Comp Name Description see also
Amoeboid-Cell-Locomotion The finger-like locomotion of a cell caused by the projection and retraction of internal actin filaments. Souther. Cell Actin-Filament Group
Cell-Locomotion The locomotion of a cell, usually accomplished internally using Actin-Filament or externally using flagella or cilia. Souther. Cell Actin-Filament Group Protein-Filament
Ensemble A collection of distinct structures which function together to carry out some task, as the respiratory enzyme complex on mitochondrial membranes. Souther.
Genome The total genetic information carried by a cell or an organism (or the DNA-Molecule that carry this information. Alberts:ECB:G-8. DNA-Molecule Gene
Group A collection of identical or functionally identical molecules which act together to perform some functional or structural role. Souther. Centriole Enzyme-Complex Histone-Complex
Centriole Short cylindrical array of microtubules, usually found (in animal cells in a paired arrangement at the center of a centrosome. Similar structures are found at the base of cilia and flagella, where they are called basal bodies. Alberts:ECB:G-4 Mitosis Microtubule Group Protein-Complex
UAG A codon in mRNA which signals the termination point for translation of a polypeptide. Souther. Ribonucleotide UMP Protein-Stop-Codon GMP AMP
Enzyme-Complex A group of enzymes which act together to provide structure or perform some function. Examples are ATP synthesis and oxidative phosphorylation enzymes. Souther. Enzyme ATP-Synthase Group ATP Protein-Complex
ATP-Synthase Membrane-associated enzyme complex that catalyzes the formation of ATP during oxidative phosphorylation and photosynthesis. Found in mitochondria, chloroplasts, and bacteria. Alberts:ECB:G-2. ATP-Synthesis Enzyme-Complex ATP Oxidative-Phosphorylation Catalyst Membrane
Histone-Complex A group of basic proteins, rich in arginine and lysine, that are associated with DNA in chromosomes. Alberts:ECB:G-9. Histone Group Protein-Complex
Pool A collection of identical or functionally identical molecules in a compartment of a cell.
Actin-Filament Protein filament, about 7nm thick, formed from a chain of globular Actin-Molecule. A major constituent of the cytoskeleton of all Eucaryotic-Cell and especially abundant in muscle cells. Alberts:ECB:G-1. Protein Actin-Molecule Eucaryotic-Cell Amoeboid-Cell-Locomotion Protein-Filament
Chemical-Sequence A sequence of monomers that form a chain, e.g. polymers. Souther:2001 Amino-Acid-Sequence Dinucleotide Nucleotide-Sequence Chemical-Object Monomer Chemical-Information-Sequence
Amino-Acid-Sequence A chain of amino-acids linked by Peptide-Bond. Souther. Carboxyl-Terminus Amino-Terminus Amino-Acid Peptide-Bond Chemical-Sequence Information-Sequence Polypeptide
Polypeptide Linear polymer composed of multiple Amino-Acid. Proteins are large polypeptides. Alberts:ECB:G-14. Amino-Acid-Sequence Macromolecule Protein Amino-Acid Protein-Domain
Protein Linear polymer of Amino-Acid linked together in a specific sequence by Peptide-Bond. Alberts:ECB-G-15. Allosteric-Protein Amino-Acid Cytoplasmic-Protein Globular-Protein Ribosomal-Protein Protein-Domain Structural-Protein Enzyme Fibrous-Protein Ubiquinated-Protein Nascent-Protein Peptide-Bond Regulatory-Protein Secreted-Protein Polypeptide
Allosteric-Protein Protein that exists in two or more conformations depending on the binding of a molecule (a ligand) at a regulatory site. Allosteric-Protein composed of multiple subunits often display a cooperative response to ligand binding. Modified from Alberts:ECB:G-1. Regulatory-Site Protein Binding-Site Allosteric-Enzyme
Allosteric-Enzyme Enzyme that exists in two or more conformations depending on the binding of a molecule [a ligand] at a site other than the catalytic site. Allosteric-Enzyme composed of multiple subunits often display a cooperative response to ligand binding. Alberts:ECB:G-1. Allosteric-Protein Enzyme Regulatory-Site Active-Site
Cytoplasmic-Protein A protein located in the cytoplasm of the cell. Souther. Protein Cytoplasm
Enzyme A protein that catalyzes a specific chemical reaction. Alberts:ECB:G-7. Addition-Enzyme Protein Enzyme-Catalysis Ligase Catalyst Peptidyl-Transferase Catabolic-Enzyme Ubiquitin-Binding-Enzyme Transfer-Enzyme Ribosomal-Peptidyl-Transferase Removal-Enzyme DNA-Helicase Synthase
Addition-Enzyme Enzyme that adds a group to an atom or molecule. Souther. Enzyme Chemical-Group Atom Add-Enzymatic Kinase Catalyst Molecule
Kinase Enzyme that transfers a phosphate group from ATP (or from another nucleoside triphosphate) onto another molecule. Alberts:ECB:G-10. Enzyme Protein-Kinase Addition-Enzyme Phosphorylation ATP Catalyst
UGA A codon in mRNA which signals the termination point for translation of a polypeptide. Souther. Ribonucleotide UMP Protein-Stop-Codon GMP AMP
Protein-Kinase Enzyme that transfers a phosphate group from ATP to a specific amino acid of a target protein. Cells contain hundreds of different Protein-Kinase, phosphorylating different sets of target proteins. Alberts:ECB:G-15. Enzyme Protein Kinase Phosphorylation ATP Catalyst
Catabolic-Enzyme An enzyme involved in the breakdown of large molecules into smaller accompanied by the release of energy. Souther (see Alberts:ECB:G-3 on catabolic). Nuclease Enzyme Protease Catalyst Lipase Catabolize
Lipase Enzyme that catalyzes the cleavage of fatty acids from from the glycerol moiety. Alberts:MBC:G-14. Enzyme Lipolysis Catalyst Catabolic-Enzyme
Nuclease Enzyme that cleaves Nucleic-Acid. Matthews:BC:1157 Enzyme Nucleic-Acid-Degradation Nucleic-Acid DNA-Mismatch-Repair-Protein Ribonuclease Deoxyribonuclease Catalyst Catabolic-Enzyme
Deoxyribonuclease Enzyme that cleaves DNA. Souther. Nuclease Enzyme DNA-Repair Catalyst
DNA-Mismatch-Repair-Protein Enzyme that helps repair mismatches in DNA Base-Pair by removing a sequence which includes the mismatched pairs. Souther. see Alberts:ECB:200-201. Nuclease Enzyme Base-Pair Catalyst DNA-Mismatch-Repair
Ribonuclease Enzyme that cleaves RNA. Souther. Nuclease Enzyme RNA Ribonucleic-Acid-Degradation Catalyst
Protease Enzyme such as trypsin that degrades proteins by hydrolyzing some of their Peptide-Bond. Alberts:ECB:G-15. Enzyme Peptide-Bond Catalyst Proteolysis Catabolic-Enzyme
DNA-Helicase An enzyme that catalyzes the separation of strands in a DNA molecule before replication. Lehninger:PBC:G-6 Enzyme DNA-Replication DNA-Regulatory-Protein Catalyst
Ligase Enzyme that joins two segments of DNA or RNA together end to end. Alberts:ECB:G-10. Enzyme RNA DNA-Ligase Catalyst Ligation
DNA-Ligase An enzyme that appends nucleotides onto the growing DNA chain during chain elongation or joins two Nucleotide-Sequence together during repair of strand breaks. Souther. see Alberts:ECB:G-10. Nucleotide-Sequence Ligase Catalyst DNA-Ligation
Peptidyl-Transferase A protein that catalyzes the transfer of a peptide group from one molecule to another, e.g. ribosomal peptidyl transferase. Enzyme Catalyst Transfer-Enzymatic
Removal-Enzyme Enzyme that removes a group from a molecule. Examples are phosphatases and deaminases. Souther. Phosphatase Enzyme Deaminase
Deaminase Enzyme that removes an amino group from a molecule. Souther. Enzyme Deamination Removal-Enzyme Catalyst
Phosphatase Enzyme that removes a phosphate group from a molecule. see Alberts:ECB:G-15 for proteins. Enzyme Removal-Enzyme Dephosphorylation Catalyst Protein-Phosphatase
Protein-Phosphatase Enzyme that removes a phosphate group by hydrolysis from a protein, usually with high specificity. Alberts:ECB:G-15. Phosphatase Enzyme Protein Dephosphorylation Catalyst
Ribosomal-Peptidyl-Transferase The enyzme that catalyzes the transfer of the growing polypeptide chain to the amino acid on the newly docked tRNA during protein synthesis. The enzyme is part of the ribosomal nuceloprotein complex. Souther. Enzyme
Synthase An enzyme involved in the synthesis of large molecules from smaller which requires the input of energy. Souther (see Alberts:ECB:G-2 on anabolic). Enzyme Biosynthesize Amino-Acyl-TRNA-Synthetase Polymerase Catalyst
Amino-Acyl-TRNA-Synthetase An enzyme that adds one of the amino acids to the end of the appropriate tRNA molecule before the tRNA binds to the ribosome during mRNA translation. Souther. Catalyst TRNA-Charging Synthase
Polymerase General term for an enzyme that catalyzes addition of subunits to a polymer. DNA polymerase, for example, makes DNA, while RNA polymerase makes RNA. Alberts:ECB:G-14. DNA-Polymerase-Replication Polymerize DNA-Polymerase Primase RNA Catalyst RNA-Polymerase Synthase
DNA-Polymerase Enzyme that catalyzes the synthesis or repair of a DNA molecule from nucleoside triphosphate precursors using a DNA template. Souther. see Alberts: ECB:G-16. Enzyme DNA-Polymerase-Repair Polymerase DNA-Synthesis Procaryotic-DNA-Polymerase Catalyst Eucaryotic-DNA-Polymerase
DNA-Polymerase-Repair Enzyme that catalyzes the repair of a DNA molecule either because of damage or because of wrong base incorporation. Also used to replace the RNA primer during DNA replication. Souther. see Alberts:ECB:196. Enzyme DNA-Polymerase RNA DNA-Repair Catalyst
Eucaryotic-DNA-Polymerase Enzyme that catalyzes the synthesis or repair of a DNA molecule from nucleoside triphosphate precursors using a DNA template in eucaryotes. Souther. see Alberts: ECB:G-16. Enzyme DNA-Polymerase
Procaryotic-DNA-Polymerase Enzyme that catalyzes the synthesis or repair of a DNA molecule from nucleoside triphosphate precursors using a DNA template in procaryotes. Souther. see Alberts: ECB:G-16. Enzyme DNA-Polymerase
DNA-Polymerase-Replication Enzyme that catalyzes the synthesis of a DNA molecule on a DNA template from nucleoside triphosphate precursors. Alberts: ECB:G-16. Enzyme Polymerase DNA-Replication Catalyst
Primase An RNA polymerase that makes the short RNA primer needed to initiate DNA chain elongation during DNA replication. see Alberts:ECB:195. Polymerase RNA DNA-Replication Catalyst
RNA-Polymerase Enzyme that catalyzes the synthesis of an RNA molecule on a DNA template from nucleoside triphosphate precursors (Alberts: ECB:G-16). Enzyme DNA-Transcription Polymerase RNA Bacterial-RNA-Polymerase Eucaryotic-RNA-Polymerase Catalyst
Bacterial-RNA-Polymerase Enzyme that catalyzes the synthesis of an RNA molecule on a DNA template from nucleoside triphosphate precursors in bacteria. (modified from Alberts: ECB:G-16). Enzyme RNA Catalyst Sigma-Factor RNA-Polymerase
Eucaryotic-RNA-Polymerase The RNA polymerase which carries out transcription in in eucaryotic organisms. RNA RNA-Polymerase
Transfer-Enzyme A protein that catalyzes the transfer of a group from one molecule to another, e.g. oxido-reductases. Souther. Oxido-Reductase Enzyme Catalyst Transfer-Enzymatic
Oxido-Reductase General name for an enzyme that catalyzes reactions in which one molecule is oxidized and the other is reduced. Enzymes of this type are often called oxidases, reductases, and dehydrogenases. Alberts:ECB:168. Transfer-Enzyme Oxidase Catalyst Oxido-Reduction-Reaction
Oxidase Enzyme that catalyzes oxidation reactions in which in which molecular oxygen serves as the electron acceptor, but neither of the Oxygen-Atom is incorporated into the product. Lehninger:PBC:G-9. Oxido-Reductase Enzyme Oxygen-Atom Peroxidase Catalyst Oxidation
Peroxidase Enzyme that catalyzes the breakdown of peroxidase. see Lehninger:PBC:G-10. Enzyme Peroxide Oxidase Catalyst Oxidation
Ubiquitin-Binding-Enzyme Specialized enzyme that tags a protein to be degraded with Ubiquitin. Souther. Enzyme Ubiquitin
Fibrous-Protein A protein with an elongated shape; typically one such as collagen or intermediate filament protein that is able to associate into long filamentous structures. Alberts:ECB:G-8. Protein Collagen
Collagen A fibrous protein rich in glycine and proline that is a major component of the extracellular matrix in animal tissues. Exists in many forms: type I, the most common, is found in skin, tendon, and bone; type II is found in cartilage; type IV is present in basal laminae. Alberts:ECB:G-5. Fibrous-Protein
Globular-Protein Any protein with an approximately rounded shape. Most enzymes are globular. Alberts:ECB:G-8. Protein
Nascent-Protein A newly synthesized protein before any modifications. Souther. Amino-Terminus Methionine Protein
Regulatory-Protein A protein whose role is to affect the activity of DNA, RNA, or proteins or other cell constituents. Souther. Protein RNA Protein-Regulatory-Protein RNA-Regulatory-Protein DNA-Regulatory-Protein
DNA-Regulatory-Protein A protein that regulates DNA replication or gene expression. Souther. Single-Strand-Binding-Protein Histone Protein-Sliding-Clamp DNA-Gyrase Regulatory-Protein DNA-Helicase
DNA-Gyrase A protein which binds to DNA and relieves torsional strain generated by DNA unwinding during replication. see Lehninger:PBC:943 DNA-Replication DNA-Regulatory-Protein Catalyst
Histone One of a group of basic proteins, rich in arginine and lysine, that are associated with DNA in chromosomes. Alberts:ECB:G-9. DNA-Regulatory-Protein
Protein-Sliding-Clamp A protein which encircles the DNA strand and holds the DNA polymerase in place during replication. Alberts:ECB:197. DNA-Polymerase Replication-Fork DNA-Replication DNA-Regulatory-Protein
Single-Strand-Binding-Protein A protein which binds to single-stranded DNA during DNA replication to prevent it from reforming the double helix Alberts:ECB:197. DNA-Sequence DNA-Regulatory-Protein DNA-Template
Protein-Regulatory-Protein A protein which regulates the activity of other proteins, usually by directly attaching to them. Souther. Ubiquitin Protein-Chaperone Regulatory-Protein
Protein-Chaperone A protein which assists in the folding or the membrane transport of another protein. Souther. Protein-Regulatory-Protein
Ubiquitin A protein which attaches to other proteins and marks them for degradation by proteasomes. Souther. Protein-Regulatory-Protein
RNA-Regulatory-Protein A protein which regulates mRNA processing or translation. Souther. Translation-Initiation-Factor Ribosome-Release-Factor Regulatory-Protein
Ribosome-Release-Factor A protein which participates in the release of the ribosome from the mRNA at the end of translation. Souther. RNA-Regulatory-Protein
Translation-Initiation-Factor A protein involved in the initiation of translation of mRNA into protein. Souther. RNA-Regulatory-Protein
