Variation during replication: Mutagenesis
- a population of bacteria is not homogenous and there is some variation from cell to cell. Mutation is a permanent, heritable alteration in the base seeucne of DNA and can result from spontaneous errors in replication, or as a consequence of the damageing effects of physical or chemical agents (mutagens). Point mutation is the simplest form of mutation where the sequence ofDNA is altered at a single position- base substitution: one nucleotide is replaced by another.
- the conseqeunces for mutation can vary dramatically and it depends on teh nature of the change and its location. If the chang is in the coding region of a gene (the region which is ultimately translated into protein) it may give rise to an alteration in the amino acid sequence at that point, which may affect the function of the protein. The atleration may have little or no effect, either because the changed codon give rise to the sme amino acid, or because the new amino acid is sufficiently similar to the original that hte function of the protein remains unaffected.
- a silent mutation occurs when a change in a base pare does not result in a change in the aminoa cid sequence in a protein
- a neutral mutation ocurs when a change in a base pair results in an amino acid change but the new amino acid has the same chemical propreties as the old amino acid.
- a missense mutation is one that results a change in amino acid wher the new amino acid has a different property than the old amino acid. The protein with the new primary structure may have reduced or no activitiy.
- a nonsense mutation results in a new stop translation codon formed before the naturally occurring one. Translation is stopped prematurely and a shoten
- replication fidelity is important to be maintained and can be controlled by DNA polymerases incorporating bases in the correct pairing (proofreading) as well as methyl-direct mismatch repair when the base has been further incorporated.
- in methyl-directed mismatch repair, 3 enzymes by (MutH to a GAYC site, MutS dimer to the mismatch site and MutL t MutS). MutL ppulls MutH to the mismatch site. MutH cutes one strand of DNA at the GAT site (the non-methylated one). exonucleases remove bases to past the mismatch site. Helicase, DNA polymerase and DNA ligase use the parent strand as a template and fill in the gaps.
- photolyase repairs UV damage as in the presence of visibly light, photolyase breaks the covalent bonds linking the two pyrimidine residues.
- general lesion repair: endonuclease cuts DNA on both sides of the lesion, DNA helicase unravels the cut strand for removal, DNA polymerase replaces nucleotides in that region and DNA ligase repairs the nick.
- Base Excsion Repair and AP site repair: occurs when a base is damaged or lost. When damaged it is removed by DNA glycosylase. This yields and AP site that must be correctly filled which is done in a similar manner to the nucleotide excision repair. (general Lesion repair)
- Recomination (post replication) repair: occurs when there is a lesion in DNA and DNA polymerase can't move through it and stops. DNA polymerase starts again further downstream of the lesion resulting in a section of single stranded DNA. THis portion of the DNA cannot be repaired byexcision repair but the gap can be filled using a portion of the DNA from the other pair of strands in a recombination process (cutting and rejoining the DNA), the original damage can now be repaired using excision repair, whiel teh gap in the other DNA molecule can be filled by DNA polymerase and DNA ligase.
- SOS repair: is used when the DNA is faced with overwhelming levels of damage preventing normal replication. This can temporarily modify or abolish specificity of the DNA polymerase. It enables DNA polymerase to continue making a new DNA strand, but may contain many mistakes.
- point mutationin asecually reproducting organisms: all ofsprign cary altered base, heritable diseases, tracking changes over time and space, identification of related organism.
- SNPs: single nucleotide polymorphisms: a single base substitution, commonly in the popultion and the presence or absence of SNPs may also provide information on importance of genes to survival.
- experimental applications: identify the function of a gene by removing activity and looking for missing proteins, identifying active sites, improve activity or toher characteristics by slective changes in amino acid sequence.