Chapter 20

In periods of nutrient deprivation, E. coli initiate a stress response that involves the coordinated regulation of gene expression. (1) Which E. coli regulatory RNA represses translation of mRNAs transcribed from the rpoS gene? (2) Which E. coli regulatory RNA represses transcription by binding to the σ70 subunit of RNA polymerase? (1) RybB; (2) RprA (1) DsrA; (2) 6S RNA (1) OxyS; (2) 6S RNA (1) OxyS; (2) RybB

(1) OxyS; (2) 6S RNA When E. coli enter the stationary phase (stop dividing because of nutrient depletion), 6S RNA molecules accumulate and bind to σ70 subunits, which, in turn, down-regulates transcription of σ70 promoters. At the same time, a different σ subunit, σS, becomes produced in response to the stress. The rposS gene, which encodes σS, is regulated by at least three sRNAs. Two of them, DsrA and RprA, stimulate translation of mRNAS transcribed off rpoS, while the third, OxyS, represses translation of this gene. Through inhibition of σ70 subunits by 6S RNAs combined with the sRNA-stimulated production of σS subunits, the appropriate genes are expressed to help E. coli survive the stationary phase.

What are three ways that prokaryotes regulate at level of translation?

1) Protein binding to sites near the RBS protein prevent access of 16S rRNA to the RBS. In this case, the protein encoded by the mRNA binds to its own RBS. 2) Intramolecular base pairing of the mRNA can interfere with base pairing by the 16S rRNA.

*****Rank the steps whereby miRNAs are generated and act to silence gene expression in order from first to last.

1) RNA polymerase transcribes the pri-miRNA in the nucleus that forms a stem loop. 2) Drosha cleaves the pri-miRNA at two sites to create a 65-70 nucleotide long pre-miRNA. 3) Dicer cleaves the loop from the pre-miRNA to a 22-nucleotide-long double-stranded RNA. 4) The double-stranded RNA is denatured to become the single-stranded guide RNA that can be incorporated into the RNA-induced silencing complex (RISC). The guide RNA brings RISC to the target mRNA. 5) RISC can repress gene expression through Silencer by clearing target mRNA or non-silencer-dependent mechanisms.

Imprinting is A) when only one of the parental alleles is expressed in the progeny B) always controlled by histones C) inherited epigenetically D) A & C E) A & B

A) Some mammalian genes are kept silent by methylation of nearby DNA sequence. Large regions of the mammalian genome are marked via methylation of DNA sequence and often DNA methylation is seen in regions that are also heterochromatic. This is because methylated sequences are often recognized by DNA-binding proteins (such as MeCP2) that recruit histone deacetylases and histone methylasaes, which tehn modify nearby chromatin. us, methylation of DNA can mark sites where heterochromatin subseuqently forms. DNA methylation lies at heart of phenomonm called imprinting. In a diploid cell, there are two copies of most genes; one copy on a chromosome inherited from the father nad the other copy on the equivalent chromosome from the mother. In the majoirty of cases, the two alleles are expressed at comparable levels. This is hardly surprising- they carry the same regulatory sequences and are in the presence of the same regulators; they are also located at the same oposition along the homologous chromosomes.

Which of following statements about lambda phage is not true? A) cro protein will bind at the Or3 site, blocking the Prm promoter and preventing transcription of cI B) cro protein binding at the Or3 site leads to transcribing more cro C) cII binds to the Pre, repressing transcription of cI. D) Or1 and Or2 and Or3 sites can both bind cI and cro.

B) cro protein binding at the Or3 site leads to transcribing more cro Repressor bound to Or1 and Or2 turns off transcription from Pr. Repressor bound at Or2 contacts RNA polymerase at Prm, activating gene expression of cI (repressor gene) Or3 lies within Prm; Cro bound there represses transcription of cI.

When lambda phage enters a cell, which of following is NOT true? A) transcription is initiated immediately from the PR and PL promoters B) PR drives the transcription of cro and cII C) cII is degraded by the FtSH protease D) If bacteria are growing well, FtSH activity is low.

