BIOL207-Chapter 17 Sapling

Select the terms that represent a mode of regulation of gene expression in eukaryotes. Acetylation mRNA capping and polyadenylation Purine ring structure B-form DNA structure Protein synthesis

Acetylation mRNA capping and polyadenylation Protein synthesis

Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation alternative splicing produces different transcripts from the same gene.

RNA processing

In Arabidopsis thaliana, the Flowering Locus C (FLC) gene codes for a regulatory protein that suppresses flowering. FLC is expressed in seedlings to prevent premature flowering. In mature plants, FLC expression decreases with cooler temperatures, and flowering occurs once sufficiently cool temperatures are reached. If small-interfering RNA (siRNA) that is complementary to FLC mRNA is introduced, how would RNA interference (RNAi) affect flowering? A-RNAi would degrade FLC mRNA and stimulate flowering. B-RNAi would bind irreversibly to FLC mRNA and stimulate flowering. C-RNAi would induce methylation of chromatin and repress flowering. D-RNAi would degrade FLC mRNA and repress flowering. E-RNAi is found in prokaryotes and would not affect Arabidopsis.

A

Each answer box represents a mechanism by which eukaryotes can regulate gene expression. Determine which of the five mechanisms each example represents. Not all examples will be used. Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation Examples: A-limited availability of initiation factors prevents translation of mRNA B-Gene inversion does not cause a loss of genetic information but may affect regulation of inverted genes. C-acetylation of histones facilitates transcription. D-alternative splicing produces different transcripts from the same gene. E-miRNAs direct cleavage of specific transcripts, usually at the 3' UTR of the target transcript F-transcriptional repressors compete with activators for DNA binding sites.

A-initation of translation B-none C-changes in chromatin structure D-RNA processing E-RNA interference F-activity of transcription apparatus

Modifications to chromatin can affect transcriptional activity by changing the accessibility of DNA to the transcription machinery. Below are descriptions of various processes that may or may not cause remodeling of chromatin. Match each description to the effect it has on transcriptional activity caused by chromatin remodeling. Activates, inactivates, activations AND inactivates, or no effect: Histone acetyltransferases attach acetyl groups to the N-terminus of histones Histone deacetylases remove acetyl groups from the N-terminus of histones Histone methylation occurs at different amino acids. RNA polymerase II binds the start site of transcription.

Activates: Histone acetyltransferases attach acetyl groups to the N-terminus of histones Inactivates: Histone deacetylases remove acetyl groups from the N-terminus of histones Activates and inactivates: Histone methylation occurs at different amino acids. No effect: RNA polymerase II binds the start site of transcription.

Identify each description as typical of eukaryotic repressors or bacterial repressors. Leave unplaced the description that is not characteristic of either group. binds to DNA-binding motifs on RNA polymerase and directly inhibits it binds to an operator downstream of the promoter site and blocks RNA polymerase binds to a silencer that uses transcriptional activator proteins to block RNA polymerase

Eukaryotic repressor: binds to a silencer that uses transcriptional activator proteins to block RNA polymerase Bacterial repressor: binds to an operator downstream of the promoter site and blocks RNA polymerase

Classify each of the characteristics below as pertaining to gene regulation in either prokaryotes or eukaryotes. Genes are located on one chromosome. Genes are located on different chromosomes. Some genes are organized into operons, and mRNA transcripts often specify more than one protein. Transcription and translation occur in the cytoplasm. Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm. mRNA splicing must occur to remove introns.

Prokaryotic gene regulation: Genes are located on one chromosome. Some genes are organized into operons, and mRNA transcripts often specify more than one protein. Transcription and translation occur in the cytoplasm. Eukaryotic gene regulation: Genes are located on different chromosomes. mRNA splicing must occur to remove introns. Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm.

Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation acetylation of histones facilitates transcription.

changes in chromatin structure

Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation limited availability of initiation factors prevents translation of mRNA

initiation of translation

How can microRNAs (miRNAs) regulate gene expression? A-prevent transcription by binding to DNA and removing transcription factors B-prevent translation by binding to tRNA and interfering with protein synthesis C-prevent transcription by binding to RNA polymerase and stopping RNA production D-prevent translation by binding to mRNA and degrading the mRNA strand

D

In eukaryotes, transcription factors and enhancer sequences are used to regulate transcription. Classify the following statements as true or false. Enhancer sequences directly alter transcription levels Enhancer sequences are composed of DNA base pairs Transcription factors always increase transcription levels. Transcription factors bind to the entire enhancer sequence. Enhancer sequences can be located thousands of base pairs downstream from the transcription start site.

True: Enhancer sequences can be located thousands of base pairs downstream from the transcription start site. Enhancer sequences are composed of DNA base pairs False: Enhancer sequences directly alter transcription levels Transcription factors always increase transcription levels. Transcription factors bind to the entire enhancer sequence.

