Scientific inquiry, phylogeny, taxonomy, properties of life, levels of analysis lecture (first lecture)

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

Campbell and Reece, Chapter 1 (but note Glossary and Index at end, and pay attention to several references to figures in other chapters)

Nature of scientific inquiry

Scientific inquiry and scientific method is based on observation - systematic, objective, repeatable
You cannot always manipulate things, examples: astronomy, studying the fossil record.
But you can make observations like the similarities in the forelimbs of birds and mammals. You can also make correlations, like overweight peope are more likely to develop type II diabetes. But correlation does not prove causation. For instance, that correlation does not prove that increasing your weight would increase your likelihood to get diabetes. Rather there could be an underlying genetic factor that could predispose you to diabetes and weight gain (in a sense, simultaneously).

Also there is experimental intervention: Propose a null hypothesis vs. an alternative hypothesis.
TRANSPARENCY (Fig. 1-19)
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 of being wrong, hence the involvement of statistics in experimental design. 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.

In summary, the step-by-step progress of science involves statistics, and asking the right questions, that can be answered appropriately (advanced statistics) is called "experimental design."

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

Ultimately, you develop theories (evolution), laws (gravity), or models that describe how things work (like negative feedback in homeostasis).

Biology is the study of life on Earth.

Consider the categories of substance (matter): (organic) Animal, Vegetable, (inorganic) Mineral "Is it animal, vegetable or mineral" - a question on an old quiz show called "20 questions"

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.
TRANSPARENCY (Fig. 26.15)
Sometimes more are also proposed. How can the number of kingdoms be subject to debate? Classification is not an exact science.
5 Kingdoms:
Monera (prokaryote)
TRANSPARENCY (Fig. 1.4)
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
Fungi
Plantae
Animalia

Autotroph vs. Heterotroph (self- other-feeder)

Phylogeny vs Taxonomy
Taxonomy is sometimes called "Systematics" and is based on the Linnean system (Linnaeus 1705-1778 botanist)
Kingdom - Phylum - Class - Order - Family - Genus - Species
TRANSPARENCY (Fig. 1.10)
TRANSPARENCY (Fig. 25.7) (The point is so fundamental that it is repeated in Chapter 25, 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. There can be various levels of artistic license in such evolutionary diagrams. Here (TRANSPARENCY) is an old (traditional) one I like to illustrate fundamental points. (There is a figure in the book TRANSPARENCY (Fig. 24.24) that is somewhat like the version I selected to show you.) Horse evolution is shown. 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). TRANSPARENCY (Fig. 19.3) - let's look ahead, and we will see that your book gives an example of different components of the hemoglobin protein.

What is unique to life? Cell membrane contains protoplasm and somehow inside, cells are "alive." Cells have very complex macromolecules (DNA, RNA, protein).
Complex
Movement, Responsiveness (irritability, sensitivity)
Development, Growth, Form
Metabolism must absorb energy Catabolic, Anabolic
Homeostasis (regulation) Thermostat, servo, negative feedback. TRANSPARENCY (Fig. 1.8)
water, food. 1 cookie/day = 25 lb/yr
Evolution is major unifying principle 3 1/2 billion yrs
History from primordial "soup" of molecules to biology, extinctions, etc.
It is impossible to overstate the importance of evolution to understanding and explaining biology.
Reproduction - "Survival" in biology is to and reproduce and produce fertile offspring. In fact, that is one definition of a species (organisms that can reproduce and produce offspring - that is why the horse and the donkey are not the same species even though they can mate to produce the mule -- the mule is sterile.)
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.

Levels of analysis
element - molecule - organelle - cell - tissue - organ -
organ system - organism - population - biosphere
(Biosphere - biology really change Earth)
Holism vs reductionism
Vitalism vs mechanism
Mentalism vs materialism
The attitude that "life is not driven by vital forces that defy explanation but by principles of physics and chemistry" is useful for this course, but does not touch the big questions of the meaning of life
Religion and science may seem at odds, but they can be reconciled.
Hopefully, learning biology should strengthen your appreciation of the wonder of creation.

A very useful site for SLU students, especially majors, is the Biology Department's web page.


This page was last updated 1/22/03

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Inorganic chemistry lecture

CHEMISTRY:

"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 104, 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.

INORGANIC CHEMISTRY
From the Los Alamos National Labs (periodic table) [note the back arrow does not work]
TRANSPARENCY (Fig. 2.10) shows some information from the first few rows of this table.
(Note the electrons and the nucleus.)
Periodic table - elements - O, C, H, Ca, P, K, S, ... are most abundant in life
TRANSPARENCY (Table 2.1) shows this.
There are also trace materials like iron and zinc.

Atoms = Elements
There are 3 particles.
TRANSPARENCY (Fig. 2.5) elaborates on Fig. 2.10, showing nucleus has neutrons and protons.
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).
TRANSPARENCY (Fig. 2.6) shows quantifying radioactivity in a scintillation counter (note, she should also be wearing safety goggles!) and microscopic audoradiography.
3. electrons, virtually no mass, involved in bonding of two major types:
(a) covalent bonding
(b) NaCl splits to Na+ (sodium) and Cl- (chloride) ions that are attracted to each other because of opposite charges TRANSPARENCY (Fig. 3.7)
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 will be very important in our discussion of how biological energy is stored (photosynthesis) and how it is released (cellular respiration)

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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

Campbell et al., Chapter 3

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.
H2O has covalent bonds, but there is some separation of charge, making it a polar molecule TRANSPARENCY (Fig. 2.13)
Water is very important as a solvent, in reactions, and in temperature regulation.
As a polar solvent, it dissolves charged molecules or ions.
A small fraction of water molecules split to H+ and OH- "ions", 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+]. TRANSPARENCY (Fig. 3.9)
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. 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

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Organic chemistry lecture

Campb ell et al., Chapter 4 and beginning of Chapter 5

ORGANIC CHEMISTRY 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.

Hydrocarbon (Hydro-carbon - prefix suggests hydrogen, suffix suggests carbon).
They are hydrophobic and nonpolar.
CH4 methane, TRANSPARENCY (Fig. 4.2) - natural gas
Gasoline has typically 8 carbons (octane) and is fluid. Long chains are thick, like oil and vasoline.
nonpolar, hydrophobic

Carbohydrate (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
Monosaccharides TRANSPARENCY (Fig. 5.3)
Hexose (hex = 6 [carbons], "-ose" always means sugar)- glucose, the most famous monosaccaccharide, is good to illustrate that monosaccharides usually assume a ring structure TRANSPARENCY (Fig. 5.4)
Pentose - ribose, deoxyribose (that are in RNA and DNA) are famous
Compound dehydration synthesis, hydrolysis (hydro-water, lysis-breakdown) TRANSPARENCY (Fig. 5.2)
In digestion, macromolecules are broken down to monomers.
Disaccharide - sucrose, lactose (milk) TRANSPARENCY (Fig. 5.5) shows maltose and sucrose, and shows dehydration synthesis.
Polysaccharides starch (plant), glycogen (glyco-sugar, gen-give birth to) (animal)
alpha 1-4 linkage TRANSPARENCY (Fig. 5.7)
Carbohydrates are used for energy.
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.
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

Lipids (fats) store more energy (2x sugar) 1 tablespoon of sugar is 50, fat 100 "Calories" = kilocaloriies
Glycerol & 3 fatty acids (16-24 C long) - triglyceride ester bonds TRANSPARENCY (Fig. 5.10), 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.
Polar phospholipids -TRANSPARENCY Fig 5.13 - contribute to membranes because polar group is hydrophilic and fatty acid (acyl) tail is hydrophobic
TRANSPARENCY (Fig. 5-12) polar-glycerol-FA1-FA2 (more double bonds, fluidity)
Here are some famous fatty acids: stearic C18, Oleic-18:1, TRANSPARENCY (Fig. 5.11)
There are also glycolipids with sugar attached to lipid in membranes.
Steroids-cholesterol TRANSPARENCY (Fig. 5.14)- fit into membranes and serve as precursors for hormones,
especially "sex hormones" like testosterone, progesterone, estrogen TRANSPARENCY (Fig. 4.8)
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.
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 (including second messengers, see Chapter 11), insulation, water loss, digestion


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Protein 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

Campbell et al., part of Chapter 5

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
The general formula is NH2-CR-COOH - amino ( -NH2 ) and acid ( -COOH ).
Peptide bonds TRANSPARENCY Fig. (5.16) involves -NH2 and -COOH getting linked with a dehydration synthesis.
There are about 20 amino acids TRANSPARENCY (Fig. 5.15). (alphabet of 20 letters)
R group varies, see figure.
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 TRANSPARENCY (Look ahead to Fig. 41.4 - corn is notoriously low in tryptophan and methionine).
Structure:
primary (the sequence) TRANSPARENCY (Fig. 5, 18)
secondary (alpha helix, beta pleated sheet) TRANSPARENCY (Fig. 5-20)
tertiary structure (disulfide and other bonds) TRANSPARENCY (Fig. 5.22)
quaternary structure (chains interact with each other) TRANSPARENCY (Fig. 5.23 - here is a really important example - hemoglobin - which has 2 alpha subunits and 2 beta subunits.)
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.
TRANSPARENCY (Table 5.1)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)
Storage
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

Especially as the focus is on proteins (this outline) and nucleic acids (soon) the field is usually called "biochemistry" or "biological chemistry." Cellular Biochemistry & Molecular Biology (BL-A302) (3 credit hours) is offered Fall semester (this year by Profs. Medoff and Bruzzini). It is geared to sophomores and is required of Biology majors (BS and BA).