D) If bacteria are growing well, FtSH activity is low. If growth is good, FtsH is very active, CII is destroyed efficiently, repressor is not made, and the phage tend to grow lytically. Under poor growth conditions, the opposite occurs: Low FtSH activity, slow degradation of CII, repressor accumulation and a tendency towards lysogenic development. Levels of CII are also modulated by phage protein CIII. CIII stabilizes CII, probably because it acts as an alternative (and thus competing) substrate for FtsH.

The RNAi pathway silences gives expression at the level of ______. A) Transcription B) Post-transcription C) Translation D) Post-transcription and translation E) Transcription and Post-transcription F) Transcription, post transcription and translation

F

Attenuator systems such as the one described for regulation of tryptophan synthesis would be just as likely to occur in eukaryotes as in prokaryotes. True False

False Regulation by attenuation requires that translation of a given transcript can begin before transcription is completed. This is not possible in eukaryotes, as the two processes are spatially separated by the nuclear membrane.

Why are fertile Calico cats always female?

Females contain two X chromosomes. Because any gene located on the X chromosome will have twice the expression in females, dosage compensation must occur as to not hinder metabolic or other cellular processes. Random inactivation of one of the X chromosomes has a result of a mosaic female; some of the cells express the paternal chromosome while others express the maternal X chromosome. In calico cats, the gene that determines whether or not fur is orange or black is located on the X chromosome- 1 allele of that gene gives rise to orange fur while another gives black. In female cats heterozygous for this gene, different patches of black and orange fur reveal regions made of cells in which one or the other chromosome was inactivated.

What is the function of the PAZ domains in Dicer and Argonaute proteins?***** In both proteins, the PAZ domains recognize and bind the 5′ end of a double-stranded RNA molecule. In both proteins, the PAZ domains recognize and bind the 3′ end of a double-stranded RNA molecule. In Dicer, PAZ recognizes and binds the 3′ end of the double-stranded pre-miRNA. In Argonaute, PAZ has RNase III activity used to cleave the target mRNA strand. In Dicer, PAZ has RNase III activity used to cleave a double-stranded pre-miRNA. In Argonaute, PAZ has RNase III activity used to cleave target mRNA strand.

In both proteins, the PAZ domains recognize and bind the 3′ end of a double-stranded RNA molecule. After the Microprocessor complex processes a pri-miRNA transcript to produce a pre-miRNA with a two-nucleotide overhang on its 3′ end, a second RNA-cleaving enzyme called Dicer further cleaves the double-stranded pre-miRNA. Dicer's PAZ domain binds the 3′ overhang of the pre-miRNA. This allows Dicer to precisely position the two RNase subunits at its opposite end and make cuts in the right location of each strand of the pre-miRNAs. This action generates an ~22-bp miRNA that will eventually become single-stranded and supply the RISC complex with its guide RNA strand. In the RISC complex, the guide RNA strand is arranged such that its 3′ end is bound by the PAZ domain of Argonaute. Once positioned within Argonaute, the guide RNA is available for binding to a complementary (target) mRNA molecule followed by cleavage of the target in the catalytic site of Argonaute.

Which of the following proteins combine to form the Microprocessor complex used to produce active miRNA?***** Drosha and Argonaute Pasha (or DGCR8) and Drosha Drosha and Dicer Pasha (or DGCR8) and Dicer

Pasha (or DGCR8) and Drosha The Microprocessor complex consists of an RNA-cleaving enzyme called Drosha and an essential specificity subunit called Pasha (DGCR8 in some organisms). This complex processes the primary miRNA (pri-miRNA) transcript producing a pre-miRNA product. The cleavage event occurs in the nucleus.

Which of the following statements about riboswitches is true?***** Riboswitches are typically found downstream of the genes they regulate. Riboswitches regulate expression of genes only at the level of transcription. Riboswitches control gene expression through changes in RNA secondary structure. Riboswitches regulate expression of genes only at the level of translation.

Riboswitches control gene expression through changes in RNA secondary structure. Riboswitches are cis-acting regulatory elements that regulate either transcription termination or translation initiation. These RNA sequence elements, which are usually located in the 5′-untranslated region (upstream) of the genes they are regulating, control gene expression in response to changes in the concentration of a small-molecule ligand usually produced by the gene under their regulation. Riboswitches accomplish this via changes in their secondary structure, which in turn is determined by whether or not its ligand is bound to its aptamer. When the aptamer is not bound to its ligand, transcription or translation is switched "on." When the aptamer is bound to its ligand, the secondary structure of the expression platform is altered in a manner that results in transcription or translation being switched "off."

