BIOC Exam 4 practice questions
The bacterial sigma factor dissociates from the RNA polymerase
Before the elongation phase
The original duplex DNA template _____ in semiconservative DNA replication
Is separated into single strands before replication
____is directly involved in protein synthesis.
Ribosomal RNA
When there is no lactose in a cell, transcription of the lac operon _____
is inhibited
What are the two main types of stem cells?
somatic and embryonic
The function of CRP in lac operon expression is to _____ the promoter by causing RNA polymerase to _____
stimulate, bind tighter
The __________ strand of DNA is transcribed into mRNA
template
The function of the lac operon is to provide
the enzymes needed to utilize the disaccharide lactose.
Long noncoding RNA (lncRNA) is generated from
the transcription of genomic DNA.
If DNA replication takes place before uracil is removed, then a C-G base pair mutates to a __(1)___ base pair because a(n) ___(2)___ residue is inserted opposite the ___(3)___ residue after one round of replication.
(1) T-A; (2) adenine; (3) uridine
If DNA replication takes place after uracil is removed, but before the a basic site can be repaired, then a C-G pair mutates to a ___(4)___ base pair because a(n) ___(5)___residue is inserted opposite of the a basic site and in place of the ___(6)___ residue after one round of replication.
(4) G-C; (5) cytosine; (6) guanine
How is the Ames test used to quantitate mutagenic potential of chemical compounds?
-The chemical compound to be tested is added to a filter paper disk and placed on agar plates containing the tester Salmonella strain; potent mutagens result in MORE colonies forming on histidine free plates as compared to control plates. -The Salmonella test strain used in the Ames test contains a mutation in the histidine biosynthetic pathway, which is used to identify compounds that induce back mutations to permit bacterial growth
What explains the observation that a single eukaryotic protein coding gene can give rise to multiple different proteins, i.e., why are there only ~25,000 human genes in the genome, but ~150,000 different proteins in the human "proteome?"
-mRNA transcripts from the same gene can be differentially spliced to include/exclude exons. -Genes can contain more than one polyadenylation site, which alters the 3' of the mRNA transcript and the inclusion/exclusion of exons.
Nirenberg and colleagues determined a portion of the genetic code using filter binding assays that included ribosomes, trinucleotides and tRNA molecules charged with radioactively-labeled amino acids. Choose the answer below that correctly answers the following three questions in order: 1) If the trinucleotide sequence is CAG, which amino acid will be bound to the filter paper? 2) If the wobble position of the trinucleotide sequence is changed to a U, which amino acid will be bound to the filter paper? 3) True or False: Two distinct tRNA molecules with different anticodon sequences MUST be used to recognize the codons AGA and AGG
1) Gln, 2) His, 3) False
Match the name of the DNA repair mechanism with the correct description.
1) Mismatch repair - Functions with DNA replication to remove incorrect nucleotides from the nascent strand. 2) Base-excision repair - Requires an endonuclease to remove an a basic nucleotide before DNA Pol I can replace a portion of the strand. 3) Nucleotide-excision repair - Is needed to repair chemical damage in DNA effecting more than one nucleotide, such as cyclobutane pyrimidine dimers. 4) Direct Repair - Repairs nucleotide bases without requiring DNA ligase
Put the 10 steps shown below describing the spliceosome reaction cycle into the correct order.
1.RNA Pol II finishes transcribing across an entire intron and is in the middle of a 3' exon. 2.The U1-U2 snRNP complex binds to the GU sequence at the 5' end of the intron. 3.The U2 snRNP translocates to the adenine residue at the intronic branch site. 4.The U4-U5-U6 tri-snRNP complex binds to U2 at the branch point along with the U1 snRNP. 5.The U1 and U4 snRNPs dissociate from the precatalytic complex leaving U2-U5-U6 behind. 6.The hydroxyl group of the branch point adenine attacks the phosphate at the 5' end of the intron. 7.The hydroxyl group at the 3' end of the upstream exon attacks the phosphate at the 3' end of the intron. 8.The U2-U5-U6 snRNP complex is bound to the lariat RNA structure and dissociates from mRNA. 9.The U2, U5, and U6 snRNPs dissociate from the lariat RNA structure and intronic RNA is released. 10.The U2 snRNP is released from the complex and the U5 and U6 snRNPs associate with U4 snRNP.
