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Total questions: 165
Worksheet time: 2hrs 4mins
The specificity of an enzyme for its substrate is determined by all of the following except
size of active site
shape of active site
presence or absence of charge within active site pocket
all of these determine how specific an enzyme to its substrate
Where are hydrophobic residues likely to be found in a cytoplasmic (non-membrane) protein?
Buried in the center of the protein, shielded from the external, aqueous
environment
Exposed on the surface of the protein so they can interact with water.
Interacting with hydrophilic residues to provide balance to the protein structure.
Forming ionic bonds with charged R-groups in the peptide chain.
Protein secondary structure is the result of
Peptide bonds between adjacent amino acids
Hydrogen bonds forming along the peptide backbone.
Covalent bonds between R-groups.
Hydrogen bonds between R-groups
A Western Blot uses an antibody to detect a specific protein. How does an antibody recognize a protein? (no answer)
a. By adding a biotin label and isolating it using avidin or streptavidin.
b. By binding to epitopes on the protein’s surface through its variable domains.
c. By precipitating the protein’s coding sequence.
d. By binding to DNA sequences in its promoter and turning on transcription of its
When separating proteins using SDS-PAGE (PAGE=polyacrylamide gel electrophoresis),
why do we use SDS?
a. To refold the protein and restore activity
b. To make the sample bubbly because bubbles are great.
c. To remove cell fragments that may be attached to the proteins.
d. To denature the protein and give it a net negative charge proportional to its size.
Co-immunoprecipitation is used to
a. Determine if two proteins interact with the same antibody.
b. Analyze DNA sequence of a protein.
c. Determine if two proteins interact with each other.
d. Identify chemical groups that have been added to the protein post-translationally.
In yeast 2-hybrid screening, the interaction between the “bait” and “prey” proteins
a. Identifies the function of protein of interest by its mass-to-charge ratio.
b. Depends on having SDS in the reaction.
c. Causes the cell to lyse and release the proteins into the lysate.
d. forms an intact transcription factor that turns on the expression of a reporter gene
What is the proteome?
a. The total set of proteins in the cell at any given point.
b. The number of genes that are expressed in a specific growth condition.
c. The total set of proteins encoded by the organism’s genome.
d. The number of expressed genes.
Using phage display, researchers can
a. Screen for protein based on function, and then also discover its coding
sequence.
b. Precisely measure the molecular weight of the protein and identify it.
c. Show that two proteins interact through the expression of a reporter gene.
d. Isolate a specific protein with an antibody against a protein tag, like His.
What information does MALDI-TOF or electrospray mass spectroscopy give us about a protein?
It tells us an exact molecular weight, from which we can determine the protein’s
identity.
It identifies sites for protein-protein interactions.
It identifies the precise nucleotide sequence for protein-DNA interactions.
It calculates the overall charge for the protein.
Alternative sigma factor RpoH is active at high temperatures but not at normal temperatures – why?
It is targeted for degradation at normal temperatures; at high temperatures, chaperonin degrades misfolded proteins instead.
b. It is transcribed only when temperatures exceed 60C.
c. It needs the cascade mechanism of activation.
d. Anti-sigma factor binds at lower temperatures while anti-anti sigma factor is active at high
temperatures.
Question 2
NusG binds to RNA polymerase and causes the polymerase to transcribe downstream genes. In this example, NusG is acting to
Repress the expression of downstream genes.
Block termination of transcription.
Inhibit the binding of alternative sigma factors.
Transfer phosphate groups to the ribosome.
In prokaryotes, Crp binds DNA. upstream of the RNA polymerase in the regulatory region of the lac operon. Based on where it binds, It is most likely to
Act as an activator, turning on transcription of lacZ, lacY and lacA.
Acts as a repressor, preventing transcription of lacZ, lacY and lacA
Has no effect on transcription.
Increase the rate of degradation of the transcript.
Which of the following is an example of negative regulation?
a. A gene is switched on in the presence of an activator.
b. A gene is de-repressed.
c. A gene is induced.
d. A gene is switched off by a repressor protein.
All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT
Regulating access to DNA
Controlling recognition of promoter regions through sigma factors
Using anti-termination proteins to transcribe downstream sequences
Regulating activation of the protein.
Which of the following is TRUE for an activator?
It blocks the binding of RNA polymerase.
The signal molecule causes it to come off of the DNA
Interaction with an inducer can cause the activator to bind DNA.
It binds to the operator sequence in the promoter.
For an operon, turning on transcription at the promoter
Starts transcription of only non-coding RNA sequences.
Turns off translation of monocistronic DNA.
