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BIOCHEMISTRY 1 > Molecular biology > Flashcards

Molecular biology Flashcards

1
Q

DNA Polymerase 1

A
  • prokaryotes
  • gene A
  • replication, recombination and repair
    1. 5’-3’ DNA dependent DNA polymerase ⇒ replace primer
    2. 3’-5’ exonuclease ⇒ proof reading
    2. 5’-3’ RNA dependent DNA polymerase
  • gap filling following DNA replication, repair and recombination
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2
Q

DNA Polymerase alpha

A
  • eukaryotes
    1. 5’-3’ DNA dependent RNA polymerase
    2. Primase activity
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3
Q

DNA Polymerase 2

A
  • prokaryotes
  • gene B
  • not DNA dependent
  • DNA proofreading and repair
  • mitochondrial DNA synthesis
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4
Q

DNA Polymerase beta

A
  • eukaryotes

- repair

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5
Q

DNA Polymerase 3

A
  • prokaryotes
  • gene B
  • 5’-3’ DNA dependent DNA polumerase
  • 3’-5’ exonuclease
  • subunits:
    • alpha: polymerase
    • epsilon: 3’-5’ exonuclease
    • theta: assist epsilon
  • Associated accessory proteins:
    • beta x2: sliding clamp increase processibility
    • tao: dimerise 2 core proteins ⇒ tethring
    • gamma
    • delta
    • delta’
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6
Q

DNA Polymerase epsilon

A
  • eukaryotes
    1. 5’-3’ DNA dependent DNA polymerase
    2. synthesis of leading strand
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7
Q

DNA A Protein: Initator

A
  • prokaryotes
  • binds Ori sequence
  • unwinds DNA
  • load Helicase
  • 150 to 250 bp
  • ATP dependent
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8
Q

DNA polymerase gamma

A
  • eukaryotes
    1. DNA dependent DNA polymerase
    2. Synthesis of Mt DNA
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9
Q

DNA B: Helicase

A
  • prokaryotes
  • DNA B is not an active helicase when in the P/dnaB/O complex
  • P is removed by heat shock proteins (dnaK, dnaJ, GrpE)
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10
Q

DNA Polymerase delta

A
  • eukaryotes
    1. 5’-3’ DNA dependent DNA polymerase
    2. synthesis of lagging stand
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11
Q

DNA C: Deliver and loads helicase

A
  • prokaryotes
  • stabilizes DNA B ⇒ DNA C leaves the complex
  • binding of C to B is ATP dependent
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12
Q

ORC

A
  • eukaryotes
  • ORC= origine replication compkex
  • binds a 11 bp sequence called origin replication element ORE, fond in ARS
  • DUE= DNA unwinding element
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13
Q

SSB

A
  • prokaryotes

- stabilizes unwound DNA

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14
Q

RPA

A
  • eukaryotes

- replication protein A

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15
Q

DNA G

A
  • prokaryotes

- prime DNA synthesis

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16
Q

RNAase

A
  • eukaryotes

- eukaryotic polymerase don’t have exonuclease activity

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17
Q

Gyrase

A
  • prokaryotes

- negatively supercoil DNA (topoisomerase2)

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18
Q

RNAase H

A
  • both prokaryotes and eukaryotes
  • 3’-5’ exonuclease
  • remove RNA primer
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19
Q

DNA ligase

A
  • both prokaryotes and eukaryotes

- ligates the okasaki fragments of the lagging stand ⇒ ATPase

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20
Q

Prokaryotic transcription

A
  • RNA transcript ⇒ mRNA
  • RNA can be polycitronic ⇒ encode for new proteins
  • transriptic + translation simultaneously and same place
  • RNA polymerase enoguh for transcription
  • TATA box closer to coding part of gene
  • 1 RNA polymerase
  • shorter life time of mRNA
  • RNA polymerase slides along double helix DNA until reaches promoter sequence
  • promoter sequence recognized by sigma factor
  • once RNA pol. reaches promoter ⇒ it latches on
  • helix is opened in front of it and polymerization begins
  • sigma factor is released
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21
Q

Eukariotic transcription

A
  • RNA transcript is modified
  • mRNA only encodes 1 protein (monocitronic)
  • transcription happens before, in the nucleus ⇒ translation in cytosol
  • RNA polymerase requires transcription factors
  • TATA box further from coding part of gene
  • 3 RNA polymerase
  • longer lifetime of mRNA because of cap/tail
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22
Q

