BIO - TERMS - MOLECUL Flashcards
(139 cards)
1
Q
Absorption spectrum
A
A plot of wavelength of incident light versus amount of light absorbed. Organic molecules show absorption spectra in both the infrared and the ultraviolet regions of the electromagnetic spectrum.
2
Q
Achiral
A
Having a lack of handedness. A molecule is achiral if it has a plane of symmetry and is thus superimposable on its mirror image.
3
Q
activated carrier
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Small diffusible molecule that stores easily exchangeable energy in the form of one or more energy-rich covalent bonds. Examples are ATP, acetyl CoA, FADH2, NADH, and NADPH.
4
Q
alloreactivity
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The recognition by T cells of MHC molecules other than self. Such responses are also called alloreactions or alloreactive responses.
5
Q
amorphous
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A term describing a solid in which atoms or molecules do not have any long-range order.
6
Q
Amorphous ice/vitrified ice
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Form of solidified water in which molecules are randomly arranged in a glass-like solid state; this is in contrast to crystalline ice where molecules are regularly arranged in a lattice needing more space.
7
Q
anaerobic respiration
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Respiration in which the final electron acceptor in the electron transport chain is an inorganic molecule other than molecular oxygen (O2); for example, a nitrate ion or CO2.
8
Q
analyte
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A molecule to be analyzed by mass spectrometry.
9
Q
Angle strain
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The strain introduced into a molecule when a bond angle is deformed from its ideal value. Angle strain is particularly important in small-ring cyclo alkanes, where it results from compression of bond angles to less than their ideal tetrahedral values.
10
Q
Annulation
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The building of a new ring onto an existing molecule.
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Q
anoxygenic
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Not producing molecular oxygen; typical of cyclic photophosphorylation.
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Q
Antiaromatic
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Referring to a planar, conjugated molecule with 4n π electrons. Delocalization of the p electrons leads to an increase in energy.
13
Q
aptamer
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Oligonucleotide that binds specifically to one molecular target, usually selected by an iterative cycle of affinity-based enrichment (SELEX).
14
Q
Aromaticity
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The special characteristics of cyclic conjugated molecules, including unusual stability and a tendency to undergo substitution reactions rather than addition reactions on treatment with electrophiles. Aromatic molecules are planar, cyclic, conjugated species with 4n + 2 π electrons.
15
Q
asymmetric cell division
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Cell division in which some important molecule or molecules are distributed unequally between the two daughter cells, causing these cells to become different from each other.
16
Q
ball-and-stick molecular model
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A model that represents atoms as balls and chemical bonds as sticks; how the two connect reflects a molecule’s shape.
17
Q
band theory
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A model for bonding in atomic solids based on molecular orbital theory in which atomic orbitals combine and become delocalized over the entire crystal.
18
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bent geometry
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A molecular geometry in which the angle between three bonded atoms is approximately 109° (but could be less).
19
Q
bond order
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For a molecule, the number of electrons in bonding orbitals minus the number of electrons in nonbonding orbitals divided by two; a positive bond order implies that the molecule is stable.
20
Q
Bridgehead
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An atom that is shared by more than one ring in a polycyclic molecule.
21
Q
Carboxylation
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The addition of CO2 to a molecule.
22
Q
catenane
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Two or more circular polymeric molecules interlinked by one or more noncovalent topological links, resembling the links of a chain.
23
Q
Cation radical
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A reactive species, typically formed in a mass spectrometer by loss of an electron from a neutral molecule and having both a positive charge and an odd number of electrons.
24
Q
cellulose microfibril
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Highly ordered crystalline aggregate formed from bundles of about 40 cellulose chains, arranged with the same polarity and stuck together in overlapping parallel arrays by hydrogen bonds between adjacent cellulose molecules.
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Chair conformation
A three-dimensional conformation of cyclohexane that resembles the rough shape of a chair. The chair form of cyclohexane is the lowest-energy conformation of the molecule.
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Chelators
Small molecules that bind a metal with high affinity.
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chemical biology
Name given to a strategy that uses largescale screening of hundreds of thousands of small molecules in biological assays to identify chemicals that affect a particular biological process and that can then be used to study it.
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chemoattractant
A diffusible molecule that acts over a distance to attract growing axons.
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chemorepellent
A diffusible molecule that acts over a distance to repel growing axons.
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Chiral environment
The chiral surroundings or conditions in which a molecule resides.