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The nucleic acids lecture

One "gene" codes for one "protein"
Central Dogma (of cell biology) TRANSPARENCY (Fig. 5.28)
DNA (nucleus, virus) ONE GENE
/ transcription
mRNA (nucleus to cytoplasm in eukaryotic cell, although retrovirus, like HIV, makes DNA from a template of RNA using an enzyme called reverse transcriptase).
/ translation
Protein ONE PROTEIN
RNA's: m (messenger), r (ribosomes), t (transfers aa's)
Nucleic acids: nucleotide = sugar, PO4 & base (no essential nucleic acids) TRANSPARENCY (Fig. 5.29)
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
TRANSPARENCY (Fig. 1.5) so fundamental, it is the 5th figure in the whole book
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.
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.
4 x 4 x 4 - there is a 3 letter word (codon) consisting of 4 letters for each amino acid.
It takes a longer macromolecule of DNA to code for a protein than the protein it codes for.
Nucleotides are also usded (1) in the molecules ATP (used for energy and to donate phosphate to reactions), (2) cAMP and cGMP (c=cyclic, intracellular signalling molecules where diester bonds make the molecule cyclic) and (3) and (combined with other groups) coenzymes
DNA is a double helix, with A across from T and C across from G TRANSPARENCY (Fig. 5.30); this pairing is essential for DNA to reproduce itself. In making RNA, the same pairing applies except that U is across from A.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.
TRANSPARENCY (Fig. 5.19) shows that a 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 Blacks of equatorial African origin. Homozygous, it is very bad, but heterozygous, it confers resistance to malaria.


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Control of metabolism lecture

Campbell et al. Chapter 6 is chemistry and physics oriented

Later, chapter 9 (before exam 1) we cover energy metabolism in more detail, then, (after exam 1) the reverse, namely photosynthesis, is covered in chapter 10

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

Energy saved mostly through photosynthesis
released through respiration (breathing vs. cellular)

TRANSPARENCY (Fig. 6.10) ADP plus phosphate <-> ATP involved in storage and release of energy

TRANSPARENCY (Fig. 6.8) shows ATP made of Adenine, ribose and 3 phosphates, energy stored in 3rd phosphate bond

substrate -> product

TRANSPARENCY (Fig. 6.1) is a "cartoon" to show that the body's reactions can be quite complex.
There is a staggering array of enzymes, and a lot of energy is used to power the reactions.

Reminder: enzymes are named with suffix "-ase."

TRANSPARENCY (Fig. 6.19) For instance, the body can make some amino acids (example: isoleucine) from others (example: threonine). You must consume the some (essential ones).
This transparency also reminds us of homeostasis (regulation, Chapter 1) by negative feedback)

TRANSPARENCY (Fig. 6.13) overcome energy of activation - catalysts - enzymes

TRANSPARENCY (Fig. 6.15) is an intuitive figure to show that enzyme (sucrase) binds substrate (sucrose) and eventually is recycled as it releases the products of the reaction (glucose and fructose)

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
(It is highly recommended that you read a 10 page science fiction story by Isaac Asimov called "the final 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
Exerogonic, e.g. cellular respiration C6H12O6 -> 6CO2 +6H2O + energy
the free energy is 686 kcal/mol

ATP to ADP
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.

TRANSPARENCY (Fig. 6.9) It is interesting to note that ATP delivers it's energy by transferring its phosphate to molecules, as shown in this example of the synthesis of glutamine from glutamic acid and ammonia.

TRANSPARENCY (Fig. 9.2) It is easy to mistakenly think that energy use is only by muscles, but this preview from Chapter 9 reminds you that a lot of the body's energy is used in transport and in reactions. This figure also reminds you that 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.

TRANSPARENCY (Fig. 6.16) is interesting because it will preview some stories that will come up later. 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 trypsin (proteolytic enzyme in intestine) is slightly basic.

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The cell lectures

Cell Biology

Campbell et al., Chapter 7, emphasis is on eukaryotic cells

Euglena complex Eukaryotic cell - self sufficient, swim, see, photosynthesize
TRANSPARANCY (Fig. 28.3)
Prokaryote, Eukaryote
Protozoan vs. Metazoan complex, starts as 1 cell.
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)
(2) ALL CELLS HAVE SAME GENES - CELLS DIFFERENT BY WHICH GENES ARE TURNED ON
(3) but this can be fairly permanent, developmental change in gene regulation

Microscopy:
TRANSPARENCY (Fig. 7.1) gives relative sizes and emphasizes the importance of light and electron microscopy. (Also note that Appendix 4 on p. A-7 compares light and electron microscopes.) 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, and, at low magnification, a ribbon of sections can be seen.

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."
TRANSPARENCY (Fig. 7.8) plant cell, note cell wall, plasmodesmata, chloroplasts and large vacuole.
TRANSPARENCY (Fig. 7.7) animal cell. Below, we will go through the following structures one at a time: nucleus, endoplasmic reticulum (rough and smooth), Golgi apparatus, flagellum

Nucleus - double envelope with pores
TRANSPARENCY (Fig. 7.9)

TRANSPARENCY (Fig. 7.11) 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. 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 and barbiturates induce an increase in the "microsomal fraction," smooth ER as seen after grinding and spinning down in a centriguge tube (see TRANSPARENCY [Fig. 7.3])

TRANSPARENCY (Fig. 7.10) 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

TRANSPARENCY (Fig. 7.12) 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.
It is very interesting to consider the different routings for different proteins in the cell.
TRANSPARENCY (Fig. 8.8) 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.

TRANSPARENCY (Fig. 7.17) Mitochondria has a inner and outer membranes, the inner one with shelves called cristae.
The function of the mitochondrion in ATP production is covered more in Chapter 9.
Second semester, we introduce the speculation that mitochondria (and chloroplasts), with their double membranes, are evolved from prokaryotes, engulfed into eukaryotic cells.

TRANSPARENCY (Fig. 7.18) 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.

Lysosomes, need to introduce phagocytosis (phag - eat as in hyperphagic, eating too much, or bacteriophage, a virus that infects bacteria) TRANSPARENCY (Fig. 7.14)
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, like TRANSPARENCY Fig. 7.13 in your text.
As you will see in the membrane lecture and in the genetics coverage, there are "lysosomal storage diseases," Tay Sachs being an example where there is a log jam of turnover with a corresponding buildup.

Microtubules
centrioles and cell division TRANSPARENCY (Fig. 7.22)
flagella and cilia - "9 + 2" arrangement TRANSPARENCY (Fig 7.24)
Paramecia swimming cilia - beat reverses when bump or sperm flagella TRANSPARANCY (Fig. 7.23)
dynein motor molecule for transport TRANSPARANCY (Fig. 7.21)

TRANSPARENCY (Fig. 7.27)Microfilaments
Actin - G (globular) -> F (filamentous)
Myosin - 2 heavy chains and 4 light chains)
also many other functions, streaming and anchoring of cytoplasm

Cell junctions
TRANSPARANCY (Fig. 7.30)
Tight , Gap, Desmosome

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The membrane lecture

MEMBRANES

Campbell and Reece, Chapter 8, plus some references back to earlier chapters

Lipid biochemistry:

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. TRANSPARENCY (Fig. 8.12 shows how animal vs plant cells react to hypertonic, isotonic and hypotonic solutions.

TRANSPARENCY (Fig. 8.1) shows hydrophobic vs hydrophilic aspect of polar phospholipid

TRANSPARENCY (Fig. 5.12) [shown earlier] shows the chemical structure of a polar phospholipid)

TRANSPARENCY (Fig. 7.6) 2 two dense lines in EM with osmium (Robertson)

TRANSPARENCY (Fig. 8.2) bilayer (Davson-Danielli)
vs.
TRANSPARENCY (Fig. 8.6) Fluid mosaic Singer and Nicolson

TRANSPARENCY (Fig. 8.7) Here is a famous membrane protein, rhodopsin, the molecule we see with, and how 7 hydrophobic alpha helices fit into the hydrophobic part of the membrane.

TRANSPARENCY (Fig. 8.3) 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 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.
Amphipathic
(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.

TRANSPARENCY (Fig. 8.4) Double bonds make more fluid, cholesterol makes less fluid.

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.

TRANSPARENCY (Fig. 8.16) Diffusion
(1) Lipid makes a barrier to anything polar
(LATER: steroid hormones can go in)
(2) Channels (for ions, electrical conductances)
The 1991 Nobel Prize in physiology and medicine was awarded to prize was awarded jointly to: ERWIN NEHER and BERT SAKMANN for their discoveries concerning the function of single ion channels in cells; in 1963 the prize was awarded jointly to: SIR JOHN CAREW ECCLES , SIR ALAN LLOYD HODGKIN and SIR ANDREW FIELDING HUXLEY for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cell membrane (in summary, the topic of ion channels is pretty fundamental).
(3) A large fraction of the cell's energy (ATP) goes to pumping ions (active transport)
This creates an ion imbalance, sodium Na+ high outside cell, potassium K+ high inside.
This gives rise to the membrane electrical potential (voltage) important in nerve and muscle cells.