Activates transcription of a single gene.
Initiates transcription of a polycistronic mRNA.
Gene expression in eukaryotic cells is most often regulated by controlling
translational repression.
inversion of DNA segments.
degradation of mRNA.
transcriptional initiation.
There are multiple ways that a repressor protein can be regulated. In the case of the repressor Mlc, unphosphorylated PtsG keeps Mlc at the membrane. By keeping Mlc at the membrane.
Mlc binds to alternative sigma factors and holds them at the membrane.
Mlc cannot bind to DNA and inhibit transcription of genes.
the operator sequences in the promoters of certain genes can now be bound by activators and transcribed.
PtsG stops transporting glucose across the membrane, and the cell stops transcription to survive under starvation conditions.
In eukaryotic transcription, the mediator complex
Integrates the signals of activators and enhancers binding to DNA to start transcription
Removes repressors so activators can bind.
Neutralizes repressors and activators.
Has no effect on transcription.
CG islands are _____ and are usually the target of _____.
CG poor; acetylation of DNA sequences
CG poor; phosphorylation of histones
CG rich; methylation of DNA
CG rich; methylation of histones
Sliding of nucleosomes on DNA
Leads to compaction of nucleosome and less accessible DNA.
Can expose new promoter sites.
Inactivation of sequences on the Y chromosome.
Removes acetyl groups from histone tails.
Ferritin mRNA has a stem-loop structure that is bound by the iron-regulatory protein and blocks the production of ferritin. This is an example of
Translational repression
Transcriptional repression
Activation of translation
Transcriptional attenuation
Where does transcription occur in eukaryotes?
In the nucleus
On methylated CG islands
In the cytoplasm
On ribosomes.
When cells are given the signal to grow, the small subunit of the ribosome can be phosphorylated. This leads to
Preventing any mRNAs from associating with the ribosome
Increasing the translation of specific groups of mRNAs.
Destruction of ribosomes
Shredding RNAs that come in contact with the ribosome
RNA-dependent RNA polymerase increases the effect of RNAi by
Creating more dsRNA to be cleaved by Dicer into siRNAs
Transcribing more RISC mRNA
Translating more Dicer mRNA
Converting miRNA into siRNA
Binding of a ribosomal protein to its own mRNA
Blocks its own translation and keeps balance between ribosomal proteins and rRNAs
Enhances the amount of rRNA available
Prevents the degradation of mRNA
Activates translation.
All of the following are ways to regulate translation EXCEPT for
Controlling the rate of mRNA degradation
Antisense RNA binding to mRNA
Cleaving mRNA to reveal ribosome binding sites
Sliding nucleosomes along DNA expose promoter regions
SiRNA perfectly pairs with its target while miRNA has mismatches with its target – what is the functional outcome of this?
a. There’s no functional difference between siRNA and miRNA.
b. miRNA translationally represses the mRNA, while siRNA binding to an mRNA leads to the
degradation of the mRNA
c. siRNA activates translation while miRNA blocks it.
d. siRNA holds the mRNA, while the miRNA makes more copies of it.
What additional information does footprint analysis give you over using gel shift assay?
How many pieces of DNA each proteins binds
The exact nucleotide location of DNA-protein binding
What sequences are required for transcription
If there’s activity at the regulatory region
Which technique is used to monitor the expression of genes whose products are hard to detect?
DNA footprinting
Primer extension
Gene fusion to a reporter gene
ChlA-PET
You want to find out how many copies of a particular mRNA are in a cell – which technique would you use?
RNA-Seq
Quantitative PCR
Chromatin immunoprecipitation
Footprint analysis
Gel mobility shift assays can be used to determine
The ability of a protein to bind to an rRNA sequence
The ability of DNA to bind to an RNA sequence
The ability of a protein to bind to a DNA sequence
The ability of RNA to bind to another RNA sequence
In _____, interacting protein and DNAs are crosslinked and pulled down with an antibody against the protein. This identifies what proteins and DNA sequences interact with each other.
a. Chromatin immunoprecipitation
b. SAGE
c. Gel shift assay
d. DNA microarray
The antibiotic resistance gene for tetracycline encodes
A transferase that adds acetyl groups onto tetracycline
A channel that pumps tetracycline out of the cell.
An enzyme that degrades tetracycline structure
A kinase that phosphorylates the antibiotic
The following are characteristics of plasmids EXCEPT
Plasmids are contained within their own protein capsid.
Plasmids self-replicate using rolling circle replication or bidirectional replication
Plasmids are commonly circular, double-stranded DNAs that remain separate from the host
chromosome.
