BIO 201 with Todd Hennessey, First week of notes.
BIO 201 with Todd Hennessey, First week of notes. BIO 201
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This 0 page Class Notes was uploaded by ChiWai Fan on Thursday January 14, 2016. The Class Notes belongs to BIO 201 at University at Buffalo taught by TODD HENNESSEY in Spring2015. Since its upload, it has received 258 views. For similar materials see CELL BIOLOGY in Biology at University at Buffalo.
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Date Created: 01/14/16
Jan 27 2016 and Jan 292016 Cell Biology ChiWai Fan Information credited to Professor Todd Hennessey Notes edited by Chi Wai Fan Weak acids Not all the acid molecules dissociate into ions Example water H20 H OH How can you tell how much H is dissociated pH 0 Only strong acids completely dissociate pH tells you how much it has dissociated pH is a way to express H H means concentration of hydrogen ions also called protons pH log H pH 7 means neutral Ex If pH 70 the H 10 x 10397M H or 00000001M H If pH 20 the H 10 x 10392M or 001M H 1 Which of these two above has a lower pH pH20 lt pH70 2 Which is more acidic pH20 is acidic Acidic lt pH70 lt alkaline or basic 3 Which has a higher H pH20 has a higher H than pH70 Low pH means high H Vice versa High pH means low H A bufferis a weak acid and its corresponding base Example HCO3 H gt H2CO3 Within the buffering range additions of either acid or base have less effect Tvnes of Bonds and Interaction 1 Covalent bonds 2 Noncovalent bonds A Ionic or electrostatic bonds full charges B Hydrogen bonds partial charges C Van der Waals interactions 3 Hvdroohobic aooreoations Not bonds interactions or even forces between molecules They are hydrophobic exclusions from water COVALE NT BONDS Electrons Are Shared in Covalent Bonds llycl rogen atoms 2 H l l Covalent bond Hydrogen molecule 1H2 i Covalent bonds atoms share one or more pairs of electrons H H I ll Il H Single Bonds I l H H H H trouble Bonds H Hi HG EH Triple Bundle I i i i Neil ewyetel Na he 5 ienie wmzl 5 tell E I in the e Ii etel NIH ii fiIl il Iii Lam Mart and Cl Linehareed manual izire lmie e are negative Celina115 ere p eit39ree eIONC DISSOCIATION Ionic electrostatic bonds Ionic bonds exist between two compounds with FULL and opposite charges gt A salt crystal NaCI is held together by ionic bonds gt As the salt crystal dissolves the salt dissociates into Na ions and CI ions gt If 10 mole of NaCl dissociates fully in water it will yield 10 mole of Na ions and 10 mole of CI ions What is amole3 It is an amount not a concentration 10 mole 602 x 1023 molecules HYDROGEN BONDS Hlyregeri tad Partial Charges Hemee n have prete i ne Between an eleel39Iel and e reerbex39jr39lie acid Between nucleic acid beeee paeire L r I Heel Hagen bends eexl39ii be SEEN h h39i E Fi F39 F115 I 391quot cm 93 j mmulm39dg These are netthe enly Hinds ef in ll idl EllInd HuiRum MAE LII EDEIEIJnhnll39i39iJrglIiSQnnl ljlhow do bonds stay together Hytlrgerl binds can be between or within molecules Two we ller molecules parts of one large molecule lei two large mallowas iiquot mnimilm 91quot LLBum WTEmu EE How aboutthe UthEFt EE on nonco valentboncls l lLI nnumbered page 34 Cell and Molecular Biology1mm 2005 John Wiley 8 Saonsi VAN DER WAAL INTERACTIONS l lnot hydrophobic bonds EXAMPLE a GECKO climbing on walls is done by van der waal interactions because the interaction is distance depended 1 Van der waals interactions are distance dependent 2 They are very weak individually but many together are strong like a zipper Example at a party you nd a girl attractive when you walk up to her you nd her still attractive But when you39re too closely in her face it won t be very attractive Hydrophobic Aggregations Hvdr0philic quotWater lovingquot Usually either charged or polar and water soluble Water is hydrophilic Hvdr0phobic quotWater fearingquot Usually nonpolar uncharged and not very water soluble Fats are hydrophobic BASIC THERMODYNAMICS p146 147 1 First law 0 Energy cannot be created or destroyed It is always conserved Energy is always there 0 However different types of energy can be interconverted Ex thermo energyljlight energychemical energy 2 Second law 0 The Universe always tends towards disorder F Entropy is always increasing The amount of energy which is unavailable to do useful work is TAS T Temperature 