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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
what does transcription initiation & elongation generate
a pre-mRNA that must be processed to yield mature mRNA that can be translated into protein
26
transcription - three major steps in converting pre-mRNA to functional mRNA within the ---------
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
steps & define 5' cap on eukaryotic mRNAs
= 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
RNA splicing sites x3
1. 5' splice site 2. branch point 3. 3'splice site
29
The two reactions in RNA splicing & completion
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
transcription - polyadenylation & termination
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
what is a poly A tail & function
= 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
summary of transcription steps x6
1. assembly of initation complex 2. elongation 3. termination 4. processing & polyadenylation 5. RNA splicing
33
two critical regions in tRNA
1. anticodon = a set of three consecutive nucleotides that pairs with the complementary codon in the mRNA 2. 3' amino acid binding site
34
another name for the third position in a codon
the wobble = a mismatch can be tolerated in the third position (must involve a purine & a pyrimidine)
35
aminoacyl tRNA synthetases
= 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
how amino acids are joined together (translation)
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
where does protein synthesis occur
ribosomes
38
4 key regions in ribosomes & function
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
where do ribosomes come from
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
Translation - initiation steps
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 6. 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
Translation - elongation steps
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
what provides the energy for translation elongation
GTP cleavage
43
translation - termination
eRF1 release factor bind to the stop codon in the A site & release the polypeptide = this leads to ribosome separation
44
where does translation occur
cytoplasm
45
summary of translation
1. pre-RNA produced 2. 5'capping, polyadenylation & splicing to create mature mRNA 3. mature mRNA leaves nucleus 3. mRNA translated till stop codon 4. polypeptide chains synthesised from amino to carboxyl end

hc (11 decks)

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