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by: Noah Wyman


Marketplace > University of Kentucky > Arts and Sciences > A&S 100 > SP INTRO CRSE INTRO INTERNATNAL STUDIES
Noah Wyman
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This 60 page Class Notes was uploaded by Noah Wyman on Friday October 23, 2015. The Class Notes belongs to A&S 100 at University of Kentucky taught by Staff in Fall. Since its upload, it has received 12 views. For similar materials see /class/228227/a-s-100-university-of-kentucky in Arts and Sciences at University of Kentucky.




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Date Created: 10/23/15
How Cells Harvest Chemical Energy cargo 60 gt boo2 s Introduction to Cell Metabolism Glycolysis Aerobic Cell Respiration Anaerobic Cell Respiration Fermentation Breathing and Cell Respiration are related EmilH RIMES Muscle cells Danrrying out Sugar 02 gt ATP CO2 H20 Cellular Respiration uses oxygen and glucose to produce Carbon dioxide water and ATP a caugo 69 gt 6 CO 6 293 Glucose Oxygen gas Carbon Water Energy dioxide How efficient is cell respiration Energy released Gasoline energy from glucose converted to u banked in ATP Energy released from glu se as heat and light 100 About 40 25 Burning glucose Burning gasoline in an experiment in cellular respiration in an auto engine Reduction and Oxidation Oxidation is losing electrons Reduction is gaining electrons SH ZO6 602 gt GCOZ 6H20 l j ATP Gain of hydrogen atoms Glucose Energy Glucose gives off energy as it is oxidized Reduction and Oxidation LRIG Gain or loss of electrons is often in the form of hydrogen The hydrogen is then passed to a coenzyme such as NAD H O H gt O2H NAD 2H gt lIESEJ u H 2H 2e Reduction and Oxidation What are some common coenzymes NAD and FAD illNEH When reduced gain electrons energy and hydrogens Reduction and Oxidation These coenzymes are very important for cell respiration because they transfer highenergy electrons to electron transport systems ETS m NAD H Reduction and Oxidation As the electrons move from carrier to carrier energy is released in small quantities Dos Os Electron tr g ETS Generation of ATP There are two ways to generate ATP Chemiosmosis SubstrateLevel Phosphorylation Generation of ATP Chemiosmosis quotquot Cells use the energy released by falling electrons in the ETS to pump H ions across a membrane Uses the enzyme ATP H synthase quot 439 Generation of ATP Chemiosmosis ATP synthase H lntzrmembrane 39 Proton channel campanment oilW T quot939 mitochondrial membrane 39 synthgspe W n39quot Sun 01 ATP lynthuls A B Generation of ATP Substrate Level Phosphorylation ATP can also be made by transferring Generation of ATP Substrate Level Phosphorylation I Alum ADP ATP can also be made by transferring phosphate groups from organic SUbStrate molecules to ADP 8 MW product Flgure 7B General Outline Glucose 1 Glycolysis oxy9equot Pyruvic Acid No oxygen Aeroblc Anaeroblc Transition Reaction Fermentation Krebs Cycle ETS 36 ATP 5 I I 9A fuel d magi Glucose mo ecueis energize e Glycolysis quotSm PI quot o Glucoses phosphate W 39 Fructose 6 phosphate Energy ln 2ATP 3 u StepoA six carbon oqoaoom intermediate splits into two three carbon 2 interm edlates Fructose 16 diphosphate Glyceraldehyde 3 phosphate 3935 com rm l o Step 9 A redox 1 W reaction generates 1 m3 Liza m 13 Dlphosphoglycerlc acid 5 m quot3 2 molecules 3 l Steps 9 oATP 3 Phosphoglyceric acid Energy Out 4 ATP and pyruvic acid 90 2 molecules are produced 3 2 Phosphoglyceric acid woo 2 molecules l mp H 2 Phosphoglyceric acid 30 2 molecules NET 2 ATP 2NADH 9 Pyruvicatid 2 molecules ooo per glucose molecule phosphate groups from organic SUbStrate molecules to ADP 8 e Aime product Flgure 7B Glycolysis Where The cytosol What Breaks down glucose to pyruvic acid 2 ADP 2 2 OOOOOO V 2 0 0 0 2 NAD 2 rm 2 HT General Outline Glucose 1 Glycolysis oxygen Pyruvic Acid No oxygen Aerobic Anaeroblc Transition Reaction Fermentation