Biolchem 415: Lec. 3

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Biolchem 415: Lec. 3
2015-04-14 23:59:19

Flashcards that correspond to University of Michigan Biolchem 415 Lecture 3.
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  1. What are proteins?
    Linear polymers of 20 different amino acids
  2. What is primary structure?
    Sequence of amino acids that compose the polypeptide chain
  3. The α-amino carboxylic acids (amino acids) can be one of two steroisomers, which is biologically relevant?
    • The L isomer with S stereochemistry is biologically relevant.
    • The D isomer with R stereochemistry is not
  4. What happens to amino acids at pH 7 (assuming the side chain does not possess an ionizable group)?
    They are zwitterionic (both groups are charged--positive and negative and have a neutral pH)
  5. Which amino acid is non-chiral?
    Glycine, R=H
  6. What is special about proline?
    Proline is a cyclic amino acid and an aliphatic amino acid
  7. Which amino acids have hydroxyl groups? Why is that important?
    Serine and Threonine. Hydroxyl groups can form H-bonds with water and other molecules
  8. Why is cysteine a special amino acid?
    The sulfhydryl group (-SH) can oxidize to form a disulfide bond with a neighboring cysteine (termed cystine)
  9. How can you calculate the degree of protonation of amino acid side chains?
    From pH and pKa values of their side chains using the Henderson-Hasselbalch equation
  10. What does the ionization state at pH 7 have to do with a protein's amino acid charge?
    Ionization state determines their overall charge
  11. What are the hydrophobic amino acids?
    Aliphatic and aromatic amino acids--limited solubility of side chains in water.
  12. What is the difference between an essential and nonessential amino acid?
    • Nonessential: synthesized in humans
    • Essential: not generated in humans, must be supplied through our diet
  13. What is primary structure?
    Amino acid sequence
  14. What is secondary structure?
    Local conformation of peptide backbone
  15. What is tertiary structure?
    Interaction of different secondary structures in the same polypeptide
  16. What is quaternary structure?
    Interaction of different polypeptides in a protein containing two or more polypeptides
  17. What is a peptide?
    A short polymer of amino acids
  18. What is the first residue in a protein and why?
    N-terminal because it has a free amine group
  19. What is the last residue in a protein and why?
    C-terminal because it has a free carboxylate group
  20. What bond links amino acids?
    Peptide bond.
  21. What can cause disulfide bonds? Disulfide bond example?
    Cysteine side groups form disulfide bonds between peptide chains of amino acids. Ex: disulfide bonds crosslink the A and B chains of insulin
  22. What is the favored conformation for peptide bonds?
    Trans conformation--side chains are well separated and prevents energetically unfavorable steric clashes
  23. What are the psi and phi angles?
    • Psi (ψ): Cα-C bond
    • Phi (φ): Cα-N bond
  24. What are Ramachandran plots?
    Determine the most favorable orientation of Cα bond angles. Plot psi and phi torsional angles in a polypeptide chain. Darkest colors indicate where angles are energetically favorable
  25. What is Aspartame composed of?
    Aspartate and the methyl ester of Phenylalanine
  26. What are the hydrolysis products of Aspartame?
    • Aspartate, Phenylalanine, and Methanol
  27. What is Aspartame's relationship with PKU?
    Individuals with phenylketonuria (PKU), a genetic defect in metabolizing phenylalanine, must avoid ingesting aspartame.