Molecular Biology Exam 2: Chapters 8, 9, 10

Match the images above of DNA binding domains to their names #1 #2 #3 #4 #5

#1 Beta sheets/strands #2 basic region leucine zipper (bZIP) #3 Zinc finger domain #4 loop #5 homeodomain

What effects do DNA methylation have on gene expression?

Genes can be activated or repressed on a case by case basis

Put the steps to 5' capping of an RNA in chronological order

- 5' capping begins when RNA is only 20-30 nt long - RNA 5' triphosphatase removed one phosphate from the 5' end of the RNA - Guanyl transferase attaches 1 guanosine monophosphate through a 5'-5' triphosphate linkage - Guanine is methylated by guanine-7-methyltransferase

What features of a processed RNA increase its stability? Select the 5 correct answers.

- 5' methylated cap in eukaryotes - ARE (AU-rich elements in the 3' UTRs of some eukaryotic RNAs) - stem-loop structures - Presence of a triphosphate at the 5' end of RNA-bacteria - Poly(A) tail in eukaryotes

What are two functions of the C-terminal domain of RNA polymerase II?

- Involved in the transition from initiation to elongation - Phosphorylated CTD recruits RNA processing enzymes that modify the RNA while it is still being transcribed

Other than RNA polymerase, what additional 3 classes of enzymes are needed for transcription to occur? Mark all three correct answers

- Nucleosome remodeling enzymes - Histone chaperones - Histone modifying enzymes

Put the following steps of transcription, capping, and polyadenylation in chronological order i got this one wrong on the quiz

- RNA polymerase II transcribes 20-30 nucleotides - 5' capping enzyme complex is recruited by partially phosphorylated CTD of RNA pol II - Additional phosphorylation of CTD during transcription elongation - Recruitment of intron splicing machinery - Transcription past 3' end processing signals leads to recruitment of 3' end processing complex - Intron spliced RNA is cleaved and polyadenylated

Put the following steps of allosteric transcription termination in order

- RNA polymerase II transcribes through the polyadenylation and 3' processing signals - RNA processing complexes associate with the 3' processing signals on the RNA transcript and with the phosphorylated CTD of RNA pol II - Recognition of processing signals and/or cleavage at processing sites causes RNA transcript to be released from the polymerase - The RNA polymerase is released from the DNA

Put the following steps of the torpedo model of eukaryotic transcription termination in chronological order

- RNA polymerase II transcribes through the polyadenylation and 3' processing signals - The 3' processing signals on the RNA transcript are recognized by RNA processing complex - The majority of the length of the RNA transcript (from the 5' end to the 3' processing signals) is cleaved at the 3' processing signals - A 5' to 3' ribonuclease that was hitching a ride on the RNA polymerase comes free and chews the remaining piece of RNA that was transcribed 3' of the 3' processing signals - The RNA polymerase II disassociates from the DNA

If an RNA nucleoside is incorrectly matched to the DNA template strand, this can cause a distortion in the RNA-DNA hybrid. This distortion causes the RNA polymerase to stall, and then backtrack- sliding backward along the DNA. What happens next?

- RNA polymerase slides backward along the DNA - 3' end of RNA transcript protrudes through the funnel region of the RNA polymerase - Transcript cleavage factors bind to the RNA polymerase and extend into the funnel. They position a magnesium ion in the active site which activates a water molecule for hydrolysis (carried out by the RNA polymerases endonuclease activity) of the phosphodiester bond to cleave the protruding 3' end of the RNA. - RNA polymerase corrects the RNA:DNA mismatch and then continues elongation

What 3 events are associated with promoter clearance

- RNA polymerase undergoes a conformational change that makes it grip the DNA template more stably - Removal of loop of sigma (bacterial) or TFIIB (eukaryotic) from the active site of the RNA polymerase - TFIIH phosphorylates the CTD of the large subunit Rpb1

How are riboswitches different from how transcription attenuation works in the trp operon system?

- Riboswitches have sequences of RNA that directly bind a metabolite which allows a downstream termination structure to form - In the trp operon transcription attenuation system the presence of trp allows tRNAs to be charged with it so that the ribosome doesn't pause and this allows a downstream attenuator structure to form

What are the commonalities between group II introns and spliceosomal introns? Mark the 3 correct answers.

