(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 3’end 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. (10 pts) The tetrahymena precursor large subunit rRNA self splices. via a two-step process to form the mature 28S rRNA. (23 pts) A. C. with the help of anadded small molecule. In your answer. B. 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. (8 pts) Give two reasons why V/D/J recombination is frequently unsuccessful in yielding an mRNA that is translated into a functional immunoglobulin. (5 pts) Why are introns in eukaryotic protein-coding genes almost always > 65 nt in length? . Write a detailed chemical mechanism for the first step in this process.

C. (18 pts) A. (3 pts) Within the glycogen structure. (10 pts) Using electron pushing. present the detailed chemical mechanism for the reaction below HO O 2- O3POCH2CHCH O + HOCH2CCH2OPO32- B.3. (5 pts) Briefly explain the effect of activated phosphorylase kinase on glycogen breakdown and formation. what is a reducing end? .

(5 pts).4. Why is the potential -0.42V at pH 7? What would the value of Δε be at pH 6? ο ο . (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. (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. (20 pts) A. Describe the function that capping serves in eukaryotic translation. D. The Δε for the standard H2 electrode is 0 volts. Write the half reaction for this electrode. (5 pts) Draw the the chemical structure of the 5’-cap.

. (15 pts) A. (4 pts) Draw the structure of a glycerophospholipid that has two fatty acyl groups (cis 9-hexadecanoic acid and trans.5. (4 pts) Which triacylglycerol yields more energy on oxidation. D. (4 pts) Explain why adipocytes need glucose as well as fatty acids in order to synthesize triacyl glycerols. one containing three moles of linolenic acid (18:2) or one containing three moles of stearic acid (18:0)? Explain your answer. trans 6. 9-octadienoic acid) and a phosphorylcholine head group. (3 pts) Why aren’t triacylglycerols significant components of lipid bilayers? C. B.

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