INTRGEN - Essentials of Genetics Chapter 15

inducible

produce certain enzymes only when specific chemical substrates are present
production is "on" when inducer is present
OFF AND WE'RE TURNING IT ON

inducer

reflecting the old of the substrate

constitutive

enzymes that are produced continuously, regardless of the chemical makeup of the environment

repressible

the presence of a specific molecule inhibits gene expression
production is "off" when a product is present

negative control

gene expression occurs unless it is shut off by some form of a regulator molecule

positive control

transcription only occurs if a regular molecule directly stimulates RNA production

cis-acting site

a regulatory region on the same DNA molecule located upstream of the gene cluster it controls
-bister

trans-acting molecules

molecules that bind to cis-acting sites that control transcription of the gene cluster

lac operon

three genes and an adjacent regulatory region that function together to provide a rapid response to the presence or absence of lactose
-Negative inducible operon

structural genes

genes encoding for the primary structure of the enzyems

permease

an enzyme that facilitates the entry of lactose into the bacterial cell

transacetylase

an enzyme that may be involved in the removal of toxic by-products of lactose digestion from the cell

gratuitous inducers

behave like natural inducers, but they do not serve as substrates for the enzymes that are subsequently synthesized

constitutive mutants

in cells that contain these, enzymes are produced regardless of the presence or absence of lactose

repressor gene

lack of it that causes gene regulation to be lost

operator region

adjacent sequences of DNA in the lac operon

operon model

a group of genes is regulated and expressed together as a unit

allosteric

reversible interacts with another molecule, causing both a conformational change in the repressor's three-dimentional shaped a change in its chemical activity

repressor

inhibits the action of RNA polymerase, effectively repressing the transcription of structural genes by binding to the DNA sequence of the operon region

regulation of repressor is

under negative control because transcription only occurs when the repressor fails to bind to the operator region

Jacob and Monod

operon theory

B-galactosidase

cleave lactose into is components, glucose and galactose

catabolite-activating protein (CAP)

helps activate expression of the lac operon, but is able to inhibit expression when glucose is present

catabolite repression

inhibid expression when glucose is present

cyclic adenosine monophosphate (cAMP)

CAP must be bound to it in order for CAP to bind to the lac operon promoter

adenyl cyclase

catalyzes the conversion of ATP to cAMP

role of glucose in catabolite repression

inhibit the activity of adenyl cyclase, causing a decline in the level of cAMP in the cell. Cap can then not form the camp-cap complex that is essential to the positive control of transcription of the lac operon

CAP exerts

positive control over lac gene expression by interacting with RNA polymerase at the lac promoter and by responding to the levels of cyclic AMP in the bacterial cell

corepressor

participates in repression

lac operon is

inducible

trp operon is

repressible-- in the presence of tryptophan, the repressor binds to the regulatory region of the trip operon and represses transcription initiation

attenuation

when repressed, initiation of transcription still occurs at a low level., but is subsequently terminated at a point about 140 nucleotides along the transcript
-further diminishes the expression of the operon

attenuator

the site involved in attenuation is located 115 to 140 nucleotides into the leader sequence

terminator

mRNA folds into hairpins and acts as a terminator structure, and transcription is almost always terminated prematurely, just beyond the attenuator

antiterminator hairpin

transcription proceeds past this if tryptophan is scarce, and the entire mRNA is subsequently produced

riboswitches

mRNA sequences (or elements) present in the 5'-untranslated region (5'UTR) upstream from the coding sequences. Capable of binding with small molecule ligands, such as metabolites, whose synthesis or activity is controlled by the genes encoded by the mRNA

Two important domains within a riboswitch

ligand binding site and the expression platform, which is capable of forming the terminator

attenuation and riboswitches regulate gene expression by

introducing alterations to mRNA secondary structure, leading to premature termination of transcription

eukaryotic gene regulation

regulate their growth and division to occur at appropriate places in the body and at appropriate times during development

eukaryotic cells contain a ___ amount of DNA than do prokaryotes

greater; can modify the structural organization to influence gene expression

Pro vs. Euk mRNA

Euk- wide range of half lives
Pro- decay quickly

In eukaryotes, translation rates

can be modulated, as well as the way proteins are processed, modified, and degraded

RNA polymerase __ has the most complex and diverse mechanisms

II

Two structural features of eukaryotic genes distinguish them from the genes of prokaryotes

1. eukaryotic genes are situated on chromosomes that occupy a distinct location within the cell--the nucleus
2. eukaryotic DNA is combined with histones and nonhistone proteins to form chromatin--the compactness of these chromatin structures is inhibitory to many processes, including transcription, replication, and DNA repair

chromosome territory

a discrete domain that each chromosome occupies and stays separate from others

interchromosomal domains

channels between chromosomes that contain little or no DNA

transcription factory

nuclear sites at which most RNA polymerase II transcription occurs. Contain the majority of active RNA polymerase and other transcription facotrs

chromatin can be modified in three ways

1. changes in the nucleosome composition that can affect gene transcription
2. histone modification such as acetylation, phosphorylation, and methylation
3. the repositioning or removal of nucleosomes on DNA, brought about by chromatin remodeling complexes

