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.
بطاقات هذه الرزمة
البطاقة ١
السؤال
When a card asks for an amino acid’s side-chain charge, which charges should you leave out?
الإجابة
The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.
البطاقة ٢
السؤال
Can an uncharged amino-acid side chain still be polar?
الإجابة
Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.
البطاقة ٣
السؤال
Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?
الإجابة
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.
البطاقة ٤
السؤال
Alanine side chain → polarity group?
الإجابة
Nonpolar. Its methyl group has no polar functional group.
البطاقة ٥
السؤال
Serine side chain at pH 7 → polarity/charge group?
الإجابة
Polar, predominantly uncharged. It contains a hydroxyl group.
البطاقة ٦
السؤال
Aspartate side chain at pH 7 → acid/base group and predominant charge?
الإجابة
Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
البطاقة ٧
السؤال
Valine side chain → polarity group?
الإجابة
Nonpolar. It is a branched hydrocarbon side chain.
البطاقة ٨
السؤال
Glutamine side chain at pH 7 → polarity/charge group?
الإجابة
Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.
البطاقة ٩
السؤال
Lysine side chain at pH 7 → acid/base group and predominant charge?
الإجابة
Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.
البطاقة ١٠
السؤال
Phenylalanine side chain → polarity group?
الإجابة
Nonpolar. Its benzyl group contains an aromatic ring.
البطاقة ١١
السؤال
Glycine → polarity group in this deck’s convention?
الإجابة
Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.
البطاقة ١٢
السؤال
Threonine side chain at pH 7 → polarity/charge group?
الإجابة
Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.
البطاقة ١٣
السؤال
Glutamate side chain at pH 7 → acid/base group and predominant charge?
الإجابة
Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.
البطاقة ١٤
السؤال
Leucine side chain → polarity group?
الإجابة
Nonpolar. It is a branched hydrocarbon side chain.
البطاقة ١٥
السؤال
Cysteine at pH 7 → group in this deck’s convention?
الإجابة
Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.
البطاقة ١٦
السؤال
Arginine side chain at pH 7 → acid/base group and predominant charge?
الإجابة
Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.
البطاقة ١٧
السؤال
Tryptophan → polarity group in this deck’s convention?
الإجابة
Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.
البطاقة ١٨
السؤال
Proline → polarity group in this deck’s convention?
الإجابة
Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.
البطاقة ١٩
السؤال
Asparagine side chain at pH 7 → polarity/charge group?
الإجابة
Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.
البطاقة ٢٠
السؤال
Isoleucine side chain → polarity group?
الإجابة
Nonpolar. It is a branched hydrocarbon side chain.
البطاقة ٢١
السؤال
Histidine → acid/base family?
الإجابة
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.
البطاقة ٢٢
السؤال
Tyrosine at pH 7 → group in this deck’s convention?
الإجابة
Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.
البطاقة ٢٣
السؤال
Methionine side chain → polarity group?
الإجابة
Nonpolar overall. Its sulfur is part of a thioether, not a thiol.
البطاقة ٢٤
السؤال
Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?
الإجابة
Glycine. Its small R group also permits more backbone conformations than most residues.
البطاقة ٢٥
السؤال
Which two standard amino acids have side-chain amide groups?
الإجابة
Asparagine and glutamine. Their amides are polar and uncharged at pH 7.
البطاقة ٢٦
السؤال
For a single ionizable side-chain group, what does pH below its pKa favor?
الإجابة
The protonated form. Whether that form is neutral or positive depends on the group.
البطاقة ٢٧
السؤال
Which two standard amino acids have aliphatic alcohol side chains?
الإجابة
Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.
البطاقة ٢٨
السؤال
Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?
الإجابة
Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.
البطاقة ٢٩
السؤال
Which three standard amino acids are conventionally called the branched-chain amino acids?
الإجابة
Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.
البطاقة ٣٠
السؤال
Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?
الإجابة
Aspartate and glutamate.
البطاقة ٣١
السؤال
Which standard amino acid closes its side chain back onto the backbone nitrogen?
الإجابة
Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.
البطاقة ٣٢
السؤال
For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?
الإجابة
1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.
البطاقة ٣٣
السؤال
Which three standard amino acids form the usual ‘aromatic amino acids’ study group?
الإجابة
Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.
البطاقة ٣٤
السؤال
Cysteine versus methionine: which side chain can make the usual protein disulfide link?
الإجابة
Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.
البطاقة ٣٥
السؤال
For a single ionizable side-chain group, what does pH above its pKa favor?
الإجابة
The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.
البطاقة ٣٦
السؤال
At pH 7, why is aspartate usually charged while asparagine is uncharged?
الإجابة
Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.
البطاقة ٣٧
السؤال
Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?
الإجابة
Histidine. Its protonation depends on pH and its local pKa.
البطاقة ٣٨
السؤال
Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?
الإجابة
Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.
البطاقة ٣٩
السؤال
Glycine versus proline: which generally allows more backbone conformations?
الإجابة
Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.
البطاقة ٤٠
السؤال
Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?
الإجابة
Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.
البطاقة ٤١
السؤال
Must every nonpolar side chain lie inside a water-soluble globular protein?
الإجابة
No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.
البطاقة ٤٢
السؤال
Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?
الإجابة
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.
البطاقة ٤٣
السؤال
Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?
الإجابة
Neutral thiol. pH is below pKa, so the protonated S–H form predominates.
البطاقة ٤٤
السؤال
At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?
الإجابة
Glutamate. Glutamine’s side-chain amide is neutral.
البطاقة ٤٥
السؤال
Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?
الإجابة
Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.
البطاقة ٤٦
السؤال
Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?
الإجابة
+1. pH is below pKa, favoring the protonated amino group.
البطاقة ٤٧
السؤال
Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?
الإجابة
−1. pH is above pKa, favoring the deprotonated carboxylate.
البطاقة ٤٨
السؤال
Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?
الإجابة
No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.
البطاقة ٤٩
السؤال
With a histidine side-chain pKa of 6.0, does the label ‘basic amino acid’ imply a predominantly +1 side chain at pH 7?
الإجابة
No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.
البطاقة ٥٠
السؤال
Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?
الإجابة
No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.
البطاقة ٥١
السؤال
Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?
الإجابة
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.
البطاقة ٥٢
السؤال
At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?
الإجابة
No. The two forms occur in equal proportions, giving an ensemble-average charge of +0.5. Each form still has charge 0 or +1.
البطاقة ٥٣
السؤال
Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?
الإجابة
−1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.
البطاقة ٥٤
السؤال
At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?
الإجابة
Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.
البطاقة ٥٥
السؤال
A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?
الإجابة
The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.
البطاقة ٥٦
السؤال
Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?
الإجابة
Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.
٥٦ بطاقة
Amino Acid Side-Chain Properties Flashcards: Polarity & Charge
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