0 A S Change in entropy This is Why a perpetual motion machine is impossible in our world because there is loss of entropy Surmundings SYSTEM AND SURROUNDINGS gt Energy of the Universe energy of the system energy of the surroundings 0 To conserve the energy of the Universe a change in energy of the system must have an opposing change in the energy of the surroundings So o A system can be a de ned space a physically bounded space an amount of matter etc o If one changes the other has got to change ENTROPY The system I Iquot quoti Fla 1 13 7 L Lquot r Encraase 391quot ti 1 J t a in E39FIIQTGEIEquot iquot I Ellh iyr 7 A V 3 dramas if FE E all A r LE itquot in u t Marti disorderand ASsys gt 0 implies that this system becomes more disordered during the reaction ASsys lt 0 implies that this system becomes less disordered more ordered during the reaction AS of the Universe A5 of the system AS of the surroundings First and second laws together The energy of the Universe is constant but entropy continues to increase gt The total energy change AH is equal to the sum of the change in energy that is available to do useful work AG and the change in entropy TAS AH AG TAS Total energy usable energy unusable energy H is enthalpy Total energy change AH AG is the change in free energy energy available to do useful work Can a reaction be driven by a change in entropy of the surroundings Some energy will always get loss You ll never going to get ALL energy out because some will escape or be used up That39s why there s no such thing as quotperpetual motionquot Gibb s Free energy AG AH TAS AG must be negative for a reaction to proceed spontaneously as written Reactants D Products AG Gproducts Greactants The reaction will go if it proceeds to a lower state of free energy What does this mean to us 1 A reaction can be driven by changes in either the system or surroundings 2 AG must be negative for a reaction to proceed as written This can be driven by either AH or TAS or both 3 A reaction can be driven by an increase in entropy of the surroundings even if the system becomes more ordered and no work is done O v Can h yrophobic molecules aggregate spontaneousy with no AH in water if the system becomes more ordered Cell Biology on Jan 29 2016 Notes edited by Chi Wai Fan Lecture by Professor Todd Hennessey Gibb s Free energy AG AH TAS AG free energy must be negative for a reaction to proceed spontaneously as written Reactants D products AG Gproducts Greactants The reaction will go if it proceeds to a lower state of free energy If Free energy of reactants is higher than free energy of products then AG is negaUve Ex Rock up on top of hill wants to roll down a hill Change in Gibb s free energy or AG Enderganie Eeaetien Emergenit Reaetiun pruduuta amuunl all energy required II39E39EIE39EHIHIHIE arnuunl all energy releaaed iree energy illea energy Pi dm murae ui reattian euulrae all reattian fur ie ehmm ehmte The diagrm fur ie ehmm aimIre Tlhe petm al ef ie the level If pruriuet ee ie lewet level ez r Ir iv meet The a fa This tun neaeiante ie released in this reeeliu The manual DE The manual 0f ie which ie re eaeed timing the median ie ml which ie Zleee thm ETD 1 Products have lower free energy than reactant Exergonic a Energy released b This has a AG Why We want AG to make things happen 45 Gproducts Greactants 2 8 6 2 Products have a higher free energy than products Endergonic a Needs energy b This has a AG Why This happens in a cell all the time 3 Coupled reaction You want a AG to make things happen that usually don39t happen You couple AG with AG and run on if AG is bigger than AG What does this mean to us 1 A reaction can be driven by changes in either the system Q surroundings AS of the Universe 45 of the system AS of the surroundings 2 AG must be for a reaction to proceed as written This can be driven by either AH or TAS or both AG AH us A reaction can be driven by an increase in entropy of the surroundings even if the system becomes more ordered and no work is done yes as long as surroundings become more disordered gt Can hydrophobic molecules aggregate spontaneously with no AH in water if the system becomes more ordered gt It39s an entropy party Bunch of attractive people networking All attracted to each other but don39t want to stay there for too long water molecules love binding to other water molecules but hydrophilic