Molec Bio Exam 3B

Where are hydrophilic residues likely to be found in a cytoplasmic (non-membrane) protein?

A. Buried in the center of the protein, shielded from the external, aqueous environment. (→ this is hydrophobic)

B. Exposed on the surface of the protein so they can interact with water.

C. Interacting with hydrophobic residues to provide balance to the protein structure.

D. Clustering with hydrophobic R-groups in the peptide chain.

B. Exposed on the surface of the protein so they can interact with water.

The specificity of an enzyme for its substrate is determined by all of the following except:

A. Size of active site

B. Shape of active site

C. Presence or absence of charge within active site pocket

D. All of these determine how specific an enzyme is for its substrate.

D. All of these determine how specific an enzyme is for its substrate.

Unlike proteins that have only a single subunit, a protein that is composed of multiple subunits has:

A. Primary structure

B. Secondary structure

C. Tertiary structure

D. Quaternary structure

D. Quaternary structure

Protein secondary structure is the result of:

A. Peptide bonds between adjacent amino acids

B. Hydrogen bonds forming along the peptide backbone.

C. Covalent bonds between R-groups.

D. Hydrogen bonds between R-groups

B. Hydrogen bonds forming along the peptide backbone.

An enzyme is denatured when:

A. Its secondary structure is changed and this speeds up the reaction.

B. Its primary structure is altered and this alters the speed of its reaction.

C. Its 3D shape is altered and it can no longer work.

D. Its 3D shape remains the same but it can no longer work.

C. Its 3D shape is altered and it can no longer work.

If hydrogen bonds are critical for secondary structure, what can stabilize tertiary structure?

A. Hydrophobic repulsion of R groups.

B. Hydrogen bonds between R groups.

C. Hydrophobic interactions between different subunits.

D. Peptide bonds between neighboring amino acids.

B. Hydrogen bonds between R groups.

The first level of protein (primary) structure begins with having

A. The correct linear sequence of amino acids.

B. Multiple subunits come together.

C. Hydrogen bonding between chemical groups in the protein backbone.

D. Interactions between amino acid R-groups.

A. The correct linear sequence of amino acids.

Allosteric enzymes are regulated by:

A. Substrate analogs binding and blocking inhibitors from binding.

B. Binding of a signaling molecule, which changes the shape and activity of the active site.

C. The unfolding of zinc fingers.

D. The cleavage of peptide bonds between subunits.

B. Binding of a signaling molecule, which changes the shape and activity of the active site.

A Western Blot uses an antibody to detect a specific protein. How does an antibody recognize a protein?

A. By binding to DNA sequences in its promoter and turning on transcription of its gene sequence.

B. By adding a biotin label and isolating it using avidin or streptavidin.

C. By precipitating the protein's coding sequence.

D. By binding to epitopes on the protein's surface through its variable domains.

D. By binding to epitopes on the protein's surface through its variable domains.

Leucine residues within leucine zipper motifs:

A. Interact directly with DNA.

B. Form the interaction domain between two protein subunits.

C. Are hydrophilic and remain exposed on the protein surface.

D. Serve as phosphorylation sites and regulate activity.

B. Form the interaction domain between two protein subunits.

When separating proteins using SDS-PAGE (PAGE=polyacrylamide gel electrophoresis), why do we use SDS?

A. To denature the protein and give it a net negative charge proportional to its size.

B. To make the sample bubbly because bubbles are great.

C. To refold the protein and restore activity

D. To remove cell fragments that may be attached to the proteins.

A. To denature the protein and give it a net negative charge proportional to its size.

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. Forms an intact transcription factor that turns on the expression of a reporter gene.

C. Depends on having SDS in the reaction.

D. Causes the cell to lyse and release the proteins into the lysate.

B. Forms an intact transcription factor that turns on the expression of a reporter gene.

Co-immunoprecipitation is used to:

A. Determine if two proteins interact with the same antibody.

B. Analyze DNA sequence of a protein.

C. Identify chemical groups that have been added to the protein post-translationally.

D. Determine if two proteins interact with each other.

D. Determine if two proteins interact with each other.

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.

C. The total set of proteins encoded by the organism's genome.

In prokaryotic transcription, cells may use default sigma factors or alternative sigma factors to recognize the promoter of genes. Do cells use alternative sigma factors all the time for all of their transcription?

A. Yes, because the cell needs to be able to respond to its environment quickly and alternative sigma factors need less regulation.

B. Yes, as long as anti-sigma factors are inactivating default sigma factors.

C. No, because alternative sigma factors are active only under specific conditions and with specific sequences in promoter.

