- Proteins
Here are some examples of what proteins do:

Proteins are embedded in the plasma membrane, although the more hydrophilic areas of these proteins "stick out" into the cells interior and outside of the cell.

Some of these proteins function as gates that will, in exchange for a price, allow certain molecules to cross into and out of the cell. These integral proteins are sometimes known as channels or pumps depending on whether Energy is required for the transport (see porin below).

Markers; these marker proteins (along with their attached carbohydrates), function in the recognition of self. One type is called Major Histocompatibilty proteins (MHCs). When a heart-transplant patient rejects his/her new heart, it is because their body didn't recognize the MHCs on the surface of the new hearts cells.

Cell adhesion molecules (CAMs) hold cells together. When you pickup a KFC chicken liver the cells don't just fall apart all over the table. Liver cells are held to liver cells, but not to some other kinds of cells, by CAMs. CAMs bind cells into tissues.

PORIN The cells of many the Gram-positive bacteria contain a channel (porin) for the passage of hydrophilic solutes. The protein is aptly named Porin. The bacterial membrane acts as a protection system against noxious macromolecules like proteases and bile-salt micelles. This protection system should nevertheless allow free access of small biomolecules like mono- and disaccharides, and amino acids to the cytoplasmic membrane. The bacteria need these molecules to grow. The proteins allowing for rapid diffusion of these molecules across the outer membrane are called porins.

This is a good molecule on which to practice your "Chime skills". First practice manipulating the molecule in 3-D. see if you can peer down the middle of this barrel-like molecule. After you have mastered this, use the right mouse button to change the display, color, or even add atoms (H's) to the display.

Enzymes - Perhaps the most important function of Proteins is acting as enzymes. As we have seen before, enzymes are reusable;They are not consumed in a reaction. They act as Catalysts for the thousands of biochemical reactions in our bodies. As the substrates are used up during a reaction (converted to products), the chance of their colliding with enzyme molecules decreases, this results in a fall in the amount of product being produced (reaction rate).

Most biological enzymes are proteins. They perform the chemical reactions in cells. Not all proteins are enzymes, but most enzymes are proteins. Enzymes have a special affinity for the substrate. They fit together, matching in shape and charge. The part of the enzyme where the substrate fits, is called the active site. The residues in the active site are in the right 3D conformation to bind and modify the substrate.

The image on the left shows an enzyme bound to its substrate (arrow). Each enzyme can only catalyze a few type of reactions because only certain substrates will fit into the active site.

Enzymes are named in a way that describes their substrates and the type reaction they perform. Alcohol Dehydrogenase is an enzyme that removes a Hydrogen from alcohol. It is very important in detoxifying Alcohol, like when you have a "Hangover". Almost all enzymes end with the -ase suffix. The enzyme Lactase catalyzes the reaction lactose --> glucose + galactose.

More on Protein Structure (protein structure is real important).