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INTRODUCTORY BIOCHEMISTRY
BIOL0280
Third Midterm Examination
April 30, 2013
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DO NOT WRITE YOUR NAME ON THIS EXAM
Make sure that your Banner ID is on every page. This is the only way we have of matching you
with your exam after grading it. Please work independently. Read each question carefully
before answering. Unless otherwise indicated, there is only one correct answer for each
multiple-choice question. Points are indicated by the question within brackets [ ]. There are no
calculators or other electronic devices needed or allowed on this exam. All hats must be
removed during the exam. Exams will be photocopied before being returned.
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Exam total __________/ 100
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1. [2 points] Biological amines are generated by
.
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of
2. [2 points] The hormones epinephrine and norepinephrine are derived biosynthetically from:
A) arginine.
B) histidine.
C) isoleucine.
D) tryptophan.
E) tyrosine.
Circle the correct answer
3. [4 points] Draw the structure of UMP in the space provided below. Your answer must be
completely correct to receive credit.
4. [2 points] Ribonucleotide reductase is a key enzyme in nucleotide biosynthesis.
In one sentence, describe its biochemical function.
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5. [4 points] Explain the function of the two regulatory sites of ribonucleotide reductase,
and list molecules that bind to each of these two regulatory sites.
6. [2 points] The difference between a ribonucleotide and a deoxyribonucleotide is:
A) a deoxyribonucleotide has an —H instead of an —OH at C-2.
B) a deoxyribonucleotide has α configuration; ribonucleotide has the β configuration at C-1.
C) a ribonucleotide has an extra —OH at C-4.
D) a ribonucleotide has more structural flexibility than deoxyribonucleotide.
E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.
Circle the correct answer
7. [2 points] Which of the following are possible base compositions for double-stranded DNA?
A)
%A
5
%G
45
%C
45
%T
5
%U
0
B)
20
20
20
20
20
C)
35
15
35
15
0
D) All of the above.
E) None of the above.
Circle the correct answer.
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8. [2 points] In the Watson-Crick model of DNA structure (now called B-form DNA):
A) a purine in one strand always hydrogen bonds with a purine in the other strand.
B) A–T pairs share three hydrogen bonds.
C) G–C pairs share two hydrogen bonds.
D) the 5' ends of both strands are at one end of the helix.
E) the bases occupy the interior of the helix.
Circle the correct answer.
9. [2 points] Nucleosomes:
A) are important features of chromosome organization in bacteria.
B) contain proteins that are rich in acidic amino acids.
C) are composed of protein and RNA.
D) bind DNA in the form of a solenoidal supercoil.
E) occur in chromatin at irregular intervals along the DNA molecule.
Circle the correct answer.
10. [6 points] Calculate values for the following topological properties of a closed-circular DNA
molecule containing 2,000 base pairs (for simplicity, assume there are 10 base pairs per turn in
the relaxed DNA).
(a) What is the linking number (Lk) when the DNA is
relaxed?
(b) What is the linking number (Lk) when the DNA has
been underwound by 2 turns?
(c) Will the DNA in (b) adopt positive or negative
supercoils?
11. [2 points] When a DNA molecule is described as replicating bidirectionally, that means that
it has two:
A) chains.
B) independently replicating segment.
C) origins.
D) replication forks.
E) termination points.
Circle the correct answer.
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12. [8 points] Briefly describe the biochemical role of the following enzymes in DNA replication
in E. coli:
(a) DNA helicase
(b) Primase
(c) the 3' → 5' exonuclease activity of DNA polymerase
(d) the 5' → 3' exonuclease activity of DNA polymerase I
13. [6 points] In the space below, draw the product of the deamination reaction for the base
shown on the left:
deamination
Name the bases:
Which repair pathway is most likely to repair this lesion?
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14. [5 points] Below, an RNA molecule is being transcribed from a strand of DNA.
(a) Label the 5' and 3' ends of the RNA molecule.
(b) Label the 5' and 3' ends of the DNA template strand.
(c) Using an arrow, indicate the direction of synthesis.
15. [5 points] For each of the following statements, indicate with a P if the statement applies
only to prokaryotes, an E if the statement applies only to eukaryotes, and a B if the statement
applies to both eukaryotes and prokaryotes.
___ RNA polymerase initiates transcription de novo, with no requirement for a primer.
___ Promotor sequences have little intrinsic affinity for RNA polymerase.
___ A single RNA polymerase transcribes genes that encode mRNAs, tRNAs, and rRNA.
___ Sigma (σ) subunit detaches from RNA polymerase after transcription has initiated.
___ At the 5' end of the mature mRNA there is a cap consisting of a guanosine joined to the
5'-terminal nucleotide through a 5' to 5' triphosphate group.
