**The evolution, homeostasis and reproduction (first) lecture

To regard man, the most ephemeral and rapidly evolving of all species, as the final and unsurpassable achievement of creation, especially in his present-day particularly dangerous and disagreeable stage of development, is certainly the most arrogant and dangerous of all untenable doctrines. If I thought of man as the final image of God, I should not know what to think of God. But when I consider that our ancesters, at a time fairly recent in relation to earth's history, were perfectly ordinary apes, closely related to chimpanzees, I see a glimmer of hope. It does not require considerable optimism to assume that from us human beings something better and higher may evolve. Far from seeing in man the irrevocable and unsurpassable image of God, I assert--more modestly and, I believe, in greater awe of the Creation and its infinite possibilities--that the long-sought missing link between animals and the really humane being is ourselves!
-Konrad Lorenz, On Aggression

Biology is the study of life on Earth.

Audesirk, Audesirk and Byers, Chapter 1, Many selections throughout text

Today's musical selection
Sam Cooke "What a wonderful world" ("Don't know much about biology...")

What is unique to life?

Fig. 1-2
Cell membrane contains protoplasm and somehow inside, cells are "alive."
(1) Complex - Cells have very complex macromolecules (DNA, RNA, protein).
In general, entropy (disorder) increases [we will return to this point in a later lecture]. However, in Biology, small systems are defined, enclosed in cells, that defy this generalization
(2) Movement, Responsiveness (irritability, sensitivity, excitability)
(3) Development, Growth, Form
(4) Metabolism - exchange energy
-Catabolic (breakdown)
-Anabolic (build-up)
*(6) Homeostasis (regulation)
Example#1 Thermostat, servo mechanism, negative feedback.
Example#2 Weight regulation 1 cookie/day = 25 lb/yr
*(7) Evolution is major unifying principle
Life on Earth is 3 1/2 billion yrs old (and presumably all organisms have common ancestor)
History from primordial "soup" of molecules to biology, extinctions, etc.
*(8) Reproduction -
"Survival" in biology is to and reproduce and produce fertile offspring.
Example#1- One species definition: Reproduce, fertile offspring
Horse - donkey (differenty species) mate to produce the mule -- the mule is sterile: Mule, (here is my late friend's dad proudly posing with his Missouri mules)
Example#2- Consider this: so much energy is devoted to reproduction that reproductive structures constitute most of the human diet. Oh? Well, grain, fruit (and vegetables that are fruits), dairy products and eggs.

The virus story

Figure E9-1
To tell the next story, let us introduce reproduction in the bacteriophage (a virus that "eats" bacteria). Is a virus alive? Compare the terms "infectious" with "living." Is the virus the oldest form of life because it is so simple? (Made up of just Protein and DNA) No, it cannot be because it is a Parasite and therefore could not exits until its host existed.

Figure E9-2
(Alfred Hershey & Martha Chase 1952 work) radioactive sulfur seen in protein coat of bacteriophage, radioactive phosphorus seen in bacteria where DNA is orchestrating the manufacture of new virus.

"Is it animal, vegetable or mineral"
- a question on an old quiz show called "20 questions"

Fig. 1-11
Kingdoms (At one time, 2 kingdoms were proposed (plants and animals), but there were problems, for instance some organisms have properties of both kingdoms. Now 5 are generally accepted.

Sometimes more are also proposed. How can the number of kingdoms be subject to debate? Classification is not an exact science.
5 Kingdoms:

Kingdoms and domains

Monera (prokaryotes) are very diverse (2 of the 3 domains)

These cells do not have a nucleus. The suffix "karyote" refers to the nucleus, and comes up in words like "perikaryon" (the part of a nerve cell near its nucleus) and "karyotype" (the chromosomal constitution of a cell).
The other four kingdoms have eukaryotic cells.
Protista (single celled "plants" and "animals") are also very diverse

Do they make their own food?

Fig. 1-10
Fig. 28.1
Autotroph vs. Heterotroph (self- other-feeder)
Food web (from ecology chapter)

Phylogeny vs Taxonomy

Fig 18-5
Fig. 18-6
Fig. 24-1
Taxonomy is sometimes called "Systematics" and is based on the Linnean system (Linnaeus 1705-1778 botanist)

Table 18-1
Kingdom - Phylum - Class - Order - Family - Genus - Species

(phylogeny and systematics.) Here, domain is more inclusive than kingdom
Genus - Species: binomial nomenclature
Phylum = Division for plants fungi bacteria
Homo sapiens people
Drosophila melanogaster fruit flies
Canis familiaris dogs
In phylogeny we try to draw conclusions (and diagrams) of how related organisms are.

Figure 18-5
There can be various levels of artistic license in such evolutionary diagrams.

Here is a display at the Carnegie museum in Pittsburgh. It is actually a graph. Diversity is on the X axis (abscissa). That diversity in this example is the location on Earth. The Y axis (ordinate) is time with long ago on the bottom and now on top and split up into epochs of the geological time scale (Eocene, etc.). Of note is that animals lower in the diagram are not just "simpler" animals of today. Rather, today's animals are only at the top, and some further down may be extinct, for instance, horses in the New World until they were re-introduced.

Such a diagram branches out, hence the term "divergent evolution," a concept so fundamental that you should see it now even though evolution will be covered in detail in the last quarter of the semester. One very fundamental concept is that of homology. The wing of a bird and the flipper of a porpoise are homologous and are descended from the same common structure that led to your arm and hand.

Molecular biologists borrowed this strategy and produce divergent evolution diagrams of their own (at first much to the chagrin of the comparative anatomists).

Levels of analysis

Fig. 1-1
element - molecule - organelle - cell - tissue - organ -
organ system - organism - population - biosphere

Questions used in 2007 & 2008 relating to this outline

These days, autotrophs are almost exclusively
(a) herbivores.
*(b) photosynthetic.
(c) predators.
(d) prokaryotes.
(e) ruminants.

I said that a phylogenetic diagram was like a graph. What is on the ordinate (Y-axis)?
(a) binomial nomenclature
(b) bacteria on the left, people on the right
(c) kingdom on the left, species on the right
(d) the independent variable
*(e) time from long ago to present

Comparative anatomy shows similarities in human and bird forelimbs, since humans and birds had a common ancestor. The forelimbs are called
(a) metabolic.
(b) metazoans.
(c) homeostatic.
*(d) homologous.
(e) prokaryotic.

You look at an amoeba in the microscope. Where might you put it in a phylogenetic diagram of eukaryotes?
(a) at the middle at the bottom.
*(b) at the left at the top.
(c) right next to Drosophila melanogaster.
(d) beside all the others that have the nitrogen-containing polysaccharide chitin.
(e) with ancient organisms.

In the food web, high level consumers (predators) would be considered to be
(a) more evolved than anybody else.
*(b) heterotrophs.
(c) lacking in catabolic metabolism.
(d) higher in entropy than any other organism.
(e) ruminants.

The mule was used as an example to show
(a) some organisms of the past are now extinct.
(b) the forelimbs of vertebrates are not homologous.
(c) the dangers of anabolic steroids.
(d) not all reproducing "organisms" are considered to be alive.
*(e) the horse and donkey are different species.

In the Hershey-Chase Experiment, phosphorus and sulfur were used because phosphorus is found in ____________ while sulfur is found in ______________.
(a) Cell membrane, Lipids
(b) Vesicles, Proteins
*(c) DNA, Proteins
(d) Proteins, RNA
(e) Bacteria, Lipids

Why don't most people gain or lose a lot of weight rapidly?
*(a) They eat the right amount.
(b) They count calories rather than kilocalories.
(c) They adjust their caloric loss through the urine to compensate for overeating or undereating.
(d) Antidiuretic hormone (ADH) regulates weight.
(e) Parathormone (PTH) mediates the storage of extra energy.

Terms like Homo sapiens
(a) demonstrate the concept of homology.
*(b) are derived from the Linnean system of taxonomy.
(c) tell you the phylogeny.
(d) tell us the kingdom and phylum in Latin.
(e) relate tissues to organs.

I said that the tree of life is like a graph. What is on the X-axis (abscissa) of the tree of life?
A) Binomial nomenclature.
B) The species is on the left and the genus is on the right.
C) Catabolic is on the left and metabolic is on the right.
*D) Diversity.
E) The dependent variable.

Disorder increases according to the second law of thermodynamics.
A) Homeostasis is the word biologists use for disorder.
B) This is exemplified by anabolic reactions.
*C) Although biology is complex, this law still applies to the whole universe.
D) Entropy is the fundamental unifying principle in biology.
E) Comparative anatomy was used to demonstrate that disorder applies to biology.

Your lab partner tells you that the Paramecium cell you see in the microscope is very primitive. You offer the following correction:
*A) They are present-day organisms with a 3 & 1/2 billion year geneology just like you.
B) Viruses (not Paramecia) are primitive, but cells arose later (than viruses) in the history of life.
C) Because they have photosynthesis, they must be very old.
D) Although Paramecia are prokaryotes without organelles, they are autotrophic.
E) Bacteriophage have infected those Paramecia.

What kind of an organism is a bacteriophage?
A) It is a eukaryote.
B) Scientists consider it to be a predator in the food chain.
C) It is an autotroph.
D) It is a bacterium.
*E) It is not an organism since it is not cellular.

Radioactive phosphorus vs. radioactive sulfur were used by Hershey and Chase
A) to identify membrane glycolipids.
*B) to show that DNA, not protein, is the hereditary macromolecule.
C) to diagnose brain tumors.
D) to show that water dissolves hydrophobic ions.
E) to show the age of fossils and rocks.

Untreated diabetic patients
*A) are the only people who excrete calories.
B) are the only people who have catabolic metabolism.
C) have resistance to malaria.
D) were classified by Linnaeus.
E) are protostomes.

In one table I showed you, it was claimed that bacteria and protists could be either autotrophic or heterotrophic. This dichotomy applies to
A) whether the organism is diploid or haploid
*B) whether they make their own food.
C) presence of a nucleus.
D) embryonic development.
E) whether they are gymnosperms or tracheophytes.

Questions used in 2002 relating to this outline (as well as other outlines)

You were presented with the classification of the wolf (Animalia - Chordata - Mammalia - Carnivora - Canidae - Canis - lupis). Which group would have the most species in it?
*(a) phylum
(b) class
(c) order
(d) family
(e) genus

What happens when bacteriophage T2 infects a bacterium?
(a) Phage RNA enters the cell.
*(b) Only viral DNA enters the bacterium.
(c) Only viral protein enters the bacterium.
(d) The entire virus, enzymes and membranes and all, enter.
(e) The virus injects a poison into the bacterium to kill it.

About how long ago did the first cells appear?
(a) 3.5 million years
*(b) 3.5 billion years
(c) after photosynthesis evolved
(d) not until there was sexual reproduction
(e) 1.5 billion years ago when eukaryotes came into existence

"Membership" in this group is sometimes defined by ability to mate and bear fertile offspring:
(a) species.
(b) genus.
(c) family.
(d) order.
(e) class.

Bacteriophage were used
(a) to obtain temperature resistant enzyme for PCR.
(b) to make a cDNA library.
(c) by Hershey and Chase to show that DNA but not protein was the hereditary material.
(d) to show that the lac operon is regulated by presence of lactose.
(e) for gene therapy.

This page was last revised 6/8/09

**The strong inference (scientific method) lecture

"Strong Inference"

I keep six honest serving men
(They taught me all I knew);
Their names are What and Why and When
And How and Where and Who. - Kipling

If I have seen further, is is by standing on the shoulders of giants
-Sir Isaac Newton Letter to Robert Hooke 5 February 1675

A dwarf standing on the shoulders of a giant may see farther than a giant himself
- Robert Burton (1577-1640) The anatomy of melancholy

Audesirk et al., Chapter 1, pp. 610-611 & 629 (also pay attention to several figures and readings in other chapters)

Today's musical selection
Tina Turner One of the living

Nature of scientific inquiry

Fig. 1-4
Scientific inquiry and scientific method is based on observation - systematic, objective, repeatable

Figure 14-7
You cannot always manipulate things, example: studying the fossil record.
But you can make observations like the similarities in the forelimbs of birds and mammals.

Think about high school geometry. In the text book, there are "postulates" that we assume must be true and "theorems" that can be proven. In the home work, there are "if - then" problems in which something iis assumed ("if"), a conclusion ("then") can be worked out by applying the theorems and postulates step-by step.

There are various kinds of science.
Some scientists make models (mathematical or electrical) of biological systems that have predictive value. Other scientists collect descriptive data that further substantiates a global theory.

Fig. 1-10
(Already shown in first lecture outline)
Model: energy flow in biology

Is there one right kind of science?

"Strong inference" is the title of a paper by John R. Platt (Science, 146, 347-353, 1964) in which he criticizes some approaches to science. Here are some quotes:
"...some fields of science are moving forward much faster than others"
"Those rapidly moving fields are fields where a particular method of doing scientific research is systematically used and taught, an accumulative method of inductive inference that is so effective that I think it should be given the name of 'strong inference.'"
"Strong inference consistds of...:
(1) Devising alternative hypotheses;
(2) Devising a crucial experiment ... with alternative outcomes ... each of which will ... exclude one or more of the hypotheses"
"It is like climbing a tree."
"[focus] on the exclusion of a hypothesis"
"How small and elegant an experiment can you perform?
"You must study the simplest system you think has properties you are interested in." (attributed to C. Levinthal
"...there is no such thing as proof in science... science advances only by disproofs." (attributed to Karl Popper

Doing an experiment

In an experiment:
An independent variable is what we manipulate, typically graphed on the abscissa (X-axis)
A dependent variable is what we measure, typically graphed on the ordinate (Y-axis)
Control - other variables are to be controlled
The population is everything out there
The sample is what, out of the population, we measure (to make inferences about the population)
Sampling - random sampling is best
Descriptive statistics gives us averages (means)
as well as measurements of how variable the data are (standard deviations)
In inferential statistics we propose a null hypothesis vs. an alternative hypothesis.

Doing statistics

Hypotheses are small questions. You "test" these hypotheses - answers (in the form of "rejecting the null hypothesis") are never certain but rather involve an acceptably low probability (usually 5%) of being wrong, hence the involvement of statistics in experimental design.

Enter (stage left): Statistics

"There are three kinds of lies: lies, damn lies and statistics"
Benjamin Disraeli (quoted in Mark Twain's autobiography, Chapter 29)

Enter (stage left) The normal distribution

Figure 15-13
(I just needed a picture showing the normal distribution)
Figure 15-13 will be shown again in the context of genetic basis of evolution

Area under the curve = 1
Middle of the curve is the mean, 0 in the "standard" normal distribution
variation is indicated by standard deviation
z-score indicates the number of standard deviations away from the mean the a score is
About 5% of the curve is 2 or more standard deviations from the mean

Central limit theorem:
The distribution of sample averages approaches the normal distribution as the sample size increases
(It's a theorem, that means it can be proven, it's not just an idea)

"The results are significant beyond the 0.05 level." (This its typical) This means that the results could have happened by chance (rather than because of our independent variable) 5% of the time

"It has been proven beyond a shadow of a doubt using the scientific method" - Nonsense!

Collect more data, and you will be more certain. You can only reject the null hypothesis. You can not accept (or prove) the null hypothesis. In other words, "absence of data is not the same as data of absence."

Thought problem & story

Suppose someone says that a certain plant is extinct. How can he know? To state that for certain would require examination of every square inch of the Earth. Most naturalists admit that they can say for (fairly) certain if a bird species is gone. The reason is that birds are so conspicuous and that there are so many well-trained bird-watchers. Birds do go extinct! Here is a SLIDE I took at the Smithsonian natural history museum of Martha, the last passenger pigeon who died 1 pm Sept 1, 1914 at the Cincinnatti Zoo. The famous ornithologist Audubon, saw them darken the skies hundreds of times during their migration. However, the ivory-billed woodpecker was considered extinct after its last sighting in 1944. Then it was (presumably) seen again in 2004 (although there remains some uncertainty.

"We have no evidence showing that (whatever)" - Nonsense!

In summary, the step-by-step progress of science involves statistics, and asking the right questions, that can be answered appropriately. A course in advanced statistics is usually called "experimental design" because you cannot even do the right experiment without the right design, controls, and statistics in mind.

Your faculty are scientists

"Publish or perish." Perhaps you have heard that expression. In my opinion, "a university is a community of scholars dedicated to the acquisition and disemination of knowledge." Faculty are expected to do research as well as to teach courses and are usually granted tenure only if their research publications are favorably viewed by their peers (at other universities)

Watch out!

Sometimes "scientists" are not completely honest when there is a conflict of interest


Fig. E9-3
Science is a human endeavor.
See story on p. 155 about Maurice Wilkins and Rosalind Franklin
See story on p. 156 about James Watson and Frances Crick
1962 Nobel Prize in Physiology and Medicine
American chemist Linus Pauling might have made discovery but he was not allowed to go to a meeting where data were presented because of strong anti-Communist movement in the US in the early 1950's

Scientific revolutions

Book by Thomas Kuhn (1962)
"paradigm" - set of beliefs shared by the scientific community
When too many contradictions accumulate - "paradigm shift"

Questions used in 2007 & 20008 relating to this outline

I said that "absence of data is not the same as data of absence" to paraphrase
(a) "the sample must be random."
(b) "observations must be unbiased."
*(c) "you never accept the null hypothesis."
(d) "not all science is based on experiments."
(e) "publish or perish."

Description of a hypothesis:
(a) It unifies all the observations in a field.
*(b) It should be stated in a way so that it can be disproved.
(c) Like a postulate in geometry, we must assume it is true.
(d) Like a theorem in geometry, it can be proved.
(e) It is used to describe a process and to make predictions.

It is reasonable to hypothesize that the average height of the Bio 110 class can be estimated by the average of the Tuesday morning lab because
(a) students were not biased when they did those measurements.
(b) we controlled all other variables in this experiment.
*(c) there is no reason to think it is not a random sample.
(d) we measured a population, not a sample, Tuesday morning.
(e) height is an independent variable.

The normal distribution is used because
*(a) it can be proven that the sample means are normally distributed.
(b) it is how the independent variable is related to the dependent variable.
(c) it is systematic, objective and repeatable.
(d) it is the best description of how postulates and theorems work in a high school geometry "if-then" homework problem.
(e) it is the best way to graph homology on a taxonomic tree.

The ivory-billed woodpecker
(a) has wings that are not homologous to human forelimbs.
(b) is dangerous because it has prions.
(c) was found on the Galapagos by Darwin.
*(d) was thought to be extinct but may not be.
(e) became extinct in the Old World and then was re-introduced from the New World.

Why do scientists study a sample instead of a population?
A) A sample is more accurate.
B) A population is random.
*C) A population is too big to study.
D) The sample is like a theorem while the population is like postulate.
E) Only with the sample can you prove the null hypothesis.

Which is true about the discovery of the structure of DNA?
A) American Linus Pauling discovered it.
B) Nobody believes Watson and Crick's model because they had a conflict of interest.
C) It's primary structure is the sequence of amino acids in it.
*D) The Nobel Prize went to three men, and Rosalind Franklin did not share the award.
E) It can be altered by exposure to the abnormal structure of a prion.

The null hypothesis
A) is the same as a law.
B) is the same as a model.
C) is the same as a theory.
*D) cannot be accepted, it can only be be rejected.
E) allows us to have a "paradigm shift" (scientific revolution).

I want to test a drug, so I do a clinical trial. I give half the subjects the drug and half the people a "placebo" (a dud). Why?
A) The placebo guarantees that the researchers do not have a conflict of interest.
B) The placebo guarantees that the sample is random.
C) The placebo guarantees that the observations are repeatable.
D) If we are testing a diabetes drug, we should give overweight people the drug and thin people the placebo.
*E) The people getting the placebo serve as the control group.

I calculate the mean from my sample. What is true about the sample mean?
*A) The distribution of sample means is described by the normal distribution.
B) It is the same as the standard deviation.
C) It is the same as the median.
D) It is the same as the population mean.
E) It is one of the controlled variables.

What is the significance of the "tails" (more than 2 standard deviations from the mean) of the normal distribution?
A) Homology is in the tails while analogy is in the rest of the distribution.
B) If it is in the tails, scientists consider it to be a law, while the rest of the distribution is a model.
*C) It has to do with disproving the null hypothesis.
D) The tail on the left is the dependent variable and the tail on the right is the independent variable.
E) The mean is in the tail on the left while the median is in the tail on the right.

Question used in 2002 relating to this outline

A small scientific question which the typical biologist "tests" with an experiment is called a
(a) theory.
*(b) hypothesis.
(c) model.
(d) correlation.
(e) law.

This page was last revised 6/8/09


**The chemistry and water lecture

"Water, water everywhere
And all the boards did shrink
Water, water everywhere
nor any drop to drink."

-Samuel Taylor Coleridge
The rime of the ancient mariner


Audesirk, Audesirk and Byers, Chapter 2 (and a table in chapter 34)

Today's musical selection
Tom Lehrer, the elements

"Inorganic chemistry" is an expression for first year college chemistry.
Second year college chemistry is "organic chemistry," the chemistry of carbon (C) based molecules.
In Bio 110, we have the good fortune of summarizing these 2 yrs of chemistry in a few lectures!

Substance is composed of Mass (matter), and Energy is also important, but, in biology, we will focus only on that energy which is biologically useful.


From the Los Alamos National Labs (periodic table)

Figure 2-1
Atoms = Elements
There are 3 particles.
electrons and the nucleus (Protons and Neutrons)

Table 2-1
Periodic table - elements - O, C, H, Ca, P, K, S, ... are most abundant in life
There are also trace materials like iron and zinc.

1. Protons determine the atomic number (integers in order, top of each box on the periodic table).
2. Neutrons plus protons determne weight (bottom of box).

These are not integers because there are several isotopes such as 3H (tritium), 14C. The 14 is a superscript, and this is pronounced "C-14." Isotopes are radioactive, and decay with a characteristic half-life. In biology, radioactive isotopes are used for radiocarbon dating and to label molecules (radioactive tracers) and for autoradiography (exposing film),...

Box E2-1
PET scan (positron emission tomography)

3. electrons, virtually no mass, involved in bonding of two major types:

Figure 2-6a
(a) covalent bonding

Fig. 2-4
(b) NaCl splits to Na+ (sodium) and Cl- (chloride) ions that are attracted to each other because of opposite charges

Figure 2-3
If light is absorbed by a pigment, the electron is excited, and, if the molecule fluoresces, the exctation in the electron comes back down; electrons are very important for how biological energy is stored (photosynthesis) and how it is released (cellular respiration)


The body is approxamately 2/3 water. In addition, as you will see repeatedly this semester, water is incorporated into many organic molecules.

Molecules - the next higher level of integration above atoms, generally aggregates of atoms linked by covalent bonds. Because water is so fundamental, we start with water as an example molecule.

Figure 2-6b
H2O has covalent bonds, but there is some separation of charge, making it a polar molecule
Water is very important as a solvent, in reactions, and in temperature regulation.
As a polar solvent, it dissolves charged molecules or ions.

Figure 2-14
A small fraction of water molecules split to H+ and OH- "ions", ...

Figure 2-15
...and if there is an excess of H+, the solution is an acid; if OH- predominates, it is a base. The pH scale runs from 0 (acid) to 7 neutral to 14 base (alkaline). The pH = -log [H+].

Other important properties of water:
(1) It has a very high specific heat measured in calories (1 cal is the energy to heat water 1oC); units of energy (the "calories" you "count" when dieting are actually kcal). In this regard, big bodies of water can moderate the climate (cooler in summer, warmer in the winter), the "sea climate."
(2) It has an extremely high heat of vaporization (about 540 cal/g, actually 576 at 37oC), important in body cooling via sweating and panting.
(3) It organizes matter by adhesion and cohesion and because molecules can be hydrophilic or hydrophobic.

Figure 2-12
Consider a container of Italian dressing, where the oil floats on the watery liquid, and the oil is organized into small spheres when the bottle is shaken well

Oxygen - an integrative story

Pineapple juice (or other acidic juices like lemon juice) keeps the potato slice on the right from turning brown.
(The acidity blocks an enzyme that causes oxidation of the amino acid tyroosine.)
In general, oxygen is a necessary evil, necessary because we need it for metabolism, evil because oxidation is "biological rusting."

Table 34.3
Vitamin E (tocophorol) [and several otther nutrients] are antioxidants.

Preview of coming attractions (concerning oxygen)
(1) aerobic metabloism
(2) absent in primordial atmosphere
(3) precursor of Ozone (blocks ultraviolet light from Sun)

Questions used in 2007 & 2008 relating to this outline

What do we mean by 14C when carbon usually has 6 protons and 6 neutrons?
(a) The difference between 12 and 14 is made up by two extra electrons.
(b) This carbon has 7 protons and 7 neutrons.
(c) 14C is a famous polar solvent.
(d) This is a charged ion.
*(e) It wouldn't be carbon if it didn't have 6 protons, so it must have 8 neutrons.

It is true that hydrogen and oxygen are covalently bound in water, but that is not the whole truth. Why not?
(a) Water is not polar.
(b) If the pH is 7, it can never be true.
*(c) Water can divide to hydroxyl and hydrogen ions.
(d) Water fluoresces.
(e) Water cannot become part of an organic molecule.

After an electron is excited, energy may be released when the electron drops back to its lower energy shell. How is this energy release witnessed?
(a) NaCl is covalently bound.
(b) The pH gets lower.
(c) By ADP converting to ATP plus inorganic phosphate.
(d) By the half life.
*(e) Light is emitted.

It takes 1 calorie to raise the temperature of 1 ml of water 1 oC. Why is sweating so useful to cool you when you are hot?
(a) The half life of sweat is different
(b) Water organizes hydrophobic and hydrophilic molecules
(c) Water is needed for hydrolysis.
*(d) The heat of vaporization is way more than 1 calorie.
(e) Some water is incorporated into organic molecules.

In biology, sodium is found in what form?
(a) As a radioactive isotope.
(b) As a high, i.e. acidic, pH.
(c) In pentoses.
(d) Covalently bound to chloride.
*(e) As an ion.

"Oxygen has 8 protons and 8 neutrons." True in general, but why is the atomic mass 15.999 instead of 16?
*(a) Perhaps some atoms have less than 8 neutrons.
(b) Perhaps some atoms have less than 8 protons.
(c) Because there are not enough electrons.
(d) Oxygen is the backbone of organic molecules because it makes four bonds.
(e) Oxygen molecules that are in hydrocarbons have less.

Electrons are important in pigments and also for
(a) atomic weight.
(b) the "sea climate."
(c) hydrophobicity.
(d) the resting potential
*(e) chemical bonding.

Atoms or molecules that have gained or lost electrons are termed
A) acids.
B) bases.
C) polymers.
*D) ions.
E) radioactive.

If a substance measures 7 on the pH scale, that substance
*A) has equal concentrations of H+ and OH- ions.
B) is exemplified by stomach acid.
C) is alkaline.
D) probably lacks OH- ions.
E) is basic.

Which four elements make up approximately 96% of living matter?
A) carbon, sulfur, phosphorus, helium
*B) carbon, hydrogen, nitrogen, oxygen
C) carbon, sodium, chlorine, magnesium
D) carbon, oxygen, sulfur, calcium
E) oxygen, hydrogen, calcium, sodium

In what way is 14C, used in radiocarbon dating fossils, different from normal carbon?
A) Its atomic weight is lower.
B) It has more protons.
*C) It has more neutrons.
D) It is oxidized.
E) It is an ion

If you cut open a potato, it will turn brown if you do not dip it into pineapple juice (or something else acidic) because of an enzyme, an amino acid and what else?
*A) oxygen
B) nitrogen
C) carbon
D) sulfur
E) phosphorus

What determines the atomic number of an atom?
A) number of electrons if it is an ion
B) total number of protons, neutrons and electrons
C) arrangement of neutrons in the atomic nucleus
*D) number of protons in the atomic nucleus
E) the total number of protons plus neutrons

The way that light from the Sun interacts with matter is
A) to change the pH.
B) to create positron emission tomography.
C) change the atomic weight.
D) convert a neutron into a proton.
*E) excite an electron.

Polar covalent bonds form
A) after the half-life has occurred.
*B) when electrons are shared, but unequally (example: water).
C) ions are formed.
D) an acid and base are combined.
E) charged atoms are attracted to each other.

Sweating is a useful cooling mechanism for humans because
*A) water takes up a great deal of heat in changing from its liquid state to its gaseous state.
B) it takes one calorie to heat one milliliter of water one degree Centigrade.
C) water can exist in three states at temperatures common on Earth.
D) water is an outstanding solvent.
E) water ionizes readily.

Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

A given element with a given integer atomic number might not have an integer atomic weight because of
*(a) a variable number of neutrons.
(b) a variable number of protons.
(c) unsaturated bonds.
(d) the fact that light excites the electron orbitals.
(e) covalent bonds.

Because of the half-life of 14C, you may be able to determine
(a) whether your solvent is a polar solvent.
(b) whether an organism is a prokaryote or a eukaryote.
(c) whether a reaction is anaerobic.
*(d) the age of a fossil.
(e) number of amino acids in a protein.

Charged atoms such as Na+ are called
(a) isotopes.
*(b) ions.
(c) covalent bonds.
(d) molecules.
(e) neutrons.

All of the following are used in living systems. Which is least abundant?
(a) carbon
(b) nitrogen
(c) hydrogen
*(d) iron
(e) oxygen

This page was last revised 6/9/09


**The organic chemistry lecture

"He said science was going to discover the basic secret of life someday," the bartender put in. He scratched his head and frowned. "Didn't I read in the paper the other day where they'd found out what it was?"
"I missed that," I murmured.
"I saw that," said Sandra. "About two days ago."
"That's right," said the bartender.
"What is the secret of life?" I asked.
"I forget," said Sandra.
"Protein," the bartender declared. "They found out something about protein."
"Yeah," said Sandra, "that's it."

-Kurt Vonnegut, Jr. Cat's Cradle

Audesirk, Audesirk & Byers Chapter 3

Today's musical selection
Bush The chemicals between us

is the chemistry of carbon (C) which makes 4 bonds.
In "Star Trek" (the first movie), people were called "carbon based units" by the alien.


(Hydro-carbon - prefix suggests hydrogen, suffix suggests carbon).
They are hydrophobic and nonpolar.
CH4 methane, - natural gas
Fossil fuel, but also in primordial atmosphere, oddly
Gasoline has typically 8 carbons (octane) and is fluid. Long chains are thick, like oil and vasoline.
nonpolar, hydrophobic


Figure 3-4
(Carbo-hydrate is also sort of a compound word, carbon, but note that "hydrate" suggests water, not hydrogen) - the general formula is Cn(H2O)n
Hexose (hex = 6 [carbons], "-ose" always means sugar)- glucose, the most famous monosaccaccharide, is good to illustrate that monosaccharides usually assume a ring structure

Figire 3-6
Pentose - ribose, deoxyribose (that are in RNA and DNA) are famous

Figure 3-7
Compound dehydration synthesis, hydrolysis (hydro-water, lysis-breakdown)
In digestion, macromolecules are broken down to monomers.
Disaccharide - sucrose, lactose (milk)

in milk, so all babies can digest it
Europeans evolved with dairy husbandry and so can enjoy milk as adults
Many Asians and Africans cannot
later we will see that the lac operon controls enzymes for lactose utilization in bacteria

Figure 3-8
Polysaccharides starch (plant), glycogen (glyco-sugar, gen-give birth to) (animal)
alpha 1-4 linkage
Carbohydrates are used for energy.

Figure 3-9
Carbohydrates are used for structure: cellulose (beta-1,4 glucoses), the most plentiful biological molecule on Earth,
Carbohydrates are used for bulk since people cannot digest fiber, but termites & cattle can. This introduces the topic of symbiosis (living together) and mutualism (where it is to the benefit of both organisms since, for termites, zooflagellates, which are protozoa, break down cellulose and for cattle, bacteria do the job.

Other functions
Carbohydrates are used for structure in some proteins
Carbohydrates contribute to exoskeleton in arthropods, a polymer called chitin that has some nitrogen and is also in cell walls of fungi


(fats) store more energy (2x sugar) 1 tablespoon of sugar is 50, fat 100 "Calories" = kilocaloriies

Figure 3-11
Glycerol & 3 fatty acids (16-24 C long) - triglyceride ester bonds
note the dehydration synthesis
The -COOH defines an organic acid such as a fatty acid, otherwise the molecule is a hydrocarbon.
C-C (single bond) vs. C=C (double bond) unsaturated (vs saturated with H's), with several, it is referred to as "polyunsaturated" PUFA = polyunsaturated fatty acid
Animal fats tend to be saturated, bad for arteries leads to atherosclerosis; vs vegetable fats better.

Figure 3-15
Polar phospholipids - contribute to membranes because polar group is hydrophilic and fatty acid (acyl) tail is hydrophobic
polar-glycerol-FA1-FA2 (more double bonds, fluidity)
Here are some famous fatty acids: stearic C18, Oleic-18:1
There are also glycolipids with sugar attached to lipid in membranes.

Figure 3-16
Steroids-cholesterol - fit into membranes and serve as precursors for hormones,
especially "sex hormones" like testosterone, progesterone, estrogen
Howard Cossel "anabolic steroids" (metabolic: catabolic vs anabolic) - androgens, the hormones like testosterone that favor nitrogen retention (muscle growth)
Salts of cholesterol are in bile (from liver) that acts like a detergent to emulsify fats to aid in digestion.
Interestingly, cholesterol is required in animals and is an "essential" nutrient in insects that cannot synthesize it; too much bad in people, and that can be controlled by diet though people also biosynthesize cholesterol.

Other functions
Waxes: fatty acid + long chain alcohol (instead of glycerol) prevent water loss also used for structure in nbee hive.
Blubber, especially in warm blooded cetaceans, serves as insulation.
In summary, lipids are used for energy, structure, hormones, insulation, water loss, digestion


Proteins and nucleic acids make up 2/3 of dry weight of the body
short = "Peptides", medium = polypeptide, long = "protein" (hundreds, thousands)
Proteins are very important because chains of amino acids can be very complex

Figure 3-18
Amino acid
The general formula is NH2-CR-COOH - amino ( -NH2 ) and acid ( -COOH ).

Figure 3-20
Peptide bonds involves -NH2 and -COOH getting linked with a dehydration synthesis.

There are about 20 amino acids (alphabet of 20 letters)
R group varies
If you made a peptide 4 amino acids long, there would be 20 x 20 x 20 x 20 = 160,000 different possibilities, hence the complexity.
About half of the amino acids are "essential" meaning that they cannot be made by metabolic conversion from other molecules and thus need to be eaten - corn is notoriously low in tryptophan and methionine).

primary (the sequence)
secondary (alpha helix, beta pleated sheet)
tertiary structure (disulfide and other bonds)
quaternary structure (chains interact with each other)
(here is a really important example - hemoglobin - which has 2 alpha subunits and 2 beta subunits.)

Beyond 4 levels
There are so many levels of protein structure above these 4, glycosylation (adding a sugar), phosphorylation, chopping fragments out of the protein, and other post-translational modifications, that you will have to wait until a more advanced course to really focus on them.

Protein diversity makes for individuality, and at the level of the immune system, proteins (antigens) determine self vs non-self.

Proteins can serve for:
Structure (example keratin which is in hair)
Enzymes - Their names end in the suffix -ase), that are catalysts (molecules that influece the rate of a reaction).
Antibodies (used against antigens)
Transport (example hemoglobin)
Motility and contraction
Hormones and neurotransmitters (often smaller fragments of a larger precursor, a prohormone)
Receptors (for hormones and neurotransmitter)
Energy - though the use of protein for energy is not efficient and NH3, released in catabolism of amino acids, is toxic and must be eliminated, sometimes as urea, sometimes as uric acid.
Venoms, toxins

Questions used in 2007 and 2008 relating to this outline

If it were in a polyunsaturated fatty acid, how many bonds does a carbon have?
(a) 1
(b) 2
(c) 3
*(d) 4
(e) 5

Explain "corn is not a good source of essential amino acids."
(a) It does not have all 15 amino acids.
(b) The proteins of corn have been hydrolyzed.
*(c) It does not have all the amino acids required in the human diet.
(d) These are the amino acids used for energy in catabolism.
(e) Corn is missing pyruvate, a very important amino acid.

The dehydration synthesis combines [A] to [B] in fat molecules
(a) [A] carbohydrate; [B] water
(b) [A] one amino acid; [B] another
(c) [A] one amino acid; [B] ammonia
(d) [A] glycogen; [B] glucose
*(e) [A] glycerol; [B] fatty acids

The lipids in membranes have two fatty acids. In place of the third, there is a
(a) glycerol.
(b) steroid.
*(c) polar group.
(d) hydrocarbon.
(e) saturated amino acid.

Lipids store twice as much energy as carbohydrates. How is that energy measured?
*(a) in "calories"
(b) by the length of the chain
(c) by tonicity (hypertonic, isotonic, hypotonic)
(d) by the first law of thermodynamics
(e) by oxidation - reduction

What is considered bulk or fiber for humans but can be used for energy by termites and cattle?
*(a) cellulose
(b) those amino acids that are not essential
(c) disaccharides
(d) long chain fatty acids
(e) It depends on whether the humans in question are lactose intolerant.

What kind of molecule is octane?
(a) a monosaccharide
*(b) a hydrocarbon
(c) glycogen
(d) a steroid
(e) a polypeptide

What kind of molecule is ribose?
*(a) a pentose
(b) an enzyme
(c) chitin
(d) a polysaccharide
(e) an anabolic steroid

Which of the following is NOT an organic molecule?
A) a polypeptide
B) nucleic acid
C) cellulose
*D H2O
E) a monounsaturated fatty acid

Macromolecules are synthesized by removing (what?) from the building blocks?
A) carbon.
B) covalent bonds.
*C) water.
D) oxygen.
E) peptides.

