Denaturation of a protein involves the breakdown of noncovalent bonds between amino acid residues. The formation of noncovalent bonds, such as hydrogen bonding and van der Waals forces, lead to higher order structures such as secondary, tertiary, and quaternary structure. Upon denaturation these noncovalent bonds in the protein chain are broken and the protein reverts back to its primary structure. The primary structure of a protein consists of the amino acid sequence joined together by peptide bonds (covalent bond). Covalent bonds are much stronger and more permanent that hydrogen bonds and other intermolecular forces, and can endure denaturation. Environmental conditions such as temperature and pH contribute to denaturation of a protein.

Recall that all amino acids have a carboxylic acid, amino group, hydrogen, and a functional group attached to their central carbon. In nonpolar amino acids the functional group will not contain any groups capable of protonation or deprotonation. The changes due to the pH in a nonpolar amino acid will only involve the amino and carboxylic acid groups.

A solution with pH of 13 is very basic. The carboxylic acid will be deprotonated and the amine will be intact (neither protonated nor deprotonated). The deprotonated carboxylic acid will give an overall charge of  to the molecule.

Hydrolysis reactions involve breakdown of molecules (lysis) in the presence of water. Water is a reactant in hydrolysis reactions. Dehydration synthesis reactions involve formation of bonds between molecules (synthesis) and removal of water at the end of the reaction (dehydration). Water is a product in dehydration synthesis reactions.

During the formation of peptide bonds a hydroxyl group from carboxylic acid and a hydrogen atom from the amino group are released and form water. Formation of peptide bonds is a dehydration synthesis reaction because bonds are synthesized and water is released.

Formation and destruction of bonds within macromolecules always involve a hydrolysis or a dehydration synthesis reaction. Esterification and hydrogenation reaction refer to other organic chemistry processes.

Proteins are made up of amino acids that undergo a series of dehydration reactions, which link them together to form the primary structure of a protein. Amino acids are linked together by peptide bonds, while nucleic acids are linked via phosphodiester bonds. The secondary structure of the protein is formed by hydrogen bonding between the amino acid backbones. Every protein will have primary and secondary structure, and thus will have hydrogen bonding.

Disulfide bridges help to construct tertiary structure, but only occur between cysteine residues. Cysteine will not necessarily be present in every protein, and there are some proteins that cannot form disulfide bridges. Similarly, not all proteins will contain glycine.

Aldehyde groups are frequently found in carbohydrates, but do not often appear in proteins.

Whenever you think about disulfide bonds you should think about cysteine. Cysteine contains a sulfur atom in a sulfhydryl group that is capable of forming a disulfide bridge with another sulfur atom in another cysteine residue. These disulfide bridges contribute to the overall three-dimensional structure of the protein, namely the tertiary structure).

Quaternary structure results from the joining of multiple polypeptide subunits and is driven by hydrophobic interactions. Tertiary structure is also driven by hydrophobic interactions, but also relies on intermolecular forces between amino acid function groups, such as the cysteine sulfhydryl.

To block a receptor protein, a molecule must structurally resemble the natural ligand. The active sites of proteins are highly specific, and will only bind certain molecules. The chemical formula, electrons, and bonding in the molecule can all influence small regions of the molecule's structure, but the overall shape must ultimately match the active site of the target protein.

Though proteins may be found on the cellular membrane, they are not a primary component. The cell membrane is known as the "phospholipid bilayer," as it is primarily composed of a double layer of lipids. Proteins may be attached to the surface or fully integrated into the bilayer, and serve as a means of signaling, transport, and adhesion.

Proteins are a primary component of the endocrine system, and several signaling hormones are made of peptides. The proteins action and myosin are directly involved in muscle contraction and for the structural basis of the sarcomere. Enzymes are a special class of catalytic proteins. Chaperone proteins and ion channels help transport molecules through the body; many nonpolar molecules must bind to a protein to travel through the blood.

An enzyme lowers the energy of the transition state, which makes the chemical reaction proceed faster. Enzymes speed up many chemical reactions in processes like DNA synthesis and glycolysis. They are also proteins, so they're composed of amino acids.

Polypeptides are are polymers of amino acids. Proteins consist of one or more polypeptide chains folded in a certain shape. Polysaccharides are polymers of monosaccharides and do not contain amino acids. Cellulose is a polysaccharide that is a major component of plant cell walls.

The amino acid sequence is the primary structure of a protein, which is held together by peptide bonds. The secondary structure involves hydrogen bonding between the backbones of amino acids. Tertiary structure describes the unique folding pattern of a polypeptide as a result of intermolecular forces such as hydrogen bonds, hydrophobic interactions and covalent bonds such as disulfide bridges. Tertiary structure is the result of the amino acid side chains interacting with each other. Quaternary structure is the interaction of two or more polypeptide chains with each other.