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