Biochemistry Test 2
Name: _____________________ October 19, 2007
Possible: 108 pts
1. (18 pts) Sketch the polypeptide, His—Asp—Gln. Show the atoms in their usual ionization states at physiological pH, which is about 7.4.
2. (4 pts) Atoms cannot rotate freely about all of the bonds in the polypeptide backbone. On your figure above, indicate for the central amino acid which bond(s) in the backbone can rotate.
The two bonds are shown in red, above.
3. (4 pts) Here is a figure representing a protein. Give the terms used to describe the indicated regions of secondary structure.
4. (3 pts) Complete this phrase:
All of the information required for a protein to fold is contained in its…
Amino acid sequence
This Page: 29 pts
5. (2 pts) Below is a comparison of the amino acid sequence in a portion of myoglobin, α-hemoglobin, and ß-hemoglobin.
The shapes of the three proteins are, in fact,
a)
Nearly identical.
b) Almost completely different.
c) So different as to be uncomparable.
6. (4 pts) Give one example of how the amino acid composition of the protein collagen contributes to its three-dimensional structure.
Collagen contains Lys, which forms cross-links to hold collagen fibers together.
It contains Gly, which, due to its small side chains, allows the fibers to form a triple-helix.
It contains Pro, and hydroxyproline, which give the individual fibers a left-handed helix.
7. Fetal hemoglobin has a higher oxygen affinity than adult hemoglobin.
a) (3 pts) Why is this advantageous for the developing fetus?
It allows oxygen to be transferred from the mother to the fetus.
b) (1 pt) In the graph below, which curve represents fetal hemoglobin? (Y represents the percent of the hemoglobin bound to oxygen.)
Curve A
represents fetal hemoglobin
This Page: 10 pts
c) (8 pts) One of the fetal hemoglobin chains differs slightly from the chain in adult hemoglobin. The fetal chain has fewer Lys and His residues, giving it fewer positive charges in its central cavity, compared to adult hemoglobin. Explain why fetal hemoglobin has a higher oxygen affinity than does adult hemoglobin. (The answer has to do with 2,3-bisphosphoglycerate, BPG, which has a charge of -5 under physiological conditions.)
BPG binds to the central cavity of hemoglobin, lowering its affinity for oxygen. In fetal hemoglobin, there are fewer positive charges in this central cavity, so BPG is not attracted as strongly, so the oxygen affinity is not reduced as much as it is in adult hemoglobin.
8. (15 pts) Chymotrypsin, trypsin, and elastase are members of a family of enzymes referred to as serine proteases. The enzyme papain (found in papaya) is also a protease, but is a member of a family of enzymes referred to as cysteine proteases. The amino acids in papain’s active site that are critical for peptide bond hydrolysis are a protonated histidine and a deprotonated cysteine. Using what you know about chymotrypsin’s mechanism, draw a reaction mechanism for the hydrolysis of a peptide bond by papain.
The mechanism is basically the same as what was done on the quiz, except that serine is replaced by cysteine.
This Page: 23 pts
9. (5 pts) The amino acid Asp 189 lies at the base of the substrate specificity pocket in the enzyme trypsin. How is this related to trypsin’s substrate specificity?
Asp has a negatively charged side chain, which attracts positively charged groups. So, trypsin would be expected to be specific for residues with positively charged side chains, such as Lys.
10. (5 pts) Below are the structures of serine proteases from different sources. How do these illustrate convergent evolution?
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Structure of subtillisin, from
bacteria. Its structure and amino acid
sequence are quite different from the serine proteases in mammals. |
Structures of chymotrypsin, trypsin, and elastase,
from mammals |
Convergent evolution is when different pathways lead to the same result. Bacteria and mammals appear to have independently evolved proteases that do nearly the same things. Evidence that they evolved independently is that the structures and sequences are different.
11. (6 pts) You are a physician and you have a patient who is suffering from premature pancreatic zymogen activation, which means that the pancreatic enzymes are being activated in the pancreas (rather than in the small intestine) and pancreatic tissue is being damaged as a result. Which would be most effective: a chymotrypsin inhibitor, or a trypsin inhibitor? Explain your answer.
Chymotrypsinogen is activated by trypsin. Also, trypsin will activate trypsinogen. Therefore, a trypsin inhibitor would prevent both trypsinogen and chymotrypsinogen from being activated.
This Page: 16 pts
12. (6 pts) From the plot below, estimate values of KM and Vmax.
The Vmax is approximately 30 µM/s and the KM is approximately 5 µM.
13. Decamethonium, a muscle relaxant, is an inhibitor of acetycholinesterase. The normal substrate for acetycholinesterase is acetylcholine. Structures of both molecules are shown.
a) (3 pts) What kind of inhibitor is decamethonium? Competitive
b) (2 pts) Can inhibition by decamethonium be overcome in vitro by adding large amounts of substrate? Yes
c) (2 pts) Does this inhibitor bind reversibly or irreversibly to the enzyme? Reversibly
This Page: 13 pts
14. Cytidine deaminase catalyzes the following reaction:
Both of the compounds below inhibit the reaction.
1.2 ´ 10-12 M 3
´ 10-5 M
The compounds have KI values of 3 ´ 10-5 M and 1.2 ´ 10-12 M.
a) (2 pts) Assign the appropriate KI value to each inhibitor.
b) (2 pts) Which compound is the more effective inhibitor? A
c) (3 pts) Give a structural basis for your answer to b).
Compound A resembles the transition state more closely than does compound B.
15. (6 pts) A reaction is carried out in the presence and absence of an inhibitor, and initial velocities are plotted versus substrate concentration. The results are shown in the graph. What type of inhibitor is this? Explain.
This is a mixed inhibitor. Both Vmax and KM are changed.
This Page: 13 pts
16. Aspartate transcarbamoylase (ATCase) catalyzes the formation on N-carbamoyl aspartate from carbamoyl phosphate and aspartate, a step in the multienzyme process that synthesizes cytidine triphosphate, CTP.
Kinetic studies of ATCase activity as a function of aspartate concentration yield the results below.
a) (1 pt) Is ATCase an allosteric enzyme? Yes
b) (3 pts) How do you know? The plot has a “sigmoidal” shape.
This Page: 4 pts