• Proteins are made of amino acids, in long chains (polymers).

A chain of amino acids; each amino acid is represented by a red ball. The different amino acids shown are Proline (Pro), Lysine (Lys), Phenylalanine (Phe), etc.	A structural representation of a chain of amino acids. Actual proteins are considerably larger, typically consisting of hundreds or thousands of amino acids.

• A short chain of amino acids is referred to as a peptide (or oligopeptide); a long chain of many (hundreds or thousands) amino acids is referred to as a polypeptide. 
• Each cell makes thousands of different KINDS of proteins.
• Different kinds of proteins are composed of a different sequence of amino acids. 
• For example, the first six amino acids in actin (a protein involved in muscle contraction and the cytoskeleton) are: Methionine, then cysteine, then aspartic acid, then asparagine, then asparagine, then valine.
• The first six amino acids in beta-globin (part of hemoglobin, the protein that transports oxygen in our blood) are: Methionine, then valine, then glutamine, then leucine, then serine, then serine.
• Proteins typically consist of MANY amino acids. For example, actin consists of more than 300 amino acids. A complete hemoglobin molecule has around 600 amino acids. A single antibody molecule (part of the immune system) contains about 1,400 amino acids or more.
• The SAME protein consists of the SAME sequence of amino acids. For example, if actin is a protein consisting of a chain of 376 amino acids, then EVERY actin protein will be 376 amino acids long, and EVERY actin protein will have the same amino acid sequence, starting with methionine, cysteine, aspartic acid, asparagine, asparagine, and valine.

• Amino acids are the subunit that are extended in a long chain to become proteins. 
• There are 20 different amino acids. All cells in all organisms (bacteria, protozoa, fungi, plants, and animals) use these 20 amino acids to make proteins.
• The names of the 20 amino acids are:

Alanine	Arginine	Asparagine	Aspartic Acid	Cysteine
Glutamine	Glutamic Acid	Glycine	Histidine	Isoleucine
Leucine	Lysine	Methionine	Phenylalanine	Proline
Serine	Threonine	Tryptophan	Tryrosine	Valine

• Different amino acids have different chemical structures. For example: 

Structure of the amino acid Aspartic Acid.	Structure of the amino acid Tryptophan.

• As a result, different amino acids have different chemical properties. Each kind of protein is a unique combination of different amino acids, and the properties of a protein are determined by the amino acids used to make it. 

For example, proteins that are found in membranes contain many hydrophobic amino acids, because the interior of membranes is a hydrophobic environment. These two diagrams of transport proteins show the location of the protein IN the cell membrane. Here, the protein is a blue oval/cylinder.	This structural diagram of a transport protein (in red) shows its close association with the membrane lipids (green).

• Proteins have up to four levels of structure. 
• Part of what makes a protein function the way it does is its particular three-dimensional structure (shape).
• The amino acid sequence of a particular protein determines its shape (also called conformation.
• The organization of protein structure is divided into four levels, called primary, secondary, tertiary, and quaternary.

The primary structure of a protein is simply the sequence of amino acids.

• The secondary structure of a protein is the initial arrangement of the primary structure. 

Sometimes part of the amino acid sequence folds into a coil called a helix. The diagram shows a model of the structure of a protein that contains many helices (coils). The line (red and green) represents the amino acid chain; it is coiled into numerous separate helices. EACH coil shown is a separate unit of secondary structure.
Sometimes part of the amino acid sequence folds into a sheet of parallel strands. This diagrammed protein (a snake venom molecule) illustrates how a long chain of amino acids (the grey and blue line) can form back-and-forth rows called a sheet. Unlike the helices, the amino acid chain does NOT form coils here.
The complete protein may have some parts where the secondary structure is a helix, and other parts where the secondary structure is a sheet. There may also be sections where the secondary structure is neither helix nor sheet (these sections are sometimes called random coil). Shown here is a diagram of a special receptor on the surface of most human cells. The protein has a "floor" of sheet structure and "sides" of alpha helix. The shapes of the different parts of the protein form a groove (like a hot dog bun); small molecules can bind within the groove. NOTE that each coil and sheet is a separate region of secondary structure.