Krebs Cycle ETS 36 ATP General Outline of Aerobic Respiration Glycolysis Transition Reaction Krebs Cycle Electron Transport System General Outline of Aerobic Respiration Glycolysis Transition Reaction Krebs Cycle Electron Transport System Transition Reaction Each pyruvic acid molecule is broken down to form CO2 and a twocarbon acetyl group which enters the Krebs cycle NAD o O o k w 00 60A Pyruvic Acid Acetyl CoA O Coenzyme A Krebs Cycle Where In the Mitochondria What Uses Acetyl CoA to generate ATP NADH FADHZ and C02 300m yCoA I lt 0 f 3 FIB r QSNAD39 m w Krebs Cycle Mitochondria Central vacuole Krebs Cycle Products of the a m Krebs cycle um J W cm mu Kgt0 quot10 MOO Putnam uKeloghnnrlll Hunt NAn39 Um J rm 50mm Anna co 0mm Succlnyl coA KMquot cycle accur limit for such glucose lmmlng glycnlysls General Outline of Aerobic Respiration Glycolysis Krebs Cycle Electron Transport System Electron Trans ortS stem Protein complex space In her mitochondrial Mitochondrial atrix ELECTRON TRANSPORT CHAIN ATP Figure 6 12 SYNTHASE Electron Transport System Electron transport chain Elemntrlnsponchlln Imumamb compmuch cnemIosmmlc phosphnrylalkm Electron Transport System For each glucose molecule that enters cellular respiration chemiosmosis produces up to 38 ATP molecules Overview of Aerobic Respiration cwmv em mwm Wm mm m mvwmmwmmv Nutrients Glucose H Glycolysis 2 Cy oplum Pyruvm Min Mllochondrlcn amp CEIIanI39I respiratlon overview General Outline Glucose 1 Glycolysis oxygen Pyruvic Acid No Oxygquot Aerobic AnaerobIc Transition Reaction Fermentation Krebs Cycle ETS 36 ATP Fermentation Requires NADH generated by glycolysis Where do you suppose these reactions take place Yeast produce carbon dioxide and ethanol Muscle cells produce lactic acid Only a fewATP are produced per glucose Fermentation awnm om MEGmw mu canqu Fermentation n v urnIide mpmmm mmvulni Alcoholic larmanrallnn alum gt200 Elhnnol Lmlc ncl rrmnmlon Glucw 2000 Pymvlc mm 2 2000 C 39 mm min Gene Expression Protein Synthesis I Central dogma I How are genes expressed overview I Protein structure I Genetic code I Gene expression transcription I Gene expression translation I Control of gene expression I Mutations E 71 George Beadle l a Edward Ta rum One GeneOne Enzyme Hypothesis W When a protei is needed by a cell the genetic code for that protein must he read from the DNA an proce W W synthesis of a 19 singlestranded RNA molecule 39 usIng the DNA template 1 strand of DNA is transcribed x x Minn conversion of a quot RN 0 pram messenger RNA sequence into the amino acid sequence of a polypeptide ie protein synthesis Prmein Both processes occur v 7 nucleus whereas translation occurs in the cytoplasm 2mm Highmolecularweight nitrogencontaining organic compound I Composed of one or more polypeptides I Polypeptides are composed of amino acids AA The sequence of AA gives the polypeptide its 3D shape and its properties in the cell Contains the following bonded to a central carbon atom I Amino grouP MHz Typically charged in the cell NH3 and C00 I Carboxyl group COOH I Hydrogen atom I R group different in each amino acid R group ozcarbon differs in each atom R amino acid T 9 9 H H Amino group Carboxyl group Structures common to all amino acids 20 erent am no a s occu I ng cell Abbreviated with 3 and 1letter codes J Classified into four chemical groups based on the composl ion of Rgro p 1 Aci ic n 2 2 Basic n 3 3 Neutral and polar hydroph lc n 6 4 Neutral and nonpolar hydrophobic n 9 Fig Ac c and basic amino acids Acidic Basic law quot o H N N l i Aspumc acid Q Us 5quot Asp my c 7C gxrc zi NH M m ooc o law H of H N 2 CH c c Gl mmic am quotaquot quotl H A I I lain lm c H V V rum aoc p 0 2 c a N c ml W m 39ooc mm Iv I c ic rc u Hi n CH Hlsl mi ouc HC N N Fig I Neutral nonpolar Hart T W 11470quot c 76H 75 l lsoiuucino 2 5 7 llla l 00 L llyplopllan v EH N Tm im ooc J m if cquot M c ccquot CN Leunine 39 39 lull in 3 CHa ltgt 3353quot 3900 CH cuc H w H NN l i 