some mixture of multiple choice, short-answer, and medium-length answer questions have about 3 hour to finish it. there are three part of the question it will focus on the third part which releat to the biosynthesis of Proteins and RNA processing, Transfer RNA:Structure, function, specificity and activation, The ribosome: structure and biogenesis, Mechanism of translation, Antibiotics and toxins that impair protein synthesis, Protein modification, sorting and intracellular targeting, mRNA processing: Spliceosomal Introns, Alternative mRNA splicing, Catalytic RNA, and RNA EDITING. one of other topic releated to Denaturation, renaturation of nucleic acids , Restriction enzymes / restriction analysis , Recombinant DNA, Nucleic acid sequencing , Gene structure — prokaryotic vs. eukaryotic, Transcription and its control, chromatin. the last topic releated to DNA as genetic material, Nucleotides, Polynucleotide structure,Topoisomerases and Nucleases, DNA replication, DNA repair ,QUESTIONS FROM A FINAL EXAM
Note: Some details may have been taught the year this exam was taken that we did not see this
(c) (6 marks) List THREE features of the process of protein
translation, other than the use of different proteins and RNA
species, that DIFFER between prokaryotes and eukaryotes. Clearly
indicate HOW they differ.
(d) (3 m a r k s) List T H R E E examples of modified bases (or
base modifications) of RNA. Indicate in which molecule and
where in the molecule they occur.
(e) (2 m a r k s ) Name two r o l e s of modified nucleosides in
tRNA molecules (not necessarily the ones mentioned in part d
of this question).
(g) ( 2 m a r k s ) Provide one reason why analyzing the
proteome (the collection of all proteins in an organism)
suggests a much larger number of genes than is revealed by
sequencing the genome.
(i) ( 4 m a r k s ) Name 2 different experimental
approaches/techniques/observations used in investigating
ribosomes that led to the identification of the ribosome as a
ribozyme. Briefly describe the supporting data from each approach.
True or False:
(i) In eukaryotic mRNA splicing, introns are removed from the
primary transcript by a mechanism analogous to the removal
of Group I introns.
(ii) mRNAs with premature stop codons are marked for
degradation by a cellular mechanism called Nonsense-Mediated
The nucleolus can be distinguished from the rest of the nucleus
because of the abundance of factors involved in mRNA
(iv) Many substitutions in the 3rd base of a codon are silent
thanks to the degeneracy of the genetic code.
(v) In the process of translation, the antibiotic puromycin causes
elongation arrest by blocking the A site.
(vi) The signal recognition particle (SRP) plays an important role
in translation and intracellular protein trafficking: the SRP (1)
binds to the amino-terminal signal sequence of newly formed
polypeptide chains and to the ribosome, (2) temporarily stops
translation, and (3) binds to the SRP receptor protein
embedded in the mitochondrial membrane.
(vii) The splicing of introns from pre-mRNAs in eukaryotes relies
on the presence of a branchpoint “A” residue usually found
near the 5’ end of the intron.
(viii) RNA interference (RNAi) is a gene-silencing pathway that is
initiated by the presence of double- stranded RNA molecules,
leading to the targeting and degradation or a reduced level of
translation of specific mRNAs.
(ix) miRNA are small RNA molecules encoded in the genome with the
purpose of repressing expression of genes of exogenous origin only.
(use a genetic code table from your textbook or the Internet)
Given the following template strand of DNA
3’ – CCTACGTAATAACATCACCACGGATTGG – 5′
(a) ( 2 m a r k s ) WRITE (in the 1-letter short-hand form) the
sequence of the mRNA transcribed from the W-strand.
INDICATE the 5′ and 3′ ends.
. (b) ( 1 m a r k ) CIRCLE the initiation and termination codons in
this mRNA. Label them INI (for initiation) and TER (for
. (c) ( 2 m a r k s ) WRITE (in the 3-letter short-hand form) the
amino acid sequence of the peptide encoded by this mRNA
starting at the initiation codon. INDICATE the amino (N) and
carboxyl (C) ends.
(d) ( 2 m a r k s ) In the mRNA transcribed from the wild-type W-strand,
some codons could be changed without affecting the
resulting peptide sequence. EXPLAIN, giving one example.
(e) ( 1 m a r k ) In a mutant form of the gene, the A-T base pair at position number 11 is
reversed (i.e., it becomes T in the W-strand and A in the C-strand). WRITE the sequence of the
peptide specified by the mRNA transcribed from the mutant W-strand.
(f) (2 marks) Assume the mRNA in (a) is eukaryotic and that the
first in-frame termination codon is 900 nucleotides after the
initiation codon rather than where it is shown. If the mutation
described in (e) occurred in this gene, what would be the
effect on expression of the protein. Briefly explain your
(g) (2 marks) Assume the eukaryotic gene described in (f) is not
mutated. Would you expect the sequence of the encoded
protein to differ in any way depending on whether the protein
is destined to function in the cytosol or be exported out of
the cell? Explain.
. (h) (2 marks) Mention a molecular process that can result in the
same protein product as in (e) even though the gene is not
mutated at the DNA level. Briefly explain your answer.
(i) (2 marks) In the wheat mitochondrial gene encoding subunit 2
of cytochrome oxidase (cox2), the gene sequence predicts
that amino acid at position 235 should be threonine; however,
a methionine residue is actually found at this position in the
Cox2 protein. Account for this observation.
