Biochemistry Exam 3

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Biochemistry Exam 3

Questions and Answers
  • 1. 
    The component(s) of DNA which is responsible for the absorbance band at 250-270 nm is
    • A. 

      Bases, pentoses, and phosphates all contribute

    • B. 

      Only bases

    • C. 

      Only bases and pentoses

    • D. 

      Only pentoses and phosphates

  • 2. 
    The oligonucleotide, AUGGp, has all these properties except
    • A. 

      Composed of ribonucleotides

    • B. 

      Contains a 3' phosphate

    • C. 

      Composed of deoxyribonucleotides

    • D. 

      Contains three phosphodiester bonds

  • 3. 
    An individual heterogeneous nuclear RNA (hnRNA)
    • A. 

      Contains intron sequences not found in the final mature mRNA.

    • B. 

      Contains exon sequences which are removed prior to translation.

    • C. 

      Encodes more than one protein.

    • D. 

      Can be found in the cytoplasm.

  • 4. 
    The RNA molecules which are involved in processing the hnRNA are
    • A. 

      MRNA

    • B. 

      TRNA

    • C. 

      RRNA

    • D. 

      SnRNA

  • 5. 
    What statement is incorrect about the different RNA molecules?
    • A. 

      TRNAs contain numerous intramolecular hydrogen bonds between bases.

    • B. 

      There are more distinct tRNA molecules than there are rRNA molecules.

    • C. 

      RRNAs are complexed to proteins in the ribosome.

    • D. 

      The most abundant RNA molecule in the cell is mRNA.

  • 6. 
    Which of the following is not a characteristic for DNA synthesis?
    • A. 

      DNA polymerase adds nucleotides in a 5'--> 3' direction

    • B. 

      A primer strand of DNA must contain a free 3'-OH end

    • C. 

      The primer strand of DNA determines which nucleotides are added next

    • D. 

      The correct complementary hydrogen bonding between base pairs is the primary check on the fidelity of the newly synthesized DNA

  • 7. 
    A DNA is found to exhibit a melting temperature of 75 C in 0.1 M NaCl. Under what experimental conditions would the Tm be increased?
    • A. 

      Decreasing the concentration of DNA.

    • B. 

      Increasing the concentration of NaCl in the solution.

    • C. 

      Adding 1% urea (an organic denaturant).

    • D. 

      All of the above.

  • 8. 
    A feature which is distinctive to Z-DNA is
    • A. 

      A left-handed helix

    • B. 

      It has 12 bases per turn

    • C. 

      It is found in vivo

    • D. 

      All of the above

  • 9. 
    The linking number of a highly supercoiled plasmid can be readily changed without producing a relaxed DNA by
    • A. 

      Changing the temperature

    • B. 

      Increasing salt concentration

    • C. 

      The action of topoisomerase

    • D. 

      The action of a nuclease such as pancreatic DNase

  • 10. 
    Which of the following double-stranded DNAs may convert to a cruciform structure?
    • A. 

      ATGCATGCATGCATGC / TACGTACGTACGTACG

    • B. 

      CATTAAGCAGTGCTTAAGA / GTAATTCGTCACGAATTCT

    • C. 

      ATATATATGCGCGCGCGC / TATATATACGCGCGCGCG

    • D. 

      AAAAAAAAACCCCCCCCC / TTTTTTTTTGGGGGGGG

  • 11. 
    Which statement is incorrect about the structure of native E. coli chromosomal DNA?
    • A. 

      The DNA is primarily in the B-helix.

    • B. 

      The DNA is circular and supercoiled

    • C. 

      The DNA exists as a right-handed double helix.

    • D. 

      The DNA is one large linear piece about 4000 kb in length.

  • 12. 
    E. coli DNA polymerase I has all the following characteristics except
    • A. 

      A 5'-3' exonuclease activity on a second subunit in the polymerase

    • B. 

      A 3'-5' exonuclease activity

    • C. 

      A 5'-3' DNA polymerase activity

    • D. 

      Modest processivity (ca. 20 nucleotides)

  • 13. 
    In the repair of DNA, the E. coli DNA polymerase involved performs which function in addition to its polymerase activity?
    • A. 

      It recognizes the abnormality in the duplex DNA structure.

    • B. 

      It nicks the DNA to provide a 3'-OH.

    • C. 

      It removes the damaged section of DNA with its 5'-3' exonuclease activity.

    • D. 

      It ligates the DNA after the repair synthesis.