water molecules want to bond to everyone if someone comes in their way they don39t like it gt Some unattractive people hydrophobic slipped in unattractive people don t even want to play with other unattractive people It isn39t too bad if a few get in But what happens if you get a whole bunch of unattractive people they get excluded If you let this go for an in nite time you want to let this go to a lowest state of free energy where you don t have to do much gt Lowest state of free energy for water molecule is maximum entropy to do that they got to squeeze out unattractive things quotHydrophobic exclusion aggregationquot pushes away those unattractive people gt If you add anything to pure water they don39t like it They can tolerate for a while sugar if added too much the sugar will precipitate out gt Excluded unattractive people become an ordered system it is okay if surrounding is more disordered Water molecules bind reversiny to other water molecules by hydrogen bonding Water loves to bind to water Narcissistic hydrophilic Water is in its optimal thermodynamic state maximum entropy when each water molecule can bind to as many other water molecules as possible To a matter of extend It is thermodynamically unfavorable to get in the way of this but it happens all of the time They aren39t attracted to each other they39re pushed aside How much of an unfavorable thermodynamic condition can water tolerate If too many hydrophobic lipids are suspended in water they aggregate This hydrophobic aggregation is driven by exclusion of the hydrophobic molecules from water not by bonds or interactions between the hydrophobic molecules There is no such thing as quotHydrophobic interactionsquot gt Can there be any other types of interactions between completely hydrophobic compounds 0 Because hydrophobic aggregation caused Van der Waals interactions There are no hydrophobic interactions What39s the point gt A hydrophobic aggregation in water is driven by an increase in entropy of water Lipids will spontaneously form aggregation in water without any extra energy added This is AG Once formed it can be stabilized by Van der Waals interactions but these are not quothydrophobic bondsquot gt Can a reaction ever happen if it causes an increase in order Two Worlds in a Cell Polar aqueous hydrophilic Water soluble compounds found here Some examples Cytoplasm and nucleoplasm Matrix of mitochondria aquatic worlds inside cell Lumen of ER Golgi or lysosomes will cover later ll Non Polar lipidlike hydrophobic The membrane is nonpolar world it is hydrophobic Water insoluble compounds seen here Example membranes In Between Amphipathic Amphipathic means quottwo naturesquot One end is polar and the other end is nonpolar but seldom 5050 One end is hydrophilic and the other end is hydrophobic Neutral Detergent has to be amphipathic All detergents must have polar and nonpolar parts Membrane phospholipids Exam lea NIemhrane P1105 39lmli ids Hydmph ic head Hydmphabic tail Clari cation on amphipathic compounds In general 1 If it is more hydrophobic than hydrophilic it should be a membrane lipid Mn plar part Polar part Hydrophobic tail and hydrophilic head Amphipathic compound that39s more nonpolar than polar If it is more hydrophilic than hydrophobic it should be a water soluble detergent Mn plar part Polar part Hydrophobic head and hydrophilic tail More polar than nonpolar which is bad A detergent micelle when washing clothes you soluble greasy dirt These are Anionic detergents in water there s also cation ones and neutral to a certain degree for different purposes detergent shampoo soap They are amphipathic Their hydrophilic heads face the water Their hydrophobic tails face away from the water forced into facing the greasy dirt ordered system but you get more disorder by getting greasy dirt out In the middle of this micelle is a piece of greasy dirt hydrophobic What causes this to form Hydrophobic aggregation or AG of water The increase entropy of surroundings that drives this NOT hydrophobic bonds or interactions This is how the rst cell formed What is a micelle You don39t want to see micelle in your cell you want to see it in your laundry 0 A glab of detergent around a piece of nonwater soluble substance Figure 220 tell and Molecular Biology life M 20015 John Wiley 5 Sons
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