文稿教案成果repair

1、Chapter 16Mutations and DNA RepairA mutation is a change in the nucleotide sequence of a short region of a genome, including point mutations, insertion or deletion of one or a few nucleotides.Transitions, transversions.All cells possess DNA-repair enzymes that attempt to minimize the number of mutat

2、ions that occur.Most mutations are deleterious or neutral, only a few are adaptive.With a single-celled organism such as a bacterium or yeast, all genome alterations that are not lethal or reversible are inherited by daughter cells and e permanent features of the lineage that descends from the origi

3、nal cell in which the alteration occurred. In a multicellular organism, only those events that occur in germ cells are relevant to genome evolution. Changes to the genomes of somatic cells are unimportant in an evolutionary sense, but they will have biological relevance if they result in a deleterio

4、us phenotype that affects the health of the organism.16.1 MutationsHow they arise; The effects they have on the genome and on the organism in which the genome resides; Whether it is possible for a cell to increase its mutation rate and induce programmed mutations under certain circumstances.16.1.1 T

5、he causes of mutationsSpontaneous errors in replication that evade the proofreading function of the DNA polymerases. Other mutations arise because a mutagen has reacted with the parent DNA, causing a structural change that affects the base-pairing capability of the altered nucleotide. Errors in repl

6、ication are a source of point mutationsWithout enzymes, the error rate would be 5%-10%.From correct to errorEach nucleotide base can occur as either of two alternative tautomers, structural isomers that are in dynamic equilibrium. The equilibrium is biased very much toward one form.Replication error

7、s can also lead to insertion and deletion mutationsFrameshift mutationsReplication slippage: Insertion and deletion mutations are particularly prevalent when the template DNA contains short repeated sequences, such as those found in microsatellites.Template strand and its copy shift their relative p

8、ositions so that part of the template is either copied twice or missed out.Replication slippage is probably also responsible for the trinucleotide repeat expansion diseases.Once the expansion reaches a certain length it appears to e susceptible to further expansion in subsequent rounds of replicatio

9、n, so that the disease es increasingly severe in succeeding generations.Mutations are also caused by chemical and physical mutagensDNA damaging factors are not equal to mutagens.Mutagens cause mutations in three different waysAct as base analogs;React directly with DNA (base deamination, alkylation,

10、 flat molecules that can slip between base pairs in the double helix);Do not themselves affect DNA structure, but instead cause the cell to synthesize chemicals such as peroxides that have a direct mutagenic effect.A certain amount of base deamination occurs spontaneously, with the rate being increa

11、sed by chemical mutagens. UV98.5% of the human genome can be mutated without significant effect.16.1.2 The effects of mutationsMutations occur in intron or at exon-intron boundaries.The effects of mutations on multicellular organismsIn fact, most somatic cell mutations have no significant effect, ev

12、en if they result in cell death, because there are many other identical cells in the same tissue and the loss of one cell is immaterial. An exception is when a mutation induce tumor formation or other cancerous activity.Mutations in germ cells are more important because they can be transmitted to me

13、mbers of the next generation and will then be present in all the cells of any individual who inherits the mutation.Loss-of-function/Gain-of-function mutations, usually dominant or recessive?The effects of mutations on microorganismscan also be described as loss-of-function or gain-of-functionAuxotro

14、phs/Conditional-lethal/Inhibitor-resistant/Regulatory mutantsIn addition to these four categories, many mutations are lethal and so result in death of the mutant cell, whereas others have no effect. The latter are less common in microorganisms than in higher eukaryotes, because most microbial genome

15、s are relatively compact, with little non-coding DNA. 16.1.3 Hypermutation and the possibility of programmed mutationsIs it possible for cells to utilize mutations in a positive fashion, either by increasing the rate at which mutations appear in their genomes, or by directing mutations towards speci

16、fic genes? Both types of event might appear, at first glance, to go against the accepted wisdom that mutations occur randomly.Darwinian theory, Lamarckian theory.But, as we shall see, hypermutation and programmed mutations are possible without contravening the Darwinian dogma.Hypermutation occurs wh

17、en a cell allows the rate at which mutations occur in its genome to increase Generate a diverse array of immunoglobulin proteins, mutation rates are 6-7 orders of magnitude greater than the background mutation rate experienced by the rest of the genome.Programmed mutations appear to support the Lama

