Protein Structure

A protein is a molecule that consists of amino acids joined together by covalent bonds. The code for this sequence of amino acids is preserved in a gene.

Last time we said the second thing we need to know about proteins is that each different kind of protein has a specific three-dimensional “shape” that is well designed to direct it’s own specific job for maintaining the life of that cell. The shape of the protein is perfect for whatever job it is supposed to do and is also perfect to interact with the source of energy that is needed to do that job.
The idea of “shape,” I am embarrassed to tell you this, is something of a metaphor for a set of characteristics that make up a protein in it’s final configuration, and also make it capable of adjusting to the conditions around it so that it can do its function(s) in an automatic response to those conditions.

Of course, we can’t really see what a protein is doing, so we require models that are based on the unchanging natural laws of chemistry and physics and the behaviors of the proteins, as they can be measured in various kinds of environments. I will try to describe a model for protein shapes.

Proteins are made of amino acids. Proteins are usually big molecules. Amino acids are rather small molecules. Molecules are atoms joined together with energy bonds, or they are bigger molecules made by joining together smaller molecules.

We should remember that atoms and molecules cannot be joined in just any old combination, but that every kind of atom is different in its distribution of energy. Some kinds of atoms join with others more strongly or less strongly or not at all. The distribution of energy in an atom, if the atom is part of a molecule, influences the distribution of energy in the molecule. And that is influenced by the energy of the environment. The environmental energy is usually measured as pH (that is, whether the environment more acid or more basic).

So. It is complicated.

We do not need to discuss all those complications. We only need to know they exist and understand that the “shape” of a molecule depends on the energy interactions among the atoms in the molecule and also the pH of the environment. We also need to know that the energy reactions are of two major sorts:

1. Covalent energy bonds are very strong and do not change without the help of an enzyme;
2. Weak energy bonds are constantly readjusting themselves depending on local conditions.

The primary structure of proteins consists mostly of the covalent bonds that attach one amino acid to the next amino acid in a long (or sometimes shorter) string of amino acids. These are the essential amino acids that we must eat in our diets in order to be healthy.

AminoAcid → AminoAcid → AminoAcid → AminoAcid → AminoAcid
(those arrows are strong covalent bonds)

The genetic code determines which amino acid will be where in this string and how long the string will be. Every different kind of protein has its own unique sequence of the specific kinds of amino acids, because it is made by its own specific gene.  The gene carries the code for the primary structure of the protein. We will discuss this later, but we have already said the function of many or most genes is to preserve this code and also to make sure the proteins are produced at the right time and place in the cell.

Once the sequence of the protein is firmly fastened together by covalent (strong) energy bonds that join the amino acids end to end, then there may or may not be one or a few covalent bonds created that join the sides of one or a few amino acids.  If these are present, they bend the protein molecule into its secondary structure.

The protein is then released into the cell where it folds up into a tertiary structure or shape. The tertiary structure of a protein.  The covalent bonds are formed by enzymes, but the tertiary structure is automatic as the protein folds up in response weak energy bonds that form among the various amino acids.

The weak bond is shown between the sides of two amino acids by the gray arrow; the strong bonds between their ends as black arrows. There are several different kinds of weak bonds.  Some weak bonds are stronger than others, all of them can be influenced by the pH of the environment.  The ends of every amino acid are the same.  This is why every amino acid as able to make a strong covalent bond with every other amino acid.  The sides of every kind of amino acid are different.  The proteins fold up, after the strong bonds are formed, because the sides of some of the amino acids will attract each other, some will repel each other and they will all finally settle into the configuration that is most comfortable for them all together.

Sometimes proteins pair up with other proteins by weak bonding or strong bonding.  Hemoglobin is an example. It consists of four molecules of protein — two of one kind and two of another kind.  These function together to carry red blood cells in the blood. If a protein consists of more than one chain of amino acids (polypeptide chain), its final structure is referred to as  its quaternary structure.

So, that is why proteins come in different shapes. The thing to remember from all this information is that each protein has the right shape to do one specific function in the cell. The covalent bonds make sure the primary structure is strong, and the weak bonds of the protein can adjust themselves to make the shape change just slightly when the conditions change.