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Chromophore-binding domain
Part of a photoreceptor molecule that binds the chromophore; absorbs light and triggers activity of the output-domain that links photoreceptor activity to downstream signaling.
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CIIV
An early endocytic compartment containing MHC class II molecules in dendritic cells.
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collision model
A model of chemical reactions in which a reaction occurs after a sufficiently energetic collision between two reactant molecules.
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column chromatography
Technique for separation of a mixture of substances in solution by passage through a column containing a porous solid matrix. Substances are retarded to different extents by their interaction with the matrix and can be collected separately from the column. Depending on the matrix, separation can be according to charge, hydrophobicity, size, or the ability to bind to other molecules.
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Compatible solutes
Small molecules involved in the osmoregulation of the cell (osmoprotectants, osmolytes).
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conduction band
In band theory, the band of energy levels that forms from antibonding molecular orbitals.
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Conformational analysis
A means of assessing the energy of a substituted cycloalkane by totaling the steric interactions present in the molecule.
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Conjugation reactions
Reactions in which a hydrophilic molecule becomes covalently linked to a chemical.
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contact-dependent signaling
Form of intercellular signaling in which signal molecules remain bound to the surface of the signaling cell and influence only cells that contact it.
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contour length
The length of a helical polymeric molecule as measured along its helical axis.
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crystalline
A term that describes a solid in which atoms, molecules, or ions are arranged in patterns with long-range, repeating order.
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decomposition reaction
A chemical reaction in which bonds are broken to produce smaller parts from a large molecule.
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Degree of unsaturation
The number of rings and/or multiple bonds in a molecule.
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dehydration synthesis
Chemical reaction in which water is formed during formation of a complex molecule.
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Dieckmann cyclization reaction
An intra molecular Claisen condensation reaction of a diester to give a cyclic b-keto ester.
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dimerization
An event in which two molecular complexes interact and proceed to perform a purposeful function.
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doubly labeled water (DLW)
Tool used to assess energy expenditure based on estimations of CO2 production; uses water molecules with isotopes of hydrogen ²H and ¹⁸O.
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Eclipsing strain
The strain energy in a molecule caused by electron repulsions between eclipsed bonds. Eclipsing strain is also called torsional strain.
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Electron-dot structure
A representation of a molecule showing valence electrons as dots.
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Electrostatic potential maps
Molecular representations that use color to indicate the charge distribution in molecules as derived from quantum-mechanical calculations.
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Entropy change (DS)
The change in amount of molecular randomness. The entropy change that occurs during a reaction is a measure of the difference in randomness between reactants and products.
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ESI
Electrospray ionization; a “soft” ionization method used for mass spectrometry of biological samples of very high molecular weight.
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ethylene
Small gas molecule that is a plant growth regulator influencing plant development in various ways including promoting fruit ripening, leaf abscission, and plant senescence and functioning as a stress signal in response to wounding, infection, and flooding.
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excited state
An energy-rich state of an atom or molecule, produced by the absorption of light energy; as distinct from ground state.
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Fischer projections
A means of depicting the absolute coniguration of a chiral molecule on a lat page. A
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fraction
A portion of a biological sample that has been subjected to a procedure designed to separate macromolecules based on a property such as solubility, net charge, molecular weight, or function.
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Frontier orbitals
The highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbitals.
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gas
A state of matter in which atoms or molecules have a great deal of space between them and are free to move relative to one another; lacking a definite shape or volume, gases always assume the shape and volume of their containers.
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glycerol
(glis′er-ol) Chemical component of a triglyceride molecule.
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Ground-state electron coniguration
The most stable, lowest-energy electron coniguration of a molecule or atom.
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high-energy phosphate
A molecule that can quickly release phosphate for ATP production (e.g., guanosine triphosphate, creatine phosphate).
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homophilic
Binding between molecules of the same kind, especially those involved in cell–cell adhesion.
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Hückel 4n 1 2 rule
A rule stating that monocyclic conjugated molecules having 4n 1 2 p electrons (n 5 an integer) are aromatic.
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hydrogen bonding
The forming of a hydrogen bond. Hydrogen bonds form when polar molecules containing hydrogen atoms bond directly to small electronegative atoms such as fluorine, oxygen, and nitrogen.
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hydrophobic force
Force exerted by the hydrogen-bonded network of water molecules that brings two nonpolar surfaces together by excluding water between them.
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Integrating
A technique for measuring the area under an NMR peak to determine the relative number of each kind of proton in a molecule.
