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