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MIMS > Proteins, Molecules & Enzymes Lent Term > Flashcards

Proteins, Molecules & Enzymes Lent Term Flashcards

1
Q

Nucleosome Components

A

2 units of H2A, H2B, H3 and H4

1 unit of H1 outside

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2
Q

SMC protein names and model

A

Cohesin and Cadherin: p-extrusion model

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3
Q

Regions in Chromatin with different densities

A

Heterochromatin: high nucleosome density
Euchromatin: Transcriptional

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4
Q

Helicases (Eukaryotic and prokaryotic)

A

MCM

DnaB

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5
Q

Origin Recogition Complexes

A

DnaA to ORiC

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6
Q

DNA Polymerases

A
  • Requires RNA primase
  • Sliding Clamp: PCNA
    Pol 3: Replisome + trombone model
    Pol1: Removes RNA primase + high fidelity
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7
Q

Telomeres Sequences and limit

A

TTAGGG, Hayflick Limit

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8
Q

Chromatin Immunoprecipitation

A
  • Fixation Formaldehyde

- Specific DNA binding Sites

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9
Q

DNA footprinting

A
  • General DNA binding
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10
Q

cDNA Libraries

A
  • mRNA content: no promoters / regulatory elements etc
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11
Q

Gel Electrophoresis

A
  • Ethidium Bromide Dye
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12
Q

PCR requirements

A
  • ss DNA primers

- Heat stable thermoaquatus polymerase

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13
Q

Genome Sequencing Basic Units

A
  • Chain termination 2,3 Deoxynucleotides
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14
Q

HiC (Hi chromosome capture)

A

Adjacent Strands Crosslinked & ligated

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15
Q

Base Excision Repair Key terms

A
  • Glycolase

- Abasit Site

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16
Q

NER

A
  • TF2H unwinding

- Xeroderma Pigmentosum

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17
Q

MMR

A
  • Methylated Mother Strand

- Hereditory nonpolyposis colorectal cancer

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18
Q

NHEJ

A
  • For making Ab genes / immunocompetence
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19
Q

HR

A
  • Holiday Junctions
  • Meiosis
  • BRCA gene
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20
Q

Photoreactivation

A

NER: Thymidine Dimer

21
Q

Genomic Imprinting Where?

A

CpG islands

22
Q

Core Enzyme + holoenzme

A

S factor recognises promoter

Heat shock S factor

23
Q

Pre-Initiation Complex Factors

A

TF2D with TATA binding Protein (TBP) and TBP Associated Factors (TAFs) with RNA POL2

24
Q

Eukaryotic and Prokaryotic Promoters

A 
Pribnow box (-10) and -35 box
TATA box (Core promoter element)
25
Q

Termination of Transcription

A

Rho Independent: Hairpin CG pause, long chain of U’s for dissociation
RHo Dependent: Hairpin CG pause, Rho to dissociate RNA pol

26
Q

Bacterial Response to external elements

A

Catabolite Activator (CAP) –> Via CAMP –> Binds DNA: PROMOTING
Lac Operon: Lactose presence releases DNA Operon
increased Transcription of B-galactosidase

27
Q

Eukaryotic Response Elements

A

CREB: Camp Response Elements
GRE: dissociation + dimerisation + move into nucleus

28
Q

Histone Acetylases

A

Increase Transcription by losening Histone Charge

  • CREB Binding Protein
  • GRE is the OPPOSITE
29
Q

Cell Specific Transcription Factors

A

MyoD in myoblasts

Oct-2 IG genes in B cell lymphocytes

30
Q

Name of mRNA 5’ Cap

A

G5’ppp’5N +2nd methyl group added

31
Q

Splicesome Key Steps

A
  1. 2’OH Nucleophilic Attach by Branch A to 5’ end OH
  2. Formation of Lariat Structure
  3. 3’OH nucleophilic Attack by 5’ end to 3’end of intron
32
Q

Splicesome Components

A

SSnRNP’s (U2 and U6 core)

33
Q

Frasier Syndrome

A

Kidney / Urogenital Defects
+/- KTS isoforms: 1:2 instead of 2:1
+ isoforms dont bind DNA

34
Q

Degradation of mRNA

A

5’ - 3’ Exonuclease

  • Deadenylation of 3’ Poly A tail
  • Decapping
35
Q

Initiation of Translation on Ribosomes (what consensus) in Bacteria

A
  1. Shine-Dalgarno Consensus 5’ end

Attracts 30s ribosome

36
Q

Whats the initiator tRNA?

A

Met-tRNAi + met tRNA (elongation)

37
Q

What is IRES and viruses involved

A

Internal Ribosome Entry Site:

Hep C IRES: Virus deactivates normal translation mechanisms, uses IRES for its own proteins

38
Q

Scanning Ribosome Model in Eukaryotes

A

40s Binds 5’ Cap (Eukaryotic INitiation Factor- EIF4)

Met-TRNAI Locks on

39
Q

Actual process of Translation (steps)

A
  1. Subsequent Aminoacyl-TRNA binds to A site
  2. Peptide Bond formation (transfer of peptide from P to A)
  3. Translocation from A to P
  4. Discharged tRNA leaves through E site
40
Q

Assistance in Translation:

A
  1. Elongation Factor Proteins 1: initial Aminoacyl-tRNA A site binding
  2. EFP 2: Translocation of ribosome
  3. Peptidyl Transferase
41
Q

Global Modification of Translation Control

A

Eukaryotic INitiation Factor 2 (binds 40s subunit) and phosphorylation

42
Q

Specific translation Modifications:

A

Ferritin MRNA (Sequesters Iron)
Low Iron –> Iron Regulatory Protein Increases inhibition
Iron Response Element in 5’UTR inhibited –> No ferritin

43
Q

Riboswitches

A

Thiamine Levels directly control rate of thiamine synthesis: AA’s post translation

44
Q

Proteasome Steps

A
  1. Recognition
  2. Disassociation (Ub spat Out)
  3. Translocation: fed into shaft (2 outer and 2 inner rings)
  4. Destruction: protein degraded
45
Q

Ub ligation

A

E1-UB Activating Enzyme
E2-UB conjugating enzyme
E3-UB ligase

46
Q

Streptomycin and mRNA translation

A

Binds 30s subunit

47
Q

Epigenetic Proteins

A

DNA methyltransferases & DNA maintenance

48
Q

Epigenetic Wiping Stages

A
  1. Prospermatogoia during sperm development
  2. Right after birth during oocyte phase maturation
    2nd: right after fertilisation

MIMS (5 decks)

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