1 Biology 321 W2012 The Molecular Biology of Mutation Part 1 Breakthrough of the Year: Human Genetic Variation Science 318: 1842 Dec. 21, 2007 http://fire.biol.wwu.edu/trent/trent/humanvariation.pdf This article details some of the common sequence variations that have been found when comparing individual human genome sequences including single nucleotide polymorphisms (SNPs), gene copy number variations (CNVs) and other structural rearrangements23 • Digital technology has spawned an surfeit of information that is extremely fragile (compared to paper) and therefore inherently impermanent • Moreover, nondigital materials often remain intelligible following modest deterioration, whereas digital sources such as CDs frequently become unusable at the first sign of corruption http://chnm.gmu.edu/digitalhistory/preserving/1.php4 Data currently being stored in magnetic or optical media will probably become unrecoverable within a century or less (estimates vary). This will be due to the combined effects of 1. software obsolescence 2. obsolescence of hardware for retrieval 3. decay of the storage medium (aka material deterioration). New approaches are required that will permit retrieval of information stored for centuries or even millennia5 This human-generated digital technology contrasts with the impressive information storage “technology” that evolution has produced and refined over the past 3+ billion years Our personal digital archive is NOT plagued by problems of chemical fragility or by obsolescent retrieval systems6 DNA has three properties that recommend it as a vehicle for long-term information storage: • First, DNA has stood the informational "test of time" during the billions of years since life emerged. Non-replicating DNA molecules are quite robust.  good chemical stability • Second, because DNA is our genetic material, methods for both storage and reading of DNA-encoded information is central to technological civilizations and undergo continual improvements.  DNA-R-US • Third, use of DNA as a storage medium permits each segment of information to be stored in an enormous number of identical molecules. This extensive informational redundancy would strongly mitigate effects of any losses due to stochastic decay.  easy to make copies via PCR Bottom Line: Data retrieval of information stored in DNA should ideally require minimal prior knowledge beyond a familiarity with molecular biological techniques (DNA sequencing and PCR --polymerase chain reaction)7 The changing definition of the gene: Mendelian: the fundamental functional unit of heredity that carries information from one generation to the next Biochemical: a unit of heredity that specifies the production of a polypetide Molecular: a segment of DNA composed of a transcribed region and adjacent regulatory regions that control transcription8 permanent archive of genetic instructions DNA   mRNA   PROTEINS 1Control of Biological processes/Specification of organism 2 Conversion of genetic information into a different chemical form: Translation from one chemical language to another Short stretches of DNA are copied or transcribed rRNA tRNA siRNA miRNA and others short-term, throw-away copy9 Our focus with respect to molecular genetics will be on: • how mutations come about • how mutations affect gene function • techniques available to directly assess genotype at the DNA level10 Sex, Errors and the Genome by Mark Ridley Natural History (6/2001) “At conception, human embryos average about 200 copying errors and about 50% of the embryos have a botched number of chromosomes. “ WHO IS TO BLAME?11 When a thirty year old man breeds with a 30 year old woman: • his DNA (in his sperm cells) has been copied 430 times against her 33 cell division (in egg cells). • with thirteen times as many errata in his DNA, about 185 of the 200 copying mistakes in each human conception may come from the sperm. • however, a woman’s eggs are more likely to carry serious errors in chromosome numbers, and these errors increase with maternal age.12 Sex, Errors and the Genome by Mark Ridley Natural History (6/2001) MUTATIONS: MOTHER VERSUS FATHER As their life spans stretch out, men and women travel different evolutionary roads, and the amount of DNA copying that goes on in their gonads contributes to the error level of their genomes in different ways. Men manufacture sperm throughout their lives. About 40 cell divisions in the reproductive cells have occurred in a human male by the time he reaches puberty. After that, the DNA in his sperm is copied every sixteen days, or 23 times per year. A twenty-year-old man's genome has been copied more than 200 times, and a forty-year-old's more than 600 times. Compare that with the average adult male rat: its DNA has been copied only 58 times in its short life, and the DNA in its spermatozoa is therefore relatively error free. A female human, on the other hand, already possesses her lifetime supply of eggs--with about 33 cell divisions behind them--by the time she is a late-stage fetus. When a thirty-year-old man breeds with a thirty-year-old woman, his DNA has been copied 430 times against her 33. With about thirteen times as many errata in his DNA, about 185 of the 200 copying mistakes in each human conception may come from the sperm. However, a woman's eggs are more likely to carry serious errors in chromosome numbers, and these errors increase with maternal age. Some disorders, such as Down syndrome, are the result of eggs that deliver the wrong number of chromosomes during conception. All the DNA messages in a sperm and an egg can be compared with all the text in two sets of encyclopedias. If publishers made errors in book production at the same rate fathers and mothers do in transcribing their DNA, buyers of Britannica would receive sets with 200 printing errors on average, and half the time they'd be sent the wrong number of books.13 MUTATION JARGON GENE MUTATION = POINT MUTATION (scales of mutation is small and is localized to a specific region, a single nucleotide or a few adjacent base pairs) ↓ at the DNA level: Ë single base pair substitutions: transitions & transversions Ë single (or a few) base pair addition or deletion: indels Ë gene mutation by transposon insertion at the level of