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