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FSU PCB 3063 - Exam 3

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PCB 3063General GeneticsLecture Notes Exam 3This set of notes is long! If you want to find notes for a specific date (ex: 3/17) or topic(initiation), press Ctrl F on your keyboard (Command F for Mac users) and type in what youwant to find. It’ll search the document for whatever specific word/phrase you typed in and saveyou the time of scrolling through everything!--------------------Start Exam 3Fri 3/7Nucleotide bases: Pairing:G- guanine C- cytosine G-C, 3 bondsA- adenine A-T, 2 bonds (easier to break)T- thymine A-U in RNAU- uracil, replaces T in RNAPyramidine- C and T (also U), smaller Purine- G and A, largerDNA has 2’deoxyribose sugarRNA has ribose sugarPolymer- DNA/RNA chain, longRuns 5’-3’DNA read 3’-5’ and written 5’-3’DNA must have: replication, storage, expression, mutation/variationGriffith experimentInjected mice w/ deadly bacteria to see if they’d liveSmooth bacteria=killed, rough=lived, heated smooth=livedRough + heated smooth=killedDiscovered transformation- rough bacteria took on properties of smoothInspired research to figure out what transformation factor wasScientists were down to 2 possible answers: DNA or proteinMcCarty experimentTook smooth bacteria, centrifuged it + heated it + separated it out from solutionRemoved carbs + lipids + protein – stripped it bareTook samples of it, added dif enzymes and put it with living rough bacteriaAdded protease- ate away protein, rough bacteria became smoothAdded ribonuclease- ate ribosomes, rough bacteria became smoothAdded deoxyribonuclease- ate DNA, rough bacteria stayed sameResults pointed to DNA as transforming factorHershey-Chase experimentWanted to see if DNA or protein is used to copy virusesUsed radioactive labels to mark DNA and proteinP32- DNA (phosphate used to build DNA structure)S35- protein (sulfur used in protein structure)Put virus in solution w/ E coli to infect and one of the radioactive markersLet virus reproduce and infect fresh set of E coliAfter 2nd reproduction, examined empty viral shells + infected bacteria + new virusesP32 solution- shells unlabeled, bacteria labeled, new viruses labeledViral DNA passed on to infected bacteria and new virus copiesS35 solution- shells labeled, bacteria unlabeled, new viruses unlabeledViral proteins stayed within the virus’s shellShowed DNA was transforming factorDNA strand absorbs the most UV light at wavelength=260 nmProtein absorbs the most at 280 nmUsed to prove that DNA is the heritable factorAt 260 nm, DNA mutates the mostDNA alphabet analogy:4 letters (nucleotides)3 letters per word (trinucleotide)64 words (20 amino acids)There are many words in a sentenceEach sentence means a proteinMelting- Double-stranded DNA splits into 2 single strandsAnneal- 2 single strands combine into d-stranded DNAMatching base pairs recombineRepetitive sequences anneal faster than unique onesReplicationInitiation- start at origin of replication (replicon)Elongation- adding on bases as copy is being written, added 5’-3’Proofreading- exonuclease removes mismatched basesRequired: template, DNA polymerase enzyme, deoxynucleotides, 3’OH primer attachedDNA polymerase- builds DNAPrimer- bit of RNA, attaches itself, shows where to startdATP- deoxy adenine triphosphate1 deoxyribose sugar + 1 base (like adenine) + 3 phosphate groupsReplication fork- where DNA helix unzipsSense strand- leading, runs 3’-5’, fast copying, storage, nontemplateAntisense strand- lagging, runs 5’-3’, Okazaki fragments, usable, templateOkazaki fragments- bits of DNA that were copied in pieces + need to be attachedDNA strands are antiparallel- run in opposite directionsConservative replication- new strand just like old oneDispersive replication- new + old strands made from pieces of each otherSemi-conservative replication- new strand made from old strand templateCorrect methodMeselson-Stahl experimentWorked with E coli, which use N14 in their body structurePut N14 E coli in N15, let them integrate the heavier atoms into system + replicatePut N15-labeled E coli into N14 solutionCentrifuged solution to see how much heavier the cells becameCentrifuge- spin test tube around v. fast, heavier bits collect at bottomResults pointed to semi-conservative replicationTaylor’s experimentTook DNA chromosomes and exposed to radiationTook pictures that revealed radioactivityWhen they divided, both sister chromatids had radioactive labelsWhen they divided again, one had the labels and the other was “fresh”Results pointed to semi-conservative replicationConstancy- population has almost identical genesCentral dogma- DNA  RNA  proteinRetroviruses: RNADNA  RNA  protein (retro=backwards)RNA virus: RNA 1  RNA 2  proteinDNA-RNA library analogy:DNA is like a libraryYou can’t check out any of the books but you can read themIf you need information for something, you have to write it down (transcription)You find the book you’re looking for and open it (initiation)Then you take out your notebook and copy down what it says (elongation) Your handwriting is different than the book’s (use U for T in RNA)You stop when you’ve written everything you need (termination)Then you leave and use the info for whatever you needed it for (protein synthesis)DNA/RNA moleculeNucleotide base- G, C, A, T/UPentose sugar- 5 of them, deoxyribose=DNA, ribose=RNAPhosphate groupMon 3/17Chargoff’s Rule[purines] = [pyrimidines][G or A] = [C or T][A + T] not = [C + G]Watson + Crick observations of DNADouble-strandedStrands made of DNA polymers held by hydrogen bondsHelix spiralAnti-parallel- both strands run in opposite directionsComplimentary- bases on one strand mirrored by those on the otherDNA structurePrimary- 1D, single strand, sequence of single polymerSecondary- 2D, bent strand, local folding in a given areaTertiary- 3D, structure of single moleculeQuaternary- 4D, orientation of 2+ molecules to each otherBase pair made of 1 purine + 1 pyrimidineSpace of 3.4 angstroms between paired basesOne complete twist of helix = 34 angstroms (= 10 base pairs?)Helix width = 20 angstroms = 2 nanometersB-DNA- usual form of DNARight-handed helixZ-DNA- left-handed helix, mostly G+C basesA-DNA- when purified from salty environmentDNA has a negative chargeRNA:Transcription- use DNA template to make RNA, writing down instructionsTranslation- use RNA to make protein, following instructionsReplication- use RNA template to make another RNA, making another copy of instructionsGoes only up to secondary


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