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INTRODUCTORY BIOCHEMISTRY
BIOL0280
Third Midterm Examination
April 28, 2015
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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 for each question are indicated within brackets []. There are
no calculators or other electronic devices needed or allowed on this exam. All hats
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1. [2 points] The enzyme cofactor for decarboxylation reactions in the synthesis of biological
amines is
A) dopamine
B) biotin
C) PLP
D) TPP
E) FMH
Circle the correct answer.
2. [2 points] Name the first two degradation products in the breakdown of heme.
biliverdin and bilirubin
3. [4 points] Draw the structure of GTP in the space provided below. Your answer must be
completely correct to receive credit.
4. [2 points] One amino acid directly involved in the purine biosynthetic pathway is:
A) alanine.
B) aspartate.
C) glutamate.
D) leucine.
E) tryptophan
Circle the correct answer.
5. [2 points] Purine nucleotide and Histidine synthesis both use which pair of molecules early
in the pathways?
A) Phosphoribosyl pyrophosphate and ATP
B) Xylulose 5-phosphate and ATP
C) GTP and Ribulose 5-phosphate
D) Pyridoxal phosphate and ATP
E) NAD(P)H and ATP
Circle the correct answer.
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6. [2 points] Indicate whether the following statements are true or false by circling True or
False.
True / False Difluoromethylornithine is a suicide inhibitor of ornithine decarboxylase
True / False Aspartate transcarbamoylase is regulated by CTP and ATP.
True / False In nucleotide biosynthesis, the pyrimidine ring is derived from carbamoyl
phosphate and aspartate.
True / False Thymidylate synthase catalyzes the conversion of dUTP to dTTP.
7. [4 points] Draw an adenine – thymine base pair in the space provided below in the correct
base-pairing orientation and indicate hydrogen bonds with dashed lines. Must be completely
correct to receive credit.
8. [2 points] Name at least two DNA binding motifs found in DNA binding proteins.
helix-turn-helix, zinc finger, homeodomain, leucine zipper, basic helix-loop-helix
9. [2 points] Fill in the blanks in the following sentences describing supercoiling.
Supercoiling serves to relieve _______strain________ in DNA. Most cellular DNA is
___underwound_______ and supercoiling stabilizes ______underwinding_______.
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10. [4 points] Define, in the context of DNA structure, the term “topoisomers.”
Topoisomers are different forms of a closed-circular DNA molecule that differ only in a
topological property such as their linking number (Lk).
11. [2 points] A commonality between type I and type II topoisomerases is that they both:
A) change the linking number in increments of 1.
B) require ATP.
C) go through a mechanism using a covalent enzyme-substrate intermediate.
D) are inhibited by quinoline antibiotics.
E) All of the above
Circle the correct answer.
12. [2 points] Which of the following contributes to the structure of nucleosomes?
A) Plectonemic supercoiled DNA
B) Relaxed closed-circular DNA
C) Solenoidal supercoiled DNA
D) Spacer DNA
E) Z (left-handed) DNA
Circle the correct answer.
13. [2 points] The DNA in a bacterial (prokaryotic) chromosome is best described as:
A) a single circular double-helical molecule.
B) a single linear double-helical molecule.
C) a single linear single-stranded molecule.
D) multiple linear double-helical molecules.
E) multiple linear single-stranded molecules.
Circle the correct answer.
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14. [2 points] An Okazaki fragment is a:
A) fragment of DNA resulting from endonuclease action.
B) segment of DNA that is an intermediate in the synthesis of the lagging strand.
C) fragment of RNA that is a subunit of the 30S ribosome.
D) piece of DNA that is synthesized in the 3' à 5' direction.
E) segment of mRNA synthesized by RNA polymerase.
Circle the correct answer.
15. [2 points] Which of the following is not required for elongation during DNA replication in E.
coli?
A) DnaB (helicase)
B) DnaG (primase)
C) DnaC
D) β-sliding clamp
E) Clamp loader
Circle the correct answer.
