Ch. 14 - Gene regulation Flashcards
CAP
- catabolite activator protein
- binds to DNA to activate gene transcription
gene regulation
- the ability of calls to control their level of gene expression
- ensures that proteins are produced at the right time and in the right amounts
- saves energy - only produces when needed
constitutive genes
- “housekeeping genes”
- unregulated and have essentially constant levels of expression
- encodes proteins that are constantly required for the survival of an organism (often metabolic enzymes)
gene regulation in eukaryotes
- necessary for cell differentiation
- organism’s genomes are all the same but proteomes are different
- different genes expressed and in different amounts
prokaryotic gene regulation
- responds to changes in the environment
- ex: when lactose is present, two proteins are made
1. lactose permease - transports lactose into the cell
2. beta-galactosidase - breaks down lactose
developmental gene regulation in mammals
ex: hemoglobin in fetal vs adult humans
- fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin
- helps fetus to harvest oxygen from maternal blood
- promotor should remain inactive once out of utero
where gene regulation occurs in bacteria
- most commonly occurs at the level of transcription
- can control rate of translation
- also regulated at protein/post-translation level
where gene regulation occurs in Eukaryotes
- transcriptional most common
- RNA processing (not in bacteria)
- translational
- post-translation
regulatory transcription factors
- protein that binds to DNA, usually in the vicinity of a promoter
- affects the rate of transcription of one or more nearby genes
- in both prokaryotes and eukaryotes
regulatory sequence
- sequence of DNA that acts as a binding site for a regulatory protein
- influences rate of transcription
repressors
- transcription factors that inhibit transcription
- negative control
- when downstream from the promoter, it prevents the RNA polymerase from binding
activators
- transcription factors that increase the rate of transcription
- positive control
- changes the shape of DNA so that its more accessible by the RNA polymerase
small effector molecules
- molecule that affects gene transcription by binding to a regulatory transcription factor
- causes conformational change in TF, causing it to either bind or release DNA
two domains of regulatory transcription factors that respond to small effector molecules
- site where protein binds to DNA
- site specifically for the small effector molecule
polycistronic mRNA
- mRNA that contains coding sequences for two or more proteins
- allows coordinated regulation of a group of genes with a common function
- operons are polycistronic
lac operon
operon in genome of E.coli that contains the genes necessary to metabolize lactose
components of the lac operon
- lacP
- 3 structural genes
- lacZ
- lacY
- lacA
- lacO
- CAP site
lacP
- promoter region of the lac operon
lacZ
- codes for the protein beta-galactosidase
- converts a small percentage of lactose into allolactose
lacY
- codes for lactose permease
- membrane protein required for the transport of lactose into the cytoplasm
lacA
- codes for galactoside transacetylase
- transacetylase covalently modifies lactose and lactose analogues by attaching an acetyl group
- prevents toxic buildup
lacO
- operator
- regulatory site/sequence that provides binding site for repressor protein
CAP site
- regulatory site that binds the activator protein
lacI gene
- codes for the lac repressor protein
- constitutively expressed
- not considered part of the lac operon
CAP
- catabolite activator protein
- activator protein for the lac operon
what happens at the lac operon when lactose is absent
- lac repressor protein binds to the nucleotides of the lac operator site
- prevents RNA polymerase from transcribing lacZ, Y, and A
- polymerase can bind to the promoter region, but cant get past the operator
is the lac operon inducible or repressible?
inducible
- its turned on in the presence of allolactose
what happens at the lac operon when lactose is present
- allolactose binds to the lac repressor, removing it from the DNA
- induces transcription of the lac operon
is the lac operon under negative or positive control?