Plasmids can contain genes that give the host cell a competitive advantage in its environment.
Adding chemical groups to an antibiotic can provide resistance to a cell by
Changing the shape of the antibiotic so that it no longer fits in the ribosome and blocks translation
Modifying its activity and preventing transcription
Sequestering the antibiotic in the cytoplasm
Shattering the antibiotic
Where are plasmids found?
Eukaryotes only
Prokaryotes only
Eukaryotes and prokaryotes
Prokaryotes and viruses
Which of the following might be plasmid-encoded?
Toxins
Antibiotic resistance
Plant hormones
All of the above
Bacteriocin plasmids encode toxins that will kill other bacteria (for example, ColE2). Why are the bacteria that carry these plasmids not killed?
These plasmids also contain antibiotic resistance genes.
These plasmids have immunity genes that protect against the toxin.
These plasmids are methylated and the toxin genes are not expressed.
These plasmids have a structure similar to heterochromatin in the region of the toxin gene
The Ti plasmid induces tumor growth in plants by expressing genes for
Auxins and cytokinins
Carbohydrate metabolism
Chlorophyll degradation
Self-replication
If bacteria is grown in the presence of ampicillin, the resistant cells survive because
they have mutant ribosomes that are not recognized by ampicillin.
they pump ampicillin out of the cell.
they store ampicillin in the nucleoid
they produce beta-lactamase, an enzyme that degrades ampicillin
How is the copy number of a plasmid maintained?
By limiting the amount of nucleotides in a cell
Via plasmid incompatibility
Through RNA I and RNA II interactions that block the formation of a primer for DNA synthesis
By providing a nutrient that stimulates growth of the plasmid.
Specific regulators
control large numbers of genes in response to a broad, general signals
control large numbers of genes in response to a specific signal
control small numbers of genes in response to broad, general signals
control small numbers of genes in response to a specific signal
Euchromatin
is only found in prokaryotes and forms when the chromosome is bound by accessory factors
Has acetylated histones that compact the DNA and do not allow gene expression to occur.
is densely-packed chromatin that easily gathers together the components necessary for gene
transcription
is loosely-packed chromatin that allows the transcriptional machinery to assemble at promoter
regions
Acetylated histones________________
form highly condensed heterochromatin
are a target of proteases.
allow DNA to be replicated after the cell divides
prevent nucleosomes from becoming highly condensed.
In eukaryotes, negative regulation occurs by
obstructing RNA polymerase II.
interfering with activators.
interfering with repressors
binding of repressors to operators.
What describes the type of viral growth in which the virus exists in the host cell but does not replicate aggressively and cause the cell to burst?
Active infection
Exponential phase
Latency
Lytic growth
Sliding of nucleosomes on DNA
Leads to compaction of nucleosome and less accessible DNA
Inactivation of sequence son the Y chromosome
Can expose new promoter sites
Removes acetyl groups from histones tails
Which of the following is(are) an example(s) of positive regulation of prokaryotic transcription?
An unphosphorylated channel holds the repressor at the cell membrane and doesn’t allow it to bind DNA
Arginine and Arg R repressor bind the DNA and shut off expression of genes involved in arginine synthesis
LacI binds to the operator and prevents the polymerase from binding
Arabinose binds AraC, AraC then binds the promoter region and allows for polymerase
bindin
The antibiotic resistance gene for ampicillin encodes
A transferase that adds acetyl groups onto the antibiotic
A channel that pumps ampicillin out of the cell
An enzyme that destroys (degrades) ampicillin structure
A kinase that phosphorylates the antibiotic
Bacteriocin plasmids encode toxins that will kill other bacteria (for example, CoIE2). Why are the bacteria that carry these plasmids not killed?
These plasmids also contain antibiotic resistance genes
These plasmids are methylated and the toxin genes are not expressed
These plasmids have a structure similar to heterochromatin in the region of the toxin gene
These plasmids have immunity genes that protect against the toxin
When cells are given the signal to grow, the small subunit of the ribosome can be phosphorylated. This leads to
Increasing the translation of specific groups of mRNAs
Preventing any mRNAs from associating with the ribosome
Destruction of ribosomes
Shredding RNAs that come in contact with the ribosomes
Which of the following is FALSE for a repressor?
Its binding to DNA provides the polymerase with access to the promoter.
It blocks the binding of RNA polymerase
The signal molecule binding causes it to come off of or bind to the DNA.
It binds to the operator sequence in the promoter.
Gene expression in eukaryotic cells tends to be more complicated than it is in prokaryotes. For example, repressor rarely just bind DNA and block the polymerase from binding. Which of the following is an example of negative regulation in eukaryotes?
