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Amino Acid Side-Chain Properties Flashcards: Polarity & Charge

56 flashcards on amino acid side-chain groups, charge at pH 7, and common property distinctions, with supplied-pKa reasoning and key exceptions.

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Practice amino acid side-chain properties with 56 original flashcards for learners who already recognize the 20 standard amino-acid names. The cards ask you to recall a named amino acid’s property group, identify an amino acid or a specified set from a functional-group clue, distinguish commonly confused properties, and infer predominant side-chain charge from supplied pH and pKa values.

The reference pH is 7. Charge means the R group alone, excluding backbone groups and peptide termini. Ordinary charge statements use a simple aqueous reference model, not a guarantee about a particular site inside a protein. The calculations supply their pKa assumptions; one cysteine example changes the pH to 9.3, and one histidine example supplies a shifted local pKa. You do not need to memorize exact pKa values.

This deck uses a four-group study convention: nonpolar (glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan); polar and predominantly uncharged at pH 7 (serine, threonine, asparagine, glutamine, cysteine, tyrosine); acidic (aspartate, glutamate); and basic (lysine, arginine, histidine). These are broad labels. Tryptophan has a polar hydrogen-bond donor; cysteine can behave hydrophobically; tyrosine is both aromatic and polar. Histidine belongs to the basic family but is mostly neutral at pH 7 when its side-chain pKa is 6.0. Aromaticity, polarity, and charge are not mutually exclusive descriptors.

The sequence starts with charge scope and classification, introduces the 20 amino acids in an interleaved order, then moves through property clues, comparisons, and pH reasoning. Related recall directions are separated so a nearby answer is less likely to give away the next one. Glycine’s flexibility, proline’s ring and backbone donor exception, cysteine’s disulfides, aromatic side chains, and acid-versus-amide distinctions receive focused practice.

The deck does not test one-letter or three-letter codes, structure drawings, exact pKa memorization, pI calculations, codons, dietary requirements, clinical decisions, or full-course/exam coverage. Broad clues are only reversed when the requested answer is a clear amino acid or an explicitly requested set. Structure and code recognition are covered separately in the amino acid structures and codes deck.

The questions, answers, examples, sequence, and metadata were independently authored from common biochemical facts. Fact checks used EMBL-EBI’s side-chain chemistry and ionisation guidance, plus ChEBI’s chemical classification. No source passages, exercises, or diagrams were copied. The cover is an original AI-generated conceptual illustration, not a chemical model.

Original text, organization, metadata, and generated cover are offered under CC0 1.0 to the extent applicable rights exist. This dedication does not cover source materials or anyone else’s rights. This is an independent study resource, not affiliated with or endorsed by EMBL-EBI or any course or examination provider.

Cartes de ce paquet

  1. Carte 1

    Question

    When a card asks for an amino acid’s side-chain charge, which charges should you leave out?

    Réponse

    The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.

  2. Carte 2

    Question

    Can an uncharged amino-acid side chain still be polar?

    Réponse

    Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.

  3. Carte 3

    Question

    Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?

    Réponse

    No. They describe different features. A ring can be aromatic while another feature makes the side chain polar or basic. Group labels are a study convention, not an exhaustive chemical description.

  4. Carte 4

    Question

    Alanine side chain → polarity group?

    Réponse

    Nonpolar. Its methyl group has no polar functional group.

  5. Carte 5

    Question

    Serine side chain at pH 7 → polarity/charge group?

    Réponse

    Polar, predominantly uncharged. It contains a hydroxyl group.

  6. Carte 6

    Question

    Aspartate side chain at pH 7 → acid/base group and predominant charge?

    Réponse

    Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.

  7. Carte 7

    Question

    Valine side chain → polarity group?

    Réponse

    Nonpolar. It is a branched hydrocarbon side chain.

  8. Carte 8

    Question

    Glutamine side chain at pH 7 → polarity/charge group?

    Réponse

    Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.

  9. Carte 9

    Question

    Lysine side chain at pH 7 → acid/base group and predominant charge?

    Réponse

    Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.

  10. Carte 10

    Question

    Phenylalanine side chain → polarity group?

    Réponse

    Nonpolar. Its benzyl group contains an aromatic ring.

  11. Carte 11

    Question

    Glycine → polarity group in this deck’s convention?

    Réponse

    Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.

  12. Carte 12

    Question

    Threonine side chain at pH 7 → polarity/charge group?

    Réponse

    Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.

  13. Carte 13

    Question

    Glutamate side chain at pH 7 → acid/base group and predominant charge?

    Réponse

    Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.

  14. Carte 14

    Question

    Leucine side chain → polarity group?

    Réponse

    Nonpolar. It is a branched hydrocarbon side chain.

  15. Carte 15

    Question

    Cysteine at pH 7 → group in this deck’s convention?

    Réponse

    Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.

  16. Carte 16

    Question

    Arginine side chain at pH 7 → acid/base group and predominant charge?

    Réponse

    Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.

  17. Carte 17

    Question

    Tryptophan → polarity group in this deck’s convention?