TRANSPARENCY (Fig. 8.15) how pump molecule uses ATP to make sodium and potassium gradients.

run in reverse, makes energy, motor - generator analogy ENERGY - Chap 9

BULK TRANSPORT:
phagocytosis - cell eating
pinocytosis - cell drinking
receptor mediated endocytosis - clathrin coated

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

TRANSPARENCY (Fig. 8.9) 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.
(4) cells are joined by proteins
(5) cells communicate by proteins
(6) cells hook to extracellular proteins by proteins

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The metabolism lecture

Biological Energy

Campbell and Reece Chapter 9 - is written backwards - very advanced details at beginning and fundamental information at end

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.
Marathon - 3000 Cal aerobic. 100 yd dash -anaerobic

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.

TRANSPARENCY (Fig. 9.19) 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).

TRANSPARENCY (Fig. 9.1) photosynthesis to make glucose, cellular respiration to release energy
Reaction [for glucose, C6(H2O)6]: C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O

TRANSPARENCY (Fig. 9.16) Overall, 1 glucose can give up to 38 ATP's, a few from glycolysis and the rest from the mitochondrion

TRANSPARENCY (Fig. 9.4) It is important to introduce 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)

TRANSPARENCY (Fig. 9.8) Glycolysis is a compound word glyco-sugar, lysis-splitting. 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"

TRANSPARENCY (Fig. 9.18) 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.

TRANSPARENCY (Fig. 9.17) fermentation - as in yeast is anaerobic. In cytosol. KINASE
i.e. without oxygen Substrate level phosphorylation makes ATP
Phosphoenolpyryvic acid (PEP) -> pyrivic acid

TRANSPARENCY (Fig. 9.10) Pyruvic acids generate 2 acetic acids, become Acetyl CoA's.
Kreb's cycle = citric acid cycle = TCA (tricarboxylic acid cycle) TRANSPARENCY (Fig. 9.11)
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.

TRANSPARENCY (Fig. 9.5) 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

TRANSPARENCY (Fig. 9.15) 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

TRANSPARENCY (Fig. 9.6) (like Fig 9.16 but with different emphasis)

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The photosynthesis lecture

PHOTOSYNTHESIS

Campbell et al., Chapter 10

Photoautotrophs (chemoautotrophs barely significant)
6 CO2 + 6 H2O --> C6H12O6 + 6 O2
6 CO2 + 12H2O --> C6H12O6 + 6 O2 + 6H2O actually
light for energy, corn photosynthesis up with greater light

Spectrum light comes in waves (also photons)
TRANSPARENCY (Fig. 10.5)
X,Gamma, UV, "visible," IR, radio, radar
Visible: 400 -700 nm (10-9), mm wavelength
short: ionize (damage), middle: excite electrons (reactions), long: vibrate molecules (heat, waste)
Sun cut-off 300 nm because of ozone (O3), peak at visible wavelengths, tail way out to long wavelengths
DNA 260 nm (absorption peak and possible damage)
Protein 280 nm (absorption peak and possible damage)
terrestrial life could only evolve after ozone
evolution of "vision" to use the light that is present:
also "near" UV (UVA, 300-400 nm), visible, IR (snakes).
SHOW UV LAMP
Plants also use visible light

TRANSPARENCY (Fig. 10.7) "the process of science" absorption spectrum
white light split into spectrum and monochromatic wavelength picked through slit
Here is my monochromator with yellow light feeding through the slit

TRANSPARENCY (Fig. 10.8) Pigments
Chlorophyll absorb MOSTLY long wavelengths
Antenna pigments (including carotenoids) absorb shorter wavelengths and transfer energy to chlorophylls
TRANSPARENCY (Fig. 10.6) Leaves are green because they absorb all but green light
Fall colors are because carotenoids remain after chlorophyll is lost
In summary, leaves get most of the ight available

Leaves
Must increase area. Problems with water loss (considering area of leaves for light capture)
Cuticle
Stoma close at night (except in CAM (crassulacian acid metabolism)
plants, desert succulants, store CO2 in organic acids
and close if too hot
light and low CO2 cause stomata to open

Chloroplast TRANSPARANCY (Fig. 10.4)
-- grana stacks
-- stroma (dark reactions) fluid matrix
-- thykaloid space (light reactions)
---------(lamellae) fret connect stacks
intracellular symbiote theory for chloroplasts and mitochondria

Light reactions
TRANSPARENCY (Fig. 10.12)
H2O used
H2O split to electrons, H+, O
electron transport gives bits of energy to molecules transporting electrons
electron donors, acceptors, transport
"Photosystem" = several hundred "antenna" + trap chlorophyll a
electron and light to PSII (680 nm chlorophyll)
ADP + P --> ATP
then electron to PSI 700 nm chlorophyll
2 H+ + NADP+ --> NADPH (reduction) (O2 used or put out)
O2 not put into carbohydrate TRANSPARENCY (Fig. 10.3)
at night, use O2, put out CO2
in grana of chloroplasts


TRANSPARENCY (Fig. 10.17)
ATP + NADPH to dark reactions (light independent) CO2 used
12 NADPH --> 12 NADP (give H to carbohydrate)
18 ATP --> 18 ADP + 18 P (give energy)
CO2 fixation and reduction C and O2 to carbohydrate
(not O of H2O, covered above)
Calvin cycle, 1961 Nobel, 14C,
add CO2 to "rubisco"
(glyceraldehyde 3-phosphate 3 carbon sugar made) -> sugar
C3 (3-phosphoglyceric acid after CO2 added to rubisco
TRANSPARENCY (Fig. 10.18) C4 sugar cane, crab grass (for hot and dry)
(a 4-carbon compound, anatomy of leaf different)
ADP, P, and NADP to light reactions
SUMMARY TRANSPARANCY like Fig. 10.20


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The signal transduction lecture

Signal transduction

Campbell and Reece, Chapter 11

The plasmalemma (cell membrane) makes a barrier. Already, we covered how specific molecules (channels) can make membrane permeable to ions. That allows electrical excitability. Now we cover other widespread ways to get signals across the membrane.

TRANSPARENCY (Fig. 11.3) there are several kinds of ways to get signals around the body, the most famous of which are synapses from one nerve cell to another (or to another kind of cell) and hormones. Endocrine glands (as opposed to exocrine glands that have ducts like those involved in digestive secretions) secrete into the blood stream. Although the figure implies that the hormone goes into the cell, as is the case with steroids (lipids that can cross the hydrophobic membrane) this chapter covers membrane receptors.

TRANSPARENCY (Fig. 11.9) some receptors are channels, including many famous neurotransmitter receptors

The 1991 Nobel Prize in Physiology and Medicine was awarded jointly to ERWIN NEHER and BERT SAKMANN for their discoveries concerning the function of single ion channels in cells.

The 1963 Nobel Prize in Physiology and Medicine was was awarded jointly to: SIR JOHN CAREW ECCLES , SIR ALAN LLOYD HODGKIN and SIR ANDREW FIELDING HUXLEY for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in
the peripheral and central portions of the nerve cell membrane.

TRANSPARENCY (Fig. 11.12) ATP ->(adenylyl cyclase)-> cAMP (cyclic, second messenger) plus pyrophosphate ->(phosphodiesterase)-> AMP

The 1971 Nobel Prize in Physiology and Medicine went to EARL W. JR. SUTHERLAND for his discoveries concerning the mechanisms of the action of hormones (the discovery of second messengers)

TRANSPARENCY (Fig. 11.5) signal molecule -> receptor -> pathway (cascade) ->response

TRANSPARENCY (Fig. 11.6) one of the most famous receptors is a protein with 7 membrane-spanning alpha helices, the G-protein coupled receptor, examples being rhodopsin (the molecule of visual transduction), and various hormone and transmitter receptors.

TRANSPARENCY (Fig. 11.7) G-protein is activated by binding GTP, inactivated as GTPase activity converts GTP to GDP + Phosphate. (note that an enzyme is later in the cascade)

The 1994 Nobel Prize in Physiology and Medicine was awarded jointly to: ALFRED G. GILMAN and MARTIN RODBELL for their discovery of G-proteins and the role of these proteins in signal transduction in cells.

TRANSPARENCY (Fig. 11.13) An example of a G-protein cascade using epinephrine (adrenalin) and utilizing cAMP to activate PKA (a kinase phosphorylates a protein)

TRANSPARENCY (Fig. 11.15) Some G-protein cascades make second messengers (IP3 and DAG) from the membrane lipid PIP2, note that calcium ion becomes a third messenger. The right side of this diagram implies that one type of cell may have sever interacting signal mechanisms. Also note that the "cellular responses) seem to be going on in the cytoplasm in this example.

TRANSPARENCY (Fig. 11.8) Some receptor molecules are themselves enzymes such as this receptor tyrosine kinase (a receptor that is an enzyme that phosphorylates the protein on the tyrosine amino acid).

TRANSPARENCY (Fig. 11.10) Ultimately many signals change the transcription of certain genes, and steroid hormones are a model for this. Notably, they go through the membrane, and the receptor is in the cytoplasm and/or the nucleus.

TRANSPARENCY (Fig. 11.17) Importantly, many signal transduction cascades, especially those involved in development, affect which genes are active via transcription factors. Remember, different cells have the same genes of the whole genome but have different subsets of these genes expressed.

