Week 11 - Gene Regulation Flashcards
Examples of Control Points
DNA Structure Transcription mRNA processing RNA stability Translation Post-translation modification
DNA Binding Proteins
Proteins with discrete domains that bind to DNA
- binding domains 60-90 nt
- form H-bonds with bases or interact with sugar-phosphate backbone
Dynamic interaction
Riboswitches
Regulatory sequence in mRNA
Influence formation of secondary structures
Usually in 5’ UTR of mRNA
Form compact stem and hairpin loop structures
Stabilised by binding of a small regulatory molecule
- creates terminator signal
- masks a ribsome binding site
Two-component Systems
Involve 2 proteins
- one transmembrane sensor protein
- one intracellular response regulator protein
Sensor protein
- becomes externally dephosphorylated in response to a stimulus
- internal protein kinase acquires phosphate from ATP
Response Regulator Protein
- receives P from protein kinase
- activates gene transcription
Hormones
Animal equivalent of responding to environmental condition
Steroid hormones diffuse across cell membrane
Interact with hormone receptor
Complex binds to DNA to regulate gene expression
Gene Regulation Categories
Inducible - genes that are normally off but can be switched on
Constitutive - genes that are always on
Repressible - genes that are normally on but can be switched off
Both inducible and repressible can be under positive and negative control
Positive - gene expression controlled by activator
Negative - gene expression controlled by a repressor
Cis and Trans
Cis - next to or on same DNA strand as gene it controls
Trans - across from and refers to a mobile factor that can act from anywhere
Gene Regulation in Prokaryotes: Operons
Control is at transcription
Operon theory of gene regulation:
- genes expressed in groups at a single regulatory region
- regulatory region upstream from gene
- transcription factors bind to regulatory region and control transcription
Regulatory regions of operons are cis-acting elements
Factors that bind to the regulatory region are trans-acting elements
Lac Operon of E.coli
Controls metabolism of lactose
3 structural genes - repressor, promoter and operator regulatory region
Lac Operon - No lactose present
No enzymes produced
- repressor protein expressed
- binds to operator
- RNA pol binds to promoter but can’t transcribe past repressor
Lac Operon - Lactose present
Enzymes produced
Lactose metabolised
- repressor protein expressed
- lactose acts as inducer and binds to repressor causing allosteric shift
- repressor can’t bind to operator
- RNA pol binds to promoter and transcription proceeds
- lactose converted to galactose and glucose
Lac Operon - Glucose and lactose present
No enzymes produced Lactose not metabolised - no cAMP present - no cAMP-CAP complex formed - CAP can't bind to promoter - RNA polymerase binding is weak - transcription doesn't occur
Function of the cAMP-CAP complex
Binds to promoter and stabilises binding of RNA pol to promoter
Tryptophan Operon
Repressible
Two levels of control
- Allosterically activated repressor
- Attenuation
Trp Operon Allosterically activated Repressor - Tryptophan absent
- repressor protein produced
- can’t bind to operator
- RNA pol binds to promoter and transcription proceeds
Trp Operon Allosterically activated Repressor - Tryptophan present
- repressor protein produced
- inducer binds to repressor, causing allosteric shift
- altered repressor binds to operator
- transcription can’t proceed
Trp Operon Attenuation
mRNA transcript of leader sequence can form either of two stem-loop structures
One allows transcription to continue and other doesn’t
Trp Operon Attenuation - Tryptophan present
Trp-charged tRNA available Ribosome moves quickly to next codons Prevents formation of 2:3 stem-loop Transcription stops PHOTO page 43
Trp Operon Attenuation - Tryptophan absent
Trp-charged tRNA scarce and takes long time to arrive
Ribosome stalled allowing 2:3 loop to form
Transcription continues
PHOTO page 44
Sequence Dependent Promoters
Recognition site for machinery of transcription
Two types:
- core
- regulatory
Common Characteristics of Promoters
Essential for efficient transcription
Mutations in this region alter transcription rate
Number and location varies
Core Promoters
Specify: - basal level of transcription - start site of transcription - direction of transcription Activated by general transcription factors
Regulatory Promoters
Specify enhanced level of transcription
Work in either orientation
Activated by transcriptional activator proteins
Enhancers
Essential to achieve maximum possible level of transcription
Control time and tissue specific transcription
Interact with multiple regulatory proteins and transcriptional activator proteins
Key features of Enhancers
Position related to a gene is not fixed
Orientation can be inverted
Can be moved to another gene and still work
Different enhancers have different enhancement capability
Silencers
Repress transcription initiation
Transcription Factors
Act on promoters
Trans-acting
Can be expressed in tissue specific or time dependent manner
How do promoters, enhancers and silencers affect transcription?
Two stage process
- Assembly of pre-initiation complex
- general TF’s assemble at TATA box of promoter and forms PIC
- recruits RNA pol 2 - Interaction between PIC, RNA pol and TF’s
- activator proteins create link between enhancer TF’s and PIC basal TF’s by looping DNA to bring both complexes close to each other
Chromatin Remodelling
Altering association of DNA with histone proteins in nucleosomes to allow transcription
Steps:
- loosening of DNA wound around histone core
- temporary separation of DNA from histone core
- dividing histone core into two, exposing central DNA
Alternative Splicing
Formation of different versions of mRNA from the same pre-mRNA molcules Changes in splicing can alter: - enzyme activity - receptor binding capacity - protein localisation in cell