Ribosomal-Protein A protein that is part of the ribosome. There are 50 or more distinct proteins associated with ribosomal RNA in the ribosome. Souther. Protein RNA Procaryotic-Ribosomal-Protein
Procaryotic-Ribosomal-Protein A protein that is part of the procaryotic ribosome. There are 50 or more distinct proteins associated with ribosomal RNA in the ribosome. Souther. RNA Ribosomal-Protein
Secreted-Protein A protein that is secreted from the cell. Souther. Protein
Structural-Protein A protein that provides structure to the cell, such as the proteins forming the cytoskeleton or the nuclear lamina. Souther Protein Actin-Molecule Tubulin-Molecule
Actin-Molecule A globular protein that polymerizes into actin filaments. see Alberts:ECB:G-1. Polymerize Actin-Filament Globular-Protein Structural-Protein
Tubulin-Molecule A globular protein that polymerizes into microtubules. Alberts:ECB:G-18. Structural-Protein
Ubiquinated-Protein Protein which has been tagged with ubiquitin, which marks it for degradation by proteasomes. Souther. Protein Ubiquitin
Protein-Domain Compact and stably folded region of polypeptide. Alberts:ECB:G-6. Protein Polypeptide
Chemical-Information-Sequence A sequence which encodes information. Biological examples are DNA, RNA, and the amino acid sequence of proteins (which determines folding). Souther. RNA Chemical-Object Chemical-Sequence Information-Sequence
Dinucleotide A sequence of two nucleotides. Larger sequences (3-50) are termed oligonucleotides. Souther 5-Prime-Nucleotide Phosphodiester-Bond Nucleoside-Triphosphate Carbon-Atom Chemical-Sequence Pentose 3-Prime-Nucleotide
Nucleotide-Sequence A sequence of nucleotides which forms a nucleotide polymer. Souther:2001 Polynucleotide Free-Nucleotide-Sequence RNA-Noncoding-Sequence Regulatory-Sequence Oligonucleotide 3-Prime-Nucleotide RNA-Sequence 5-Prime-Nucleotide DNA-Sequence Coding-Sequence Ribosome-Binding-Site Nucleotide Chemical-Sequence Internal-Nucleotide-Sequence
Coding-Sequence A DNA or RNA sequence which contains genetic information, encoded in nucleotide triplets, termed codons. Souther. RNA-Coding-Sequence RNA DNA-Coding-Sequence Nucleotide-Sequence Codon Information-Sequence DNA-Gene-Coding-Sequence
Codon Sequence of three nucleotides in DNA or mRNA that represents the instruction for incorporation of a specific amino acid into a polypeptide chain. Alberts:ECB:G-5. Protein-Initiator-Codon RNA-Codon Coding-Sequence DNA-Codon Nucleotide RNA-Anticodon
DNA-Codon Sequence of three nucleotides in a DNA molecule that represents the instruction for incorporation of a specific amino acid into a polypeptide chain. cf Alberts:ECB:G-5 (codon). Deoxyribonucleotide DNA-Coding-Sequence Codon
Protein-Initiator-Codon The start codon for translation of mRNA into protein. Sequence is AUG. Souther. Ribonucleotide RNA-Regulatory-Sequence UMP Codon GMP AMP
RNA-Anticodon Sequence of three nucleotides in a transfer RNA molecule that is complementary to the three nucleotide codon on a messenger RNA molecule; the anti-codon is matched to a specific amino acid covalently attached to the transfer RNA molecule. Alberts:ECB:G-2. RNA Codon Nucleotide
RNA-Codon Sequence of three nucleotides in a RNA molecule that represents the instruction for incorporation of a specific amino acid into a polypeptide chain. cf Alberts:ECB:G-5 (codon). Ribonucleotide RNA Amino-Acid Codon Protein-Stop-Codon Gene-Expression
Protein-Stop-Codon A codon in mRNA which signals the termination point for translation of a polypeptide. Souther. RNA-Codon RNA-Regulatory-Sequence GCA-Codon UUA UAG UGA
GCA-Codon A codon in mRNA which signals the termination point for translation of a polypeptide. Souther. Protein-Stop-Codon
UUA A codon in mRNA which signals the termination point for translation of a polypeptide. Souther. Ribonucleotide UMP Protein-Stop-Codon AMP
DNA-Coding-Sequence A region of the DNA which codes for all or part of a protein or RNA. It may include noncoding regions, as for example in Eucaryotic-Gene which include Regulatory-Sequence. Souther. RNA Cistron DNA-Codon Internal-DNA-Sequence Eucaryotic-Gene Regulatory-Sequence DNA-Sequence Exon Coding-Sequence 3-Prime-Deoxyribonucleotide Transcription-Unit 5-Prime-Deoxyribonucleotide Gene
Cistron The smallest unit of DNA that must be intact to code for the amino acid sequence of a polypeptide; thus, the coding part of a gene, minus 5' and 3' untranslated sequences and regulatory elements. Matthews:BC:1150. DNA-Coding-Sequence DNA-Codon
Exon Segment of a eucaryotic gene that is transcribed into RNA and codes for the amino acid sequence of part of a protein. Alberts:ECB:G-7. RNA DNA-Coding-Sequence Eucaryotic-Gene
Gene Region of DNA that controls a discrete hereditary characteristic of an organism, usually corresponding to a single protein or RNA. Alberts:ECB:G8. Genes generally include both transcription units and flanking Regulatory-Region, but in operons they lack flanking regions, ie, Procaryotic-Gene include flanking Regulatory-Region when alone, but not when part of an operon. Souther. RNA DNA-Coding-Sequence Procaryotic-Gene DNA-Codon Eucaryotic-Gene DNA-Template DNA-Strand Regulatory-Region
Eucaryotic-Gene Region of DNA that controls a discrete hereditary characteristic, usually corresponding to a single protein or RNA. This definition includes the entire functional unit, encompassing coding DNA-Sequence, noncoding regulatory DNA-Sequence, and introns Alberts:MBC:G-10. RNA DNA-Sequence DNA-Gene-Coding-Sequence Gene
Procaryotic-Gene Region of procaryotic DNA that controls a discrete hereditary characteristic, usually corresponding to a single protein or RNA. Most Procaryotic-Gene are part of operons. Souther. RNA Operon Gene
Transcription-Unit A stretch of DNA that is naturally transcribed in a single operation to produce a single primary transcript. Can be (the coding part of) an operon or a gene. Strachan:HMG:556. Includes untranslated regions as well as the cistron. Souther DNA-Transcription DNA-3prime-UTR DNA-Coding-Sequence DNA-5prime-UTR Cistron DNA-Codon Template
DNA-Gene-Coding-Sequence Physical and functional unit of heredity, which carries information from one generation to the next. In molecular terms, it is the entire DNA sequence - including exons, introns, and noncoding transcription control regions - necessary for production of a functional protein or RNA. (Lodish:MCB:G-7). Note: this is the definition for gene, but applies to operons as well. DNA-Sequence RNA Coding-Sequence Operon Eucaryotic-Gene
Operon A set of contiguous prokaryotic structural genes that are transcribed as a unit, along with the adjacent regulatory elements that control their expression. Matthews:Biochemistry:1158. DNA-Gene-Coding-Sequence
RNA-Coding-Sequence A region of the RNA which codes for all or part of a protein. Souther. RNA Coding-Sequence RNA-Sequence
DNA-Sequence A nucleotide sequence of deoxyribonucleotides. Souther. Deoxyribonucleotide Nucleotide-Sequence Internal-DNA-Sequence DNA-Noncoding-Sequence Polydeoxyribonucleotide DNA-Gene-Coding-Sequence DNA-Substance Damaged-DNA-Sequence DNA-Coding-Sequence 3-Prime-Deoxyribonucleotide DNA-Template 5-Prime-Deoxyribonucleotide
3-Prime-Deoxyribonucleotide Nucleotide at the end of a DNA sequence which is connected within the sequence only at the 5' OH. At the end of a molecule the 3'-OH is free. Souther. Deoxyribonucleotide DNA-Sequence 3-Prime-End Nucleotide DNA-Strand Nucleoside-Monophosphate
5-Prime-Deoxyribonucleotide Nucleotide at the end of a DNA sequence which is connected within the sequence only at the 3' OH. If the DNA-Sequence is free, the 5' phosphoryl group is a triphosphate rather than a monophosphate. Souther. Deoxyribonucleotide DNA-Sequence Phosphoryl-Group 5-Prime-End Triphosphate Nucleotide Monophosphate
Damaged-DNA-Sequence A region of the DNA which has missing, mismatched, or altered bases or Base-Pair. Souther. DNA-Sequence Base-Pair
DNA-Noncoding-Sequence A region of the DNA which does not code for any known product, either protein or RNA. Souther. DNA-3prime-UTR DNA-Sequence RNA DNA-5prime-UTR Intron Non-Transcribed-Region Spacer-DNA-Region
DNA-3prime-UTR The sequence at the end of the transcription unit which is not translated. Souther. DNA-Noncoding-Sequence
DNA-5prime-UTR The sequence at the beginning of the transcription unit which is not later translated Souther. DNA-Noncoding-Sequence
Intron Region of a eucaryotic gene that does not code for protein but is transcribed into an RNA molecule and then excised by RNA splicing to produce mRNA. Alberts:ECB:G-10. RNA Intron-Branch-Sequence Intron-End-Sequence DNA-Noncoding-Sequence Intron-Beginning-Sequence
Non-Transcribed-Region Sequences of DNA which are not transcribed and do not play any role in regulation. The so-described 'junk' or 'spacer' DNA. Souther. DNA-Noncoding-Sequence
Spacer-DNA-Region The DNA region between Genes which is not transcribed. Can be up to 100,000 nucleotides long. Alberts:ECB:218. DNA-Noncoding-Sequence
DNA-Template A DNA sequence which is copied during DNA replication or repair. Polynucleotide DNA-Sequence DNA-Synthesis Gene
Internal-DNA-Sequence A region of the DNA which is internal, thus having no free 5' or 3' end. Souther. DNA-Sequence Internal-Nucleotide-Sequence
Polydeoxyribonucleotide A molecular chain of deoxyribonucleotides chemically bonded by a series of phosphodiester linkages. Alberts:ECB:G-14. Polynucleotide Deoxyribonucleotide D-CMP D-TMP Internal-DNA-Sequence D-GMP DNA-Substance DNA-Sequence DNA-Strand DNA-Strand-Fragment D-AMP
DNA-Strand One of two complementary anti-parallel chains that make up the DNA double helical molecule. Souther. Eucaryotic-DNA-Strand Free-Nucleotide-Sequence 3-Prime-End Carbon-Atom 5-Prime-End Nitrogen-Atom DNA-Region Polydeoxyribonucleotide DNA-Noncoding-Sequence Nitrogenous-Base DNA-Gene-Coding-Sequence DNA-Replication Covalent-CN-Bond Template Nucleotide Deoxyribose Deoxyribose-Monophosphate
Eucaryotic-DNA-Strand One of two strands that make up the DNA double helix. The two strands run antiparallel and are held together by Hydrogen-Bond between the bases. Souther. Hydrogen-Bond DNA-Strand Template Eucaryotic-Gene DNA-Region DNA-Noncoding-Sequence DNA-Gene-Coding-Sequence
DNA-Strand-Fragment A part of a DNA strand with free ends. Souther. Free-Nucleotide-Sequence Okazaki-Fragment Polydeoxyribonucleotide
Okazaki-Fragment A short length of DNA produced on the lagging strand during DNA replication, discovered by R. Okazaki. They are rapidly joined by DNA ligase to form a continuous DNA strand. Alberts:MBC:G-17. Free-Nucleotide-Sequence DNA-Synthesis DNA-Strand-Fragment
Free-Nucleotide-Sequence A nucleotide sequence with a free 5'-triphosphate and free 3'-OH, i.e. a sequence which is not an internal sequence. Examples include DNA-Strand, Free-Nucleotide. Souther. Phosphodiester-Bond Nucleotide-Sequence Nucleoside-Triphosphate Carbon-Atom 3-Prime-Nucleotide 5-Prime-Nucleotide Free-Nucleotide DNA-Strand DNA-Strand-Fragment Nucleoside-Monophosphate Pentose
Free-Nucleotide A nucleotide which is not part of DNA or RNA, and is free in the medium. Souther. Free-Nucleotide-Sequence RNA Nucleotide
Internal-Nucleotide-Sequence A region of a nucleotide sequence which is internal, thus having no free 5' or 3' end. Souther. Internal-RNA-Sequence 3-Prime-End Nucleotide-Sequence Internal-DNA-Sequence 5-Prime-End 3-Prime-Deoxyribonucleotide Nucleoside-Monophosphate 5-Prime-Deoxyribonucleotide
Nucleotide Nucleoside with one or more phosphate groups joined in ester linkages to the sugar part. DNA and RNA are polymers of nucleotides. Alberts:ECB:G-13. Deoxyribonucleotide RNA Nucleotide-Sequence Phosphoryl-Group Nucleoside-Triphosphate Carbon-Atom 5-Prime-Nucleotide Ribonucleotide Oxygen-Atom Free-Nucleotide Nucleoside Covalent-CO-Bond Nucleoside-Monophosphate Monomer Hydroxyl-Group Pentose
Internal-RNA-Sequence A region of the RNA which is internal, thus having no free 5' or 3' end. Souther. RNA Internal-Nucleotide-Sequence RNA-Sequence
5-Prime-Nucleotide Nucleotide at the end of a sequence whose 5' end either bears a free triphosphate (free sequences like DNA-Strand or DNA-Strand-Fragment) or whose 5' end is attached to a neighboring sequence (internal sequences like introns or Regulatory-Sequence). Souther. Nucleotide-Sequence Intron 5-Prime-End Nucleotide DNA-Strand Internal-Nucleotide-Sequence Regulatory-Sequence DNA-Strand-Fragment
Deoxyribonucleotide Nucleotide containing 2-deoxy-D-ribose as the pentose component. Lehninger:PBC:G-3. D-CMP D-TMP Adenine D-GMP Monophosphate Nitrogenous-Base Guanine 3-Prime-Deoxyribonucleotide Nucleoside Nucleotide 5-Prime-Deoxyribonucleotide Deoxyribose Cytosine Thymine D-AMP
D-AMP Deoxyadenosine monophosphate. One of the four nucleotides in DNA, containing deoxyribose and adenine. Souther. Deoxyribonucleotide D-TMP Carbon-Atom Monophosphate Oxygen-Atom Covalent-CO-Bond Deoxyribose Nucleoside-Monophosphate Deoxyadenosine
D-CMP Deoxycytidine monophosphate. One of the four nucleotides in DNA, containing cytosine and deoxyribose. Souther. Deoxyribonucleotide Deoxycytidine Carbon-Atom D-GMP Monophosphate Oxygen-Atom Covalent-CO-Bond Deoxyribose Nucleoside-Monophosphate
D-GMP Deoxyguanosine monophosphate. One of the four nucleotides in DNA, containing deoxyribose and guanine. Souther. Oxygen-Atom Deoxyribonucleotide D-CMP Deoxyguanosine Carbon-Atom Covalent-CO-Bond Nucleoside-Monophosphate Deoxyribose Monophosphate
D-TMP Deoxythymidine monophosphate. One of the four nucleotides in DNA, containing deoxyribose and thymine. Souther. Deoxyribonucleotide Carbon-Atom Deoxythymidine Monophosphate Oxygen-Atom Covalent-CO-Bond Deoxyribose Nucleoside-Monophosphate D-AMP
Nucleoside-Monophosphate A nucleotide in which the 5' terminal group is a monophosphate. Souther. CMP D-CMP TMP 3-Prime-Ribonucleotide D-TMP UMP GMP D-GMP Monophosphate 3-Prime-Nucleotide 3-Prime-Deoxyribonucleotide Nucleotide AMP D-AMP
3-Prime-Nucleotide Nucleotide at the end of a sequence whose 3' end either bears a free hydroxyl group (free sequences like DNA strands or DNA-Strand-Fragment) or whose 3' end is attached to a neighboring sequence (internal sequences like introns or Regulatory-Sequence). Souther. 3-Prime-End Nucleotide-Sequence Intron Nucleotide DNA-Strand Internal-Nucleotide-Sequence Regulatory-Sequence Nucleoside-Monophosphate DNA-Strand-Fragment Hydroxyl-Group