RNA polymerase

A
  • prokaryotes
    1. alpha: recognise regulatory factors
    2. beta: polymerase activity, binds Mg2+ ions and composes the catalytic subunit
    3. beta’: binds DNA template
    4. w: unknown function
    5. sigma: enables the core enzyme to recognize and bind the promoter region to form the pre initiation complex PIC
    6. 30-50bp/min
    7. no proof reading
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23
Q

RNA Polymerase 1

A
  • eukaryotes
    1. forms rRNA
    2. found in the nucleolus
    3. insensitive to alpha-amantinin
24
Q

RNA Polymerase 2

A
  • eukaryotes
    1. mRNA
    2. IncRNA
    3. miRNA
    4. SnRNA
    5. found in nucleus
    6. high sensitivity to alpha-amantinin
25
Q

RNA Polymerase 3

A
  • eukaryotes
    1. tRNA
    2. 5s rRNA
    3. intermediate sensitivity to alpha-amantinin
26
Q

Prokaryotic RNA Polymerase complex

A
  • promoter sequence
  • sigma binds promoter sequence
  • upstream from transcription start site, we have a consensus sequence to which RNA polymerase binds to form the closed complex
  • more proximal to transcription start site⇒ TATA box
  • it binds to transcription factor and therefor indicates where transcription should be initiated from
27
Q

Eukaryotic RNA Polymerase complex

A
  • TATA box bind to TBP (subunit of TFIID)
  • TAFs bind downstream promoter elements DPE and initiator sequence INR
  • Caat box
    • upstream cis-acting element
    • binds with CTF
    • increase the frequency of transcription
  • GC box
    • upstream cis-acting element
    • bind Sp1
    • increase the frequency of transcription
  • TFIID⇒ complex consisting of TBP and 14 TAFs
  • TFIIA,B,D ⇒ transcription initiation site ⇒ F, E, H
28
Q

Spliceosome

A
  • macromolecular complex responsible for precursor mRNA splicing
  • consists of:
    • U1: within the snRNP complex binds first by base pairing to the 5’ exon - intron boundary
    • U2: within snRNP complex, binds to branch site ⇒ exposes nucleophilic A residue
    • U4/U5/U6: within snRNP complex mediates ATP-dependent protein-mediated unwinding that results in disruption of the base paired U4-U6 complex with the release of U4. U6 is then able to interact with U2 and then U1
    • U5: enhances elignment
29
Q

Splicing

A
  • starts with a cut at 5’ junction between intron and exon. Done by nucleophile attack from adenine just upstream from 3’ end
  • the free 5’ forms a loop with adenine. ⇒ 5’-2’ phosphodiester bond
  • second cut at junction of intron and 3’ exon. The 3’-OH of upstream exon attacks the 5’ phosphate of downstream exon-intron junction ⇒ loop is released ⇒ 5’ and 3’ extremities of the eons are ligated to form a continuous segment
30
Q

tRNA

A
  • 3 loops
  • 4 arms
  • nucleotide derivates are present like iodine, pseudouridine, dihydrouridine
  • phosphate at 5’ end
  • CCA sequence at 3’ end where AA are bound
  • part containing 3’ and 5’ arm: acceptor arm
  • D-loop⇒ aminoacyl-tRNA-synthase bound
  • anticodon loop ⇒ anticodon
  • T-loop ⇒ binding site for ribosome
  • recognition + attachement:
    • AA + ATP⇒ aminoacyl-AMP + PPi
    • Aminoacyl-AMP + tRNA ⇒ aminoacyl-tRNA + AMP
  • A site: binds aminoacyl-tRNA
  • P site: occupied by peptide-tRNA
  • E site: occupied by empty tRNA
31
Q

rRNA

A
  • large 60s subunit (3RNA + 49proteins)

- small 40s subunit (1RNA + 33 proteins)

32
Q

miRNA

A
  • pri-miRNA are 5’-capped and 3’-polyadenylated
33
Q

snRNA

A
  • U1, U2, U4, U5, U6 are involved in intron removal and processing of mRNA precursors into mRNA
  • U7 nRNA involved in production of correct 3’ ends of histone mRNA - which lacks a poly(A) tail
34
Q

siRNA

A
  • RNA silencing and post transcriptional regulation of gene expression by: cleavage of mRNA strand, destabilization of mRNA through shortening of poly A tail, less efficient translation of mRNA into proteins by ribosomes
35
Q

IF-1

A
  • prokaryotes

- complex with small subunit

36
Q

IF-2

A
  • prokaryotes
  • binds to GTP, it attaches to the initiator aminoacyl-tRNA ⇒ joins the small subunit and the mRNA ⇒ it goes directly into P-site where binds to AUG
  • when binding of large subunit ⇒ hydrolysis of GTP on IF-2
  • IF-1 and 2 are released
  • the 2 subunits unite ⇒ elongation begins
37
Q

