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