Chp 14- Gene Expression at the Molecular Level III: Gene Regulation

CpG islands

A cluster of CpG sites.CG refers to the nucleotides of C and G in DNA and p refers to a phosphodiester linkage between the nucleotides containing those bases.

iron regulatory protein (IRP)

An RNA-binding protein that regulates the translation of the mRNA that encodes ferritin.

regulatory elements

DNA sequence that is recognized by regulatory transcription factors and regulates the expression of genes

general transcription factors (GTFs)

Five different proteins that play a role in initiating transcription at the core promoter of protein-encoding genes in eukaryotes.

regulatory sequence

In the regulation of transcription, a DNA sequence that functions as a binding site for regulatory transcription factor proteins, influence rate of transcription

which of the following is NOT a level at which gene regulation occurs in bacteria?

RNA modification

alternative splicing

The splicing of pre-mRNA in more than one way to create two or more different polypeptides from the same gene

operator (lac O)

a DNA sequence in bacteria that is recognized by activator or repressor proteins that regulate the level of gene transcription

ATP-dependent chromatin-remodeling complexes

a collection of proteins that alters chromatin structure

histone variant

a histone protein that has a slightly different amino acid sequence from the standard histone proteins.

enhancers

a regulatory elements in eukaryotes that increases the rate of transcription when bound by an activator protein

The trp operon is considered___ operon because the protein-enconding genes necessary for tryptophan synthesis are not expressed when the level of tryptophan in the cell is high.

a repressible

lac repressor

a repressor protein that regulates the lac operon

iron regulatory element (IRE)

a response element within the ferritin mRNA to which the iron regulatory protein binds

what is the biological advantage of alternative splicing?

allows a single gnee to encode two or more polypeptids . This enables organisms to have smaller genomes, which are more efficeint and easier to package into a cell

_______ refers to the process that allows a single type of pre-mRNA to give rise to multiple types of mRNAs due to different patterns of intron and exon removal

alternative splicing

in bacteria, the unit of DNA that contains multiple genes under the control of a single promoter is called____. The mRNA produced from this unit is referred to as ___mRNA a. an operator, a polycistronic b. a template, a structural c. an operon, a polycistronic d. an operon, a monocistronic e. a template, a monocistronic

c. an operon, a polycistronic

When an activator interacts with mediator, how does this affect the function of RNA polymerase?

causes RNA polymerase to proceed to the elongation stage of transcription

open conformation

chromatin that can be transcribed into RNA

closed conformation

chromatin that cannot be transcribed into RNA

genes that are expressed at all times at relatively constant levels are known as ______ genes

constitutive

regulatory elements that function to increase transcription levels in eukaryotes are called

enhancers

the iron regulatory protein (IRP) binds to the iron regulatory element (IRE) when iron levels are _____ and _______ translation of ferritin mRNA

low, inhibits

core promoter

refers to the TATA box and the transcriptional start site of a eukaryotic structural gene

operon

set of two or more genes in bacteria that are under the transcriptional control of a single promoter

what are the two opposing effects that histone modifications may have on transcription?

some histone modifications enhance transcription, whereas others inhibit it

preinitiation complex

the assembles structure consisting of RNA polymerase II and transcription factors (GTFs) at the TATA box prior to trasncription of eukaryotic protein-encoding genes

histone code hypothesis

the idea that the pattern of histone modification is recognized by proteins and this plays a role in the expression of eukaryotic genes

combinatorial control

the phenomenon whereby a combination of many factors determines the expression of any given gene

positive control

transcription regulation by activator proteins

negative control

transcription regulation by repressor proteins

CAP site

1/2 regulatory sites near the lac promoter; this site is a DNA sequence recognized by caltabolite activator protein (CAP)

TATA box

1/3 ft found in promoters of many protein-encoding genes in eukaryotes; the others are the transcriptional start site and regulatory elements

what is the difference between inducible and repressible operon? Give an example of each.

In an inducible operon, the presence of a small effector molecule causes transcription to occur. An example is the lac operon, which is nduced with allolactose, In repressible operons, a small effector molecule inhibits trasncription. An example is the trp operon, which is repressed by high levels of tryptophan. The effects of these small molecules are mediated through regulatory proteins that bind to the DNA

chromatin

The complex of DNA and proteins that makes up eukaryotic chromosomes.

mediator

a large protein complex that plays a role in initiating transcription at the core promoter of protein-encoding genes in eukaryotes

basal transcription

a low level of transcription resulting from just the core promoter's action.

small effector molecules

a molecule that affects gene transcription by binding to a regulatory transcription factor, causing a conformational change in that protein

DNA methylation

a process in which methyl groups are attached to cytosines in DNA

methyl-CpG-binding proteins

a protein that binds methylated DNA sequences and inhibits transcription

coactivator

a protein that increases the rate of transcription but does not directly bind to the DNA itself

regulatory transcription factors

a proteins that binds to DNA, usually in the vicinity of a promoter, and affects the rate of transcription of one or more nearby genes

corepressor

a small effector molecule that binds to a repressor protein, thereby causing the repressor protein to bind to DNA and inhibit transcription

histone acetyltransferase

an enzyme that attached acetyl groups to the amino terminal tails of histone proteins

DNA methyltransferase

an enzyme that attaches methyl groups to bases in DNA

polycistronic mRNA

an mRNA that contains the coding sequences for two or more protein-encoding genes

lac operon

an operon in the genome of E. coli that contains the genes for the proteins that allow the bacterium to metabolize lactose

trp operon

an operon of E. Coli that encodes enzymes requires to make the amino acid tryptophan, a building block of cellular proteins.

the presence of _______ in a bacterium's environment prevents CAP from binding to the DNA, resulting in _________ in transcription of the lac operon

glucose, a decrease

catabolite repression

in bacteria, a process whereby transcriptional regulation is influenced by the presence of glucose

Nucleosome-free region (NFR)

in eukaryotes, a site in the chromatin in which the DNA is not wrapped around histone proteins to form nucleosomes

What are the advantages of having both an activator and a reperssor protein?

in the case of bacterial metabolism sugars, the reprressor keeps the lac operon turned off unless lactose is present in the environment. The activator allows the bacterium to choose between glucose and lactose

cell differentiation

process by which cells become specialized into particular types

For the lac operon, what would be the expected effects of a mutation in the operator site that prevented the binding of the repressor protein? a. the operon would always be tured on. b. the operon would always be turned off. c. the operon would always be turned on,except when glucose is present. d. the operon would be turned on only in the presence of lactose. e. the operon would be turned on only in the presence of lactose and the absence of glucose.

the operon would always be turned on, except when glucose is present

transcriptional start site

the site in a eukaryotic promoter where transcription begins.

silencers

a regulatory element in eukaryotes that prevents transcription of a given gene when buond by a repressor protein

inducer

a small effector molecule that increases the rate of transcription of a gene

repressors

a transcription factor that binds to DNA and inhibits transcription

activators

a trasncription factor that binds to DNA and increases the rate of transcription

repressible operon

a type of operon for which a small effector molecule inhibits transcription

inducible operon

a type of operon for which the presence of a small effector molecule causes transcription to increase

Transcriptional regulation often involved a regulatory protein that binds to a segment of DNA and small effector molecule that binds to the regulatory protein. Does each of the following terms apply to a regulatory protein, a segment of DNA, or a small effector molecule? A. repressor B. inducer C. operator D. corepressor E. activator

a. regulatory protein b. small effector molecule c. segment of DNA d. small effector molecule e. regulatory protein

catabolite activator protein (CAP)

activator protein for the lac operon

transcription factors that bind to DNA and stimulate transcription are

activators