PROTEINS FUNCTION ACCORDING TO THEIR SHAPES

In molecules with a limitless range of potential shapes, the things that can be accomplished are just as limitless.  Here we will deal with just a few very important but general applications to which proteins are put in living systems, and please note that these designations are artificial labels and some proteins can reasonably be included in more than one group:

Some protein types have relatively stable forms and functions:

STRUCTURAL ELEMENTS, especially on small scales like on and within cells.  On a cellular level, proteins take the forms you might associate with construction materials:  cables, struts, and sheets.  Cells with particular forms are held in those shapes by proteins.  Above the cell level, proteins are common in structural elements, such as cartilage, but there are non-proteins found at that level as well, like the starch cellulose in plants or the salt calcium carbonate in bones.

MOVEMENT ELEMENTS.  With very few exceptions, any kind of visible movement in living things, whether the movement of microscopic cell parts or the movement of your own arm, is exerted by protein systems.  Force for movement is generally exerted as a pull, which can come from compression of a spring-like protein or the movement of two proteins across one another, shortening the length of the complex.

COMMUNICATION MOLECULES.  These may work several different ways, and this is a function often performed by non-proteins as well.  Communication may be over distances, as is done by protein-based hormones, smell-message pheromones, or neurotransmitters carrying nerve impulse messages across tiny gaps (synapses) between nerves in a sequence, or communication may be across barriers, as is accomplished by many proteins embedded in cell membranes that carry signals in and out.  Another type of protein that could be considered in this group are antibodies, which are created by the immune system with two active domains.  One end of the molecule has domains specifically built to attach to antigens, molecules (usually protein-based) that have gotten into the body but which are different from any of the body's molecules - they are foreign, and automatically treated as being dangerous.  An important source of antigens is external molecules on disease-causing invaders like viruses and bacteria, but any foreign molecule of sufficient size can stimulate an antibody response.  The other antibody domain is the communications domain, activated when antibody-antigen binding changes the shape of the antibody molecule;  this marks molecules and the invaders carrying them for various responses designed to remove them.  If your immune system is working properly, you currently have antibodies in circulation to every disease organism (among other things) that you have even been exposed to, which will prevent new individuals carrying an old disease from being able to "set up shop" in your system.  Simply put, the antibodies will "flag" returning invaders for immediate removal.

Some proteins function through changes and transitional forms.   Most of these are capable of temporarily binding other molecules, called substrates or ligands, and doing something with them, as antibodies above were mentioned doing:

CARRIERS / TRANSPORTERS.  Proteins may form temporary complexes with atoms and molecules that increase solubility, to move materials around in circulation fluids, or may pass materials through barriers such as cell membranes.  A well-known carrier in humans are our lipoproteins, lipid-carriers implicated in arterial problems.

RECEPTORS.  These proteins change in response to some input, often when another molecule connects to it temporarily.  Living things have many different types of receptors, for things like communications molecules, nutrients, smells and tastes, and even wavelengths ("colors"), levels of light, and magnetic fields.

CONTROL AND REGULATION MOLECULES.  These are directly involved in adjusting the function of metabolic systems, often by attaching to molecules that are vital to the flow of a particular process or pathway.

ENZYMES.   Important enough that several later sections will be spent discussing their operations, these are the catalysts used in almost every known biological systems.  A catalyst speeds up the rate at which a chemical reaction takes place by reducing the amount of energy it takes to get it started (activation energy).  Enzymes bind to substrates, bringing potential pieces together in synthesis reactions (anabolism) so that they bind together, or grabbing larger molecules and stressing them in ways that bring them to split into separate pieces in breakdown reactions (catabolism).  Enzymes are usually very specific for substrates;  very few will react with multiple substrates.  This three-dimensional pickiness, which is also found in things like receptors and other binding proteins, is called specificity or stereospecificity.  Any kind of chemistry that occurs in organisms only occurs because specific enzymes exist for any given step of any given process.  For example, sucrase is a digestive enzyme used to break down table sugar, sucrose, but it cannot react with the similar molecule in sucralose, known commercially as Splenda^TM.  Enzyme types are usually named with an -ase ending;  like carbohydrates, however, all enzymes don't have this ending, but chemicals with this ending are all enzymes.  Like any catalyst, when an enzyme has contributed to a chemical change, it returns to its original form, ready to help again.  However, just because an enzyme emerges from a reaction in the same form it started as does not mean that it doesn't change while the reaction is going on.  The old image of a solid lock-and-key does not give a truly accurate idea of how these molecules work.

PRIONS.  These were at one time important functional proteins, but accidentally became twisted into a dangerous new form that could cause other copies of the proteins to change to prions - these are the closest thing nature gets to actual zombies!  These can cause diseases by shutting down the protein's original function, and some cause infectious diseases.

As mentioned earlier, this is just a list of major functions performed by proteins, without getting into the long list of more minor activity, and proteins often resist categorization and could be put into multiple classes from this list.