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Protein Structure

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Protein Structure
Protein Structure

Protein Structure

Credit: Mariana Ruiz Villarreal

Protein Structure

Proteins are biological polymers composed of amino acids. Amino acids, linked together by peptide bonds, form a polypeptide chain. One or more polypeptide chains twisted into a 3-D shape form a protein. Proteins have complex shapes that include various folds, loops, and curves. Folding in proteins happens spontaneously. Chemical bonding between portions of the polypeptide chain aid in holding the protein together and giving it its shape. There are two general classes of protein molecules: globular proteins and fibrous proteins. Globular proteins are generally compact, soluble, and spherical in shape. Fibrous proteins are typically elongated and insoluble. Globular and fibrous proteins may exhibit one or more of four types of protein structure. These structure types are called primary, secondary, tertiary, and quaternary structure.

Protein Structure Levels

The four levels of protein structure are distinguished from one another by the degree of complexity in the polypeptide chain. A single protein molecule may contain one or more of the protein structure types.
  • Primary Structure - describes the unique order in which amino acids are linked together to form a protein. Proteins are constructed from a set of 20 amino acids. Generally, amino acids have the following structural properties:

    • A carbon (the alpha carbon) bonded to the four groups below:


    • A hydrogen atom (H)
    • A Carboxyl group (-COOH)
    • An Amino group (-NH2)
    • A "variable" group or "R" group
    All amino acids have the alpha carbon bonded to a hydrogen atom, carboxyl group, and amino group. The "R" group varies among amino acids and determines the differences between these protein monomers. The amino acid sequence of a protein is determined by the information found in the cellular genetic code. The order of amino acids in a polypeptide chain is unique and specific to a particular protein. Altering a single amino acid causes a gene mutation, which most often results in a non-functioning protein.

  • Secondary Structure - refers to the coiling or folding of a polypeptide chain that gives the protein its 3-D shape. There are two types of secondary structures observed in proteins. One type is the alpha (α) helix structure. This structure resembles a coiled spring and is secured by hydrogen bonding in the polypeptide chain. The second type of secondary structure in proteins is the beta (β) pleated sheet. This structure appears to be folded or pleated and is held together by hydrogen bonding between polypeptide units of the folded chain that lie adjacent to one another.

  • Tertiary Structure - refers to the comprehensive 3-D structure of the polypeptide chain of a protein. There are several types of bonds and forces that hold a protein in its tertiary structure. Hydrophobic interactions greatly contribute to the folding and shaping of a protein. The "R" group of the amino acid is either hydrophobic or hydrophilic. The amino acids with hydrophilic "R" groups will seek contact with their aqueous environment, while amino acids with hydrophobic "R" groups will seek to avoid water and position themselves towards the center of the protein. Hydrogen bonding in the polypeptide chain and between amino acid "R" groups helps to stabilize protein structure by holding the protein in the shape established by the hydrophobic interactions. Due to protein folding, ionic bonding can occur between the positively and negatively charged "R" groups that come in close contact with one another. Folding can also result in covalent bonding between the "R" groups of cysteine amino acids. This type of bonding forms what is called a disulfide bridge. Interactions called van der Waals forces also assist in the stabilization of protein structure. These interactions pertain to the attractive and repulsive forces that occur between molecules that become polarized. These forces contribute to the bonding that occurs between molecules.

  • Quaternary Structure - refers to the structure of a protein macromolecule formed by interactions between multiple polypeptide chains. Each polypeptide chain is referred to as a subunit. Proteins with quaternary structure may consist of more than one of the same type of protein subunit. They may also be composed of different subunits. Hemoglobin is an example of a protein with quaternary structure. Hemoglobin, found in the blood, is an iron containing protein that binds oxygen molecules. It contains four subunits: two alpha subunits and two beta subunits.
Protein Structure Determination

The three-dimensional shape of a protein is determined by its primary structure. The order of amino acids establishes a protein's structure and specific function. The distinct instructions for the order of amino acids are designated by the genes in a cell. When a cell perceives a need for protein synthesis, the DNA unravels and is transcribed into an RNA copy of the genetic code. This process is called DNA transcription. The RNA copy is then translated to produce a protein. The genetic information in the DNA determines the specific sequence of amino acids and the specific protein that is produced. Proteins are examples of one type of biological polymer. Along with proteins, carbohydrates, lipids, and nucleic acids constitute the four major classes of organic compounds in living cells.

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