Amino Acid Side-Chain Properties Flashcards: Polarity & Charge

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1. カード 1

   質問

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

   回答

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

2. カード 2

   質問

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

   回答

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

3. カード 3

   質問

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

   回答

   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. カード 4

   質問

   Alanine side chain → polarity group?

   回答

   Nonpolar. Its methyl group has no polar functional group.

5. カード 5

   質問

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

   回答

   Polar, predominantly uncharged. It contains a hydroxyl group.

6. カード 6

   質問

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

   回答

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

7. カード 7

   質問

   Valine side chain → polarity group?

   回答

   Nonpolar. It is a branched hydrocarbon side chain.

8. カード 8

   質問

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

   回答

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

9. カード 9

   質問

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

   回答

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

10. カード 10

    質問

    Phenylalanine side chain → polarity group?

    回答

    Nonpolar. Its benzyl group contains an aromatic ring.

11. カード 11

    質問

    Glycine → polarity group in this deck’s convention?

    回答

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

12. カード 12

    質問

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

    回答

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

13. カード 13

    質問

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

    回答

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

14. カード 14

    質問

    Leucine side chain → polarity group?

    回答

    Nonpolar. It is a branched hydrocarbon side chain.

15. カード 15

    質問

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

    回答

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

16. カード 16

    質問

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

    回答

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

17. カード 17

    質問

    Tryptophan → polarity group in this deck’s convention?

    回答

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

18. カード 18

    質問

    Proline → polarity group in this deck’s convention?

    回答

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

19. カード 19

    質問

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

    回答

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

20. カード 20

    質問

    Isoleucine side chain → polarity group?

    回答

    Nonpolar. It is a branched hydrocarbon side chain.

21. カード 21

    質問

    Histidine → acid/base family?

    回答

    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. カード 22

    質問

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

    回答

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

23. カード 23

    質問

    Methionine side chain → polarity group?

    回答

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

24. カード 24

    質問

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

    回答

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

25. カード 25

    質問

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

    回答

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

26. カード 26

    質問

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

    回答

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

27. カード 27

    質問

    Which two standard amino acids have aliphatic alcohol side chains?

    回答

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

28. カード 28

    質問

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

    回答

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

29. カード 29

    質問

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

    回答

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

30. カード 30

    質問

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

    回答

    Aspartate and glutamate.

31. カード 31

    質問

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

    回答

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

32. カード 32

    質問

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

    回答

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

33. カード 33

    質問

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

    回答

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

34. カード 34

    質問

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

    回答

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

35. カード 35

    質問

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

    回答

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

36. カード 36

    質問

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

    回答

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

37. カード 37

    質問

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

    回答

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

38. カード 38

    質問

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

    回答

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

39. カード 39

    質問

    Glycine versus proline: which generally allows more backbone conformations?

    回答

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

40. カード 40

    質問

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

    回答

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

41. カード 41

    質問

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

    回答

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

42. カード 42

    質問

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

    回答

    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. カード 43

    質問

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

    回答

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

44. カード 44

    質問

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

    回答

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

45. カード 45

    質問

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

    回答

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

46. カード 46

    質問

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

    回答

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

47. カード 47

    質問

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

    回答

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

48. カード 48

    質問

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

    回答

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

49. カード 49

    質問

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

    回答

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

50. カード 50

    質問

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

    回答

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

51. カード 51

    質問

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

    回答

    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. カード 52

    質問

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

    回答

    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. カード 53

    質問

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

    回答

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

54. カード 54

    質問

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

    回答

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

55. カード 55

    質問

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

    回答

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

56. カード 56

    質問

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

    回答

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

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Amino Acid Side-Chain Properties Flashcards: Polarity & Charge

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