Proteins are formed when amino acids join through peptide bonds, which is why they are also called polypeptides. The peptide bonds between the amino acids are formed by a process called dehydration synthesis. The conformation of a protein is dependent upon physical and chemical conditions of its surrounding environment such as pH and temperature. A protein’s sequence of amino acids (a simple organic compound containing both a carboxyl and an amino group) determines how it functions. Proteins have four levels of structure: Primary, secondary, tertiary, and quaternary. The tendency of nonpolar molecules in a polar solvent to interact with one another is called the hydrophobic effect. Proteins have hydrophobic amino acids, such as glycine, clustered together within the protein. It is the amino acids with hydrophobic side chains becoming clusters at the core of a protein as a polypeptide folds into its functional shape. Hydrogen bonding between amino groups and carboxyl groups in a protein sheet cause certain patterns of folding to occur. These hydrogen bonds cause the amino acid chain to fold or coil. This can result in two specific shapes. An alpha helix occurs when the hydrogen bonds form in a chain causing a spiraling pattern. Beta sheets form when chains that are parallel to each other link to create a pleated shape. These folding patterns make up the secondary structure of a protein.Van der Waals interactions are defined as ever-changing “hot spots of positive/negative charge” that enable atoms to stick together, due to the constant and “unsymmetrical” motion of electrons (1). Van der Waals forces are able to do this because “slight differences in the dipole moment of two parts of the protein chain” allow these two parts to become linked together (3). Due to this linking, proteins are able to fold into the different structures that allow them to function properly. Van der Waals interactions also contribute to the strength of the hydrophobic effect because non-polar atoms are especially favored in this type of interaction (2). Mad Cow disease is a brain disorder in adult cattle, affecting a cow’s nervous system, causing a cow to lose its ability to do normal things (5). Researchers believe that the infectious agent that causes mad cow disease is an abnormal version of a protein normally found on cell surfaces, called a prion (4). This protein becomes altered and destroys nervous system tissue, specifically the brain and spinal cord. The human version of mad cow disease is called Creutzfeldt-Jakob disease. It gradually destroys brain cells and is believed to be caused by eating beef products contaminated with central nervous system tissue, such as brain and spinal cord, from cattle infected with mad cow disease. People with this disease will have difficulty controlling their body movements, speech, and dementia. Similar to mad cow disease, Creutzfeldt-Jakob Disease happens when a prion protein, an “abnormal kind of amyloid”, causes abnormalities in other proteins. The buildup and malformation of prions on the brain cells ultimately leads to brain damage and death.