Which of the following correctly matches an organic polymer with its respective monomers?
*A) protein and amino acids
B) carbohydrates and polysaccharides
C) hydrocarbon and monosaccharides
D) polar phospholipid and steroids
E) glycerol and glycogen

The fiber in your diet is really
A) a polypeptide.
B) a polyunsaturated fatty acid.
C) starch.
D) keratin, a structural protein.
*E) a polysaccharide.

In a biological membrane, the phospholipids are arranged with the fatty acid chains facing the interior of the membrane. As a result, the interior of the membrane is
*A) hydrophobic.
B) hydrophilic.
C) charged.
D) polar.
E) filled with water.

When hemoglobin is shown as two alpha chains linked to two beta chains, this represents which level of protein organization?
A) glycosylation
B) posttranslational modifications
C) primary structure
*D) quaternary structure
E) phosphorylation

What type of chemical reaction results in the breakdown of organic polymers into their respective subunits?
A) dehydration
B) oxidation
C) reduction
D) ionization
*E) hydrolysis

Where is glycogen stored in vertebrate animals?
A) brain and kidneys
*B) liver and muscles
C) heart and bones
D) pancreas and blood
E) adipose tissue

The group of biological molecules most diverse in structure is
A) disaccharides.
B) lipids.
*C) proteins.
D) polyunsaturated fatty acids
E) steroids

Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

Which would have the greatest potential for variability?
(a) a nucleotide 3 base pairs long
*(b) a peptide 3 amino acids long
(c) a hydrocarbon 3 carbons long
(d) a glycogen chain 3 glucose molecules long
(e) ATP

Those amino acids your metabolism cannot synthesize from other amino acids are called
(a) polyunsaturated.
(b) isotopes.
(c) vital.
(d) exerogonic.
*(e) essential.

Certain chemical modifications of a protein are called "post-translational."
(a) Post-translational modifications include "high" levels of structural organization such as alpha helix vs. beta pleated sheet.
(b) "Post-translational" would be the term applied to the association of two alpha subunits and two beta subunits in hemoglobin.
(c) "Post-translational" refers to the sequence of amino acids coded in that protein's "gene" (DNA coding sequence).
(d) For a protein to become an antigen (a non-self protein), it must be modified post-translationally.
*(e) "Post-translational" is after the manufacture of protein from a template of mRNA.

Steroids are
(a) hydrophilic.
(b) hydrocarbons.
(c) carbohydrates.
(d) triglycerides.
*(e) lipids.

In terms of biological reactions, what is the opposite of dehydration synthesis?
(a) transcription
(b) anabolic metabolism
(c) entropy
(d) photosynthesis
*(e) hydrolysis

Which does NOT have nitrogen in it?
(a) deoxyribonucleic acid
(b) chitin
*(c) starch
(d) protein
(e) urea

Kilocalories, those "calories" you count when you are dieting, are a measurement of
(a) water content of food and drink you consume.
(b) amino acid content of food.
*(c) energy available in food.
(d) relative fat content of food.
(e) relative carbohydrate content of food.

People with type I diabetes mellitus need to inject insulin
(a) because they have a mutation that puts valine in the 6th amino acid position of the beta chain of hemoglobin.
*(b) that is a protein hormone.
(c) because it is an enzyme used in digestion.
(d) to replace the missing gonadal steroids.
(e) to activate the sodium-potassium pump.

Enzymes are indicated by the suffix
(a) -ose.
*(b) -ase.
(c) -eic.
(d) -some.
(e) -karyote.

What type of molecule is cellulose?
(a) triglyceride
(b) nucleic acid
(c) polypeptide
(d) polyunsaturated fatty acid
*(e) carbohydrate

Vegetable oils would be higher (than animal fats) in
*(a) fatty acids with double bonds.
(b) triglycerides in which each acyl group is saturated with as many -H's as possible.
(c) all essential amino acids.
(d) uric acid.
(e) mutations.

Triglycerides with some double bonds are called
(a) enzymatic.
(b) ionic.
*(c) polyunsaturated.
(d) hydrolytic.
(e) radioactive.

Which does not have sugar in it?
(a) starch
(b) glycoproteins and glycolipids
(c) glycogen
*(d) testosterone
(e) sucrose

Which is not true about hemoglobin?
(a) It contains iron.
(b) It is in red blood cells.
(c) It is altered in sickle cell anemia.
*(d) It is an enzyme that makes DNA from a template of mRNA.
(e) It is a protein used for the transport of oxygen.

Reactions by which amino acids are used for energy, yielding nitrogenous wastes, might be referred to as:
*(a) catabolic.
(b) anabolic.
(c) prokaryotic.
(d) eukaryotic.
(e) autotrophic.

Which is NOT a carbohydrate?
(a) lactose
*(b) cholesterol
(c) glycogen
(d) Cn(H2O)n
(e) chitin

Enzymes function for
(a) motility.
(b) energy storage.
*(c) catalysis.
(d) attacking antigens.
(e) storage of hereditary information.

The liver bile salts that are secreted into the intestines are most closely related to
(a) cellulose.
(b) membrane glycolipids.
(c) ATP.
*(d) cholesterol.
(e) antibodies.

About how many different amino acids are used by living things?
(a) 10
*(b) 20
(c) 40
(d) 64
(e) 100

Arrangement of membrane lipids depends largely on
*(a) polar and hydrophobic portions of the molecules.
(b) ions.
(c) collagen.
(d) hydrolysis.
(e) radioactivity.

The term "unsaturated," as in "polyunsaturated" refers to
(a) whether all of the essential amino acids are there.
(b) whether an electron is missing.
(c) whether the third nucleotide in the codon is required to specify the amino acid.
(d) whether an element has an extra neutron.
*(e) whether there are double bonds.

This page was last revised 6/17/09


**The cell lecture

Amoebas are very small
Oh ah ee oo there's absolutely no strife
living the timeless life
I don't need a wife
living the timeless life
If I need a friend I just give a wriggle
Split right down the middle
And when I look there's two of me
Both as handsome as can be
Oh here we go slithering, here we go slithering and squelching on
-Incredible string band, A very cellular song

Cell Biology

Audesirk, Audesirk & Byers Chapter 4

Today's musical selection
Five blobs - The blob

Figure E42a
Euglena complex Eukaryotic cell - self sufficient, swim, see, photosynthesize

Figure 4-20

Figure 4-3

Figure E42c
Protozoan (Paramecium)
vs. Metazoan complex, starts as 1 cell.

Figure 4-10
divide (Mitoses) - daughter cells
become specialized

control of gene expression (in multicellular organism):
(1) different genes turned on in different cells (and at different times)
(3) but this can be fairly permanent, developmental change in gene regulation

Figure 4-1
gives relative sizes and emphasizes the importance of light and electron microscopy.

Dyes (that absorb light) are used to highlight substructures in cells. Consider, for instance, the word "chromosome" which translates to "colored body."

Similarly, electron dense materials, heavy metals like osmium, uranium and lead create an electron density in the EM.

Since I have done some EM, I offer these pictures to give you a feeling of how EM is done. Sections are cut with an ultramicrotome using a diamond knife and sections, floated onto water are picked up on small copper grids. The grid is put into an evacuated column in the EM (like Figure E41c), and, at low magnification, a ribbon of sections can be seen.

Figure. 4-2
The cell membrane is a selective barrier to polar, charged, hydrophilic molecules and ions. These need to be pumped at the expense of energy or come through specific channels (pore molecules) through the membrane (more later in membrane coverage).

Eukaryotic cells have specific little bodies that are the small cell parallel of organs in the body, and hence they are called "organelles."

Figure 4-4
plant cell, note cell wall, plasmodesmata, chloroplasts and large vacuole.

Figure 4-3 (again)
animal cell. Below, we will go through the following structures one at a time: nucleus, endoplasmic reticulum (rough and smooth), Golgi apparatus, flagellum

Figure 4-9a
Nucleus - double envelope with pores

Figure 4-12
Ribosomes & RER (rough endoplasmic reticulum) where mRNA is translated into protein, "rough" describing the ribosomes that can be seen in the electron microscope. Also, here is an EM from my work showing RER.

Figure 4-12 (continued)
There is also smooth ER where reactions other than protein synthesis take place, such as steroid hormone synthesis, detoxification of substances in liver. Liver hepatocytes detoxify. Barbiturates induce an increase in the "microsomal fraction," smooth ER as seen after grinding and spinning down in a centriguge tube

Figure 4-11
Also free ribosomes and polysomes in the cytoplasm that make proteins that go to different places.
Protein synthesis - goes at 10 amino acids per second

Figure 4-13
Golgi apparatus receives vesicles from ER (at cis face) and send secretory products that bleb off (from trans side) reactions after protein synthesis (post-translational modification of proteins) take place in Golgi complex.

Figure 4-14
It is very interesting to consider the different routings for different proteins in the cell.
this figure ("sidedness of the plasma membrane") reminds us that inside the ER, Golgi complex, or vesicle is outside the cell, much like inside the gut is outside the body.

Figure 4-17
Mitochondria has a inner and outer membranes, the inner one with shelves called cristae.
The function of the mitochondrion in ATP production

Theory that mitochondria (and chloroplasts), with their double membranes, are evolved from prokaryotes, engulfed into eukaryotic cells; They have some genes.

Also mitochondria are intimastely involved in programmed cell death (apoptosis)

Figure 4-18
chloroplast with 2 membranes plus granum with thylakoid membranes, frets and stroma. Note that the pigmernts for photosynthesis, in order to be absorbed by light, are deployed in multiple layers of membranes.

Figure 4-15
Lysosomes, need to introduce phagocytosis (phag - eat as in hyperphagic, eating too much, or bacteriophage, a virus that infects bacteria)
Lysosomes merge and digest.
This also applies to autophagy, where cell eats itself in a process of turnover of its components.
Here is a picture from my own work of lysosomes merging with recycled membranes in the Drosophila visual receptor,

Figure 4-7
flagella and cilia - "9 + 2" arrangement
Paramecia swimming cilia - beat reverses when bump

Figure 4-8
sperm flagella, cilia to clear mucus from trachea

Figure 4-6
(will be covered in muscle lectures)
also many other functions, streaming and anchoring of cytoplasm

Questions used in 2007 and 2008 relating to this outline

Posttranslational modifications are changes that are made to
(a) phage.
(b) cells when they are being prepared for microscopy.
(c) bacterial DNA.
(d) mitochondria.
*(e) proteins.

The Golgi apparatus receives vesicles from
(a) chromosomes.
(b) the nucleolus.
*(c) the rough endoplasmic reticulum.
(d) the cell wall.
(e) autophagy.

To "attack" antigens, an antibody
(a) uses phagocytosis.
(b) injects its RNA into the cell.
(c) must be polyunsaturated
(d) must reside within the lysosome.
*(e) is put out of the cell by exocytosis.

The primary structure of a protein
(a) depends on whether it is a "self" vs. a "non-self" protein.
(b) has to do with whether there is an alpha helix or a beta sheet.
*(c) depends on the sequence of amino acids.
(d) depends on glycosylation.
(e) is exemplified by the alpha and beta chains in hemoglobin.

ATP, is made
(a) by chopping out fragments from a protein.
*(b) in cytoplasm and mitochondria.
(c) during apotosis.
(d) by plasmids.
(e) by smooth endoplasmic reticulum.

(a) have a cell wall made of chitin.
(b) are metazoans with different genes active in different cells of the body.
(c) are so small that they can only be seen in the electron microscope.
*(d) have photosynthesis.
(e) are prokaryotes.

Mitochondria and chloroplasts are thought to have originated about 1.5 billion years ago
(a) when the microsomal fraction assembled into the smooth endoplasmic reticulum.
(b) as vesicles that blebbed off of the Golgi apparatus.
*(c) when prokaryotes became engulfed into the primordial eukaryotic cell.
(d) because of a mass extinction.
(e) because of genetic drift.

Ribosomes exist as free ribosomes, polysomes, and
(a) attached to the basal body.
(b) attached to the Golgi complex.
(c) attached to the chromosomes.
*(d) attached to the rough endoplasmic reticulum.
(e) in the spindle apparatus.

In phagocytosis, a food vacuole (endosome) merges with
*(a) a lysosome.
(b) a cilium.
(c) a microfilament.
(d) plasmodesmata.
(e) a nephridium.

Ribosomes are the site of synthesis of
B) phagocytosis.
D) nucleoli.
*E) proteins.

Which of the following is associated with rough endoplasmic reticulum?
A) chlorophyll
*B) ribosomes
C) cholesterol
D) microtubules
E) mitosis

What is not characteristic of a prokaryotic cell?
A) a cell membrane
*B) a nuclear membrane
C) a cell wall
D) plasmids

Receptors are membrane proteins that would be synthesized on ribosomes
*A) on the rough endoplasmic reticulum
B) on the smooth endoplasmic reticulum
C) on the Golgi complex
D) in the chloroplast
E) in the nucleus

Which organelle does one expect to be most abundant in cells that need lots of biological energy like cardiac muscle cells?
A) vacuoles
B) lysosomes
C) Golgi complexes
D) smooth ER
*E) mitochondria

If all the lysosomes within a cell suddenly ruptured, what could occur?
A) If it were a prokaryotic cell, it would become a eukaryotic cell.
B) If it were a Paramecium, it would swim backwards.
*C) The macromolecules in the cell cytoplasm would be broken down.
D) Antibody proteins would be exocytosed.
E) Proteins would be translated from DNA in vesicles.

Cells that primarily produce steroid hormones, as well as liver cells that destroy toxins, have large quantities of
A) apoptosis.
*B) smooth endoplasmic reticulum.
C) cell walls.
D) heavy metals.
E) flagella

The Golgi packages materials into ________ for transport or exocytosis.
A) cilia
B) plasmids
*C) vesicles
D) vacuoles
E) nucleoli

Which organelle would a white blood cell use to destroy a bacterium it has phagocytosed?
A) nucleus
B) mitochondrion
*C) lysosome
D) polysome
E) flagellum

Which order describes the flow between endoplasmic reticulum (ER), exocytotic vesicles, and Golgi apparatus in the export of protein from the cell?
A) From Golgi to ER to vesicle.
*B) From ER to Golgi to vesicles.
C) From vesicles to Golgi to ER.
D) From Golgi to vesicle to ER.
E) From vesicles to ER to Golgi.

Questions used in 2002 relating to this outline (and other outlines)

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the plasmalemma; B to mediate transcription.
(e) A in the desmosome; B to carry the genetic code for each protein.

Lysosomes would function to
(a) make glucose from CO2 and H2O using energy from light.
(b) modify proteins coming from the endoplasmic reticulum.
(c) allow cells to move ("swim").
*(d) break down membrane-enclosed cellular waste or food.
(e) carry oxygen from the lungs to the tissues.

In which cellular organelle is most of the ATP produced from thorough glucose catabolism?
(a) nucleus
(b) rough endoplasmic reticulum
*(c) mitochondrion
(d) flagellum
(e) chloroplast

If a biochemist grinds up liver and isolates microsomes as fraction in the centrifuge tube, what would this organelle with enzymes for detoxifying alcohol, drugs or toxins, be as seen in an electron microscope?
*(a) smooth endoplasmic reticulum
(b) tight junction
(c) nuclear envelope
(d) microtubules
(e) contractile vacuole

When you see dark areas in transmission electron microscopy or what appear to be membrane proteins in freeze-fracture, you are actually seeing
(a) colored dyes such as those that make chromosomes to appear as colored bodies.
*(b) heavy metals such as osmium, lead, uranium and platinum.
(c) individual molecules.
(d) the effects of radioactive isotopes.
(e) covalent and ionic bonds.

This page was last revised 6/18/09


**The membrane lecture



Audesirk, Audesirk & Byers Chapter 5

Today's musical selection
Ray Charles America the Beautiful

Lipid biochemistry:

Figure 5-10
Get a good source of membranes: red blood cells (erythrocytes) from adult human have only plasmalemma. Gorter and Grendel showed in1925 that there was enough lipid to make two layers.
Put red blood cells into distilled water, they burst from hyposmotic shock and become only "ghosts" - membrane only.

Membrane structure

Figure 5-3
shows hydrophobic vs hydrophilic aspect of polar phospholipid
bilayer (Davson-Danielli)

Figure 5-2
shows the chemical structure of a polar phospholipid)

Figure 5-1
Fluid mosaic Singer and Nicolson
Proteins (channels, pumps, receptors, etc.) among lipids

Figure 5-4
Double bonds make more fluid, cholesterol makes less fluid.

Techniques to study membranes

Freeze fracture EM. Membrane is ripped in half, and membrane proteins are shadowed.

Picture I made freeze fracture replicas with this apparatus. Specimen is prepared, frozen to liquid nitrogen temperature, put inside a vacuum, smashed with a razor, blasted from an angle with a platinum gun (to shadow protein with electron dense metal), blasted from above with a carbon gun (to hold replica together), then the tissue is dissolved away.

Here, from my research, is an example of how things look. Picture shows visual membranes in Drosophila. High vitamin A has membranes full of protein (rhodopsin) while vitamin A deprivation eliminates this protein.

Membrane lipid types

Membrane lipids are composed of:
(1) Phospholipids such as phosphatidylcholine (lecithin)
I did some research on the phospholipids of the Drosophila head. Using radioactively lbeled phosphate, many different phospholipids are visualized after they have been separated on a TLC (thin layer chromatography) plate.
(2) Cholesterol
(3) Glycolipids such as one that accumulates in Tay-Sachs, a hereditary lysosomal storage disease,1/30 Am. Jews carry, recessive, fatal at 6 mo - 5 yr
The sugar groups of glycoproteins and glycolipids are on the outside of the membrane.

Signal transduction

It used to be thought that lipids just sit there. In the 1980's it became clear that they turn over metabolically and that some products of membrane lipid turnover are important mediators of intracellular signalling. This is very fundamental and will come up repeatedly in biology.

How do molecules get across the membrane?

Lipid makes a barrier to anything polar
(steroid hormones can go in)
Channels (for ions, electrical conductances)

Figure 5-12
how pump molecule uses ATP to make sodium and potassium gradients.

Bulk transport

Figure 5-15
phagocytosis - cell eating
pinocytosis - cell drinking

Figure 5-16

Figure 5-14
receptor mediated endocytosis - clathrin coated

Figure 5-19
Also holes in membranes from one cell to another are important:
(1) Gap junctions (animals)
(2) Plasmodesmata (plants)

shows some other functions of membrane proteins

(1) in addition to transport,
(2) many enzymes are on the membrane
(3) receptors for hormones, neurotransmitters and developmental signals are on the membrane.

Figure 5-18
(4) cells are joined by proteins
(5) cells communicate by proteins
(6) cells hook to extracellular proteins by proteins

Questions used in 2007 and 2008 relating to this outline

A red blood cell ghost was used to study
(a) lysosomal storage diseases.
(b) nuclei.
*(c) membranes.
(d) the genetic code.
(e) the action potential.

A TLC (thin layer chromatography) plate could be used to
(a) model continental drift.
(b) allow Cl- (chloride ions) to pass out of the cell.
(c) demonstrate phagocytosis.
(d) visualize proteins in a carbon-platinum replica of the membrane.
*(e) separate membrane lipids chemically.

Clathrin coated pits are part of what process?
(a) meiosis
(b) apoptosis
(c) hydrolysis
*(d) endocytosis
(e) transcription

It would take energy in the form of ATP to transport Ca2+ ions from [A] to [B].
(a) [A] coated pit; [B] coated vesicle
*(b) [A] inside the cell; [B] outside the cell
(c) [A] microfilament; [B] microtubule
(d) [A] omega figure; [B] coated pit
(e) [A] nucleus; [B] rough endoplasmic reticulum

The function of a gap junction is
(a) to hold cells together.
*(b) allow confluence of cytoplasm of adjacent cells.
(c) receptor mediated endocytosis.
(d) to allow a white blood cell to "eat" bacteria.
(e) to make the plant cell wall permeable.

Pseudopods might be used by Amoebae to eat Paramecia by a process called
(a) exocytosis.
(b) phosphorylation
(c) hydrophobicity.
(d) autoradiography.
*(e) phagocytosis.

Which is true about glycolipids?
(a) They are the rigid motile elements of cilia and flagella.
(b) They are the universal currency of biological energy.
(c) They are phosphorylated peptides.
*(d) They accumulate in victims of Tay-Sachs disease.
(e) Phosphatidylcholine is the predominant type.

Tight junctions are used
*(a) to keep layers of cells from leaking.
(b) to hold the tRNA to the DNA.
(c) in the Kreb's cycle.
(d) in flagella.
(e) to coat vesicles used in bulk transport.

The central concept of the fluid mosaic model is that
*(a) there is enough lipid in membranes to make two layers.
(b) mRNA can pass freely from the cytoplasm to the nucleus.
(c) ions can pass through the hydrophobic layer.
(d) 38 pyruvates are made from one glycogen.
(e) the cell membrane is the only membrane in eukaryotic cells.

*A) are found in cell membranes.
B) are completely hydrophilic.
C) are completely hydrophobic.
D) are made in the mitochondria.
E) allow water and ions to move from outside the cell into the cell.

In general, which of the following is largely responsible for moving substances across the plasma membrane?
A) the bilayer of lipids
B) carbohydrates
*C) proteins
D) nucleic acids
E) cytoskeleton

Which of the following would not be found in a membrane?
*A) cellulose
B) cholesterol
C) phospholipid
D) channel protein
E) receptor protein

Glucose gets into the cell
A) by drifting through the lipid bilayer like steroid hormones do.
*B) with the aid of transport proteins.
C) only when ADP plus phosphate is converted into ATP.
D) with the help of a protein named clathrin.
E) by exocytosis.

What does a cell use exocytosis for?
A) to move away from danger
B) to create identical "daughter" cells
C) to keep a layer of cells from leaking (between the cells) like a sieve.
D) to move bad cholesterol (LDL) into the cell
*E) to release substances from the cell

What is not characteristic of a prokaryotic cell?
A) a cell membrane
*B) a nuclear membrane
C) a cell wall
D) plasmids

Receptors are membrane proteins that would be synthesized on ribosomes
*A) on the rough endoplasmic reticulum
B) on the smooth endoplasmic reticulum
C) on the Golgi complex
D) in the chloroplast
E) in the nucleus

The feature that creates a barrier to the movement of ions across the membrane is
A) channel proteins
B) cellulose
C) lactase
*D) fatty acids
E) vitamin E

How are plasma membranes BEST described?
A) a double layer of phospholipid molecules with hydrophobic tails directed toward the cytoplasm of the cell
B) a single layer of phospholipid molecules with water molecules attached along one side
C) a double layer of phospholipid molecules with hydrophilic heads directed toward each other
*D) a double layer of phospholipid molecules with hydrophobic tails oriented toward each other
E) a single layer of phospholipids with tails pointed to the inside of the cell

Within the fluid mosaic of a plasma membrane, what is the role of proteins?
A) They bind estrogen and testosterone since these molecules cannot cross the membrane.
B) They are the site of ADP formation.
C) They cause arteriosclerosis.
D) They are the site of transcription.
*E) They serve as channels and receptors and for transport.

The dominant type of lipid found in cell membranes is
A) the ribosome.
B) vitamin A.
*C) phospholipid.
D) a glycoprotein.
E) the type that accumulates in Tay-Sach's Disease.

Glucose gets into the cell
A) through coated pits
*B) with the aid of proteins.
C) when ADP plus phosphate is converted into ATP.
D) with the help of clathrin.
E) by exocytosis.

If red blood cells are taken from the body and placed into a hypotonic solution (like distilled water), what happens to the cells?
*A) The cells swell and burst because water moves into the cells.
B) The cells shrivel up because water leaves the cells.
C) Gap junctions will form.
D) "Good cholesterol" (LDL) will be transported.
E) Desmosomes and tight junctions will form.

Sometimes, the cytoplasm of a cell will have too many calcium (Ca2+) ions. How does the cell re-establish its normal calcium homeostasis?
A) by receptor-mediated endocytosis
B) phagocytosis
C) osmosis
D) through plasmodesmata
*E) active transport

The electric signal goes from one myocardial (heart muscle) cell to the next through
A) coated pits.
B) desmosomes.
*C) gap junctions.
D) glycolipids.
E) active transporters that utilize ATP.

Questions used in 2002 relating to this outline (and other outlines)

One reason that membrane lipids are arranged the way they are is because of
(a) essential amino acids.
(b) ionic bonds.
*(c) hydrophobic fatty acids.
(d) hydrolysis of bonds.
(e) the half life.

A cell's membrane consists principally of two layers of
(a) hydrocarbon.
(b) disaccharides.
(c) cellulose.
*(d) lipid.
(e) collagen.

This page was last revised 7/8/08


**The metabolism lecture


Any plant or man who dies
adds to Nature's compost heap
becomes the manure without which
nothing could grow nothing could be created
Death is simply part of the process
Every death even the cruellest death
Drowns in the total indifference of Nature
Nature herself would watch unmoved
if we destroyed the entire human race
I hate Nature
-Peter Weiss ... Marat ...Sade 1965

Audesirk, Audesirk & Byers Chapters 6 & 8

Today's musical selection
Jay and the Americans - Only in America


Metabolism is the general term for two kinds of reactions:
(1) catabolic reactions (breakdown)
(2) anabolic reactions (constructive)

Energy saved mostly through photosynthesis (Chapter 7, does not fit in this one semester)
released through "respiration" ("respiration" applies to breathing and cellularrespiration)

Figure 6-8
ADP plus phosphate <-> ATP involved in storage and release of energy
ATP made of Adenine, ribose and 3 phosphates, energy stored in 3rd phosphate bond

Figure 6-5
"Burning" glucose

Figure 6-3
substrates (reactants)-> products

Figure 6-13
Simplified metabolic pathways
Reminder: enzymes are named with suffix "-ase."

Figure 6-14
overcome energy of activation - catalysts - enzymes


Energy - kinetic and potential (later, discussing bioelectricity, potential will also be Volts)
First law of thermodynamics - energy of universe is constant
Second law - things become more disordered
Humanities: a 10 page science fiction story Isaac Asimov, The last Question in which it is asked what happens after the universe is dissipated.)
Energy flows as entropy increases.
In general, heat is waste and not useful.
BTU's (British thermal units, which can be converted to calories) imply that energy and heat are related.
Heat stored in energies of covalent bonds in kcal / mol
Free energy can be used for work = what is stored in bonds minus what is wasted as heat

Figure 6-3
e.g. cellular respiration C6H12O6 -> 6CO2 +6H2O + energy
the free energy is 686 kcal/mol


Figure 8-10
Store glucose energy into ATP
38 of them generated when respiration is complete
40.3% efficient, the rest is heat, usually considered as waste but useful in temperature regulation in warm blooded animals, homoiotherms, homeotherms.

It is easy to mistakenly think that energy use is only by muscles. However, a lot of the body's energy is used in transport and in reactions. ATP transfers its 3rd phosphate to molecules and the phosphate is then released as inorganic phosphate to be eventually added to ADP to make ATP.

Figure 6-19
Optimum tempreature for human enzyme may be near 37oC, body temperature. For a thermophilic bacterium, it may be very high, useful in PCR (polymerase chain reaction). Also, optimum pH for pepsin (proteolytic enzyme in stomach) is acidic while for amylase (polysaccharide enzyme in saliva) is slightly basic.

Biological Energy

Reminder - "count" "calories"= kcal
2000 per day for a sedentary woman
Important that we do not lose calories (through urine or feces) except through urine in untreated diabetes.

Figure (Chapter 6 opener)
(also Chapter 6 case study, energy unleashed, p. 101 and revisited, p. 113)
Marathon - 3000 Cal aerobic. 100 yd dash -anaerobic

Figure 6-10
ATP's 3rd phosphate bond has lots of energy, and breaking that bond releases the energy, but interestingly, how cells use energy is to put that phosphate from ATP onto a molecule like an ion pump or muscle's myosin molecule.

We get our energy mostly from (1) glucose, (2) glycogen (glyco-sugar, gen-give rise to) in muscle for use in muscle and in liver for glucose release to blood, (3) amino acids (with NH3 as waste), or (4) fat (mostly fatty acids are chopped down 2 carbons at a time to give acetic acid into acetyl CoA in the Kreb's cycle).

photosynthesis to make glucose, cellular respiration to release energy
Reaction [for glucose, C6(H2O)6]: C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O


Figure 8-10
Overall, 1 glucose can give up to 38 ATP's, a few from glycolysis and the rest from the mitochondrion


Figure 8-2
NAD+ plus 2 H <-> NADH in oxidation - reduction reactions as a way to carry electrons.
lose electrons - oxidation (NAD+ is oxidized)
nicotinamide adenine dinucleotide
add electrons - reduction (NADH is reduced)

Figure 8-1
Glycolysis is a compound word
Glucose is split into 2 pyruvic acids
Use 2 ATP's make 4, net 2 make 2 NADH's plus 2 H+'s, the H+'s come from from "sugar"

Anaerobic glycolysis

Figure 8-4
without oxygen, make ethanol or lactate (lactic acid).
Anaerobic glycolysis is used to deliver ATP quickly but wastefully (squandering glucose).
Make ATP's but need to regenerate NAD+ from NADH] to make.
Lactic acid contributes to fatigue in muscle and oxygen debt, and the liver eventually reconverts.
Anaerobic cellular "respiration" is needed in times of extreme exertion because the heart (cardiac output) is the limiting factor in delivery of oxygen to muscle.
Lactic acid is also made by bacteria in yogurt, sour cream, and cheese.

Krebs cycle

Figure 8-9
Pyruvic acids generate 2 acetic acids, become Acetyl CoA's.
Kreb's cycle = citric acid cycle = TCA (tricarboxylic acid cycle)
Takes place in the mitochondrion
A few ATP's are made plus NADH's and FADH2 are generated
Notice that CO2 is generated here.

The1953 Nobel prize in Physiology and Medicine was divided equally, one half awarded to: SIR HANS ADOLF KREBS for his discovery of the citric acid cycle and the other half to: FRITZ ALBERT LIPMANN for his discovery of co-enzyme A and its importance for intermediary metabolism.

Electron transport

Figure 8-8
sugar-H2 + NAD+ -> (DEHYDROGENASE) "sugar" + NADH + H+
(in other words, H is split to H+ and e-)
Electron transport and oxidative phosphorylation use oxygen
cytochromes - these are iron - containing pigments (iron is in the form of heme)
Iron is not abundant, but it is important in biology.
NADH and FADH2 give electrons to cytochromes and oxygen

Protons pumped, then flow down gradient making ATP's.
Something like an ion pump (we will cover that a lot later in the semester) in reverse is how most ATP is made, H+ (pH, proton) gradient runs through that molecule, like water running through turbines generating electricity, to generate electricity

Questions used in 2007 and 2008 relating to this outline

"Thermophilic" is a term applied to
(a) warm blooded animals.
(b) enzymes like pepsin that function well in stomach acid.
(c) entropy.
*(d) bacteria whose enzymes are used in PCR (the polymerase chain reaction).
(e) counting calories.

Hydrogen ions are pumped across a membrane, then, when they run back, they generate ATP. This is a simplified statement of
(a) thermodynamics.
(b) anaerobic glycolysis.
(c) the role of lactic acid in fatigue.
*(d) the electron transport chain.
(e) translation.

686 kcal per mole describes
(a) acetyl CoA.
*(b) energy from glucose breakdown.
(c) NAD+ and NADH.
(d) homeotherms.
(e) urea formation resulting from amino acid catabolism.

"Exerogonic" is a term applied to
(a) cell drinking.
(b) the "central dogma" of cell biology.
*(c) reactions.
(d) protein synthesis.
(e) apoptosis.

About what fraction of ATP is made by glycolysis when respiration is aerobic?
*(a) 1/16
(b) 1/4
(c) 1/2
(d) 3/4
(e) 15/16

In the delivery of biological energy
(a) sucrase gets used up when it generates glucose and fructose.
(b) the mitochondria use CO2 to produce O2.
(c) heat and entropy are captured and stored in ADP.
(d) glucose is taken into muscle (when insulin is low) where it is converted into triglycerides.
*(e) phosphate is typically transferred from ATP to another molecule.

Questions used in 2002 relating to this outline (and other outlines)

In the delivery of biological energy
(a) sucrase gets used up when it generates glucose and fructose.
*(b) phosphate is typically transferred from ATP to another molecule.
(c) heat and entropy are captured and stored in ADP.
(d) the end-product feeds back to inhibit the rate-limiting enzyme.
(e) the mitochondria use CO2 to produce O2

A reaction that requires oxygen is called
(a) autotrophic.
(b) fermentation.
(c) anabolic.
(d) reduction.
*(e) aerobic.

Kilocalories, those "calories" you count when you are dieting, are a measurement of
(a) water content of food and drink you consume.
(b) amino acid content of food.
*(c) energy available in food.
(d) relative fat content of food.
(e) relative carbohydrate content of food.

The fundamental function of aerobic respiration in cells is
(a) production of glucose.
*(b) the release of energy.
(c) storage of entropy.
(d) the replication of DNA.
(e) biosynthesis of triglycerides.

In which cellular organelle is most of the ATP produced from thorough glucose catabolism?
(a) nucleus
(b) rough endoplasmic reticulum
*(c) mitochondrion
(d) flagellum
(e) chloroplast

If animal muscle cells are depleted of sufficient levels of oxygen during use, anaerobic glycolysis will result and pyruvic acid will be converted into
*(a) lactic acid.
(b) carbon dioxide.
(c) glucose.
(d) glycogen.
(e) oxygen.

Energy that is not converted to useful energy is usually given off as
A) radioactivity.
C) pH.
*D) heat.
E) ethanol.

At the end of glycolysis, the original carbons of the glucose molecule form
A) carbon dioxide.
B) hydrogen ions (H+) plus electrons (e-).
*C) two molecules of pyruvic acid.
D) two fatty acid chains.
E) sucrose.

H+ (hydrogen ions) run across a membrane protein to generate most of the ATP
A) during glycolysis.
B) during fermentation.
C) during the Krebs cycle
D) when pyruvic acid is converted to Acetyl CoA.
*E) in the mitochondrion.

Entropy is a measure of
A) anabolic reactions.
B) enzymes.
C) fermentation.
D) lactic acid.
*E) disorder.

During glycolysis, the net production of ATP is
A) one molecule.
*B) two molecules.
C) 34 molecules.
D) 36 molecules.
E) 38 molecules.

A "high-energy" bond in an ATP molecule is located between
*A) the second and third phosphate groups.
B) acetic acid and acetyl CoA.
C) the cytoplasm and the mitochondrion.
D) the production of CO2 and the production of H2O.
E) pyruvate and lactic acid

Why are enzymes important?
A) They are carbohydrates.
B) They are the basis of the laws of thermodynamics.
C) They are the universal "currency" of energy in biological systems.
*D) They catalyze reactions at body temperature
E) They are only important in the laboratory in PCR (polymerase chain reactions).

When the breakdown of glucose happens with insufficient oxygen,
A) water and carbon dioxide are formed.
B) NH3 is formed.
C) that is when the electron transport chain is used
*D) it is called anaerobic glycolysis.
E) it is called the Krebs cycle

What results if glucose is metabolized under aerobic conditions (the reactions are allowed to go to completion)?
A) Acetic acid comes out of the mitochondrion to become ethanol.
*B) 36 or 38 ATP molecules are made.
C) Oxygen is not used since it is not available.
D) Lactic acid is formed in muscle.
E) Carbon dioxide plus water are converted to glucose.

This page was last revised 6/24/09


**The DNA lecture

DNA - the molecule of heredity


Audesirk, Audesirk & Byers Chapter 9, part of Chapter 10 and several figures from other chapters

Today's musical selection
Waltz round the cycle


Figure 9-1
It was not until the 1940's that it was proved that DNA was the material of heredity.
(work of Griffith and Avery) S (smooth) bacteria kill mouse, R (rough) not, DNA from S can transform R to make them deadly.

Central dogma

Figure 10-3
One "gene" codes for one "protein"
Central Dogma (of cell biology)
DNA (nucleus, virus) ONE GENE
mRNA (nucleus to cytoplasm in eukaryotic cell)

Figure E19-2a
retrovirus, like HIV, makes DNA from a template of RNA using an enzyme called reverse transcriptase.

Figure 10-2
RNA's: m (messenger), r (ribosomes), t (transfers aa's)

Table 10-1
Nucleic acids: nucleotide = sugar, PO4 & base (no essential nucleic acids)
Sugar (ribose or deoxyribose), phosphate (PO4), base
4 bases in DNA: Adenine, Guanine, Thymine, Cytosine
4 bases in RNA: The same except Uracil instead of Thymine
purines - A & G, pyrimidines - C, T, U

How can DNA lead to so much biological variability?

Two in a row nucleotides in a row would give 4 x 4 = 16 possibilities.
This is < 20, the number of amino acids, so 2 would not be enough for code.
It takes a longer macromolecule of DNA to code for a protein than the protein it codes for.

Table 10-3
(The genetic code)
4 x 4 x 4 - there is a 3 letter word (codon) consisting of 4 letters for each amino acid.
However 4 x 4 x 4 = 64 is more than enough (redundant) and the word for this is degeneracy, in that there are several codes for certain of the amino acids.

DNA has a built in way to reproduce itself accurately...

Figure 9-6
DNA is a double helix, with A across from T and C across from G
this pairing is essential for DNA to reproduce itself.
DNA is quite stable and accurate in its replication.

...and to orchestrate transcription and translation

Figure 10-9
In making RNA, the same pairing applies except that U is across from A.

More detail on DNA replication

Figure E9-7
each strand contains all the information necessary, put into action by each strand being capable of organizing the other strand; but instead of the two strands separating entirely and generating the daughter strand, numerous bubbles form where the parental strand is copied at the replication fork.

