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gene expression Flashcards

1
Q

transcription define & what involves

A

process of DNA being copied into RNA

  1. DNA
  2. transcription factors
  3. RNA polymerase
  4. ATP
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2
Q

translation define

A

process where RNA direct synthesis of proteins (nucleotides translated into amino acids)

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3
Q

the phosphodiester linkages connects to which carbons on the sugars

A

3’C of one sugar & 5’C of another sugar

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4
Q

single ring amino acid in DNA

A

pyrimidine bases - uracil & cytosine

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5
Q

double ring amino acid in DNA

A

purine bases - guanine & adenine

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6
Q

non-coding strand of DNA

A

the template strand used in transcription, different depending on gene

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7
Q

coding strand of DNA

A

non-template strand used in transcription, complimentary to the RNA new strand

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8
Q

transcription steps

A
  1. initiates at TTS (embedded in a core promoter)
  2. core promoter assembles preinitiation complex
    3.
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9
Q

what direction does RNA synthesis occur

A

5’ to 3’ direction

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10
Q

does transcription need a primer

A

no

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11
Q

define high processivity

A

carry out continuous DNA synthesis with little dissociation

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12
Q

does RNA polymerase have high or low processivity

A

high (starts & finishes transcription)

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13
Q

three type of RNA polymerase

A

RNA polymerase I - transcribes pre-RNA
RNA polymerase II
RNA polymerase III

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14
Q

what is the pre-initiation complex in transcription

A

complex of the general transcription factors & RNA polymerase

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15
Q

enhancers define

A

they are locally regulatory sequences that activate promoters. bind transcription factors, cofactors which increase transcription from the core promoter

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16
Q

Transcription promoters

A
  1. TATA box (30bp upstream of TSS)
  2. initiator (Inr) motif = overlaps with TSS = binds TAF1 more abundant than TATA
  3. DPE = increases TFIID binding in TATA-less promoters
  4. BRE sequence enhances binding of TFIIB to promoters
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17
Q

CpG islands

A

regions of elevated GC in promoters
- have distinct chromatin modifications & involved in constitutive gene expression

= promoter regions with high guanine and cytosine

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18
Q

Pre-initiation core

A
  • RNA polymerase (I, II, or III)
  • TATA box-binding protein (TBP: required for both TATA-box-less promoters)
  • general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF for pol II) or related proteins for I & III.
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19
Q

Transcription initiation & elongation with polymerase II

x7

A
  1. TFIID contains the TATA box binding protein & binds to the core promoter
  2. TFIID recruits TFIIA = stabilises the TBP-DNA complex
  3. TFIIB required to recruit the RNA pol II, interacts with BRE motif
  4. TFIIF recruits RNA pol II, stabilises the complex & influences the selection of the transcription start site
  5. TFIIE recruits & stimulates TFIIH = binds to RNA pol II = unwinds DNA to form an open complex.

TFIIH = has kinase, helicase & ATPase activity

  1. As DNA unwinds RNA pol moves down the template DNA strand 3’ to 5’ direction = adds nucleotides to the 3’ end of growing change
  2. TFIIH-CDK7 phosphorylates RNA pol II, regulating the switch to elongation. Pol II associates with elongation factors to increase elongation rate.
20
Q

Polymerase I transcription termination

A

transcription stopped by termination factor recognising terminator sequences. in mammals 18bp terminator Sal box recognised by TTFI

21
Q

Polymerase II transcription termination

A

transcription can continue for 100-1000s of nucleotides beyond the end of the gene. termination is coupled to RNA processing & the poly A tail is necessary

22
Q

Polymerase III transcription termination

A

transcription terminates at the T-rich sequences located a short distance from the mature 3’ end & involves a limited number of auxiliary factors

23
Q

core promoter determines ——- in transcription

A

the burst size

24
Q

enhancer increase —— in transcription

A

bursting frequency form their target core promoter

25
Q

what does transcription initiation & elongation generate

A

a pre-mRNA that must be processed to yield mature mRNA that can be translated into protein

26
Q

transcription - three major steps in converting pre-mRNA to functional mRNA within the ———

A

nucleus.