12H 3 L I e H Glycine c inking 5 Jigsaw Giyl icl ooc iiiHoo H3N c Alanlna H 7 393 CH1 Praline 75quot Ala A HC c Pro in some H H Hzquot H on Y H Vallne Val m Fig Neutral polar Hxn c l HIN T s Tyrasine 7 7 Aspurugme E CMO on M m f cquot if quotquot2 A N mac 7 3900 0 mm r i HN T Gluinmme Senna 7 cicHoH 5m 5 3 272 quotquot2 15ml rev 130 race 0 HN H Haw H H OH l l lc meaning C 7cH2 SH cysmine m 41 race Eys lCl ooc cu Amino acids are joined to form unbranched polypeptides by a peptide bond J Peptide bond covalent bond between the carboxyl group of one amino acid and amino group of the next amino acid Aminn acid Amino acid Polypeptide R o H 0 quot2 quot1 o H o l I I H l HJN39 C C Hw c c H N c CN c c I I A I l l 0 mo R1 0 H Camuxyl gm 39 PLImux Carboxyl group and Clerminal end J The N terminus is at the beginning of the polypeptide chain and the C terminus is at the end of the polypeptide chain Prote ns show four h erarch al levels of structural organ a o 1 Primam structure amino acid sequence Determined by the genetic code of the mRNA 2 Secondary structure folding and twisting of a single polypeptide chain Result of weak Hbonds and electrostatic interactions eg uhelix coiled and pleated sheet zigzag 3 Tertiam structure three dimensional shape or conformation of a Ingle polypeptide chain Results from the different R groups 4 guaternam structure association between polypeptides in multisubunit proteins eg hemoglobin Occurs only with two or more polypeptides Electrons shared between carbonyl group and p plum bond c el same charactenslics oi double bonds Primary Structure sequence of amino acids I Nterminus Cterminus H n o H o uouno iHiiliirH u T H Peptide ne39nicic Nice icic Nice ecec Necec Nececr Mad l x b ckbune H u an cu cu Jquot gquot Czlllwxyl group Ammo mu 39 Slde chains Secondary structure a Hydrogen bonds form between peptide chains a Hydrogen bonds Vorm between peptide chains quot 739 n n i 39 MEL c in pleated sheet 39 E chgrw u cw quot Innic bond Hip H Hydrugen bond between H2797 quot5 Disul de bond M Ma side she mostly at uhslices mnslly oi upleamd sheets disuliide bands Quaternary Structure a Cro protein a dimer b Hemoglobin a tetramer Mum Cod an an m lnlnmaliunll mm an autumn A V n o a o a 7 c p z n H u a E a Genetic Codequot 39 5 5 a 1 u u r 7 v J w How does DNA make proteins K x mm L y um quot w M z m DNA 9 Protein The enetic code how do nucleotides s eci 20 amino acids Yhsm m 4 RNA hue m c A G and they must speciiy an amino was quot 7 3 Hawmany OAGUGGC ruuu man bases speclfy 5 s n D mm a single amino 1 14 V lt acid I szm 2 Bans a Bans a Busls I maximum Manda ammo aclds nldx xa5 ammuaclda smeolnmmonlyuzses U U U 339 U A U G U U U U 5 U U l U U 2 Phase mm could spzclly I z a a I 2 a 4 quot Vquot39 39quot C quot c u c c c A c u c 2 iv a r c c c cl A G 5 e I E 5 5 7 2 4 All AC AA AG AA AAr AAu AAf 4 lt 20 Not enough a w n 2 a m n 2 l ELI GS 511 EC 56 GG GOA He is a u u 15 3 u l lGlt20Nmenough l 34 gt 20 Momlhan ennugh Hypnlheals A codun ls Masses long Allemauve hypothesls Acwdnn is 1 nr2basas lang Experimental semp Parent DNA sequence Pam DNA sequence Parent DNA immense lbnsapairdalmian h 2basepalrdalnllnn 39 3hainpnir nlelion delelions Ibasepalr delatlnns or 2hase pair delelians 39 39939e aquot quot Raiding lrame ul biplnl code Paw DNA sewn Q quotWe Wm 4 i amass delellun u n y mm in mm m an Canclusio m M The genetic code is a triplet code A set of 3 consecutive nucleotides make a codon in mRNA code which corresponds to one amino acid in a polypeptide chain 1 19605 Francis Crick et al 2 Studied frameshift mutations in bacteriophage T4 amp E coli induced by the mutagen proflavin 3 Proflavin caused the insertionldeletion indels of a base pair in the DNA 1 Discovered that frameshift mutations insertion or deletion resulted in a different sequence of amino acids a Wildlype b Frameshilimulalinn by deleiian delzled DNA 539 ACGACG ACG ACGIACG 339 539 ACGCGACGACBACGA 339 3 19976 qci39rscitcg 