Amino Acid Side-Chain Properties Flashcards: Polarity & Charge

Question 1

When a card asks for an amino acid’s side-chain charge, which charges should you leave out?

Accepted Answer

The backbone amino and carboxyl groups, including peptide termini. Count only the R group’s charge.

Question 2

Can an uncharged amino-acid side chain still be polar?

Accepted Answer

Yes. Uneven electron distribution can make a group polar without giving it a net charge; a hydroxyl group is an example.

Question 3

Are ‘aromatic,’ ‘polar,’ and ‘basic’ mutually exclusive amino-acid labels?

Accepted Answer

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.

Question 4

Alanine side chain → polarity group?

Accepted Answer

Nonpolar. Its methyl group has no polar functional group.

Question 5

Serine side chain at pH 7 → polarity/charge group?

Accepted Answer

Polar, predominantly uncharged. It contains a hydroxyl group.

Question 6

Aspartate side chain at pH 7 → acid/base group and predominant charge?

Accepted Answer

Acidic; −1. The side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.

Question 7

Valine side chain → polarity group?

Accepted Answer

Nonpolar. It is a branched hydrocarbon side chain.

Question 8

Glutamine side chain at pH 7 → polarity/charge group?

Accepted Answer

Polar, uncharged. Its amide group does not behave like glutamate’s carboxylate.

Question 9

Lysine side chain at pH 7 → acid/base group and predominant charge?

Accepted Answer

Basic; +1. Its terminal side-chain amino group is predominantly protonated under the usual aqueous reference conditions.

Question 10

Phenylalanine side chain → polarity group?

Accepted Answer

Nonpolar. Its benzyl group contains an aromatic ring.

Question 11

Glycine → polarity group in this deck’s convention?

Accepted Answer

Nonpolar. Its R group is just hydrogen; the grouping does not imply a large hydrophobic side chain.

Question 12

Threonine side chain at pH 7 → polarity/charge group?

Accepted Answer

Polar, predominantly uncharged. Its hydroxyl group contributes polarity despite the methyl group beside it.

Question 13

Glutamate side chain at pH 7 → acid/base group and predominant charge?

Accepted Answer

Acidic; −1. Its side-chain carboxyl group is predominantly deprotonated under the usual aqueous reference conditions.

Question 14

Leucine side chain → polarity group?

Accepted Answer

Nonpolar. It is a branched hydrocarbon side chain.

Question 15

Cysteine at pH 7 → group in this deck’s convention?

Accepted Answer

Polar, predominantly uncharged. The side-chain thiol is usually mostly protonated. Cysteine can also behave hydrophobically, so classification schemes differ.

Question 16

Arginine side chain at pH 7 → acid/base group and predominant charge?

Accepted Answer

Basic; +1. The guanidinium group is predominantly protonated under the usual aqueous reference conditions.

Question 17

Tryptophan → polarity group in this deck’s convention?

Accepted Answer

Nonpolar overall, with a polar feature. Its large aromatic indole group is hydrophobic, but its N–H can donate a hydrogen bond.

Question 18

Proline → polarity group in this deck’s convention?

Accepted Answer

Nonpolar. Its side chain also closes a ring with the backbone nitrogen, restricting backbone motion.

Question 19

Asparagine side chain at pH 7 → polarity/charge group?

Accepted Answer

Polar, uncharged. Its amide group is distinct from aspartate’s carboxylate.

Question 20

Isoleucine side chain → polarity group?

Accepted Answer

Nonpolar. It is a branched hydrocarbon side chain.

Question 21

Histidine → acid/base family?

Accepted Answer

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.

Question 22

Tyrosine at pH 7 → group in this deck’s convention?

Accepted Answer

Polar, predominantly uncharged. Its phenolic hydroxyl adds polarity to an aromatic, partly hydrophobic side chain; other schemes group it with the aromatics.

Question 23

Methionine side chain → polarity group?

Accepted Answer

Nonpolar overall. Its sulfur is part of a thioether, not a thiol.

Question 24

Which standard amino acid has hydrogen as its R group and no chiral alpha carbon?

Accepted Answer

Glycine. Its small R group also permits more backbone conformations than most residues.

Question 25

Which two standard amino acids have side-chain amide groups?

Accepted Answer

Asparagine and glutamine. Their amides are polar and uncharged at pH 7.

Question 26

For a single ionizable side-chain group, what does pH below its pKa favor?

Accepted Answer

The protonated form. Whether that form is neutral or positive depends on the group.

Question 27

Which two standard amino acids have aliphatic alcohol side chains?

Accepted Answer

Serine and threonine. Tyrosine’s hydroxyl is phenolic, attached directly to an aromatic ring.

Question 28

Which standard amino acid supplies the side-chain sulfur atoms of a protein disulfide bond?

Accepted Answer

Cysteine. Oxidation of two cysteine thiols can produce a covalent S–S link.

Question 29

Which three standard amino acids are conventionally called the branched-chain amino acids?

Accepted Answer

Valine, leucine, and isoleucine. All three have nonpolar hydrocarbon side chains.

Question 30

Which two standard amino acids usually have negatively charged side-chain carboxylates at pH 7?

Accepted Answer

Aspartate and glutamate.

Question 31

Which standard amino acid closes its side chain back onto the backbone nitrogen?

Accepted Answer

Proline. The ring restricts backbone flexibility; an internal proline residue also lacks the usual peptide N–H donor.

Question 32

For a single ionizable side-chain group, what is the protonated:deprotonated ratio at pH = pKa?

