Lecture Two - Amino Acids

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Lecture Two - Amino Acids
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2013-09-09 17:37:59
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Biochemistry Lecture Two Amino Acids Section One
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Biochemistry
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  1. What are the most abundant of Macromolecules in cells?
    Proteins
  2. How do proteins have such a diverse range of functions (and therefore structures)?
    Variable Size and Physical Properties
  3. How are genes expressed? (What is the final product of gene expression)?
    Proteins
  4. What is a Heteropolymer?
    A polymer composed of repeat units made up of different monomers.
  5. What are proteins made of?
    Linear, Heteropolymers of amino acids.
  6. Do all organisms use the same Amino Acids?
    Yes.
  7. How many different Amino Acids are used in Living Organisms?
    ~20
  8. What is the structure of a generic amino Acid?
    An Amino Group and a Carboxylate group Covalently attached to a Tetrahedral α-Carbon.
  9. How are Amino Acids classified?
    Based upon the physiochemical properties of the R-Group.
  10. What is a Zwitterion?
    A species containing both a Positive and a Negative charge.
  11. How are Amino Acids pH sensitive?
    Their Carboxyalate and Amino groups can be either Protonated or Deprotonated depending on the pH.
  12. What is the structure of the Amino Acids in the physiological pH range (pH5-8)?
    The Carboxylate and Amino groups are Completely Ionized.

