Ch. 15: Regulation of Gene Expression

positive gene regulation

a regulatory protein interacts directly w/ the genome to switch transcription on

activation domain

binds other regulatory proteins or components of the transcription machinery, facilitating a series of protein-protein interactions that result in enhanced transcription of a given gene

DNA methylation

the addition of methyl groups on the DNA bases (usually cytosine) of plants, animals, and fungi; inactivates transcription

histone acetylation

the attachment of acetyl groups to certain amino acids of histone proteins; appears to promote transcription by opening up the chromatin structure

histone methylation

the attachment of methyl groups to histone proteins can lead to the condensation of chromatin and reduced transcription

RNA interference (RNAi)

the blocking of gene expression by siRNAs; used as a means of disabling specific genes to investigate their function

trp operator

the trp repressor binding site; located within the trp promoter

corepressor

A lack of which of the following molecules would result in the cell's inability to "turn off" genes? A) corepressor B) ubiquitin C) operon D) promoter E) inducer

decreased chromatin condensation

A researcher found a method she could use to manipulate and quantify phosphorylation and methylation in embryonic cells in culture. In one set of experiments she succeeded in decreasing methylation of histone tails. Which of the following results would she most likely see? A) decreased binding of transcription factors B) increased chromatin condensation C) activation of histone tails for enzymatic function D) inactivation of the selected genes E) decreased chromatin condensation

The amount of protein produced by the target gene may be significantly reduced.

A researcher introduces double-stranded RNA into a culture of mammalian cells. The double-stranded RNA corresponds to a region of a protein-coding gene of interest. How may the introduced RNA affect gene expression in these cells? A) The overall rate of transcription in the cell may be significantly reduced. B) The amount of protein produced by the target gene may be significantly reduced. C) The overall rate of translation in the cell may be significantly reduced. D) The overall rate of transcription in the cell may be significantly increased. E) The amount of mRNA produced by the target gene may be significantly increased.

piRNA

Among the newly discovered small noncoding RNAs, one type reestablishes methylation patterns during gamete formation and blocks expression of some transposons. These RNAs are called: A) piRNA B) siRNA C) RNAi D) snRNA E) miRNA

RNA polymerase must bind to the promoter, and the repressor must be inactive.

For a repressible operon to be transcribed, which of the following must occur? A) RNA polymerase and the active repressor must be present. B) RNA polymerase cannot be present, and the repressor must be inactive. C) A corepressor must be present. D) RNA polymerase must bind to the promoter, and the repressor must be inactive.

They allow the expression of many or even all of the genes in a genome to be compared at once.

How have DNA microarrays had such a huge impact on genomic studies? A) They allow the expression of many or even all of the genes in a genome to be compared at once. B) They allow physical maps of the genome to be assembled in a very short time. C) They can be used to introduce entire genomes into bacterial cells. D) They can identify the function of any gene in a genome.

Beta galactosidase will not be produced.

If an experimenter moves the promoter for the lac operon to the region between the beta galactosidase (lacZ) gene and the permease (lacY) gene, which of the following would be likely? A) The three genes will be expressed normally. B) Beta galactosidase will not be produced. C) The operon will no longer be inducible. D) RNA polymerase will no longer transcribe permease. E) The cell will continue to metabolize but more slowly.

piwi-associated RNAs (piRNAs)

RNAs that induce formation of heterochromatin, blocking expression of some parasitic DNA elements in the genome (transposons); appear in the germ cells of many animal species to help reestablish appropriate methylation patterns in the genome during gamete formation

Changes in technology as well as our ability to determine how much of the DNA is expressed have now made this possible.

Since Watson and Crick described DNA in 1953, which of the following statements might best explain why the function of small RNAs is still being explained? A) The functions of small RNAs could not be approached until the entire human genome was sequenced. B) Changes in technology as well as our ability to determine how much of the DNA is expressed have now made this possible. C) Ethical considerations prevented scientists from exploring this material until recently. D) Watson and Crick described DNA but did not predict any function for RNA. E) As RNAs have evolved since that time, they have taken on new functions.

DNA methylation and histone acetylation

Two potential functions that eukaryotic cells perform to regulate transcription are: A) DNA acetylation and methylation B) DNA methylation and histone amplification C) DNA methylation and histone acetylation D) DNA amplification and histone methylation E) histone amplification and DNA acetylation

bind to the repressor protein and activate it

What is the role of a molecule that controls a repressible operon? A) bind to the operator region and block the attachment of RNA polymerase to the promoter B) bind to the promoter region and decrease the affinity of RNA polymerase for the promoter C) bind to the repressor protein and deactivate it D) bind to the repressor protein and activate it E) increase the production of inactive repressor proteins

continuous transcription of the structural gene controlled by that regulator

What would be the result of a mutation that deactivates the regulatory gene of a repressible operon in an E. coli cell? A) inactivation of RNA polymerase by alteration of its active site B) continuous transcription of the structural gene controlled by that regulator C) irreversible binding of the repressor to the operator D) continuous translation of the mRNA because of alteration of its structure E) complete inhibition of transcription by the structural gene controlled by that regulator

a short double-stranded RNA, one of whose strands can block gene expression

Which of the following best describes siRNA? A) a short double-stranded RNA, one of whose strands can block gene expression B) an RNA sequence that can block the expression of some transposons C) a portion of rRNA that allows it to bind to several ribosomal proteins in forming large or small subunits D) a double-stranded RNA that is formed by cleavage of hairpin loops in a larger precursor

It attaches to proteins that are marked for destruction in the cell.