- The 3' end of EX1 attacks the 5' end of EX2 in the second splicing reaction - Both have an A at the branchpoint sequence whose OH group is used to attack the GU at the 5' end of IN1 in the first splicing reaction - Both types of introns form a lariat structure during splicing

Put the following steps of intron splicing performed by a spliceosome in chronological order

- U1 binds to GU at 5' end of IN1 - U2 displaces BBP (Branchpoint Binding Protein) at the A branchpoint - U4-U5-U6 complex displaces U2AF65 and U2AF35 - A rearrangement of the snRNPs releases the U1 and U4 snRNPs and the first transesterification reaction occurs to form the lariat intermediate - Further rearrangements bring the two splice sites together and then the two exons are spliced together and the lariat released

When TFIIH phosphorylates serine 5 on RNA polymerase II in eukaryotes, this causes the following events to occur. Put them in the correct chronological order from first to last.

- negative elongation factors bind RNA polymerase II and cause transcription arrest - The 5' capping enzyme adds a methylated guanosine to the 5' end of the RNA transcript - p-TEFb phosphorylates serine 2 on the CTD of RNA polymerase II - elongation resumes

When a new RNA nucleotide is added to the growing RNA chain in the 5' to 3' direction, based on complementary base pairing to the DNA template strand, —---- phosphate groups are removed from that incoming RNA nucleotide?

2

What does the 5' cap consist of and how is it joined to the RNA?

A 7-methylguanine ribonucleotide is bonded via a 5' to 5' triphosphate linkage to the 5' end of the RNA

Where are intronic and exonic splicing enhancers located?

At non-splice site regulatory sequences; bind proteins that increase the ability of spliceosomes to recognize nearby splice sites

There are two types of transcription termination in E. coli- intrinsic termination and Rho-dependent termination. Match the enzymes, DNA sequences, or proteins with their function. Bacterial intrinsic terminator sequences Mechanism of bacterial intrinsic transcription termination Bacterial Rho enzyme Ribosomes

Bacterial intrinsic terminator sequences Inverted repeat sequence on the DNA followed by 8-10 A's Mechanism of bacterial intrinsic transcription termination Inverted repeat RNA hairpins and weak A-U base pairing in the DNA-RNA hybrid cause transcription arrest and disassociation of the RNA polymerase Bacterial Rho enzyme Recognizes and binds to rut sites on the RNA transcript. Pulls the RNA transcript away from the RNA polymerase Ribosomes Can compete with Rho binding thereby preventing premature transcription termination

What is the advantage of alternative splicing?

Can be used in a regulated way to obtain different proteins produced from the same initial RNA transcript

Match the information about the 3 most common RNA edits Deamination of cytidine to uridine methylation of adenosine Deamination of adenosine to inosine

Deamination of cytidine to uridine Occurs in many plant mitochondrial and chloroplast mRNAs and the mRNA encoding mammalian apolipoprotein methylation of adenosine affects RNA splicing to use of RNA for translation and RNA decay Deamination of adenosine to inosine Converted nucleotide is recognized as guanosine and that can change the amino acids used during translation due to a change in codon

What is the advantage of several RNAs being contained in one precursor RNA

Each of the RNAs are made in the same amounts because their transcription is all driven by the same promoter

Match the features to exon definition or intron definition model Exon definition- interacting snRNPs Exon definition- effect of mutation of 5' splice site Intron definition Intron definition- effect of mutation of 5' splice site

Exon definition- interacting snRNPs The 5' and 3' ends of an exon are brought together by interactions of the U1 snRNP bound to the 5' end of the second intron and the U2 complex bound to the 3' end of the first intron Exon definition- effect of mutation of 5' splice site exon exclusion Intron definition Introns are defined by interactions between the sequential 5' and 3' splice site bound factors bound within 1 intron Intron definition- effect of mutation of 5' splice site intron inclusion

During Group I intron splicing, where does the guanosine nucleotide come from, whose 3' OH group is used to break the boundary between EX1 and IN1?

Floating around in the nucleus

How does the Mediator complex assist in the activation of many RNA polymerase II transcribed genes?

Interacts with regulatory proteins that bind upstream of the promoter region

What happens under conditions of low tryptophan and high tryptophan? Low trp concentrations first effect Low trp concentrations second effect Low trp conc third effect High trp conc first effect High trp conc 2nd effect High trp conc 3rd effect

Low trp concentrations first effect Ribosome stalls on leader sequence 1 Low trp concentrations second effect Leader sequences 2 and 3 form stem-loop Low trp conc third effect RNA polymerase proceeds through the entire operon High trp conc first effect the ribosome does not stall on leader sequence 1 and proceeds into leader sequence 2 High trp conc 2nd effect Leader sequences 3 and 4 form stem-loop High trp conc 3rd effect Transcription is terminated before the trp genes can be transcribed