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Intramolecular, intermolecular
A reaction that occurs within the same molecule is intramolecular; a reaction that occurs between two molecules is intermolecular.
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Invariant
Constant, unchanging, usually referring to the portion of a molecule that is the same across species.
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ion-sensitive indicators
Molecules whose light emission reflects the local concentration of a particular ion; some are luminescent (emitting light spontaneously) while others are fluorescent (emitting light on exposure to light).
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ionization
The separation (dissociation) of a molecule into ions.
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ionizing power
The ability of radiation to ionize other molecules and atoms.
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JAK inhibitors (Jakinibs)
Small molecule kinase inhibitors with relative selectivity for one or more of the JAK kinases.
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kahweol
A molecule found in coffee beans that may have several health benefits, including preventing bone breakdown. May also have anticancer and anti- inflammatory properties.
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Kelvin scale
The temperature scale that assigns 0 K (-273 °C or -459 °F) to the coldest temperature possible, absolute zero, which is the temperature at which molecular motion virtually stops.
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L-selectin
Adhesion molecule of the selectin family found on lymphocytes. L-selectin binds to CD34 and GlyCAM-1 on high endothelial venules to initiate the migration of naive lymphocytes into lymphoid tissue.
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LIP22
The initial cleaved fragment of invariant chain bound to MHC class II molecules.
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liquid
A state of matter in which atoms or molecules pack about as closely as they do in solid matter but are free to move relative to each other; liquids have a fixed volume but not a fixed shape.
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local mediator
Extracellular signal molecule that acts on neighboring cells.
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MALDI
Matrix-assisted laser desorption ionization; a soft ionization method used for mass spectrometry of biological samples of very high molecular weight.
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mean free path
The average distance that a molecule in a gas travels between collisions.
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melting point
The temperature at which the molecules of a solid have enough thermal energy to overcome intermolecular forces and become a liquid.
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membrane associated ring finger (C3HC4) 1, MARCH-1
An E3 ligase expressed in B cells, dendritic cells, and macrophages that induces the constitutive degradation of MHC class II molecules, regulating their steadystate expression.
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mixed lymphocyte reaction (MLR)
A test for histocompatibility in which lymphocytes from donor and recipient are cultured together. If the two people are histoincompatible, the recipient’s T cells recognize the allogeneic MHC molecules on the cells of the other donor as ‘foreign’ and proliferate.
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molecular element
Those elements that do not normally exist in nature with single atoms as their basic units; elements with diatomic or polyatomic molecules as their basic unit.
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molecular geometry
The geometrical arrangement of atoms in a molecule.
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Molecular ion
The cation produced in a mass spectrometer by loss of an electron from the parent molecule. The mass of the molecular ion corresponds to the molecular weight of the sample.
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molecular mass
The sum of the atomic masses of all atoms making up a molecule.
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Molecular mechanics
A computerbased method for calculating the minimum-energy conformation of a molecule.
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nanotechnology
Making molecular- or atomic-sized products.
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Noncovalent interactions
One of a variety of nonbonding interactions between molecules, such as dipole–dipole forces, dispersion forces, and hydrogen bonds.
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octahedral geometry
The molecular geometry of seven atoms with 90° bond angles.
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Optically active
A property of some organic molecules wherein the plane of polarization is rotated through an angle when a beam of plane-polarized light is passed through a solution of the molecules.
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PAMP (pathogen-associated molecular patterns)
Molecules present on pathogens and not self.
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permanent dipole
A molecule with a permanent dipole always has a slightly negative charge at one end and a slightly positive charge at the other.
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phosphorescence
The long-lived emission of light that sometimes follows the absorption of light by certain atoms and molecules.
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photoactivation
Technique for studying intracellular processes in which an inactive form of a molecule of interest is introduced into the cell, and is then activated by a focused beam of light at a precise spot in the cell.
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Plane of symmetry
A plane that bisects a molecule such that one half of the molecule is the mirror image of the other half. Molecules containing a plane of symmetry are achiral.
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Plasticizers
Small organic molecules added to polymers to act as a lubricant between polymer chains.
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Polarizability
The measure of the change in a molecule’s electron distribution in response to changing electrostatic interactions with solvents or ionic reagents.
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pressure
A measure of force exerted per unit area; in chemistry, most commonly the force exerted by gas molecules as they strike the surfaces around them.
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Prochiral
A molecule that can be converted from achiral to chiral in a single chemical step.
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reversible reaction
A chemical reaction in which the end-products can readily revert to the original molecules.
