CHEM 4600 1st EditionExam # 1 Study GuideReview***Memorize Amino Acids***1. Structure2. 1 Letter Symbol3. 3 Letter Symbol1. Organica. Review basic structures of molecules.i. Phenyl, Carboxyl, Ester, Ether, Alcohol, Ketone, Aldehydeii. Amine, Schiff Baseiii. Thioester (Unstable)iv. Phosphate, Phosphodiester2. Biologya. DNA <= => RNA => Protein3. Chemistrya. Atomsi. Most (if not all) properties of atoms are defined by valence electronsii. Octet Rule1. Atoms try to have full outer shellsa. Some atoms give up electrons while others receive electrons to get a full outer shellb. Electronegativity (EN)– Tendency of an atom to gain bonding pairs to fill/empty their outer shell. Based on atoms pull of electrons toward their nucleus.a. EN can determine the type of bond between atoms1. Molecule 1 – Molecule 2 = ENb. Moleculesi. Bonds1. Covalent Bondsa. Equal sharing of electronsb. ~ 350 kJ / molc. Electronegativity < .4d. Ex. Carbon --- Carbona. EN of carbon = 2.5b. 2.5 – 2.5 = 02. Polar Covalent Bonda. Unequal sharing of electronsb. .5 < EN < 1.2c. Ex. Oxygen --- Hydrogena. EN of oxygen = 3.5b. EN of Hydrogen = 2.3c. 3.5 – 2.3 = 1.23. Ionic Bonda. Stealing of electrons of one atom by anotherb. EN > 1.21c. Ex. Sodium --- Chlorinea. EN of Chlorine = 3.0b. EN of Sodium = .9c. 3.0 - .9 = 2.1c. Molecules Interacting with Other Moleculesi. Non-covalent bonds – Intermolecular Forces (IMF)1. Van der Waalsa. Induced Dipole : Induced Dipolea. An uncharged molecule is induced with a charge, causing a charge on the neighboring molecule.b. ~ 1 kJ / mol2. Hydrogen Bondsa. Stronger that Van der Waalsb. ~ 4-20 kJ / molc. Sharing of Hydrogen – H+a. Needs a donor with H+1. Only with Highly EN atoms: Usually N, O, or F2. EN atoms de-shield H+3. Ex. Ethanol b. Needs an acceptor without H+1. Has to be a highly EN atom: UsuallyN, O, or F2. Ex. Diethyl Etherc. Linear1. 180⁰ +/- 20⁰3. Electrostatic Interactionsa. Ionic Interactions – “Salt Bridges”b. ~ 5 kJ / mola. About as strong as an H-Bondc. Made with + (or partial +) and – (or partial -)4. Hydrophobic Interactionsa. Non-polar molecules attempt to get away from H20a. Nonpolar likes Nonpolarb. Polar likes Polar / Waterb. Strongest IMF - ~7-10 kJ / molc. Hydrophobic Effect : Exclusion of Non-Polar substances by waterd. Water surrounds nonpolar molecule;a. Causes more dirorder = more ∆S = more entropy ( + )b. ∆G = ∆H - T∆S1. ∆G = Gibbs Free Energy; -∆G is spontaneous rx2. ∆H = Enthalpy; Change in Heat3. T = Temperature; Kelvind. H20 is awesomei. Dielectric Constant1. Makes ionic bonds weaker through electrostatic interactionsa. NaCl –H2O -> Na+ + Cl-ii. Specific Heat Capacity1. Raise 1g of H2O by 1C = 4.184 J / mol Ciii. Liquid at room temperature1. Solid Liquid and Gas between 0C and 100Civ. Universal Solventv. High Surface Tension1. Coheres to self instead of adhere to other molecules2. Capillary Action: Ability to move togethervi. Neutral pH4. pHa. pH = -log [H+]i. On a scale of 1 to 141. 1: Strong Acid2. ~3 – 7: Weak Acida. Doesn’t completely dissociate3. 7: Neutral4. ~7 – 11: Weak Base5. 