BI210 - Prokaryotic and Eukaryotic Gene Regulation

how do prokaryotes approach sugar and amino acid needs

• if glucose present → used for metabolism

• if no glucose → use other sugars

• if amino acids presents → used in translation

• if no amino acids → synthesized using gene products

what are two main strategies employed by prokaryotes to regulate gene expression at level of transcription

• modify promoter region

  • modify accessibility of promoter to RNA pol

• organization of related genes in efficient units

what are sigma factors

help RNA pol bind to correct promoter and activate it

housekeeping sigma factor

sig. 70

heat stress sigma factor

sig. 32

why would the heat stress sigma factor be important and what types of genes does it tend to upregulate

bacteria activates genes to help it cope w/ high temperatures

what is an operon

transcriptional unit comprised of multiple adjacent genes that are under control of single promoter

what is trp operon used for

encodes machinery to produce tryptophan

what is lac operon used for

encodes machinery to use lactose

what type of operon is the lac operon

negative inducible

when is the lac open active

when there is high lactose

what is an inducer

inactivates repressor

how does glucose concentrations affect lac operon function

low lactose = no enzymes

high lactose = enzymes

why is glucose more vital than lactose

primary sugar energy source for most pro and euk

what is CAP and cAMP and how does it regulate lac operon

prevent cells from breaking down lactose when glucose present

• low glucose = high cAMP

• high glucose = low cAMP

negative control

repressor

positive control

activator

inducible

off until turned on

repressible

on until turned off

6 main targets for eukaryotic gene regulation

• chromatin modifications

• transcriptional initiation

• post-transcriptional processing

• mRNA stability

• translational initiation

• post-translational processing and stability

epigenetics

study of mechanisms for regulating gene activity independent of DNA sequence

acetylation

addition of acetyl group to chemical compound

• HAT

• results in euchromatin

deacetylation

removal of acetyl group from chemical compound

• HDAC

• results in heterochromatin

what amino acid is targeted with acetylation

lysine

how does acetylation result in changes in DNA-histone interactions

weakens interaction between histones and DNA

what is methylation

addition of methyl group to chemical structure

where are methyl groups attached in DNA

cytosine residues @ CpG islands

what are CpG islands and where are they found

CG rich regions found upset of coding regions in promoters

what are DNMTs and what molecule do they use as a methyl donor

catalyze methylation

• use SAM as donor

relationship between methylation and gene expression

results in heterochromatin

how does nutrition affect epigenetics

folic acid and B vitamins important for generating SAM

response elements and where are they found

bind transcription factors

enhancers

promote transcription

silencers

inhibit transcription

transcription factors

facilitate transcription

• help RNA pol find specific promoter activating transcriptional initiation complex

up regulation

more transcription

down regulation

less transcription

what is deadenylation-dependent pathway and how does is degrade mRNA

AU rich sequences in 3’ trigger RNAses to destroy poly A tail

• loss of tail → activation of cap removal enzymes

RNAi

RNA interference

Dicer

enzyme that cuts double stranded RNA segments to yield small siRNA and miRNA mol.

RISC

small siRNA and miRNA mol. interact w/ RISC to destroy RNA

four ways translation is regulation during initiation

• binding of inhibitors to 5’ UTR

  • prevent scanning

• modification to kozak sequence

  • makes recognition and identification of correct start codon difficult

• variations in length of poly A tail

  • longer tail → more activating proteins binding

• incorporation of additional AUG in 5’ UTR

  • complicate identification of correct start codon

how might chemical modifications affect protein function

glycosylation

• attachment of carb group important for cell attachment and signaling

examples of chemical modification that affect protein function

amino acid modification

ubiquitination

proteins marked specifically for destruction w/ ubiquitin

how are ubiquitinated proteins degraded

proteins broken down amid their amino acids recycled by proteosome

N-end rule

amino acid found at end of amino terminus of protein impacts overall stability

what would you expect to happen to protein that had unstable N-end amino acids

targeted for degradation

• FLWY