  1. adding a 5’ cap & a 3’ poly A tail to the transcript = protective role
  2. removal of introns = RNA splicing
  3. joining expressed exons
27
Q

steps & define 5’ cap on eukaryotic mRNAs

A

= 7-methylguanosine cap added to the 5’end of mRNA = helps prevent degradation & helps ribosome attach to mRNA to begin translation

  1. phosphatase removes 5’ phosphate
  2. Guanyl transferase adds GMP to RNA with a 5’ to 5’ link
  3. methyl transferase adds methyl groups
28
Q

RNA splicing sites x3

A
  1. 5’ splice site
  2. branch point
  3. 3’splice site
29
Q

The two reactions in RNA splicing & completion

A
  1. Branching = the branch point adenosine attacks the phosphodiester group at the 5’ splice site, producing a cleaved 5’ exon & a lariat-intron-3’ exon intermediate = cuts sugar phosphate backbone
  2. exon ligation = newly exposed 3’ OH of the 5’ exon attacks the phosphodiester group of the 3’ splice site, ligating the 5’ & 3’ exons to form mRNA & release the lariat intron

completion = mRNA is released, intron lariat is degraded & spliceosome disassembled

30
Q

transcription - polyadenylation & termination

A
  1. cleavage at 3’ end of mRNA is catalysed by the CPSD enzyme
  2. CPSF binds to polyadenylation signal AAUAAA
    (occurs 10-30 nucleotides upstream of the poly A tail)
  3. proteins CstF bind GU-rich sequences located downstream of cleavage site = these proteins add specifically to cleavage process & they also bind to RNA polymerase II = this links transcription elongation & termination
  4. the enzyme poly A polymerase adds a chain of 200 adenines to RNA
31
Q

what is a poly A tail & function

A

= long chain of adenine residues added to the 3’ end of mRNA = polyadenylation

  • increases transcript stability & allows export of the mRNA from the nucleus into the cytoplasm
32
Q

summary of transcription steps x6

A
  1. assembly of initation complex
  2. elongation
  3. termination
  4. processing & polyadenylation
  5. RNA splicing
33
Q

two critical regions in tRNA

A
  1. anticodon = a set of three consecutive nucleotides that pairs with the complementary codon in the mRNA
  2. 3’ amino acid binding site
34
Q

another name for the third position in a codon

A

the wobble = a mismatch can be tolerated in the third position (must involve a purine & a pyrimidine)

35
Q

aminoacyl tRNA synthetases

A

= enzyme that attaches the appropriate amino acid to the corresponding tRNA

  • links the amino acid to rRNA by high energy bond & this bond drives the formation of the peptide bonds that link amino acids in the growing polypeptide bond
36
Q

how amino acids are joined together (translation)

A

via the formation of a peptide bond between the carboxyl (C-) group at the end of a growing polypeptide chain & a free amino (N-) group on an incoming amino acid

  • protein synthesised from its N terminal end to its C-terminal end
37
Q

where does protein synthesis occur

A

ribosomes

38
Q

4 key regions in ribosomes & function

A
  1. mRNA binding site
  2. Aminoacyl (A) site = binds the new tRNA molecule carrying the next amino acid
  3. Peptidyl (P) site = holds the tRNA to which the nascent polypeptide is attached
  4. Exit (E) site = exit site for tRNA as they leave ribosome after their amino acid has been added
39
Q

where do ribosomes come from

A

60S & 40S ribosomal units are assembled in the nucleus. exported into the cytoplasm where they join together on an mRNA molecule, near the 5’ end to synthesise proteins

40
Q

Translation - initiation steps

A
  1. 40S ribosomal unit interacts with 3 eukaryotic initiation factors (eIF) to form the preinitiation complex
  2. joins the initiator tRNA^met (carries methionine) & eIF5
  3. initator complex is formed by the binding of mRNA with eIF4
  4. initiator complex scans along the mRNA in search of the start codon - usually the first AUG (methionine) embedded in a consenus sequence known as the Kozak sequence ACCAUGG

= locating the start codon leads to the recruitment of the 60S subunit to form 80S ribosome complex

  1. the eIF proteins dissociate once the 80s ribosome is formed
    - the initiator tRNA^met is located at the P site & the a site is vacant waiting for the arrival of the second tRNA
41
Q

Translation - elongation steps

A

recruitment of elongation factor (EF) proteins facilitate:

  1. recruitment of charged tRNAs into the A site
  2. formation of a peptide bond between sequential amino acids
  3. translocation of the ribosome in the 3’ direction along the mRNA

continues until stop codon as not anticodons for them

42
Q

what provides the energy for translation elongation

A

GTP cleavage

43
Q

translation - termination

A

eRF1 release factor bind to the stop codon in the A site & release the polypeptide = this leads to ribosome separation

44
Q

where does translation occur

A

cytoplasm

45
Q

summary of translation

A
  1. pre-RNA produced
  2. 5’capping, polyadenylation & splicing to create mature mRNA
  3. mature mRNA leaves nucleus
  4. mRNA translated till stop codon
  5. polypeptide chains synthesised from amino to carboxyl end

hc (11 decks)

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