Biochemistry

Amino Acids, Proteins, and Enzymes

Proteins are formed from a sequence of amino acids linked by peptide bonds.

Proteins are important to a vast array of functions in living things, from catalyzing reactions to providing structure and conveying messages within the body. They are absolutely vital to life and are produced by transcription and translation of DNA and RNA.

Proteins are made up of long, polymerized chains of amino acids. An amino acid is a protein-building molecule that contains an amino group (NH2{{-}\rm{NH_2}}), a carboxyl group (COOH{{-}\rm{COOH}}), and between them a carbon atom attached to a side chain. The side chain, known as "the R group," gives the amino acid its identity and contributes to its structure and function of the protein.

Amino Acid Structure

An amino acid consists of an amino group, a carboxyl group, and an R group. The R group may have a variety of characteristics that will ultimately contribute to the structure and function of the resulting protein.
There are 20 different amino acids used in the synthesis of proteins. Some have polar side chains that will form hydrogen bonds in water, and others have nonpolar side chains. In addition, some side chains are positively charged, some negatively charged, and some are neutral.

Amino acids are joined together by peptide bonds that result from a dehydration synthesis reaction. A peptide bond is a covalent amide (CONH{{-}\rm{CONH}{-}}) bond that forms between two adjacent amino acids along the same peptide chain. The bond forms between the amine (NH2{{-}\rm{NH_2}}) group, or amino group, of one amino acid and the carboxyl (COOH{{-}\rm{COOH}}) group of another. In forming the bond, the COOH{{-}\rm{COOH}} group loses a hydroxide ion (OH) while the amine group loses a hydrogen ion (H+), producing a molecule of water. The nitrogen atom of the amine group then bonds to the carbon atom of the COOH{{-}\rm{COOH}} group, creating a peptide bond. The process is repeated for every amino acid added to the chain.

Structure and Function of Amino Acids

Proteins can have four levels of structure, called primary, secondary, tertiary, and quaternary structure, and the function of a protein depends on its structure.

For all proteins, the shape of the molecule determines how it interacts with other molecules and therefore determines its function. There are four structural levels to a protein. A protein's primary structure is the sequence of amino acids linked by peptide (amide) bonds to form a polypeptide chain. Proteins tend to be large molecules, and each protein has its own unique primary structure. Many proteins are between 200 and 400 amino acids long but can have up to several thousand.

The secondary structure of a protein is the initial folding of the amino acid polymer that arises from hydrogen bonding between the amine and carboxyl groups of amino acids in neighboring parts of the chain. This secondary structure appears in two variations. One type of secondary structure is the alpha helix, a helical structure of proteins that adopts a right-handed-spiral conformation, where chain backbone NH{\rm{N}{-}\rm{H}} groups form hydrogen bonds with C=O{\rm{C}{=}\rm{O}} groups of nearby amino acids along the protein chain. Hydrogen bonds form between the amine group of one amino acid and the carboxyl group of the amino acid four spaces past it on the same chain. The second variation of a protein's secondary structure is a beta pleated sheet, a structure of amino acids that takes the shape of a pleated sheet folded at regular intervals. The shape is held in place by hydrogen bonds that form between adjacent amino acids on different chains. To picture secondary structures, it's important to remember that proteins (and all molecules) exist as three-dimensional structures in space, even though they are commonly represented as two-dimensional structures on paper. A protein may have a secondary shape that is entirely composed of one of these structures or a mixture of both.

Levels of Protein Structure

A protein can be defined by four levels of structure: the sequence of amino acids, the inclusion of beta sheets or alpha helices, the attraction between beta sheets and alpha helices, and the number of amino acid chains.
The tertiary structure of a protein is produced by interactions between the R groups of the amino acids in the chain and with the environment around them. The portions of the chain with polar R groups are located on the outside of the structure, facing the polar, aqueous environment. Nonpolar side chains are located near the inside of the protein. For example, amino acids with opposing charges that wind up near each other may form ionic bonds. In addition, the sulfur atoms in cysteine, an amino acid with the structure HO2CCH(NH2)CH2SH, can form covalent bonds with one another through oxidation, forming disulfide bridges that play an important role in stabilizing the protein structure. Primary, secondary, and tertiary structures all occur within the same amino acid chain. However, many large proteins have a quaternary structure, which is two or more chains of proteins that interact with one another. In these proteins, each folded amino acid strand is called a subunit. The subunits may all be the same, or they may be different. They are held together by the same forces that stabilize the secondary and tertiary structures—hydrogen bonds and disulfide linkages.

Quaternary Structure of Hemoglobin

Hemoglobin is the iron complex that binds oxygen. The quaternary structure shows that hemoglobin is made of two identical copies of two different subunits, known as an α1\alpha_1 globin chain and an α2\alpha_2 globin chain. These proteins contain heme, a ringed molecule with an iron ion (Fe2+) in the center.

Enzymes

Enzymes are proteins that catalyze reactions in biological systems, and the structure of an enzyme is specific to the shape of the substrate molecule on which it acts.

Many important chemical reactions in the human body, such as extracting energy from food or copying DNA, would happen extremely slowly if it weren't for enzymes. Enzymes are proteins with precise shapes that allow them to catalyze biological reactions. Each reaction requires its own specific enzyme, and each enzyme has its own unique shape.

Each enzyme contains an area called the active site, which is the place on an enzyme where the substrate binds and the reaction occurs. A substrate is a molecule that is acted upon by an enzyme by binding to the enzyme's active site. The binding of the enzyme to the substrate can change the substrate in a number of ways, allowing it to carry out a function. The binding of the enzyme may pull the substrate apart, bring molecules close enough together to react, or affect the configuration of electrons on the substrate, altering its ability to bond with particular nearby molecules.

The function of an enzyme can be affected by factors that influence the hydrogen bonding or disulfide bridges, which are bonds between two sulfur atoms forming the general structure R1SSR2{\rm{R_1}{-}\rm{S}{-}\rm{S}{-}\rm{R_2}}, that stabilize the shape of the enzyme. These bonds are very sensitive to changes in temperature and pH. Enzymes in conditions other than their optimal temperature or pH may become denatured (structurally altered), losing their shape and therefore becoming unable to carry out their functions.