biochemistry Test one

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biochemistry Test one
2012-02-03 20:20:54

amino acids
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  1. What are the three parts of the amino acid?
    • Amino group
    • carboxylic acid
    • R group
  2. Which part gives the amino acids it’s distinct structure
    The R group
  3. What is Glycene’s distinct structure group
    Hydrogen is it's R group
  4. What is a carbon with four different substitutions
    asymmetrical and optically active
  5. L amino acids are ----------- incorporated
  6. D amino acids are made by
    enzymatically made and it's sometimes ribosomally made
  7. D amino acids have evidence that they arose by past------
    transcriptional isomerazation
  8. In what environment is the amino acid completely protanated and what are the charges?
    very low pH, the carboxylic acid and amino group have positive charges
  9. What is the state of the amino acid at the Physiological pH and what is the Physiological pH?
    The carboxylic acid will ionize by the amino acid has the hydrogen on it. and the physiological ph is a ph of 6.5
  10. How will you be able to pull the hydrogen off the amino group? What will the charge?
    by raising the alkalinity and you will have a negative species
  11. What is a double charge and when do you normally see them?
    zwitter ion, and you normally see them in physiological pHs
  12. What cause discourages ionization?
    surrounded by hydrophobic groups
  13. what bond encourages ionization and which bond discourages it?
    Ionic bonds encourage ionization, and hydrogen bonds discourage ionization
  14. What is the PK3?
    the ionization constant of the R group
  15. Examples of Hydrophobicity
    Oil and grease
  16. true/false R groups only have hydrophobic properties
    False. R groups can have both properties of hydrophobic and hydrophilic
  17. Globular proteins are viewed as --------- because
    creme filled chocolates because they have a hydrophilic outside layer and a hydrophobic center.
  18. What interacts with water and is responsible for the water solubility of proteins?
    hydrophilic amino acids
  19. what bonds does the hydrophilic amino acids tend to have?
    ionic and hydrogen
  20. acidic amino acids have additional ------- and where are they attached?
    carboxylic acids and they are attached to the alpha carboxylic acid not the Carbon
  21. the core part of the acidic amino acid is the------
    alpha carboxylic acid
  22. the--------is blocked so the---------stands out
    alpha carboxylic acid, R group
  23. Aspartic acid has what attached to it?
    one methylated group
  24. Glutamic acid has what attached to it?
    2 methylated groups
  25. At what pH are Aspartic and glutamic acid ionized?
    physiological pH
  26. What are lysosymes able to do?
    they cleave carbohydrates due to the environment
  27. the amide on aspartic acid makes it------
  28. the amide on glutamic acid makes it-----
  29. what two acidic amino acids can be amidated?
    Glutamic acid and Aspartic acid
  30. T/F amides are negatively charged
    False, they have no charge
  31. to be hydrophobic it must be------
  32. to be hydrophilic it must be -------
  33. what is electron greedy on the amino acid?
    the carbonyl's oxygen. the electrons are presumably shared betwwn a carbon and oxygen but they spend more the oxygen. this way giving the O a neg. charge and the C a positive charge
  34. why is the carbonyl group able to interact with water?
    Because it is polar due to the slight charges on the carbon and oxygen.
  35. what can attach to asparagine? And where are they attached?
    carbohydrates, and the sugars attach to the Nitrogen sometimes known as N-linked sugars
  36. what are glycoproteins?
    Proteins that have sugars attached
  37. Glutamines are involved in -------
    cross-linking, they are 1 or 2 covalent links that can occur n proteins.
  38. How many amino acids can have carbohydrates attached?
    Three: asparagine being one
  39. Lysine has an extra--------group
    amino group
  40. Lysine can cross-link with what?
  41. What bond forms between the peptide chain of glutamine and the peptide chain of lysine?
  42. what is the enzyme that removes the amide to form the isopeptide bond between glutamine and lysine?
  43. when we couple amino acids together (glutamine & lysine) we see that the alpha carboxylic acid will form -------. In addition, amino groups form------- with-------.
    • will form the same type of modified amides
    • schiff bases
    • aldehydes
  44. what is in the active site of amylases that are involved with a number of aldehydes?
  45. What modifications can lysine undergo?
    • acetalation
    • methylation
  46. what group does arginine have attached by a carbon chain?
    guanidinium group
  47. what is not involved with schiff bases?
  48. Why is Histadine considered basic?
    Because it has a aninozole group that is protanated with a positive charge.
  49. What is the PK3 of histadine?
    6.5 (physiological pH)
  50. the Pka is the PH when ----
    when 50% of the groups are ionized
  51. what would you have to drop the pH down to to protanate half the aminozoles on the histadine?
    6.5 (histadine is not charged at 6.5)
  52. Proteins that are sensitive to pH have a critical -------- environment.
  53. what is the critical function of histadine?
    It acts as a pH sensor.
  54. T/F aminozole can resonate
  55. What holds iron in place in hemoglobin?
  56. what drives the folding process of proteins?
    Hydrophobic amino acids trying to get away from water comes together and forms the core
  57. what stabilizes the folding of proteins?
    Van der waal bonds between the hydrophobic amino acids
  58. Hydrophobic amino acids are also important in ------
    membrane proteins
  59. what are the membrane proteins made of?
    hydrophobic alpha helix
  60. How can you find where the alpha helixes are in the membrane?
    By a hydropathy plot
  61. the membrane proteins can also form -----------
    Hydrophobic pockets
  62. what does the negative numbers mean on the hydropathy plot?
    hydrophilic molecules
  63. what does the positive value mean in the hydropathy plot?
    Hydrophobic molecule
  64. what are examples of molecules that are carried in the hydrophobic pockets?
    • steroids
    • fatty acids
    • cholesterol
    • hydrophobic amino acids
  65. what amino acid forms the basis for all the other amino acids? Also known as the smallest.
  66. Glycene is the only amino acid that is not---------because------
    optically active because you have two identical substitutions on it
  67. what is just a teeny bit hydrophobic?
  68. Alanine is usually found at----------
    at the interface between the lipid and the hydrophilic cytosol
  69. Valine, Leucine, Isoleucine and Methonine are all very-----
  70. what amino acid deals with packing? what bond is used?
    Methionine, van der waals
  71. what are aromatic hydrophobic amino acids?
    • tyrosine
    • phenylalanine
    • typtophan
  72. what is involved in signaling growth factors and signaling mitogenesis?
    Phosphorylated Tyrosine
  73. where does the amino acid have to be to be phosphorylated?
    exposed to the surface
  74. tyrosine and tryptophan are usually found------
    in binding pockets
  75. what happens if the proteins use a ionic bond to bind a ligand?
    The ionic bond attracts water and you will have a sphere of hydration that blocks the access of the ligand to the binding site.
  76. what is the unique characteristics of tyrosine and typtophan?
    they are hydrophobic enough to dispel the sphere of hydration but they still hydrogen bond with the ligand.
  77. what two amino acids have hydroxyl R groups?
    Serine and threonine
  78. Serine and threonine can be ----------- and they are very involved in ----------
    • phosphorylated
    • enzyme regulation
  79. which amino acids can attach sugars to their oxygen?
    serine and threonine