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FUN E > E8 Regulation of gene expression > Flashcards

E8 Regulation of gene expression Flashcards

1
Q

how can a cell be changed in terms of protein and RNA?

A
  • 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
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2
Q

describe glucocorticoid receptors and how they enter the nucleus

A
  • 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
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3
Q

how does the glucocorticoid hormone change transcription of a cell without entering the cell?

A
  • 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
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4
Q

what processes mediate switching in signal transduction?

A
  • phosphorylation and dephosphorylation
  • relays of phosphorylating can be started
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5
Q

what is the function of a protein kinase?

A
  • enzyme that adds a phosphate
  • phosphorylating can switch signalling on
  • makes proteins active
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6
Q

what is the function of a phosphatase?

A
  • enzyme that removes a phosphate
  • dephosphorylation can switch signalling off
  • usually deactivates a protein
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7
Q

what does the signal transduction cascade do?

A
  • amplifies signal and carries it into the cell
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8
Q

what is a receptor kinase? what happens when it is active and inactive?

A
  • allosteric switch (embedded in membrane)
  • inactive when no hormone / growth factor is bound
  • when activated, intracellular kinase is activated by phosphorylation
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9
Q

what happens when intracellular kinase is activated by phosphorylation?

A
  • process passes a signal through the cell membrane by activating an enzyme that will phosphorylate internal targets
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10
Q

what is a common feature of cancer in terms of receptor kinases?

A

over activation of receptor kinases

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11
Q

what could cancer drugs be in order to block or reduce receptor activation?

A

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

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12
Q

state the 5 common mechanisms for the control of gene expression

A
  • regulation of transcription
  • splicing
  • regulation of translation
  • regulation of mRNA degradation
  • regulation of protein degradation
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13
Q

describe regulation of transcription as a mechanism to control gene expression

A
  • main control of gene expression
  • regulates the amount of pre-mRNA synthesised
  • transcription factors binding to DNA to cause transcription
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14
Q

describe splicing as a mechanism to control gene expression

A
  • 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)
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15
Q

describe regulation of translation as a mechanism to control gene expression

A
  • 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
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16
Q

describe regulation of mRNA degradation as a mechanism to control gene expression

A
  • 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
17
Q

describe regulation of protein degradation as a mechanism to control gene expression

A
  • 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
18
Q

what 2 categories do the 5 mechanisms of gene expression control fit into? state which mechanisms go where

A

nuclear recognition and cytoplasmic regulation

nuclear regulation
- regulation of transcription
- splicing

cytoplasmic regulation
- regulation of translation
- regulation of mRNA degradation
- regulation of protein degradation

19
Q

describe splicing

A
  • 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)
20
Q

how can exons be skipped in splicing and what can this allow for?

A
  • 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
21
Q

how can splicing cure cancer?

A
  • can splice around mutations and leave out mutated mRNA
22
Q

what do mRNAs acquire as well as removal of introns?

A
  • a cap structure at their 5’ end and a poly(A) tail at the 3’ end
23
Q

describe capping

A
  • 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
24
Q

describe polyadenylation

A
  • 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
25
Q

what is cordycepin?

A
  • 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
26
Q

describe the steps of pre-mRNA processing

A
  1. transcription, 5’ capping
  2. endonuclease, cleavage at poly(A) site
  3. poly(A) polymerase and ATP, polyadenylation
  4. RNA splicing

end up with mature mRNA ready for translation - has a cap, poly(A) tail and is spliced

27
Q

what factors determine the amount of a protein in the cell?

A
  • mRNA degradation rate
  • translation efficiency
  • degradation rate of the protein
28
Q

what is post-transcriptional regulation mediated by?

A

small RNAs and RNA binding proteins

29
Q

what is splicing regulated by?

A

RNA binding proteins and small RNAs which bind to introns

30
Q

what is mRNA specific translation regulation dependent on?

A
  • sequence specific RNA binding proteins
  • base pairing of microRNAs being recruited to the mRNA
31
Q

what can miRNAs be made from?

A

genes that don’t produce proteins

32
Q

what is mRNA decay mediated by?

A

sequence specific RNA binding proteins or by base pairing with miRNAs

33
Q

describe miRNAs and their importance

A
  • important for medicines
  • considered the future for some diseases
  • recognise a range of target mRNAs by base pairing
  • key regulators of gene expression
34
Q

what feature of proteins can make them difficult to access for proteases?

A
  • proteins with well-structured domains
35
Q

how are most proteins degraded? describe the process

A
  • 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
36
Q

what is ubiquitin mediated degradation often linked to?

A

signal transduction by phosphorylation

37
Q

describe an example of why you want to be sensitive to new signalling of protein degradation if it comes

A
  • 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

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