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