The Shine-Dalgarno sequence of mRNA base pairs with the _____ rRNA within the prokaryote _____ ribosomal subunit
16S, 30S
The E. coli MutS-MutL-MutH protein complex is responsible for mediating mismatch repair. Use Figure 20.37 to put the following 10 steps in the correct order describing mismatch repair in E. coli.
1__ MutH proteins bind to hemimethylated GATC sites in DNA near the mismatch mutation. 2__ Homodimer of MutS protein binds to the mismatch mutation in double stranded DNA. 3__ MutL protein forms a complex with MutS through an ATP-dependent association. 4__ The DNA is threaded through the MutS-MutL complex in the direction of MutH. 5__ A MutS-MutL-MutH complex loops out the mutated DNA using ATP hydrolysis. 6__ The endonuclease activity of MutH makes a single strand cut in the daughter DNA. 7__ MutS-MutL-MutH dissociates and daughter DNA is removed by an exonuclease. 8__ Single strand DNA binding protein binds to the parental DNA strand to protect it. 9__ DNA Pol III resynthesizes the daughter strand and the DNA nick is sealed by ligase. 10__The daughter strand DNA is methylated at the adenine residue within GATC sequences.
If the following mRNA was added to a cell-free translation system, how many unique protein sequences would be generated based on codon usage? 5'-ACCACCACCACCACCACCACCACCACCACCACC-3'
3
Put the following steps in the correct order to synthesize DNA. 1. Addition of an RNA primer 2. Extension of the RNA primer 3. Conversion of double-stranded DNA to single-stranded DNA 4. Synthesize new DNA
3,1,2,4
All DNA is synthesized in the ___________ direction
5' → 3'
Both prokaryotes and eukaryotes recognize the mRNA sequence _____ as a translational start codon
5'-AUG-3'
Radioactively-labeled aminoacyl-tRNA with the anticodon of 5'-CUG-3' was used in the Nirenberg-Leder experiment. They found that radioactivity was retained on the filter, which meant that _____ was the sequence of the mRNA used in the experiment
5'-CAG-3'
Based on the sequence of the double stranded DNA shown above, which sequence below corresponds to the mRNA transcript?
5'-CGCUAUAGCGUUU-3'
If one parent has Lynch syndrome, but the other does not, what is the likelihood that the child will also have Lynch syndrome?
50%
A Holliday junction can best be defined as a region of ________________
A quadruplex DNA structure
What accounts for the high fidelity of DNA polymerization?
Active site geometry ensures that only correct sized nucleotide base pairs are formed, and 3' to 5' proofreading removes incorrect nucleotides.
Place the following steps i n the correct order describing the steps required for synthesis of a membrane-bound protein: A. GTP binds to SRP B. Protein synthesis occurs on free ribosomes C. Protein synthesis halts D. SRP binds to the signal peptide sequence
B,D,C,A
Francis Crick hypothesized that the Genetic Code must require 3 nucleotides in the mRNA to specify each amino acid based on a simple calculation. What was the logic behind this calculation?
Based on the number of known amino acids and the number of known nucleotide bases
Why do BRCA1/BRCA2 mutations cause cancer?
Because BRCA1/BRCA2 are DNA repair enzymes, and therefore mutations in BRCA1/BRCA2 will result in unrepaired DNA damage that could lead to cancer.
The roles of U1, U2, U4, U5, and U6 in the spliceosome complex are to
Bind mRNA and facilitate the splicing reaction
The best description of how allosteric regulation works is that a ligand _____ the transcriptional regulatory protein, which _____ the protein's affinity for DNA
Binds to; causes conformational changes that affect
The Tus-Ter complex terminates DNA synthesis in E. coli by
Blocking the opening of helicase
The Tus-Ter complex terminates E. coli DNA synthesis by ____________.
