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by: Shawn Pfannerstill IV


Shawn Pfannerstill IV
GPA 3.56


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Class Notes
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This 11 page Class Notes was uploaded by Shawn Pfannerstill IV on Thursday October 22, 2015. The Class Notes belongs to PHIL 142 at University of California Santa Barbara taught by Staff in Fall. Since its upload, it has received 79 views. For similar materials see /class/227178/phil-142-university-of-california-santa-barbara in PHIL-Philosophy at University of California Santa Barbara.

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Date Created: 10/22/15
Lecture 1 Foundations of Biochemistry Learning goals To think about What is biochemistry What is life To understand some things about Physical foundations of life The molecular logic of life Study Resources httpllbcswhfreemancomllehningerl httpllwwwworthpublisherscomllehningerl lming PHlNEIHES DF El lMMIETW W W 39 rigg ifig lg Emw E Hip fxi Lehnlnger Prlncmles of s Biochemistry vis vitais NH2 M N A N am 5 HCN k l a I In N N httpllwwwchemucsbedulkaljulchem142A gt living graphs titration ligand binding enzyme kinetics gt mechanism and technique animations gt technique animations gt online quizzes and flashcards Albert Lehninger 19171986 CI Citric acid cycle occurs in mitochondria CI Mechanism of oxidative phosphorylation CI Mitochondrial structure and function CI Bioenergetics CI Author of classic textbooks 0 Biochemistry 19701983 0 The Mitochondrion 1964 o Bioenergetics 19651974 Image and more httpwwwmedicalarchivesjhmiedulsgmlllehningerhtml FEE H I I FEES UF Ell l39l IMSTRV Biochemistry What s this Biochemistry is a science dealing with the chemistry of living matter Important topics that biochemical research addresses include gt structure and properties of biological macromolecules gt interactions of biological macromolecules with other molecules gt storage transmission and expression of heritable information genes gt molecular origin of diseases and ways to combat diseases gt transformation and use of energy by living organisms Biochemistry and Other Physical Organic chemistry Chemistry K t amp g InorganIc Chemistry of me lcs chemistry l thermodynamlcs4 l carbon compounds H20 39 Medicine I E Health of 39 I Vng things Molecular Cb Biotechnology biology 8 I Engl Blology neering Cells and larger materials living structures equipment Mathematics and computer science Data analysis modeling Visualization RR Biochemistry is a Science Dealing with the Chemistry of Living Matter We know quite well what is chemistry But what is living matter Lehnlnger PlillClpiBS m 5 Biochemistry Textbook life is characterized by Degree of complexity N Extraction transformation and systematic use of energy to create and maintain structure and to do work Capacity for precise selfreplication Ability to sense and respond to changes in surrounding Building blocks eg amino acid alanine Mw 75 204 Da C39 N O H S and Se Life is Complex Macromolecules eg proteins Mw 10000300000 D 1003000 amino acids Living organisms have internal structures with defined functions eg ribosome 30 nm in diameter 00 000 large number or E13ll34rl2u393lem39iues 33m different compounds 30 different pmieins eg mitochondrion 15 um long The cell 5100 pm in diameter taungm zml Dennil hunk Mummy HK l mm mm BaCterium Interacting galaxies Microprocessor The simplest bacterium Our galaxy contains Core of AMD S Opteron Mycoplasma genitalium has 100 billion stars 100 Million transistors 580000 basePa PNA and all the elements in about 200 mm2 486 types f pr tem5 lt 20 chemical elements lt 20 chemical elements m 9 EL m as 59mm 9 magehtt9ll astr n my my hi ma e ms a ae m Mum w Extraction Transformation and Systematic use of Energy to Create and Maintain Structure and do Work by lifeless chemistry by living organisms BelousovZhabotinsky reaction Aggregation of social amoeba KBrO339v malon39c ac39dv Mnsom Dictiostelium discoideumon agar plates heated solution of sulfuric acid htt dict baseor ltutoriall http onllneredwoodscccaus h h instructdarnoIdDEPro39ISQQSIGabeD WWW Capacity