5'->3' direction replication fork
DNA helicase and leading strand DNA polymerase
lagging strand:
DNA polymerase makes one piece at a time
DNA ligase puts pieces together


Figure 12-29
Sickle-cell anemia

Figure 9-8
DNA is quite stable and accurate in its replication. However, sometimes factors such as chemical mutagens and ionizing radiation cause alterations called mutations. In the fully evolved organism, mutations are usually deliterious, but they can sometimes create an advantage. On the evolutionary time scale, mutations have been the driving force of divergent evolution and adaptive radiation.

Disorder which turns human red blood cells (erythrocytes) sickle shaped (sickle cell anemia) is caused by a mutation substituting Val for Glu at amino acid #6 in the beta chain of hemoglobin. This disorder is high in African-American of equatorial African origin. Homozygous, it is very bad, but heterozygous, it confers resistance to malaria.

Orientation for using microscopes in cell lab (and other labs)

Fig. 1 - Start with the lowest power objective with the stage all the way up
Fig. 2 - Best to use your left hand on the focus knobs...
Fig. 3 - ...so that your right hand is available to move the slide

To find and focus your specimen:
(1) put a landmark, like the edge of the cover slip or a highly stained part of the slide in the light beam
(2) [from the stage up position with the lowest power objective, see above] move the slide's landmark back and forth (right hand) (or up and down) continuously while moving the stage down (left hand)
(3) when the landmark is in focus, find the specimen
(4) the microscope is parfocal, meaning that you can then go to higher power objectives and be reasonably close to focus

Questions used in 2007 and 2008 relating to this outline

In the genetic code, how many different triplets are there?
(a) 3
(b) 4
(c) 16
(d) 20
*(e) 64

What substance from S bacteria convert R bacteria into a form that is lethal to mice?
*(a) DNA
(b) NADH
(c) Glycogen
(d) ATP
(e) Protein

In transcription,
(a) mRNA is used to make protein.
(b) the ribosomes are used.
*(c) DNA is used to make mRNA.
(d) the anticodon is matched to the codon.
(e) RNA is used to make DNA.

HIV (human immunodeficiency virus)
(a) remains outside the cell like a bacteriophage.
(b) is made up of DNA and protein.
(c) is the only virus (or organism) with degeneracy in its genetic code.
(d) works backwards by using anticodons instead of codons.
*(e) uses reverse transcriptase.

How might a complementary vs. a template DNA strand differ?
(a) Across from U would be A.
*(b) Across from A would be T.
(c) Across from C would be C.
(d) Across from G would be glycine.
(e) Across from DNA would be RNA.

Replication forks would be used in conjunction with
*(a) DNA polymerase.
(b) translation.
(c) reverse transcriptase.
(d) sickle cells.
(e) heterozygous mutations.

A ribosome is used to assist in the process of
(a) transcription.
(b) copying DNA into mRNA.
*(c) translation.
(d) conversion of ATP to ADP.
(e) dehydration synthesis.

Transfer RNA (tRNA) is used in the process of
(a) oxidative phosphorylation.
(b) exocytosis.
(c) producing a karyotype.
(d) crossing over.
*(e) translation.

Which is NOT true about HIV (Human Immunodeficiency Virus)?
(a) It goes into the cell it infects.
*(b) It belongs to the kingdom of protista.
(c) Causing AIDS, it preferentially depletes helper T cells.
(d) Its hereditary material is RNA.
(e) Reverse transcriptase is already present.

A ribosome is used to assist in the process of
(a) transcription.
(b) copying DNA into mRNA.
*(c) translation.
(d) conversion of ATP to ADP.
(e) dehydration synthesis.

Transfer RNA (tRNA) is used in the process of
(a) oxidative phosphorylation.
(b) exocytosis.
(c) producing a karyotype.
(d) crossing over.
*(e) translation.

Which is NOT true about HIV (Human Immunodeficiency Virus)?
(a) It goes into the cell it infects.
*(b) It belongs to the kingdom of protista.
(c) Causing AIDS, it preferentially depletes helper T cells.
(d) Its hereditary material is RNA.
(e) Reverse transcriptase is already present.

Because of degeneracy of the DNA code,
A) the HIV retrovirus disobeys central dogma.
B) most mutations are bad.
C) both strands can be used for DNA to reproduce itself, but only one strand can be used to code for a specific protein.
D) it takes four nucleotides in a row to determine one amino acid.
*E) it might be possible to have a mutation in the DNA without changing the protein it codes for.

Which is NOT true about hemoglobin?
A) It contains iron.
B) It is in red blood cells.
C) It is altered in sickle cell anemia.
*D) It is an enzyme that makes DNA from a template of mRNA.
E) It is a protein used for the transport of oxygen.

Which would have the greatest potential for variability?
*A) a peptide 3 amino acids long
B) a nucleotide chain 3 base pairs long
C) a hydrocarbon 3 carbons long
D) a glycogen chain 3 glucose molecules long

What was the main point of Griffith's experiments with pneumonia in mice?
A) A mutation is how the R strain becomes the S strain.
B) DNA was reverse transcribed into RNA using DNA ligase.
C) Protein carries the code for heredity.
D) RNA is translated into DNA.
*E) There is a substance present in dead bacteria that can cause a heritable change in living bacteria.

DNA has
A) A, U, G, and C bases.
B) only purines.
C) anticodons.
*D) C, T, A, and G bases.
E) all 5 bases: A, U, G, T, and C.

The DNA of a certain organism has guanine as 30% of its bases. What percentage of its bases would be adenine?
A) 0%
B) 10%
*C) 20%
D) 30%
E) 40%

For the DNA sequence GCCTAT in the template DNA strand, the sequence found in the complementary DNA strand is

How does the Watson and Crick model of DNA structure help explain DNA replication?
A) Uracil is always across from Thymine.
*B) Precise base pairing allows the base sequence to be copied.
C) Methionine is the amino acid for the stop codon.
D) Some amino acids are purines and these are mutated to different amino acids, pyrimidines.
E) It doesn't; DNA never replicates.

A stretch of DNA 10 nucleotides long can have how many possible sequences of the four bases?
A) one
B) four
C) ten
D) hundreds
*E) way more than any of the above

Questions used in 2002 relating to this outline (and other outlines)

Which would have the greatest potential for variability?
(a) a nucleotide 3 base pairs long
*(b) a peptide 3 amino acids long
(c) a hydrocarbon 3 carbons long
(d) a glycogen chain 3 glucose molecules long
(e) ATP

Which nucleotide base is used in RNA but not DNA?
(a) cytosine
(b) adenine
(c) thymine
*(d) uracil
(e) guanine

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the plasmalemma; B to mediate transcription.
(e) A in the desmosome; B to carry the genetic code for each protein.

Making mRNA from a template of DNA is called
(a) respiration.
(b) glycolysis.
(c) motility.
*(d) transcription.
(e) fluorescence.

Because of degeneracy of the DNA code,
(a) the HIV retrovirus disobeys central dogma.
(b) most mutations are bad.
(c) both strands can be used for DNA to reproduce itself, but only one strand can be used to code for a specific protein.
(d) it takes four nucleotides in a row to determine one amino acid.
*(e) it might be possible to have a mutation in the DNA without changing the protein it codes.

Which is a purine base of a nucleotide?
*(a) adenine
(b) ribose
(c) phenylalanine
(d) lactic acid
(e) actin

Which is not true about hemoglobin?
(a) It contains iron.
(b) It is in red blood cells.
(c) It is altered in sickle cell anemia.
*(d) It is an enzyme that makes DNA from a template of mRNA.
(e) It is a protein used for the transport of oxygen.

A ligase would be used in
(a) control of gene transcription.
(b) synthesis of DNA from the hereditary molecule in the HIV (human immunodeficiency virus).
(c) western blotting.
(d) lagging strand replication.
(e) cutting open a plasmid to prepare for cloning a gene.

In the 1940's, Avery and others showed DNA was the important part of smooth bacterial extract that made rough bacteria pathogenic in Griffith's experiment. The phenomenon Griffith demonstrated is called
(a) transformation.
(b) conjugation.
(c) cloning.
(d) hybridization.
(e) operon regulation.

This page was last revised 6/26/09

**The central dogma lecture

Central dogma and proteins


Audesirk, Audesirk & Byers Chapter 10

Today's musical selection
Lewis Lee Attack of the killer tomatoes

Central Dogma of cell biology (review)

Figure 10.3
(reverse transctiption, using reverse transcriptase enzyme, in AIDS-causing retrovirus HIV)
As you will eventually see, there is more to it than this, like RNA processing,

Genetic code (partly a review)

Table 10-3
3 letter code for aa's (codons)
Note, with 20 amino acids, and 4 x 4 x 4 = 64 codons, there is redundancy, called "degeneracy."
For instance, (top left) for phenylalanine, code can be UUU or UUC.
(It is interesting to contemplate that if a mutation converted UUU to UUC or vice versa, the amino acid would still be the same.)
There are 3 stop codons
Methionine is the start codon

Study question: Is this code for RNA or DNA?
Answer: RNA (You can tell when you notice that U is one of the four bases specified)

Figure 10-9
combining the information from the last 2 figures, here is a diagram of what nucleotide sequences might be for DNA and RNA and the amino acid sequence would be.
(It is interesting to contemplate that only one of the two DNA strands would work, the "template DNA strand" or the sense strand [the other being "the complementary DNA strand" or the antisense strand])

Example: Hemoglobin

Table 10-4
On the topic of mutations, consider that if CTT changes to CAT, Glu -> Val, the sickle cell anemia mutation.
When one amino acid is changed to another, this is a missense mutation.


(1) change base in degenerate 3rd position - no effect
(2) change a base that matters - "missense" - the protein will have a different amino acid
(3) change base so that there is a stop codon - "nonsense" the protein will not be full length
(4) insertion or deletion - many amino acid changes and/or premature stop
To understand this last point, I introduce the expression "open reading frame;" even though you could conceivably start anywhere, only if you start in right place (the right one of 3 nucleotides) for a normal (non-mutant) gene will the reading proceed for a reasonable distance without hitting a stop codon.

Transcription and translation

Figure 10-4a
RNA polymerase makes mRNA
(I'll say more about the "promoter" later)

Figure 10-5
What transcription looks like

In general, there are 3 RNA's, t (transfer), m (messenger), and r (ribosomal).
(1) Ribosome is the machinery, and it is big.
(2) mRNA codes for the protein.
(3) Many different tRNA's read (by base pairing, using the anticodon) each codon and carry one amino acid to the growing peptide chain.

Figure 10-8 (I will show Fig. 10-8 b, f, and i)
step by step, peptide is elongated, aminoacyl tRNA (tRNA with amino acid hooked to it) brings in amino acid.
eventually, when one of the 3 stop codons is encountered, the protein is released.

Question: What is a gene?

One theoretical answer: The DNA sequence that codes for one protein.
But: In eukaryotes there is way too much DNA.
(1) There are extra stretches of DNA interspersed in the coding sequence.
(That will be one topic we cover here.)
(2) There are places between "genes," some of which regulate the genes because of:

The need for gene regulation

In multicellular eukaryotic organism,
(but this can be fairly permanent, development gene regulation)

Prokaryote example, the lac operon

Figure 10-10
(relates to fundamental topic of gene regulation) lac operon - genes for enzymes for metabolism of lactose, the disaccharide in milk. When lactose is present, allolactose pulls repressor off of operator so that RNA polymerase can move from promoter to make mRNA for genes (lacZ, lacY and lacA) that code for their respective enzymes (beta-galactosidase, permease and transacetylase, enzymes for lactose metabolism. The bacterium "does not bother" making lactose metabolizing enzymes unless lactose (the sugar in milk) is present. Note that one mRNA is for 3 proteins, never the case in eukaryotes.

The 1965 Nobel Prize was shared by FRANÇOIS JACOB and JACUES MONOD who established the operon model.

Lactose digestion in humans

Box on p. 113
(also reference in digestion chapter
All infants can digest lactose, obviously
There is a racial difference in whether adults have lactase.
Blacks and Asians are likely to be lactose intolerant
Caucasians are usually lactose tolerant
Europeans evolved with dairy husbandry

Eukaryotic gene structure and RNA processing

Figure 10-7
RNA polymerase II makes "pre-mRNA"
methylated G nucleotide - at 5' cap
extra copied after end of gene is not capped, degraded
poly-A tail 100-200 residues of adenylic acid
site shows where end of gene transcription should be.
primary transcript
Exons are spliced together and form the coding sequence, and introns are spliced out.

Question: Is this splicing useful in any way? (other than to get rid of junk DNA)
Answer: Different exons can be spliced together (for instance in different tissues) to make several different proteins from the same gene.

Promoting gene action

Note that there are places "upstream" of the "gene" (coding sequence), the promoter, where transcription factors (proteins) bind to notify RNA polymerase to do its job. Since the 1980's, there has been a lot of interest in "promoter bashing," determining properties of the transcription factors and the DNA sequences they interact with. Here is where many hormones and signaling pathways determine a cell's specifics

Questions used in 2007 and 2008 related to this outline

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the microsomal fraction; B to mediate transcription.
(e) A in the intercalated disk; B to carry the genetic code for each protein.

A poly-A tail characterizes
(a) the intron.
*(b) mRNA.
(c) the operator.
(d) methionine.
(e) the anticodon.

In eukaryotes, what gets spliced to what?
(a) The promoter to the coding sequence.
(b) The lacZ, LacY and LacA genes.
(c) The template and complementary DNA strands.
(d) Jacob to Monod.
*(e) One exon to another.

An amino acid can be coded for by more than one codon. What is this called?
(a) Heterozygosity
*(b) Degeneracy
(c) Nondisjunction
(d) Translation
(e) Nonsense mutations

The tRNA molecule for which amino acid binds to the start codon during translation?
(a) Tyrosine
(b) Glucose
(c) Arginine
(d) Glycine
*(e) Methionine

Humans only have a fraction of their DNA that codes for proteins. Where is this? (a) in ribosomes
(b) in operators
(c) in promoters
(d) in introns
*(e) in exons

What factor accounts for the variety of cell types in different tissues?
(a) Some cells are homozygous, others are heterozygous.
(b) Different cells have different subsets of genes.
*(c) Different genes are expressed.
(d) Different cells contain different sets of chromosomes.
(e) Some mRNAs are translated; others are not.

The codons on the table for the genetic code are triplets from
(a) the template DNA strand.
(b) the sense DNA strand.
(c) the complementary DNA strand.
*(d) mRNA.
(e) the RNA sequence of ribosomal RNA (rRNA)

What would happen if a codon for an amino acid were mutated into a stop codon?
(a) Lactose intolerance would result.
(b) There would be a missense mutation.
*(c) The growing peptide would be ejected from the ribosome prematurely.
(d) Not much since the change would be in the third base.
(e) People would suffer from sickle cell anemia.

In the lac operon, RNA polymerase would be blocked if (what) were present?
*(a) The repressor.
(b) Introns.
(c) The operator.
(d) The promoter.
(e) Lactose.

DNA polymerase had already duplicated the DNA to make two identical copies of all the genetic material. Where are these two copies?
(a) in the two kinetochores
(b) in the two centrioles
*(c) in the two sister chromatids
(d) in the two homologues
(e) one in the autosome, the other in the sex chromosome
Which of the following is TRUE of the genetic information in the cells of your body?
A) Different kinds of cells contain different genetic information.
B) Each type of cell contains only the genetic information it needs to be that type of cell.
*C) The genetic information in all somatic cells (this excludes gametes) is identical.
D) Growth, development, and differentiation result from mutations in DNA.
E) Meiosis ensures that each somatic cell will be different.

The number of consecutive mRNA bases needed to specify one amino acid is
*A) 3.
B) 4.
C) 20.
D) 64.
E) many more than any of the above numbers .

"Val is substituted in place of Glu in the sixth position of the beta chain of hemoglobin."
A) This a nonsense mutation.
B) This could only happen if the deletion of one base pair offset the open reading frame.
C) This is because of regulation of the lac operon.
*D) This is a result of a mutation in DNA that causes sickle cell anemia.
E) This is because of degeneracy in the genetic code.

The number of different possible codons is
A) 3.
B) 4.
C) 20.
*D) 64.
E) way higher than any of the above numbers.

"Splicing" is a term applied to
A) the polycistronic (multi-gene) mRNA of bacteria.
*B) putting together exons to make mRNA from pre-mRNA.
C) the release of mRNA from DNA when the RNA polymerase reaches the end of the gene.
D) what happens at the ribosome when a stop codon is encountered.
E) regulating which genes are expressed in different cells.

What would happen if the complementary DNA strand were transcribed into mRNA instead of the template strand?
A) It seems to me it ought to work if RNA polymerase just went the other way along the DNA double helix.
B) That is precisely what happens in the checkpoint letting cells in G0 go on into prophase.
C) That is precisely what the cause of missense mutations is.
D) Lactose would be bound to the repressor.
*E) A ridiculous mRNA would be made and the translation machinery would encounter stop codons.

All of the following occur during DNA replication EXCEPT
A) separation of parental DNA strands.
B) use of parental DNA as a template.
*C) translation into RNA.
D) synthesis of a new strand to make double-stranded DNA.
E) use of DNA polymerase.

When comparing DNA and RNA, we find
A) RNA has the sugar deoxyribose while DNA has no sugar.
B) DNA is a chain of nucleotides while RNA is a chain of amino acids.
C) DNA is used for translation while RNA is used for transformation.
*D) adenine pairs with different bases in DNA and RNA.
E) cytosine pairs with different bases in DNA and RNA.

Questions used in 2002 relating to this outline (and other outlines)

The central dogma of cell biology
(a) postulates that protein is transcribed directly from DNA.
*(b) runs in reverse with the virus that causes AIDS.
(c) applies to how one DNA strand has the information to synthesize the other strand.
(d) states that amino acid sequences are translated into nucleotide sequences.
(e) explains the plasmid.

(a) are "jumping genes" with inverted repeats at their ends.
(b) are the type of virus that "eat" bacteria.
(c) are only found in prokaryotes.
*(d) are the parts of eukaryotic pre-mRNA that are spliced out to make mRNA.
(e) cause mad cow disease.

In prokaryotes, transcription
(a) makes a molecule with introns and exons.
(b) makes proteins.
(c) makes transcription factors.
*(d) makes mRNA.
(e) takes place in the nucleus.

Anticodon is a term applied to
(a) ribosomal subunits.
(b) the DNA template.
*(c) aminoacyl-tRNA.
(d) the exon.
(e) the poly-A tail.

Reverse transcriptase would work on [A] to form [B].
(a) [A] bacteria; [B] bacteriophage
(b) [A] pre-mRNA; [B] mRNA
(c) [A] mRNA; [B] protein
(d) [A] DNA; [B] PCR reaction products
*(e) [A] RNA; [B] DNA

If the sequences of bases along the template strand of DNA is A-G-A-T, what is the sequence along the mRNA strand?
(a) A-G-A-T
*(b) U-C-U-A
(c) A-T-C-T
(d) A-G-A-U
(e) U-A-G-A

Sickle cell anemia is a
*(a) missense mutation.
(b) nonsense mutation.
(c) frameshift.
(d) thymine dimer.
(e) result of telomerase.

The codes for leucine include CUU, CUC, CUA, and CUG. A nucleotide substitution in the third position of the codon would
*(a) have no effect on the final protein.
(b) have no effect on the exact mRNA sequence.
(c) cause the protein synthesis to stop prematurely.
(d) not even change which tRNA molecule recognizes the codon.
(e) result in an amino acid substitution.

Which enzyme is the hallmark of HIV (human immunodeficiency virus) that causes AIDS (acquired immunodeficiency virus)?
(a) primase.
(b) nuclease.
(c) telomerase.
(d) hemoglobin.
*(e) reverse transcriptase.

Codons such as CUG would be found
*(a) on the mRNA.
(b) on an antibody.
(c) in the restriction endonuclease.
(d) on the ribosome.
(e) on the template DNA.

Nonsense mutations are
(a) codons changed to start.
*(b) codons changed to stop.
(c) codons changed to codons for another amino acid.
(d) mutations in the position that defines degeneracy of DNA.
(e) jumping genes.

One thing that is unique to gene transcription in bacteria is
*(a) several enzymes might be coded for by one mRNA.
(b) introns are spliced out.
(c) there is processing of a pre-mRNA to mRNA before mRNA leaves the nucleus.
(d) genetic information is carried by RNA that is transcribed to DNA.
(e) the hereditary information is carried by proteins.

The genetic code for Met (the amino acid methionine), AUG, is unique because
(a) it is a DNA sequence.
(b) it is the sort of palindrome that is cut by a restriction enzyme.
(c) it is also the binding site for a helix turn helix molecule.
*(d) it is also the start codon.
(e) it is also the stop codon.

This page was last revised 6/30/08

**The mitosis lecture

cell division

Audesirk, Audesirk & Byers part of Chapter 11

In second grade, my health teacher read us the book "Mickey the microbe," and I learned that bacteria could "multiply and divide;" I was envious since I was not going to learn how to multiply and divide until 4th grade.

Figure 4-10
Chromosome = colored body.

Figure 11-3
Understand: concepts of 2n is diploid, prophase, metaphase, anaphase.
interphase is when the cell actually functions -
unwound chromatin vs. condensed chromosomes
cell cycle:interphase G1, S, G2, mitosis
G = gap, S = synthesis
arrest in G1 if postmitotic these are the cells which age

Some cells do not divide, others do

In many cell types, for instance brain (CNS Neurons) and heart (myocardial cells) - not divide, which is why stroke and heart attack are so damaging (no new cells replaced by mitosis) vs. in intestines, cells are constantly replaced by mitoses from stem cells since, in that milieu, cells digest themselves.
Centromere (on chromosome) = kinetochore (where microtubules attach)

Figure 11-10
(This figure shows a lot and we will spend some time on it.)
homologues do not line up (contrast with meiosis, next lecture),
DNA had already doubled (S=synthesis)
prophase, centrioles, spindle
Centromere (on chromosome) = kinetochore (where microtubules attach)
later (metaphase) chromosomes line up at metaphase plate, centromeres divide
anaphase, chromosomes separate
telophase when cells separate followed by cytokinesis.

Cell division in eukaryotes to make genetically identical daughter cells
FUNDAMENTAL: multicellular, all cells have same genes (except germ cells)

Human chromosomes

Figure 11-6
observe at metaphase block w drug colchicine
(they are duplicated - sister chromatids.)

Figure 11-9
look different, i.e. where centromere is and size
46 chromosomes (23 pairs [since we are diploid, 2n] one from father and one from mother)
22 pairs of autosomes and 2 sex chromosomes, XX female, XY male
there are two homologues in a pair

Figure 11-13
Progress through cell cycle is controlled

Figure 11-14
Very specific molecules control progress through cell cycle.

Figure 11-15
Many of the signal transduction cascades control this cell cycle.

Figure E11-3
When things go wrong with these controls, cancer occurs.

Questions used in 2007 and 2008 related to this outline

If p53, the tumor suppressor, is mutated,
(a) chromosomes are not divided equally to the two daughter cells.
(b) the homologues never line up next to each other.
(c) chromosomes get stuck at the metaphase plate.
*(d) damaged DNA gets replicated.
(e) cyclin never gets made.

DNA polymerase had already duplicated the DNA to make two identical copies of all the genetic material. Where are these two copies?
(a) in the two kinetochores
(b) in the two centrioles
*(c) in the two sister chromatids
(d) in the two homologues
(e) one in the autosome, the other in the sex chromosome

If a cell exits from the cell cycle to function as a non-dividing cell, from which step does it exit?
*(a) G1, the first gap
(b) S, the synthesis phase
(c) metaphase
(d) cytokinesis
(e) mitosis

Retinoblastoma (Rb) informs us about normal vs abnormal regulation of cell division. When it was stated that cyclin dependent kinase phosphorylates Rb, what is Rb?
(a) some DNA
*(b) a protein
(c) an extracellular growth factor that signals the cell
(d) the centriole
(e) the sister chromatin

The centriole pair organizes a structure for chromosome motility called
(a) interphase.
(b) the metaphase plate.
(c) the karyotype.
(d) colchicine.
*(e) the spindle.

Where did the two homologues come from?
(a) one from the template strand, one from the complementary strand
(b) one from cyclin, one from cyclin dependent kinase
(c) one from the autosome, one from the XY pair
*(d) one from the mother, one from the father
(e) one from p53, one from retinoblastoma

What about mitosis in myocardial (heart muscle) cells?
(a) They undergo mitosis after DNA synthesis is complete.
(b) The p53 molecule cannot block cyclin phosphorylation.
(c) Growth factors present after stroke regulate mitosis in these cells.
*(d) They are in G0.
(e) Colchicine locks them in metaphase.

Why might you want to block mitosis with colchicine?
*A) to prepare a karyotype
B) because of all the DNA damage done by cyclin
C) in situations where p53 does not bind to the membrane growth factor receptor
D) to prevent eye cancer (retinoblastoma)
E) to give the homologues a chance to line up

When does the DNA replicate itself in a eukaryotic cell?
A) prophase
B) metaphase
C) anaphase
D) telophase
*E) interphase

When a eukaryotic cell undergoes mitosis
A) each daughter cell receives exactly half the genetic information in the parent cell.
*B) each daughter cell receives a nearly perfect copy of the parent cell's genetic information.
C) a haploid chromosomal number is passed on to each daughter cell.
D) genetic information is randomly parceled out to the daughter cells.
E) one of each of the two homologues goes to each daughter cell.

The cells of the intestinal epithelium are continually dividing
A) because they are in G0.
B) because p53 is mutated.
*C) to replace dead cells lost from the surface of the intestinal lining.
D) because they do not have autosomes, but they do have sister chromatids.
E) because that is where gametes are made.

If there are 12 chromosomes in an animal cell in the G1 stage of the cell cycle, what is the diploid number of chromosomes for this organism?
A) 6
*B) 12
C) 24
D) 36
E) 48

The microtubules of the mitotic spindle attach to a specialized structure in the centromere region of each chromosome, called the
*A) kinetochore.
B) nucleolus.
C) metaphase plate.
D) chiasma.
E) centriole.

In the human karyotype, you see X-shaped bodies.
A) Each side of the X is one of the strands (template or complementary) of the DNA double helix.
B) This appearance applies to the X chromosome only.
C) This is only the case for XXY (Klinefelter's syndrome) males.
D) At this stage, the genetic material is called "chromatin."
*E) Two copies of one chromosome are still connected at the centromere.

A homologous pair of chromosomes
*A) consists of two chromosomes, one from each parent, with the same genes.
B) consists of two chromosomes having identical alleles.
C) would be one chromosome after it has duplicated before mitosis.
D) might be found in one sperm cell.
E) is found only in haploid cells

Sister chromatids are
A) X chromosomes.
B) specialized gamete-forming cells.
C) inactivated chromosomes (Barr bodies).
D) the same as homologous chromosomes.
*E) duplicated chromosomes held together by a common centromere.

Questions used in 2002 relating to this outline (and other outlines)

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

A pair of sister chromatids might be X-shaped in the microscope
(a) only for the X chromosome.
(b) during the G2 of interphase.
(c) because of the centriole pair.
(d) in anaphase.
*(e) when they are joined at the centromere.

Karyotypes are produced from
(a) gametes.
*(b) cells arrested in metaphase.
(c) nuclei of myocardial dells.
(d) haploid cells.
(e) cells in meiosis.

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

The kinetochore is most closely associated with
(a) interphase chromatin.
(b) the stamen.
(c) the G protein linked signal transduction cascade.
(d) the part of the gene to which steroid hormone receptors bind.
(e) the centromere.

What is cytokinesis?
(a) the way useful energy is obtained after light excites an electron
(b) the arrest of neurons in adult human central nervous system in G1
(c) the final processes of cell division
(d) how cAMP becomes inactivated
(e) a way to test for genetic or chromosomal abnormalities

A protein called p53 is
(a) coded by the C. elegans gene that promotes cell death.
(b) deficient in sickle cell anemia.
(c) the G protein coupled receptor.
(d) obtained from bacteria that live in hot springs.
(e) a tumor suppressor.

This page was last updated 6/30/09

**The meiosis lecture


Sex, meiosis and biological variability


Audesirk, Audesirk & Byers part of Chapter 11

Today's musical selection
Let me tell you about the birds and the bees

Eukaryotes, diploidy, and sexual reproduction

1-1.5 billion years ago, eukaryotic cells originated. Perhaps diploidy soon evolved because lethal and detrimental mutations would be over-ridden by dominant wild-type genes. Sexual reproduction and meiosis arose and gave rise to a powerful mechanism to insure biological variability, shuffling the genetic deck. Variability is very fundamental in evolution since new varieties may be more adapted and hence survive (to reproduction) better as selection pressures change.

Figure 11-20
Humans are diploid
Our gametes (sperm and eggs) are haploid
When sperm fertilizes egg, a diploid zygote is formed

With two homologous chromosomes...

Figure 11-16
...one is from the father and one is from the mother.
Both copies (alleles) of a gene might be the same (homozygous)...
...or they may be different

human and other life cycles

Figure 11-27
haploid (n), diploid (2n), gametes, ova, sperm, fertilization, zygote.

Figure 11-25
Note that while meiosis creates haploid gametes in humans, there are many organisms where meiosis creates a gamete-forming organism (alternation of generations, haploid life cycles).

(Previously, I described how mitosis creates two identical diploid "daughter" cells; here, you can see that mitosis can also create haploid cells from haploid cells in protists, fungi and plants.)

(An anthropocentric view is that meiosis only makes haploid gametes, but here you can see that it can make haploid organisms, again in protists, fungi and plants.)


Figure 11-21
(We will spend a long time with this figure.)
Meiosis. Note that there are two homologous chromosomes, 23 pairs for the human diploid number, 46. Theoretically, one could go to each gamete with one meiotic division. Instead, they align, duplicate, and divide twice.
Homologous chromosomes separate in first division
Sister chromatids separate in second division

Awesome variability

for 2 pairs of chromosomes, there are 4 possible combinations of chromosomes (centromeres) in the zygote. For 46 chromosomes, there are 2 to 23 power = 8.4 million.

The story goes that the king offered to pay the inventor of chess who wanted one grain of wheat for one square on the chess board, 2 for the second and so on. The king readily agreed but then found out that that was more wheat than the country would produce for decades, so he had the inventor beheaded instead. Behold the power of 2 to the power of (whatever).

Figure 11-22
Tetrad (bivalent), homologues have duplicated and are aligned next to eachother
Crossing-over (recombination) increases this beyond measure(shown for one pair of chromosomes)

Coming attractions

Unequal crossing over and gene duplication as major means of protein family evolution

Figure 12.33
Errors in meiosis (nondisjunction) can lead to offspring with aneuploidy (the wrong number of chromosomes) such as trisomy 21

Questions used in 2007 and 2008 relating to this outline

In the bivalent there is/are [A] sister chromatids and [B] homologues
(a) [A] 1; [B] 1
(b) [A] 1; [B] 2
(c) [A] 2; [B] 1
*(d) [A] 2; [B] 2
(e) none of the above

What is the end result of spermatogenesis in the human male?
(a) Four diploid daughter cells
*(b) Four haploid gametes
(c) Four identical chromosomes lined up next to each other
(d) Two haploid spores
(e) Two haploid zygotes

"Meiosis creates haploid gametes." Why is this not the whole truth?
*(a) Meiosis creates haploid organisms when there is alternation of generations.
(b) Heterozygous gametes are not haploid.
(c) Many gametes are diploid.
(d) In plants, meiosis creates zygotes.
(e) In Protista, it is alleles that are made, not gametes.

Two different but closely related proteins may have arisen, over evolutionary time, by a process of
(a) trisomy.
(b) mitosis.
(c) fertilization.
(d) nondisjunction.
*(e) unequal crossing over.

A pair of sister chromatids might be X-shaped in the microscope
*(a) when they are joined at the centromere.
(b) during the G2 of interphase.
(c) because of the centriole pair.
(d) in anaphase.
(e) only for the X chromosome.

The tetrad would form
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Two to the twenty-third power = 8.4 million. Why are there even more possible gametes than that in the human?
(a) Diploidy adds to variability.
*(b) Crossing over adds to variability.
(c) Homozygosity adds to variability.
(d) That's how it would be if there were just one meiotic division, but there are two.
(e) That's how it would be in interphase, but gametes are in prophase.

If a human does not possess 46 chromosomes, what is the term for the abnormal chromosome number?
(a) loci
*(b) aneuploidy
(c) hybrids
(d) recessives
(e) bivalents

What processes take place during Anaphase II?
*(a) Centromeres divide and sister chromatids move to opposite poles.
(b) Centromeres do not divide and sister homologues move to opposite poles.
(c) Centromeres divide and bivalents move to opposite poles.
(d) Sister homologues attach to spindle fibers from opposite poles.
(e) Tetrads attach to spindle fibers from opposite poles.

What constitutes a tetrad (bivalent)?
(a) Sister chromatids aligned next to each other.
*(b) Duplicated homologous chromosomes aligned next to each other.
(c) Homologous chromosomes aligning at the center of the cell during anaphase I.
(d) The karyotype when mitosis is blocked with colchicine.
(e) Homologous chromosomes that are connected during telophase I.

"Mitosis creates genetically identical diploid daughter cells." Why is this statement not the whole truth?
(a) In the retrovirus, it makes identical RNA strands.
(b) It's not true at all; mitosis makes haploid gametes.
*(c) When there is alternation of generations, there can be mitosis of haploid cells.
(d) In the central dogma of cell biology, it makes proteins.
(e) It's not true at all; it is meiosis that makes identical diploid cells.

Children with Down syndrome
(a) are heterozygous.
*(b) have 47 chromosomes.
(c) accumulate glycolipids from an enzymatic deficiency.
(d) have a mutation of a gene on chromosome 21.
(e) are born when older men decide to have children.

Name a cell that could have 22 autosomes and one Y chromosome.
(a) a human egg
*(b) a human sperm
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

What is a major source of genetic variation in sexual reproduction?
A) mitosis
B) alternate splicing
*C) crossing over
D) nondisjunction
E) DNA replication

Drosophila have 4 pairs of chromosomes. How many possible arrangements of chromosomes are possible in the gametes owing only to independent assortment (i.e. discounting recombination)?
A) 2
B) 4
C) 8
*D) 16
E) 32

Which of the following statements is FALSE?
A) Meiosis separates homologous chromosomes during anaphase I.
B) Meiosis separates sister chromatids during anaphase II.
C) In plants, meiosis produces spores rather than gametes.
*D) The karyotype is produced from gametes.
E) In animals, it is meiosis that produces sperm and eggs.

If there are 12 chromosomes in a cell that has just completed meiosis II, what is the number of chromosomes in the zygote?
A) 6
B) 12
*C) 24
D) 24 pairs
E) There is no answer because it would be different if there were alternation of generations.

Where does recombination occur?
A) at centromeres
B) at kinetochores
C) at Barr bodies
D) in zygotes
*E) at chiasmata

Name a cell that could have 22 autosomes and one Y chromosome.
A) a human egg cell
*B) a human sperm cell
C) a human diploid cell
D) a body cell from a Klinefelter's syndrome individual
E) a cell from a Turner's syndrome individual

When sperm and egg form the zygote, this is called
A) nondisjunction.
B) meiosis.
C) mitosis.
*D) fertilization.
E) crossing over.

In flowering plants, meiosis
A) makes gametes just as it does in animals.
B) makes sperm and eggs.
*C) gives rise to a separate gamete-forming organism.
D) makes zygotes, in contrast with the situation for animals.
E) makes all the cells of the plants.

Nondisjunction of chromosome #21 in humans leads to
A) Tay-Sachs disease.
B) Crossing over.
C) Klinefelter's syndrome.
D) Turner's syndrome.
*E) Down's syndrome.

Questions used in 2002 relating to this outline (and other outlines)

Disregarding crossing over, in meiosis, [A] separate in the first division, while [B] separate in the second division.
(a) A-single DNA strands, B-centrioles.
(b) A-alleles, B-genes.
(c) A-homozygotes, B-heterozygotes.
(d) A-chromatin, B-tetrads.
*(e) A-homologous chromosomes, B-sister chromatids.

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

Name a cell that could have 22 autosomes and one Y chromosome.
*(a) a human sperm cell
(b) a human ovum
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

When sperm and egg form the zygote, this is called
(a) nondisjunction.
(b) meiosis.
(c) mitosis.
(d) crossing over.
*(e) fertilization.

The tetrad would form
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Haploid is a term that would apply to
(a) interphase.
(b) chromosomes viewed for the karyotype.
(c) daughter cells of a mitotic division
*(d) gametes.
(e) zygotes.

In flowering plants, meiosis
(a) makes gametes just as it does in animals.
(b) makes sperm and eggs.
(c) makes zygotes, in contrast with the situation for animals.
*(d) gives rise to a separate gamete-forming organism.
(e) makes all the cells of the plants.

When does crossing over occur?
(a) during G2
(b) during fertilization
(c) during mitosis
*(d) when the tetrad is present
(e) during interphase

Crossing over occurs
(a) during the preparation of the karyotype.
(b) in the G1 portion of the cell cycle.
*(c) during meiosis.
(d) only during interphase.
(e) after gametes are haploid.

Making haploid cells from diploid cells is called
(a) nondisjunction.
*(b) meiosis.
(c) mitosis.
(d) mapping.
(e) fertilization.

Nondisjunction of chromosome #21 in humans leads to
(a) Tay-Sachs disease.
(b) Crossing over.
(c) Klinefelter's syndrome.
(d) Turner's syndrome.
*(e) Down's syndrome.

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

This page was last updated 6/30/09

**the genetics lecture


This land is your land
and this land is my land
from California to the New York Island
from the redwood forest to the Gulf Stream waters
This land was made for you and me.
-Woody Guthrie


Many people may think of "genetics" as one type of biotechnology. Actually, genetisists studied progeny of crosses of living organisms (fruit flies or pea plants), or, alternatively pedigrees (family trees say of humans). Also, the outcomes of the genetic crosses told us more about meiosis than anything else.

