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WorksheetsMolecular Exam 3
Total questions: 76
Worksheet time: 38mins
Would removing the Shine-Dalgarno sequence from an mRNA affect eukaryotic translation?
Yes, the small subunit would not bind.
No, eukaryotic translation relies on their cap structure to assemble the ribosome and find the first AUG, not a
Shine-Dalgarno sequence.
Yes, the initiator tRNA would not be able to bind the A site.
No, because eukaryotic translation uses elongation factors to assemble the ribosome.
Bacteria can transcribe and translate the same mRNA; why can this NOT happen in eukaryotes?
This happens all the time in eukaryotes
mRNA is in the nucleus while ribosomes are in the nucleolus.
mRNAs are transcribed and processed in the nucleus, while translation only occurs in the cytoplasm.
Eukaryotic RNA polymerases and ribosomes are too big to be on the same piece of mRNA at the same time
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 is for 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?
By binding to epitopes on the protein’s surface through its variable domains.
By binding to DNA sequences in its promoter and turning on transcription of its gene sequence.
By adding a biotin label and isolating it using avidin or streptavidin.
By precipitating the protein’s coding sequence.
When separating proteins using SDS-PAGE (PAGE=polyacrylamide gel electrophoresis), why do we use SDS?
To make the sample bubbly because bubbles are great.
To denature the protein and give it a net negative charge proportional to its size.
To refold the protein and restore activity
To remove cell fragments that may be attached to the proteins.
Co-immunoprecipitation is used to
Determine if two proteins interact with the same antibody.
Analyze DNA sequence of a protein.
Determine if two proteins interact with each other.
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
Identifies the function of protein of interest by its mass-to-charge ratio.
Depends on having SDS in the reaction.
Causes the cell to lyse and release the proteins into the lysate.
Forms an intact transcription factor that turns on the expression of a reporter gene.
In prokaryotic transcription, cells may use default sigma factors or alternative sigma factors at the 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
Yes, as long as antisigma factors are inactivating default sigma factors.
No, because all prokaryotic genes are found in clusters and the operon requires the default sigma factor.
All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT
Regulating access to DNA and the promoter region
Controlling recognition of promoter regions through sigma factors
Using anti-termination proteins to transcribe downstream sequences
Regulating activation of the translated protein.
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.
Which of the following is FALSE for a repressor?
It blocks the binding of RNA polymerase.
The signal molecule binding causes it to come off of or bind to the DNA
Its binding to DNA provides the polymerase with access to the promoter.
It binds to the operator sequence in the promoter.
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.
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.
Would removing the Shine-Dalgarno sequence from an mRNA affect prokaryotic translation?
No,because prokaryotic translation uses elongation factors to assemble the ribosome.
Yes, the small subunit would n o t bind.
Yes, the initiator tRNA would not be able to bind the Asite.
No, eukaryotic translation relies on their cap structure to assemble the ribosome and find the first AUG, not a Shine-Dalgarno sequence.
In translation, release factors
help the ribosome release the amino acids on the charged tRNAs.
help terminate transcription.
exchange uncharged tRNA molecules in the ribosome for tRNAs associated with amino acids.
recognize the stop codon and help dissociate the ribosome
A triplet of three nucleotides found on the mRNA that codes for an amino acid is the
peptide
anticodon
codon
trio
During translation, elongation factors, like EF-G,can
During translation, elongation factors, like EF-G, can
act as internal ribosome entries and allow translation of a second cistron.
assist stalled ribosomes by providing a stop codon.
shift the tRNAs in the A and P sites to the P and E sites, respectively.
add additional sequence to the mRNA and increase the size of the protein.
All of the following are required for translation EXCEPT
RNA polymerase
mRNA
tRNA
rRNA
What happens to a protein tagged with ubiquitin?
It is brought to the membrane, where it is allowed to continue translation and translocation across the membrane.
It is targeted to the proteasome for degradation
It remains within the ribosome.
It is secreted from the cell in its active state.
If resources are scarce in bacteria, how is protein translation slowed?
Ribosomes are held on mRNA, making a polysome.
More release factors are translated, which dissociates the ribosomes into large and small subunits.
ribosome Modulation Factor, RMF, binds ribosomes, causing them to form dimers and blocking them from interacting with mRNAs.
elF2 remains bound to GDP and stays in an inactive state.
Protein primary structure is the result of
Hydrogen bonds forming along the peptide backbone.
Peptide bonds between adjacent amino acids
Covalent bonds between R-groups.
Hydrogen bonds between R-groups
The specificity of an enzyme for its substrate is determined by all of the following except
Size of active site
Shape of active site
Hydrophobic residues on the cytoplasmic surface of the enzyme.
Presence or absence of charge within active site pocket
If hydrogen bonds are critical for secondary structure, what stabilizes tertiary structures?
