Chapter 13 Gene Regulation

Select all of the following that form the pre-initiation complex in eukaryotic transcription, including the binding site

- RNA polymerase II - core promoter - GTFs

Eukaryotic gene expression can be regulated at which levels?

- RNA processing - transcription - translation

What are the two components of the core promoter?

- TATA box - transcriptional start site

Histone modifications can result in:

- activation of transcription - loosening of chromatin

Which of the following factors help to increase transcription levels in eukaryotes?

- binding of an activator protein to DNA - loosening of chromatin structure

How can faster regulation of gene regulation be achieved in eukaryotes?

- controlling the steps in RNA processing - controlling the steps after an RNA is made

Place the steps in gene expression in correct order from first to last

- convert chromatin to an open conformation - transcribe the gene - process the RNA and export from the nucleus - make the protein via translation

Which of the following accurately describe the role of chromatin packing in the expression of eukaryotic genes?

- loosely packed chromatin allows GTFs and RNA polymerase to access the promoter site and transcription can take place - tightly packed chromatin is difficult or impossible to transcribe

How can DNA methylation inhibit transcription?

- methylation can convert DNA from an open conformation to a closed one - methylation can prevent an activator from binding to an enhancer

Small RNAs that silence gene expression are called:

- microRNAs - short-interfering RNAs

Match the type of transcription factors with the proper form of transcriptional regulation repressor activator regulatory transcription factors

- negative control - positive control - both positive and negative control

Match each regulated step of eukaryotic gene expression with the appropriate description transcription RNA processing translation post-translation

- the amount of RNA synthesized from a gene is regulated - two or more different types of mRNAs are created from a single gene - the amount of protein synthesized from a mRNA is regulated - protein function is affected by feedback inhibition, covalent modifications, and degradation

What are two major benefits of gene regulation?

- the conservation of energy - expression of genes at appropriate times

What are the effects of binding of an mRNA to its target?

- the mRNA is silenced - the mRNA is degraded

The enzyme _____ _____ is responsible for covalently attaching methyl groups to DNA

DNA methylase

How does gene regulation differ between prokaryotes and eukaryotes?

Eukaryotes process mRNA transcripts in ways that prokaryotes do not

The process by which an miRNA silences the expression of an mRNA is called _____ _____

RNA interference

What is basal transcription?

The low level of transcription activated by the core promoter alone

What is cyclic AMP (cAMP)?

a small effector molecule involved in the positive control of the lac operon

When the sugar _____ binds to the repressor protein, this causes a conformational change that prevents the repressor from binding to the _____ site

allolactose; operator

The process whereby different transcripts are made from a single gene is called _____ _____

alternative splicing

In eukaryotes, the rate of transcription of genes is influenced by regulatory transcription factors called _____ and _____. These proteins bind to regulatory elements and control the gene expression rate

repressors; activators

What is chromatin?

the complex formed by DNA and its associated proteins

Which of the following are ways of regulating gene expression in BOTH prokaryotes and eukaryotes?

- post-transiational regulation - regulation of translation - regulation of transcription

Control of gene expression takes place at what levels in eukaryotes?

- post-translation - processing of mRNA - translation - transcription

At what levels does gene regulation occur in prokaryotes?

- post-translation - translation - transcription

Match the features of transcriptional regulation on the left to the organisms using them on the right activator and repressor proteins regulate genes genes organized individually genes organized in operons

- prokaryotes and eukaryotes - eukaryotes - prokaryotes

The lac repressor protein prevents the enzyme _____ _____ from transcribing the genes in the lac operon

RNA polymerase

What is the CAP site for lac operon?

The sequence of nucleotides that is recognized by an activator protein

In eukaryotic DNA, regulatory elements known as _____ play a role in the ability of RNA polymerase to begin transcription, thereby increasing the rate of transcription

enhancers

The process in which the information in a gene is made into the functional gene product is termed gene _____

expression

Different cell types, such as skin cells and nerve cells, have different morphologies because _____ are expressed and regulated in different ways in different cells

genes

Of the four possible environments E. coli could encounter with regard to lactose and glucose, which has the highest levels of lac operon transcription?

high lactose and low glucose

Covalent modification to _____ proteins can affect gene expression by activating or silencing the transcription of genes

histone

When there are low levels of trytophan in the cell, the transcription of the trp operon is _____

increased

The genes found in the lac operon of E. coli are used for the metabolism of _____

lactose

Transcription rate of the lac operon is very high when _____ levels are high and _____ levels are low. This is because the protein _____ is bound to the DNA, and the lac repressor is not bound to the _____ site

lactose; glucose; CAP; lacO

What are small effector molecules?

molecules that bind to transcription factors and change their conformation

When transcription is regulated by repressor proteins, this is called:

negative control

The lacO site of the lac operon is called the _____ and is the site where the repressor protein binds

operator

A _____ is a cluster of genes that are part of a single transcription unit that is under the control of a single promoter

operon

The catabolite activator protein (CAP) is involved in _____ control of the lac operon

positive

The _____ is the collection of all proteins that are expressed in a cell:

proteome

What happens when the corepressor binds to the trp repressor?