539 DNA a39 Tgcecmcrscrecr 539 mRNA 5 AcqggeggqchaAcg 3 mHNA 539 AqqchAccAcGAceA 339 Pnlypepiide quot39Thn l mian n nip Polvvemide THrArg Arg Arg Argw DNA mRNA Poiypepwe Lima ULTNI 2 Also discovered that r mutants treated with proflavin could be restored to the wild type W I deletion corrects insertion or vice versa 5 Combination of three r mutants routinely yielded revertants unlike other multiple combinations Normal mHNA AUG AQNQAUEAAEQQQQUQEHNQGQ yEQGAA Aminuacids Mel Thr His Asn Gly Phe Val Trp cys Glu 3 4 mutations 3 3 i mRNA Aug m gime uucaUAzuee usuzaAA Amino acids Fhe Val Trprs Glu Incorrect amino acids in polypeplide Three nearhyim ign restore the reading frame giving normal or nearnormal function Second lener c A u c uuu m ucu UAu Ty ueu Cys u U uuc m use 5quot UAC m use 0 e um Le UCA 5 i v u i A we L use use Trp a W cuu ccu CAU Hjs ceu u c we LE ccc pm mac H ccc mg c CUA L CCA P CAA G CGA R A 1 one CCG CA6 Q CGG 6 2 Z AUU ACU AAU Asn AGU Se U A Auc Act Tquot no N Ass 5 cquot AU ACA m AAA L AGA A Y My AUG Me ACG AM 10 A56 R G M GUU ch GAU Asp can u G GUC Val GCC Ah GAC 3 sec my c GUA W1 GCA W GAA a GGA G A sue ace GAG E GGG a I chain termination cudun stop Initiation codaquot Characteris ics of the genetic code written as in mRNAI 5 to 3 2quot Code is triplet N Code is comma free mRNA is read continuously 3 bases at a time without skipping bases in Code is nonoverlapping P Code is almost universal 5quot Code is degenerate 18 of 20 amino acids are coded by more than one codon 9 Code has start and stop signals Wobble occurs in the tRNA anticodon 3rd base is less constrained and pairs less spec cally a Secondary structure of tRNA W I Proposed by Francis Crick in 1966 I Occurs at 3 end of codonS end of anticodon I Result of arrangement of Hbonds of base pairs at the 3rd pos I Degeneracy of the code is such that wobble always results in translation of the same amino acid I Complete set of codons can be read by fewer than 61 tRNAs 5 in J 3 serum Leu i Lau 3 539 Identical 3 5 G pairs with U or C leuclne La c pairs with G La x lRNAs k 1 A pairs with u L 3 39 39 7 W pairswitii AorG G A G g A G I Inosine pairs with A u or c 1 i E quwal I I quble u c pairing 3 u U pairing 1 posttranscription modified purine mRNA c 539 3i 539 3r PHE SER TVR cvs PHE SER TVR cvs LEU SER STOP STOP LEU SER STOP TRP LEU PRO HIS ARG LEU PRO HIS ARG LEU PRO GLN ARG LEU PRO GLN ARG ILE THR ASN SER ILE THR ASN SER ILE THR Lvs ARG MET THR LVS ARG VAL ALA ASP GLV VAL ALA ASP GLV VAL ALA GLU GLV VAL ALA GLU GLV n 5 PHE SER TVR cvs g o PHE SER TVR cvs g E LEU SER STOP STOP g LEU SER STOP TRp 395 LEU PRO HIS ARG E LEU PRO HIS ARG LEU PRO GLN ARG z LEU PRO GLN ARG j ILE THR ASN SER E ILE THR ASN SER g ILE THR Lvs ARG z MET THR LVS ARG 5 VAL ALA ASP GLV VAL ALA ASP GLV g a VAL ALA GLU GLV 5 z VAL ALA GLU GLV g 10 Evolution of the genetic cod Some codons are inherently conservative by nature whereas others are more adical Phe Leu Ile Met Val 15 codons with T at 2nd pos possess 104 possible evolutionary pathways Only 12 115 result in moderately or radically dissimilar amino acid changes Most changes are nearly neutral because they result in substitution of similar amino acids Evolution of the genet code cont I average similar codons specify similar amino acids such that single base changes re u t in small chemical changes to polypeptides DNA gt RNA gt Protein Step 1 Transcription 11 NonIamplale caning Skand DNA Wmsphodlesier mm s lonlmlJ by RNA pulymnmsa nner base pairing uccm39s 0 5 a quot a as v P Pi P I oi 7 i on f E 339 on on i 77 Hydrugenhandsmrmimrween 7 mnplmmnmly base pails DNAmmpIme r t t t t 5 m P P r F P Holoenzyme Core enzyme HOW TRANSCRIPTION BEGINS Promoter an nontemplate strand 35 box 10 box cTGTI GA ATTAATCATCGAACTAQ T AGTACGC Upstrea v 39 1 site DNA w Sigma W 1 lt a Downstream DNA r K I RNA polymerase 1 Initiation begins Sigma binds to promoter region of DNA 12 HOW TRANSCRIPTION BEGINS Template strand