Hydrophobic repulsion of R groups.
Hydrophobic interactions between different subunits.
Peptide bonds between neighboring amino acids.
Hydrogen bonds between R groups.
Where are hydrophilic residues likely to be found in a cytoplasmic (non-membrane) protein?
Buried in the center of the protein, shielded from the external, aqueous environment.
Interacting with hydrophobic residues to provide balance to the protein structure.
Exposed on the surface of the protein so they can interact with water.
Forming covalent bonds with charged -groups in the peptide chain.
Metal ions and cofactors
Give the protein extra mass required for function.
Help the protein fold properly and maintain its structure and activity.
Are only useful when isolating the protein.
Tether the protein to the plasma membrane.
Some activators of transcription are examples of allosteric proteins, meaning
They absorb or emit light.
They refold unfolded proteins.
Their structure must stay the same at all times in order to be active.
The binding of a signal molecule to one part of the protein changes its shape and activity.
Leucine residues within leucine zipper motifs
Interact directly with DNA.
Are hydrophilic and remain exposed on the protein surface.
Serve as phosphorylation sites and regulate activity.
Form the interaction domain between two protein subunits.
An enzyme is denatured when
Its three-dimensional (3D) configuration is changed and it can no longer work.
Its three-dimensional (3D) configuration stays the same but it can no longer work.
Its secondary structure is altered and this increases the rate of its reaction.
Its primary structure is altered and this alters its reaction.
In a-helix (alpha-helix), where are the R-groups located?
Hidden within the core of the helix
Projecting parallel to the H-bonds along the axis.
Extending outward from the helix.
Alternating between extending outward from or into the helix
When separating proteins using SDS-PAGE(PAGE=polyacrylamide gel electrophoresis), why do we use SDS?
To denature the protein and give it a net negative charge proportional to its size.
To clean the sample and remove oils from the protein.
To refold the protein and restore activity
To remove cell fragments that may be attached to the proteins.
How does an antibody recognize a protein?
By precipitating the protein's coding sequence.
By binding to DNA sequences in its promoter and turning on transcription of its gene sequence
By adding a biotin label and isolating it using avidin or streptavidin.
By binding to epitopes on the protein's surface through its variable domains.
In yeast 2-hybrid screening, the interaction between the"bait" and "prey" proteins
Identifies the function of protein of interest by its mass-to-charge ratio.
Forms an intact transcription factor that turns on the expression of a reporter gene.
Depends on having SDS in the reaction.
Causes the cell to lyse and release the proteins into the lysate.
Co-immunoprecipitation is used to
Analyze DNA sequence of a protein.
Determine if two proteins interact with the same antibody.
Identify chemical groups that have been added to the protein post-translationally.
Determine if two proteins interact with each other.
What is the benefit of expressing your protein of interest with a protein tag, like FLAG- or His-tag?
The protein tag provides a fluorescent label that allows for cell sorting.
The addition of the tag allows you to isolate the protein easily, without having to make an antibody specific to your protein
The protein tag denatures the protein and gives it a negative net charge that permits separation by SDS-PAGE.
Transcription is activated by the DNA-binding domain of the protein tag.
In prokaryotic transcription, cells may use default sigma factors or alternative sigma factors at the promoter. Do cells use alternative sigma factors all the time for all of their transcription?
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, because the cell needs to be able to respond to its environment quickly and alternative sigma factors need less regulation.
Yes, as long as antisigma factors are inactivating default sigma factors.
What information does MALDI-TOF or electrospray mass spectroscopy give us about a protein?
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.
It tells us an exact molecular weight, from which we can determine the protein's identity.
How are polyacrylamide gels and column chromatography similar to each other?
They allow us to screen for proteins and their coding sequences based on function.
These techniques separate proteins based on size and/or charge.
Both identify proteins without having specific antibodies against the proteins of interest.
They provide the molecular weight of the protein, including any modifications that may be present.
For an operon, turning on transcription at the promoter
Initiates transcription of a polycistronic mRNA.
Activates transcription of a single gene.
Starts transcription of only non-coding RNA sequences.
Turns off translation of monocistronic DNA.
All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT
Regulating access to DNA and the promoter region
Controlling recognition of promoter regions through sigma factors
Controlling activation of the translated protein.
Using anti-termination proteins to transcribe downstream sequences
Using phage display, researchers can
Show that two proteins interact through the expression of a reporter gene.
Isolate a specific protein with an antibody against a protein tag, like His.
Screen for protein based on function, and then also discover its coding sequence.
Precisely measure the molecular weight of the protein and identify it.
Global regulators of transcription
control small numbers of genes in response to broad, general signals.
control large numbers of genes in response to a broad, general signals.
control small numbers of genes in response to a specific signal.
control large numbers of genes in response to a specific signal.
