2010 Biochem Review

2010 Biochem Review - BIOMG 3310 Course Review Monday,...

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BIOMG 3310 Course Review Monday, December 8, 2010 PEPTIDES AND AMINO ACIDS general structure (do not memorize side chains) meaning of pK a 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 Φ,Ψ rotation restrictions Ramachandran Map understand what info is in a Ramachandran Map! OBSERVED STRUCTURES α -helix, β -sheet, turns, collagen: general properties (don't memorize Φ,Ψ ) 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 G o 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 O 2 in lungs, but gives up O 2 to tissue low O 2 affinity when BPG bound low O 2 affinity at low pH higher O 2 affinity for fetal Hb role of ion pairs in deoxyHb R and T states cooperativity (O 2 ) allostery (O 2 , H + , BPG, CO)
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specificity: what is the basis? what are "cofactors"? rxn rate increase: basic kinetics; data of kinetics; why rxns take time G o vs progress of rxn: be able to draw an elementary rate constant corresponds to a particular G o barrier transition state: definition in general, what catalysts do to speed rxn enzyme kinetics: Michaelis-Menten kinetics: know/use equation K m , V m (know definitions) V m = k cat [E] total , but k cat can be combo of rate constants Lineweaver-Burk plot (but do not memorize equations for finding Km or Vm for inhib) enzyme inhibition: charge on ionizable AA residues (pH effects) competitive, non-competitive, irreversible chymotrypsin (do not memorize each intermediate; no detailed mechanism question on final exam) ENZYME REGULATION regulate enzyme concentration 1. synthesis and 2. degradation regulate enzyme activity allosteric (R and T states): non-covalent or covalent aspartate carbamoyl transferase glycogen phosphorylase phosphofructokinase pyruvate kinase covalent zymogens phosphorylation/dephosphorylation lipid structure: fatty acids and triglycerides (Do know how to abbreviate; do not learn all the different phospholipid headgroups) lipid bilayer: general permeability properties membrane proteins: integral or peripheral membrane transport: passive transport vs active transport ENERGETICS "high-energy compounds" - be able to explain
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This note was uploaded on 12/10/2011 for the course BIO BM 3310 at Cornell.

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2010 Biochem Review - BIOMG 3310 Course Review Monday,...

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