BIOBM 310 Course Review.docVIP

BIOBM 3310 Course Review Monday, December 8, 2008 PEPTIDES AND AMINO ACIDS ? general structure (do not memorize side chains) ? meaning of pKa and how to do Henderson-Hasselbalch calculation ? categories of AA (polar vs nonpolar) ??draw peptide bond PROTEIN STRUCTURE ? forces ? folding constraints: bond angles, lengths, and size of atoms ?? ???? rotation restrictions ??Ramachandran Map draw Ramachandran Map or describe in words OBSERVED STRUCTURES ? ?-helix, ?-sheet, turns, collagen: general properties (dont memorize ????) ? I, II, III, IV and folds (structural domains) ??transient IV structure (e.g. transcription complexes; insulin signaling complex) ? commonly observed structures: Zn-fingers; P-loops FORMATION/LOSS OF PROTEIN STRUCTURE ? Go vs structural coordinates know how to show relatively lower or higher stability on such diagrams ? denaturation: loss of function caused by partial/complete loss of native struct. ? folding: largest single driving force is hydrophobic interaction info to fold is in sequence molten globule some proteins assist folding or prevent aggregation: disulfide isomerase prolyl isomerase chaperones-- how they work HEMOGLOBIN ? special properties: sat. with O2 in lungs, but gives up O2 to tissue low O2 affinity when BPG bound low O2 affinity at low pH higher O2 affinity for fetal Hb role of ion pairs in deoxyHb R and T states cooperativity (O2) allostery (O2, H+, BPG, CO) ENZYMES AND CATALYSIS ? specificity: what is the basis? ? what are cofactors? ? rxn rate increase: basic kinetics; data of kinetics; why rxns take time ? Go vs progress of rxn an elementary rate constant corresponds to a particular Go barrier ? transition state: definition what catalysts do: ? enzyme kinetics: Michaelis-Menten kinetics: know/use equation Km, Vm (know definitions) Vm = kcat[E]total, but kcat can be combo of rate constants Lineweaver-Burk plot (but do not memorize equations for finding Km or Vm for inhib) enzyme inhibit