MOL

 214  
Exam  1  
 
March  5,  2014  
 
 
 
 
Your  exam  code  number  is:    
 
Write  this  number  on  each   key  
page  of  your  exam.  
 
 
 
DO  NOT  write  everything  you  know  about  a  topic,  this  will  waste  your  time.    If  you  provide  more  than  one  
answer  for  a  question  only  your  first  answer  will  be  graded.  
 
If  you  need  extra  space,  continue  only  on  the  back  of  the  page  that  the  question  is  written  on.    Clearly  
label  that  you  are  using  the  back  for  your  answer.  
 
Remember  to  write  legibly,  if  we  can’t  read  it,  we  can’t  grade  it!  
 
 
 
 
 
 
I  pledge  my  honor  that  I  have  not  violated  the  honor  code  during  this  
examination.  

 
Signature:  __________________________________  
 
Printed  Name:  ___________________________  
 Exam  number:______________________  
Multiple Choice Questions:

1. Which of the following statements about the newly synthesized strand of a human chromosome is
correct? (3)
(a) It was synthesized from a single origin solely by continuous DNA synthesis.
(b) It was synthesized from a single origin solely by discontinuous DNA synthesis.
(c) It was synthesized from a single origin by a mixture of continuous and discontinuous DNA
synthesis.
(d) It was synthesized from multiple origins solely by continuous DNA synthesis.
(e) It was synthesized from multiple origins solely by discontinuous DNA synthesis.
(f) It was synthesized from multiple origins solely by a mixture of continuous and discontinuous
DNA synthesis.
(g) It was synthesized from multiple origins by either continuous or discontinuous DNA synthesis,
depending on which specific daughter chromosome is being examined.

2. Which of the following statements does not describe both eukaryotic and prokaryotic transcription? (3)
(a) Promoter elements in the DNA sequence are required for polymerase binding.
(b) Proteins interact with the RNA polymerase and control its binding to DNA.
(c) RNA polymerase opens a double-stranded DNA molecule to expose the template strand.
(d) RNA polymerase can transcribe in either direction once it binds to a promoter sequence.
(e) None of above.

3. Which of the following is required for both splicing and transcription termination in eukaryotes? (3)
(a) A hairpin
(b) RNA polymerase II C-terminal domain
(d) snRNPs
(e) poly(A) polymerase
(f) a nuclease

4. In 2031, the newest Mars expedition returns with samples of

single-celled Martian life forms. You are running a laboratory that
is part of the consortium characterizing the proteome of the
creatures. Pictured is an amino acid present in proteins from the
Martian cells. You wish to study its chemical properties in earthly
cells. Which of the following amino acids do you think you could
most readily replace in a bacterial peptide with the least
perturbation? (3) (A chart of amino acid structures is given on the
last page of the exam)
(a) glycine
(b) histidine
(c) proline
(d) glutamic acid
(e) phenylalanine

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5. Which of the following types of bonds would you expect to form between the R groups of two polar,
charged amino acids? (3)
(a) disulfide bond
(b) electrostatic interaction
(c) hydrophobic interaction
(d) peptide bond
(e) hydrogen bond

6. Which of the following bonds/interactions is strongest? (3)

(a) ionic bond
(b) electrostatic interaction
(c) hydrophobic interaction
(d) peptide bond
(e) hydrogen bond

7. You are studying a membrane protein with four transmembrane alpha helices that assemble into a tight
bundle called a 4-helix bundle (illustrated above). Which of the following best describes the structure of
the 4-helix bundle? (3)
(a) A 4-helix bundle is an example of primary structure.
(b) A 4-helix bundle is an example of secondary structure. This  question  had  a  typo  (it  was  incorrect  to  
(c) A 4-helix bundle is an example of tertiary structure. talk  about  bases  in  proteins).    We  accepted  
(d) A 4-helix bundle is an example of quaternary structure. (e),  which  was  the  only  technically  correct  
answer  in  that  respect,  as  well  as  (a),  which  
would  have  been  correct  if  not  for  the  typo.  
8. Which of the following is the strongest prediction you can make about the transmembrane portion of this
4-helix bundle? (3)
(a) There will be mostly hydrophobic bases on the portions facing the outside of the bundle.
(b) There will be mostly hydrophilic bases on the portions facing the outside of the bundle.
(c) There will be mostly hydrophobic bases on the portions facing the inside of the bundle.
(d) There will be mostly hydrophilic bases on the portions facing the inside of the bundle.
(e) There will be mostly small side chains on the portions facing the inside of the bundle.

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Short  Answer  Questions  
 
9. In  the  early  1900s  scientists  showed  that  chromosomes  were  the  basis  for  inheritance,  but  the  
predominant  hypothesis  was  that  proteins  were  the  hereditary  material.    Why  was  this  the  
prevailing  model?  (4  pts)  
 
 
 
Chromosomes  are  made  of  proteins  and  DNA.    Proteins  were  known  to  have  20  amino  acids  
as  building  block  choices,  while  DNA  has  only  four  bases.    Proteins  could  code  for  much  
greater  variety  in  their  amino  acid  sequence  than  DNA  could  in  its  nucleotide  sequence.  
 
