Molecular Biology Ch 8-13 (Fall 2021- Petrik)

Match the images above of DNA binding domains to their names (there will be pictures that are numbered)

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

The complementarity of bacterial sRNAs are their mRNA targets are usually only -- bp. This base pairing is often discontinuous, but there does need to be a region of continuous base pairing for the interaction. This continuous region is often --, and can base pair with --.

10-20; conserved; multiple mRNA targets

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? (fill in the blank)

2.0

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 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

If there is incorrect codon/anticodon matching in the ribosome P site, what happens? Put the below steps in chronological order

A conformational change in the ribosome is triggered More mis-incorporations occur due to mismatching Premature termination The polypeptide is degraded by cellular peptidases and proteases

Match the names and functions of different enzymes and other proteins involved in miRNA processing in eukaryotes Drosha Dicer DGCR8 TRBP2 pre-miRNA pri-miRNA PAZ

A nuclear class 2 RNAseIII enzyme that is part of the microprocessor complex that removes the 5' and 3' extensions off the pri-mRNA Together with its accessory protein (both in the cytoplasm) cleaves the pre-miRNA into miR:miR* RNA binding protein that with Drosha forms the Microprocessor complex accessory RNA binding protein that interacts with DICER to cut off the loop from the pre-miRNA Partially processed miRNA transcript in which the 5' and 3' extensions have been removed but the loop is still present at the opposite end Initial stem-loop structure of the miRNA gene transcript with 5' and 3' extensions and a loop Domain of Drosha and Dicer that secures the 3' end of the RNA

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

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

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

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

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

Binds to the core enzyme to convert it to the holoenzyme Binds to the -10 promoter sequence Binds to the -35 promoter sequence Used in response to specific signals or stress conditions to express response genes.

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

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

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

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

When any of the 3 normal stop codons are misread by aminoacyl-tRNA species (often due to specific sequence elements in the mRNA) such that termination of translation fails to occur, this is called:

Nonsense suppression

Which types of domains exhibit more variety in structures- RNA binding domains or DNA binding domains? (type answer)

RNA binding domains

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

RNA polymerase

Put the following steps of transcription, capping, and polyadenylation in chronological order

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

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

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

Put the 3 broad steps of ribosome rescue (occurs if ribosome pausing or arrest occurs) in chronological order

The mRNA is targeted for decay The truncated protein is targeted for proteolysis The ribosomes are recycled

Put the below steps of how high tryptophan levels affects ribosome stalling and thus also transcription termination in the tnaCAB trp utilization operon

The ribosome stalls on the trp-stalling peptide sequence within tnaC Rho protein is blocked from binding the nascent RNA RNA polymerase is not disassociated from the mRNA before reaching downstream genes Transcription elongation continues into tnaA and tnaB genes

Put the 3 broad steps of translation initiation in chronological order

The small ribosomal subunit identifies the initiation codon within the mRNA A methionyl-tRNA is loaded into the P site of the ribosome where it base pairs with the initiation codon The large ribosomal subunit must join the small subunit

Why is the +1 frameshifting that can occur during translation to produce bacterial termination factor RF2 called a programmed frameshifting event?

This frameshifting only occurs when RF2 concentrations are low, which slows down termination, allowing the frameshift to occur which allows continued translation to produce more RF2.

How is eukaryotic translation initiation most often regulated at a gene specific level?

Via interactions of various factors such as proteins or RNAs with the 3'UTR of the transcript

Other than RNA polymerase, what additional 3 classes of enzymes are needed for transcription to occur? Mark all three correct answers a Nucleosome remodeling enzymes b Primase c Histone chaperones d Histone modifying enzymes

a. Nucleosome remodeling enzymes c. Histone chaperones d. Histone modifying enzymes

What 3 events are associated with promoter clearance a RNA polymerase undergoes a conformational change that makes it grip the DNA template more stably b Removal of loop of sigma (bacterial) or TFIIB (eukaryotic) from the active site of the RNA polymerase c The single stranded DNA primer that the first RNA nucleotide binds to is removed d TFIIH phosphorylates the CTD of the large subunit Rpb1