16. [2 points] When bacterial DNA replication introduces a mismatch in a double-stranded
DNA, the methyl-directed repair system:
A) cannot distinguish the template strand from the newly replicated strand.
B) changes both the template strand and the newly replicated strand.
C) corrects the DNA strand that is methylated.
D) corrects the mismatch by changing the newly replicated strand.
E) corrects the mismatch by changing the template strand.
Circle the correct answer.
17. [4 points] The high fidelity of DNA replication is due primarily to immediate error correction
by the 3' —> 5' exonuclease (proofreading) activity of the DNA polymerase. Some incorrectly
paired bases escape this proofreading, and further errors can arise from challenges to the
chemical integrity of the DNA. List the four classes of repair mechanisms that the cell can use
to help correct such errors and other DNA damage.
(1) mismatch repair, (2) base-excision repair, (3) nucleotide-excision repair, and (4) direct
repair.
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18. [2 points] In a mammalian cell, DNA repair systems:
A) are extraordinarily efficient energetically.
B) are generally absent, except in egg and sperm cells.
C) can repair deletions, but not mismatches.
D) can repair most types of lesions except those caused by UV light.
E) normally repair more than 99% of the DNA lesions that occur.
Circle the correct answer.
19. [4 points] List one basic property that distinguishes RNA polymerases from DNA
polymerases, and list one basic property they share.
Different:
RNA polymerase does not require a primer, but DNA polymerase does;
RNA polymerase lacks the 3' → 5' proofreading exonuclease activity present in DNA
polymerase.
Shared:
both enzymes use nucleoside triphosphates as substrates,
both require Mg 2+ and Zn2+,
both produce an antiparallel complement to the template
both synthesize nucleic acids in the direction 5' → 3'.
20. [4 points] For the following sequence of an RNA transcript, write down the sequences of
the DNA template and coding strands and clearly label the 5' and 3' ends of each strand.
RNA transcript:
(5') C G C U A U A G C G (3')
Template strand:
(3') G C G A T A T C G C (5')
Coding strand:
(5') C G C T A T A G C G (3')
21. [2 points] The 5'-terminal cap structure of eukaryotic mRNAs is a(n):
A) 7-methylcytosine joined to the mRNA via a 2',3'-cyclic linkage.
B) 7-methylguanosine joined to the mRNA via a 5' → 3' diphosphate linkage.
C) 7-methylguanosine joined to the mRNA via a 5' → 5' triphosphate linkage.
D) N6-methyladenosine joined to the mRNA via a 5' → 5' phosphodiester bond.
E) O6-methylguanosine joined to the mRNA via a 5' → 5' triphosphate linkage.
Circle the correct answer.
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22. [2 points] Introns:
A) are frequently present in prokaryotic genes but are rare in eukaryotic genes.
B) can occur many times within a single gene.
C) are spliced out before transcription.
D) are translated but not transcribed.
E) encode unusual amino acids in proteins.
Circle the correct answer.
23. [4 points] Indicate whether the following statements are true or false by circling True or
False.
True / False
True / False
True / False
True / False
Ribozymes are DNA molecules with catalytic properties.
Splicing involves transesterification reactions.
nuclear mRNA splicing is carried out in a complex called the spliceosome.
The mechanism of tRNA splicing is similar to group I splicing.
24. [2 points] Which one of the following is true about the genetic code?
A)
B)
C)
D)
All codons recognized by a given tRNA encode different amino acids.
It is absolutely identical in all living things.
Several different codons may encode the same amino acid.
The base in the middle position of the tRNA anticodon sometimes permits “wobble”
base pairing with two or three different codons.
E) The first position of the tRNA anticodon is always adenosine.
Circle the correct answer.
25. [4 points] Indicate whether the following statements are true or false by circling True or
False.
True / False
True / False
True / False
True / False
A ribosome is the complex within which protein synthesis occurs.
Ribosomes contain many separate proteins.
The three ribosomal RNAs in a bacterial ribosome are distributed in three
separate, large ribosomal subunits.
The catalytic machinery of the ribosome is protein-based.
