1.

(24 pts)
A. (8 pts). In the genetic code, the triplets coding for Phe are UUU and UUC. Triplets
coding for Leu are UUA and UUG, differing only in third position from Phe, whereas
those coding for Cys are UGU and UGC, differing only in the second position from Phe.
i. Since the codons for Leu and Cys each differ in only one position from the codons for
Phe, why are the codons for Leu considered to be near-cognate to the codons for Phe,
whereas the codons for Cys are considered to be non-cognate to the codons for Phe?
ii. What is the consequence of this difference (near-cognate for Leu, non-cognate for
Cys) on how errors in translation at Phe codons affect protein stability?
B. (8 pts) Shown below is a typical backbone structure of tRNA.
i. Explain the significance of the sphere
sizes shown along backbone.
ii. What role does the single stranded 3end play in ensuring the accuracy of
protein synthesis?

C. (8 pts) The release factors RF1 and RF2 share a conserved GGQ sequence. Draw a
chemical mechanism illustrating how this conserved sequence is involved in the release
of the completed peptide chain from peptidyl-tRNA.

2. (23 pts)
A. (10 pts) The tetrahymena precursor large subunit rRNA self splices, with the help of
anadded small molecule, via a two-step process to form the mature 28S rRNA. Write a
detailed chemical mechanism for the first step in this process. In your answer, please use
arrows to indicate which bonds are being formed and broken, and indicate the positions
of the two exons and the intron relative to the site of chemical reaction.
B. (8 pts) Give two reasons why V/D/J recombination is frequently unsuccessful in
yielding an mRNA that is translated into a functional immunoglobulin.
C. (5 pts) Why are introns in eukaryotic protein-coding genes almost always > 65 nt in
length?

3. (18 pts)
A. (10 pts) Using electron pushing, present the detailed chemical mechanism for the
reaction below

HO O
2-

O3POCH2CHCH

O
+ HOCH2CCH2OPO32-

B. (5 pts) Briefly explain the effect of activated phosphorylase kinase on glycogen

breakdown and formation.
C. (3 pts) Within the glycogen structure, what is a reducing end?

4. (20 pts)
A. (6 pts) How do DICER and RISC complex combine to degrade specific mRNAs? In
what compartment(s) of the cell do the various reactions involved in such degradation
take take place?
B. (4 pts) Why could adding an inhibitor molecule to a bacterial culture that stalls
ribosome-dependent protein synthesis also lead to premature termination of mRNA
transcription?
C. (5 pts) Draw the the chemical structure of the 5-cap. Describe the function that
capping serves in eukaryotic translation.
D. (5 pts). The for the standard H2 electrode is 0 volts. Write the half reaction for this
electrode. Why is the potential -0.42V at pH 7? What would the value of be at pH 6?

5. (15 pts)
A. (4 pts) Which triacylglycerol yields more energy on oxidation, one containing three
moles of linolenic acid (18:2) or one containing three moles of stearic acid (18:0)?
Explain your answer.
B. (3 pts) Why arent triacylglycerols significant components of lipid bilayers?
C. (4 pts) Explain why adipocytes need glucose as well as fatty acids in order to
synthesize triacyl glycerols.
D. (4 pts) Draw the structure of a glycerophospholipid that has two fatty acyl groups (cis
9-hexadecanoic acid and trans, trans 6, 9-octadienoic acid) and a phosphorylcholine head
group.