Note that I offer Neuro and Signal courses, relevant to this topic.

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The mitosis lecture

cell division

Campbell and Reece, Chapter 12

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.

TRANSPARANCY (Fig. 13.8) Mitosis - understand concepts of 2n is diploid, prophase, metaphase, anaphase. Chromosome = colored body.

TRANSPARENCY (from AHSturtevant and GWBeadle, An introduction to genetics, Dover, New York, 1939 and 1962) indicates that, if there are homologues, they do not line up (contrast with meiosis, next lecture), early (prophase) DNA doubles, later (metaphase) centromeres divide
TRANSPARENCIES (Figs 12.5 a & b) your book's equivlent of the above

Cell division in eukaryotes to make genetically identical daughter cells
FUNDAMENTAL: multicellular, all cells have same genes (except germ cells)
spindles (centriole, not in plant, aster, spindle)

vs. in prokaryote - round DNA linked to membrane

TRANSPARENCY (Fig. 12.4) cell cycle
interphase is when the cell actually functions - unwound chromatin vs. condensed chromosomes
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 strm cells since, in that milieu, cells digest themselves.
Centromere (on chromosome) = kinetochore (where microtubules attach)
metaphase push apart
metaphase plate
telophase when cells separate followed by cytokinesis.
cell cycle:interphase G1, S, G2, mitosis
G = gap, S = synthesis
arrest in G1 if postmitotic these are the cells which age

Karyotype TRANSPARENCY
observe at metaphase block w drug colchicine
look different, i.e. where centromere is and size
bands
TRANSPARENCY (Fig. 13.3) Your book's karyotype slide

TRANSPARENCY (Fig. 12.14) Very specific molecules control progress through cell cycle.
Many of the signal transduction cascades (previous chapter) control this cell cycle.
When things go wrong with these controls, cancer occurs.

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Meiosis lecture

Meiosis

Campbell and Reece Chapter 13

Sexual reproduction and meiosis give rise to biological variability, which is very fundamental in evolution since new varieties may be more adapted and hence survive (to reproduction) better.

Sexual reproduction probably evolved about 1.5 billion years ago, about when eukaryotic cells evolved, and probably gave an evolutionary advantage.

TRANSPARENCY (Fig. 13.4) human life cycle haploid (n), diploid (2n), gametes, ova, sperm, fertilization, zygote. Note that while meiosis creates haploid gametes in humans, there are many organisms where meiosis creates a gamete-forming organism (alternation of generations, many examples next semester).

TRANSPARENCY (Fig. 13.6) 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.

TRANSPARENCY (from AHSturtevant and GWBeadle, An introduction to genetics, Dover, New York, 1939 and 1962) details two divisions, tetrad, crossing over.
TRANSPARENCY (Fig. 13.7 A and B) Your book's version of the first division.

Awesome variability TRANSPARENCY (Fig. 13.9) for 2 pairs of chromosomes, there are 4 possible outcomes. For 46 chromosomes, there are 2 to 23 power = 8.4 million.
Crossing over increases this beyond measure.(shown for one pair of chromosomes TRANSPARENCY (Fig. 13.10))
story of grains of wheat on chess board

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

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Genetics lecture

Genetics

Campbell and Reece, Chapter 14

1865 Mendel TRANSPARENCY Fig. 14.1 - pea plants - purple vs. white flowers
P=parental, F1 first generation (filial)
TRANSPARENCY (Fig. 14.3) Since cells are diploid, there are two copies (alleles) at each locus, and they can be the same or different.
true-breeding = homozygous
hybrids = heterozygous
purple is dominant, white is recessive
TRANSPARENCY (Fig. 14.2) F2 has 3/1 ratio
units = gene separate Mendel's first law (segregation)

TRANSPARENCY (Fig. 14.4) 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).

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."

Mendel's Second Law TRANSPARENCY (Fig. 14.7) 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.

Here is a picture (Fig. 14.9) TRANSPARENCY showing incomplete dominance - red vs. white snapdragon cross gives pink.

wild type (with respect to a given gene) indicated by + or capital letter
The example above is simple - usually there are many alleles, many genes, and no simple dominant and recessive relationship.

Blood groups TRANSPARENCY (Fig. 14.10)
A=B (co-dominant), O is recessive -- 3 alleles

genotypes...............phenotype.........antigens..........antibodies
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.

Since I do research with Drosophila, and maintain a small genetic stock collection, I have mentored science projects at Gateway Middle School, and there are a number of useful figures. Drosophila are convenient because it takes only about 2 weeks for a new generation. If vials are cleared of adults, then any femal flies emerging in the next 6 hr will be virgin, and specific crosses can be set up at the experimenter's will.

Relevant to this lecture, as well as the next two outlines, there are two faculty members in biology who are especially interested in genetics and who teach our genetics course, Dr. Coulter and Dr. Tsubota.


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Genetic abnormalities 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

GENETIC DISORDERS IN PEOPLE

Campbell and Reece, Chapter 14

Sickle cell anemia
TRANSPARENCY (Fig. 14.15) If homozygous, red blood cells have abnormal shape
hgb clumps in low O2, heterozygotes (trait) largely normal
TRANSPARENCY (Fig. 5.19) [review from earlier chapter]
2 alpha, 2 beta. Beta 146 aa, 6th valine instead of
glutamic acid, GUG instead of GAG
2 SLIDES blacks, heterozygous gives resistance to malaria
TRANSPARENCY (Fig. 23.10) sickle cell anemia correlates with malaria.

Hemophelia (4 SLIDES)
pedigree
Victoria, Nicholas II & Alexandra - Alexis, Rasputin
on X
problem with AIDS for clotting factor

Tay Sachs, inbreeding, incest taboos
east Europe ghettos, 1/30 Am. Jews carry
lipidosis, detect by 6 mo, die by 5
Genetic counseling - ressive 2 carriers = 1/4

Amish Ellis van Creveld syndrome - short arms legs extra fingers. 1720-1780 200 from Switzerland to PA now about 8000 in Lancaster

PKU phenyl keton uria phenylalanine to tyrosine lophenylac
(diet costs $1000/yr)
1/10000
Hard for PKU female to have non-PKU child

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
SLIDE Woody Guthrie died of it, his son Arlo, in the movie Alice's restaurant worries about it
Big family tree in Venezuela studied by Nancy Wexler (Fig. 14.16) -> get gene
one of a group of triplet repeat diseases, in this case, CAG (codes for glutamine
very bad do victims want to know?
does wife have a right to know?
if amniocentesis, may say husband has

MILD

eye color >2 genes 2 completely dominant alleles can have 5 colors if AaBb x AaBb light and dark blue and 3 shades of brown

color blindness (next semester) complicated
x-linked
SLIDE 3 cone types red (yellow) green blue

Albinism (SLIDE Winter, SLIDE siamese cat)
TRANSPARENCY Albino tiger cover of Science

Eugenics - Galton 1880's, immigration restrictions 1920's
counseling
TRANSPARENCY (Fig. 14.17) amniocentesis abortion, but late, ethical & emotional problems
chorionic villus biopsy - earlier detection
artificial insemination
Genetic engineering

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Chromosomes and their abnormalities lecture

The gingham dog and the calico cat
Side by side on the table sat;
...
There was going to be a terrible spat.
...
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)

Chromosomes

Campbell and Reece., Chapter 15

Of course, genes come on chromosomes.
There are autosomes and sex chromosomes.
Linkage:
Independent assortment (Mendel's 2nd law) does not apply to genes (near enough to each other) on the same chromosome.
TRANSPARENCY (Fig. 15.7) map location is based on cross-over probability (determined with a genetic cross)

TRANSPARENCY (Fig. 15.3) Sex linked inheritance in Drosophila, white x red eye cross. Note that there is no corresponding gene on the Y, hence the term hemizygous.

TRANSPARENCY (Fig. 15.8) Different organisms have different chromosomal means of sex determination.

Drosophila 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

TRANSPARENCY (Fig. 15.10) X inactivation in tortoiseshell cat
SLIDE calico cat
XX Barr body, X inactivation Mary Lyon
dosage compensation

Chromosomal Abnormalities
TRANSPARENCY (Fig. 15.11) Nondisjunction e.g. trisomy
lethal, spontaneous abortions

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 (SLIDE) 1/2000 females
spatial sense abnormal
In humans, Y determines male-ness and there are virtually no genes on Y except to differentiate testes in male. CARTOON (Science 1993 vol261 p. 679)

Autosomal aneuploidies are often lethal
Trisomy 21 = Down's syndrome
The TV show "Life goes on" featured Corkey who had 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%

In the reproduction lecture (second semester), you can see that 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).

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The DNA replication lecture

DNA replication -

Campbell and Reece, Chapter 16

History:

It was not until the 1940's that it was proved that DNA was the material of heredity.
TRANSPARENCY (Fig. 16.1) (work of Griffith and Avery) S (smooth) bacteria kill mouse, R (rough) not, DNA from S can transform R to make them deadly.

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." SLIDES (5) 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.

TRANSPARENCY (Fig. 16.2 [a and b]) (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.

TRANSPARENCY (Fig 16.10 [Overview]) The fact that bases complement each other History:
means that 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.