Nontemplate strand 2 Initiation continues Sigma opens the DNA helix transcription be ns an HOW TRANSCRIPTION ENDS r Upstream DNA Hairpin Inop N polymerase r quot r r Transcription tarminaIio n slgna RNA polymerase reaches a transcription 2 The RNA hairpin causes the RNA strand termination signai which codes for RNA to separate Irom the RNA polymerase that terms a halrpln terminating transcription singlestranded Inimn Exon DNA oniy He 53 size of gene DNA 7 I Singlestranded DNA 4 base palred wim mam size at mature RNA transcript a lntrons must be removed from RNA transcripts lntran 1 lntron 2 DNA 31 539 V Lg Promoter Exon 1 Exon 2 Exon 3 Primary FINA transcript 5 7 i r 1 a 2 3r Spliced transcript 57 r 5 J 3 Gene Expression Step 2 Translation Transla rot n s quotthe s Overv w Protein synthesis occurs on ribosomes 2 mRNA is translated 539 to 339 Protein is synthesized Nterminus to Cterminus 4 Amino acids bound to tRNAs are transported to the ribosome Facilitated by Spe cbi Complementary basepairing between the mRNA codon and the tRNA anticodon mRNA recognizes the tRNA anticodon not the amino acid ding of amino acids to their tRNAs Translat n 4 m n steps 1 Charging of tRNA 2 Initiation 3 Elongation 3 steps 1 Bin ing of the aminoacyl tRNA to the ribosome 2 Formation of the peptide bond 5quot Translocation of the ribosome to the next codon 4 Termination 14 step 1 hnrnin of tRNA 39 I 1 Amino acids are attached to tRNAs by amInoacyltRNA synthetase mluo aniu PA39 and AV hind P 39 In enzyme Enzyme camyns can lin ouminn pMJ sci u MP 10 mm P m aminmcyl AMP rm pnnnpnnins nninoacynnnnsynnn Enzyme i Mm n i in original ii sinie J L u v i P 5 AMP uncharged mam andc mi leased aaIRNAanlvms H 39 2 n n AmmuacyHRNA imam 2min Imnslels amino ac min aminnacylAMP a KR a inrm aminancyHRNA i mm in umm and mm are released lrnm ihe enzyme aamhuzym Unchalgad mm was lnxyme Steg 21 nreguirements 1 mRNA 2 Ribosom e 3 Initiator tRNA fMet tRNA in proka ryotes 4 3 Initiation factors IF1 IF2 IF3 5 M 6 GTP guanosine triphosphate 15 mmuuur 39 a n Bwnctmu INmATING TRANSLATION IN BACTERIA Rlbasnma man slte Lam nhun n homma 3 Large subunit 1 ubmme hum Ymnslnnnn mains 16 mm m mmmummumm 17 Ribasomes Frame Shift Mutations Point Mutations Silent Nonsense Missense 18 SUMMARY MMH 163 KnownYypes afP sum Missense Rewazemem Nonsense Flamesmll I Mutations Da nltlun ixample consequent Ongma DNA sequence m E Law wwgwawewuwwe 5 Change m nudsatide mm m Change In genolypz hm nu mange In dazsnmchan Aaminc 7 7 W i ulvenmypz andspui zdbycodon 3 L LB E i Change m nuzleunde rhal Change In p mayysxmume a promquot hangzs amino and spezi ed 7 bymdun TY E33 quot1 quot5 1 f lt angem nudemiuemm Premamrelerminatranpo1ypemlde a quot J lesulxs n early slop ann Isuunaxe W srow Readmg fvame ws shmed see mam lSAmasswe mmanse Ser All E W Admnun or Salmon 0 a mumm 19 Introductory Biology I What is the nature oF biological diversity and how did it arise Learning Outcomes Define biodiversity Identify unifying themes of biology Introduction to evolution descent with modification phylogeny Introduction to DNA the genetic material of cells Biodiversity The variety and variability among living organisms and the ecological complexes in which they occur Gene ic Species Ecosystem Biology the study of life at various scales Organisms are extremely diverse Organisms are extremely diverse Bacteria Organisms are extremely diverse lit v 39 r i unifying themes of biology Eukarya New properties emerge at higher levels of biological hierarchies Emergent properties complexity increases due to the arrangement and interactions of parts unifying themes of biology unifying themes of biology Organisms interact with their Structure and function are correlated environments exchanging energy and matter Matter in CO2 and nutrients Matter out O2 and decomposing biomass Energy in light Energy out heat unifying themes of biology Ulllfylng themes 0f bl0l09y Feedback mechanisms quotmm The