Bio 376 Test 1

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Author:
ccraigr
ID:
215143
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Bio 376 Test 1
Updated:
2013-04-26 10:41:23
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Bio 376 test ccraigr
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Lecture 1: Protein Folding Lecture 2: Protein Chaperones Lecture 3: Protein Degradation Mechanism Lecture 4: Protein Binding Lecture 5: Enzyme Function Lecture 6: Protein Regulation
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  1. What is a simple way to remember the hydrophobic amino acids?
    • FAMILY VW
    • Phenylalanine
    • Alanine
    • Methionine
    • Isoleucine
    • Leucine
    • Tyrosine
    • Valine
    • Tryptophan
  2. What is significant about an alcoholic R group, and what amino acids would pertain to this group?
    • 1: It is a point of phosphorylation.
    • Serine, Threonine, Tyrosine,
  3. When using a helix wheel projection, what will indicate amphipathicity?
    Segregation of hydrophobic and hydrophilic amino acids on opposite sides of the wheel indicates amphipathicity.
  4. With regard to proteins, define primary, secondary, tertiary, and quaternary structure.
    • 1. The linear sequence of amino acids
    • 2. The intermolecular forces that affect folding (H bond, london dispersion, VdW, hydrophobic interactions) including the shapes caused by these interactions (a-helices, b-sheets etc)
    • 3. The 3D structure of a single polypeptide.
    • 4. Interactions between multiple pps.
  5. Structure and role of alpha helices:
    • Found in protein alpha-keratin
    • results from N-H and C=O hydrogen bonding without involving the R groups
    • But these hydrogen bonds are on the same strand of the pp.
  6. Structure and role of beta sheets:
    • Found in protein fibroin
    • results from N-H and C=O hydrogen bonding without involving the R groups
    • These hydrogen bonds are on different strands of the pp.
  7. How does a protein "know" it is in the right shape?
    • Generally, it's final shape will minimize free energy.
    • This is not a smooth process. It can move and get stuck in local low energy points.
    • Hydrophobic colapse is a strong factor in reducing the free energy.
    • So is Weak Bond Formation,
    • and Steric Hinderences.
  8. Does a translated protein contain all the necessary information to specify it's 3D shape? What evidence is there to suggest this?
    Not counting the environment, yes. Denaturing experiments have shown that proteins can be denatured and the renatured dependent on the solvent environment that they are placed in.
  9. What is a protein domain?
    • It is an independently folded and stable portion of the polypeptide chain.
    • usually between 40-350aa
    • -Alpha Turn helix.
    • -Beta-alpha-beta propeller
    • -beta barrel
  10. Describe the different types of molecular chaperones; their structure, apearance, and function:
    • HSP 60 & 70. Different parts of the cell have different HSP's.
    • They have an affinity for exposed hydrophobic patches.
    • Often Hydrolyse ATP
    • 70 acts early, binding to 7 hydrophobic residues as the protein leaves the ribosome, it is small globular
    • 60 (chaperonin) forms a barrel like isolation chamber
  11. What classifies a protein as mis-folded?
    A misfolded protein is one that is in an incorrect low energy trough, and it does not have sufficient energy to continue folding in it's molten globule state.
  12. What problems do mis-folded proteins present for the body?
    • Exposed hydrophobic regions can corrupt other proteins.
    • This leads to: cell function disruptions, lysis, plaques.
    • Cross-beta filimentation is particularly dangerous.
    • as are prions.

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