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Part I:   [64 points]:  For multiple choice, choose the one BEST answer.  Circle its letter. Read each question
and all 5 choices carefully because more than one answer might seem correct at first glance. 1 pt each

1.  DNA pol I functions include
     a.  5'-3' exonuclease activity
     b.  elongation of DNA polymerization
     c.  initiation of DNA polymerization
     d.  a and b
     e.  all of the above

2.  Transcription begins
     a.  at the promoter
     b.  near the promoter
     c.  at the operator
     d.  a and b
     e.  all of the above

3.  Ligase
     a. links two molecules of single stranded DNA
     b. links two strands of double stranded DNA
     c. links two molecules of single stranded RNA
     d. links two strands of double stranded RNA
     e. breaks and "re-links" DNA chains

4.  A promoter is
     a.  the transcription start site
     b.  the site RNA polymerase binds DNA
     c.  the site DNA polymerase binds DNA
     d.  only found in prokaryotes
     e.  all of the above

5.  The lac operon is stimulated by
     a.  lactose
     b.  cAMP
     c.  glucose
     d.  a and b
     e.  all of the above

6.  Okasaki fragments
     a.  are a result of discontinuous DNA synthesis
     b.  are synthesized 3'-5'
     c.  are synthesized primarily by DNA pol I
     d.  a and b
     e.  all of the above

7.  DNA is synthesized
     a.  3'-- 5'
     b.  5' -- 3'
     c.  a and b are each true sometimes
     d.  N terminus -- C terminus
     e.  C terminus -- N terminus
     f.  d and e are each true sometimes

8.  cAMP regulates the lac operon by
     a. binding to the operator to up-regulate transcription
     b. binding to the lac repressor to down-regulate transcription
     c. binding catabolite activated protein; the complex  up-regulates transcription
     d.  binding catabolite activated protein; the complex  down-regulates transcription
     e.  binding glucose; the complex  down-regulates transcription
 
 

9.  Functions of, or uses for the acyl group of acetyl-CoA include
     a.  delivery from pyruvate to TCA cycle for degradation
     b.  energy resource
     c.  biosynthetic precursor
     d.  a and b
     e.  all of the above

10.  Regulation of gene expression can occur by
     a.  binding of  proteins to specific DNA sequences in prokaryotes only
     b.  binding of  proteins to specific DNA sequences in eukaryotes only
     c.  binding of  proteins to specific DNA sequences in prokaryotes and eukaryotes
     d.  binding of proteins to DNA regions regardless of DNA sequence, just shape
     e. none of the above

11.  The synthesis of RNA using  a DNA template is
     a.  transposon
     b.  transcription
     c.  translation
     d.  translocation
     e.  viral replication

12. The presence of deoxyribose in DNA, compared with ribose in RNA, accounts for
     a.  the use of thymidine rather than uracil
     b.  base pairing specificity
     c.  increased stability of DNA in aqueous environments
     d.  the helical shape of DNA
     e.  specific protein binding properties

13. Base pairing in DNA
     a. is restricted by steric hindrance
     b. restricted by size of the base
     c. restricted by ability of base to form H-bonds
     d. always purine - pyrimidine pairing
     e. all of the above

14.  Which of the following is NOT a feature of DNA?
     a.  the presence of thymine instead of uracil
     b.  DNA can not be easily denatured because of the stability of its double helix structure
     c.  it is a double helix that is easily bendable
     d.  the 3 common forms of DNA are A, B, and Z
     e.  it does not have a hydroxyl group at the 2  carbon position

15.  The rate of oxidative phosphorylation in your body is determined mainly by
     a.  how much food you eat
     b.  how much ATP you need
     c.  how much ADP you need
     d.  whether or not you are breathing
     e.  how fast glycolysis is occurring

16.  RNA is synthesized
     a.  3'-- 5'
     b.  5' -- 3'
     c.  a and b are each true sometimes
     d.  N terminus -- C terminus
     e.  C terminus -- N terminus
     c.  d and e are each true sometimes

17. In DNA replication, the lagging strand is different from the leading strand because
     a.  the lagging strand contains nicks that must be repaired by ligase
     b.  the lagging strand has RNA/DNA duplexes called  Okazaki fragments
     c.  the lagging strand elongates DNA in a 3  to 5  direction
     d.  a and b
     e.  b and c
 

