This document covers DNA damage, repair, and recombination. It begins by explaining mutagenesis, including the causes of mutations like radiation, chemicals, and errors in DNA replication. It then discusses the different types of DNA damage from physical and chemical mutagens, as well as oxidative damage and alkylation. The document outlines several DNA repair mechanisms like photoreactivation, alkyltransferase, excision repair, and mismatch repair that help repair damaged DNA. It concludes by explaining homologous recombination, site-specific recombination, and transposition that contribute to genetic recombination and diversity. The overall learning objectives are to explain these concepts of mutagenesis, DNA damage, repair mechanisms, and genetic recombination.
This document covers DNA damage, repair, and recombination. It begins by explaining mutagenesis, including the causes of mutations like radiation, chemicals, and errors in DNA replication. It then discusses the different types of DNA damage from physical and chemical mutagens, as well as oxidative damage and alkylation. The document outlines several DNA repair mechanisms like photoreactivation, alkyltransferase, excision repair, and mismatch repair that help repair damaged DNA. It concludes by explaining homologous recombination, site-specific recombination, and transposition that contribute to genetic recombination and diversity. The overall learning objectives are to explain these concepts of mutagenesis, DNA damage, repair mechanisms, and genetic recombination.
This document covers DNA damage, repair, and recombination. It begins by explaining mutagenesis, including the causes of mutations like radiation, chemicals, and errors in DNA replication. It then discusses the different types of DNA damage from physical and chemical mutagens, as well as oxidative damage and alkylation. The document outlines several DNA repair mechanisms like photoreactivation, alkyltransferase, excision repair, and mismatch repair that help repair damaged DNA. It concludes by explaining homologous recombination, site-specific recombination, and transposition that contribute to genetic recombination and diversity. The overall learning objectives are to explain these concepts of mutagenesis, DNA damage, repair mechanisms, and genetic recombination.
and recombination Learning Outcome (LO) After students learn this lecture, students are able to explain: • Mutagenesis (LO 6.1) • DNA damage (LO 6.2) • DNA repair (LO 6.3) • Recombination (LO 6.4) MUTAGENESIS Mutation ❑ Mutations are heritable permanent changes in the base sequence of DNA. ❑ Point mutations may be transitions (e.g. G-C→A-T) or transversions (e.g. G-C→ T-A). ❑ Deletions and insertions involve the loss or addition of bases and can cause frameshifts in reading the genetic code. ❑ Silent mutations have no phenotypic effect, while missense and nonsense mutations change the amino acid sequence of the encoded protein.
LO 6.1: Students are able to explain mutagenesis
Biology _ concepts and investigations-McGraw-Hill (2012)
LO 6.1: Students are able to explain mutagenesis
MUTAGENESIS Replication fidelity ❑ The high accuracy of DNA replication (one error per 1010 bases incorporated) depends on a combination of proper base pairing of template strand and incoming nucleotide in the active site of the DNA polymerase, proofreading of the incorporated base by 3’→5’ exonuclease and mismatch repair.
LO 6.1: Students are able to explain mutagenesis
MUTAGENESIS Physical mutagens ❑ Ionizing (e.g. X- and γ-rays) and nonionizing (e.g. UV) radiation produce a variety of DNA lesions. ❑ Pyrimidine dimers are the commonest product of UV irradiation.
LO 6.1: Students are able to explain mutagenesis
MUTAGENESIS Chemical mutagens ❑ Base analogs can mispair during DNA replication to cause mutations. ❑ Nitrous acid deaminates cytosine and adenine. ❑ Alkylating and arylating agents generate a variety of adducts that can block transcription and replication and cause mutations by direct or, more commonly, indirect mutagenesis. ❑ Most chemical mutagens are carcinogenic.
LO 6.1: Students are able to explain mutagenesis
MUTAGENESIS Direct mutagenesis ❑ If a base analog or modified base whose base pairing properties are different from the parent base is not removed by a DNA repair mechanism before passage of a replication fork, then an incorrect base will be incorporated. ❑ A second round of replication fixes the mutation permanently in the DNA.
LO 6.1: Students are able to explain mutagenesis
MUTAGENESIS Indirect mutagenesis ❑ Most lesions in DNA are repaired by error-free direct reversal or excision repair mechanisms before passage of a replication fork. ❑ If this is not possible, an error-prone form of translesion DNA synthesis may take place involving specialized DNA polymerases and one or more incorrect bases become incorporated opposite the lesion.