  • 14. 
    The Klenow fragment of E. coli DNA polymerase I can be used to add nucleotides to a DNA with staggered ends if the ends
    • A. 

      Are recessed with 5'-phosphates

    • B. 

      Are recessed with 3'-OHs

    • C. 

      Are extended with 5'-phosphates

    • D. 

      Are extended with 3'-OHs

  • 15. 
    Which of the following is not a characteristic of replication of the E. coli circular chromosome?
    • A. 

      Replication is bidirectional.

    • B. 

      It initiates at a unique position called oriC.

    • C. 

      Torsional stress introduced in the duplex DNA is relieved by DNA gyrase.

    • D. 

      The unwinding of the duplex DNA is driven by the translocation of the DNA polymerase.

  • 16. 
    E. coli replication on the lagging strand
    • A. 

      Is primarily carried out by DNA polymerase I

    • B. 

      Is synthesized continuously

    • C. 

      This DNA strand is synthesized in a 3'-5'direction of synthesis

    • D. 

      Is initially synthesized as Okazaki fragments

  • 17. 
    Which one of the following characteristics is not associated with E. coli primase?  
    • A. 

      It synthesizes the RNA primer in DNA replication.

    • B. 

      It is a specific RNA polymerase.

    • C. 

      It is essential for DNA replication.

    • D. 

      It is also a gyrase

  • 18. 
    The polymerase which plays a similar role as that of Prokaryotic polII in eukaryotic replication is?
    • A. 

      DNA polymerase alpha

    • B. 

      DNA polymerase delta

    • C. 

      DNA polymerase gamma

    • D. 

      DNA polymerase kappa

  • 19. 
    Which is not a property of E. coli DNA polymerase III?
    • A. 

      It is responsible for incorporating most of the nucleotides in the lagging strand.

    • B. 

      It synthesizes most of the leading strand prior to aiding in the synthesis of the lagging strand.

    • C. 

      It contains a 3¨ to 5¨ exonuclease activity.

    • D. 

      It synthesizes the leading strand and the lagging strand at the same time

  • 20. 
    Which statement is incorrect about E. coli DNA polymerase I?
    • A. 

      The cell contains more molecules of DNA pol I than DNA pol III.

    • B. 

      DNA pol I is a single polypeptide with three domains.

    • C. 

      DNA pol I is involved in the repair of UV damaged DNA.

    • D. 

      DNA pol I has a larger turnover number than DNA pol III.

  • 21. 
    Which E. coli enzyme has the greatest frequency of incorporating the incorrect nucleotide into its nucleic acid polymer?
    • A. 

      RNA polymerase

    • B. 

      DNA polymerase I

    • C. 

      DNA polymerase III

    • D. 

      Klenow fragment from DNA polymerase I

  • 22. 
    DNA-dependent RNA polymerase acts on the DNA template in eukaryotic cells in the synthesis of
    • A. 

      A 5'-3' hnRNA transcript as the RNA polymerase moves in the 3'-5' direction on the DNA template

    • B. 

      A mature RNA transcript as the RNA polymerase moves in the 5'-3' direction

    • C. 

      An RNA transcript, with the sigma subunit of polymerase dissociating after the initiation event

    • D. 

      An RNA transcript, which is complementary to the sense strand of the DNA, except for the replacement of uridines for the thymidines

  • 23. 
     The shorter the primer, the more specific the DNA. 
    • A. 

      True

    • B. 

      False

  • 24. 
     Z-DNA can be stable in A:T-rich regions allowing its transition from B-DNA form. 
    • A. 

      True

    • B. 

      False

  • 25. 
    Due to nitrogenous bases, UV abs. of DNA increases when heated above body temperature. 
    • A. 

      True

    • B. 

      False

  • 26. 
    The rate of DNA renaturation is an index of its homology. 
    • A. 

      True

    • B. 

      False

  • 27. 
    Stacked base pairs absorb less light in native DNA.
    • A. 

      True

    • B. 

      False

  • 28. 
    ________studies the way genes express, determining the differences between vertebrates. 
  • 29. 
    In a duplex circular DNA, the _____________ state has around ____________ per turn. (answer, answer)
  • 30. 
    ____________is a topoisomerase II that introduces ______________ supercoiling and promote  ________________. (answer, answer, answer)
  • 31. 
    A _______________ region is the same DNA sequence read either 5’ to 3’ or viceversa. 
  • 32. 
    When supercoiled, the _____________number increases when there are more twists.
  • 33. 
    Part 2. Determine W, T and L respectively if DNA gyrase puts 4 negative supercoils into the 200-bp circular DNA. If relaxed, what would the value of L be?
  • 34. 
    Under which of the following conditions does the melting temp. for DNA denaturation increase?
    • A. 