    • E.g Alanine...
  13. What are two other names for Zwitterions?
    • Dipolar Ions
    • Ampholytes
  14. Why are Zwitterions useful in biology?
    They can act as either an Acid or a Base.
  15. What is the pKa of an α-Carboxyl Group?
    ~2.2 (The R-Group makes a slight difference).
  16. What is the pKa of an α-Amino Group?
    ~9.4 (The R-group makes a slight difference).
  17. What percentage of α-Carboxylate will be Protonated at pH 2.2?
    50%
  18. What percentage of α-Carboxylate will be Deprotonated at pH 2.2?
    50%
  19. In terms of Acid/Base Chemistry, what might be the state of an α-Amino group at pH 3?
    *It will be protonated.
  20. Why are Amino Acids Chiral?
    The α-Carbon is covalently attached to four different groups.
  21. Name a Non-Chiral Amino Acid.
    Glycine.
  22. What are the Two Classes of Stereoisomers for Optically Active Amino Acids?
    L & D (Depending on which way they rotate plane polarized light).
  23. What Amino Acid Stereoisomers are not found in Living Systems?
    The D-Stereoisomers.
  24. What system of Labelling Stereoisomers is used in Biochemistry?
    L & D (As opposed to R,S in Synthetic Chemistry).
  25. How might you use CO-R-N to distinguish between L & D Stereoisomers?
    • 1. Rotate the Amino Acid so the H-Group faces away from you.
    • 2. Look Clockwise around the α-Carbon.
    • 3. If the Word CO-R-N is spelled, the molecule is L.
    •  If not, the molecule is D.
  26. What is the Magnitude of the Energy Difference Between L & D Stereoisomers?
    Zero. They are energetically equal.
  27. Why is only one Amino Acid Stereoisomer ever used?
    Repetitive Structures in Proteins require all Amino Acids to have the Same Configuration.
  28. What are some Repetitive Structures you might find in a Protein?
    Helices, Sheets, Turns.
  29. Could an α-Helix be composed of L & D Amino Acids?
    No, they must all be the same stereoisomer.
  30. How did the L-Stereoisomer become the dominant Amino Acid?
    Initial Random Choice carried through in Evolution.
  31. Define Polarity.
    The Magnitude of the Dipole induced in the presence of an external electromagentic field.
  32. Where in the periodic table might you look for atoms that have easily induced Dipoles?
    The Edges of rows 1-3.
  33. Where in the Periodic Table might you look for atoms that are difficult to induce dipoles in?
    The Centre of rows 1-3.
  34. What is interesting properties of Non-polar Amino Acids?
    They are relatively unreactive.
  35. Given their basic property(s) how might Non-polar Amino Acids be used living systems?
    For Structural Proteins Given their Unreactivity.
  36. An Aliphatic Amino Acid would most likely be...?
    A) Non-Polar
    B) Polar (Charged)
    C) Polar (Uncharged)
    A) Non-Polar
    (this multiple choice question has been scrambled)
  37. Methionine is...?
    A) Non-Polar
    B) Polar (Charged)
    C) Polar (Uncharged)
    A) Non-Polar
    (this multiple choice question has been scrambled)
  38. Proline is...?
    A) Non-Polar
    B) Polar (Charged)
    C) Polar (Uncharged)
    A) Non-Polar
    (this multiple choice question has been scrambled)
  39. What two Classifications does Glycine fall under?
    Non-Polar & Polar
  40. What is a useful property of Aromatic Amino Acids?
    They ansorb UV light.
  41. What is Unique about Proline?
    It is cyclic whereby it's R-Group chain covantly attaches to the α-Amino group.
  42. Why is Leucine non-polar?
    It has an Aliphatic Chain which makes it difficult to induce any dipoles.
  43. Where might Glycine be useful in polypeptide structure?
    It can be used to do tight turns due to it's low hydroxyl group.
  44. How is proline useful in Polypeptide Structure?
    It forces Kinks in the chain.
  45. An Amino Acid with a Hydroxyl Group might be?
    A) Polar (Uncharged)
    B) Polar (Charged)
    C) Non-Polar
    A) Polar (Uncharged)
    (this multiple choice question has been scrambled)
  46. An Amino Acid with a Thiol Group might be?
    A) Non-Polar
    B) Polar (Charged)
    C) Polar (Uncharged)
    C) Polar (Uncharged)
    (this multiple choice question has been scrambled)
  47. An Amino Acid with a Carboxyamide might be?
    A) Polar (Charged)
    B) Non-Polar
    C) Polar (Uncharged)
    C) Polar (Uncharged)
    (this multiple choice question has been scrambled)
  48. Serine, Threonine and Cysteine are often involved in _________ reactions.
    Enzymatic
  49. Glycine, Tyrosine and Cysteine fall into two categories. Which are they?
    • Polar (Uncharged)
    • Non-Polar
  50. Three Amino Acids can be Polar (Uncharged) or Non-Polar. What are they?
    • Tyrosine
    • Cysteine
    • Glycine
  51. When might Cysteine be considered non-polar?
    When it has formed a Disulfide bridge.
  52. How is Cystine (Be careful) formed?
    Spontaneously from two Cysteines in the presence of Oxidizing Agents.
  53. What is Cystine? (Be Careful).
    A comound formed from two Cysteines whereby the two Thiol Groups become covalently bonded, producing a Disulfide Bridge.
  54. What is special about Cystine? (Be Careful).
    It is VERY non-polar.
  55. What are Polar (Charged) Amino Acids?
    Polar Amino Acids that are partially or fully ionized at neutral pH.
  56. What two functional groups show up in the Polar (Charged) Amino Acids?
    • Carboxylate
    • Amine
  57. What charges might an Amine group on an Amino Acid carry?
    • Neutral (0)
    • Positive (+1)
  58. What charges might a Carboxylate group on an Amino Acid carry?
    • Neutral (0)
    • Negative (-1)
  59. What is the pKa of Cysteine's R-Group?
    8.4
  60. What is the pKa of Tyrosine's R-Group?
    10.5
  61. What is the pKa of Histidine's R-Group?
    6.0
  62. What is the pKa of Lysine's R-Group?
    10.5
  63. What is the pKa of Arginine's R-Group?
    12.5
  64. What is the pKa of Aspartate's R-Group?
    3.9
  65. What is the pKa of Glutamate's R-Group?
    4.1
  66. What is the name of a Proline Residue?
    Prolyl.
  67. What is the name of a Tryptotophan Residue?
    Tryptotophanyl
  68. What is the name of a Glutamate Residue?
    Glutamyl
  69. What is the three letter code for Glycine?
    Gly
  70. What is the three letter code for Serine?
    Ser
  71. What is the three letter code for Histidine?
    His
  72. What is the three letter code for Isoleucine?
    Lle
  73. What is the three letter code for Tryptophan?
    Trp
  74. What is the three letter code for Asparagine?
    Asn
  75. What is the three letter code for Glutamine?
    Gln
  76. Explain why a curve like the one shown might be the result of an Amino Acid Titration
    .
    At a low pH addition of OH causes deprotonation of the α-Carboxylate which acts like a buffer, slowing down the rate of pH change and creating the first plateu.

