Office: room 436B Morill 4S 5:15-6:15 WednesdayTA: [email protected] 4:15-5:15 WednesdayEmail prof/TA before hoursCafé conference roomExam 1: Fri 10/1 lectures 1-11Exam 2: Mon 10/22 lectures 13-20Exam 3: Wed 11/14 lectures 22-29Final (noncumulative) lectures 31-39We use model organisms to study processes that are essential to humans and human disease9/7/12 NotesBefore every exam, there will be a review session IN CLASS the day before~Chapter 2~Electrons determine how a given atom will interact with other atomsSpecifically electrons in the outer shellIonic bond (electrostatic attraction) = transfer of electrons (positive and negative charge)Covalent bond = sharing of electronsEx: water (polar covalent bond – asymmetry of charge)Ex: oxygen (non-polar covalent bond)Ethane has one bond between C (swivel) and ethene has a double bondSaturated fats have hydrogens while unsaturated fats have a double bond (shorter and ridged  kinks)Unsaturated fats are more fluidEx: butter is saturated and olive oil is unsaturatedHydrophobic vs. hydrophilic“phobic” = water fearingmolecules with non-polar covalent bondsex: fats and hydrocarbons“philic” = water lovingmolecules with polar covalent bondsex: acids, bases, alcoholmolecules with positive and negative ionsex: NaClPhospholipids have both phobic and philic parts (amphipathic)Macromolecules are made up of many subunits linked together by covalent bondsSugar – polysaccharide (glycocidic bonds)Amino acid – protein (peptide bonds)DNA/RNA – nucleic acid (phosphodyester bonds)Condensation reactions create covalent bonds (dehydration synthesis)  take away waterHydrolysis reactions break them  add waterStrength of bondsCovalent-ionic-hydrogen-van der WaalsHydrogen bonding (F,O,N) = special form of polar interaction with hydrogen between two electron attracting atomsVan Der Waal = flickering of electron cloud inducing charge BETWEEN atomsHydrophobic force = water forces hydrophobic groups togetherDNA StrandA T G C A T CT A C G T A GCovalent and hydrogen bonds in DNAC and G are stronger because they make 3 hydrogen bonds while A and T make only 2!Heating up DNA, denaturation and breaks the hydrogen bonds, not the covalent bondsAmino AcidAmino N-terminus (basic and positive b/c gain hydrogen)R functional groupCarboxyl C-terminus (acidic and negative b/c lose hydrogen)Lysine (basic + charge)Glutamic acid (acidic – charge)Glutamine (polar uncharged)Glycine and Leucine (non-polar, hydrophobic)All is determined by the R group!Determines the shape of the protein9/10/12 NotesThe Second Law of ThermodynamicsDisorder (entropy) must always be increasing YET life generates incredible orderFree energy (G)Disorder/entropy must always be increasingA reaction with a negative delta G is energetically favorableCan occur spontaneouslyA reaction with a positive delta G is an energetically unfavorableOnly if it is coupled with an energetically favored one to be unfavoredThe net free energy is negative (law is satisfied)Energy is derived from the oxidation of glucose (sucrose+fructose)The chemical bond energy in food molecules is harnessed by living cellsCalorie = the amount of energy to heat 1 mL of water to 1 degree CelsiusIn a cell, the break down of glucose is coupled to utilized energy for multiple purposesEnzymes catalyze a reaction while not changing itself!Catalysts lower the activation energy of a reaction to speed up the process  on a particular pathwayThree processes are used to derive energy from sugars1. Glycolysis (cytosol)2. Krebs/Citric Acid Cycle (mitochondria)3. ETC/oxidative phosphorylation“Carrier molecules” = allow us to couple the energetically favorable process of “burning” food to the energetically unfavorable process of staying aliveEx: ATP, NADPH, NADH, FADH2, Acetyl CoAPhosphate, electrons and hydrogens, acetyl groupsHydrolysis of ATP is favorable (negative delta G)Phosphorylation = the addition of a phosphate groupWhen there is a hydroxal (alcohol group -OH), they can be phosphorlyatedKinase is the enzyme that sticks phosphate groupsPhosphatase is the enzyme that removes phosphate groupsA hydride ion is a proton and 2 electronsGlycolysisInput: glucose, 2 ATPOutput: 2 NADH, 4 ATP, 2 pyruvate (net of 2 ATP)Pyruvate goes to the Krebs cycleNADH goes to the ETC (donates electrons and protons)9/12/12 NotesKrebs CycleWithin the mitochondrial matrixCoenzyme A converts pyruvate into acetyl CoASugars, fats, and amino acids help create acetyl CoAIn the beginning, there is citrate which in the end is turned into oxaloacetate after 8 steps and the cycle repeats with oxaloacetate turning into citrateAcetyl CoA + oxaloacetate = citrateCarbon dioxide is released as a waste productNADH funnels energy to the ETC  make ATPKey features of the Krebs cycleInput: Acetyl CoA (derived from sugars, proteins, fats)Output: Carbon dioxide, 3 NADH, 1 FADH2, 1GTP (used by enzymes)NADH and FADH2 go to the ETCAs long as Acetyl CoA is there, the cycle will continue!ETC is in the inner membrane of the mitochondrionOrganization of the mitochondrionMatrix, inner membrane (cristae – inner folds), outer membrane, intermembrane spaceOxidative phosphorlyation takes place in and across the inner membraneETC  electrochemical proton gradient  ATP synthaseEach NADH molecule donates 2 electrons to the ETCUbiquinone (carry 2 electons/in the membrane due to hydrophobic tail)Cytochrome C (electrostatic interactions because on the outer membrane/1 electon)They have increasing affinity for electronsETC – each component is reduced and is energetically favorable9/14/12 NotesPathway of the ETCNADH dehydrogenase complex  ubiquinone  cytochrome b-c1 complex  cytochrome C  cytochrome oxidase complexSOMETIMES electrons prematurely leak into oxygen from the ETC and turn into superoxide (02-)A reactive oxygen species (ROS) that can wreak havocProton pumping yields a protein gradient with two properties (voltage difference and pH difference across the membrane)Most of the proton motive force comes from membrane potentialATP synthase is imbedded in the inner membrane of the mitochondria (acts like a rotary motor)ATP synthase harnesses the proton motive force to convert the energy from the flow of protons across the inner membrane into ATP generation (95% of ATP generation!)Composed of the electric motor, rotation of the axle, rotation of F1 and generation of ATPMembrane potential  mechanical energy  chemical energyATP synthase