Chapter 15: Gene Regulation in Eukaryotes

Structural features of regulatory transcription factors allow them to bind to DNA.

- Domains are regions of transcription factors that have specific functions. - A domain that has a similar structure in many different proteins is called a motif.Transcription factors often contain - helix called the recognition helix, which makes contact with and recognizes a base sequence along the major groove of the DNA.

Regulatory transcription factors must be regulated by the following

- the binding of an effector molecule. An example is steroid hormones - Protein-protein interactions. An example is the formation of homodimers and heterodimers - Covalent modification of the transcription factor. An example is the addition of a phosphate group

How many promoters are in an operon

1

(Comprehension Q) A bidirectional enhancer has the following sequence: 5'-GTCA-3' 3'-CAGT-5' Which of the following sequences would also be a functional enhancer?

5'-TGAC-3' 3'-ACTG-5'

motif

A domain that has a similar structure in many different proteins

activator

A transcription factor that increases the rate of transcription is called an ____ , and the DNA sequence it binds to an enhancer.

Nucleosome rearrangement may be altered b

ATP-dependent chromatin remodeling

Which of the following combinations will cause the rate of transcription to increase? An activator plus an inducer An activator plus an inhibitor A repressor plus a corepressor

An activator plus an inducer

In eukaryotes, gene transcription can be regulated by the binding of repressors to silencers. Which of the following does NOT correctly describe the function of silencers? Can be found in introns Can work at a distance (even several kilobases away) due to the formation of a DNA loop via an interaction between the mediator complex and repressor Can function bi-directionally -Can work even at a distance (even several kilobases away) due to the formation of a DNA loop via an interaction between TFIID and repressor.

Can work even at a distance (even several kilobases away) due to the formation of a DNA loop via an interaction between TFIID and repressor.

In eukaryotes, gene transcription can be regulated by the binding of activators to enhancers. Which of the following does NOT correctly describe the function of enhancers?

Can work even in a distance (even several kilobases away) due to the formation of a DNA loop via an interaction between TFIID and activator

All remodeling complexes have a catalytic ATPase subunit that is similar to other motor proteins, called ____ , that move along the DNA.

DNA translocases

Which of the following is NOT involved in transcriptional activation? Histone modifications Changes in histone composition within nucleosomes Demethylation of DNA Changes in nucleosome locations

Demethylation of DNA

(Comprehension Q) Which of the following events is NOT involved in transcription of eukaryotic genes? -Histone deacetylation ahead of RNA polymerase - Re-formation of nucleosomes behind RNA polymerase - Histone acetylation ahead of RNA polymerase - Histone eviction ahead of RNA polymerase

Histone deacetylation ahead of RNA polymerase

How can methylation at a CpG island affect transcription?

It may promote the binding of methyl-CpG binding proteins, which coverts the chromatin to a closed conformation to inhibit transcription.

Methylated DNA sequences are inherited during cell division.

Maintenance methylation is involved in the process of genomic imprinting and appears to be involved in cell differentiation.

methylation may convert the chromatin from an open to closed conformation.

Methyl-CpG-binding proteins recognize methylated CG sequences and recruit other proteins to the area, compacting the DNA.

Steriod hormones act as effector molecules for transcription activators. Which of the following is NOT involved in the mechanism by which steroid hormones regulate gene expression? -Phosphorylation of steroid receptors -Binding of hormones to steroid receptors -Binding of hormone-bound steroid receptors to a regulatory element. -Dimerization of hormone-bound steroid receptors

Phosphorylation of steroid receptors

Steriod hormones act as effector molecules for transcription activators. Which of the following is NOT involved in the mechanism by which steroid hormones regulate gene expression? Binding of hormones to steroid receptors Phosphorylation of steroid receptors Binding of hormone-bound steroid receptors to a regulatory element. Dimerization of hormone-bound steroid receptors

Phosphorylation of steroid receptors

transcription factor.

Proteins that influence the ability of the RNA polymerase to transcribe a gene

When a repressor interacts with mediator, whats the result? RNA pol can't bind to core promoter XXXX no TFIID can't bind to core promoter Histone replaces from core promoter RNA pol is unable to switch to elongation of transcription

RNA polymerase is unable to switch to the elongation stage of transcription.

