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