Accepted Answer

1:1. Half is protonated and half is deprotonated in the simple two-state acid–base model.

Question 33

Which three standard amino acids form the usual ‘aromatic amino acids’ study group?

Accepted Answer

Phenylalanine, tyrosine, and tryptophan. Histidine’s imidazole is chemically aromatic too, but introductory grouping tables usually place histidine with the basic amino acids.

Question 34

Cysteine versus methionine: which side chain can make the usual protein disulfide link?

Accepted Answer

Cysteine. It has a thiol; methionine has a thioether and does not form this cysteine-type disulfide link.

Question 35

For a single ionizable side-chain group, what does pH above its pKa favor?

Accepted Answer

The deprotonated form. For a carboxyl group this is negative; for a protonated amine losing its proton, it is neutral.

Question 36

At pH 7, why is aspartate usually charged while asparagine is uncharged?

Accepted Answer

Aspartate has a side-chain carboxylate (−1); asparagine has a neutral amide. Similar names do not mean the same functional group.

Question 37

Which standard amino acid has an imidazole side chain that can switch between neutral and +1 forms?

Accepted Answer

Histidine. Its protonation depends on pH and its local pKa.

Question 38

Which standard amino acid combines a phenyl ring with a phenolic hydroxyl group?

Accepted Answer

Tyrosine. The hydroxyl makes this aromatic side chain more polar than phenylalanine’s.

Question 39

Glycine versus proline: which generally allows more backbone conformations?

Accepted Answer

Glycine. Its tiny R group imposes little steric restriction; proline’s ring constrains the backbone.

Question 40

Why can tryptophan donate a side-chain hydrogen bond despite being grouped as nonpolar overall?

Accepted Answer

Its indole N–H can donate a hydrogen bond. A large hydrophobic group can still contain a polar site.

Question 41

Must every nonpolar side chain lie inside a water-soluble globular protein?

Accepted Answer

No. Burial of nonpolar groups is a tendency, not a rule for every residue. Protein shape and local interactions also matter.

Question 42

Assume histidine’s side-chain pKa is 6.0. At pH 7.0, is its predominant side-chain charge 0 or +1?

Accepted Answer

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.

Question 43

Assume cysteine’s thiol pKa is 8.3. At pH 7.0, which form predominates: neutral thiol or negative thiolate?

Accepted Answer

Neutral thiol. pH is below pKa, so the protonated S–H form predominates.

Question 44

At pH 7, which has a predominantly −1 side chain: glutamate or glutamine?

Accepted Answer

Glutamate. Glutamine’s side-chain amide is neutral.

Question 45

Assume tyrosine’s phenolic pKa is 10.1. At pH 7.0, is its side chain predominantly neutral or negative?

Accepted Answer

Neutral. The phenolic hydroxyl is mostly protonated because pH is below pKa.

Question 46

Assume lysine’s side-chain pKa is 10.5. At pH 7.0, is its side chain predominantly neutral or +1?

Accepted Answer

+1. pH is below pKa, favoring the protonated amino group.

Question 47

Assume aspartate’s side-chain pKa is 3.9. At pH 7.0, is its side chain predominantly neutral or −1?

Accepted Answer

−1. pH is above pKa, favoring the deprotonated carboxylate.

Question 48

Can a standard aqueous pKa value determine a buried protein side chain’s charge with certainty?

Accepted Answer

No. Nearby charges, solvent exposure, and other local interactions can shift pKa. Use a value appropriate to that site when it is known.

Question 49

With a histidine side-chain pKa of 6.0, does the label ‘basic amino acid’ imply a predominantly +1 side chain at pH 7?

Accepted Answer

No. ‘Basic’ describes proton-accepting chemistry; the predominant charge at a stated pH follows the pKa. Here the side chain is mostly neutral.

Question 50

Does a predominantly neutral tyrosine side chain at pH 7 make tyrosine nonpolar in this deck’s grouping?

Accepted Answer

No. Its hydroxyl is polar even when uncharged. This deck groups tyrosine as polar, uncharged and also recognizes its aromatic character.

Question 51

Does an internal proline residue have the same backbone N–H hydrogen-bond donor as most peptide residues?

Accepted Answer

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.

Question 52

At pH = pKa, a side chain switches between 0 and +1. Is each individual side chain charged +0.5?

Accepted Answer

No. The two forms occur in equal proportions, giving an ensemble-average charge of +0.5. Each form still has charge 0 or +1.

Question 53

Assume cysteine’s thiol pKa is 8.3. At pH 9.3, what is its predominant side-chain charge?

Accepted Answer

−1. Deprotonated thiolate predominates; the thiolate:thiol ratio is 10:1 in the simple model.

Question 54

At pH 7, which pair is a plausible side-chain salt bridge: lysine–glutamate or leucine–valine?

Accepted Answer

Lysine–glutamate: their usual side-chain charges are +1 and −1. A salt bridge still requires suitable proximity and environment.

Question 55

A histidine site has a measured side-chain pKa of 8.0. At pH 7.0, which side-chain form predominates?

Accepted Answer

The protonated +1 form. pH is below this site’s pKa; use the supplied local value rather than a generic histidine value.

Question 56

Phenylalanine versus tyrosine: which has the side-chain hydroxyl that adds polarity?

Accepted Answer

Tyrosine. Phenylalanine lacks that hydroxyl; both contain an aromatic ring.

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Amino Acid Side-Chain Properties Flashcards: Polarity & Charge