1. What are proteins and peptides made of, and what is unique about the bond that connects these components?
    Proteins and peptides are made up of amino acid that are joined by peptide bonds. The difference is that proteins are bigger in size, hence have a greater molecular weight, peptides are small in nature.
  2. What are some functinos that proteins serve?
    Catalyzing biochemical pathways, found in contractile structures, carrying O2 and CO2 from cells, transport, etc. 
  3. Describe the general solubility properties of proteins
    • 3 general categories:
    • fibrous and insoluble
    • globular and soluble
    • fibrous and soluble
  4. What is the primary structure of proteins?
    the amino acid sequence
  5. What is secondary structure?
    alpha helix, beta pleated sheet, beta turns, and random coiling

    The local 3D folding of the chain.
  6. What is tertiary structure?
    the general 3D structure of the protein
  7. What is quaternary structure?
    formed when multiple polypeptide chains interact by non covalent bonds to form one single structure

    The arrangement of chains in a multichain protein.
  8. What are the commonly occuring modifications of amino acids found in some proteins?
    • acetylation at the N-terminus
    • carboxylation (addition of COOH)
    • hydroxylation (addition of OH)
    • glycosylation (addition of glucose)
    • phosphorylation
    • disulfide linkages

    (Good Day CHAP)
  9. What amino acids are sometimes found phosphorylated in proteins?
    • serine
    • threonine
    • tyrosine
  10. Describe alpha helix
    • tightly coiled
    • stabilized by H bonds between imido groups and carbonyl oxygens
    • 3.66 amino acids per turn
  11. Describe beta-pleated sheets
    • Result of neighboring chains (or long regions of same chain) bonding via H bonds, perpindicular to axis of chain.
    • Antiparallel sheet is the most stable
  12. Describe beta turns
    • Reverse turns
    • H-bonding of amino acids 3 sequences apart
    • Cause a U turn
  13. What stabilizes higher order in proteins?
    • 1. electrostatic attractions
    • 2. internal H bonding
    • 3. van der waals / london dispersion forces
    • 4. entropy driven hydrophobicity (gibbs free energy change)
  14. What amino acids are likely to carry a charge on side chains at a neutral pH?
    • Aspartic acid and glutamic acid have negative charges.
    • Tyrosine and cysteine have negative charges.
    • Lysine, arginine, histidine carry positive charges.
  15. What are zinc fingers?
    • A loop of about 12 amino acids.
    • Result from zinc ion being complexed to 4 aa's - usually cysteines and histidines
  16. What are kringle domains?
    • Conserved sequences.
    • They fold into large loops stabilized by 3 disulfide bridges.
    • Important in protein-protein interactions w/ blood.
    • Coagulation factors
  17. What are leucine zippers?
    Arrangements of leucines along one side of alpha helix between 2 proteins - these proteins can form dimers leaving basic aa regions to bind DNA
  18. How can proteins be denatured?
    • detergents
    • chaotropic agents
    • high temp
    • drastic pH changes
    • organic solvents
  19. What is the hydrophobic effect?
    When the hydrophobic regions of the protein in its tertiary structure are moved inward and hydrophilic regions move to the outside of the protein.
Card Set
Introduction to Biochemistry