1. Write out the different mechanisms for the GU-AG intron, Group I intron, and
splicosome intron splicing.
2. Why can’t eukaryotic transcription be regulated by attenuation?
3. Draw out the steps for the initiation, elongation, and release of the polypeptide
during translation of an mRNA sequence. Use pictures and diagrams to help
4. Define the following terms:
a. Initiation factors
b. Elongation factors
c. Release factors
d. Post-translational modification
e. Synonyms
f. Nonsense mutation
g. Nonsense suppressor
h. Missense suppressor
i. Frameshift suppressor
j. Amber codon
k. Transitions
l. Transversions
m. 5-bromouracil
n. 2-aminopurine
o. essential amino acids
p. nonessential amino acids
5. What is the product of the reaction of guanine with nitrous acid? Is this
mutagenic? Explain.
xanthine can base pair with C has 2 H bonds instead of 3. Therefore it is not mutagenic.
6. The fingerprint of a protein from a phenotypically revertant mutant of
bacteriophage T4 indicates the presence of an altered tryptic peptide with respect
to the wild type. The wild-type and mutant peptides have the following sequences:
Wild type
Cys-Glu-Asp-His-Val-Pro-Gln-Tyr-Arg
Mutant
Cys-Glu-Thr-Met-Ser-His-Ser-Tyr-Arg
Indicate how the mutant could have arisen and give the base sequences, as far as possible,
of the mRNAs specifying the two peptides. Comment on the function of the peptide in
the protein.
1. Write out the urea cycle showing all structures and intermediates.
a. How is the urea cycle regulated?
b. What other pathways are linked to the urea cycle?
2. Define glucogenic and ketogenic.
3. Which amino acids are glucogenic? Which amino acids are ketogenic? Which
amino acids are both glucogenic and ketogenic?
4. Which amino acids are degraded to pyruvate? Which amino acids are degraded to
acetyl-CoA? Which amino acids are degraded to -ketoglutarate? Which amino
acids are degraded to succinyl-CoA? Which are degraded to acetoacetate? What
pathways do these molecules go to?
5. Show the PLP-dependent mechanisms for the cleavage of a C-H bond, C- C
bond, C-COO- bond, and C- C bond. Name an enzyme for each of these
reactions. What pathways are these enzymes associated with?
6. How can a PLP-dependent enzyme catalyze a deamination? Show a plausible
mechanism.
7. Starting from threonine, show the pathways to make glucose and palmitate. Show
all chemical structures, co-factors, and enzymes with names involved with these
pathways. How are these pathways regulated?
8. Starting from glucose, show the pathways leading to the production methionine.
Show all chemical structures, co-factors, and enzymes with names involved with
these pathways. How are these pathways regulated?
9. Which amino acids are the essential amino acids? Which are the nonessential
amino acids?
10. Write the pathway for the formation of chorismate, a key intermediate in
biosynthesis of pre-aromatic compounds. Show all structures and indicate the
cofactors and class names for all enzymes. You need not name all intermediates
but you should name important ones.
11. How is Glutamine Synthetase regulated? List all effectors, inhibitors and
activators.
12. Draw the structure of an active biopterin. What enzyme uses biopterin? What
reaction does it catalyze? How is this cofactor regenerated? What is the NIH
shift?
13. Heme is derived from what precursor molecules?
14. What types of reactions utilize THF cofactors?
15. What amino acid can be produced from pyruvate? Oxaloacetate? ketoglutarate?