Audesirk, Audesirk & Byers part of Chapter 12

Today's musical selection
Nervous Norvus - Transfusion

Mendel's work

Figure 12-2
1865 Mendel

Figure 12-3
pea flowers
(might seem strange to think about sexual reproduction in plants)
presumably genes are lined up along chromosomes, each at its own place
thus "locus" is a word for a gene

Figure 12-4
- purple vs. white flowers (phenotype)
P=parental, F1 first generation (filial)

Since cells are diploid, there are two copies (alleles) at each locus, and they can be the same or different.

Figure 12-6
true-breeding = homozygous PP or pp (genotype)

Figure 12-7
hybrids = heterozygous (Pp)
purple (P) is dominant, white (p) is recessive
Thus Pp genotype has purple phenotype

Figure 12-5
F2 has 3/1 ratio
units = gene separate Mendel's first law (segregation)

Figure 12-11
Punnett square
shows haploid gametes (ova and sperm) and genotypes and phenotypes

Mutations - variation and evolution (many are bad also recessive, many are neutral, some might be good under the right environmental circumstances. They can be caused by ionizing radiation or chemicals (mutagens which are also carcinogens).

Taboos against insest-
People carry several detrimental or lethal alleles (such as those discussed later in this outline). They are usually not expressed because they are recessive and heterozygous. Inbreeding is a problem because related people would have mutations in the same genes, resulting in a homozygous recessive expression. "Hybrid vigor" refers to a stronger genetic constitution in organisms with more heterozygosity (and hence more genetic variability

Mendel (knew about Darwin but Darwin did not know about Mendel)
"...this seems to be the one correct way of finally reaching the solution to a question whose significance for the evolutionary history of organic forms must not be underestimated."

Figure 12-14
Mendel's Second Law
The law of independent assortment
green-yellow, round-wrinkled
dihybrid cross (two genes each on a separate chromosome, two alleles each) fill in "Punnett square"
Independent assortment does not apply to linked genes. i.e. genes that are on the same chromosome.

A few human examples

Figure 12-24
Here is a picture showing incomplete dominance (hair texture)

Table 12-1
Blood groups
A=B (co-dominant), O is recessive -- 3 alleles

IA IA or IA i...........A......................A.....................anti-B
IB IB or IB i...........B......................B.....................anti-A
IA IB......................AB....................A and B..........anti neither
ii ............................O......................none................anti both

O universal donor, AB universal recipient

Question: What is unusual about this situation? Answer: There are already antibodies even though there was no previous exposure to antigens.

Genetic disorders in people

Figure 12-29
Sickle cell anemia
If homozygous, red blood cells have abnormal shape
hgb clumps in low O2, heterozygotes (trait) largely normal
2 alpha, 2 beta. Beta 146 aa, 6th valine instead of
glutamic acid, GUG instead of GAG
blacks, heterozygous gives resistance to malaria

Figure 12-31
Victoria, Nicholas II & Alexandra - Alexis, Rasputin
on X
problem with AIDS for clotting factor

Lethals detrimentals
- everyone carries several recessives, but different
become homozygous if inbreeding

Huntington's - chorea - age 40's or 50's death in 10-20 years
By that age, person has probably already reproduced
autosomal dominant - 50:50 chance to pass on mapped to chromosome #4
Woody Guthrie died of it

Figure E12-1
Cystic fibrosis
lungs fill up with thick mucus
cloned as CFTR, mutation in Cl- transport, children have salty sweat
Life is short, chest must be thumped to clear lungs

Some others we will not take the time to cover
Tay-Sachs disease
Phenylketonuria (PKU)

Mild disorders

Figure 12-30
color blindness

Figure 12-28
Melanin formed from polymerization of dopa quinones derived from the amino acid tyrosine

Figure 12-26
Himalayan rabbit (like Siamese cat)
"temperature sensitive" presumably missense mutation, enzyme works if cool but body heat denatures it

Questions used in 2007 and 2008 related to this outline

A dihybrid cross was presented to explain
*(a) the 9:3:3:1 ratio.
(b) genetics of blood groups.
(c) sex-linked (X-linked) diseases.
(d) the Hardy-Weinberg ratio.
(e) cephalization.

What blood type is known as the universal donor?
(a) AB
(b) A
(c) B
(d) C
*(e) O

Why is a Siamese cat's nose black?
*(a) There is a temperature sensitive missense mutation.
(b) Cats are mosaic for whether there is a mutation on of the X chromosomes.
(c) Because of convergent evolution.
(d) There was an evolutionary bottleneck.
(e) Because of homeostasis.

Why are some people from African descent resistant to malaria?
(a) They use banked umbilical blood in Africa.
(b) Hemophelia heterozygotes are immune.
(c) They have Down's syndrome.
(d) They are carriers of PTC insensitivity.
*(e) They are heterozygous for sickle cell anemia.

Why does Huntington's disease create such a dilemma?
(a) If they knew how antisocial they were expected to be, they would consider it the self-fulfilling prophesy.
(b) Much of what we know was presented by a nineteenth century British physician with an unsavory attitude toward non-European races.
*(c) Most people did not show symptoms until they already had children.
(d) Though retarded, children with Huntington's disease are pleasant and happy.
(e) Richard Speck, accused murderer of 8 student nurses in Chicago in 1966, had Huntington's disease.

In genetics, if there are two or more different copies of a gene possible, they are referred to as
(a) pedigrees.
(b) homologues.
*(c) alleles.
(d) kinetochores.
(e) filials.

A pea that is heterozygous for purple colored flowers is crossed with a plant having white flowers. What is the makeup the F1 generation?
*(a) 1/2 purple, 1/2 white
(b) 1/4 purple, 3/4 white
(c) all purple
(d) 1/2 pink, 1/2 purple
(e) 1/3 white, 2/3 purple

What genetic disorder relates the history of Europe's royal families and a unique evolutionary selection pressure in the first years of the AIDS epidemic?
(a) Down syndrome
(b) albinism
(c) Huntington's disease
*(d) hemophelia
(e) green-wrinkled syndrome

What is true about people with type AB blood?
(a) They are universal donors.
(b) On the surface of their red blood cells, they do not have A or B glycoproteins (antigens).
(c) They are homozygous dominant.
(d) They are homozygous recessive.
*(e) They don't have antibodies against A or B glycoproteins.

Which statement is false?
(a) Meiosis leads to segregation of two alleles at one locus in plants.
(b) Separate male and female structures in pea flowers allowed Mendel to cross-fertilize.
(c) Mendel knew about Darwin and thought his own genetic studies could help to explain evolution.
(d) The F2 ratio of 3:1 describes phenotypes, not genotypes.
*(e) Plants do not reproduce sexually.

Most people are not born with fatal genetic diseases. Why not?
*(a) Detrimental mutations are usually heterozygous recessive.
(b) The only mutations that can possibly be detrimental are autosomal dominant.
(c) Mutations only occur on extra chromosomes produced by nondisjunction.
(d) Mutations only occur on the Y chromosome.
(e) Most parents do not have detrimental mutations.

Cystic fibrosis
(a) causes spastic movements referred to as "chorea."
*(b) results in thick mucus in the lungs.
(c) is the cause of red-green color blindness.
(d) only begins to appear in people in their 50's.
(e) probably first appeared in Queen Victoria.

What would have happened if Mendel had done his dihybrid cross using two traits that were near each other on the same chromosome?
(a) That is what he did and how he got the 3/1 ratio.
(b) That is what he did and how he got the 9/3/3/1 ratio.
*(c) His ratio would not have been 9/3/3/1 and he might have discovered linkage.
(d) That is what he did and how he obtained the ratio of ABO blood groups.
(e) He would have discovered Klinefelter syndrome.

In the US, sickle cell anemia is most common among Afro-Americans because
(a) it is a mutation in the enzymes that form melanin.
(b) it is an example of convergent evolution.
(c) the antibodies are already present in the blood, even before exposure to the antigen.
(d) it is on the X chromosome, and Afro-Americans are mosaics for which X is active.
*(e) it confers resistance to malaria.

Cystic fibrosis is a genetic disease that leads to the production of excessive thick mucous in the respiratory tract, leading to frequent and serious respiratory infections. The defect is due to
*A) faulty transport of chloride (Cl-) ions.
B) antibodies attacking antigens on red blood cells.
C) bleeding into the mucous because of a mutation that originated in Queen Victoria.
D) a dominant gene defect that is not expressed until about age 50.
E) faulty melanin synthesis.

Which is NOT a difference between the examples of Mendel's dihybrid cross (YyRr) and the ABO blood groups?
A) There are two alleles per gene only for the Mendel example.
B) There are two alleles in one gene that are equally dominant only for the blood groups.
C) There are two genes (loci) only for the Mendel example.
D) ABO blood groups cannot be used to demonstrate independent assortment while Mendel's work on peas can.
*E) Antibodies and antigens apply only for peas.

Gregor Mendel concluded that two units determined pea flower color, and each sperm cell or egg cell contains only one unit. Each individual unit is a(n) ________.
A) chromosome.
*B) allele.
C) trait.
D) homozygote.
E) gamete.

According to the Law of Segregation, in an organism with the genotype Aa,
A) A and a will blend and never be passed on to progeny intact.
B) the organism can have a as its genotype
C) the gametes can be AA, Aa or aa.
*D) half the gametes will have A and half will have a.
E) the phenotype of the gametes can be either A or a.

Red-green colorblindness
A) explains the black extremities on the otherwise white Himalayan rabbit.
B) is dominant.
C) results from nondisjunction.
*D) is on the X chromosome.
E) would be lethal if hemizygous.

Sickle-cell anemia
A) is expressed only after the age of 50.
B) explains the appearance of the calico cat.
C) was the blood disorder in the Russian royal family.
*D) confers resistance to malaria.
E) is caused by a stop codon.

In flowering plants, meiosis
A) makes gametes just as it does in animals.
B) makes sperm and eggs.
*C) gives rise to a separate gamete-forming organism.
D) makes zygotes, in contrast with the situation for animals.
E) makes all the cells of the plants.

Which of the following statements is FALSE?
A) Individuals with the same phenotype might have different genotypes.
*B) Matings between individuals with dominant phenotypes cannot produce offspring with recessive phenotypes.
C) Matings between individuals with recessive phenotypes do not produce offspring with dominant phenotypes.
D) Mating between heterozygotes produce a 3:1 ratio of dominant:recessive phenotypes.
E) Mating between heterozygotes produce a 1:2:1 ratio of genotypes.

Blood typing is often used as evidence in paternity cases in court. In one case, the mother had blood type B and the child had blood type O. Which of the following blood types could the father NOT have?
A) A
B) B
*C) AB
D) O
E) Both choices C and D are correct.

Questions used in 2002 relating to this outline (and other outlines)

What is one reason that type O individuals would be especially useful in a blood drive?
*(a) They are universal donors.
(b) They are universal recipients.
(c) They have A and B antigens as well as antibodies against A and B.
(d) They are homozygous dominant.
(e) They are the only people that are not mutant.

A pea plant with purple flowers is referred to as Pp. Pp
(a) is the plant's phenotype.
(b) indicates that the plant is homozygous.
(c) are only seen in the F2 of a cross of purple- and white-flowered pea plants.
*(d) is the plant's genotype.
(e) is a gamete.

Which is a dominant lethal mutation which probably would not be expressed until after affected men and women have had children?
(a) Down's syndrome
(b) PKU
*(c) Huntington's chorea
(d) Tay Sachs disease
(e) Sickle cell anemia

What made the example of the ABO blood groups an interesting contrast with the pea crosses used to exemplify Mendel's first and second laws?
(a) There were more than two loci.
(b) There are no homozygotes.
(c) There are no genotypes, only phenotypes.
(d) The genes are sex-linked.
*(e) There were three alleles.

Mendel's second law
(a) explains how both yellow or green pea bearing plants would be seen in subsequent generations if homozygous yellow or green pea bearing plants are crossed.
*(b) applies to two alleles of two genes on two different chromosomes.
(c) is the law of segregation.
(d) was used by Darwin to explain some aspects of evolution.
(e) is how linked genes are mapped on one chromosome.

Mendel's laws of segregation and independent assortment apply to
(a) mitosis.
(b) non-disjunction.
*(c) meiosis.
(d) linkage.
(e) mapping.

Which is a mutation?
(a) Klinefelter's syndrome
*(b) Tay Sach's disease.
(c) Down's syndrome
(d) XYY
(e) Turner's syndrome

Hemophelia is a sex-linked recessive allele. If a mother and father have a daughter with hemophelia, which of the following statements is the only one which MUST be correct on the basis of this information?
*(a) The father has hemophelia.
(b) The mother has hemophelia.
(c) Both father and mother have hemophelia.
(d) The daughter inherited all hemophelia alleles from the mother.
(e) Half of the mother's sons would have hemophelia.

Most people are not born with fatal genetic diseases. Why not?
(a) Most parents do not have detrimental mutations.
(b) The only mutations that can possibly be detrimental are autosomal dominant.
(c) Mutations only occur on extra chromosomes produced by nondisjunction.
(d) Mutations only occur on the Y chromosome.
*(e) Detrimental mutations are usually heterozygous recessive.

Which statement applies to the Siamese cat having white fur with black extremities?
*(a) A mutation makes an enzyme for melanin synthesis temperature-sensitive.
(b) Black vs. white depends on which X chromosome is active.
(c) There is incomplete dominance like for snapdragon flower color.
(d) The cat is heterozygous for the body color gene.
(e) Sons of such a female cat will be either black or white.

To analyze a situation like hemophelia in Queen Victoria's family, you use
(a) a Punnett square.
(b) a dihybrid cross.
(c) a pedigree.
(d) PCR.
(e) a northern blot.

Human evolution takes place in a changing environment of medical intervention (allowing survival of some people with genetic disorders). After treatment that helped this condition were established, the early years of the AIDS pandemic created a particularly harsh selection pressure against people with
(a) Tay-Sachs disease.
(b) Turner's syndrome.
(c) anthrax.
(d) hemophelia.
(e) PKU.

The famous American folk singer Woody Guthrie, as well as a large population from Venezuela, had this genetic disorder:
(a) Tay Sach's disease.
(b) PKU.
(c) Klinefelter's syndrome
(d) Huntington's disease.
(e) sickle cell anemia.

This page was last updated 7/9/09


 **The chromosome lecture


The gingham dog and the calico cat
Side by side on the table sat;
'T was half-past twelve and (what do you think!)
Nor one nor t'other had slept a wink!
The old Dutch clock and the Chinese plate
Appeared to know as sure as fate
There was going to be a terrible spat.
(I wasn't there; I simply state
What was told to me by the Chinese plate!)

The gingham dog went "bow-wow-wow!"
And the calico cat replied "mee-ow!"
The air was littered, an hour or so,
With bits of gingham and calico,
While the old Dutch clock in the chimney-place
Up with its hands before its face
For it always dreaded a family row!
(Now mind: I'm only telling you
What the old Dutch clock declares is true!)

The Chinese plate looked very blue,
And wailed, "Oh, dear! What shall we do!"
But the gingham dog and the calico cat
Wallowed this way and tumbled that,
Employing every tooth and claw
In the awfullest way you ever saw-
And, oh! How the gingham and calico flew!
(Don't fancy I exaggerate-
I got my news from the Chinese plate!)

Next morning, where the two had sat
They found no trace of dog or cat;
And some folks think unto this day
That burglars stole that pair away!
But the truth about the cat and pup
Is this: They ate each other up!
Now what do you really think of that!
(The old Dutch clock it told me so,
And that is how I came to know.)

The Duel
by Eugene Field (1850-1895)

(Poems of Childhood)



Audesirk, Audesirk & Byers part of Chapter 12, and several other figures

Today's musical selection
Beatles Ob la di
A cover of this song was the theme for the TV situation comedy Life goes on where Corky has Down syndrome

Of course, genes come on chromosomes.
There are autosomes and sex chromosomes.

Sex linkage

Figure 12-21

Figure 12-22
sex determination

Figure (Chapter 10 opener)
Case study - Vive la difference Chapter 10, p. 167
Case study revisited Chapter 10, p. 186
Different organisms have different chromosomal means of sex determination (dimorphism).
Sry gene on Y codes for TDF (testicular determining factor)
In female, Wolffian ducts degenerate and Mullerian ducts develop into oviducts, uterus, and cervix (default pathway).
In male, testes make testosterone and MIH (Mullerian inhibiting factor), Mullerian ducts degenerate, Wolffian ducts become epididymus, vas deferens and seminal vesicles (active, not default)
urogenital groove becomes external genitals

In humans, Y determines male-ness and there are virtually no genes on Y except to differentiate testes in male.
Why map the Y? Science 261, 1993, p. 679
A guy bashing joke with genes like "inability to say 'I love you'" over the phone called "ME-2"
However, I am showing this picture to also make a serious point -- genes eventually get assigned to locations on the chromosome, but first, genetic linkage must be established
Independent assortment (Mendel's 2nd law) does not apply to genes (near enough to each other) on the same chromosome.
map location is based on cross-over probability (determined with a genetic cross)

Figure 12-23
Sex linked inheritance in Drosophila, white x red eye cross. Note that there is no corresponding gene on the Y, hence the term hemizygous.
males are XY, but tissues that are XO are male (though if fly or germ cells are X0, fly is sterile) and XX tissues are female, thus sex is based on number of X chromosomes. grasshopper XO male

Figure 10-13
X inactivation in calico cat

Figure 10-12
XX Barr body, X inactivation Mary Lyon
dosage compensation

Chromosomal abnormalities

Figure 12-32
Chromosomal Abnormalities
Nondisjunction e.g. trisomy
lethal, spontaneous abortions

Table 12-2
X abnormalities survive
Klinefelter's XXY
Supermale XYY
1968 prison if taller than 71 inches 1/11 XXY or XYY
population XXY - .08-.092%
XYY - .069-.095%
Research to find if people have X or Y abnormalities is controversial, for instance because of self-fulfiling prophesy.
It was widely rumored that Richard Speck, known for his mass murder of 8 student nurses in Chicago in 1966, was XYY.
Turner X0 1/2000 females
spatial sense abnormal

Figure 12-33
Autosomal aneuploidies are often lethal
Trisomy 21 = Down's syndrome
(the term "Mongulism" is used less in this era of political correctness, especially in light of Down's unsavory attitude toward non-European races in his writings)
retarded but nice, increases with increasing maternal age and is in percents for women over 40
age 40 almost 1% age 50 almost 10%

Figure 12-34
Here is a graph of that increase with age

Figure E13-5
Many couples choose to test the chromosomes of the fetus using amniocentesis of chorionic villus sampling

All human "eggs" are already made around the time of birth (while sperm are made throughout life). It seems likely that either "eggs" suffer from aging (alternatively the good ones are used in the earlier reproductive years).

Questions used in 2007 & 2008 related to this outline

What would have happened if Mendel had done his dihybrid cross using two traits that were near each other on the same chromosome?
(a) That is what he did and how he got the 3/1 ratio.
(b) That is what he did and how he got the 9/3/3/1 ratio.
*(c) His ratio would not have been 9/3/3/1 and he might have discovered linkage.
(d) That is what he did and how he obtained the ratio of ABO blood groups.
(e) He would have discovered Klinefelter syndrome.

Why is there a relatively high frequency of X chromosomal aneuploidies?
(a) The X chromosome is not subject to amniocentesis.
(b) The X chromosome is even smaller than chromosome 21.
(c) There are many nondisjunctions when mitosis involves the X chromosome.
*(d) All but one X chromosome is inactivated.
(e) X chromosomal abnormalities are not detected in chorionic villus sampling.

The human Y chromosome
(a) has most of the genes that are on the X.
*(b) is important for sex determination.
(c) is not as important for sex determination as the number of X chromosomes.
(d) is seen histologically as the Barr body
(e) is the cause of coat color mosaicism in the Siamese cat

A female fruit fly homozygous for red eyes is mated to a white eyed male.
*(a) Male and female offspring are red eyed.
(b) Female offspring have red eyes but males have white eyes.
(c) Female offspring have white eyes but males have red eyes.
(d) Female and male offspring have white eyes.
(e) Female and male offspring have pink eyes, halfway between red and white.

Amniotic fluid
(a) is used for chorionic villus sampling.
*(b) should contain no maternal cells.
(c) is used for cloning.
(d) is the source of prions.
(e) would be present only if nondisjunction had occurred during mitosis.

Which is a way to test for chromosomal abnormalities in the embryo?
(a) gel electrophoresis
(b) administering dopamine
(c) using rubella
(d) testing for chorionic gonadotroin
*(e) chorionic villus sampling

Children with Down syndrome
(a) are heterozygous.
*(b) have 47 chromosomes.
(c) accumulate glycolipids from an enzymatic deficiency.
(d) have a mutation of a gene on chromosome 21.
(e) are born when older men decide to have children.

Name a cell that could have 22 autosomes and one Y chromosome.
(a) a human egg
*(b) a human sperm
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

A human female has one X chromosome with the normal gene and the other with the recessive mutated gene.
(a) She passes the normal gene to her daughters and the mutated gene to her sons.
(b) She is called "hemizygous."
(c) All her daughters are carriers since she passes both X chromosomes to daughters.
*(d) She is a mosaic of cells expressing one or the other X.
(e) Her sons would have Klinefelter's syndrome

The testicular determining factor is found in what chromosome in humans?
(a) X
(b) #21
*(c) Y
(d) No single chromosome; it is explained by polygenic inheritance.
(e) The chromosome has not been identified yet.

"Early female sexual development is the default." Meaning?
(a) Like with fruit flies, two X chromosomes specify female development.
*(b) Ducts become female genitals in the absence of factors present in the male.
(c) Many genes specifying male characteristics are mapped to the Y chromosome.
(d) Since females have two X chromosomes and males have one, it is no wonder males and females are different.
(e) That is the statement that got Lawrence Summers fired as president of Harvard.

'Dosage compensation explains the high prevalence of abnormalities like Turner's syndrome and Klinefelter's syndrome.' Dosage of
*A) genes on the X chromosome
B) p53
C) colchicine
D) polar bodies
E) antibodies

Chromosome map position
A) was first determined in Darwin's classic genetic experiments.
*B) is based on the cross-over frequency for linked genes.
C) is determined by the normal distribution.
D) was 9:3:3:1 when Mendel figured it out.
E) is calculated using the Punnett square.

Amniotic fluid
A) causes mutations.
B) is hybrid in the F1 generation.
C) is the universal donor in blood transfusions.
D) is produced by the Sry gene on the Y chromosome.
*E) can be used to screen for chromosomal and genetic abnormalities in the fetus.

The failure of chromosomes to distribute equally to gametes is called
*A) nondisjunction.
B) conjugation.
C) segregation.
D) inversion.
E) independent assortment.

Which disorder is more common among the babies of older mothers?
A) Turner syndrome
C) hemophelia
D) Huntington's disease
*E) Down syndrome

Klinefelter syndrome
A) results when detrimental alleles become homozygous because of incest.
B) is an autosominal dominant disorder.
C) females would lack a Barr body.
*D) results from sex chromosomal nondisjunction.
E) is because of crossing-over.

Questions used in 2002 relating to this outline (and other outlines) [some overlap particularly with genetics questions]

In your genetics coverage, you were introduced to the term "locus." Of the following, which would be the best term to substitute for "locus?"
(a) true-breeding
(b) hybrid
(c) chromosome
*(d) gene
(e) allele

Most people have two copies of chromosome 21. These two copies would be called
(a) alleles.
(b) tetrads.
*(c) homologues.
(d) spindles.
(e) centromeres.

Name a cell that could have 22 autosomes and one Y chromosome.
*(a) a human sperm cell
(b) a human ovum
(c) a human diploid cell
(d) a body cell from a Klinefelter's syndrome individual
(e) a cell from a Turner's syndrome individual

Which is a dominant lethal mutation which probably would not be expressed until after affected men and women have had children?
(a) Down's syndrome
(b) PKU
*(c) Huntington's chorea
(d) Tay Sachs disease
(e) Sickle cell anemia

Which is a mutation?
(a) Klinefelter's syndrome
*(b) Tay Sach's disease.
(c) Down's syndrome
(d) XYY
(e) Turner's syndrome

A person has 44 autosomes plus one X chromosome plus one Y chromosome. Which statement is true for this person?
*(a) The Y chromosome came from the father.
(b) The X chromosome becomes a Barr body.
(c) The X chromosome could have come from either the father or the mother.
(d) The Y chromosome's inactivation is described by the Mary Lyon hypothesis.
(e) This person has Klinefelter's syndrome.

Which statement applies to the Siamese cat having white fur with black extremities?
*(a) A mutation makes an enzyme for melanin synthesis temperature-sensitive.
(b) Black vs. white depends on which X chromosome is active.
(c) There is incomplete dominance like for snapdragon flower color.
(d) The cat is heterozygous for the body color gene.
(e) Sons of such a female cat will be either black or white.

To see whether your baby would be born with trisomy-21, you could use
(a) recombinant DNA.
(b) a microarray.
*(c) chorionic villus sampling.
(d) autoradiography.
(e) reverse transcriptase.

Which is the best statement about human chromosomes?
(a) Presence of two X chromosomes causes development of the female.
(b) Dosage compensation in females works by X chromosome inactivation.
(c) Male development begins under the control of the one X chromosome.
(d) The male genome is haploid while the female genome is diploid.
(e) The Y chromosome has all the same loci as the X chromosome.

This page was last updated 7/13/09

**Prions viruses prokaryotes

I have heard it was the opinion of others that it [the plague] might be distinguished by the party's breathing upon a piece of glass, where, the breath condensing, there might living creatures be seen by a microscope, of strange, monstrous, and frightful shapes, such as dragons, snakes, serpents, and devils, horrible to behold.
-Daniel Defoe
A Journal of the Plague Year, 1721

Our townsfolk were not more to blame than others; they forgot to be modest, that was all, and thought that everything was still possible for them; which presupposed that pestilences were impossible. They went on doing business, arranging for journeys, and formed views. How should they have given a thought to anything like plague, which rules out any future, cancels journeys, silences the exchange of views. They fancied themselves free, and no one will ever be free so long as there are pestilences.
-Albert Camus
The plague

I had a little bird,
Its name was Enza.
I opened the window,
And in-flu-enza.
-- Children's Skipping Rhyme, 1918

Audesirk, Audesirk & Byers part of Chapter 19,

Today's music selection
Huey "Piano" Smith Rockin' pneumonia and the Boogie Woogie Flu


(conventional wisdom that DNA or RNA are required)

Figure (chapter 3 opener)
Prion diseases
Creutzfeldt - Jakob Disease (CJD) "Spongiform" (brain turns to sponge) degeneration.
There were seemingly esoteric* cases of spongiform encephalitis.
* for instance afflicting Jews in Lybia who thought raw sheep eyeballs were a delicacy.
Kuru was a disease in New Guinea among cannibals.
D. Carleton Gadjusek (1976 Nobel Prize) thought it was a slow virus.
Scrapie in sheep so named because they roll around with intense itching.

Personal reflection. Since we did a sheep brain dissection in physiological psychology lab at Hopkins, I wondered if rubber gloves were necessary. Since Baltimore was close to Bethesda, I called. Gadjusek was away, studying some remote tribe, but I spoke with his coworker (Gibbs) who thought formaldehyde might not kill the virus. Then I got on their mailing list and, once a month or so, got an inch thick envelope full of case studies of diseases in far away places. I had to move to Missouri (in 1979) to make it stop.

Stanley Pruisinger 1980's proposes "prion" (protenaceous infectious particle).
That a disease could be transmitted without virus or bactera was heresy at the time.
But he had strong evidence and won the 1997 Nobel Prize.
Normal protein (PrP-C [control]) is altered by altered form (PrP-Sc [scrapie])
In the 1990s when the term "mad cow disease," was applied to observations in Britain, it seemed like a joke.
Now "BSE" (bovine spongiform encephalitis) is no laughing matter.
In meat industry, having matter from other animals in the feed is really bad.
Can disease spread from animal to animal? (probably)
Can disease spread from animal to human? (probably)
Cases in Canada, mainland Europe, and even in the US are in the news.
Should "downers" ("cows" that have dropped to the ground) be slaughtered for food?
How is it that meat from one downer can be sold in many different states and, only later, the announcement is made that it had BSE?


not in 5 kingdoms (recall question on whether viruses are "alive") makes it virtually impossible for an introductory textbook to have a good place to cover viruses

Figure 19-11
These are electron micrographs
Being small (Protein and DNA) they pass through fine filters, hence an old term, "filterable"

Figure 19-13
(review from first lecture)
Bacteriophage (phage-eat) protein and DNA
lytic cycle - bacterial cells lyse.

Viruses cause lots of disorders: measles, smallpox, chicken pox, mumps, rabies, flu = influenza, herpes, AIDS, mononucleosis, polio, colds, rubella (German measles), yellow fever, hepatitis


Some very fundamental terminology:
Antigen - non-self protein (e.g. virus coat)
Antibody to antigen made by B lymphocytes (white blood cells)


Vaccines - active immunity (like disease)
memory cells of immune system

Figure E36-1
Edward Jenner credited with "vaccination" -1796 "encowment" cowpox, smallpox
Actually the English aristocrat Lady Mary Wortley Montague introduced the Turkish technique of innoculating with weakened smallpox in the early 1700's
Smallpox is so completely eliminated that one issue is whether to get rid of lab virus.
Passive immunity - give antibodies


Figure Chapter 36 opener
Case study Chapter 36 Fighting the flu (p. 721) snd revisited (p. 738)

Figure E36-2
Box on fighting influenza
change (mutate) also exchange with birds (ducks) and pigs

Humanities Gina Kolata, Flu: The story of the great influenza pandemic of 1918 and the search for the virus that caused it, New York, Farrar Straus and Giroux, 1999

1918 20-200 million died worldwide, H1N1 (hemagglutinin, neuraminidase)
1957 Asian bad H2N2
1968 Hong Kong bad H3N2 (70,000 died in 6 wks)
Worry in 1973 that there would be a swine flu pandemic
Worry now that there will be an avian (bird) flu pandemic H5N1

Figure E19-2b
Not always does cell burst. Here you see how the virus takes over the cells machinery to make its own DNA and to make proteins etc after transcription of its DNA into RNA


Figure 19-12
Structurally (and chemically) not all viruses are as simple as bacteriophage, and sometimes RNA is the hereditary material

Figure E19-2a
The retrovirus, HIV (Human Immunodeficiency Virus that leads to AIDS, acquired immunodeficiency syndrome) deserves special attention. Its hereditary material is RNA. It is called a retrovirus because it comes pre-packaged with functional reverse transcriptase enzyme to make DNA out of RNA. The DNA that is made gets incorporated into the cell's own genome.

Figure (Chapter 18 opener)
Case study - origin of a killer, Chapter 18, p. 357

Figure 18-8
Case study revisited
Evolutionary relationships for HIV


2 of 3 domains
Kingdom? (monera)
bacteria, also blue-green algae (cyanobacteria)
(algae = aquatic plants)

Figure 1-5
Penicillin, an antibiotic, kills bacteria
Penicillin was discovered by Fleming and developed by Florey and Chain. They shared the 1945 Nobel Prize

Figure 19-1b
Here is a picture of E. coli (Escherichia coli), the most famous bacterium from genetics and molecular studies - this picture was found at the microbe zoo site
circular DNA
prokaryote, (karyon as in "karyotype," refers to the nucleus)
genophore - bacterial chromosome
Reproduction by fission, "Multiply and Divide"

also DNA transferred: (1) transformation (earlier coverage, DNA from smooth transforming rough) , transduction (from phage

Figure 19-8
conjugation (like mating)
Plasmids - little circles of DNA - very useful in molecular biology and easy to identify since they carry antibiotic resistance

Figure 19-1
-diplococcus - two
-streptococci-string (e.g. strep throat)
-staphylococci-grapes (e.g. staph infections)
spirilla and spirochetes-spiral

One characteristic of monera is that they have a rigid cell wall made of peptidoglycan. That means that they must absorb, they cannot ingest. The chemiheterotrophs (saprobes) are therefore good at biodegradation because they must put out "digestive" enzyme

Figure 19-2
Even though they are rigid, they have flagella (very different from eukaryotic flagella), and organisms like the famous E. coli have positive and negative chemotaxes.

Figure 19-4
Aerobic vs anaerobic -
The story about anaerobic bacteria that is so famous that everybody should know it. It is about botulism toxin from Clostridium botulinum, endospores killed only with high temperature. They are obligate anaerobes, and the endospores survive in improperly canned goods, 1 g kill 15 million by blocking release of vesicles that contain neurotransmitter substances. "Botox" is used as cosmetic, injected into face, blocks muscles, less wrinkles.

Figure 19-5
Thermoacidophyles hot sulfur (heat stability important in enzymes used for PCR, refer back to biotech lecture).

cell wall, Gram stain
Gram positive-heavy wall, Negative-stain wash out
Antibiotics like penicillin G for Gram + like strep, gonorrhea, syphilis


Famous traditional STD's (VD's) gonorhea, syphilis (spirochete)
famous recent worry Lyme disease from ticks
recently understood that ulcers are caused by Helicobacter pylori
bubonic plague rats flea middle ages

Figure Chapter 15 opener
Tuberculosis TB consumption sanatoriums
Humanities suggestion - Eugene O"Neill Long day's journey into night
Current events - May 2007 - a patient with antibiotic resistant TB is quaranteened

diphtheria, some pneumonia, paratyphoid, scarlet fever
tetanus muscle clamp lockjaw anaerobic puncture (like botulism, toxin affects neural transmission)
whooping cough (pertussis) DPT vaccine (toxin very important in studying signal transduction)
strep throat (leads to rheumatic fever)
typhoid fever carriers*
cholera fatal diarrhea (toxin very important in studying signal transduction)
leprosy leper colonies,
Salmonella (food = "ptomane" poisoning),
(evolution of resistance in meat and eggs with antibiotics fed in animal husbandry)
evololution of antibiotic resistance in syphilis (spirochete), gonnorhea
toxic shock (tampons)
Leigionnaires' (1970's Philadelphia, took several years to find cause)
Staphylococcus = acne,
some pneumonia, paratyphoid, scarlet fever, dysentery
chlamydia like virus common STD (VD)
Rocky Mountain spotted fever typhus (Rickettsia like virus)
mycoplasmas - smallest cells

Figure - chapter opener
(Case study- agents of death Chaspter 19, p. 371 and case study revisited p. 384)
Anthrax (mostly cattle [also humans, mail terror attacks of Fall, 2001])
fire blight (apple, pear)
crown galls (plants)

*Typhoid Mary (Mary Mallon) Irish immigrant, in the 1900-1906 period, cases involved in her being a cook until epidemiological investigation found her. She had an infection in her gallbladder. Detained at Riverside Hospital for 3 years. Later, released then detained again for the rest of her life (25 years) - died in 1938. Caused 1300 cases of typhoid fever.

nitrogen fixation,
actinomycetes produce streptomycin, chloramphenicol,
tetracycline, cyanobacteria (blue-green) algae
nitrogen fixation nodules - alfalfa, soy clover
for rice blue green algae - cyanobacteria heterocysts
yogart, cheeze, saurkraut, coco
enzymes for industry
Chemisynthetic use sulfur, ammonia, nitrite,
put out sulfates and nitrates for soil.
cows sheep goats cellulose
make vit K and B12

For further study: Here is a site entitled "Communicable Disease Surveillance and Response (CSR)" which is of relevance to this and other chapters. And here is Disease information from the Centers for Disease Control, also relevant to several chapters, especially this one.

Questions used in 2007 & 2008 relating to this outline

Vaccination is more successful for smallpox than flu because
(a) passive immunity is conferred for smallpox.
(b) antibiotics work so well for smallpox.
*(c) evolution in animal hosts takes place in flu.
(d) smallpox is a bacterium while flu is a retrovirus.
(e) flu is caused by a proteinaceous particle.

Mad cow disease is most closely related to
(a) typhoid.
(b) antibiotic resistance.
(c) herpes.
*(d) scrapie.
(e) the H1N1 strain.

Fleming accidentally dropped a colony of Penicillium onto a plate of
(a) viruses.
*(b) bacteria.
(c) algae.
(d) antibiotics.
(e) plasmids.

One particular concern about rubella (German measles) is that
(a) it is killing all the chimpanzees.
(b) it killed over 20 million people in 1918 and it could strike again.
(c) even though eliminated worldwide, we should not eliminate the last repositories of viruses in case terrorists have it in their possession.
(d) the DNA reverse transcribed from its RNA gets incorporated into the host cell's genome.
*(e) it can cross the placenta.

An important laboratory test is the Gram stain. What structure does it target?
(a) alleles for purple flowers
(b) eukaryotic chromosomes at the metaphase plate
(c) DNA in gel electrophoresis
(d) protein coat of virus
*(e) cell wall of bacteria

It has recently been understood that Helicobacter pylori causes what aliment in humans?
(a) sexually stransmitted diseases (STDs)
(b) Down syndrome
*(c) ulcers
(d) Bubonic plague
(e) Turner's syndrome

What is the proper scientific nomenclature for rod shaped bacteria?
(a) cocci
*(b) bacilli
(c) spirilla
(d) streptococci
(e) staphylococcus

The lytic cycle applies to reproduction
(a) of DNA during the S phase of the cell cycle.
(b) of herpes virus.
*(c) of bacteriophage.
(d) of the karyotype.
(e) of bacteria.

Evolution of antibiotic resistance is of particular concern in
(a) biodegradation.
(b) polymerase chain reaction (PCR).
(c) endospores.
*(d) the meat industry.
(e) the digestion of cellulose by ruminants.

