cap 15

gene expression

the process by which the information within a gene is accessed, first to

synthesize RNA and polypeptides, and eventually to affect the properties of cells and the phenotype of

multicellular organisms.

gene regulation

the phenomenon in which the level of gene expression can vary under different conditions

combinatorial control

the combination of many factors that regulate eykaryotic genes

determines the expression of any given gene.

transcription factor

a category of proteins that influence the

ability of RNA polymerase to transcribe DNA into RNA.

general transcription factor

required for the binding of RNA polymerase to the

core promoter and for progression to the elongation stage.

regulatory transcription factors

serve to regulate the rate of transcription of target genes.

domains

regions in transcription factor proteins that have specific functions

motif

the structurally similar region of a domain in many different proteins

recognition helix

an alpha helix that makes contact with and recognizes a base sequence along the major groove of the DNA

homodimer

two identical transcription factors come together to form this structure

heterodimer

two different transcription factors come together to form this structure

regulatory elements

cis-acting regulatory sequences that are located in the same

chromosome as the gene they regulate; may be close to or far way from the core promoter.

enhancer

a DNA region, usually 50–1000 bp in length, that contains one or more regulatory elements

activator

a regulatory transcription factor that when it binds to an enhancer increases the rate of transcription

repressors

a regulatory transcription factor that when it binds to an enhancer prevents transcription from occurring

up regulation

a phenomenon, type of regulation, in which an activator binds to an enhancer and stimulates transcription 10- to 1000-fold

down regulation

a phenomenon in which the binding of repressors inhibit transcription and results in this type of regulation

orientation independent

a characteristic of regulatory elements and the enhancers that contain them

• a regulatory element can function in either the forward or the reverse

  direction

closed conformation

a chromatin conformation in which transcription may be difficult or impossible

open conformation

a chromatin conformation in which is more easily accessed by transcription factors and RNA polymerase, allowing transcription to occur.

chromatin remodeling

dynamic changes in the structure of chromatin that occur during the life of a cell.

• In this process, the energy of ATP hydrolysis is used to drive changes in the positions and/or compositions of nucleosomes, making the DNA more or less amenable to transcription.

atp dependent chromatin remodeling complexes

a set of diverse multiprotein machines that reposition and

restructure nucleosomes.

dna translocase

a catalytic ATPase subunit that moves along the DNA. is found in all chromatin remodeling complexes

histone variants

altered histones that resulted from accumulated mutations in genes that change the amino acid sequences of histone proteins.

histone acetyltransferases

proteins that acetylate positively charged lysines within the core histone

proteins

histone deacetylases

remove acetyl groups from acetylated histones and thereby favor a tighter

contact between histones and the DNA.

histone code hypothesis

a hypothesis that establishes that the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure.

dna methylation

a process in which a methyl group can be attached to the cytosine base in DNA

dna methyltransferase

an enzyme that attaches a methyl group to the carbon at the number 5 position of the cytosine base, forming 5-methylcytosine

CpG islands

a dinucleotide of C and G in DNA that is connected by a phosphodiester

linkage

housekeeping genes

genes that code proteins required in most cells of a

multicellular organism

tissue specific genes

genes that are highly regulated and may be expressed only in a particular cell type.

methyl CpG binding proteins

proteins that contain a domain called the methyl-binding domain that recognizes a methylated CpG island. Once bound to the DNA, it recruits to that region other proteins that inhibit transcription.

de novo methylation

the methylation of DNA that was previously unmethylated.

maintenance methylation

a process in which the hemimethylated DNA is efficiently recognized by DNA methyltransferase, which makes it fully methylated. this preserves the

methylated condition in future cells.

gene activation

a series of events that enable a gene to be transcribed to produce an RNA molecule.

nucleosome free region

a region of DNA where nucleosomes are not found.

coactivators

proteins that increase the rate of transcription but do

not bind directly to the DNA.

insulator

a structure that limits genetic interactions to a specific region

closed complex

complex in which dna strands are bound to each other

open complex

complex in which dna strands are separated

TFIIH

a component of the preinitiation complex that has a subunit that functions as a DNA translocase, tracking along the DNA and leaving unwound DNA in its wake

• separates DNA strands

promoter escape

a process in which release of RNA polymerase II is released from the binding of GTF and mediator

proximal promoter pausing

a phenomenon in which RNA polymerase II pauses in RNA synthesis while it is still fairly close to the transcriptional start site,

steroid receptor

a type of regulatory transcription factor

• the steroid hormone binds directly to the protein.

cAMP response element-binding protein

a 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).

gene repression

any mechanism that inhibits the transcription of a gene and thereby results in a lower level of RNA

synthesis from that gene.

repressor

a protein that binds directly to a DNA sequence and inhibits transcription

basal transcription

transcription that occurs from a core promoter

without the aid of enhancers, activators, and coactivators

gene silencing

long term repression in which a gene is subjected to changes in

chromatin structure that are more permanent in nature

epigenetics

changes passed from mother to daughter cells