DNA Repair + Pathology (Week 2)

BER pathway

Goal is to excise and repair lesions of DNA damage, often from reactive-oxidative species

ROS, tumor

__ potentially inhibit repair of DNA via down-regulation of certain initial proteins of the BER pathway

• Buildup of carcinogenic mutations → __ progression

Endogenous DNA damage

• Replication stress/errors, ROS, infections

• Intrinsic instability of DNA (i.e. hydrolysis, oxidation, methylation)

Exogenous DNA damage

• Chemical radials, ionizing irradiation, UV-light

DNA repair, cell cycle checkpoint, apoptosis, transcriptional activation

4 classes of safeguard to DNA damage

Natural Errors

Methods include DNA Polymerase base selection, proofreading, mismatch repair

Mismatch Repair (MMR), colon

__ __ comes in post-replication and naturally detect errors and repair (natural error method)

• Useful for detecting underlying __ cancers

Dam methylase

Recognize GATC sites on bacterial DNA strands separated with only 1 methyl group and add new methyl groups for symmetry (natural error - MMR method)

Msh, Mut

Mismatch repair heterodimers in human cells are known as __

Mismatch repair heterodimers in bacteria are known as __

Endogenous/exogenous DNA damage checkers

Base excision repair, nucleotide excision repair, recombination, polymerase bypass

do not, block

Recombination + polymerase bypass __ (do/do not) remove DNA damage but instead remove its __ replication

Base excision repair (BER), single, uracil

__ __ __ is the major pathway for repair of a __ base modification, __ misincorporation = deamination of C, alkylation, oxidative damage

DNA glycosylases, AP endonuclease, DNA polymerase, ligase

In BER

1. __ __ recognize specific lesion and remove base at glycosidic bond, produce Apurinic/apyrimidinic (AP) site by base “flipping out”

2. __ __ incises phosphodiesterase backbone adjacent to AP site

3. AP nucleotides are removed by exonuclease/__ __ and patch refilled by DNA synthesis and __

Nucleotide excision repair (NER), pyrimidine

__ __ _Repairs bulky lesions and is a multienzyme complex

This also repairs __ dimers

Nuclease, helicase, polymerase, ligase

In NER

1. Excision __ leaves to phosphodiester backbone

2. DNA __ removes single strand

3. DNA __ adds new nucleotides

4. DNA __ seals openings

Double-stranded break

Homologous Recombination (HR) and Non-Homologous End Joining (NHEJ) are used for repair of a __-__ __ of DNA

>

HDR fidelity _ (< / = / >) NHEJ fidelity

Structure

__ of DNA polymerase is conserved across most cells

bypass polymerases, distributive polymerization

As a last resort, cells employ “__” __ - with loosened specificity allow for progression of DNA replication

• exhibit __ __ - meaning low accuracy and will fall off

Xeroderma pigmentosum (XP)

Sun sensitivity with severe sunburn, erythema from minimal sun exposure, freckle pigmentation of face

childhood skin cancers, NER

Associated risks of Xeroderma pigmentosum include an increased prevalence of __ onset __ __

• Diagnosis is made from viewing dysregulation of __ repair mechanism

UV-light induced damage

Condition that induces covalent linkages between consecutive bases of C and T bases on nucleotide chain in vicinity of carbon-carbon double bonds

NER, BER, pyrimidine

__ and __ help against __ dimers present from UV-light damage

Benzopyrene, lung

__ is an aromatic hydrocarbon that forms covalent DNA adducts after metabolic activation → Mutations → __ cancer

NRTI Drugs

Phosphorylated and inhibit action of HIV reverse transcriptase

• halts conversion of viral RNA to double stranded DNA

Vorinostat

Histone deacetylase inhibitors that correct aberrant balance between acetylated and deacylated histones

Deacetylated, acetylation, T cell lymphoma

For Vorinostat

Genes are turned off when histones are __ (i.e. tumor suppressor gene turned off in cancer)

Regulate transcription of genes with __ → preventing tumorigenesis of cutaneous _ __ __

Nucleosomes, histones

• During eukaryotic replication

  1. __ are disrupted → Each ds strand is 1/2ved

  2. New __ are added by chromatin assembly factors