3-Prime-Ribonucleotide Nucleotide at the end of a RNA sequence which is connected within the sequence only at the 5' OH. At the end of a molecule the 3'-OH is free. Souther. Ribonucleotide RNA 3-Prime-End Nucleotide Nucleoside-Monophosphate Hydroxyl-Group RNA-Sequence
AMP Adenosine monophosphate. One of the four nucleotides in RNA. AMP is produced by the energetically favorable hydrolysis of ATP. Alberts:ECB:G-2. RNA UMP Carbon-Atom Ribose ATP Monophosphate Adenosine Ribonucleotide Oxygen-Atom Covalent-CO-Bond Nucleotide Nucleoside-Monophosphate
CMP Cytidine monophosphate. One of the four nucleotides in RNA and DNA. Souther. Ribonucleotide Oxygen-Atom RNA Cytidine Carbon-Atom Covalent-CO-Bond GMP Ribose Nucleoside-Monophosphate Monophosphate
GMP Guanosine monophosphate. One of the four nucleotides in RNA. Souther. Ribonucleotide CMP Oxygen-Atom RNA Guanosine Carbon-Atom Covalent-CO-Bond Ribose Nucleoside-Monophosphate Monophosphate
TMP Thymidine monophosphate. One of the four nucleotides in DNA. Souther. Ribonucleotide Oxygen-Atom Carbon-Atom Covalent-CO-Bond Thymidine Ribose Nucleoside-Monophosphate Monophosphate
UMP Uridine monophosphate. One of the four nucleotides in RNA. Souther. Uridine RNA Carbon-Atom Ribose Monophosphate Ribonucleotide Oxygen-Atom Covalent-CO-Bond Nucleoside-Monophosphate AMP
Nucleoside-Triphosphate A nucleotide in which the 5' terminal group is a triphosphate. Souther. Carbon-Atom ATP Monophosphate CTP TTP Oxygen-Atom UTP Nucleoside Covalent-CO-Bond Triphosphate Nucleotide Pentose
ATP Adenosine triphosphate. The principle carrier of chemical energy in cells. The terminal phosphate groups are highly reactive in the sense that their hydrolysis, or transfer to another molecule, takes place with release of a large amount of free energy. Alberts:ECB:G-2. Cell Nucleoside-Triphosphate Carbon-Atom Ribose Monophosphate Adenosine Molecule Ribonucleotide Oxygen-Atom Covalent-CO-Bond Triphosphate Phosphate Chemical-Energy Chemical-Bond-Energy-Transfer
CTP Nucleoside triphosphate used in the synthesis of RNA and DNA. Souther. Ribonucleotide Oxygen-Atom RNA Cytidine Nucleoside-Triphosphate Nucleoside Carbon-Atom Triphosphate Covalent-CO-Bond Ribose Monophosphate
TTP Nucleoside triphosphate used in the synthesis of DNA. Souther. Ribonucleotide Oxygen-Atom Nucleoside-Triphosphate Nucleoside Carbon-Atom Triphosphate Covalent-CO-Bond Thymidine Ribose Monophosphate
UTP Nucleoside triphosphate used in the synthesis of RNA. Souther. Uridine RNA Nucleoside-Triphosphate Carbon-Atom Ribose Monophosphate Ribonucleotide Oxygen-Atom Nucleoside Covalent-CO-Bond Triphosphate
Ribonucleotide Nucleotide containing D-ribose as the pentose component. Lehninger:PBC:G-12. CMP Uracil TMP 3-Prime-Ribonucleotide UMP Phosphoryl-Group 5-Prime-Ribonucleotide GMP Ribose Adenine ADP ATP Nitrogenous-Base CTP Guanine TTP UTP GTP Nucleoside Nucleotide AMP Cytosine
5-Prime-Ribonucleotide Nucleotide at the end of a RNA sequence which is connected within the sequence only at the 3' OH. If at the end of a molecule the free 5' OH is connected to a triphosphate rather than a monophosphate. Souther. Ribonucleotide RNA 5-Prime-End Nucleotide Hydroxyl-Group RNA-Sequence
ADP Nucleoside that is produced by hydrolysis of the terminal phosphate of ATP. Alberts:ECB:G-1 Ribonucleotide Oxygen-Atom Diphosphate Nucleoside Covalent-CO-Bond Carbon-Atom Phosphate Ribose ATP Monophosphate Adenosine
GTP Major nucleoside triphosphate used in the synthesis of RNA and in some energy-transfer reactions. Has a special role in microtubule assembly, protein synthesis, and cell signaling. Alberts:ECB:G-9. Ribonucleotide Oxygen-Atom RNA Guanosine Carbon-Atom Triphosphate Covalent-CO-Bond Ribose Monophosphate
Oligonucleotide A molecular chain of nucleotides chemically bonded by a series of phosphodiester linkages. Alberts:ECB:G-14. Arbitrarily defined in this KB to be between 3 and 49 nucleotides long, shorter Nucleotide-Sequence are called oligonucleotides. Note: the current lengths are arbitrary. All source so far consulted just say a 'short' nucleotide sequence. Souther. Macromolecule 5-Prime-Nucleotide 3-Prime-End Phosphodiester-Bond Nucleotide-Sequence 5-Prime-End Carbon-Atom Nucleotide Pentose 3-Prime-Nucleotide
Polynucleotide A molecular chain of nucleotides chemically bonded by a series of phosphodiester linkages. Alberts:ECB:G-14. Arbitrarily defined in this KB to be at least 50 nucleotides long, shorter Nucleotide-Sequence are called oligonucleotides. Note: the current lengths are arbitrary. All source so far consulted just say a 'long' nucleotide sequence. Souther. 3-Prime-End Phosphodiester-Bond Nucleotide-Sequence 5-Prime-End Carbon-Atom Polydeoxyribonucleotide 3-Prime-Nucleotide 5-Prime-Nucleotide Macromolecule DNA-Template Nucleotide Polyribonucleotide Pentose
Polyribonucleotide A polymer of ribonucleotides. Example is RNA. Souther. Polynucleotide Ribonucleotide CMP Poly-A-Tail RNA Phosphodiester-Bond UMP RNA-Molecule GMP AMP
Poly-A-Tail The polyadenylate chain added to the end of a newly synthesized mRNA in eucaryotes. Souther. Polyribonucleotide AMP
RNA-Molecule Polymer formed from covalently linked ribonucleotide units. Alberts:ECB:G-16 RNA-Transcript Polymer Ribonucleotide RNA Polyribonucleotide MRNA
MRNA RNA molecule that specifies the amino acid sequence of a protein. Produced by RNA splicing (in eucaryotes) from a larger RNA molecule made by RNA polymerase as a complementary copy of DNA. It is translated into protein in a process catalyzed by ribosomes. Alberts:ECB:G-11 RNA Protein-Initiator-Codon RNA-Translated-Region Eucaryotic-MRNA RNA-Molecule Protein-Stop-Codon Ribosome-Binding-Site Procaryotic-MRNA
Eucaryotic-MRNA RNA molecule that specifies the amino acid sequence of a protein, produced by RNA splicing from a larger RNA molecule made by RNA polymerase as a complementary copy of DNA. It is translated into protein in a process catalyzed by ribosomes. Alberts:ECB:G-11 RNA-5prime-UTR RNA RNA-Translated-Region Poly-A-Tail MRNA RNA-3prime-UTR
Procaryotic-MRNA RNA molecule that specifies the amino acid sequence of a protein. Made by RNA polymerase as a complementary copy of DNA. It is translated into protein in a process catalyzed by ribosomes. Alberts:ECB:G-11 RNA RNA-Translated-Region Protein-Initiator-Codon Protein-Stop-Codon Gene-Transcript RNA-3prime-UTR RNA-5prime-UTR Series MRNA Gene
RNA-Transcript RNA product of DNA transcription (Alberts:MBC:1994). Functional-RNA-Transcript RNA RRNA Bacterial-RNA-Transcript RNA-Molecule Eucaryotic-RNA-Transcript TRNA Gene-Transcript
Bacterial-RNA-Transcript RNA product of DNA transcription in bacteria. Alberts:MBC:1994. RNA-Transcript RNA
Gene-Transcript The RNA transcript of a single gene, which is the rule for an mRNA transcript in eucaryotes. In procaryotes the mRNA transcript may code for several genes. Souther. RNA-Transcript RNA
Eucaryotic-RNA-Transcript The DNA transcription product in eucaryotes. Souther. RNA-Transcript Primary-RNA-Transcript
Primary-RNA-Transcript The newly transcribed RNA molecule before any modifications have been made to it in the nucleus. Souther. RNA-5prime-UTR RNA Eucaryotic-Gene Eucaryotic-RNA-Transcript RNA-3prime-UTR
Functional-RNA-Transcript The RNA transcript after all the post-transcription processing has been completed. (Compare with Primary Transcript). Souther. RNA-Transcript RNA Functional-MRNA-Transcript
Functional-MRNA-Transcript The RNA transcript after all the post-transcription processing has been completed, which includes RNA capping, polyadenylation, and splicing. Souther. Functional-RNA-Transcript Ribonucleotide RNA Phosphodiester-Bond Poly-A-Tail Nucleoside Covalent-CO-Bond Carbon-Atom Nucleotide Ribose 7-Methyl-Guanosine Hydroxyl-Group Methyl-Group Functional-Vertebrate-MRNA-Transcript AMP
Functional-Vertebrate-MRNA-Transcript The RNA transcript in vertebrates after all the post-transcription processing has been completed. Differs from lower organisms in that the RNA capping involves methylating the ribose of the second ribonucleotide as well. Souther. Ribonucleotide RNA Carbon-Atom Ribose Covalent-Bond Functional-MRNA-Transcript Hydroxyl-Group Methyl-Group
RRNA Any one of a number of specific RNA molecules that form part of the structure of a ribosome and participate in the synthesis of proteins. Alberts:ECB:G-16. Eucaryotic-RRNA RNA-Transcript RNA Procaryotic-RRNA
Eucaryotic-RRNA Eucaryotic rRNA molecule. Souther. RRNA
Procaryotic-RRNA Procaryotic rRNA molecule. Souther. RRNA
TRNA Small RNA molecule used in protein synthesis as an adaptor between a specific codon in mRNA, and specific amino acids. Each type of tRNA molecule is covalently linked to a particular amino acid and recognizes a particular codon or set of codons by base-pairing. Alberts:ECB:G-18. RNA-Transcript Procaryotic-TRNA RNA Eucaryotic-TRNA Nucleotide Amino-Acid-Binding-Site RNA-Anticodon
Eucaryotic-TRNA Eucaryotic tRNA molecule. Souther. TRNA
Procaryotic-TRNA Procaryotic tRNA molecule. Souther. TRNA
Regulatory-Sequence A sequence of nucleotides that regulates the the synthesis of DNA, RNA, or protein. Souther. RNA RNA-Regulatory-Sequence Nucleotide-Sequence DNA-Regulatory-Sequence
DNA-Regulatory-Sequence A sequence of DNA deoxyribonucleotides on a DNA strand that regulates the replication or transcription of DNA. Souther. TATA-Box CTGGCGGC-Like-Sequence Regulatory-Sequence Replication-Origin-Sequence Terminator TTTT-Like-Sequence Promoter GCCGCCAG-Like-Sequence TTGACA-Like-Sequence
Series A collection of identical or functionally identical molecules which repeat in a linear manner along some structure. Examples: Protein-Filament made up of molecules attached end to end, the series of hydrogen bonds in DNA, etc. Souther. Protein-Filament
CTGGCGGC-Like-Sequence A DNA consensus sequence that forms part of the terminator for DNA transcription. Alberts:ECB:217. DNA-Regulatory-Sequence
GCCGCCAG-Like-Sequence A DNA consensus sequence that forms part of the terminator for DNA transcription. Alberts:ECB:217 Deoxyribonucleotide D-CMP DNA-Regulatory-Sequence D-GMP D-AMP
Promoter Nucleotide sequence in DNA to which RNA polymerase binds to begin transcription. Alberts:ECB:G-15. TATA-Box RNA Deoxyribonucleotide DNA-Regulatory-Sequence Nucleotide TTGACA-Like-Sequence
Replication-Origin-Sequence A DNA sequence that attracts initiator proteins for DNA translation. Alberts:ECB:190 Deoxyribonucleotide D-TMP DNA-Regulatory-Sequence D-AMP
TATA-Box A DNA consensus sequence that forms part of the promoter for DNA transcription. Alberts:ECB:217 Deoxyribonucleotide D-TMP DNA-Regulatory-Sequence D-AMP
Terminator A DNA sequence that appears at the end of a transcriptional unit and signals the end of transcription. Lehninger:PBC:G-13. TTTT-Like-Sequence CTGGCGGC-Like-Sequence Deoxyribonucleotide GCCGCCAG-Like-Sequence DNA-Regulatory-Sequence Terminator-Region
TTGACA-Like-Sequence A DNA consensus sequence that forms part of the promoter for DNA transcription. Alberts:ECB:217. Deoxyribonucleotide D-CMP D-TMP DNA-Regulatory-Sequence D-GMP D-AMP
TTTT-Like-Sequence A DNA consensus sequence that forms part of the terminator for DNA transcription. Alberts:ECB:217. Deoxyribonucleotide D-TMP DNA-Regulatory-Sequence
RNA-Regulatory-Sequence A sequence of mRNA ribonucleotides on an RNA transcript that regulates the processing of RNA or translation of RNA. Souther. Protein-Initiator-Codon RNA Intron-Branch-Sequence Intron-End-Sequence Protein-Stop-Codon Regulatory-Sequence Intron-Beginning-Sequence
Intron-Beginning-Sequence The sequence that identifies the 5' splice site on an intron. Souther. RNA-Regulatory-Sequence
Intron-Branch-Sequence The conserved sequence within an intron containing an adenine which attacks and breaks the bond between the last exon nucleotide and the first (5') intron nucleotide. Souther. RNA-Regulatory-Sequence
Intron-End-Sequence The sequence that identifies the 3' splice site on an intron. Souther. RNA-Regulatory-Sequence
Ribosome-Binding-Site A binding site on the ribosome that contains a nucleotide sequence which matches a complementary sequence on tRNA or mRNA. Souther. Nucleotide-Sequence Binding-Site
Microtubule Long, stiff, cylindrical intracellular structure, 20 nanometers in diameter, composed of the protein tubulin; one of the major components of the cytoskeleton, used by Eucaryotic-Cell to regulate their shape and control their movements. Alberts:ECB:G-11. Series Eucaryotic-Cell Protein-Filament Tubulin-Molecule
RNA-Noncoding-Sequence The part of messenger RNA which is not translated. Souther. RNA-5prime-UTR RNA Nucleotide-Sequence RNA-3prime-UTR
RNA-3prime-UTR The sequence at the end of the mRNA which is not translated. In eucaryotes, it is partly trimmed and a poly-A tail is added. Souther. RNA-Noncoding-Sequence
RNA-5prime-UTR The sequence at the beginning of the mRNA which is not translated. In eucaryotes, it is partly trimmed and a poly-A tail is added. Souther. RNA-Noncoding-Sequence
RNA-Sequence A nucleotide sequence of ribonucleotides. Souther. RNA-Coding-Sequence Ribonucleotide Internal-RNA-Sequence Nucleotide-Sequence 3-Prime-Ribonucleotide 5-Prime-Ribonucleotide
Information-Sequence A sequence which encodes information. Biological examples are DNA, RNA, and the amino acid sequence of proteins (which determines folding). Souther. Amino-Acid-Sequence Genetic-Information-Sequence RNA Coding-Sequence Information Chemical-Information-Sequence
Genetic-Information-Sequence A genetic sequence which encodes information. Souther. Information-Sequence
Protein-Filament A linear chain of protein molecules. As microtubules, Actin-Filament, and Intermediate-Filament, they constitute much of the cytoskeleton of all eucaryotic cells and especially abundant in muscle cells. see Alberts:ECB:16. Intermediate-Filament Protein Microtubule Compound-Protein Series Actin-Filament
Intermediate-Filament Fibrous protein filament (10 nm in diameter) that forms ropelike bundles in animal cells. Often provides tensile strength to withstand tension applied to the cell from outside. Alberts:ECB:G-10. Protein Series Protein-Filament
Information Knowledge communicated or received concerning a particular fact or circumstance. RHCD:1st Revised: 684. Information-Sequence
Nuclear-Pore Channel through the nuclear envelope that allows selected molecules to move between the nucleus and cytoplasm. Alberts:ECB:G-13. Nucleoplasm
Atomic-Region A region of the atom. Souther. Atomic-Nucleus Electron-Shell
Atomic-Nucleus The central part of an atom containing protons and neutrons. Souther. Atomic-Region
