The Biology and Genetic Base of Cancer. 2 (Mutation)

Gene Chemical bases DNA Molecule Chromosome From cellular to molecular biology

Mutation the effect from chromosome to Protein

Mutation …Bad ….Good It is good, it is bad also!!  Mutation in the long term it is essential to our existance.  Without mutation there Could be no change and without change life cannot evolve. Ex. Adaptive mutation

Definition of mutation A change in DNA 1. Arrangement. 2. Context. 3. Dosage. 4. Sequence.

Causes of mutations

Size of mutation  Point mutation.  Submicroscopic mutation.  Microscopically visible mutation.  Loss of a whole chromosome.

Somatic or germinal? Types of mutations

Del(5)(p15) Germinal mutation

Normal 1 st event2 nd event Born with mutation 2 nd event  Familiar.  Sporadic. Type of Mutations

Mutation Chromosomal level Aneuploidy, robertsonian translocation Change in DNA sequence arrangement Genomic regional level – e.g. translocation, inversion, Retrotransposition. Change in sequence context Wh ole gene level – e.g. whole gene deletion or duplication Change in gene dosage Nucleotide level – e.g. change, deletion, duplication of one or a few bases Change of nucleotide sequence

Acquired mutations

Hereditarymutations

Methods detect mutations Three common methods

For acquired mutation

Mutation Chromosomal level Aneuploidy, robertsonian translocation Change in DNA sequence arrangement Genomic regional level – e.g. translocation, inversion, Retrotransposition. Change in sequence context Wh ole gene level – e.g. whole gene deletion or duplication Change in gene dosage Nucleotide level – e.g. change, deletion, duplication of one or a few bases Change of nucleotide sequence

Mutation reflects the event, not its consequences  Does a mutation need to relate to an effect (gain, loss or alteration) on gene function?  Is a new sequence change with no effect on the individual a mutation?  Context may be important e.g. “polymorphism” that leads to disease susceptibility e.g. new recessive mutation e.g. point mutation with no effect on the protein sequence

Mutation may be viewed as the engine that drives evolution Is mutation rate determined (selected) by evolution? mutation rate as a balance between benefit and liability  too low leads to a species that is not adaptive.  too high leads to a species in which there is disease and decreased fitness. Mutation rate reflects:  Replication error: the major contributor.  Copying, proofreading, repair tuned to the optimum error rate  Damage and repair: may be primarily somatic.  Other biological processes with built-in error rates (e.g. recombination)

Types of mutations  Point mutations: Change of the normal base to another  Possible consequences:  Silent mutation: No consequence  Missense mutation: changes the codon to one encoding a different amino acid  Nonsense mutation: Changes codon from one encoding an amino acid to a stop codon  Splice site alteration: can abolish or create a splice site  Regulatory region mutation: Can result in net increased or decreased gene expression

Deletion DuplicationInversion

What is the mutation rate Overall rates consider the fidelity of DNA replication  - in vitro fidelity, studies in model organisms  – 10 –11 per bp per replication (10 -6 – 10 –8 per gene per division)  - Deleterious mutation rate (# per zygote) is difficult to accurately determine  - Disease-based estimate: extrapolate from incidence of one disease  - individual genes may not be representative  - Population-based estimate: molecular clock based on species divergence  - estimate the “neutral” mutation rate in non-coding vs. coding  - infer the lost, presumably deleterious, mutations lost  - extrapolate over the whole genome  - use time since split, generation time, gene number estimates  - estimated 3 deleterious mutations/zygote

 6. In the face of the deleterious mutation rate, how can a species persist?  - The rate of accumulation of deleterious mutations must be balanced by loss  - Highly deleterious mutations are purged individually (Haldane)  - Mildly deleterious mutations persist initially and are then lost by selection, drift  - Crow: quasi truncation selection model:  - assume 3 new deleterious mutations per generation  - assume mutations persist for 100 generations  - question: what level of loss (genetic death) is needed to balance the load?  - average of 16% reproduction failure  - as the load increases, a point is reached at which fitness decreases  - a probabilistic model relating load to fitness (reproduction)  - variables that could affect the result  - number of mutations, persistence  - environmental improvements lead to increased tolerance  - medical intervention leads to increase tolerance

Types of mutation  Point mutations: single nucleotide changes synonymous (silent), nonsynonymous (missense, nonsense)  - microdeletions/duplications – one or a few nucleotides  - may be mediated by short repeated sequences  - larger deletions/duplications – large portions of a gene or genes  - single gene or contiguous gene disorders  - often mediated by larger repeat elements: e.g. LINE1, Alu  - microsatellite repeat deletion/expansion – CA or trinucleotide repeats

Major mutation types  Single base substitutions that cause premature termination of protein synthesis, change of amino acid, suppress termination of protein translation, alter level of gene expression, or alter patterns of mRNA splicing  Translocations, that bring disparate genes or chromosome segments together  Deletions of a few nucleotides up to long stretches of DNA  Insertions and duplications of nucleotides up to long stretches of DNA  Many different mutations can occur within a given gene, although it appears that genes have different degrees of mutability  Different mutations affecting a gene can result in distinct clinical syndromes

Types of mutations  Translocations:  Fusion of one chromosomal segment or gene fragment with another  May result in disruption of gene(s)  May result in a hybrid gene with novel function or combination of the functions of both genes

Location, location, location