"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

CHEMISTRY:

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

Today's musical selection
Tom Lehrer, the elements

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

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

INORGANIC CHEMISTRY

From the Los Alamos National Labs (periodic table)

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

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

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

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

Box E2-1
...and
PET scan (positron emission tomography)

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

Figure 2-6a
(a) covalent bonding

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

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

Water

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

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

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


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

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


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

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

Oxygen - an integrative story

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

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

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

Questions used in 2007 & 2008 relating to this outline

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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This page was last revised 6/9/09