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

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

acetyltransferases; adding acetyl groups; increasing transcription

Translation in bacteria is globally downregulated in response to --. If an uncharged tRNA binds to the A site in the ribosome, this is recognized by the -- protein, which then produces (p)pppGpp (also known as --), which activates the stringent response pathway.

amino acid starvation; RelA; magic spot

Large non-cognate amino acids are rejected from the -- site of the tRNA based on size exclusion. Smaller non-cognate amino acids are occasionally initially accepted and activated and moved to the editing site, but then rejected pre-transfer to the tRNA and --. If a non-cognate amino acid gets activated and charged onto the tRNA in the amino-acylation site, it can be hydrolyzed post-transfer from the tRNA in the -- site.

amino-acylation site; hydrolyzed; editing

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 details about features of the mRNA used for bacterial translation initiation to the name of the feature. A bacterial mRNA molecule that is polycistronic means that: Shine-Dalgarno sequence anti-Shine-Dalgarno sequence Purpose of Shine-Dalgarno sequence

each open reading frame has its own initiation and termination codons A polypurine tract thatis located 6-8 nt of the AUG initiation codon Polypyrimidine tract in the 3' end of the 16S rRNA in the small ribosomal subunit. To guide the small ribosomal subunit so that it's P site is surrounding the AUG start site

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

general transcription factors

Match the following features of Class I versus Class II aminoacyl-tRNA synthetases Class I: Where does the synthetase recognize the acceptor stem of the tRNA? Class II: Where does the synthetase recognize the acceptor stem of the tRNA? Class I- where does the synthetase attach the amino acid to the ribose of the adenosine? Class II- where does the synthetase attach the amino acid to the ribose of the adenosine?

minor groove major groove 2' OH 3' OH

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

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

nonsense-mediated decay; uses EJCs that recruit RNases used when an mRNA completely lacks a stop codon Used when an mRNA has a problematic coding sequence that stalls translation Used by bacteria when an mRNA is truncated and lacks a stop codon which stalls the ribosome

Signal cascades often work by a stimulus binding to a --, which auto-phosphorylates itself. The phosphate group is then passed to a chain of proteins, ending at a -- with an effector domain. This then triggers downstream responses to the presence of the environmental stimulus.

receptor kinase; response regulator

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

Define the following translation related terms Codon Anticodon Aminoacyl-tRNA synthetases tRNA ribosome ribosome small subunit ribosome large subunit

sequence of 3 nucleotides in an mRNA that code for an amino acid A region in the tRNA that base pairs with the codon of mRNA Enzymes that attach the appropriate amino acid to the various tRNAs RNAs that decode mRNA and participate in the synthesis of polypeptides A large molecular machine composed of RNA and protein and performs protein synthesis Subunit of ribosome that deciphers the mRNA Subunit of ribosome that mediates the formation of peptide bonds between amino acids

Match the following features to the large or small ribosomal subunits The subunit where interactions between mRNA and tRNA take place The subunit where peptide bond formation takes place Large subunit How many antibiotics work

small subunit large subunit Location of the exit tunnel for the polypeptide blocking the exit tunnel

If a regulatory RNA is encoded on the DNA in a region far distant from its target, the regulatory RNA is said to be --. In contrast, if the regulatory RNA is encoded on the DNA as a small subregion of the target, the regulatory RNA is said to be --.

trans-encoded; cis-encoded

-- associates with the A site; -- associates with the E site, and -- is a GTPase that helps to direct f-Met-tRNAfMet to the AUG in the -- site.

IF1; IF3; IF2; P site

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 below steps of eukaryotic non-stop or no-go decay allowing mRNA decay and ribosomal rescue in chronological order.