What disorder would you be avoiding by making certain that your home-canned foods and the containers are hot enough?
(a) west Nile encephalitis
(b) polio
(c) tetanus
*(d) botulism
(e) ulcers

Shortly after the 9/11 attacks on the World Trade Center and the Pentagon, there were mail attacks with what disease?
(a) botox
(b) avian flu
(c) smallpox
*(d) anthrax
(e) fire blight

Plasmids are found in
*A) bacterial cells.
B) the virus that causes AIDS (acquired immunodeficiency syndrome).
C) vaccines.
D) hemaglutinin and neuraminidase.
E) antigens.

What allows Clostridium botulinum to flourish in improperly canned garden goods?
A) reverse transcriptase
B) flagella
*C) endospores
D) peptidoglycan
E) antibiotics

Cyanobacteria are _____________ .
A) saprobes.
*B) photosynthetic.
C) heterotrophic.
D) eukaryotic.
E) the cause of bovine spongiform encephalitis (mad cow disease).

Bacteria cause (or contribute to) which of these disorders?
A) tuberculosis (TB, consumption)
B) anthrax
C) ulcers
D) strep throat
*E) all of these

For which of the following diseases would antibiotics be useful?
A) smallpox
*B) plague
C) H1N1 ("Spanish") influenza
D) scrapie
E) measles

Creutzfeldt-Jacob disease (CJD) is caused by
*A) a protenacious infectious particle.
B) an anaerobic bacterium.
C) viruses that can also live in swine and birds.
D) an RNA-containing virus.
E) peptidoglycan.

Prions are known to cause
A) sickle cell anemia
B) colds
*D) mad cow disease
E) influenza

Flagellated bacteria
A) have internal organelles such as mitochondria.
B) use the flagella to exchange sperm and eggs for sexual reproduction.
*C) can move toward attractants like nutrients.
D) are not considered to be officially "alive" by biologists.
E) are eukaryotes.

The bacterial cell wall contains
A) adrenalin.
*B) peptidoglycan.
C) chitin.
D) triglycerides.
E) glycogen.

How do Gram-positive bacteria necessarily differ from Gram-negative bacteria?
A) how much they weigh
B) whether they have DNA or not
C) whether they translate RNA to DNA or reverse translate DNA into RNA
*D) staining properties
E) whether they have a nucleus or not

Which of the following may be contained in a virus?
B) mitochondria
C) cytoplasm
D) ribosomes
E) lysosomes

Questions used in 2002 relating to this outline (and other outlines)

The first vaccination, in the late 1700's was against
(a) polio.
(b) Asian flu.
*(c) small pox.
(d) a retrovirus.
(e) E. coli.

A Nobel Prize relates to mad cow disease, caused by a
(a) virus.
*(b) protein.
(c) bacterium.
(d) plasmid.
(e) transposon.

Reverse transcriptase would work on [A] to form [B].
(a) [A] bacteria; [B] bacteriophage
(b) [A] pre-mRNA; [B] mRNA
(c) [A] mRNA; [B] protein
(d) [A] DNA; [B] PCR reaction products
*(e) [A] RNA; [B] DNA

Which enzyme is the hallmark of HIV (human immunodeficiency virus) that causes AIDS (acquired immunodeficiency virus)?
(a) primase.
(b) nuclease.
(c) telomerase.
(d) hemoglobin.
*(e) reverse transcriptase.

Vaccination confers active immunity by
*(a) stimulating your immune system to make antibodies.
(b) stimulating your immune system to make antigens.
(c) stimulating your immune system to make prions.
(d) stimulating your immune system to make transposons.
(e) giving a person antibodies made by another person when (s)he overcame the disease.

Clostridium botulinum
(a) is a methanogen, making swamp gas.
(b) was used by terrorists in Fall, 2001 in the US Postal Service.
(c) is a photoautotroph.
*(d) have a toxin that, although deadly, is used as a cosmetic.
(e) reproduces sexually but, since the offspring are not fertile, is not considered to be a species.

Which live in salty areas like the Dead Sea?
(a) cyanobacteria
(b) Helicobacter pylori
*(c) extreme halophiles
(d) E. coli
(e) the bacterium whose DNA polymerase is used in the PCR reaction

(a) causes ulcers
(b) is spread by the bite of a tick.
(c) caused the Black Plague in the Middle Ages.
*(d) comes from anaerobic bacteria.
(e) is a sexually transmitted disease

Mary Mallon, an Irish immigrant, worked as a cook in the early 1900's until she was incarcerated and is believed to have infected 1300 people with
(a) typhoid.
(b) small pox.
(c) hepatitis B.
(d) AIDS.
(e) syphilis.

(a) are drugs that kill bacteria.
(b) are made by your immune system to attack microbes.
(c) are the portions of the antigen that antibodies attack
(d) are on red blood cells and are responsible for ABO blood groups.
(e) should be used to treat disorders like influenza.

Some viruses use the mosquito as an intermediate host. Of the following, this applies to the one causing
(a) Lyme disease
(b) small pox
(c) polio
(d) West Nile encephalitis
(e) Klinefelter's syndrome

Which is not caused by a virus?
(a) small pox
(b) AIDS
(c) polio
(d) cholera
(e) flu

This page was last updated  7/13/09

I'm a biologist. I'm in the biology department.
You're the one! You're the one's going to make all that trouble ... making everyone the same, rearranging the chromozones, or whatever it is. Isn't that right?
NICK (with that small smile)
Not exactly: chromosomes.
Biology, hunh?
I read somewhere that science fiction is really not fiction at all ... that you people are rearranging my genes, so that everyone will be like everyone else. Now I won't have that! It would be a shame. I mean ... look at me! Is it really such a good idea ... if everyone was forty something and looked fifty-five?
-Edward Albee, Who's Afraid of Virginia Woolfe?1962

"In the year 6565, ain't gonna need no husband, won't need no wife.
You'll pick your son, pick your daughter too
from the bottom of a long glass tube.
Woh - woh."
-Rick Evans (Zager and Evans), Zerland Music, 1969
In the Year 2525 (Exordium & Terminus)

Audesirk, Audesirk & Byers Chapter 13, Selections from Chapters 4, 9, 11 & 40

Today's musical selection
Wierd Al Yankovic - I think I'm a clone now


The word "clone" has three meanings:
(1) Grow an organism from a somatic cell's nucleus
(2) Chop off a gene and grow it in another cell
(3) (as a noun) The group of cells descended from one cell (not discussed further in this outline)

Dolly, etc

One of the best known to the lay public started when a sheep named Dolly was made from a nucleus from another sheep. Text box "carbon copies" (pp. 202-204, Chapter 11) discusses similarities with any asexual reproduction used in agriculture.

1950's work on amphibians - Since all nuclei should have all the genes, any nucleus should work to make whole organism, here taken out of an intestine cell. But not all cells work, so put it in an egg where it is certain that the nucleus already there has been destroyed.

Figure E-11-1
1997 work to make sheep Dolly. Nuclear transfer by removal followed by cell fusion. Need surogate mother.
Cloning has been extremely controversial, and human cloning was banned. Some scientists hoping to advance medical treatments would like to distinguish "theraputic cloning" from cloning to produce a person genetically identical with the donor. Some think the issue would be simplified by use of the term "nuclear transplantation."


Figure 9-1
Transformation in bacteria

Figure 9-2
Molecular mechanism of transformation

Figure 4-20
Bacterial cells have circular chromosome plus plasmids

Gene cloning

Figure 13-1
In lay terms, cloning is chopping a gene at both ends, putting it in and growing it up in bacteria. Plasmids are important. This allows manufacture of proteins of interest, and examples are given: growth hormone and a clot dissolving enzyme. Also, bacteria can be altered with inserted genes so that they do useful things like clean up oil spills. Crops can also be altered like inserting resistance to pests.

Figure 13-9
restriction nucleases often cut at "palindromes"
"restriction" restrict phage infections in bacteria
"Able was I ere I saw Elba" Napoleon "Madam I'm Adam" first sentence
Eco R1 E. coli
staggered cuts with single stranded cohesive ends

The1978 Nobel prize in Physiology and Medicine was awarded jointly to: WERNER ARBER , DANIEL NATHANS and HAMILTON O. SMITH for the discovery of restriction enzymes and their application to problems of molecular genetics

Figure 13-10
(How to put Bt [a gene from Bacillus thuringiensis] into plants using Agrobacterium tumefaciens for insect resistance)
If the same restriction enzyme is used to cut a piece of DNA with the gene of interest and the plasmid, they will have complementary sticky ends and will stick together.


It's a lot of trouble to clone a gene.

Figure E9-7
DNA polymerase works on single stranded DNA.

The1993 Nobel Prize in Chemistry was shared and awarded in part to KARY B. MULLIS for his invention of the polymerase chain reaction (PCR) method.

Figure 13-3
One strand is sense strand, the other is the antisense strand, and they are antiparallel.
If you know sequence at beginning and end of the gene, you make one primer for the sense strand at the beginning of the gene and another for the antisense strand at the end of the gene.
These will copy gene and then continue beyond in the first round, which is a small problem.
But on next round, going the other way stops at the end of the gene.

Figure E13-1
If 98oC to denature, cool to 60oC for polymerase to add to prime, that would require new polymerase at each cooling, but Thermus aquaticus from Yellowstone hot spring polymerase.
It all becomes very automated, and here's a picture I shot of one of the Biology Department's PCR machines.

DNA profiles

Figure 13-5
Gel electrophoresis

Figure 13-11
(Example of diagnosing sickle cell anemia)
restriction fragment length polymorphisms (RFLP)
In general, a marker is something like fruit fly eye color (something that has a phenotype (trait)), that can be used for genetic mapping but RFLPs can be markers too. This is the older method behind DNA fingerprinting

Figure 13-7
Now short tandem repeats (STRs) provide most unequivocal profiling
"...a perfect match...means that there is less than one chance in a trillion..." (recall scientific method)

Figure 13-12
Microarray - test for expression of all the genes (supplies are expensive)


Figure (Chapter 13 opener)
Chapter 13 case study (guilty or innocent) p. 251 and revisited p. 271. Case of Earl Ruffin in prison 21 years before DNA evidence showed him innocent

Figure E40-3
(look ahead to p. 831 box on Hi-tech reproduction)
Now cloning is controversial. In the 1970's, in vitro fertilization was controversial.


Figure E13-4
GMO stands for "genetically modified organisms." In this country, environmental groups such as Greenpeace, have spearheaded the opposition to GMO. At the economic level, the US, a major agricultural exporter and with big biotech firms, opposes trade sanctions and labeling requirements. At the level of the world trade organization, (WTO), especially the European union (EU), there is consumer anxiety, witnessed by terms such as "Frankenfoods." Clearly, there can be wonderful achievements, such as the recent expression of beta-carotene in rice; in many third world areas, rice is so preponderant in the diet that people suffer from vitamin A deficiency. But there are dangers such as the possibility that sterility alleles will transfer from patented crop to other plants.

Questions used in 2007 & 2008 relating to this outline

Nuclear transplantation was used
(a) for in vitro fertilization.
(b) to transform R-strain bacteria with S-strain DNA.
*(c) to clone Dolly.
(d) to clone a gene.
(e) to create DNA arrays.

Golden rice with beta carotene
(a) was crossed with green rice by Mendel.
(b) solves the problem of vitamin B deficiency.
(c) was a product of stem cell research.
*(d) should be good for vision.
(e) arose by sympatric speciation.

Gel electrophoresis can separate globin alleles by
(a) color.
(b) histology.
(c) symmetry.
(d) hydrophobicity.
*(e) length.

What is a danger of genetically modified agriculture mentioned in class?
*(a) Sterility alleles might be spread.
(b) It led to the Irish potato famine.
(c) Autotrophs would go extinct.
(d) Genetically modified plants lack a vascular system.
(e) Genetically modified plants are susceptible to penicillin.

Sticky ends refer to
*(a) DNA cut by restriction endonucleases.
(b) Gram stining.
(c) implantation into a surrogate mother.
(d) Creutzfeld-Jacob disease (CJD).
(e) transfer RNA (tRNA).

In the polymerase chain reaction (PCR)
(a) theraputic cloning is achieved.
(b) an enzyme is used to cut a gene and a plasmid.
(c) a gene is inserted into a plant using Agrobacterium tumefaciens.
(d) a protein is mass produced using bacteria.
*(e) a defined length of DNA is amplified.

RFLPs (restriction fragment length polymorphisms) can be used for
(a) in vitro fertilization.
*(b) genetic profiling.
(c) achieve conjugation in bacteria.
(d) copying DNA to another copy after everything had been heated to denature DNA.
(e) preventing the evolution of antibiotic resistant bacteria.

One, two or three bands on a gel representing homozygous sickle globin, homozygous normal and heterozygous respectively
(a) allowed Earl Ruffin to be freed after 21 years in prison.
*(b) were created when one enzyme cut different DNA sequences to different numbers and lengths.
(c) would be of little value without a surrogate mother.
(d) represent the amino acid sequence of alpha and beta chains of hemoglobin.
(e) allowed insertion of a Bacillus thuringiensis gene into a bacterium.

What property of DNA allowed more unequivocal identification of people by DNA fingerprinting?
*(a) short tandem repeats (STRs)
(b) divergence
(c) heterozygosity
(d) poly-A tails
(e) dominance

The polymerase chain reaction (PCR) is used
A) for "theraputic cloning" (nuclear transfer).
B) ligation of separate DNA fragments copied on the lagging strand.
C) allowing restriction enzymes to cut DNA at palindromes.
*D) making many copies of a small amount of DNA.
E) "cloning" (chopping off a gene at both ends and sticking it into a bacterium).

Specific fragments of DNA on a gel can be visualized using
*A) DNA probes.
B) in vitro fertilization.
C) Bacillus thuringiensis.
D) a surrogate mother.

The molecules used to cut DNA in recombinant DNA research are called
A) DNA polymerases.
B) DNA ligase.
*C) restriction enzymes.
D) Agrobacterium tumefaciens.
E) Frankenfoods.

In addition to DNA ligase, what would be a typical enzyme necessary to put your gene of interest into a plasmid?
A) DNA polymerase
*B) Eco R1
C) the one from thermophilic bacteria from hot springs
D) RNA polymerase.
E) hydrolysis enzyme

Differences in RFLP banding patterns indicate that
A) one of the X chromosomes is inactivated.
B) mRNA is not transcribed.
C) two genes are not linked.
D) a nucleus has been transplanted.
*E) the two different DNAs being tested possess different base pairs.

To clone Dolly, they needed an egg (with its nucleus removed), a nucleus from a somatic cell and
A) sticky ends.
B) primers.
C) the Bt gene.
*D) a surrogate mother.
E) gel electrophoresis.

DNA fragments created by restriction enzymes are separated from one another by
A) crossing over.
B) short tandem repeats.
C) apoptosis.
D) polymerase chain reaction.
*E) gel electrophoresis.

Which of the following can be used to produce genetic profiles of people?
A) the number of introns in a chromosome
B) Bt (a gene from Bacillus thuringiensis)
C) cloning
*D) short tandem repeats (STRs)
E) plasmids

To join a fragment of human DNA to plasmid DNA, both the human DNA and the bacterial DNA must be first treated with the same
A) polyunsaturated fatty acid.
B) RNA polymerase.
*C) restriction enzyme.
D) lipid soluble vitamin.
E) hydrolysis enzyme

Questions used in 2002 relating to this outline (and other outlines)

A disease-causing allele of a gene can be mapped to a "marker" that is a nearby alteration in DNA sequence called a(n)
(a) autoradiogram.
(b) PCR primer.
(c) G protein.
(d) hybridization.
*(e) RFLP (restriction fragment length polymorphism).

Which of the following has plasmids?
(a) HIV
(b) flu
*(c) E. coli
(d) small pox
(e) T4

PCR is used to
(a) determine the sizes of different restriction fragments.
(b) insert a new gene in gene therapy
*(c) make multiple copies of a gene of interest.
(d) identify protein in a blot.
(e) get rid of p53.

Which would most likely be a line from Weird Al Yankovic's song "I think I'm a clone?"
(a) "You people are rearranging my genes."
(b) "The basic secret of life is something about protein."
(c) "The gingham dog and the calico cat side by side on the table sat."
(d) "Northern blot, Southern blot, Western blot, all around the blot blot."
(e) "They took a donor's body cell and fertilized a human egg."

This page was last updated 7/23/09

 **The evolution vs intelligent design lecture



 And God saw every thing that he had made, and, behold, it was very good. And the evening and the morning were the sixth day.
-The first book of Moses, called GENESIS, Chapter 1, verse 31

...like one of those sticklike male insects I once watched in horror as a child which, even during the very act of mating, is calmly devoured by the female headfirst right down to his rutting abdomen...
-Michael Curtis Ford The ten thousand, a novel of ancient Greece


Audesirk, Audesirk & Byers Selections from Chapters 14-16 & 18
plus (obviously) I had to shop around a lot for figures (in Chapters 1, 23, 26, 27 & 43)

Today's musical selection
Gene McDaniels One hundred pounds of clay

Evolution vs Intelligent design

Lamarck (1744-1829) use and disuse. Giraffe example

Figure E14-1
Darwin (1809 - 1882) survival of the fittest
(1) survival means to reproduce
(2) fittest may have as much to do with likelihood of reproducing as toughness

Voyage of HMS Beagle 1831 - 1836 Book 1839
Galapagos -
volcanic, 600 mi from Ecuador, 1 million yrs (young)
"tortoises" - Darwin was impressed with DIVERSITY (not so much in England)

Figure E43.3
(Islands are particularly interesting. For instance birds on islands w/o predators like dodo, have relaxed selection pressure until environment changes - humans with clubs arrive.)

Figure 14-5
Darwin's finches
13 species diversity
woodpecker finch - twig to get insects (tongue short)
(could not compete)
The idea is that the ancestor colonized these islands recently (relative to the geological time scale), and there has been divergent evolution to make different species that have different adaptations for survival in terms of feeding (like type of beak) or where they nest. There are niches that eventually get filled.

Influences on Darwin:
Malthus Essay on the Principle of Population 1798 (philosopher of gloom - population will grow exponentially, and resources will at best increase linearly so that eventually there will be a struggle for survival.
Lyell geology, earth changes slowly
Origin of species 1859 Alfred Wallace 1858

Voyage of HMS Beagle - Controversy, skipper Fitzroy commit suicide
Thomas Huxley (Huxleys) (vs. Bishop Samuel Wilberforce 1860)
British Asdsociation for the Advancement of Science
"would have rather been descended from an ape than from a cultivateed man who prostituted the gifts of culture and eloquence to the service of predjudice and falsehood"

Scopes (John) "monkey trial" Dayton Tenn. 1925
Clarrence Darrow
William Jennings Bryant silver-tongued orator, former Pres candidate, died after
Curtis of UMC was a witness
found guilty and fined $100
Humanities: Jerome Lawrence and Robert E. Lee published their dramatized account of the trial in Inherit the Wind.

Power point slides
Creationism - from an early 1960's paper by George Wald on the Origin of life
Bible - note how short the story of creation is
Fundamentalism,equal time in text book controversies,
Now called "intelligent design"

SLU's Biology department felt the need to post a statement about evolution in answer to attacks from proponents of so-called "intelligent design."Evolution


Origin of the species
survival of the fittest,
Natural selection,
selection pressure,
adaptation for survival, homology
divergent evolution
adaptive radiation
convergent evolution, analogy

Origin of the species

(MANY) - 1.6 million known - maybe several million more
maybe 100 x as many in the past
mass extinctions, most past species gone

Figure 16-8
One species definition: Reproduce, fertile offspring
Tiger - lion: (different species)
there are many limitations to this theory (especially it only applies to sexually reproducing species)


Figure 26-10
think of survival of fittest
pack of wolves kill elk


Survival = Reproduce

Figure 23.18
(I just needed a picture)
Praying mantis
So predatory that the female eats the male' head first
the rest of the body completes copulation

Figure 15-12
Sexual selection

(Examples from chapter 27, community interactions [ecology])

Figure 27.5
camouflage - cryptic coloration

Figure 27.7
Warning coloration (opposite strategy of crytic coloration)

Figure 27-8
Mimicry - viceroy
Monarch, milk weed, digitalis 1 trial learning

Natural selection

As an extension of the idea of "natural selection", we should consider selection after human influences:

Figure (Chapter 15 opener)
(Chapter 15 case study, evolution of a menace, p. 295 and revisited p. 311)
antibiotic resistance

Not everything has a purpose

Figure (Chapter 14 opener)
(What good are wings on ostrich?)
(Case study - what good are wisdom teeth? chapter 14, p. 277 and revisited p. 292)
vestigial structures - human appendix, male nipples

divergent evolution

Figure 14-7
comparative anatomy (and embryology)

Figure 1-11
tree (on a grand scale)

Figure 18-6
tree (on an intermediate scale)

Figure E18-1
Tree (on a small scale)

convergent evolution

Figure 14-9
In addition to divergent evolution, there is convergent evolution (like insects and birds both have wings but not derived from a primordial anatomical structure in a common ancester) and coevolution, the latter being a topic at the interface between evolution and ecology (Chapters toward the end of the book)

(many possible examples)
based on symbiosis (living together)
Pollination, cross pollination - avoid inbreeding

Figure 43-17

Figure 43-16
(UV ultraviolet)

Figure 43-19
Hummingbirds, (red)
honey possom

Figure 43-20
Orchid - wasp (coevolution, mimicry)

Questions used in 2007 & 2008 relating to this outline

The idea that available niches will eventually get filled best describes
(a) the influence that Malthus had on Darwin.
*(b) the finches Darwin studied on the Galapagos.
(c) the infertility of a tiger-lion hybrid.
(d) cryptic coloration (camouflage) in the example of a moth that looks like a bird dropping.
(e) Lamarck's idea that acquired characteristics are inherited.

"Analogy" is the term selected instead of "homology" to distinguish
(a) extinction of the dinosaur from the many periods of extinction over geological time.
(b) coevolution from warning coloration.
*(c) convergent evolution from divergent evolution.
(d) the wing of a bird from the human hand and arm.
(e) Darwin's theory from Lamarck's theory.

Ultraviolet (UV) light is most relevant to
(a) attraction of the peahen to the most extravagant peacock.
(b) birds avoiding viceroy butterflies when monarch butterflies are poisonous.
(c) real wings vs vestigial wings.
*(d) pollination of some flowers by bees.
(e) survival of the genes vs survival of the individual in the praying mantis example.

The story about big red flowers like columbine and trumpet vine relates to
(a) divergent evolution in an island system.
(b) mimicry used to avoid predation by birds.
(c) exponential vs linear growth curves.
(d) what defines a species when sexual reproduction is not relevant.
*(e) coevolution with the humming bird as a pollinator.

What term best relates the forelimb skeletons of birds, bats, and pterodactyl?
(a) convergent evolution
(b) coevolution
*(c) homology
(d) allopatric
(e) sexual selection

What is an example of a vestigial structure?
(a) islets of Langerhans
(b) taste buds
(c) the rumen of a cow
(d) a male peacock's tail
*(e) human appendix

Questions used in 2002 relating to this outline (and other outlines)

Who thought that characteristics acquired during life could be passed on to the next generation?
(a) Alfred Wallace, 1858 author
*(b) Lamarck
(c) the school teacher John Scopes
(d) the geologist Lyell
(e) Malthus, author of Essay on the Principle of Population

Numerous vacant niches are a model for the evolution of
(a) melanotic moths during the industrial revolution.
*(b) "Darwin's finches" on the Galapagos Islands.
(c) the Missouri mule.
(d) antibiotic resistance.
(e) the curious mating habits of the praying mantis.

When structures in two different species are evolved from a common ancestor, this is an example of
*(a) homology.
(b) coevolution.
(c) convergent evolution.
(d) sexual selection.
(e) altruism.

According to Darwin's theory of evolution, present day giraffes came to have long necks because
(a) genetic drift makes each individual giraffe's neck longer and this longer neck trait is then passed on to each giraffe's offspring.
*(b) long necked giraffes survive to reproductive age because they are better adapted to eat while short necked giraffes die young.
(c) use of the neck enlarges it and each giraffe passes on its neck characteristics determined by such use vs. disuse.
(d) all giraffes reproduce similarly, but, after the reproductive part of the life span is passed, long necked giraffes can live to an older age.
(e) the bottleneck phenomenon eliminated short necks.

All of the following organisms have forelimbs which are examples of homologous structures except which one?
(a) Whale
(b) Bird
(c) Bat
*(d) Insect
(e) Human

Exponential growth, when plotted as a graph,
(a) looks like a line.
*(b) is a curve with increasing upward slope.
(c) goes straight across.
(d) goes up, then down.
(e) goes down then up.

Some of Darwin's ideas on the struggle for survival developed only after reading
*(a) Essay on the Principle of Populations by Thomas Malthus.
(b) On the Tendency of Varieties to Depart Indefinitely from the Original Type by Alfred Wallace.
(c) Mendel's Laws of Segregation and of Independent Assortment.
(d) The play Inherit the Wind.
(e) The transcripts from the Scopes "monkey trial."

The peacock is a classic example of
(a) altruism.
*(b) sexual selection.
(c) sympatric speciation.
(d) mimicry.
(e) the bottleneck effect.

Which would be an example of "convergent evolution"?
(a) the similarity of your arm and a chicken wing
(b) the idea that present-day bacteria and people have a common ancester in a cell from long ago.
(c) the fact that trumpet flowers are pollinated by humming birds
(d) the carniverous behavior during mating in the praying mantis
*(e) the fact that bats and bees both have wings

How does a bee's ability to see ultraviolet light fit in with evolution?
A) It makes those bees more attractive (sexual selection).
B) Those bees filled one niche on the Galapagos Islands.
*C) It contributes to coevolution of pollinators with flowering plants.
D) Bees use ultraviolet light for camouflage (cryptic coloration).
E) Ultraviolet vision is considered vestigial.

The incorrect theory that "organisms can modify their bodies through use or disuse of parts, and that these modifications can be passed on to their offspring" was formulated by
A) Malthus.
B) Darwin.
*C) Lamarck.
D) Wallace.
E) Lyell.

When unrelated organisms living under similar environmental demands evolve superficially similar structures, it is called
A) adaptive radiation.
B) divergent evolution.
*C) convergent evolution.
D) coevolution
E) homology

Boa constrictor snakes have tiny pelvic girdles and leg bones within their bodies. Because these structures are nonfunctional "evolutionary baggage," they are called
A) convergent.
B) analogous.
C) adaptive.
D) homologous.
*E) vestigial.

Mimicry in the viceroy butterfly relies on
A) occupied niches.
*B) warning coloration.
C) exponential population growth.
D) adaptive radiation in an island habitat.
E) sexual selection.

This page was last updated 7/28/09

** The genetic bases of evolution


 Evolution and its genetic basis


Audesirk, Audesirk & Byers Selections from Chapters 14-16 & 18

Background and review

Figure 14-7
Homology Limb
Comparative anatomy, embryology, biochemistry, molecular biology
Homology - common descent
bat (also pterodactyl, bird - fly)
dolphin (also seal - swim)
dog (also sheep - run)
human (also shrew - grasp)

Figure 18-6
Divergent (vs. convergent evolution)
Phylogenetic tree
Eukaryote evolution

isolating mechanisms

Remember, species can reproduce

Figure 16-10
speciation in the same area (sympatric)

Figure 16-9
and in different areas (allopatric). There are also other .

Moths use sex attractant pheromones from female sensed by big feathery antennae in males.
These may be molecules like acetates, chains10 to 15 carbons long.
Two similar moths in same place (sympatric) do not mate, thus seem to be 2 species (Roelofs and Comeau, Science 165, 398-400, 1969).
One uses molecule cis around one double bond, the other trans.
For that to happen, one female would have to change pheromone used and a male at the same place and time would have to have a change in preference, an amazing jump (saltation).

Divergent evolution

Figure 23-1
Comparative anatomy, embryology, biochemistry, molecular biology

Figure E18-1
can use "molecular" (biochemical) data to get relationships

Figure 14-11
also (cytochrome c sequence comparison between species)

Figure 24-1
Remember (and it is so confusing that it is hard to remember) that lower on the diagram are ancestors, not "simple" organisms that are around today.

Figure 24-2
One "left-over" that helps to confuse this issue is the old saying "Ontogeny recapitulates phylogeny." Gill pouches and tail suggest that people and birds go through a fish stage in their development.

Need to simplify by considering one gene

Box (a closer look) [p. 298, chapter 15]
The Hardy-Weinberg principle
(Orientation for next week's lab)

The Hardy-Weinberg principle describes the frequency of alleles if there is no change (a non-evolving population):
(1) large population
(2) no migration
(3) no net mutation
(4) random mating
(5) nonatural selection

I've redrawn Fig. 12-11 with p and q being the gamete probabilities in the population.
Hey, this looks like a punnet square for the F2 of a cross with one gene and two alleles, except here, we have added probabilities of the two alleles (p + q = 1) to get probabilities of the "4" genotypes (actually 3 since aA is the same as Aa)

Imagine you roll a die: Expectation - 1, 2, 3, 4, 5, and 6 each should occur 1/6 of the time. How deviant from that expectation would your outcome need to be for you to conclude that the die is "loaded?"

Restated with reference to our coverage of statistics and the scientific method, how far from expectation must the observed results be before you conclude that they show a real difference and not just chance, keeping in mind that you can never be absolutely certain?

In lab, we will simulate a sampling by selection and counting beads and thus doing the appropriate statistical test, called Chi-square

"Adaptive significance," "selection pressures" and all those favorite jargons give the false impression that everything is the way it is because of "deliberate" outcomes of evolutionary processes. But all kinds of things got to be the way they are through "accidental" processes. (Furthermore, evolution cannot make an overall master plan but rather has to build on the successes and mistakes of the past.)

Figure 15-5
Genetic drift
The frequency of alleles might change by this seemingly accidental mechanism.

Figure 15-7
The bottleneck effect.
What if some catastrophe wiped out all but a few individuals? The population would likely lose a lot of its variability as shown in this figure.

Figure 24-15c
Cheetah (very weak, genetically speaking, because of lack of heterozygosity in its genes)

Polygenic inheritance

Think about how the Hardy-Weinberg principle looks like a one-gene two-allele cross. Then remember how much more complicated the F2 Punnet square looked for Mendel's second law than for his first. My gosh, what if there were more than 2 genes and 2 alleles? This is called polygenic inheritance.

Figure 15-13
Genetic basis of variability and selection
Remember, in the genetics outline, I said (and gave this quote from Mendel):
Mendel (knew about Darwin but Darwin did not know about Mendel)
"...this seems to be the one correct way of finally reaching the solution to a question whose significance for the evolutionary history of organic forms must not be underestimated."

Figure 15-13
selection depends on variability in population
This plot of Frequency as a function of some quantitative measurement of phenotype shows a normal distribution.
Artificial selection in experiments - Directional selection

Environment changes
variability important
what is adaptive at one time may not be at another time


Figure 14-11
There's a lot of work these days with DNA sequence,
Similarities in sequences of human and mouse cytochrome c

Figure E18-1
Make a phylogenic tree using DNA

Questions used in 2007 & 2008 elated to this outline

In a population of wild flowers, there is this frequency of flower color alleles: R (red, dominant) = 0.8, r (white, recessive) = 0.2. Which describes how the r allele might be eliminated if only a few individuals from each generation reproduce?
(a) the Hardy-Weinberg theorem
(b) selection pressure
(c) sympatric speciation
(d) sexual selection
*(e) genetic drift

Long ago, some wogglebugs blew over to an island (previously devoid of wogglebugs) from the mainland and now biologists cannot get mainland and island wogglebugs to interbreed. This is
(a) genetic drift.
(b) expected from the Hardy-Weinberg principle.
*(c) allopatric speciation.
(d) comparative embryology.
(e) the Punnett square.

What is the deal with the cheetah?
(a) It cannot produce fertile offspring.
*(b) It has low heterozygosity in its genes.
(c) Sex-attractant pheromone traps have been used to eliminate this pest.
(d) It has a notocord but not a vertebral column.
(e) It is an extinct ancestor to present lions and tigers.

In a population of omicrons, the frequency of alleles for brunette fur is 0.8 while the frequency for blond is 0.2. What is the proportion of heterozygotes?
(a) 0.8
(b) 0.64
*(c) 0.32
(d) 0.2
(e) 0.04

If the tallest guy and gal in the class got married and had kids and the shortest guy and gal in the class also got married and had kids, the first couple's kids might be taller than the other couple's because of
(a) the fact that ontogeny recapitulates phylogeny.
(b) sympatric speciation.
(c) the bottleneck effect.
*(d) polygenic inheritance.
(e) Mendel's second law.

Which of the following is NOT a condition of the Hardy-Weinberg Principle?
*A) Natural selection will occur.
B) No mutations occur.
C) No gene flow will occur.
D) All mating is random.
E) Individuals will not move into or out of the population.

A small population is likely to evolve because of ________, but this is not likely to be true for large populations.
A) artificial selection
*B) genetic drift
C) mutations
D) the Hardy-Weinberg Principle
E) natural selection

Imagine that a population of deer living on an island without any predators was threatened with overpopulation. Then wolves were imported. After a few years there were fewer deer, but their average running speed had increased. This is an example of
A) inheritance of acquired characteristics.
B) theraputic cloning.
C) genetic drift.
D) the Hardy-Weinberg principle.
*E) natural selection.

According to the Hardy-Weinberg Principle, if 3/4 of the alleles in the gene pool are A1 and 1/4 are A2, what fraction of individuals has genotype A1A2 in this population?
A) 1/4
*B) 3/8
C) 1/2
D) 1/16
E) none of the above

Natural selection acts on ________ to affect the evolution of ________.
*A) phenotypes; populations
B) genotypes; populations
C) genotypes; individuals
D) genotypes; mutations
E) phenotypes; individuals

The male peacock's beautiful tail is really a trade-off between
A) natural selection and genetic drift.
*B) sexual selection and natural selection.
C) the Punnett square and natural selection.
D) disruptive selection and natural selection.
E) the bottleneck effect and allopatric speciation.

The extreme loss of genetic diversity that has occurred in cheetah populations due to overhunting is the result of
A) the Hardy-Weinberg principle.
B) sympatric speciation.
*C) a population bottleneck.
D) pheromones.
E) natural selection.

Historically, most evidence for homology and the common ancestor was based on ________.
*A) comparative anatomy.
B) cytochrome c.
C) convergent evolution.
D) RNA base sequence.
E) polygenic inheritance.

Questions used in 2002 relating to this outline (and other outlines)

In a population of wild flower, there is this frequency of flower color alleles: R (red, dominant) = 0.8, r (white, recessive) = 0.2. Which describes how the r allele might be eliminated if only a few individuals from each generation reproduce?
(a) the Hardy-Weinberg theorem
(b) punctuated equilibrium
(c) sympatric speciation
(d) altruism
*(e) genetic drift

The term "allopatric" was used in the context of
(a) whether symbiosis benefits both parties.
*(b) the formation of new species when the parent population becomes geographically isolated.
(c) whether the organism provides its own nutrition or needs to feed on others.
(d) whether the organism requires O2.
(e) whether evolution was gradual or sudden.

When structures in two different species are evolved from a common ancestor, this is an example of
*(a) homology.
(b) coevolution.
(c) convergent evolution.
(d) sexual selection.
(e) altruism.

Suppose that the red flower allele is dominant to the white flower allele and that the frequency of the red allele in the population is 0.8 while the frequency of the white flower allele is 0.2. What proportion of plants will have red flowers?
(a) 0.2
(b) 0.5
(c) 0.64
(d) 0.8
*(e) 0.96


This page was last updated 7/30/09


** Origin of life outline


In such a problem as the spontaneous origin of life...time is on its side. However improbable we regard this event...given enough time it will almost certainly happen at least once...One only has to wait: time itself performs the miracles...This is by far our most significant conclusion--that life, as an orderly natural event on such a planet as ours, was inevitable. - George Wald

Origin of life


Audesirk, Audesirk & Byers Part of Chapter 17, selection from Chapter 1

Today's musical selection
Peter, Paul and Mary Puff the magic dragon

Personal reflection. When I was in 9th grade biology (1961-1962) I read a paper (The origin of life, Scientific American, August 1954) by George Wald (who won a Nobel Prize in 1967); reading that paper had a great impact on me.

Panspermia - seeds of life distributed everywhere
Extraterrestrial origin

Spontaneous generation discredited:

Figure E1-1 (scientific inquiry box chapter 1)
(1) Redi (1600's show maggots on meat need flies to lay eggs)

Figure 17-1
(2) Pasteur microorganisms

Universe 15 - 20 billion years old
Earth 4.6 billion
Earth has water as liquid, many heavy elements

Figure 17-2
Haldane = Oparin theory, Miller & Urey experiment to reconstruct synthesis of organic molecules using water, methane, hydrogen and ammonia.

