Regulation of gene expression Flashcards
What is found on the 5’ end of pre-mRNA
cap
What is found on 3’ end of pre-MRNA
Poly(A)
What happens in eukaryotic gene expression
-RNA degrade or spliced to remove introns
What can happen to RNA other than splicing
Alternative splicing
What is alternative splicing
Where you remove one of the exons as well to produce one or more protein
Where does translation occur
cytosol
What ca happen. to RNA when in cytosol
Can degrade RNA or sequester in inactive form (stick it in such a way that it can’t be translated)
What happens afterRNA is translated
RNA translation hen could be degraded or made into protein + processed and then compartmentalised and secreted
Which type of control prevents formation of unwanted intermediates
Transcriptional control
How can there be transcriptional control (2 core mechanisms)
- Binding of sequence specific transcription factors to DNA
- Control of DNA packaging and chromatin structure
What are cis-acting sequences
Eukaryotic genes are controlled by cis-acting sequences which can be close to T site or can be further away (regulatory transcription factors)
Where are cis-acting sequences found
Either proximal to transcription start site or further away
What are cis-acting sequences recognized by
Transcription factors
What binding sites do transcription factors have
- DNA
- Transactivation domains
What are transactivation domains
Where DNA polymerase binds and is activated
What do transcription factors recognize
Discrete DNA sequence patterns
What are the two main parts of DNA
- major groove
- minor groove
What do Transcription factors usually bind to on DNA and why
Major groove because its bigger
What do Transcription factors function as and why
Dimers because it increases binding affinity and specificity and can be homo or heterodimers
What are the two types of transcription factors
General TF’s
Transcription regulators
In a eukaryotic gene, what facilitates the binding of distal TF and the gene
mediator
Why does DNA looping occur when a mediator is present
So that transcription factors that are far away from transcription start site can regulate transcription
What does the mediator bind to
Distal and proximal TF and promoter
Whatare the two types of DNA binding transcription factors
- co activators
- co repressors
What do co activators and co repressors do (DNA binding transcription factors)
-what does this require
Modify local chromatin structure to affect transcription
-requiresDNA interaction with histones
Whats a coactivator
Binds and modifies chromatin
What does a chromatin remodeling complex do
Unwinds nucleosome because it contains ATP
What does a histone modifying enzyme do
Loss of +ve charge and so reduced interaction with phosphate backbone and so it unwinds
Example of histone modifying enzyme
Histone acetyl transferase
What does histone acetyl transferase do
Acetylates lysienes in histones and gets rid of positive charge so interaction with phosphate backbone weakens
Example of a corepressor
Histone deacetylase
What does histone deacetylase do
Reduce acetyl groups and causes binding to histones again
different ways in which co repressors may work
- methylation
- Binds and prevents activator binding
- Binds with activator and reacts and so activator masked
- Single binding site on promoter and affinity for repressor is higher
How can extracellular signals link to changes in gene expression
- Activate protein synthesis f transcription factors so can regulate genes
- Ligand binding (become active transcription factors)
- Covalent modification (phosphorylation to activate transcription factors and dephosphorylation for inhibition)
- Adding of second subunit (some TF’s only active as dimers)
- Unmasking (protein bind to TF to mask signal)
- Stimulation of nuclear entry (inhibitory protein to stop nuclear localization signal)
- Proteolysis to release cytosolic part of TF bound to membrane to inactivate them
What are transcription circuits used for
Controlling of genes
gene product can positively or negatively impact gene (i.e. positive or negative feedback)
What is the flip flop device
Product of A has -ve effect on A and product of B has a -ve effect on B
What is the feed forward loop
A induces B which induces c
How to make iPS
Switch on fibroblasts
Examples of transcription factors that control cell fate decisions and/or are implicated in human disease
Oct 4
sox 2
KIF 4
MyC
What does the Pax transcription factor do
-If this is harmed, what can this cause
Controls development of neural crest cell migration
-can cause deafness, lack of iris, and eyeless embryo
Different ways od post-transcriptional RNA modification
- alternative splicing
- RNA editing
- mRNA stability
- miRNA’s
What happens in alternative pslicing
The Poly(A) cap is on a different place
What happens in RNA editing
ApoB gene (transports lipids) needs to form low density lipoproteins in liver but chylomicrons in intestine. So cytosine deaminase converts cytosine in one of the exons to Uracil in the intestine (it is a stop codon). The protein stops at that point so chylomicron is produced there
What is mRNA stability
PolyA tail and 5’ end cap loop round and bind to maintain stability. If this is disrupted then RNA is degraded
What do mIRNA’s do
human genome contains non-coding RNAs and many of these are miRNAs. These associate to form RISC (RNA induced silencing complex) which either silences or reduces transcription of mRNA
