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Glossary
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Pyrimidine A class of nucleotide base with an aromatic ring containing four carbon and two nitrogen atoms Pyrophosphate bonds The covalent bonds between adjacent, covalently linked, phosphate groups Quaternary structure A molecule structure in which two or more tertiary structures attach or associate with one another to form an even larger molecule or complex Ramachandran diagram A plot of peptide bond angles showing contours of which angles fall within certain energy ranges Random coil A conformation in which a polymer has no specific secondary structure Reference state A state of a system chosen to be used to define all other states of the system The other states of the system are defined in terms of the difference in energy (or some other quantity) between them and the reference state Often the ground state is chosen as the reference state Reflection Light (electromagnetic radiation) bouncing off a surface Refraction The bending of light (electromagnetic radiation) while passing through a surface Regulation The control of a biological process by a cell or organism, usually through some kind of a feedback mechanism Residue Each of the units or smaller molecules making up a polymer Ribose A five-carbon simple sugar (carbohydrate) commonly found in nucleotides Ribosome A complex of structural proteins, enzymes, and ribosomal RNA, a basic structure involved in protein synthesis Right-handed helix A helix that turns clockwise as you move along its length RNA (ribonucleic acid) A nucleic acid whose nucleotides contain ribose See also mRNA (messenger RNA), tRNA (transfer RNA), and rRNA (ribosomal RNA) RNA polymerase An enzyme that catalyzes the biochemical reaction to covalently link ribonucleotides together to form RNA Saccharide Another name for carbohydrate (See also monosaccharide, disaccharide, oligosaccharide, and polysaccharide) Salt bridge An ionic attraction between a positive and negative ion, usually between two parts of the same molecule (such as a protein) or between two molecules within a complex
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B i o p h y s i c s D e mys tifie D
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Saponifiable lipid A lipid that is a polymer or that contains a polymer as a major portion of its structure See also nonpolymeric lipid Saturated fatty acid A fatty acid with no double bonds in the hydrocarbon chain Scanning electron microscopy (SEM) A technique in which a beam of electrons is gradually scanned across the surface of the specimen to provide a highly magnified image of the sample Second law of thermodynamics For any process, the sum of the entropy of the system plus the entropy of its surroundings will only increase or remain constant If the process occurs in a closed system, then the entropy of the closed system will only increase or remain constant Secondary active transport An active transport where the energy needed for the transport comes from a simultaneous passive transport Secondary amine An amine covalently connected to only one hydrogen atom and with two covalent bonds to the rest of the molecule Secondary structure The simple, three-dimensional structure of a molecule Some large molecules may contain more than one secondary structure (see also tertiary structure) Sedimentation The motion of particles in a fluid under the application of a force Selectively permeable Having a quality such that some things can pass through while others cannot Self-assembly The forming of molecular structures through folding and/or through association with other molecules without need for energy input, catalysis, or other molecules that are not part of the structure Side chain In an amino acid, the atom or group of atoms, other than the amine and the carboxyl, that is attached to the alpha carbon Single bond A covalent bond in which a pair of electrons is shared between two atoms Sodium-calcium exchanger A membrane transport protein that moves three Na1 ions into the cell for every Ca21 ion that it moves out of the cell Specificity A property of some proteins and other molecules that only one certain type of molecule will bind strongly to it Spectroscopy Any of a variety of techniques that measure and present data according to a spectrum, that is across a wide range of some variable such as frequency, wavelength, energy, or mass See also EM spectroscopy
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