Which of the following is a function of the protein called ubiquitin? A) It attaches to proteins that are marked for destruction in the cell. B) It adds the 3' and 5' caps to eukaryotic pre-mRNA. C) It initiates the formation of a transcription complex. D) It assists in the removal of introns from a eukaryotic pre-mRNA.

regulatory gene

a gene that codes for a protein (e.g., a repressor) that controls the transcription of another gene or group of genes

cells can adjust the activity of enzymes already present; cells can regulate the expression of genes encoding certain enzymes

a metabolic pathway can be controlled on 2 levels:

coordinately controlled

a single "on-off switch" can control the whole cluster of functionally related genes; the key advantage of grouping genes of related function into 1 transcription unit

promoter

a site where RNA polymerase can bind to and begin transcription

corepressor

a small molecule that binds to a bacterial repressor protein and changes the protein's shape, allowing it to bind to the operator and switch an operon off (e.g., tryptophan)

inducer

a specific small molecule that binds to a bacterial repressor protein and changes its shape so that it cannot bind to an operator, thus switching the operon on (e.g., allolactose)

operon

a unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway

represses

accumulation of tryptophan (end product of pathway) _____ transcription of the trp operon, thus blocking synthesis of all the enzymes in the pathway and shutting down tryptophan production

nucleosome

basic unit of chromatin; consists of a cluster of 8 histone proteins around which the DNA double helix is wrapped; their location along a gene's promoter determines whether or not a gene is transcribed

trp operon

consists of a promoter and 5 genes encoding the polypeptide subunits of three enzymes that catalyze the anabolic pathway for tryptophan

differential regulation of transcription/activator proteins

different combinations of a few control elements in an enhancer associated w/ a gene can allow _____ in two cell types b/c each cell type contains a different group of _____

alternative RNA splicing

different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and introns; greatly multiplies the number of possible human proteins

enhancers

distal control elements located far from the gene whose transcription they regulate

operator

in bacterial and phage DNA, a sequence of nucleotides near the start of an operon to which an active repressor can attach, thus preventing RNA polymerase from attaching to the promoter and transcribing the genes of the operon

general transcription factors

located at the promoter; essential for the transcription of all protein-coding genes; a few bind to a DNA sequence (e.g., the TATA box), many bind to proteins (e.g., other _____ and RNA polymerase II)

DNA-binding domain

part of an activator's 3D structure that binds to DNA

repressor proteins

proteins that inhibit gene transcription; in prokaryotes, _____ bind to the DNA in or near the promoter, blocking the attachment of RNA polymerase to the promoter and preventing gene transcription; specific for the operator of a particular operon

negative gene regulation

regulation of both the trp and lac operons involves _____ b/c the operons are switched off by the active form of the repressor protein

cAMP receptor protein (CRP)

regulatory activator protein that binds to DNA and stimulates gene transcription; when cAMP binds to _____, it assumes its active shape and can attach to a specific site at the upstream end of the lac promoter, thus increasing affinity of RNA polymerase for the lac promoter

control elements

segments of noncoding DNA that help regulate transcription of a gene by serving as a binding site for a transcription factor; multiple are present in a eukaryotic gene's enhancer

cyclic AMP (cAMP)

small organic molecule which accumulates when glucose is scarce; interacts w/ an allosteric regulatory protein so an E. coli cell can "sense" its glucose concentration

microRNAs (miRNAs)

small, single-stranded RNA molecules; associate w/ one or more proteins in a complex that can degrade or prevent translation of an mRNA w/ a complementary sequence; (1) binds to a target mRNA w/ at least 7 complementary bases; (2) if _____ and mRNA bases are complementary all along their length, the mRNA is degraded; if the match is less complete, translation is blocked

small interfering RNAs (siRNAs)

small, single-stranded RNA molecules; associate w/ one or more proteins in a complex that can degrade or prevent translation of an mRNA w/ a complementary sequence; can also block transcription by promoting chromatin modification

repressors

some bind directly to control element DNA, blocking activator binding; others interfere w/ the activator itself so it can't bind to DNA

silencing

some repressors recruit proteins that remove acetyl groups from histones, leading to reduced transcription

"volume control"

state of CRP (w/ or w/o bound cAMP) controls the rate of transcription if the lac operon is repressor-free

"on-off switch"

state of the lac repressor (w/ or w/o bound allolactose) determines whether or not transcription of the lac operon's genes occurs at all

histone tails

the N-terminus of each histone in a nucleosome protrudes outward from the nucleosome; accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups

differential gene expression

the expression of different sets of genes by cells w/ the same genome

negative control/positive control

the lac operon is under dual control: _____ by the lac repressor and _____ by CRP

trp repressor

the protein product of a regulatory gene (trpR); an allosteric protein w/ two alternative shapes: active and inactive

specific transcription factors

the rate of gene expression can be strongly increased or decreased by the binding of _____ (either activators or repressors) to the control elements of enhancers; in eukaryotes, high levels of transcription of genes at the appropriate place and time depend on the interaction of control elements w/ _____;

inducible operon

transcription is usually off but can be stimulated when a specific small molecule interacts w/ a regulatory protein (e.g., lac operon)

repressible operon

transcription is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein (e.g., trp operon)

inactive form

trp repressor is synthesized; has little affinity for the trp operator

active form

tryptophan binds to the trp repressor at an allosteric site; trp repressor changes to _____ that can attach to the trp operator, turning the trp operon off

lac operon

w/o the repressor bound, the _____ is transcribed into mRNA, and the enzymes for using lactose are made