E8 Regulation of gene expression Flashcards
how can a cell be changed in terms of protein and RNA?
- changing a cell requires changing the synthesis and / or decay of specific proteins
- depends on how much genes are expressed and how fast proteins are degraded
- input and output should be changed accordingly to how much you need RNA or protein
describe glucocorticoid receptors and how they enter the nucleus
- gene specific transcription factors that are released from the cytoplasm upon the glucocorticoid hormone binding
- undergo conformational change that allows them to enter nucleus and bind to genes
how does the glucocorticoid hormone change transcription of a cell without entering the cell?
- peptide hormone is hydrophilic, membrane is hydrophobic and cytosol is hydrophilic
- membrane is a tight barrier and it’s difficult for hormones to translocate into the cell
- instead hormone binds to receptor on outside of cell with transmits change to the inside of the nucleus
what processes mediate switching in signal transduction?
- phosphorylation and dephosphorylation
- relays of phosphorylating can be started
what is the function of a protein kinase?
- enzyme that adds a phosphate
- phosphorylating can switch signalling on
- makes proteins active
what is the function of a phosphatase?
- enzyme that removes a phosphate
- dephosphorylation can switch signalling off
- usually deactivates a protein
what does the signal transduction cascade do?
- amplifies signal and carries it into the cell
what is a receptor kinase? what happens when it is active and inactive?
- allosteric switch (embedded in membrane)
- inactive when no hormone / growth factor is bound
- when activated, intracellular kinase is activated by phosphorylation
what happens when intracellular kinase is activated by phosphorylation?
- process passes a signal through the cell membrane by activating an enzyme that will phosphorylate internal targets
what is a common feature of cancer in terms of receptor kinases?
over activation of receptor kinases
what could cancer drugs be in order to block or reduce receptor activation?
antagonist
- prevent activation of receptor
- could be similar to the ligand for the receptor
- could be complementary to active sit or compete with the ligand
kinase inhibitor
- molecule that prevents the enzymatic activity of the receptor or downstream kinases
- could be similar to ATP
state the 5 common mechanisms for the control of gene expression
- regulation of transcription
- splicing
- regulation of translation
- regulation of mRNA degradation
- regulation of protein degradation
describe regulation of transcription as a mechanism to control gene expression
- main control of gene expression
- regulates the amount of pre-mRNA synthesised
- transcription factors binding to DNA to cause transcription
describe splicing as a mechanism to control gene expression
- determines which parts of the pre-mRNA end up in the mRNA
- involves dividing and processing of pre-mRNA (keep exons, bin introns)
- certain sequences bring in proteins that will cut out sections of the RNA (introns)
describe regulation of translation as a mechanism to control gene expression
- determines how much protein is made from a particular mRNA and therefore the protein level
- depends on the sequence and the structure of the sequence
- depends on how well the mRNA is produced
describe regulation of mRNA degradation as a mechanism to control gene expression
- determines how fast mRNA is degraded and therefore the level of an mRNA
- some mRNA may degrade very fast as the protein may have very dramatic effects so you only want them for a short time
- depends on how well the mRNA is produced
- if mRNA is degraded slowly but made fast, lots of mRNA will build up and lots of protein will be made
describe regulation of protein degradation as a mechanism to control gene expression
- determines how fast a protein is degraded and therefore the protein level
- mechanisms in the cell can down-regulate receptors and flag proteins for degradation
what 2 categories do the 5 mechanisms of gene expression control fit into? state which mechanisms go where
nuclear recognition and cytoplasmic regulation
nuclear regulation
- regulation of transcription
- splicing
cytoplasmic regulation
- regulation of translation
- regulation of mRNA degradation
- regulation of protein degradation
describe splicing
- introns are removed from the pre-mRNA (introns can be very large)
- exons are expressed
- exons and introns can be considered as each other sometimes (alternative splicing. -different cells may splice the same piece of pre-mRNA into different mature mRNA)
how can exons be skipped in splicing and what can this allow for?
- exons can be skipped by disguising them as introns so they’re not expressed
- this can then cure diseases because a slightly different protein can be translated form the same pre-mRNA
how can splicing cure cancer?
- can splice around mutations and leave out mutated mRNA
what do mRNAs acquire as well as removal of introns?
- a cap structure at their 5’ end and a poly(A) tail at the 3’ end
describe capping
- cap structure at 5’
- protects the 5’ end
- accumulation of proteins
- cap allows for translation (poor without cap)
- interacts with polyA tail when mRNA loops round
describe polyadenylation
- poly(A) tail at 3’ end
- protein sticks lots of A’s onto the RNA to make mRNA
- length of polyA tail determines how efficiently the mRNA will be used for translation
what is cordycepin?
- a polyadenylation inhibitor isolated from caterpillar fungi
- has anti-inflammatory and anti-cancer properties
- it can control polyadenylation and can inhibit the production of mRNA
describe the steps of pre-mRNA processing
- transcription, 5’ capping
- endonuclease, cleavage at poly(A) site
- poly(A) polymerase and ATP, polyadenylation
- RNA splicing
end up with mature mRNA ready for translation - has a cap, poly(A) tail and is spliced
what factors determine the amount of a protein in the cell?
- mRNA degradation rate
- translation efficiency
- degradation rate of the protein
what is post-transcriptional regulation mediated by?
small RNAs and RNA binding proteins
what is splicing regulated by?
RNA binding proteins and small RNAs which bind to introns
what is mRNA specific translation regulation dependent on?
- sequence specific RNA binding proteins
- base pairing of microRNAs being recruited to the mRNA
what can miRNAs be made from?
genes that don’t produce proteins
what is mRNA decay mediated by?
sequence specific RNA binding proteins or by base pairing with miRNAs
describe miRNAs and their importance
- important for medicines
- considered the future for some diseases
- recognise a range of target mRNAs by base pairing
- key regulators of gene expression
what feature of proteins can make them difficult to access for proteases?
- proteins with well-structured domains
how are most proteins degraded? describe the process
- by the ubiquitin-proteasome pathway
- multiple copies of ubiquitin are coupled to a lysine residue in the protein by specific ligases (polyubiquitination)
- this flags the protein
- proteasome recognises polyubiquitin chain
- then unwinds the secondary structure of the ubiquitinated protein and hydrolyses it into small peptides
what is ubiquitin mediated degradation often linked to?
signal transduction by phosphorylation
describe an example of why you want to be sensitive to new signalling of protein degradation if it comes
- activated kinase by signal transduction could phosphorylate a target protein
- don’t want the protein to be phosphorylated permanently
- ubiquitin ligase will recognise the phosphorylated protein and. perform polyubiquitination
- degradation will occur as you don’t want the protein activated forever (you wouldn’t be able to respond to new activated kinases)
- proteasome degrades the protein so the amino acids can be used to synthesis new proteins
