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