control of gene expression Flashcards
Name some functions of living organisms that the control of gene expression is critical for
development & differentiation
ability to respond to changes in the environment
maintaining the biochemistry of the cell (having the correct levels of protein products)
At which points can gene expression be controlled?
Most gene expression is controlled at the point of transcription initiation but there are other points of control. Overall RNA is a much less stable molecule compared with DNA but even different mRNAs can vary greatly in their stability or change their stability depending on cellular conditions. There are specific RNA decay pathways that target the destruction of RNAs.
Proteins can also vary in their stability and have well characterized degradation mechanisms.
What is the key to the regulation of transcription initiation?
regulating the interaction of RNA polymerase with the promoter region
What is positive regulation?
Activator proteins are required to turn transcription on
All genes have different promoter sequences although they may share some features. Thus there are some genes that could be considered as having a ‘strong’ promoter for which RNAP has a high affinity. There are other promoters that could be considered as being ‘weak’ and RNAP needs the help of activator proteins to enable it to bind and start transcription. It should be noted that in eukaryotes RNAP always has a low affinity for promoters and therefore needs activator proteins to enable transcription.
What is negative regulation?
Gene is expressed unless a repressor protein is present to turn transcription OFF
In negative regulation the gene would be transcribed unless a repressor protein blocks the activity of RNAP.
Describe the control of gene expression in prokaryotes
Prokaryotes are highly skilled at changing their gene expression to suit the prevailing environmental conditions
eg making use of different carbon sources
producing virulence factors only in the presence of a suitable host
RNA polymerase and activating proteins bind to the promoter region
Repressor proteins bind to the operator region
Many prokaryotic genes are organised into operons
Co-ordinated regulation of linked genes that are often involved in the same biological process
What is the role of the lac operon?
Allows synthesis of lactose metabolizing enzymes in E.coli when lactose is present as a carbon source
The enzyme responsible for metabolizing lactose is beta-galactosidase (cleaves lactose into glucose & galactose)
1000x more beta-galactosidase is made in the presence of lactose than in the absence
How does regulation take place in the lac operon?
Regulation is achieved via a repressor protein (LacI)
In the absence of lactose the LacI repressor binds to the operator and prevents transcription of the lac operon.
The LacI repressor is able to bind lactose. This leads to a change in the shape of LacI and it can no longer bind DNA
This type of regulation of a protein by the binding of a small molecule is known as allosteric
What is allosteric regulation?
Regulation of a protein by binding of an ‘effector’ molecule at a site other than the enzyme’s active site or DNA binding domain. Binding at the allosteric site will cause a conformational change. The LacI protein has two important sites: the DNA binding site that can recognize and bind to the operator sequence and the allosteric site that binds lactose
Summarise the process of negative regulation in the lac operon
lac structural genes are only transcribed in the presence of lactose
LacI repressor protein senses lactose
The LacI protein undergoes an allosteric change in shape in the presence of the lactose that prevents it binding to the operator sequence
How does the availability of glucose affect the expression of the lac operon?
Glucose is a better carbon source than lactose
If glucose is present then the lac genes are not expressed (this is known as catabolite repression)
Controlled by the CAP regulatory protein
Describe the relationship between glucose levels and cAMP
High glucose=inactivates adenylate cyclase
Low glucose= cAMP levels increase
cAMP is an important cellular constituent that is formed by the enzyme adenylate cyclase. High levels of glucose inactivate adenylate cyclase and therefore cAMP levels are low in the presence of glucose.
Describe how the cAMP-CAP complex activates transcription
cAMP is the allosteric regulator of the catabolite activator protein (CAP).
In the presence of cAMP, CAP is able to bind to the lac operon promoter sequence and activate transcription by helping recruit RNAP.
Thus when glucose is present, the low levels of cAMP result in failure to activate lac operon transcription.
How is chromatin opened up?
In order to open up chromatin there are regulatory proteins that are able to bind to target sequences on DNA even when it is packaged into a tight nucleosome configuration. These regulatory proteins can then modify the nucleosomes or histone components to ‘remodel’ the chromatin.
Even when RNAP has access, it alone has low affinity for promoter regions and needs additional proteins transcription factors to assemble.
Describe eukaryotic promoters
Eukaryotic promoters are complex and contain multiple binding sites (referred here as ‘elements’) for regulatory proteins usually referred to as transcription factors. The core promoter is where RNAP and ‘general transcription factors’ bind. It establishes the start site for transcription initiation and includes the TATA box and initiation site.
The promoter proximal elements are upstream of the TATA box (~-50 to -200) and these will vary from gene-to-gene. They are important in determining where, when and at what level transcription of that gene takes place. They are binding sites for regulatory proteins, some of which will be involved in opening up chromatin whereas other will be involved in recruiting RNAP.
Basal Promoter elements: set the basal level of transcription
Response elements: Allow certain genes to respond to environmental stimuli
Cell-specific elements: Located in promoters of genes expressed in only one type of tissue
There are also elements located at a distance to the transcriptional start site that can increase the level of transcription. These so called ‘enhancer’ elements can be upstream or downstream and may be many kilobases away from the start site.
