BSC2010 March 7-11
BSC2010 March 7-11 BSC 2010
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This 7 page Class Notes was uploaded by Tori Ruby on Saturday March 12, 2016. The Class Notes belongs to BSC 2010 at University of Florida taught by Staff in Winter 2016. Since its upload, it has received 17 views. For similar materials see Integrated Principles of Biology 1 in Biological Sciences at University of Florida.
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Date Created: 03/12/16
Mutation: change in the composition of the genome from parent to daughter strand o (total genomic damage-repaired damage) = mutation o Occur in both somatic and germline cells (only considering heritable mutations- which occur in germline cells) o Is the ultimate source of genetic variation (!) Categories of mutations o Nucleotide sequence mutations o Chromosomal rearrangements o Transposable elements Types of nucleotide sequence mutations o Point mutation (+ base substitution) o Insertions/deletions (“indels”) o Duplications Point mutations o Substitution of one nucleotide for another at a homologous site o Rates vary- generally around 10^-8 to 10^-10 per site per generation, varies by taxon o Occur anywhere in the DNA sequence Rate may (and does) vary with genomic text Chemical types of point mutations o o Transitions are more common- magnitude depends on gene and taxon The genetic code o Mutation- “silent” or “synonymous” substitution o Substitute a purine for pyrimidine or pyrimidine for purine Mutation- “Replacement” substitution o Substitute purine for purine or pyrimidine for pyrimidine Mutation- insertion/deletion (“indels”) o Deletion: remove a pyrimidine or purine o Insertion: dd a pyrimidine or purine o Can be one or more nucleotides Mutations occur because o Spontaneous errors in DNA replication (mismatches) o Mutagenic damage to DNA (replicating or non-replicating) o “Selfish” elements replicate themselves, often to the detriment of the host genome Causes of mismatches o Polymerase base misincorporation DNA polymerases have 3’->5’ and/or 5’->3’ exonuclease (proofreading) function o Tautomerization o Spontaneous deamination (e.g., deaminated cytosine is uracil, leads to C/G-> U/A -> T/A DNA repair o First line of defense: DNA polymerase DNA polymerase III has a “proofreading” capability If the wrong nucleotide is entered, DNA synthesis stops, the offending nucleotide is removed, and synthesis resumes Mechanisms of mutagenic damage o Base analogs: purines/pyrimidines that mimic legitimate bases pair differently o Direct damage to DNA: e.g. Deamination, alkylation, intercalating agents, UV o Indirect damage to DNA: e.g. Agents that generate oxygen free radicals Oxygen free radicals predominantly cause G/C->A/T via 5- hydroxyuracil from cytosine deamination and G/C-> T/A via 8- oxoguanine Mechanisms of DNA repair o Direct repair: damage repaired directly o Excision repair: damaged DNA excised and repaired using undamaged strand as template; base excision, nucleotide excision o Mismatch repair: recognizes misincorporated bases, removes the mispaired base, and repairs using the parent strand as a template o Recombination repair: (double stranded break repair): employs the recominational machinery o Transcription- coupled repair: (ER, specific to transcribed strand during transcription) Insertions/Deletions (indels) o Insertions Addition of nucleotides to a sequence o Deletions Deletion of nucleotides from a sequence o Result from “replication slippage” when replicating DNA reanneals at short tandem repeats Non-homologous (ectopic) recombination Chromosomal aberrations and their consequences o Non-disjunction Homologous chromosomes do not separate at meiosis I Sister chromatids do not separate at meiosis II Consequences If fertilization with a gamete with abnormal ploidy occurs, result is offspring with abnormal chromosome number, called “aneuploidy” Polyploidy o Sometimes organisms get an entire extra (haploid) set of chromosomes o 3 sets are called “triploidy” Can occur by fertilization of a diploid egg in which all chromosomes underwent non-disjunction o 4 sets are called “tetraploidy” E.g. Zygote fails to divide after DNA replication; mitosis leads to a 4n organism Duplications o Result from non-homologous recombination o Probably very important for evolution of new genes Chromosomal rearrangements o Typically from non-homologous recombination or double-stranded breaks in the chromosome o 2 types Inversions Once inversion occurs, recombination is usually prevented because recombinant gametes cannot get a full complement of genes Translocations Pieces of non-homologous chromosomes break and fuse together Often cause improper segregation of chromosomes at meiosis Transposable elements: “jumping genes” o Transposable elements are genetic elements that contain the information for their own replication o Insert into new locations in the genome Conservative transposition (cut and paste) Replicative transposition (copy and paste) o Unlike episomes or viruses, TEs never exist independent of the host genome o Most recombination requires complementary base-pairing of homologous (sequence-similar) regions of DNA Meiosis (in eukaryotes) Transformation Generalized transduction Conjugation o Transposition is a form of non-homologous recombination o TEs can move to novel sites in the genome o The simplest TEs consist of A gene that encodes an enzyme for excision an insertion of the TE sequence; transposase in DNA TEs A recognition sequence that the enzyme recognizes as the boundary of the TE o In prokaryotes Insertion sequences A transposase gene A recognition sequence that is an inverted repeat Transposase recognizes boundaries of TE inverted repeats and cuts the TE out of the donor site Transposase cleaves chromosome at target side via endonuclease Transposon is joined to the single-stranded ends at the target site Gaps are filled in by DNA polymerase I and DNA ligase Result is a new copy (copy and paste) or moved copy (cut and paste) of the TE o Composite transposable elements Contain additional genetic material besides transposase, IRs Structure consistent with two ISs close together in genome One transposase may not be functional Transposable elements (TEs) o DNA transposons Composite transposable elements Contains additional genetic material besides transposase, IRs Structure consistent with two ISs close together in genome One transposase may not be functional Prokaryotic gene regulation: metabolic control o Metabolism can be defined as the total of the chemical reactions of a cell (or organism) Must be controlled, or chaos ensues o Anabolic metabolism: building large molecules out of small molecules; requires energy input o Catabolic metabolism: breaking down large molecules into small molecules; releases energy o Direction of flux through metabolic pathway depends on cellular needs o Flux through a metabolic pathway can be regulated in two ways Activity of the enzymes themselves Regulation of enzyme activity o Competitive inhibition: inhibitor binds to active site o Non-competitive inhibition: inhibitor binds to some other part of the cell o Allosteric regulation: multiple subunits o Feedback inhibition Metabolic pathway switched off by the end- product o Cooperativity Active form stabilized by substrate Expression of genes that encode enzymes Regulation of gene expression: operon o In prokaryotes, functionally related genes often are clustered together in the genome, called “operons” o Under the control of a single promoter sequence, so are transcribed together o Single “switch” sequence controls transcription of the whole operon; called an operator o Operator controls access of RNA Pol to genes o Repressor proteins controls access of Pol to operator o Repressor protein encoded by a “regulatory” gene o Presence or absence of an end-product or precursor controls the operon “on-off switch” o Example: the E. coli trp operon o Trp operon is repressible because transcription is repressed by the presence of an end-product Repressible operons usually function in anabolic metabolism o An inducible operon becomes transcriptionally active by the presence of a precursor Example: E. coli lac operon Negative v. positive o Trp and lac operons are negative regulation: transcription switched off by active repressor o Positive regulation: transcription switched on by activator molecule Operon control: repressible v. inducible o Repressible operon: end-product turns the operon off o Inducible operon: substrate turns the operon on
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