Biochem 4000 - Lecture 1 PII

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  1. What is the key problem with using free amino acids for hydropathy?
    Hydrophobicity of a free amino acid is not the same as for the corresponding amino acid residue
  2. What effect does the main chain have on hydrophobicity?
    Charges association with the main chain dramatically reduce hydrophobicity and affect preferred conformation
  3. How can the problems of hydropathy with free amino acids be overcome?
    • Chemically synthesize R-group
    • Modified amino acids (acetylate or aminate main chain)
    • Use tripeptides (most accurate)
  4. What is the benefit of acetylating the main chain?
    Chemical modification may neutrillize main chain charges
  5. The two broad techniques for quantifying hydropathy
    • Solute partitioning
    • Structure-based determination
  6. Outline structure based hydropathy determination (quantification)
    • Calculate fraction of residue types accessible to water (requires known structure)
    • Assume solvent accessible areas are aquous (inaccessible are nonpolar)
    • Quantify with parition coefficient or solute partition formula
  7. Why does structure based hydropathy perform best on small monomeric proteins?
    Structures are better known
  8. Key problems with structure based hydropathy quantification
    • Structures elucidated in high salt, glycol or organic solvent (to stabillize)
    • Overall fold bias derived hydrophobicities
    • Structural constraints can bias derived hydrophobicities for residues with specific functions.
  9. What do partitioning and structure based methods say about residue distribution?
    • Polar charged - Least hydrophobic 
    • Polar uncharged - Intermediate
    • Nonpolar - Hydrophobic
  10. Why is cysteine ranked most hydrophobic in structure based methods?
    Prevalence of very hydrophobic disulfides
  11. Why is proline grouped with polar charged residues in solvent patitioning?
    Structural roles (change main chain direction, capping helices)
  12. Why is tryptophan non-polar in structure-based methods?
    Intermolecular interactions
  13. Why is it an issue if a residue occurs unexpectedly (e.g arginine in the core)?
    Proteins are not hugely stable. An out of place residue must be stabillized or the protein will denature
  14. What does QSAR stand for?
    Quantitative structure-activity relationship
  15. How does QSAR work?
    Perform binding and catalysis studies on related compounds
  16. Functional groups with high hydropathy tend to have...
    Low catalytic activity
  17. What is a polyprotein?
    A polypeptide transcript that can be cleaved to form many different proteins (save genomic real estate)
  18. Why can polyprotein proteases be inhibited?
    Make a peptide-like residue (replace NH2 w/ phosphate) that permanently binds to protease preventing polyprotein activity
Author:
Ant
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Card Set:
Biochem 4000 - Lecture 1 PII
Updated:
2016-02-11 21:04:23
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Biochemistry 4000
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Biochem
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