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