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Understanding how dipeptides are formed begins with the concept of peptide bond formation. A peptide bond is a covalent bond that links two amino acids together within a protein or peptide molecule. This bond is formed during a dehydration synthesis reaction, where the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another, releasing a molecule of water (H2O) in the process. The resultant bond is a stable linkage known in chemistry as an amide bond.

Peptide bonds are strong and durable, providing stability to the overall structure of proteins and peptides. However, they also allow for some flexibility, which is crucial for the protein's functional conformation. The formation of a peptide bond is an example of biochemical condensation reactions that are central to life processes. Importantly, the creation of these bonds during protein synthesis is catalyzed by ribosomes in the cell, ensuring that proteins are built quickly and accurately.

Moving to the amino acid sequence, it's essential to understand that a dipeptide consists of just two amino acids, and hence their sequence plays a crucial role in defining their characteristics. Each amino acid within a peptide or protein is like a bead on a string, where the string is the peptide bond holding them together. The order in which these 'beads' are arranged dictates the dipeptide's identity and can significantly influence its behavior and interaction with other molecules.

In the context of the exercise, the sequence distinction between Ala-Phe and Phe-Ala is what makes these two dipeptides distinct. Even with only two amino acids present, the order is enough to confer different properties on each molecule. For larger protein structures, the sequence of amino acids (known as the primary structure of a protein) is even more critical, as it ultimately determines how the protein will fold into its unique three-dimensional shape necessary for its specific function.

Lastly, the concept of protein structure is intricately linked to the peptide bond and amino acid sequence. Proteins have four levels of structure: primary, secondary, tertiary, and quaternary. The primary structure is simply the linear sequence of amino acids, just like the ones we have discussed in dipeptides. The secondary structure refers to local folded structures that form within a protein due to hydrogen bonding between the backbone constituents of amino acids. These structures include alpha helices and beta sheets.

The tertiary structure of a protein is its overall three-dimensional shape, built upon the patterns of its secondary structures, and strongly influenced by interactions among the side chains of the amino acids. Finally, the quaternary structure applies when a protein is made up of more than one polypeptide chain, describing how these multiple subunits arrange themselves in space.

Going back to dipeptides, although they don't exhibit secondary, tertiary, or quaternary structures due to their small size, understanding that they build the primary structure of proteins helps appreciate their role. Each dipeptide might represent a tiny piece of a much larger and complex protein puzzle, with every bond and sequence contributing to the big picture of biological function.