Chromatin

DNA is wrapped around protein to creat a DNA protein complex

Chromatin Remodeling

before transcription can occur the stretch of DNA containing the promoter must be released from tight interactions so that the DNA poly combines

RNA processing steps that occur in nucleus

(1) chromatin remodeling

(2) transcription

(3) RNA processing

RNA-cytoplasm

mRNA stability

Translation

Post translational modification

supercoiling

the DNA double helix is twisted on itself many times

Histones

positive charge proteins associated w/DNA in the chromatin of eukaryotic cells

Nucleosome

group of 8 histone proteins and other proteins

Linker DNA

stretch of DNA between nucleosomes

charges of DNA/histones and why

DNA (-) charged due to phosphate groupe

histones (+) charged due to lysine or arginine residues

30 nm fiber

-

H1 hisotnes interact w/ each other w/ histones in other nucleosomes to produce a tighly pack structure

-attached to proteins that form a scaffold inside nucleus

DNASE

enzyme that cuts DNA at random locations

-cannot cut DNA efficiently if moelcule is tighely complexed w/ histones

DNA needs to be relaxed

Default state of eukaryotic cells

"off" since in condensed

to start transcription must be relaxed so DNA poly can attach

how is chromatin altered?

-chromatin remodeling complexes

(series of ATP dependent rxns)

-acetylation

-methylation

Histone acetyl transferase

(HATs)

acetylate the positively charged lysine residues in histones

-when adds an acetyl growup the marked protein can act as a binding site for chromatin remodeling complexes that open the DNA)

Histone deactylase

(HDACs)

remove the acetyl gropus added by HATs

Histone code

precise patterns of chemical modifications of histones contain info

-influences whether or nota  particular gene is expressed

epigenetic inheritance

patterns of inheritance that are not due to differences in DNA sequences

promoter

site in DNA where RNA poly binds to initiate transcription

-highly conserved sequences (TATA box)

TATA binding protein

(TBP)

1st step in transcription protein binds to TATA box 

is a component of the basal transcription complex

Regulatory Sequences

sections of DNA that are involved in controlling the activity of genes

(like prokaryotic CAP binding site/operators)

promoter proximal elements

regulatory sequences in DNA that are close to a promoter and that can bind regulatory transcription factors

-have sequences that are unique to specific genes

Antibodies

proteins that bind to specific sites on other molecules

Enhancers

-regulatory elements that are far from the promoter

-can be located in:

introns

untranscribed sequences on either side of gene

can work if opposite way and if they are moved

Silencers

transcription is stopped when regulatory genes bind here

Gene

DNA that codes for a functional polypeptide of RNA molecule and regulatory sequences required for expression

Regulatory transcription factors

-proteins that bind to enhancers silencers or promoter proximal elements

-responsible for particular genes in particular cell types and particuar stages of development

Bssal Transcription Factors

 interact w/ the promoter and are not restricted to particular stages cell types

-must be present for transcription to occur

does not provide regulation

-bind to eukaryotic promoters to help initatie transcription

Mediator complex

does not bind to DNA

creates physical link btwn regulatory and basal trascription factors

3 ways of post transcriptional control

(1) splicing of mRNAs in various ways

(2) Modifying the life span of mRNAs or altering the rate at which translation is initiated

(3) activating/inactivating protiens after translation has occurred

alternative splicing

primary RNA transcript can yield more than one kind of mature processed mRNA

-different combinations of transcribed exons

lifespan of mRNA

controlled by tine, single stranded RNA moleucles that bind to complemetnary sequences in teh mRNA

-once mRNA becomes double stranded specific proteins degrade the mRNA or prevent it from being translated

RNA interference

look at picture

micro RNA

(miRNA)

small single stranded RNA associated w/proteins in an RNA induced silencing complex

-can bind to complementary sequences in mRNA molecules allowing th associated proteins to degrade the bound mRNA or inhibit translation

6 ways gene expression can be controlled

"C.T.R. M.T.A."

(1) at the level of chromatin structure

(2) transcription initiation

(3) RNA processing

(4) mRNA availability

(5) translation rate

(6) altering protein activity post translation

Post Translational Control

(1) folding

(3) chemical modificaitons

-phosphoylation

-glucyosylation

cleaving off

Proteasome

recognizes proteins that have a ubiquitin tage and cuts them into short segments

ubiquitinization

mechanism for controlling the life span of proteins in cells

Difference in gene expression in bacteria vs eukaryotic

(packing)

chromatin structure (provides - control) in eukaryotes must be opened first (default state off due to tightness)

default state of transcription in bacteria=on (no histone proteins; freely accessible promoters)

Difference in gene expression in bacteria vs eukaryotic

(alternative splicing)

RARE in bacteria 1:1

eukaryotic gene may code for thousands of distinct products

Difference in gene expression in bacteria vs eukaryotic

(complexity)

sigma - basal transcription complex

CAP , repressor and other proteins  - transcription factors in eukaryotes

Difference in gene expression in bacteria vs eukaryotic

(coordinated expression)

-bactera- genes take part in the same cellular respons are organized into operons control by single promoter

-eukaryotes- genes that are physically scattered can be expressed at the same time bc a single set of regulatory transcription facors can trigger the transcription of several genes

tumor suppressors

genes that stop or slow the cell cycle

proto-oncognes

genes that trigger cell growth and division by inititating specific phases in the cell cycle

oncogene

an allele that promotes cancer development