Concept:
Proteins are polymers of amino acids joined by peptide bonds. Most protein amino acids are alpha amino acids.
Step 1: Check Assertion (A).
Proteins are made up of alpha amino acids.
\[
A \text{ is correct}
\]
Step 2: Check Reason (R).
During denaturation, the secondary and tertiary structures are destroyed, but the primary structure generally remains intact.
\[
R \text{ is correct}
\]
Step 3: Check explanation.
The reason talks about denaturation, while the assertion talks about the basic building blocks of proteins. Therefore, Reason does not explain Assertion.
\[
\therefore \text{Correct Answer is (B)}
\]