LS3 MIDTERM II EXAM

INSTR:L.JOHNSON

February28,2014

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TestFormA
INSTRUCTIONS
Thisexamis10pageslong.Beforestartingmakesureyouhaveallthepages.
Usinganumber2pencil,onthefrontofyourscantronfillintheInstructor(Johnson),Class
(LS3),Hour(12:00or1:00),
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OnthebackofyourscantronWriteandBubbleinyourUIDandTestForm(seeabove).

1. In vitro translation was used to decipher the genetic code. In the

graph above, the bars labeled (-) represent
a. the negative control where no 14C-labeled amino acids were added to the
reaction.
b. the negative control where no Poly(U) was added to
the reaction. you dont add polyU mRNA so you
wont see any proteins being made
c. the negative control at time 0.
d. None of the above.
2. In the second step in the tRNA charging reaction, what small
molecule is released?
a. ADP
b. pyrophosphate
c. AMP
d. H2O

3. In the picture of the ribosome above, what is the order the tRNA
binding sites (from left to right)?
a. A-P-E
b. E-P-A
4. If you plated E. coli on media with glucose + X-gal, what color
would the colonies be?

5.

6.

7.

8.

9.

a. Colorless because it hasnt been mutated. If you

mutated the E.coli cells to knock out their repressors,
repressors wouldnt bind to lac operon, lac operon would be
induced. But normal repressor will bidn to lac operon and
since there is no inducer (we are using X-gal in glucose
media), it will be repressed substrate wont be broken
down wont get blue precipitate
b. blue
Suppose you knocked-out alpha 2 (so that the protein was no
longer functional) in a diploid cell. Which sets of genes would be
expressed?
a. a specific genes
b. alpha specific genes
c. haploid specific genes
d. All of the above
What do the translation factors, IF-2 and EF-Tu have in common?
a. They are both G proteins yes
b. They both play a role is escorting charged tRNAs to the A
site no, IF-2 brings initiator tRNA
c. They both undergo a conformation change upon hydrolysis
of GTP yes
d. a and b
e. a and c
Which of the following statements is true?
a. Rho-independent terminators in prokaryotes are similar to
transcription termination in eukaryotes.
b. Rho-dependent terminators in prokaryotes and
transcription termination in eukaryotes both require
special proteins.
c. Transcription termination in both prokaryotes and
eukaryotes is linked to poly-A addition no, only in
eukaryotes
A degenerate genetic code refers to
a. the ability of a tRNA to base pair with more than one codon
b. the fact that there is more than one codon per amino
acid wobble allows for degeneracy!
c. observation that the genetic code has deterioted during
evolutionary time
Peptide bond formation during translation
a. is catalyzed by the 23S rRNA yes
b. is an energetically unfavorable reaction no, it is made
favorable by charging step
c. happens spontaneously on the ribosome when both the P
and A site contain aminoacyl-tRNAs
d. All of the above.
e. a and c

10.
Using the genetic code and wobble rules on the last page
of the exam, which codon below would be recognized by a tRNA
with the anticodon 5 IAC 3?
a. 5 GUA 3
b. 5 AUG 3
c. 5 GUG 3
11.
Proteins that are secreted from the cell enter the ER
a. through a pore in the membrane after they are translated
b. through a pore in the membrane while they are
being translated
c. through a vesicle originating from the Golgi apparatus
d. directly from the cytoplasm after merging with the ER
membrane
12.
Why do aa-tRNA-EF-TU and EF-G share a similar structure?
a. Because they are both G proteins
b. Because they have similar functions
c. Because they both bind to the same site on the
ribosome both bind to the factor binding site of the
large subunit
d. Because they are both elongation factors.
13.
Which of the following motifs interact with the major
groove of DNA using an alpha helix?
a. helix-turn-helix
b. Zn finger
c. homeodomain
d. basic leucine zipper
e. All of the above the only one that doesnt is TBP
which interacts with minor groove and causes sharp
bend in the DNA
14.
If you plated E. coli on media with glucose + IPTG, what
color would the colonies be?
a. white (neutral) IPTG is an inducer; it binds to lac
repressor and blocks repression so lac operon is induced
makes B-gal but IPTG isnt a substrate so it would be
colorless
b. blue
15.
In Drosophila, when both Giant and Hunchback are at high
concentrations, is the Eve stripe 2 enhancer activating
transcription?
a. yes
b. no hunchback is an activator but giant is a
repressor
16.
Using fusion proteins, scientists found they could mix and
match DNA binding domains and activation domains to make
custom proteins. These experiments illustrated that

a. these domains acted as structural domains yes, they are

independently folding domains
b. that activators only worked in conjunction with a DNA
binding domain yes, in the control experiment when
there was no DNA binding domain there was no activation
c. repressors could be transformed into activators by the
addition of an activator domain yes, lacZ encodes for lac
repressor but was transformed to activator by adding Gal4p
activation domain
d. All of the above
17.

