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Exam 2 MCB2610 May 2014
Name_________________________
1.
In many bacteria, the electron carrier __________ is used for biosynthesis,
whereas __________ feeds the electron transport system.
a. NADPH; NADH
d. all of the above
b. FADH2; NADPH
e. none of the above
c. NADH; acetyl-S-CoA
-----------------------------2.
The enzyme pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to
pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is
an example of:
a. ATP synthesis by substrate-level phosphorylation
b. the use of a proton concentration gradient by [H+]-ATPases to
synthesize ATP
c. ATP coupled to FADH2 oxidation
d. a P-Type ATPase activity
e. none of the above
----------------------------3.
Fatty acids enter the TCA cycle after being degraded to what molecule?
a. acetyl-phosphate
d. all of the above
b. malonyl-S-CoA
e. none of the above
c. acetyl-S-CoA
----------------------------4.
Bacteria synthesize ribose for nucleotides using which pathway?
a. Embden-Meyerhoff-Parnas
d. tricarboxylic acid cycle
b. Entner-Doudoroff
e. all of the above
c. pentose phosphate shunt
----------------------------5. Which of the following is the best definition of fermentation?
A) The reduction of glucose to pyruvic acid
B) The complete catabolism of glucose to CO2 and H2O
C) The oxidation of a carbohydrate with organic molecules serving as electron
donors and acceptors
D) The production of ATP from glucose
E) The production of ethanol from glucose
----------------------------6. How does fermentation of glucose differ from the oxidation of glucose?
A) Fermentation of glucose is anaerobic; oxidation of glucose can be aerobic or
anaerobic.
B) Fermentation produces less ATP per glucose molecule than oxidation does.
C) Glucose is fermented by a different metabolic pathway than when it is oxidized
by
respiration.
D) Both a and b
E) All of the above
----------------------------7. What is the biological function of NAD+?
A) Accept electrons released by the oxidation of organic molecules
B) Provide electrons for the oxidation of glucose
C) Provide electrons for the reduction of pyruvic acid to lactic acid
D) Provide electrons for the substrate-level phosphorylation of ADP to ATP
E) None of the above
-----------------------------
8.A quorum-sensing gene system requires the accumulation of a secreted small
molecule called a(n):
a. autoinducer
d. inducer
b. activator
e. corepressor
c. repressor
----------------------------9.In a two-component signal transduction system, a _________ is transferred from a
sensor kinase to a _________ in response to an environmental signal.
a. phosphate; sensor domain
d. magnesium; sensor domain
b. phosphate; sensor phosphatase
e. magnesium; response regulator
c. phosphate; response regulator
----------------------------10. Promoters are specific sequences of __________ and in synthesizing RNA,
the polymerase moves __________ the promoter.
A) DNA / toward
B) RNA / toward
C) DNA / away from
D) RNA / away from
----------------------------11. Two-dimensional gel electrophoresis separates proteins based on:
a. charge and size.
b. size and sequence.
c. charge and amino acid content.
d. size and amino acid content.
e. charge and mass
----------------------------12. Say you were studying the genetics of a newly discovered species, Intel
degradus, and you found 6 genes scattered around the organism's linear chromosome
which allowed the organism to breakdown silicon. Further study revealed that all 6
genes were under the control of a repressor which you call slcR. In class we
discussed gene control hierarchies--the genes described above are an example of
what?
A) a regulon
B) a stimulon
C) an operon
D) a positive control system
E) a negative ground state
----------------------------13.
A consensus sequence consists of:
a. the region to which sigma factors can bind
b. the most likely base (or bases) at each position
c. hairpins in RNA to slow down or stop transcription
d. sequences to which ribosomes bind
e. primer sequences used to initiate transcription
----------------------------14.
What does it mean to say that the genetic code is redundant?
a. There is more than one kind of amino acid in proteins.
b. More than one rRNA can bind to the ribosome at the same time.
c. A codon is composed of more than one nucleotide.
d. More than one codon can specify the same amino acid.
e. All products of translation contain a certain minimum number of
mistakes, called mutations.
-----------------------------
15. Peptide bond formation effectively transfers the peptide from the tRNA in the
__________ to tRNA in the __________.
a. P-site; E-site
d. P-site; A-site
b. E-site; A-site
e. A-site; P-site
c. E-site; P-site
----------------------------16.
What is the significance of the Shine-Dalgarno sequence?
a. It is the site where RNA polymerase binds to begin transcription.
b. It is the site where a ribosome binds so that it can initiate
translation.
c. It is the site where DNA polymerase binds to begin chromosome
replication.
d. It is the site where the tRNA binds to the mRNA in translation.
e. It is the site where DNA polymerase begins synthesis of the
Okazaki fragments on the lagging strand.