continuity of life is based on heritable regulate biological information DNA systems 33525 i 7 Negative m u DNA controls the on an end product of a muggmmmmk development and process slows that process maintenance of all organisms Positive feedback less common end product Excessz swarm speeds up production ser lt is similar across species hi Pnslwe 122mm Evolution is the core unifying theme of biology It explains how all life forms can be so similar ie Possess the same genetic language and cell structure It also explains how life can be so divers He t of al isole Nothing in biology makes sense except in the light of evolution T Dobzhansky 39 ation ted the El Metabolism Catabolism Anabolism El Catabolic reactions are energy yielding El They are involved in the breakdown of more complex molecules into simpler ones El Anabolic reactions are energy requiring El They are involved in the building up of simpler molecules into more complex ones El We can consider these bioenergetics in terms of the physical laws of thermodynamics Every energy transfer or transformation increases the disorder entropy of the universequot Note especially the waste heat Energy can be transferred or transformed but neither created nor destroyedquot ir W u cnwuqmw 7005K El Organisms take in energy 398 transduce it to new forms 1st law As energy transducers organisms are less than 100 efficient 2nd law Organisms employ this energy to Grow Protect Themselves Repair Themselves Compete with other Organisms Reproduce In the process organisms generate waste chemicals amp heat I I I3 El First Law of Thermodynamics Energy can be neither created nor destroyed Therefore energy quotgeneratedquot in any system is energy that has been transformed from one state to another eg chemically stored energy transformed to heat U Second Law of Thermodynamics Efficiencies of energy transformation never equal 100 Therefore all processes lose energy typically as heat and are not reversible unless the system is open amp the lost energy is resupplied from the environment Conversion to heat is the ultimate fate of chemical energy Amount of energy required AG gt 0 Amount of energy released AG lt 0 Energy released required Reactants Free energy gt Products Free energya Progress of the reaction gt Progress of the reactio b Endergonic reaction energy required ergy released lemma rum mnsPzuunsam rm rum Manmmrmm Ar mm a Exergonic reaction en m5er Edi21m in mm ISPHIWVIBvamnCum g 2 Minus the cut forthe 2 d law Free energy gt Progress 039 Iha relation D a Exergenlr reacllon energy released Exergonic reactions can supply energy for endergonic reactions Progress ol the reactin b Emergent reaction energy required unwrime mm mm mm in mm myrnnremmmr WWW atabolic reactions provide the energy that drives anabolic reactions forward I s AB DCDEnergy r r l Phosphate groups v a39r E F Energy DG H L I 39 cumnmmsrumnamninwhimmgummawminmmings Alhlwmxusmu Anabolic reaction Movement toward Adenosine trlphosphate ATP equilibrium WE lnorganic phosphate Adenosine diphosphate ADP cmmmu 3 um no a rm 1 p m quotm Siami mm a 5 mnEmnAlmJn Mmmwul unm mpmmmmmlnm Allon 7 W mmquot quotE m m quotquot7 quotquotquot quot quotWWW M Endergonic A 39 Exercgtonlc J r A 39 39 I Anabolic V rea Ion rocess reaction r 1 p amp Exergonic Endergonic reaction reaction Energy for cellular work endergonlc energy consuming procases Energy from catabolism exergonic energy yielding processes s auwngmm ansPumnmeaMm Wblmhgut mm awmlncummlnn mmmm V a i Chemically stored energy Cowugh o zws Putnu 2mm in Mm mmquot mm aiming m was mm M Anything that doesn t require an input of energy to get started has Transition state EA with H already en ma happened is lower AG isu d hy enzyme Lowering of activation energy Products camm mashmueaum in Mmm u mammm mm mm mm 5mm mos paw mum inc mlmw um mm rimming 1 quotgm mm This is instead of adding heat heat is an inefficient means of speeding up reactions since it simply is a