Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BMS 242 - Advanced Cell and Molecular > 2!!! - Control of gene expression: RNA > Flashcards

2!!! - Control of gene expression: RNA Flashcards

1
Q

What are isoforms?

A

Multiple proteins made from the same gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are 3 ways that isoforms made?

A

From:

  • Alternative splice sites
  • Alternative start sites
  • Alternative polyadenylation (the end of the DNA)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What do some mRNAs have that can be regulated independently?

A

A second ORF

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What 3 ways gene expression be regulated?

A
  • Transcription
  • Splicing
  • Translation
  • Regulated nuclear transport
  • RNA stability
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How many genes in the human are alternatively spliced?

A

75%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How many genes in the drosophila are alternatively spliced?

A

40%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are 4 ways that alternative splicing can occur?

A

1) Optional exon
2) Optional intron
3) Mutually exclusive exons
4) Internal splice sites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are mutually exclusive exons?

A

Exons that don’t occur at the same time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

When do mutually exclusive exons usually occur?

A

When the exons code for similar proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is an internal splice site?

A

Where the 3’ OR 5’ end splice site is in the middle of the intron instead of the end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How does the cell alternatively splice sites?

A
  • Splice donor and acceptor sequences are very small (only 2 base pairs), meaning they are VERY FREQUENT
  • Splice sites are relatively simple
  • Mechanism isnt very precise - taken advantage of to produce different splice sites
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

How do RNA binding proteins assist alternative splicing?

A

They bind around the donor/acceptor splice sites and influence where splicing occurs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What affects the choice of splice site?

A
  • RNA binding proteins

- Other sequences and secondary structure in the RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Why is the splicing mechanism not very precise?

A

To take advantage of it

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the most common spliced gene?

A

Dscam in drosophila

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is Dscam involved in?

A

Specifying neurons in the brain of the drosophila

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

In what way is the Dscam gene alternatively spliced?

A

Has mutually exclusive exons

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How many different possible isoforms are there in the Dscam gene?

A

38,000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What process is used to help to understand alternative splicing in humans?

A

Sex determination in drosophila

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How is sex determined in drosophila?

A

By the amount of X chromosomes that the fly has:

  • Male = X
  • Female = XX
  • This is then translated into sex characteristics
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the three genes that regulate male or female differentiation?

A

1) sxl (sex lethal)
2) tra (transfomer)
3) dsx (double sex)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How are MALE characteristics determined in the drosophila?

A
  • Transcripts sxl and tra are spliced to give INACTIVE protein isoforms
  • dsx is ACTIVE
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What does dsx do in the active form?

A
  • Gives rise to a male specific repressor protein, which represses transcription from genes required for female development
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

How are FEMALE characteristics determined in the drosophila?

A
  • MORE transcription of sxl due to two X chromosomes
  • SMALL AMOUNT of functional sxl protein made using an alternative promoter
  • sxl binds to its own transcript in a positive feedback loop to make MORE of the active protein by REPRESSING SPLICING at this site
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

How does sxl block splicing of the sxl transcript?

A

sxl is a binding protein - binds to transcript:

  • Blocks the splice acceptor site that is used in males
  • Causes splice over and removal of the central exon
  • Activation of an alternative acceptor - joining the outside exons together (alternative combination that in the male)
  • The joining of these exons together form the active form of tra
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What does the active form of tra do in females?

What does this result in?

A

Binds to dsx mRNA with tra-2 to activate a splice acceptor in dsx mRNA:

  • This results in a change to the carboxy terminus at the end of the protein
  • Producing the female specific isoform of dsx transcription factor
  • This isoform represses male differentiation genes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

How do RNA binding proteins work to specify sex?

A
  • Can repress splicing by HIDING the splice acceptor, forcing an alternative splice site to be chosen by the splicing complex
  • Can enhance splicing at a new site by binding to the splice site and active it
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How can the site of polyadenylation of the mRNA be regulated to produce different protein isoforms?

A
  • B lymphocytes produce the
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

How do B lymphocytes produce 2 different antibody isoforms?

Why is this important in the immune response?

A

By altering where the RNA transcript is cleaved and polyadenylated

Important because B lymphocytes originally want to make antibodies that are NOT secreted and are tethered to the membrane

As these antibodies are perfected - need to be secreted, no longer have a transmembrane domain

30
Q

How many possible sites in antibodies are there for cleavage and polyadenylation?

A

2 possible sites

31
Q

What tells where to cut the preRNA to make mRNA?

A

Sequences inside the preRNA

32
Q

What is the mechanism of altering the site of cleavage and polyadenylation in antibodies?

A
  • When the cell produces the preRNA, the first stop codon is spliced out, resulting in the translation of a transmembrane domain
  • Switch to cleavage and polyadenylation earlier within the intron
  • Loss of the splice acceptor (and second stop site)
  • Intron no longer recognised, can’t be removed
  • First stop codon not removed
  • Results in the antibody being secreted
33
Q

How are alternative starts sites regulated?

A
  • Many different start sites (AUG sequence)

- Not all created equal - ribosome can skip AUG sites

34
Q

What is ‘leaky scanning’?

A

Where the ribosome skips AUG sequences

35
Q

What is the optimal sequence for the small subunit to stop and transcription to happen?

A

KOZAK sequence:

ACCAUGG

36
Q

How do proteins differ when they have alternative start sites and why?

A

Only in their N-terminus

As all the alternative starts are all in the SAME reading frame

37
Q

How do cells modify the use of their alternative start sites?

A

Using high levels of eIF-EF (initiation factor)

38
Q

What start site does eIF-4G favour?

