Download C483 Exam I 2014 Answer Key

C483 Exam I 2014 Answer Key
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? (from discussion problem set 4, no 2
and 3)
Ka = kon/koff = 1010M-1 = 107M-1S-1/X koff = 10-3 S-1
If the on rate is slowed, the off rate must slow proportionally to maintain the same
Ka. So the off rate will go down (koff will get smaller) and the lifetime of the complex
increases.
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? Many differences. Most relevant:
310 helix: 3 residues per turn, 10 atoms per H-bond loop.
Alpha helix: 3.6 residues per turn, 13 atoms per H-bond loop.
Glycine has no R group, so it has the conformational flexibility to adopt the phi, psi
angles required in a 310 helix, which is a tighter helical wind than an alpha helix and
therefore demands different phi, psi angles than an alpha helix. (ps- for those who
said glycine has “rotational freedom”, this statement is incorrect. It has the same
amide bond restrictions as other amino acids. It is conformational flexibility about
phi and psi that is important.
3) 6 pts Draw a tetrapeptide of the following structure: N,W, E, Q (ionization state
should reflect a pH of 7.0) (problem 6 in discussion problem set 2)
4) 6 pts What are the two main forces that stabilize an alpha helix? Describe them.
Problem 1 in discussion problem set 3:
H-bonding between main chain carbonyl oxygen and main chain NH bond in a 13
atom loop. Nucleophilic N-Pi star interaction between lone pair on carbonyl oxygen
and the pi star orbital of the carbonyl on an adjacent residue. (a simple drawing
would have been good here).
Problems 5-9 were drawn largely from chapter summaries
5) 5 pts How many classes of enzymes are there? 6
Name three: oxidoreductase, ligase, lyase, isomerase, transferase, hydrolase
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.
Ch 5 fig 5.5. Note Km on X axis and Vmax/2 on Y axis
Ch 5 fig 5.6
No equations necessary
7) 6 pts Name the type of reversible inhibition that best fits the descriptions below:
(ch 5 study guide problems 8,9)
Appears to decrease Km and Vmax proportionally uncompetitive inhib
Appears to decrease Vmax without changing Km noncompetitive inhib
Appears to change Km without changing Vmax compet. Inhib.
8) (2 pts each, 10 pts total) Answer the following short answer questions
a) The 3-D structure of proteins may be determined by NMR and
x-ray diffraction (crystallography)
b) Oxygen binding to hemoglobin is characterized by positive cooperativity and
allosteric regulation.
c) In proteins that contain quaternary structure, subunits are usually held together
noncovalent interactions.
d) The sequence of a polypeptide chain may be determined by the Edman
degradation procedure, in which N-terminal residues are successively cleaved.
e) The major noncovalent interactions that determine the structures of
biomolecules are electrostatic and hydrophobic
9. (2 pts each, 10 pts total) True or false
___F___Collagen is formed from three right handed helices that form a left handed
supercoil.
___T____The variable domains of antibodies are at the end of the heavy and light
chain and interact with the antigen.
___F___ After a protein is denatured with denaturing agents, it cannot be renatured.
___F____ The tertiary structure of a protein may be formed from the folding of
independent subunits to form a homodimer.
___T____Beta sandwiches are held together by hydrophobic forces.
10. (2pts each, 20 pts total) Fill in the blank (these are all from the student guide
questions)
a) A solution that contains equal, or nearly equal quantities of a weak acid and its
conjugate base is called a/an buffer
b) Within the hydrophobic interior of a protein, the attraction between two
oppositely charged functional groups is often called a salt bridge
c) The pH at which a given amino acid carries a net zero charge is referred to as
isoelectric point
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 disulfide bridge/bond
e) The Bohr effect explains why hemoglobin has a reduced affinity for oxygen when
levels of carbon dioxide and H+ are elevated.
f) The predominant type of secondary structure seen in myoglobin is alpha helix
(cal)
g) An organic molecule in erythrocytes that lowers the affinity of hemoglobin for
oxygen is 2,3-bisphosphoglycerate (or structure)
h/I) Scurvy is a condition arising from the inability to make functional collagen.
This is caused by the absence of vitamin C which makes the formation of
hydroxyproline/hydroxylysine 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)
Ch 2 question 13
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.
Ch 3 question 12
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)
see text for structures. Do not use gly, asn, trp, glu, gln, his