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