Final Study Guide

Final Study Guide - BIOBM 331 IN A NUTSHELL A complete and...

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BIOBM 331 IN A NUTSHELL A complete and comprehensive study guide for the BIOBM 331 Final Exam *Disclaimer: This study guide does not guarantee a better grade on the final exam. Its producer assumes no responsibility for any questions that appear on the exam that are not covered in this guide.
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PEPTIDES AND AMINO ACIDS General Structure •Only L isomers •H 3 N + —CHR—COO - Meaning of pKa •pH=pKa + log(un/pro) •pKa depends on local environment of ionizable group Categories of AA •Aliphatic: Gly, Ala, Val, Leu, Ile •Aromatic: Phe, Tyr, Trp •S-containing: Cys, Met •Aliphatic –OH: Ser, Thr •Acidic: Asp, Glu •Amide: Asn, Gln •Basic: Lys, Arg, His •Proline: Pro Peptide Bond •COO - + H 3 N + CO—NH + H 2 O PROTEIN STRUCTURE Forces •Hydrophobic Interaction -Entropy: Increase in water, Decrease in protein -Increases with increase in temperature ( G= H-T S) •Hydrogen Bonds -About the same in unfolded protein and water as folded protein and water -Highly directional •Electrostatic -No directionality -“Ion pair” or “Salt bridge” •Disulfide Bond -Directional •Dipole, Ion-dipole, van der Waals -Weak and weakly directional •Ring-stacking -Phe and Trp Folding Constraints •6 atoms in plane: C α —CO—NH—C α •Boltzmann: P=e -X/RT -Probability of a deviation costing energy X higher than ground state •Steric Hindrance of Atoms -Phi (N and C α ); Psi (C α and C) -Ramachandran Map *Beta sheet in upper left *Alpha helix in middle left
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OBSERVED STRUCTURES α-helix •R groups point out from axis •Helix is right-handed •NO Pro or many charged AA •Max H-Bonding •3.6 AA per 360° polar AA every 3-4 AA β-sheet •R groups above or below sheet •Antiparallel vs. parallel -Antiparallel more linear H-Bonding (stronger) Turns •Type I vs. Type II -Type II has Gly at i+2 -Pro common at i+1 Collagen •Triple helix •Pro fits well •Many chemical modifications (hydroxy-AA) I, II, III, IV and Structural Domains •Primary, secondary, tertiary, and quaternary (multiple polypeptides) structure •Structural domain = arrangement of major secondary structures -Includes different topological connections of β sheets Transient IV Structure •Signal binding/interaction domains assemble -Signal example: phosphorylation of a domain •Examples: transcription complexes, insulin signaling complex Common Structures •Zn-fingers -2 Cys-X-X-X…X-2 His -Connected to DNA transcription •P-loops FORMATION/LOSS OF PROTEIN STRUCTURE G o vs. Structural Coordinates •G o decreases greatly near native conformation (more stable) •Structural coordinate axis arbitrary Stability and G o •Lower G o = more stable Denaturation •8M Urea used to denature proteins •Mb: lower pH to protonate His, then add 8M Urea •Insulin: denatures loses some AA can’t refold Folding •AA sequence contains folding information •Helping proteins:
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-Disulfide isomerase -Prolyl isomerase (cis-trans interchange) *Peptide bond is trans
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This note was uploaded on 03/30/2008 for the course BIOBM 3310 taught by Professor Feigenson,gw during the Fall '07 term at Cornell.

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Final Study Guide - BIOBM 331 IN A NUTSHELL A complete and...

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