to Precisely Selfreplicate l Proteinoid microspheres formed artificially from Primordial soup ave membranes can divide and are subject to selection 35 billion year old fossil showing possible evidence for dividing ancient cyanobacteria It has been demonstrated recently that some proteins and nucleic acids can selfreplicate Proteinoids 1 rcnsmic wnlininndnizsIexmexl chem A hlml hila wwwgencilivs cnmRvsezrch rizngieiindysaasiinmi lesgt hlml Other Thoughts about Life NASA Life is a seltE sustained chemical system capable of undergoing Darwinian evolution Excludes single individuals Forest fire is a selfsustaining chemical system that undergoes evolution by rules similar to darvvinian evolution DD Images by NASA httg Ilwwwnasagov More Thoughts about Life Freeman Dyson Advanced Study Princeton USA Life is defined as a material s stem that can acquire store process and use information to organize i s activities Haboku Nakamura Biology Institute Konan University Kobe Japan Living beings are systems that have three simultaneous features they are selfsupported they reproduce themselves and they evolve throug interaction with e environmen Andre Brack Centre for Molecular Biophysics of CNRS France Life is a chemical system able to replicate itself through autocatalysis and to make mistakes that gradually Increase the ef CIency of the autocatalySIs Sidney Fox South Alabama University USA Living beings are proteinmade bodies formed by one or more cells that communica e with the environment through information transfer carried out by electric im ulses or chemical substances and capable of morphological evolution an metabolism growth and reproduction Carol Cleland Colorado University in Boulder USA It is a mistake to try to define 39Iife39 Such efforts reflect fundamental misunderstandings about the nature and power of definitions So What is Life Living things tend to be complex and highly organized take in energy from the environment and transform it for growth and reproduction respond to stimuli from environment and their stimulation fosters a reactionlike motion recoil and in advanced forms learning be consumers because growth includes changing biomass creating new individuals and the shedding of waste share a carbonbased chemistry depend on water and leave behind fossils with carbon or sulfur isotopes that point to metabolism selfbound selfgenerating Lifeforms on the Earth are Diverse q A dolphin and a human in Shark Bay Western Australia These two species have the most advanced vocal languages among all the species Giant bacterial colonies in Shark Bay Western Australia Many of the ancient phototrophic and heterotrophic bacteria lived in such colonial associations known as stromatolites 39 39 39 thm and Can Survive in Extreme Conditions Bacteria on the rock Image from httpwwwmspsuedul0105lrockshtml Temperature 75 C Too Cold Extremophiles can grow well El at high temperatures 95 C El at low temperatures 0 C El extreme acidities pH 1 El high salinities 5 M NaCI http Ilwww hart wiltr roka Notes Never Too Old to MakeKids Sur momwas tlmii quotharm werebom Etonyeam txi quot t Bacterial spore trapped in an ancient salt crystal in an underground cavern near Carlsbad New Mexico was revived to give offsprings shown above htt Ilwwwc talinkscomlbacteriahtml Radiation No Problem Meet the bacterium Deinococcus radiodurans gt First found in radiationsterilized foods gt Lives in cooling waters of nuclear reactors gt Tolerates Xray and yradiation doses 3000 times higherthan humans gt Tolerates UVIight doses 10000 times higher than eukaryotes gt Tolerates mutagenic chemicals if Image it Q nulltEtEsting Enviravveh urghEWNVallgagerhtml Related links h p Ideinococcus al bio orgl Can Survive on the Moon Surveyor 3 unmanned Moon probe 1967 Charles Pete Conrad Commander Apollo 12 mission quotI always thought the most significant thing that we ever found on the whole goddamn Moon was that little bacteria who came back and lived and nobody ever said shit about itquot Apollo 12 mission brought back samples of the Surveyor 3 spacecraft in 1969 1 sample out of 33 contained live bacteria Experiments Ilhtml Physical Foundations of