Amino acids are connected by peptide bonds, which are formed through a dehydration synthesis reaction. During this process, the carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water and forming a covalent bond. This linkage creates a chain of amino acids, known as a polypeptide, which folds into specific shapes to form proteins. The sequence and structure of amino acids determine the protein's function and characteristics.