(j) (2 marks) A gene encoding a protein with a mitochondrial
localization signal comes in two variants: one encodes a signal
peptide (SP) upstream of the protein and the other encodes
the SP downstream of the protein. Predict the cellular
localization of the protein product in each case explaining
Practice questions 3rd section Protein synthesis, RNA processing and RNAi
What experiment showed that protein synthesis doesn’t need DNA? What else did it show?
What does polynucleotide phosphorylase do? How did it help elucidate the genetic code?
True or False? – Explain in any case
The three letters at the 3’ end of a tRNA determine the amino acid that will be loaded into the tRNA.
A modified 5’base in the anticodon allows some tRNA to recognize more than one codon
Ribosomes are assembled with ATP spending by a specific set of enzymes and chaperones
Peptide bond synthesis at the P site of the ribosome is catalysed by specific bases of the ribosomal RNA
and specific amino acids of a ribosomal protein located within the P site
Genes for rRNA subunits are usually processed post— transcriptionally by splicing, just like mRNA
All organisms use formyl—methionine as the initiation amino acid but in eukaryotes the formyl group is
removed post— Translationally
At the DNA sequence level, the end of a gene is usually evident because of a long series of A (the poly A
In eukaryotes transcription and translation are uncoupled
Translation initiation factors are needed for accuracy in pairing a tRNA with its correct amino acid
EF—G mimics the conformation of EF—TU complexed with tRNA+amino acid
Incorporation of an incorrect amino acid elicits the NMD response to eliminate the faulty protein
The antibiotic streptomycin inhibits translation in bacteria by blocking the binding between EF-tu and
Ribosomes in the rough ER synthesize all proteins that are not Cytoplasmic
Protein glycosylation occurs in ER
“Signal peptide” refers to the region of a protein that contains the information needed to reach its final
Spliceosomal introns are generally smaller in bacteria than in Eukaryotes
Alternative splicing occurs when a gene contains both Group I and Group II introns
RNAse P is a protein that cleaves the 5’ end of a maturing tRNA
RNA editing corrects the mistakes made by the RNA polymerase by restoring the correct base in the
Describe potential effects of a mutation that impedes modification of the 5’ base at the anticodon of
What is the effect of “long range base pairing” in tRNA and rRNAs?
Describe the comparative phylogenetic approach to study the conformation of rRNA molecules
What is the “universal core” in LSU and SSU rRNA
Draw a typical bacterial transcript with 3 protein—coding regions and indicate all elements that
influence translation and their roles
Draw a scheme of an actively translating eukaryotic mRNA and indicate the elements involved and their
In a eukaryotic gene, a single mutation results in a protein that has an additional, internal segment of
300 amino acids. Explain possible causes
Draw a scheme of two proteins; one is to be secreted to the exterior and the other functions in the
For a research project, you are given a eukaryotic protein— coding gene. By analyzing the sub—cellular
localization of said protein in different tissues, you find that in the liver the protein appears in the
plasma membrane of the cells but in other organs the protein localizes to the cytoplasm. Propose a
model of the gene that explains this observation.
Compare cis (normal) splicing, trans—splicing, group I and group II splicing.
What are guide RNA? Briefly describe possible effects when one guide RNA is missing
Explain why a few molecules of dsRNA can result in the silencing of a highly expressed gene.
Finally, click here for a message from your instructors
BIOC3400 – 3rd section – Slamovits
Quick-firing questions study quiz
1- mRNA splicing occurs:
1. In the cytoplasm where RNA is translated
2. In the nucleus while the primary transcript is being synthesized
3. In the nucleus after the primary transcript is released
2- For a gene that has multiple introns, introns are spliced:
1. sequentially starting from the 5′ end
2. at the same time
3- What two snRNPs combine to form the catalytic active site for
U4 and U5
U3 and U7
U2 and B-52
U2 and U6
4- Self-splicing of Group 1 introns generates what structure?
A circular molecule
A linear molecule
5- The U1 snRNA particle initiates intron splicing by binding to:
1. The Cap
2. the 5′ splice site of the intron
3. The spliceosome
4. The polypyrimidine tract
6- The first two bases and the last two bases of nuclear introns are
Purines and pyrimidines, respectively
always GU and AG
Depends on the size of the intron
7- Which base in the branching region of introns is completely
1. All of them
2. The middle A
List all the translation factors (Initiation, elongation and termination)
with GTPase activity.
The role of EF-Tu in translation in bacterial cells is to:
1. Causes translocation
2. Recycles EF-Ts
3. Binds to, and places the aminoacyl-tRNAs into the A site of the
4. Brings chaos and destruction
The first step in translation initiation in bacteria is:
The one before the second
Attachment of small and large subunits
Recognition of mRNA
association of IF-1 and IF-3 with the 30S ribosomal subunit
Cleavage of signal peptide
Which inhibitor of protein synthesis acts through enzymatic activity?
The Shine-Dalgarno sequence occurs in what location(s) in a
polycistronic bacterial mRNA molecule?
Following the 5’cap
In the 23S rRNA
About 35 bases upstream of the initiation codon of each ORF
In the Kanto Region
The active site of the ribosome where peptide bonds are formed is a
Acidic residues of ribosomal proteins
Codon and anticodon
Nucleotides of the universal core
Wrinkles in the Speed Force
In what sense mRNA splicing and RNA editing are similar? In what
aspects they differ?
In what genetic systems are each of the mechanisms below more
• mRNA splicing
• RNA editing
• RNA interference
• Nonsense-mediated RNA decay
• tmRNA-mediated suppression of truncated mRNA
What are the substrate and product of DICER?
Compare RNA interference mechanisms for exogenous and
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