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E Coli DNA by Mind Map: E Coli DNA
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E Coli DNA

Restriction / Modification System

Modification Methylase

protect DNA from unneeded "repair"

role in repair

differentiate template strand

topoisomerases

Replication

preconditions

transcription factors, DnaA

nutrients (fixed growth vs change), magic spot

@oric

terms, IHF, R1-R5,FIS, IHF, ATP DnaBoxes

polymerization

replication errors

terms

helicase

dna gyrase

SSB

DNAPIII, structural model, holoenzyme (protein complex), domains (hand)

Primosome Assembly Site, PriA, PriB

termination

ter sites

normal

failsafe

dif

postconditions

Structure&Topology

pyrimidine

purine

major/minor groove

GC=3, AT=2

topoisomerases

precondition, relax supercoils

postcondition, add +1 or +2 twists, removes negative supercoils, change DNA topology

types, I, "steps of 1", II, steps of 2, require ATP

conformations: b, a, z DNA

bdna has 10bp/turn and is the "typical" conformation.

Linking = twists + writh (heteroduplex)

phosphodiester

sugar-phosphate

Analysis Techniques

Gel Electrophoresis

Northern Blot, RNA

Southern Blot, DNA

Western BLot, Protein

use in deletion analysis

use in restriction site mapping

restriction site mapping

DNA damage & repair

Replication Errors

Mismatch Repair System

Exonucleases

spontaneous

Oxidative, oxoG, OH radical, Superoxide

chemical damage

aflotoxin (stored grain)

bezno2pyrene(smokers)

UltraViolet Radiation

thymine dimer

Repair

reverse (undo)

excision (del, pol new)

Recombinatorial

Nucleotide Excision Repair (NER)

precondition

BIG molecules, major deformities

repairs chemical damage

repairs Ultra Violet Radiation

proteins, UvrA, UvrB, UvrC, mechanism

Base Excision Repair

precondition

mechanism & BER pathway, terms, DNA glycosylase, AP Site, AP endonuclease, DRPase, DNAPI, DNA Ligase

postcondition

small molecules, minor DNA deformities

Repairing Oxidative Damage, OH radical

New node

Glycosylates (related), DNA glycosylase, Thymine Glycol, methylation, spontaneous C-->U

Adaptive Response "methyl group repair"

methylating agents

repair proteins, Glycosylates, AlkA, inducible, recognize methyl group, Tag, not-inducible, recognize DNA damage

Directly Reversible, AlkB, turnover, inducible, ogt, No turnover (not enzyme), not inducible, Ada, inducible, mechanism

mechanism of induction

SOS response, UmuC, UmuD, RecA, also involved with recombination

DNA repair involving no lesion removal

      

recombinatorial repair

lesion bypass DNAP

damage avoidance mechanism

phenomenology

unresolved

primosome assembly

"minutes" vs 84 degrees/minutes

Recombination

Rec BCD Pathway

holiday junction

RecA protein & pathway