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.
การ์ดในเด็คนี้
การ์ด 1
คำถาม
When a card asks for an amino acid’s side-chain charge, which charges should you leave out?
คำตอบ
The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.
การ์ด 2
คำถาม
Can an uncharged amino-acid side chain still be polar?
คำตอบ
Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.
การ์ด 3
คำถาม
Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?
คำตอบ
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.
การ์ด 4
คำถาม
Alanine side chain → polarity group?
คำตอบ
Nonpolar. Its methyl group has no polar functional group.
การ์ด 5
คำถาม
Serine side chain at pH 7 → polarity/charge group?
คำตอบ
Polar, predominantly uncharged. It contains a hydroxyl group.
การ์ด 6
คำถาม
Aspartate side chain at pH 7 → acid/base group and predominant charge?
คำตอบ
Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
การ์ด 7
คำถาม
Valine side chain → polarity group?
คำตอบ
Nonpolar. It is a branched hydrocarbon side chain.
การ์ด 8
คำถาม
Glutamine side chain at pH 7 → polarity/charge group?
คำตอบ
Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.
การ์ด 9
คำถาม
Lysine side chain at pH 7 → acid/base group and predominant charge?
คำตอบ
Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.
การ์ด 10
คำถาม
Phenylalanine side chain → polarity group?
คำตอบ
Nonpolar. Its benzyl group contains an aromatic ring.
การ์ด 11
คำถาม
Glycine → polarity group in this deck’s convention?
คำตอบ
Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.
การ์ด 12
คำถาม
Threonine side chain at pH 7 → polarity/charge group?
คำตอบ
Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.
การ์ด 13
คำถาม
Glutamate side chain at pH 7 → acid/base group and predominant charge?
คำตอบ
Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
การ์ด 14
คำถาม
Leucine side chain → polarity group?
คำตอบ
Nonpolar. It is a branched hydrocarbon side chain.
การ์ด 15
คำถาม
Cysteine at pH 7 → group in this deck’s convention?
คำตอบ
Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.
การ์ด 16
คำถาม
Arginine side chain at pH 7 → acid/base group and predominant charge?
คำตอบ
Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.
การ์ด 17
คำถาม
Tryptophan → polarity group in this deck’s convention?
คำตอบ
Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.
การ์ด 18
คำถาม
Proline → polarity group in this deck’s convention?
คำตอบ
Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.
การ์ด 19
คำถาม
Asparagine side chain at pH 7 → polarity/charge group?
คำตอบ
Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.
การ์ด 20
คำถาม
Isoleucine side chain → polarity group?
คำตอบ
Nonpolar. It is a branched hydrocarbon side chain.
การ์ด 21
คำถาม
Histidine → acid/base family?
คำตอบ
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.
การ์ด 22
คำถาม
Tyrosine at pH 7 → group in this deck’s convention?
คำตอบ
Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.
การ์ด 23
คำถาม
Methionine side chain → polarity group?
คำตอบ
Nonpolar overall. Its sulfur is part of a thioether, not a thiol.
การ์ด 24
คำถาม
Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?
คำตอบ
Glycine. Its small R group also permits more backbone conformations than most residues.
การ์ด 25
คำถาม
Which two standard amino acids have side-chain amide groups?
คำตอบ
Asparagine and glutamine. Their amides are polar and uncharged at pH 7.
การ์ด 26
คำถาม
For a single ionizable side-chain group, what does pH below its pKa favor?
คำตอบ
The protonated form. Whether that form is neutral or positive depends on the group.
การ์ด 27
คำถาม
Which two standard amino acids have aliphatic alcohol side chains?
คำตอบ
Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.
การ์ด 28
คำถาม
Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?
คำตอบ
Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.
การ์ด 29
คำถาม
Which three standard amino acids are conventionally called the branched-chain amino acids?
คำตอบ
Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.
การ์ด 30
คำถาม
Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?
คำตอบ
Aspartate and glutamate.
การ์ด 31
คำถาม
Which standard amino acid closes its side chain back onto the backbone nitrogen?
คำตอบ
Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.
การ์ด 32
คำถาม
For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?
คำตอบ
1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.
การ์ด 33
คำถาม
Which three standard amino acids form the usual ‘aromatic amino acids’ study group?
คำตอบ
Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.
การ์ด 34
คำถาม
Cysteine versus methionine: which side chain can make the usual protein disulfide link?
คำตอบ
Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.
การ์ด 35
คำถาม
For a single ionizable side-chain group, what does pH above its pKa favor?
คำตอบ
The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.
การ์ด 36
คำถาม
At pH 7, why is aspartate usually charged while asparagine is uncharged?
คำตอบ
Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.
การ์ด 37
คำถาม
Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?
คำตอบ
Histidine. Its protonation depends on pH and its local pKa.
การ์ด 38
คำถาม
Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?
คำตอบ
Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.
การ์ด 39
คำถาม
Glycine versus proline: which generally allows more backbone conformations?
คำตอบ
Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.
การ์ด 40
คำถาม
Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?
คำตอบ
Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.
การ์ด 41
คำถาม
Must every nonpolar side chain lie inside a water-soluble globular protein?
คำตอบ
No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.
การ์ด 42
คำถาม
Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?
คำตอบ
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.
การ์ด 43
คำถาม
Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?
คำตอบ
Neutral thiol. pH is below pKa, so the protonated S–H form predominates.
การ์ด 44
คำถาม
At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?
คำตอบ
Glutamate. Glutamine’s side-chain amide is neutral.
การ์ด 45
คำถาม
Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?
คำตอบ
Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.
การ์ด 46
คำถาม
Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?
คำตอบ
+1. pH is below pKa, favoring the protonated amino group.
การ์ด 47
คำถาม
Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?
คำตอบ
−1. pH is above pKa, favoring the deprotonated carboxylate.
การ์ด 48
คำถาม
Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?
คำตอบ
No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.
การ์ด 49
คำถาม
With a histidine side-chain pKa of 6.0, does the label ‘basic amino acid’ imply a predominantly +1 side chain at pH 7?
คำตอบ
No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.
การ์ด 50
คำถาม
Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?
คำตอบ
No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.
การ์ด 51
คำถาม
Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?
คำตอบ
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.
การ์ด 52
คำถาม
At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?
คำตอบ
No. The two forms occur in equal proportions, giving an ensemble-average charge of +0.5. Each form still has charge 0 or +1.
การ์ด 53
คำถาม
Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?
คำตอบ
−1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.
การ์ด 54
คำถาม
At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?
คำตอบ
Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.
การ์ด 55
คำถาม
A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?
คำตอบ
The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.
การ์ด 56
คำถาม
Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?
คำตอบ
Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.
56 การ์ด
Amino Acid Side-Chain Properties Flashcards: Polarity & Charge
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