lec 2 gene regulation (rev)

Revising gene requlation for eukaryotes and prokaryotes

gene regulation

level of gene expression can change under different conditions

constitutive

unregulated genes

benefit of regulating genes

proteins will only be expressed when required

describe constitutive genes

1. constant levels of exp

2. for proteins that are continuously necessary

gene regulation is important for

1. metabolism

2. response to environmental stress

3. cell division

gene regulation can happen in

1. transcription

2. translation

3. post translation

Transcriptional regulation

most common way to regulate in bacteria by influencing the initiation of transcription

negativw control

regualtion by repressors

positive control

regulation by activatior

effector molecules

bind to regulatory proteins but not DNA directly

presence of effector molecule increase transcription

increase transcription

termed inducers

function in 2 ways:

1. bind activators and cause them to bind to DNA

2. bind repressors and prevend them from binding to DNA

genes regulated by effectors to increase their expression

inducible

effector may inhibit transcription

1. corepressors bind to repressors and cause them to bind to DNA

2. inhibitors bind to activators and prevent them from binding to DNA

genes inhibited by effector molecules

repressibles

enzyme adaptation

A particular enzyme appears in the cell only after the cell has been exposed to the enzyme’s substrate

Operon

regulatory unit consisting of a few structural genes under the control of one promoter

encodes polycistronic mRNA (2 or more structural genes)

allow the bacteria to regulate a group of genes that encode proteins with common functional goal

Two distinct transcriptional units

1. actual lac operon

   a. DNA elements:

   1) promotor (binds RNA polymerase)

   2) Operator: binds the lac repressor protein

   3) CAP site: binds the catabolite activator protein

   b. structural genes:

   1) lacZ 2) lac y 3)lacA

2. lacl gene

LacZ

encode beta-galactosidase

cleave lactose and lactose analogues

convert lactiose to allolactose(isomer)

LacY

encode lactose permease

membrane protein for the transport of lactose and its analogues

lacA

encodes galactosidase transacetylase

covalently modify lactose and its analogues

unclear functional necessity

;acI gene

not a part of the lac operon

has the i promotor

expressed constitutively at low levels

encodes the lac repressor

lac repressor function as a tetramer

only a small amount of protein is needed to repress the lac operon

The lac operon could be controlled by

1. repressor protein

2. activator protein

Controll by repressor

inducible negative control

lac repressor protein

inducer: allolactose: binds to lac repressor and inactivates it

does not completely inhibit transcription

regulation by an activator protein

catabolite repression

inducible and positive control

cAMP-CAP complex bind to CAP site near promotor and increase transcription

diauxic growth

sequential use of 2 sugars

the small effector molecule in catabollite expression

cyclic AMP

produced from ATP through adenylyl cyclase

bind to CAP

if there is glucose dec cAMP fa rate of transcription decreases

the 3 operator sites for the lac repressor

genetic and crystallographic studies

o1: next to promotor (slightly downstream)

o2: downstream in the lacZ coding region

o3; slightly upstream of the promotor

trp operon

invovlved in the biosynthesis of tryptophan amino acid

trp operon consists of

genes: trpE,D,C,B,A encode the enzymes for the synthesis

genes: trp R,L are important for the regulation of the trp operon

R: trp repressor

L: short peptide called leader peptide, functions in attenuation

Attenuation in trp operon

1. Tryptophan starved: antitermination

   no trp tRNA, and so the leader stop at the codon, allowing transcription to move on

2. Non-starved: Termination

   yes trp so no transcription

Why does attentuation occur in bacteria and not humans

Because transcription and translation are coupled

transcription begins but is terminated before entire mRNA is made

How does attenuation work:

Segment of DNA called attenuator is important for facilitating the termination

in case of trp operon termination after trpL

attenuation inhibits production of more tryptophan

Inducible vs repressible regulation

1. Inducible: operons in catabolism, substances to be broken down or related compounds act as the inducer

2. Repressible: Involved in anabolism, the product is the inhibitor or corepressor

Translational regulation is regulated by ……. in bacterial genes

binding of proteins

a translational regulatory protein recognizes sequences within mRNA

or antisense RNA

if the proteins inhibit translation

translational repressors

how to translational repressors work:

1. bind next to the shine dalgarno sequence and/ or start codon: thus hinder the ribososme from initiating translation

2. bind outside shine-dalgarno/start codon: thus stablize mRNA secondary structure that prevent initiation

antisense RNA

a strand complementary to mRNA

trait of osmoregulation (ability to control the amount of water inside the cell to prevent shrinkage or lysis

ompF (outer membrane protein)

protein in E. coli is important in osmoregulation

predominantly produced at low osmolarity (dec at high osmolarity)

at high osmolarity micF is responsible for inhibiting ompF

micF RNA

doesn’t code for a protein

complementary to ompF mRNA

antisense

at high osmolarity

block translation

Posttranslational regulation

for metabolic enzymes: feedback inhibition

final product of a pathway inhibit an enzyme that acts early in the pathway

covalent modification of protein structure

allosteric enzyme

has catalytic site to bind to the substrate

regulatory site to bind to the final product of the pathway

covalently modify proteins

1. reversible and transient: phosphorylation, acetylation,, methylation

2. irreversible: adding prosthetic groups, sugars or lipids, and proteolytic processing

Riboswitch

transcriptional regulation of thiamin pyrophosphate (TPP)

product binds to its own mRNA to prevent transcription (rho independent transcription termination)

binding of TPP to RNA will occur when present at high levels, causing changes in secondary structures of RNA TPP-bound conformation changes cause termination of transcription for genes in TPP

Translational regulation of TPP

Binding of TPP (ligand) to this mRNA allows the formation of stem-loop that sequesters the Shine-Dalgarno sequence and Translation is blocked