CDP binding the activator binding site on DNA and preventing the activator from binding.
Acetylation of histone tails
Dimers forming with partners that lack DNA binding domains
Transcription factors that have both DNA binding and activating domains
What occurs at the internal resolution sites of transposons?
It guides resolvase to recombine the DNA during replicative transposition.
It is where ribosomes bind and translate the transposase sequence.
Nucleases bind and degrade the DNA.
Transposase recognizes and cuts out the transposon at internal resolution sites
Which of the following are required for conservative transposition? Choose all that apply.
Internal resolution site
Transposase
Resolvase
Inverted repeats
Target sequences
Internal resolution site
Transposase
Resolvase
How does a virus ‘choose’ the cell it will infect?
It recognizes cell with high replication capacity.
There is no choice involved; viruses infect any cell in its environment.
It is attracted by an increasing gradient of chemokines to the cell.
It chooses cells based on its cell-surface molecules.
RNA-Seq itself is useful for determining all of the following EXCEPT
The number of gene transcripts in a cell
Regions required for transcription
Expression level differences between individual cells.
The sequences of the transcribed RNAs
Which technique is used to monitor the expression of genes whose products are hard to detect?
Gene fusion to a reporter gene
DNA footprinting
Primer extension
ChIA-PET
Histones can be modified by adding different chemical groups to amino acid residues in their N-terminal regions. Acetylation of histones tends to
Prevent nucleosomes from becoming highly condensed
From highly condensed heterochromatin
Are a target of proteases
Allow DNA to be replicated after the cell divides
Reporter systems are most useful for ___________.
Determining DNA-protein interactions
Monitoring gene expression
Identifying the product of biochemical reactions
Constructing large numbers of clones in bacteria
In eukaryotic transcription, the mediator complex
Removes repressors so activators can bind
Neutralizes repressors and activators
Integrates the signals of activators and enhancers binding to DNA to start transcription
Has no effect on transcription
SiRNA perfectly pairs with its target while miRNA has mismatches with its target - what is the functional outcome of this?
There’s no functional difference between siRNA and miRNA
siRNA activates translation while miRNA blocks it
miRNA translationally represses the mRNA, while siRNA binding on an mRNA leads to the
degradation of the mRNA
siRNA holds the mRNA, while the miRNA makes more copies of it
Methylation can have different effects depending on when and what is being methylated. If an insulator region is methylated and insulators no longer bind DNA,
Enhancers are restricted to regulating nearby genes.
DNA no longer interacts with matrix attachment regions.
The DNA is unraveled from histones.
Then enhancers can activate distant genes.
How can RNA act as a thermosensor and regulate its own translation?
RNA can be bound by attenuation proteins and stop its transcription
It is recruited by phosphorylation of the S6 protein in ribosomes.
Leader sequences in the 5’UTR can stall the ribosome and allow the pre-emptor loop to
form
Certain stem-loop structures will be more unstable at higher temperatures and unfold to
reveal Shine-Delgarno sequences.
All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT
Regulating activation of the protein
Regulating access to DNA
Controlling recognition of promoter regions through sigma factors
Using anti-termination proteins to transcribe downstream sequences
In the Ac/Ds family of transposons, Ac transposon has a complete transposase gene while Ds transposons have partial or missing transposase genes. Of the following choices, which transposons or sets of transposons can “jump”, or move from their original location? Choose all that apply
Ac transposon
None of the above
Two Ds transposons in one cell
An Ac and a Ds transposon in the same cell
The simplest transposons have
Target sequences and inverted repeats.
Inverted repeats and a gene for antibiotic resistance.
Inverted repeats and a gene for transposase.
Inverted repeats, transposase, and resolvase.
Viruses can have different genome organizations, sizes (3-1000 genes), and structures.
Which of the following is not a viral genome arrangement?
single-stranded DNA
positive single-stranded RNA
double-stranded DNA
double-stranded RNA-DNA hybrid
Place the events of viral life cycle in the proper order in which they occur:
a)Transfer of viral genome into host cell.
b)Release of new virions
c)Translation viral proteins
d)Assembly of new viral particles
e) Attach to host cell.
e,a,c,d,b
a,b,c,d,e
b,a,c,e,d
d,c,e,a,b
What will you NOT find in any virus? Choose all that apply
Outer protein coat
DNA genome
Ribosomes
RNA genome
Mitochondria
Where are plasmids found? Choose all that apply.