TRANSPARENCY (Fig. 16.13) 5'->3' direction replication fork
enzymes:
DNA helicase and leading strand DNA polymerase
lagging strand - primase makes RNA primer
DNA polymerase adds Okazaki fragment to RNA primer
primer removed and DNA replaced
DNA ligase fixes

TRANSPARENCY (Fig. 16.14) primase makes RNA primer

Mutations - variation and evolution
lots of repair mechanisms
TRANSPARENCY (Fig. 16.17) like excision of thymine dimers reacted from 260 nm light
ionizing radiation, chemicals, mistakes

TRANSPARENCY (Fig. 16.19) There are special problems at the telomeres (ends of the DNA molecules) because the above mechanisms cannot apply to both strands. Hence the need for telomerase to extend the 3' end. Eventually telomeres can become shorter.

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The central dogma lecture

Central Dogma of cell biology

Campbell et al., Chapter 17

TRANSPARENCY (Fig. 17.2)
DNA
transcription
RNA
translation
protein
As you will eventually see, there is more to it than this, like RNA processing, but first:

TRANSPARENCY (Fig. 17.4) 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.)

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)

TRANSPARENCY (Fig. 17.3) 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 sense strand).
There are 3 stop codons
Methionine is the start codon

TRANSPARENCY (Fig. 17.23) 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, as covered in the next figure.

TRANSPARENCY (Fig. 17.24 A and B) Changes in DNA, categories:
(1) change base in degenerate 3rd position - no effect
(2) change a base that matters - "missense" - the protein will have a different amino acid
Sickle cell anemia is severe. The Siamese cat presents an interesting minor (temperature sensitive) example in that it makes melanin in the cool extremities (permnissive temperature) when the enzyme is not denatured by the body's core temperature (restrictive temperature); there would be a conservative amino change.
(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.



This page was last updated 7/22/02

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Transcription and translation lecture

Transcription, translation

part of Campbell and Reece, Chapter 17

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.
Explanations:
(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:

In multicellular eukaryotic organism,
(1) ALL CELLS HAVE SAME GENES
(2) CELLS ARE DIFFERENT BECAUSE OF WHICH GENES ARE TURNED EXPRESSED
(but this can be fairly permanent, development gene regulation)
This will come up again in the Chapter 19 coverage.

TRANSPARENCY (Fig. 17.9) 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)
TRANSPARENCY (Fig. 19.11 [2 chapters ahead])
Answer: Different exons can be spliced together (for instance in different tissues) to make several different proteins from the same gene.

In general, there are 3 RNA's, t (transfer), m (messenger), and r (ribosomal).
TRANSPARENCY (Fig. 17.12) here's how they work in the cytoplasm (endoplasmic reticulum and polysomes):
(1) Ribosome is the machinery, and it is big.
(2) mRNA codes for the protein.
(3) Many different tRNA's read (by base pairing) each codon and carry one amino acide to the growing peptide chain.

TRANSPARENCY (Fig. 17.18) step by step, peptide is elongated, aminoacyl tRNA (tRNA with amino acid hooked to it) brings in amino acid.

TRANSPARENCY (Fig. 17.19) eventually, when one of the 3 stop codons is encountered, the protein is released.

TRANSPARENCY (Fig. 17.20) In polysome, you can see that the ribosome reads along the mRNA just as a tape recorder head passes along the tape.

TRANSPARENCY (Fig. 17.7) This will be the first mention (it will come up again in the next outline, and a lot in the outline after that) of how genes are regulated. Notice that there are places "upstream" of the "gene" (coding sequence), the promoter, and places like the TATA "box" 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.

This page was last updated 7/24/02

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The viruses and bacteria, diseases and immunity lecture

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


Campbell and Reece, Chapter 18

Viruses
(Continues some material from the last lecture)
Second semester (Bio 106) starts with Diversity (the march through the kingdoms). The difficulty (previous lecture) in defining a virus as alive makes it virtually impossible for an introductory textbook to have a good place to cover viruses, so here they are.

TRANSPARENCY (Fig. 18.1) Being small (Protein and DNA) they pass through fine filters, hence an old term, "filterable"
Bacteriophage (phage-eat) protein and DNA
TRANSPARENCY Fig. 18.4 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 (virus coat)
Antibody to antigen made by B lymphocytes (white blood cells)

History:

Vaccines - active immunity (like disease)
memory cells of immune system
Edward Jenner 1796 "encowment" cowpox, smallpox
Smallpox is so completely eliminated that one issue is whether to get rid of lab virus.
Passive immunity - give antibodies

Flu
1918 20 million died worldwide
1957 Asian bad
1968 Hong Kong bad (70,000 died in 6 wks)
change (mutate) also exchange with birds (ducks)

TRANSPARENCY (Fig. 18.2) Structurally (and chemically) not all viruses are as simple as bacteriophage, and sometimes RNA is the hereditary material
TRANSPARENCY (Fig, 18.3) 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

TRANSPARENCY (Fig. 18.7) 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.

That last phenomenon is one of the underlying themes of this chapter which in many ways is a hodge-podge - How do cells get changed genetically?

MONERA bacteria, also blue-green algae (cyanobacteria)
(algae = aquatic plants)

TRANSPARENCY Fig. 7.4
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 (last lecture example of DNA from smooth transforming rough) , transduction (from phage TRANSPARENCY [Fig. 18.13]), conjugation (like mating, TRANSPARENCY [Fig. 18.15])
Plasmids - little circles of DNA - very useful in molecular biology and easy to identify since they carry antibiotic resistance

Fundamental story:

(relates to fundamental topic of gene regulation) lac operon - genes for enzymes for metabolism of lactose, the disaccharide in milk TRANSPARENCY (Fig. 18.21 A & B). 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, enzymwes 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 in Physiology and Medicine was shared by FRANÇOIS JACOB and JACOUES MONOD who established the operon model.

Two other stories:

DNA is very stable, and slow mutational changes over long time periods were once thought to be the only agents of evolutionary change. Over the last few decades, and related to the idea that retroviruses can orchestrate insertions into DNA, was the idea of transposons TRANSPARENCY (Fig. 18.16). In the lab (or in nature) genes (or hunks of DNA) can insert. For instance, in fruit flies, genes can be inserted to make new transgenic Drosophila. If the "jumping gene" inadvertently jumps into the middle of another gene, it will ruin it.

The 1983 Nobel Prize in Physiology and Medicine went to BARBARA MC CLINTOCK for her discovery of mobile genetic elements.

Various spongiform encephalitis syndromes (where the brain degenerates) were once thought to be caused by slow viruses, but now are thought to be caused by protein without any hereditary material. Such disorders include Creutzfeld-Jacob Syndrome in humans, scrapie in sheep and bovine "mad cow disease." TRANSPARENCY (Fig. 18.10) shows how this might happen.

The 1997 Nobel Prize in Physiology and Medicine went to STANLEY B. PRUSINER for his discovery of Prions - a new biological principle of infection

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.

This page was last updated 7/23/02

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The gene regulation lecture

Gene regulation

Campbell and Reece, Chapter 19

TRANSPARENCY (Fig. 19.1) successive magnifications of DNA (note scales 2 to 1400 nm
A chromosome in interphase would be 5 cm in length, in mitosis, it is coiled to 5 micro meters
Histones with high charged positive a.a.'s (lysine, arginine)
Beads on a string, double helix makes 2 wraps arould protein

It is interesting to consider:
(1) Arrangement of DNA may put places near each other that are many nucleotides away.
(2) Anything happening along the DNA (RNA polymerase) must deal with this structure.

TRANSPARENCY (Fig. 19.8) expands on the information after Fig. 17.7. In addition to the "promoter" (let's call it the "proximal promoter") just upstream of the coding sequence (that place controlling which cells express the protein coded for), there are additional areas further upstream (distal and proximal control elements, enhancers, etc) that control whether the protein is expressed.

TRANSPARENCY (Fig. 19.10) There are lots of proteins that control whether or not the gene is active (transcribed into mRNA), and these are called transcription factors. Three types of domains bind DNA. (A domain is a portion of a protein.) These have certain features. (The protein jargon for such features is "motif.")
(1) Helix-turn-helix
(2) zinc finger
(3) leucine zipper

TRANSPARENCY (Fig. 19.14) (This figure will make more sense after reviewing the Chapter 11 material and the associated lecture about signal transduction.) Transcription factors are ultimately controlled by signals that come up to a cell membrane receptor. For instance (right side of the figure), a G-protein coupled receptor can affect transcription through a transduction cascade with kinases (enzymes that phosphorylate proteins). Growth factors (left side of the figure) cause a receptor tyrosine kinase (itself an enzyme) to dimerize and activate (phosphorylate itself on tyrosine residues [amino acids]). ras is an important protein in this cascade. It binds GTP, but it is a smaller GTP-binding protein than the GTP binding protein on the right side of the figure.

The example given pertains to how growth factors and growth inhibiting factors might control cell division. When cell division goes haywire, you have cancer. ras is an acronym for rat sarcoma, and a viral gene is an oncogene of a normal protooncogene. In other words, we do not have genes that cause cancer (oncogenes) but rather genes that, if mutated, cause cancer, but normally these genes encode proteins like ras that subserve important and normal functions. If this pathway activates mitosis and runs out of control, there is too much cell division. p53 is important in that it is a transcription factor controlling the manufacture of proteins that inhibit the cell cycle. A block in this pathway, and the protein is missing and cells divide too much.