Which of the following is FALSE for a repressor?
It binds to the operator sequence in the promoter.
It blocks the binding of RNA polymerase.
The signal molecule binding causes it to come off of or bind to the DNA.
Its binding to DNA provides the polymerase with access to the promoter.
Which of the following is an example of positive regulation of prokaryotic transcription?
Lacl binds to the operator and prevents the polymerase from binding.
An unphosphorylated channel holds the repressor at the cell membrane and doesn't allow it to bind DNA.
Arabinose binds AraC, AraC then binds the promoter region and allows for polymerase binding to the promoter.
Arginine and ArgR repressors bind the DNA and shut off expression of genes involved in arginine synthesis.
Crp binds upstream of the RNA polymerase in the regulatory region of the lac operon. Based on where it binds in the regulatory region, it is most likely to
Have no effect on transcription.
Act as an activator, turning on transcription of lacZ, lacY, and lacA.
Increase the rate of degradation of the transcript.
Acts as a repressor, preventing transcription of lacZ, lacY and lacA.
Heterochromatin
is only found in prokaryotes and forms when the chromosome is bound by accessory factors.
has densely-packed chromatin that easily gathers together the components necessary for gene transcription.
has non-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 promoter regions.
When there is an excess of the amino acid arginine, it acts as a co-repressor when it binds to the Arg R repressor. What does the arginine-Arg R repressor complex do next?
Falls off the operator and the RNA polymerase to bind.
Binds to the operator and prevent expression of proteins that make more arginine.
It is transported to the cell membrane, where it pumps arginine out of the cell.
It activates anti-anti-sigma factors and turns on transcription by alternative sigma factors.
Methylation can have different effects depending on when and what is being methylated. fI an insulator region is methylated and insulators no longer bind DNA,
The DNA is unraveled from histones.
Then enhancers can activate distant genes.
Enhancers are restricted to regulating nearby genes.
DNA no longer interacts with matrix attachment regions.
Gene expression in eukaryotic cells tends to be more complicated than it is in prokaryotes. For example, eukaryotic repressors rarely just bind DNA and block the polymerase from binding. Which of the following is an example of negative regulation in eukaryotes
Dimers forming with both partners having DNA binding domains
Transcription factors that have both DNA binding and activating domains.
Acetylation of histone tails.
CDO binding the activator binding site on DNA and prevents activator from binding
Gene expression in eukaryotic cells tends to be more complicated than it is in prokaryotes. For example, eukaryotic repressors rarely just bind DNA and block the polymerase from binding. Which of the following is an example of negative regulation in eukaryotes
Dimers forming with partners that lack DNA binding domains
Transcription factors that have both DNA binding and activating domains.
Acetylation of histone tails.
Methylation of insulator and enhancer domains
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 as methylated?
Of course! These cells express the same genes at the same levels, otherwise the cells would be destroyed by the immune system.
No! X-inactivation will determine which cell becomes an osteocyte and which becomes a hepatocyte.
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.
Yes! The cell functions are the same in all tissues and therefore the same genes will need to be expressed in both cell types.
Sliding of nucleosomes on DNA
Inactivates sequences on the X chromosome.
Removes acetyl groups from histone tails.
Can expose new promoter sites.
Leads to compaction of nucleosome and less accessible DNA.
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.
allow DNA to be replicated after the cell divides.
form highly condensed heterochromatin that cannot be transcribed.
are targeted by proteases and degraded.
When methylases add methyl groups to CG islands in DNA, this can block transcription factors from binding DNA, but it can provide the scaffold for bringing in histone deacetylases (HDACs). Once on DNA, what do HDACs do?
They tag the DNA and histones for degradation by the proteosome.
They recruit UBF to the methylated CG islands and turn on the transcription of rRNAs.
They remove acetyl groups from histones, leading to the aggregation of histones and silencing of DNA sequences.
They remove acetyl groups from DNA and add them to histones, thereby opening access to DNA.
When cells are given the signal to grow, the S6 protein on the small subunit of the ribosome can be phosphorylated. This leads to
Shredding RNAs that come in contact with the ribosome.
Preventing any mRNAs from associating with the ribosome
Increasing the translation of specific groups of mRNAs
Destruction of ribosomes
Where does transcription occur in eukaryotes?
In the cytoplasm
On ribosomes.
On methylated CG islands
In the nucleus
What effect does antisense RNA have on translation of its mRNA?
It hybridizes with its complementary sequence and blocks its translation.
It exposes the ribosome binding site and promotes translation.
It binds to the mRNA response elements and signals for degradation.
It slows transcription and causes early termination of translation.
Enhancers
recognize the promoter and help the polymerase bind the promoter.
are regions of DNA that are located far away from promoters they control; they can bind transcription factors and activate transcription
regions of DNA that make "local' areas of DNA and prevent chromatin from compaction from spreading.