Electron-Shell An energy level in the atom which corresponds to a discrete orbit. Each shell can accomodate only a strictly limited number of electrons. Alberts:ECB:40 Atomic-Region
Binding-Site Region on the surface of a molecule - typically a cavity or groove - that is complementary in shape to another molecule (the ligand) and therefore can bind it through the formation of multiple weak (noncovalent) bonds. cf Alberts:ECB:G-3. MRNA-Site Regulatory-Site P-Site A-Site E-Site TRNA-Initiator-Site Ribosome-Binding-Site Amino-Acid-Binding-Site Active-Site
A-Site The site on the ribosome where the incoming amino-acyl tRNA binds. Alberts:ECB:230. Ribosome Binding-Site TRNA
Active-Site Region of an enzyme surface to which a substrate molecule binds before it undergoes a catalyzed reaction. Alberts:ECB:G-1. Enzyme-Catalysis Binding-Site substrate
Amino-Acid-Binding-Site A short, single-stranded region at the 3' end of TRNA where the amino acid that matches the codon of the mRNA being translated is bound. see Alberts:ECB:226. Binding-Site TRNA TRNA-Charging
E-Site The site on the ribosome where the tRNA that has just given up the growing polypeptide chain dissociates from the ribosome. Alberts:ECB:230. Binding-Site
MRNA-Site The site on the ribosome where mRNA is bound during translation. Souther. Binding-Site
P-Site The site on the ribosome where the the tRNA holding the growing polypeptide chain binds. Alberts:ECB:230. Binding-Site
Regulatory-Site A site on a molecule to which a regulatory ligand binds and alters the activity or function of that molecule. Souther. DNA-Regulatory-Site Binding-Site Molecule
DNA-Regulatory-Site A regulatory site on the DNA molecule such as the replication origin or the promoter. Souther. Regulatory-Site
TRNA-Initiator-Site Binding-Site
3-Prime-End The region of a nucleotide sequence acid which includes the terminal nucleotide with a free 3' hydroxyl group. Souther. Nucleic-Acid-Region Nucleotide-Sequence Nucleotide Hydroxyl-Group 3-Prime-Nucleotide
Nucleic-Acid-Region A region of a nucleic acid such as the 5' end or 3' end. Souther. 3-Prime-End RNA-Region 5-Prime-End DNA-Region
5-Prime-End The region of a nucleotide sequence which includes the terminal nucleotide with a free 5' triphosphate group. Souther. 5-Prime-Nucleotide Nucleic-Acid-Region Nucleotide-Sequence Triphosphate Nucleotide
DNA-Region A region of the DNA, such as the 5' end or the replication origin. Souther Replication-Fork Nucleic-Acid-Region DNA-Non-Coding-Region
DNA-Non-Coding-Region A region which does not code for RNA or proteins. Examples include the spacer DNA-Region in eucaryotes. Souther. RNA DNA-Region
Replication-Fork The site on the DNA molecule of DNA replication. Souther. DNA-Replication DNA-Region
RNA-Region A region of an RNA molecule. In mRNA, includes untranslated and coding regions. Souther. RNA-Translated-Region RNA Nucleic-Acid-Region RNA-Coding-Region RNA-Non-Coding-Region RNA-Untranslated-Region
RNA-Coding-Region Region of the mRNA which codes for a protein. Souther. RNA-Region
RNA-Non-Coding-Region Region of the mRNA which does not code for protein. Includes the untranslated regions at either end and the introns which are spliced out. Souther. RNA-Region
RNA-Translated-Region Region of the mRNA which directs the selection of amino acids to make up a particular protein. Souther. RNA-Coding-Sequence Protein-Initiator-Codon RNA-Region Protein-Stop-Codon
RNA-Untranslated-Region Region at either end of the mRNA molecule which is not translated, e.g., the poly-A tail. Souther. RNA-Region
Protein-Binding-Site Region on the surface of a protein - typically a cavity or groove - that is complementary in shape to another molecule (the ligand) and therefore can bind it through the formation of multiple weak (noncovalent) bonds. Alberts:ECB:G-3.
Protein-Region Any region of a protein, such as the carboxy terminal or amino terminal end. Souther. Amino-Terminus Carboxyl-Terminus
Amino-Terminus That end of a polypeptide chain which carries an unattached amino acid group. Alberts:ECB:G-12 Amino-Acid-Sequence Protein-Region
Carboxyl-Terminus That end of a polypeptide chain which carries an unattached carboxylic acid group. Alberts:ECB:G-3 Protein-Region
RNA Acid consisting of a chain of ribonucleotides. Souther. Nucleic-Acid Acid RNA-Molecule
Protoplasm The organized colloidal complex of organic and Inorganic-Substance that constitutes the living cell or organelle. WNCD:947. Pool Nucleoplasm Cytoplasm Inorganic-Molecule Colloid Organic-Molecule Inorganic-Substance
Cytoplasm Contents of a cell that are contained within the plasma membrane, but, in the case of Eucaryotic-Cell, outside of the nucleus. Alberts:ECB:G-5 Procaryotic-Cytoplasm Cell Eucaryotic-Cytoplasm Protoplasm Eucaryotic-Cell
Eucaryotic-Cytoplasm The cytoplasm of Eucaryotic-Cell containing the nucleus and other organelles. Souther. Cytoskeleton Eucaryotic-Cell Centriole ATP CTP Peroxisome Vesicle Microtubule GTP Actin-Filament Cytosol Golgi-Apparatus Endoplasmic-Reticulum Cytoplasmic-Protein Functional-RNA-Transcript Intermediate-Filament UTP Pool Lysosome Cytoplasm Mitochondrion
Procaryotic-Cytoplasm The cytoplasm of Eucaryotic-Cell containing the nucleus and other organelles. Souther. Cytoplasm Eucaryotic-Cell Procaryotic-DNA
Nucleoplasm The protoplasm of the nucleus. Souther. Protoplasm Pool Nucleoside-Triphosphate Chromosome Eucaryotic-DNA-Polymerase
Regulatory-Region A region or site on DNA, RNA, or a Protein which regulates the processing or activity of the molecule. Souther RNA Protein DNA-Regulatory-Region
DNA-Regulatory-Region A region of the DNA that contains Regulatory-Sequence. Souther. Promoter-Region Regulatory-Sequence DNA-Regulatory-Sequence Terminator-Region Replication-Origin Regulatory-Region
Promoter-Region The region that encompasses the promoter, which is usually in two separate sequences. Souther. Promoter DNA-Regulatory-Region
Replication-Origin Site on a chromosome at which DNA replication begins. Alberts:ECB:G-16. Deoxyribonucleotide DNA-Replication Replication-Origin-Sequence DNA-Regulatory-Region
Terminator-Region The region which contains the terminator sequences. Terminator DNA-Regulatory-Region
Acid Molecule (or substance) that dissociates in water to release one or more protons (H+ ions). see Alberts:ECB:G-1. Pyruvic-Acid Chemical-Entity Keto-Acid Organic-Acid Molecule Acidic-Amino-Acid Hydrogen-Atom Carboxylic-Acid
Base Molecule or substance that accepts proton(s) in solution. Also used refer to the purines and pyrimidines in DNA and RNA. Alberts:ECB:G-3. Chemical-Entity Basic-Amino-Acid RNA Nitrogenous-Base Molecule
Chemical-Entity Any molecule, atom, substance, or phenomenon (e.g, a chemical bond) which has chemical properties. Souther. Acid Chemical-Object Base Chemical-Substance Chemical-Bond
Acidic-Amino-Acid An amino acid which carries a net negative charge at pH 7. Souther. Acid Amino-Acid Glutamic-Acid Aspartic-Acid
Aspartic-Acid A polar amino acid with a acetic side chain. Souther Charged-Polar-Amino-Acid Alpha-Carbon Nonessential-Amino-Acid Carbon-Atom Acidic-Amino-Acid Amino-Acid-Side-Chain Acetyl-Group Covalent-CC-Bond
Glutamic-Acid A polar amino acid with a propionic side chain. Souther Charged-Polar-Amino-Acid Alpha-Carbon Nonessential-Amino-Acid Carbon-Atom Acidic-Amino-Acid Amino-Acid-Side-Chain Propionic-Group Covalent-CC-Bond
Carboxylic-Acid Organic compounds containing the carboxy group (-COOH). This group of compounds includes Amino-Acid and fatty acids. Carboxylic-Acid can be saturated, unsaturated, or aromatic. PubMed:MeSH. Acid Amino-Acid Organic-Molecule Carboxyl-Group
Keto-Acid Organic compounds containing the carboxy group (-COOH) attached to a carbonyl group (C=O). Souther. Acid Carbon-Atom Carbonyl-Group Organic-Molecule Carboxyl-Group Covalent-CC-Bond
Organic-Acid An organic molecule or substance which acts as an acid (a hydrogen donor). Souther. Nucleic-Acid Acid Pantothenic-Acid Carbon-Atom Nucleic-Acid-Molecule
Nucleic-Acid Acid made up of chains of nucleotides. Souther. DNA-Acid RNA Organic-Acid Acid Viral-Nucleic-Acid
DNA-Acid Acid consisting of a chain of deoxyribonucleotides. Souther. Nucleic-Acid Acid
Viral-Nucleic-Acid The hereditary material of a virus, either DNA or RNA. Nucleic-Acid RNA Viral-DNA
Viral-DNA The DNA of a virus. Souther. DNA-Virus Viral-Nucleic-Acid DNA-Molecule
Nucleic-Acid-Molecule RNA or DNA; consists of a chain of nucleotides joined together by Phosphodiester-Bond. Alberts:ECB:G-13. Macromolecule Organic-Acid RNA Phosphodiester-Bond
Pantothenic-Acid An organic acid that is one of the major parts of coenzymeA. Souther. Organic-Acid
Pyruvic-Acid An intermediate compound in the metabolism of carbohydrates, proteins, and fats. PubMed:MeSH:From Stedman, 26th ed. Formula: CH3COCOOH. Souther. Acid Carbon-Atom Carbonyl-Group Methyl-Group Organic-Molecule Carboxyl-Group Covalent-CC-Bond
Lysine A basic amino acid with a butylamine side chain. Souther Charged-Polar-Amino-Acid Alpha-Carbon Basic-Amino-Acid Butylamine Carbon-Atom Amino-Acid-Side-Chain Essential-Amino-Acid Covalent-CC-Bond
Basic-Amino-Acid An amino acid which carries a net positive charge at pH 7. Souther. Charged-Polar-Amino-Acid Histidine Amino-Acid Base Lysine Arginine
Arginine A basic amino acid with a di-amido propylamine side chain CH2CH2CH2NHCH(NH2)2 Souther Propylamine Basic-Amino-Acid Carbon-Atom Nitrogen-Atom Amino-Acid-Side-Chain Essential-Amino-Acid Charged-Polar-Amino-Acid Alpha-Carbon Covalent-CN-Bond Conjugated-Double-Bond Methyl-Group Amino-Group Covalent-CC-Bond
Histidine A charged polar amino acid with an imidazole derived side chain. Souther. Charged-Polar-Amino-Acid Alpha-Carbon Basic-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Imidazole Essential-Amino-Acid Covalent-CC-Bond
Nitrogenous-Base A base containing nitrogen. Pyrimidine Purine Base
Purine A nitrogenous compound containing two fused heterocyclic rings. Two purines, adenine and guanine, commonly are found in DNA and RNA. Lodish:MCB:G-14. Heterocyclic-Compound RNA Carbon-Atom Adenine Covalent-CH-Bond Nitrogen-Atom Nitrogenous-Base Guanine Covalent-CN-Bond Pyrimidine Conjugated-Double-Bond Hydrogen-Atom Covalent-NH-Bond
Adenine A purine base which combines with a ribose base to form adenosine. Adenosine phosphates are prominent molecules in cells as ATP, cAMP, and nucleotides. Souther. Uracil Purine Carbon-Atom Covalent-CH-Bond Nitrogen-Atom ATP Adenosine Covalent-CN-Bond Conjugated-Double-Bond Thymine Hydrogen-Atom Amino-Group Covalent-NH-Bond
Guanine A purine base which combines with a ribose base to form guanosine. Guanosine phosphates are prominent molecules in cells as GTP which participates in cell signaling metabolism and nucleotides. Souther. Purine Double-Covalent-CO-Bond Carbon-Atom Covalent-CH-Bond Nitrogen-Atom Double-Covalent-CC-Bond Oxygen-Atom Guanosine Covalent-CN-Bond GTP Conjugated-Double-Bond Cytosine Amino-Group Hydrogen-Atom Covalent-CC-Bond Covalent-NH-Bond
Pyrimidine A nitrogenous compound containing one heterocyclic ring. Two pyrimidines, cytosine and thymine, are commonly found in DNA. Lodish:MCB:G-14. Uracil Heterocyclic-Compound Purine Carbon-Atom Nitrogen-Atom Covalent-CH-Bond Nitrogenous-Base Conjugated-Double-Bond Cytosine Thymine Hydrogen-Atom
Cytosine A pyrimidine base which combines with a ribose base to form cytosine. Cytosine triphosphates are one of the building block monomers for DNA and RNA. Souther. RNA Double-Covalent-CO-Bond Carbon-Atom Nitrogen-Atom Guanine Oxygen-Atom Pyrimidine Covalent-CN-Bond Conjugated-Double-Bond Hydrogen-Atom Amino-Group Covalent-NH-Bond
Thymine A pyrimidine base which combines with a ribose base to form thymidine. Thymidine triphosphates are one of the building block monomers for DNA. Souther. Carbon-Atom Double-Covalent-CO-Bond Adenine Nitrogen-Atom Oxygen-Atom Pyrimidine Covalent-CN-Bond Thymidine Methyl-Group Hydrogen-Atom Covalent-CC-Bond Covalent-NH-Bond
Uracil A pyrimidine base which combines with a ribose base to form uridine. Uridine triphosphates are one of the building block monomers for RNA. Souther. Uridine RNA Double-Covalent-CO-Bond Carbon-Atom Adenine Covalent-CH-Bond Nitrogen-Atom Double-Covalent-CC-Bond Oxygen-Atom Pyrimidine Covalent-CN-Bond Covalent-CO-Bond Hydrogen-Atom Covalent-CC-Bond Covalent-NH-Bond
Chemical-Bond Linkage between two atoms that holds them together in a chemical compound. Types found in living cells include Ionic-Bond, Covalent-Bond, polar bonds, and Hydrogen-Bond. Alberts:ECB:G-4. Chemical-Entity Hydrogen-Bond Ionic-Bond Chemical-Object Bond Covalent-Bond High-Energy-Bond Noncovalent-Bond
Covalent-Bond A stable chemical link between two atoms produced by sharing one or more electrons. Alberts:ECB:G-5 Phosphoanhydride-Bond Phosphodiester-Bond Covalent-Single-Bond Peptide-Bond Double-Covalent-Bond Chemical-Bond Thioester-Bond
Covalent-Single-Bond A stable chemical link between two atoms produced by sharing a pair of electrons. cf Alberts:ECB:G-5 Covalent-PO-Bond Atom Covalent-CN-Bond Covalent-CO-Bond Covalent-CH-Bond Covalent-Bond Covalent-CC-Bond Covalent-CS-Bond Covalent-NH-Bond
Covalent-CC-Bond Chemical bond between two carbons. Souther. Atom Covalent-Single-Bond Carbon-Atom
Covalent-CH-Bond Chemical bond between carbon and hydrogen. Souther. Atom Covalent-Single-Bond Carbon-Atom Hydrogen-Atom
Peptide-Bond Chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid - a special form of amide linkage. Alberts:ECB:G-14. Amino-Acid-Sequence Amino-Acid Covalent-Bond
Covalent-CN-Bond Chemical bond between carbon and nitrogen. Souther. Atom Covalent-Single-Bond Carbon-Atom Nitrogen-Atom
Covalent-CO-Bond Chemical bond between a carbon and a oxygen. Souther. Oxygen-Atom Atom Covalent-Single-Bond Carbon-Atom
Covalent-CS-Bond Chemical bond between a carbon and a sulfur. Souther. Atom Covalent-Single-Bond Carbon-Atom Sulfur-Atom
Covalent-NH-Bond Chemical bond between hydrogen and nitrogen. Souther. Atom Covalent-Single-Bond Nitrogen-Atom Hydrogen-Atom
Covalent-PO-Bond Chemical bond between a phosphorus and a oxygen. Souther. Oxygen-Atom Phosphorus-Atom Atom Covalent-Single-Bond
Double-Covalent-Bond A chemical bond formed when two atoms share two pairs of electrons. Alberts:ECB:45 Double-Covalent-CN-Bond Double-Covalent-CO-Bond Conjugated-Double-Bond Covalent-Bond Double-Covalent-CC-Bond