TRANSPARENCY (Fig. 19.15) here is an example (colorectal cancer) where ras is activated and p53 is inhibited.

TRANSPARENCY (Fig. 19.6) Although the title of chapter 19 is "the organization and control of eukaryotic genomes," I have concentrated on control (except for fig. 19.1). I finish with this figure because it relates to a really fundamental question I brought up in the virus lecture: How can the genome anticipate all of the antibodies that need to be made for all microbes (considering that they keep changing). Antibody has 4 chains which have constant and variable regions. The variable region is variable because there is something like RNA splicing that takes place in the DNA (!) as the B lymphocyte differentiates.

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The biotech lecture

NICK
I'm a biologist. I'm in the biology department.
...
GEORGE
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.
GEORGE
...
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

Biotech Campbell and Reece, Chapter 20

It's not possible for a professor to lecture from old notes in biolog, especially for topics like this

METHODS BOX
Protein analysis
TRANSPARENCY (Fig. 20.8)
When voltage is applied, proteins in detergent migrate through a gel based on their size.
"PAGE" (polyacrylamide gel electrophoresis) and western blotting (immunoblotting)
Here is a photo of the rig used to pour the gel with wells depicted in the transparency.
Here is a picture of the power supply and the electric hookup to make the proteins migrate.
Here is a photo of the gel with proteins spread out after the proteins have been stained.
This shows the apparatus to transfer proteins from the gel.
The blot, with radioactively labeled antibody to the protein of interest, are put together in a cassette.
Film (unexposed) and blot are sandwiched in the casette until the film is exposed, then it is developed (figure) to make an autoradiogram.
Here is some work from my laboratory to determine if a protein called PLC (phospholipase C) is decreased by vitamin A deprivation; protein molecular weights are shown.

The word "clone" has several meanings. One of the best known to the lay public started when a sheep named Dolly was made from a nucleus from another sheep. But for now:

TRANSPARENCY (Fig. 20.1) 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 disolving enzyme. Also, bacteria can be altered with inserted genes so that they do useful things like clean up oil spils. Crops can also be altered like inserting resistance to pests.

TRANSPARENCY (Fig. 20.2)
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

TRANSPARENCY (Fig. 20.3) If the same restriction enzyme is used to gut a piece of DNA with the gene of interest and the plasmid, they will have complementary sticky ends and will stick together. Though putting antibiotic resistance into bacteria may seem dangerous (and early on, precautions were regulated) this allows you to screen for bacteria that have the new plasmids you have made (since only those bacteria will survive if ther is antibiotic in the medium.

DNA has a tendency to anneal, hybridization, and this is real useful.
TRANSPARANCY (Fig. 20.4) How do you test for the gene you want?
Spread thinly on petri dish so that each clump is one clone.
Pick up some on paper denature and hybridize to radioactive probe. Do autoradiography.
Then go back to dish to recover clone.
Here's a photograph I took of a petri dish with colonies.

TRANSPARENCY (Fig. 20.6) chop up whole genome (genes which are and are not of interest)
This works pretty well except chopping chops some genes in half.
Chop plasmids (with same enzyme) mix, put back in (bacteria),
Select on antibiotic and keep growing, then you have a genomic library.

A genomic DNA library is, good for telling you introns, promotors, also, it's a big mess.
TRANSPARENCY (Fig. 20.5) it is possible to make DNA out of mRNA - cDNA (complementary).
You can make a cDNA library.
Note that the cDNA library would be specific for different cell types, deprnding on which cells are expressed.

It's a lot of trouble to clone a gene.
TRANSPARANCY (Fig. 20.7) DNA polymerase which 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.
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.
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.

TRANSPARANCY (Fig. 20.9) restriction fragment length polymorphisms
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.
TRANSPARENCY (Fig, 20.10) Southern blotting (for DNA) [northern - mRNA, western - protein]
TRANSPARENCY (Fig. 20.15) Sometimes a RFLP marker can be closely linked to a specific disease-causing genetic allele.
TRANSPARENCY (Fig. 20.17) This is the idea behind DNA fingerprinting

Get different cuts by cutting with different nucleases, use different cuts to walk to gene of interest
TRANSPARANCY (Fig. 20.11)

TRANSPARENCY (Fig. 20.16) - if a gene is in a retrovirus, it can be put into a particular somatic tissue and get incorporated into the genome. Note, there are orders of magnitude different ethical issues for the germ line!

TRANSPARENCY (Fig. 20. 14a) Microarray - test for expression of all the genes (supplies are expensive)

This page was last updated 8/2/02

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The development lectures

Development

Campbell and Reece, Chapter 21

Embryology has been fundamental in Biology since the 1800's. Most universities have (or had) courses in (animal) embryology (ours is BL A344) taught by Dr. Schreiweis, Director of Pre-Health Profession, or Dr. Medoff). Traditional animal embryology is essential in comparative biology in the classification of animals, and my lecture outline for Bio 106 (second semester) on this material can be found on the web. Also, there is substantial treatment second semester (after reproduction) on embryology. Many Universities have either replaced or supplemented their traditional embryology courses with "developmental biology" courses, material more akin to this chapter, and our course, offered only occasionally, is BLA460. Development is also predominant in biology research; at SLU, Dr. Coulter's field is developmental genetics.

The 1995 Nobel prize in Physiology and Medicine was awarded jointly to: EDWARD B. LEWIS, CHRISTIANE NÜSSLEIN-VOLHARD and ERIC F. WIESCHAUS for their discoveries concerning the genetic control of early embryonic development. This, of course, added a degree of prestige to this field which was already quite firmly established. Their work on Drosophila is covered in this chapter (p. 397 onward) and in this lecture.

There are advantages of certain organisms, Drosophila (fruit fly), mouse, Caenorhabditis elegans (round worm), zebrafish and Arabidopsis (plant)

PICTURE stages in fly life (egg, 3 larval instars, pupa, adult)
TRANSPARENCY (Fig. 21.11) This diagram summarizes some of the stages in Drosophila development, as well as presenting the additional information:
Nucleus divides to make multinucleated embryo
Then cells vs yolk are laid down in blastula
Then there are 3 larval instars
Then comes complete metamorphosis in the pupa (like the butterfly chrysalis or moth cocoon)
Finally, there is the adult (imago)

TRANSPARENCY (this figure was in earlier editions of your book, but it is not there any more) One reason Drosophila are so interesting is that, like many insects (the holometabolous insects), they undergo a complete metamorphosis. This diagram shows that there are certain tissues in the larva called imaginal disks that are determined to become adult structures but that do not differentiate until the pupa.

TRANSPARENCY (Fig. 21.12) Nurse cells in the "mother" put mRNA for a protein called bicoid in one side of the egg (hence "maternal effect genes"). When that mRNA is translated a little later in the embryo, a gradient of bicoid protein defines anterior to posterior.

As you will learn second semester (classification of animals), one fundamental aspect of the morphology of many phyla is segmentation. Just as segmentation is fundamental in comparative anatomy, the processes leading to segmentation are fundamental in comparative embryology. After the anterior-posterior axis gets laid down several types of genes lay down the segmented pattern of the larva.

TRANSPARENCY (Fig. 21.13) (work for which Nusslein-Volhard and Wieschaus won the Nobel Prize) three types of genes, gap genes, pair-rule genes and segment-polarity genes function in sequence to define segments.

TRANSPARENCY (from another book, but like Fig. 21.14) (now here is what you would call a mutant!) - legs where antenna should be. Such mutants are called homeotic mutants, and EBLewis's Nobel Prize contributions pertain to homeotic mutants.

(back to previous TRANSPARENCY) Homeotic genes act after segmentation genes.

TRANSPARENCY (Fig. 21.15) After homeotic mutants and their respective genes were elaborated in Drosophila, they were found in numerous organisms, and the mouse is shown here. Amazingly, genes are ordered along the chromosomes in the same direction as the anterior to posterior organization in the animal.

Cloning
(Not cloning as in cloning a gene, covered previously, but cloning an organism)
TRANSPARENCY (Fig. 21.6) 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.
TRANSPARENCY (Fig. 21.7) 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 is 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. (Also, the word "clone" has several meanings.) Some think the issue would be simplified by use of the term "nuclear transplantation."

Induction
TRANSPARENCY (Fig. 21.17) Cells are often told what they should become developmentally by signalling molecules and signal transduction cascades originating from cells that are nearby. In this example, the anchor cell is organizing the vulva (egg laying pore) in the nematode.

