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.
Apie šį rinkinį
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.
Šio rinkinio kortelės
1 kortelė
Klausimas
When a card asks for an amino acid’s side-chain charge, which charges should you leave out?
Atsakymas
The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.
2 kortelė
Klausimas
Can an uncharged amino-acid side chain still be polar?
Atsakymas
Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.
3 kortelė
Klausimas
Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?
Atsakymas
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 kortelė
Klausimas
Alanine side chain → polarity group?
Atsakymas
Nonpolar. Its methyl group has no polar functional group.
5 kortelė
Klausimas
Serine side chain at pH 7 → polarity/charge group?
Atsakymas
Polar, predominantly uncharged. It contains a hydroxyl group.
6 kortelė
Klausimas
Aspartate side chain at pH 7 → acid/base group and predominant charge?
Atsakymas
Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
7 kortelė
Klausimas
Valine side chain → polarity group?
Atsakymas
Nonpolar. It is a branched hydrocarbon side chain.
8 kortelė
Klausimas
Glutamine side chain at pH 7 → polarity/charge group?
Atsakymas
Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.
9 kortelė
Klausimas
Lysine side chain at pH 7 → acid/base group and predominant charge?
Atsakymas
Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.
10 kortelė
Klausimas
Phenylalanine side chain → polarity group?
Atsakymas
Nonpolar. Its benzyl group contains an aromatic ring.
11 kortelė
Klausimas
Glycine → polarity group in this deck’s convention?
Atsakymas
Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.
12 kortelė
Klausimas
Threonine side chain at pH 7 → polarity/charge group?
Atsakymas
Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.
13 kortelė
Klausimas
Glutamate side chain at pH 7 → acid/base group and predominant charge?
Atsakymas
Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
14 kortelė
Klausimas
Leucine side chain → polarity group?
Atsakymas
Nonpolar. It is a branched hydrocarbon side chain.
15 kortelė
Klausimas
Cysteine at pH 7 → group in this deck’s convention?
Atsakymas
Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.
16 kortelė
Klausimas
Arginine side chain at pH 7 → acid/base group and predominant charge?
Atsakymas
Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.
17 kortelė
Klausimas
Tryptophan → polarity group in this deck’s convention?
Atsakymas
Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.
18 kortelė
Klausimas
Proline → polarity group in this deck’s convention?
Atsakymas
Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.
19 kortelė
Klausimas
Asparagine side chain at pH 7 → polarity/charge group?
Atsakymas
Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.
20 kortelė
Klausimas
Isoleucine side chain → polarity group?
Atsakymas
Nonpolar. It is a branched hydrocarbon side chain.
21 kortelė
Klausimas
Histidine → acid/base family?
Atsakymas
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 kortelė
Klausimas
Tyrosine at pH 7 → group in this deck’s convention?
Atsakymas
Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.
23 kortelė
Klausimas
Methionine side chain → polarity group?
Atsakymas
Nonpolar overall. Its sulfur is part of a thioether, not a thiol.
24 kortelė
Klausimas
Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?
Atsakymas
Glycine. Its small R group also permits more backbone conformations than most residues.
25 kortelė
Klausimas
Which two standard amino acids have side-chain amide groups?
Atsakymas
Asparagine and glutamine. Their amides are polar and uncharged at pH 7.
26 kortelė
Klausimas
For a single ionizable side-chain group, what does pH below its pKa favor?
Atsakymas
The protonated form. Whether that form is neutral or positive depends on the group.
27 kortelė
Klausimas
Which two standard amino acids have aliphatic alcohol side chains?
Atsakymas
Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.
28 kortelė
Klausimas
Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?
Atsakymas
Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.
29 kortelė
Klausimas
Which three standard amino acids are conventionally called the branched-chain amino acids?
Atsakymas
Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.
30 kortelė
Klausimas
Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?
Atsakymas
Aspartate and glutamate.
31 kortelė
Klausimas
Which standard amino acid closes its side chain back onto the backbone nitrogen?
Atsakymas
Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.
32 kortelė
Klausimas
For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?
Atsakymas
1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.
33 kortelė
Klausimas
Which three standard amino acids form the usual ‘aromatic amino acids’ study group?
Atsakymas
Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.
34 kortelė
Klausimas
Cysteine versus methionine: which side chain can make the usual protein disulfide link?
Atsakymas
Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.
35 kortelė
Klausimas
For a single ionizable side-chain group, what does pH above its pKa favor?
Atsakymas
The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.
36 kortelė
Klausimas
At pH 7, why is aspartate usually charged while asparagine is uncharged?
Atsakymas
Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.
37 kortelė
Klausimas
Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?
Atsakymas
Histidine. Its protonation depends on pH and its local pKa.
38 kortelė
Klausimas
Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?
Atsakymas
Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.
39 kortelė
Klausimas
Glycine versus proline: which generally allows more backbone conformations?
Atsakymas
Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.
40 kortelė
Klausimas
Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?
Atsakymas
Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.
41 kortelė
Klausimas
Must every nonpolar side chain lie inside a water-soluble globular protein?
Atsakymas
No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.
42 kortelė
Klausimas
Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?
Atsakymas
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 kortelė
Klausimas
Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?
Atsakymas
Neutral thiol. pH is below pKa, so the protonated S–H form predominates.
44 kortelė
Klausimas
At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?
Atsakymas
Glutamate. Glutamine’s side-chain amide is neutral.
45 kortelė
Klausimas
Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?
Atsakymas
Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.
46 kortelė
Klausimas
Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?
Atsakymas
+1. pH is below pKa, favoring the protonated amino group.
47 kortelė
Klausimas
Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?
Atsakymas
−1. pH is above pKa, favoring the deprotonated carboxylate.
48 kortelė
Klausimas
Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?
Atsakymas
No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.
49 kortelė
Klausimas
With a histidine side-chain pKa of 6.0, does the label ‘basic amino acid’ imply a predominantly +1 side chain at pH 7?
Atsakymas
No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.
50 kortelė
Klausimas
Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?
Atsakymas
No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.
51 kortelė
Klausimas
Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?
Atsakymas
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 kortelė
Klausimas
At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?
Atsakymas
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 kortelė
Klausimas
Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?
Atsakymas
−1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.
54 kortelė
Klausimas
At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?
Atsakymas
Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.
55 kortelė
Klausimas
A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?
Atsakymas
The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.
56 kortelė
Klausimas
Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?
Atsakymas
Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.
56 kortelės
Amino Acid Side-Chain Properties Flashcards: Polarity & Charge
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