C483 Exam I 2014
______________________________
Name
Instructions: Please read all questions carefully. Use structures if they are called for.
Do not use acronyms unless specifically directed. If you need more space, use the
back of your paper. No calculators or electronic devices. Answers should be short
and to the point. If you have extra material that is incorrect, points will be deducted.
This is a one hour exam, but you have two hours to complete it. Good luck.
1) 6 pts Consider a protein complex with a Ka of 1010 M-1. If you make the
assumption that this complex forms at the rate of diffusion of large molecules
(roughly 107M-1S-1) what is the dissociation rate? It is often the case that complex
formation is actually quite a bit slower than the diffusion rate. If this is so, what
would it mean for the lifetime of the complex?
2) 6pts What are the major differences between a 310 helix and an alpha helix?
Why is glycine likely found so often in a 310 helix?
3) 6 pts Draw a tetrapeptide of the following structure: N,W, E, Q (ionization state
should reflect a pH of 7.0)
4) 6 pts What are the two main forces that stabilize an alpha helix? Describe them.
5) 5 pts How many classes of enzymes are there?
Name three:
_______________________
_________________________
________________________
6) 8 pts Draw a notional plot of velocity vs. substrate concentration for an enzyme
reaction. (Make sure to label your axes.) Show how you would then obtain the
relevant kinetic constants that describe enzyme activity. Show how you could
linearize this plot depict the resulting plot with relevant kinetic constants.
7) 6 pts Name the type of reversible inhibition that best fits the descriptions below:
Appears to decrease Km and Vmax proportionally ______________________________
Appears to decrease Vmax without changing Km _______________________________
Appears to change Km without changing Vmax _________________________________
8) (2 pts each, 10 pts total) Answer the following short answer questions
a) The 3-D structure of proteins may be determined by ___________________ and
__________________
b) Oxygen binding to hemoglobin is characterized by positive ______________and
________________ regulation.
c) In proteins that contain quaternary structure, subunits are usually held together
by _________________ interactions.
d) The sequence of a polypeptide chain may be determined by the ____________________
procedure, in which N-terminal residues are successively cleaved.
e) The major noncovalent interactions that determine the structures of
biomolecules are ___________________ and ____________________
9. (2 pts each, 10 pts total) True or false
______Collagen is formed from three right handed helices that form a left handed
supercoil.
________The variable domains of antibodies are at the end of the heavy and light chain
and interact with the antigen.
________ After a protein is denatured with denaturing agents, it cannot be renatured.
________ The tertiary structure of a protein may be formed from the folding of
independent subunits to form a homodimer.
_________Beta sandwiches are held together by hydrophobic forces.
10. (2pts each, 20 pts total) Fill in the blank
a) A solution that contains equal, or nearly equal quantities of a weak acid and its
conjugate base is called a/an __________________________
b) Within the hydrophobic interior of a protein, the attraction between two
oppositely charged functional groups is often called a ______________________
c) The pH at which a given amino acid carries a net zero charge is referred to as
____________________________
d) The covalent linkage formed by the oxidation of the side chains of two cysteine
residues in a peptide or protein is called a/an__________________________
e) The Bohr effect explains why hemoglobin has a ________________ affinity for oxygen
when levels of carbon dioxide and H+ are elevated.
f) The predominant type of secondary structure seen in myoglobin is _________________
g) An organic molecule in erythrocytes that lowers the affinity of hemoglobin for
oxygen is _________________________
h/I) Scurvy is a condition arising from the inability to make functional collagen.
This is caused by the absence of ________________________ which makes the formation of
____________________ impossible.
11. 7 pts (do not do the full calculation, just show how you would do it) Calculate
the percentage of aspirin that is protonated at pH 2.0. (pKa of aspirin is 3.5)
12. 10 pts. Draw a titration curve for histidine. The pKa values are 1.8, 6.0 and 9.3.
Draw the structure of histidine at each stage of its ionization. Identify the points at
which the average net charge is +2, +0.5, and -1.
Extra credit 10 pts. You must get this question completely right to get credit. No
partial credit.
Draw the structures and give the single letter code for 12 amino acids found in
proteins. You may not use amino acids referred to in questions 2, 3 and 12. (form
should be predominant one at pH 7)
Points
Possible
earned
1)6
________
2)6
________
3)6
________
4)6
________
5)5
________
6)8
________
7)6
________
8)10
________
9)10
________
10)20
________
11)7
________
12)10
________
EC10
________
Total
------------------