Name:
2 points
Chem 465
Biochemistry II
Multiple choice (4 points apiece):
1. Which one of the following is true about the genetic code?
A)
All codons recognized by a given tRNA encode different amino acids.
B)
It is absolutely identical in all living things.
C)
Several different codons may encode the same amino acid.
D)
The base in the middle position of the tRNA anticodon sometimes permits
"wobble" base pairing with 2 or 3 different codons.
E)
The first position of the tRNA anticodon is always adenosine.
2. Aminoacyl-tRNA synthetases (amino acid activating enzymes):
A)
"recognize" specific tRNA molecules and specific amino acids.
B)
in conjunction with another enzyme attach the amino acid to the tRNA.
C)
interact directly with free ribosomes.
D)
occur in multiple forms for each amino acid.
E)
require GTP to activate the amino acid.
3. Which of the following is true about the sorting pathway for proteins destined for
incorporation into lysosomes or the plasma membrane of eukaryotic cells?
A)
Binding of SRP to the signal peptide and the ribosome temporarily
accelerates protein synthesis.
B)
The newly synthesized polypeptides include a signal peptide at their
carboxyl termini.
C)
The signal peptide is cleaved off inside the mitochondria by signal
peptidase.
D)
The signal recognition particle (SRP) binds to the signal peptide soon
after it appears outside the ribosome.
E)
The signal sequence is added to the polypeptide in a posttranslational
modification reaction.
4. Which of the following statements correctly describes promoters in E. coli?
A)
A promoter may be present on either side of a gene or in the middle of it.
B)
All promoters have the same sequence that is recognized by RNA
polymerase holoenzyme.
C)
Every promoter has a different sequence, with little or no resemblance to
other promoters.
D)
Many promoters are similar and resemble a consensus sequence, which
has the highest affinity for RNA polymerase holoenzyme.
E)
Promoters are not essential for gene transcription, but can increase its
rate by two- to three-fold.
5. Protein structural motifs often have general functions in common. Which one of the
following motifs is known to be involved in protein dimer formation, but not in direct
protein-DNA interactions?
A)
â-barrel
B)
helix-turn-helix
C)
homeodomain
D)
leucine zipper
E)
zinc finger
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6. RecA protein provides the functional link between DNA damage and the SOS
response by displacing the LexA protein from its operator sites on the SOS genes.
RecA does so by:
A)
associating with polymerase holoenzyme to help it remove LexA from
operator.
B)
bending LexA operator DNA to force dissociation of LexA repressor.
C)
binding to LexA protein to weaken directly its affinity for operator sites.
D)
causing self-cleavage of LexA, thus inactivating its binding to operator.
E)
competitively binding to LexA operators and serving as an activator.
7. Which of the following is a DNA sequence?
A)
Coactivator
B)
Corepressor
C)
Enhancer
D)
Inducer
E)
Transactivator
Essay questions - answer any 5 (total of 6!)
1. Define the following terms (Please define all terms in this question)
ORF Open reading frame - an AUG codon followed by 50 or more codons
without a stop codon
Translation frameshifting When the ribosome does a stutter step and changes
the reading frame of the mRNA it is working on
Shine-Dalgarno sequence A sequence in the E coli mRNA that is ued to
assemble the ribosome at the proper spot.
Elongation factors Factors needed by the ribosome to continue the protein
synthesizing process. One is involved in bringing the charged amino acid tRNA into the
ribosome and the other is involved in moving the ribosome along the mRNA
translocation The process by which the ribosome moved on codon along the
mRNA
polysome A single mRNA to which several ribosomes are actively making
proteins
SRP Signal Recognition Particle - the protein that binds to a signal sequence
and halts protein synthesis of a ribosome until that ribosome is attached to the ER
lumen
NLS Nuclear Localization sequence the sequence in a protein that targets the
protein for transport to the nucleus
induction The process of increasing the expression of one or more genes
promoter The region on a piece of DNA that the RNA polymerase will bind to to
start making RNA
repressor A protein that binds to DNA to imped the access of an RNA
polymerase to a promoter.
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Enhancer A protein that enhances the ability of RNA polymerase to bind to a
promoter
Apatamer An RNA molecule that will bind some other small molecule
restrictive ground state. A cell in which most of the genes are turned off unless
specifically turned on.
2. Describe the system by which a tRNA gets charged with an amino acid. In your
description be sure to included details like: What are the different classes of these
enzymes and how are they different, how are the tRNA’s recognized, does any
proofreading occur, and are there any differences between prokaryotic and eukaryotic
systems?
This process is carried out by Aminoacyl-tRNA synthetases. A cell will usually
have one synthetase for each amino acid, even when there are several tRNAs for the
same amino acid. The synthetase will charge all the different tRNA for a given amino
acid because it does not ‘look’ at the anti-codon on the tRNA, but instead looks for cues
that it has the correct tRNA at other location in the tRNA 3D structure.