18. Introns are
     a.  removed from mRNAs before or during translation
     b.  excised from pre-mRNA as part of its maturation to mRNA
     c.  removed from rRNAs in the nucleolus
     d.  excised from pre-rRNA as part of its maturation to rRNA
     e.  excised from all eukaryotic pre-RNA as part of their maturation to RNA

19.  Proofreading by DNA polymerases employs
     a.  3'-5' endonuclease
     b.  3'-5' exonuclease
     c.  5'-3' endonuclease
     d.  5'-3' exonuclease
     e.  none of the above - DNA polymerases do not have nuclease activity

20.  In the absence of inducer, the lac repressor
     a. binds tightly and rapidly to the operator
     b. floats freely in the cell
     c. binds lactose or allolactose
     d. begins transcription
     e. binds tightly and rapidly to the promoter

21.  The 5'  cap
     a.  is encoded in the DNA
     b. is  added only to mRNA
     c.  is added to all RNA transcripts
     d.  a and b
     e.  all of the above

22.  Which of the following is NOT TRUE about restriction endonucleases?
     a.  they bind to either the 5  or 3  terminus and remove nucleotides one at a time
     b.  as a part of the bacterial DNA immune system, they protect the cell against entry by foreign DNA
     c.  they are enzymes that cleave double-stranded DNA at specific sites
     d.  their cleavage process often produce  sticky ends  that are used in DNA recombination
     e.  none of the above

23.  The lac operon is inhibited by
     a.  glucose
     b.  cAMP
     c.  galactose
     d.  lactose
     e.  all of the above

24. Transcription in E. coli requires
     a. core enzyme of RNA pol
     b. holoenzyme of RNA pol
     c. holoenzyme of RNA pol for initiation; core enzyme of RNA pol for elongation
     d. core enzyme of RNA pol for initiation; holoenzyme of RNA pol for elongation
     e. other:

25. How does the twisting into a helix contribute to the stability of DNA s structure?
     a.  it brings the stacked base pairs close to one another
     b.  water is excluded from the hydrophobic core
     c.  hydrophobic interactions in the core & the H bonds between bases contribute to DNA stability
     d.  the major and minor grooves allow proteins to anchor there
     e.  all of the above

26.  Nicks in DNA are repaired by
     a.  DNA pol I
     b.  DNA pol III
     c.  ligase
     d.  primase
     e.  replicase
 
 

27.  Which of the following processes are part of translation?
     a.  initiation
     b.  elongation
     c.  termination
     d.  a and b
     e.  all of the above

28.  A plasmid is
     a.  a section of DNA that has been spiced out by a restriction endonuclease
     b.  a form of DNA found in eukaryotes
     c.  a self-replicating circular piece of DNA
     d.  a replicon that has multiple origins of replication
     e.  none of the above

29.  Homologous DNA recombination plays an important role in
     a.  DNA replication
     b.  RNA replication
     c.  DNA repair
     d.  transcription
     e.  translation

30.  The poly (A)  tail
     a.  is encoded in the DNA
     b. is  added only to mRNA
     c.  is added to all RNA transcripts
     d.  a and b
     e.  all of the above

31. In prokaryotes, a cluster of genes that performs coordinated gene expression and regulations is called a(n)
     a.  intron
     b.  operon
     c.  exon
     d.  transposon
     e.  polycistron

32.  In semi-conservative replication, each replicated DNA molecule will consist of
          a.  old and new DNA dispersed on both strands
     b.  one old parental strand and one new strand
     c.  only the old parental DNA on both strands
     d.  new DNA on both strands
     e.  there is no such thing as semi-conservative replication of DNA

33. The sigma subunit of E. coli RNA polymerase is
     a. a polypeptride
     b. required for transcription initiation at promoters
     c. a protein
     d.  a and b
     e.  all of the above

34.  DNA
     a.  is comprised of two anti-parallel strands
     b.  has major and minor grooves along its surface
     c.  is negatively charged
     d.  a and b
     e.  all of the above

36. Protein is synthesized
     a.  3'-- 5'
     b.  5' -- 3'
     c.  a and b are each true sometimes
     d.  N terminus -- C terminus
     e.  C terminus -- N terminus
     c.  d and e are each true sometimes
 

37.  DNA gyrase
     a.  introduces positive or negative supercoiling in DNA
     b.  destabilizes base pairing to separate the double stranded molecule into single strands
     c.  is found at the replication fork
     d.  a and b
     e.  all of the above

38. Which of the following is (are)  involved in translation?
     a.  mRNAs
     b.  tRNAs
     c.  ribosomes
     d.  all of the above
     e.  none of the above