TRANSPARENCY (Fig. 21.18) Apoptosis -
There has been a lot of research, especially in the last 10 years, on apoptosis (programmed cell death) in which a signalling mechanism mediates the "deliberate" developmental loss of cells.
Two types of cell death:
1. necrosis - from injury, cells burst, there is inflammation
2. programmed cell death = apoptosis
In apoptosis, nuclei condense & fragment, cell is phagocytosed (by macrophages for instance), there is no inflammation, and DNA gets chopped into 50-300 bp lengths, hence "ladder" seen in gel.
examples: lymphocytes eliminated, tadpole tail lost, get rid of webs between digits
TRANSPARENCY (Fig. 21.4) C elegans usually has clearly specified cell development (cell lineage).
In C. elegans, mutants ced-3 and -4 (cell death abnormal) have 131 cells which should die but survive
ced-9, if normal, represses death
protein Ced-3 is a protease,
There is a histological technique called TUNEL (Tdt-mediated deoxyuridine triphosphate nick end labeling, of course) which stains cells which are dying of apoptosis

TRANSPARENCY (Fig. 21.9) Determination
Consider what has been stated repeatedly this semester (with various wordings), that all the cells have the same genes but express a different subset of these genes. That implies that an initially generic cell becomes determined to become a particular type of cell, then eventually differentiates into a particular cell type. What distinguishes the terminally differentiated muscle cell (the example in Fig. 21.9) from, say a visual receptor is that the muscle cell expresses muscle proteins (like actin and myosin) (while the visual receptor expresses proteins of the visual cascade like rhodopsin, the visual pigment). This figure shows that transcription factors (here MyoD) regulate what genes are expressed.

NOTE:
(1) Before cells are determined and differentiated (referred to above as "generic," these cells can become anything, hence they are called "pluripotent."
(2) Even though determined and differentiated cells have all the genes other cells have, they permanently lose their pluripotency.

TRANSPARENCY (Fig. 21.8)
Stem cell research
Because cells lose their pluripotency, researchers have focussed on their discovery that embryonic stem cells are better at differentiating into cells that can repair cell damaged areas such as in the case of spinal cord injury; the issue is very controversial because it may encourage practitioners to create and destroy human embryos for no other purpose than to harvest stem cells. For this reason, for humans, only the use of some 60 cell lines that are already in culture is permitted.
Several colleagues and I are collaborating to cure blindness in a mouse mutant with cells that started as embryonic and were induced to become precursors of nerve cells; identified by green fluorescent protein, here is a cell that has been put into the retina and is beginning to show a neuron-like phenotype.

This page was last updated 7/31/02

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The evolution vs special creation lecture

Natural selection

Campbell and Reece, Chapter 22 (but lecture goes way beyond chapter)

NATURAL SELECTION; ORIGIN OF THE SPECIES
As an extension of the idea of "natural selection", we should consider selection after human influences:
DDT resistance
TRANSPARENCY (Fig. 22.12)
antibiotic resistance-STD and in agriculture
even antiviral drug resistance now that there are antiviral drugs that are used

THE SPECIES CONCEPT

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

One species definition: Reproduce, fertile offspring
Hereford Brahman (same species) SLIDE
Tiger - lion: (different species) Tigon, SLIDE
Horse - donkey (differenty species): Mule, SLIDE (here is my friend's late dad proudly posing with his Missouri mules)
there are many limitations to this theory (especially it only applies to sexually reproducing species)

THINKING ABOUT "SURVIVAL OF THE FITTEST"

Natural selection, selection pressure, survival of the fittest, adaptation for survival, adaptive radiation.
Survival = Reproduce
Ultimately, survival is not of the individual but of genes.

vestigial structures - human appendix, male nipples
comparative anatomy and embryology
Convergent evolution -wing of insects and birds

Natural selection, SURVIVAL (to reproduce)
of THE FITTEST (English peppered moth example) SLIDE
camouflage - cryptic coloration

Warning coloration (opposite strategy of crytic coloration)
SLIDE poisonous snake
Mimicry - viceroy SLIDE
Monarch, milk weed, digitalis 1 trial learning SLIDE

Altruism - parental, survival of genes (birds) etc
SLIDE - poison arrow frog
wolf spiders
Honeybees Queen, workers, drone (SLIDE)

Sexual selection - SLIDE think of survival of fittest
(cheetah and Thomson's gazelle Serengeti)
- Peacock SLIDE

Praying mantis SLIDES

EVOLUTION VS CREATIONISM

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

Darwin (1809 - 1882) survival of the fittest
Important:
(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
TRANSPARENCY (Fig. 22.5)
Galapagos - "tortoises" - Darwin was impressed with DIVERSITY (not so much in England)
"Darwin's finches" - TRANSPARENCY - (an interesting diagram from another book)
also TRANSPARENCY (Fig. 1.17) [so fundamental that the authors moved it to Chapter 1!)
Darwin's finches
(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.)
volcanic, 600 mi from Ecuador, 1 million yrs (young)
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. With reference to "ecology" lectures second semester, there are niches that eventually get filled.

Influences on Darwin:
TRANSPARENCY (Fig. 22.1)
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 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
Play: Jerome Lawrence and Robert E. Lee published their dramatized account of the trial in Inherit the Wind.

Creationism - TRANSPARENCY from an early 1960's paper by George Wald on the Origin of life
TRANSPARENCY Bible - note how short the story of creation is
Fundamentalism,equal time in text book controversies,

PUTTING DIVERGENT EVOLUTION INTO PERSPECTIVE

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)

Coevolution-
Symbiosis (living together)
Parasitism & Mutualism (for mutual benefit)
Bacteria in gut, E.coli, superinfection after
broad-spectrum antibiotic
Nitrogen fixation
Microorganisms in termite gut - cellulose
Lichens-fungi and algae or blue green algae
Oxpecker on giraffe (SLIDE)
Raven on African bufallo (SLIDE)
Cleaner wrass, red snapper, sabre toothed blenny
(SLIDES) mimicry
Estrilded finch & brood parasite long tailed paradise
willow bird (mimicry) (SLIDE)
Pollination, cross pollination - avoid inbreeding
salvia male and female mature differently
carrion flower beetles, flies
Bees, (UV ultraviolet) Hummingbirds, (red)
Bats honey possom
(SLIDES)
Orchid - wasp (coevolution, mimicry)SLIDE
on flower beetles, flies
Bees, (UV ultraviolet) Hummingbirds, (red)
Bats honey possom
(SLIDES)

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The evolution and genetics lecture

Evolution and its genetic basis

Campbell and Reece, Chapter 22 - Descent with modification: A Darwinian view of life
and Chapter 23 - The evolution of populations
and Chapter 24 - The origin of the species
(also, I will jump about several chapters here)

Homology Limb TRANSPARENCY (Fig. 22.14)
Comparative anatomy, embryology, biochemistry, molecular biology
Homology - common descent
forelimbs:
bat (also pterodactyl, bird - fly)
whale (also seal - swim)
cat (also sheep - run)
human (also insectivore - grasp)

Divergent (vs. convergent evolution)
Phylogenetic tree TRANSPARENCY (Fig. 24.24) Horse evolution

TRANSPARENCY (Fig. 24.17) controversy
Gradual vs. sudden, gaps in fossil record, dramatic events

Drawings like this next one confuse the issue since butterflies (as if they were all from today's world) are drawn while the time line suggests that the ones at the bottom of the figure are obviously ancestral.

TRANSPARENCY (Fig. 24.6) speciation in the same area (sympatric) and in different areas (allopatric. There are also other isolating mechanisms.

STORY
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).

Comparative anatomy, embryology, biochemistry, molecular biology
TRANSPARENCY (Table 22.1) - can use "molecular" (biochemical) data to get relationships (here amino acid differences in a part of hemoglobin).

TRANSPARENCY (Fig. 25.8) at the beginning of the semester, I did some hand waving about the relationship between phylogeny and taxonomy, and I do it again with this figure (professors are good at hand waving). While taxonomy and phylogeny are different, they are related in that more inclusive levels of taxonomy are related to a common ancester in phylogeny.

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. 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.

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."

TRANSPARENCY (Fig. 23.3B) The Hardy-Weinberg "theorem"
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)

"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.)

TRANSPARENCY (Fig. 23.4) Genetic drift The frequency of alleles might change by this seemingly accidental mechanism.

TRANSPARENCY (Fig. 23.5) 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.

Think about how the Hardy-Weinberg principle looks like a one-gene two-allele cross. Then remember how much ore 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.

TRANSPARENCY (Fig. 23.12) - 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
Hirsch-Hadler maze to divide Drosophila into normal distribution
Selection for behavior (that was news at the time) - geotaxis or phototaxis.

METHODS

TRANSPARENCY (Fig. 25.13) There's a lot of work these days with DNA sequence, but similarities in certain stretches can only be made after adjusting for big changes (like gaps).

TRANSPARENCY (Fig. 25.UN1)Make a phylogenic tree using DNA

TRANSPARENCY (Fig. 25.17) Cladistics - compare how many differences there are with an outgroup.

SLU's Biology department well represented in evolution: Drs Aspinwall, Barber, Bernhardt, Mayden, and Wood.


Biology majors (BA and BS) in this department must take a course in evolution (BL A301).

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The origin of life lecture

ORIGIN OF LIFE ON EARTH

Campbell and Reece, Chapter 26

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), tha reading that paper had a great impact on me.

Panspermia - seeds of life distributed everywhere
Extraterrestrial origin
Spontaneous generation discredited:
(1) Redi (1600's show maggots on meat need flies to lay eggs)
(2) Pasteur microorganisms
TRANSPARENCY (Fig. 26.9)

Universe 15 - 20 billion years old
Earth 4.6 billion
Earth has water as liquid, many heavy elements

TRANSPARENCY (Fig. 26.4) Haldane = Oparin theory, Miller & Urey experiment to reconstruct synthesis of organic molecules using water, methane, hydrogen and ammonia.