DNA methylation

the addition or removal of methyl groups to or from bases in DNA
-most often involves cytosine

evidence for methylation

-large transcriptionally inert regions of the genome, such as the inactivated X chromosome in mammalian species, are often heavily methylated
-methylation patterns are tissue specific and, once established, are heritable for all cells of that tissue

as in prokaryotes, eukaryotic transcription is controlled by

trans-acting regulatory proteins that bind to specific cis-acting sites located in and around eukaryotic genes

cis acting sites

do not, by themselves, regulate gene transcription, they are essential because they position regulatory proteins in regions where those proteins can act to stimulate or repress transcription of the associated gene

promoter

region of DNA that binds one or more proteins that regulate transcription initiation
-located immediately adjacent to the genes they regulate
-specify where transcription begins and in the direction of transcription along the DNA

promoter elements

within the promoters
-short nucleotide sequences that bind specific regulatory factors

two subcategories within eukaryotic promoters

core and proximal

core promoters

determine the accurate initiation of transcription by RNA polymerase II

Proximal promoter elements

this that modulate the efficiency of basal levels of transcription

focused promoters

specify transcription initiation at a single specific nucleotide
-usually associated with genes whose transcription levels are highly regulated

dispersed promoters

direct initiation from a number of weak transcription start sites located over a 50- to 100- nucleotide region
-associated with genes that are transcribed constitutively

enhancers

cis regulators because they function when adjacent to the structural genes they regulate
-can be located on either side of gene, at some distance from, or even within the gene
-responsible for time and tissue specific gene expression

silencer

another type of cis-acting transcription regulatory element that represses the level of transcription initiation
-act in tissue- or temporal-specific ways to control gene expression

transcription factors

eukaryotic promotors, enhancers, and silencers that influence transcription initiation by acting as binding sites for transcription regulatory proteins
-bind to cis-acting regulatory sites within or adjacent to a gene promoter

activators

increase the levels of transcription initiation

repressors

reduce transcription levels

general transcription factors

needed to initiate both basal-level and enhanced levels of transcription. assemble at the promoter in a specific order

pre-initiation complex

formed from general transcription factors assembling at the promoter and provides a platform for RNA polymerase to recognize and bind to the promoter

Transition factors act by

enhancing or repressing the association of general transcription factors at the promoter
may also assist in chromatin remodeling and the release of RNA polymerase II from the promoter

post transcriptional regulation

modification of eukaryotic nuclear RNA transcripts prior to translation

alternative splicing

can generate different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins with similar or different functions

proteome

the numbers of proteins an organism can make

spliceopathies

defects in the regulation of RNA splicing

steady-state level

an mRNA's amount in the cell as determined by a combination of the rate at which the gene is transcribed and the rate at which the mRNA is degraded

p53 protein

essential to protect normal cells from the effects of DNA damaged other stresses
-levels low levels under normal conditions

Ubiquitin

a small protein that tags other proteins for degradation by proteolytic enzymes

RNA interference

repressing translation in the cytoplasm and triggering the degradation of mRNAS
-introduction of darn into a cell causes specific degradation of mRNA's containing the same sequence

RNA induced gene silencing

RNA interference AND acting in the nucleus to alter chromatin structure and bring about repression of transcription

two short RNA molecules involved in RNA-induced gene silencing

small interfering RNA and microRNA

constitutive enzymes

always produced

adaptive/ facultative enzymes

made when needed

Positive- _____
Negative- _____

pos- activator
neg- repressor

Job of repressor

stop transcription

transcriptional control

can be negative or positive

catabolic repressor

repress genes required to metabolize other sugars if glucose is present

CAP

Catabolite activator protein; enhances RNA polymerase binding to promoter

Glucose levels regulate

cAMP levels

CAP-cAMP

Binds to DNA and bends it, makes it more accessible

trp operon

repressible-- normally on, must be turned off

Differences in prokaryotic and eukaryotic gene regulation

1. eukaryotic genes are not organized into operons
2. chromatin effects gene expression in euks
3. regulation of gene expression has more layers in euks

Acetylation

of histones "opens" chromatin, allowing transcription

methylation

of histones can change he packing of chromatin, allowing transcription or cause tighter binding--heterochromoatin

methylation of DNA

associated with transcriptionally inactive parts of chromosomes

Two functions of transcriptional activator proteins

1. bind to DNA in regulatory promoter
2. interact with other compounds

Enhancers and silencers

alter transcription at a distant promoter

Insulator

boundary element- limits range of enhancer/ silencer

Multiple response elements

allow for varied expression
response is varied depending on heavy metal concentration

coordinated expression

(ala bacterial operon) can be essential

the amount of mRNA is carefully regulated

1. transcription
2. persistence of mRNA (turnover)

Dicer

recognizes double stranded RNA cuts up

RITS

RNA induced transcriptional silencing

transient thing

momentarily shuts of gene expression