IF-3

A
  • prokaryotes
  • complex with small subunit
  • when released ⇒ binding of large subunit
38
Q

eIF-2

A
  • eukaryotes
  • binds AA-tRNA to 5’-cep of mRNA
  • GTP binding protein involved un bringing the initiation or tRNA to the P site of the pre-initiation complex
  • formation of 43S pre-initiation complex
39
Q

eIF-2a

A
  • eukaryotes
  • is phosphorylated by at least four different protein kinases (HCR, PKR, PERK, GCN2)
  • binds tightly to and inactivates GTP-GDP recycling protein eIF-2b⇒ prevent formation of 43s pre initiation complex and blocking protein synthesis
40
Q

eIF-3

A
  • eukaryotes
  • eIF-3 and eIF-1a bind to newly dissociated 40s ribosomal subunit. ⇒ delays its reallocation with 60s subunit and allows other transition initiation factors to associate with the 40s subunit
  • binds with high affinity to 4G component of 4F, and it links this complex to 40s ribosomal subunit
41
Q

eIF-4

A
  • eukaryotes
  • eIF-4a
  • eIF-4g: interacts with eIF3; poly A tail binging
  • eIF-4e: rate limiting step that binds to 5’cap
  • eIF-4b: reduces complex secondary structure of 5’ end of mRNA through its ATP- dependent helices activity
  • eIF-4bp: inhibit complex assembly
  • eIF-4 a+g+e⇒4f
42
Q

EF-TU

A
  • prokaryotes

- elongation factor thermo-unstable mediates the entry of aminoacyl-tRNA to the entry A site

43
Q

EF-TS

A
  • prokaryotes

- serves as guanine exchange factor for EF-TU, catalyzing the release of GDP from EF-TU

44
Q

EF-G

A
  • prokaryotes
  • catalyses the translocation of the tRNA and the mRNA down the ribosome at the end of each round of polypeptide elongation
45
Q

eEF-1a

A
  • eukaryotes
  • formas a ternary complex with GTP and the entering aminoacyl-tRNA.
  • complex allows the correct AA-tRNA to enter A-site with the release of EF1A-GDP and phosphate
  • GTP hydrolysis is catalysed by an active site on ribosome; hydrolysis induces a conformational change in the ribosome concomitantly increasing affinity for tRNA
46
Q

eEF-1b

A
  • eukaryotes

- acts as guanine exchange factor for alpha, and catalyses the release of GDP from alpha

47
Q

eEF-2

A
  • eukaryotes
  • binds to and displaces the peptide tRNA from the A site to the P site
  • in turn the deacetylated tRNA is on the E site from which it leaves the ribosome
  • EF2-GTP complex is hydrolyzed to EF2-GDP, effectively moving the mRNA forward by one codon and leaving the A site open for occupancy by another ternary complex of AA tRNA-EF1a-GTP and another cycle of elongation
48
Q

RF-1

A
  • prokaryotes
  • termination factor
  • trigger hydrolysis of ester bond in peptide-tRNA + release of new protein
  • recognise stop codon resides in A site
  • bound by complex consisting of RF3-GTP
  • complex + peptide transferase promotes hydrolysis of bond between peptide and tRNA occupying P site
  • thus a water molecule rather than amino acid is added. this hydrolysis releases the protein and tRNA from P site
49
Q

RF-2

A
  • prokaryotes

- trigger hydrolysis of ester bond in peptide-tRNA + release of new protein

50
Q

RF-3

A
  • prokaryotes
  • catalyses release of RF1 and 2
  • bound to GTP
51
Q

eRF in eukaryotes

A
  1. primary transcript has 20 nucleotides cleaved downstream from recognition sequence
  2. enzyme polyA polymerase adds poly A tail ⇒ protects 3’end from endonuclease attack. + involved in transport of mRNA to cytoplasm
52
Q

Actinomycin D

A
  • intercalated between C and G pairs in DNA

- inhibits transcription, elongation in prokaryotes and eukaryotes

53
Q

Rifampicin

A
  • binds to beta subunit of the prokaryotes RNAP

- blocks promoter clearance

54
Q

Alpha-amatinin

A
  • blocks translocation of RNA polymerase during phosphodiester bond formation
55
Q

Chloramphenicol

A
  • inhibitor of translation

BIOCHEMISTRY 1 (9 decks)

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