BIOL 1951 Quiz 7

1) regulatory elements 2) TATA box 3) Transcriptional start site

3 common factors common among most promoters for eukaryotic protein-encoding genes

1) Transcription (how much mRNA made) 2) Translation (ability of mRNA to be translated into a protein) 3) Post-translation (protein is controlled after it is synthesized)

3 different levels of gene regulation in bacteria

lacZ, lacY, lacA

3 genes in the Lac Operon

1) RNA Polymerase II 2) General transcription factors (GTFs) 3) Mediator

3 types of proteins that play a role in initiating transcription at the core promoter (TATA box + trascriptional start site)

1) change locations of nucleosomes 2) evict histone octamers from DNA - creating gaps where nucleosomes are not found 3) replace standard histone proteins with histone variants (slightly different AA sequence)

3 ways that ATP-dependent chromatin remodeling complexes change chromatin sturcture

1) Transcription (most common) 2) RNA Modification 3) Translation 4) Post translation

4 levels of gene regulation in eukaryotic cells

1) Influence interactions bt DNA and histones 2) Provide binding sites that are recognized by other proteins

Affects of covalent modifications on histone protein tails

inducible operon

An operon under positive control. It is usually "off" but can be turned "on" via an inducer. Ex = the lac operon

regulatory sequence

Binding site for proteins that influence transcription (regulatory transcription factors)

allolactose

Inducer of the lac operon; structurally similar to lactose; generated by b-galactosidase

DNA methylation

The addition of methyl groups (—CH3) to cytosine bases of DNA after DNA synthesis

1) Conserves energy 2) ensures that genes are expressed in the appropriate cell types and at the correct stage of development

Why is gene regulation necessary?

cis-acting elements

a DNA segment that must be adjacent to to the gene(s) that it regulates

iron regulatory protein (IRP)

a translational regulatory protein that recognizes iron response elements that are found in specific mRNAs. It may inhibit translation or stabilize the mRNA.

lacZ gene

protein encoding gene in the lac operon that encodes B-galactosidase

small effector molecules

with regard to transcription,refers to a molecule that exerts its effects by binding to a regulatory transcription factor,causing a conformational change in the protein.

repressible operon (trp operon)

-repressor is initially inactive -corepressor (tryptophan) binds to the repressor and makes it active

TATA box

A promoter DNA sequence crucial in forming the transcription initiation complex.

polycistronic mRNA

A single molecule of messenger RNA that encodes more than 1 protein that results from a group of genes transcribed as a single unit

cyclic AMP (cAMP)

A small effector molecule formed from ATP that controls CAP

DNA methyltransferase

An enzyme that catalyzes the methylation of DNA by attaching methyl groups to DNA bases (cytosine)

regulatory elements

DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

Catabolite repression of the lac operon

E. coli prefers to use glucose(catabolite) as its carbon source so it represses the lac operon because its is a waster of energy to make product and then use glucose instead

F' factor

F factors that carry genes that were originally found within the bacterial chromosome

DNA methylation

Modification of DNA structure from DNA methyltransferase that typically inhibits the transcription of eukaryotic genes

chromatin

Substance found in eukaryotic chromosomes that consists of DNA tightly coiled around histones

operator

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

transcription factor II D (TFIID)

a GTF that binds to the TATA box that can be repressed or enhanced by the binding of silencers or enhancers

merozygote

a bacterial cell that contains an F' factor

lac operon

a gene system whose operator gene and three structural genes control lactose metabolism in E. coli

CpG islands

a group of CG sequences that may be clustered near a promoter region of a gene. The methylation of the cytosine bases usually inhibits transcription.

basal transcription

a low level of transcription resulting from just the core promoter and no TATA box

lac repressor

a protein that binds to the operator site of the lac operon and inhibits transcription of lacA, lacX, and lacY

CAP site (in lac operon)

a regulatory sequence recognized by an activator

operon

a set of 2 or more genes in bacteria that are under the transcriptional control of a single promoter

Nucleosome-free region (NFR)

a site in the chromatin in which the DNA is not wrapped around histone proteins to form nucleosomes wherein the core promoter is found in active genes

gene regulation

ability of an organism to control the expression on their genes

genome, proteomes

all differentiated cells have the same ____ but different _____

cis-effect

an effect on gene expression due to genetic sequences that are within the same chromosome and often are immediately adjacent to the gene of interest

trans-effect

an effect on gene expression that occurs even though two DNA segments are not physically adjacent to each other. Trans-effects are mediated through by genes that encode regulatory proteins.