Conjugated-Double-Bond A double bond which exists in alteration with single bonds in a carbon skeleton. WHS:PBC-5th:61. Atom Carbon-Atom Double-Covalent-Bond
Double-Covalent-CC-Bond Double covalent bond between two carbons. Souther. Atom Carbon-Atom Double-Covalent-Bond
Double-Covalent-CN-Bond Double covalent bond between carbon and nitrogen. Souther. Atom Carbon-Atom Double-Covalent-Bond Nitrogen-Atom
Double-Covalent-CO-Bond Double covalent bond between carbon and oxygen. Souther. Oxygen-Atom Atom Carbon-Atom Double-Covalent-Bond
Phosphoanhydride-Bond A chemical bond formed between two phosphate groups. Souther. Covalent-Bond Monophosphate
Phosphodiester-Bond A covalent chemical bond formed when two hydroxyl groups are linked in ester linkage to the same phosphate group, as in the case of adjacent nucleotides in RNA or DNA. Alberts:ECB:G-14. RNA Covalent-Bond Nucleotide
Thioester-Bond High-energy bond formed by a condensation reaction between an acid (acyl) group and a thiol group (-SH); seen, for example, in acetyl CoA and in many enzyme- substrate complexes. Alberts:ECB:G-17. Covalent-Bond substrate
Atom The smallest particle of an element that still retains its distinctive chemical properties. Alberts:ECB:G-2. Proton Carbon-Atom Nitrogen-Atom Oxygen-Atom Phosphorus-Atom Chemical-Object Electron Hydrogen-Atom Sulfur-Atom
High-Energy-Bond Covalent bond whose hydrolysis releases an unusually large amount of free energy under the conditions existing in a cell. Examples include the Phosphodiester-Bond in ATP and the thioester linkage in acetyl CoA. Alberts:ECB:G-9 Phosphodiester-Bond ATP Chemical-Energy Chemical-Bond
Noncovalent-Bond Chemical bond in which, in contrast to a covalent bond, no electrons are shared. NonCovalent-Bond are relatively weak, but they can sum together to produce strong, highly specific interactions between molecules. Alberts:ECB:G-13 Hydrogen-Bond Ionic-Bond Chemical-Bond
Hydrogen-Bond A weak chemical bond between an electronegative atom such as nitrogen or oxygen and a hydrogen atom bound to another electronegative atom. Alberts:ECB:G-9. Atom Hydrogen-Atom Noncovalent-Bond
Ionic-Bond Attractive force that holds together two ions, one positive and the other negative. Alberts:ECB:G-10 Anion Cation Ion Noncovalent-Bond
Chemical-Object Any object which is typically described in terms of its chemical properties. Includes atoms, molecules, and Chemical-Group like methyl group. Souther. Chemical-Entity Chemical-Group Atom Electron-Carrier Ion Molecule Subatomic-Particle Hydrophobic-Structure Electron-Acceptor Electron-Donor Chemical-Substance Chemical-Sequence Hydrophilic-Structure
Carbon-Atom The fundamental building block of living systems. Souther. Alpha-Carbon Atom Proton Neutron Electron
Alpha-Carbon The central carbon atom in an alpha amino acid, to which the carboyxl and Amino-Group and the side chain group are attached. Souther. Acid Amino-Acid Carbon-Atom Amino-Group
Hydrogen-Atom A colorless, odorless, flammable element that combines with oxygen to form water. The lightest of all elements. RHCD:1st Revised:649. Atom Proton Electron
Nitrogen-Atom A colorless, odorless element constituting about 4/5ths of the volume of the atmosphere and is present in combined form in animal and vegetable tissues, especially in proteins. RHCD:1st Revised:901. Atom Proton Neutron Electron
Oxygen-Atom An element that is found free as a colorless tasteless odorless gas in the atmosphere of whicdh it forms about 21 percent or combned in water, in most rocks and minerals, and in numerous organic compounds, that is capable of combining with all elements except the inert gases, is active in physiological processes, and is involved especially in comobustion processes. Websters 9th NCD:843. Atom Proton Neutron Electron
Phosphorus-Atom A solid, nonmetallic element that is a necessary constituent for bones and nerves, and as a phosphate forms high-energy bonds that provide the energy for all biosynthetic reactions. Souther. Atom Proton Neutron Electron
Sulfur-Atom A nonmetallic element that occurs either free or combined especially in sulfides and sulfates, and is a constituent of proteins. Websters 9th NCD:1180. Atom Proton Neutron Electron
Chemical-Group Set of covalently linked atoms, such as a hydroxyl group or an amino group, tht occurs in many different molecules and has a distinctive chemical character. Alberts:ECB:G-4. Ethyl-Group Propyl-Group Amido-Group Ethanol-Group Butyl-Group Acetamino-Group Isopropyl-Group Propionic-Group Methyl-Group Amino-Group Propylamine Phosphoryl-Group Methanol-Group Formyl-Group Amino-Acid-Side-Chain Carbonyl-Group Propionamino-Group Isobutyl-Group Butylamine Thiol-Group Chemical-Object Acetyl-Group Hydroxyl-Group Carboxyl-Group
Acetamino-Group A chemical group derived from acetamine. CH3-CONH2. Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Amido-Group Hydrogen-Atom Covalent-CC-Bond
Acetyl-Group A chemical group derived from acetic acid. Alberts:ECB:G-1 Chemical-Group Carbon-Atom Covalent-CH-Bond Carboxyl-Group Hydrogen-Atom Covalent-CC-Bond
Amido-Group Molecule containing a carbonyl group linked to an amine. Alberts:ECB:G-1. Chemical-Group Oxygen-Atom Covalent-CN-Bond Carbon-Atom Double-Covalent-CO-Bond Molecule Amino-Group
Amino-Acid-Side-Chain A chemical group which is attached to the alpha carbon in alpha Amino-Acid. For living organisms, there are about 20 different side chains yielding 20 different Amino-Acid which make up proteins. Souther. Chemical-Group Alpha-Carbon Amino-Acid
Amino-Group Weakly basic functional group, derived from ammonia (NH3). In aqueous solution an amino group can accept a proton and carry a positive charge. Alberts:ECB:G-2 Chemical-Group Nitrogen-Atom Hydrogen-Atom
Butyl-Group Hydrophobic chemical group derived from butane. Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-CC-Bond
Butylamine Amine derived from butane. CH3-CH2-CH2-CH2-NH3. Souther. Chemical-Group Covalent-CN-Bond Carbon-Atom Covalent-CH-Bond Amino-Group Hydrogen-Atom Covalent-CC-Bond
Carbonyl-Group Chemical group consisting of a carbon atom linked to an oxygen atom by a double bond. Alberts:ECB:G-3. Chemical-Group Oxygen-Atom Carbon-Atom Double-Covalent-CO-Bond
Carboxyl-Group Chemical group consistingt of a carbon atom linked both to an oxygen atom by a double bond and to a hydroxyl group. Molecules containing a carboxyl group are weak acids (Carboxylic-Acid). Alberts:ECB:G-3. Chemical-Group Oxygen-Atom Carbon-Atom Covalent-CO-Bond Double-Covalent-CO-Bond Carboxylic-Acid Hydrogen-Atom
Ethanol-Group Alcohol derived from ethane. Souther. Chemical-Group Alcohol Carbon-Atom Covalent-CH-Bond Amino-Acid-Side-Chain Oxygen-Atom Covalent-CO-Bond Hydroxyl-Group Hydrogen-Atom
Ethyl-Group Hydrophobic chemical group derived from Ethane. Alberts:ECB:G-11. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-CC-Bond
Formyl-Group Chemical group consisting of a carbon atom linked to an oxygen atom by a double bond. Alberts:ECB:G-3. Chemical-Group Oxygen-Atom Carbon-Atom Double-Covalent-CO-Bond Covalent-CH-Bond Hydrogen-Atom
Hydroxyl-Group Chemical group consisting of a hydrogen atom linked to an oxygen, as in an alcohol. Alberts:ECB:G-9. Chemical-Group Oxygen-Atom Hydrogen-Atom
Isobutyl-Group Hydrophobic chemical group derived from butane. (CH3)2-CH2CH3. Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-CC-Bond
Isopropyl-Group Hydrophobic chemical group derived from Isopropane. Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-CC-Bond
Methanol-Group Alcohol derived from methane. Souther. Chemical-Group Alcohol Carbon-Atom Covalent-CH-Bond Amino-Acid-Side-Chain Oxygen-Atom Covalent-CO-Bond Hydroxyl-Group Hydrogen-Atom
Methyl-Group Hydrophobic chemical group derived from methane. Alberts:ECB:G-11. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom
Phosphoryl-Group A chemical group made up of 1 at least one phosphorus and 4 oxygens. Normally acidic in the cell. Souther. Chemical-Group Diphosphate Triphosphate Phosphate Monophosphate
Diphosphate A compound containing a two phosphate groups in a chain, linked by Phosphoanhydride-Bond. Souther. Oxygen-Atom Phosphorus-Atom Phosphoanhydride-Bond Phosphoryl-Group Monophosphate
Monophosphate A compound containing a single phosphate group. Souther. Covalent-PO-Bond Oxygen-Atom Phosphorus-Atom Phosphoryl-Group
Triphosphate A compound containing a three phosphate groups in a chain. Souther. Oxygen-Atom Phosphorus-Atom Phosphoanhydride-Bond Phosphoryl-Group Monophosphate
Propionamino-Group Amine derived from Propionamino acid. CH2-CH2-CONH3 Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Amido-Group Hydrogen-Atom Covalent-CC-Bond
Propionic-Group Acidic chemical group derived from propane. CH3-CH2-COO- Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Carboxyl-Group Hydrogen-Atom Covalent-CC-Bond
Propyl-Group Hydrophobic chemical group derived from propane. CH3-CH2-CH2- Souther. Chemical-Group Carbon-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-CC-Bond
Propylamine Amine derived from propane. CH3-CH2-CH2-NH3. Souther. Chemical-Group Covalent-CN-Bond Carbon-Atom Covalent-CH-Bond Amino-Group Hydrogen-Atom Covalent-CC-Bond
Thiol-Group Chemical group containing sulfer and hydrogen found in the amino acid cysteine and other molecules. Two sulfhydryls can join to produce a disulfide bond. Alberts:ECB:G-17 Chemical-Group Hydrogen-Atom Sulfur-Atom
Electron-Acceptor Atom or molecule that takes up electrons readily. Upon gaining an electron, it is said to be reduced. Alberts:ECB:G-7 Atom Chemical-Object Reduction
Electron-Carrier Molecule such as cytochrome C that transfers an electron from a donor molecule to an acceptor molecule. Alberts:ECB:G-7 Chemical-Object NAD-Plus FADH2 Molecule Electron-Transfer
FADH2 Major electron carrier in metabolism; produced by reduction of FAD during the oxidation of catabolites such as succinate. Alberts:ECB:G-7 Electron-Carrier Electron-Transfer
NAD-Plus Molecule that participates in an oxidatin reaction by accepting a hydride ion (H-) from a donor molecule thereby producing NADH, which serves as an activated carrier of electrons; important in the energy-producing breakdown of sugars and fats. Alberts:ECB:G-12. Electron-Carrier Molecule
Electron-Donor Atom or molecule that gives up electrons readily. In the process, it is said to become oxidized. Alberts:ECB:G-7 Atom Chemical-Object Oxidation
Hydrophilic-Structure Any chemical object which attracts water. Souther. Chemical-Object
Hydrophobic-Structure Any chemical object which repels water. Souther. Chemical-Object
Ion Atom or molecule carrying an electrical charge, either positive or negative. Alberts:ECB:G-10 Atom Chemical-Object Anion Cation
Anion A negatively charged ion. Alberts:ECB:G-2. Ion
Cation A positively charged ion. Alberts:ECB:G-3. Hydronium-Ion Hydrogen-Ion Ion
Hydrogen-Ion A proton in aqueous solution - the basis of acidity. Such protons readily combine with Water-Molecule to form H3O+, so that Hydrogen-Ion in a strict sense are a rarity. Alberts:ECB:G-9. Cation Water-Molecule
Hydronium-Ion The positive ion resulting from the addition of a proton to a water molecule. Souther. Oxygen-Atom Inorganic-Molecule Cation Hydrogen-Atom
Molecule Group of atoms joined together by Covalent-Bond. Alberts:ECB:G-12. Peroxide Polar-Molecule Atom Activated-Carrier Coenzyme Chemical-Object Nonpolar-Molecule Covalent-Bond Inorganic-Molecule Group Organic-Molecule
Activated-Carrier Small molecule carrying a chemical group in a high-energy linkage, serving as a donor of energy or of the chemical group in may different chemical reactions. Examples include ATP, acetyl CoA, and NADH. Alberts:ECB:G-1. ATP Molecule High-Energy-Bond
Coenzyme Small molecule tightly associated with an enzyme that participates in the reaction that the enzyme catalyzes, often by forming a transient covalent bond to the substrate. Examples include biotin, NAD+, and coenzymeA. Alberts:MBC:G-6 CoenzymeA substrate Molecule Enzyme-Activation
CoenzymeA Small molecule used in the enzymatic transfer of acyl groups in the cell. Alberts:ECB:G-5 Coenzyme Pantothenic-Acid
Inorganic-Molecule Molecule lacking a carbohydrate skeleton. Souther. Carbon-Dioxide Nitrogen-Molecule Hydronium-Ion Phosphate Oxygen-Molecule Water-Molecule Molecule
Carbon-Dioxide Chemical group consisting of a carbon atom linked to two Oxygen-Atom by Covalent-Bond. Souther. Oxygen-Atom Carbon-Atom Double-Covalent-CO-Bond Covalent-Bond Inorganic-Molecule
Nitrogen-Molecule Molecule made up of two or more Nitrogen-Atom. Souther. Dinitrogen Nitrogen-Atom Inorganic-Molecule Molecule
Dinitrogen Molecule made up of two covalently bonded nitrogen atoms. Souther. Nitrogen-Molecule Nitrogen-Atom Molecule
Oxygen-Molecule Molecule made up of two or more Oxygen-Atom. Souther. Oxygen-Atom Inorganic-Molecule Molecule Dioxygen
Dioxygen Molecule made up of two covalently bonded Oxygen-Atom. Souther. Oxygen-Atom Oxygen-Molecule Molecule
Phosphate A compound containing phosphate. In cells, they are normally acidic. Oxygen-Atom Phosphorus-Atom Phosphoryl-Group Inorganic-Molecule
Water-Molecule Molecule made up of two Hydrogen-Atom each covalently bonded to the same oxygen atom. Souther. Oxygen-Atom Inorganic-Molecule Molecule Hydrogen-Atom
Nonpolar-Molecule Molecule that lacks any local accumulation of positive or negative charge. Nonpolar-Molecule are generally insoluble in water. Alberts:ECB:G-13. Nonpolar-Amino-Acid Molecule
Nonpolar-Amino-Acid Amino-Acid with side chains which are hydrophobic. see Alberts:ECB:61. Isoleucine Methionine Amino-Acid Cysteine Leucine Alanine Phenylalanine Tryptophan Proline Glycine Nonpolar-Molecule Threonine Tyrosine Valine
Alanine A nonpolar amino acid with a methyl side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Nonessential-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Covalent-CC-Bond
Cysteine A nonpolar amino acid with a Thiol-methyl side chain. Souther Nonessential-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Nonpolar-Amino-Acid Alpha-Carbon Thiol-Group Methyl-Group Sulfur-Atom Covalent-CS-Bond Covalent-CC-Bond
Glycine A nonpolar amino acid. Glycine is the simplest amino acid with hydrogen atom as the side chain. Souther Nonpolar-Amino-Acid Nonessential-Amino-Acid Amino-Acid-Side-Chain Hydrogen-Atom
Isoleucine A nonpolar amino acid with a 1-methyl-isopropyl side chain. Souther. Nonpolar-Amino-Acid Alpha-Carbon Isopropyl-Group Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Essential-Amino-Acid Covalent-CC-Bond