How does glucose affect the levels of cAMP in the cell?

a. At high glucose levels, adenylcyclase is stimulated to make
cAMP.
b. At high glucose levels, adenylcyclase is inhibited
from making cAMP.
c. At low glucose levels, adenylcyclase is stimulated to make
cAMP.
d. At low glucose levels, adenylcyclase is inhibited from
making cAMP.
18.
Which of the following transcription factors does not bind
DNA in the presence of an allosteric effector?
a. CAP
b. lac repressorthe allosteric effect is the inducer
c. AraC
d. trp repressor
19.
Which of the following is true of prokaryotic transcription
initiation?
a. Abortive initiation occurs because sigma factor is
blocking the RNA exit channel. yes
b. When RNA polymerase binds a promoter without sigma
factor, there is no abortive initiation it wouldnt bind
promoter w/o sigma factor
c. Abortive initiation only occurs at weak promoters.
d. Abortive initiation is associated with release of RNA
polymerase and initiation must be started again.
20.
General transcription factors in eukaryotes
a. are needed at all promoters during transcription initiation
yes
b. perform many of the roles that sigma factor performs in
prokaryotes yes?
c. are released from Pol II when it escapes the promoter yes
d. b and c
e. All of the above
21.
What two steps in eukaryotic transcription initiation require
ATP?

22.

a. binding promoter and phosphorylation of the CTD

b. binding the general transcription factors and unwinding the
DNA
c. unwinding the DNA and phosphorylation of the CTD
The 5 cap on eukaryotic mRNAs refers to a
a. guanosine added to the 5 end in a 5 ppp 3 linkage
b. guanosine added to the 5 end in a 5 pp 3 linkage
c. guanosine added to the 5 end in a 5 ppp 5 linkage
d. guanosine added to the 5 end in a 5 pp 5 linkage

23.
Consider the primary transcript above that is spliced in the
brain to yield a mRNA containing exons 1,2,3,5 and 6. Which sites
would have to be blocked to obtain this spliced product?
a. Intron 3 5 splice site, intron 3 3 splice site, 1st Poly(A) site
b. Intron 3 3 splice site, intron 4 5 splice site, 1st
Poly(A) site
c. Intron 3 5 splice site, intron 4 3 splice site, 1st Poly(A) site
d. Intron 4 5 splice site, intron 4 3 splice site, 1st Poly(A) site

24.

In the diagram above, exon 1 in the final mRNA is

a. the coding region for the N-terminus of the protein exon 1
isnt translated so it cant be part of the coding region
b. contains part of the 5 UTRexons contain the UTRs
c. contains the first AUG used in translation it isnt
translated so no
d. a and c
e. All of the above.
25.
For translation to initiate at an AUG in prokaryotes, what
else must be present?
a. 5 cap
b. 5 triphosphate
c. Kozak sequence
d. Shine-Delgarno sequence
26.
TBP differs from most DNA binding proteins because
a. it uses an alpha helix to bind to the minor groove

27.

b. it uses a beta sheet to bind to the major groove

c. it uses an alpha helix to bind to the major groove
d. it uses a beta sheet to bind to the minor groove
TFIIH
The Gal3p transducer induces transcription by
a. binding to Gal80p and allowing activation the
Gal80p is an anti-activator blocking Gal4p; when
Gal3p binds to Gal80, Gal4 can open and activate
b. binding to Gal4p and stimulating activation binds to
gal80 NOT gal4
c. binding to galactose and then binding to DNA doesnt
bind to DNA
d. binding to the UAS and blocking Gal4p binding doesnt
bidn to DNA

28.
The stripe 2 enhancer for Eve gene is regulated by two
activators and two repressors that compete for overlapping
binding sites. Suppose Kruppel and Bicoid bind the same
sequence, but Kruppel has a higher affinity.
a. This observation would suggest the the Kd for Kruppel is
higher than Bicoid (larger number).
b. This observation would suggest the the Kd for
Kruppel is lower than Bicoid (smaller number).-->
lower Kd = higher affinity
29.
Which of the genes below are examples of a specific
genes?
a. a pheromone
b. a receptor
c. alpha receptor
d. a and b
e. a and c
30.
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 splicing occurs at RNA level not genomic level;
you can create alternate proteins not alternate 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.
31.
The second transesterification reaction that takes place
during splicing
a. after U1 has left the spliceosome yes, U1 and U4 leave
before catalysis
b. involves the 5 splice site 3OH attacking the 3 splice site
phosphate yes

c. is coupled to ATP hydrolysis no, ATP not needed bc

energy is stored in bonds
d. a and b
e. All of the above
32.
Charging of tRNAs by aminoacyl tRNA synthetases is
coupled to the hydrolysis of ATP. Why is this necessary?
a. If the amino acid is not attached to the tRNA, it cant be
used for protein synthesis.
b. Some of the potential energy of the ATP is retained
in the amino acyl bond, making peptide bond
formation energetically favorable.
c. ATP hydrolysis is a commonly coupled to reactions through
transfer reactions.
33.
Which of the following proteins is both an inducer and
substrate?
a. cAMP not a substrate or inducer; it is allosteric effector
b. arabinose yes; arabinose binds to AraC and changes
AraC conformation so that AraC is no longer binding to I1
and O2 and can instead bind to I1 and I2. It is a substrate
bc the Ara operon metabolizes arabinose
c. X-Gal substrate not an inducer
d. IPTG inducer not substrate
e. tryptophan
34.
During activation of transcription in eukaryotes, corepressors include
a. histone acetyl transferases co-activators
b. histone deacetyl transferases yes, de-acetylation
will keep nucleosome blocking the TATA box and
gene
c. histone remodeling protein co-activators
d. a and c
e. b and c

Wobble Rules