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.
About this deck
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.
Cards in this deck
Card 1
Question
When a card asks for an amino acid’s side-chain charge, which charges should you leave out?
Answer
The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.
Card 2
Question
Can an uncharged amino-acid side chain still be polar?
Answer
Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.
Card 3
Question
Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?
Answer
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.
Card 4
Question
Alanine side chain → polarity group?
Answer
Nonpolar. Its methyl group has no polar functional group.
Card 5
Question
Serine side chain at pH 7 → polarity/charge group?
Answer
Polar, predominantly uncharged. It contains a hydroxyl group.
Card 6
Question
Aspartate side chain at pH 7 → acid/base group and predominant charge?
Answer
Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
Card 7
Question
Valine side chain → polarity group?
Answer
Nonpolar. It is a branched hydrocarbon side chain.
Card 8
Question
Glutamine side chain at pH 7 → polarity/charge group?
Answer
Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.
Card 9
Question
Lysine side chain at pH 7 → acid/base group and predominant charge?
Answer
Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.
Card 10
Question
Phenylalanine side chain → polarity group?
Answer
Nonpolar. Its benzyl group contains an aromatic ring.
Card 11
Question
Glycine → polarity group in this deck’s convention?
Answer
Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.
Card 12
Question
Threonine side chain at pH 7 → polarity/charge group?
Answer
Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.
Card 13
Question
Glutamate side chain at pH 7 → acid/base group and predominant charge?
Answer
Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
Card 14
Question
Leucine side chain → polarity group?
Answer
Nonpolar. It is a branched hydrocarbon side chain.
Card 15
Question
Cysteine at pH 7 → group in this deck’s convention?
Answer
Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.
Card 16
Question
Arginine side chain at pH 7 → acid/base group and predominant charge?
Answer
Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.
Card 17
Question
Tryptophan → polarity group in this deck’s convention?
Answer
Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.
Card 18
Question
Proline → polarity group in this deck’s convention?
Answer
Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.
Card 19
Question
Asparagine side chain at pH 7 → polarity/charge group?
Answer
Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.
Card 20
Question
Isoleucine side chain → polarity group?
Answer
Nonpolar. It is a branched hydrocarbon side chain.
Card 21
Question
Histidine → acid/base family?
Answer
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.
Card 22
Question
Tyrosine at pH 7 → group in this deck’s convention?
Answer
Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.
Card 23
Question
Methionine side chain → polarity group?
Answer
Nonpolar overall. Its sulfur is part of a thioether, not a thiol.
Card 24
Question
Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?
Answer
Glycine. Its small R group also permits more backbone conformations than most residues.
Card 25
Question
Which two standard amino acids have side-chain amide groups?
Answer
Asparagine and glutamine. Their amides are polar and uncharged at pH 7.
Card 26
Question
For a single ionizable side-chain group, what does pH below its pKa favor?
Answer
The protonated form. Whether that form is neutral or positive depends on the group.
Card 27
Question
Which two standard amino acids have aliphatic alcohol side chains?
Answer
Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.
Card 28
Question
Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?
Answer
Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.
Card 29
Question
Which three standard amino acids are conventionally called the branched-chain amino acids?
Answer
Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.
Card 30
Question
Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?
Answer
Aspartate and glutamate.
Card 31
Question
Which standard amino acid closes its side chain back onto the backbone nitrogen?
Answer
Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.
Card 32
Question
For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?
Answer
1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.
Card 33
Question
Which three standard amino acids form the usual ‘aromatic amino acids’ study group?
Answer
Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.
Card 34
Question
Cysteine versus methionine: which side chain can make the usual protein disulfide link?
Answer
Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.
Card 35
Question
For a single ionizable side-chain group, what does pH above its pKa favor?
Answer
The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.
Card 36
Question
At pH 7, why is aspartate usually charged while asparagine is uncharged?
Answer
Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.
Card 37
Question
Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?
Answer
Histidine. Its protonation depends on pH and its local pKa.
Card 38
Question
Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?
Answer
Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.
Card 39
Question
Glycine versus proline: which generally allows more backbone conformations?
Answer
Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.
Card 40
Question
Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?
Answer
Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.
Card 41
Question
Must every nonpolar side chain lie inside a water-soluble globular protein?
Answer
No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.
Card 42
Question
Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?
Answer
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.
Card 43
Question
Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?
Answer
Neutral thiol. pH is below pKa, so the protonated S–H form predominates.
Card 44
Question
At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?
Answer
Glutamate. Glutamine’s side-chain amide is neutral.
Card 45
Question
Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?
Answer
Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.
Card 46
Question
Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?
Answer
+1. pH is below pKa, favoring the protonated amino group.
Card 47
Question
Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?
Answer
−1. pH is above pKa, favoring the deprotonated carboxylate.
Card 48
Question
Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?
Answer
No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.
Card 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?
Answer
No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.
Card 50
Question
Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?
Answer
No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.
Card 51
Question
Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?
Answer
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.
Card 52
Question
At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?
Answer
No. The two forms occur in equal proportions, giving an ensemble-average charge of +0.5. Each form still has charge 0 or +1.
Card 53
Question
Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?
Answer
−1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.
Card 54
Question
At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?
Answer
Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.
Card 55
Question
A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?
Answer
The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.
Card 56
Question
Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?
Answer
Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.
56 cards
Amino Acid Side-Chain Properties Flashcards: Polarity & Charge
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