the repressor binds to the operator and prevents transcription

Which of the following is a repressible operon?

the trp operon

In both prokaryotes and eukaryotes, most gene regulation occurs when cells regulate the level of _____ of a gene

transcription

What step in gene expression is regulated by microRNAs and short-interfering RNAs?

translation

Match he small effector molecules with the correct operons trp operon lac operon

trp operon: - tryptophan - corepressor lac operon: - allolactose - inducer

When is a gene "turned off"?

when no mRNA is transcribed from the gene

The trp operon is regulated by a _____ protein that is encoded by the trpR gene

repressor

What are the three ways activators and repressors influence transcription?

- regulate the function of RNA polymerase by interacting with GTFs - control RNA polymerase function via mediator proteins - Recruit proteins that influence the level of DNA compaction at the promoter site

What are the three features common to most promoters that are needed for the initiation of transcription of protein coding genes in eukaryotes?

- regulatory elements - transcriptional start site - TATA box

For initiation of eukaryotic transcription at the core promoter, three types of proteins are needed: RNA polymerase _____, GTFs and a large protein complex called _____

II; mediator

_____ control is transcriptional regulation by activator proteins

positive

What is the role of repressor proteins in the regulation of transcription?

repressor proteins bind to DNA and decrease the rate of transcription

What molecules can influence transcription by binding to enhancers or silencers?

repressors and activators

According to the histone code hypothesis, proteins recognize histones based on:

the covalent modifications

How does the mediator protein interact with RNA polymerase and the GTFs during the initiation of transcription?

the mediator protein controls interaction between the pre-initiation complex and other regulatory elements

Which of the following are similarities between eukaryotic and prokaryotic transcriptional regulation?

- small effector molecules are involved in gene regulation - proteins influence the ability of RNA polymerase to bind to the DNA

How can gene regulation be specific?

- specific genes are expressed at different developmental stages - specific genes are expressed only in certain cells - specific cells differ in expression levels from cell to cell

Match each protein or group of proteins with its role in transcription RNA polymerase general transcription factors activators

- synthesis of RNA from a DNA template - required for binding to the core promoter and initiating transcription - binding to enhancer sequences and interactions with other proteins

A small effector molecule that increases the rate of transcription is called a _____

inducer

An operon that can be turned on in the presence of a small effector molecule is said to be _____ operon

inducible

The lacl gene encodes the lac _____

repressor

What is cell differentiation?

the process by which cells become specialized in different types

Which of the following are ways that translation can be regulated?

- small RNA molecules control translation of the mRNA - stabilizing an mRNA - degrading an mRNA - RNA-binding proteins control translation of the mRNA

When glucose is present in a bacterial cell, it can act to repress the expression of the lac operon because it is preferentially used compared to other sugars. What form of transcriptional regulation is this?

catabolite repression

Order the components of a eukaryotic promoter in the most common organization from the 5' end at the top to the 3' end at the bottom

regulatory elements TAT box transcriptional start site

An operon in which a small effector molecule prevents transcription is called a _____ operon

repressible

What is the order of steps that activator proteins take in order to promote the unraveling of compact chromatin at the site of gene transcription?

- transcriptional activator binds to an open enhancer site - activators recruit chromatin remodeling proteins - compared chromatin is loosened - trancription occurs

Match the operon with the small effector molecule on the repressor protein The repressor proteins binds to the operator in the presence of the small effector molecule The repressor proteins binds to the operator in the absence of the small effector molecule

- trp operon - lac operon

How does the presence of lactose in the cell influence the transcription of the lac operon?

- when lactose is present, the lac repressor protein does not bind to the operator site and transcription can occur - when lactose is present, transcription of the lac operon is high

When chromatin is tightly packed, this is called the _____ conformation, and when it is loosely packed, this is called the _____ conformation

closed; open

In many multicellular species a combination of many different factors determines the regulation of gene expression. This is called:

combinatorial control

The protein encoded by the lacl gene functions to:

prevent transcription of the lac operon

Regulatory transcription factors influence the expression of genes by binding directly to DNA at or near the _____ site of a gene

promoter

How does cAMP play a role in the transcription of the lac operon?

cAMP binds to CAP and together they bind to the DNA, which enhances transcription of the lac operon

When _____ binds to CAP, the resulting complex binds to the CAP site near the lac _____. This causes a bend in the DNA that enhances the ability of RNA polymerase to bind, and so the transcription rate is increased

cAMP; promoter

Match each term with the correct description activators enhancers repressors silencers

- proteins that bind to DNA and increase transcription - DNA sequences that increase transcription - proteins that bind to DNA and inhibit transcription - DNA sequences that prevent transcription

When a gene has constant levels of expression over time in a cell, it is:

constitutive gene