    Réponse

    Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.

  18. Carte 18

    Question

    Proline → polarity group in this deck’s convention?

    Réponse

    Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.

  19. Carte 19

    Question

    Asparagine side chain at pH 7 → polarity/charge group?

    Réponse

    Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.

  20. Carte 20

    Question

    Isoleucine side chain → polarity group?

    Réponse

    Nonpolar. It is a branched hydrocarbon side chain.

  21. Carte 21

    Question

    Histidine → acid/base family?

    Réponse

    Basic. Its imidazole can accept a proton. ‘Basic’ does not mean mostly +1 at pH 7: with a side-chain pKa of 6.0, most molecules have a neutral side chain.

  22. Carte 22

    Question

    Tyrosine at pH 7 → group in this deck’s convention?

    Réponse

    Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.

  23. Carte 23

    Question

    Methionine side chain → polarity group?

    Réponse

    Nonpolar overall. Its sulfur is part of a thioether, not a thiol.

  24. Carte 24

    Question

    Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?

    Réponse

    Glycine. Its small R group also permits more backbone conformations than most residues.

  25. Carte 25

    Question

    Which two standard amino acids have side-chain amide groups?

    Réponse

    Asparagine and glutamine. Their amides are polar and uncharged at pH 7.

  26. Carte 26

    Question

    For a single ionizable side-chain group, what does pH below its pKa favor?

    Réponse

    The protonated form. Whether that form is neutral or positive depends on the group.

  27. Carte 27

    Question

    Which two standard amino acids have aliphatic alcohol side chains?

    Réponse

    Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.

  28. Carte 28

    Question

    Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?

    Réponse

    Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.

  29. Carte 29

    Question

    Which three standard amino acids are conventionally called the branched-chain amino acids?

    Réponse

    Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.

  30. Carte 30

    Question

    Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?

    Réponse

    Aspartate and glutamate.

  31. Carte 31

    Question

    Which standard amino acid closes its side chain back onto the backbone nitrogen?

    Réponse

    Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.

  32. Carte 32

    Question

    For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?

    Réponse

    1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.

  33. Carte 33

    Question

    Which three standard amino acids form the usual ‘aromatic amino acids’ study group?

    Réponse

    Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.

  34. Carte 34

    Question

    Cysteine versus methionine: which side chain can make the usual protein disulfide link?

    Réponse

    Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.

  35. Carte 35

    Question

    For a single ionizable side-chain group, what does pH above its pKa favor?

    Réponse

    The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.

  36. Carte 36

    Question

    At pH 7, why is aspartate usually charged while asparagine is uncharged?

    Réponse

    Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.

  37. Carte 37

    Question

    Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?

    Réponse

    Histidine. Its protonation depends on pH and its local pKa.

  38. Carte 38

    Question

    Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?

    Réponse

    Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.

  39. Carte 39

    Question

    Glycine versus proline: which generally allows more backbone conformations?

    Réponse

    Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.

  40. Carte 40

    Question

    Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?

    Réponse

    Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.

  41. Carte 41

    Question

    Must every nonpolar side chain lie inside a water-soluble globular protein?

    Réponse

    No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.

  42. Carte 42

    Question

    Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?

    Réponse

    0

    pH is one unit above pKa, so neutral:protonated is 10:1; about 9% is +1. This is a supplied-pKa model, not a universal protein value.

  43. Carte 43

    Question

    Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?

    Réponse

    Neutral thiol. pH is below pKa, so the protonated S–H form predominates.

  44. Carte 44

    Question

    At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?

    Réponse

    Glutamate. Glutamine’s side-chain amide is neutral.

  45. Carte 45

    Question

    Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?

    Réponse

    Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.

  46. Carte 46

    Question

    Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?

    Réponse

    +1. pH is below pKa, favoring the protonated amino group.

  47. Carte 47

    Question

    Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?

    Réponse

    −1. pH is above pKa, favoring the deprotonated carboxylate.

  48. Carte 48

    Question

    Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?

    Réponse

    No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.

  49. Carte 49

    Question

    With a histidine side-chain pKa of 6.0, does the label ‘basic amino acid’ imply a predominantly +1 side chain at pH 7?

    Réponse

    No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.

  50. Carte 50

    Question

    Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?

    Réponse

    No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.

  51. Carte 51

    Question

    Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?

    Réponse

    No. Its backbone nitrogen has no attached hydrogen in the peptide chain. This is a backbone consequence of its ring, not a side-chain charge.

  52. Carte 52

    Question

    At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?

    Réponse

    No. The two forms occur in equal proportions, giving an ensemble-average charge of +0.5. Each form still has charge 0 or +1.

  53. Carte 53

    Question

    Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?

    Réponse

    −1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.

  54. Carte 54

    Question

    At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?

    Réponse

    Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.

  55. Carte 55

    Question

    A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?

    Réponse

    The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.

  56. Carte 56

    Question

    Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?

    Réponse

    Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.

Abstract teal protein ribbon with colorful side branches on a dark blue background; conceptual illustration.

56 cartes

Amino Acid Side-Chain Properties Flashcards: Polarity & Charge

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