Gene expression - C&M

efficiency

regulation maintains ____

energy

expressing all genes would require a massive amount of ____

space

cells are kept to a manageable size

time

genes can be expressed as needed & more rapidly

gene expression

different cell types exhibit differential ____ _______:

• eye vs. liver cell

prokaryotic regulation

• transcription/translation occur simultaneously in the cytoplasm

• regulation occurs at the transcriptional level

eukaryotic regulation

• transcription & RNA processing occurs in the nucleus

• translation takes place in the cytoplasm

gene expression is regulated during:

1. transcription

2. translation

3. post-translational modification of proteins

prokaryotic DNA

• circular chromosome located in nucleoid region of cytoplasm

• operons — organized blocks of proteins w/ similar function/in the same biochemical pathway

3 molecules that regulate operons

1. repressors — suppress transcription

2. activators — increase transcription

3. inducers — may suppress/activate transcription depending on cell needs

trp repressor operon - when tryptophan is plentiful

• 2 tryptophan molecules bind the repressor protein at the operator sequence

• complex physically blocks the RNA polymerase from transcribing the tryptophan genes by binding to operator

trp repressor operon - when tryptophan is absent

• repressor protein doesn’t bind to operator

• RNA polymerase can access the operator & the genes are transcribed

negative regulators

proteins that bind to the operator & silence trp expression

• ex. trp repressor operon - tryptophan absent

CAP - positive regulator

glucose supplies become limited in cell:

• cAMP levels increase

• cAMP binds to the __ protein

• cAMP/__ protein complex binds to an operator region upstream of the genes required to use other sugar sources

positive regulators

proteins that bind the promoter in order to activate gene expression

• ex. CAP protein

lac operon - inducer operon

proteins that activate/repress transcription:

• activation/repression depends on the local environment & cell needs

eukaryotic epigenetic regulation

first level begins w/ control of access to DNA & occurs before TRANSCRIPTION begins

transcription factors

proteins that control the transcription of genetic information from DNA —> RNA

human genome

• 20,000 genes

• 23 chromosomes

• DNA is compacted w/ histones

• expressed genes must be unwound & made available to polymerases

nucleosomes

these control access to DNA:

• when spaced closely together

  • transcription factors cannot bind

  • gene expression = OFF

• when spaced far apart, the DNA is exposed

  • transcription factors can bind

  • gene expression = ON

epigenetic regulation

“around genetics” temporary changes to nuclear proteins & DNA that don’t alter nucleotide sequence but do alter gene expression

chemical tags

these are added to histones & DNA:

• phosphate, methyl, acetyl groups

• not permanent — can be added/removed

acts as signals to tell histones if region of chromosome should be open or closed.

unwinding & opening

_____ & _____ of DNA allows transcription factors to:

• bind promoters & other upstream regions

• initiate transcription

eukaryotic transcription

requires RNA polymerases, which also require transcription factors:

• these factors bind the promoter sequence & other DNA regulatory sequences

promoter

region of DNA upstream of coding sequence (a few nucleotide to 100’s of nucleotides long)

TATA box

a series of thymine & adenine dinucleotides w/in the promoter just upstream of the transcriptional start site

TFIID

a transcription factor that binds the TATA box:

• recruits additional transcription factors to form a complex here

RNA polymerase can bind to upstream sequence:

• phosphorylated & part of protein is released from DNA

• in proper orientation for TRANSCRIPTION

enhancer

a DNA seuqence that promotes transcription:

• made of distal control elements — short DNA sequences

• activators bind to those & interact w/ mediator proteins & transcription factors

eukaryotic post-transcription

in eukaryotes…

RNA transcripts must be processed into final form before translation can begin modification:

• this step can be regulated to control gene expression

evolution of alternative splicing

1. splicing requires proper ID of introns

2. errors could lead to splicing out of an intervening exon

3. usually would be deleterious to organism…

4. but could produce a protein variant w/o loss of original protein

5. new variant might’ve had an adaptive advantage

untranslated regions (UTRs)

the protein-coding region of mRNA is flanked by 5’ & 3’ _______ ____.

RNA stability

RNA-binding proteins at UTRs influence ___ _____:

• can increase/decrease length of time mRNA is present in cytoplasm

• regulate mRNA localization & protein translation

5’ cap & poly-A tail

a GTP molecule that prevents degradation of transcript

• other does the same thing

microRNAs (miRNAs)

short RNA molecules (21-24 nucleotides) that recognize specific sequences of mRNA:

• associate w/ ribonucleoprotein complex — RNA-induced silencing complex (RISC)

• RISC/miRNA bind to & degrade the mRNA

initiation complex & translation rate

1. translation controlled by proteins that bind & initiate process (formation of this complex)

2. eukaryotic initiation factor-2 (eIF-2) — first protein to bind & form complex

(she said not to go through whole process; slide 30)

3 tRNA binding sites

1. A-site (acceptor) — charged tRNAs enter here

2. P-site

3. E-site

chemical modifications

these affect protein activity:

• can be added/removed

• also length of time they exist in cell

• can alter epigenetic accessibility, transcription, mRNA stability, or translation

  • all resulting in changes in expression of various genes