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