Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25dancing1Library: storing information2What’s in a word❖Base: opposite of acid (i.e., sucks up protons)Base: opposite of acid (i.e., sucks up protons)❖Base: component of nucleotides, such as you met in Base: component of nucleotides, such as you met in lablab❖Kinda like John, your best pal vs. john, where you Kinda like John, your best pal vs. john, where you poop:poop:Not good to confuse the two!Not good to confuse the two!3How far can we get How far can we get on first principles?on first principles?Life is presumably possibleLife is presumably possiblemaybe even consistent with physical lawsmaybe even consistent with physical lawsWhat do (all!) organisms’ What do (all!) organisms’ instructionsinstructions looklook like? like?4This.5Ways to look at ‘em6Never forget: it’s a braille world7❖There is There is nothingnothing comparable to sight or sound comparable to sight or sound❖As a molecule, either you touch it, or you are As a molecule, either you touch it, or you are ignorant of it. Period.ignorant of it. Period.❖As a molecule, either you touch it, or you are As a molecule, either you touch it, or you are ignorant of it. Period.ignorant of it. Period.❖Yeah, I said that twiceYeah, I said that twiceGeneral & SpecificShake hands with 3 people near youShake hands with 3 people near youHow many of these interactions How many of these interactions failedfailed??Could you Could you recognizerecognize your different partners in the your different partners in the dark?dark?Pair up. Design a handshake where A can shake Pair up. Design a handshake where A can shake with B, but not A:A nor B:B. It’s gotta work in the with B, but not A:A nor B:B. It’s gotta work in the dark/under the tabledark/under the tableHow can we do this with C, H, N, O?How can we do this with C, H, N, O?9G:A-D-DT:O-N-OSecret society handshakesMore common; less helpful1011What nature came up withFreeman, Biological Science, 4.6b❖Four similar unitsFour similar units❖Rigid platforms (rings Rigid platforms (rings with double bonds)with double bonds)❖‘‘Decorated’ with... our Decorated’ with... our pals! Donors, pals! Donors, acceptorsacceptorsFailure: it’s why things work❖If anybody can shake hands with anybody, there is no If anybody can shake hands with anybody, there is no recognitionrecognition--no --no informationinformation in the handshakein the handshake❖Hydrophobic exclusions never fail--any grease-on-Hydrophobic exclusions never fail--any grease-on-grease action at any angle is ‘exciting’ to the grease action at any angle is ‘exciting’ to the surrounding waterssurrounding waters❖Ionic interactions never fail--they fade, but still ‘count’ Ionic interactions never fail--they fade, but still ‘count’ ❖Hydrogen interactions are Hydrogen interactions are greatgreat at failing--they have at failing--they have to be the right to be the right distancedistance the right the right alignmentalignment12Summary❖Structure of the bases allows them to ‘call for’ or Structure of the bases allows them to ‘call for’ or match with their partnersmatch with their partners❖All a polymerase (copier) needs to do is ALLOW All a polymerase (copier) needs to do is ALLOW and RECOGNIZE matching. and RECOGNIZE matching. ❖It never needs to be ‘aware’ of what the It never needs to be ‘aware’ of what the ‘template’ (existing) base is, what base is ‘template’ (existing) base is, what base is neededneeded, what base is visiting, what base is visiting❖Just: “Does this new thing ‘fit’ to the existing Just: “Does this new thing ‘fit’ to the existing thing?”thing?”❖Pretty cool, eh?Pretty cool, eh?13Assembly Assembly instructionsinstructions14Yes, we hate you (naming names)❖The ‘normal’ numbers ID The ‘normal’ numbers ID positions on the base (green)positions on the base (green)❖So sugar gets ‘primed’ So sugar gets ‘primed’ numbers, pronounced ‘one numbers, pronounced ‘one prime’, ‘2 prime’...prime’, ‘2 prime’...❖New stuff is added @ the 3’ by New stuff is added @ the 3’ by joining something hanging off joining something hanging off the 5’the 5’15A,G,C,T,URiboseThe two connectorsDeOxy(Found in the nucleus)AcidSimple solutions appear over & over16❖Amino acids have a common chassis (amino group-Amino acids have a common chassis (amino group-alpha carbon-COOH group) & a decoration (side chain)alpha carbon-COOH group) & a decoration (side chain)❖Nucleic acids do tooNucleic acids do too--the --the basesbases are the ‘interesting’ are the ‘interesting’ decorationsdecorations❖though not as varied as amino acids!though not as varied as amino acids!The ‘backbone’❖The major polymers (nucleic acid; The major polymers (nucleic acid; protein) have common elements protein) have common elements (‘backbones’ or chassis) PLUS (‘backbones’ or chassis) PLUS distinctive elements (for nucleic acid, distinctive elements (for nucleic acid, basesbases; for proteins, ; for proteins, side chainsside chains))❖In (DNA & RNA), there’s a sugary bit In (DNA & RNA), there’s a sugary bit attached to on oxygened-up attached to on oxygened-up phosphorous (A.K.A. phosphate)phosphorous (A.K.A. phosphate)17Fig 4.3Boring...Boring...Boring...Boring...Ooh!Ahh!Oh my!****your exclamation of pleasure hereHow does a copier know what to do?18Template(the source information)Primerthing being added TOThink ‘prime the pump’--start it upFig. 14.6This is the same chemistry as ATPase!What it looks like❖Two strands, ‘complemTwo strands, ‘complemeentary’ntary’❖Each is all the info needed to Each is all the info needed to make the othermake the other❖So pull them apart, So pull them apart, createcreate a a new match one-by-onenew match one-by-one❖Poof! Where there was one, Poof! Where there was one, twotwo19http://www.champaignschools.org/staffwebsites/isabelgi/Soph_Bio/DNAreplication.htmReview!❖Take happy moleculeTake happy molecule❖Lure last P with accessible forbidden fruit (oxygen Lure last P with accessible forbidden fruit (oxygen from water)from water)❖Delight in wrecking homesDelight in wrecking homes20Ade-P-O-P-O-POHHAde-P-O-P-O--POHH--Ade-P-O-P-OOHP::Putting the poly in