Paramagnetic, PCR, Periplasm, Peroxidase, Phagocyte, Phosphatase, Phosphorylation, Photolysis, Photosynthesis, Photosystem, Phytochelatin, Picket-fence porphyrin, Plasma, Plasmid, Plastocyanin, Polydentate, Polyhedral symbol, Polymerase chain reaction, Porphyrin, Power saturation, Primary structure, Prokaryote, Promoter, Prosthetic group, Protoporphyrin IX, Pterin, Quaternary structure, Racemic, Radical, Radionuclide, Rate-controlling step, Redox potential, Reductase, Reductive elimination, Regulation , Relative configuration, Relaxation, Resonance Raman spectroscopy, Ribonucleic acids (RNA), Ribonucleotide reductases, Ribosomes, Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), Rieske iron-sulfur protein, RNA, Rubisco, Rubredoxin, Rubrerythrin, Rusticyanin.
Substances having a positive magnetic susceptibility are paramagnetic. They are attracted by a magnetic field.
See polymerase chain reaction.
The fluid occupying the space between the inside and outside cellular membranes of bacteria.
A heme protein (donor:hydrogen-peroxide oxidoreductase, EC class 1.11.1) which catalyzes the one-electron oxidation of a substrate by dihydrogen peroxide. Substrates for different peroxidases include various organic compounds, cytochrome c, halides, and Mn2+.
A cell which is able to ingest, and often to digest, large particles such as bacteria and dead tissue cells.
An enzyme that catalyzes the hydrolysis of orthophosphoric monoesters. Alkaline phosphatases (EC 220.127.116.11) have an optimum pH above 7 and are zinc-containing proteins. Acid phosphatases (EC 18.104.22.168) have an optimum pH below 7 and some of these contain a dinuclear center of iron, or iron and zinc.
A process involving the transfer of a phosphate group (catalyzed by enzymes) from a donor to a suitable acceptor; in general an ester linkage is formed, for example:
A light-induced bond cleavage. The term is often used incorrectly to describe irradiation of a sample.
A metabolic process in plants and certain bacteria, using light energy absorbed by chlorophyll and other photosynthetic pigments for the reduction of CO2, followed by the formation of organic compounds. See also photosystem.
A membrane-bound protein complex in plants and photosynthetic bacteria, responsible for light harvesting and primary electron transfer. Comprises light-harvesting pigments such as chlorophyll; a primary electron-transfer center, and secondary electron carriers. In green plant photosynthesis, Photosystem I transfers electrons from plastocyanin to a [2Fe-2S] ferredoxin, and contains iron-sulfur proteins. Photosystem II transfers electrons from the oxygen-evolving complex to plastoquinone, and contains an iron center.
A peptide of higher plants, consisting of polymers of 2-11 glutathione (-glutamyl-cysteinyl-glycine) groups, which binds heavy metals.
A porphyrin with a protective enclosure for binding oxygen at one side of the ring that is used to mimic the dioxygen-carrying properties of the heme group. See also biomimetic.
In biology this term has the following three meanings :
(1) Fluid component of blood in which the blood cells and platelets are suspended ('blood plasma').
N.B. Note the distinction between plasma, which describes a part of the blood (the fluid part of blood, outside the blood cells) and serum, which describes a fraction derived from blood by a manipulation (the fluid which separates when blood coagulates).
(2) Fluid component of semen produced by the accessory glands, the seminal vesicles, the prostate, and the bulbo-urethal glands.
(3) Cell substance outside the nucleus (cytoplasm).
An extrachromosomal genetic element consisting generally of circular double-stranded DNA, which can replicate independently of chromosomal DNA. R-plasmids are responsible for the mutual transfer of antibiotic resistance among microbes. Plasmids are used as vectors for cloning DNA in bacteria or yeast host cells.
An electron transferprotein, containing a type 1 copper site, involved in plant and cyanobacterial photosynthesis, which transfers electrons to Photosystem I.
See chelation, donor atom symbol.
The polyhedral symbol indicates the geometrical arrangements of the coordinating atoms about the central atom. It consists of one or more capital italic letters derived from common geometric terms (tetrahedron, square plane, octahedron, etc.) which denote the idealized geometry of the ligands around the coordination center, and an arabic numeral that is the coordination number of the central atom. The polyhedral symbol is used as an affix, enclosed in parentheses, and separated from the name by a hyphen. Examples are T-4, SP-4, TBPY-5, SPY-5, OC-6, andCU-8.
Polymerase chain reaction (PCR)
A laboratory technique, to rapidly amplify pre-determined regions of double stranded DNA. Generally involves the use of a heat-stable DNA polymerase.
A macrocyclic molecule that contains four pyrrole rings linked together by single carbon atom bridges between the alpha positions of the pyrrole rings. Porphyrins usually occur in their dianionic form coordinated to a metal ion.
A phenomenon used in electron paramagnetic resonance spectroscopy to estimate the electron-spin relaxation times, providing information about distances between paramagnetic centers.
The amino-acid sequence of a protein or nucleotide sequence of DNA or RNA.
A unicellular organism characterized by the absence of a membrane-bound nucleus. See also eukaryotes.
The DNA region, usually upstream to the coding sequence of a gene or operon, which binds and directs RNA polymerase to the correct transcriptional start site and thus permits transcription at a specific initiation site.
N.B.In catalysis a promoter is used differently: a co-catalyst usually present in much smaller amounts than the catalyst.
