Biochemistry Test one

  1. what amino acid does not have a free amino group but one attached to a side chain and a cyclic structure?
  2. what are the consequences of not having a freee amino group?
    forms a kink in the bond and its only compatible with a unique proline helix.
  3. Proline is "sticky" and seeks out other polyprolines because------
    because it is hydrophobic
  4. Proline seeks out polyprolines and forms very important proteins for------
    transcription factors
  5. proline can also act as a molecular switch because
    they have double bonds in the middle of the chain and the energy difference in proline allows it to flip back and forth between cis and trans.
  6. All peptid bonds except for proline strongly favor ------ conformation
  7. what does selinocysteine have attached to it?
  8. what creates one of the termination codons
  9. what does selinocysteine do?
    • has no genetic code
    • creates one of the termination codons
    • used in a number of redox enzymes
  10. Proline has a lot of-----
    random structures
  11. what are Primary structures?
    amino acid sequence
  12. how are the electrons shared between carbon and oxygen dispersed?
    they are dispersed between the carbonyl and a peptide bond
  13. How does the peptide bond get partial double bond like characteristics?
    Sometimes we see peptide bond where the second electron is dispersed between the carbonyl and peptide bond.
  14. What conformation is it when the chains in front of the bond and behind it are facing on opposite sides?
    Trans conformation
  15. What conformation is it when the chains in front of the bond and behind it are on the same side?
    Cis conformation
  16. In general which conformation is less?
    Trans, so all peptides not involving proline are in trans.
  17. Cis can reach up to ------- of these peptide bonds involving proline
  18. Only time you will see a stable Cis conformation is....
    with proline
  19. Trans is only --------kilocalorie per mole than the cis when it is on the amino side of the proline
  20. when do ionic bonds occur?
    between oppositely charged species
  21. if you double the distance of an ionic bond what happens to the energy? why is this when ionic bonds are strong?
    • the weaker the bond, it would cut the energy in half.
    • Because it is neutralized by its own strength.
  22. van der waals forces are-------
    non-covalent bonds between electrically neutral molecules
  23. what bond attracts water and acquires a sphere of hydration that interferes with the bond?
    Ionic bonds
  24. where do you usually see conserved ionic bonds?
    places like the interface between proteins, where you can basically exclude water
  25. Where do dipole-dipole bonds occur?
    Between the carbonyls
  26. the bond between two carobnyls is how much energy compared to an ionic bond?
    it would by -9.3 kj/mole almost 1/10th the energy in an ionic bond
  27. what happens to the energy if you double the distance of the dipole-dipole bond?
    If you double the distance between the two species with the bond the energy goes from 1/10th the energy in an ionic bond to 1/8th the energy.
  28. when does dispersion occur?
    when you have two aromatic rings that involves the interatcion of the P orbitals.
  29. when do hydrogen bonds occur and what is the strength of the bonds?
    Hydrogen bonds occur when a hydrogen is shared between groups. the bond is ntermediate in strength (-20 to -30 kj/mole)
  30. what is one of the most important bonds to proteins?
    Hydrogen bonds
  31. what is the length of a fixed hydrogen bond?
  32. How many types of secondary structures are there?
  33. What is random structure very important in?
    in binding in molecular assembly and also in protein modification
  34. 1/3 to 1/2 of eukaryotic proteins have at least--------amino acids
  35. what is another name for the random structure in eukaryotic proteins?
    intrinsicially disordered peptides
  36. when would it be difficult for modifying enzymes to get to the site on the protein?
    if the protein was very tight, so most often these sites are on loose sections of the protein.
  37. what is the advantage of random structures when it comes to molecular recognition? (2 things)
    • there is more versatility and the structure can recognize ligands
    • it has a larger capture radius which means that the kinetics of association are much faster
  38. upon modification random structures receive------
    stability but these regions can also function exclusively as random structures
  39. what are entropic chains?
    functioning random structures.
  40. What are entropic spring used for?
    They are used by entropic chains to keep proteins apart.
  41. what is the largest protein in the body?
  42. where is Titan located?
    found in the sarcomere
  43. what are titans?
    It is random structure that can elongate and shorten without disrupting the structure of the overall protein.
  44. what runs from the M line to the Z line?
  45. What are entropic clots?
    the ends of peptide chains that close channels (nervous system). they are random structures.
  46. What bond does beta structure use?
    Hydrogen bonds
  47. chains of amino acids share hydrogens between their nitrogen and the oxygen of the adjacent chain are called------
    anti-parallel beta sheet
  48. what does a beta-pleated sheet look like?
    The R groups of the protein chains get in the way so that the chain has to 'pucker' to throw the R groups above or below the sheet.
  49. why can't the R groups be between the beta-pleated sheet?
    Because they would interfere with hydrogen bonding
  50. when can't you have a pure beta sheet?
    when you have a parallel beta sheet
  51. what is the one way you can have a pure beta structure?
    if the beta strand is circular
  52. T/F Beta structures are very rich in hydrophilic amino acids
    False, hydrophobic
  53. where do you often see beta structures?
    in the center of globular proteins because they are hydrophobic
  54. you have reached the limit in protein structure when----
    a protein has only one binding domain
  55. hemoglobin consists of --------- helixes
  56. what has four helixes that line up together to form an alpha helical bundle
    Myoheryhrin (sp??)
  57. The way secondary domains fold on each other is known as----
    tertiary structure
  58. what is the difference between secondary and tertiary structures for fibrous proteins like silk and intermediate filaments?
    both the same except for the globular proteins have multiple domains that fold on one another.
Card Set
Biochemistry Test one
Protein structure