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CMB2001 - Eukaryotic Control of Gene Expression > Lectures 7-8: Post-transcriptional control of gene expression (pt1) > Flashcards

Lectures 7-8: Post-transcriptional control of gene expression (pt1) Flashcards

1
Q

What are the 4 main controls during protein synthesis?

A

1 - transcription control
2 - RNA processing control
3 - translational control
4 - protein activity control

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2
Q

What are the problems with the different protein synthesis control processes?

A

Genetic diseases are caused by defects in these events
Viruses alter or use these events to their advantage

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3
Q

Do transcription levels effect the amount of mRNA produced?

A

No

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4
Q

When are the Cap and poly A tail added?

A

Added post-transcriptionally (not encoded in the genome)

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5
Q

Why is the poly A tail added?

A

For stability

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6
Q

What are the different primary transcript processes?

A

Capping, Splicing, Polyadenylation and editing

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7
Q

Why does primary transcript processing take place and how?

A

They are coupled to transcription via the RNA polymerase II CTD (C-terminal domain) which acts as a landing pad

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8
Q

What is the structure and synthesis of the m7G cap?

A

Takes place on all RNA polymerase II RNAs
RNA initially contains triphosphate at 5’ end
2 step event: GpppN structure then methylation
Methylation alters chemical behaviour of the base

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9
Q

What are the functions of the m7G cap?

A

Protects mRNA from degradation by 5’-3’ nucleases
Facilitates splicing
Facilitates export from the nucleus
Critical for translation of most mRNAs
Functions mediated through protein binding (CBP80/20 nucleus and eIF4 cytoplasm)
Switches function based on location

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10
Q

How are exons presented in the pre-mRNA sequence?

A

They are not a continuous coding stream

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11
Q

What happens to mRNA if introns are not spliced out?

A

A truncated protein forms that can be degraded or have a detrimental effect

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12
Q

What is the gene with the largest mRNA and introns?

A

Dystrophin - gene linked to duchenne muscular dystrophy

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13
Q

What are the different conserved sequences in introns?

A

5’ splice site
3’ splice site
Branch site

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14
Q

What is the function of the conserved sequences in introns?

A

They define the limits of exons and introns
Recruit splicing machinery required to remove introns and join exons

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15
Q

What are the 2 steps of splicing introns?

A

Step 1: cut at 5’ splice site
Creation of bond between 5’ end of intron and branch site
Step 2: cut at 3’ slice site to release intron lariat
Ligation of 2 exons

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16
Q

What are the reactions that take place when splicing exons?

A

2 trans-esterification reactions (chemical)

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17
Q

What is the spliceosome?

A

An enzymatic complex that catalyses the removal of introns
Requiring ATP
>200 proteins that assemble onto each intron
Proteins: RNA-binding proteins, ATPases, GTPases
Contain several snRNPs (U1, U2, U4, U5 & U6)

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18
Q

What are snRNPs?

A

Small nuclear ribonucleoprotein particles
Stable RNA - protein complexes in the nucleus
Do not code for protein
Base-pair wit conserved sequences in the intron
(splicing catalysed by snRNAs NOT snRNPs)

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19
Q

What structural properties do snRNPs have?

A

Main: Sm ring
Sm binding site - conserved sequence on all molecules
Allows the binding of subset proteins

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20
Q

How was the function of snRNP ring determined?

A

Anti-Sm and Lupus
Anti-Sm antibodies react against the Sm proteins
Anti-Sm antibodies are very rare unless you have systemic lupus erythematosis (SLE)

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20
Q

How is slicing catalysed?

A

By RNA

21
Q

How is the proteome expanded in alternative splicing?

A

Different genes can be mixed and matched to produce different isoforms meaning different proteins are produced

22
Q

What are the different types of alternative splicing?

A

Exon skipping
Intron retention
Mutually exclusive exons
Alternative 5’ splice site
Alternative 3’ splice site

23
Q

How do mutations impact alternative splicing?

A

It can lead to less isoforms of genes

24
Q

How is alternative splicing regulated?

A

Using activators- intronic and exonic splicing enhancers (ISE) (ESE)
Using repressors - intronic and exonic splicing silencers (ISS) (ESS)

25
Q

How do mutations effect splicing?