18、rckian theory of evolutionE. coli seems to be able to direct mutations toward genes whose mutation would be advantageous under the environmental conditions that the bacterium is encountering.Cairns J, Overbaugh J, Miller S (1988) The origin of mutants. Nature. 1988 Sep 8;335:142-145.An apparent incr

19、ease in mutation rate arising from modifications to the normal DNA repair process does not contradict the dogma regarding the randomness of mutations.Foster PL (1999) Annu Rev Genet. 33:57-88.Roth, J.R., et al. (2006) Annu. Rev. Microbiol. 60: 477-501.Something not newOxidativedamage to guanine mult

20、iplets often results from attacks to DNA from a distanceSpacing between adjacent base pairs in DNA (3.4 )is similar to the planar spacing in graphite. The close proximity of aromatic base-pairs allows for significant orbital overlap along the DNA helix, resulting in pi-stacking of the DNA bases. The

21、 structural similarity between graphite, a known conductive material, and DNA was an initial clue to the conductivity of DNA. Decades of research have now established that electrons as well as electron holes are readily transported through the DNA pi-stack.Single base mismatches, base modifications

22、and lesions, and even protein binding events that kink the DNA duplex or flip out a base are sufficient to interrupt DNA charge transfer.Arnold AR, Grodick MA, Barton JK: DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016, 23(1):183-197.Something not newDNA charge transf

23、er (CT)G is the most easily oxidized of the DNA basesThe presence of adjacent G further lowers the guanineoxidation potential. Guanine doublets and triplets are electron hole sinks within DNA. Oxidative damage can be generated from a distance via DNA CT and that this damage is localized to these low

24、 potential guanine multiplets. Arnold AR, Grodick MA, Barton JK: DNA Charge Transport: from Chemical Principles to the Cell. Cell Chem Biol 2016, 23(1):183-197.Programmed mutations appear to support the Lamarckian theory of evolutionE. coli seems to be able to direct mutations toward genes whose mut

25、ation would be advantageous under the environmental conditions that the bacterium is encountering.Cairns J, Overbaugh J, Miller S (1988) The origin of mutants. Nature. 1988 Sep 8;335:142-145.An apparent increase in mutation rate arising from modifications to the normal DNA repair process does not co

26、ntradict the dogma regarding the randomness of mutations.Foster PL (1999) Annu Rev Genet. 33:57-88.Roth, J.R., et al. (2006) Annu. Rev. Microbiol. 60: 477-501.16.2. DNA Repair16.2.1 Direct repair systems fill in nicks and correct some types of nucleotide modificationOnly a few types of damaged nucle

27、otide can be repaired directly: NicksSome forms of alkylation damage Cyclobutyl dimers16.2.2 Excision repairHuman genome sequences contain just a single gene coding for a protein involved in direct repair, but have at least 40 genes for components of the excision repair pathways.Base excision repair

28、 Nucleotide excision repair 16.2.3 Mismatch repair: correcting errors of replicationThe repair must be made in the daughter polynucleotide because it is in this newly synthesized strand that the error has occurred; the parent polynucleotide has the correct sequence. How does the repair process know

29、which strand is which? 6-methyladenines and 5-methylcytosines in E. coli.E. coli has at least three mismatch repair systems, called long patch, short patch and very short patch, the names indicating the relative lengths of the excised and resynthesized segments.In eukaryotes, possibilities include a

30、n association between the repair enzymes and the replication complex, so that repair is coupled with DNA synthesis, or use of single-strand binding proteins that mark the parent strand.16.2.4 Repair of DNA breaks16.2.5 Bypassing DNA damage during genome replicationIf a region of the genome has suffe

31、red extensive damage then it is conceivable that the repair processes will be overwhelmed. The cell then faces a stark choice between dying or attempting to replicate the damaged region even though this replication may be error-prone and result in mutated daughter molecules.SOS response, which enabl

32、es the cell to replicate its DNA even though the template polynucleotides contain AP sites and/or cyclobutyl dimers and other photoproducts resulting from exposure to chemical mutagens or UV radiation that would normally block, or at least delay, the replication complex.Other similar polymerases found in E. coli and eukaryotic cells.When it encounters a damaged position in the template DNA, the polymerase selects a nucleotide more or less at random, although with some p