Integrate all of the signals coming into the transcription apparatus and determine whether or not transcription will be activated
Ferritin mRNA has a stem-loop structure that is bound by the iron-regulatory protein, which blocks the production of ferritin.This is an example of
Transcriptional attenuation
Transcriptional repression
Translational repression.
Activation of translation
How can RNA act as a thermosensor and regulate its own translation?
Leader sequences in the 5'UTR can stall the ribosome and allow the pre-emptor loop to form.
It is recruited by phosphorylation of the S6 protein in ribosomes.
RNA can be bound by attenuation proteins and stop its transcription.
Certain stem-loop structures will be more unstable at higher temperatures and unfold to reveal Shine-Dalgarno sequences.
Riboswitches can alternate between forming pre-emptor stem loops or terminator stem loops. What causes the switch between the two forms?
Signal metabolite binding, shifting to the loop structure that forms a terminator loop or occludes the Shine-Dalgarno sequence.
Upstream open reading frames in the 5' UTR.
A decrease in temperature shifts the structure back to the pre-emptor loop.
Protein binding to the 3'UTR of the mRNA.
In one mechanism of transcription attenuation, the ribosome moves through the leader region of the mRNA quickly, a terminator loop forms, and transcription stops. Could this same regulatory mechanism be at work in eukaryotes?
No, because the Shine-Dalgarno motif is removed from eukaryotic mRNAs.
Yes, ribosomes bound to the 5' end of mRNAs would release the transcription apparatus from the 3' end
No, because phosphorylation of the ribosome prevents it from acting with all mRNAs.
No, because transcription and translation occur in separate cell compartments, and not on the same mRNA at the same time.
CsrA stabilizing some mRNAs while triggering the destruction of others is an example of
Preferential translation of certain classes of mRNAs by modifying the ribosome.
Regulating the rate of RNA degradation
Making untranslatable RNA open for translation.
Transcriptional attenuation
Which of the following is an example of a translational activator?
Iron response protein
Attenuation protein bound with its amino acid
Ribosomal proteins binding to their own mRNA
cPABP (chloroplast polyadenylated binding protein)
The first level of protein (primary) structure begins with having
multiple subunits come together
hydrogen bonding between chemical groups in the protein backbone
the correct linear sequence of amino acids
interactions between amino acid R-groups
What is the proteome?
the total set of proteins encoded by the organism's genome
the total set of proteins in the cell at any given point
the number of genes that are expressed in a specific growth condition
the number of expressed genes
Which of the following is TRUE for a repressor of prokaryotic transcription?
Its binding to DNA is not regulated by signal molecules
It can block the binding of RNA polymerase to the promoter
Its binding to DNA provides the polymerase with access to the promoter
It binds to the Shine-Dalgarno sequence and blocks the ribosome from binding
All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT
regulating access to DNA and the promoter region
inhibiting translation through regulatory proteins binding to mRNA sequence
controlling recognition of promoter regions through sigma factors
using anti-termination proteins to transcribe downstream sequences
specific regulators of transcription
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 a specific signal
control small numbers of genes in response to broad, general signals
an operon is
where the repressor binds and prevents transcription
a cluster of genes in prokaryotes that has its transcription controlled by the same regulatory regions
downstream of the promoter and can sometimes be found in the gene sequence
compacts DNA in prokaryotic cells
The regulatory region of the lac operon has an up stream activator site that bind Crp and an operator that binds lac repressor. If both Crp and lac repressor are bound, what happens to transcription of the downstream genes?
transcription is turned off because the polymerase cannot bind
transcription is activated and the genes are transcribed
transcription can be turned on if lactose binds Crp and causes it to come off the DNA
transcription is blocked by the formation of a DNA loop, which prevents the RNA polymerase from binding to the DNA
In eukaryotic transcription, the mediator complex
removes repressors so activators can bind
integrates the signals of activators and enhancers binding to the DNA to start transcription
neutralizes repressors and activators
has no effect on transcription
HATs (histone acetyl transferases) add acetyl groups to histone tails and can slide nucleosomes on DNA, which
leads to compaction of nucleosome and less accessible DNA
inactivation of sequences on the Y chromosome
can expose new promoter sites
removes acetyl groups from histone tails
Which of the following is an example of regulation designed to produce a quick response>
repressor binding to operator
having RNA secondary structure block the Shine-Dalgarno sequence
phosphorylation of a protein to activate it
instability of mRNA
Sometimes, prokaryotic mRNAs are processed, too. AdhE mRNA needs to be cleaved before it can be translated why?
the cleaved part of the RNA is needed to sequester proteins that will degrade the mRNA
The secondary structure of the mRNA blocks the ribosome binding site and coding sequence
cleavage removes the thermosensor
so it can phosphorylate the ribsome