 
10. A  newly  discovered  protozoan  has  a  genome  that  is  40%  Adenine.    What  is  the  percentage  of  
Guanine?  (2)  
 
10%  
 
 
11. Griffith  discovered  a  “transforming  principle”  based  on  experiments  mixing  heat-­‐killed  S  and  live  
R  bacterial  strains.  Two  decades  later,  Avery  MacLeod,  and  McCarty  determined  the  identity  of  the  
"transforming  principle".    What  was  the  key  evidence  that  they  provided?  (5)  
 
 
 
After  separating  the  lipids  and  carbohydrates  from  the  proteins  and  nucleic  acids  of  
bacterial  cell  extracts,  Avery  et  al.  subjected  the  proteins  and  nucleic  acids  to  selective  
degradation  (by  proteases,  RNase,  and  DNase).    The  fact  that  transformation  was  abolished  
only  by  DNase  was  strong  evidence  that  DNA  was  the  agent  of  transformation.  
 
 
 
 
12. One  of  the  critical  experiments  showing  that  DNA  was  the  hereditary  material  was  performed  by  
Hershey  and  Chase  using  bacteriophage  that  infect  E.  coli.    An  important  technological  advance  for  
their  experiment  was  the  invention  of  the  Waring  blender.    Why  was  this  important  for  their  
experiment?  (5)  
 
The  goal  of  this  experiment  was  to  determine  whether  it  is  the  protein  or  DNA  that  
provides  the  information  for  generating  new  bacteriophage.    The  interpretation  of  the  
experiment  depended  on  their  being  able  to  determine  whether  it  was  the  DNA  or  the  
protein  that  was  what  was  injected  into  the  cell.    To  be  able  to  distinguish  this,  they  had  to  
be  able  to  follow  the  protein  (phage  body)  and  the  DNA  and  that  meant  that  they  had  to  be  
able  to  separate  the  phage  bodies  from  the  cell,  which  is  what  they  used  the  blender  to  do.  
 
 
 
   

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13. Below  is  an  illustration  of  the  restriction  maps  of  a  plasmid  vector  and  a  molecule  of  DNA  
containing  a  gene  you  wish  to  clone  into  the  vector,  as  well  as  the  specificities  of  several  
restriction  endonucleases  available  to  you  for  the  cloning  experiment.    

 
 
  Which  enzymes  should  be  used  to  cut  the  vector,  and  which  to  cut  out  the  gene  of  interest?  (4)  
 
 
The  vector  should  be  cut  with  BsiWI  and  the  gene  of  interest  should  be  cut  out  with  BsrGI  and  
BSiWI.  
 
 
 
14. Why  is  DNA  helicase  required  for  DNA  replication  in  the  cell  but  not  for  PCR  or  DNA  sequencing?  
(4)  
 
 
Helicase  is  an  enzyme  that  separates  the  two  strands  of  a  DNA  double  helix.    This  is  unnecessary  
during  PCR  and  sequencing  reactions  because  heat  is  used  to  separate  the  two  strands  in  PCR.  
 
15. Label  the  5’  and  3’  ends  of  each  parental  DNA  strand.  (2)  

 
   

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16. Three  different  types  of  nucleotides  are  shown  below.    For  each  molecule,  specify  whether  DNA  
polymerase  could  add  the  molecule  to  a  strand  of  DNA  that  it  is  polymerizing.    If  your  answer  is  no,  
explain  briefly  why  the  molecule  cannot  be  added.  (4.5)  
 

no;$DNA$pol$can$only$
no;$this$is$a$
add$nucleotide$ yes$
ribonucleotide$
triphosphates$

 
 
17. Could  DNA  polymerase  extend  a  strand  by  adding  deoxynucleotide  triphosphates  to  molecules  
ending  with  the  structures  shown  below?    Again,  give  a  brief  explanation  for  cases  in  which  your  
answer  is  no.  (4.5)  
 

no;$dideoxynucleotides$
yes$ yes$
are$chain$terminators/$
there$is$no$3′$OH$to$add$to$
 
 
18. Why  can’t  all  DNA  mutations  be  corrected  by  the  proofreading  activity  of  DNA  polymerase?  (4)  
 
Proofreading  only  corrects  mismatched  base  pairs  arising  during  replication.    Polymerase  
thus  cannot  correct  spontaneous/chemically  induced  base  modifications,  non-­‐mismatch  
mutations  like  insertions/deletions/double  strand  breaks,  or  a  mutation  of  the  template  
strand  which  can  be  replicated  (“incorrectly”,  but  as  normal).    No  credit  for  answers  
concerning  proofreading  error  rate,  beneficial  mutations,  hereditary  mutations,  or  other  
answers  which  avoided  discussing  how  the  actual  mechanism  of  proofreading  could  be  
bypassed  by  a  specific  alternate  mutational  mechanism.  
 