Match each protein or other type of molecule with its mode of action Operator Enhancer Activator Repressor Co-activator Co-repressor Architectural DNA-binding proteins locus control regions allosteric effectors

Operator DNA sequence in bacteria that is bound by an activator or repressor Enhancer DNA sequence in eukaryotes that is distal from the promoter but can be bound by regulatory proteins to affect transcription Activator Protein that when bound to DNA increases transcription Repressor Protein that when bound to DNA decreases transcription Co-activator Protein that doesn't bind directly to the DNA but interacts with the activator to increase transcription Co-repressor Protein that doesn't bind directly to the DNA but interacts with the repressor to decrease transcription Architectural DNA-binding proteins Promotes looping of DNA so that activators or repressors bound to DNA a significant distance from the promoter can still interact with RNA polymerase locus control regions in higher eukaryotes these contain a combination of enhancers and insulator elements allosteric effectors small molecules that bind to regulatory proteins and change their shape thus allowing or preventing their ability to bind to DNA

Which types of domains exhibit more variety in structures- RNA binding domains or DNA binding domains?

RNA binding domains

What enzyme unwinds the DNA double helix at the promoter during transcription?

RNA polymerase

Match each RNA polymerase with its function RNA polymerase I RNA polymerase II RNA polymerase III RNA polymerase IV and V (plants only)

RNA polymerase I Transcribes ribosomal RNA (rRNA) RNA polymerase II Transcribes mRNA and small regulatory RNAs RNA polymerase III Transcribes tRNA and 5S RNA and snRNA RNA polymerase IV and V (plants only) Transcribes siRNA

What is one cause of RNA polymerase being so stably associated with the DNA template during transcription elongation, leading to high processivity?

RNA polymerase associates with the RNA-DNA hybrid

Match the following mechanisms to what that mechanism is called Recognition and removal of an mRNA that has a premature stop codon non-stop decay no-go decay tmRNA mediated decay

Recognition and removal of an mRNA that has a premature stop codon nonsense-mediated decay; uses EJCs that recruit RNases non-stop decay used when an mRNA completely lacks a stop codon no-go decay Used when an mRNA has a problematic coding sequence that stalls translation tmRNA mediated decay Used by bacteria when an mRNA is truncated and lacks a stop codon which stalls the ribosome

Match the functions to the proteins other than snRNPs that are important for intron splicing or recognition thereof SR proteins EJC Prp8 ATPases

SR proteins Bind to exons and help recruit spliceosomes to splice sites EJC Bind to exon-exon junctions to mark the RNA as processed Prp8 Found near the active site of the spliceosome and believed to be important for catalysis ATPases Help with structural rearrangements of snRNPs during spliceosome assembly

Match the following components of the bacterial RNA polymerase with facts about each Sigma Factor Domain 2 of sigma factor Domain 4 Alternative sigma factors

Sigma Factor Binds to the core enzyme to convert it to the holoenzyme Domain 2 of sigma factor Binds to the -10 promoter sequence Domain 4 Binds to the -35 promoter sequence Alternative sigma factors Used in response to specific signals or stress conditions to express response genes.

The -- subunit of TFIID binds to the TATA box element of eukaryotic promoters, whereas the -- subunits of TFIID mediate recognition of other core promoter elements or have enzymatic activities necessary for transcription activation of gene specific transcriptional regulators.

TBP; TAF

The following eukaryotic general transcription factors are placed in order of binding to the promoter. Match the function of each GTF TFIID: TBP subunit TFIIB TFIIA TFIIF TFIIE TFIIH

TFIID: TBP subunit Binds in minor groove of DNA at the TATA box that and introduces 90 degree bend in the DNA that interacts with regulatory factors TFIIB Recognizes BRE promoter element; binds asymmetrically to control direction of transcription. Stabilizes early transcribing complex TFIIA Further enhances TBP and TFIIB interactions with DNA TFIIF Present in a complex with RNA polymerase; both recruited after TFIIA. Suppresses non-specific DNA binding TFIIE Recruits TFIIH TFIIH Uses ATP to power promoter unwinding and phosphorylates the CTD of RNA polymerase subunit Rpb1

Match the following features with their description Terminator polyadenylation signal sequence U-rich or GU-rich region CA cleavage site alternative polyadenylation sites

Terminator located downstream of 3' regulatory sequences polyadenylation signal sequence Directs cleavage at the CA cleavage site U-rich or GU-rich region CA cleavage site is located between polyadenylation signal sequence on 5' end and this sequence on 3' end CA cleavage site Poly(A) tail is added after this sequence alternative polyadenylation sites Can allow inclusion or removal of regulatory sequences

How does the CCA adding enzyme specifically add CCA (no other bases and in that order) to the 3' end of a tRNA?