Leucine A nonpolar amino acid with a isobutyl side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Carbon-Atom Amino-Acid-Side-Chain Isobutyl-Group Essential-Amino-Acid Covalent-CC-Bond
Methionine A nonpolar amino acid with a methyl-thio-ethyl side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Ethyl-Group Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Essential-Amino-Acid Covalent-CC-Bond Sulfur-Atom Covalent-CS-Bond
Phenylalanine A nonpolar amino acid with a methyl side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Phenyl-Group Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Essential-Amino-Acid Covalent-CC-Bond
Proline A nonpolar amino acid with a propyl side chain whose distal end is attached to the amino group to form a five-membered ring structure. Souther. Nonpolar-Amino-Acid Alpha-Carbon Propyl-Group Nonessential-Amino-Acid Covalent-CN-Bond Carbon-Atom Nitrogen-Atom Amino-Acid-Side-Chain Amino-Group Covalent-CC-Bond
Threonine An uncharged polar amino acid with an ethanol side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Carbon-Atom Amino-Acid-Side-Chain Ethanol-Group Essential-Amino-Acid Covalent-CC-Bond
Tryptophan A nonpolar amino acid with an indole side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Carbon-Atom Indole Amino-Acid-Side-Chain Methyl-Group Essential-Amino-Acid Covalent-CC-Bond
Tyrosine An uncharged polar amino acid with a phenol side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Nonessential-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Methyl-Group Phenol Covalent-CC-Bond
Valine A nonpolar amino acid with a propyl side chain. Souther Nonpolar-Amino-Acid Alpha-Carbon Carbon-Atom Isopropyl-Group Amino-Acid-Side-Chain Essential-Amino-Acid Covalent-CC-Bond
Organic-Molecule Molecule containing hydrocarbon(s). Souther. Pyruvic-Acid Keto-Acid Alcohol Lipid Ring-Compound Molecule Carbohydrate Polymer Sugar-Phosphate Nucleoside Substrate Monomer Carboxylic-Acid Ligand
Alcohol Organic compound containing a hydroxyl group bound to a saturated carbon atom - for example ethyl alcohol. Alberts:ECB:G-1. Methanol-Group Covalent-CO-Bond Carbon-Atom Ethanol-Group Hydroxyl-Group Organic-Molecule
Carbohydrate General term for sugars and related compounds with the general formula (CH2O)n. Alberts:ECB:G-3. Monosaccharide Organic-Molecule
Monosaccharide Any sijmple sugar with the formula (CH2O)n where n = 3-7. Alberts:MBC:G-16. Monosaccharides are the basic unit of sugars and polysaccharides. Souther. Carbohydrate Hexose Monomer Pentose
Hexose A six-carbon monosaccharide. Lodish:MCB:G-8. Monosaccharide Glucose Carbon-Atom
Glucose A six-carbon sugar that plays a major role in the metabolism of living cells. Stored in polymeric form as glycogen in animal cells and as starch in plants. Alberts:ECB:G-8. Oxygen-Atom Carbon-Atom Covalent-CO-Bond Hexose Covalent-CH-Bond Hydroxyl-Group Hydrogen-Atom Covalent-CC-Bond
Pentose A five-carbon monosaccharide. The pentoses deoxyribose and ribose are present in DNA and RNA respectively. Lodish:MCB:G-13. Monosaccharide RNA Carbon-Atom Ribose Covalent-CH-Bond Oxygen-Atom Covalent-CO-Bond Deoxyribose Hydroxyl-Group Hydrogen-Atom Covalent-CC-Bond
Deoxyribose A pentose which forms the carbohydrate moiety of nucleotides which constitute DNA. Souther. Methanol-Group Carbon-Atom Covalent-CH-Bond Oxygen-Atom Covalent-CO-Bond Hydroxyl-Group Pentose Hydrogen-Atom Covalent-CC-Bond
Ribose A Ribose which forms the carbohydrate moiety of nucleotides, both when free and when incorporated into RNA. Souther. RNA Carbon-Atom Covalent-CH-Bond Oxygen-Atom Covalent-CO-Bond Hydroxyl-Group Pentose Hydrogen-Atom Covalent-CC-Bond
Ligand Molecule such as a hormone or a neurotransmitter that that binds to a specific site on a protein. Alberts:ECB:G-10. Protein Organic-Molecule Molecule
Lipid Organic molecule, generally containing hydrocarbon chains, that is insoluble in water but dissolves readily in nonpolar organic solvents. One class, phospholipids, forms the structural basis of Biological-Membrane. Alberts:ECB:G-10. Biological-Membrane Organic-Molecule
Monomer Small molecule that can be linked to others of the same type to form a larger molecule. Alberts:ECB:G-12. Monosaccharide Polymer Amino-Acid Nucleotide Organic-Molecule
Amino-Acid Organic molecule containing both an amino group and a carboxyl group. Alpha Amino-Acid (those in which the amino and Carboxyl-Group are linked to the same carbon atom) serve as the building blocks of proteins. Alberts:ECB:G-2. Covalent-CH-Bond Essential-Amino-Acid Nonpolar-Amino-Acid Alpha-Carbon Formylmethionine Amino-Group Nonessential-Amino-Acid Amino-Acid-Side-Chain Neutral-Amino-Acid Peptide-Bond Acidic-Amino-Acid Monomer Polar-Amino-Acid Carboxyl-Group Hydrogen-Atom Covalent-CC-Bond
Essential-Amino-Acid Amino acid that cannot be synthesized by humans (and other vertebrates) and must be obtained from the diet. Lehninger:PBC:G-5. Isoleucine Methionine Histidine Amino-Acid Lysine Leucine Phenylalanine Tryptophan Threonine Arginine Valine
Formylmethionine Methionine modified with a formyl group attached to the amino nitrogen. It is the amino acid which initiates peptide chain formation in bacteria. Souther. see Alberts:ECB:231 Methionine Amino-Acid Double-Covalent-CN-Bond Carbon-Atom Formyl-Group Nitrogen-Atom Amino-Group
Neutral-Amino-Acid Amino-Acid
Nonessential-Amino-Acid Amino acid that can be made by humans and other vertebrates from simple precursors, and thus is not required in the diet. Lehninger:PBC:G-9. Amino-Acid Cysteine Glutamic-Acid Aspartic-Acid Glutamine Serine Alanine Proline Glycine Asparagine Tyrosine
Asparagine A polar amino acid with a acetamino side chain. Souther Alpha-Carbon Nonessential-Amino-Acid Uncharged-Polar-Amino-Acid Carbon-Atom Acetamino-Group Amino-Acid-Side-Chain Covalent-CC-Bond
Glutamine A polar amino acid with a propionic side chain. Souther Alpha-Carbon Nonessential-Amino-Acid Uncharged-Polar-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Propionamino-Group Covalent-CC-Bond
Serine An uncharged polar amino acid with a methanol side chain. Souther Alpha-Carbon Nonessential-Amino-Acid Methanol-Group Uncharged-Polar-Amino-Acid Carbon-Atom Amino-Acid-Side-Chain Covalent-CC-Bond
Polar-Amino-Acid Amino-Acid with side chains which are hydrophilic. see Alberts:ECB:61. Charged-Polar-Amino-Acid Polar-Molecule Amino-Acid Uncharged-Polar-Amino-Acid
Charged-Polar-Amino-Acid A polar amino acid bearing a charge. Souther. Basic-Amino-Acid Glutamic-Acid Aspartic-Acid Polar-Amino-Acid
Uncharged-Polar-Amino-Acid A polar amino acid with neutral charge. Souther. Asparagine Polar-Amino-Acid Glutamine Serine
Nucleoside Compound composed of a purine or pyrimidine base linked to either a ribose or a deoxyribose sugar. Alberts:ECB:G-13. Uridine Deoxycytidine Deoxyguanosine Purine Deoxythymidine Nitrogenous-Base Adenosine Organic-Molecule Cytidine Guanosine Pyrimidine Thymidine Pentose Deoxyadenosine
Adenosine A nucleoside containing adenine that when joined with a monophosphate group forms one of the four nucleotides in RNA. As a nucleoside triphosphate it is the principle energy yielding molecule in the cell. Souther. RNA Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Adenine Ribose
Cytidine A nucleoside containing cytosine that when joined with a monophosphate group forms one of the four nucleotides in RNA. Souther. RNA Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Ribose Cytosine
Deoxyadenosine A nucleoside containing adenine and deoxyribose that when joined with a monophosphate forms one of the four nucleotides in DNA. Souther. Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Adenine Deoxyribose
Deoxycytidine A nucleoside containing cytosine and deoxyribose that when joined with a monophosphate group forms one of the four nucleotides in DNA. Souther. Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Deoxyribose Cytosine
Deoxyguanosine A nucleoside containing guanine and ribose that when joined with a monophosphate forms one of the four nucleotides in RNA. Souther. RNA Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Deoxyribose Guanine
Deoxythymidine A nucleoside containing thymine and deoxyribose that when joined with a monophosphate group forms one of the four nucleotides in DNA. Souther. Nucleoside Carbon-Atom Covalent-Bond Nitrogen-Atom Deoxyribose Thymine
Guanosine A nucleoside containing guanine and ribose that when joined with a monophosphate forms one of the four nucleotides in RNA. Souther. RNA Carbon-Atom Nitrogen-Atom Ribose Guanine Covalent-CN-Bond Nucleoside 7-Methyl-Guanosine
7-Methyl-Guanosine A modified guanosine which is attached to the 5' end of newly made mRNA during RNA capping. Alberts:ECB:218. RNA Guanosine Carbon-Atom Covalent-CO-Bond Nitrogen-Atom Methyl-Group MRNA Guanine
Thymidine A nucleoside containing thymine and ribose. Souther. Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Ribose Thymine
Uridine A nucleoside containing uridine that when joined with a monophosphate group forms one of the four nucleotides in RNA. Souther. Uracil RNA Covalent-CN-Bond Nucleoside Carbon-Atom Nitrogen-Atom Ribose
Polymer Large and usually linear molecule made by linking together multiple identical or similar units (monomers) in a repetitive fashion. Alberts:ECB:G-14 Macromolecule Monomer Organic-Molecule
Macromolecule Polymer molecule, such as a protein, nucleic acid, or polysaccharide, with a molecular mass greater than a few thousand daltons. Alberts:ECB:G-11 Polynucleotide Nucleic-Acid-Molecule Oligonucleotide Nucleoprotein Polymer Polysaccharide Monomer Polypeptide
Nucleoprotein Organic molecule containing both nucleic acid and protein(s). Examples are ribosomes and SNRPs. Souther. Macromolecule Polynucleotide SnRNP Protein Ribonucleoprotein Sigma-Factor
Ribonucleoprotein A nucleoprotein that makes up part of a ribosome. Souther. Nucleoprotein
Sigma-Factor A subunit of procaryotic RNA polymerase which interacts with the promoter to signal the polymerase to initiate transcription at a specific sequence in template DNA. Lodish:MCB:347. RNA Nucleoprotein RNA-Polymerase
SnRNP A nucleoprotein enzyme involved in the splicing of mRNA. Alberts:ECB:220 Protein RNA Nucleoprotein
Polysaccharide Linear or branched polymer composed of sugars. Examples are glycogen and cellulose. Alberts:ECB:G-14. Cellulose Macromolecule
Cellulose Structural polysaccharide consisting of long chains of covalently linked glucose units. It provides tensile strength in plant cells. Alberts:ECB:G-4. Polysaccharide
Ring-Compound Compound in which some or all of its member atoms are joined in a ring. Heterocyclic-Compound Aromatic-Compound Organic-Molecule
Aromatic-Compound A ring compound containing the benzene ring. Souther. Phenyl-Group Ring-Compound Toluene Phenol Benzene
Benzene A six-carbon ring with the carbons attached to each other by Conjugated-Double-Bond. Souther. Aromatic-Compound Carbon-Atom Conjugated-Double-Bond Covalent-CH-Bond Hydrogen-Atom
Phenol A six-carbon ring alcohol with the carbons attached to each other by Conjugated-Double-Bond and containing one alcohol group. Souther. Aromatic-Compound Carbon-Atom Conjugated-Double-Bond Covalent-CH-Bond Hydroxyl-Group Hydrogen-Atom
Phenyl-Group A six-carbon ring with the carbons attached to each other by Conjugated-Double-Bond. Souther. Aromatic-Compound Carbon-Atom Conjugated-Double-Bond Covalent-CH-Bond Hydrogen-Atom
Toluene Methylbenzene. Souther Aromatic-Compound Carbon-Atom Conjugated-Double-Bond Methyl-Group Hydroxyl-Group Hydrogen-Atom Benzene
Heterocyclic-Compound A ring compound in which there are two or more ring members. In organic compounds the other atom is typically nitrogen or oxygen. Souther. Pyrimidine Ring-Compound Purine
Substrate The molecule on which an enzyme acts. Alberts:ECB:G-17. Catalysis Organic-Molecule
Sugar-Phosphate A deoxyribose sugar phosphate. Souther Oxygen-Atom Carbon-Atom Covalent-CO-Bond Monophosphate Deoxyribose Organic-Molecule Deoxyribose-Monophosphate
Deoxyribose-Monophosphate A deoxyribose sugar phosphate. Souther Oxygen-Atom Sugar-Phosphate Carbon-Atom Covalent-CO-Bond Monophosphate Deoxyribose
Peroxide Molecule containing two covalently bonded oxygen atoms. Souther. Oxygen-Atom Molecule
Polar-Molecule A molecule in which the bonding electrons are attracted more strongly to some atoms than to others, thereby creating an uneven (or polarized) distribution of electric charge. Alberts:ECB:G-14. Polar-Amino-Acid Molecule
Subatomic-Particle A particle that is one of the constituents of an atom. Souther. Proton Chemical-Object Neutron Electron
Electron Fundamental subatomic particle with a unit negative charge. Alberts:ECB:G-7. Subatomic-Particle
Neutron Fundamental subatomic particle found in the atomic nucleus; it has a mass similar to that of a proton, but no electric charge. Alberts:ECB:G-12. Subatomic-Particle
Proton Positively charged subatomic particle found in atomic nuclei. Also exists as an independent chemical species as a positive hydrogen ion (H+). Alberts:ECB:G-15. Subatomic-Particle
Chemical-Substance A substance composed of atoms or molecules. Souther. Chemical-Solution Organic-Substance Chemical-Entity Chemical-Mixture Inorganic-Substance
Chemical-Mixture An aggregate of two or more substances that are not chemically united and that exist in no fixed proportion to each other. RHCD:856. Chemical-Substance Colloid
Colloid A mixture of a solid, liquid, or gas that does not in a solid, liquid, or gas that does not separate out upon standing, such as an emulsion, foam, smoke, or fog. RHCD:264 cf colloidal system. Protoplasm Chemical-Mixture
Chemical-Solution The homogeneous mixture of a solid, liquid, or gas within a liquid or sometimes a solid or gas. WNCD:1123. Chemical-Substance Aqueous-Solution
Aqueous-Solution A solution in which water is the solvent for dissolved particles. Souther. Chemical-Solution Water Cytosol
Cytosol Aqueous solution of large and small molecules that fills the main compartment of the cytoplasm. Excludes membrane-bounded organelles such as endoplasmic reticulum and mitochondria. Alberts:ECB:G-6. Aqueous-Solution
Inorganic-Substance Any chemical substance which does not contain hydrocarbons. Water Chemical-Substance
Water Water as a substance. Souther. Water-Molecule Inorganic-Substance
Organic-Substance Any substance containing hydrocarbons. Souther. DNA-Substance Chemical-Substance
