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biochem > TMC2 - Transcription > Flashcards

TMC2 - Transcription Flashcards

1
Q

Transcription of genes is also referred
to as

A

gene expression

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2
Q

largest human gene

A

Dystrophin

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3
Q

functions of some of these non-coding RNAs

A
  • ribosomal RNAs (rRNAs) which form part of the ribosome
  • transfer RNAs (tRNAs) – serve as adapters - link the correct amino acid with the correct codon within the ribosome during translation
  • small nuclear RNAs which play a role in RNA splicing
  • microRNAs (miRNAs) which play a role in gene regulation
    -long non coding RNAs (lncRNAs)
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4
Q

DNA or RNA on the left of any chosen point in DNA
or RNA

A

upstream or 5’ of the point.

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5
Q

How is transcription coupled to translation in
prokaryotes

A
  • Ribosomes bind to RBS on the mRNA – bind close to the start codon on the 5’ end of mRNA
  • binds as soon as it is synthesised and before
    the transcript is completed.
  • Translation begins at the first AUG downstream from
    the RBS.
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6
Q

typical polyadenylation sequence

A

AAUAAA

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7
Q

In eukaryotes, RNA encoding proteins is processed and
transported out of the nucleus before it can be translated.
What are the typical steps?

A
  • gene transcribed into pre mRNA in the nucleus
  • Introns removed from the pre mRNA through splicing – giving us mRNA
  • mRNA then cleaved close to a sequence called the poly adenylation site – located at 3’ end of mRNA
  • Polyadneylation sequence is typically AAUAAA
  • Enzyme called polyA polymerase adds a large number of A’s to the 3’ end of mRNA.
  • A modified guanine- called 7-methylguanine is added to the 5’ end of mRNA with an unusual 5’ to 5’ triphosphate linkage.
  • Once 7-methylguanine is added - mRNA is said to be capped.
  • Fully processed mRNA exported through a nuclear pore to the cytoplasm where translation takes place.
  • Ribosomes typically bind to the the CAP and start
    translation at the first AUG downstream from the CAP.
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8
Q

where do ribosomes bind on eukaryotic mRNA for translation and where does translation start

A

to the 7-methylguanine CAP
start translation at the first AUG downstream of the CAP (3’ of the CAP)

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9
Q

which end of mRNA is the CAP added to and the poly-A tail added to

A

CAP – 5’ end
poly-A tail – 3’ end

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10
Q

how is the CAP added to mRNA (like thru what linkage)

A

the CAP - 7-methylguanine is added to the 5’ end of mRNA thru a 5’ to 5’ triphosphate linkage

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11
Q

start codon

A

AUG - methionine

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12
Q

where is the polyA signal seq. located

A

downstream of stop codon to the 3’ end of mRNA

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13
Q

where does cleavage occur in polyadenylation

A

10-30 bases downstream of the polyA signal sequence

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14
Q

enzyme for polyadenylation

A

polyA polmerase

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15
Q

where is mRNA transcripted and translated

A

transcription (including going from premRNA to mRNA) - nucleus (exported thru nuclear pore)
translation - cytoplasm

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16
Q

in what cells are transcription and translation coupled

A

prokaryotic

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17
Q

process of polyadenylation

A

-PolyA signal sequence downstream of of stop codon
- specialised proteins bind to this sequence – cause cleavage of sequence about 10-30 bps downstream of codon
- polyA polymerase then adds a few 100 bps to the end of e cleaved mRNA

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18
Q

after mRNA is modified…

A
  • It leaves the nuclues through the nuclear pores
  • Then translated in the cytoplasm
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19
Q

Functions of the CAP (7-methylguanine)

A
  1. TRANSLATION: the cap binding complex (eIF4) binds cap, the ribosomes then bind to this complex in eukaryotes and starts translation at the first AUG downstream of the cap.
  2. TRANSPORT of mRNA out of the nucleus.
  3. SPLICING and POLYADENYLATION
  4. PROTECTION of the mRNA from degradation by 5’ exonucleases.
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20
Q

Function of Poly A tail

A
  1. TERMINATION of the mRNA transcript
  2. TRANSPORT of mRNA out of cell
  3. PROTECTION from exonucleases that degrade RNA.
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21
Q

what does RNA polymerase use as RNA precursors

A

it uses nucleotide triphosphates (ATP, CTP, GTP,
UTP) as RNA precursors.

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22
Q

what does RNA poly. incorporate into the growing RNA chain

A

It incorporates nucleotide monophosphates
(AMP, CMP, GMP, UMP) into the growing RNA chain

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23
Q

What is released from each nucleotide incorporated by the RNA polym.

A

pyrophosphate (PPi)

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24
Q

which strand does RNA have the same sequence as

A

the DNA coding strand (but complementary to DNA template strand and also U’s instead of T’s)

25
Q

what are the precursors of RNA

A

ATP, CTP, GTP, UTP

26
Q

what are the precursors of RNA often called

A

NTPs

27
Q

how many high energy phosphate bonds does each NTP have

A

2

28
Q

which enzyme can synthesise from scratch - does not need a primer

A

RNA polymerase

RNA polymerase (unlike DNA polymerase) can synthesise RNA from scratch on a DNA template i.e. it can synthesise RNA de novo, it does not require requires a primer.