means of At a given quot 39 increasing the temperature random jostlings of catalyzed reactions molecules can run faster because less energy is required to achieve the transition state lnlllal substrate lhreanina Active aim vailnhls Thrennlne ln acuve site Feedback inhibition 553 Enzymes in single pathway ggm39ic 39 a may be colocalized so that 39quot quot the product of one enzyme increases the local concentration of the Q 5235331 A substrate for another cum c was Furon Elmlm in MW 1 Putnam Esipm in 0mm All mu rui iv Evolution is the core unifying theme of biology It explains how all life forms can be so similar ie Possess the same genetic language and cell structure It also explains how life can be so diverse Nothing in biology makes sense except in the light of evolution T Dobzhansky Background By the 1800 s scientists knew that only simple fossils were found in older rock and complex fossils only in younger rock Scientists wanted to explain how new life forms appeared and why some life forms disappeared completely Charles DanNin ship s naturalist 18311836 He studied the unusual combination of animal species which inhabited the isolated Galapagos Islands W K Tl Darwin observed that each island had its own species of animals which differed noticeably from related animals only a few miles The core unifying theme of biology Evolutionchange in he genetic composition of a popula ion over time Darwin referred to evolution as descent with modification He proposed that the mechanism was natural selection Why The core unifying theme of M biology y He saw that individuals in populations varied anc that the variation was heritab e He saw that populations were producing more offspring than could survive He saw that species tended to be suited to their environment He concluded that individuals with traits that are better suited to the environment are more likely to survive and reproduce This will lead to changes in the gene pool over time mp l evulman berks evedulevusnelevul l lllMechanisms smm Descent with Modification 39I39IIE IIIS I39ORY or III ON EARTH Biological evolution is descent with modification This definition encompasses smallscale evolution changes in gene frequency in a population from one generation to the next and largescale evolution the descent of different species from a common ancestor over many generations Evolution helps us to understand the history of life Biological evolution is not simply a matter of change over time Lots ofthings change over time but they aren39t examples of biological evolution because they don39t v involve descent through genetic inheritance no in The central idea of biological evolution is that all life on Earth shares a common ancestor just as cousins share a common grandmother Ibo use i an ID a ueua uuaivous E as i amg u nmm a uaua 39 2 Through the process of descent with modification the common ancestor of life on Earth gave rise to the fantastic diversity that we see documented in the fossil record and around us today The central ideas of evolution are that life has a history it has changed over time and that different y species share common ancestors 0 We can explore how evolutionary change and evolutionary relationships are represented in family treesquot how these trees are constructed and how this knowledge affects biological classification Descent with modification from a common ancestor but what has been modified Evolution only occurs when there is a change in gene frequency within a population over time These genetic differences are heritable and can be passed onto the next generation Family Tree The process of evolution produces a pattern of relationships between species As lineages evolve and split and modifications are inherited their evolutionary paths diverge This produces a branching pattern of evolutionary relationships By studying inherited characteristics and other historical evidence we can reconstruct evolutionary relationships