Figure 17-3
Early atmosphere (there's still some debate): Nitrogen (N2), Hydrogen (reducing = build-up), Methane (for C, H), Ammonia (for N, H), Carbon dioxide (for C, O), Water (for H, O), also some Hydrogen - sulfide (S), CO (carbon monoxide)

No (or very little) Oxygen O2 (oxidizing = break-down) or Ozone O3 (block UV)

Now N2 78%, O2 21%, CO2 0.3% + others (Argon)

Primordial hot dilute soup
"chemical" vs. "biological" evolution
amino acids hook together with "geologically relevant" heating like lava
amino acids - proteins, nucleotides - RNA, DNA, ATP
Eventually, DNA became the major hereditary molecule because it is so stable.
Probably RNA was the first hereditary material.
Vesicles, protocells
In the laboratory, such protobionts have been made.
Prokaryotes 3 & 1/2 billion years ago

Figure 17-4
then Eukaryotes (1 & 1/2 billion years ago)
Origin of mitochondria and chloroplasts as endosymbionts

Ferment (energy and CO2) (anaerobic = w/o oxygen)

Photosynthesis 6 CO2 + 6 H2O -- C6H12O6 (glucose) + O2

Animals - motility, sensory

Respiration (metabolism, aerobic)

Ozone (O3) from O2
Prior to that, all life had to be in the sea for protection from ultraviolet light
(depletion with freon = fluorocarbons)

Invasion of land had special requirements:
(1) vascular system to transport nutrients, wastes, gasses and hormones for multicellular organisms, (2) support on land where gravity is more of a concern
(3) mating without water

Questions used in 2007 & 2008 relating to this outline

Spontaneous generation
*(a) is accepted as how life originated even though it was disproved in classic experiments by Redi (for flies) and Pasteur (for bacteria).
(b) relates to the observation that embryos have gill slits and tails while adults do not.
(c) is the expression used to describe continental drift.
(d) describes how mitochondria and chloroplasts originated in early eukaryotes.
(e) is a process in which the allele frequency changes if only a few individuals of the population mate.

The earliest heredity may have been based on
*(a) RNA.
(b) DNA.
(c) proteins.
(d) chloroplasts.
(e) autotrophs.

"Reducing atmosphere" refers to
(a) global warming.
*(b) hydrogen favoring constructive reactions.
(c) oxygen.
(d) depletion of ozone.
(e) nitrogen.

There is a consensus that (what gas?) was missing from or very low in the prebiotic atmosphere?
(a) water
*(b) oxygen
(c) ammonia
(d) methane
(e) hydrogen

Endosymbiotes relate to
(a) the Irish potato famine.
(b) the Hardy-Weinberg principle.
(c) the pollen tube.
(d) xylem and phloem.
*(e) organelles in eukaryotic cells.

In the history of life, the earliest nutrition for catabolism
(a) was provided by photosynthesis.
*(b) was anaerobic.
(c) was present in protostomes.
(d) was a product of mitochondria.
(e) required the use of oxygen.

Most scientists think that global warming results from
(a) freon leaking from air conditioners.
*(b) carbon dioxide from fossil fuels.
(c) abundance of the primordial "hot dilute soup."
(d) an asteroid impact.
(e) elimination of habitats.

Why is ozone depletion a big problem?
*(a) Ultraviolet light reaches Earth.
(b) Melting polar ice caps will inundate low altitude cities.
(c) Acromegaly results.
(d) Osteoporosis results.
(e) Diuresis results.

All experiments that simulate conditions in Earth's early atmosphere assume that it did NOT contain which gas?
A) water vapor
B) methane
*C) oxygen
D) hydrogen
E) carbon dioxide

Carbon dioxide
A) was the main ingredient in the "primordial hot dilute soup."
B) was responsible for the "reducing" reactions of the primordial atmosphere.
*C) is increasing in the atmosphere presently and is a greenhouse gas.
D) is created because of Freon leaking from air conditioners.
E) is offloaded from the blood to tissues in the systemic circulation.

Why was fermentation needed by the earliest organisms for energy production?
*A) Since photosynthesis had not yet evolved, there was no oxygen.
B) There were chloroplasts in cells, but there were not mitochondria yet.
C) The cells were autotrophs, and that's what autotrophs do for metabolism
D) Without ozone, there was no ultraviolet (UV) light.
E) With only a two-chambered heart, there was poor gas exchange in these organisms.

Louis Pasteur's experiment illustrated that
A) spontaneous generation does occur.
B) mitochondria were incorporated as endosymbiotes.
C) phospholipids will spontaneously form a bilayer in water.
D) some complex molecules associated with living organisms can be synthesized by heating and cooling a solution of simple molecules and providing an electric spark.
*E) microbes will not grow in a nutrient broth that has been sterilized unless they are allowed to enter by opening the vessel to the air.

It has been proposed that the first atmosphere of Earth had all the following gases EXCEPT
A) H2.
B) H2O.
*C) O2.
D) CH4.
E) water vapor.

A) was used in the metabolism of the earliest organisms, the autotrophs.
B) is a big problem because of the use of fossil fuels.
C) was the source of sulfur in the earliest organic molecules.
*D) could not have appeared in the atmosphere until after photosynthesis.
E) was incorporated into the earliest eukaryotic cells to become organelles.

In the most ancient life forms, what was hypothesized to be the first self-replicating hereditary molecule because it had some enzymatic capabilities?
C) protein
D) methane
E) carbohydrate

The scenario of prebiotic (chemical) evolution leading to the origin of life on Earth is plausible because
A) DNA was already present in the primordial atmosphere.
*B) there was a vast period of time for simple chemicals to form complex molecules that eventually became enclosed simple cells.
C) even today, the ocean is a hot dilute soup of organic molecules that form into cells.
D) Francesco Redi proved that spontaneous generation occurred.
E) extraterrestrial organic molecules were known to have arrived.

Questions used in 2002 relating to this outline (and other outlines)

Which gas was probably not abundant (during chemical and early biological evolution) until after the origin of photosynthesis?
*(a) ozone
(b) carbon dioxide
(c) methane
(d) nitrogen
(e) water vapor

Why was it important in an evolutionary context to have early reproducing molecules enclosed into coacervates?
(a) because nutrients were scarce
(b) to compete with the abundant chemiautotrophs
*(c) so that the peptides translated would reside near the RNA
(d) because aerobic processes were beginning to degrade RNA
(e) because DNA, unlike proteins, can have properties like enzymes

(a) was released when the Cambrian exploded.
(b) served as the energy source of ancient bacteria.
(c) causes programmed cell death.
(d) arrived on Earth from the asteroid that arrived at the end of the Cretaceous.
*(e) is used to date fossils.

Which form of life came into existence first?
(a) flowering plants
*(b) prokaryotes
(c) invertebrates
(d) eukaryotes
(e) reptiles

The first biological organisms
(a) were probably eukaryotes.
(b) were probably autotrophs.
*(c) were probably heterotrophs.
(d) probably used DNA as their hereditary molecule.
(e) were probably photosynthetic.

Organic compounds break down spontaneously in the presence of what substance? Hence, life probably never would have emerged if the atmosphere were the same billions of years ago as it is today.
(a) hydrogen
(b) water
(c) nitrogen
*(d) oxygen
(e) methane

Chemical evolution before the origin of life on Earth is believed to have taken place
(a) about 4000 years before Christ.
(b) about 10,000 years ago.
(c) about 1,000,000 years ago.
(d) about 1,000,000,000 years ago.
*(e) before any of the above.

The "atmosphere" in the Miller-Urey experiment was "reducing" because it contained what substance which would have promoted the formation of organic molecules through reduction reactions.
(a) Argon
(b) O2
*(c) H2
(d) N2
(e) CO2

Which would have come first?
(a) sexual reproduction
*(b) heterotrophic prokaryotes
(c) incorporation of bacteria (that eventually became mitochondria) into eukaryotes
(d) incorporation of photosynthetic bacteria (that eventually became chloroplasts) into the precursors of plant cells
(e) the invasion of land

Among his many contributions, Louis Pasteur is known for
*(a) a classic experiment disproving spontaneous generation.
(b) prosecuting the Scopes "monkey trial."
(c) publishing a theory much like Darwin's at about the same time.
(d) developing a way to distinguish bacteria with different cell wall-membrane geometry.
(e) visiting the Galopagos Islands.

About how long ago did the first cells appear?
(a) 3.5 million years
(b) 3.5 billion years
(c) after photosynthesis evolved
(d) not until there was sexual reproduction
(e) 1.5 billion years ago when eukaryotes came into existence

There are very few fossils, except for stomatolites (that are like current mats of prokaryotes)
(a) in the Jurassic period
(b) in the Permean extinction
(c) at the Cretaceous-Tertiary boundary.
(d) during the part of the Paleozoic era before the Carboniferous period.
(e) in the Precambrian

Why do scientists think RNA was the hereditary molecule in the earliest organisms?
(a) RNA is more stable than DNA.
(b) RNA has fewer nucleotides and thus it is simpler.
*(c) RNA has properties like enzymes (usually proteins).
(d) The earliest organisms were viruses, and these contain only RNA.
(e) It was not until later that proteins evolved to take over hereditary function.

Which is thought to have happened most recently?
(a) the first protobionts.
(b) the first heterotrophic prokaryotes
(c) oxygen production by photosynthesis.
(d) incorporation of bacteria that eventually became mitochondria into eukaryotic cells.
*(e) incorporation of bacteria that would eventually become chloroplasts into plant cells.

This page was last updated 8/3/09

And has not such a Story from of Old
Down Man's successive generations roll'd
Of such a clod of saturated Earth
Cast by the Maker into Human mold?
--Omar Khayyam, Rubaiyat, FitzGerald, Fifth Edition

Audesirk, Audesirk & Byers Part of chapter 17, selections from Chapters 18 & 25

Today's musical selection
Irish Rovers - The unicorn song

History of life on Earth

molten rock solidifies 3.8 bya
Box, scientific inquiry, How do we know how old a fossil is?
40K -> 40Ar, bubbles out of molten rock, trapped in solid rock,
1.25 billion yr half life


Numbers (e.g. -570-) are million years ago

Table 17-1
(Useful to present in reverse, start at the beginning)

Precambrian 4.6 Earth

chemical evolution
biological evolution
RNA as hereditary molecule
Then DNA

very first life 3.5 1st fossils
these would have been anaerobic heterotrophs
3.5 Photosynthesis -> oxygen begins 2,200

2000 (million years ago = 2 billion) eukaryotes
diploidy and sexual reproduction around that time
then they get symbiotes, first mitochondria then chloroplasts
(endosymbiosis was covered in cell lecture)
1200 1st multicellular eukaryotes

O2 high to O3
(ozone, blocks UV, 260 nm damages DNA, 280 damages protein, now freon depletes)



Cambrian explosion (many species formed)

Figure 17-10
Mass extinctions

Coal deposited before and after Carboniferous, but Carboniferous is central.
Frequently flooded swamps with vascular plantscaused "reducing" conditions.
Petroleum from microscopic organism deposits often found near deposits of foraminiferans.
(Also associated with Carboniferous but quite extensive time span.)

Figure 17-11
Plate tectonics (actually not widely understood until the 1970's)
Pangaea, continental drift

Permian extinction, lose ocean habitat
Pangaea formed


Triassic 1st dinosaurs
Pangaea breakup
End of Triassic, mass extinctions, possibly global warming


Jurassic Dinosaurs, 1st birds
mammals flower plant
(Hard to imagine mammals would surpass dinosaurs, but adaptations to survival)


Cretaceous flowering plants
Mass extinctions - meteorite iridium -2.5 tril.tons 11km

- 65 million -



adaptive radiation of mammals & birds
...(other epochs)...


Quarternary Pleistocene (epoch) 4 ice ages
to MO, Ohio R.
mammoths die out
first Homo


Figure 17-12
Primitive primates (prosimians) lemurs, tree shrews
New world monkeys spider monkeys, prehensile tail
Old world monkeys (more "evolved") baboons, macaques (rhesus) color vision
(rhesus used in research - centers)
Animal activists give primate researchers a hard time

Figure 25-13
Figure 25-14
(baboons - very interesting social life)

Great apes -

Figure 18-3
Chimpanzee chromosomes like ours

Figure 25-17
Famously studied by Jane Goodall

present controversy used in AIDS research

Gorilla - very different in zoos,
Studied by Schaller
Dian Fossey studied them and was murdered by poachers in 1985
Gorillas in the mist was a movie about her

Orangutan, Gibbon


Figure 17-14
fossils not in good places
scavange, animals, native groups want buried
Famous hoax, Piltdown man, confused issue
Discoveries continue
Organization (diagram) changes
Excitement, for instance Ice-man
4 million yrs ago, before that "hominids"
Australopithecus afarensis Lucy 2.8 - 3.6 MYA
walked upright before brain grew
Australopithecus africanus (tool use) East Africa

Homo habilis

Figure 17-15
(crude chipped stones) (stone age)

Homo erectus (Java, Peking)
1.5 million yrs ago

Homo neanderthalensis
200,000 yrs ago
co-existed with Homo sapiens
did they compete? did they interbreed?

Homo sapiens

Figure 17-17
paint in caves

Figure 17-16

Figure 17-18
out of Africa

Figure (Chapter opener)
Case study little people big story
Homo floresciensis

Questions used in 2007 & 2008 relating to this outline

Which form of life came into existence first?
(a) flowering plants
(b) reptiles
(c) invertebrates
*(d) prokaryotes
(e) eukaryotes

When Pangaea was formed
(a) the Cambrian explosion blew up the dinosaurs.
(b) coal was deposited.
(c) so were the first cells.
*(d) coastal habitats were lost.
(e) RNA replaced DNA as the hereditary molecule.

Dinosaurs are thought to have gone extinct
(a) in the Quaternary period during the ice ages that wiped out the mammoth.
(b) when ozone was depleted.
*(c) at the Cretaceous-Tertiary boundary when an asteroid or comet crashed into Earth.
(d) because they got buried in frequently flooded swamp forests in the Carboniferous period.
(e) when oxygen started to appear in the atmosphere.

About how long ago did the first cells appear?
*(a) 3.5 billion years
(b) 1.5 billion years ago when eukaryotes came into existence
(c) 3.5 million years
(d) not until there was sexual reproduction
(e) after photosynthesis evolved

There is a consensus that humans originated
(a) because of a mutation in their closest relatives, the New World monkeys.
(b) in Indonesia.
(c) while dinosaurs were still dominant.
(d) in Peking.
*(e) in Africa.

(a) were the earliest humans.
(b) are the recently-discovered small people nicknamed "Hobbits."
*(c) co-existed with Homo sapiens.
(d) were in the species Australopithecus, and Lucy is a famous fossil.
(e) are the missing link between prosimians and modern humans.

The geological time scale corresponds to sequences of rock formations and fossils that have been grouped into four broad eras (ordered from long ago to now)
(a) Precambrian, Mesozoic, Cenozoic, Pleistocene.
(b) Cenozoic, Mesozoic, Precambrian, Paleozoic
(c) Precambrian, Paleozoic, Cenozoic, Pleistocene.
(d) Paleozoic, Precambrian, Mesozoic, Cenozoic.
*(e) Precambrian, Paleozoic, Mesozoic, Cenozoic.

Most scientists attribute the mass extinction of the dinosaurs to
A) loss of habitat.
B) hunting by primitive humans.
C) plate tectonics.
D) predation by mammals.
*E) a meteor impact.

The endosymbiotic hypothesis accounts for the origin of which cell structure?
*A) chloroplast
B) cell wall
C) chromosome
D) plasma membrane
E) ribosome

The first cells were
A) deposited and are now the coal of today.
*B) from 3.5 billion years ago.
C) photosynthetic, somewhat like cyanobacteria of today.
D) terrestrial (land-dwelling).
E) eukaryotes.

The worst mass extinction event of all time
A) occurred when the mammoths went extinct.
B) happened because of the Cambrian explosion.
C) accompanied the 4 ice ages that drove the dinosaurs extinct.
D) was 4 billion years ago.
*E) was at the end of the Permian period.

Humans first appeared in the
A) Mesozoic era.
B) Carboniferous period.
C) Jurassic period.
*D) Quaternary period.
E) Precambrian era.

In addition to Homo, another genus of hominids was
A) the chimpanzee.
B) the Lemur.
C) the Neanderthal.
D) the Piltdown man.
*E) Australopithecus.

Hominids originated in
*A) Africa.
B) Peking.
C) Indonesia.
D) North America.
E) Australia.

Geologists can determine the age of a rock by measuring ________ in the rock.
A) ions
B) chitin
*C) the proportion of potassium-40 to argon-40
D) Euglena
E) coal

Hobbit-sized hominid fossils recently discovered on a remote oceanic island belonged to
A) the genus Australopithicus afarensis.
B) the same species as the cave man in the stone age.
C) the same species as us.
*D) the species Homo floresiensis.
E) the genus Homo neanderthalensis.

Questions used in 2002 relating to this outline (and other outlines)

Which gas was probably not abundant (during chemical and early biological evolution) until after the origin of photosynthesis?
*(a) ozone
(b) carbon dioxide
(c) methane
(d) nitrogen
(e) water vapor

"Pangaea" is a term applied to
(a) present day drift of land masses.
(b) a period in the Paleozoic era.
*(c) a supercontinent in the Paleozoic era.
(d) a domain in the 3-domain system.
(e) the shape of a bacterial cell.

(a) was released when the Cambrian exploded.
(b) served as the energy source of ancient bacteria.
(c) causes programmed cell death.
(d) arrived on Earth from the asteroid that arrived at the end of the Cretaceous.
*(e) is used to date fossils.

Which form of life came into existence first?
(a) flowering plants
*(b) prokaryotes
(c) invertebrates
(d) eukaryotes
(e) reptiles

The first biological organisms
(a) were probably eukaryotes.
(b) were probably autotrophs.
*(c) were probably heterotrophs.
(d) probably used DNA as their hereditary molecule.
(e) were probably photosynthetic.

Chemical evolution before the origin of life on Earth is believed to have taken place
(a) about 4000 years before Christ.
(b) about 10,000 years ago.
(c) about 1,000,000 years ago.
(d) about 1,000,000,000 years ago.
*(e) before any of the above.

Coal was formed
(a) from organisms killed during the Permean extinction.
(b) from flowering plants in a reducing atmosphere.
*(c) from primitive vascular plants in the Carboniferous period.
(d) from mats of Precambrian photosynthetic prokaryotes.
(e) from deposits of foraminiferans.

The dinosaurs disappeared abruptly before the close of the Cretaceous because
*(a) there was a profound shift in climate probably caused by collision with an asteroid.
(b) of the most recent ice age.
(c) there were sudden, massive upheavals in Earth's crust.
(d) of a pathogenic bacterium specific to dinosaurs.
(e) of the Hardy-Weinberg theorem.

The geological time scale corresponds to sequences of rock formations and fossils that have been grouped into four broad eras (ordered from long ago to now)
(a) Precambrian, Mesozoic, Cenozoic, Pleistocene.
(b) Cenozoic, Mesozoic, Precambrian, Paleozoic
(c) Precambrian, Paleozoic, Cenozoic, Pleistocene.
(d) Paleozoic, Precambrian, Mesozoic, Cenozoic.
*(e) Precambrian, Paleozoic, Mesozoic, Cenozoic.

Which would have come first?
(a) sexual reproduction
*(b) heterotrophic prokaryotes
(c) incorporation of bacteria (that eventually became mitochondria) into eukaryotes
(d) incorporation of photosynthetic bacteria (that eventually became chloroplasts) into the precursors of plant cells
(e) the invasion of land

Organisms that do not use oxygen in the process of respiration are
(a) heterotrophic.
(b) haploid.
*(c) anaerobic.
(d) symbiotic.
(e) eukaryotic.

Why do scientists think RNA was the hereditary molecule in the earliest organisms?
(a) RNA is more stable than DNA.
(b) RNA has fewer nucleotides and thus it is simpler.
*(c) RNA has properties like enzymes (usually proteins).
(d) The earliest organisms were viruses, and these contain only RNA.
(e) It was not until later that proteins evolved to take over hereditary function.

At the end of the Paleozoic, continents merged to Pangaea, and the loss of costal habitats contributed to which extinction?
(a) Precambrian
(b) Ordovician
(c) Devonian
*(d) Permean
(e) Cretaceous

Which is thought to have happened most recently?
(a) the first protobionts.
(b) the first heterotrophic prokaryotes
(c) oxygen production by photosynthesis.
(d) incorporation of bacteria that eventually became mitochondria into eukaryotic cells.
*(e) incorporation of bacteria that would eventually become chloroplasts into plant cells.

Fossil fuels
(a) are composed of carbon dioxide precipitated out in rock by chemical action.
(b) are the remains of plants and animals of hundreds of millions of years ago.
(c) are the only form of carbon stored long-term by biological organisms long ago.
(d) deplete the ozone layer when burned.
(e) have caused an increase in atmospheric nitrogen when burned.

This page was last updated 8/5/09

**March through the kingdoms


I believe a leaf of grass is no less than the journey work of the stars
-Walt Whitman (Leaves of Grass)

What's in a name? That which we call a rose
By any other name would smell as sweet.
--William Shakespeare, Romeo and Juliet

I sometimes think that never blows so red
The Rose as where some buried Caesar bled;
That every Hyacinth the Garden wears
Dropt in her Lap from some once lovely Head.
--Omar Khayyam, Rubaiyat, FitzGerald, Fifth Edition

Selections from Chapters 20-22, Figure from Chapter 4

Today's musical selection
The who, Boris the spider

"March through the kingdoms"

As a follow-up to evoltion and history of life, this outline introduces diversity of organisms. We already covered one kingdom (Prokaryotes), and I will cover animals in the next outline. That means we will hurry through 3 kingdomes in this outline. This would have been three or more lectures in a two semester course for biology majors. In special attention to feedback from Fall 2007 students (assessment), the coverage is abridged from the 2007 coverage. Also, we have gone to some lengths to integrate this coverage better with newly-developed laboratory coverage.


Figure 4-3
Animal cell to remind you about nucleus and organelles

Table 20-1
A staggering diversity
Heterotrophs and Autotrophs
A simple view - 3 groups:
Protozoans - "first animals"
Phytoplankton (floating plants) ["phyto" as in "phytonutrients" (from "plants")]
Ones like fungi

Figure 20-1
Amoebas are among the most famous

Figure 20-3
Giardia causes diarrhea

Figure 20-5
Euglena- little green fungus-like animals chloroplasts, eye, flagellum

Figure 20-6
Trypanosoma -African sleeping sickness, tsetse fly

Figure 20-10
Dinoflagellata 2 flagella photosynthetic, armor

Figure 20-11
red tides, blooms fill fish, make shellfish poisonous

Figure 20-12
malaria (Plasmodium) mosquitos
red blood cells rupture (Life cycle)
selection in Blacks for sickel cell anemia
molecule and blood cell

Figure 20-13

Figure 20-14
Paramecium , Didinium,

Figure 20-15A
Foraminifera have limestone shells,
Foramin - with windows
Petroleum accumulation (centered in Carboniferous period) is from deposits of microscopic organisms and is often associated with deposits of foriminifera.

Figure 20-8
Pastures of the sea - phytoplankton

Figure 20-7
Irish potato famine (late blight)1845-1847
8 million to 4 million, 1 million die, emmigrate
dangers of monocrop agriculture

Figure 20-9a
Brown algae have holdfasts, air-filled floats

Figure 20-9B
Giant kelp - divers can get stuck
Xanthophyll is the accessory light harvesting pigment

Figure 20-19
Red algae
sheets, mostly in oceans;
deep - use green light - phycobilins are the accessory pigment
frame for coral reefs; used to make agar (used in research and Chinese deserts)


What I thought when I was a kid - 2 types of plants -
nasty weeds hard to kill,
pretty flowers hard to grow

Figure 21-1
Considerable emphasis will be on reproduction.
Human reproduction is hard enough to understand -- plants reproduction is ridiculous.
Alternation of generations.
This is more than just haploid gametes (sperm and eggs) vs. adult form as in human.
In alternation of generations, each form is multicellular
sporophyte is diploid makes spores
(diploid = 2 copies of each gene)
male and female gametophytes are haploid make sperm egg
(haploid = one copy of each gene)

Figure 21-11
male part-stamen: anther, filament
female part-carpel: stigma, style, ovary
see how pollen grain grows to tube to deliver sperm
that is the gametophyte

Figure 21-2
evolution and diversity of plants
Angiosperms are by far most numerous

Transition to land required
(1) O2 -> O3 (ozone) to block UV (ultraviolet light) that damages proteins and DNA
(2) Vascular system (like your circulation) - xylem (for water) and phloen (for sugar)
(3) support (lignin)
(4) sexual reproduction that does not rely on water

Figure 21-4
Bryophytes (transitional land plants, mosses, liverworts)
The "Plant" that you see is gametophyte which is unusual
makes this comparison for moss, fern and flowering plant

seedless vascular plants

Figure 21-5 C
Ferns Plant is diploid- sporophyte
makes spore
Fern with sori, clusters of sporangia
Frequently flooded swamp forests in carboniferous create "reducing" (in the chemical sense of the word) conditions, and coal is formed from lots of ferns back then.

Seed plants

Figure 21-9
Gymnosperms (naked seed = no fruit)
male & female cones

Figure 21-10
Angiosperms (flowering plants) fruit
235,000 species (successful)
class - monocotyledons
class - dicotyledons (eudicots, a different term, a clade that is most of the dicots)


Even though mushrooms stick out of the ground, fungi are not like plants. Especially, fungi are heterotrophic
Fungi usually filaments, except yeast; heterotrophs, chitin cell walls, sometimes parasitic, otherwise saprobic or mutualistic.
Reproduction by budding, fragmentation of hyphae (rows of cells), or spores

Figure 22-3
(Evolution) diversity

Figure 22-10
Fairy ring
mycelium (mushroom shown here) most underground, reproductive part emerges quickly above ground when it is moist. Composed of strands (hyphae).

Figure 22-5
Zygomycota "zygote fungi" ex: Rhyzopus - bread mold
Life cycle
States: Haploid, diploid, dikaryotic
Processes: Plasmogamy & karyogamy

Figure 22-6
Ascomycota (sac fungi reproduce by spore sacs)
8 ascospores in ascus are neatly arranged for genetic "tetrad analysis."

Figure 22-7B

Figure 22-8
Basidiomycota "club fungi"
Life cycle
Mushrooms (Agaricus) the reproductive structure is above ground, the rest is under ground
Corn smut
wheat rust
Poisons (Psilocybin)


Ringworm, Athlete's foot - parasites

Figure 22-16
Candida (yeast) problem in AIDS


Penicillium Here is a picture, from the Microbe zoo
(Antibiotic - 1928 Alexander Fleming found mold killed bacteria, later, Howard Florey and Ernst Chain developed, 1945 Nobel Prize in Physiology and Medicine)
Saccharomyces brewers & bakers yeasts ascomycota

Figure 22-13
Mycorrhizae w/ roots of 80% of vascular plants
Plants - absorption of water and nutrients

Figure 22-11
Figure 22-12
Lichens mutualism (or controlled parasitism) of fungus and algae

Questions from 2007 & 2008 relating to this outline

An example of a gametophyte is
(a) the cellular slime mold.
(b) sperm.
(c) the dinoflagellate that causes red tides.
*(d) pollen.
(e) the Trypanosomes transmitted to humans by the tsetse fly.

The mosquito transmits (what?) to humans?
*(a) Plasmodium, the parasite that causes malaria
(b) diatoms
(c) sporopyhtes
(d) phytoplankton
(e) sickle cell anemia

Ciliates belong to the kingdom of
(a) archaea.
*(b) protists.
(c) fungi.
(d) plants.
(e) animals.

Which productive autotrophs are called "pastures of the sea?"
*(a) diatoms
(b) Giardia
(c) trypanosomes
(d) amoebas
(e) cephalopods

Euglena is referred to as an autotroph because
*(a) it has photosynthesis.
(b) it belongs to the plant kingdom.
(c) it cannot move.
(d) it vanished in a mass extinction.
(e) it is a gametophyte.

A vascular system exists for ferns but not for
(a) any chordate.
(b) monocotyledons.
(c) earthworms.
(d) people.
*(e) bryophytes.

How the mycelium obtains its nutrition explains
*(a) the fairy ring.
(b) the gastrovascular cavity.
(c) anabolic steroid abuse by some athletes.
(d) the bird's gizzard.
(e) autotrophs.

In the microscope lab, you saw (or tried to see) an amoeba and a paramecium. What kingdom (assuming 5 kingdoms) did they come from?
A) monera
*B) protista
C) plants
D) fungi
E) animals

What do mosses lack that is present in ferns and seed plants?
A) protostomes
B) alternation of generations
C) sexual reproduction
D) membership in the plant kingdom
*E) true vascular tissue and lignin

What kingdom (assuming 5 kingdoms) did coal come from
A) monera
B) protista
*C) plants
D) fungi
E) animals

Fossil remains of (what?) are found in association with petroleum deposits.
A) saprobes
*B) foraminifera
C) mammoths
D) dinosaurs
E) monera

15. "Animal-like protista" would
A) be in one of the two domains of prokaryotes.
B) accumulate and eventually become the coal deposits of today.
*C) be heterotrophic.
D) have cell walls made of chitin.
E) be called metazoa.

Pollen is
*A) the male gametophyte.
B) the vascular system of tracheophytes.
C) very concentrated in blooms (red tides) of dinoflagellates.
D) underground in the fairy ring.
E) a lichen.

"Forests" of giant kelp off the coast of Monterrey, CA are
A) heterotrophs.
*B) protists.
C) gymnosperms.
D) predators.
E) monocotyledons.

All but one are associated with protists.
A) malaria
B) African sleeping sickness
C) diatomaceous earth
*D) penicillin
E) Euglena

Ringworm and athlete's foot come from what kingdom?
A) monera
B) protista
C) plants
*D) fungi
E) animals

Questions used in 2002 relating to this outline (and other outlines)

Trichinella are
(a) larvae (maggots) of holometabolous flies.
(b) parasites in the kingdom Protista.
*(c) nematodes.
(d) chordates.
(e) deuterostomes.

What is the closest approximation to fertilization found in the fungus?
*(a) karyogamy
(b) formation of the sporophyte
(c) mitosis
(d) formation of the megaspore
(e) fragmentation of hyphae

Which disorder is caused by an apicomplexan, transmitted to people by the mosquito, and involves infection of red blood cells by merozoites?
(a) ring worm
(b) cirrhosis
(c) ulcer
*(d) malaria
(e) red tide

"Meiosis makes haploid gametes, while mitosis makes diploid daughter cells." This statement is, of course, wrong. Which is an example of why it is wrong?
(a) Plants do not have sperm.
(b) In plants, meiosis makes diploid cells.
(c) There is no meiosis in the sexual reproduction of protistans.
(d) Sometimes haploid cells have meiosis.
*(e) Sometimes haploid cells have mitosis.

Penicillin is derived from
(a) red algae.
(b) diatoms.
(c) oomycotes, fungus-like protistans.
*(d) a fungus.
(e) the medicinal leech.

Which are productive autotrophs?
*(a) diatoms
(b) Giardia
(c) trypanosomes
(d) yeasts
(e) cephalopods

Mushrooms might be found in a circle because
(a) of the highly organized products of meiosis in the ascus.
(b) sperm can only fertilize eggs in the damp soil.
(c) of the mutualistic association of algae and fungi.
(d) the spores from the previous mushrooms land in a circle.
*(e) the mycelium expands outward as it exhausts organic matter.

Mushrooms might be found in a circle because
(a) of the highly organized products of meiosis in the ascus.
(b) sperm can only fertilize eggs in the damp soil.
(c) of the mutualistic association of algae and fungi.
(d) the spores from the previous mushrooms land in a circle.
*(e) the mycelium expands outward as it exhausts organic matter.

On the underside of a green fern leaf, you see sori where
(a) O2 and H2O goes out and CO2 goes in.
*(b) spores are formed.
(c) syngamy takes place.
(d) fertilization takes place.
(e) karyogamy takes place.

Which is an example of a pheromone-mediated aggregation of free-living amoeboid cells into a colony for the sake of producing spores?
(a) eumetazoa
(b) osteichthyes
(c) prosimians
(d) lichens
*(e) slime mold

Bryophytes differ from flowering plants in that they
(a) are dioecious.
(b) have naked seeds.
(c) are considered to be members of the kingdom Protista.
*(d) lack vascular tissue.
(e) are phytoplankton.

Chitin, a nitrogen-containing polysaccharide, is present in arthropod exoskeleton and
(a) loose connective tissue.
*(b) cell walls of fungi.
(c) the cytoplasm to bind calcium ions.
(d) xylem.
(e) meristems.

The male portion of a complete flower that releases the pollen is the
(a) filament.
*(b) anther.
(c) ovary.
(d) stigma.
(e) style.

This page was last updated 8/7/09

**The animal diversity lecture


starfish and giant foams
greet us with a smile
-Jimi Hendrix



Audesirk, Audesirk & Byers Chapter 23 and 34, references to Chapters 33 & 41

Today's musical selection
Simon and Garfunkel At the zoo

here is a comprehensive site on animal diversity

Former view: Protozoans vs Metazoans.
Oversimplification (but close to the truth): vertebrates and invertebrates

The overall diversity is awesome, much more than you might want to know, so simplification is important to show fundamental points

Major developments with multicellularity:

Instead of just saying each type of organism and its characteristics, the invertebrate coverage will use examples to discuss these developments.

The first 3 slides pertain to the gut arrangement

Figure 23-5
primitive: sponges

Figure 23-7
two way: cniderans, flat worms

Figure 23-13
one way: (two openings) roundworms & up, Mollusk is shown

Figure 23-2
symmetry: none, "radial" (even star fish is bilateral), bilateral

Figure 23-11
cephalization (not shown in figure, but there is a tendency for nervous system to concentrate in head)

Figure 23-3
body cavity (coelom with peritoneum) acoelomates vs pseudocoelomates
body cavity seen above roundworms

Figure 41-3
Zygote, Cleavage, Ball, Infold,- gastrulation
protostome: molluscs, annelids, arthropods
blastopore becomes mouth
deuterostome: echinoderms, chordates
blastopore becomes anus

Figure 23-1
All in one figure Animal diversity
(even though arthropods and molluscs can be high, comparative embryology tells us that echinoderms are closer)

When you're big, you need:also need:

Figure 23-5
body support (example - spicules in sponge)

Figure 23-11
integration: nervous system and hormones

Figure 33-4

Disorders caused by invertebrates:

flatworms -

Figure 23-10
- tapeworms

flukes (parasites) Shistosoma 1 Trematoda Snails water Africa


Caenorhabditis elegans genetics

Figure 23-26
Trichinella (pork)
dog heart worms

Some other major points about invertebrates:

Figure 23-11 (Earthworm)
Segmentation is very important

Molluscs (we eat them)
Gastropod (stomach - foot) snails
Pelecypoda (clams and bivalves)
Cephalopoda squid octopus

Figure (chapter opener) and case study
squids can be biggest invertebrates

Figure 23-21
Arthropods (insect example)
2/3 species are insects
many are pests
Departments of Entomology in large universities
Fruitfly Drosophila is very useful in genetics

Figure 23-18
Exoskeleton must molt
made of chitin, a nitrogen-containing polysaccharide also found in fungus cell walls

Chordates -

Figure 24-1
major developments
notochord (becomes support usually), dorsal nerve, pharyngeal gill slits, tail

Figure 41-4
Famous "straw man"
"Ontogeny recapitulates phylogeny" gills, tail, etc

Figure 24-4
jawless fish - lampreys

Figure 24-5
cartilagenous fish

Figure 24-6
ray finned fish.
most diverse vertebrates

Figure 24-8
Amphibia metamorphosis interest in development

Figure 24-9
Reptiles internal fertilization.

Figure 24-11
Birds -separate evolution from reptiles.

Mammals (named after mammary glands) adaptive radiation from reptiles

Figure 24-13
Monotremes (egg, platypus)

Figure 24-14
Marsupials (pouch) (opposums, kangaroo)

Figure 24-15

Questions used in 2007 & 2008 related to this outline

Protostomes and deuterostomes differ with respect to what dichotomy?
(a) whether the mature organism is a gametophyte or a sporophyte
(b) whether the organisms are self-feeders or other-feeders
*(c) whether the blastopore becomes the mouth or the anus
(d) whether meiosis makes gametes or spores
(e) whether cells have a nucleus or not

Which shows cephalization?
(a) mosses
(b) lichens
*(c) earthworms
(d) sponges
(e) kelp

Trichinosis, contracted by people if they eat undercooked pork, is caused by
(a) fungi.
(b) staphylococci called MRSA.
(c) deuterostomes.
(d) chordates.
*(e) roundworms.

Lampreys are
(a) invertebrates but not chordates.
(b) ray-finned fish.
*(c) jawless fish, predatory to fish.
(d) terrestrial plants that do not have vascular tissue.
(e) mutualistic symbiotic relationships between algae and fungi.

A monotreme is
(a) a cartilaginous fish, and the ray is an example.
*(b) a mammal, and the platypus is an example.
(c) a reptile and the tadpole is an example.
(d) a placental mammal and the opossum is an example.
(e) a marsupial and the shark is an example.

Which of the following animal phyla is distinguished by a lack of tissues?
A) echinoderms
B) flatworms
C) annelids
D) roundworms
*E) sponges

What DON'T earthworms have?
A) cephalization
B) a coelom
*C) radial symmetry
D) a digestive system
E) segmentation

Why do they call the cavity of a jellyfish a "gastrovascular" cavity?
A) because it is the same as the intraperitoneal cavity
B) because it is a one-way gut with a mouth and an anus
*C) because it serves for circulation and digestion
D) because the jellyfish is famous for having 5 hearts
E) because jellyfish are bilaterally symmetric

What the blastopore eventually becomes is most relevant to
A) whether the fish have jaws.
*B) whether the animal is classified as a protostome or a deuterostome.
C) whether the animal is a parasite.
D) whether sexual reproduction can only be achieved in water.
E) whether the animal is a chordate or a vertebrate.

Why do insects need to molt their cuticles (exoskeletons)?
A) to dispose of their nephridia
B) so their blood can continue to transport oxygen in a closed circulatory system
C) if they did not, they would not have mesoderm
D) that is how ectoderm and endothelium develop
*E) to grow

Which of these groups is characterized by having a true coelom?
A) sponges
B) jellyfish
*C) insects
D) flatworms
E) roundworms

A tadpole is a(n) _________.
A) bony fish
B) cartilaginous fish
C) jawless fish
*D) amphibian
E) invertebrate

Which of these groups is characterized by having a pseudocoelom?
*A) roundworms
B) annelids
C) arthropods
D) chordates
E) cnidarians

The Trichinella worm, which causes trichinosis, is a(n) ________.
A) autotroph.
B) prokaryote.
C) chordate.
*D) roundworm.
E) protostome.