Ribosome encounters long string of A's with no stop codon in it Ribosomes stall and stack up An endonuclease known as Cue2 cleaves the mRNA in the A site of stalled or stacked ribosomes Termination factors Pelota and Hbs1 associate with the ribosome A site ABCE1-GTP is recruited by Pelota and Hbs1 ABCE1's GTPase activity provides energy for dissociation of the ribosomal subunits and release of the tRNA with bound polypeptide and the mRNA and termination factors

How are premature stop codons recognized in the mRNAs of higher eukaryotes?

Ribosomes encounter a stop codon upstream of a exon junction complex tag the mRNA transcript and trigger recruitment of Upfs 1, 2, 3, eRF1, and eRF3-GTP to degrade the mRNA and protein

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

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 exclusion Introns are defined by interactions between the sequential 5' and 3' splice site bound factors bound within 1 intron intron inclusion

Which of the below statements is NOT accurate? a decoding region of the small ribosomal subunit is rRNA b The part of the large ribosomal subunit that interacts with the aminoacyl end of the tRNAs is rRNA c It is the protein part of snRNPs that are involved in processing of introns in mRNA processing d There are no protein elements within 18 angstroms of the region where peptide bond formation occurs

c. It is the protein part of snRNPs that are involved in processing of introns in mRNA processing

Eukaryotic translation elongation is inhibited due to -- phosphorylation, which is a critical factor involved in the -- step of elongation.

eEF2; translocation

Match features of eukaryotic versus bacterial initiator tRNAs Bacteria: Type of methionine on the initiator tRNA Eukaryotes: Type of methionine on the initiator tRNA Bacteria: Unusual base pairs at the top of the acceptor stem Eukaryotes: Base pairs at the top of the acceptor stem Base pairs in common at anticodon stem between bacteria and eukaryotes

formylated methionine methionine C-A A-U at 1st position and C-G at 3rd position 3 consecutive G-C base pairs

What effects do DNA methylation have on gene expression?

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

During translation initiation, initiation factors load the -- site of the -- subunit of the ribosome with methionine-loaded --.

P; small; initiator tRNA-Met

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

Transcribes ribosomal RNA (rRNA) Transcribes mRNA and small regulatory RNAs Transcribes tRNA and 5S RNA and snRNA Transcribes siRNA

siRNAs are derived from long dsRNAs present in the -- from exogenous or endogenous sources. They are cleaved into 20-25 bp double stranded fragments by the action of -- with its accessory RNA binding protein --.

cytoplasm; Dicer; TRBP2

MicroRNAs are created by -- , whereas siRNAs are derived from --. Repeat associated small interfering RNAs are derived from transcription of repetitive regions of the genome, and include mammalian -- that bind to the Piwi class of Argonaute proteins.

transcription of miRNA genes to make a stem-loop structure that will be processed; cleavage of longer duplex RNAs in the cytoplasm; piRNAs

There are ________ amino acids that are encoded by _________ codons that base pair with the anticodons of _________ tRNAs. The reason that there can be fewer tRNAs than codons is due to ________ pairing where there is promiscuity in the reading of the 3rd RNA codon position by the first position of the anticodon of the tRNAs. (fill in blanks)

20 61 40 wobble

There are typically -- aminoacyl tRNA synthetases, one for each amino acid. One given aminoacyl tRNA synthetase can add its amino acid onto more than one tRNA, these sets of tRNAs that get charged with the same amino acid are called --. This reaction requires energy provided by the release of pyrophosphate from --. The AMP bound amino acid is then transferred to the 2' or 3' OH of the ribose of the -- of the 3' CCA tail of the tRNA.

20; isoacceptors; ATP; adenosine

Class I release factors bind in the ______ site of the ribosome upon recognizing a stop codon, and facilitate release of the polypeptide from the peptidyl tRNA. Class II release factors are types of enzymes called ______ and promote different facets of the termination process in bacteria and eukaryotes. (fill in blank)

A GTPases

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

What is the name of the elongation factor that is a GTPase and promotes structural rearrangements of the ribosome during translocation?

