Luo_Lecture7 Includes Summary

7/27/2019 Luo_Lecture7 Includes Summary

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Molecular Biology

Principles and Practice

DNA Mutation and Repair

Copyright 2012 by W. H. Freeman and Company

Michael M. Cox Jennifer A. Doudna Michael ODonnell


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Lesion: site of DNA damage

Mutation: permanent base change

bad - result in amino acid change that makes protein

non-functional

good - evolution (rare)

silent mutation - no functional impact

Lesion v.s. mutation


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Sources of DNA damage

Endogenous damages: internal agents fromnormal metabolic byproducts

Reactive oxygen species

Exogenous damages: external agents UV radiation from the sun

X-rays and gamma rays

Hydrolysis or thermal disruption

Plant toxins Man-made mutagenic chemicals

Viruses

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UV-induced DNA damages

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UV light

UV-A: 320-400 nm majority of UV light reaching earth

does little DNA damage

UV-B: 295-320 nm

~10% of UV light reaching earth

responsible for most of DNA damage in skin

UV-C: 100-295 nm

includes wavelength of maximum DNA absorbance (260 nm)

little reaches earth's surface due to ozone layer

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Two pathways for

UV-induced DNA damage

both involve dimer formation between

adjacent pyrimidine rings on same strand

cyclobutane pyrimidine dimer (CPD)

accounts for 75% of UV induced damage

(6-4) photoproducts

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UV-induced cyclobutane

pyrimidine dimer formation

thymine-thymine dimers are most common

cytosine-thymine and cytosine-cytosine dimers also form at slower rates

Adapted from Friedberg, E. C., et al. DNA Repair and Mutagenesis, 2/3. ASM

Press, 2005.7


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UV-induced

(6-4) photoproduct formation

Adapted from Friedberg, E. C., et al. DNA Repair and Mutagenesis, 2/3. ASM

Press, 2005.8


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Cyclobutane pyrimidine dimers produce

a kink in DNA

Reproduced from Park, H., et al., Proc. Natl. Acad. Sci. USA 99 (2002): 15965-

15970. Copyright 2002, National Academy of Sciences, USA. Photo courtesy

of ChulHee Kang, Washington State University.

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Other DNA damages

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DNA has three

types of bondssusceptible to

hydrolytic cleavage

phosphodiester bonds, N-glycosylic bonds, and bonds

linking exocyclic amine groups to bases are susceptible

Adapted from Doetsch, P. W. Encyclopedia of Life Sciences. John Wiley &

Sons, Ltd., April 2001. [doi: 10.1038/npg.els.0000557]. 11


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AP site formation by

N-glycosyl bond cleavage

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Water-mediated deamination

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Transition and transversion mutations

caused by deamination

Transversion

Transition

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DNA damage by hydroxyl radical

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8-oxoguanine base pairs with C or A

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Alkylating agents damage DNA

transfer methyl, ethyl, or larger alkylgroups to DNA

alkylation takes place at: nitrogen and oxygen atoms external to the base

ring systems

nitrogen atoms in the base ring systems exceptthose linked to deoxyribose

non-bridging oxygen atoms in phosphate

groups

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Methylation results in

mutation of GC pair to AT


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Summary What I learned in this

lecture. Mutations: Permanent base changes

Sources of DNA damage: Endogenous (reactive o2 species) or exogenous (external agents: UV

rays, X-RAYS, gamma rays, hydrolysis or thermal disruption, plant toxins, chemicals, viruses)

UV: two pathways for UV-induced DNA damage both involve dimer formation btwn adjacent

pyrimidine rings on same strand

cyclobutane pyrimidine dimer (CPD)

(6-4 photoproducts)

--cyclobutane pyrimidine dimer produces a kink in DNA

Other DNA damages

DNA has three types of bonds susceptible to hydrolytic cleavage. WHAT ARE THEY 1)phosphodiester

bonds 2)N-glycosylic bonds 3)exocyclic amine groups to bases

-When DOES AN AP SITE FORM? When the N-glycosylic bond in cleaved, this will lead us to an

opening of the ribose ring!

-Water also cleaves the exocylic amine (the amine groups on the bases). WHAT are the RESULTS of

this EXOCYCLIC AMINE BONDs BREAKING? Transition and transversion mutations! TRANSITIONAND TRANSVERSION MUTATIONS ARE CAUSE BY DEAMINATION!

-SIDE BAR: DNA DAMAGE can also occur by hydroxyl radical. Ex: guanine 8-oxoguanine.

-8-OXOGUANINE base pairs with C or A (GAC) GAGA AND CHRISTINE

-Alkylating agents damage DNA! Where does alkylation take place? N and O external to ring system, N

in base ring system except those linked to deoxyribose, non-bridging oxygen atoms in phosphate

groups

-METHYLATION RESULTS IN MUTATION FROM GC pair to AT! 19

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Luo_Lecture7 Includes Summary