A tightly bound, specific nonpolypeptide unit in a protein determining and involved in its biological activity. See also cofactor.
The porphyrin ligand of heme b. Heme b is a Fe(II) porphyrin complex readily isolated from the hemoglobin of beef blood, but also found in other proteins including other hemoglobins, myoglobins, cytochromes P-450, catalases, peroxidases as well as b type cytochromes. Protoporphyrin IX contains four methyl groups in positions 2, 7, 12 and 18, two vinyl groups in positions 3 and 8 and two propionic acid groups in positions 13 and 17.
2-Amino-4-hydroxypteridine. See also molybdopterin
The level of structural organization in oligomeric proteins (i.e., those composed of more than one subunit) represented by the number and arrangement of the subunits and the interactions between them.
Pertaining to a racemate, an equimolar mixture of a pair of enantiomers. It does not exhibit optical activity.
A molecular entity possessing one or more unpaired electrons, formerly often called "free radical". A radical may be charged, positively (radical cation) or negatively (radical anion). Paramagnetic metal ions are not normally regarded as radicals.
A radioactive nuclide. The term nuclide implies an atom of specified atomic number and mass number. In the study of biochemical processes, radioactive isotopes are used for labelling compounds that subsequently are used to investigate various aspects of the reactivity or metabolism of proteins, carbohydrates and lipids or as sources of radiation in imaging. The fate of the radionuclide in reactive products or metabolites is determined by following (counting) the emitted radiation. Prominent among the radionuclides used in biochemical research are : 3H, 14C, 32P, 35Ca, 99mTc, 125I and 131I. See also imaging.
A rate-controlling (rate-determining or rate-limiting) step in a reaction occurring by a composite mechanism is an elementary reaction, the rate constant for which exerts a dominant effect - stronger than that of any other rate constant - on the overall rate.
Any oxidation-reduction (redox) reaction can be divided into two half reactions: one in which a chemical species undergoes oxidation and one in which another chemical species undergoes reduction. If a half-reaction is written as a reduction, the driving force is the reduction potential. If the half-reaction is written as oxidation, the driving force is the oxidation potential related to the reduction potential by a sign change. So the redox potential is the reduction/oxidation potential of a compound measured under standard conditions against a standard reference half-cell. In biological systems the standard redox potential is defined at pH = 7. 0versus the hydrogen electrode and partial pressure of hydrogen = 1 bar. See also electrode potential.
The reverse of oxidative addition.
Refers to control of activity of an enzyme (system) or gene expression.
The configuration of any stereogenic (asymmetric) centre with respect to any other stereogenic centre contained within the same molecular entity. A stereogenic unit is a grouping within a molecular entity that may be considered a focus of stereoisomerism.
If a system is disturbed from its state of equilibrium it relaxes to that state, and the process is referred to as relaxation.
Resonance Raman spectroscopy
A spectroscopic technique increasingly used in bioinorganic chemistry for characterization and assignment of vibrations directly connected with a chromophore, as well for the assignment of the chromophore. The excitation frequency is applied close to the absorption maximum of the chromophore. Particularly useful for deeply coloured species.
Ribonucleic acids (RNA)
Linear polymer molecules composed of a chain of ribose units linked between positions 3 and 5 by phosphodiester groups. The bases adenine or guanine (via atom N-9) or uracil or cytosine (via atom N-1), respectively, areattached to ribose at its atom C-1 by -N-glycosidic bonds (see nucleotides). The three most important types of RNAs in the cell are: messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA).
Enzymes (EC 22.214.171.124-2), which catalyze the reduction of ribonucleotide diphosphates or triphosphates to the corresponding deoxyribonucleotides by a radical-dependent reaction. The enzyme of animal, yeast and aerobic E. coli cells contains an oxo-bridged dinuclear iron center and a tyrosyl radical cation, and uses thioredoxin, a thiol-containing protein, as reductant. At least three other ribonucleotide reductases are known from bacteria, containing, respectively, an iron-sulfur cluster with a glycyl radical, adenosyl cobalamin, and a dinuclear manganese cluster.
A subcellular unit composed of specific rRNA and proteins that are responsible for the translation of mRNA into protein synthesis.
Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
A magnesium-dependent enzyme (EC 126.96.36.199), the primary enzyme of carbon dioxide fixation in plants and autotrophic bacteria. It catalyzes the synthesis of 3-phospho-D-glycerate from ribulose bisphosphate and also the oxidation of ribulose bisphosphate by O2 to 3-phospho-D-glycerate and 2-phosphoglycolate.
Rieske iron-sulfur protein
An iron-sulfur protein of the mitochondrial respiratory chain, in which the [2Fe-2S] cluster is coordinated to two sulfur ligands from cysteine and two imidazole ligands from histidine. The term is also applied to similar proteins isolated from photosynthetic organisms and microorganisms, and other proteins containing [2Fe-2S]clusters with similar coordination.
See ribonucleic acids.
See ribulose-1,5-bisphosphate carboxylase/oxygenase.
An iron-sulfur protein without acid-labile sulfur, in which an iron center is coordinated by four sulfur-containing ligands, usually cysteine. The function, where known, is as an electron carrier.
A protein assumed to contain both a rubredoxin-like iron center and a hemerythrin-like dinuclear iron center.
An electron transferprotein, containing a type 1 copper site, from the periplasm of the iron-oxidizing bacterium Thiobacillus ferrooxidans.
Return to home page for Glossary of terms used in Bioinorganic Chemistry.