    As the OH increases further the α-Carboxylate becomes completely ionized (deprotonated) and the rate of pH change increases again.

    With a continued addition of OH the pH will become suitable to deprotonate the α-amino group which will cause a plateu in the same way the α-carboxylate did.
  77. What might alter the shape of a Titration Curve of an Amino Acid?
    • Ionizable R-groups
    • Peptide bonds
  78. What does "OH Equivalency Added" mean?
    • The amount of OH added relative to the initial substrate (Amino Acid) concentration.
    • (If 1 Mol of substrate is added, the OH Equivalency is simply the OH concentration).
  79. Can titrations be used to identify Amino Acids?
    Sometimes. Often however the pKas of the α-Carboxylate and α-Amino groups are degenerate.
  80. Look at the following Titration Curve of an Amino Acid. What is a suitable suggestion for the identity of the Amino Acid?
    Glycine
  81. What is the Isoelectric Point?
    The point at which the total charge of an Amino Acid (peptide or protein) is Zero.
  82. For a simple Amino Acid, such as Glycine, how might you determine the pH of it's Isoelectric Point?
    Take the average of the pKA's of it's α-Carboxy α-Amino ends.
  83. What feature of some R-groups makes it harder to calculate the Isoelectric point?
    Ionizability (Ionizable R-Groups give more complex titration curves).
  84. Given the following, how might you calculate the pK of an acid?
    pH
    [A-]
    [HA]
    • Simply rearrange the Equation,
  85. What kind of Amino Acid might give a Titration Curve like the following?
    An Amino Acid with an Ionizable R-group.
  86. How do you find the Isoelectric point on a more complex titration curve?
    Take the average of the pKas bounding the species with a net charge of zero.
  87. How might you determine where the species with a net charge of Zero is?
    • start with a fully protonated structure of the Amino Acid
    • Deprotonate stepwise as though OH was gradually being added (Acids first) until a species with no charge arises.
    • Find the plateues to either side of this species and take their average pKa.
  88. What sort of reaction forms Peptide Bonds?
    Condensation
  89. How many N and C termini will a polypeptide consisting of four Amino Acid residues have? What about a polypeptide with ten residues?
    Only ever two. One for each (N at one end, C at the other).
  90. To what end of a polypeptide are Amino Acids added?
    Only ever to the N-Terminus.
  91. Are peptide bonds ionizable?
    No
  92. Define the term Residue with respect to Biochemistry.
    An Amino Acid in an Oligo- or polypeptide, protein; a peptide unit.
  93. Define the term Oligopeptide.
    Short polymer of Residues; up to 10-20 residues.
  94. Define the term Polypeptide.
    Longer polymer of Residues; larger sizes.
  95. Define the term Protein with respect to Biochemistry.
    One or more polypeptide chains.
  96. How might you name a polypeptide chain?
    Name all the constituent residues by their residue names, except the last one which has its Amino Acid name.
  97. How might you name the following polypeptide?
    Serine-Tryptophan-Phenylalanine
    Seryltryptophanylphenylalanine.
  98. Seven Hundred Amino Acids have been detected in living organisms.
    Why do people say there are only 20?
    Only ~20 of the ~700 amino acids known are common to all life. Some organisms have variations outside of the common 20.
  99. What are Ornithine and Citrulline?
    Non-standard Amino Acids that are Metabolic Intermediates in Urea biosynthesis.
  100. How do Non-standard Amino Acids come about?
    Post Translational Modifications.
  101. How are Post Translational modifcations to residues carried out?
    Specific enzymes target specific residues to modify them.
  102. 4-Hydroxyproline is a Non-Standard Amino Acid. Low levels can cause?
    Scurvy
  103. What are some useful biological functions of modified Amino Acids?
    • Neurotransmitters
    • Allergic Response
  104. What is the function of the Non-Standard Amino Acid Dopamine?
    A neurotransmitter.
  105. What is γ-Aminobutyric Acid?
    Also known as GABA. It is a neurotransmitter.
  106. Is Histamine an Amino Acid?
    Yes. It is a Non-Standard Amino acid used in Allergic Responses.
  107. What is a Catecholamine?
    A Non-Standard Amino Acid that has been modified to have it's α-Carboxylate removed.

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