14: Strong Baseii. Acid = H+ donor / e- acceptor1. Ex. Strong Acid – HCl =H2O=> Cl- + H+2. Ex. Weak Acid – CH3COOH <=H2O=> CH3COO- + H+iii. Base = H+ acceptor / e- dororiv. Buffers – Resist Change in pH1. Normally a weak acid or a weak basea. Resists change2. pH + pOH = 14a. [H+] + [OH-] = 10^-14b. If [H+] increases, [OH-] decreasesc. If [OH-] increases, [H+] decreasesd. HA  A- + H+a. Protonated anion  Anion + Proton3. La Chateliers’ Principle – LCPa. Equilibrium with shift in response to a change in any of the followinga. Concentrationb. Pressurec. Temperatured. Volume4. Strength of a Buffera. Pka = -log kaa. ka = acid dissociation constantb. pka = pH at which protonated to deprotonated ratio is ~1:1c. ka = ( [H+] [A-] ) / [HA]d. log ka = log [H+] + log [A- / HA]e. –log ka = -log [H+] + log [A- / HA]f. –pka = -pH + log [ A- / HA]g. pH = pka + log [A- / HA]5. pKaa. Strength of Acida. CH3COOH pka = 4 and pH = 41. pH = pka + log [A- / HA]2. 4 = 4 + log [A- / HA]3. 0 = log [A- / HA]4. 10^0 = A- / HA5. 1 = A- / HA6. 1:1 = A-:HAb. Buffering Rangea. +/- 1 pH unit from pka1. If pka = 4 then buffer pH = 3-5a. 10:1 ratio or 1:10 ratio of A-:HAc. Charge at pHa. Point where H+ is lost due to pH1. If pH > pka then H+ is lost2. If pH < pka then H+ is gained6. Buffers in usa. Cell Cytoplasm buffer – Phosphate Buffera. H2PO4-1 <=6.8=> HPO4-2 + H+ <=> PO4-3 + H+b. Blood Buffer – Carbonate Buffera. H2CO3 <=6.1=> HCO3- + H+ =Enz=> CO2 + H2Ob. ^Carbonic Acid ^Bicarbonate5. Amino Acidsa. pka / pHi. pka C1. 1.8 – 3.02. –COOH  COO- + H+ii. Pka N1. 9-102. –NH3+  NH2 + H+iii. At pH = 71. COO-2. NH3+iv. pka R – Some AA have ionizable “R” groups1. Cys, Tyr, Asp, Glua. Have extra e- when pH exceeds pka of R Groupb. Asp and Glu act as nucleophile at pH = 7a. Accept H+ / donate e-2. His, Lys, Arga. Have extra proton when pH is below pka of R Groupb. Lys and Arg act as electrophiles at pH = 7a. Donate H+ / Accept e-v. Why does Cys have a pka but Ser does not1. Ser has a pka = 19b. Charges of AA at certain pH’si. pI = -log [I]1. Isoelectric pointa. pH where a majority of the species has a charge of 02. pI = (pkaC + pkaN) / 2a. If R group exists, pI is determined with the pH’swhere charge starts being 0 and where it stops being 0ii. Aliphatic AA’s1. Gly, Ala, Val, Leu, Ils, Proiii. Polar Non-Charged AA’s1. Ser, Thr,Cys,Asn,Glniv. Hydrophobic AA’s1. Metv. Aromatic AA’s1. Phe, Tyr, Trpvi. Bases AA’s1. Lys,Argvii. Both Acid and Base AA’s1. Hisviii. Acids AA’s1. Asp,Gluc. Put AA’s togetheri. AA’s are combined through a dehydration synthesis1. H2O is lost and a bond is formed2. The Amino terminus of one AA bonds with the Carboxy terminus of another AAa. H+ is lost from Aminob. OH- is lost from Carboxyii. Always forms from N  Ciii. Nomenclature1. Monomer = Amino Acid2. ~2 – 15 Amion Acids = Peptide3. ~15 – 40 Amino Acids = Polypeptide4. ~40+ Amino Acids = Proteiniv. Structure1. 1⁰ = Just Peptide Chain2. 2⁰ = H-Bonds between peptide backbonea. α-Helixa. 3.6 AA per turn1. Oxygen on Co carbon H-Bond with H on Nitrogen2. Almost all are right handed / clockwise3. Not all of the AA can be in an α-helix, since their side chains disrupt the helixb. β-Sheetsa. Fully Extended peptide1. β-Sheet bonds to another β-Sheeta. Parallel H-Bondi. + / - 20⁰ from 180⁰b. Anti-Parallel