[{"data":1,"prerenderedAt":1608},["ShallowReactive",2],{"mdc-i3lm0m-key":3},{"data":4,"body":5},{},{"type":6,"children":7},"root",[8,17,23,109,121,125,131,136,184,187,193,198,264,274,277,283,360,363,369,413,416,422,427,455,465,468,474,483,501,510,523,526,532,541,559,568,581,584,590,618,621,627,636,649,658,671,674,680,711,714,720,740,743,749,757,793,796,802,807,830,833,839,844,877,880,886,891,909,912,918,957,960,966,989,992,998,1003,1022,1042,1045,1051,1056,1074,1085,1088,1094,1107,1110,1116,1121,1150,1158,1161,1167,1172,1185,1188,1194,1199,1202,1208,1251,1254,1260,1278,1281,1287,1300,1303,1309,1345,1348,1354,1367,1370,1376,1394,1397,1403,1426,1429,1435,1458,1461,1467,1490,1493,1499,1517,1520,1526,1559,1562,1568,1573,1596],{"type":9,"tag":10,"props":11,"children":13},"element","h2",{"id":12},"page-1-why-study-proteins",[14],{"type":15,"value":16},"text","🧬 Page 1 — Why study proteins?",{"type":9,"tag":18,"props":19,"children":20},"p",{},[21],{"type":15,"value":22},"Proteins are central to life and biology:",{"type":9,"tag":24,"props":25,"children":26},"ul",{},[27,39,51,71,99],{"type":9,"tag":28,"props":29,"children":30},"li",{},[31,33],{"type":15,"value":32},"They act as ",{"type":9,"tag":34,"props":35,"children":36},"strong",{},[37],{"type":15,"value":38},"scaffolds, machines, signals, transporters, and catalysts",{"type":9,"tag":28,"props":40,"children":41},{},[42,44,49],{"type":15,"value":43},"Understanding ",{"type":9,"tag":34,"props":45,"children":46},{},[47],{"type":15,"value":48},"structure ↔ function",{"type":15,"value":50}," is key to medicine, biotechnology, and biology",{"type":9,"tag":28,"props":52,"children":53},{},[54,56,61,63],{"type":15,"value":55},"Proteins are ",{"type":9,"tag":34,"props":57,"children":58},{},[59],{"type":15,"value":60},"much more complex than DNA",{"type":15,"value":62},":",{"type":9,"tag":24,"props":64,"children":65},{},[66],{"type":9,"tag":28,"props":67,"children":68},{},[69],{"type":15,"value":70},"20 amino acids vs 4 nucleotides",{"type":9,"tag":28,"props":72,"children":73},{},[74,76],{"type":15,"value":75},"The combinatorial explosion is enormous:",{"type":9,"tag":24,"props":77,"children":78},{},[79,89],{"type":9,"tag":28,"props":80,"children":81},{},[82,84],{"type":15,"value":83},"A 37-AA protein → ",{"type":9,"tag":34,"props":85,"children":86},{},[87],{"type":15,"value":88},"20³⁷ ≈ 1.37 x 10⁴⁸ possible sequences",{"type":9,"tag":28,"props":90,"children":91},{},[92,94],{"type":15,"value":93},"One copy of each would weigh ",{"type":9,"tag":34,"props":95,"children":96},{},[97],{"type":15,"value":98},"1.5x Earth's mass",{"type":9,"tag":28,"props":100,"children":101},{},[102,104],{"type":15,"value":103},"Average human protein length: ",{"type":9,"tag":34,"props":105,"children":106},{},[107],{"type":15,"value":108},"~373 amino acids",{"type":9,"tag":18,"props":110,"children":111},{},[112,114,119],{"type":15,"value":113},"🧠 ",{"type":9,"tag":34,"props":115,"children":116},{},[117],{"type":15,"value":118},"Key idea:",{"type":15,"value":120}," proteins are chemically diverse, structurally complex, and biologically powerful",{"type":9,"tag":122,"props":123,"children":124},"hr",{},[],{"type":9,"tag":10,"props":126,"children":128},{"id":127},"page-2-what-this-lecture-covers",[129],{"type":15,"value":130},"🧪 Page 2 — What this lecture covers",{"type":9,"tag":18,"props":132,"children":133},{},[134],{"type":15,"value":135},"Overview of core protein chemistry:",{"type":9,"tag":24,"props":137,"children":138},{},[139,144,149,154,159,164,169,174,179],{"type":9,"tag":28,"props":140,"children":141},{},[142],{"type":15,"value":143},"Amino acids as building blocks",{"type":9,"tag":28,"props":145,"children":146},{},[147],{"type":15,"value":148},"Zwitterions & charge behavior",{"type":9,"tag":28,"props":150,"children":151},{},[152],{"type":15,"value":153},"Chirality",{"type":9,"tag":28,"props":155,"children":156},{},[157],{"type":15,"value":158},"Structures & naming conventions",{"type":9,"tag":28,"props":160,"children":161},{},[162],{"type":15,"value":163},"Amino-acid similarities & abundance",{"type":9,"tag":28,"props":165,"children":166},{},[167],{"type":15,"value":168},"Charge, pI, pH",{"type":9,"tag":28,"props":170,"children":171},{},[172],{"type":15,"value":173},"Protein structural hierarchy",{"type":9,"tag":28,"props":175,"children":176},{},[177],{"type":15,"value":178},"Secondary structure elements",{"type":9,"tag":28,"props":180,"children":181},{},[182],{"type":15,"value":183},"Databases & tools",{"type":9,"tag":122,"props":185,"children":186},{},[],{"type":9,"tag":10,"props":188,"children":190},{"id":189},"️-page-3-amino-acids-as-zwitterions",[191],{"type":15,"value":192},"⚖️ Page 3 — Amino acids as zwitterions",{"type":9,"tag":18,"props":194,"children":195},{},[196],{"type":15,"value":197},"In water at physiological pH:",{"type":9,"tag":24,"props":199,"children":200},{},[201,231,254],{"type":9,"tag":28,"props":202,"children":203},{},[204,206,211],{"type":15,"value":205},"Amino acids exist as ",{"type":9,"tag":34,"props":207,"children":208},{},[209],{"type":15,"value":210},"zwitterions",{"type":9,"tag":24,"props":212,"children":213},{},[214],{"type":9,"tag":28,"props":215,"children":216},{},[217,222,224,229],{"type":9,"tag":34,"props":218,"children":219},{},[220],{"type":15,"value":221},"NH₃⁺ (positive)",{"type":15,"value":223}," and ",{"type":9,"tag":34,"props":225,"children":226},{},[227],{"type":15,"value":228},"COO⁻ (negative)",{"type":15,"value":230}," simultaneously",{"type":9,"tag":28,"props":232,"children":233},{},[234,236],{"type":15,"value":235},"pH controls protonation state:",{"type":9,"tag":24,"props":237,"children":238},{},[239,244,249],{"type":9,"tag":28,"props":240,"children":241},{},[242],{"type":15,"value":243},"Low pH → fully protonated",{"type":9,"tag":28,"props":245,"children":246},{},[247],{"type":15,"value":248},"Neutral pH → zwitterion",{"type":9,"tag":28,"props":250,"children":251},{},[252],{"type":15,"value":253},"High pH → deprotonated",{"type":9,"tag":28,"props":255,"children":256},{},[257,259],{"type":15,"value":258},"The graph shows ",{"type":9,"tag":34,"props":260,"children":261},{},[262],{"type":15,"value":263},"species distribution vs pH",{"type":9,"tag":18,"props":265,"children":266},{},[267,268,272],{"type":15,"value":113},{"type":9,"tag":34,"props":269,"children":270},{},[271],{"type":15,"value":118},{"type":15,"value":273}," amino acids are never “neutral” in solution",{"type":9,"tag":122,"props":275,"children":276},{},[],{"type":9,"tag":10,"props":278,"children":280},{"id":279},"page-4-chirality-the-corn-rule",[281],{"type":15,"value":282},"🔄 Page 4 — Chirality & the CORN rule",{"type":9,"tag":24,"props":284,"children":285},{},[286,298,308,345],{"type":9,"tag":28,"props":287,"children":288},{},[289,291,296],{"type":15,"value":290},"All amino acids except ",{"type":9,"tag":34,"props":292,"children":293},{},[294],{"type":15,"value":295},"glycine",{"type":15,"value":297}," are chiral at Cα",{"type":9,"tag":28,"props":299,"children":300},{},[301,303],{"type":15,"value":302},"Nature uses ",{"type":9,"tag":34,"props":304,"children":305},{},[306],{"type":15,"value":307},"only L-amino acids",{"type":9,"tag":28,"props":309,"children":310},{},[311,316,317],{"type":9,"tag":34,"props":312,"children":313},{},[314],{"type":15,"value":315},"CORN rule",{"type":15,"value":62},{"type":9,"tag":24,"props":318,"children":319},{},[320,325,335],{"type":9,"tag":28,"props":321,"children":322},{},[323],{"type":15,"value":324},"View from H → Cα",{"type":9,"tag":28,"props":326,"children":327},{},[328,330],{"type":15,"value":329},"Read ",{"type":9,"tag":34,"props":331,"children":332},{},[333],{"type":15,"value":334},"CO → R → N",{"type":9,"tag":28,"props":336,"children":337},{},[338,340],{"type":15,"value":339},"Clockwise = ",{"type":9,"tag":34,"props":341,"children":342},{},[343],{"type":15,"value":344},"L-isomer",{"type":9,"tag":28,"props":346,"children":347},{},[348,353,355],{"type":9,"tag":34,"props":349,"children":350},{},[351],{"type":15,"value":352},"Isoleucine & threonine",{"type":15,"value":354}," have ",{"type":9,"tag":34,"props":356,"children":357},{},[358],{"type":15,"value":359},"two chiral centers",{"type":9,"tag":122,"props":361,"children":362},{},[],{"type":9,"tag":10,"props":364,"children":366},{"id":365},"page-5-carbon-naming-α-β-γ",[367],{"type":15,"value":368},"🔢 Page 5 — Carbon naming (α, β, γ…)",{"type":9,"tag":24,"props":370,"children":371},{},[372,385,403],{"type":9,"tag":28,"props":373,"children":374},{},[375,377],{"type":15,"value":376},"Side-chain carbons are named:",{"type":9,"tag":24,"props":378,"children":379},{},[380],{"type":9,"tag":28,"props":381,"children":382},{},[383],{"type":15,"value":384},"α, β, γ, δ, ε, ζ, η",{"type":9,"tag":28,"props":386,"children":387},{},[388,390,395],{"type":15,"value":389},"Example: ",{"type":9,"tag":34,"props":391,"children":392},{},[393],{"type":15,"value":394},"lysine",{"type":9,"tag":24,"props":396,"children":397},{},[398],{"type":9,"tag":28,"props":399,"children":400},{},[401],{"type":15,"value":402},"Long aliphatic chain ending in ε-NH₃⁺",{"type":9,"tag":28,"props":404,"children":405},{},[406,408],{"type":15,"value":407},"Important for ",{"type":9,"tag":34,"props":409,"children":410},{},[411],{"type":15,"value":412},"mechanisms, mutations, PTMs",{"type":9,"tag":122,"props":414,"children":415},{},[],{"type":9,"tag":10,"props":417,"children":419},{"id":418},"page-6-aliphatic-amino-acids",[420],{"type":15,"value":421},"🧱 Page 6 — Aliphatic amino acids",{"type":9,"tag":18,"props":423,"children":424},{},[425],{"type":15,"value":426},"Nonpolar, hydrophobic side chains:",{"type":9,"tag":24,"props":428,"children":429},{},[430,435,440,445,450],{"type":9,"tag":28,"props":431,"children":432},{},[433],{"type":15,"value":434},"Glycine (0 carbons)",{"type":9,"tag":28,"props":436,"children":437},{},[438],{"type":15,"value":439},"Alanine (1)",{"type":9,"tag":28,"props":441,"children":442},{},[443],{"type":15,"value":444},"Valine (3)",{"type":9,"tag":28,"props":446,"children":447},{},[448],{"type":15,"value":449},"Leucine (4)",{"type":9,"tag":28,"props":451,"children":452},{},[453],{"type":15,"value":454},"Isoleucine (4, branched)",{"type":9,"tag":18,"props":456,"children":457},{},[458,459,463],{"type":15,"value":113},{"type":9,"tag":34,"props":460,"children":461},{},[462],{"type":15,"value":118},{"type":15,"value":464}," increasing carbon count → increased hydrophobicity",{"type":9,"tag":122,"props":466,"children":467},{},[],{"type":9,"tag":10,"props":469,"children":471},{"id":470},"page-7-aromatic-imino-acids",[472],{"type":15,"value":473},"🌸 Page 7 — Aromatic & imino acids",{"type":9,"tag":18,"props":475,"children":476},{},[477,482],{"type":9,"tag":34,"props":478,"children":479},{},[480],{"type":15,"value":481},"Aromatic amino acids",{"type":15,"value":62},{"type":9,"tag":24,"props":484,"children":485},{},[486,491,496],{"type":9,"tag":28,"props":487,"children":488},{},[489],{"type":15,"value":490},"Phenylalanine",{"type":9,"tag":28,"props":492,"children":493},{},[494],{"type":15,"value":495},"Tyrosine",{"type":9,"tag":28,"props":497,"children":498},{},[499],{"type":15,"value":500},"Tryptophan (largest, absorbs UV strongly)",{"type":9,"tag":18,"props":502,"children":503},{},[504,509],{"type":9,"tag":34,"props":505,"children":506},{},[507],{"type":15,"value":508},"Proline",{"type":15,"value":62},{"type":9,"tag":24,"props":511,"children":512},{},[513,518],{"type":9,"tag":28,"props":514,"children":515},{},[516],{"type":15,"value":517},"Imino acid (side chain bonds back to backbone N)",{"type":9,"tag":28,"props":519,"children":520},{},[521],{"type":15,"value":522},"Rigid → disrupts helices",{"type":9,"tag":122,"props":524,"children":525},{},[],{"type":9,"tag":10,"props":527,"children":529},{"id":528},"page-8-charged-side-chains",[530],{"type":15,"value":531},"⚡ Page 8 — Charged side chains",{"type":9,"tag":18,"props":533,"children":534},{},[535,540],{"type":9,"tag":34,"props":536,"children":537},{},[538],{"type":15,"value":539},"Basic (positively charged)",{"type":15,"value":62},{"type":9,"tag":24,"props":542,"children":543},{},[544,549,554],{"type":9,"tag":28,"props":545,"children":546},{},[547],{"type":15,"value":548},"Lysine",{"type":9,"tag":28,"props":550,"children":551},{},[552],{"type":15,"value":553},"Arginine",{"type":9,"tag":28,"props":555,"children":556},{},[557],{"type":15,"value":558},"Histidine (aromatic + titratable near pH 7)",{"type":9,"tag":18,"props":560,"children":561},{},[562,567],{"type":9,"tag":34,"props":563,"children":564},{},[565],{"type":15,"value":566},"Acidic (negatively charged)",{"type":15,"value":62},{"type":9,"tag":24,"props":569,"children":570},{},[571,576],{"type":9,"tag":28,"props":572,"children":573},{},[574],{"type":15,"value":575},"Aspartate",{"type":9,"tag":28,"props":577,"children":578},{},[579],{"type":15,"value":580},"Glutamate",{"type":9,"tag":122,"props":582,"children":583},{},[],{"type":9,"tag":10,"props":585,"children":587},{"id":586},"page-9-hydroxyl-side-chains",[588],{"type":15,"value":589},"💧 Page 9 — Hydroxyl side chains",{"type":9,"tag":24,"props":591,"children":592},{},[593,598,603,608,613],{"type":9,"tag":28,"props":594,"children":595},{},[596],{"type":15,"value":597},"Serine",{"type":9,"tag":28,"props":599,"children":600},{},[601],{"type":15,"value":602},"Threonine",{"type":9,"tag":28,"props":604,"children":605},{},[606],{"type":15,"value":607},"Tyrosine\nContain -OH groups:",{"type":9,"tag":28,"props":609,"children":610},{},[611],{"type":15,"value":612},"Hydrogen bonding",{"type":9,"tag":28,"props":614,"children":615},{},[616],{"type":15,"value":617},"Phosphorylation sites (Ser, Thr, Tyr)",{"type":9,"tag":122,"props":619,"children":620},{},[],{"type":9,"tag":10,"props":622,"children":624},{"id":623},"page-10-amide-sulfur-side-chains",[625],{"type":15,"value":626},"🔗 Page 10 — Amide & sulfur side chains",{"type":9,"tag":18,"props":628,"children":629},{},[630,635],{"type":9,"tag":34,"props":631,"children":632},{},[633],{"type":15,"value":634},"Amide",{"type":15,"value":62},{"type":9,"tag":24,"props":637,"children":638},{},[639,644],{"type":9,"tag":28,"props":640,"children":641},{},[642],{"type":15,"value":643},"Asparagine",{"type":9,"tag":28,"props":645,"children":646},{},[647],{"type":15,"value":648},"Glutamine",{"type":9,"tag":18,"props":650,"children":651},{},[652,657],{"type":9,"tag":34,"props":653,"children":654},{},[655],{"type":15,"value":656},"Sulfur-containing",{"type":15,"value":62},{"type":9,"tag":24,"props":659,"children":660},{},[661,666],{"type":9,"tag":28,"props":662,"children":663},{},[664],{"type":15,"value":665},"Methionine (thioether)",{"type":9,"tag":28,"props":667,"children":668},{},[669],{"type":15,"value":670},"Cysteine (thiol → disulfide bonds)",{"type":9,"tag":122,"props":672,"children":673},{},[],{"type":9,"tag":10,"props":675,"children":677},{"id":676},"️-page-11-drawing-amino-acids-exercise",[678],{"type":15,"value":679},"✏️ Page 11 — Drawing amino acids (exercise)",{"type":9,"tag":24,"props":681,"children":682},{},[683,688],{"type":9,"tag":28,"props":684,"children":685},{},[686],{"type":15,"value":687},"Practice drawing amino acids from memory",{"type":9,"tag":28,"props":689,"children":690},{},[691,693],{"type":15,"value":692},"Reinforces:",{"type":9,"tag":24,"props":694,"children":695},{},[696,701,706],{"type":9,"tag":28,"props":697,"children":698},{},[699],{"type":15,"value":700},"Backbone",{"type":9,"tag":28,"props":702,"children":703},{},[704],{"type":15,"value":705},"Side-chain diversity",{"type":9,"tag":28,"props":707,"children":708},{},[709],{"type":15,"value":710},"Chirality awareness",{"type":9,"tag":122,"props":712,"children":713},{},[],{"type":9,"tag":10,"props":715,"children":717},{"id":716},"page-12-genetic-code-organization",[718],{"type":15,"value":719},"🧬 Page 12 — Genetic code organization",{"type":9,"tag":24,"props":721,"children":722},{},[723,728],{"type":9,"tag":28,"props":724,"children":725},{},[726],{"type":15,"value":727},"Codons encoding similar amino acids cluster together",{"type":9,"tag":28,"props":729,"children":730},{},[731,733,738],{"type":15,"value":732},"Stop codons can be ",{"type":9,"tag":34,"props":734,"children":735},{},[736],{"type":15,"value":737},"repurposed",{"type":15,"value":739}," for special amino acids",{"type":9,"tag":122,"props":741,"children":742},{},[],{"type":9,"tag":10,"props":744,"children":746},{"id":745},"page-13-pam-matrices",[747],{"type":15,"value":748},"📊 Page 13 — PAM matrices",{"type":9,"tag":18,"props":750,"children":751},{},[752],{"type":9,"tag":34,"props":753,"children":754},{},[755],{"type":15,"value":756},"PAM = Point Accepted Mutations",{"type":9,"tag":24,"props":758,"children":759},{},[760,765,783],{"type":9,"tag":28,"props":761,"children":762},{},[763],{"type":15,"value":764},"Measures evolutionary substitution probability",{"type":9,"tag":28,"props":766,"children":767},{},[768,770],{"type":15,"value":769},"Example:",{"type":9,"tag":24,"props":771,"children":772},{},[773],{"type":9,"tag":28,"props":774,"children":775},{},[776,778],{"type":15,"value":777},"Tyr ↔ Phe appears ",{"type":9,"tag":34,"props":779,"children":780},{},[781],{"type":15,"value":782},"6.6x more often than random",{"type":9,"tag":28,"props":784,"children":785},{},[786,788],{"type":15,"value":787},"Used in ",{"type":9,"tag":34,"props":789,"children":790},{},[791],{"type":15,"value":792},"sequence alignment",{"type":9,"tag":122,"props":794,"children":795},{},[],{"type":9,"tag":10,"props":797,"children":799},{"id":798},"page-14-the-22-amino-acids",[800],{"type":15,"value":801},"🌟 Page 14 — The 22 amino acids",{"type":9,"tag":18,"props":803,"children":804},{},[805],{"type":15,"value":806},"Beyond the standard 20:",{"type":9,"tag":24,"props":808,"children":809},{},[810,820],{"type":9,"tag":28,"props":811,"children":812},{},[813,818],{"type":9,"tag":34,"props":814,"children":815},{},[816],{"type":15,"value":817},"Selenocysteine (U)",{"type":15,"value":819}," — encoded by UGA",{"type":9,"tag":28,"props":821,"children":822},{},[823,828],{"type":9,"tag":34,"props":824,"children":825},{},[826],{"type":15,"value":827},"Pyrrolysine (O)",{"type":15,"value":829}," — encoded by UAG\nUsed in specific organisms and enzymes",{"type":9,"tag":122,"props":831,"children":832},{},[],{"type":9,"tag":10,"props":834,"children":836},{"id":835},"page-15-one-letter-codes",[837],{"type":15,"value":838},"🔠 Page 15 — One-letter codes",{"type":9,"tag":18,"props":840,"children":841},{},[842],{"type":15,"value":843},"Rules:",{"type":9,"tag":24,"props":845,"children":846},{},[847,852,857,862,867,872],{"type":9,"tag":28,"props":848,"children":849},{},[850],{"type":15,"value":851},"First letter used unless conflict",{"type":9,"tag":28,"props":853,"children":854},{},[855],{"type":15,"value":856},"Smallest amino acid gets priority\nSpecial codes:",{"type":9,"tag":28,"props":858,"children":859},{},[860],{"type":15,"value":861},"X = any amino acid",{"type":9,"tag":28,"props":863,"children":864},{},[865],{"type":15,"value":866},"B = Asn/Asp",{"type":9,"tag":28,"props":868,"children":869},{},[870],{"type":15,"value":871},"Z = Gln/Glu",{"type":9,"tag":28,"props":873,"children":874},{},[875],{"type":15,"value":876},"J = Leu/Ile",{"type":9,"tag":122,"props":878,"children":879},{},[],{"type":9,"tag":10,"props":881,"children":883},{"id":882},"page-16-hydrophobicity",[884],{"type":15,"value":885},"🌊 Page 16 — Hydrophobicity",{"type":9,"tag":18,"props":887,"children":888},{},[889],{"type":15,"value":890},"Hydrophobicity measured as:",{"type":9,"tag":24,"props":892,"children":893},{},[894,899,904],{"type":9,"tag":28,"props":895,"children":896},{},[897],{"type":15,"value":898},"ΔG of transferring AA from membrane interior → water",{"type":9,"tag":28,"props":900,"children":901},{},[902],{"type":15,"value":903},"High positive ΔG = hydrophobic",{"type":9,"tag":28,"props":905,"children":906},{},[907],{"type":15,"value":908},"Charged AAs strongly unfavorable in membranes",{"type":9,"tag":122,"props":910,"children":911},{},[],{"type":9,"tag":10,"props":913,"children":915},{"id":914},"️-page-17-ionization-of-glycine",[916],{"type":15,"value":917},"⚖️ Page 17 — Ionization of glycine",{"type":9,"tag":24,"props":919,"children":920},{},[921,939,944],{"type":9,"tag":28,"props":922,"children":923},{},[924,926],{"type":15,"value":925},"Two pKa values:",{"type":9,"tag":24,"props":927,"children":928},{},[929,934],{"type":9,"tag":28,"props":930,"children":931},{},[932],{"type":15,"value":933},"pK₁ (COOH) ≈ 2.3",{"type":9,"tag":28,"props":935,"children":936},{},[937],{"type":15,"value":938},"pK₂ (NH₃⁺) ≈ 9.6",{"type":9,"tag":28,"props":940,"children":941},{},[942],{"type":15,"value":943},"pI ≈ 6.0",{"type":9,"tag":28,"props":945,"children":946},{},[947,949],{"type":15,"value":948},"Titration curve shows charge transitions:",{"type":9,"tag":24,"props":950,"children":951},{},[952],{"type":9,"tag":28,"props":953,"children":954},{},[955],{"type":15,"value":956},"+1 → 0 → -1",{"type":9,"tag":122,"props":958,"children":959},{},[],{"type":9,"tag":10,"props":961,"children":963},{"id":962},"pages-18-20-titration-of-all-amino-acids",[964],{"type":15,"value":965},"📉 Pages 18-20 — Titration of all amino acids",{"type":9,"tag":24,"props":967,"children":968},{},[969,974,979,984],{"type":9,"tag":28,"props":970,"children":971},{},[972],{"type":15,"value":973},"Side chains add extra pKa values",{"type":9,"tag":28,"props":975,"children":976},{},[977],{"type":15,"value":978},"Basic AAs can reach +2",{"type":9,"tag":28,"props":980,"children":981},{},[982],{"type":15,"value":983},"Acidic AAs can reach -2",{"type":9,"tag":28,"props":985,"children":986},{},[987],{"type":15,"value":988},"Histidine is special (pKa ≈ 6)",{"type":9,"tag":122,"props":990,"children":991},{},[],{"type":9,"tag":10,"props":993,"children":995},{"id":994},"page-19-henderson-hasselbalch",[996],{"type":15,"value":997},"🧮 Page 19 — Henderson-Hasselbalch",{"type":9,"tag":18,"props":999,"children":1000},{},[1001],{"type":15,"value":1002},"Used to calculate:",{"type":9,"tag":24,"props":1004,"children":1005},{},[1006,1011],{"type":9,"tag":28,"props":1007,"children":1008},{},[1009],{"type":15,"value":1010},"Fraction protonated vs deprotonated",{"type":9,"tag":28,"props":1012,"children":1013},{},[1014,1015,1020],{"type":15,"value":389},{"type":9,"tag":34,"props":1016,"children":1017},{},[1018],{"type":15,"value":1019},"Cys-S⁻ at different pH",{"type":15,"value":1021},"\nFormula:",{"type":9,"tag":18,"props":1023,"children":1024},{},[1025,1027,1033,1035,1040],{"type":15,"value":1026},"pH = pKa + log(",{"type":9,"tag":1028,"props":1029,"children":1030},"span",{},[1031],{"type":15,"value":1032},"base",{"type":15,"value":1034}," / ",{"type":9,"tag":1028,"props":1036,"children":1037},{},[1038],{"type":15,"value":1039},"acid",{"type":15,"value":1041},")",{"type":9,"tag":122,"props":1043,"children":1044},{},[],{"type":9,"tag":10,"props":1046,"children":1048},{"id":1047},"pages-21-22-environmental-effects-on-pka",[1049],{"type":15,"value":1050},"🌍 Pages 21-22 — Environmental effects on pKa",{"type":9,"tag":18,"props":1052,"children":1053},{},[1054],{"type":15,"value":1055},"pKa depends on environment:",{"type":9,"tag":24,"props":1057,"children":1058},{},[1059,1064,1069],{"type":9,"tag":28,"props":1060,"children":1061},{},[1062],{"type":15,"value":1063},"Nearby charges shift pKa",{"type":9,"tag":28,"props":1065,"children":1066},{},[1067],{"type":15,"value":1068},"Hydrophobic environments favor neutral states",{"type":9,"tag":28,"props":1070,"children":1071},{},[1072],{"type":15,"value":1073},"Proteins tune pKa to enable catalysis",{"type":9,"tag":18,"props":1075,"children":1076},{},[1077,1078,1083],{"type":15,"value":113},{"type":9,"tag":34,"props":1079,"children":1080},{},[1081],{"type":15,"value":1082},"Key insight:",{"type":15,"value":1084}," pKa is not fixed inside proteins",{"type":9,"tag":122,"props":1086,"children":1087},{},[],{"type":9,"tag":10,"props":1089,"children":1091},{"id":1090},"️-page-23-protein-visualization-light",[1092],{"type":15,"value":1093},"👁️ Page 23 — Protein visualization & light",{"type":9,"tag":24,"props":1095,"children":1096},{},[1097,1102],{"type":9,"tag":28,"props":1098,"children":1099},{},[1100],{"type":15,"value":1101},"Aromatic AAs absorb UV",{"type":9,"tag":28,"props":1103,"children":1104},{},[1105],{"type":15,"value":1106},"Choice of wavelength (λ) matters for detection",{"type":9,"tag":122,"props":1108,"children":1109},{},[],{"type":9,"tag":10,"props":1111,"children":1113},{"id":1112},"page-24-amino-acid-analysis-aaa",[1114],{"type":15,"value":1115},"🧪 Page 24 — Amino acid analysis (AAA)",{"type":9,"tag":18,"props":1117,"children":1118},{},[1119],{"type":15,"value":1120},"Process:",{"type":9,"tag":1122,"props":1123,"children":1124},"ol",{},[1125,1135,1140,1145],{"type":9,"tag":28,"props":1126,"children":1127},{},[1128,1130],{"type":15,"value":1129},"Hydrolyze protein in ",{"type":9,"tag":34,"props":1131,"children":1132},{},[1133],{"type":15,"value":1134},"6 M HCl",{"type":9,"tag":28,"props":1136,"children":1137},{},[1138],{"type":15,"value":1139},"Label amino groups fluorescently",{"type":9,"tag":28,"props":1141,"children":1142},{},[1143],{"type":15,"value":1144},"Separate chromatographically",{"type":9,"tag":28,"props":1146,"children":1147},{},[1148],{"type":15,"value":1149},"Quantify peaks\nLimitations:",{"type":9,"tag":24,"props":1151,"children":1152},{},[1153],{"type":9,"tag":28,"props":1154,"children":1155},{},[1156],{"type":15,"value":1157},"Asn, Gln, Trp destroyed or lost",{"type":9,"tag":122,"props":1159,"children":1160},{},[],{"type":9,"tag":10,"props":1162,"children":1164},{"id":1163},"page-25-amino-acid-abundance",[1165],{"type":15,"value":1166},"📈 Page 25 — Amino acid abundance",{"type":9,"tag":18,"props":1168,"children":1169},{},[1170],{"type":15,"value":1171},"Based on:",{"type":9,"tag":24,"props":1173,"children":1174},{},[1175,1180],{"type":9,"tag":28,"props":1176,"children":1177},{},[1178],{"type":15,"value":1179},"207,132 protein sequences",{"type":9,"tag":28,"props":1181,"children":1182},{},[1183],{"type":15,"value":1184},"75 million amino acids\nShows natural AA frequency biases",{"type":9,"tag":122,"props":1186,"children":1187},{},[],{"type":9,"tag":10,"props":1189,"children":1191},{"id":1190},"page-26-amino-acid-properties",[1192],{"type":15,"value":1193},"📚 Page 26 — Amino-acid properties",{"type":9,"tag":18,"props":1195,"children":1196},{},[1197],{"type":15,"value":1198},"Derived from large-scale sequence alignments\nUsed to infer conservation and function",{"type":9,"tag":122,"props":1200,"children":1201},{},[],{"type":9,"tag":10,"props":1203,"children":1205},{"id":1204},"️-page-27-protein-structure-hierarchy",[1206],{"type":15,"value":1207},"🏗️ Page 27 — Protein structure