Amino Acids Structural Features and Ionizable Groups

Practice flashcards covering amino acid classifications, structural features, symbols, pKa values, imino acids, and ionizable groups in proteins.

At what pH is the ionization status of amino acids presented in the structural feature tables?

The ionization status is shown at physiologic pH ($7.4$).

What are the three-letter symbol, one-letter symbol, and $pK_a$ values for Glycine?

Glycine symbol: Gly [G], with $pK_1 (\text{a-COOH}) = 2.4$ and $pK_2 (\text{a-NH}_3^+) = 9.8$.

What are the symbols and $pK_a$ values for Alanine?

Alanine symbol: Ala [A], with $pK_1 (\text{a-COOH}) = 2.4$ and $pK_2 (\text{a-NH}_3^+) = 9.9$.

What are the symbols and $pK_a$ values for Valine?

Valine symbol: Val [V], with $pK_1 (\text{a-COOH}) = 2.2$ and $pK_2 (\text{a-NH}_3^+) = 9.7$.

Which amino acids belong to Category 1 (aliphatic side chains)?

Glycine, Alanine, Valine, Leucine, and Isoleucine.

What are the symbols and $pK_a$ values for Leucine and Isoleucine?

Leucine: Leu [L], $pK_1 = 2.3$, $pK_2 = 9.7$. Isoleucine: Ile [I], $pK_1 = 2.3$, $pK_2 = 9.8$.

Which amino acids belong to Category 2 (side chains containing hydroxylic groups)?

Serine, Threonine, and Tyrosine.

What are the $pK_1$, $pK_2$, and R Group $pK_3$ values for Serine and Threonine?

Serine: Ser [S], $pK_1 = 2.2$, $pK_2 = 9.2$, $pK_3 = \text{about } 13$. Threonine: Thr [T], $pK_1 = 2.1$, $pK_2 = 9.1$, $pK_3 = \text{about } 13$.

What are the symbols and $pK_a$ values for Tyrosine?

Tyrosine symbol: Tyr [Y], with $pK_1 = 2.2$, $pK_2 = 9.1$, and R Group $pK_3 = 10.1$.

In addition to Category 2 (hydroxylic groups), which category does Tyrosine also belong to?

Category 6 (amino acids with side chains containing aromatic rings).

Which amino acids belong to Category 3 (side chains containing sulfur atoms)?

Cysteine and Methionine.

What are the $pK_a$ values for Cysteine and Methionine?

Cysteine: Cys [C], $pK_1 = 1.9$, $pK_2 = 10.8$, $pK_3 = 8.3$. Methionine: Met [M], $pK_1 = 2.1$, $pK_2 = 9.3$ (no R group $pK_3$).

Which amino acids belong to Category 4 (side chains containing acidic groups or their amides)?

Aspartic acid, Asparagine, Glutamic acid, and Glutamine.

What are the R Group $pK_3$ values for Aspartic acid and Glutamic acid?

Aspartic acid (Asp [D]): $pK_3 = 3.9$. Glutamic acid (Glu [E]): $pK_3 = 4.1$.

Why do Asparagine and Glutamine not have an R Group $pK_3$ value listed?

Because their amide side chains are not ionizable.

What are the symbols and $pK_a$ values for Asparagine and Glutamine?

Asparagine: Asn [N], $pK_1 = 2.1$, $pK_2 = 8.8$. Glutamine: Gln [Q], $pK_1 = 2.2$, $pK_2 = 9.1$.

Which amino acids belong to Category 5 (side chains containing basic groups)?

Arginine, Lysine, and Histidine.

What are the symbols and R Group $pK_3$ values for Arginine, Lysine, and Histidine?

Arginine: Arg [R], $pK_3 = 12.5$. Lysine: Lys [K], $pK_3 = 10.8$. Histidine: His [H], $pK_3 = 6.0$.

Which amino acids belong to Category 6 (side chains containing aromatic rings)?

Histidine, Phenylalanine, Tyrosine, and Tryptophan.

What are the symbols and $pK_a$ values for Phenylalanine and Tryptophan?

Phenylalanine: Phe [F], $pK_1 = 2.2$, $pK_2 = 9.2$. Tryptophan: Trp [W], $pK_1 = 2.4$, $pK_2 = 9.4$.

Why is Proline categorized as an imino acid?

Its side chain forms a cyclic structure that covalently bonds back to the nitrogen of its amino group, creating a secondary amine.

What are the symbol and $pK_a$ values for Proline?

Symbol: Pro [P], with $pK_1 (\text{a-COOH}) = 2.0$ and $pK_2 (\text{a-NH}_3^+) = 10.6$.

Why do the $pK_a$ values of free amino acids only approximate their $pK_a$ values in proteins?

Functional groups and the local environment surrounding the ionizable group in proteins affect its $pK_a$, making relatively large variations from solution $pK_a$ common.

According to the summary table of ionizable groups in proteins, what are the $pK_a$ ranges for Aspartic Acid/Aspartate and Glutamic Acid/Glutamate?

Aspartic Acid/Aspartate (Asp, D): $pK_a = 3.9\text{-}4.0$. Glutamic Acid/Glutamate (Glu, E): $pK_a = 4.0\text{-}4.5$.

According to the summary table, what are the $pK_a$ values for Histidine, Cysteine, and Tyrosine in proteins?

Histidine (His, H): $pK_a = 6.0\text{-}7.0$. Cysteine (Cys, C): $pK_a = 8.0\text{-}9.0$. Tyrosine (Tyr, Y): $pK_a = 10.0\text{-}10.3$.

According to the summary table, what are the $pK_a$ values for Lysine, Arginine, and Serine in proteins?

Lysine (Lys, K): $pK_a = 10.4\text{-}11.1$. Arginine (Arg, R): $pK_a = 12.5$. Serine (Ser, S): $pK_a = 13.0$.

What are the $pK_a$ values for the N-terminus and C-terminus in proteins?

N-terminus: $pK_a = 9.6$. C-terminus: $pK_a = 2.5$.

At physiologic pH ($7.4$), which ionizable groups predominate in their deprotonated conjugate base form in proteins?

Aspartic Acid/Aspartate, Glutamic Acid/Glutamate, Histidine, and the C-terminus.

At physiologic pH ($7.4$), which ionizable groups predominate in their protonated acid form in proteins?

Cysteine, Tyrosine, Lysine, Arginine, Serine, and the N-terminus.

What information does this summary table provide about ionizable groups in proteins?

It lists the acid form, conjugate base form, and $pK_a$ values for amino acid side chains and terminal groups in proteins, indicating which form predominates at physiologic pH ($7.4$).