Final answer:
Protein structure is maintained primarily by hydrogen bonds and disulfide linkages, which are crucial for stabilizing different levels of protein folding.
Step-by-step explanation:
The two covalent bonds responsible for the maintenance of protein structure are hydrogen bonding and disulfide linkages. Hydrogen bonds form between highly electronegative atoms like oxygen or nitrogen and a hydrogen atom that is covalently bonded to another electronegative atom. These bonds are crucial for maintaining both the primary and secondary structures of proteins.
Disulfide linkages, on the other hand, occur when two cysteine amino acids come close together during protein folding and their sulfhydryl groups form a covalent bond, resulting in a cystine. This type of bond significantly stabilizes the protein's tertiary structure.