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