Sharks and rays are _________.
A) bony fish
*B) cartilaginous fish
C) jawless fish
D) amphibians
E) invertebrates

A marsupial is a(n) _________.
A) amphibian
B) reptile
C) bird
*D) mammal
E) mollusk

Protostomes and deuterostomes differ with respect to what dichotomy?
A) whether the mature organism is a gametophyte or a sporophyte
B) whether the nervous system is mostly in the head or not
*C) whether the blastopore becomes the mouth or the anus
D) whether meiosis makes gametes or spores
E) whether the animal is a protozoan or a metazoan

Questions used in 2003 relating to this outline

Trichinella are
(a) larvae (maggots) of holometabolous flies.
(b) parasites in the kingdom Protista.
*(c) nematodes.
(d) chordates.
(e) deuterostomes.

Chitin, a nitrogen-containing polysaccharide, is present in arthropod exoskeleton and
(a) loose connective tissue.
*(b) cell walls of fungi.
(c) the cytoplasm to bind calcium ions.
(d) xylem.
(e) meristems.

Protostomes and deuterostomes differ with respect to what dichotomy?
(a) whether the mature organism is a gametophyte or a sporophyte
(b) whether there is a lateral meristem or not
(c) whether the blastopore becomes the mouth or the anus
(d) whether meiosis makes gametes or spores
(e) whether both sexes or only one sex are housed within one mature plant

this page was last updated 8/12/09


**The structure function lecture

An introduction to animal struture and function


Audesirk, Audesirk & Byers Chapter 31
From Chapter 39, Health watch (p. 810) and Case study (Hidden hazards of space travel, p 797 & 810)

Today's musical selection
Weird Al Yankovic Like a surgeon


Figure 1-1
levels of integration
Animal organismal biology:
Cells (like chief cells) -> Tissues (like gastric mucosa) -> Organs (like stomach) -> Organ systems (like digestive system)

Figure 31-3
A simplified Organism
Emphasis: Cells -> Tissues -> Organs
Note that topographically, digestive system is outside body.

Table 31-1
Organ systems
(Chapters 32-39 will cover this material System by System)
(Cells were emphasized earlier this semester)

There are several general classes of tissues

Close relationship with week 10 lab, histology

Figure 31-4
Epithelial tissue
Usually there are on a basal lamina - extracellular material.
Columnar, cuboidal and squamous
Simple, pseudostratified and stratified

(work I did with researcher at Lions eye bank on preservation of cornea for transplantation)
There are interesting junctions between cells which often make the sheet of cells into a good barrier.

Figure 31-9
Striated (striped) muscle (voluntary, skeletal) - Cardiac muscle - Smooth muscle (run by the autonomic nervous system)

Figure 31-10
To coordinate, there will need to be systems of integration (nervous and hormonal systems)

There are several classes of Connective Tissue:

Figure 31-7

Figure 31-8

Figure 31-5

Figure 31-6
Importance of extracellular material - chondroitin sulfate

On the topic of extracellular material
Some SEMs and TEMs I made some years ago from cornea of human eye donors showing neatly arranged alternating directions of collagen fibers (recall that cornea is transparent - proteins should not absorb visible light)


Figure 31-2
negative feedback - set point (like how you set a thermostat) - "servo mechanism"
how thermostat works in the body

Suspended animation

Figure (chapter 31 opener)
Ground squirrels hybernate near freezing, metabolism drops by 97%
Several cases of people being revived after being chilled to life-stopping temperatures
Open heart surgery, lower body temp to 65 degrees F


Figure (chapter 39 opener)
Figure E39-2
Famous issue - did the woman fall and break her hip or did a him fracture make her fall?
Astronauts lose bone mass
Estrogen replacement in postmenopausal women increases risk of heart attack (2002 Women's Health Initiative)
(1) better drugs
(2) better diagnoses (of bone mineral density)
(3) new appreciation of genetic factors
Turnover of calcium is normal in regulating blood calcium levels by hormones
Parathyroid hormone (PTH) works with osteoclasts to increase blood calcium by borrowing it from bone.
Vitamin D, fat soluable, (complicated but involves sunlight) helps calcium absorption from the gut.
Rickets is a bone deformation in infants from low vitamin D
Osteoclasts degrade bone (formed from macrophage)
Drugs like Fosamax interfere with osteoclasts
Osteoprotegerin (OPG) is protein from a gene that interferes with osteoclasts
Osteoblasts add mineral (formed from stromal cell)
Estrogen promotes these cells
Considerable attention given to factors regulating cell development
SERM (selective estrogen receptor modulator)
ANGELS (activators of non-genomic estrogen-like signalling)

Demonstration of LabScribe and iWorx

Questions used in 2007 & 2008 related to this outline

All of the following are considered the four types of tissue except
A) epithelial tissue.
B) connective tissue.
C) muscle tissue.
D) nerve tissue.
*E) mesoderm tissue.

The pads that line joints are formed from
A) bone.
*B) cartilage.
C) adipose tissue.
D) fat.
E) dendrites.

Blood is considered to be a connective tissue and so is (are)
*A) bone.
B) basal lamina.
C) endoderm.
D) metazoa.
E) simple squamous cells.

*A) are affected by parathyroid hormone (PTH).
B) are an ancient genus of hominids found in Indonesia.
C) are involved in the set point for human temperature regulation.
D) give the sponge some rigidity.
E) are the cells of adipose tissue.

Groups of tissues that function together
*A) form an organ.
B) would be exemplified by the digestive system.
C) are composed of columnar epithelial cells.
D) have the individual as the next higher level of organization.
E) make up the basement membrane.

In the cornea of the eye, there are
A) axons.
B) servo mechanisms.
C) hypothalamic control centers that regulate the set point.
D) pigments that absorb visible wavelengths of light.
*E) transparent cells and proteins.

The concept of the set point is used to describe
(a) the stripes seen in skeletal muscle in the microscope.
(b) squamous connective tissue.
(c) where to put the stethoscope when measuring blood pressure.
*(d) negative feedback in physiological systems.
(e) different levels of integration from cell to organ system.

Dendrites are a component of
(a) chondroitin sulfate.
(b) the apical (top) surface of cells lining the trachea.
(c) platelets.
(d) a columnar epithelial layer.
*(e) nerve cells.

Estrogen replacement therapy was a standard treatment
(a) for the fibrillin mutation that caused Olympic medalist Flo Hyman's aorta to rupture.
(b) to cure heart murmurs.
*(c) to prevent osteoporosis.
(d) for vitamin B deficiency.
(e) myocardial infarction.

Temperature maintenance in animals is controlled by
*A) the hypothalamus.
B) oxytocin.
C) positive feedback.
D) the cerebellum.
E) the cerebral cortex.

Which would NOT have a positive or negative effect on bone density?
A) weightlessness in space travel
B) estrogen
C) vitamin D
D) osteoclasts
*E) the thalamus

"Simple squamous" is a term applied to
A) tissue layers after gastrulation.
B) the cell walls of fungi.
*C) animal epithelial tissues.
D) the theory that a prokaryotic symbiote evolved into a eukaryotic plastid.
E) a life cycle stage unique to protista.

Questions used in 2003 relating to this outline

"Simple squamous" is a term applied to
(a) plant cells with a function of support.
(b) the cell walls of fungi.
*(c) animal epithelial tissues.
(d) the theory that a prokaryotic symbiote evolved into a eukaryotic plastid.
(e) a life cycle stage unique to protista.

The basal lamina
(a) has plasmodesmata.
(b) closely resembles the cell walls of fungi.
(c) forces extracellular water into cells in plant roots.
(d) is the structure specialized for water excretion in fresh water protistans.
*(e) is an extracellular layer juxtaposed to epithelia.

Which would cause the bones to release calcium?
(a) cortisol
(b) glucagon
(c) vitamin D
(d) calcitonin
*(e) parathyroid hormone

Rickets can be prevented by supplements of
(a) steroids.
(b) insulin.
(c) growth hormone.
(d) T3 and T4.
*(e) vitamin D.

Which would be most likely to slow the development of osteoporosis?
(a) vitamin A
(b) iodine
*(c) vitamin D
(d) magnesium
(e) organophosphates

this page was last updated 8/13/08


**The circulation lecture

The first time ever I held you near
and felt your heart beat close to mine
I thought our joy would fill the world
and would last till the end of time, my Love.
--Peter, Paul and Mary



Audesirk, Audesirk & Byers Chapter 32, Case study, Chapter 12

Today's musical selection
Huey Lewis and the News Heart of rock and roll

Pep talk

Figure (chapter 12 opener)
Flo Hyman, 1984 Olympic silver medalist, died at age 32 when her aorta ruptured.
She had a dominant mutation of fibrillin

Figure (chapter 13 opener)
St. Louis Cardinals pitcher Darryl Kile died at age 33 in 2002.
He had blocked coronary arteries, and there was a family history


In multicellular metazoan, need a vascular system (in terestrial plants above mosses, xylem and phloem)
Circulation : Cardiovascular system

Figure 32-1
Open circulation Blood = interstitial fluid - hemolymph is term for blood - most molluscs and all arthropods have open circulation
hemocoel is the space where the blood is
- important in insects that gas transport (via air filled trachea) does not rely on circulation being closed
Closed circulation - annelids, cephalopods, echinoderms, vertebrates

Figure 32-2
Chambers of heart -
Fish have 2 chambers (gills and body "wired" in series)
The "circuit" is "in series" - heart -> gills -> body -> back to heart
Amphibia and reptiles have 3 chambers (2 atria, 1 ventricle)
As long as blood does not fully mix, there is some separation of non-oxygenated blood to the pulmonary circulation and of oxygenated blood to the systemic circulation

Anatomy of the heart

Figure 32-3
Note that right is drawn on left as if looking into the chest of a supine subject

Figure 32-2
Here is the circuit: LA - LV - Arteries (aorta, etc.) (blood pressure taken here) - Arterioles (regulate blood flow to muscles, brain, digestion, kidneys and skin) - Capillaries (near, exchange, WBC's) - venules - veins (no pressure, valves)- RA - RV - Pulmonary arteries - Lung capillaries - Pulmonary veins -

Heart valves and sounds

Figure 32-3
pulmonary valve (semilunar) feeds pulmonary arteries
aortic valve (semilunar) feeds aorta
These valves snap shut from arterial back pressure at the end of systole to make second heart sound- "dub"
Superior and inferior vena cava feed right atrium -> ventricle via tricuspid (atrio-ventricular) valve.
Pulmonary veins feed left atrium -> ventricle via bicuspid (atrioventricular) valve.
Tricuspid & bicuspid snap shut at start of ventricular contraction to make first heart sound- "lub."
If there is backslosh through valves, this is called a heart murmur.

Blood vessels

Figure 32-14
artery is like hose
blood flow to emptying into vascular bed: regulation by smooth muscle of arteriole
capillary is one layer of endothelial cells

Figure 32-16
Blood moves slowly and with very little pressure in veins. Movement in veins is mostly passive with a series of valves and where contraction of skeletal muscles helps

Figure 32-17
Lymphatic circulation helps to percolate interstitial fluid back to circulation

Cardiac cycle and blood pressure

Figure 32-5
cardiac cycle
Diastole (between heart beats), systole is during ventricular contraction, hence terms systolic and diastolic blood pressure.
Ventricle fills during diastole.
Ventricle empties during systole.
Ventricular pressure builds during systole.

Measuring blood pressure

It is arterial blood pressure that is usually measured.

Figure 32-6
close off artery, when it opens (systolic pressure), blood flow is turbulent and noisy (Korotkoff sounds), when it is always open (diastolic pressure), blood flow is no longer noisy
Blood pressure is measured in arteries
High blood pressure is called the "silent killer."
hypertension 45 million Americans - salt intake is still debated, >140/95 high 140/70 normal
high diastolic is especially bad

Myocardial cells

Figure 32-4
Heart muscle cells branch and come together and are joiined at intercalated discs with gap junctions that spread the electrical signal from cell to cell.
cardiac muscle - automatic (explained below)
here is a picture from our histology course of heart muscle cells joined at intercalated discs

Electrical activity of heart cells

Figure 32-7
Electrical - SA (sinoatrial) node (or electrical pacemaker) - spread - automatic.
Sympathetic nervous system speeds it up, parasympathetic nervous system slows it down.
AV (atrioventricular node) is eventually stimulated.
If it were not, it is also automatic but slower and would generate a heart beat in the venticals.
Bundle of His, bundle branches, and Purkinje fibers get ventricular depolarization to happen almost synchronously.


This will be covered in lab
Because a lot of cells in heart work together, and because extracellular fluid has high conductivity, electrical activity can be recorded non-invasively.
P is atrial depolarization.
QRS is ventricular depolarization.
T is ventricular repolarization.


Figure W32-1
A layer of fat with ccholesterol between media and externa
ulceration lining lumen
atherosclerosis - hardening of the arteries - plaques
atheroma with macrophages
Cholesterol is a problem

Heart attack

Myocardial cells not regenerate (by mitosis in the adult). This is why heart attack is so damaging. The same is true for the nerves in the central nervous system where similar damage is called stroke.
Coronary arteries clog -> myocardial infarction - coronary thrombosis - ischemia (too little blood flow for oxygen delivery)
Angina, chest pain, and referred pain
Heart muscle is aerobic
Anaerobic metabolism would build up lactic acid and cause pain (angina pectoris)
In CPR (cardiopulmonary resuscitation) chest pressure keeps blood flowing a little and rescue

Platelet aggregation - thrombus (local), embolism (from elsewhere) cause ischemia
tissue plasmogen activator (TPA) dissolve clots
aspirin inhibits clotting, coumaden is a strong anticoagulant

Figure E32-2
catheter with balloon angioplasty insert stent

Figure E32-3
bypass operations, replace coronary artery with vessel from somewhere else in the body,

Risk facrors for heart attack
(1) High blood pressure (the silent killer) -- Wiggers diagram --heart has to work harder to open semilunar valves.
(2) prior heart attack
(3) smoking
(4) diabetes
(5) family history -

Prevention -
(1) exercise - increase HDL (endothelial cells do not take up)
(2) antioxidants (oxidized LDLs in endothelial cells are bad)
(3) alcohol in moderation (but people who die of cirrhosis rarely have atherosclerosis)
(4) statins

Questions used in 2007 & 2008 related to this outline

A thrombus is
A) a blood vessel that feeds the heart.
B) the smooth muscle that controls blood flow to a capillary bed from an arteriole.
C) a phagocytic cell full of cholesterol.
*D) a blood clot that clogs an atherosclerotic artery.
E) the muscle cells that regrow after a heart attack.

An open circulatory system
A) is present in amphibia and reptiles.
B) feeds the lungs in humans.
*C) percolates hemolymph into and out of the hemocoel in insects.
D) refers to the valves between the ventricles and the arteries.
E) is exemplified by the cardiovascular system in birds and mammals.

Which is one reason heart signals can be recorded by connections to the wrists and ankle?
A) because of ischemia.
*B) because there is little electrical resistance in extracellular fluid.
C) because of angina.
D) because of Korotkoff sounds.
E) because of the endothelium.

The "silent killer" is
A) plaque.
C) heart murmers.
D) diabetes.
*E) high blood pressure.

What keeps blood moving forward through veins in the body's systemic circulation?
A) the driving force of blood pressure.
*B) valves.
C) the AV node.
D) the pulmonary circulation.
E) systole.

The right ventricle sends blood to the
A) aorta.
B) left atrium.
C) vena cava.
*D) pulmonary circulation.
E) lymph vessels.

Balloon angioplasty
A) is used to record the electrocardiogram.
B) measures the diastolic blood pressure.
*C) is used to open atherosclerotic coronary arteries.
D) conducts the electrical signal across intercalated discs.
E) triggers the heartbeat.

Insects have
*(a) an open circulatory system and separate gas transport via air-filled trachea.
(b) a circulatory system that is more like that of vertebrates than of arthropods.
(c) xylem and phloem.
(d) 5 hearts and a closed circulatory system.
(e) a three-chambered heart where one ventricle might allow mixing of systemic and pulmonary blood.

Why is the wall of the right ventricle thinner than that of the left ventricle?
(a) The right ventricle creates systolic blood pressure while the left ventricle determines diastolic blood pressure.
*(b) There is not as much pressure in pulmonary circulation as there is in the systemic circulation.
(c) The right ventricle creates hypertension while the left ventricle is for lower pressure.
(d) The right ventricle makes Korotkoff sounds while the left ventricle makes lub-dub sounds.
(e) The right ventricle pumps to the aorta while the left ventricle pumps to the left atrium.

Atrioventricular valves are open
(a) never.
(b) when muscles contract against the veins.
(c) when stress regulates blood flow to different beds of capillaries.
*(d) during diastole.
(e) while the ventricles are pushing blood into the arteries.

Blood pressure measurements involve
(a) listening to the "lub-dub" heart sounds.
*(b) listening for turbulent blood flow in an artery.
(c) measurements from veins.
(d) electrical measurements from heart muscle.
(e) coronary bypass

Intercalated discs hold heart muscle cells together. What other function do they serve?
(a) They help in the conversion of CO2 plus H2O to H2CO3.
(b) They allow HDL buildup in atherosclerotic plaques.
*(c) They allow electrical connection by gap junctions.
(d) They keep blood from flowing backwards during ventricular contraction.
(e) They hold open a partially closed coronary artery.

Electrical activity in the heart usually starts in the
*(a) SA node.
(b) pulmonary arteries.
(c) thrombus.
(d) medulla of the brain.
(e) angina pectoris.

The term for too little blood flow for adequate oxygen delivery is
(a) laryngitis.
(b) cirrhosis.
(c) hypertension.
(d) peristalsis.
*(e) ischemia.

Amphibia and reptiles
A) have a two-chambered heart.
*B) have a three-chambered heart.
C) have an open circulatory system like an insect.
D) have multiple hearts like an earthworm.
E) do not have a vascular system.

How is the amount of blood flow to the different capillary beds of the body regulated?
A) by valves
B) by the cerebral cortex
C) by the size of the veins
*D) by smooth muscle of arterioles
E) by insulin

Diastolic and systolic blood pressures
A) are from systemic and pulmonary circulations respectively.
B) are from atria and ventricles respectively.
C) should be the same as eachother in healthy people.
D) are measured from veins.
*E) are measured from arteries.

Questions used in 2003 relating to this outline

Blood goes from the right ventricle to the
(a) pulmonary vein.
*(b) pulmonary artery.
(c) aorta.
(d) vena cava.
(e) right atrium.

(a) reduces HDL.
(b) reduces LDL.
(c) restores the heart beat.
*(d) circulates oxygenated blood to the brain.
(e) prevents atherosclerosis.

During atrial and ventricular diastole
*(a) AV valves (tricuspid and bicuspid valves) are open.
(b) semilunar valves are open.
(c) the QRS complex of the ECG is generated.
(d) ventricles contract.
(e) blood pressure measured with a cuff on the arm is highest.

The SA node
(a) can have its lumen clogged by a thrombus in a heart attack.
*(b) initiates the electrical activity in the heart beat.
(c) requires a nerve connection, and the heart would stop in severe polio.
(d) is the part of the brain that stimulates breathing when O2 is low.
(e) connects the hypothalamus to the anterior pituitary.

How does electrical excitation spread throughout the heart?
(a) via plasmodesmata
(b) by neurotransmitters
(c) by interleukins
*(d) by gap junctions
(e) by neurons

this page was last updated 8/13/09

**The respiration lecture




Audesirk, Audesirk & Byers Chapter 33

Today's musical selection
Bobby "Boris" Pickett Monster Mash
Happy Halloween


Figure 33-7
Nasal - moisture (smell) sniffing
Pharynx - larynx
Vocal cords larynx (laryngitis) "voice box"
Equal time to creationism : "Adam's apple"
Further down cilia sweep mucus, bacteria, dust up
(histology picture of cilia)
Cilia sweep from pharynx to esophagus (where you can swallow "crud")
Smoking paralyses ciliary sweep (more crud, less sweeping, famously asbestos is worse in smokers)

Figure 33-11
Trachea - rings of cartilage to hold tube open like a vacuum cleaner hose
2 bronchi
Inflammation of the bronchi is called bronchitis.

Asthma bronchioconstriction, use epinephrine . Epinephrine was in inhalers. Terbutaline is an anti beta 2 drug. Singulair is an antileukotriene. Because inspiration helps to open the bronchioles, breathing out (this is counterintuitive) is most difficult.

Alveoli 600 million in human 50 x skin area
Here is a picture from our histology course showing how thin the cell layers of alveoli are.

Emphysema - alveoli merge, often results from smoking, increased muscular effort in breathing- smoetimes they have a hunch back from using back to help breathe. These are the people older than they look pulling a dolly of oxygen around with them.

Figure 33-9
Air sacs (alveoli) are close to capillaries.
Note, red vs blue for arteriole vs venule is reversed for pulmonary circulation, obviously.

Figure 33-2
Here is the cardio-respiratory system with blue blood and red blood


Figure 33-11
Inspiration - pressure in lungs is lower than atmospheric, obviously, and expiration, pressure is higher.
Mechanisms involved - move rib cage and diaphragm mostly, and others as well.

Figure 33-8
Heimlich maneuver

Figure 33-9
Water's surface tension would tend to collapse (close) alveoli. Alveolar cells secrete surfactant (surface active agent), phosphatidylcholine plus phosphatidylglycerol, that decreases surface tension. RDS (respiratory distress syndrome) aflicts premature babies since surfactant production does not start until late.

Figure E12-1
Cystic fibrosis is from mutation in CFTR (cystic fibrosis transmembrane regulator), a chloride channel, results in viscous mucus.

Control of ventillation

Introduction: The receptors that are sensitive to changes in the concentrations of CO2 and H+ are located within the arterial system and the medulla of the brain. Excitation of these receptors trigger neural reflexes which alter the respiratory rate and depth. Additionally, other parts of the nervous system influence the basic ventilation pattern established by the respiratory center.

Summary. A common misconception is that variation in the O2 levels within the system cause changes in the ventilation rate. Actually, the O2 concentration, under normal conditions, has little to do with the determination of respiratory rate. The critical determining factor is the level of CO2 and/or the level of free protons circulating in the blood. For example, an increase in CO2 or H+ levels will induce changes which result in an acceleration of the ventilation rate and volume until these levels return to the normal range. Conversely, conditions associated with alkalosis and lower than normal CO2 levels depress the ventilation rate.

Hyperventillation - blow off CO2 and desire to breathe less, can hold breath.

Transport of O2 and CO2

Figure 33-10
The trouble is that oxygen does not dissolve well in water, 66 x as much oxygen is in blood, with its hemoglobin, than in plasma.
Everyone should know that hemoglobin is composed of 2 alpha chains, 2 beta chains, and heme with iron in it.
From tissue to blood:
CO2 transported as bicarbonate, bound to hemoglobin, and dissolved in blood
CO2 dissolves better than O2 in water
Red blood cells CO2 + H2) -> (carbonic anhydrase)-> H2CO3 (carbonic acid).
then H2CO3 -> H+ and HCO3- (bicarbonate)

Questions used in 2007 & 2008 relating to this outline

What would you do if a person were choking?
(a) a stress electrocardiogram
(b) balloon angiography
(c) administer heme
(d) buy time in suspended animation
*(e) the Heimlich maneuver

Where are there cilia in the respiratory system?
*(a) in the trachea
(b) in the hemoglobin
(c) in the alveoli
(d) in the pharynx (Adam's apple)
(e) in the diaphragm

Why might you inhale epinephrine?
(a) to treat RDS (respiratory distress syndrome)
(b) to eliminate an embolism lodged in a coronary artery
(c) to decrease cholesterol build-up
*(d) in case of asthma
(e) to treat referred pain

Why would a premature baby have trouble breathing?
(a) too much LDL
(b) not enough precapillary sphincters.
*(c) no surfactant
(d) backslosh through semilunar valves.
(e) emphysema

Carbon dioxide is transported in the blood by being dissolved in plasma, bound to hemoglobin and (what)?
(a) as H+ in the medulla.
*(b) as bicarbonate.
(c) as phosphatidylcholine.
(d) as cholecystokinin.
(e) through a chloride channel.

Which is a genetic disorder caused by faulty chloride transport in the lungs?
(a) asthma
*(b) cystic fibrosis
(c) emphysema
(d) respiratory distress syndrome
(e) Parkinsons disease

Breathing is achieved by raising and lowering the rib cage and (what)?
(a) the AV node.
(b) bronchitis.
(c) peristalsis.
(d) gallbladder.
*(e) the diaphragm.

Which is bad for the lungs, especially the lungs of smokers?
*A) asbestos.
B) surfactant.
D) bicarbonate.
E) epinephrine.

Cystic fibrosis is a disease
A) of coronary arteries caused by cholesterol buildup.
B) of the liver caused by too much alcohol consumption.
C) of the kidneys caused by low aldosterone.
D) caused by duplication of the inner cell mass.
*E) of the lungs caused by faulty chloride transport.

Which of the following is part of the gas-exchange portion of the human lung?
*A) alveoli
B) pharynx
C) bronchi
D) bronchioles
E) larynx

Which structure prevents foods and liquids from entering the lungs?
A) larynx
B) pharynx
*C) epiglottis
D) bronchi
E) bronchioles

The highest percentage of carbon dioxide is transported
A) into the left ventricle.
*B) as bicarbonate ions in the plasma.
C) as carbon dioxide attached to hemoglobin.
D) as carbon dioxide dissolved in plasma.
E) into the medulla as a high pH (alkaline) well-buffered fluid.

During inhalation, the diaphragm
A) contracts and is dome-shaped.
B) relaxes and is dome-shaped.
C) relaxes and is flattened.
*D) contracts and is flattened.
E) causes the belly to get smaller.

The cells lining the conducting portion of the human respiratory system secrete
*A) mucus.
B) hemoglobin.
C) epinephrine.
D) adrenalin.
E) carbonic anhydrase.

What decreases the surface tension of water in the alveoli?
A) asbestos.
*B) surfactant.
D) bicarbonate.
E) epinephrine.

Questions used in 2003 relating to this outline

Cystic fibrosis is a disease
(a) of coronary arteries caused by cholesterol buildup.
(b) of the liver caused by too much alcohol consumption.
(c) of the kidneys caused by low aldosterone.
(d) caused by duplication of the inner cell mass.
*(e) of the lungs caused by faulty chloride transport.

Exchange of carbon dioxide and oxygen takes place between the capillaries in the lungs and the
(a) bronchi.
(b) larynx.
(c) trachea.
*(d) alveoli.
(e) pharynx.

this page was last revised 8/13/09

**The digestion lecture




Audesirk, Audesirk & Byers Part of Chapter 34, Selections from other chapters

Today's musical selection
Weird Al Yankovic Eat it


Figure 3-2
break down long chain proteins, polysaccharides and nucleic acids into monomers
recall hydrolysis (opposite of dehydration synthesis) (hydro-water lysis-break apart)
if not broken down, proteins which are non-self would make a big antigen invasion

Figure 3-8
Starch (glycogen, animal starch , is much like this)

Figure 3-9
Cellulose (also a polymer of glucose, but not digested, "fiber" contributres to bulk and "regularity")

Comparative biology

Figure 34-4
In sponge, Collar cell

Figure 34-5
In Hydra and flatworm, gastrovascular - digestive and circulatory systems are combined

Figure 34-6
Rumen - bacteria - ruminants - chew cud not acid - pensive "ruminate"
fermentation then feed to other chambers

Input - output

Figure 34-9
Tube - Alimentary canal
One emphasis will be on how the human digestive system invests many juices (hydrolases = enzymes which catalyse hydrolysis)
Some glands have ducts and these are called exocrine glands.
This is in contrast with endocrine glands (ductless, for hormones, which are also involved in digestion)

Table 34-4
Sources and sites of secretions

Overall anatomy
(from mouth to stomach)

Figure 34-7
Mouth - teeth,

Figure 34-8
birds have gizzard - stones to break up seeds, sort of a lapidary device (this is why you give pet bird gravel),
gizzard is near the stomach and near the bird's center of gravity -- not only do birds need to be light to fly but also balanced, and teeth, which are heavy and in the mouth, would upset the center of gravity
Crop is used for storage in birds

lubrication, salivary amylase to disaccharide maltose - starch tastes sweet (only starch in mouth)
-ase enzymes

Figure 34-10
Pharynx swallowing

Figure 34-11
Esophagus - bolus, peristalsis

Figure 34-12
Lower esophagesl sphincter


Figure 34-12
Stomach - gastric mucosa - mucus protect
HCl kill bacteria, stop amylase
From chief cell: pepsinogen ---(HCl, pepsin))--> pepsin (proteolytic)

Figure E34-2
Heartburn, antacids, ulcer (although it is now known that a specific bacterium, Helicobacter pylori, is associated with ulcer)
very little absorption in stomach - exceptions: aspirin, alcohol

Figure 6-19
The optimum pH for pepsin (proteolytic enzyme in stomach) is acidic while for trypsin (proteolytic enzyme in intestine) is slightly basic. And for salivary amylase, it is neutral.

Figure 34-12 (again)
Pyloric sphincter regulates emptying of acidic gastric juice to duodenum.
In duodenum, bile from liver and bicarbonate and enzymes from pancreas add to enzymes from small intestine

Figure E34-1
Gastric bypass and band


enzymes - lactase, maltase, sucrase, others
mitosis - since cells digest themselves
absorption - food and water

Figure 34-14
Villi (big) increase surface area. Mitoses in crypts.

Here is a micrograph from our histology course dramatizing the tremendous increase in apical surface area of intestinal cells caused by the microvillar brush border.
The microvilli in the intestines have a special name, the brush border.


Figure 34-13
Pancreas is responsible for dumping in many of the enzymes

"pro..." as in "procarboxypeptidase and "...ogen" as in "chymotrypsinogen" --a peptide fragment is cut off from a larger precursor protein to make active enzyme; there are many examples like this in biology, for instance prohormones cleaved to make active peptide hormones.
Pancreas puts out bicarbonate (alkaline) to neutralize stomach acid.
Optimum pH for for trypsin is 8.
Pancreas and common bile duct (from liver and gall bladder) dumping into duodenum.
When I took organic chemistry lab (1966-7) we used gall stones for a cholesterol extraction.
Note: Islets of Langerhans (endocrine tissue) in pancreas where alpha cells make glucagon and beta cells make insulin.


Figure 34-13
Liver contributes to fat digestion via bile salts, salts of cholesterol, that emulsify fats
Very few enzymes.
Emulsify fats (salts of cholesterol)
Iron recycling.
Eliminate some wastes to feces.


Portal blood veins (circulatory system "wired" in series is unusual, another famous example being the hypothalamus of the brain which feeds to the pituitary gland and kidney cortex to medulla). Via hepatic portal vein pick-up from small intestine is first delivered to liver cels. There, "microsomal fraction" (how biochemists view the smooth endoplasmic reticulum) has enzymes to detoxify. Enzymes like those that detoxify drugs like barbiturates are increased on exposure to toxins (inducible). Alcohol -(alcohol dehydrogenase (ADH) )-> aldehyde - (aldehyde dehydrogenase)-> acetic acid. With AcetylCoA, acetic acid can add to fatty acid chains 2 carbons at a time. There is a fatty metamorphosis of the liver from one binge. Continued heavy drinking leads to scarring and cirrhosis.

Erythrocyte iron recycling, bile pigment (bilirubin) ->urobilinogen turns feces dark.
Also colors urine.
Hepatitis (disorder which spills bile into blood) - turns skin yellow (jaundice) (feces are not as dark, urine is darker)


Table 34-5
Local hormones control digestion - Many found later in other places

Figure 34-16
from stomach:
food stimulates gastrin which, in turn, stimulates gastric juice until there is a low (acidic) pH

from duodenum:
Cholecystokinin (CCK) - liver and pancreas
Secretin for bicarbonate release
Gastric inhibitory peptide to slow gastric emptying and stimulate insulin

Questions used in 2007 & 2008 relating to this outline

Which is NOT a function of the liver?
*(a) providing digestive enzymes
(b) emulsifying fats
(c) recycling erythrocytes
(d) detoxifying what intestines absorb
(e) eliminating wastes through feces

Which is NOT true of the pancreas?
(a) Insulin-secreting cells are located there.
(b) Its exocrine secretions go into the small intestine.
(c) It makes bicarbonate to neutralize acidity of what the stomach sends to the intestines.
(d) It makes precursors for digestive enzymes.
*(e) It is the source of salts of cholesterol.

Why do birds have a gizzard?
(a) the site of collar cells, since they have no tissues or organs
*(b) instead of teeth, for grinding
(c) manufacture of bilirubin
(d) alcohol metabolism, the microsomal fraction
(e) to house symbiotic bacteria, for cellulose digestion

The word for the apical surface of intestinal cells
(a) peristalsis
(b) pyloric sphyncter
(c) Helicobacter pylori
(d) brush border
(e) cholecystokinin

The pH optimum for pepsin is
(a) neutral.
(b) a higher number that that for salivary amylase or trypsin.
*(c) about 2.
(d) why it stops working once it reaches the stomach.
(e) alkaline.

Which comes from the pancreas?
(a) thyroxin
*(b) chymotrypsinogen
(c) pepsin
(d) bile
(e) vitamin K

A disorder involving iron recycled in the liver:
*(a) jaundice
(b) ulcer
(c) scurvey
(d) diabetes
(e) malaria

In addition to being the organ where insulin is made, the pancreas also secretes
A) bile.
B) surfactant.
C) ozone.
*D) precursors of digestive enzymes.
E) antigens.

The rumen of a ruminant
*A) has microbes that help in cellulose digestion.
B) is the site of action of the famous enzyme gastrin.
C) grinds up hard seeds with the aid of gravel.
D) was the first prototypical cell.
E) is lined with rings of cartilage that keep this windpipe from collapsing.

The largest variety of digestive enzymes comes from the
A) large intestine.
*B) pancreas.
C) stomach.
D) mouth.
E) liver.

What is the hepatic portal vessel?
A) It is inside an embryonic membrane.
B) It is the true body cavity for animals above the flat worm.
*C) It carries blood from the intestines to the liver.
D) It is the valve between the atria and the ventricles.
E) after gastrulation, it will become the gut.

Chymotrypsinogen is
*A) the precursor of an enzyme that comes from the pancreas.
B) the term for smooth muscle contractions that moves food through the gut.
C) the cause of ulcers.
D) what endocytosed (phagocytosed) food particles merge with in the sponge's collar cells.
E) a hormone that stimulates gastric secretions.

The liver's contribution to digestion is that its secretions
A) break down cellulose.
B) include pepsin.
C) include insulin.
D) are involved in acid reflux.
*E) emulsify fats.

Cirrhosis is caused by
A) grinding action in the gizzard.
B) hydrolysis.
*C) alcoholism.
D) Helicobacter pylori.
E) symbiosis with microorganisms that digest cellulose

Starch is digested by
A) the gall bladder.
B) pepsin.
C) beta cells in the islets of Langerhans.
D) bile.
*E) amylase.

The optimum pH for pepsin is
A) referred to as "peristalsis."
B) neutral.
C) basic.
*D) acidic.
E) the way it is because it preserves the brush border.

Questions used in 2003 relating to this outline

Famous for its function at low pH.
*(a) pepsin
(b) ethylene
(c) bile
(d) amylase
(e) kinase

The largest variety of digestive enzymes function in the
(a) large intestine.
(b) mouth.
(c) stomach.
*(d) small intestine.
(e) liver.

Cellulose looks most like
*(a) glycogen.
(b) octane.
(c) hemoglobin.
(d) tRNA.
(e) triglyceride.

What is the hepatic portal vessel?
(a) It is what defines the chordate.
(b) It is the gastro-vascular cavity of the flat worm.
(c) after gastrulation, it is the cavity that will become the gut.
(d) It connects the gall bladder to the duodenum.
*(e) It carries blood from the intestines to the liver.

The liver bile salts that are secreted into the intestines are most closely related to
(a) cellulose.
(b) membrane glycolipids.
(c) ATP.
*(d) cholesterol.
(e) antibodies.

this page was last revised 8/17/09


**The nutrition lecture

The King asked
The Queen, and
The Queen asked
The Dairymaid:
"Could we have some butter for
The Royal slice of bread?"
"You'd better tell
His Majesty
That many people nowadays
Like marmalade
The King sobbed, "Oh, deary me!"
And went back to bed.
He whimpered,
"Could call me
A fussy man;
I only want
A little bit
Of butter for
My bread!"