D. No, because all prokaryotic genes are found in clusters and the operon requires the default sigma factor.

C. No, because alternative sigma factors are active only under specific conditions and with specific sequences in promoter.

What is the benefit of expressing your protein of interest with a protein tag, like FLAG- or His-tag?

A. The protein tag provides a fluorescent label that allows for cell sorting.

B. The protein tag denatures the protein and gives it a negative net charge that permits separation by SDS-PAGE..

C. Transcription is activated by the DNA-binding domain of the protein tag.

D. The addition of the tag allows you to isolate the protein easily, without having to make an antibody specific to your protein.

D. The addition of the tag allows you to isolate the protein easily, without having to make an antibody specific to your protein.

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:

A. Acts as a repressor, preventing transcription of lacZ, lacY and lacA.

B. Have no effect on transcription.

C. Increase the rate of degradation of the transcript.

D. Act as an activator, turning on transcription of lacZ, lacY and lacA.

D. Act as an activator, turning on transcription of lacZ, lacY and lacA.

All of the following are examples of where the cell can regulate at the transcriptional level EXCEPT

A. Regulating access to DNA and the promoter region

B. Controlling recognition of promoter regions through sigma factors

C. Regulating activation of the translated protein.

D. Using anti-termination proteins to transcribe downstream sequences

C. Regulating activation of the translated protein.

For an operon, turning on transcription at the promoter

A. Initiates transcription of only non-coding RNA sequences.

B. Starts transcription of a polycistronic mRNA.

C. Turns off translation of monocistronic DNA.

D. Activates transcription of a single gene.

B. Starts transcription of a polycistronic mRNA.

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?

A. Falls off the operator and allow the RNA polymerase to bind.

B. It is transported to the cell membrane, where it pumps arginine out of the cell.

C. it activates anti-anti-sigma factors and turns on transcription by alternative sigma factors.

D. Binds to the operator and prevent expression of proteins that make more arginine.

D. Binds to the operator and prevent expression of proteins that make more arginine.

Specific regulators of transcription

A. control small numbers of genes in response to a specific signal.

B. control large numbers of genes in response to a broad, general signals.

C. control large numbers of genes in response to a specific signal.

D. control small numbers of genes in response to broad, general signals.

A. control small numbers of genes in response to a specific signal.

The regulatory region of the Lac operon has an upstream 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?

A. Transcription is turned off because the polymerase cannot bind.

B. Transcription is activated and the genes are transcribed.

C. Transcription can be turned on if lactose binds Crp and causes it to come off the DNA.

D. Transcription is blocked by the formation of a DNA loop, which prevents the RNA polymerase from binding to the DNA.

A. Transcription is turned off because the polymerase cannot bind.

Euchromatin

A. is only found in prokaryotes and forms when the chromosome is bound by accessory factors.

B. Has acetylated histones that compact the DNA and do not allow gene expression to occur.

C. is loosely-packed chromatin that allows the transcriptional machinery to assemble at promoter regions.

D. is densely-packed chromatin that easily gathers together the components necessary for gene transcription.

C. is loosely-packed chromatin that allows the transcriptional machinery to assemble at promoter regions.

Which of the following is FALSE for a repressor?

A. It blocks the binding of RNA polymerase.

B. Its binding to DNA brings RNA polymerase to the promoter.

C. The signal molecule binding causes it to come off of or bind to the DNA.

D. It binds to the operator sequence in the promoter.

B. Its binding to DNA brings RNA polymerase to the promoter.

Gene expression in eukaryotic cells tends to be more complicated than it is in prokaryotes. For example, repressors rarely just bind DNA and block the polymerase from binding. Which of the following is an example of negative regulation in eukaryotes?

A. Dimers forming with partners that have DNA binding domains.

B. Transcription factors that have both DNA binding and activating domains.

C. Acetylation of histone tails.

D. CDP binding the activator binding site on DNA and preventing the activator from binding.

D. CDP binding the activator binding site on DNA and preventing the activator from binding.

Where does transcription occur in eukaryotes?

A. On methylated CG islands

B. In the nucleus

C. In the cytoplasm

D. On ribosomes.

B. In the nucleus

Sliding of nucleosomes on DNA

A. Can expose new promoter sites.

B. Leads to compaction of nucleosome and less accessible DNA.

C. Inactivation of sequences on the Y chromosome.

D. Removes acetyl groups from histone tails.

A. Can expose new promoter sites.

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,

A. Enhancers are restricted to regulating nearby genes.

B. DNA no longer interacts with matrix attachment regions.

C. The DNA is unraveled from histones.

D. Then enhancers can activate distant genes.

D. Then enhancers can activate distant genes.

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

A. Translational repression.

B. Transcriptional repression

C. Activation of translation

D. Transcriptional attenuation

A. Translational repression.

In eukaryotic transcription, the mediator complex

A. Removes repressors so activators can bind

B. Neutralizes repressors and activators.

C. Has no effect on transcription.

D. Integrates the signals of activators and enhancers binding to DNA to start transcription.

D. Integrates the signals of activators and enhancers binding to DNA to start transcription.

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?

