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Amino Acids

Tier 3 · #22 of 33 · moderate yield · topic 1.4 — every high-yield fact from the book chapter, exam-ready.

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  1. Front
    What four groups are bonded to the alpha-carbon (Cα) of a standard amino acid ?
    Back
    A carboxyl group (–COOH) , an amino group (–NH₂) , a hydrogen atom , and a variable side chain (R group)
  2. Front
    All amino acids found in human proteins are in which stereochemical configuration?
    Back
    L-configuration
  3. Front
    At physiological pH 7.4, the dominant form of an amino acid carries one positive and one negative charge with zero net charge. What is this form called?
    Back
    A zwitterion
  4. Front
    Which standard amino acid is the only one whose alpha-carbon is achiral (optically inactive) , and why?
    Back
    Glycine — its R group is a second hydrogen , so Cα is not bonded to four different groups
  5. Front
    Cloze: An ____ is a derivative of ammonia (NH₃) in which one or more hydrogens are replaced by a carbon-containing group.
    Back
    amine
  6. Front
    How many carbon groups are on the nitrogen of a primary , secondary , and tertiary amine , respectively?
    Back
    Primary = 1 (R–NH₂), secondary = 2 (R–NH–R'), tertiary = 3 (R–N(R')R'')
  7. Front
    Why can a tertiary amine NOT act as a hydrogen-bond donor?
    Back
    It has no N–H bond — there is no hydrogen on the nitrogen to donate
  8. Front
    Are amines acids or bases, and what ion forms when an amine accepts a proton?
    Back
    Weak bases ; accepting a proton forms a positively charged ammonium ion
  9. Front
    What intermediate forms when a primary amine condenses with an aldehyde or ketone (losing the N–H and forming a C=N double bond)?
    Back
    A Schiff base
  10. Front
    Which cofactor forms a Schiff base with an active-site lysine , a mechanism central to transamination ?
    Back
    Pyridoxal phosphate (PLP)
  11. Front
    Which single feature of an amino acid determines its solubility, charge, and reactivity?
    Back
    The side chain (R group)
  12. Front
    Name the seven nonpolar, aliphatic amino acids .
    Back
    Glycine , Alanine , Valine , Leucine , Isoleucine , Methionine , Proline
  13. Front
    Why is proline a 'helix-breaker'?
    Back
    Its side chain loops back to the backbone nitrogen (making it a secondary amine ), creating rigidity that prevents the phi/psi angles needed for an alpha-helix
  14. Front
    Among the standard amino acids, proline is unusual because its backbone nitrogen is what type of amine?
    Back
    A secondary amine
  15. Front
    Name the five polar, uncharged amino acids .
    Back
    Serine , Threonine , Cysteine , Asparagine , Glutamine
  16. Front
    Which amino acid's thiol (–SH) group can be oxidized to form a disulfide bond ?
    Back
    Cysteine
  17. Front
    What is the only covalent cross-link formed between standard amino acid side chains in protein structure?
    Back
    The disulfide bond (–S–S–) , formed between two cysteines
  18. Front
    Name the three aromatic amino acids .
    Back
    Phenylalanine , Tyrosine , Tryptophan
  19. Front
    Which aromatic amino acid absorbs UV light most strongly, and at what wavelength is absorbance used to estimate protein concentration?
    Back
    Tryptophan ; absorbance at ~280 nm
  20. Front
    Which aromatic amino acid is the precursor to melanin and thyroid hormones ?
    Back
    Tyrosine
  21. Front
    Name the two acidic amino acids .
    Back
    Aspartic acid (Asp) and Glutamic acid (Glu)
  22. Front
    What net charge do aspartate and glutamate carry at pH 7.4?
    Back
    −1
  23. Front
    Name the three basic amino acids .
    Back
    Lysine (Lys) , Arginine (Arg) , Histidine (His)
  24. Front
    What is the approximate side-chain pKa of histidine 's imidazole ring ?
    Back
    ~6.0
  25. Front
    Histidine is classified as basic, but what is its actual charge state at pH 7.4?
    Back
    Mostly uncharged (only a small fraction is positive) — it does NOT carry +1 at physiological pH
  26. Front
    Why is histidine the premier catalytic residue in enzyme active sites?
    Back
    Its imidazole pKa (~6.0) is near physiological pH, so it can accept and donate protons (act as a proton shuttle) at pH 7.4
  27. Front
    What term describes the ability of amino acids to act as either an acid or a base depending on pH?
    Back
    Amphoteric
  28. Front
    What is the approximate pKa of the alpha-carboxyl group of an amino acid?
    Back
    ~2–3
  29. Front
    What is the approximate pKa of the alpha-amino group of an amino acid?
    Back
    ~9–10
  30. Front
    Cloze: For any ionizable group, if pH < pKa the group is predominantly ____.
