Glossary, the structure of life

Acquired immunodeficiency syndrome (AIDS) A viral disease caused by the human immunodeficiency virus (HIV).

Active site The region of an enzyme to which a substrate binds and at which a chemical reaction occurs.

AIDS Acquired immunodeficiency syndrome—an infectious disease that is a major killer worldwide.

Alpha helix A short, spiral-shaped section within a protein structure.

Amino acid A chemical building block of proteins. There are 20 standard amino acids. A protein consists of a specific sequence of amino acids.

Angstrom A unit of length used for measuring atomic dimensions. One angstrom equals 10-10 meters.

Antibiotic-resistant bacteria A strain of bacteria with slight alterations (mutations) in some of their molecules that enable the bacteria to survive drugs designed to kill them.

Atom A fundamental unit of matter. It consists of a nucleus and electrons.

AZT (azido-deoxythymidine) A drug used to treat HIV. It targets the reverse transcriptase enzyme.

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).

Beta sheet A pleated section within a protein structure.

Chaperones Proteins that help other proteins fold or escort other proteins throughout the cell.

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.

Cyclooxygenases Enzymes that are responsible for producing prostaglandins and other molecules in the body.

Deoxyribose The type of sugar in DNA.

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.

Enzyme A substance, usually a protein, that speeds up, or catalyzes, a specific chemical reaction without being permanently altered or consumed. Some RNA molecules can also act as enzymes.

Gene A unit of heredity. A segment of DNA that contains the code for a specific protein or protein subunit.

Genetic code The set of triplet letters in DNA (or mRNA) that code for specific amino acids.

HIV protease An HIV enzyme that is required during the life cycle of the virus. It is required for HIV virus particles to mature into fully infectious particles.

Human immunodeficiency virus (HIV) The virus that causes AIDS.

Inhibitor A molecule that “inhibits,” or blocks, the biological action of another molecule.

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.

Kilodalton A unit of mass equal to 1,000 daltons. A dalton is a unit used to measure the mass of atoms and molecules. One dalton equals the atomic weight of a hydrogen atom (1.66 x 10-24 grams).

MAD See multi-wavelength anomalous diffraction.

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.

Messenger RNA (mRNA) An RNA molecule that serves as an intermediate in the synthesis of protein.Messenger RNA is complementary to DNA and carries genetic information to the ribosome.

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.

mRNA Messenger RNA.

Multi-dimensional NMR A technique used to solve complex NMR problems.

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.

NMR Nuclear magnetic resonance.

NMR-active atom An atom that has the correct magnetic properties to be useful for NMR. For some atoms, the NMR-active form is a rare isotope, such as 13C or 15N.

NOESY Nuclear Overhauser effect spectroscopy.

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.

NSAIDs Non-steroidal anti-inflammatory drugs such as aspirin or ibuprofen.

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.

Nuclear Overhauser effect spectroscopy (NOESY) An NMR technique used to help determine protein structures. It reveals how close different protons (hydrogen nuclei) are to each other in space.

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.

Nucleus (pl. nuclei) 1.The membrane-bounded center of a cell, which contains genetic material. 2.The center of an atom, made up of protons and neutrons.

Phosphate group A chemical group found in DNA and RNA, and often attached to proteins and other biological molecules. It is composed of one phosphorous atom bound to four oxygen atoms.

Photosynthesis The chemical process by which green plants, algae, and some bacteria use the Sun’s energy to synthesize organic compounds (initially carbohydrates).

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.

Reverse transcriptase An enzyme found in retroviruses that copies the virus’ genetic material fromsingle-stranded RNA into double-stranded DNA.

Ribose The type of sugar found in RNA.

Ribosomal RNA RNA found in the ribosome.

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.

Side chain The part of an amino acid that confers its identity. Side chains range from a single hydrogen atom (for glycine) to a group of 15 or more atoms.

Signal transduction The process by which chemical, electrical, or biological signals are transmitted into and within a cell.

Structural biology A field of study dedicated to determining the detailed, three-dimensional structures of biological molecules to better understand the function of these molecules.

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.

Structure-based drug design An approach to developing medicines that takes advantage of the detailed, three-dimensional structure of target molecules.

Substrate A molecule that binds to an enzyme and undergoes a chemical change during the ensuing enzymatic reaction.

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.

Transcription The first major step in protein synthesis, in which the information coded in DNA is copied (transcribed) into mRNA.

Translation The second major step in protein synthesis, in which the information encoded in mRNA is deciphered (translated) into sequences of amino acids. This process occurs at the ribosome.

Virus An infectious microbe that requires a host cell (plant, animal, human, or bacterial) in which to reproduce. It is composed of proteins and genetic material (either DNA or RNA).

Virus particle A single member of a viral strain, including all requisite proteins and genetic material.

X-ray crystallography A technique used to determine the detailed, three-dimensional structure of molecules. It is based on the scattering of X-rays through a crystal of the molecule under study.

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connie dello buono

Health educator, author and enterpreneur or ; cell 408-854-1883 Helping families in the bay area by providing compassionate and live-in caregivers for homebound bay area seniors. Blogs at Currently writing a self help and self cure ebook to help transform others in their journey to wellness, Healing within, transform inside and out. This is a compilation of topics Connie answered at and posts in this site.

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