A. They remove acetyl groups from histones, leading to the aggregation of histones and silencing of DNA sequences.

B. They remove acetyl groups from DNA and add them to histones, thereby opening access to DNA.

C. They tag the DNA and histones for degradation by the protesome.

D. They recruit UBF to the methylated CG islands and turn on the transcription of rRNAs.

A. They remove acetyl groups from histones, leading to the aggregation of histones and silencing of DNA sequences.

Sometimes, prokaryotic mRNAs are processed, too. AdhE mRNA needs to be cleaved before it can be translated - why?

A. The cleaved part of the RNA is needed to sequester proteins that will degrade the mRNA.

B. The secondary structure of the mRNA blocks the ribosome binding site and coding sequence.

C. Cleavage removes the thermosensor.

D. So it can phosphorylate the ribosome.

B. The secondary structure of the mRNA blocks the ribosome binding site and coding sequence.

When cells are given the signal to grow, the S6 protein on the small subunit of the ribosome can be phosphorylated. This often leads to

A. Increasing the translation of specific groups of mRNAs

B. Preventing any mRNAs from associating with the ribosome

C. Destruction of ribosomes

D. Shredding RNAs that come in contact with the ribosome.

A. Increasing the translation of specific groups of mRNAs

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?

A. No, because the Shine-Dalgarno motif is removed from eukaryotic mRNAs.

B. No, because transcription and translation occur in separate cell compartments, and not on the same mRNA at the same time.

C. Yes, ribosomes bound to the 5' end of mRNAs would release the transcription apparatus from the 3' end.

D. No, because phosphorylation of the ribosome prevents it from acting with all mRNAs.

B. No, because transcription and translation occur in separate cell compartments, and not on the same mRNA at the same time.

How can RNA act as a thermosensor and regulate its own translation?

A. Leader sequences in the 5'UTR can stall the ribosome and allow the pre-emptor loop to form.

B. Certain stem-loop structures will be more unstable at higher temperatures and unfold to reveal Shine-Dalgarno sequences.

C. It is recruited by phosphorylation of the S6 protein in ribosomes.

D. RNA can be bound by attenuation proteins and stop its transcription.

B. Certain stem-loop structures will be more unstable at higher temperatures and unfold to reveal Shine-Dalgarno sequences.

Non-coding RNA functions in all of the following ways EXCEPT:

A. To form pores that allow movement between the nucleus and cytoplasm

B. To function in defense against invading nucleic acids.

C. To give structure to DNA in the nucleus.

D. To link together enhancer regions with mediators and transcription complexes.

A. To form pores that allow movement between the nucleus and cytoplasm

What effect does antisense RNA have on translation of its RNA?

A. It binds to the mRNA response elements and signals for degradation.

B. It slows transcription and causes early termination of translation.

C. It hybridizes with its complementary sequence and blocks its translation.

D. It exposes the ribosome binding site and promotes translation.

C. It hybridizes with its complementary sequence and blocks its translation.

What best describes how circRNAs form?

A. Back-splicing to remove introns and join exon ends into a circular piece of RNA.

B. Splicing of primary transcript into a linear mRNA with a 5'cap and 3'tail.

C. Digestion of tRNAS with RNases remove D- and T-loops.

D. Splicing from introns into short fragments that can then ligate together.]

A. Back-splicing to remove introns and join exon ends into a circular piece of RNA.

What RNA can act as a transfer RNA, messenger RNA, and gets stuck ribosomes 'unstuck'?

A. gRNAs

B. miRNAs

C. tmRNAS

D. snoRNAs

C. tmRNAS

In prokaryotes, small regulatory RNAs (sNAs) like RyhB and anti-bfr hybridize with the 5' end of their target mRNA sequences, which

A. Increases transcription of the target mRNA.

B. Removes intron sequences from the target mRNA.

C. Converts the mRNA into tiRNA.

D. Blocks ribosome binding and translation of the mRNA.

D. Blocks ribosome binding and translation of the mRNA.

Small nuclear RNAs (snRNAs) are examples of ribozymes that

A. Assemble ribosomes in the nucleolus.

b. Regulate translation based on temperature-dependent structural changes of RNA.

