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LS3 MIDTERM II EXAM

INSTR:L.JOHNSON

March1,2013

NAME:_________________________________
(last)
(first)
I.D. #__________________________________
TA___________________________________
TestFormB
INSTRUCTIONS
Thisexamis10pageslong.Beforestartingmakesureyouhaveallthepages.
Usinganumber2pencil,onthefrontofyourscantronfillintheInstructor(Johnson),Class
(LS3),Hour(12:00or1:00),
WriteandBubbleinyourUID,yourlastnameandfirstname.
OnthebackofyourscantronWriteandBubbleinyourUIDandTestForm(seeabove).

1. During translation, peptide bond formation involves a


nucleophilic attack. Which atom acts as the nucleophile?
a. The oxygen from the carboxyl terminus of the growing
peptide chain.
b. The oxygen from the carboxyl terminus of the incoming
amino-acyl tRNA.
c. The nitrogen from the amino terminus of the growing
peptide chain.
d. The nitrogen from the amino terminus of the
incoming amino-acyl tRNA.--> proteins synthesized N C
2. What concept below best explains how 40 tRNAs can read 61
codons?
a. Wobble-pairing
b. Degenerate code each amino acid has several codons
c. tRNA synthetases charge all tRNAs for one amino acid
d. All of the above.
3. Assume there is only one tRNA for cysteine. Using the genetic
code and wobble rules on the last page of the exam, which
anticodon below would you expect to find on the cysteine tRNA?
(make sure it doesnt recognize any non-cysteine codons)
a. 5 GCA 3
b. 5 ACG 3
c. 5 ICA 3
d. 5 ACI 3

4. Which of the following conclusions are consistent with the data


shown above.
a. -galactosidase is less stable than its mRNA.
b. Addition of the inducer slows the growth rate of the cell.
c. Elimination of the inducer has a drastic effect on the levels
of -galactosidase.
d. Addition of the inducer leads to an increase in mRNA
followed by an increase in protein shows that
regulation is happening at level of transcription
2

5. Which of the following is true of prokaryotic translation initiation?


a. The small ribosomal subunit scans the mRNA for the first
AUG no, this is eukaryotes
b. The small ribosomal subunit scans the mRNA for a TATA
sequence no, euk
c. The small ribosomal subunit binds IF1 in the A site
and IF3 in the E site yes
d. The small ribosomal subunit contains the 23S rRNA.--> no,
23srRNA is large subunit
e. All of the above.
6. Which of the following proteins can bind to the A site of the
ribosome?
a. RF1
b. RF2
c. RRF
d. All of the above.
7. Which of the following molecules is not an allosteric effector?
a. IPTG IPTG is an inducer therefore it is an effector
b. X-GAL X-gal is substrate but not inducer; NOT effector!
c. Arabinose binds to AraC and changes its conformation so
it is an effector
d. tryptophan
e. cAMP binds to CAP so it is an effector
8. The elongations factors, EF-Tu and EF-G
a. are both G poteins.--> yes
b. both play a role is escorting charged tRNAs to the A site.-->
no, EF-G does translocation
c. both undergo a conformation change upon hydrolysis of
GTP yes; EF-Tu hydrolyzes and lets go of charged tRNA;
EF-G hydrolyzes and pushes tRNAs into next site
d. a and b
e. a and c
9. Which of the following DNA binding motifs grasp DNA like a pair
of scissors?
a. Helix-turn-helix no
b. Zn finger no
c. Homeodomain no
d. Basic leucine zipper yes, have DNA binding domain
(basic charged region) followed by Leucine zipper that has
a leucine every 7th a.a.
e. All of the above.
10.
Which of the following proteins is under positive allosteric
control:
a. IF1
b. Gal80p
c. CAP- allosteric effector cAMP binds to it and it can activate

d. Lac repressor
e. Sigma factor
11.
Which of the following factors play a role in two stages of
translation (initiation, elongation, termination)?
a. EF-Tu
b. EF-G elongation, termination (translocates)
c. IF3 initiation, termination (dissociates the ribosome
subunits)
d. a and b
e. b and c
12.
Pol II transcripts are modified at the 5 end with
a. ATP in a 5-3 linkage
b. ATP in a 5-5 linkage
c. GTP in a 5-3 linkage
d. GTP in a 5-5 linkage
13.
Charging of tRNAs by amino acyl synthetases is a two step
process. The first step can be described as:
a. Transesterification
b. Phospho-transfer reaction
c. Adenylylation
d. Hydrolysis
14.
In the second step in the tRNA charging reaction, the
nucleophile is
a. The 2OH on ATP
b. The carboxyl oxygen on the amino acid
c. The 3 OH on the tRNA everything is always 35
d. The nitrogen on the amino acid

15.

16.

a.
b.
c.
a.
b.
c.
d.

