1.

(26 pts)
a. (4 pts) Draw the structures of -carboxyGlu and of -N-acetylLys
COO-

COO-

NH3+

CH

COO-

CH2

CH

CH2
CH2
+

H3N

CH

CH2

O
C

CH2 O

O-

HN C CH3

b. (12 pts) For the peptide IHERW

i. Draw its covalent structure

ii. Calculate its approximate pI value

Low pH 3 positive charges, R+H+N terminal
High pH 2 negative charges, E+C terminal
Therefore, to get to pI, have to remove one positive charge, which will come mostly from His.
approximate pI is 0.5 (6.04 + 9.76) = 7.9

The

Or:
At low pH, 3 positive charges, when pH=2.5, C terminal and E are half deprotonated and the net charge is 2.
Increase pH to 6.04, , C terminal and E are fully deprotonated with H half deprotonated and the net charge is 0.5.
Increase pH to 9.76, C terminal and E,H are fully deprotonated with N terminal half deprotonated and the net
charge is -0.5. pI is the average of pKs which are related with the neutral species, 0.5 (6.04 + 9.76) = 7.9.
c. (5 pts) At physiological pH, polylysine assumes a random coil conformation. At what pH might it form an
helix? Why?
At physiological pH (~7), lysine is positive charged and the positive change repels each other, preventing
formation of compact helix structure. If we increase pH to about 10.54, when Lysine is half deprotonated,
then polylysine can form an helix.
d. (5 pts) Identify the structures shown. Why does a Gly residue favor the structure on the right more than an
Ala residue?

Left, type 1 turn; Right, type 2 turn

Gly has a smaller sidechain (H) compared with Ala (CH3), which reduces the steric clash between O of residue
2 and C-B (side chain)of residue 3.
2.
a. Provide a thermodynamic rationale for why many proteins can be denatured by storage
at cold temperatures.
G=H-TS
In the process to form native protein, generally, H is positive but smaller than TS. The
overall G is negative which indicates it is a spontaneous process.
At cold temperatures, T drops dramatically and TS becomes smaller. The overall G is
less negative or even positive. In other words, many proteins are likely to be denatured at
cold temperatures.

b. Compare the advantages and disadvantages in determining protein structure by X-ray

crystallography vs. nuclear magnetic resonance.

c. How is ICH2CO2H used in sequencing proteins? Include in your answer what it reacts with and the products
that are formed.
Blocks SH groups formed on reduction; prevents reformation of S-S bonds; allows separation of peptide
fragments held together by a cystine (S-S) linkage
ICH2CO2Reduction of disulfide bonds ( ---SS---)- ---SH HS---

2 ---SCH2CO2- + 2I-

d. How is CNBr used in sequencing proteins? Include in your answer what it reacts with and the products that
are formed.
Cleaves proteins at Met residues

e. Draw the structure of two strands of an antiparallel -sheet containing three amino acids per strand (you need
not specify the substitution at the -carbons). In the first strand, what is the distance between the -carbons in
residues 1 and 3? 7

3. a. In the equation below, identify what the following symbols stand for:
s, M, D. Why is s proportional to M2/3?

s=

w r
2

M(1- v r )D
RT

s, sedimentation coefficient; w
, angular velocity of rotormolecular massD, diffusion constant
D is inversely proportional to the radius of a spherical particle; M is proportional to the radius cubed.
Therefore, D is proportional to M-1/3; s is proportional to MD, or M2/3
b. Explain with a diagram why loops connecting antiparallel strands in -sheets are shorter than loops
connecting -strands.

Antiparallel

Parallel

c. What does hydropathy measure?

Tendency of a side chain to occupy the hydrophobic interior of a protein
d. List the following bond types in order of increasing bond strength:
C-H covalent bond, London dispersion force, ionic interaction, hydrogen bond
London dispersion force < hydrogen bond < ionic interaction < C-H covalent bond

4. (15 pts)
RNAse A catalyzes the hydrolysis of RNA chains by a two-step mechanism. Draw the mechanism, and
indicate in each step where general acid and general base catalysis plays a role.

Step 1
His 12 acts as general base in partially removing proton from 2-OH, which
converts 2-O into a potent nucleophile that attacks phosphoryl group
His 119H+ acts as general acid in partially protonating leaving group 5-oxygen
Step 2
His 119 acts as general base in partially removing proton from attacking
H2O, which converts water oxygen into a potent nucleophile that attacks
phosphoryl group. His 12H+ acts as general acid in partially protonating
leaving group 2-oxygen
Step 2 is essentially the reverse of step 1