A

The first AUG site

39
Q

What happens with HIV enters the cell as an RNA genome?

A

It is converted into DNA by reverse transcriptase and inserted into the host genome

40
Q

When HIV DNA is inserted into the host genome, what can happen?

A

The entire genome is transcribed

Can undergo alternative splicing to give rise to many different protein isoforms

41
Q

Wha is the full-length un-spliced HIV RNA needed for?

A

To make new virions to infect the the next stage

42
Q

What is the full-length un-spliced HIV RNA needed for?

A

To make new virions to infect the the next cell

43
Q

What helps full-length, un-spliced RNAs to leave the nucleus?

A
  • Retroviruses produce a REV (a protein)
  • REV goes back into the nucleus and binds to the introns of a full-sized RNA transcript, escorts the RNA out of the nucleus
44
Q

Why don’t un-spliced RNAs leave the nucleus?

A

This is a checkpoint

45
Q

What monitors the levels of HIV?

A

Levels of rev protein (produced by reteroviruses)

46
Q

What targets mRNA to a specific part of the cell?

A

Signals in the untranslated region of mRNA (UTR)

47
Q

Where is the UTR in mRNA?

A

Between:

  • The 5’ end and the start codon
  • The stop codon and the 3’ polyadenylation site
48
Q

What structure do the 3’ UTR in the mRNA form?

What is this recognised by and what does this allows?

A

Stem loop structures

Recognised by cellular proteins which are localised to one side of the cell

This traps the RNA at a specific point in the cell - when translated, there is a higher concentration of the protein on one side of the cell compared to the other

49
Q

What do many mRNA have in their 3’ and 5’ UTR?

A

Translational control elements

50
Q

What can regulate the transcriptional control elements in the 5’ and 3’ UTR?

A

Ferrtin - proteins that stores ion in the cell (reducing available Fe)

Transferrin - receptor that imports ion into the cell (increasing available Fe)

51
Q

What happens where is low Fe in the cytoplasm?

A
  • Aconitase binds to the stem loops of 5’ UTR of ferritin mRNA and BLOCK TRANSLATION
  • Fe not stored
  • Also binds to stem loops of 3’ UTR of transferrin mRNA and BLOCKS DEGREDATION
  • More receptors, more Fe into the cell
52
Q

What type of protein is Aconitase?

A

An RNA binding protein

53
Q

How does Aconitase block the translation of ferritin?

A

Prevents the small subunit from moving from the cap

54
Q

How does Aconitase block the degradation of ferritin?

A

By stabilising the mRNA

55
Q

What happens when there is high Fe in the cytoplasm?

A
  • Aconitase binds to Fe in the cytoplasm and goes through a conformational change
  • Aconitase releases mRNAs on ferritin and transferrin
  • Ferritin now translated and transferrin mRNA destabilised
56
Q

Is aconitase specific or not specific to certain mRNAs?

A

Specific

57
Q

How can the cell modify ALL translation? (globally)

A

By using eIF2 and eIF-2B

58
Q

What 2 situations is global control of translation needed?

A

1) When the cell becomes infected with a virus - slows down to prevent further infection
2) When the cell starves - runs out of energy

59
Q

What is the mechanism of the global control of translation by eIF2 and eIF-2B?

A

Normally:
1) eIF2/GTP binds to Met tRNA - start scanning and progress from the cap

2) eIF-2b binds to eIF-2 and knocks off GDP - allowing GTP to bind and activate eIF-2 and recycling eIF-2b

When the cell enters rest phase:
1) Phosphorylates eIF-2 - causing it to bind tightly to eIF-2, blocking the recycling

2) Less active eIF-2 in the cytoplasm

60
Q

What must eIF2 be bound to to be active?

A

GTP

61
Q

What is required for the dissociation of GDP from eIF2?

A

eIF-2b

62
Q

What are IRES?

What do they allow?

A

Internal ribosomal entry sites
- Stem loops in RNA, between ORFs that can initiate the formation of the ribosome independant of the cap/polyA initiation complex

Allow more than one gene to be present on an mRNA
(2 exons, 2 ORF)

63
Q

Where are IRES’s common?

A

In viruses

64
Q

How does the IRES work?

A

Imitates the cap structure, allowing the small subunit to work

65
Q

What initiation factor binds to the IRES stem loop and is required for IRES based induction?

A

eIF-4G

66
Q

What are the levels of eIF-4G in the cell?

A

Regulated

67
Q

How do viruses favour the translation of their transcripts?

A

Cleave the hosts eIF-4G into a form that no longer binds eIF-4E but still binds IRES sequence

68
Q

What is eIF-4G usually required for in the cell?

A

Binds to the polyA tail and eIF-4E (which is bound to the cap on the mRNA) - to form the looped structure of mRNA to ensure both ends are present before leaving the nucleus

69
Q

Apart from in viruses, when else is eIF-4G cleaved and why?

A

During apoptosis:
- Genes required during cell death are usually in the second ORF (favoured during cell death)

  • Utilise this to activate the IRES and continue to be translated
70
Q

How can RNA stability be regulated in order to regulate translation?

A

1) Exonuclease - chews down the polyA tail
- At 30nt - the mRNA is decapped and recognised for degredation

2) Some mRNAs are favoured and RE-ADENYLATED in the cytoplasm - extending their half life
3) Proteins target RNAs to degrade them more quickly

71
Q

What does DAN do?

A

Competes with eIF-4E to bind to the cap and promotes degredation

BMS 242 - Advanced Cell and Molecular (24 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions