CHAPTER 12 Molecular Mechanisms of Mutation and DNA Repair 12 1 Mutations are classified in a variety of ways Mutagens increase the chance that a gene undergoes mutation Most mutations are spontaneous each gene has characteristic rate of mutation probability of undergoing a change in DNA increase rate with mutagen so mutation is induced Germ line mutations are inherited somatic mutations are not A somatic mutation yields an organism that is genotypically a mixture mosaic of normal and mutant tissue Most common cancers result from somatic cell mutations Conditional mutations are expressed only under certain conditions Conditional mutations produce changes in phenotype in one set of environmental conditions restrictive conditions but not in permissive conditions A temperature sensitive mutation is a conditional mutation whose expression depends on temperature Proteins containing amino acid replacements are often temperature sensitive An example of temperature sensitivity is the Siamese cat which has a black pigment melanin that is temperature sensitive and the pathway is blocked at normal body temperature Mutations can affect the amount or activity of the gene product os the time or tissue specificity of expression A loss of function mutation complete gene inactivation or a nonfunctional gene Ex deletion of gene amino acid replacement that inactivates protein Hypomorphic mutation reduces expression Ex nucleotide substitution LEAKY Hypermorphic mutation greater than normal level of gene expression A gain of function mutation alters the action of a gene making it active in a type of cell or tissue where the gene is not normally active Most loss of function and Hypomorphic mutations are recessive whereas many gain of function mutations are dominant Expression of a wildtype gene in an abnormal location is also called ectopic expression 12 2 Mutations result from changes in DNA sequence A base substitution replaces one nucleotide pair with another The simplest type of mutation is a base substitution Transition mutations replace one pyrimidine with the other or one purine with the other there are four possible transition mutations Transversion mutations replace a pyrimidine with a purine or the other way around there are eight possible transversion mutations One would expect a 1 2 ratio in transitions to transversions Spontaneous base substitutions are biased in favor of transitions Among spontaneous base substitutions the ratio of transitions to transversions is approximately 2 1 Mutations in protein coding regions can change an amino acid truncate the protein or shift the reading frame Missense mutations or nonsynonymous mutations result in one amino acid being replaced with another Ex R408W Phenylketonuria Most transition mutations in the third codon position do not change the amino acid that is encoded Synonymous substitutions or silent substitutions are not detectable by changes in phenotype A nonsense mutation creates a new stop codon almost always resulting in loss of gene function Frameshift mutations shift the reading frame of the codons in the mRNA Unless it is very near the carboxyl terminus of a protein a frameshift mutation usually results in the synthesis of a nonfunctional protein Sickle cell anemia results from a Missense mutation that confers resistance to malaria Sickle cell anemia results from a single amino acid replacement and is hereditary mutant gene for beta globin sixth codon glutamic exchanged fro valine needle like crystals RBC either destroyed or clump together and clog capillaries It is caused by Plasmodium falciparum In people with the mutant hemoglobin infection with malaria is less likely and also less severe Any change in the active site of an enzyme usually decreases enzymatic activity In the human genome some trinucleotide repeats have high rates of mutation Dynamic mutations contain genetic instability in X chromosomes FRAGILE X which is highly variable in severity has paradoxical pattern of inheritance 1 5 males carrying fragile X chromosome are phenotypically normal heterozygous daughters of a transmitting male often have affected children of both sexes caused by trinucleotide repeat normal 6 54 copies affected 230 2300 copies The trinucleotide repeat in the X chromosome in transmitting males is called the premutation Trinucleotide premutation when transmitted by females often increases in copy number trinucleotide expansion Excessive CGG copies cause loss of function of FMR1 gene lack of FRMA mRNA There is 80 that premutation will undergo amplification Dynamic mutation genetic diseases Myotonic dystrophy CTG repeat female transmission Kennedy disease AGC Friedreich ataxia AAG Spinocerebellar ataxia type 1 AGC male transmission and Huntington AGC male transmission Molecular mechanism for trinucleotide expansions is replication slippage or slipped strand mispairing where replication complex momentarily dissociates from the template strand 3 end backtracks along the template corrected by nucleotide excision repair where expanded region is introduced into the template strand FMR1 inactivation is associated with enzymatic addition of a methyl CH3 to each of the cytosine nucleotides in the 5 region In mammals cytosine methylation occurs preferentially at CG dinucleotides FMRP fragile X mental retardation protein is an RNA binding protein that binds with the 5 end of certain mRNAs and regulates translation into protein or localization in the cytoplasm 12 3 Transposable elements are agents of mutation McClintock and kernel mottling element Dissociation Ds involving transposition moving to new position Ds only moves if Activator Ac is also present transposable elements 50 of the human genome consists of transposable elements Some transposable element transpose via a DNA intermediate others via RNA intermediate The presence of target site duplication is characteristic of most transposable element insertions and it results from asymmetrical cleavage of the target sequence Transposase determines the distance between the cuts made in the target DNA strands Ds is of a large class of elements called DNA transposons which transpose via cut and paste transposition where transposon is cleaved from one position in the genome and the same molecule is inserted somewhere else Terminal inverted repeats is where a sequence is repeated in inverted orientation at each end of the element The presence of an Ac element provides transactivation that enables a Ds element to