EFG in bacteria (eEF2 in eukaryotes)

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

GAPs (GTPase-activating proteins) and GEFs (Guanine-nucleotide exchange factors) both play roles in GTP hydrolysis during translation. Interestingly, it is documented that the ribosome itself can act as a __________ in its interaction with EFTu to allow full acceptance of the aminoacyl-tRNA into the A site and release of EFTu-GDP (fill in blank)

GAP

Conformational changes of the G530, A1492, A1493 amino acids in the 16S rRNA A site of the bacterial ribosome rearrange when a cognate tRNA anticodon-mRNA codon interaction occurs. These structural changes are thought to be critical for triggering _________ activation by EFTu and for accommodation of the cognate tRNA in the A site.

GTPase

In the case of amino acid starvation in eukaryotes, uncharged tRNAs are bound by the protein --. There, its -- domain phosphorylates the translation initiation factor --. This phosphorylated translation initiation factor is therefore unable to bind to -- and guide it to the P site of the small ribosomal subunit, but rather is bound its guanine nucleotide exchange factor (GEF), eIF2B.

Gcn2; kinase; initiator tRNAiMet

What is the name of the chaperone protein that binds to both sRNAs and their targeted mRNAs? What is the term for mRNAs that can bind to sRNAs to prevent them from binding to their target mRNAs?

Hfq; sponge or decoy mRNAs

Although tRNAs are often drawn as a cloverleaf shaped structure, in actuality, they form a -- shaped structure. The 5' and 3' ends of the tRNA together form the -- stem, at the 3' end of which is the --. The 3 nucleotides of the anticodon are typically stacked on one another in a structure known as a --.

L; acceptor; 3' CCA tail; U-turn

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

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

During translation termination, the polypeptide is released from the ribosome. Ribosome recycling occurs next. Match the features of bacterial versus eukaryotic ribosome recycling Bacteria Step 1: Which two factors bind in the ribosome A site? Bacteria Step 2 Bacteria Step 3 Eukaryotes: Step 1 Eukaryotes : Step 2 Eukaryotes: Step 3

RRF and EGF-GTP Disassociation of the 2 ribosomal subunits IF3 binds to the small ribosomal subunit and the peptidyl tRNA disassociates wit the P site. eRF1 is still in the A site and ABCE1 interacts with it there where ATP hydrolysis occurs eIF2D allows ejection of the mRNA and the deacylated tRNA eIF1 + eIF1A + eIF3 stabilize the dissociated state of the ribosomal subunits by binding to the small subunit

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

Ribosome stalls on leader sequence 1 Leader sequences 2 and 3 form stem-loop RNA polymerase proceeds through the entire operon the ribosome does not stall on leader sequence 1 and proceeds into leader sequence 2 Leader sequences 3 and 4 form stem-loop Transcription is terminated before the trp genes can be transcribed

What are the 3 RyhB regulatory RNA mechanisms that occur under low iron conditions?: What happens to translation of non-essential iron using enzymes? How is RNaseE dependent cleavage of transcripts for non-essential iron using enzymes affected? RyhB effect on transcripts encoding proteins needed to facilitate iron uptake

RyhB RNA binds near the start codon blocking translation of non-essential iron using enzymes RyhB recruits RNaseE to degrade non-essential iron using enzymes' mRNA transcripts RyhB recruits the ribosome to translate transcripts whose enzymes are needed to facilitate iron uptake

In contrast to differing temperature altering mRNA folding, thus blocking or allowing access to the -- sequence, mRNA specific translation regulation can instead occur by the biosynthesis product or intermediate binding to the mRNA, altering its structure. The altered mRNA structure blocks access to this important mRNA sequence necessary for translation initiation. The mRNA structure in this 2nd mechanism, which is dependent on a product or biosynthesis intermediate binding to the mRNA is called a --.

