Bio 301, Biochemistry I
Midterm Examination I, November 8, 2006
Name:
(Multiple choice questions, each 3 points, have only one answers)
1. Which of the following amino acids has an uncharged side chain under physiological
conditions?
a. Arginine
b. Aspartate
c. Glutamate
d. Lysine
e. Threonine
2. Which amino acid has a side chain whose pKa is closest to neutral pH?
a. Histidine
b. Isoleucine
c. Lysine
d. Methionine
e. Tyrosine
3. Which of the following best describes an alpha-helical region of a polypeptide?
a. Left-handed, 5.4 aa/turn
b. Left-handed, 6.5 aa/turn
c. Right-handed, 3.6 aa/turn
d. Right-handed, 7.0 aa/turn
e. Right-handed, 10.5 aa/turn
4. Which of the following best describes the arrangement of amino acid side chains in an alpha
helix?
a. The side chains point outward away from the helical axis.
b. The side chains point inward toward the center of the helix.
c. The side chains point toward the N-terminal end of the helix.
d. The side chains point toward the C-terminal end of the helix.
e. The side chains point toward the nearest beta sheet.
5. Which of the following amino acids is found most frequently at beta turns in the secondary
structures of proteins? Explain why?
a. Histidine
b. Leucine
c. Methionine
d. Proline
e. Tryptophan
6. Which of the following best describes the structural backbone of nucleic acids?
a. … – base – sugar – base – sugar – …
b. … – base – phosphate – base – phosphate – …
c. … – base – phosphate – sugar – base – phosphate – sugar – …
d. … – phosphate – sugar – phosphate – sugar – …
e. … – phosphate – phosphate – sugar – phosphate – phosphate – sugar – …
7. Which of the following best describes the structure of DNA?
a. two parallel strands, covalently attached to each other
b. two parallel strands, noncovalently attached to each other
c. two strands without polarity, noncovalently attached to each other
d. two antiparallel strands, covalently attached to each other
e. two antiparallel strands, noncovalently attached to each other
8. Which of the following best describes the structure of B form DNA?
a. Left-handed, 10.5 bp/turn
b. Left-handed, 12 bp/turn
c. Right-handed, 10.5 bp/turn
d. Right-handed, 21 bp/turn
e. Right-handed, 3.4 bp/turn
9. Which of the following most accurately describes the charge state of DNA under physiological
conditions?
a. Roughly uniformly positively charged along its length
b. Roughly uniformly negatively charged along its length
c. Roughly uniformly uncharged along its length
d. Heterogeneously charged, with some regions positive and some regions negative
e. Heterogeneously charged, with some regions negative and some regions neutral
10. DNA is less susceptible than RNA to alkaline hydrolysis. Which of the following contributes
most to this difference?
a. DNA is double stranded, whereas RNA is single stranded.
b. DNA has 2’ hydrogen atoms, whereas RNA has 2’ hydroxyl groups.
c. DNA includes thymine bases, whereas RNA includes uracil bases.
d. DNA seldom forms nonWatson-Crick base pairs, whereas RNA does so more readily.
e. DNA seldom adopts stable tertiary structure folds, whereas RNA does so more readily.
11. Which of the following best describes the TATA box?
a. It is a sequence in chromosomes that marks replication origins.
b. It is a sequence in the promoter region of genes that marks transcription start sites.
c. It is a sequence in primary transcripts that marks cleavage and polyadenylation sites.
d. It is a sequence in primary transcripts that marks splice sites.
e. It is a sequence in mRNAs that marks translation start sites.
12. Which of the following best characterizes the function of enhancers in gene regulation?
a. They are DNA sequences that directly bind RNA polymerase and regulate transcriptional
initiation.
b. They are DNA sequences that directly bind TFIID, and regulate transcriptional initiation.
c. They are DNA sequences that directly bind transcription factors and regulate
transcriptional initiation.
d. They are DNA sequences that directly bind transcription factors and regulate
transcriptional elongation.
e. They are mRNA sequences that directly bind initiation factors and regulate translational
initiation.
13. Which of the following best characterizes the termination of transcription?
a. The sequence signals for termination of transcription are contained within the transcript
itself.
b. The transcriptional termination sequence is a site in the DNA approximately 30 base pairs
downstream of the actual termination point.
c. Transcription terminates when the polymerase reaches a stop codon.
d. Transcription terminates when the polymerase reaches the promoter of the adjacent
downstream gene.
e. Transcription terminates when the polymerase reaches the start codon of the adjacent
downstream gene.
14. Which of the following is an accurate statement regarding the relationship between primers
and nucleic acid synthesis?
a. Primase catalyzes the de novo polymerization of DNA.
b. RNA polymerase II initiates RNA synthesis by elongation of a DNA primer.
c. During DNA replication, every Okazaki fragment synthesized by DNA polymerase III is
elongated from a separate RNA primer.
d. During DNA replication, leading strands are synthesized by DNA polymerase III without
utilizing a primer.
e. During DNA replication, primers are used to initiate DNA synthesis, and these primers are
incorporated into the final daughter strand products.
15. Which of the following post-transcriptional processes can lead to the production of multiple
protein isoforms from a single gene?
a. Alternative splicing
b. Capping
c. Nonsense mediated decay
d. Polyadenylation
e. RNA interference
16. Which of the following best describes the degeneracy of the genetic code?
a. Some codons are specified by multiple amino acids; these amino acids are usually similar
in chemical properties.
b. Some amino acids are specified by multiple codons; these codons usually differ only at
the first position.
c. Some amino acids are specified by multiple codons; these codons usually differ only at
the second position.
d. Some amino acids are specified by multiple codons; these codons usually differ only at
the third position.
e. Some amino acids are specified by multiple codons; these codons are usually unrelated in
sequence.
17. Which of the following best characterizes the relationship between amino acids and tRNAs?
a. The activation of an amino acid by formation of an aminoacyl-tRNA is coupled to the
hydrolysis of ATP to AMP + 2 Pi.
b. The conformation of an aminoacyl-tRNA facilitates the direct interaction between the
amino acid and its appropriate codon in the mRNA-ribosome complex.
c. Formation of the ester linkages between a tRNA and its corresponding amino acid is
catalyzed by the tRNA itself.
d. A tRNA binds to its appropriate amino acid through a covalent linkage of the amino acid’s
side chain to the base of the nucleotide immediately 5’ of the anticodon.
e. A tRNA is a six-nucleotide RNA molecule consisting of an anticodon followed by a CCA
sequence that accepts amino acids.
18. A) Draw a tripeptide. You may show the side chains of the amino acids with an –R if you like.
B) Explain what properties of a polypeptide can form regular secondary structures such as helices and - pleated sheets.
C) Describe and compare -helical and - pleated sheet structures.
19. What is salting out? Explain how it works. Explain how you would use to purify proteins.
20. Describe how would you determine the aminoacid sequence of a protein with 250 residues.
Explain each step in detail.
21. Describe the biochemical use of the following reagents:
a) CNBr
b) Urea
c) -Mercaptoethanol
d) Dabsy chloride
e) 6 N HCl
22. The gene encoding a protein with a single disulfide bond undergoes a mutation that
changes a serine residue into a cysteine residue. You want to find out whether the
disulfide pairing in this mutant is the same as in the original protein. Propose an
experiment to directly answer this question.