galactoside transacetylase

an enzyme that covalently modifies lactose and lactose analogs by attaching an acetyl group (COCH3) to prevent toxic build-up of these proteins in the cytoplasm

histone acetyltransferase

an enzyme that loosens the compaction of chromatin by attaching acetyl groups to histone proteins. Aids in transcription

allolactose

an inducer that binds to the lac repressor to cause a conformational change that prevents the lac repressor from binding to the operator site

open conformation of chromatin

chromatin that can be transcribed into mRNA because it is accessible to GTFs and RNA polymerase II

closed conformation of chromatin

chromatin that cannot be transcribed into mRNA

preinitiation complex

cluster of transcription factors (GTFs) and other proteins that recruit RNA polymerase II at the TATA box

combinational control

combination of many factors determines the expression of any given gene

ATP-dependent chromatin remodeling complexes

complex of proteins that alter chromatin structure by using energy from ATP hydrolysis. This altering of chromatin structure can incr or prevent transcription of DNA into mRNA

cAMP + CAP

complex that binds to CAP site near the lac promoter and causes the DNA to bend in a way that enhances the ability of RNA polymerase to bind to the promoter (positive control)

Mediator

composed of many proteins that bind together to form an elliptically shped complex that partially wraps itself around RNA polymerase II and GTFs to 'mediate' the interactions between the preinitiation complex and regulatory transcription factors

1) genes in eukaryotes almost always regulated individually,not in operons 2) more complexity in eukaryotic gene regulation 3) eukaryotic genes = controlled by many factors (combinational control)

differences between gene regulation in eukaryotes and bacteria

lactose high, glucose high

environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein CAP does not bind to CAP site; inhibits transcription. Bacterium uses glucose

lactose high, glucose low

environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein binding of RNA polymerase to promoter is enhanced by CAP binding. Transcription rate is high.

lactose low, glucose high or low (doesnt matter)

environmental condition that an E. Coli bacterium might experience with regard to glucose and lactose wherein the lac repressor prevents transcription of the lac operon

lactose permease

enzyme in bacterium E. Coli that functions to transport lactose into a cell. Very little of this enzyme is produced if lactose is not available in the environment.

β-Galactosidase

enzyme that catalyzes the breakdown of lactose as well as converts a small amount of lactose into allolactose, a structurally similar sugar

lacI gene

gene adjacent to the lac operon that encodes the lac repressor

transcription

in bacteria, gene regulation most often occurs at the level of ____

catabolite repression

key function of CAP

lacI-

mutant lacI strain that inhibits synthesis of a functional lac repressor and prevents the lac repressor from inhibiting transcription

trp operon

operon in e. coli that encodes enzymes that are required to make the amino acid tryptophan

gene expression

process by which a gene produces its product and the product carries out its function

lacP

promoter of the lac operon that's involved in the transcription of 3 protein-encoding genes

histone code hypothesis

proposes that specific combinations of modifications help determine chromatin configuration and influence transcription

lacA

protein encoding gene in the lac operon that encodes galactoside transacetylase

lacY

protein encoding gene in the lac operon that encodes lactose permease

regulatory transcription factors

proteins that bind to regulatory sequences in the DNA in the vicinity of a promoter and affect the rate of transcription of one or more nearby genes.

methyl-CpG-binding proteins

proteins that change chromatin structure by binding to methylated sequences and recruiting other transcription inhibiting proteins

coactivators

proteins that increase the rate of transcription but do not directly bind to the DNA itself, instead bind to activators and can stimulate the function of the mediator

core promoter

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

alternative splicing

regulated process during gene expression that results in a single gene coding for multiple proteins at different stages of development, different cell types, an/or in response to a change in environmental conditions

Enhancers

regulatory elements that increase the rate of transcription

silencers

regulatory elements that prevent transcription of a given gene

repressors

regulatory transcription factors that bind to the DNA and decrease the rate of transcription (negative control)

activators

regulatory transcription factors that bind to the DNA and increase the rate of transcription (positive control)

inducer

small effector molecule that causes transcription to increase

catabolite activator protein (CAP)

the activator protein for the lac operon- positively controls this operon

histone variants that promote transcription

the nucleosome free region is often flanked by...

cell differentiation

the process by which a cell becomes specialized into particular types (muscle cells, neurons, etc)

repressible

the trp operon is an example of a _____ operon because it is regulated by a repressor protein that's encoded by the trpR gene

repressible operon

transcription is usually on, but can be inhibited (repressed) when a specific small effector molecule binds to a regulatory protein (example tryptophan)

positive control

transcriptional regulation by activator proteins

negative control

transcriptional regulation by repressor proteins

domains

two functional regions on repressors and activators that respond to small effector molecules

1) Repressors 2) activators

types of regulatory transcription factors

allows bacterium to coordinately regulate a group of genes that encode proteins whose functions are used in a common pathway

what is the advantage of having an operon?

allolactose

whether or not the lac repressor bids to the lac operator depends on...