16. [2 points] A branched (“lariat”) structure is formed during:
A) attachment of a 5' cap to mRNA.
B) attachment of poly(A) tails to mRNA.
C) processing of preribosomal RNA.
D) splicing of all classes of introns.
E) splicing of group II introns.
Circle the correct answer.
17. [2 points] Splicing of introns in nuclear mRNA primary transcripts requires:
A) a guanine nucleoside or nucleotide.
B) endoribonucleases.
C) polynucleotide phosphorylase.
D) RNA polymerase II.
E) small nuclear RNAs (snRNAs).
Circle the correct answer.
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18. [6 points] The template strand of a segment of double-stranded DNA contains the
sequence:
(5ʹ′)CTT TGA TAA GGA TAG CCC TTC(3ʹ′)
(a) What is the base sequence of the mRNA that can be transcribed from this strand? Be
certain to label all 5ʹ′ and 3ʹ′ ends in your answer.
(b) What amino acid sequence could be coded by the mRNA base sequence in (a), using
only the first reading frame starting at the 5' end? (You may refer to the genetic code on
the last page of the exam.)
(c) Suppose the other (complementary) strand is used as a template for transcription. What
is the amino acid sequence of the resulting peptide, again starting from the 5' end and
using only the first reading frame?
19. [7 points] Match the factor or enzyme at the left with the stage(s) of protein synthesis at
which it acts. If a factor or enzyme participates in two stages of protein synthesis, indicate both
of them.
A) RF
Amino acid activation
B) EF-G
Initiation
C) aminoacyl-tRNA
D) Shine-Dalgarno sequence
E) IF-3
Elongation
Termination
20. [2 points] Approximately how many high-energy phosphate bonds must be consumed to
incorporate one amino acid into a protein? (I.e., per peptide bond.)
A) 0
B) 1
C) 2
D) 4
E) 8
Circle the correct answer.
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21. [10 points] In one or two sentences, define the following terms with respect to regulation of
transcription:
(a) Constitutive
(b) Induction
(c) Repression
(d) Repressor
(e) Co-activator
22. [4 points] In prokaryotes such as E. coli, many operons that encode enzymes involved in
amino acid biosynthesis begin with a sequence coding for a leader peptide. This peptide has
no known enzymatic function and is rich in the amino acid that is synthesized by the enzymes
coded for in the operon. What is the function of this leader peptide?
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23. [2 points] Certain restriction enzymes produce cohesive (sticky) ends. This means that
they:
A) cut both DNA strands at the same base pair.
B) cut in regions of high GC content, leaving ends that can form more hydrogen bonds than
ends of high AT content.
C) make a staggered double-strand cut, leaving ends with a few nucleotides of singlestranded DNA protruding.
D) make ends that can anneal to cohesive ends generated by any other restriction enzyme.
E) stick tightly to the ends of the DNA they have cut.
Circle the correct answer.
24. [3 points] Match each vector with the appropriate method used for its introduction into host
cells:
(a) Electroporation
Plasmid
(b) Transformation
Bacteriophage λ
(c) Infection
BAC (Bacterial Artificial Chromosome)
25. [3 points] In order to amplify Gene X shown below using PCR, to what region and strand
would the two oligonucleotide primers anneal?
A) Region A and B of the top strand.
B) Region A of both strands.
C) Region A of the top strand and region B of the bottom strand.
D) Region A of the bottom strand and region B of the top strand.
E) None of the above.
Circle the correct answer and draw the primers on the diagram.
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26. [5 points] A plasmid that encodes resistance to ampicillin and tetracycline is digested with
the restriction endonuclease PstI, which cuts the plasmid at a single site in the ampicillinresistance gene. The cut plasmid DNA is then ligated with a PstI digest of human DNA and
introduced into E. coli cells.
(a) What antibiotic would you put in an agar plate to ensure that the cells of a bacterial
colony contain the plasmid?
(b) What will the antibiotic-resistance phenotypes be of the bacteria growing on the plate?
(In your answer, use tetR to refer to tetracycline resistance, tetS to refer to tetracycline
sensitivity, ampR to refer to ampicillin resistance and ampS to refer to ampicillin
sensitivity.)
(c) Which phenotype will indicate the presence of plasmids that contain human DNA
fragments? Provide a brief explanation.
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The Genetic Code:
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