Proteins

Proteins | Protein Structure | Protein Folding | Movies

The human body makes at least 50,000 different proteins, and possibly twice that many. They are the essential working parts of living matter. If a cell is thought of as a house, then proteins are just about everything in it. They are the furniture, the fixtures, the lumber.

Like those objects, each protein has a particular shape and function. The shapes and functions, in fact, are inextricably linked. Hemoglobin's shape lets it carry oxygen. Collagen's makes it a good connective tissue. Insulin fits in spaces like a key, enabling it to turn things on and off.

Proteins are polymers composed of some 20 amino acids. Proteins have different functions; they can provide structure (ligaments, fingernails, hair), help in digestion (stomach enzymes), aid in movement (muscles), and play a part in our ability to see (the lens of our eyes is pure crystalline protein) . Proteins are formed in a series of highly controlled reactions. Amino acids are polymerized into a polypeptide chain on ribosomes in the cell. The process of making a protein involves various parts of a cell, the nucleus and the cytoplasm (The insides of a cell is shown in the drawing below ... the cytoplasm is everything purple and the gray area is the nucleus). The cell spends 25 kcal/mol of amino acids for the formation of the peptide bonds and in translating messenger RNA to polypeptide and in making the translation as accurate as possible.

Image courtesy of National Health Museum

Once a protein is made it moves a particular part of the cell where it is needed, or the cell packages it up and sends to other another cell or other parts of the body. This process is like putting groceries (proteins) in a bag at the store (the cytoplasm where they are made), taking them home (moving them somewhere else), then using them for various purposes (eggs for cooking, milk for drinking, candies for munching ...).

Hemoglobin binds to the oxygen in the lungs through its iron core, then carries and releases oxygen throughout the body. Hemoglobin is one example of a multisubunit protein. Hemoglobin has an alpha2beta2 structure. It consists of four polypeptides, two alpha subunits and two beta subunits. Each subunit also contains a nonprotein group called heme that is essential for hemoglobin's function (i.e. oxygen transport).

Insulin is an essential protein which initiates sugar absorption to the cells.

Peptides

Image courtesy of National Health Museum

Proteins consist of a polypeptide backbone with attached side chains. Each type of protein differs in its sequence and number of amino acids; therefore, it is the sequence of the chemically different side chains that makes each protein distinct. The two ends of a polypeptide chain are chemically different: the end carrying the free amino group (NH3+, also written NH2) is the amino, or N-, terminus, and that carrying the free carboxyl group (COO-, also written COOH) is the carboxyl, or C-, terminus. The amino acid sequence of a protein is always presented in the N to C direction, reading from left to right.

Peptides (and proteins) are made by joining amino acids together via amide bonds.

Amides are made by condensing together a carboxylic acid and an amine:

Any number of amino acids can be joined together to form peptides of any length.

Small peptides (containing less than a couple of dozen amino acids) are sometimes called oligopeptides. Longer peptides are many times called polypeptides.

Notice that peptides have a "polarity"; each peptide has only one free a-amino group (on the amino-terminal residue) and one free (non-sidechain) carboxyl group (on the carboxy-terminal residue):

A Tetrapeptide

When thinking about peptide (and protein) structure, it is often times useful to distinguish between the peptide "backbone" and the sidechains. The backbone atoms consist of the peptide amide units and the alpha carbons; the sidechains consists of the remaining atoms in the molecule (i.e. the "R" groups of each amino acid):

You can view many movies of computer simulations of Protein Folding:(http://folding.stanford.edu/movies/)

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Author: Tug Sezen

Reference: G. E. Schulz and R.H. Schirmer (1979), Principles of Protein Structure; Springer-Verlag