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.
TRANSPARENCY (Fig. 26.11) Probably RNA was the first hereditary material.
polysaccharides
Coacervates (microspheres, protobionts) = droplets, aggregates
TRANSPARENCY (Fig. 26.12)In the laboratory, such protobionts have been made.
Prokaryotes then Eukaryotes
Fossil record rich back to 600 million yrs old
TRANSPARENCY (Fig. 25.2) 14C dating in fossils is important
Earth and Mars 4 1/2 billion yrs. old
first 1/2 billion yrs unsuitable for life
3.2-3.5 billion yrs ago first fossils
Precambrian - Salt marsh - blue-green algae, no fish algal mats rock fossils

Ferment (energy and CO2) (anaerobic = w/o oxygen)

Photosynthesis 6 CO2 + 6 H2O -- C6H12O6 (glucose) + O2

Animals - motility, sensory

Respiration (metabolism, aerobic)

Ozone from O2 (before all life in sea)
(depletion with freon = fluorocarbons)

Invasion of land - vascular, support, mating without water

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History of life lecture

"History of life on Earth"
Campbell and Reece, Chap. 25

GEOLOGICAL TIME
TRANSPARENCY (Table 25.1)
ERA, PERIOD, EPOCH
Numbers (e.g. -570-) are million years ago

(Useful to present in reverse, start at the beginning)

Precambrian 4.6 Earth
3.8 rocks
very first life 3.5 1st fossils
prokaryotes (useful to consider that bacteria cannot eat because of cell wall)
3.3 Photosynthesis -> oxygen begins 2,500

1700 (million years ago = 1.5 billion) eukaryotes

1000 1st multicellular eukaryotes

O2 high to O3

-570-

Paleozoic

Cambrian Cambrian explosion
Ancient all inv.groups
in 10 mill yr.

-510-

Ordovician 1st vertebrates,
plants to land
invertebrates
At the end, there was an mass extinction (including trilobites) probably caused by sea level fluctuations.

-439-

Silurian arthropods to land
1st vascular plants

-409-

Devonian age of many fish
first amphibian,
insects
Late there was a mass extinction possibly caused by an impact and cooling) including placoderms (extinct fish with jaws)

-363-

Carboniferous Amphibians dominate, 1st reptiles
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.)

-290-

TRANSPARENCY (Fig. 25.3) Plate tectonics (actually not widely understood until the 1970's)
TRANSPARENCY (Fig. 25.4) Pangaea, continental drift

Permian Appalacians (large time span, Ordovician to Triassic)
Permian extinction, lose ocean habitat
Pangaea formed

-245-

Mesozoic

Triassic 1st dinosaurs
Pangaea breakup
ferns, gymnosperm forests
End of Triassic, mass extinctions, possibly global warming

-208-

Jurassic Dinosaurs, 1st birds
mammals flower plant
(Hard to imagine mammals would surpass dinosaurs, but adaptations to survival)

-145-

Cretaceous flowering plants
Rockies (started earlier, still lifting)
Mass extinctions - meteorite iridium -2.5 tril.tons 11km
TRANSPARENCY (Fig. 25.6)
TRANSPARENCY (Fig. 25.5) dramatizes mass extinctions and explosions. consider that because of human influences, we may be presently in a period of mass extinctions

- 65 million -

Cenozoic

Teritiary

Paleocene (epoch) adaptive radiation of mammals & birds
...(other epochs)...
Pliocene

-1.8-

Quarternary Pleistocene (epoch) 4 ice ages
to MO, Ohio R.
mammoths die out
first Homo

TRANSPARENCY (Fig. 16.1) review, as a phylogenetic tree

Recent (epoch) - history

Volcanic eruptions:

Francis, Self: The eruption of Krakatau, Nov 83 Sci Am
1883, 20 km3
SLIDE Krakatau

Tambora, Indonesian Island of Sumbawa, April, 1815, 150-180 km3
New England (1816) snow in June and killing frost in August
Stommel,Stommel: The year without summer, SciAm June 79

Nuclear winter:

Ehrlich et al., Long term biological consequences of nuclear war, Sci. 222, 1983, 1293-1300

Turco et al., Nuclear Winter: Global consequences of multiple nuclear explosions, Sci. 222, 1983, 1283-1292

Turco et al., The climatic effects of nuclear winter, Sci. Am. Aug., 1984, 33-43.

When combined with the prompt destruction from the nuclear blast, fires and fallout and the later enhancement of solar ultraviolet radiation due to ozone depletion long term exposure to cold, dark and radioactivity could pose a serious threat to human survivors and to other species.
ruction from the nuclear blast, fires and fallout and the later enhancement of solar ultraviolet radiation due to ozone depletion long term exposure to cold, dark and radioactivity could pose a serious threat to human survivors and to other species.

Extinctions still going on today, lots of public worry about "charismatic megavertebrates" but many other species going.

W.W. Gibbs On the termination of Species, Scientific American, November 2001, 40-49.


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The monera lecture

Monera

Campbell and Reece, Chapter 27
Note that Appendix Three will also be useful for the diversity lectures

This will be the first in the diversity lectures (march through the kingdoms)
prokaryotes (this lecture), eukaryotes (the other kingdoms)
TRANSPARENCY (Fig. 26.15) 5 kingdoms
When I went to school, there were 2 kingdoms, the other 3 evolved since then.
Seriously there were too many problems with trying to call everything either animals or plants.
TRANSPARENCY (Fig. 27.2) Here is an alternative 3 domain model, 2 of which are prokaryotes.

When I was in second grade, the school health teacher, Mrs Parker, read us a book, Mickey the Microbe, and that experience makes me an expert on microbiology.

TRANSPARENCY (Fig. 27.3)
Shape
cocci-blob (Fig. 27.3 A)
diplococcus - two
streptococci-string (e.g. strep throat)
staphylococci-grapes (e.g. staph infections)
bacilli-rod (Fig. 27.3 B)
spirilla and spirochetes-spiral (Fig. 27.3 C)

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

TRANSPARENCY (Fig. 27.2)
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.

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 endotoxins are present 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.

Archaebacteria
methanogens (swamp gas)
Extreme halophiles [they like salt] (Fig. 27.14)- (purple membranes contain bacteriorhodopsin - covered later).
Thermoacidophyles hot sulfur (heat stability important in enzymes used for PCR, refer back to biotech lecture).

EXCEPTION to autotrophs being photosynthetic:
Chemisynthetic use sulfur, ammonia, nitrite, put out sulfates and nitrates for soil.

Eubacteria-largely chemiheterotroph
TRANSPARENCY (Fig. 27.5) cell wall, Gram stain
Gram positive-heavy wall, Negative-stain wash out
Antibiotics like penicillin G for Gram + like strep, gonorrhea, syphilis

TRANSPARENCY - Fig. 27.13 - (1) Bacteria (diverse domain); (2) Archaea (medium domain) [(1) and (2) are this chapter]; and (3) Eukarya (the other 4 kingdoms)

Disease-

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
Tuberculosis TB consumption sanatoriums
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
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.

Advantages-biodegradation,sewage
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

This page was last updated 7/31/02

return to Bio 104 Syllabus

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The semester wrap-up issues lecture

Monera

Campbell and Reece, Chapter 27
Note that Appendix Three will also be useful for the diversity lectures

This will be the first in the diversity lectures (march through the kingdoms)
prokaryotes (this lecture), eukaryotes (the other kingdoms)
TRANSPARENCY (Fig. 26.15) 5 kingdoms
When I went to school, there were 2 kingdoms, the other 3 evolved since then.
Seriously there were too many problems with trying to call everything either animals or plants.
TRANSPARENCY (Fig. 27.2) Here is an alternative 3 domain model, 2 of which are prokaryotes.

When I was in second grade, the school health teacher, Mrs Parker, read us a book, Mickey the Microbe, and that experience makes me an expert on microbiology.

TRANSPARENCY (Fig. 27.3)
Shape
cocci-blob (Fig. 27.3 A)
diplococcus - two
streptococci-string (e.g. strep throat)
staphylococci-grapes (e.g. staph infections)
bacilli-rod (Fig. 27.3 B)
spirilla and spirochetes-spiral (Fig. 27.3 C)

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

TRANSPARENCY (Fig. 27.2)
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.

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 endotoxins are present 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.

Archaebacteria
methanogens (swamp gas)
Extreme halophiles [they like salt] (Fig. 27.14)- (purple membranes contain bacteriorhodopsin - covered later).
Thermoacidophyles hot sulfur (heat stability important in enzymes used for PCR, refer back to biotech lecture).

EXCEPTION to autotrophs being photosynthetic:
Chemisynthetic use sulfur, ammonia, nitrite, put out sulfates and nitrates for soil.

Eubacteria-largely chemiheterotroph
TRANSPARENCY (Fig. 27.5) cell wall, Gram stain
Gram positive-heavy wall, Negative-stain wash out
Antibiotics like penicillin G for Gram + like strep, gonorrhea, syphilis

TRANSPARENCY - Fig. 27.13 - (1) Bacteria (diverse domain); (2) Archaea (medium domain) [(1) and (2) are this chapter]; and (3) Eukarya (the other 4 kingdoms)

Disease-

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
Tuberculosis TB consumption sanatoriums
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
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.

Advantages-biodegradation,sewage
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

This page was last updated 7/31/02

return to Bio 104 Syllabus

return to Stark home page