Genetics Ch 15

Three classes of proteins involved in transcription activation

1) General transcription factors (basal transcription) 2) Activators (trans-activation) 3) Coactivators

Three common ways the function of regulatory transcription factors can be modulated

1. Binding of a small effector molecule 2. Protein-protein interactions 3. Covalent modification

Three common interactions that communicate the effects of regulatory transcription factors are...

1. TFIID-direct or through coactivators 2. Mediator 3. recruiting proteins that affect nucleosome composition

What is the size of the nucelosome-free region found at the core-promoter of active genes?

150 bp

What percentage of human genes encode transcription factors?

2-3%

DNA methyltransferase is an enzyme that attaches a methly group to the _________ position of the ________ base

5; cytosine

Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin remodeling complexes?

ATP hydrolysis

What is the name for stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites that are found near gene promoters?

CpG islands

What is the function of a helix-turn-helix?

DNA binding

What is the function of zinc finger?

DNA binding

A change in chromatin structure that silences gene expression

DNA methylation

Which enzyme catalyzes the formation of 5-methyltransferase?

DNA methyltransferase

The ATPase subunit of chromatin-remodeling complexes

DNA translocase

Function as enhancers located near dozens of different genes, so the hormone can activate many genes

Glucocorticoid Response Elements

These influence nutrient metabolism in most cells; they promote glucose utilization, fat mobilization and protein breakdown

Glucocorticoids

These include estrogen and testosterone; they influence the growth and function of the gonads

Gonadocorticoids

The function of TFIID to bind to the ________ box and recruit RNA _________ ___ to the core promoter

TATA; polymerase II

TFIID binds to _______ the box and helps recruit RNA polymerase II to the core _______.

TATA; promoter

Which organism has the highest amunt of DNA methylation? a. vertebrates b. yeast c. Drosophila

a. vertebrates

A regulatory protein that increases the rate of transcription

activator

A regulatory transcription factor that enhances the rate of transcription

activator

What effect can ATP-dependent chromatin remodeling have on transcription?

both activation and repression

•Steroid hormones are produced by __________ ________

endocrine glands

Sequence that the activator binds to

enhancer

The binding of a regulatory transcription factor to a ___________ can stimulate transcription 10 to 1000-fold, which is called ________ regulation

enhancer; up

Activators are proteins that bind to _________

enhancers

Iron response elements (IREs) can be found in the 5'-UTR of _______ mRNA and in the 3'-UTR of ______ _____ mRNA

ferritin; transferrin receptor

The ENCODE Consortium is attempting to list all ________ ______ in the human genome

functional elements

The ultimate action of a steroid hormone is to affect ______ ______

gene transcription

Factors that are required for the binding of the RNA pol to the core promoter and its progression to the elongation stage; and are necessary for basal transcription

general transcription factors

The central goal of the Encyclopedia of DNA Elements (ENCODE) Consortium is to make a comprehensive list of functional elements in the ___ ___, including those that control gene expression.

human genome

Many response elements are orientation ___________ or _________

independent; bidirectional

Chromatin is accessible to transcription factors; transcription can take place

open conformation

What is the function of leucine zipper?

protein dimerization

A regulatory protein that decreases the rate of transcription

repressor

The cAMP __________ element binding protein (__________ protein) is a regulatory transcription factor that is activated in response to signaling molecules that increase cytoplasmic cAMP

response; CREB

Sequence that the repressor binds to

silencer

Regulatory transcription factors that respond to steroid hormones

steroid receptors

Genes that are highly regulated and may be expressed only in certain cell types

tissue-specific genes

The transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with __________ _________ _________

general transcription factors

A domain that has a very similar structure in many different proteins

motif

Nucleosomes containing the histone variant ________, which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone __________

H2A.Z; H2A

Segments of DNA that insulate a gene from the regulatory effects of other genes; some act as barriers to chromatin remodeling, others block the effects of enhancers

Insulators

_________ can change in location along a DNA molecule, by replacement of a standard histone with a histone variant, and thorugh covalent modifications on histone tails

Nucleosomes

CREB protein becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of ______

cAMP

Mediator phosphorylates the _______-terminus of RNA polymerase II, stimulating progression to the __________ stage of transcription.

carboxyl; elongation

Methylated DNA sequences are inherited during _____ ______

cell division

Regulatory transcription factors recognize ____ _________ elements located near the core promoter

cis regulatory

Transcription may be difficult or impossible, if chromatin is in a _______ confirmation

closed

Chromatin is very tightly packed; transcription may be difficult or impossible

closed conformation

Activator proteins often increase transcription through an interaction with ____________

coactivators

DNA sequences that are analogous to the operator sites found near bacterial promoters are called ______ elements or _______ sequences

control; regulatory

DNA methylation is the _______ attachment of methly groups to DNA

covalent

The methylation of DNA that was previously unmethylated

de novo methylation

ATP-__________ ________ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes

dependent chromatin

Transcription factor proteins contain regions called __________ that have specific functions

domains

Transcription factor proteins contain regions, called ________, that have specific functions

domains

The dimerization of two identical proteins results in a ____________

homodimer

Genes that code for proteins that are required in most cells of a multicellular organism

housekeeping genes

In order to regulate the translation of both ferritin and transferrin receptor mRNAs, the iron regulatory protein (IRP) binds to the _____ ____ _____ of the mRNAs

iron response element

Positively charged _______ within core histone proteins can be acetlyated by histone ___________

lysines; acetyltransferases

The protein compex that mediates the interaction between RNA polymerase II and regulatory transcription factors

mediator

CpG islands near the promoters of tissue-specific genes are often ______.

methylated

If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be __________. If the same sequence of nonmethylated DNA is introduced into a cell, it will be _____________ in daughter cells.

methylated; unmethylated

The core promoter of active genes is found in a(n) ____-free region, which is a segment of DNA that is missing histones.

nucleosome

Found at the beginning and end of many genes. Nucleosomes tend to be precisely positioned near the beginning and end of a gene, but are less regularly distributed elsewhere

nucleosome-free region

The phenomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene ___________

regulation

Regulatory transcription factors that serve to regulate the rate of transcription of target genes; they influence the ability of RNA pol to begin transcription of a particular gene

regulatory transcription factors

Coactivators usually contain a ________ domain that promotes the activation of RNA polymerase.

transactivation

A protein that influences the ability of RNA polymerase to transcribe a given gene

transcription factors

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

transcription factors

If chromatin is in a closed conformation, nucleosome position and histone composition make it difficult for __________ ________ to gain access to and bind their target sequences in the promoter _______

transcription factors; DNA

True or False: A transcription factor can have multiple domains

true

True or False: Cells modulate the function of their regulatory transcription factors

true

True or False: DNA methylation is inheritable

true

True or False: Most regulatory transcription factors do not bind directly to RNA polymerase

true

True or False: The methylation state of DNA is inherited during cell division

true

The cytosines in CpG islands near housekeeping genes are _______

unmethylated

In general ___ CpG islands correlate with active genes, and ___ CpG islands correlate with suppressed genes.

unmethylated; methylated

An enhancer is a DNA element that can be bound by a regulatory transcription factor, which leads to ______ _______

up regulation

Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone _______

variants

Eukaryotes 4 families of chromatin remodelers:

• SWI/SNF • ISWI • INO80 • Mi-2