Endoplasmic reticulum
Mammalian cells
Viruses
bacteria
What determines if two plasmids are ‘incompatible’?
they produce toxins that kill the host cell.
they have the same DNA sequences in their replication genes
they are transferable from one host to another
they carry genes for antibiotic resistance.
CG islands are found in DNA and are usually the target of methylases. Would you expect
osteocytes (bone cells) and hepatocytes (liver cells) to have the same genes methylated?
No! X-inactivation will determine which cell becomes an osteocyte and which becomes a hepatocyte
Of course! These cells express the same genes at the same levels, otherwise the cells would be destroyed by the immune system.
Yes! The cell functions are the same in all tissues and therefore the same genes will need to be expressed in both cell types.
Of course not! These are different cells needing tissue-specific genes to be expressed
so some methylated genes will be the specific to the tissue.
Which technique crosslinks protein and DNAs, pulls down the crosslinked complex with an antibody the protein, and thereby allows us to identify what proteins and DNA sequences interact with each other?
SAGE
Gel shift assay
Chromatin immunoprecipitation
DNA microarray
Euchromatin ________________.
Is only found in prokaryotes and forms when the chromosome is bound by accessory factors
Has acetylated histones that compact the DNA and do not allow gene expression to occur
Is loosely-packed chromatin that allows the transcriptional machinery to assemble at promoter
regions
Is densely-packed chromatin that easily gathers together the components necessary for gene transcription
Crp binds upstream of the RNA polymerase in the regulatory region of the lac operon. It is most likely to
Acts as a repressor, preventing transcription of lacZ, lacY, lacA
Act as an activator, turning on transcription of lacZ, lacY, and lacA
Has no effect on transcription
Increase the rate of degradation of the transcript
What additional information does footprint analysis give you over using gel shift assay?
How many pieces of DNA each proteins binds
What sequences are required for transcription
The exact nucleotide location of DNA-protein binding
If there’s activity at the regulatory region
Global regulators _______________.
Control large numbers of genes in response to a specific signal
Control large numbers of genes in response to a broad, general signals
Control small numbers of genes in response to broad, general signals
Control small numbers of genes in response to a specific signal
Both conservative and replicative transposition result in movement of the transposon; however, only replicative transposition
Transfers the transposon to the new location without copying it
Has transposase that cuts at inverted repeats and target sequences.
Produces a second copy of the transposon sequence.
Inserts the transposon sequence into target sequences
How is rolling circle plasmid replication different from bi-directional replication?
There is only one replication fork in the intact replication bubble.
Rolling circle replication is only used to copy viral genomes.
Rolling circle replication uses reverse transcriptase to copy the DNA sequence.
One strand is nicked and unwound to act as template.
In prokaryotic transcription, cells may use default sigma factors or alternative sigma factors at promoter. Do cells use alternative sigma factors all the time for all of their transcription?
Yes, because the cell needs to be able to respond to its environment quickly and alternative sigma factors need less regulation.
No, because alternative sigma factors are active only under specific conditions and with
specific sequences in promoter
No, because all prokaryotic genes are found in clusters and the operon requires the default sigma factor.
Yes, as long as antisigma factors are inactivating default sigma factors.
All of the following statements about transposable elements are true EXCEPT
Transposable elements insert at target sites in host DNA.
Transposable elements are pieces of DNA that are inserted into a larger piece of DNA.
Transposable elements self-replicate like plasmids and viruses do.
Transposable elements replicate when the host DNA replicates.
How is the copy number of a plasmid regulated in a host cell?
By sense and antisense RNAs that block the formation of a primer for DNA synthesis
By providing a nutrient that stimulates growth of the plasmid.
By limiting the amount of nucleotides in a cell
Via plasmid incompatibility
Which of the following is TRUE for plus-strand RNA viruses but NOT for minus-strand RNA viruses?
The complementary strand is transcribed, and the double stranded RNA is inserted into the host genome.
Only plus-strand RNA viruses have a high mutational rate that can the virus evade the host’s immune response.
The plus-strand can be directly translated into a polyprotein that then gets cleaved into
smaller functional proteins.
Another plus-strand is first made for plus-strand RNA viruses and translated into viral proteins.
Ferritin mRNA has a ste,-loop structure that is bound by the iron-regulatory protein and blocks the production of ferritin. This is an example of
Transcriptional repression
Translational repression
Activation of translation
Transcriptional attenuation
All virus replication requires
Transfer of viral mitochondria
Host cell machinery
Reverse transcription of RNA into DNA
Functioning viral ribosomes
Since transposition events can damage DNA sequences, how is the amount of active
transposase regulated in the cell? (choose all that apply)
Its activity is regulated by phosphorylation.
