Week 1 Notes (8/25)
Week 1 Notes (8/25) BSC 450
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This 6 page Class Notes was uploaded by Jordana Baraad on Friday August 28, 2015. The Class Notes belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 75 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.
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Date Created: 08/28/15
BSC 450 Ch 2 Water and Aqueous Forces Enzymes work bec of weak forces Decrease activation energy In Terms of Thermodynamics Gibbs Free Energy Formula AG AH T AS AG free energy lt 0 favorable gt0 not favored AH enthalpy important in electrostatics Affected by partial and full charges in restricted space T temperature in degrees Kelvin AS entropy measure of disorder Increasing entroypy more disorder favorable Decreasing entropy more order not favored In cell temperature and pressure are STEADY Must nd other ways to change the reaction Types of Bonds and Forces Covalent CH bond sharing 2 delocalized electrons Stable and strong bec electrons shared equally 410 kJ mol required to break this bond Weak Forces many required to break C H covalent bond 520 kJ mol required to break this bond 4 types weak forces 1 hydrogen bonding ie H20 2 electrostatic interactions full positive or negative charge 3 Van der Waal s forces interactions a Can occur between any 2 molecules b Key factor distance between molecules 0 Electron cloud interaction gives partial charge 4 hydrophobic effect hydrophobic molecules ONLY a clump to avoid contact with hydrophilic solutions and air b form lipid bilayers and clathrates Chemical Nature of Water ALWAYS present in the cellular environment Sometimes unhelpful bec competes with intended reactions Water bridges networks of water molecules that link nearby hydrogen bond Acceptors ie carbohydrates and donor proteins ie amides Water interacts with its own molecules above all others UNIQUE property eg water molecules in glass stay together to avoid contact with air or glass Accounts for Adhesion Cohesion Surface tension Hydrogen bond bond between H and an electronegative atom in water oxygen is the electronegative atom HO hydrogen bond is POLAR Partial neg charge on oxygen Partial pos charge on hydrogen When a hydrogen bond forms AH decreases as opposite partial charges come together AS decreases bec hydrogen bonds are HIGHLY ORDERED Unfavorable from a free energy standpoint Known as entropic penalty Cellular reactions must account for this Water Can Shield Charges Effectively Solubility of ionic compound ex NaCl is FAVORABLE Complete hydration reached when ALL Cl neg charge molecules surrounded by pos H atoms ALL Na pos charge molecules surrounded by neg O atoms Solubility of carbohydrate ex Glubcose is FAVORABLE Hydroxyl group on glucose used for bonding Hydration makes it harder for ions to reassociate Ex Of water competing for interactions Hydrogen Bonds in Water are Dynamic see youtube demonstration water molecules form purple bonds bonds forming and breaking AT THE SAME TIME called ickering ickering is an IMPORTANT ability of water way of evading entropic penalty from hydrogen bonding energy released balances out energy required must look at energy in entire system not just bond in question in this class the system is the cell Hydrogen Bonds Carbonyl CO and imino groups hydrogen acceptors Hydroxyl HO and ether ester groups hydrogen donors Carbonyl reaction with water HOH V hydroxyl ROH Hydroxyl reaction desired Reaction conditions must make it more favorable than water reaction Enzyme active sites pockets in cell Where water is excluded so it can t compete with the reaction Properties of Hydrogen Bonds Strength determined by 1 distance between donor D and acceptor A Typically 23 Angstrom difference 2 bond angle Straight angles v bent angles Smaller distance btwn greater distance btwn Opposite partial charges opposite partial charges Stronger weaker Importance of Hydrogen Bonds source of unique properties of water structure and function of proteins structure and function of DNA structure and fnction of polysaccharides binding of substrates to enzymes binding of hormones to receptors matching of mRNA and tRNA Linus Pauling Hbond most important Hbonds WEAK yet CRITICAL to the body s chemistry H20 chain in cytochrome f Important in electron transfer H hopping Room for exactly 5 molecules Hbonded H20s as part of protein s sugar binding site Hydrogen bonds allow proper alignment Enzyme and substrate must face one another Electrostatic Interactions in an Aqueous Environment FULL formal charges pos or neg Couloumb s Law formula to calculate force exerted by 2 opposite charges Hydrophobic environment INCREASES force of attraction btwn opposite charges Helpful to ionize compounds pH relevant AG v distance graph Positive curving slope AG inversely proportional to between opposite charges F 3932le IE39 F Van der Waals Forces Result from Induced Dipoles VERY WEAK 48 kCal mol Can occur between ANY 2 ATOMS Key factor is distance Electrostatic type of interaction Distortion of electron cloud leads to formation of partial charge Transient Attractive force Substances in enzyme active site are within Van der Waals distance What About Nonpolar Amphipathic Molecules 4 hydrophobic effect hydrophobic molecules have no charge amphipathic molecules contain polar and nonpolar entities clathrate water molecules form a cage around a hydrophobic molecule HIGHLY ORDERED More ordered than surrounding noncaging water which is ickering AS decreases order increases large entropic hit Flickering H20s disorder offsets high order of clathrate Water Surrounding Nonpolar Solutes Has Lower Entropy eX Methane hydrates in ocean after BP oil spill H2O molecules surround CH4 molecule Micelle polar on outside nonpolar inside Nonpolar molecules not bonded just grouped together Interact preferentially to avoid H2O lesser of 2 eyils hydrophobic effect holds cell membranes together Hydrophobic Effect Defined as the association of nonpolar molecules in aqueous solutions Protein folding Proteinprotein association Formation of lipic micelles membranes Binding of steroid hormones to receptors nonpolar molecules DO NOT BIND eX magic sand interacts with itself not water even when submerged stays dry Multiple Weak Interactions Act Additiyely Img I ordered water interacting with substrate and enzyme Img 2 disordered water displaced by enzymesubstrate interaction Enzymesubstracte interaction stabilized by hydrogen bonding ionic and hydrophobic interactions DNA approx 2 m strands held together by Hbonds Thousands of Hbonds contribute to great overall stability Individual Hbonds weak ease of breakability allows for replication Held together buy PROBABILITY HIGH chance that l Hbond canwill be broken at a given time LOW chance that ALL Hbonds canwill be broken at a given time Complex Biomolecules Are Formed Based on Weak Forces Img 1 Atomic Force imaging of cell membrane islands lipid rafts Specific groupings of lipids Formed Via hydrophobic effect Van der Waals Forces some Hbonding 1mg 2 Rubisco xes atmospheric CO2 Held together by weak forces KNOW FOR EXAM Look at a molecule and be able to tell which of the weak forces interactions plays a role EX Determine in amino acids
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