Biochemical Genomics Block II sample questions

Multiple Choice

1. Primase enzymes catalyze:
   a) The initiation of replication by laying down RNA primers
   b) The initiation of replication by laying down DNA primers
   c) The termination of replication by connecting primers to newly synthesized DNA
   d) The process of DNA repair by "priming" the replacement DNA
   e) None of the above

2. Taq polymerase:
   a) Catalyzes the synthesis of DNA from RNA
   b) Is a heat resistant DNA polymerase often used in the PCR technique
   c) Is a thymine-specific eukaryotic DNA repair enzyme
   d) Is one of the two primers used during the PCR method
   e) Is involved in creating many copies of new DNA during times of growth in the human body

3. DNA replication is:
   a) Dispersive and unidirectional
   b) Conservative and unidirectional
   c) Conservative and bidirectional
   d) Semiconservative and unidirectional
   e) Semiconservative and bidirectional

4. Okazaki fragments are:
   a) Fragments of DNA cut by restriction enzymes
   b) Fragments of DNA synthesized in the lagging strand of DNA
   c) Areas of mutated DNA that are repaired by DNA Polymerase I
   d) Nucleotide primers
   e) None of the above

5. Which of the following drugs targets the alpha subunit of DNA gyrase:
   a) Coumermycin
   b) Novobiocin
   c) Ciprofloxacin
   d) AZT
   e) None of the above

6. DNA gyrase:
   a) Creates supercoils in prokaryotic DNA, making it more tightly coiled
   b) Cuts both strands of prokaryotic DNA, relaxing the DNA
   c) Cuts only one strand of eukaryotic DNA, relaxing the DNA
   d) Is involved in eukaryotic DNA repair
   e) Is a target for AZT

7. All of the following are examples of spontaneous mutations EXCEPT:
   a) A tautomer is incorporated into a growing strand of DNA
   b) Cytosine can be spontaneously deaminated, incorporating a uracil in its place
   c) A particular strand of DNA is rich in GC regions, so the supply of dGTP is depleted. A polymerase adds a dATP instead.
   d) Replication machinery "slips" on a VNTR, shortening the length of one of the DNA strands.
   e) All of the above are examples of spontaneous mutations.

8. Which of the following mutations would be considered a transition:
   a) CTTAGA -> CTTTAGA
   b) CTTAGA -> GTTAGA
   c) CTTAGA -> TCTAAG
   d) CTTAGA -> CTCAGA
   e) CTTAGA -> CTTAGT
   

9. Thalassemia may result from:
   a) Defects of mRNA processing
   b) Deletion of the LCR
   c) Point mutations within promoters
   d) Mutations affecting translation
   e) All of the above

10. Xeroderma Pigmentosum:
    a) Is a sex-linked recessive syndrome
    b) Involves a defect in base excision repair
    c) Can be traced to a mutation in a single gene
    d) Patients are sensitive to sunlight
    e) All of the above

11. DNA damage that can be repaired directly in humans:
    a) Methylation
    b) Cyclobutyl dimers
    c) Misincorporated DNA
    d) Any helix distorting mutation
    e) Glycosylation

12. A protein that regulates the cell cycle, and can signal apoptosis if there is too much DNA damage/mutation is/are:
    a) Ku
    b) BRCA I
    c) p53
    d) MutH
    e) All of the above

13. Recombination occurs in the following order:
    I. Holiday junction formation
    II. Nicking the DNA
    III. Ligating the DNA
    IV. Strand invasion
    V. Rotation of the intermediate and strand cleavage

    a) II -> V -> IV -> I -> III
    b) II -> IV -> I -> V -> III
    c) III -> IV -> II -> V -> I
    d) III -> IV -> I -> II -> V
    e) IV -> II -> V -> I -> III

14. Which of the following is NOT an example of a vector in cell-based cloning?
    a) Bacteriophage
    b) YAC: Yeast Artificial Chromosome
    c) Plasmid
    d) Human gamete cell
    e) All of the above are used in cell-based cloning

15. Introducing DNA into a bacterial cell is called:
    a) Transformation
    b) Transfection
    c) Transposition
    d) RFLP insertion
    e) Isoschizomerization