Regulatory transcription factors (activators/repressors) interact with

TFIID and mediator

Most regulatory transcription factors do not bind directly to the RNA polymerase. Instead, they interact with

TFIID or mediator

Which of the following does NOT happen for the CREB protein to activate gene expression? Covalent modification of the CREB protein The binding of a small effector molecule to the CREB protein. protein-protein interactions (dimer formation)

The binding of a small effector molecule to the CREB protein.

characteristics typical of a eukaryotic gene that can be transcribed?

The core promoter is found in a nucleosome-free region.

With regard to lac operon regulation via catabolite activator protein (CAP), which statement is correct in absence of glucose?

The level of cAMP is high enough to bind to CAP, so CAP is able to bind to the CAP site to increase transcription.

regulatory transcription factors

These proteins typically recognize cis regulatory elements that are similar to operators in bacteria

Histone acetyltransferases place an acetyl group on positively changed lysines within the core histone proteins.

This eliminates the positive charge on the lysine side chain, thereby disrupting the electrostatic attraction between the histone protein and the negatively changed DNA backbone. This leads to a more open chromatin structure.

repressors

Transcription factors that decrease the rate of transcription are called ____, and the DNA sequence they bind to is called a silencer.

Binding of ( ) to ( ) decreases the rate of transcription.

a repressor, a silencer

Chromatin remodeling change chromatin structure by

a. changing nucleosome position b. histone eviction c. replacing histones with variants

Particular amino acids in the amino-terminal tails of standard histones and histone variants are subject to several types of covalent modifications, including

acetylation, methylation, and phosphorylation.

Which of following will cause rate of transcription to increase: - activator plus inducer - activator plus corepressor

activator plus inducer

The binding of ( ) to the lac repressor disables the lac repressor to bind to the ( ) site, thereby ( ) transcription. glucose, CAP, increasing allolactose, operator, increasing glucose, CAP, inhibiting allolactose, operator, inhibiting

allolactose, operator, increasing

Binding of ( ) to ( ) increases the rate of transcription.

an activator, an enhancer

Tightly packed chromatin is said to be in the

closed configuration.

Regulatory transcription factors can be modulated by

covalent modifications protein-protein interactions the binding of small effector molecules

Which of the following is NOT involved in transcriptional activation: -Histone Mods -changes in histone composition within nucleosomes -demethylation of DNA -Changes in nucleosome locations

demethylation of DNA

What of the following is an advantage of gene regulation?

efficiency: only make proteins when they are needed. Development: only make proteins at particular stages of development. Specialization: only make proteins in particular cell types.

TFIID

general transcription factor that binds to the TATA box and is needed to recruit RNA polymerase II to the core promoter

General transcription factors

help the RNA polymerase bind to the core promoter.

Another way for methylation at a CpG island to affect transcription is that

it may prevent the binding of an activator to an enhancer, thereby decreasing transcription.

One way for methylation at a CpG island to affect transcription is that It may enhance the binding of an activator to an enhancer to increase transcription. It may promote the binding of methyl-CpG binding proteins, which increases transcription. it may prevent the binding of an activator to an enhancer, thereby decreasing transcription. It may enhance the binding of an activator to a silencer to decrease transcription.

it may prevent the binding of an activator to an enhancer, thereby decreasing transcription.

NFR

lanked by two-well positioned nucleosomes that are termed the -1 and +1 nucleosomes. These may contain histone variants that are important in regulation of transcription.

with regard to lac operon regulation via catabolite activator protein (CAP) which of the following statements is correct in presence of glucose?

level of cAMP is too low to bind to CAP so CAP is unable to bind to the CAP site. This fails to activate the transcription of the lac operon.

methylation of CpG islands

may inhibit binding of transcription factors.

Eukaryotic genes are flanked by

nucleosome-free regions and well-positioned nucleosomes

Chromatin in the _____ configuration is more accessible to transcription factors and RNA polymerase.

open

The primary function of mediator is to control whether or not RNA polymerase is able to

proceed to the elongation stage of transcription.

Transcription factors often contain helix called the

recognition helix, which makes contact with and recognizes a base sequence along the major groove of the DNA.

Regulatory transcription factors

regulate the rate of gene transcription.

CREB protein

regulatory transcription factor that becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of the molecule cyclic adenosine monophosphate (cAMP)

A chromatin-remodeling complex may

replace standard histones with histone variants change the loaction of nucleosomes evict histones from DNA

DNA methylation may regulate genes in a tissue-specific manner.

silences gene expression

Combinatorial control refers to the phenomenon that

the combination of many factors determines the expression of any given gene.

For active genes or those genes that can be activated

the core promoter is found at a nucleosome-free region (NFR). This is typically 150 bp in length.