In most proteins, once the secondary structure has formed, the secondary structure is further arranged into clumps called tertiary structure. Several examples of tertiary structure are visible above . Tertiary structure is simply the grouping of different separate secondary structures, such as multiple helices or multiple sheets or a combination of helices and sheets.

Quaternary Stucture: Some complete proteins actually consist of more than one separate polypeptide (long chain of amino acids). For example, hemoglobin consists of FOUR separate polypeptide chains - two alpha-globin polypeptides plus two beta-globin polypeptide chains. When multiple separate polypeptide chains are required to make the complete protein, the protein has quaternary structure.

• In summary, there are up to four levels of protein structure: 
 

Primary Structure	The amino acid sequence.
Secondary Structure	Initial folding of the amino acid sequence into helixes and sheets.
Tertiary Structure	Arrangements and groupings of the secondary structure into clumps.
Quaternary Structure	Arrangement of separate tertiary structures, when multiple amino acid chains are required to make a single protein.

• Protein structure can change. 
• Protein primary structure is strong and stable, because the amino acids are connected to each other by covalent bonds.
• Secondary, Tertiary, and Quaternary structure in proteins are held together primarily by hydrogen bonds and other weak interactions. 
• Small changes in structure often happen during protein functioning. In other words, proteins can change shape. In fact, this is how many proteins do their jobs: by moving and changing shape. For example, some enzymes attach two substrate molecules by flexing and literally smashing the two substrate molecules together to make a product. The particular shape of a protein is sometimes called its conformation.
• If all of the hydrogen bonds break at the same time, the protein can completely unravel. If this happens, the protein will lose all structure except for the primary structure. When a protein loses its structure, it is denatured. 
• You've probably conducted experiments in protein denaturation at home. When eggs cook, the proteins denature, and because they are unable to re-form the correct secondary and tertiary structure, the process is irreversible (cooked eggs don't revert back to the liquid state when they cool). Some proteins CAN correctly reverse the denaturation process by themselves. An example is gelatin: you can melt Jello, let it solidify, remelt it, and re-solidify it as many times as you want.
• Allosteric Modification: The function of some proteins is regulated by causing a conformation change - causing a change in the three-dimensional shape of the protein. For example, sometimes an enzyme is activated (or inactivated) if some regulatory molecule binds to the enzyme. When the regulatory molecule binds, it causes the enzyme to change shape, causing it to gain (or sometimes to lose) its function. Sometimes a protein can be turned "off" or turned "on" when a molecule binds and causes a change in shape.
• Types of Proteins: There are many different kinds of proteins in cells. They perform a variety of functions in cells. All proteins, however, consist of chains of amino acids arranged into secondary, tertiary, and perhaps quaternary structure. 
• Enzymes - proteins that enable specific chemical reactions to occur, such as conversion of starch to glucose. Most enzymes only catalyze ONE kind of chemical reaction. For example, the eight chemical reactions of glycolysis (breakdown of glucose to pyruvate) each require a different kind of enzyme.
• Transporters - Proteins that help other molecules move into or out of cells.
• Movement - Proteins move molecules within cells, and help cells and organisms move through the world.
• Structural - Proteins give cells their shape, and help the cells of multicellular organisms stay attached. In humans, hair and nails are mostly protein.
• Other Proteins - have specialized functions. Many hormones are small proteins. Many bacterial toxins (molecules that are released by the bacteria, causing disease symptoms) are also proteins. Some proteins, such as receptors, are involved in transmitting information into the cell from the outside. 
• Where do proteins come from? 
• Proteins are made by ribosomes, in the process of protein synthesis, also called translation.
• The instructions for protein synthesis - the code for the correct order and number of amino acids for each protein - is contained in the DNA (in the genes, on the chromosomes). In fact, this is a main function of the genetic material - to store the instructions that allow the cell to make proteins.

A. The Basic Chemistry of Biology

B. The Molecules of Biology

1. Water - Structure and properties, hydrogen bonding, hydrophilic and hydrophobic, diffusion, osmosis.

2. Amino Acids and Proteins; Protein structure, conformation, and allosteric modification (you are here).

3. Sugars and Polysaccharides

4. Nucleotides and Nucleic Acids

5. Lipids and Membranes (general information; more detail on membranes)