29
Q

direction of RNA synthesis by RNA polym.

A

RNA Pol synthesises RNA in a 5’ to 3’ direction.

RNA polymerase (like DNA polymerase) can only attach an incoming NTP to the 3’ OH group on a ribose

30
Q

what bond does RNA polym. catalyse the formation of

A

5’-3’ phosphodiester bond
between the phosphate on the 5’ carbon of incoming NTP and 3’OH on another nucleotide.

31
Q

what is consumed and released during the catalysis reaction of RNA polym. during RNA synthesis

A

High energy NTP consumed
pyrophosphate (PPi) released

32
Q

RNA synthesis mechanism (ie. Transcription)

A
  1. Precursors of RNA – ATP, CTP, GTP and UTP (NTPs collectively).
    Each NTP has two high energy phosphate bonds.
  2. RNA synthesis carried out by enzyme RNA polymerase (RNA Pol).
  3. RNA polymerase uses one DNA strand as a template to synthesise a complementary strand of RNA.
  4. RNA polymerase (unlike DNA polymerase) can synthesise RNA from scratch on a DNA template – it does not require require a primer.
  5. RNA Pol synthesises RNA in a 5’ to 3’ direction(like DNA polymerase) – attaches an incoming NTP to the 3’ OH group on a ribose
  6. RNA polymerase catalyses the formation of a 5’ -3’ phosphodiester bond between the phosphate on the 5’ carbon of incoming NTP and 3’OH on another nucleotide.
  7. A high energy NTP is consumed in the reaction and pyrophosphate (PPi) is released.
  8. Like DNA synthesis, the template dictates the nucleotides incorporated into the RNA i.e. the nucleotides incorporated are complementary to the sequence of the DNA template.
33
Q

Transcription - elongation

A

RNA polymerase often attempts transcription initiation several times before really starting. Eventually it grips the template firmly and shifts into elongation phase and transcribes a gene.

34
Q

Transcription - torsional strain

A

As RNA polymerase synthesises RNA from a DNA template it unwinds the DNA. Thus coiling builds up in the DNA in front of the RNA polymerase and causes torsional stress i.e. the DNA essentially becomes overcoiled - called supercoiled.

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

35
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

36
Q

What happens to the DNA in front and behind RNA pol.

A

In front – overwound/supercoiled
behind – underwound

37
Q

supercoiling and proper level of coiling restored by which enzyme

A

topiosomerase

38
Q

Transcription - termination

A

RNA is released from the RNA:DNA hybrid bubble at a
termination point and the RNA polymerase dissociates.
A defined terminator causes termination in most cases in
prokaryotes - the mechanism of transcription termination in
eukaryotes is less clear.

38
Q

Transcription - termination

A

RNA is released from the RNA:DNA hybrid bubble at a
termination point and the RNA polymerase dissociates.
A defined terminator causes termination in most cases in
prokaryotes - the mechanism of transcription termination in
eukaryotes is less clear.

38
Q

Transcription - termination

A

RNA is released from the RNA:DNA hybrid bubble at a
termination point and the RNA polymerase dissociates.
A defined terminator causes termination in most cases in
prokaryotes - the mechanism of transcription termination in
eukaryotes is less clear.

39
Q

start point of a gene to which RNA polymerase binds

A

promoter

40
Q

The end point of a gene where RNA polymerase stops is
called

A

terminator

41
Q

The exact position on the DNA where RNA polymerase
begins synthesis of the RNA is called

A

+1

42
Q

where are promoters located on a gene

A

immediately upstream of the gene

43
Q

Promoter – important points

A
  1. Promoters are typically located immediately upstream of the gene.
  2. Every gene that is transcribed has a promoter.
    RNA polymerase binds directly or indirectly to the promoter.
  3. The DNA in the promoter region is melted and RNA polymerase begins transcription.
  4. The transcription start site on the DNA is called the +1 site.
  5. RNA polymerase transcribes right through the gene and stops at a terminator site.
44
Q

Essential elements in transcription

A

DNA
Promoter
RNA polymerase
ATP, CTP, GTP, UTP
Transcription start site
Terminator site
RNA splicing (eukaryotes)
RNA capping (eukaryotes)
RNA polyadenylation (eukaryotes)
Export out of the nucleus (eukaryotes)

45
Q

Essential elements in translation

A

RNA
CAP (eukaryotes)
Ribosome binding site (prokaryotes)
5’ UTR
Start codon - AUG
Coding sequence (CDS)
Stop codon
3’ UTR
PolyA tail
Ribosomes
tRNAs
Amino acids

46
Q

verage number of exons per human gene

A

9

47
Q

pre- mRNA made of

A

Each gene including its exons and introns are transcribed into pre-mRNA.

48
Q

frequency of introns in diff types of cells

A

Introns are rare / absent in prokaryotes. Introns are infrequent in lower eukaryotes and very frequent in higher eukaryotes.

49
Q

Alternative splicing

A

Alternative (RNA) splicing of genes can occur whereby different combinations of exons are spliced together.
generates different proteins from the same genes
very frequent in higher eukaryotes.

50
Q
A

…

biochem (10 decks)

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