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L08 & 09 - Origins of Variation

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Biology 1001A
Tom Haffie

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L08 –Origins of Variation More on Inheritance of Sameness Mutations are highly important to the evolutionary process - ultimate source of variability in offspring - provides a basis for natural selection - most of the mistakes that occur are base-pair mismatches Proofreading Mechanisms - proposed in 1972 by Arthur Kornberg - depends on ability of DNA polymerases to back up and remove mistakes - has to happen immediately after the nucleotide is added - nucleotide cannot remain as it cannot form proper H-bonds & shape of helix is distorted - overall error rate is low (1 mispair per 1mil nucleotides) - essential, as if it is altered to work less efficiently you get 1 mistake per 1000- 10000 nucleotides (experimentally proven in prokaryotes AND eukaryotes) Errors that escape proofreading - another round of correction by DNA repair mechanisms - increase accuracy BEYOND 1 in a million errors - mispairs cannot form proper bonds/ hold the shape of the helix - repair enzymes move alone double helix and remove mismatches - gap left by mismatch removal is filled w/ DNA polymerase and completed by DNA ligase , sealing the continuous molecule - same repair mechanisms can repair damage done to DNA by chemicals and radiation - REPAIR MECHANISMS ARE INFINITELY IMPORTANT ex. Individuals with xeroderma pigmentosum, a disorder in which the repair mechanism is faulty may develop skin cancer very quickly due to the unrepaired alterations in their DNA. This is if they are exposed to sunlight . Mobile Elements (Mechanisms that promote Inheritance of Difference) - sometimes called jumping genes - elements move from place to place within a genome of a cell - cut and paste different DNA elements and recombine DNA - VERY active in plants (ex. Pigmentation gene)  Insertion Sequence Elements and Transposons - mobile elements are known as transposable elements - mechanism of movement: transposition - occurs by cut and paste process (piece of DNA backbone is cut out and incorporated somewhere else ) or copy and paste wherein two copies remain, in the original spot and in the new spot - TE’s do not exist free of DNA in which they are integrated - cause important genetic changes - TE - biological mutagens that increase genetic variability - in bacterial chromosomes, move b/w chromosomes and plasmids, and between plasmids - frequency of transposition is low but constant for any given TE. - Some are specific, some are random - Insertion sequences and transposons Insertion sequences often enclose transposons b/c IS have repeat genes and transposons have sections of DNA to be transposed - many antibiotics are less effective due to resistance in transposons - movement to plasmids aids in antibiotic resistance (through conjugation) -  Transposable Elements were first discovered in Eukaryotes - discovered in corn by a geneticist who noticed leaf colour had the ability to change rapidly under certain conditions - alleles were mapped and it was discovered: alleles moved frequently; they can move place to place - changes could be so frequent that they could be noticed across ONE developing kernel - conclusions were accepted when TE’s were discovered in other eukaryotes  Transposons vs Retrotransposons - distinguished by TE movement - eukaryotic transposons similar to bacterial transposons - retrotransposons transpose by copy-and-paste method - Process: 1. Retrotransposon is transcribed into a complementary DNA copy via reverse transcriptase (makes a DNA copy from RNA template) - 2. DNA copy is inserted into location in backbone - 3. Genes are duplicated and passed on w/ replication and cell division - may become a permanent part of the DNA of the species - mutations may accumulate in TE: can make it nonmobile - this is a reason why DNA contains so much nonfunctional DNA Retrotransposons vs. Retroviruses - reverse transcription is common between the two - both incorporate genetic recombination - inserted viral DNA is known as provirus - together occupy 40% of genome - -can cause deletions and translocations of DNA - can disturb normal gene expression / protein synthesis - can lead to cancer, abnormalities in gene expression HAPPY MEDIUM – Variation and Sameness - variation must occur to evolve a species - sameness accounts for quality control - genetic recombination is essential to contribute to change and evolution Insertion sequences - simple, contain genes only for transposition - contains gene for transposase, enzyme for recombination rxns for inserting or removing TE’s. - each end has an inverted repeat sequence (same DNA sequence in opp directions) - enables transposase to recognize ends of TE in transposition How much human variation is there? - Venter individual genome sequence showed 1.2 mil variants - ¼ of variants are SNP (single nucleotide polymorphisms) - ¾ are CNV (copy number variations), inversions, etc - MOST differences are larger rearrangements than single base pairs - Each person has ~1000 CNV affecting 35% of genes (and consequently, proteins) - Humans are far more variable than once thought - Each person has 300 variables in insertion of retro elements (due to mobile element transposition) Bacterial Transposons - genes in bacteria code for their own mobility - code for transposase (a recombinase which makes cuts in DNA backbones) - transposase initiates replication and movement of DNA to another side - transposons are relocated when moved in between IS - many transposons code for antibiotic resistance Retrotransposons - move via RNA - reverse transcribe genes and insert them in DNA - can move w/in genomes - retroviruses are embedded in genome (cannot move/produce protein and becomes genomic junk) - VERY significant source of mutation and variat
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