Which of the following occurs as a result of an abundance of tryptophan in E. coli? The 5 trp genes (TrpA - TrpE) are transcribed, but not translated. Stalling of the ribosome at trp codons in the leader sequence The leader sequence is not transcribed. The 5 trp genes (TrpA - TrpE) are not transcribed.

The 5 trp genes (TrpA - TrpE) are not transcribed. When trp is abundant, the genes involved in tryptophan synthesis are negatively regulated at the level of transcription.

The two-hybrid assay takes advantage of which property of transcriptional activators? The ability to bind DNA The ability of domains to interact even when they are on separate proteins The ability of an acidic domain to block transcription.

The ability of domains to interact even when they are on separate proteins

How does the source and generation of miRNAs differ from those of siRNAs?

The genome encodes pri-miRNAs that form a secondary structure (stem-loop) after being transcribed. pri-miRNAs are processed by Drosha to cleave the lower stem from the upper stem, and these pre-miRNAs can then be further processed by Dicer to liberate mature mRNAs. siRNAs arise from double-stranded RNAs that form when two complementary RNAs base-pair. After processing by Dicer, they look similar to the processed miRNAs and inhibit gene expression in a similar manner.

Which of the following features of the trp operon is likely least essential to the process of attenuation? The ability of sequences within the leader mRNA to pair with one another Transcription and translation of the leader sequence occur simultaneously. The order of the structural genes, E, D, C, B, A Trp codons near the beginning of the leader sequence

The order of the structural genes, E, D, C, B, A Because each gene encodes an enzyme involved in the trp synthetic pathway, the order in which the genes occur is likely not important in terms of the attenuation process.

Which of following about riboswitches is false? They regulate gene expression at level of transcription or translation. They are regulatory elements found in the 3' unsaturated regions Each riboswitch has two components: the aptamer and the expression platform Conformational changes in the secondary RNA structure are induced upon binding of small-molecule ligands such as metabolites or uncharged tRNA to the aptamer. Conformational changes in the secondary structure result in either termination of transcription or inhibtion of translation.

They are regulatory elements found in the 3' unsaturated regions

Which of the following statements about the function of regulatory RNAs in X-chromosome inactivation is NOT true?***** When Xic is transcribed, a regulatory RNA called Xist is produced. Inactivated X-chromosomes are much less acetylated than the rest of the genome. Xist RNAs produced by one X-chromosome can initiate inactivation of genes located on the other X-chromosome (they are trans-acting regulators). Xist coats the X-chromosome from which it was transcribed, which leads to the recruitment of other factors that modify and condense the chromatin.

Xist RNAs produced by one X-chromosome can initiate inactivation of genes located on the other X-chromosome (they are trans-acting regulators). The regulatory RNA that initiates X-chromosome inactivation is called Xist. This RNA is transcribed from the Xic gene found on the X- chromosome. It is believed that Xist RNAs produced by one X-chromosome are can only coat genes on that same X-chromosome. The reason why Xist is only cis-acting is not yet clear.

In which of the following pre-mRNA sequence elements can pre-miRNAs be coded?***** exons and introns introns and noncoding regions exons, introns, and noncoding regions noncoding regions

exons, introns, and noncoding regions Pre-miRNAs can be found any part of a pre-mRNA transcript, meaning exons, introns, or noncoding regions.

Which of following regulatory RNAs is NOT found in bacteria? sRNAs miRNAs Riboswitches CRISPRs

miRNAs

Which of the following is a shared characteristic of miRNAs and siRNAs?***** miRNAs and siRNAs are both processed in the cytoplasm by the protein Dicer. miRNAs and siRNAs are both processed in the nucleus by the protein Drosha. miRNAs and siRNAs are both made from large hairpin precursors. miRNAs and siRNAs are both processed in the nucleus by the protein Dicer.

miRNAs and siRNAs are both processed in the cytoplasm by the protein Dicer. Dicer processes pre-miRNAs in the cytoplasm to produce the mature miRNA used in the RISC complex. Similarly, Dicer processes long double-stranded RNA molecules into short siRNAs that are subsequently used in RISC or RITS complexes.