CLAIMS
The patent application's list of claims defines the composition and utility of the invention. The claims also describe obvious variations on the invention to prevent others from easily engineering around the patent. For example, for a method of immobilizing proteins on a surface, the first claim may describe the invention in detail and specify the use of a biotin tag on the protein that will bind streptavidin attached to the surface. The second claim may assert that the method in the first claim can also be modified to use a histidine-tag and nickel coating in place of biotin and streptavidin. Other claims may mention other binding-reagent pairs. Without supporting evidence, claims worded too broadly may be challenged and invalidated (e.g. you cannot simply claim "any method of attaching a protein to a surface").
Patent litigation has been compared to cards... a full house of claims beats three of a kind. The stronger your claims, the less likely someone will challenge you in court.
The claims made in the patent cannot be purely theoretical. To patent a particular molecule, you must have successfully synthesized it and provided evidence that the molecule actually has the uses for which you seek patent protection. For example, there is much confusion over the patenting of genes. Like any other chemical entity, a gene may be considered for patenting. The gene must be cloned and its composition (sequence) described. However, because the patent must also describe a use, such as synthesis of the protein that the gene encodes, the inventor must demonstrate that a specific protein can actually be produced from the cloned gene and that this protein is likely to have further application, such as protein replacement therapy for a disease or screening of small-molecular inhibitors. The patent can also be worded to cover gene variants so that one could not change the sequence slightly to get around the patent.