----------------------------17. Which of the following sequences would pair with the sequence
5’ UACCAGCUG 3’?
A) 3’ GTCGACCAT 5’
B) 3’ ATGGTCGAC 5’
C) 5’ GUCGACCAU 3’
D) 5’ ATGGTCGAC 3’
E) 5’ AUGGUCGAA 3’
----------------------------18. The E site on the ribosome is the site where
A) ribosomes enter to begin translation.
B) tRNA enters the ribosome.
C) tRNA is released from the ribosome.
D) ribosomes exit to end translation.
E) mRNA binds to the ribosome.
----------------------------19. What is the role of sigma70 in E. coli?
A) To guide RNA polymerase to generic, housekeeping promoters
B) To guide RNA polymerase to heat shock promoters
C) To guide DNA polymerase to generic, housekeeping promoters
D) To guide DNA polymerase to heat shock promoters
E) To stop transcription at Shine-Dalgarno sequences
----------------------------20.
The smallest cellular genomes identified thus far are those of:
a. E. coli
d. Mycoplasma
b. Staphylococcus
e. yeast
c. Streptococcus
----------------------------21.
Accidental errors during replication are corrected by the DNA proofreading
activity intrinsic to:
a. DNA polI
d. DNA polIV
b. DNA polII
e. DNA polV
c. DNA polIII
-----------------------------
22.
When the chromosome replicates, how is the newly made strand related to its
template strand?
a. The two strands have identical sequences and are parallel to each
other.
b. The two strands have complementary sequences and are parallel to
each other.
c. The two strands have identical sequences and are antiparallel to
each other.
d. The two strands have complementary sequences and are antiparallel
to each other.
e. The two strands have identical sequences and are antiparallel to
each other, except that U replaces T.
----------------------------23. Imagine that you are designing an artificial chromosome to carry a large set of
genes that encode proteins that can convert lead to gold. Your first task is to
make an OriC region that will allow the chromosome to be replicated. Which of the
following sequences would be your best choice for the region of your new OriC that
will separate during the open-complex-formation step of replication?
A.
5’ GGATTTTATTAAATCAATCA 3’
3’ CCTAAAATAATTTAGTTAGA 5’
B.
5’ GATCGATCGATCGATCGATC 3’
3’ CTAGCTACCTAGCTAGCTAG 5’
C.
5’ GGCACGAATCGCGGGCAATC 3’
3’ CCGTGCTTAGCGCCCGTTAG 5’
D.
5’ TCGATCGATCGATCGATCGA 3’
3’ AGCTAGCTAGCTAGCTAGCA 5’
E.
5’ GCGCGGGCGCGCCGCGGCGC 3’
3’ CGCGCCCGCGCGGCGCCGCG 5’
----------------------------24. Imagine had identified an organism that you thought was a new pathogen, which,
unfortunately, you were having trouble getting to grow. In desperation, you had the
organism sequenced and after analyzing the genome you found that it lacked
superoxide dismutase, and was lac-. Of the conditions listed below, which would be
your best option for getting growth?
A) Minimal
B) Minimal
C) Minimal
D) Minimal
E) Minimal
-------
medium
medium
medium
medium
medium
with
with
with
with
with
H2O2 as an oxygen source
glucose as a carbon source,
lactose as a carbon source,
glucose as a carbon source,
lactose as a carbon source,
in
in
in
in
an
an
an
an
aerobic environment
anaerobic environment
anaerobic environment
anaerobic environment
25. The E. coli chromosome is about 4 million basepairs in size. If DNA polymerase
moves at a rate of 1000 basepairs per second, how long will it take to replicate
the chromosome (be careful!).
A) About
B) About
C) About
D) About
-------
4000 minutes
15 minutes
35 minutes
70 minutes
26. Imagine that you have found a set of 8 genes that causes a bacterium
(Facilemelodius rouge) to glow red in the presence of easy-listening music. One of
the genes encodes a protein that senses the music, and you name it ezlS. A quick
mapping of the remaining 7 elz genes shows that they are in 3 clusters at different
spots on the bacterial chromosome. Upon inactivating ezlS you discover that the
cells always red even in the presence of an extremely strong repressor like
Genkenuberstein's metal masterpiece “Speed Rune”. Which of the following statements
is true based on the information given above?
A. The 7
B. The 7
C. The 7
D. The 7
------27.
A.
B.
C.
D.