hierarchy",{"type":9,"tag":1122,"props":1209,"children":1210},{},[1211,1221,1231,1241],{"type":9,"tag":28,"props":1212,"children":1213},{},[1214,1219],{"type":9,"tag":34,"props":1215,"children":1216},{},[1217],{"type":15,"value":1218},"Primary",{"type":15,"value":1220}," — sequence",{"type":9,"tag":28,"props":1222,"children":1223},{},[1224,1229],{"type":9,"tag":34,"props":1225,"children":1226},{},[1227],{"type":15,"value":1228},"Secondary",{"type":15,"value":1230}," — helices, sheets",{"type":9,"tag":28,"props":1232,"children":1233},{},[1234,1239],{"type":9,"tag":34,"props":1235,"children":1236},{},[1237],{"type":15,"value":1238},"Tertiary",{"type":15,"value":1240}," — 3D fold",{"type":9,"tag":28,"props":1242,"children":1243},{},[1244,1249],{"type":9,"tag":34,"props":1245,"children":1246},{},[1247],{"type":15,"value":1248},"Quaternary",{"type":15,"value":1250}," — subunit assembly",{"type":9,"tag":122,"props":1252,"children":1253},{},[],{"type":9,"tag":10,"props":1255,"children":1257},{"id":1256},"page-28-peptides-vs-proteins",[1258],{"type":15,"value":1259},"🔗 Page 28 — Peptides vs proteins",{"type":9,"tag":24,"props":1261,"children":1262},{},[1263,1268,1273],{"type":9,"tag":28,"props":1264,"children":1265},{},[1266],{"type":15,"value":1267},"Peptide: short, flexible",{"type":9,"tag":28,"props":1269,"children":1270},{},[1271],{"type":15,"value":1272},"Polypeptide: longer chain",{"type":9,"tag":28,"props":1274,"children":1275},{},[1276],{"type":15,"value":1277},"Protein: folded, functional\nResidue mass = AA - H₂O",{"type":9,"tag":122,"props":1279,"children":1280},{},[],{"type":9,"tag":10,"props":1282,"children":1284},{"id":1283},"️-page-29-peptide-orientation",[1285],{"type":15,"value":1286},"➡️ Page 29 — Peptide orientation",{"type":9,"tag":24,"props":1288,"children":1289},{},[1290,1295],{"type":9,"tag":28,"props":1291,"children":1292},{},[1293],{"type":15,"value":1294},"N-terminus → C-terminus",{"type":9,"tag":28,"props":1296,"children":1297},{},[1298],{"type":15,"value":1299},"Backbone direction matters",{"type":9,"tag":122,"props":1301,"children":1302},{},[],{"type":9,"tag":10,"props":1304,"children":1306},{"id":1305},"page-30-peptide-bond-geometry",[1307],{"type":15,"value":1308},"🔄 Page 30 — Peptide bond geometry",{"type":9,"tag":24,"props":1310,"children":1311},{},[1312,1317],{"type":9,"tag":28,"props":1313,"children":1314},{},[1315],{"type":15,"value":1316},"Planar due to partial double bond",{"type":9,"tag":28,"props":1318,"children":1319},{},[1320,1322],{"type":15,"value":1321},"Two conformations:",{"type":9,"tag":24,"props":1323,"children":1324},{},[1325,1335],{"type":9,"tag":28,"props":1326,"children":1327},{},[1328,1333],{"type":9,"tag":34,"props":1329,"children":1330},{},[1331],{"type":15,"value":1332},"Trans",{"type":15,"value":1334}," (favored)",{"type":9,"tag":28,"props":1336,"children":1337},{},[1338,1343],{"type":9,"tag":34,"props":1339,"children":1340},{},[1341],{"type":15,"value":1342},"Cis",{"type":15,"value":1344}," (rare; more common with Pro)",{"type":9,"tag":122,"props":1346,"children":1347},{},[],{"type":9,"tag":10,"props":1349,"children":1351},{"id":1350},"pages-31-32-φ-and-ψ-angles",[1352],{"type":15,"value":1353},"📐 Pages 31-32 — φ and ψ angles",{"type":9,"tag":24,"props":1355,"children":1356},{},[1357,1362],{"type":9,"tag":28,"props":1358,"children":1359},{},[1360],{"type":15,"value":1361},"Backbone flexibility defined by φ (phi) and ψ (psi)",{"type":9,"tag":28,"props":1363,"children":1364},{},[1365],{"type":15,"value":1366},"Rotations determine folding possibilities",{"type":9,"tag":122,"props":1368,"children":1369},{},[],{"type":9,"tag":10,"props":1371,"children":1373},{"id":1372},"page-33-ramachandran-plot",[1374],{"type":15,"value":1375},"📊 Page 33 — Ramachandran plot",{"type":9,"tag":24,"props":1377,"children":1378},{},[1379,1384,1389],{"type":9,"tag":28,"props":1380,"children":1381},{},[1382],{"type":15,"value":1383},"Shows allowed/disallowed φ-ψ combinations",{"type":9,"tag":28,"props":1385,"children":1386},{},[1387],{"type":15,"value":1388},"Glycine more flexible",{"type":9,"tag":28,"props":1390,"children":1391},{},[1392],{"type":15,"value":1393},"Proline more restricted",{"type":9,"tag":122,"props":1395,"children":1396},{},[],{"type":9,"tag":10,"props":1398,"children":1400},{"id":1399},"pages-34-35-α-helices",[1401],{"type":15,"value":1402},"🌀 Pages 34-35 — α-helices",{"type":9,"tag":24,"props":1404,"children":1405},{},[1406,1411,1416,1421],{"type":9,"tag":28,"props":1407,"children":1408},{},[1409],{"type":15,"value":1410},"Right-handed 