Chapter 21 Biochem - Prokaryotic transcription

Gene

the basic physical and functional unit of heredity.

what are chromatins made of

Euchromatin (light color, active genes (being transcribed)

Heterochromatin (dark color, inactive genes)

What is chromatin

DNA plus protein

Histone

The protein that DNA wraps around when being compressed

Nucleosome

Histone proteins + DNA

Linker DNA

between nucleosomes, more vulnerable to degradation.

What does the write function do on a histone tail

adds modification

What does the erase function do on a histone tail

removes modification

What does the read function do on a histone tail

binds to modification to

Three most common modifiers

Acetylation

Methylation

Phosphorylation

Histone Acetylation

An acetyl group is added to a lysine amino acid

in the histone, neutralizing its positive charge. Reduces the negative DNA’s affinity for the

histone. Compacting the DNA

is Histone Acetylation on active or inactive

active

Acetyl groups are written by

Histone Acetyl Transferases

Acetyl groups are erased by

Histone DeACetylases

Acetyl reader

bromodomain

Histone Methylation

A methyl group is added to an arginine or lysine amino

acid in the histone

is Histone Methylation work on active or inactive dna

Context dependent

Methyl groups are written by

Histone Methyl

Transferases

Methyl groups are erased by

Histone DeMethylases

Methyl reader domain

chromodomain

Histone Phosphorylation

A phosphate group is added to a serine, threonine, or tyrosine amino acid in the histone. Opens up the DNA by making it more negatively charged. Used for gene repair

is Histone Phosphorylation on active or inactive DNA

active

Phosphate groups are added by

Histone Kinases

Phosphate groups are removed by

Histone Phosphatases

Phosphate reader domain

14-3-3 domain

DNA Methylation

Adds a methyl group to cytosine to deactivate genes

is DNA Methylation active or inactive?

inactive

Promoter

Site where the RNA polymerase and other transcription factors bind – controls when

and how much the gene is expressed

RNA-coding region

Part of the gene that is actually transcribed into RNA.

Terminator

Site where transcription finishes

Upstream

towards the promoter

Downstream

towards the terminator

Transcription Factor

Binds the promoter, basic machinery needed for RNA polymerase to bind

TATA box

consensus sequence recognized by transcription factors

Transcriptional activators and co-activators

Bind Promoters and Enhancers. Activators stimulate transcription but are not required like

Transcription Factors.

Transcriptional Repressors

Binds to silencers

Enhancer

DNA sequence stimulating transcription from a distance away from promoter

Insulator

DNA sequence that blocks or insulates the effect of enhancers

Mediators

Scaffolding proteins that hold the complex together

TFIID

recognizes TATA box

TFIIH

Helicase

activity aids

in creating

transcription

bubble

The Lac (lactose) operon structural genes (prok)

lacZ, lacY, and lacA

The Lac (lactose) operon regulatory genes (prok)

lacI

The Lac (lactose) operon regulatory elements (prok)

lacO and lacP

The LacZ gene encodes β-galactosidase

Enzyme converts

disaccharide lactose to monosaccharides glucose and

galactose.

The LacY gene encodes permease

which transports lactose into the bacterial cell

The LacA gene encodes the enzyme transacetylase

its exact function is unknown, but it may be involved in removal of toxic by-products of lactose digestion from the cell

repression loop

Binding of repressor to operators O1 & O3 or O2 & O3

what does a repression loop do

Prevents RNA polymerase access to the promoter

• Represses transcription of the structural genes

When lactose binds an allosteric site on the repressor

it loses the ability to bind the operator and repress

transcription

if no lactose is present with lac operon

Enzymes not needed expression of

genes encoding enzymes repressed.

if lactose is present with lac operon

Indirectly induces activation of

genes by binding repressor.

if all lactose is metabolized with lac operon

none available to bind to

repressor—transcription repressed.

Activator

exerts positive control over lac operon

What does cap do

binds to a cap binding site and facilitates transcription

What happens to CAP if high levels of glucose are present

Diminishes expression of operon when glucose is

present

What does cAMP do

helps bind CAP to a promoter

what type of relationship does glucose and cAMP have

inverse

Low lactose, low glucose

No expression

Low lactose, high glucose

No expression

High lactose, high glucose

Some expression

High lactose, low glucose

High expression

what are the three major requirements for transcription

DNA template, raw materials, and a transcription aperatace

RNA Polymerase

Enzyme that directs the synthesis of RNA using DNA template

promotor

Specific D NA sequences in the 5′ region upstream of the

initial transcription point.

RNA polymerase σ factor

responsible for promoter recognition.

Cis-acting DNA elements

elements are adjacent parts of the same DNA molecule.

Trans-acting RNA & protein factors

factors bind to cis-acting DNA elements to influence gene expression

What is the first step of transcription

Initiation

what is initation?

DNA double helix is denatured at the transcription

start site

• The DNA unwound to make the template strand

accessible for RNA polymerase

• Interaction of promoters and RNA polymerase

regulates efficiency of transcription

• RNA polymerase and other DNA binding proteins

often bind to specific consensus sequences

consensus sequences

The average strand that gets bonded to

what is step 2 of transcription

elongation

Elongation

σ subunit dissociates from the RNA polymerase

holoenzyme one initiation is complete and

elongation starts

• Elongation proceeds under direction of the core

enzyme

• As mRNA emerges from the RNA polymerase

ribosomes bind to it and begin translation

what is step 3 of transcription

RNA Polymerase traverses the entire gene until a

termination nucleotide sequence is encountered

Intrinsic (Rho Independent)

Hairpin and UA repeats

destabilize the polymerase and cause it to release the

RNA & DNA

Rho Dependent

the Rho protein separates the RNA &

DNA and removes the polymerase

Polycistronic Transcription

Multiple genes are transcribed together