Review Questions

Proteins

1. Why are proteins so important to living organisms?

Every cell in every organism is built of thousands of different proteins.
There are an estimated 1 billion different proteins in all of life. Proteins
are supporters, enzymes, receptors, communicators, transporters,
movers, and defenders. Proteins are the body and run the body.
Proteins are the machinery of life.

2. What is a protein’s conformation?

Proteins are sophisticated organic compounds. Every protein is folded
into a complicated three-dimensional shape. The 3-D shape of a
protein is called its “conformation”.

3. Why is a protein’s conformation important?

The shape of a protein is essential to its function. For example,
enzymes are proteins that facilitate chemical reactions. Each enzyme
has an active site; a space that binds only binds to a particular
molecule. If the shape of the active site changes, the enzyme ceases
to function. Every protein is adapted for a job. If a protein has a wrong
shape, more than likely, the protein can’t do its job. “Form follows
function”
4. How do we know what a folded protein looks like?
Biochemists use a technique called x-ray diffraction. They first
crystallize a protein. Crystals have a regular repeating internal
structure. By bombarding the crystal with short wavelength x-rays and
examining how the x-rays diffract off the crystals, biochemists can
determine the shape of the protein. So far, the shape of approximately
different 45,000 proteins has been discovered.

5. What is the monomer of proteins?

The monomer of proteins is the amino acid.

6. What is the polymer of proteins?

The polymer of proteins is a long chain of amino acids called a
polypeptide.

7. Why are there so many different kinds of proteins?

The human body is built and run by 100,000 to 150,000 different kinds
of proteins. The diversity of proteins compared to carbohydrates, lipids,
and nucleic acids, is monumental. This diversity comes from the large
pool of different kinds of amino acids. There are 20 different amino
acids found in all living organisms. Recently two more were discovered
but they are limited to a few obscure microbes.

If you have a protein that is made of just one amino acid, there are 20
different proteins that can result. If you have a protein made from just
two amino acids, there can be 400 different proteins (202 or 20 x 20 =
400). A protein built of just three amino acids can result in 8000
different proteins (203 or 20 x 20 x 20 = 8000). A four amino acid chain
can result in 160,000 different proteins (204 or 20 x 20 x 20 x 20 =
160,000). As you can see, just a small chain of amino acids can
produce huge numbers of different combinations. The typical protein
has a chain of 500 amino acids; that would make 20500 different
proteins. No wonder proteins are the most diverse and sophisticated
molecules!
8. Describe the structure of an amino acid.

9. What makes one kind of amino acid different from another?

The big difference between amino acids is the R group. R is a
chemist’s shorthand for remainder or variable. Each amino acid is
exactly the same except for the R group. That little side chain
represented by the will be different depending on the kind of amino
acid. For example, glycine has a hydrogen atom as its R group,
whereas alanine has a methyl group (CH3).
10. Why does stale urine smell like ammonia?
When we eat a protein, most of the amino acids are used as building
blocks for making other proteins. However, sometimes an amino acid
is used as fuel. Before the chemical energy of amino acid can be
harvested, the amino group (NH2) on the molecule has to be removed
(deamination). The free amino group quickly bonds to a free hydrogen
and forms NH3; ammonia. Ammonia is toxic to cells, so it is combined
with carbon dioxide to make urea. Urea is also toxic but not as bad as
pure ammonia. The body rids itself of the urea through the urine. Urine
that has been exposed to the air and bacteria will start to smell like
ammonia. Bacteria break down the urea and ammonia is released. Our
urinary system really exists for the dealing with the toxic by-product of
protein metabolism.

11. How are amino acids bonded together to form a polypeptide?

Dehydration synthesis joins amino acids together. The amino acids in
a polypeptide are covalently bonded to each other. The covalent bond
is called a “peptide bond”.

12. Why and how does a protein fold?

Protein folding can best be understood by exploring four levels of
increasing structural complexity in the conformation of the protein. The
simplest level is called the primary structure. Although a protein looks
like a tangled mass, it really is just a single polypeptide. The primary is
simply the linear sequence of amino acids in a polypeptide. Even
though this is the least complicated level, it really is the most important.
The sequence of amino acids determines the final conformation of the
protein. “The beginning determines the end”
Soon after a polypeptide is made, it will spontaneously start to fold.
Among the first folds is the secondary structure. There are two types of
folding in the secondary structure; the alpha helix and the pleated
sheet. In the 1930’s, a chemist named Linus Pauling discovered the
alpha helix. The alpha helix is a delicate coil of polypeptide.

How does the alpha helix form? The region around the peptide bond is
polar. There is a slight positive charge near the hydrogen (bonded to
nitrogen) and a slight negative charge near the oxygen (bonded to
carbon). Weak hydrogen bonds form between adjacent amino acids. In
fact, each amino acid will form a hydrogen bond with another one four
amino acids down the chain. All this hydrogen bonding makes a coil.

The pleated sheet is also formed through hydrogen bonding because

of the polarity near the peptide bonds. But instead of making a coil, it
will bond to an adjacent polypeptide or to itself, if the polypeptide is
folded back. The structure looks like a fan, with alternating ridges and
valleys.
The next level is called the tertiary level. Tertiary means “third”. The
polypeptide continues to bond to itself but this time the individual
amino acids join to each other by bonds between their R groups.
Remember, the 20 kinds of amino acids differ because of their R
groups. These R groups also have different chemical bonding. There
are R groups that form covalent bonds, some that form ionic bonds,
and still others that form hydrogen bonds. For example, cysteine is an
amino acid that has a sulfadryl group (-SH) for its R group. If a cysteine
gets in close proximity with another cysteine down the chain, they will
form a covalent bond between the two sulfurs (called a disulfide
bridge). The tertiary structure is an aggregation alpha helices and
pleated sheets in twists and tangles. For a protein that is composed of
a single polypeptide, this is the most complicated level of organization.
 The final level of protein organization is called the quaternary structure.
Quaternary means “fourth”. This level only occurs when there is more
than one polypeptide in a protein. Composed of four polypeptides,
hemoglobin is a good example. The individual polypeptides in the
quaternary structures are joined to each other by bonds between the
R-groups, just like the tertiary level.

13. Which level of protein organization is the most important in

determining the final conformation?

The primary structure is the most important. If an amino acid is missing

or out of sequence, it may cause the succeeding levels to fold
differently. Most genetic diseases are caused by malformed proteins.
Take sickle cell anemia for instance. Sickle cell is caused by
abnormally-shaped hemoglobin. The only difference between normal
and sickle cell hemoglobin is one different amino acid. In normal
hemoglobin, the amino acid in position #6 is glutamic acid. In sickle
cell, it is valine. That one small difference changes the conformation to
such an extent that it causes a nasty genetic disease affecting millions.