39.  -  52.  Fill in the following table: put a check if the characteristic is true of the indicated process
 
 
 
 

DNA synthesis
RNA synthesis
 

requires DNA template
 
 
 

product is complete complementary representation of template
 
 
 

5' --> 3' ONLY
 
 
 

occurs in nucleus (in eukaryotes)
 
 
 

reaction driven by hydrolysis of nucleoside triphosphate --> pyrophosphate
 
 
 

requires primer
 
 
 

template is fully conserved and unchanged
 
 
 

53. -  64.   Match the enzyme with the function - be sure to choose the BEST answer (do not use a subset if the
entire set is also a choice)

      53.  destabilizes DNA base pairs                      a.  helicase
                                                  b.  DNA pol I
      54.  synthesizes RNA using a DNA template                  c.  RNA polymerase
                                                  d.  gyrase
      55.  synthesizes DNA using a DNA template                  e.  primase
                                                  f.  DNA pol III
      56.  synthesizes DNA using an RNA template                 g.  aminoacyl tRNA synthetase
                                                  h.  topoisomerase
      57.  transcribes a short RNA strand for replication initiation       i.  DNA pol II
                                                  j.  ligase
      58.  main DNA repair enzyme                      k. phosphofructokinase
                                                  m. exonuclease
      59.  synthesizes tRNA                            p.  reverse transcriptase
                                                  r.  DNA polymerase
      60.  aminoacylates tRNA                          s.  RNAase
                                                  t.  restriction endonuclease
      61.  main replication enzyme                          w.  single stranded DNA binding
                                                                 protein
      62.  cleaves DNA at specific sequences                x.  none of the above

      63. cleaves RNA at specific sequence

      64.  synthesizes RNA using an RNA template

EXTRA CREDIT: Write you own question and answer it.  HINT: this is you opportunity to show what you
know.  Do not ask yourself a question if you aren't sure of the answer.  Ask the question you were sure would
be on the exam, so you studied the material, and then somehow it was left off!  Your score will depend on the
quality of the question as well as the answer - up to a possible maximum of  5 points. [you may use one of the above
instead of omitting it, if you choose]

Part II:  [40 points]  Answer 4 (omit 2)  10 points each:   Be sure that your answers address the questions.  Be
focussed and clear.

1.  The following terms are used to describe protein structure.  For each, state whether it is likely to be subject
to alteration by a single base pair mutation in a gene's coding region (Always - Never - Sometimes).  Explain -
briefly.
      a. primary structure
 

      b. secondary structure
 

      c. tertiary structure
 

      d. quaternary structure
 
 

      e. disulfide bonds
 
 

2. Why is protein generally considered to be the final product of gene expression (rather than, e.g.,
carbohydrates or lipids)? Where do other biological molecules, like lipids and carbohydrates, come from? Does
the genome control their production - and if so, how?
 
 
 
 
 
 
 
 
 
 
 
 
 
 

3.  What are the major important features or characteristics required for a useful vector?
     (a) expression vector?
     (b) cloning vector?
In addition to specific restriction sites, list (at least) 3 other types of DNA sequences or elements which need to
be found in a vector in order for it to be used (a) for the expression of a recombinant protein in a eukaryotic
cell or (b) for generating many copies of the DNA.   While your description of these genetic elements may be
in general terms, be sure that you state clearly what task they are intended to accomplish.   Explain why each of
these is important. 4.  If a human gene is isolated from a cDNA library and also from a genomic DNA library, would you expect
the sequences of these isolated DNAs to be the same or different?  Explain.  Which would you choose to use if
your goal was to produce large quantities of the encoded polypeptide?  Explain.  Which would you choose to
use if your goal was to study how this gene is regulated in people?  Explain.
 
 
 
 
 
 
 
 
 
 
 
 

5.  Gene regulation may occur at any of several reactions.  Briefly outline the scheme of gene expression,
pointing out the major regulatory steps.  Which of these do you think might be likely targets for intervention?
Explain your logic.  (Note - there are many possible answers here).
 
 
 
 
 
 
 
 
 
 
 
 
 

6.  What do you think is the most exciting, interesting, potentially useful (etc.) part of the current and
developing genetic and molecular technology.  Explain your answer USING SPECIFIC EXAMPLES of
techniques and potential.  [Note: while this asks for your opinion, and as such, any opinion may be stated, the
score will depend on the cogent defense of that opinion!]