A frameshift is necessary to translate the complete functional protein.
It is quickly tagged with ubiquitin and degraded by the proteosome.
The first open reading frame makes a transcriptional regulator to block its transcription.
RNA-dependent RNA polymerase increases the effect of RNAi by
Transcribing more RISC mRNA
Translating more Dicer mRNA
Creating more dsRNA to be cleaved by Dicer into siRNAs
Converting miRNA into siRNA
Gel mobility shift assays can be used to determine
The ability of a protein to bind to a DNA sequence
The ability of a protein to bind to an rRNA sequence
The ability of DNA to bind to an RNA sequence
The ability of RNA to bind to another RNA sequence
By radiolabeling DNA and protein of bacteriophage, Hershey and Chase saw radiolabel only on DNA in new virions. Why wasn’t the radiolabel also detected on the viral proteins?
The protein cut off its radiolabel so the protein coat can be assembled.
The envelope that surrounds the bacteriophage prevents the radiolabel on proteins from
being detected
The protein coat stays outside and doesn’t get into the new viral particles, only viral DNA
goes into the cell
A frameshift causes the proteins’ radiolabel to be removed during replication
Primer extension is used to ______________.
Locate the binding of RNA polymerase
Determine the interaction of RNA and proteins
Generate primers for PCR
Determine the transcriptional start site
Which of the following are characteristics common to plasmids? Choose all that apply.
Cause their host cell to burst and release plasmid.
Contained within protein coat.
Carry sequence that directs replication.
Circular, double stranded DNA
Plasmids often help their host cells by providing additional genes that help the host survive in certain environments. How does the kanamycin-resistance gene help bacteria survive when the host cells are grown in the presence of the antibiotic kanamycin?
It adds chemical groups onto kanamycin so it no longer fits in the ribosome.
Resistance is through beta-lactamase, an enzyme that degrades kanamycin
The cell survives because kanamycin is stored in the nucleoid.
It encodes a pump that moves kanamycin out of the cell.
For an operon, turning on the transcription at the promoter
Initiates transcription of a polycistronic mRNA
Starts transcription of only non-coding RNA sequences
Turns off translation of monocistronic DNA
Activates transcription of a single gene
You’ve heard about protein-tagging systems that add a molecule to your protein and let you purify your protein from cells, identify your protein without having a specific antibody against it, or isolate your protein and its binding partners. What do you need to know about the protein to “tag” it?
Its molecular weight and charge
Where it localizes in the cell
When it is expressed
Its coding sequence
Which of the following is an example of negative regulation?
A gene is switched off by a repressor protein
A gene is switched on in the presence of an activator
A gene is de-repressed
A gene is induced
X-inactivation _________________.
Only occurs in males
Prevents transcription of one of the two X chromosomes in females
Is the deactivation of both X chromosomes in all females
Occurs by the action of histone acetylation
Acetylated histones ____________.
Prevent nucleosomes from becoming highly condensed
From highly condensed heterochromatin
Are a target of proteases
Allow DNA to be replicated after the cell divides
In eukaryotes, negative regulation occurs by ________________.
Obstructing RNA polymerase II
Interfering with repressors
Interfering with activators
Binding of repressors to operates
Levels of transcription for a specific gene are measured using all of the following except ____________
Quantitative PCR
Primer extension
Reporter genes
SAGE
Protein-tagging systems allow proteins to be expressed with a handy “tag” that then allow them to be isolated or detected - but what else do you need to have to make these tagged proteins?
RNA thermosensors to regulate the system by temperature
The nucleotide sequence that codes for your protein of interest
An antibody that recognizes the amino acid sequence of your gene of interest
Xgal to detect active luciferase
A method that uses an antibody to detect a specific protein is called ___________
Phage display
Mass Spectrometry
Yeast two hybrid system
Western blot
Which method allows a researcher to screen for a protein based on its function, and find its nucleotide sequence, too?
Phage display
Co-immunoprecipitation
RT-PCR
Intein trapping
Which of the following is NOT used in a Western blot?
Antibody
RNA probe
Acrylamide gel
SDS
NusG, an anti-termination factors, binds to RNA polymerase and causes the polymerase to
Immediately stop transcribing and release from the template
Ignore transcription termination signals and transcribe downstream genes
Return to the promoter region
d. Methylate the gene sequence and permanently turn off gene transcription
Which of the following is TRUE for an activator?
It blocks the binding of RNA polymerase.
The signal molecule causes it to come off of the DNA
Binding of the signal molecule to the activator causes the activator to bind to DNA
It binds to the operator sequence in the promoter.