Shine-Dalgarno; riboswitch

Put the following steps of tmRNA:SmpB mediated ribosomal rescue from truncated mRNAs in bacteria in chronological order

SmpB partner protein binds in ribosome A site because there is no mRNA in the A site Alanine from acceptor arm of tmRNA is peptide bonded to the truncated polypeptide template mRNA is released and subsequently degraded by RNases Short ORF on tmRNA is translated to 10 amino acids added onto the polypeptide Translation meets stop codon on tmRNA Free ribosomes are liberated and tagged polypeptide is degraded by proteases

Match the following facts to each question about translation elongation After the very first initiator tRNA-Met is loaded into the P site - where is the the next charged tRNA loaded? elongation factor Tu in bacteria or elongation factor eEF1A in eukaryotes GTP hydrolysis Site where peptidyl bond formation occurs Process where the tRNA in the A site moves to the P site and the one in the P site moves to the E site Factor that promotes translocation Recognizes stop codons Additional GTPase involved in translation termination Process by which the large and small ribosomal subunits dissociate from each other thereby releasing the final tRNA and mRNA

The A site Loads the aminoacyl-tRNAs onto the ribosome Source of energy that EF Tu uses for loading charged tRNAs onto the ribosome Attached to the amino acid attached to the tRNA in the A site translocation EFG in bacteria; eEF2 in eukaryotes Class 1 release factors Class 2 release factors ribosome recycling

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

The lambda repressor protein that represses lytic growth Promotes the lysogenic pathway by recruiting RNA polymerase to the PRE promoter to initially drive expression of cI gene Binds to the PRM promoter and represses transcription of the cI gene- thereby promoting the lytic cycle 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

Match the following features of how bacterial regulatory RNAs most often work Way that the majority of sRNAs in bacteria are encoded: antisense or cis or trans Act as full length transcripts or are processed to shorter fragments from larger fragments Degree of complementarity to the mRNA target

Trans-encoded Act as full length transcripts Limited complementarity to mRNA target

What features of a processed RNA increase its stability? Select the 5 correct answers. a 5' methylated cap in eukaryotes b Poly(A) tail in bacteria c ARE (AU-rich elements in the 3' UTRs of some eukaryotic RNAs) d introns e stem-loop structures f Presence of a triphosphate at the 5' end of RNA-bacteria g Poly(A) tail in eukaryotes

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

How are riboswitches different from how transcription attenuation works in the trp operon system? a Riboswitches have sequences of RNA that directly bind a metabolite which allows a downstream termination structure to form b Riboswitches bind RNA polymerase in the center of their multi-stem loop structure c Transcription attenuation occurs when transcription has been paused but then binding of a protein to the DNA template allows transcription to resume d 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 stucture to form

a. Riboswitches have sequences of RNA that directly bind a metabolite which allows a downstream termination structure to form d. 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 stucture to form

Match the following protein factors and RNA sequences with their functions binds to the 5' cap Binds to the poly(A) tail eIF4G Pre-initiation complex Kozak Recognition of AUG initiator start codon by the PIC causes eIF5B-GTP hydrolysis

eIF4E PABPs Binds to both PABPs and eIF4E which allows the mRNA to form a closed loop structure The small 40S ribosomal subunit bound with several translation initiation factors Sequence in the 5' UTR that surrounds the first AUG; the PIC scans from the 5' end of the mRNA to this sequence to locate the translation start codon Release of eIF1 and Pi and Eif2 Ribosome subunit joining occurs and release of additional initiation factors from the complex

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

gene upstream of the lac operon that expresses the lac repressor binds to operator and blocks expression when lactose is unavailable binds to lac repressor and thereby prevents its binding to the operator molecule that is in high concentration when glucose levels are low and binds to CAP activator 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

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

When iron levels are low in eukaryotic cells, iron response proteins bind to -- in the -- of the ferritin mRNA, blocking access of the ribosome to the AUG start site.

iron response elements; 5' UTR

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

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

Which of the below components have been found to be important in examples of incorporation of non-standard amino acids into proteins with specialized functions? a mRNA elements such as stem-loops b Removal of the methyl group from the 5' methylguanine cap on the mRNA as a mechanism to tag mRNAs that have codons needing modified charged tRNAs c specialized tRNA d dedicated aminoacyl-tRNA synthetase

a. mRNA elements such as stem-loops c. specialized tRNA d. dedicated aminoacyl-tRNA synthetase