LO 6.1: Students are able to explain mutagenesis
DNA DAMAGE DNA lesions ❑ The chemical reactivity of DNA with exogenous chemicals or radiation can give rise to changes in its chemical or physical structure. ❑ These may block replication or transcription and so be lethal, or they may generate mutations through direct or indirect mutagenesis. ❑ The chemical instability of DNA can generate spontaneous lesions such as deamination and depurination.
LO 6.2: Students are able to explain DNA damage
DNA DAMAGE Oxidative damage ❑ Reactive oxygen species such as superoxide and hydroxyl radicals produce a variety of lesions including 8-oxoguanine and 5-formyluracil. ❑ Such damage occurs spontaneously but is increased by some exogenous agents including λ-rays.
LO 6.2: Students are able to explain DNA damage
DNA DAMAGE Alkylation ❑ Electrophilic alkylating agents such as methylmethane sulfonate and ethylnitrosourea can modify nucleotides in a variety of positions. ❑ Most lesions are indirectly mutagenic, but O6-alkylguanine is directly mutagenic.
LO 6.2: Students are able to explain DNA damage
DNA DAMAGE Bulky adducts ❑ Bulky lesions such as pyrimidine dimers and arylating agent adducts distort the double helix and cause localized denaturation. ❑ This disrupts the normal functioning of the DNA.
LO 6.2: Students are able to explain DNA damage
DNA REPAIR Photoreactivation ❑ Cleavage of the cyclobutane ring of pyrimidine dimers by DNA photolyases restores the original DNA structure. ❑ Photolyases have chromophores which absorb blue light to provide energy for the reaction.
LO 6.3: Students are able to explain DNA repair
DNA REPAIR Alkyltransferase
❑ An inducible protein specifically removes an alkyl
group from the O6 position of guanine and transfers it to itself, causing inactivation of the protein.
LO 6.3: Students are able to explain DNA repair
DNA REPAIR Excision repair ❑ In nucleotide excision repair, an endonuclease makes nicks on either side of the lesion, which is then removed to leave a gap. ❑ This gap is filled by a DNA polymerase, and DNA ligase makes the final phosphodiester bond. ❑ In base excision repair, the lesion is removed by a specific DNA glycosylase. ❑ The resulting AP site is cleaved and expanded to a gap by an AP endonuclease plus exonuclease. ❑ Thereafter, the process is like nucleotide excision repair.
LO 6.3: Students are able to explain DNA repair
DNA REPAIR Excision repair
LO 6.3: Students are able to explain DNA repair
DNA REPAIR Mismatch repair ❑ Replication errors which escape proofreading have a mismatch in the daughter strand. ❑ Hemimethylation of the DNA after replication allows the daughter strand to be distinguished from the parental strand. ❑ The mismatched base is removed from the daughter strand by an excision repair mechanism.
LO 6.3: Students are able to explain DNA repair
DNA REPAIR Hereditary repair defects ❑ Mutations in excision repair genes or a translesion DNA polymerase cause different forms of xeroderma pigmentosum, a sun-sensitive cancer-prone disorder. ❑ Excision repair is also defective in Cockayne syndrome.
LO 6.3: Students are able to explain DNA repair
RECOMBINATION Homologous recombination ❑ The exchange of homologous regions between two DNA molecules occurs extensively in eukaryotes during meiosis. ❑ In prokaryotes, recA-dependent recombination involves a four-stranded Holliday intermediate which can resolve in two ways. ❑ The integrity of DNA containing unrepaired lesions can be maintained during replication by homologous recombination.
LO 6.4: Students are able to explain recombination
RECOMBINATION Homologous recombination
LO 6.4: Students are able to explain recombination
RECOMBINATION Site-specific recombination ❑ The exchange of nonhomologous regions of DNA at specific sites is independent of recA. ❑ Integration of bacteriophage into the E. coli genome involves recombination at a 15 bp sequence present in both molecules and specific protein integration factors. ❑ Site-specific recombination also accounts for the generation of antibody diversity in animals.
LO 6.4: Students are able to explain recombination
RECOMBINATION Transposition ❑ Replicated copies of transposable DNA elements can insert themselves anywhere in the genome. ❑ All transposons encode a transposase which catalyzes the insertion. ❑ Retrotransposons replicate through an RNA intermediate and are related to retroviruses.
LO 6.4: Students are able to explain recombination