Acetylated histones________________
form highly condensed heterochromatin
Never exist in the nucleus
Allow nucleosomes to be less aggregated
are a target of proteases.
Which of the following is an example of small molecules acting as a co-repressor and turning off transcription?
A unphosphorylated channel (PtsG) binding to a repressor and keeping the repressor at the cell membrane
Arginine and ArgR repressor interacting with each other and then binding to the operator region
of genes in the Arg biosynthesis pathwa
Oxidation of the activator Fnr to hide DNA binding sites
Transfer of phosphate groups between multiple regulatory proteins
Euchromatin _______________
Is only found in prokaryotes
Is loosely packed chromatin
Does not allow gene expression to occur
Is densely packed chromatin
Insulator regions in DNA can be bound by insulator binding proteins, and
Extend the reach of enhancers to distant promoter sequences
Restrict enhancers to acting upon local genes
Deacetylate histone tails and cause compaction
Inactivate transcription by blocking activator binding sites
Methylation of DNA and deacetylation of histones
Turns on gene transcription
Tends to silence and inactivate genes
Targets mRNAs for degradation
Creates regions of euchromatin
A protective mechanism in eukaryotic cells that destroy mRNAs with the exact same sequence as siRNAs is
Nonsense mediated decay
CRISPR
RNA interference
The proteasome
All of the following are ways to regulate translation EXCEPT for
Controlling the rate of mRNA degradation
Insulator creating loops of DNA
Antisense RNA binding to mRNA
Modifying ribosomes
Without cleavage of adhE mRNA, no translation occurs, why?
Introns need to be spliced out first
Cleavage removes secondary structure and exposes the ribosome binding site
The repressor binding site is removed by cleavage
The activator binding site is added back on the 3’UTR
Rolling circle replication _____________.
Begins when the origin of replication is pulled apart to generate a replication bubble
Begins when the origin of replication is nicked and one strand is unrolled
Occurs at the origin of vegetative replication
Occurs when a plasmid replicated in step with host cell division
Plasmids are incompatible and will not exist in the same cell after multiple rounds of division when
They are transferable
They have similar DNA sequences in the replication genes
They produce toxins.
They carry genes for antibiotic resistance
Choose the characteristic that is NOT found in a plasmid
Origin of replication
Circular
Double-stranded RNA
Double-stranded DNA
Which of the following is not an inducer of the lac operon?
a. allo-lactose
b. IPTG
c. glucose
d. Lactose
Gratuitous inducers
are metabolized like the natural inducer
are not broken down
are nutrient sources
are competitive inhibitors
All of the following are examples of transcriptional regulation in prokaryotes except
binding of a repressor to an operator
premature termination of RNA polymerase during transcription elongation
binding of cAMP-CRP complex to the lac operon of Escherichia coli
over-riding termination by anti-terminator proteins
All of
the following are associated with two-component regulatory systems except .
gratuitous inducer
phosphorelay
DNA binding regulator
sensor kinase
Autoregulation occurs when .
IPTG binds to LacI
allo-lactx-inarose binds to LacI
a repressor binds to its own gene to prevent transcription
CRP binds to cAMP and the the lac operon
Which of the following is the MOST commonly used as a control point in eukaryotic transcription?
initiation
elongation
termination
RNA processing
Housekeeping genes are always .
off until needed
on
induced
Repressed
X-inactivation
only occurs in males
is the deactivation of both X chromosomes in all females
shuts down one of the two X chromosomes in females
occurs by the action of histone acetylation
Xist is
a gene encoding an untranslated RNA involved in X-inactivation
the heterochromatin of inactivated X chromosomes
is a gene that is only found on active X chromosomes
helps inactivate the X chromosome of males
Specific transcription factors .
a. modulate gene expression in response to a specific stimulus
b. are not able to enter the nucleus of eukaryotes and instead help regulate gene expression at the post-transcriptional level
c. bind to target mRNAs prior to translation
d. prevent RNA polymerase II from binding to the DNA
RNA interference is triggered by
a. dsDNA
b. dsRNA
c. ssDNA
d. ssRNA
Riboswitches
can bind small molecules
are useful in translational control
are found on the 5’ end of the mRNA
are all of the above
Which statement is false?
Nucleases are not part of the RNAi scenario.
Some small RNAs help stabilize the mRNA and protect it from degradation.
RNAi is a form of gene silencing that involves degradation of target RNAs.
Riboswitches bind small molecules.
Proteins that prevent translation of mRNA are called
nucleases
translational repressors
proteases
mRNA silencers
Which nuclease is responsible for generating siRNA?
