Proteins, Molecules & Enzymes Lent Term

Question 1

Nucleosome Components

Answer 1

2 units of H2A, H2B, H3 and H4

1 unit of H1 outside

Question 2

SMC protein names and model

Answer 2

Cohesin and Cadherin: p-extrusion model

Question 3

Regions in Chromatin with different densities

Answer 3

Heterochromatin: high nucleosome density
Euchromatin: Transcriptional

Question 4

Helicases (Eukaryotic and prokaryotic)

Answer 4

MCM

DnaB

Question 5

Origin Recogition Complexes

Answer 5

DnaA to ORiC

Question 6

DNA Polymerases

Answer 6

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

Question 7

Telomeres Sequences and limit

Answer 7

TTAGGG, Hayflick Limit

Question 8

Chromatin Immunoprecipitation

Answer 8

• Fixation Formaldehyde

- Specific DNA binding Sites

Question 9

DNA footprinting

Answer 9

• General DNA binding

Question 10

cDNA Libraries

Answer 10

• mRNA content: no promoters / regulatory elements etc

Question 11

Gel Electrophoresis

Answer 11

• Ethidium Bromide Dye

Question 12

PCR requirements

Answer 12

• ss DNA primers

- Heat stable thermoaquatus polymerase

Question 13

Genome Sequencing Basic Units

Answer 13

• Chain termination 2,3 Deoxynucleotides

Question 14

HiC (Hi chromosome capture)

Answer 14

Adjacent Strands Crosslinked & ligated

Question 15

Base Excision Repair Key terms

Answer 15

• Glycolase

- Abasit Site

Question 16

NER

Answer 16

• TF2H unwinding

- Xeroderma Pigmentosum

Question 17

MMR

Answer 17

• Methylated Mother Strand

- Hereditory nonpolyposis colorectal cancer

Question 18

NHEJ

Answer 18

• For making Ab genes / immunocompetence

Question 19

HR

Answer 19

• Holiday Junctions
• Meiosis
• BRCA gene

Question 20

Photoreactivation

Answer 20

NER: Thymidine Dimer

Question 21

Genomic Imprinting Where?

Answer 21

CpG islands

Question 22

Core Enzyme + holoenzme

Answer 22

S factor recognises promoter

Heat shock S factor

Question 23

Pre-Initiation Complex Factors

Answer 23

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

Question 24

Eukaryotic and Prokaryotic Promoters

Answer 24

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

Question 25

Termination of Transcription

Answer 25

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

Question 26

Bacterial Response to external elements

Answer 26

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

Question 27

Eukaryotic Response Elements

Answer 27

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

Question 28

Histone Acetylases

Answer 28

Increase Transcription by losening Histone Charge - CREB Binding Protein - GRE is the OPPOSITE

Question 29

Cell Specific Transcription Factors

Answer 29

MyoD in myoblasts | Oct-2 IG genes in B cell lymphocytes

Question 30

Name of mRNA 5' Cap

Answer 30

G5'ppp'5N +2nd methyl group added

Question 31

Splicesome Key Steps

Answer 31

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

Question 32

Splicesome Components

Answer 32

SSnRNP's (U2 and U6 core)

Question 33

Frasier Syndrome

Answer 33

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

Question 34

Degradation of mRNA

Answer 34

5' - 3' Exonuclease - Deadenylation of 3' Poly A tail - Decapping

Question 35

Initiation of Translation on Ribosomes (what consensus) in Bacteria

Answer 35

1. Shine-Dalgarno Consensus 5' end | Attracts 30s ribosome

Question 36

Whats the initiator tRNA?

Answer 36

Met-tRNAi + met tRNA (elongation)

Question 37

What is IRES and viruses involved

Answer 37

Internal Ribosome Entry Site: | Hep C IRES: Virus deactivates normal translation mechanisms, uses IRES for its own proteins

Question 38

Scanning Ribosome Model in Eukaryotes

Answer 38

40s Binds 5' Cap (Eukaryotic INitiation Factor- EIF4) | Met-TRNAI Locks on

Question 39

Actual process of Translation (steps)

Answer 39

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

Question 40

Assistance in Translation:

Answer 40

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

Question 41

Global Modification of Translation Control

Answer 41

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

Question 42

Specific translation Modifications:

Answer 42

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

Question 43

Riboswitches

Answer 43

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

Question 44

Proteasome Steps

Answer 44

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

Question 45

Ub ligation

Answer 45

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

Question 46

Streptomycin and mRNA translation

Answer 46

Binds 30s subunit

Question 47

Epigenetic Proteins

Answer 47

DNA methyltransferases & DNA maintenance

Question 48

Epigenetic Wiping Stages

Answer 48

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