    Back
    protonated
  31. Front
    When a carboxyl group is protonated (pH < pKa), what is its charge?
    Back
    Neutral (–COOH = 0)
  32. Front
    When an amino group is protonated (pH < pKa), what is its charge?
    Back
    Positive (–NH₃⁺ = +1)
  33. Front
    Define the isoelectric point (pI) .
    Back
    The pH at which an amino acid or protein carries zero net charge (positive and negative charges exactly balance)
  34. Front
    For a neutral amino acid (e.g. glycine ), how is pI calculated?
    Back
    pI = (pKa1 + pKa2) / 2 — average of the alpha-carboxyl and alpha-amino pKa values
  35. Front
    For an acidic amino acid (Asp/Glu) , which two pKa values are averaged to get the pI?
    Back
    pKa1 (alpha-carboxyl) and pKR (side-chain carboxyl) — pI = (pKa1 + pKR)/2
  36. Front
    For a basic amino acid (Lys/Arg/His) , which two pKa values are averaged to get the pI?
    Back
    pKa2 (alpha-amino) and pKaR (side-chain amino) — pI = (pKa2 + pKaR)/2
  37. Front
    Calculate the pI of glycine (pKa1 = 2.34, pKa2 = 9.60).
    Back
    pI = (2.34 + 9.60)/2 = 5.97 (~6, slightly acidic)
  38. Front
    What is the approximate pI of aspartic acid ?
    Back
    ~2.77–2.85
  39. Front
    What is the approximate pI of glutamic acid ?
    Back
    ~3.22
  40. Front
    Approximately what pI ranges do neutral , acidic , and basic amino acids fall into?
    Back
    Neutral ~5–6 ; acidic ~3 ; basic ~9–11
  41. Front
    Worked: at pH 7.4, what is the net charge on aspartic acid (pKa1=2.0, pKR=3.7, pKa2=9.8)?
    Back
    −1 (alpha-COO⁻ = −1, side-chain COO⁻ = −1, alpha-NH₃⁺ = +1; sum = −1)
  42. Front
    What is the common trap when assigning aspartate 's charge at pH 7.4 — why is it −1, not −2?
    Back
    The alpha-amino group is still protonated (pH 7.4 < pKa ~9.8), contributing +1 that offsets one of the two −1 carboxylates
  43. Front
    At pH 7.4, what is the net charge on lysine (pKa1=2.2, pKa2=9.0, pKaR=10.5)?
    Back
    +1 (alpha-COO⁻ = −1, alpha-NH₃⁺ = +1, side-chain NH₃⁺ = +1; sum = +1)
  44. Front
    In electrophoresis, if pH < pI, the molecule is net positive and migrates toward which electrode?
    Back
    The cathode (negative electrode)
  45. Front
    In electrophoresis, if pH > pI, toward which electrode does the ( net negative ) molecule migrate?
    Back
    The anode (positive electrode)
  46. Front
    At what pH does an amino acid fail to migrate in an electric field?
    Back
    When pH = pI (zero net charge)
  47. Front
    An amino acid has pI 9.75. At pH 7.4, which electrode does it migrate toward?
    Back
    The cathode (negative electrode) — pH 7.4 < pI, so it is net positive
  48. Front
    How is a peptide bond formed between two amino acids?
    Back
    By a dehydration (condensation) reaction between the alpha-carboxyl of one and the alpha-amino of the next, releasing water
  49. Front
    By convention, peptides are written from which terminus on the left to which on the right?
    Back
    N-terminus (free amino end) on the left to C-terminus (free carboxyl end) on the right
  50. Front
    Approximately what percent double-bond character does the peptide (C–N) bond have, due to resonance?
    Back
    ~40%
  51. Front
    What is the key structural consequence of the peptide bond's partial double-bond character?
    Back
    No free rotation around the bond ; the six atoms of the peptide group are coplanar
  52. Front
    Which configuration (cis or trans) is the peptide bond almost always found in, and why?
    Back
    Trans — adjacent alpha-carbons on opposite sides minimize steric clashes
  53. Front
    The peptide-bond dipole (δ+ on N, δ− on O) makes what kind of interaction in secondary structure possible?
    Back
    Hydrogen bonding in alpha-helices and beta-sheets
  54. Front
    Cloze: ____ protein structure is the amino acid sequence.
    Back
    Primary
  55. Front
    What does secondary protein structure refer to?
    Back
    Local patterns of backbone hydrogen bonding — alpha-helices and beta-sheets
  56. Front
    What distinguishes tertiary from quaternary protein structure?
    Back
    Tertiary = the complete 3D fold of a single polypeptide chain; quaternary = the arrangement of multiple polypeptide subunits
  57. Front
    Exam trap: 'The predominant ionic form of glutamic acid at pH 7.4 has net charge 0.' True or false, and why?