Blocking the opening of the DNA helix at the fork by helicase
Which statements below describe three similarities between Group II self-splicing RNA mechanisms and spliceosome-mediated RNA splicing mechanisms?
Both use the same two transesterification reactions Both require a branch site adenine residue Both release the intron as a lariat RNA structure
Place the following steps in the elongation phase of mRNA translation into the proper order. Peptide bond formation occurs GTP is hydrolyzed, and the ribosome moves one codon in the 3' direction GTP is hydrolyzed, and EF-Tu GDP is released tRNA is released from the E site
C,A,B,D
tRNA is _____ before binding to the ribosome to allow for translation to occur
Charged with an amino acid
Which enzyme synthesizes the RNA primer for DNA replication?
DNA primase
Individuals with mutations of BRCA have increased incidence of cancer because of their___________
Decreased ability to repair double-strand DNA breaks
If a protein is covalently modified by ubiquitin, it will be _____
Degraded by the proteasome
When the trp operon is attenuated, then _____ occurs
Disruption of transcriptional elongation by RNA polymerase
Which of the following statements is correct regarding self-splicing introns?
Group I introns use an exogenous guanosine as a cofactor
What are the functions of the HAT and HDAC enzymes with regard to regulating gene expression in eukaryotic cells?
HAT activates the gene and HDAC represses the gene
If 15N DNA (heavy) replicated using conservative replication in 14N (light) media, the outcome would be different than semi-conservative replication, and in this case, the two daughter DNA double strands would be ______________after one generation.
Heavy only for one daughter DNA and light only for the other daughter DNA
What are the functions of enzymes helicase and gyrase in DNA replication?
Helicase unwinds DNA and gyrase relieves the torsional strain
Why do helicase and gyrase need to work together to keep the replication fork moving forward?
Helicase unwinds the DNA and gyrase relieves the torsional strain created by the unwinding
What would it mean if fewer colonies were observed on the plate if the compound were first treated with rat liver extract as compared to not treating the compound?
If fewer colonies were observed, then enzymes in the rat liver extract modified the compound to make it less potent.
What would it mean if more colonies were observed on the plate if the compound were first treated with rat liver extract as compared to not treating the compound?
If more colonies were observed, then enzymes in the rat liver extract modified the compound to make it more potent.
Histone acetylation leads to _____ with regard to transcriptional regulation
Increased transcriptional activity
Introducing genes encoding the proteins Oct4, Sox2, c-Myc, and Klf4 into a differentiated cell causes _____
Induction of the pluripotent state
When the Trp repressor is bound to the trp operon, it results in the _____ by RNA polymerase
Inhibition of transcriptional initiation
Assume that you have identified all the cis-acting sites in a prokaryotic genome for a particular trans-acting transcription factor. What is the function of this transcription factor when binding to these sites?
It is not possible to predict the function from the sites since could activate or repress at different sites
What is the function of the enzyme telomerase in eukaryotic DNA synthesis?
It synthesizes DNA on the lagging strand at the ends of chromosomes
The function of the beta-clamp in DNA replication is to __
Keep the Pol III complex associated with the DNA.
The main difference between group I and group II introns is _____
Linear versus lariat intron products
Which DNA repair mechanism is required to fix replication errors in E. coli?
Mismatch repair
The figure below shows _____ autoregulation and that _____
Negative; reaches a steady state of expression
Conservative replication predicts that bacteria grown in 15N media for multiple generations, and then switched to 14N media for one generation, will have DNA strands of
One high density strand and one low density strand
Semiconservative replication predicts that bacteria grown in 15N media for multiple generations, and then switched to 14N media for one generation, will have DNA strands of _
One high density strand and one low density strand.
How can antiparallel DNA strands (one and the other is ) be synthesized in such a way that the replication fork moves in only one direction?
One of the strands is synthesized using Okazaki fragments
A lipid-modified protein is most likely localized to the _____
Plasma membrane
RNA is more susceptible to backbone hydrolysis than DNA because of the ___
Presence of a 2' OH group.
