gene regulation

Big theme: Gene expression is regulated

not all geens are expressed at the same time

constitutive genes are always expressed- always on

But many important genes are not always expressed —> related to energetics

prokaryotic gene regulation

Regulation can happen during transcription initiation

Lac operon model

found in ecoli- gut bacteria→ human intestine

adjusts gene expression based on diet

Human drinks milk→ E.coli digests lactose

Induction

turning on gene expression

inducer

compund that stimulates gene expression

inducible gene

gene activated by inducer- default state is off

turned on when needed

contrasts with constitutive genes

operon

complex of dna consisting of

multiple elements

groups of genes with associated/ related functions

associated regulatory dna sequences

only found in prokaryotes (w/ very few exceptions)

An operon is a group of functionally related genes, along with regulatory DNA sequences, that are controlled together and are commonly found in prokaryotes.

Exp: Lac operon

Contains:

promoter- rna polymerase binding site, not transcribed

operator- on/ off switch sequence for gene expression

3 genes: lacz, lacy, laca → dont need to know these

negative regulation of lec operon

governed by the presence of absence of → inducible

no lactose→ negative regulation is ACTIVE, operon is off, no gene expression

lactose is present→ operon is induced, negative regulation is INACTIVE

when off genes are on

involves repressor

repressor

repressor gene codes for repressor protein- down regulates gene expression when active

constitutive expression

not apart of operon

easier explanation: when bound to the operator, it prevents or reduces transcription of the structural genes-> not part of operon but regulates.

it isconstitutively expressed, meaning it continuously produces repressor proteins that regulate gene expression.

Lac repressor activity No lactose scenario

repressor binds operator

The RNA polymerase can bind to the promotor, but can not transcribe genes bc repressor is preventing operator

This prevents the cell from wasting energy making proteins it doesn't currently need.

Lac repressor activity lactose available scenario

Lactose enters the cell and is converted to allolactose (lactose isomer)

allolactose is the inducer (cmpd stim gene expression)

allolactose induces the lac operon by inactivating pressor protein→ changes shape of repressor

Binds 2nd site on repressor protein- inactivates repressor→ can no longer bind operator

Result:

LOW levels of lac expression

1 long mrna w/ all 3 genes, each with their own start and stop codons are being transcribed → eventually translated as 3 sep polypeptides

Prokaryotes have no nucleus and transcription typically occurs in the nucleus then the cytoplasm so the process becomes simultaneous. even though all three genes are on ONE mRNA, they each have their own translation initiation and termination signals. Therefore, the ribosome can translate the three coding regions into three separate proteins.

Positive regulation of lac operon

Regulation by activator that binds DNA to stimulate transcription

HIGH expression when active

responds to the presence or absence of glucose

Ecoli prefers glucose over lactose so when both are present, ecoli will use the glucose first but in the scenario glucose isnt present, it settles for lactose

Lac promoter (binding site) is inefficient

It has a low affinity for RNApolymerase

Solution? Catabolite activator protein (CAP)

CAP increases affinity of promoter for RNA polymerase

CAP is inactive alone→ active when bound to cyclic acid (CAMP)

CAMP- indicates if we are out of glucose or not

cAMP levels are inversely related to glucose availability.

In general, cAMP should be low

Glucose availability	cAMP levels
High glucose	Low cAMP
Low glucose	High cAMP

How CAP cAMP works

Low glucose-cAMP increases

cAMP binds to CAP

CAP-cAMP binds CAP binding site in lac promoter (next to rna poly bonding site)

Bends double helix and increases RNA polymerase binding

summary

1. Negative control = repressor

Negative control means a protein (the repressor) blocks transcription.

• Absence of lactose: Repressor is active and binds the operator → transcription is blocked → operon OFF.

• Presence of lactose: Allolactose binds the repressor, making it inactive → transcription can occur.

So: Negative control represses gene expression when lactose is absent.

2. Positive control = CAP-cAMP

Positive control means a protein helps increase transcription.

• Presence of glucose: cAMP is low → CAP is inactive → little activation of transcription.

• Absence of glucose: cAMP is high → binds CAP → CAP-cAMP helps RNA polymerase bind → increased transcription.

So: Positive control upregulates gene expression when glucose is absent.

Lactose	Glucose	lac operon expression
Absent	Present	OFF
Absent	Absent	OFF
Present	Present	LOW
Present	Absent	HIGH

eukaryotic gene regulation

Every level is regulated (unlike prokaryotes)

Regulation of chromatin structure

If dna is loosely packed, genes can be active → euchromatin

if densely packed, no gene expression→ heterochromatin

Modified via DNA methylaton → condenses→ causes gene expression to decrease

regulation of transcription initiation

Generally more complex than prokaryotes

involves DNA sequences and transcription factors→ proteins that bind dna

promote or inhibit transcription initiation

Post transcriptional regulation

length of poly a tail affects level of translation

alternative splicing: diff polypeptides from same gene via inclusion/exclusion of exons

post transitional regulation

polypeptides processed and modified→ final protein

must be folded correctly

chemical modifications affect level of activity

Sometimes a protein is made, but it isn't functional yet. The cell needs to modify it to activate it or change how it works→ “batteries not included”