E.
elz
elz
elz
elz
genes
genes
genes
genes
form
form
form
form
a regulon
a regulon
an operon
an operon
under
under
under
under
negative
positive
negative
positive
control
control
control
control
Consider the molecule shown below, in what structure would it be found?
DNA
Ribosomes
mRNA
Two of the above
All of the above
----------------------------28.
Consider the following piece of DNA. Which part of it is the very oldest?
TTAGATCTCGGATTACGTATTCGACGTAGCGGCTAGCTCTCGGCAGGATCGGCTCGAGAATCGGTTCAGGATCGGC 3’
3’ AATGGCTAGCCTAATGCATAAGCTGCATCGCCGATCGAGAGCCGTCCTAGCCGAGCTCTTAGCCAAGTCCTAGCCG 5’
/
/
methyl
methyl
A. The left end of the top strand
B. The right end of the top strand
C. The left end of the bottom strand
D. The right end of the bottom strand
----------------------------29. During DNA replication in E. coli, all newly synthesized strands of DNA begin
with a small piece of RNA. Why?
A. Because DNA PolIII cannot start a new DNA chain but it can add dNTPs to a piece
of RNA.
B. Because DNA ligase cannot seal nicks in DNA, but it can seal nicks between
RNA and DNA.
C. Because RNA is more stable than DNA.
D. Because the leading strand is made in many small fragments.
E. Because the lagging strand is made in many small fragments.
-----------------------------
30.
Which of the following statement about the DNA duplexes shown below is true?
#1 5’ TTCGATCC 3’
3’ AAGCTAGG 5’
#2 3’ CCTAGCTT 5’
5’ GGATCGAA 3’
A. Only #1 is incorrectly drawn.
B. #1 and #2 show the same molecule.
C. Both #1 and #2 are incorrectly drawn.
D. Only #2 is incorrectly drawn.
------------------31 Your friend, Newton G.C. Finster, has fallen hard for his Bio107 lab partner
Anita Taratina. After searching the Web has found a perfect gift which he wants to
use to declare his affection. Fig YY, at the end of the exam, shows this gift-it’s a ring and finger made, each made of a piece of single stranded DNA that has
paired with itself. Knowing that you’re in MCB2610 Newton asks you what you think
of this opportunity. After looking at the gift, you wonder about his sense of
taste, but offer him the following advice based on what you’ve learned about DNA
structure. (By the way, don’t worry about the AT finger melting apart--the gift
comes with a self-cooling storage system.)
A. Don’t by the set, because
assemble as advertised.
B. Go ahead and buy the set,
C. Don’t by the set, because
assemble as advertised.
D. Don’t by the set, because
advertised.
---------------------
she’ll be getting a finger, but the ring won’t
the DNA should form the structures as advertised
she’ll be getting a ring, but the finger won’t
neither the ring nor the finger will assemble as
32. The normal mutation rate for most bacteria is on the order of 10-9 mutations per
base pair. However, one can often isolate “mutator” strains of bacteria which
mutate at a much higher rate. Suppose that you have isolate a bacterial species
which converts gold to lead (Leadto goldus), and you were interested in finding a
mutant which did the reverse reaction. If, with wild-type L. goldus (average 10-9
mutations per base pair and genome size of 3 million base pairs) you found the
mutant you wanted once in every million colonies, how often you find the same type
of mutant if you used a “mutator” strain with a mutation rate of 10-5 muations per
base pair?
33. In the November 1999 issue of the Journal of Bacteriology, Ding et. al
describe a protein from Acetivibrio cellulolyticus which functions as a scaffold to
hold seven proteins needed to degrade cellulose. The protein is called scaffoldin
and the sequence for the promoter region and the first part of the gene is given
below:
-35
-10
5’ATTCTATTTATCCCAAGTGTTCTCTGGTAACATATTTGTTTCGTACAAGTTTTACTTATTAACATGAG
AGACAATAACTAACATGTATTAGGTATTTGTTTTTTTTGGGTACCTTAAAGATCTTTAAATAGATCATATAA
Shine-Dalgarno
AAATAAAATTTTGGGAGGAACGGTTAAATGAAAAAGGTTATCAGTATCAGTATTGATTTTAGCTATCG-3’
A. The nontranscribed strand is shown above.
be.
Show about where the +1 site would
B. What are the first six amino acids of scaffoldin?
end of the exam for the decoding.
Use the codon table at the
34. Explain why the molecule shown below inhibits the genome replication of HIV.
35. Draw a diagram of the Lac region of E. coli when lactose is absent. Include the
following items:
LacI tetramer, Lac promoter region with -35, -10, +1 sites, The start codon of lacZ
operators O1 and O3 and looped DNA.
Fig. YY. Ring and finger