The acid-base behavior of amino acids is an especially favorite MCAT topic. In neutral solution, typically the carboxyl groups are ionized to be negatively charged and amine groups are ionized to be positively charged.
In peptide bond formation, the amine group of one amino acid reacts with the carboxyl group of another in an acyl exchange mechanism, forming an amide linkage.
There will definitely be questions on the new MCAT which rely on you being able to identify the characteristics of a particular amino acid, such as knowing that valine is non-polar from memory or that lysine has a basic side-chain.
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