Repressor

a transcription factor that prevents mRNA synthesis by binding to the operator of a gene

Insulator

a transcriptional element that blocks the signal between enhancers and promoters

Malaria is a life-threatening illness caused by Plasmodium parasites that are transmitted to humans by infected Anopheles mosquitoes. Freitas-Junior et al. (2005) describe how multiple Plasmodium species evade host immune systems via antigenic variation, wherein the parasites regularly change the antigens on their surfaces to evade detection by host immune cells. The mechanism that varies antigen expression is epigenetic: histone proteins associated with a suite of antigen-coding genes are repeatedly chemically modified, such that chromatin structure changes over time, producing variation in expression of particular antigen-coding genes. What chemical changes in histone proteins are responsible for changes in gene expression? A-addition or removal of methyl and acetyl groups within the tail domains of histones B-addition or removal of methyl and acetyl groups within the globular domains of histones C-proteolytic cleavage of the globular and tail domains of histone proteins into oligopeptides D-removal of electrically-charged functional groups from the tail domains of histones E-addition of acidic groups and removal of alkaline groups within the tail domains of histones

A

How are proteins regulated after translation? Click all that apply. A-active proteins can be inactivated by post-translational modification B-proteins that are no longer required can be transported out of the cell C-proteins can be tagged with small molecules and subsequently degraded D-inactive proteins can be activated by phosphorylation E-existing mRNA molecules can be degraded to produce fewer proteins

A, C, D

How do cells regulate gene expression using alternative RNA splicing? Alternative RNA splicing determines how fast certain proteins are translated. Alternative RNA splicing determines which proteins are produced from each gene. Alternative RNA splicing determines which genes are transcribed to mRNA. Alternative RNA splicing determines which genes are overexpressed.

Alternative RNA splicing determines which proteins are produced from each gene.

Select the post-translational modifications of histones that are most commonly associated with changes in transcription levels in eukaryotes. A- acetylation and lipidation B- nitrosylation and ubiquitination C- methylation and acetylation D- phosphorylation and glycosylation

C

Which description applies to post-translational gene regulation? A-processing of exons in mRNA that results in a single gene coding for multiple proteins B-heritable changes in gene expression that occur without altering the DNA sequence C-protein modifications such as addition of a functional group, or structural changes such as folding D-mRNA modifications such as additions of a 5' cap and 3' poly-A tail and removal of introns E-a gene cluster controlled by a single promoter that transcribes to a single mRNA strand

C

Which description applies to epigenetic gene regulation? A-mRNA modifications such as additions of a 5\' cap and 3\' poly-A tail and removal of introns B-protein modifications such as addition of a functional group, or structural changes such as folding C-a gene cluster controlled by a single promoter that transcribes to a single mRNA strand D-processing of exons in mRNA that results in a single gene coding for multiple proteins E-heritable changes in gene expression that occur without altering the DNA sequence

E

Which of the following post-translational modifications generally targets a protein for degradation in eukaryotes? A-nitrosylation B-methylation C-lipidation D-acetylation E-ubiquitination

E

Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation miRNAs direct cleavage of specific transcripts, usually at the 3' UTR of the target transcript

RNA interference

Drosophila sex determination involves the regulation of alternative RNA splicing by the sex-lethal (Sxl), transformer (tra), and doublesex (dsx) genes. Match each effect on Drosophila sexual development with the gene deletion that would cause it. Gene deletion options: Sxl, tra, dsx A-absence of female-determine regulatory protein yields male trains in females B-male-specific splicing of ddx yields male trains in females C-absence of male-determining regulatory protein yields female traits in males D-male-specific splicing of tra yields male trains in females

Sxl deletion: D tra deletion: B ddx deletion: A and C

Five mechanisms: changes in chromatin structure, activity of transcription apparatus, RNA processing, RNA interference, initiation of translation transcriptional repressors compete with activators for DNA binding sites.

activity of transcription apparatus

Enhancer I can stimulate the transcription of gene A, but the insulator blocks its effect on gene B. Enhancer II can stimulate the transcription of gene B, but the insulator blocks its effect on gene A. What would be the effect of moving the insulator to a position between enhancer II and the promoter for gene B? The newly positioned insulator prevents enhancer II form stimulating the transcription of gene B. The newly positioned insulator allows enhancer II to hyperactive gene B transcription. The newly positioning of the insulator prevents gene A expression. The newly positioned insulator allows enhancer I to activate gene B transcription.

The newly positioned insulator prevents enhancer II form stimulating the transcription of gene B.

Operator

a short DNA sequence that can be recognized by a repressor protein

Growth in nutrient-rich medium represses expression of the yeast serine biosynthesis gene SER3. Martens et al. repressed SER3 expression and found a highly transcribed region of DNA upstream of the SER3 gene. This upstream region contains a non-protein-coding gene called SRG1. An RNA polymerase binds the SRG1 promoter and transcribes the SRG1 gene through the adjacent SER3 promoter, which leads to the repression of SER3. Mutations in the SRG1 promoter remove the repression of SER3. Which of the following statements explains how SRG1 transcription represses SER3 transcription? Transcription machinery on the SRG1 gene prevents binding of transcription factors on the SER3 promoter, blocking SER3 transcription. The protein product of the SRG1 gene binds to the SER3 promoter and prevents its transcription. SRG1 RNA modifies the histones in the region of the SER3 promoter, creating a heterochromatic region around the SER3 gene. The SRG1 transcription process occurs at such a high rate that it titrates basal transcription factors away from other initiation sites.

Transcription machinery on the SRG1 gene prevents binding of transcription factors on the SER3 promoter, blocking SER3 transcription.

Promoter

a DNA sequence located near the start of a gene that RNA polymerase binds to initiate transcription

Regulatory Gene

a gene that controls the expression of one or more genes by promoting or inhibiting transcription

Inducer

a molecule that activates mRNA synthesis by disabling the protein that prevents transcription