Amino Acids and Proteins

Proteins are very abundant in living systems and are very diverse in functionality. They may serve as enzymes. They may serve in transport and storage, or they may be structural, regulatory, or protective proteins. Each protein has a unique function, and like their diverse functionality, proteins have a variety of structures. All proteins, however, consist of a long chain of amino acids linked by peptide bonds. An amino acid is an organic molecule that contains a carboxyl group (${-}{\rm{COOH}}$), an amino group (${-}{\rm{NH}}_2$), and a functional (R) chain, which is a group of atoms unique in its structure and function. All proteins are made up of different combinations of the same 20 amino acids. The amino group of one amino acid bonds with the carboxyl group of another amino acid. As with other molecules, they form through a condensation reaction. Two amino acids linked together are known as a dipeptide, and three or more amino acids linked together are known as a polypeptide. The overall shape of a protein can be either fibrous or globular. Fibrous proteins have polypeptide chains that are arranged as strands or sheets, and globular proteins have polypeptide chains that are folded into compact, rounded shapes. A protein's function is completely dependent on its structure, so when describing proteins, it is important to discuss the many structural levels of proteins. The primary structure of proteins is the specific sequence of amino acids. This sequence is unique for each protein. A protein's primary structure influences the protein's overall shape in two main ways. It allows hydrogen bonds to form between different amino acids along the length of the chain, referred to as a protein's secondary structure. This structure is determined by hydrogen bonding between amino and carboxyl groups of different amino acids, excluding the R groups. These bonds give rise to either a coiled (helical) or extended, pleated sheet pattern. The protein's primary structure also puts R groups in positions that allow them to interact with one another. This unique three-dimensional structure is referred to as a protein's tertiary structure, which includes the interaction of R groups with other R groups. Some proteins do not work alone and are instead identified as small protein subunits called polypeptides that are held together by weak chemical bonds and disulfide bridges to create a quaternary protein structure. An example is hemoglobin. Hemoglobin is actually made up of four individual polypeptides bonded together to perform the task of binding to oxygen atoms in blood. Proteins can also bond to other organic compounds to perform specific functions. Lipoproteins are proteins that are combined with cholesterol, triglycerides, and phospholipids. Glycoproteins are proteins that are combined with saccharides. Since each protein's structure is so specific and its function is dependent upon its structure, any change to that structure will alter the protein's ability to function. Denaturation is a process where the molecular structure of a protein is modified in such a way that hydrogen bonds are broken, causing proteins to lose their higher-ordered, three-dimensional structure. That is, proteins lose their structure in their natural or native state, returning to a structure that consists of a string of amino acids. The denatured proteins are classified as nonfunctional. Typically, environmental exposures such as changes in temperature or pH and the presence of chemicals such as strong acids or bases can create denatured proteins. For example, consider the effects of denaturation on hemoglobin. As blood, which contains hemoglobin, is heated, this external stressor causes the protein to lose its native quaternary structure, creating a protein molecule that no longer possesses an oxygen-carrying ability. Certain denaturation processes, such as with hemoglobin, are reversible. However, there are other denaturation processes that are irreversible, which is applicable to the albumin protein in an egg. As an egg is cooked, the clear, liquid egg white becomes an opaque white solid.