A

Loss of normal function or only one protien isoform

26
Q

What are examples of diseases that contain mutations causing defects in splicing?

A

Spinal muscular atrophy
Retinitis pigmentosa
Myotonic dystrophy

27
Q

Where does polyadenylation take place?

A

It takes place at a site downstream from a conserved AAUAAA 10-35 nucleotide sequence
G/U or U rich tract just downstream of poly(A) site
U-rich upstream ‘USE’

28
Q

What proteins are required for polyadenylation?

A

Cleavage and polyadenylation specificity factor (CPSF) - binds AAUAAA
Cleavage stimulatory factor (CstF) - binds G/U
Poly(A) polymerase

29
Q

How does the conserved sequence impact polyadenylation?

A

A signal is received do cleave endonuclease and adds the As by polyA polymerase

30
Q

Why is the poly A tail significant?

A

All mRNAs have 3’ poly(A) tail (not histones etc)
Approx 250 nucleotides long
Bound by poly A-binding protein
Enhances export of RNA
Stabilises the 3’ end of the mRNA
Enhances translation of mRNA

31
Q

What is RNA editing?

A

Nucleotide alterations which result in different or additional nucleotides in the mature RNA

32
Q

Where does RNA editing occur?

A

mRNA, tRNA and rRNA

33
Q

What are the 2 types of RNA editing?

A

Insertion/deletion
Modification (point)

34
Q

What is the significance of RNA editing in medicine and development?

A

Disease - Atherosclerosis
Brain function - human (depression)
Development - Drosophila
Parasites - Typanosoma Leishmania and Trypanosoma mitochondria (drug target)

35
Q

What is a marked nucleotide base modification?

A

A reversible process where a methyl group is added which binds different proteins

36
Q

What is altered identity base modification?

A

Flipping of nucleotides, purine to different purine and pyrimidine to pyrimidine

37
Q

What are the effects of mRNA editing?

A

Creation of start codons (insertion and flipping)
Creating of new ORFs by nucleotide insertion (insertion and flipping)
Creation of stop codons (insertion and flipping)

38
Q

How does deamination take place?

A

Using deaminase enzyme

39
Q

What is the change from adenosine to inosine the same as?

A

Adenosine to guanosine (equivalent of A to G)

40
Q

What is cytidine deamination?

A

apoB mRNA editing using the APOBEC-1 enzyme
Both forms of apoB-100 & 48 circulate in the blood and have different functions
The long form of very low density lipoproteins linked to atherosclerosis

41
Q

What happens when Adenosine is changed to inosine in the Q/R site of glutamate receptors?

A

L-glutamate excitatory neurotransmitter
Editing decrease Ca2+ permeability of channels containing the R version
Editing varies in different parts of body
Editing carried out by ADAR2
Mutations in ADAR2 gene in mice lead to seizures, post-natal death, neurodegeneration in hippocampus

42
Q

What are properties of the nuclear pore?

A

Hydrophobic
Contain cytoplasmic filaments
Cage-like structure

43
Q

How is tRNA export mediated?

A

Using Exp-t and ran GTP

44
Q

How is miRNA export mediated?

A

Exp-5 and ran GTP

45
Q

How is snRNA export mediated?

A

CRN1, ran GTP, CBC and PHAX

46
Q

How is mRNA export mediated?

A

TAP/Mex67, p15/Mtr2, CBC and ALY/Yra1

47
Q

How is rRNA export mediated?

A

CRM1, Arx1, Mex67, Mtr2, ran GTP and Nmd3

48
Q

Why is mRNA localised?

A

For protein synthesis
Generates cell polarity
Prevents expression in wrong place
Promotes efficiency of subsequent protein targeting
Local control of translation

49
Q

What are examples of localised protein synthesis generating cell polarity?

A

Drosophila embryo - bicoid, nanos
Drosophila - neuroblasts
Fibroblasts - β-actin
Yeast mRNA - Ash1

50
Q

How does diffusion-based localisation occur?

A

mRNAs freely diffuse in the cytoplasm and are locally entrapped by anchor proteins

51
Q

How does active transport based-localisation occur?

A

mRNA recognised by specific trans-acting factors in the nucleus
Cytoplasmic factors ensure transport along a polarised cytoskeleton

CMB2001 - Eukaryotic Control of Gene Expression (4 decks)

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