(15) 1a. Draw the structure of thefollowing peptide at pH 7 (structures of aa side- chains are on sale for 1 pt each!):
(10) b. Draw a titration curve
for a peptide having the same amino acid residues as (a) above
from pH 2-12 (assume that it is soluble) indicating approximate
pKavalues. Label axis, buffer regions, and approximate
(10) 2. Discuss the concept of
domains in protein structure. Include in your discussion the relation
between genes and domains, the potential consequences for adaptive
evolution, and the effects/consequences of domain structure on
protein folding and function.
(8) 3. Circle the best answerfor each of the following:
a. Glycolytic enzymes are synthesized:in
the cytosol, on the endoplasmic reticulum, on the rough endoplasmic
reticulum, in the golgi complex.
b. Of the following amino acids,those
which are most likely to be found in a proteins interior are:
(ala, ser, & cys), (gly, leu, & pro), (tyr, glu,&
ala), (his, arg, & gly).
c. The most important force or
bond in causing a protein to fold up into a compact form is: hydrogen
bonding, disulfide bonding, hydrophobic forces, van der Waals
d. The most important/characteristic
"bond" type for maintaining secondary structures in
protein assemblies is: hydrophobic, van der Waals, hydrogen, covalent,
(9) 4. Briefly discuss the roles
of disulfide bonds (if any) in each of the following: protein
folding, protein structure, and protein function.
(14) 5. On the axis below draw typical kinetic curves for an allosteric enzyme such as we discussed in class under the following conditions: a) with no effectors present, b) in the presence of a positive effector, and c) in the presence of a negative effector. Label them!
d. Which of these curves shows
the least cooperatively? Explain briefly why this should be so.
e. Challenge question:
What would the effect of a competitive inhibitor on this enzyme
if it were present at less than half saturating concentration?
As your answer you can draw the curve for this situation on the
plot above - label it!
(12) 6. List and describe as briefly
as possible the six levels of protein structure we have discussed
(8) 7. A typical plot for enzyme activity as a function of temperature is shown below. Describe/explain the phenomena underlying this curve.
(12) 8. Consider the process of protein folding and Briefly answer the following questions:
a. Why is it often said that proteins
do not achieve the folded state with the lowest global free energy?
b. Why are alpha-helices so commonin
c. What advantage is there to
breaking a large protein up into domains?
d. How do chaperones aid proteins in achieving their native folded structures?
Last modified 17 August 2007