      Smaller DNA fragments

    • B. 

      Higher G-C contents in DNA

    • C. 

      Higher A-T contents in DNA

    • D. 

      A and c are correct

    • E. 

      None are correct

  • 35. 
    Which of the following statements is true about chromosomes?
    • A. 

      They must be packed around the cell membrane.

    • B. 

      They can exist as unwrapped DNA.

    • C. 

      Genetic information is not located in these structures.

    • D. 

      As part of their structure, chromatin contains histones wrapped by DNA.

    • E. 

      None of the above.

  • 36. 
    Which of the following is not true about tRNA and rRNA?
    • A. 

      TRNA can self-base pair forming loops and base pair with non-canonical bases

    • B. 

      TRNA can carry at least one amino acid and contain an anticodon.

    • C. 

      RRNA is used for ribosome assembly as large and small units that are exported to the cytosol.

    • D. 

      RRNA can self-base pair with its complementary strand in a double stranded structure.

    • E. 

      Ribosomes contain rRNA as well as proteins except that the former is greater in number.

  • 37. 
    The separation of a double-stranded DNA will form two template strands. 
    • A. 

      True

    • B. 

      False

  • 38. 
    DNA replication mainly occurs in a conservative manner. 
    • A. 

      True

    • B. 

      False

  • 39. 
    In E.coli, only one replication fork is needed to replicate a new DNA strand. 
    • A. 

      True

    • B. 

      False

  • 40. 
    RNA can form an unstable hybrid structure with DNA. 
    • A. 

      True

    • B. 

      False

  • 41. 
    The unwinding of DNA is an energetically favorable process to allow replication. 
    • A. 

      True

    • B. 

      False

  • 42. 
    Template strands are only copied continuously. 
    • A. 

      True

    • B. 

      False

  • 43. 
    In E. coli, the replication fork copies DNA continuously and segmented in a 360o direction. 
    • A. 

      True

    • B. 

      False

  • 44. 
    DNA is unwound by gyrase without breaking it. 
    • A. 

      True

    • B. 

      False

  • 45. 
    Eukaryotic DNA can contain more than 2 replication forks. 
    • A. 

      True

    • B. 

      False

  • 46. 
    Replication occurs mainly during the G2 and G1 phases where cell growth occurs. 
    • A. 

      True

    • B. 

      False

  • 47. 
    Bidirectional replication starts at the_______________, moving replication forks in opposite direction.
  • 48. 
    A_______________ is bound to Ter locus to prevent helicase activity.
  • 49. 
    High_______________means a high number of successive cycles of nucleotide addition.
  • 50. 
    A primer needed for replication is formed by a_________________.
  • 51. 
    The process in which an RNA template is transcribed to cDNA is executed by _______________.
  • 52. 
    Which of the following is true of replication?
    • A. 

      It creates a complementary strand relying upon base-stacking interactions.

    • B. 

      Usually, one replication fork must move 360o around the entire chromosome in E.coli.

    • C. 

      DNA Pol I adds a new nucleotide to the 5’-end of an existing DNA molecule.

    • D. 

      DNA Pol I adds a new nucleotide to the 3’-end of the template strand.

    • E. 

      An antiparallel DNA strand is produced and a pyrophosphate is released.

  • 53. 
    DNA Pol III
    • A. 

      Synthesizes Okazaki fragments.

    • B. 

      Functions mainly in DNA repair.

    • C. 

      Polymerizes DNA in a 5’--> 3’ direction

    • D. 

      A and c are correct.

    • E. 

      None of the above.

  • 54. 
    Which of the following statements is not true?
    • A. 

      Replication occurs during the S phase of the eukaryotic cell cycle.

    • B. 

      Helicase is an ATP-dependant protein that unwinds DNA during replication.

    • C. 

      DNA Pol I uses its 3’--> 5’ exonuclease activity to remove primers.

    • D. 

      Ligase seals nicks in DNA by covalently linking Okazaki fragments.

    • E. 

      DNA Pol I has two types of exonuclease activities.

  • 55. 
    Reverse transcriptase
    • A. 

      Can be a telomerase that uses its own RNA as template.

    • B. 

      Is contained in all RNA tumor viruses.

    • C. 

      Allows the transcription of cDNA from an RNA template to form a DNA:RNA hybrid.

    • D. 

      Can be inhibited by HIV therapy.

    • E. 

      All of the above