Transcription Flashcards
What are transcription factors
Proteins that regulate transcription
Have DNA binding domain and transactivating domain
~10% genes code for transcription factors
Examples of transcription factors
Helix-turn-helix - In all organisms
Zinc finger domain - Common in humans
Coiled coil domains - In leucine zipper and helix-loop-helix motifs
What are activators and repressors?
Activators are proteins that increase transcription
Repressors are proteins that decrease transcription
What do activators and repressors bind to?
Regulatory DNA sequences called operators
What can RNA polymerase holoenzyme always transcribe?
Any gene with a functional promoter
Where can enhancers be found?
Up or downstream of gene
Enhancers - increase transcription
Silencers - decrease transcription
What genes control gene expression in bacteria?
Constitutive and regulated genes
Constitutive genes
Encode proteins cell always needs
Regulated genes
Expression only required under certain circumstances
Expression in bacteria regulated at transcription level
Operons
Genes expressed to encode proteins that work together is co-ordinated by organisation of genes into operons
Operon genes transcribed together to one polycistronic mRNA - translated into separate proteins
What occurs when lactose added to sole carbon source in E. coli?
- Increase in lac mRNA transcript
- Rapid synthesis of lactose-metabolizing enzymes
Beta-galactosidase hydrolyses lactose to glucose and galactose
Lactose converted to allolactose
Permease enables lactose to enter cell
How are lac genes expressed
lac operon (lacZ, lacY, lacA) transcribed to produce mRNA
mRNA forms beta-galactosidase (lacZ), Permease (lacY), Transacetylase (lacA)
lacI upstream of operon - express lac repressor and has own promoter
When does lacI bind lac operator
When no lactose is present
RNA pol can’t bind promoter
No transcription
What occurs with lacI when lactose present
allolactose binds lacI, altering shape
Transcription occurs
What occurs in transcription when glucose present
- Inactivates adenylyl cyclase
- Low cAMP levels
cAMP indicates glucose levels
cAMP high = low glucose
What is CAP protein?
Catabolite activator protein
CAP dimerizes in cAMP presence
Dimerized CAP binds DNA
Bends DNA by 90 degrees
What occurs when CAP-cAMP binds CAP operator?
RNA polymerase holoenzyme binds promoter
Activates more then 100 promoters in E. coli in low glucose levels
Name 2 molecules that combine lac operon regulation
lac repressors and CAP-cAMP
Explain mRNA in tryptophan biosynthesis
5 genes encoding enzymes expressed in operon as polycistronic mRNA
When is trp operon turned off
excess tryptophan
Regulatory gene is trpR
Tryptophan-mediated repression
trpR encodes aporepressor
No binding of TrpR aporepressor in absence of tryptophan
Aporepressor activated by binding tryptophan in excess tryptophan
Binds operator, prevents transcription
Regulation acts as on/off switch
Explain second regulatory mechanism of trp operon
Tryptophan starvation - Maximal expression of trp genes
tryptophan limited - less than maximal expression of trp genes
Attenuation produces short transcripts that don’t encode structural proteins
Termination at attenuator site with trpL leader region of operon
Attenuation is based on fact bacterial transcription coupled to translation
trp operon regulation at initiation
Absence of trp - No repression - transcription
Presence of excess trp - TrpR aporepressor + tryptophan co-repressor bind operator - No transcription
What are riboswitches?
Portion of transcript
Bind small molecule that controls RNA secondary structure, regulating transcription/translation
2 regions of riboswitch
Aptamer - Binds metabolite
Expression platform - control transcription or translation
Adenine riboswitch
- Regulates adenine synthesis and transport in B. subtilis
What does gene expression depend on with adenine riboswitches?
Whether terminator or anti-terminator forms
Low adenine - regions 2 and 3 form anti-terminator, prevents regions 3 and 4 forming terminator
High adenine - adenine binds aptamer leading to regions 3 and 4 pairing and forming terminator
