Biochemistry Study Questions -- Protein Structure and Function (Chapter 3)

1. Classify each of the 20 amino acids according to the side chain on the alpha-carbon
into one of the following groups: aliphatic, aromatic, sulfur containing, aliphatic
hydroxyl, basic, acidic, or amide derivative. The amino acids with aliphatic side chains
are glycine, alanine, valine, leucine, and isoluecine methionine and proline (the last are
hydrophobic amino acids.) Phenylalanine, tyrosine and tryptophan are the amino acids
with aromatic side chains. The amino acids with sulfur are cystine and methionine .
Serine and threonine contain aliphatic hydroxyl side groups. The amino acids with basic
groups are lysine, arginine, and histidine while the amino acids with acidic groups are
aspartate and glutamate.

2. How might a change in the pH alter protein structure and function? Changing the ph
can change the charge associated with the amino acid. In an acidic solution the amine is
protonated and the carboxylic acid part is neutral. In a basic solution, the amine is neutral
while the carboxylic acid part is negatively charged.

3. Draw a peptide bond. What are the unique characteristics of this bond and how do
these characteristics influence the structure of proteins? A peptide bond is a bond
between the amino group of one amino acid and the carboxylic acid of another amino
acid. When this happens there is a loss of a water molecule. In any peptide bond the
amino group of the 1st amino acid is always given the number 1. Peptide bonds are
kinetically stable and can last for many years. A polypeptide chain consists of a
backbone and side chains which can undergo hydrogen bonding.

4. Give two examples of modified amino acids. How might each of these modifications
alter the function of the protein? Adding a phosphate to an amino acid changes the charge
on that amino acid which in turn can change the structure and function of the protein.

5. Compare and contrast alpha-helices and beta-sheets with respect to H-bonding, shape,
and ability to form coiled coils. The alpha-helix is a rod-like coiled structure that is
stabilized by hydrogen bonding with the side chains oriented towards the outside of the
helix. A beta sheet is is a fully extended peptide chain form by two or more B strands
linked together by hydrogen bonds. Beta sheets are not planar with the sheets on the
outside likely curving. Alpha helices are able to form coiled coils while B sheets are not.

6. List the amino acids with side chains that can participate in the formation of H-bonds
and indicate which functional groups can serve as a donor or acceptor. The amino acids
with acidic and basic functional groups are the ones that can undergo hydrogen bonding
with the basic functional groups accepting the proton and the acidic functional groups
donating a proton.

7. Describe what is meant by the terms primary, secondary, and quaternary structure.

Primary- the sequence of amino acids in a peptide chain

 Secondary- alpha-helices and beta sheets

Tertiary- the overall folding of the molecule

Quaternary- interactions between subunits of a molecule

8. What is a zwitterion? Under what conditions is a zwitterion likely to be found? A

zwitterion is a dipolar amino acid the exists in a neutral Ph.

9. Why is histidine often found at the active sites of proteins? It is found in many active
sites because it is able to do a proton transfer which is helpful in many acylation and
deacylation mechanisms.

10. What types of disulfide bonds can be formed? What is the difference in the oxidized
and reduced forms of cysteine? Two cystine molecules come together to form a
disulfide bond or you can form a sulfhydral bond. The oxidized form of cystine contains
the sulfide bond while the reduced form is just the unreacted cysteine.

11. What is the importance of determining the primary structure of a protein? The
primary structure can tell you the amino acid sequence which is useful in determining the
mechanism of action and the three dimensional structure. This can lead to determining
abnormal functioning and figuring out a way to fix it.

12. Describe how a folded protein differs from an unfolded protein. Describe the
transition of a protein from a folded to unfolded state (native to denatured state). Folded
proteins are functional proteins while unfolded proteins are non-functional. Once the
protein begins to become unfolded it becomes easier to get the rest of the protein to
unfold, it is an all or none process.

13. How do proteins which exhibit quaternary structure differ from proteins which do
not? Protein the exhibit quaternary structure have more than one subunit which allows
them to exhibit this structure.

14. Each protein has a beginning and an end. How would one tell the beginning of a
protein from the end? The beginning of the protein is the amino group while the end is
the carboxylic acid group.

15. What effect would treatment of a protein with beta-mercaptoethanol or urea have on
the structure or function of the protein? Treating it with those two things tends to
denature the protein and inactivate it, but it can be re-oxidized in the presence of these
same two compounds. NOT ALL PROTEINS CAN RENATURE.