3.6₁₃ helix",{"type":9,"tag":28,"props":1412,"children":1413},{},[1414],{"type":15,"value":1415},"3.6 residues/turn",{"type":9,"tag":28,"props":1417,"children":1418},{},[1419],{"type":15,"value":1420},"H-bond: n → n+4",{"type":9,"tag":28,"props":1422,"children":1423},{},[1424],{"type":15,"value":1425},"Helical wheel reveals amphipathic nature",{"type":9,"tag":122,"props":1427,"children":1428},{},[],{"type":9,"tag":10,"props":1430,"children":1432},{"id":1431},"pages-36-37-β-sheets",[1433],{"type":15,"value":1434},"🧵 Pages 36-37 — β-sheets",{"type":9,"tag":24,"props":1436,"children":1437},{},[1438,1443,1448,1453],{"type":9,"tag":28,"props":1439,"children":1440},{},[1441],{"type":15,"value":1442},"Parallel vs antiparallel",{"type":9,"tag":28,"props":1444,"children":1445},{},[1446],{"type":15,"value":1447},"H-bond geometry differs",{"type":9,"tag":28,"props":1449,"children":1450},{},[1451],{"type":15,"value":1452},"Side chains alternate up/down",{"type":9,"tag":28,"props":1454,"children":1455},{},[1456],{"type":15,"value":1457},"Turns often i → i+3",{"type":9,"tag":122,"props":1459,"children":1460},{},[],{"type":9,"tag":10,"props":1462,"children":1464},{"id":1463},"page-38-structural-distances",[1465],{"type":15,"value":1466},"📏 Page 38 — Structural distances",{"type":9,"tag":24,"props":1468,"children":1469},{},[1470,1480],{"type":9,"tag":28,"props":1471,"children":1472},{},[1473,1475],{"type":15,"value":1474},"α-helix: ",{"type":9,"tag":34,"props":1476,"children":1477},{},[1478],{"type":15,"value":1479},"1.5 Å/residue",{"type":9,"tag":28,"props":1481,"children":1482},{},[1483,1485],{"type":15,"value":1484},"β-strand: ",{"type":9,"tag":34,"props":1486,"children":1487},{},[1488],{"type":15,"value":1489},"3.5 Å/residue",{"type":9,"tag":122,"props":1491,"children":1492},{},[],{"type":9,"tag":10,"props":1494,"children":1496},{"id":1495},"page-40-collagen-triple-helix",[1497],{"type":15,"value":1498},"🧬 Page 40 — Collagen triple helix",{"type":9,"tag":24,"props":1500,"children":1501},{},[1502,1507,1512],{"type":9,"tag":28,"props":1503,"children":1504},{},[1505],{"type":15,"value":1506},"Special case",{"type":9,"tag":28,"props":1508,"children":1509},{},[1510],{"type":15,"value":1511},"Rich in Gly-Pro-Hyp",{"type":9,"tag":28,"props":1513,"children":1514},{},[1515],{"type":15,"value":1516},"Left-handed helices assemble into right-handed triple helix",{"type":9,"tag":122,"props":1518,"children":1519},{},[],{"type":9,"tag":10,"props":1521,"children":1523},{"id":1522},"page-41-protein-databases-tools",[1524],{"type":15,"value":1525},"🔍 Page 41 — Protein databases & tools",{"type":9,"tag":24,"props":1527,"children":1528},{},[1529,1534,1539,1544,1549],{"type":9,"tag":28,"props":1530,"children":1531},{},[1532],{"type":15,"value":1533},"UniProtKB (Swiss-Prot & TrEMBL)",{"type":9,"tag":28,"props":1535,"children":1536},{},[1537],{"type":15,"value":1538},"NCBI Protein",{"type":9,"tag":28,"props":1540,"children":1541},{},[1542],{"type":15,"value":1543},"ExPASy ProtParam",{"type":9,"tag":28,"props":1545,"children":1546},{},[1547],{"type":15,"value":1548},"ProtPi",{"type":9,"tag":28,"props":1550,"children":1551},{},[1552,1554],{"type":15,"value":1553},"Structures: ",{"type":9,"tag":34,"props":1555,"children":1556},{},[1557],{"type":15,"value":1558},"RCSB PDB",{"type":9,"tag":122,"props":1560,"children":1561},{},[],{"type":9,"tag":10,"props":1563,"children":1565},{"id":1564},"final-takeaway",[1566],{"type":15,"value":1567},"🧠 Final takeaway",{"type":9,"tag":18,"props":1569,"children":1570},{},[1571],{"type":15,"value":1572},"Proteins are:",{"type":9,"tag":24,"props":1574,"children":1575},{},[1576,1581,1586,1591],{"type":9,"tag":28,"props":1577,"children":1578},{},[1579],{"type":15,"value":1580},"Chemically diverse",{"type":9,"tag":28,"props":1582,"children":1583},{},[1584],{"type":15,"value":1585},"Structurally hierarchical",{"type":9,"tag":28,"props":1587,"children":1588},{},[1589],{"type":15,"value":1590},"Environment-dependent",{"type":9,"tag":28,"props":1592,"children":1593},{},[1594],{"type":15,"value":1595},"Evolutionarily optimized",{"type":9,"tag":18,"props":1597,"children":1598},{},[1599,1601,1606],{"type":15,"value":1600},"Mastering ",{"type":9,"tag":34,"props":1602,"children":1603},{},[1604],{"type":15,"value":1605},"amino acids → bonds → angles → structures",{"type":15,"value":1607}," is the foundation of protein science.",1775084282664]