C. Create proteins by decoding mRNA sequences.

D. Splice together exons and remove introns from mRNAs.

D. Splice together exons and remove introns from mRNAs.

A protective mechanism in eukaryotic cells that destroys mRNA with the same sequence as dRNA is

A. Nonsense mediated decay

B. CRISPR

C. RNA interference

D. The proteasome

C. RNA interference

Which long non-coding RNA is correctly matched with its function?

A. Xist RNA: interacts with one of the two X chromosomes and inactivates it.

B. Circular RNAs: encircles insulator regions and blocks enhancer activity.

C. Enhancer RNA: acts as a "sponge" and hybridizes with miRNAs.

D. Architectural RNA: acts as scaffold supporting structures at the cell membrane.

A. Xist RNA: interacts with one of the two X chromosomes and inactivates it.

Where do miRNAs come from?

A. They are the degradation products of viruses.

B. They are the fragments of tRNAs.

C. They are trimmed from pri-miRNAs made by the cell.

D. They arise from riboswitches in the 5'UTRs of mRNAs.

C. They are trimmed from pri-miRNAs made by the cell.

The nuclease that cleaves dRNA into fragments is:

A. Dicer

B. Slicer

C. RISC

D. Ribonuclease H

A. Dicer

How does a Class 2 CRISPR mechanism differ from Class 1 mechanism?

A. Class 1 CRISPR systems have trans-activating RNA that guides the complex to the target.

B. Class 2 mechanisms use a single effector protein and make double strands break in the target DNA

C. Class 2 nucleases degrade the target sequences from their 5' ends.

D. Class 1 CRISPR mechanisms do not require cRNAs binding to the target DNA.

B. Class 2 mechanisms use a single effector protein and make double strands break in the target DNA

How does the RISC complex know which RNA sequences to target?

A. It acts preferentially with non-methylated RNA.

B. It is recruited by Dicer to DNA sequences.

C. It is guided by the miRNA or siRNA associated with the complex.

D. It recognizes dRNA structures.

C. It is guided by the miRNA or siRNA associated with the complex.

How does siRNA and miRNA binding differ, and what outcome does that have on its target sequence?

A. miRNA binding activates RdRP, which amplifies the signal and degrades more RNA.

B. SiRNA forms a stem loop structure that attenuates transcription.

C. SiRNA is a perfect match to its target and causes the RNA to be destroyed by RISC.

D. miRNA binds circRNA and blocks enhancer activity.

C. SiRNA is a perfect match to its target and causes the RNA to be destroyed by RISC.

What is found in the CRISPR locus?

A. Pri-miRNAs that will be processed into miRNAs for RNAi.

B. Coding sequence for zinc finger proteins.

C. Long non-coding RNAs that give structure to the genome.

D. Clusters of short sequences, originally from viruses that invaded the cell.

D. Clusters of short sequences, originally from viruses that invaded the cell.

dCas9 does not have nuclease activity, but can still affect gene expression. How?

A. By destroying ssDNA as the RNA is being transcribed.

B. By binding to the promoter region and blocking polymerase from binding and transcribing downstream gene

C. By preventing the CRISPR transcript from being processed into mature crRNAs.

D. By repressing the transcription of tracRNA

B. By binding to the promoter region and blocking polymerase from binding and transcribing downstream gene

BQ1. Describe 2 ways double-stranded RNA can be introduced into cells to target specific sequences by RNA interference.

Microinjection: Injecting dsRNA directly into cells introduces RNAi molecules to target specific sequences.

Transfection: Using carriers like liposomes, dsRNA is delivered into cells to trigger RNAi.

BQ2. Briefly describe 3 ways transcription can be regulated.

Promoter control: Transcription factors bind to promoters to activate or repress transcription.

Enhancers and silencers: Distant DNA elements increase or decrease transcription through mediator proteins.

Epigenetic changes: DNA methylation or histone modifications alter chromatin structure, affecting gene access.

BQ3. How do 2-dimensional gels separate proteins?

2D gels separate proteins by charge and size. The charges go through a pI and follow a pH gradient until the negative or positive charge is neutral. For size, the SDS page helps guide the proteins as they are traveling. The bigger the protein, the slower it travels and vice versa.

BQ4. How do each of the following protein motifs interact with DNA: leucine zippers, zinc fingers, and helix-turn-helix motifs.

Leucine zippers: Use a dimer of alpha helices to bind DNA through basic residues in their structure.

Zinc fingers: Use zinc ions to stabilize their structure and interact with specific DNA bases in the major groove.

Helix-turn-helix: Fit into the major groove of DNA using one recognition helix to bind specific sequences.