The conformational shape of the CCA enzyme nucleotide binding pocket changes after each added nucleotide to only accommodate the next needed nucleotide

Why does the 2 step transesterification reaction of intron splicing not require ATP?

The energy gained from breaking the first phosphodiester bond between EX1 and IN1 is used for an equal energy requiring formation of a 2nd phosphodiester bond between EX1 and EX2

Match the following features of either RNAi or CRISPR Type of nucleic acid for RNAi Type of nucleic acid for CRISPR RNA directed cleavage that occurs in eukaryotes RNA directed cleavage that occurs in bacteria and archaea CRISPR RNAi

Type of nucleic acid for RNAi Long dsRNAs are cleaved by DICER into 20-30 nt fragments Type of nucleic acid for CRISPR Foreign DNA is integrated into the CRISPR locus RNA directed cleavage that occurs in eukaryotes RNAi RNA directed cleavage that occurs in bacteria and archaea CRISPR CRISPR Integrated DNA is transcribed and processed; the processed guide RNA directs cleavage of homologous foreign DNA or RNA RNAi Cleaved siRNAs are loaded onto Argonaute protein and direct the protein to homologous RNA sequence to degrade it

Histone -- alter the chemical structure of histone proteins by --, resulting in --.

acetyltransferases; adding acetyl groups; increasing transcription

The function of the N protein whose expression is driven by the PL promoter is to --. The Q gene is downstream of the PR and tR. If the Q gene is expressed to make the Q protein, it's function is to --.

bind to nut sites and prevent termination at tR and tL terminators; relieve transcriptional pausing to allow transcription of late lytic genes

Match the following components that affect lambda transcription initiation with their function cI cII Cro RecA

cI The lambda repressor protein that represses lytic growth cII Promotes the lysogenic pathway by recruiting RNA polymerase to the PRE promoter to initially drive expression of cI gene Cro Binds to the PRM promoter and represses transcription of the cI gene- thereby promoting the lytic cycle RecA Its production is part of the bacterial SOS response which is triggered by DNA damage. This protein cleaves cI protein so it disassociates from operators that overlap the PR and PL promoters and this allows transcription of early lytic genes

What do eukaryotes and archaea use target their RNA polymerases to promoters?

general transcription factors

Proteins binding to DNA can recruit histone deacetylases, which remove acetyl groups from histones and make DNA more --, thereby -- gene expression in the region.

heterochromatic; silencing

Match the enzyme or protein with its function. Note that both eukaryotic and prokaryotic proteins or enzymes are discussed in this question. histone chaperone proteins histone modifying enzymes E. coli DNA gyrase E. coli DNA topoisomerase I

histone chaperone proteins Assist in removing histones in front of the RNA polymerase and re-adding them to the DNA behind the RNA polymerase histone modifying enzymes perform chemical modification to histones that signal histone chaperone proteins E. coli DNA gyrase removes positive supercoils ahead of the transcribing polymerase E. coli DNA topoisomerase I Removes negative supercoils behind the RNA polymerase

match the following components of the lac operon gene expression regulation system with its mode of action/function lacI lac repressor Lactose cAMP CAP protein

lacI gene upstream of the lac operon that expresses the lac repressor lac repressor binds to operator and blocks expression when lactose is unavailable Lactose binds to lac repressor and thereby prevents its binding to the operator cAMP molecule that is in high concentration when glucose levels are low and binds to CAP activator protein CAP protein If cAMP levels are high because glucose levels are low AND there is lactose present- then it can increase transcription of the operon to high levels

When a bacterial cell has endured DNA damage, the bacteriophage lambda will transition to the -- life cycle. This process is called --.

lytic; induction

A protein binds to the trp operon's operator sequence to decrease its transcription in the presence of tryptophan. This protein is a/an -- protein. But it can only bind when it has the correct shape. The molecule tryptophan is an -- which allows the protein to bind.

repressor; allosteric effector

What two types of chemical modifications are most common in rRNAs, and what performs these modifications?

ribose 2'-O-methylation and psuedouridylation; snoRNP

Some RNA processing complexes are ribonucleoproteins. Some RNPs have an RNA component that has catalytic activity. These are called --. Also involved in RNA processing are a specific type of RNA, called a --, that directs proteins to carry out reactions at specific targeted RNA sequences.

ribozymes; guide RNA