Biochemistry See pages 21 28 in the 4th edition See pages 6 12 in the 3rd edition Solar Energy OUTPUT form of Ilght my Longe thymahm Images httpIliamaicauarizonaeduliclnats1011Ilectureslch02lch02htm h c 39 tt IIwwwchemwmedulchemWWWl ourseslchem105l ro eclsl rou 3Ia e3htm From sunlight plants green bacteria cyanobacteria From fuels animals most bacteria Energy input is needed in order to maintain complex structures and be in a dynamic steady state away from the equilibrium Image http llwwwmelburtontaxiderm coml Isolated closed and open systems httpl cafemais nc mlmugs html http lwww r chard sangster comlwait htm 39 39 39 qallervl Danes0001 0301 2614 0127 html The Molecular Logic of Life We look at the chemistry that is behind Maintaining homeostasis Accelerating reactions Organization of metabolism and signaling Storage and transfer of information Image Waterfall by MC Escher httpwwwwu39 39 39 39 quot y Diamonds are Forever Macromolecules Die before Us Most macromolecules are being degraded and synthesized continuously through the life of organism s thesis Precursors yn Hemoglobin Breakdown products amino acids Iquot in erythrocyte quot2 amino acids degradation gt When r1 r2 the concentration of hemoglobin is constant Reasons for such dynamic steady state eliminate macromolecules that are damaged allows fine control of the amount of molecules Some exceptions Lens proteins ofthe eye Why DNA in some cells eg in a mammalian egg Concentration of Many Small Molecules in the Cell Remains Constant r2 Waste CO2 t Food Inge ion Glucose utilization r3 Storage fats carbohydrates 1n blood r4 Other products When r1 r2 r3 r4 the concentration of glucose in blood is constant 1 Dynamic steady state applies to a chemical species or to a specific process Homeostasis applies to the whole organism For a fine distinction between these terms please see hi39tnlwvwv ruf rice edu 39 39 39 39 39 39 39 Life can t be too slow How to speed things up Higher temperatures Used rarely eg incubation of eggs Remember 10 degrees C gt 2 X rate increase Higher concentration of reactants Used rarely because it is costly Remember v k AB for A B gt C Lower activation barrier by catalysis Used widely because allows great control Remember ingENZYMEHSUBSIRATE V7 Km SUBSTRATE Change the reaction by coupling to a fast one Catalysis More realistically simplified scheme Unrealistically simplified scheme Activation barrier transition state 7 clwati n barrier transition state 3 chctants A Frau energy a Free energy 6 Products lBl Reaction coordinate 1A gt Bl Reaction coordinate A gt El A catalyst is a compound that increases the rate of a chemical reaction by providing an alternative reaction mechanism Review of kinetics amp catalysis httpWWW I 39 demon cn 39 quot quot 39quot quot 39 htm Energy Coupling Reaction 2 AT A ADP P Reaction 3 inc s gt glucose Siphosphate ADP Reaction 1 use P glucose 6 phosphate Free energy G AGS AGl AG2 Reaction coordinate ATP Chemical Currency of Energy r12 N C H i Ii 0 O39 O l l C CH O O l T O IIT O CHZ O N N O O O H H H OH OH Series of Related Reactions Forms a Pathway enzyme 1 B enzyme 2 C vnzynu 3 enzymel E enzyme 4 4 g gt F What kind of pathways can you think of Metabolic Pathway produces energy or valuable materials Signal Transduction Pathway transmits information Metabolic Pathways Map exnasv m quotiquot 39 39 H hemindex Digital map at http Detailed View of the Map II I l nun m 5quot cuccao H H HYDROXYI PHENYLPYRUVATE A F H CHICO COOH szo IN DINYDIO 1 BIOP39I39EIIN mo TRANSAMlNASE W E LTYIOSINE cocmcoos idMill pumm H W ALANINE v 00 u quot PHENYL lGLU I mxo Gems NA 1 PYMJVATE AM clumu39re LPHENYLALANINE u mw I gm 0 BIOPTEIIN u9ooou H E H 00M 1 N c TYROSINE TIANSAMINASE Some practical uses of metabolic maps Follow the fate of metabolites and building blocks Identify enzymes that act on these metabolites Identify points and agents of regulation Identify sources of metabolic diseases Signal Transduction Pathways lnsulln Fla Insulin Ha I Insulin quotsulln Insulin Insulin Rh Insulin Rb Illiulln rm 5139 1quot rm and Insulin an GDPp quot hinrnrfn Maps available a 39


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