AZT is useful in the treatment of AIDS-HIV because it _
Prevents new DNA from being replicated
Excess exposure to ultraviolet light can cause damage because it _
Produces photoproducts.
A Holliday junction can best be defined as a region of_
Quadruplex DNA
The primary function of transcriptional activator proteins is to ____
Recruit other transcription factors to the gene promoter
The initiation of transcription in eukaryotes _____
Requires many more transcription factors than prokaryotic transcription
The spliceosome _____
Resembles group II introns in its mechanism and product
Given that rod cell apoptosis is the primary effect of autosomal dominant PRPF31 mutations in retinitis pigmentosa patients, what explains progressive total blindness in these patients as a result of secondary cone cell deterioration?
Rod cell apoptosis results in reduced secretion of the cone protective factor, RdCVF, which is required for cone cell viability.
What is the difference between a somatic mutation and a germline mutation?
Somatic mutations occur during a lifetime and are not inherited; germline mutations exist in gametes and are inherited by offspring
Why does RNA contain uracil and DNA contain thymine?
Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-G base pair to a T-A base pair
The role of Mg2+ in DNA replication is to _____ the incoming deoxynucleotide
Stabilize the negative charges on
Prokaryotic and eukaryotic DNA polymerases rarely make mismatched base pairs because ____________
The active site does not fit mismatches well
The Ames test is designed to identify mutation rates using a strategy based on ___________
The frequency of new mutations that compensate for an existing mutation
Which of the following statements is correct regarding spliceosome-mediated trans splicing?
The spliceosome mechanism involves two transesterification reactions
Which statement below most accurately describes the function of trans- and cis-acting factors in mediating gene regulation?
Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences
The control point for prokaryotic gene regulation primarily occurs at the point of ____
Transcriptional initiation
The _____ requires hydrolysis of GTP as a key step in the insertion of a newly synthesized protein into the ER lumen
Transfer of the signal peptide sequence into the translocon
When tryptophan levels inside a bacterial cell are elevated then _____
Trp repressor is bound to DNA
The precatalytic spliceosome complex includes the U1, U2, U4, U5, and U6 sn RNP molecules. Which statement below correctly describes the RNA-RNA base pairing interactions required for formation of the precatalytic spliceosome complex?
U1 snRNA base pairing with the 5' end of the intron; U2 snRNA base pairing with intron sequences at the branch point; U6 snRNA base pairing with U2 snRNA; U6 snRNA base pairing with U4 snRNA
The 3'-hydroxyl group used to initiate DNA synthesis comes from_
a RNA primer
When a cytosine is deaminated to form uracil and removed by glycosylase enzymes, a(n) __________ site is generated.
abasic
In the Nirenberg-Leder experiment, the _________ was radioactively-labeled.
aminoacyl-tRNA
Inosine is formed by
deamination of adenosine
Individuals with mutations of BRCA have increased incidence of cancer because of __
decreased ability to repair double-strand DNA breaks.
iPS cells can be defined as __________ cells.
dedifferentiated
The name of the enzyme responsible for generating siRNA is
dicer
Homologous recombination repairs
double-strand breaks in DNA.
A reporter gene can be defined as a gene that_________________.
encodes a product that is easy to detect
One of the most common binding interactions between proteins and DNA are _____ bonds
hydrogen
The DNA sequence of prokaryotic gene promoters are
largely conserved.
DNA foot printing technique is used to identify the
location of a DNA binding protein on DNA
Which amino acid residues on histones are acetylated?
lysine
A common RNA base modification is _____
methylation
The MutS-MutL-MutH protein complex is required for
mismatch DNA repair
Together, the eight histone molecules are called the histone _____
octamer
If tRNAs are charged with radioactively-labeled amino acids in an in vitro system, then over time the radioactivity will be located in newly synthesized __________.
protein
The antibiotics streptomycin, tetracycline, and chloramphenicol all interfere with
protein synthesis.
The _____ contains the enzymes and proteins required to replicate DNA
replisome
RNA interference is mediated by __________ leading to mRNA degradation.
siRNA