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BM210 > RNA > Flashcards

RNA Flashcards

1
Q

what is the difference between a nucleotide and a nucleoside?

A

nucleotide- this a base bonded to a 5-membered ribose ring
nucleoside - this is a nucleoside bonded to one or more phosphates (they’re the same apart from the phosphates in the nucleoside)

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2
Q

what is DNA made up of?

A

its made up of bases, you know the bases and 2 antiparallel strands, the stands have a sugar-phosphate backbone on the outside, whilst the bases are on the inside

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3
Q

how are the strands of DNA kept together?

A

by H bonds and van der waals forces

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4
Q

what phase of the cell cycle does DNA replication take place in?

A

the S phase of the cell cycle

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5
Q

what is primase and what does it do?

A

its an enzyme that makes random primers to provide a free 3’ end for DNA replication
it also proof reads the strand to make sure there’s no mistakes

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6
Q

what way does the newly formed DNA grow?

A

it grows from 5’ to 3’
but it copies a complimentary copy of the DNA going from the 3’ end towards the 5’ end

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7
Q

what type of fragments grow on the lagging strand?

A

Okazaki fragments

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8
Q

what is mRNA?

A

it is the template for the synthesis of proteins and is transcribed by RNA polymerase II

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9
Q

what is mRNA transcribed by?

A

RNA polymerase II

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10
Q

what is tRNA?

A

it carries amino acids to the ribosome

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11
Q

what is tRNA transcribed by?

A

RNA polymerase III

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12
Q

what is rRNA?

A

it is a component of ribosomes

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13
Q

what is rRNA transcribed by?

A

RNA polymerase I

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14
Q

describe the steps of tRNA synthesis?

A

there are 3 steps
1. the amino acid activation step
2. the transfer of amino-acyl-AMP to a specific tRNA
3. the process is driven by hydrolysis of PPi

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15
Q

what is the overall word equation for tRNA synthesis?

A

amino acid + ATP + tRNA + H2O > amino-acyl-tRNA + AMP + 2 Pi

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16
Q

what does the anti-codon pair with in tRNA synthesis and why does it do that?

A

it pairs with the codon to ensure specificity and that the correct amino acid is brought to the ribosome

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17
Q

what are tRNA synthetases?

A

they link the amino acid with the specific tRNA
they also have proof reading ability in the CCA arm, it can read the amino acid to check its the right one

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18
Q

what is the structure of tRNA?

A

its a clover leaf structure

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19
Q

what are the names of the steps in mRNA synthesis?

A

initiation
elongation
termination

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20
Q

what happens in initiation in mRNA synthesis?

A

RNA polymerase and transcription factors gather at promoter sites then synthesis is initiated

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21
Q

where does initistion occur on the DNA strand?

A

at the promoters, these are places that have any number of boxes at them

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22
Q

what are the names of the boxes and where are they on the template strand in mRNA polymerase?

A

TATA box- found at -25 bp from synthesis site
CAAT box- found at -75bp from synthesis site
GC box- found wherever GGCCGG is

23
Q

where does initaition begin for mRNA synthesis

A

it starts at +1 because that is where the TATA box is telling it to start

24
Q

In what direction is mRNA synthesised along the DNA strand and what synthesises it?

A

5’>3’ by RNA polymerase II

25
Q

what happens in termination in mRNA synthesis?

A

the RNA polymerase stops at a defined site

26
Q

what is splicing for?

A

it to get rid of introns and stop the mRNA from degrading

27
Q

how is the mRNA transcript stabilised?

A

the mRNA transcript is stabilised by modifications by adding a cap at the 5’ end and a poly A tail at the 3’ end
- this happens by the methylation of bases at either side of the coding region
a 5’ to 5’ triphospahte also protects it

28
Q

when does capping happen?

A

it happens when the pre-mRNA is ~25 nucleotides long
the process involves specific proteins which enhance the stability`

29
Q

what does every intron begin with and end with?

A

begins with AG and ends with G

30
Q

what molecule is key to splicing?

A

pyrimidine-rich tract (Py)n with a specific adeninie

31
Q

what do splicing proteins recognise?

A

they recognise different sites by the bases that are there

32
Q

how is a splicosome created?

A

by splicing proteins recruiting other proteins into a complex

33
Q

what is alternative splicing?

A

it is the creation of different mRNA transcripts which can have different functions for the proteins they create

34
Q

what is an example of a protein made by alternative splicing?

A

antibodies on the cell surface are examples

35
Q

is the effect of controlling RNA splicing by RNA binding proteins positive or negative?

A

trick question
it can be both
if it isn’t controlled though, mutations can occur and cause disease by affecting splicing

36
Q

how do RNA molecules self-slice and how is it a good thing?

A

they can act as enzymes to slice themselves by folding into distinct structures
the short sequences of nucleotides can base-pair with others to cause it to fold and can drive slicing of the structure

37
Q

how can RNA interference be exploited? and how can it be used in cell biology?

A

it can be exploited to ‘silence’ the expression of specific genes in different organisms
its used in cell biology to examine the function of a particular gene product

38
Q

what happens ex-vivo in CRISPR?

A

the cells are isolated from the patient and treated, edited and then re-engrafted back into the patient
the target cells are then able to survive in vitro and go back to the target tissue after being transplanted back in the body

39
Q

what happens in vivo in CRISPR?

A

engineered nucleases are deeliveded by both viral and non-viral approaches
they’re directly injected into the patient for systemic/ targeted tissue effect

40
Q

what happens in CAR-T therapy?

A

t cells are collected by the patient
then they’re isolated, engineered and modified, then they’re bound to an antigen
then CAR can transmit signals and activate the modified t cells
CAR recognition can allow the t cells to bypass MHC limitation and give it an advantage towards tumours

41
Q

what are enhancers?

A

they control the transcription process far away from the promoter

42
Q

how do enhancers work?

A

they turn on/off genes
theyre also sites that transcription factors can bind to
this can all influence gene expression

43
Q

what is the transcription start site in protein synthesis?

A

it is the AGU on the mRNA which is the GO codon

44
Q

what is the initiation codon for translation?

A

MET

45
Q

what is mRNA read in at the ribosome?

A

its read in lots of 3 nucleotides which make up codons

46
Q

what subunits make up the ribosomes?

A

50S and 30S rRNA subunits

47
Q

what are the P, A and E sites?

A

P site- where the peptode grows from
A site - the tRNA binds to this part and brings in the next amino acid
E site- this is where the tRNAs exit the ribosome

48
Q

where is the growing polypeptide released from in the ribosome?

A

the tunnel

49
Q

what is the complex in tanslation made up of?

A

its made up of the initiation factors, the tRNA bound to the MET, GTP and the 30S ribosome subunit

50
Q

what does the complex formed in translation do?

A

it scans the mRNA looking for the AGU (GO) codon
then when it finds the codon, the other ribosomal units are recruited with more initiation factors to make the 80S initiation complex

51
Q

how many codons is MET coded for?

A

1

52
Q

what is involved in the selective control of gene expression?

A

enhancers
DNA modifications
epigenetics

53
Q

what are the regulatory steps you can take for DNA replication?

A

selective control of gene expression
control of mRNA synthesis rates
mRNA stability
mRNA processing
protein synthesis and degradation rates

BM210 (13 decks)

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