Chapter 16: Mechanisms of Genetic Variation

types of mutations

• spontaneous

• induced

• transition

• transversion

mutation

• a stable, heritable change in the genomic nucleotide sequence

  • this can be a single base change → point mutation

    • spontaneous or induced mutations

  • changes of several bases or larger → insertions, deletions, inversions, duplications, and translocations

• can be spontaneous or induced (physical and chemical mutagens)

• base pair substitutions, deletion or insertion

spontaneous mutation

• arise occasionally in the absence of any added agent

• without exposure to external agents → they are often the result of errors in replications or lesions to the DNA

• tautomerization: due to DNA replication, there are errors in replication can be due to tautomeric shifts = base substitutions

  • transitions and transversion mutations

• lesions in the structure of DNA

  • loss of a nitrogenous base creating an apurinic or apyrimidinic site can cause spontanous mutations

induced mutations

result of exposure to a mutagen (physical or chemical agent) that damage DNA, alter its chemistry or interfere with its functioning

• base analogs

• specific mispairing

• intercalating agents

transition mutation

substitution of one purine for another or of one pyrimidine for another

transversion mutation

substitution of a purine for a pyrimidine or vice versa

base analogs

structurally similar to normal nitrogenous bases and can be incorporated into DNA during replication → exhibit base-pairing properties different from the bases they replace

specific mispairing

occurs when mutagen is a DNA modifying agents that changes a base’s structure and thereby alters its pairing characteristics

intercalating agents

become inserted between the stacked bases of the helix, distort the DNA and thus induce single nucleotide pair insertions or deletions

detection and isolation of mutants (mutagens and carcinogens)

• carcinogens are cancer causing agents = mutagens

  • therefore tests for mutagenicity can be used as a screen for carcinogenic potential

• ames test

ames test

• widely used mutagenicity test

• detects an increase in reversion of special strains of salmonella typhimurium from histidine auxotrophy to prototrophy after exposure to carcinogen

DNA repair

• attempt to correct mistakes or damages in the DNA → cells have the ability to repair damaged DNA by:

  • proofreading by DNA polymerases

  • excision repair

  • direct repair of thymine dimers

  • mismatch repair

  • recombinational repair

  • SOS response

proofreading by DNA polymerases

immediately repairs many replication errors

nucleotide excision repair

damaged area is excised, producing a single stranded gap → the gap is filled in by DNA polymerase I and DNA ligase joins the new fragment into the existing DNA strand

base excison repair

DNA glycosylases remove the damged base and signals AP nucleases to mark the damaged DNA, which is then excised and repaired by DNA polymerase I and ligase

direct repair of thymine dimers

alkylated bases occurs through photoreactivation or the action of alkyl or methyltransferases

mismatch repair

• system corrects replication errors that result in mismatched base pairs

  • detected by MutS and repaired through excision by MutH

recombinational repair

recombination with an undamaged molecule, is used to restore DNA that has damage in both strands through the action of RecA protein

SOS response

• repair is a type of recombination repair that depends on the RecA protein

  • used to repair excessive damage that halts replicaiton → error prone process that results in many mutations

• RecA derepresses the synthetic of a variety of DNA repair genes

  • very serious damage is treated by translesion DNA synthesis that is highly error prone

transposable elements

• transposons

• insertion sequences

transposition

movement of pieces of DNA around the genome

transposons

segments of DNA that can move about chromosomes → jumping genes

• carry other genes in addition to those needed for transposition

insertion sequences

contain genes only for those enzymes required for transportation

• are bound on both ends by inverted terminal repeat sequences

creating genetic variability

• recombination

• horizontal gene transfer in bacteria or archaea

• vertical gene transfer

• exogenote

  • conjugation, transformation, transduction

recombination

process by which one or more nucleic acid molecules are rearranged or combined to produce a new nucleotide sequence

• mutant or wild type alleles can be exchanged

horizontal gene transfer

moves genes from one mature, independent organism to another

vertical gene transfer

transmission of genes from parents to offspring

exogenote

donor DNA that enters the bacterium by one of several mechanisms

conjugation

direct transfer from donor bacterium to recipient while the two are temporarily in physical contact

transformation

transfer of a naked DNA molecule

transduction

transfer mediated by a bacteriophage

bacterial conjuation

• the transfer of genetic information via direct cell contact → mediated by fertility factors (F plasmids)

• F+ F- mating

• Hfr conjuation

F+ F- mating

• in E. coli and other gram negative bacteria, an F plasmid moves from the donor (F+) to a recipient (F-) while being replicated

  • replication is by the rolling circle mechanism where the 3’ end is extended from a nick in one DNA strand, following around the circular genome and displacing the 5’ end

  • the displaced strand is transferred via a sex pilus and then copied to produce double stranded DNA

    • donor retains the other parental DNA strand and its complement → recipient becomes F+ and the donor remains F-

  • chromosomal genes are not transferred

high frequency of recombination (Hfr) conjugation

• F plasmid integration into the host chromosome results in an Hfr strain of bacteria

• mechanics of conjugation of Hfr strains are similar to those of F+ strains

• initial break for rolling circle replication is at the integrated plasmid’s origin of transfer site

  • part of the plasmid is transferred first

  • chromosomal genes are transferred next

  • the rest of the plasmid is transferred last

rolling circle replication

• enzyme cuts one strand of plasmid DNA while the other strand is in tacked

• the cut strand rolls off and passes through the conjugation pilus to the other bacteria

• DNA synthesis then produced a new complementary strand to replace the strand that left

bacterial transformation

• a naked DNA molecule from the envrionment is taken up by the cell and incorporated into its chromosome in some heritable form

• competent cell→ one that is capable of taking up DNA and therefore acting as a recipient

  • only a limited number of species are naturally competent

  • mechanics of the natural transformation process differ from species to species

• species that are not normally competent can be made competent by calcium chloride treatment and other methods that make the cells more permeable to DNA

bacterial transduction

• transfer of bacterial genes by viruses → occurs as the result of the reproductive cycle of the virus

  • lytic cycle

  • lysogeny

lytic cycle

viral reproductive cycle that ends in lysis of the host cell → viruses that use this cycle are called virulent bacteriophages

lysogeny

reproductive cycle that involves maintenance of the viral genome within the host cell without immediate lysis of the hostg

generalized transduction

transfer of any portion of the bacterial genome → occurs during the lytic cycle of virulent and temperate bacteriophage

specialized transduction

transfer of only specific portions of the bacterial genome → carried out only by temperate phages that have integrated their DNA into the host chromosome at a specific site in the chromosome