According to the hybrid states model, during translocation, after peptide bond formation, the tRNA first moves spontaneously with respect to the -- subunit. There is then a global rotation of the -- subunit. EFG then promotes movement of the anticodon and -- domain of the ribosome (connected to the polypeptide). During the final step, the ribosome ratchets back to its unrotated conformation.

large; small; elbow

How do erythromycin and streptomycin antibiotics work?

Block the exit channel of the ribosome for the polypeptide; cause shape changes to the small subunit so near-cognate tRNAs are accepted and leading to incorrect proteins

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

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

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

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

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

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

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

Put the steps of the eukaryotic RQC (Ribosomal Quality Control) pathway to degrade incomplete proteins into chronological order.

Stalled ribosome subunit dissociation recruits NEMF and Ltn1 NEMF replaces 40S small ribosomal subunit and interacts with the 60S large ribosomal subunit NEMF adds alanine and threonine amino acids to the C terminus of the polypeptide Ltn1 ubiquitinates the incomplete protein Incomplete protein is degraded by the proteasome

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

What are the commonalities between group II introns and spliceosomal introns? Mark the 3 correct answers. a The 3' end of EX1 attacks the 5' end of EX2 in the second splicing reaction b 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 c Both use snRNPs in their splicing mechanisms d Both types of introns form a lariat structure during splicing

a. The 3' end of EX1 attacks the 5' end of EX2 in the second splicing reaction b. 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 d. Both types of introns form a lariat structure during splicing

Viruses disrupt host translation- how do they themselves get their RNAs translated- what are the two mechanisms we discussed in class? a Viruses use IREs (initiation response elements) in the 5' UTRs of their RNAs that directly recruit ribosomes at non-AUG start codons using a reduced set of initiation factors b Viruses can use guide RNA mediated RNA editing to alter the mRNAs of host initiation or elongation factors that they use so that only unaltered mRNAs that the host would use are inhibited c Viruses can use sequences in the 5' or 3' UTRs of their RNAs to mimic the initiator tRNA that would normally be recruited by eIF2 if they have inhibited the action of host eIF2 d Viruses can produce their own translation factors and proteins faster and more abundantly than their mechanisms to inhibit the host's translation factors and proteins work

a. Viruses use IREs (initiation response elements) in the 5' UTRs of their RNAs that directly recruit ribosomes at non-AUG start codons using a reduced set of initiation factors c. Viruses can use sequences in the 5' or 3' UTRs of their RNAs to mimic the initiator tRNA that would normally be recruited by eIF2 if they have inhibited the action of host eIF2

What are two functions of the C-terminal domain of RNA polymerase II? a Be bound by DNA binding proteins to help recruit the RNA polymerase to the correct location in the promoter b Involved in the transition from initiation to elongation c Carries along the small ribosomal subunit to allow simultaneous transcription and translation in bacteria d Phosphorylated CTD recruits RNA processing enzymes that modify the RNA while it is still being transcribed

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

During translation initiation in eukaryotes, the mRNA forms a closed loop complex through the interactions of _________ that is bound to the 5' methylated guanine cap with PABPs that are bound to the poly(A) tail, and with eIF4G that binds to each of these to allow formation of the closed loop. Translation initiation can be globally regulated by the reduction in transcription of _________ in response to external stimuli, it being phosphorylated in response to external stimuli reducing its binding to the 5' cap. and its binding to _________ which compete for its binding to eIF4G. (fill in the blank)

eIF4E eIF4E 4E-BPs

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

located downstream of 3' regulatory sequences Directs cleavage at the CA cleavage site CA cleavage site is located between polyadenylation signal sequence on 5' end and this sequence on 3' end Poly(A) tail is added after this sequence can allow inclusion or removal of regulatory sequences

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

lytic; induction