Ribonuclease P
Dicer
Slicer
RISC
In bacteria, the system destroys incoming viral DNA and RNA.
a. RISC
b. Dicer
c. Slicer
d. CRISPR
The blocking of translation of an mRNA by miRNA occurs because the miRNA .
binds to the 3’-UTR of the mRNA and prevents translation
targets the mRNA for degradation by Slicer
binds to the 5’-UTR to prevent the ribosome from binding
folds into alternative stem-loop structure and protects the mRNA from nuclease
cleavage
How might the potential binding of a protein to a specific fragment of DNA be investigated?
primer extension
western blotting
gel mobility shift assays
isoelectric focusing
Which of the following techniques would not be useful for determining the number of mRNA copies present in a cell?
SAGE
DNA microarrays
Quantitative PCR
Primer extension
DNase I protection assays or DNA footprinting is useful for
determining the start of transcription
determining the location of a DNA binding sequence
preventing contamination of RNA in primer extension samples
none of the above
Microarrays and SAGE have the ability to monitor
large numbers of mRNAs simultaneously
small numbers of specific mRNAs
proteins expressed under a given condition
the binding of a protein to a DNA or RNA molecule
A specific mRNA may be detected using
a. Southern
b. Western
c. Northern
d. Southwestern
Bidirectional replication for F-plasmids occurs at the
origin of vegetative replication
origin of transfer
origin of chromosomal replication
linear ends
Which one of the following organisms does not have plasmids?
a. bacteria
b. viruses
c. yeast
d. Archaea
Plasmids in the same family are incompatible because .
they are transferable
they produce toxins
they carry genes for antibiotic resistance
they have similar DNA sequences in the replication genes
The early genes of viruses are transcribed by
host RNA polymerase
viral RNA polymerase
DNA polymerase
rolling circle replication
Viral protein coats are called
a. capsomeres
b. envelopes
c. capsids
d. Cloaks
Plaques are the result of
bacteria infecting viruses
viruses infecting bacteria
viruses lysing bacteria
Lysogens
All viruses are
a. parasitic
b. saprophytic
c. enveloped
d. Bacteriophages
Enveloped viruses only infect
a. plants
b. bacteria
c. animals
d. Yeast
The next step of viral propagation following attachment and entry is .
genome replication
assembly
viral protein manufacture
release of new virions
Which enzyme is required for RNA viruses to replicate their genomes?
reverse transcriptase
RNA replicase
DNA polymerase
host RNA polymerase
Defective copies of transposable elements that are found in genomes are called
junk DNA
transposable elements
retrotransposons
Introns
Resolvase is needed for
conservative transposition
replicative transposition
simple transposons
Retrotransposons
Internal resolution sites of complex transposons are recognized by
a. Dicer
b. cointegrase
c. recombinase
d. Resolvase
All transposons have all of the following characteristics except
the gene for transposase
inverted repeats
resolvase
antibiotic resistance genes
Reverse transcriptase is needed for
the movement of retrotransposons
the integration of RNA transposons
the transcription of RNA transposons
the excision of retrotransposons
Conservative transposition
generates a copy of the transposon
generates double-stranded breaks in the DNA
occurs only for RNA transposons
has no detrimental effects on the host genome.
Where might mobile DNA elements be found?
plasmids
chromosomes
viral genomes
all of the above
Any DNA or RNA molecule that has an origin of replication is called a
mobile element
transposon
replicon
Integron
What is the purpose of the inverted repeats at the ends of DNA-based transposons?
The inverted repeats are recognized by enzymes that move the elements.
The inverted repeats are the sites of transfer.
The inverted repeats are recognized by restriction enzymes that cut out the transposon.
The inverted repeats are magnets for nucleases
Which method allows a researcher to find a gene based upon the protein that it encodes?
Co-immunoprecipitation
RT-PCR
Phage display
Intein trapping
You’ve cloned your protein of interest and added a MBP tag to it. What benefit do you get from the MBP tag?
You can purify your protein
You can use the MBP to isolate your protein and its binding partners
You can now identify your protein without having a specific antibody against it
All of these
NusG binds to RNA polymerase and causes the polymerase to transcribe downstream genes. NusG is an example of
A co-repressor
An anti-termination factor
An activator
A phosphorelay system
Attenuation of RNA involves the formation of alternate stem-loop structures
a. False
b. True
When cells are given the signal to grow, the S6 protein on the small subunit of the ribosome can be phosphorylated. This leads to
Preventing any mRNAs from associating with the ribosome
Increasing the translation of specific groups of mRNAs
Destruction of ribosomes
Shredding RNAs that come in contact with the ribosome.