26. [2 points] Aminoacyl-tRNA synthetases (amino acid activating enzymes):
A) in conjunction with another enzyme attach the amino acid to the tRNA.
B) recognize specific tRNA molecules and specific amino acids.
C) interact directly with free ribosomes.
D) activate amino acids bound to the ribosome.
E) require GTP to activate the amino acid.
Circle the correct answer.
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27. [6 points] Briefly describe the role of the following components in bacterial protein
synthesis.
(a) Initiation factor 2 (IF-2)
IF-2 is a protein factor that, when bound to GTP, brings the fMet-tRNAfMet to the initiation
complex (the ribosome).
(b) Release factors
Release factors are proteins that bring about the release of the finished polypeptide when the
ribosome encounters a termination codon in the mRNA.
(c) Elongation factor G (EF-G)
EF-G participates in the translocation of the ribosome down the mRNA by one codon after
each peptide bond is formed.
28. [4 points] Fill in the blanks in the following sentences about gene regulation.
RNA polymerase binds to DNA at ________promoters_______.
______Repressors__________ impede access of RNA polymerase to the DNA and
________activators________ enhance access of RNA polymerase to DNA.
Prokaryotic genes are regulated in units called _____operons______.
29. [2 points] The binding of CRP (cAMP receptor protein of E. coli) to DNA in the lac operon:
A) assists RNA polymerase binding to the lac promoter.
B) is inhibited by a high level of cAMP.
C) occurs in the lac repressor region.
D) occurs only when glucose is present in the growth medium.
E) prevents repressor from binding to the lac operator.
Circle the correct answer
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30. [6 points] Describe in one or two sentences the role of each of the following types of
proteins in the regulation of gene expression in eukaryotes:
(a) basal transcription factors
Basal transcription factors bind to the promoter region and recruit RNA polymerase to the
promoter.
(b) transactivators
Transactivators bind to DNA (at enhancer sites) and interact with coactivators to activate
transcription.
(c) coactivators.
Coactivators interact with both transactivators and RNA polymerase (but not with DNA) to
activate transcription.
31. [2 points] Which of the following is not part of miRNA formation?
A) Pri-miRNA
B) Pre-miRNA
C) Dicer
D) RISC
E) Pseudouridine
Circle the correct answer.
32. [2 points] Restriction enzymes:
A) act at the membrane to restrict the passage of certain molecules into the cell.
B) are highly specialized ribonucleases that degrade mRNA soon after its synthesis.
C) are sequence-specific DNA endonucleases.
D) are very specific proteases that cleave peptides at only certain sequences.
E) catalyze the addition of a certain amino acid to a specific tRNA.
Circle the correct answer.
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33. [2 points] A convenient cloning vector with which to introduce foreign DNA into E. coli is
a(n):
A) yeast transposable element.
B) E. coli chromosome.
C) messenger RNA.
D) plasmid.
E) yeast “ARS” sequence.
Circle the correct answer.
34. [2 points] The PCR reaction mixture does not include:
A) oligonucleotide primer(s).
B) all four deoxynucleoside triphosphates.
C) DNA containing the sequence to be amplified.
D) DNA ligase.
E) heat-stable DNA polymerase.
Circle the correct answer.
35. [4 points] What is the essential difference between a genomic library and a cDNA library?
A genomic library contains (in principle) all of the sequences present in the chromosome(s),
including DNA sequences that are not transcribed. Because a cDNA library is made as a
DNA copy of mRNA, it contains only those DNA sequences that are expressed in the cell.
36. [2 points] The technique known as two hybrid analysis for detecting interacting gene
products depend on:
A) direct binding of a Gal4p activation domain to a DNA sequence in the promoter region.
B) having a promoter that responds directly to one of the two proteins whose interactions is
being measured.
C) hybridization of DNA segments corresponding to the two genes being examined.
D) stimulation of transcription by interaction of two Gal4p domains via fused protein
sequences.
E) activation of DNA polymerase by the nearby binding of hybridizing protein complexes.
Circle the correct answer.