Test One ID Terms

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Test One ID Terms
2014-09-17 22:20:54
Test one
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  1. van der Waals contacts
    As atoms get closer to eac other, electron clouds interact wit each other. At optimal distances, attractive forces keep them together
  2. hydrophobic interactions
    This occurs when a hydrophobic molecule is placed in an aqueous environment. Because they are unable to hydrogen bond, initially, the water molecules break their hydrogen bond with one another and form cages around the structure, which makes the solution more ordered, thus decreasing entropy and being unfavorable. As a result of this unfavorability, the hydrophobic molecules seek one antoher out, facilitated by water molecules, to decrease their surface area exposed to water. Water is then allowed to hydrogen bond with bulk water.
  3. lactoferrin
    Binds iron and undergoes a substantial change in conformation that allows other molecuels to distinguish between the iron bound and iron free forms
  4. dipolar ions (zwitterions)
    The form of the amino acid in which the amino group is protonated and the carboxyl group is deprotonated, leading to a molecule with two different charges; neutral due to having both charges
  5. Hydrophobic effect
    The tendency of hydrophobic groups to come together in an attempt to avoid the water
  6. 1.32 Angstroms
    The C—N distance in a peptide bond, demonstrating that it has slight double bond character due to the moving around of electrons between nitrogen and oxygen
  7. Phi bond
    The angle of rotation about the bond between the nitrogen and the alpha carbon atoms
  8. Psi bond
    Angle of rotation about the alpha carbon and the carbonyl carbon atoms
  9. Translation
    A rise in the alpha helix structure; 1.5 angstroms along the helix axis and a rotation of 3.6 residues per turn
  10. Supersecondary structure
    Certain combinations of secondary structure that are present in proteins and exhibit similar functions
  11. motifs
    Shapes of polypeptides
  12. Beta turns
    Motifs that connect different strands of secondary structure, stabilized by hydrogen bonds. i binds to the amino acid at residue I + 3; stabilizes abrupt changes in the poplypeptide
  13. Alpha helical coiled coil
    When two helices come together to form one larger helix
  14. Domain
    When polypeptide chains fold into two or more compact regions that may be connected by a flexible segment of polypeptide chain; also, when a region of proteins that exists exactly the same in numerous proteins because it copies itself into genes. This subportion is unique from the rest fof the protein function and folds individually
  15. Bovine ribonuclease
    Cow enzyme with enzymatic activity; chops up RNA
  16. Levinthal’s paradox
    the difference between the calculated and actual folding times that reveals that proteins don’t fold by trying every confirmation but must instead follow a partly defined pathway
  17. pKa
    tells how acidic or not a given hydrogen atom in a molecule is/ describes the susceptibility of a proton to removal by reaction with a base
  18. backbone of the amino acid
    • eeverything but the R group
    • alpha carbon
    • amino and COOH (both are ionizable)
  19. inflection point
    point on chart that marks significant move, either up or down
  20. secondary structure
    interaction betwen amino acids that is localized
  21. Ramachandran chart
    a chart that maps the phi and psi angles that are allowed or restricted
  22. prosthetic groups
    groups that can be inorganic or organic that bind to proteins to enhance their function; bind after the protien takes its native conformation; can covalently bind, but doesn't usually