 
 
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19. Exposure  of  DNA  to  nitrous  acid  results  in  conversion  of  adenine  to  hypoxanthine.    What  type  of  
mutation  would  you  classify  this  as?  (3)  
    (a)   Depurination  
    (b)   Deamination  
    (c)   Oxidation  
    (d)   Thymidine  dimer  formation  
   
  The  altered  A  base  pairs  with  C  (cytosine).    Why  is  this  a  problem  if  there  are  still  2  hydrogen  bonds  
formed  between  the  altered  A  and  the  C?  (3)  
 
 
 
Because  A  is  supposed  to  pair  with  T.    When  the  hypoxanthine  is  replicated  or  transcribed  
erroneously,  problems  may  result.  
 
 
 
 
 
20. You  have  managed  to  purify  telomerase  from  a  newly  discovered  protozoan.    You  test  the  enzyme  
in  a  reaction  with  artificial  telomeres  and  radioactive  dGTP  and  run  a  gel  to  analyze  the  products.    
Surprisingly,  you  find  that  the  bands  on  the  gel  differ  by  12  bases.    Explain  the  property  of  your  
telomerase  that  must  be  different  from  other  known  telomerases.    (4)  
 
 
The  telomerase  RNA  must  be  twice  as  long  as  standard  telomerase  RNA  –  must  have  two  
units  of  a  6-­‐base  repeat  or  a  12  base  repeat.  
 
 
 
 
21. Most  of  the  cells  in  the  human  body  are  not  replicating.    What  stage  of  the  cell  cycle  are  they  in?  
(2)  
 
G0.    (We’ll  also  accept  something  along  the  lines  of  “a  special,  extended  G1  phase.”    Simply  
“G1”  is  incorrect.)    
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22. In  a  project  for  your  thesis,  you’ve  been  studying  the  yeast  cell  cycle.    You  want  to  use  Western  
blotting  to  detect  a  cyclin  and  a  CDK  in  a  time  course  of  an  actively  growing  culture  of  yeast  cells.    
You  intended  to  prepare  two  separate  blots  and  apply  an  antibody  to  cyclin  to  one  of  them  and  an  
antibody  to  CDK  to  the  other,  but  you  accidentally  added  both  antibodies  to  one  of  your  blots.    
Which  set  of  bands  corresponds  to  the  cyclin,  and  which  to  the  CDK?  (2)    
   
 
 
The  top  set  of  bands  are  the  cyclin,  
and  the  bottom  set  are  the  CDK.  
 
 
 
 
 
 
   
 
 
 
 
  Why  was  it  necessary  for  you  to  perform  a  Western  blot  to  identify  these  proteins  instead  of  just  
staining  the  SDS-­‐polyacrylamide  gel  with  protein  dye?  (3)  
 
 
  The  stain  labels  all  the  cellular  proteins  so  it  will  be  difficult  to  tell  which  protein  is  cyclin  or  
Cdk.  
 
 
 
 
 
23. Walther  Flemming  was  the  first  to  observe  chromosomes  and  describe  mitosis.    How  is  the  
structural  organization  of  chromatin  during  mitosis  different  from  its  organization  during  the  G1  
phase  of  the  cell  cycle?  (4)  
 
 
During  G1  (or  interphase  in  general)  chromatin  is  packed  more  loosely.    When  the  cell  enters  
mitosis,  chromatin  packs  much  more  tightly  to  form  the  chromosomes  that  are  visible  at  
metaphase.  
 
 
 
 
 
 
   

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24. Pictured  above  is  the  beginning  of  a  bacterial  transcription  unit,  including  its  promoter.    Write  out  
the  sequence  of  the  first  6  bases  of  the  mRNA  transcript  according  to  convention  (4)  
 
 
          CGUCAC  
 
 
 
25. Based  upon  the  results  of  DNA  sequencing  of  the  human  genome,  it  is  estimated  that  there  are  
around  25,000  genes  in  the  human  genome.    However,  the  number  of  different  types  of  proteins  is  
much  higher  than  this.    Why?  (4)  
 
 
    Alternative  splicing  can  produce  many  different  proteins  from  a  single  gene.  
 
 
 
 
26. Secondary  structure  is  stabilized  by  hydrogen  bonds  between  atoms  of  the  polypeptide  backbone  
rather  than  between  the  side  chains.    How,  then,  do  the  side  chains  exert  any  influence  over  the  
structure  of  a  protein?  (4)  
 
 
  H-­‐bonds  of  the  backbone  are  essential  for  secondary  structure  (and  the  nature  of  the  amino  
acid  side  chains  can  influence  whether  there  is  more  alpha  helix  or  beta  sheet)  but  the  side  
chains  are  primarily  responsible  for  the  tertiary  structure  of  the  protein.      
 
 
 
 
27. Name  two  properties  by  which  proteins  can  be  separated.    Provide  a  technique  for  each  property  
that  can  be  used  to  separate  proteins  based  on  this  property.  (4)  
 
There  are  many  possible  answers,  including  size,  charge,  shape/affinity,  hydrophobicity,  
which  can  be  separated  by  different  techniques  (SDS  PAGE,  ion  exchange,  affinity,  and  
hydrophobic  interaction  chromatography).    
If  chromatography  is  listed  as  the  method,  the  type  of  chromatography  should  be  specified.  
 
 
 
   

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