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Ring-lip
A molecular motion that interconverts two chair conformations of cyclohexane. The effect of a ring-lip is to convert an axial substituent into an equatorial substituent.
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Saturated
A molecule that has only single bonds and thus can’t undergo addition reactions. Alkanes are saturated, but alkenes are unsaturated.
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scanned-probe microscopy
Microscopic technique used to obtain images of molecular shapes, to characterize chemical properties, and to determine temperature variations within a specimen.
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secondary valence
The number of molecules or ions directly bound to the metal atom in a complex ion; also called the coordination number.
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seesaw geometry
The molecular geometry of a molecule with trigonal bipyramidal electron geometry and one lone pair in an axial position.
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sickle-cell anemia
A human disease characterized by defective hemoglobin molecules in individuals homozygous for a mutant allele coding for the chain of hemoglobin.
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singlet oxygen
Highly reactive molecular oxygen (O2 -).
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size-exclusion chromatography
A procedure for the separation of molecules by size, based on the capacity of porous polymers to exclude solutes above a certain size; also called gel filtration.
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solid
A state of matter in which atoms or molecules are packed close to one another in fixed locations with definite volume.
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space-filling molecular model
A representation of a molecule in which atoms fill the space between each other to more closely represent how a molecule might appear if scaled to visible size.
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square planar geometry
The molecular geometry of a molecule with octahedral electron geometry and two lone pairs.
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square pyramidal geometry
The molecular geometry of a molecule with octahedral electron geometry and one lone pair.
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Stereochemistry
The branch of chemistry concerned with the three-dimensional arrangement of atoms in molecules.
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structural formula
A molecular formula that uses lines to represent covalent bonds and shows how the atoms in a molecule are connected or bonded to each other.
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Symmetry plane
A plane that bisects a molecule such that one half of the molecule is the mirror image of the other half. Molecules containing a plane of symmetry are achiral.
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synthesis reaction
A chemical reaction in which two or more atoms combine to form a new, larger molecule.
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T-shaped geometry
The molecular geometry of a molecule with trigonal bipyramidal electron geometry and two lone pairs in axial positions.
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Tautomeric shift
The transfer of a hydrogen atom from one position in an organic molecule to another position.
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temperature
A measure of the average kinetic energy of the atoms or molecules that compose a sample of matter.
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tetrahedral geometry
The molecular geometry of five atoms with 109.5° bond angles.
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thermal energy
A type of kinetic energy associated with the temperature of an object, arising from the motion of individual atoms or molecules in the object; see also heat.
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Thermodynamic activity
Used here as a measure of the ‘escaping tendency’ of a molecule from its formulation. By definition, a thermodynamic activity of 1 equates to a saturated solution, or suspension, as the molecules in a saturated solution have the greatest ‘escape tendency’.
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Torsional strain
The strain in a molecule caused by electron repulsion between eclipsed bonds. Torsional strain is also called eclipsing strain.
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transport
Process by which substances and molecules are transferred from one area of the body to another, or from outside a cell to inside a cell.
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trigonal planar geometry
The molecular geometry of four atoms with 120° bond angles in a plane.
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trigonal pyramidal geometry
The molecular geometry of a molecule with tetrahedral electron geometry and one lone pair.
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Unsaturated
A molecule that has one or more multiple bonds.
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valence
The combining capacity of an atom or a molecule.
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valence band
In band theory, the band of energy levels that forms from bonding molecular orbitals.
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valence shell electron pair repulsion (VSEPR) theory
A theory that allows prediction of the shapes of molecules based on the idea that electrons—either as lone pairs or as bonding pairs—repel one another.
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VCAM-1
An adhesion molecule expressed by vascular endothelium at sites of inflammation; it binds the integrin VLA-4, which allows effector T cells to enter sites of infection.
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white phosphorus
An unstable allotrope of phosphorus consisting of P4 molecules in a tetrahedral shape, with the phosphorus atoms at the corners of the tetrahedron.
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α2-Macroglobulin
A circulating protease inhibitor with a very high molecular weight (725,000 D).
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Highest occupied molecular orbital (HOMO)
The symmetries of the HOMO and LUMO are important in pericyclic reactions.
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kinetic molecular theory
A model of an ideal gas as a collection of point particles in constant motion undergoing completely elastic collisions.
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Lowest unoccupied molecular orbital (LUMO)
The symmetries of the LUMO and the HOMO are important in determining the stereochemistry of pericyclic reactions.
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molecularity
The number of reactant particles involved in an elementary step.