DNA-Substance DNA as the substance which makes up the hereditary material of the cell. Souther. Organic-Substance
Organic-Structure A structure made up of Organic-Molecule, such as the plasma membrane, organelles, etc. Souther. Organic-Complex Organic-Compartment Cytoskeleton Cell-Wall Organic-Layer Subcellular-Compartment Organic-Molecule Membrane
Cell-Wall Mechanically strong fibrous layer deposited by a cell outside its plasma membrane. Prominent in most plants, bacteria, algae, and fungi but not present in most animal cells. Alberts:ECB:G-4. Cell Organic-Structure Plasma-Membrane
Cytoskeleton System of Protein-Filament in the cytoplasm of a eucaryotic cell that gives the cell a polarized shape and the capacity for directed movement. Its most abundant components are Actin-Filament, microtubules, and Intermediate-Filament. Alberts:ECB:G-5. Intermediate-Filament Cell Organic-Structure Microtubule Actin-Filament Group Protein-Filament
Living-Group Any functionally related group of living entities, like the cells of an organ, a population of individuals, an ecological community, etc. Souther. Biological-Kingdom
Biological-Kingdom Highest biological taxonomic category. Organisms have been classically divided into 5 kingdoms. Souther. Procaryotes Living-Group
Procaryotes The taxonomic division consisting of single-celled non-nucleated organisms (see Procaryote). Souther. Procaryote Biological-Kingdom
Organism Single or multicellular entities which are free living and capable of reproduction. Souther. Cell Eucaryote Multicellular-Organism Unicellular-Organism
Eucaryote Living organism composed of one or more cells with a distinct nucleus and cytoplasm. Alberts:ECB:G-7. Organism Eucaryotic-Cell
Multicellular-Organism An organism composed of more than one cell. Souther. Invertebrate-Organism Organism Cell
Invertebrate-Organism A multicellular organism lacking a vertebral cord. Souther. Multicellular-Organism
Unicellular-Organism An organism consisting of a single cell. Souther. Procaryote Organism Cell
Procaryote Single-celled organism distinguished by the absence of a distinct nucleus. modified Alberts:ECB:G-14. Plasma-Membrane Bacterium Cytoplasm Unicellular-Organism Cell-Wall
Bacterium Member of one of the two classes of procaryotes, the other group being the archaea. Souther. Procaryote
Sub-Organismal-Entity Suborganismal 'living' components of organisms, including systems, organs, tissues, and cells. Souther. Cell
Cell The basic unit from which living organisms are made, consisting of an aqueous solution of Organic-Molecule enclosed by a membrane. All cells arise from existing cells, usually by a process of division into two. (Alberts:ECB:G-3). Plasma-Membrane Cytoplasm Eucaryotic-Cell Sub-Organismal-Entity Organic-Molecule
Eucaryotic-Cell Cells which contain a nucleus and other organelles in addition to cytoplasm. Modified from Alberts:ECB:9 Cell Eucaryotic-Cytoplasm Nucleus Eucaryotic-Plasma-Membrane
Virus Infectious particle consisting of nucleic acid (RNA or DNA) enclosed in a protein coat; replicates by parasitizing the reproductive machinery of a host cell, from which new virus particles ar released to infect other cells. Often the cause of disease. (Alberts:ECB:G-18.) DNA-Virus RNA Viral-Nucleic-Acid Protein-Coat
DNA-Virus A virus which contains DNA (cf RNA Virus whose particles contain RNA. Souther. Virus RNA Protein-Coat Viral-DNA
Membrane A thin, soft, pliable sheet or layer. Webster's 9th NCD:741. Rough-Endoplasmic-Reticulum Biological-Membrane Organic-Structure Smooth-Endoplasmic-Reticulum
Biological-Membrane Thin sheet of lipid molecules and associated proteins that encloses all cells and forms the boundaries of many eucaryotic organelles. Alberts:ECB:G-11 as 'membrane'. Internal-Membrane Plasma-Membrane Sub-Organismal-Entity Membrane
Internal-Membrane Eucaryotic cell membrane other than the plasma membrane. The membrane that surrounds an organelle is an example. Alberts:ECB:G-10 Biological-Membrane Nuclear-Envelope
Nuclear-Envelope Envelope surrounding the nucleus in a eucaryotic cell. It consists of two lipid bilayer membranes - an outer and an inner - and is perforated by Nuclear-Pore. Alberts:ECB:G-13. Internal-Membrane Group Nuclear-Pore Lipid-Bilayer
Plasma-Membrane Membrane that surrounds a living cell. Alberts:ECB:G-14 Cell Biological-Membrane Protein Group Eucaryotic-Plasma-Membrane Membrane Lipid-Bilayer
Eucaryotic-Plasma-Membrane Membrane that surrounds a eucaryotic cell. Alberts:ECB:G-14 Eucaryotic-Cytoplasm Plasma-Membrane Eucaryotic-Cell Membrane
Rough-Endoplasmic-Reticulum Region of the endoplasmic reticulum associated with ribosomes; involved in the synthesis of secreted and membrane-bound proteins. Alberts:ECB:G-16. Membrane
Smooth-Endoplasmic-Reticulum Region of the endoplasmic reticulum not associated with ribosomes; involved in synthesis of lipids. Alberts:ECB:G-17. Lipid-Synthesis Membrane
Organelle A discrete structure or subcompartment of a eucaryotic cell specialized to carry out a particular function; especially a cellular substructure that is visible in the light microscope. Examples include mitochondria and the Golgi apparatus. (Alberts:ECB:G-13). Any membrane bound structure found in the cytoplasm of cells. Lodish:MCB:G-13. Golgi-Apparatus Internal-Membrane Endoplasmic-Reticulum Organic-Compartment Vesicle Peroxisome Lysosome Cytoplasm Mitochondrion Centrosome Nucleus
Organic-Compartment A compartment within a living structure, surrounded by a membrane. Examples are chambers of the heart, and the nucleus of the cell. Organelle Organic-Structure
Centrosome Centrally located organelle of animal cells that is the primary microtubule-organizing center and is duplicated to form the spindle poles during mitosis. In most animal cells it contains a pair of centrioles. Alberts:ECB:G-4 Mitosis Organelle Centriole
Endoplasmic-Reticulum Labyrinthine, membrane-bounded compartment in the cytoplasm of Eucaryotic-Cell, where lipds are secreted and membrane-bound proteins are made. Alberts:ECB:G-7 Organelle Internal-Membrane Eucaryotic-Cell Subcellular-Compartment
Golgi-Apparatus Membrane-bounded organelle in Eucaryotic-Cell, where the proteins and lipids made in the endoplasmic reticulum are modified and sorted. Alberts:ECB:G-8. Organelle Vesicle Eucaryotic-Cell
Lysosome Intracellular membrane-bound organelle containing digestive enzymes. The interior of a lysosome is strongly acidic, and its enzymes are active at an acid pH. Alberts:ECB:G-11. Nuclease Phosphatase Organelle Pool Protease Catabolize Lipase
Mitochondrion Membrane-bound organelle, about the size of a bacterium, that carries out oxidative phosphorylation and produces most of the ATP in Eucaryotic-Cell. Alberts:ECB:G-11. Oxido-Reductase Organelle Pool ATP Eucaryotic-Cell
Nucleus The major organelle in Eucaryotic-Cell, containing DNA organized into chromosomes. Alberts:ECB:G-13 Organelle Nucleoplasm Chromosome Eucaryotic-Cell Group Nuclear-Envelope
Peroxisome Small, membrane-bounded organelle that uses molecular oxygen to oxidize Organic-Molecule. Contains some enzymes that produce hydrogen peroxide and others that degrade hydrogen peroxide. Alberts:ECB:G-14. Organelle Pool Peroxidase Organic-Molecule
Vesicle Small, membrane-bounded, spherical organelle in the cytoplasm of a eucaryotic cell. Alberts:ECB:G-18. Organelle
Organic-Complex A complex of several organic constituents, such as the nucleolus or extracellular matrix, which serves some structural or functional role. Souther:2001. Molecular-Complex Organic-Structure Extracellular-Matrix Nucleic-Acid-Complex
Extracellular-Matrix Complex network of polysaccharides (such as glycosaminoglycans or cellulose) and proteins (such as collagen) secreted by cells. A structural component of tissues that also influences their development and physiology. Alberts:ECB:G-7. Organic-Complex Protein Polysaccharide Group
Molecular-Complex An assembly of molecules, usually macromolecules, held together by nonCovalent-Bond and performing a specific function, such as DNA replication or the synthesis of phospholipids. Alberts:ECB:G-12. Organic-Complex Nucleoprotein-Complex Protein-Complex Molecule
Nucleoprotein-Complex A complex made up of proteins and Nucleic-Acid. Examples include chromosomes, and the SNRP splicing complex. Souther. Ribosome Polynucleotide Nucleic-Acid Protein Polyribosome Chromatin Molecular-Complex SnRNP-Ensemble Nucleolus Chromosome Replication-Machine
Chromatin Complex of DNA, histones, and nonhistone proteins found in the nucleus of a eucaryotic cell. The material of which chromosomes are made. Alberts:ECB:G-4. Nucleoprotein-Complex
Chromosome Long, threadlike structure composed of DNA and associated proteins that carries part or all of the genetic information of an organism. Alberts:ECB:G-4 Eucaryotic-DNA Histone Nucleoprotein-Complex Chromatin DNA-Molecule Histone-Complex
Nucleolus Structure in the nucleus where ribosomal RNA is transcribed and ribosomal subunits are assembled. Alberts:ECB:G-13. RNA Nucleoprotein-Complex
Polyribosome A mRNA-ribosome complex made up of several ribosomes spaced along a mRNA. Alberts:ECB:232 Ribosome Series Nucleoprotein-Complex MRNA
Replication-Machine The multiprotein complex that promotes DNA synthesis at the replication fork. Lehninger:PBC:G-12. Single-Strand-Binding-Protein Primase Protein-Sliding-Clamp DNA-Polymerase-Replication Pool DNA-Gyrase Nucleoprotein-Complex DNA-Template DNA-Helicase
Ribosome Particle composed of ribosomal RNAs and ribosomal proteins that associates with messenger RNA and catalyzes the synthesis of protein. Alberts:ECB:G-16. RNA Procaryotic-Ribosome Nucleoprotein-Complex Bound-Ribosome Eucaryotic-Ribosome Free-Ribosome
Bound-Ribosome Ribosomes that are bound to the endoplasmic reticulum. Areas with bound ribosomes are called rough endoplasmic reticulum. Souther. Ribosome Internal-Membrane Endoplasmic-Reticulum
Eucaryotic-Ribosome Ribosome found in cytoplasm of eucaryotes. Souther. Ribosome MRNA-Site P-Site A-Site Ribonucleoprotein RRNA Ribosomal-Protein E-Site TRNA-Initiator-Site
Free-Ribosome Ribosomes that are free in the cytoplasm. Souther. Ribosome Cytoplasm
Procaryotic-Ribosome Ribosome found in cytoplasm of procaryotes. Souther. Ribosome Procaryotic-Ribosomal-Protein Ribonucleoprotein Procaryotic-RRNA
SnRNP-Ensemble A complex of nucleoprotein enzymes involved in the splicing of mRNA. Alberts:ECB:220 SnRNP Nucleoprotein-Complex
Protein-Complex A group of proteins which act together to provide structure or perform some function. They are often held together by weak bonds such as Hydrogen-Bond. Examples: histones and the mitotic spindle. Souther. Hydrogen-Bond Protein Compound-Protein Centriole Protein-Coat Molecular-Complex Enzyme-Complex Proteasome Histone-Complex
Compound-Protein A protein made up of polypeptide subunits held together by nonCovalent-Bond. The structure formed by these subunits is called quaternary structure. Examples include microtubules, hemoglobin. Souther. Protein-Filament Protein-Complex
Proteasome Large protein complex in the cytosol that is responsible for degrading cytosolic proteins that have been marked for destruction by ubiquitination or by some other means. Alberts:ECB:G-14. Protease Proteolysis Group Protein-Complex
Protein-Coat The viral protein(s) which cover and protect the viral nucleic acid. Protein-Complex
Nucleic-Acid-Complex A group of Nucleic-Acid which act together to provide structure or perform some function. They are often held together by weak bonds such as Hydrogen-Bond. Examples: DNA double helix and Base-Pair. Souther. G-C-Base-Pair Organic-Complex Hydrogen-Bond Nucleic-Acid Nucleotide-Sequence A-U-Base-Pair Base-Pair DNA-Molecule DNA-Molecule-Segment
A-U-Base-Pair The base pair resulting from the hydrogen bonding of adenine and uracil in RNA-Molecule. Souther. Hydrogen-Bond Uracil RNA-Molecule Nitrogen-Atom Adenine Nucleic-Acid-Complex DNA-Molecule Oxygen-Atom Base Amino-Group Hydrogen-Atom
Base-Pair Two nucleotides in an RNA or a DNA molecule that are paired by Hydrogen-Bond - for example, G with C, and A with T or U. Alberts:ECB:G-3. Hydrogen-Bond RNA Pyrimidine A-T-Base-Pair Purine Nucleotide Nucleic-Acid-Complex DNA-Molecule
A-T-Base-Pair The nucleotide base pair resulting from the hydrogen bonding of adenine and thymine in DNA-Molecule. Souther. Hydrogen-Bond D-TMP Base-Pair Nitrogen-Atom Adenine DNA-Molecule Oxygen-Atom Nucleotide Thymine Amino-Group Hydrogen-Atom D-AMP
DNA-Molecule Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information. Alberts:ECB:G-6 Hydrogen-Bond Genetic-Information-Storage Base-Pair Nucleic-Acid-Complex Bacterial-DNA Eucaryotic-DNA DNA-Substance Series Genome DNA-Strand Viral-DNA Procaryotic-DNA Replication-Origin
Bacterial-DNA Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information in bacteria. Alberts:ECB:G-6. Operon DNA-Strand DNA-Molecule Gene
Eucaryotic-DNA Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information in eucaryotes. Alberts:ECB:G-6. DNA-Strand DNA-Molecule DNA-Gene-Coding-Sequence Gene
Procaryotic-DNA Double-stranded polynucleotide formed from two separate chains of deoxyribonucleotide units; serves as the carrier of genetic information in procaryotes. Alberts:ECB:G-6. Operon DNA-Strand DNA-Molecule Gene
DNA-Molecule-Segment A segment of a DNA molecule. Souther. DNA-Substance Hydrogen-Bond DNA-Sequence Series Base-Pair Nucleic-Acid-Complex
G-C-Base-Pair The base pair resulting from the hydrogen bonding of Guanine and Cytosine in RNA-Molecule. Souther. Hydrogen-Bond D-CMP RNA-Molecule Nitrogen-Atom D-GMP Nucleic-Acid-Complex DNA-Molecule Guanine Oxygen-Atom Cytosine Amino-Group Hydrogen-Atom
Organic-Layer A layer made up of Organic-Molecule, such as the bimolecular layer that makes up the plasma membrane. Souther:2001. Organic-Structure Organic-Molecule Lipid-Bilayer
Lipid-Bilayer A bimolecular leaflet made up of lipid molecules, forming the basic structure of the plasma membrane, organelle membranes, etc. Souther. Lipid Organic-Layer Group Molecule
Subcellular-Compartment A compartment within the cell, surrounded by a membrane. Examples are mitochondrial matrix, the nucleoplasm, and the compartment within the endoplasmic reticulum. Organic-Structure Internal-Membrane
Acid-Substance Substance that dissociates in water to release protons (H+ ions) thereby producing a low pH; these protons associate with water, generating hydronium (H3O+) ions. Alberts:ECB:G-1.