    Back
    FALSE — glutamate's pI is ~3.22; at pH 7.4 (far above pI) both carboxyls are deprotonated and the amino group is protonated , giving net −1
  58. Front
    Why are D-amino acids relevant in biology even though they are absent from human proteins?
    Back
    They occur in nature, notably in bacterial cell walls
  59. Front
    Why do amino acids dissolve readily in water and migrate in an electric field?
    Back
    They exist as charged (ionic) species — zwitterions — not as simple neutral molecules
  60. Front
    What is the name of arginine 's positively charged side-chain group, and its approximate pKa?
    Back
    A guanidinium group ; pKa ≈ 12.5
  61. Front
    What is the name of lysine 's positively charged side-chain group, and its approximate pKa?
    Back
    An ε-amino group ; pKa ≈ 10.5
  62. Front
    Rank the side-chain pKa values of the three basic amino acids from lowest to highest.
    Back
    Histidine imidazole (~6.0) < lysine ε-amino (~10.5) < arginine guanidinium (~12.5)
  63. Front
    What is the approximate length of a peptide bond , and what does that value indicate about the bond?
    Back
    ~1.33 Å — intermediate between a pure single and a pure double bond (reflecting its ~40% double-bond character)
  64. Front
    Reacting an amine with an acid such as HCl produces what kind of product?
    Back
    A water-soluble ammonium salt
  65. Front
    Why are poorly water-soluble drugs containing an amine group often formulated as their hydrochloride salts ?
    Back
    Reacting the amine with HCl forms a water-soluble ammonium salt , improving solubility
  66. Front
    What is the approximate pKa range of the side-chain carboxyl group (pKR) of the acidic amino acids Asp and Glu ?
    Back
    ~3.7–4.3
  67. Front
    At pH 7.4 (well above its pKR of ~3.7–4.3), what is the charge on the side-chain carboxyl of aspartate or glutamate ?
    Back
    Deprotonated, −1 (–COO⁻)
  68. Front
    Besides being classified as basic, what type of side chain (in terms of ring character) does histidine have?
    Back
    An aromatic imidazole side chain
  69. Front
    When you add strong acid (lower the pH below the carboxyl pKa), what happens to the carboxylate and the molecule's net charge?
    Back
    The carboxylate is protonated (–COO⁻ + H⁺ → –COOH), so the molecule gains a net positive charge
  70. Front
    When you add strong base (raise the pH above the amino pKa), what happens to the ammonium group and the molecule's net charge?
    Back
    The ammonium is deprotonated (–NH₃⁺ → –NH₂ + H⁺), so the molecule gains a net negative charge
  71. Front
    The pI is NOT the pH at which every ionizable group is neutral. What is it actually defined as?
    Back
    The pH at which the positive and negative charges exactly balance (zero NET charge)
  72. Front
    Conceptually, why does an acidic amino acid (Asp/Glu) need a LOW pH to reach zero net charge?
    Back
    A low pH is needed to protonate (suppress ionization of) its side-chain carboxyl so the negative charges no longer outweigh the positive amino group
  73. Front
    Conceptually, why does a basic amino acid (Lys/Arg) need a HIGH pH to reach zero net charge?
    Back
    A high pH is needed to deprotonate both amino groups so the positive charges no longer outweigh the negative carboxyl
  74. Front
    What force drives nonpolar (hydrophobic) side chains to cluster in the interior of a folded protein?
    Back
    The hydrophobic effect
  75. Front
    Match the stabilizing interaction to its level of protein structure: backbone amide hydrogen bonds stabilize which level?
    Back
    Secondary structure ( alpha-helices and beta-sheets )
  76. Front
    At which level(s) of protein structure do hydrophobic core packing and salt bridges between charged side chains act as stabilizers?
    Back
    Tertiary structure
  77. Front
    Disulfide bonds act as covalent cross-links stabilizing which level(s) of protein structure?
    Back
    Tertiary and quaternary structure
  78. Front
    Name the physiologically important protein given in the chapter as a classic example of disulfide-bond -stabilized structure.
    Back
    Insulin
  79. Front
    What makes the alpha-carbon (Cα) of every standard amino acid except glycine a chiral (asymmetric) center?
    Back
    It is bonded to four different groups (–COOH, –NH₂, –H, and a unique side chain)
  80. Front
    All three aromatic amino acids share what laboratory-exploited property?
    Back
    They absorb ultraviolet (UV) light , used to detect and quantify proteins
  81. Front
    Which nonpolar amino acid contains sulfur, and in what form is that sulfur (vs cysteine's)?
    Back
    Methionine — its sulfur is in a thioether (–S–CH₃) , unlike cysteine 's free thiol (–SH)

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