Let's analyze each statement regarding the optical activity and stereochemistry of amino acids derived from natural proteins.

Amino Acids Stereochemistry

Amino acids, except glycine, are chiral molecules containing a stereogenic center (chiral carbon) at the alpha-carbon. This chirality leads to optical activity and the possibility of different stereoisomers (D and L isomers).

Statement Analysis:

Statement A: All alpha-amino acids have the D stereochemical configuration.

This statement is incorrect. Natural proteins are primarily composed of L-alpha-amino acids. The D-amino acids are found in some peptides, cell walls of bacteria, and antibiotics, but are not the standard building blocks of proteins synthesized by ribosomes.

Statement B: All L-amino acids have the (S) absolute configuration except cysteine, which has the (R) absolute configuration.

This statement is generally correct. The L/D designation is based on the configuration relative to glyceraldehyde. The R/S designation is based on the Cahn-Ingold-Prelog priority rules applied to the groups around the chiral center. For most L-amino acids, following the priority rules (NH\(_2\) > COOH > R group > H), the configuration at the alpha-carbon is (S). However, in cysteine, the priority order is NH\(_2\) > CH\(_2\)SH > COOH > H. When determining the R/S configuration, if the lowest priority group (H) is pointing away, you trace from priority 1 to 2 to 3. For cysteine, this tracing goes clockwise, resulting in an (R) configuration, even though it is an L-amino acid. Thus, L-cysteine has the (R) absolute configuration.

Statement C: All D-amino acids have the (S) absolute configuration except cysteine, which has the (R) stereochemical configuration.

This statement is incorrect. D-amino acids generally have the (R) absolute configuration (except for D-cysteine, which would be (S)). The statement incorrectly mixes absolute (R/S) and stereochemical (D/L) configuration systems and incorrectly assigns (S) to D-amino acids in general.

Statement D: In the absolute configuration system, L-threonine and L-isoleucine are (2S, 3R)-threonine and (2S, 3S)-isoleucine diastereomers, respectively.

This statement is correct. Threonine and isoleucine are amino acids with two chiral centers (at the alpha-carbon, C2, and on the side chain, C3). For L-threonine, the configuration at C2 is (S) and at C3 is (R), making it (2S, 3R)-threonine. For L-isoleucine, the configuration at C2 is (S) and at C3 is (S), making it (2S, 3S)-isoleucine. Diastereomers are stereoisomers that are not mirror images of each other. Since L-threonine and L-isoleucine have different configurations at C3 while sharing the same configuration at C2, they are diastereomers.

Correct Statements Combination

Based on the analysis:

• Statement A is incorrect.
• Statement B is correct.
• Statement C is incorrect.
• Statement D is correct.

Therefore, the combination of all correct statements is B and D.