both
is the lac repressor cis- or tans-effect
trans-effect
trans-effect
- form of genetic regulation that can occur even though two DNA segments are not physically adjacent
cis-effect
- DNA segment that must be adjacent to the gene(s) that it regulates
role of cAMp in lac operon
- cAMP binds to CAP, which attaches to the CAP site and induces translation of the lac operon
- bends the DNA in a way that helps RNA polymerase bind
positive control of lac operon
cAMP and CAP bind at the CAP site to promote binding of RNA polymerase
- positive because it enhances the binding of RNA polymerase
relationship between glucose and cAMP
- inverse relationship
- high glucose = low cAMP
- low glucose = high cAMP
- glucose inhibits the production of cAMP
Lactose operon in high lactose and high glucose
- operon is shut off
- glucose uptake causes cAMP levels to drop
- CAP does not activate transcription
- bacterium uses one sugar at a time (glucose) to conserve energy
lac operon when lactose is high and glucose is low
- operon is turned on
- allolactose levels rise and prevent the lac repressor from binding to the operator
- Cap is bound to CAP site
- bacterium uses lactose
lac operon in low lactose (regardless of glucose)
- operon is shut off
- in low lactose, there is no allolactose so lac repressor prevents transcription
trp operon
- operon in E.coli that encodes enzymes require to make the amino acid tryptophan
- tryptophan acts as a small repressor molecule/corepressor
- when tryptophan is present, it can bind to its repressor to stop transcription
- without tryptophan, repressor doesn’t bind and more tryptophan can be synthesized
trpR gene
- encodes repressor protein that regulates the trp operon
tryptophan
- small repressor molecule/corepressor that attaches to repressor to inhibit the trpR gene
lac vs trp repressors
- lac repressor binds to its operator in the absence of its small effector molecule and trp binds in the presence
- lac is inducible (allolactose induces transcription)
- trp is repressible (tryptophan represses transcription)
difference in eukaryotic transcription vs. prokaryotic
similarities:
- both have activator and repressor proteins that influence the ability of RNA polymerase to initiate transcription
- both have small effector molecules for regulation
differences:
- eukaryotic genes always organized individually
- regulation of eukaryotes is more intricate
core promoter
- TATA box and transcriptional start site of a eukaryotic protein-encoding gene
regulatory element
- DNA sequence in eukaryotes that is recognized by regularity transcription factors and regulates the expression of genes
- silenvers and enhancers
- where the enhancers and repressors bind
TATA box
- found in the promoter of protein-encoding genes
- only in eukaryotes
- usually 25 bp upstreams from a transcriptional start site
- determines the precise starting point for transcription
transcriptional start site
- site in a eukaryotic promoter where transcription begins
three main parts of the promoter region of eukaryotic protein-encoding genes
- regulatory elements
- TATA box
- transcriptional start site
three proteins that mediate transcription
- RNA polymerase II
- 5 different general transcription factors (GTFs)
- mediator
mediator complex
- large protein complex that plays a role in initiating transcription at the core promoter
- can change how the polymerase interacts with GTFs, controlling the rate of transcription
- mediates interactions with activators and repressors that bind to enhancers or silencers
what two molecules must be at the core promoter before transcription can be initiated
GTFs and RNA polymerase II
pre initiation complex
- assembled GTFs and RNA polymerase II at the TATA box
- form basal transcription apparatus
transcriptional regulation
- activator and repressor proteins regulate the transcription of a nearby gene
- bind to enhancer and silencer elements (sequences)
- some regulatory elements are thousands of nucleotides away from the coding elements (bend the DNA)
effect of chromatin packing on gene expression
- transcription difficult or impossible in heterochromatin (closed)
- euchromatin allows easy access (open conformation)
three changes to chromatin structure from ATP-dependent chromatin-remodeling complex
- the relative positions of nucleosomes changes
- histone octamers are removed, leaving gaps where nucleosomes are not found
- change in the composition of nucleosomes by replacing histones with histone variants
histone acetyltransferase
- enzyme that attaches acetyl groups to histone proteins so they don’t bind as tightly
- aids in transcription
histone code
- different amino acids in the amino terminal tails of histone proteins are subject to several types of covalent modification
- common targets for modification because it influences transcription
- pattern of modifications affects the degree of chromatin compaction
DNA methylation
- DNA methylase attaches methyl groups
- usually inhibits translation
- common in some eukaryotes
- methylate CpG islands
- closes conformation, or prevents activator from binding to inhibit translation
when is gene expression most commonly regulated in eukaryotes
- transcription
alternative splicing (general)
- increases proteome size without increasing genome
- order of exons is maintained, so products will be similar
- increases biological complexity
Iron regulatory protein (IRP)
- binds to ferritin mRNA to prevent production of ferritin when iron levels are low
- binds to the IRE (iron regulatory element)
- when iron levels are high, iron can bind to IRP to release it from the IRE, allowing the production of ferritin
combinatorial control
- the combination of many factors determines the expression of a given gene
ex: - one or more activators or repressors may affect the ability of RNA polymerase to initiate transcription
- regulatory transcription factors may be modulated in several ways
- compaction of chromatin, DNA methylation
modulation
- small effector molecules, protein-protein interactions, and covalent modifications can modulate activators and repressors
