Lecture 8 - Regulation of Gene Expression Flashcards
Levels of gene expression control (3)
- Before transcription starts
- After transcription/before translation
- Post translationally
Transcriptional regulation has __ regulatory elements.
two
- Promoter - region upstream of a gene where RNA polymerase binds and regulation of gene expression occurs.
- Enhancer - sequence of DNA that positively regulates gene expression upon binding of an activator from the distance.
Transcriptional regulation involves __ regulatory proteins.
two
- Activator - protein that binds to a regulatory element to increase gene expression
- Inhibitor - protein that binds to a regulatory element to decrease gene expression.
There are __ types of transcriptional regulation.
two
- Negative regulation - a repressor protein prevents transcription.
- Positive regulation - an activator protein stimulates transcription.
Transcriptional regulation: Regulation of a gene depends on the recruitment/inhibition of ___ _______ to the ____. Prokaryotes and Eukaryotes differ by…
RNA polymerase; promoter.
Prokaryotes: sigma factor binds to -10 and -35 sites
-10: 5’-TATAAT-3’
-35: 5’-TTGACAT-3’
Eukaryotes: General Transcription Factor II D binds to TATA box.
E. coli prefers ___ as a source of energy, but it can also use ___. It regulates genes encoding for proteins involved in the digestion of these energy sources. ___ _____ is used to regulate digestion of lactose.
glucose; lactose
lac operon
Operon
a set of genes that are regulated under the same regulatory elements.
Lac Operon has ___ genes that code for ___ proteins
three
- B-galactoside permease: carrier protein that moves lactose into the cell
- B-galactosidase: enzyme that hydrolyses lactose
- B-galactoside transacetylase: transfers acetyl groups from acetyl CoA to certain B-galactosides.
Lac Operon is an example of _____ regulation.
Negative.
- expression of the lac operon is off in the absence of lactose.
- the lac repressor is a protein that binds to the Lac operon promoter and inhibits its expression.
- when lactose is absent, the lac repressor is active
- when lactose is present, the lac repressor is inactive.
When lactose is present, _____ is produced. Binding of _____ to the ___ ______ induces a _______ _____ that _____ binding to the promoter.
allolactose
allolactose; lac repressor; conformation change; inhibits
Lac operon can also be an example of _____ regulation.
positive
- glucose is still E. coli’s preferred energy source.
- lac operon has a “weak” promoter. The sigma factor binds poorly to the -10 and -35.
- low glucose environment produces an accumulation of cAMP
- cAMP-receptor protein CRP (catabolite activator protein) requires binding of cAMP to be able to bind to the promoter.
- CAP (cAMP-CRP complex) is an activator.
Binding of ____ to promoter will recruit ___ _______ and therefore ________ transcription.
CAP; RNA polymerase; enhance
Regulation of trp operon: Trp operon codes for enzymes that catalyze the synthesis of ______ (2)
tryptophan
- activated when trp is low
- high levels of trp will induce the trp to bind to and activate repressor.
There are ___ levels of gene regulation in eukaryotes
six
- transcriptional level
- DNA packing - histone modifications
- DNA methylation
- Post transcriptional regulation
- Translational level
- Post translational regulation
Eukaryotic transcriptional regulation: ___ ________ __ can only bind to the promoter after _____ _________ _____ have assembled on the _________. ____ binds to the ______ box; then other factors bind to form an _______ ______. Assembly of ___ ______ will _____ transcription.
RNA polymerase II; general transcription factors; chromosome.
TFIID; TATA; initiation complex.
core complex; initiate
There are ___ regulatory elements for eukaryotic transcriptional regulation.
two
- Enhancers: regulatory sequences where transcription factors bind to activate transcription or increase rate of transcription.
- Silencers: sequence of DNA where transcription factors bind to repress transcription.
Enhancers/ DNA looping (2)
- enhancer is a regulatory element that act at a distance
- DNA has the capacity to bend >150 bp.
- this is true for both euks and proks
- an activator can bind and recruit the RNA polymerase.
If genes have common regulatory sequences, they can be regulated by the ___ transcription factors
same
DNA packing: ____ modifications
histone
- eukaryotic cells have their DNA packed by histones which are proteins that help with DNA packing.
Histones (4)
- H2A, H2B, H3 and H4 are known as the core histones
- Nucleosomes form when two of each of the core histones come together in an octamer where DNA can bind.
- Ionic interactions hold the nucleosomes together
- negative charge of phosphates (DNA) interacts with positive charge of amino acids on the histones
- DNA packing is determined by interactions between histones and the DNA
Chromatin remodeling
RNA polymerase needs to be able to access the genes to be able to transcribe them
- RNA polymerase and transcriptional factors cannot transcribe areas of packed DNA.
Histone modifications - acetylation (2)
- histone acetyltransferases (HATs) add an acetyl group at the end of a conserved Lys
- acetylation of histones disturbs histone-DNA interaction opening nucleosomes which allow accessibility of DNA. Histone acetylation correlates with active genes.
Histones can also be modified by ___ and ____
methylation and phosphorylation
methylation: inactivates genes
phosphorylation: effects depend on which amino acids are involved.
DNA methylation
- catalyzed by DNA methyltransferase
- usually occurs in regions rich with C and G doublets (CpG islands): high methylation of CpG islands correlates with regions of low transcription (gene silencing)
DNA packing: two types of chromatin
- euchromatin - diffuse, light-straining; contains DNA that is transcribed.
- heterochromatin - condensed, dark-staining; contains genes not transcribed.
Imprinting (2)
- in mammals, eggs and sperm develop different methylation patterns
- for about 200 genes, offspring inherit and inactive (methylated) copy and an activated (demethylated) one.
X-inactivation (4)
- males (XY) and females (XX) contain different numbers of X-linked genes, yet for most genes transcription rates are similar.
- early in development, one of the X chromosomes in females is inactivated. Which X chromosome gets inactivated is random in each cell.
- RNA transcribed from Xist (X inactivation-specific transcript) binds to the chromosome, spreading the inactivation.
- The DNA is heavily methylated, and unavailable for transcription, except for the Xist gene.
Post transcriptional regulation: Alternative Splicing (3)
- different mRNAs can be made from the same gene.
- there are many more human mRNAs than there are coding genes.
- specific sequences identify the presence of an intron
- snRNPs bind to these sequences and recruit components of the spliceosome
- by changing the capacity of snRNPs to recognize an intron, you can alter gene expression.
Post transcriptional regulation: MicroRNAs (miRNA)
- microRNAs are small RNAs (~22 nucleotides long) that produce a hairpin
- they can target mRNA for degradation or translational repression
- miRNA’s target complementary sequences
- miRNAs have many targets as complementarity does not have to be perfect.
Translation level: Repression
- miRNAs can inhibit translation
- GTP cap on 5’ end of mRNA can be modified since euks need 5’-cap for translational initiation
- repressor proteins can block translation directly
Translational level: Repression by ______
Riboswitch
- translational repressor proteins can bind to noncoding regions of mRNA and block translation by preventing it from binding to a ribosome.
Post translational regulation: degradation & modification
Proteins can be targeted for destruction when ______ attaches to it and attracts other ______, forming a ______ chain.
This ______ protein is recognized by the ________ and _____.
ubiquitin; ubiquitins; polyubiquitin
polyubiquitin; proteasome; degraded.
