Chemistry 

- a quick review and a study guide

A.) Element- (1) a substance that can't be decomposed into other substances. (2)
a substance where all of the atoms have the same number of protons (atomic
number) although the number of neutrons may differ (the atomic weights may
differ). The different atomic weight variants of an element are called
the isotopes of that element. (for example, c12, c13, and c14 are all isotopes of
carbon, all have 6 protons but each has a different number of neutrons).

Protons and neutrons are found in the nucleus of the atom while

the electrons are located in various orbitals or shells which surround
the nucleus. These orbitals have specific numbers of electrons that they can
accommodate. (how do the shells differ in their electron capacity?)

If an atom is neutral then it has an equal number of protons and electrons.

Neutral atoms are especially stable if their orbitals are filled to capacity. This is
the case with noble gases.

However, the atoms of most elements have incompletely filled orbitals and

these atoms form bonds to achieve stability. (see pg. 25, table 2.2).

Ions and ionic bonds

Electrons are lost or gained in the unfilled shell. The atom becomes charged --

either positive (cation) or negative (anion). (see pg. 27, fig. 2.2).
Charged atoms (or molecules) of opposite charge are attracted to each other and
can form reversible, ionic bonds with each other. Ionic compounds dissolved in
water conduct electricity very well. Dissolved ions are therefore
called electrolytes.

Covalent bonds

In covalent bonds, pairs of electrons are shared between atoms in order to fill

their outer shells. (see pg. 28, figure 2.3).

Hydrogen bonds

Covalently bonded atoms may be electrically neutral however the electrons may

not be evenly distributed across the molecule. Such molecules will have
oppositely charged areas that can be attracted to other charged molecules. A
good example of this occurs between water molecules where such electrostatic
bonds are called hydrogen bonds. (see page 29, figure 2.4).

Hydrophobic bonds

This non-covalent bond describes the interaction of non-polar, hydrophobic

molecules when they are put into water. Hydrophobic bonds are very important
in the formation of membranes and in enzyme-substrate binding.

The molecules of life

Water

Hydrogen bonds between water molecules contribute to water's high boiling

point. Water molecules actually repel each other at freezing; this means
that frozen water is less dense than liquid water. Also, the hydrogen bonds can
absorb and hold on to energy; this makes water a good temperature buffer (ie.:
water changes temperature slowly).

The polar nature of water molecules contributes to water's excellent solvent

properties. (see page 34, figure 2.6).

Water can ionize to form hydrogen (+) ions and hydroxyl (-) ions. The

concentration of these ions determines the ph of water or other solutions. (see
pgs. 35-36; figs. 2.7 and 2.8).

Organic compounds

Organic molecules can be acidic or basic. They may have other charged groups
attached. They can be polar or non-polar. They can
be hydrophilic or hydrophobic. (page 37 gives a good overview of the chemistry
of carbon. Moreover, table 2.3 summarizes the most important functional groups
found on organic molecules.)

Carbohydrates - sugars and their polymers.

Monosaccharides - the simple sugars. We will be most concerned with

the pentose and the hexose sugars.
Disaccharides - 2 covalently bonded monosaccharides. (see page 38).

Polysaccharides - polymers of monosaccharides and disaccharides. Some,

like chitin and cellulose, are structural polysaccharides. Others,
like starch and glycogen, are food storage molecules. Incidentally, all four of the
polysaccharide examples are polymers of glucose. (see lewis pg 46 for a good
discussion of how these four polysaccharides are constructed.)

Lipids - are nonpolar molecules that are insoluble in water. (see pages 39-41).

Lipids are composed of glycerol and fatty acids: depending on how many fatty
acids are attached to the glycerol, these may be monoglycerides, diglycerides or
triglycerides. Depending on how many hydrogens are attached to the fatty acids
(or how many double bonds are present), these may be saturated or
unsaturated. If liquid, these lipids are called oils; if solid, these lipids are called
fats or waxes. Phospholipids are a special class of diglyceride that has a
phosphate group attached to it. Phospholipids are an important component of
membranes.

Steroids represent another class of lipids that are structurally very different from
the glycerides described above. (see page 41).

Proteins - these large molecules are polymers of amino acids. Proteins contain a

significant amount of nitrogen in addition to the carbon, hydrogen, and oxygen
they contain. Proteins serve many essential purposes in the cell. They can
be structural proteins such as collagen and keratin. Most other proteins such
as enzymes, antibodies, cell surface receptors, and the various carrier
molecules are actively involved in many of the biochemical reactions of the cell or
the multicellular organism. Each of these proteins has the ability to specifically
recognize and bind to its unique substrate.

Proteins or polypeptides are polymers of amino acids. (see page 42, fig. 2.15 for a
description of amino acid. See page 43, table 2.4 for a listing of the twenty
common amino acids -- note the r-groups). Each different amino acid has a
unique r-group which gives each amino acid unique chemistry. The amino acids
are covalently linked to each other via peptide bonds. (see page 44, fig. 2.17 for a
description of peptide bond formation). Once polymerized, the r-groups of the
various amino acids interact with each other and with the solution environment
the protein finds itself in. This then causes the polypeptide to assume a shape or
conformation. Therefore the amino acid sequence determines the conformation
of the protein and this, in turn, determines the function of the protein. (see
page 45, fig. 2.18 for a description of the conformation levels of proteins).

It is important to remember that protein shape is sensitive to ph, temperature

and dissolved salts. By changing these variables the activity or function of the
protein will be altered. If the protein's shape is altered so severely that the
protein no longer functions, the protein is said to be denatured.

Nucleic acids - both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are

polymers of nucleotides. (see page 47, figs. 2.20 and 2.21 for a description of
nucleotides).

Nucleotides have three essential parts: (1) a sugar -- either ribose or

deoxyribose; (2) a base -- either a purine such as a guanine (g) or adenine (a) or
a pyrimidine such as thymine (t), cytosine (c) or uracil (u); and (3) a phosphate
group.

Nucleotides can be covalently linked into a single strand of nucleic acid by forming
covalent bonds between the phosphate groups and the 3' oh group of the sugars
of a series of nucleotides. A single-stranded piece of nucleic acid can base-
pair or hybridize with a complementary piece of nucleic acid by forming non-
covalent hydrogen bonds between complementary bases. The biochemically
complementary bases are a-t, a-u , and g-c. Double-stranded nucleic acids can be
melted into single strands in the laboratory by raising the temperature and they
will hybridize again when the temperature is lowered. Within the cell, melting and
reannealing is done by enzymes.

Note that ATP is a nucleotide as is camp.