The reaction involves a two step process. In the first step the amino acid is
reacted with ATP to form aminoacyl-AMP. This intermediate remains bound on the
synthetase and in the second step either the 2' or the 3' OH of the sugar at the 3' end of
the tRNA attacks the aminoacyl-AMP to form the aminoacyl-tRNA. (Class I synthetases
use the 2' OH, class II synthetases use the 3'OH). IN both classes the amino acid is
eventually transferred to the 3' OH.
In this process there are two or three binding steps that are used to make sure
the correct amino acid is bound to the correct tRNA. The first binding step is when the
synthetase binds the amino acid and attached it to the AMP. In a proofreading step
there is a second site on the synthetase that will hydrolyse an AMP bound to the
incorrect amino acid. Many Synthetases also have an additional proofreading site to
hydrolyze incorrect amino acid-tRNA’s.
3. Describe the system (all the steps and proteins involved) by which nuclear proteins
are imported into the nucleus.
Here I was looking for a diagram like Figure 27-42 of your text.
Importin á binds to NLS sequence in protein and Importin â bind to á. This
complex is then imported into the nucleus at the nuclear pore. In the nucleus RanGTP
binds to importin â and releases it from the complex. Then a secod Ran GTP and CAS
protein bind importin á to completely release the protein in the nucleus. Both the
RanGTP-âimportin and RanGTP-CAS-áimportin complexes are exported out of the
nucleus to the cytosol where the GTP is hydrolyzed to GDP and the importins are
released to complex with more nuclear proteins. RanGDP then binds with Nuclear
Transport factor 2 (NTF2) to get transported back into the nucleus, where RanGEF
replaced the GDP with GTP so the RanGTP can continue its work.
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4. In the previous chapter we talked about several ways the structure of the mRNA
modified in Eukaryotic cells. In this chapter we see how some of these structures are
important in the binding of the mRNA to the ribosome. What are these structures, and
how are they used in ribosome binding.
A diagram like figure 27-27 will help.
The two structures I wanted you to remember were the 5' cap and the polyA tail.
The 5' cap is bound by the eTF4E to the 40S subunit of the ribosome. In the initiation
process the first AUG after this 5' cap becomes the site of initiation. The polyA tail is
bound by the PAB (poly A binding Protein)
5. One of the new emerging fields in gene regulation and control is control of gene
expression by RNA. Describe at least two systems where RNA controls gene
expression.
E coli rpoS (RNA polymerase sigma factor) an example of in trans regulation
While low levels of this mRNA are expressed in E coli, the mRNA is not
translated because a hairpin forms in the mRNA structure that inhibits Ribosome
binding. Under certain conditions E coli will express either the DsrA (Downstream
region A) or the RprA (Rpos regulator RNA A) RNA’s. Both of these RNA’s have a
region that can bind to ½ of the hairpin on the RNA polymerase sigma factor mRNA
thus removing the hairpin and allowing Ribosomal binding and translation of the mRNA.
These interactions require the addition of a RNA chaperone called Hfq that encourages
the formation double stranded RNA structures.
Riboswitches in TPP (an example of in cis regulation)
In this case the mRNA has a complex structure that includes an aptamer, a
region of the RNA that can bind another small molecule, in this case, TPP.
As the mRNA is being transcribed from DNA, the apatamer structure binds to
TPP. In some organisms this binding makes a poly U structure form tat signals the
RNA polymerase to terminate the message before it get to the genes needed for TPP
synthesis. In other organisms the RNA is transcribed, but the binding of TPP to the
aptamer forms a structure that blocks ribosome binding, and blocks the translation
process. In yet other organisms the binding of TPP to the aptamer changes the splicing
and changes the message that way.
6. Using the yeast galactose gene as a model, describe the steps involved in
expressing a eukaryotic gene.
A diagram like either 28-29, 28-31, or 28-32 is helpful.
First an transcription activator like Gal4p binds to the DNA enhancer sequence in
a transcriptionally inactive section of heterochromatin. IN the case of the Gal gene an
additional protein, Gal80p binds to the Gal4p an nothing further happens. However if
Galatose is present, in binds to the Gal3p which then interacts with Gal 80p to release it
from the Gal4p and allow it to start acting like an activator.
In this case, the Gal3P forms interact with SAGA complex to start acetylating
histones in the region and SW1/SNF to start remodeling the chromatin into more active
‘euchromation’. It can now form a complex with Mediator and TBP to bind ot the TATA
box at the start of the Gal Gene. Now additional facotr get added and the RNA
polymerase initiation complex forms so the mRNA for the Gal gene can be transcribed.
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1C
2A
3D
4D
5D
6D
7C