F BICH 410 Final Exam Study Guide Unit 1 What is biochemistry o The study of life on the molecular level List the noncovalent forces in order from strongest to weakest o Noncovalent forces are 10 100 times weaker than covalent o Ionic van der waals dipole dipole London dispersion Who discovered the polarity or unequal sharing of water electrons o Linus Pauling What is another name for ionic interactions o Salt bridges When is the equations for Keq o Keq H A HA What are the possible relationships of molecules to water o Hydrophobic nonpolar and aggregate together ie hydrocarbons hydrophilic polar and amphipathic both polar nonpolar and cause micelles bilayers to form What is the relationship between Ka ionization constant and pKa o logka pka What is the relationship between pKa and the strength of the acid o Smaller pka stronger acid larger ka stronger acid What is Henderson Hasselbachs equation o pH pKa log deprotonated protonated What is the relationship between protonation pH and pka o pH pKa more dissociated or protonated o pH pKa less dissociated or deprotonated What is a titration curve o When you add strong base to a weak acid and measure the average pH What is the inflection point o When acid base and ph pka What is a buffer o Buffers resist changes in pH The greater the concentration of weak acid with its conjugate base the better the resistance of the buffer to change It is a good buffer when the pka the desired ph What are good biological buffers o H2PO42 HPO42 is the principal buffer intracellularly ph 7 These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute o CO2 g H20 H aq HCO3 aq major buffer intercellularly ie in blood What can induce changes in blood chemistry o Respiratory alkalosis hyperventilation leads to a decrease in CO2 so body pushes rxn to left causing decrease in H so pH increases o Respiratory acidosis hypoventilation causes and increase in CO2 so leads the reaction to push towards the right causing decrease in pH o Metabolic alkalosis increase in blood pH which decreases breathing rate CO2 and H2O react o Metabolic acidosis decrease in blood pH which increases breathing rate H and HCO3 What do thermodynamics kinetics and equilibrium represent o Thermodynamics predicts if reaction is possible o Kinetics expresses how fast process will occur o Equilibrium determines how far reaction will go What is the equilibrium constant and its relationship with 1 o Keq products reactants o Keq 1 reactants dominate o Keq 1 products dominate What is enthalpy and its relationship to a reaction o Enthalpy H change in H change in Energy PV o Exothermic reactions heat evolved new more stable bonds when change in H 0 o Endothermic reactions heat absorbed new less stable bonds when change in H O What is a van t Hoff plot o A what to determine the enthalpy change through determining the slope of a graph with the equation enthalpy r d lnKeq d 1 T What is a standard state o A defined set of conditions denoted by the not superscript What is a bio standard stae o When water and H both use a value of 1 regardless of what the reaction gives you Denoted by What is entropy and its relationship to a reaction o Entropy S measure of disorder o Delta S 0 final state has more order not favorable o Delta S 0 final state has less order favorable What is the relationship of H S and free energy o Delta G Delta H TdeltaS o Delta G 0 and the entropic and enthalpic changes are equal equilibrium o Delta G 0 exergonic reaction energy released o Delat G 0 endergonic reaction energy required What is the equation to find delta G at standard conditions o Delta Go RTln products reactants What is the relationship between delta G and Keq o Delta G 0 keq 1 Delta G 0 keq 1 How do you find Delta G at a specific set of conditions o Delta G deltaGo RTlnKeq Are thermodynamic state functions additive o Yes consequently you can couple reactions What does an Amino Acid Contain o And alpha C a side group R a carboxyl group an amino group o What are the classifications of Amino acids Nonpolar L P A V M F W I Polar noncharged G S N Q T Y C Acidic D E Basic K R H o Which is the only amino acid not chiral Glycine o Who discovered the 1 letter naming system Margret Dayhoff o Which Amino acids can be detected by UV Aromatic R group amino acids F Y W Know structure of all Amino Acids Are there amino acids beyond the 20 o Yes such as selenocysteine and pyrroline These are all amino acids that are altered from the original 20 and then replace the orginal amino acids in the chain and can have important functions in peptides What is pKa of all amino acids o Alpha COOH 2 2 alpha NH3 9 5 o R 12 5 T 13 S 13 Y 10 K 10 5 o D 3 9 E 4 3 H 6 C 8 What is the relationship between pH and pKa o Ph PKA protonated ph pka deprotonated Be able to draw amino acids and specific pH by changing the ionization of each ionizable form What is the isoelectric point pi o pH at which a zwitterion structure where no net charge exists is known o pI 1 2 pKi pKj Which Amino acids have two chiral centers o Ile and Thr Which amino acid can form disulfide bonds o Cys Which amino acid is cyclic to a primary amine o Pro allows for rigid structure What amino acid for predominates in nature o L amino group to the left on a fischer projection All L amino acids are S except for o Cys because of the priority the S takes attached to the alpha C What denotes the second sterocenter in Ile and Thr o The addition of allo onto the amino acid name Who first described the peptide bond and what does it consist of o Pauling And a peptide bond is the condensation of Amino acids and has two possible resonance structures with 6 planar atoms due to the double bond character What are individual amino acids called in a peptide bond o Residues and yl replaces the ide What is the pKa of COOH and NH3 in peptide o COOH 3 5 NH3 8 5 How should you draw a peptide bond o Always start with Nterminus and end with C terminus Be able to draw peptide at different ph find pI and find net charge What is the size of a protein o Average formula weight of amino aicd is 110D How are proteins classified o By shape and function ie fibrous globular membrane What are the levels of protein structure o Primary sequence o Secondary local structure alpha beta o Tertiary overall 3D structure o …