and represent them on a family treequot called a phylogeny DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKAHVA v339 s ca QM c ya v quotf Kg Understanding a phylogeny is a lot like reading a family tree The root of the tree represents the ancestral lineage and the tips ofthe branches represent the descendents of that ancestor As you move from the root to the tips you are moving forward in time DESCENDENTS 1 2 3 4 RECENT ANCESTOR PAST When a lineage splits speciation it is represented as branching on a phylogeny When a speciation event occurs a single ancestral lineage gives rise to two or more daughter lineages K SPECIATION EVENT ANCESTRAL LINEAGE Phylogenies trace patterns of shared ancestry between lineages Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages I Uqu i Still on b I Unique history of C Shared history of B and C A clade is a grouping that includes a common ancestor and all the descendents living and extinct ofthat ancestor Using a phylogeny it is easy to tell if a group of lineages forms a clade Imagine clipping a single branch offthe phylogeny all ofthe organisms on that pruned branch make up a clade I Aclade I Aclade Not a clade Not a clade Clades are nested within one another they form a nested hierarchy A clade may include many thousands of species orjust a few Some examples of clades at different levels are marked on the phylogenies below Notice how clades are nested within larger clades To build a phylogenetic tree biologists collect data about the characters of each organism they are interested In Characters are heritable traits that can be compared across organisms such as physical characteristics morphology genetic 39 sequences and behavioral traits Shared Derived Characters A shared character is one that two lineages have in common and a derived character is one that evolved in the lineage leading up to a clade and that sets members ofthat clade apart from other individuals Example fish have scales and mammals have hair Having hair is a derived character for mammals because only the mammals have ancestors with hair Shared derived characters can be used to group organisms into clades For example amphibians turtles lizards snakes crocodiles birds and mammals all have or historically had four limbs Sharks Ray nned shes Amphibians Turtles Lizards Snakes Crocodiles Birds Mammals Four limbs evolved here 10 Substate Active site En co p Enzyme substrate complex 9 m mir wmm o pnm ax tem peratu retfor Obtwm a temperature for typmal huma enzyme enzyme qfihe rmupmkz Optima pH forpepsm stomach 39en z W a IE h A v 39 r x I u L ir quotL lt 5 h I I 1 L 77 x H 1 r f A 1 H X ay beam cwguaum mulecme m a x lemmas n mumI chemoI slmclure D A Itruclum nucleotide Adenlne A Three postulated methods of DNA Replication WWWltIWNNNNM WWWw SemiConservative WltWWW Conservative WOWltZ WWW Dispersive T 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aukaryoles DNA nplicauon begins a many sues along the glanl DNA molecula ofeach e ronlosoma b In his micrograph mm repllcalion bubbles are vislhle along the cullumd Chin Se at each bubble TEM arguwnupnne makhane am pm lolnod hy mama bondlna 39 Adding bases o can only add nucleotides to 339 end of a growing DNA strand 9 strand only grows 5 gt3 Limits of DNA polymerase o can only buiid qntp 3 end of an existing DNA strand Qrkaz ki fragments 6 joined byJig39ase Limits of DNA olym39erase II o can only buii d onto and of an ezjs ng DNA stand RNA primer 0 buiit by m o serves as starter seq uenoe for DNA pollmefase Ill Hut DNA palyr39 e rasel still quot u 39 63 endof All39DNjA polymerases can nlyadd 03 encl ofran 39exnsling DNA strand Lass ofhases a 39veryre Ii 7 n romosnme sget shutter w h each replicatinn i squot R a t n 0f chram mes 394 mitto5u cejld Telnr ena se 5 enzyme extend5 tglqmare v v antadd DNA bases at 539 and nmrent lave afaptivity in differemgglls 5 Why hi gh in stem Sells 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