In the image above, the gene is being transcribed


from right to left
from left to right
There is not sufficient information to determine the
direction of transcription.
Pol II transcripts are modified at the 3 end
by cleavage followed by addition of poly-A yes
by termination followed by addition of poly-A no,
termination happens separately and a while after cleavage
to protect them from degradation yes
a and c
4

17.
is

e. b and c
The expression of eve in stripe 2 of the Drosophila embryo
a.
b.
c.
d.

activated by bicoid and hunchback


activated by giant and bicoid
repressed by kruppel and hunchback
repressed by bicoid and kruppel.
18.
Which of the following factors has helicase activity?
a. TFIIA
b. TFIIB
c. TFIID
d. THIIE
e. TFIIH has helicase activity and CTD phosphorylation
19.
Which of the following factors phosphorylates the Pol II CTD
during initiation?
a. TFIIA
b. TFIIB
c. TFIID
d. THIIE
e. TFIIH
20.
Which of the following is true of eukaryotic translation
initiation?
a. The 5 cap on the mRNA is recognized by an initiation
factor.--> yes, 5 cap is recognized by eIF4
b. The initiating tRNA is charged with methionine and then
modified by formylation.
c. The Shine-Dalgarno sequence base pairs to the 16S rRNA.
d. IF1 binds and blocks the A site.
e. All of the above are true.
21.
Phosphorylation of the Pol II CTD
a. recruits polyadenylation enzymes yes
b. recruits capping enzymes
c. promotes escape from the promoter it loosens the tail so
the polymerase can loosen its grip on transcription factors
and the promoter and start moving along the DNA
d. recruits splicing enzymes
e. All of the above.
22.
When E. coli is grown in media containing both glucose and
lactose
a. the lac operon is induced but transcription is not
activated yes; induced because allolactose will bind to lac
repressor to prevent it from binding the DNA
b. the lac operon is activated but not induced no, activator
CAP-cAMP isnt binding
c. the level of transcription from the lac operon is considered
basal yes, neither activator nor repressor bound

d. a and c
e. b and c
23.
The Torpedo Model refers to
a. how DNA is synthesized at the replication fork.
b. how RNA is terminated in eukaryotes polymerase keeps
transcribing after cleavage, the 3 end is
exposed/uncapped, RNase jumps up and starts chewing the
RNA
c. how RNA is terminated in prokaryotes
d. how translation is terminated
24.
Which of the following is NOT true about yeast mating type
control?
a. Mcm1 in combination with 1 activates specific genes
true
b. Haploid specific genes are on unless repressed in a diploid
cell true
c. Mcm1 in combination with a1 activates a specific genes
MCM1 will express a1 by itself
d. a1 and 2 combine to form a repressor true; they repress
alpha 1

25.
In the graph above, the peaks of radioactivity look different
from the peaks of OD 260 because
a. the radioactivity is only measuring mRNA and the OD260 is
measuring rRNA.
b. the radioactivity is only measuring newly synthesized RNA
and the OD260 is measuring total RNA, which is mostly
rRNA.
c. the radioactivity is measuring RNA and the OD260 is
measuring protein.
d. All of the above.
26.
Which of the following factors recognizes the TATA box?
a. TFIIA
b. TFIIB
c. TFIID contains TBP as one of its proteins
6

27.

28.

29.

d. THIIE
e. TFIIH
The Gal80p repressor inhibits transcription by
a. binding to Gal3p and blocking activation
b. binding to Gal4p and blocking activation gal80 is really
an anti-activator
c. binding to the GAL1 operator and blocking RNA polymerase
d. binding to the UAS and blocking Gal4p binding
General transcription factors in eukaryotes
a. bind to enhancers to regulate transcription in a tissue
specific manner no, general transcription factors bind to
promoter
b. are responsible for recognizing the TATA box yes
c. are needed at all promoters during transcription initiation
yes
d. b and c
e. all of the above
Alternative splicing
a. allows exons to be spliced together in reverse order.
b. allows exons to be spliced together in the DNA to create
new genes.
c. allows exons to be spliced together in more than one way
to encode more than one protein from a single gene.
d. All of the above.

30.
The first transesterification reaction that takes place during
splicing
a. is catalyzed by snRNPs yes
b. involves the branch point 2OH attacking the 3 splice site
no; A 3 OH attacks 5 splice site!!!
c. occurs after activation of the snRNP by adenylylation
d. a and b
e. all of the above
31.
Which of the following is NOT true of splicing?
a. U2 snRNP binds to the branch point true
b. U1 snRNP binds to the 3 splice site false; U1 binds to 5
splice site
c. The formation of the spliceosome brings the 5 and 3
splice sites near each other
d. A lariat is formed in the intron.
32.
Which of the following is NOT true of the lac and ara
operons?
a. They are both regulated by activators and repressors
b. Their respective repressors have two DNA binding sites and
can cause loops to form in the DNA yes; lac has 2
operators and ara has I1, I2, and O2

c. They are both repressed when lactose or arabinose,


respectively, are absent
d. CAP-cAMP activates both operons when glucose levels are
high not true; glucose needs to be low to make cAMP
33.
During activation of transcription in eukaryotes, coactivators include
a. histone acetyl transferases yes
b. histone deacetyl transferases no
c. histone remodeling proteins yes
d. a and c
e. b and c
34.
What would you predict would happen if a eukaryotic in
vitro translation system was given a prokaryotic polycistronic
mRNA?
a. It would translate each ORF present on the mRNA.
b. It would translate only the first ORF present on the mRNA
c. It would not translate it at all without a 5 cap.

35.
When Jacob and Monod screened for repressor mutants
E.coli, what did they put in their media?
a. Glucose didnt use lactose as sugar source bc needed it
to not be an inducer
b. X-GAL turned blue when broken down by B-gal
c. IPTG no, would act as an inducer which they didnt want
d. a and b
e. a and c
36.
Experiments not described in class showed that when a
eukaryotic mRNA was hybridized to its genomic DNA, regions
were observed that looped out (were not complementary). This
result is cartooned below.
1
2

In this cartoon, which strand represents the DNA?


a. 1
b. 2
37.
Which term below describes the process of movement of
the ribosome to the next codon?

a.
b.
c.
d.

translation
translocation
transformation
transcription

Wobble Rules

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