Energy The capacity to do work. RHCD:438. Chemical-Energy
Chemical-Energy Energy produced by or stored in chemical properties or property differentials, such as Chemical-Bond, such as charge gradients, density gradients, etc. Souther. Activation-Energy Energy Chemical-Bond-Energy Chemical-Bond
Activation-Energy Extra energy that a molecule must acquire in order to surmount an energy barrier so as to undergo a particular chemical reaction. Alberts:ECB:G-1. Chemical-Energy
Chemical-Bond-Energy The strength of the chemical linkage between two atoms, measured by the energy in kilocalories/mole needed to break it. Alberts:ECB:G-3. Chemical-Energy
Particulate-Matter Matter made up of particles. Souther. Phagocytose
Add-Enzymatic The enzymatic addition of a group to an atom or molecule. Souther. Chemical-Group Cell Atom Addition-Enzyme Chemical-Object Phosphorylation Molecule
Phosphorylation The transfer of a phosphate to a molecule. The bond formed is high energy and permits the charged molecule to undergo reactions that would otherwise be energetically unfavorable. Souther. Cell Add-Enzymatic Phosphoryl-Group Kinase Oxidative-Phosphorylation Molecule
Oxidative-Phosphorylation Process in bacteria and mitochondria in which ATP formation is driven by the transfer of electrons from food molecules to molecular oxygen. Involves the intermediate generation of a pH gradient across the membrane, which drives ATP synthesis by a chemiosmotic coupling. Alberts:ECB:G-13p Cell Phosphorylation ATP Oxygen-Molecule Monophosphate ADP Oxidation
Catabolize Cellular process whereby complex molecules are degraded to simpler ones and energy is released. Lodish:MCB:G-2. Lipolysis Nucleic-Acid-Degradation Glycolysis Chemical-Object Ribonucleic-Acid-Degradation Proteolysis Sub-Organismal-Entity Catabolic-Enzyme
Glycolysis The catabolic pathway by which a molecule of glucose is broken down into 2 molecules of Pyruvic-Acid. Lehninger:PBC:G-6. Cell Pyruvic-Acid Glucose Group Catabolize Catabolic-Enzyme
Lipolysis The catabolic pathway by which lipids are hydrolyzed. Souther. Lipid Catabolize Sub-Organismal-Entity Lipase
Nucleic-Acid-Degradation The hydrolytic breakdown of Nucleic-Acid. Souther. Polynucleotide Nuclease Nucleic-Acid Pool Nucleotide-Sequence Catabolize
Proteolysis The catabolic pathway by which lipids are hydrolyzed. Souther. Protein Pool Amino-Acid Protease Catabolize Sub-Organismal-Entity
Ribonucleic-Acid-Degradation The hydrolytic breakdown of RiboNucleic-Acid. Souther. Pool Ribonuclease Catabolize RNA-Sequence
Mitosis Division of the nucleus of a eucaryotic cell, involving condensation of the DNA into visible chromosomes. Alberts:ECB:G-12. Centrosome Nucleus
Detach-Enzymatic The removal of a group from a molecule, such as a phosphate, amino group, etc. Souther. Cell Enzyme Chemical-Object
DNA-Replication A process by which a copy of a DNA molecule is made. Alberts:ECB:G-6. Biosynthesize Deoxyribonucleotide DNA-Polymerase Pool DNA-Strand DNA-Molecule Replication-Origin
DNA-Synthesis A process by which a copy of all or part of a DNA molecule is made or repaired. Souther. Biosynthesize Cell Hydrogen-Bond DNA-Chain-Elongation Deoxyribonucleotide DNA-Polymerase 5-Prime-End Procaryotic-DNA-Synthesis DNA-Lagging-Strand-Synthesis Organelle Virus DNA-Sequence Replication-Fork Pool Nucleotide
DNA-Lagging-Strand-Synthesis The synthesis of a daughter strand using the lagging strand as the template. The lagging strand runs 5' to 3' so the daughter strand is synthesized 3' to 5', therefore discontinuously. The resulting 'Okazaki-Fragment' must be stitched together by a DNA ligase. Souther. Deoxyribonucleotide DNA-Sequence Pool DNA-Synthesis Replication-Machine DNA-Molecule-Segment Molecule
Procaryotic-DNA-Synthesis A process by which a copy of all or part of a procaryotic DNA molecule is made. Souther. Procaryote DNA-Synthesis Procaryotic-DNA-Polymerase
DNA-Transcription Copying of one strand of DNA into a complementary RNA sequence by the enzyme RNA Polymerase. Alberts:ECB:1998. Biosynthesize Cell Ribonucleotide RNA-Transcript RNA Polymerase Pool Eucaryotic-DNA-Transcription Transcription-Unit RNA-Polymerase
Eucaryotic-DNA-Transcription Copying of one strand of DNA into a complementary RNA sequence by the enzyme RNA Polymerase in eucaryotes. cf Alberts:ECB:G-18 DNA-Transcription Ribonucleotide RNA Polymerase Eucaryotic-DNA-Strand Pool Eucaryotic-Cell Eucaryotic-RNA-Transcript
Catalysis A chemical reaction whose rate is facilitated by the presence of a substance which is not altered by the reaction. Souther. Enzyme-Catalysis Chemical-Object Catalyst
Enzyme-Catalysis A chemical reaction whose rate is facilitated by the presence of an enzyme which is not altered by the reaction. Souther. Cell Enzyme Chemical-Object Catalysis
Metabolize The sum of processes by which a particular substance is handled by the body. Webster's Ninth Collegiate Dictionary - under Metabolism. Enzyme Chemical-Object
Polymerize To link together many identical or similar units (monomers) in a repetitive fashion. Alberts:ECB:G-14; derived from definition of polymer. Polymer Monomer
Produce-Enzymatic Any Enzymatic reaction process which requires enzymes, including anabolic, catabolic, and transfer reactions. Souther, 2001. Biosynthesize Cell Enzyme Chemical-Object RNA-Translation
Biosynthesize The production of a more complex substance from simpler substances by a living entity. Souther, 2001. DNA-Transcription Produce-Enzymatic Enzyme Protein-Synthesis Lipid-Synthesis Chemical-Object DNA-Synthesis DNA-Replication ATP-Synthesis
ATP-Synthesis The synthesis of ATP from ADP and and a monophosphate group. Souther. Biosynthesize Cell ATP-Synthase Monophosphate Mitochondrion ADP ATP
Lipid-Synthesis The synthesis of lipids. Souther. Biosynthesize Cell Lipid Smooth-Endoplasmic-Reticulum
Protein-Synthesis The commonest form of gene expression in which proteins are synthesized as directed by a gene via the intermediary of RNA which is translated into protein. Souther. Biosynthesize DNA-Transcription RNA Protein Amino-Acid Pool Gene-Expression RNA-Translation MRNA Chemical-Information-Sequence Gene
RNA-Translation The synthesis of a protein from amino acids guided by mRNA. Souther. Amino-Acid-Sequence Amino-Acid Produce-Enzymatic Ribosomal-Peptidyl-Transferase
Enzyme-Activation To put into a state where it a can participate in an action. Souther. Cell Enzyme Coenzyme
Attach-Enzymatic The attachment or addition of a group to a molecule, such as a phosphate, amino group, etc. Souther. DNA-Chain-Elongation Cell Enzyme Chemical-Object TRNA-Charging Ligation
DNA-Chain-Elongation The process of adding deoxyribonucleotides to the end of a growing DNA sequence during DNA replication or repair. Souther Deoxyribonucleotide DNA-Sequence DNA-Polymerase Attach-Enzymatic
Ligation The joining of the 3' end of one nucleic acid strand with the 5' end of another, forming a continuous strand. see Lodish:MCB:G-10. definition for ligase. Nucleotide-Sequence Ligase Attach-Enzymatic DNA-Ligation
DNA-Ligation The joining of the 3' end of one nucleic acid strand with the 5' end of another, forming a continuous strand. see Lodish:MCB:G-10. definition for ligase. DNA-Sequence 3-Prime-Deoxyribonucleotide Ligase 5-Prime-Deoxyribonucleotide Ligation
TRNA-Charging The attachment of an amino acid to the appropriate tRNA during RNA translation. Souther. Cell RNA Amino-Acyl-TRNA-Synthetase Amino-Acid TRNA Attach-Enzymatic
Endocytose Uptake of material into a cell by an invagination of the plasma membrane leading to internalization in a membrane- bounded vesicle. Alberts:ECB:G-7. Cell Pinocytose Phagocytose
Phagocytose The process by which particulate matter is engulfed by a cell. Prominent in predatory protozoa, such as Amoeba proteus, and to certain specialized cells of multicellular animals such as macrophages. Alberts:ECB:G-14. Particulate-Matter Cell Endocytose
Pinocytose Uptake of fluid by a cell by means of endocytosis Alberts:ECB:G-14. Cell Endocytose
Remove-Enzymatic The enzymatic removal of a group from an atom or molecule. Souther. Cell Deamination Chemical-Object Removal-Enzyme Dephosphorylation
Deamination The loss or removal of an amino group from a molecule. Souther. Cytosine-Deamination DNA-Strand Amino-Group Remove-Enzymatic Deaminase
Cytosine-Deamination The loss of an amino group from a cytosine base in a DNA molecule. Souther, see Alberts:ECB:202. Uracil Deamination DNA-Strand Cytosine Amino-Group
Dephosphorylation The removal of a phosphoryl group from a molecule. The resulting molecule is less charged energetically and is said to be deactivated. Souther. Phosphatase Phosphoryl-Group Molecule Remove-Enzymatic
Electron-Transfer The transfer of electrons from one molecule to another. Souther. Cell Electron-Carrier Electron Molecule
Energy-Transfer The transfer of energy from one entity to another. Souther. Energy Chemical-Energy-Transfer
Chemical-Energy-Transfer The transfer of chemical energy from one entity to another. Souther. Chemical-Entity Energy-Transfer Chemical-Energy Chemical-Bond-Energy-Transfer
Chemical-Bond-Energy-Transfer The transfer of chemical energy from one molecule to another. Souther. Chemical-Bond-Energy Molecule Chemical-Bond Chemical-Energy-Transfer
Gene-Expression The process by which a gene exerts its effect on a cell or an organism, usually by directing the synthesis of an RNA molecule that can be translated into a protein with a characteristic activity. Alberts:ECB:G-8. The product of gene expression may also be rRNA or tRNA. Souther. Protein-Synthesis Macromolecule DNA-Transcription RNA Gene Chemical-Information-Sequence
Information-Transfer The transfer of information from one entity to another. Souther. Information
Depurination The spontaneous loss of a purine from a DNA strand. Souther, see Alberts:ECB:202. Purine DNA-Strand
Oxidation The loss of electrons from an atom or molecule as occurs when hydrogen is removed from a molecule or oxygen is added. Lodish:MCB:G-13 Cellular-Respiration Citric-Acid-Cycle Chemical-Object Electron Oxidative-Phosphorylation Oxidase Oxido-Reduction-Reaction
Cellular-Respiration The process by which glucose is broken down to CO2 and water. Normally, ATP is generated in the process. Substages include glycolysis, citric acid cycle, and oxidative phosphorylation. Souther. Glucose Glycolysis Water ATP Carbon-Dioxide Oxygen-Atom Citric-Acid-Cycle Oxidative-Phosphorylation Oxidation
Citric-Acid-Cycle Central metabolic pathwya in all aerobic organisms that oxidizes Acetyl-Group derived from food molecules to CO2. In Eucaryotic-Cell these reactions are located in the mitochondrial matrix. Alberts:ECB:G-4. Acetyl-Group Eucaryotic-Cell Oxidation
Oxido-Reduction-Reaction The simultaneous loss of electrons from one molecule (oxidation) and gain of by a second molecule of electrons (reduction) by transfer from the first to the second. Souther. Enzyme Chemical-Object Electron Reduction Oxidation
Donate-Molecular The donation of energy or of a chemical entity by a chemical object such as an atom or molecule. Souther. Chemical-Entity Chemical-Object
Reduction The gain of electrons by an atom or molecule as occurs when hydrogen is added from a molecule or oxygen is removed. Lodish:MCB:G-15 Chemical-Object Electron Oxido-Reduction-Reaction
Transfer-Enzymatic The transfer of a group from one molecule to another, such as a phosphate, amino group, etc, facilitated by enzyme(s). Souther. Enzyme Sub-Organismal-Entity Molecule
Diffuse The spread of molecules and small particles from one location to another through random, thermally-driven movements. Alberts:ECB:G-6. Molecule
Replace-Biological The substitution or replacement of one molecule or chemical group by another. Souther. Enzyme Chemical-Entity Sub-Organismal-Entity Molecule
Replace-Enzymatic The substitution or replacement of one molecule or chemical group by another. Souther. Enzyme Chemical-Object Damaged-DNA-Repair DNA-Repair DNA-Mismatch-Repair Sub-Organismal-Entity Molecule Hydrogen-Atom
Damaged-DNA-Repair A DNA repair system that identifies DNA damaged by environmental stimuli, such as UV radiation and repairs it. Souther, see Alberts:ECB:204. DNA-Polymerase-Repair DNA-Sequence DNA-Synthesis DNA-Strand Base-Pair Replace-Enzymatic Deoxyribonuclease DNA-Ligase DNA-Ligation
DNA-Mismatch-Repair A DNA repair system that identifies base pair mismatches, excises a region of the DNA strand containing the mismatch(es), and resynthesizes the missing nucleotide pairs. Paraphrased from Alberts:ECB:200. DNA-Polymerase-Repair DNA-Sequence DNA-Synthesis DNA-Strand Base-Pair Replace-Enzymatic Deoxyribonuclease DNA-Ligase DNA-Ligation
DNA-Repair Collective term for the enzymatic processes that correct deleterious changes affecting the continuity or sequence of a DNA molecule. Alberts:ECB:G-6. Cell DNA-Polymerase-Repair Deoxyribonuclease DNA-Ligase DNA-Ligation Enzyme DNA-Sequence DNA-Synthesis DNA-Strand Replace-Enzymatic Group
Genetic-Information-Storage Genetic-Information-Sequence Nucleotide-Sequence
Information-Storage Information
Carrier The object or medium which transports the object moved during a move event.
Catalyst A molecule that accelerates a chemical reaction without itself undergoing a change. Alberts:ECB:G-3. Enzyme Catalysis
Bond A uniting or binding element or force. Websters 9th NCD:166 Chemical-Bond
Template
substrate
Indole An azole ring fused to a benzene ring. Souther. Covalent-CN-Bond Carbon-Atom Nitrogen-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-NH-Bond Covalent-CC-Bond Double-Covalent-CC-Bond
Imidazole An imino 5 membered ring. Souther. Covalent-CN-Bond Carbon-Atom Conjugated-Double-Bond Nitrogen-Atom Covalent-CH-Bond Hydrogen-Atom Covalent-NH-Bond Double-Covalent-CC-Bond