The Structures of Life
Bacterium (pl. bacteria) A primitive, one-celled microorganism without a nucleus. Bacteria live almost everywhere in the environment. Some bacteria may infect humans, plants, or animals. They may be harmless or they may cause disease.
Base A chemical component (the fundamental information unit) of DNA or RNA. There are four bases in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G). RNA also contains four bases, but instead of thymine, RNA contains uracil (U).
Chemical shift An atomic property that varies depending on the chemical and magnetic properties of an atom and its arrangement within a molecule. Chemical shifts are measured by NMR spectroscopists to identify the types of atoms in their samples.
COX-1 (cyclooxygenase-1) An enzyme made continually in the stomach, blood vessels, platelet cells, and parts of the kidney. It produces prostaglandins that, among other things, protect the lining of the stomach from digestive acids. Because NSAIDs block COX-1, they foster ulcers.
COX-2 (cyclooxygenase-2) An enzyme found in only a few places, such as the brain and parts of the kidney. It is made only in response to injury or infection. It produces prostaglandins involved in inflammation and the immune response. NSAIDs act by blocking COX-2. Because elevated levels of COX-2 in the body have been linked to cancer, scientists are investigating whether blocking COX-2 may prevent or treat some cancers.
DNA (deoxyribonucleic acid) The substance of heredity. A long, usually double-stranded chain of nucleotides that carries genetic information necessary for all cellular functions, including the building of proteins. DNA is composed of the sugar deoxyribose, phosphate groups, and the bases adenine, thymine, guanine, and cytosine.
Drug target See target molecule.
Electromagnetic radiation Energy radiated in the form of a wave. It includes all kinds of radiation, including, in order of increasing energy, radio waves, microwaves, infrared radiation (heat), visible light, ultraviolet radiation, X-rays, and gamma radiation.
Isotope A form of a chemical element that contains the same number of protons but a different number of neutrons than other forms of the element. Isotopes are often used to trace atoms or molecules in a metabolic pathway. In NMR, only one isotope of each element contains the correct magnetic properties to be useful.
Megahertz A unit of measurement equal to 1,000,000 hertz. A hertz is defined as one event or cycle per second and is used to measure the frequency of radio waves and other forms of electromagnetic radiation. The strength of NMR magnets is often reported in megahertz, with most NMR magnets ranging from 500 to 900 megahertz.
Molecule The smallest unit of matter that retains all of the physical and chemical properties of that substance. It consists of one or more identical atoms or a group of different atoms bonded together.
Multi-wavelength anomalous diffraction (MAD) A technique used in X-ray crystallography that accelerates the determination of protein structures. It uses X-rays of different wavelengths, relieving crystallographers from having to make several different metal-containing crystals.
Non-steroidal anti-inflammatory drugs A class of medicines used to treat pain and inflammation. Examples include aspirin and ibuprofen. They work by blocking the action of the COX-2 enzyme. Because they also block the COX-1 enzyme, they can cause side effects such as stomach ulcers.
Nuclear magnetic resonance (NMR) spectroscopy A technique used to determine the detailed, three-dimensional structure of molecules and, more broadly, to study the physical, chemical, and biological properties of matter. It uses a strong magnet that interacts with the natural magnetic properties in atomic nuclei.
Nucleotide A subunit of DNA or RNA that includes one base, one phosphate molecule, and one sugar molecule (deoxyribose in DNA, ribose in RNA). Thousands of nucleotides join end-to-end to create a molecule of DNA or RNA. See base, phosphate group.
Prostaglandins A hormone-like group of molecules involved in a variety of functions in the body, including inflammation, blood flow in the kidney, protection of the stomach lining, blood clotting, and relaxation or contraction of muscles in the lungs, uterus, and blood vessels. The formation of prostaglandins is blocked by NSAIDs.
Protein A large biological molecule composed of amino acids arranged in a specific order determined by the genetic code and folded into a specific three-dimensional shape. Proteins are essential for all life processes.
Receptor protein Specific proteins found on the cell surface to which hormones or other molecules bind, triggering a specific reaction within the cell. Receptor proteins are responsible for initiating reactions as diverse as nerve impulses, changes in cell metabolism, and hormone release.
Resistance See antibiotic-resistant bacteria. Viruses can also develop resistance to antiviral drugs.
Retrovirus A type of virus that carries its genetic material as single-stranded RNA, rather than as DNA. Upon infecting a cell, the virus generates a DNA replica of its RNA using the enzyme reverse transcriptase.
RNA (ribonucleic acid) A long, usually single-stranded chain of nucleotides that has structural, genetic, and enzymatic roles. There are three major types of RNA, which are all involved in making proteins: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). RNA is composed of the sugar ribose, phosphate groups, and the bases adenine, uracil, guanine, and cytosine. Certain viruses contain RNA, instead of DNA, as their genetic material.
Structural genomics A field of study that seeks to determine a large inventory of protein structures based on gene sequences. The eventual goal is to be able to produce approximate structural models of any protein based on its gene sequence. From these structures and models, scientists hope to learn more about the biological function of proteins.
Synchrotron A large machine that accelerates electrically charged particles to nearly the speed of light and maintains them in circular orbits. Originally designed for use by high-energy physicists, synchrotrons are now heavily used by structural biologists as a source of very intense X-rays.
Target molecule (or target protein) The molecule on which pharmaceutical researchers focus when designing a drug. Often, the target molecule is from a virus or bacterium, or is an abnormal human protein. In these cases, the researchers usually seek to design a small molecule—a drug—to bind to the target molecule and block its action.