-Alan Alexander (AA) Milne



Audesirk, Audesirk & Byers Chapter 34, Specified figures elsewhere

Today's musical selection
Jim Backus and Phyllis Diller Delicious (you tube: http://www.youtube.com/watch?v=7NUtJoDG3sE) lyrics

It is worth mentioning that hunger and satiety are complex
In old work on brain lesions, the hypothalamus was thought to have hunger and satiety centers,
Hypothalamus is important in many motivated behaviors including thirst and sex drive
Now it is known that there are hormones like leptin

Figure (chapter 34 opener)
Your case study describes Carre Otis who, like many others, suffered pathological weight loss
anorexia nervosa
bulemia nervosa
(or taking laxatives)


Energy (calories - kilocalories)
2000-3000/day 250 extra/day add 25 lb/yr regulation
do not lose calories in feces, urine (except diabetes)
sweat (all systems efficient)

Table 34-1
Calories of food and calories burned by various activities

Amino acids

"Precursors" building blocks 9 essential amino acids
corn very low in lysine and isoleucine,
beans low in tryptophan and methionine

Figure 34-2
Kwashiorkor - Africa - disease of child new baby born
some essential fatty acids
even cholesterol essential to life, essential in insect diet


Table 34-3
Vitamins not synthesized (in most cases), and are not metabolized
Fat soluable
A is usually considered to be the "chromophore" (pigmented portion) of the visual pigment (rhodopsin)
retinoic acid and steroid hormone receptors act by regulating transcription (into mRNA) of specific genes
Some of my main research interests concern vision and vitamin A: see site 1, site 2, site 3, and site 4

Personal reflection:
The main source of vitamin A in the diet is carotenoids. For 10 years, I have attended a special interest dinner at the vision meeting: "Nutrition" (carotenoids) and I am happy to report that the food they serve is high in carotenoids (note the bright colors)

E (antioxidant) Oxygen is a necessary evil. fat soluable
K (coagulation), normally made by gut bacteria, can have hypervitaminosis which would cause thromboses

Special note:
You are in the Doisy College, and the generosity of the Doisy family to Saint Louis University has been great. Edward A Doisy was SLU's only Nobel Prize winner, and he shared the 1943 Nobel Prize "for his discovery of the chemical nature of vitamin K."
D - also like a hormone, affects bone,

Figure 34-2c
D deficiency leads to a disorder in young people known as rickets with skeletal abnormalities witnessed as bowleggedness, sunshine creates vitamin D in the skin, and hence the expression "sunshine vitamin D." Rickets was in cool climate areas where people are dressed and/or indoors. Now the problem is solved by adding vitamin D to milk, but in the old days thay gave cod liver oil, and fish (especially livers) are high in the fat soluable vitamins most notably A and D

Water soluable
C colds? The Nobel Prize winning chemist Linus Pauling (later in his career) became a strong advocate of the wonders of vitamin C. Does it help for cancer? Scurvey is the name of the vitamin C deficiency, and all sorts of things go wrong. On voyages, sailers were deprived of fresh fruits and came down with scurvey. In the1700's the British figured this out and stocked the ships with citrus fruits and hence British sailers were called "Limeys"
B complex there are 12 B vitamins and some are Kreb's cycle coenzymes, hence these vitamins are important in metabolism
Beriberi - B1 thiamin deficiency

Figure 34-2b
pellagra niacin deficiency


Ca - used in bone, but really importantly in muscle and nerve
P - phosphate - used in ATP etc.
Na, Cl, K - electrolytes which regulate cell electrophysiology
Iodine - used in the hormone thyroxine -

Figure 37-9
deficiency causes goiter (thyroid gland in neck gets very big), iodine is in seafood so deficiencies used to be found mainly inland, now iodine is added to iodized salt
Iron, cobalt, copper - hemoglobin - anemia
Zn is an important mineral (but otherwise some heavy metals like lead and mercury are very toxic

Questions used in 2007 & 2008 related to this lecture

Why is cholesterol NOT considered to be essential in the human diet
(a) It contributes to atherosclerosis.
(b) It serves no useful function.
(c) There is actually a "good" kind of cholesterol, namely LDL (low density lipoprotein).
*(d) Our bodies would biosynthesize cholesterol even if we do not eat any.
(e) It is bad for you.

Some people take an aspirin a day, and it decreases the chance of heart attack. Which vitamin has the opposite effect on blood clotting?
(a) A
(b) C
(c) D
(d) E
*(e) K

Beta carotene, present in green, yellow and red vegetables,
*(a) renders vitamin A, used in rhodopsin, our visual pigment.
(b) causes kwashiorkor.
(c) is a heavy metal, but, unlike lead, it is not toxic.
(d) prevents colds according to chemistry Nobel Prize winner Linus Pauling.
(e) causes anemia.

Goiter, a hypertrophied thyroid gland
(a) results from lack of "sunshine" vitamin D.
(b) is treated with cod liver oil.
*(c) results from iodine deficiency.
(d) was a problem until biotechnology created golden rice.
(e) leads to acromegaly.

Leptin is produced
(a) from a precursor called pellagra.
*(b) by adipose tissue.
(c) by the hypothalamus.
(d) only in people with anorexia nervosa.
(e) in the posterior pituitary.

Partially hydrogenated vegetable oil is
(a) what they give people who have rickets.
*(b) used in some fried food and bad for you.
(c) another expression for omega-3 fatty acids.
(d) good for you and present in sea food.
(e) the reason that olive oil is good for you.

Which of the following would prevent rickets?
*(a) sunshine
(b) adrenalin
(c) Prozac
(d) fibrinogen
(e) dopamine

(a) is the major extracellular protein of connective tissue.
(b) is what actin is made of.
(c) decreases surface tension in alveoli.
*(d) is a glucose polymer that humans cannot hydrolyze.
(e) is created when hemoglobin is recycled by the liver.

(a) is caused by over-activity of the brush border.
*(b) would be prevented by cod liver oil.
(c) are the sounds coming from leaky heart valves.
(d) can be prevented by vitamin K.
(e) happens when alveoli are clogged with viscous mucus.

Iodine is added to salt
A) to help hemoglobin to carry oxygen.
B) as a chromophore so that light is absorbed by the pigment we see with.
*C) for adequate thyroid hormone.
D) to improve bone health.
E) because it assists osteoclasts in their regulation of blood calcium.

What would happen if you had too little vitamin K?
*A) You would have excessive bleeding.
B) Your bones would be depleted of calcium.
C) You would get osteoporosis.
D) Your cells would be damaged by oxidation.
E) Your eyesight would not be good.

Which is a water soluble vitamin that, according to chemistry Nobel Laureate Linus Pauling, is good against the common cold?
A) A
B) B
*C) C
D) D
E) E

The main dietary source of vitamin A is
A) iodine.
B) tocopherol.
*C) carotenoids.
D) trans fats.
E) scurvey.

People used to take cod liver oil because it was rich in
A) essential amino acids.
*B) vitamin D.
D) sodium chloride.
E) cholesterol.

Doisy won a Nobel Prize for
A) proposing that vitamin C cured the common cold.
B) showing that the B complex vitamins were involved in the Kreb's cycle.
C) studies of the importance of thyroid hormone.
*D) research on a lipid soluble vitamin involved in blood clotting.
E) revising the "food pyramid."

"Sunshine" is a term applied to
A) retinoic acid.
B) anemia.
C) monosaturated fatty acids.
D) rhodopsin.
*E) vitamin D.

Adequate caloric intake but protein malnutrition leads to
*A) kwashiorkor.
B) goiter.
C) diuresis.
D) hemorrhage.
E) rickets.

As a food item, corn is notorious for
A) being high in saturated fats.
B) being the cause of pellagra.
C) causing an increase in LDL.
D) being responsible for anorexia nervosa.
*E) lacking several essential amino acids.

Questions used in 2003 related to this outline

A disorder of too little iodine intake as an adult is
(a) cirrhosis.
(b) polio.
(c) cystic fibrosis.
*(d) goiter.
(e) schizophrenia.

Which is a fat soluable vitamin that functions in vision and is related to retinoic acid, an important regulator of development?
*(a) A
(b) B
(c) C
(d) D
(e) E

Which would be most likely to slow the development of osteoporosis?
(a) vitamin A
(b) iodine
*(c) vitamin D
(d) magnesium
(e) organophosphates

this page was last updated 8/17/09

**The excretion lecture

And then Pantagruel had a sudden, urgent need to piss. and he pissed all over their camp, so thoroughly and in such quantities, that his private and personal flood drowned everyone for ten miles around.
Francois Rabelais - Gargantua and Pantagruel



Audesirk, Audesirk & Byers Chapter 35

Today's musical selection
Frank Zappa and the Mothers of invention, Don't eat the yellow snow

Kidneys, transplantation, dialysis

Figure E35-2
Consider the work of the kidneys
Dialysis10 hr 2 times per week

Figure (chapter opener)
This is why transplant important, and there is difficulty getting a compatable donor

In the 1978 thriller movie Coma, unscrupulous doctors harvest organs from the amazing number of patients they have who slip into a coma for seemingly unexplained reasons.

Cell makes wastes go to plasma
heart pumps 7000 l/day (32 55 gal drums)
1/4 (8 55 gal drums) through kidneys
Glomerulus - Bowman's capsule 180 l/day filter
1 l urine/day


(for ions)
Hypertonic (concentrated), isotonic, hypotonic (dilute)
Nitrogenous waste is from catabolism of amino acids and nucleotides
Water animals - nitrogenous waste can be ammonia (toxic)

Comparative biology

Figure 35-1
There is a tradition in undergraduate biology to emphasize comparative aspects:
("nephron" is the term for "higher" organisms)
Protonephridia in planaria
earthworm has nephrostome with nephridiopore in each segment in close juxtaposition with vascular system.
Insect Malpighian tubule puts out uric acid and rectum recovers water and other molecules

Figure 35-8
Freshwater fish - gills leak water in, pump salt in, TRANSPARENCY Fig. 44.14 dilute urine
Salt water fish, gills lose water- pump salt out through gills, not much urine
(When we get to neurons, we will see how universal ion pumping is.)
Salmon (which move from fresh to salt to fresh water) must adapt
Cartilagenous fish keep urea in blood for equal tonicity- need to dialyse meat for preparation
Marine birds - nasal salt gland

Figure 35-9
Kangaroo rat - metabolic water, hypertonic urine
Uric acid (birds, reptiles, insects)

Nitrogen - An integrative story

Although 78% of the atmosphere is nitrogen in the form of N2, this is fairly unreactive.
Thus there are these important processes: N2 to NH3 nitrogen fixation, NH3 to NO3- (nitrate) nitrification, NO3 to NH3 (nitrate reduction) in plant roots.
Also nitrogen is recycled.
In Pacific, off the coast of Peru, the Humbolt current causes an upwelling of nutrients, anchovies thrive, bird droppings (guano) were used as fertilizer.
El Nino (the Child, named not for misbehavior but because it comes near Christmas) is a periodic climate misbehavior that disrupts this.


Figure 35-3
kidney, ureter, bladder, urethra

Figure 35-4
Pelvis=basin; Medulla=marrow; Cortex=bark ("medulla" and "cortex" are terms used a lot, like in brain and in adrenal gland)
many blood vessels - kidney is supplied by major blood vessels
Renal artery and vein branches near eachother

Figure 35-5
each kidney has 1 million nephrons
Blood flow in glomeruli
Glomerulus - Bowman's capsule filter 180 l/day (throwing out the baby with the bath water)
blood and osmotic pressures drive
Glomerulus - capillaries a sieve
here is a picture from the histology course
another picture highlights glomerulus by dye injected into artery
large molecules dye do not pass
- small molecules dye passes through
blood proteins and cells do not pass
urinalysis strips test if blood, cells or protein is present

Figure 35-6
Need for resorption
Proximal Convvoluted tubule - bring back amino acids, glucose note active (NaCl) vs passive (water) transport

Figure E35-1
Na pump
6% of body's energy at rest
Countercurrant system
Ascending loop - salt resorbed but not water
Ascending loop of Henle - salt outward resorption is stimulated by aldosterone

Figure 35-7
ADH (vasopressin) makes water follow back into interstitial fluid which is hypertonic from salt
alcohol and caffeine inhibit ADH, hence diuresis (excessive urination)
regulation of ADH (from hypothalamus to pituitary) and relation to thirst

Posterior pituitary

Figure 37-8
(related to kidney coverage)
neurosecretion from hypothalamus (peptides)
oxytocin (milk, delivery)
(synthetic to induce labor)

Chapter 38 case study ("How do I love thee?")
hormones involved in love, oxytocin called the trust hormone

Covered in Excretion lecture: ADH action on kidney
vasopressin (ADH), H2O and blood pressure
alcohol, caffein inhibit anti [diuresis] hormone


Filter, resorb (salt and water)
Sweat pores not as good -which is why gatorade tastes good to athletes
especially bad in cystic fibrosis (salty sweat) molecular genetics shows a chloride channel defect
Kidney also secretes - pump out (penicillin)

Questions used in 2007 and 2008 related to this outline

Where does the ADH-dependent water resorption occur in the kidney?
(a) in the urethra
(b) in Bowman's capsule
(c) in the afferent arteriole
(d) in the bladder
*(e) in the collecting duct

To regulate osmolarity, salt water fish
(a) pump uric acid out through the fins.
(b) move water in through the gills by osmosis.
(c) have kidneys that excrete large amounts of dilute (hypotonic) urine.
*(d) pump salt out through the gills.
(e) move salt in through the gills by osmosis.

What is urea?
*(a) nitrogenous waste
(b) the tube connecting the kidney to the bladder
(c) the organ for excretion in the insect
(d) the hormone that helps the kidney maintain isotonic body fluids
(e) the unit of the kidney, 1 million per kidney

What happens in the proximal tubule of the nephron?
(a) Aldosterone is secreted.
(b) Filtration takes place.
*(c) Water and nutrients are resorbed.
(d) Memory cells of the immune system are stored.
(e) Urine exits from the bladder.

The Kangaroo rat, a desert animal
(a) is considered to be a producer by ecologists.
(b) uses dialysis.
(c) has diuresis.
*(d) excretes hypertonic urine.
(e) loses glucose through its urine.

What is the fundamental unit of the kidney in humans?
(a) oligodendroglia
(b) the polymorphonuclear granulocyte
*(c) the nephron
(d) the Malpighian tubule
(e) the urethra

"Secretion" (as opposed to excretion)
A) refers to active transport of water in the proximal tubule.
*B) refers to output of wastes in the distal tubule.
C) refers to the passive salt transport in the proximal tubule.
D) refers to the salt transport in the collecting duct.
E) refers to the filtration in the glomerulus.

What does the Humboldt current have to do with nitrogenous wastes?
A) The flame cell of the flatworm creates the Humboldt current.
B) This is the part of the nephron between proximal and distal tubules where there is a flow (current) of urine.
*C) Because it creates a rich marine environment, nitrogen-rich bird droppings are on the islands.
D) El nino is high in nitrogen.
E) The Humboldt current dilutes nitrogenous wastes in the kangaroo rat.

Where does ADH exert its influence in the kidney?
*A) collecting duct
B) loop of Henle
C) proximal tubule
D) distal tubule
E) glomerulus

After a salmon has returned to its mating area
A) it should need to pump salt out by active transport through its gills.
B) it should need to put out small amounts of salty urine.
C) its malpighian tubules would need to get rid of more urea.
*D) it should need to excrete copious amounts of dilute urine.
E) its osmoregulation would be no different than when it grew for 5 years in the ocean.

Why did they refer to the blood vessel returning blood from the glomerulus as an "arteriole?"
*A) because of the portal system
B) because the extracellular fluid in the kidney medulla is isotonic
C) because blood flows straight into the ureter
D) because it returns blood straight to the vena cava
E) because this is where water, salt and nutrients are secreted

What is the correct order of flow?
A) Bowman's capsule, urethra, loop of Henle
*B) proximal tubule, collecting duct, ureter
C) bladder, distal tubule, glomerulus
D) loop of Henle, collecting duct, proximal tubule
E) ureter, urethra, collecting duct

Where is dilute urine first formed by filtration of the blood?
A) the proximal tubule
B) the loop of Henle
C) the Purkinje cell
*D) the glomerulus
E) the kidney's medulla

ADH (antidiuretic hormone)
A) is no longer needed now that they add vitamins A and D to milk.
*B) is regulated by the hypothalamus that monitors your state of hydration.
C) is why you should soak shark meat in water before cooking and eating it.
D) is a hormone that tells your brain how hungry you should be.
E) has its effects on osteoclasts.

Which is NOT true about aldosterone?
A) It comes from the adrenal cortex.
B) The gland it comes from is near the kidney anatomically.
C) It has its effects in the kidney.
D) It mediates salt reuptake.
*E) It is a peptide.

this page was last updated 6/30/09

**Blood and immunity

Blood and antibodies


Audesirk, Audesirk & Byers Chapter 36 (and part of Chapter 32) (a little from Chapter 5)

Today's musical selection
Foreigner Hot blooded

Overview of blood cell types

Table 32-1
plasma and hematocrit (formed elements), Buffy coat between

I. Plasma - (serum lacks fibrinogen) fluids, nutrients, O2, CO2, ions
proteins (synthesized in liver except gamma globulins)(clotting)

II. Hematocrit
Erythrocytes 5-6 million/ml
Leucocytes 5-10 thousand/ml
Platelets 250,000-400,000/ml formed from megacaryocytes
(antibodies) ions, wastes, hormones

Blood clotting

Figure 32-8c
Platelets 250,000/ml from megacaryocytes

Figure 32-12
Clotting Platelet adhesion then fibrin (from fibrinogen)
activated Hageman factor
prothrombin -> thrombin
fibrinogen ->fibrin
Hemophelia is famous disorder


Figure 32-8a
Red blood cells (corpuscles) (erythrocytes)
no nuclei
O2 transport, hemoglobin, anemia
last 120 days, made in marrow, recycled
iron recycling in liver is what makes feces dark (and skin yellow in jaundice [hepatitis]) - bile pigments

Polymorphonuclear granulocytes

Figure 32-8b
There are non-specific responses to injury

White blood cells (leucocytes as in leukemia)
Polymorphonuclear granulocytes (phagocytosis, etc)

neutrophil (60-70%) phagocytosis
here is a picture from our histology course of a neutrophil showing the complex nucleus
chemotaxis after 30-60 min
more synthesized especially in bacterial infection
reset thermostat (pyrogens)

eosinophil (1.5%) phagocytosis
allergic and parasitic inflamation

basophil (0.1%) histamine containing
like mast cells

Phagocytosis and review slides

Figure 5-15c
Phagocytosis (cell eating), fusion of primary lysosome, formation of secondary lysosome
white blood cell engulfing bacterium

Figure 36-4
macrophage eating E. coli


Figure 32-8b
Mononuclear cells
monocytes (5%) (as in mononucleosis) (phagocytosis)
late chemotaxis become macrophages
alveolar macrophages in lungs
Kupffer's cells in liver


Figure 36-5
Inflammation and phagocytosis
Triad redness, warmth, swelling
Histamine (from mast cells, platelets)


There are specific responses involving antibodies and other mechanisms

T-cells (80%) (thymus - near heart) cell
(transplant) cytotoxic, suppressor, helper (AIDS)
B-cells (20%) (bone marrow, actually bursa of Fabricius) (become plasma cells)

Active and passive immunity

When I was a kid, nearly everybody got measles, mumps, and chicken pox. We were presumably immune for life (active immunity). When we had the disease was part of out health record.

Vaccines - active immunity (like disease)
memory cells of immune system
Edward Jenner 1796 "encowment"
Farmers were less likely to get smallpox because they got a related disease, cowpox
When I was a kid, you could not enroll in school without the scar
Smallpox is so completely eliminated that one issue is whether to get rid of lab virus.

When I was a kid, there was (still) a polio epidemic.
A kid at a birthday party I went to got polio, so I went to the family doctor for gamma globulin, passive immunity
(1954 Salk vaccine injected, soon Sabin vaccine in sugar cube)


Humoral immunity - B cells

Figure 36-9
clones of plasma cells and memory cells derived from B cells for specific antigens

Figure 36-11
Another version of this figure

Figure 36-6
Antigen (virus or bacterial coat, usually not self)
2 long chains and 2 short chains, variable region at the end of all 4 makes it specific for antigen

Figure 36-8
An amazing mechanism where the gene is rearranged accounts for diversity.

IgG most abundant, monomer, cross placenta
Antibodies cross placenta, also in mother's milk, and late weaning covers until child's own antibodies are formed.

Figure 36-13
IgE allergy, bind to mast cells (histamine)


Figure 36-11
helper T cells express CD4
antigen presenting macrophage
MHC major histocompatability complex 20 genes 50 alleles each
Class II MHC only on macrophages (and B lymphocytes)
antigen presented by to B cell

Figure 36-10
cytotoxic (killer) T cells express CD8
Class I MHC - actually on lots of cells (including the infected cellsshown here)
[try to match MHC (tissue typing) for transplantation]

Questions used in 2007 & 2008 related to this outline

Phagocytosis is a term for
(a) self-induced vomiting to lose weight.
(b) the kind of inflammation mediated by histamine.
(c) the network of molecular transformations mediating blood clotting.
(d) histological staining with histamine.
*(e) eating of bacteria by white blood cells.

If you are given an injection of antibodies, this is called
(a) active immunity.
*(b) passive immunity.
(c) vaccination.
(d) major histocompatability complex.
(e) histamine.

How does a B lymphocyte help after infection?
*(a) It makes antibody.
(b) It makes antigen.
(c) It destroys infected cells.
(d) It causes inflammation.
(e) It expresses CD8 and hence activates killer T cells

How can so many antibodies be made against the vast array of possible antigens?
(a) Each different antibody is coded by a different gene in your genome.
(b) Alternative splicing of RNA.
*(c) Recombination on chromosomes produces different antibody genes.
(d) That's what histamine is used for.
(e) Different antibodies come from different polymorphonuclear granulocytes.

Which does not apply to blood clotting?
(a) hemophelia.
(b) fibrin.
(c) prothrombin.
*(d) mast cells.
(e) platelets.

A newborn baby might have some immunity because
(a) memory cells cross the placenta.
(b) cytotoxic T cells cross the placenta.
*(c) antibodies cross the placenta.
(d) Hageman factor crosses the placenta.
(e) of active immunity in the baby's own neutrophils.

(a) are used for dialysis.
(b) are peptide hormones.
(c) make antigens.
(d) are histamine-secreting cells.
*(e) are the source of platelets.

Which is a lymphocyte?
(a) an osteoblast
(b) Paramecium
(c) a T cell
(d) the glomerulus
(e) macrophage

Upon the first exposure to non-self proteins, what does the immune system do to allow quick antibody production the next time?
(a) The erythrocyte engulfs the bacterium.
(b) Pyrogens are secreted from the thymus.
(c) Mast cells are converted to red blood cells.
*(d) Antigens bind to B-cells.
(e) Killer-plasma cells attack and kill infected cells.

Fibrinogen is involved in
A) cell-mediated immunity.
B) humoral immunity.
C) inflammation.
*D) blood clotting.
E) antibody formation.

Why might an infant, at the moment of birth, have some of the mother's immunities?
A) because of prothrombin
B) because of platelets
*C) because of IgG
D) because of killer T cells
E) because of megakaryocytes

Some macrophages present viral antigens on their surface. How did they get those antigens?
A) by using pyrogens
*B) by phagocytosing the virus
C) by using eosin
D) by releasing histamine
E) These macrophages were memory cells, so they "remembered" the antigens.

Plasma cells are derived from
A) polymorphonuclear granulocytes.
B) mast cells.
C) basophils.
D) erythrocytes.
*E) B lymphocytes.

"Antibodies on only one B cell can bind an antigen," according to one figure. What happens then?
A) Prothrombin gets activated to thrombin.
B) Erythrocytes get recycled in the liver.
*C) Some become memory cells to jump start a future response.
D) Phagocytic cells mop up the debris.
E) Helper T cells kill the B cell.

Helper T cells are involved in
*A) cell-mediated immunity.
B) humoral immunity.
C) inflammation.
D) blood clotting.
E) chemotaxis.

83. Which is a phagocytic white blood cell?
A) plasma cell
*B) neutrophil
C) platelet
D) interstitial cell
E) Purkinje cell

Questions used in 2002 relating to this outline (and other outlines)

The CD4 and CD8 proteins are expressed by [A] and [B] respectively.
(a) [A] steroid hormone cells; [B] peptide hormone cells.
(b) [A] adrenal cortex; [B] adrenal medulla.
*(c) [A] helper T cells; [B] killer T cells.
(d) [A] alpha cells in the islets of Langerhans; [B] beta cells in the islets of Langerhans.
(e) [A] erythrocytes; [B] leukocytes.

Macrophages are derived from
(a) a clone of memory cells.
(b) the pituitary.
(c) plasma cells.
*(d) monocytes.
(e) the thyroid.

Chemotaxis is a term applied to
*(a) monocytes and polymorphonuclear granulocytes migrating to the site of an injury.
(b) dilute urine moving from Bowman's capsule to the proximal convoluted tubule.
(c) the sperm being attracted to the egg.
(d) the forward flow of blood through veins.
(e) the transport of CO2 in the blood.

Vasodilation would occur
(a) during diastole.
(b) in laryngitis.
(c) during inhalation.
*(d) during the inflammatory response.
(e) when veins like the vena cava regulate blood flow to vascular beds.

Which cells are most depleted by infection with HIV (human immunodeficiency virus)?
(a) erythrocytes
(b) eosinophils
*(c) helper T cells
(d) monocytes
(e) macrophages

.A highly variable region is the hallmark of which of the following?
*(a) an antibody molecule
(b) pro-opiomelanocortin
(c) the cervix
(d) the cardiac orifice
(e) the vascular cambium

this page was last updated 8/17/09



Audesirk, Audesirk & Byers Chapter 37

Today's musical selection
Weird Al Yankovic Pancreas

Figure (Chapter 37 opener)
case study "losing on artificial hormones"
Of course testosterone and other anabolic steroids favor muscle growth.
Also stimulants, growth hormone, diuretics, masking compounds, erythropoietin (EPO), more.
Box and paper detail the work of Prof. Don Catlin
Paper is dated 2004, so there have been many further cases.
Tour de France, Olympics, etc. - baseball is a special case because of a century of worship of records and record holders.
Hard for those who do the testing to stay ahead of new and innovative cheaters
New steroids like THG (tetrahydrogestrinone)
Testosterone itself is hard to judge, because it is naturally occuring, but synthetic has lower 13C/12C.
Also there's blood doping
There are so many health (and legal and career) dangers of messing around!
Balco (Bay Area Laboratory Cooperative) provides know-how and drugs and is networked with athletes.


Table 37-1
Metazoans (animals with more cells than protozoans) require systems of integration
INTEGRATION: Hormones, paracrine (local) & nervous system
"endocrine" - ductless, into blood stream
vs. exocrine (like digestive - saliva etc.)

Figure 37-2
Three steps:
cells with blood vessels for release
hormone transported in the circulation
target cell with receptor

Two mechanisms

Figure 37-3
(1) receptor molecule on membrane

Figure 37-4
(2) enter cell and bind receptor


Figure 37-1
I. Traditionally, this material starts with a picture of the major glands

Figure 37-6
II. Then it covers Pituitary three ways
(1) posterior pituitary
(2) anterior pituitary as "master gland" (and the other glands it controls)
(3) anterior pituitary (affects not mediated through other glands)

III. Then it covers other glands (not controlled by the pituitary)

Posterior pituitary

Figure 37-8
(related to kidney coverage)
neurosecretion from hypothalamus (peptides)
oxytocin (milk, delivery)
(synthetic to induce labor)

Chapter 38 case study ("How do I love thee?")
hormones involved in love, oxytocin called the trust hormone

Covered in Excretion lecture: ADH action on kidney
vasopressin (ADH), H2O and blood pressure
alcohol, caffein inhibit anti [diuresis] hormone

Anterior pituitary

Figure 37-10
Secretion of releasing (and inhibiting) hormones (peptides) at pituitary stalk
Portal system
Anterior pituitary and its hormones (peptides)
Thyroid hormones
Influence on metabolism, but not as obviously as epinephrine, insulin, glucagon or even glucocorticoids.
Negative feedback with pituitary
Hypothalamus -TRF-> + Ant. Pituit. -TSH->+ Thyroid -> thyroxine-
- neck thyroxin (T4), triiodothyroxine (T3) iodine, sea food (and iodized salt)
T3 and T4 (Fig. 11.3 shown in an earlier lecture)

Figure 37-9
Goiter (thyroid overgrows if too little iodine in diet)
Cretinism if too little in infant, hypothyroid, hyperthyroid
Change in salmon during salt to fresh water change, metamorphosis in frog
Problem of radioactive iodine (like from reactor leaks) - helps to take large doses of non-radioactive iodine to compete

Table 37-3
So many more examples!

Non-trophic hormones
(not where pituitary acts as master gland to control other glands)

GH - 200 a.a. -bone, muscle, not fat,

Figure 37-7
GH - gigantism (bones grow long if too much GH when young), dwarfism (if too little GH when young), acromegaly (bones grow too thick if too much GH when already grown up, danger of GH abuse), abuse by body builders, dangers of extracts,, now available through recombinant DNA research

"Master Gland"
sex hormones from pituitary (more details later):
LH (female) = ICSH (male); (luteinizing) (interstitial cell)
FSH (follicle)

Adrenal cortex

Figure 37-13
Adrenal cortex - Glucocorticoids stimulate metabolism, inhibits inflamation.
Mineralocorticoids, the best known being Aldosterone helps kidney retain salt
Adrenalectomy causes salt loss and salt appetite.
Sweat glands are not as efficient at retaining salt as kidney.
That is why "Gatorade" (electrolyte) is used by athletes.
Salt is also lost in cystic fibrosis (mutation of CFTR (cystic fibrosis transmembrane conductance regulator)

Adrenal medulla

Table 37.2
while on the topic of the adrenal gland,
Adrenal medulla - Epinephrine, (alias adrenalin) - activates body
Autonomic (vs voluntary) motor control: sympathetic (vs parasympathetic)
Sympathetic nervous system uses norepinephrine at postganglionic synapses.
Sympathetic - "fight or flight"
Helps in metabolism to release glucose to blood stream
Muscles activity up, peripheral circulation and digestion inhibited
Heart rate goes up

Glucose (insulin and Glucagon) and diabetes

Figure 37-12
In pancreas, which is largely a digestive exocrine gland, there are also islets of Langerhans (as shown in this picture from our histology course) which are the endocrine glands where the beta cells make insulin and the alpha cells make glucagon
Pancreas Insulin- sugar uptake into cells (blood sugar down), make glycogen in muscle & liver

Diabetes mellitus

Type 1 autoimmune disease beta cells are destroyed, young people, insulin dependent
inject insulin. protein, must inject
(vs steroid like "the pill" which can be taken orally)
Type 2, older people, genetic, correlated with overweight, non-insulin dependent
sugar in urine-
Eye problems (too many new blood vessels - angiogenesis) and cardiovascular problems
Brain is not insulin-dependent - coma from too much insulin because no glucose for brain
Glucagon mobilize sugar to blood like adrenalin
sugar regulates insulin and glucagon

Calcium homeostasis

Figure 37-11
Parathyroid - parathormone - blood Ca2+ up (from bones)
near thyroid gland in neck

Thyroid - thyrocalcitonin - blood Ca2+ down
Vitamin D sunlight, rickets, fish oil, hormone, absorption from gut
Osteoporosis - bone deterioration with age especially in women
Ca2+ very important, muscle (later), nerve (later)


Menopause (pause in the menes) ["change of life" at about 50] - lack of estrogen.
(Some hysterectomy or ovarian cancer surgeries might also deplete because of ovarectomy).
Many symptoms, hot flashes most obvious short term effect.
Osteoporosis most obvious long term effect.
For me, this site worked with explorer, not netscape - estrogen (hormone) replacement therapy
Hotly contested (a lot of negative press lately), partly because estrogen increases chances of breast cancer.
There is a drug, Tamoxifen that blocks estrogen's effects, differently in different tissues.

Signal transduction

Figure 37-4
steroid hormone
gene transcription
signal transduction for G protein coupled receptor

Prostaglandins, etc

Table 37-2
prostaglandins (mediators of inflammation) are derived from fatty acid (arachidonic acid, 20:4) using cyclooxygenase (COX)
NSAIDS (non-steroidal anti-inflammtory drugs) aspirin, ibuprofen, inhibit prostaglandin synthesis by inhibiting cyclooxygenase (COX-1 & 2) nonspecifically, problems in stomach
Celebrex, Vioxx, Bextra inhibit prostaglandin synthesis by inhibiting cyclooxygenase (COX-2); popular for arthritus, but Merck pulled Vioxx 10/04 for increasing cardiovascular problems, and later Bextra was pulled.
Aspirin is anti-inflammatory, analgesic, antipyretic, anticoagulant, implicated in Reye's syndrome.

Questions used in 2007 relating to this outline

How might the authorities know whether a competitor had taken anabolic steroids.
(a) Look at the ratio of paracrine to endocrine secretions.
*(b) Look at the ratio of 13C/12C in testosteone.
(c) Check for acromegaly.
(d) Look at the ratio of CD4- vs CD8-expressing cells.
(e) Directly test for diuretics.

The pituitary is called the "master gland of the body" because
(a) most of the steroids are produced there.
(b) most of the exocrine secretions come from there.
(c) that is where insulin comes from.
*(d) it makes peptides that control other glands
(e) all the hormones that control calcium are located there.

Which of the following would prevent rickets?
*(a) sunshine
(b) adrenalin
(c) Prozac
(d) fibrinogen
(e) dopamine

"Endocrine secretions bind to G protein-coupled receptors on the cell's membrane."
(a) So do the antigens presented by macrophages.
(b) So do exocrine secretions.
(c) From there, they move in to bind to mRNA
*(d) By contrast, steroid hormones bind to receptors inside the cell.
(e) This is true for endocrine secretions but never for neurotransmitter substances.

A portal vessel connects the hypothalamus to the
(a) islets of Langerhans.
(b) interstitial cells between seminiferous tubules.
(c) mammary gland.
(d) collecting ducts shared among nephrons.
*(e) anterior pituitary.

Why would active people (e.g. athletes) prefer electrolyte drinks (e.g. Gatorade)?
*(a) because of salt loss by sweat glands
(b) to prevent insulin shock
(c) because activity inhibits oxytocin release from the adrenal medulla
(d) to make up for iodine deficiency
(e) because electrolytes are used for blood doping

Steroid hormones come from the gonads and the
(a) hypothalamus
*(b) adrenal cortex
(c) pancreas
(d) fat cells of adipose tissue
(e) thyroid

Why can't people with type I diabetes just eat their insulin?
(a) It would upset the homeostasis regulating thyroxne.
(b) That would cause osteoporosis.
(c) That would cause acromegaly.
(d) That would inhibit the formation of prostaglandins.
*(e) It's a protein and would be hydrolyzed.

Which of the following is delivered from the hypothalamus to the pituitary?
(a) inhibin
(b) vitamin D
(c) bicarbonate
*(d) GnRH (gonadotropin releasing hormone)
(e) progesterone

A "hormonal" disorder of too little vitamin D in toddlers is
(a) dwarfism.
(b) cretinism.
*(c) rickets.
(d) goiter.
(e) scurvey.

If a woman's contractions were too weak during labor, the obstetrician might add a synthetic version of (what?) to the intravenous drip?
(a) IgG
*(b) oxytocin
(c) thyroid hormone
(d) troponin
(e) glucagon

Questions used in 2002 relating to this outline (and other outlines)

Which is likely to be an autoimmune disease?
(a) acromegaly
(b) bronchitis
(c) myocardial infarction
*(d) diabetes
(e) cystic fibrosis

Classic experiments in which the adrenal gland was removed in rats
(a) demonstrated that the adrenal gland produces an antipyretic substance and is thus the center for temperature regulation.
(b) eliminated problems associated with ingesting radioactive iodine.
(c) caused a decrease in helper T cells.
(d) resulted in increased muscle mass because of anabolic steroids.
*(e) showed that there is an increased salt appetite.

Which would cause the bones to release calcium?
(a) cortisol
(b) glucagon
(c) vitamin D
(d) calcitonin
*(e) parathyroid hormone

Which is delivered via the portal vessel from the hypothalamus to the pituitary?
(a) angiotensin
(b) thrombin
(c) bicarbonate
*(d) peptide releasing factors
(e) steroid hormones

A disorder of too little thyroid hormone as an infant is
(a) dwarfism.
*(b) cretinism.
(c) rickets.
(d) laryngitis.
(e) emphysema.

Angiogenesis in the retina would most likely occur from
*(a) diabetes.
(b) vitamin D deficiency.
(c) Addison's disease.
(d) cretinism.
(e) cancer.

The prescription drugs for osteoarthritis, Vioxx and Celebrex, work
(a) as narcotic analgesics.
*(b) by targeting conversion of arachidonic acid to prostaglandins by COX-2.
(c) by inhibiting pituitary release of endorphins.
(d) to regulate calcium homeostasis.
(e) to stimulate inflammation.

To induce stronger uterine contractions, a synthetic version of what hormone is given?
(a) androgen
(b) estrogen
(c) progesterone
*(d) oxytocin
(e) FSH

ADH (antidiuretic hormone) affects
(a) the Malpighian tubules.
*(b) water recovery in the collecting duct.
(c) conversion of carbonic acid to bicarbonate in the blood stream.
(d) emergence of the adult insect from the pupa case.
(e) the transition from marine to fresh water physiology in salmon.

Rickets can be prevented by supplements of
(a) steroids.
(b) insulin.
(c) growth hormone.
(d) T3 and T4.
*(e) vitamin D.

Beer and coffee cause excessive urination
(a) by stimulating glomerular filtration.
(b) just because of the water they contain.
(c) by activating angiotensin.
(d) by activating interstitial cell stimulating hormone.
*(e) by inhibiting a hormone from the posterior pituitary.

Insulin shock
*(a) would happen when blood sugar gets too low.
(b) is from insufficient insulin.
(c) could only occur in untreated diabetics.
(d) is just another word for diabetes.
(e) commonly occurs when there are too many alpha cells in the islets of Langerhans.

A disorder of too little iodine intake as an adult is
(a) cirrhosis.
(b) polio.
(c) cystic fibrosis.
*(d) goiter.
(e) schizophrenia.

A disorder of too much growth hormone as an adult is
*(a) acromegaly.
(b) multiple sclerosis.
(c) treated by non-steroidal anti-inflammatory drugs (NSAIDS).
(d) gigantism
(e) cretinism

Which endocrine gland is involved in calcium regulation?
*(a) parathyroid
(b) pancreas
(c) juxtaglomerular apparatus
(d) interstitial cells
(e) pituitary

Which would be most likely to slow the development of osteoporosis?
(a) vitamin A
(b) iodine
*(c) vitamin D
(d) magnesium
(e) organophosphates

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