16. All of the following are diagnostic of CML EXCEPT:
    a) Splenomegaly
    b) High WBC counts
    c) The presence of the Philadelphia chromosome
    d) BCR/ABL fusion transcript product
    e) All of the above are diagnostic of CML

17. Regarding the mechanism for Gleevec:
    a) It generally inhibits tyrosine kinase activity
    b) It dephosphorylates ATP before it can bind to the tyrosine kinase
    c) It works on PDGF, c-kit, ABL, and BCR/ABL
    d) All of the above
    e) None of the above

18. Regarding Rb:
    a) It is a tumor suppressor gene
    b) Unphosphorylated Rb inhibits cell division
    c) Phosphorylated Rb allows the cell to enter the S phase
    d) Papilloma virus allows for unchecked growth by keeping Rb "turned on"
    e) All of the above

19. All of the following are involved with RFLP analysis EXCEPT:
    a) DNA extraction
    b) Cutting DNA with a restriction enzyme
    c) Creating a cDNA library
    d) Using a gel to separate DNA by size
    e) All of the above are involve with RFLP analysis

20. The following DNA can be used to identify suspects in criminal proceedings:
    a) Hair left by the suspect
    b) Finger nail scraping (victim's fingernail)
    c) An aborted fetus
    d) A hydatiform mole
    e) All of the above

21. A technique allowing us to examine the expression of a gene in a given tissue is called:
    a) Southern blotting
    b) Northern blotting
    c) Eastern blotting
    d) Western blotting
    e) None of the above

22. The first step in screening a library is:
    a) Denaturing the DNA
    b) Lysing the cells that harbor the plasmids
    c) Hybridization of the DNA to a probe
    d) Transfer of the DNA to a support system
    e) Exposure to reveal the identity of the clone

23. DNA can be radiolabelled by:
    a) Adding a radiolabelled dNTP to the 3' end of the DNA using polynucleotide kinase
    b) DNA polymerase I can be used to incorporate a radiolabelled dNTP internally in the DNA
    c) Random priming can be used by incorporating a radiolabelled RNA primer into the DNA
    d) All of the above
    e) None of the above

    True/False

24. Loss of heterozygosity refers to inheriting a mutated allele from one parent, after which only one gene must be mutated before a phenotype is observed.
    
25. Cancer can result from the misincorporation of one nucleotide into a strand of DNA.
    
26. Sickle cell anemia results from a single DNA mutation.
    
27. Thalassemia is a hemoglobinopathy.
    
28. Recombination occurs in somatic cells, albeit with low frequency.
    
29. LINES and SINES are examples of transposable elements in human DNA.
    
30. Alternative splicing accounts for the diversity of T cells, so they may recognize millions of different antigens.
    
31. Chromosome walking through a cDNA library would allow an investigator to find a promoter sequence in a gene of interest.
    
32. Non-hematopoietic stem cells have been shown in research to develop into neurons in sites of spinal cord injury.
    
33. The exciting new drug Gleevec functions by reducing the activity of the BCR/ABL transcript, rather than killing rapidly dividing cells.
    
34. The advantage of RFLP analysis over PCR is that less product is needed in order to determine a sample sequence.
    
35. DNA spots on a chip can be hybridized to a probe to identify which genes are present in a given sample.
    
36. Low temperature and high salt concentration are considered highly stringent conditions.
    
37. RT-PCR can be performed to assess if a gene is transcribed in a given circumstance.
    
38. Eukaryotic DNA heated to 95 degrees Celsius will denature.

    Matching

39. Convert cytosine to uracil and adenine to hypoxanthine.
    
40. Act by adding an alkyl group to the N7 position of a purine.
    
41. Planar fused ring structures that insert in between stacked based.
    
42. Catalyzes the formation of pyrimidine dimers, causing a local distortion of DNA.
    
43. Affect base pairing because they resemble a natural base, but base pair with different partners.
    
44. Ethidium Bromide
45. Nitrous acid and its derivatives (found in hot dogs!)

    a) UV light
    b) Base analog(s)
    c) Alkylating agent(s)
    d) Deaminating agent(s)
    e) Intercalating agent(s)
    

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