Glossary

Glossary and Overviews

2007-12-31T23:59:00.000-08:00

There are two alphabetic indexes for the Glossary :
▫Sections▫ at the top of the sidebar show all o-o items o-o beginning with indicated letter. ◦Items◦, lower on sidebar, provide links to listed o-o items o-o beginning with indicated letter. The body of each o-o item o-o provides links to more detailed items on the Companion Sites. Iconic links to site maps for the Companion Sites are provided at the base of the sidebar at left. The alphabetic o-o items o-o also provide direct links to more detailed items on the companion sites.

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Overview:

Scientific theories of biological evolution seek to explain the mechanisms of the observable fact of biological evolution. Scientists observing biological evolution first sought to explain observed morphological changes over time – phenotypic evidence of changes in body structure found in the fossil record. Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – that is, a genetic alteration in the intergenerational frequency of alleles in populations.

There are two basic types of mechanism involved in biological evolution. First are the genetic sources of alteration of a gene within the genotype of an individual (mutations). Duplication mutations have been particularly important in evolutionary history. Second are those statistical mechanisms that determine the fate of an altered allele. These are the mechanisms that increase or decrease frequency of an allele (a form of a gene at a locus) within a population. Evolution is expected to occur when selection acts on a trait that has a heritable basis of phenotypic variation.

Biochemistry includes the study of ions, inorganic molecules, and organic molecules involved in biological processes – for example, structural molecules, transport molecules, and metabolic pathways. • Molecules in Pathways •

Molecular genetics is the study of molecules and mechanisms involved in genetic inheritance. Archival information molecules are long polymers of deoxyribonucleic acid (DNA) comprising bases in specific sequence. The bases adenine (A), thymine (T), cytosine (C), and guanine (G), function as codon triplets – sequences of three bases that code for specific amino acids or for translation initiation (start codons) or termination (stop codons). Uracil is substituted for thymine in RNA.

The segments of DNA that contain protein-coding instructions are called genes, and these gene sequences comprise a portion of the total genome of a cell. The genome includes both the genes (coding-sequences, domains) and the non-coding sequences – both exons, which include open reading frames, and introns.

Because the 64 possible combinations of G-A-T-C code for only the 20 amino acids commonly found in proteins, the code is 'degenerate' (redundant) with more than one triplet combination coding for each amino acid. (This code reduncancy provides hereditary stability by reducing mutation errors.) The double helix of DNA comprises paired nucleotide strands in which the nucleobases are hydrogen bonded to complementary bases in the adjacent chain. Adenine pairs with thymine or uracil (A-TU), and cytosine pairs with guanine (CG).

During cellular reproduction, strands of archival DNA are copied or replicated. Transcription is the first step in gene expression – DNA instructions are converted into mRNA codons, rRNAs, miRNAs, and tRNAs. Coding instructions of nucleotide sequences in archival DNA, which have been transcribed and processed into mRNAs are then translated into polypeptides and proteins at cytoplasmic ribosomes. Translation is the ultimate step in gene expression, in which archival genetic instructions are converted into specified sequences of amino acids in peptides, polypeptides, and proteins.

In prokaryotic cells – without a nuclear membrane – translation into polypeptides and proteins may begin prior to termination of transcription. The molecular genetics of eukaryotic cells is more complicated than that of prokaryotes. Various molecules of ribonucleic acid (RNA) participate in the transcription of the DNA code into processed mRNA in a series of RNA processing stages including capping, polyadenylation, and pre-mRNA splicing.

Following pre-mRNA processing, RNAs undergo extranuclear transfer. Mature RNAs may undergo post-transcriptional modulation (via miRNAs) before translation of the archival DNA instructions into specific sequences of amino acids in the polypeptides and proteins that participate in cellular function and structure. Transfer RNAs (tRNA) deliver specific amino acids to the cytoplasmic ribosomes along the rough endoplasmic reticulum. Ribosomal RNAs participate in assembly of polypeptides and proteins at ribosomes. Here RNAs serve as ribozymes – non-proteinaceous enzymes.

A number of processes are involved in control of cellular function through the maintenance of accuracy of genetic inheritance – damage to DNA is repaired, and faulty RNA is destroyed by nonsense-mediated decay or nonstop decay.

DNA damage may result from replication errors, incorporation of mismatched nucleotides (substitution errors – transitions and transversions), damage by oxygen radicals, hydroxyl radicals, ionizing or ultraviolet radiation, toxins, alkylating agents, and chemotherapy agents. A number of vital mechanisms repair DNA damage to bases (including C to T, C to U, and T U mismatch) and to strands, including double strand breaks. All organisms, prokaryotic and eukaryotic, utilize at least three enzymatic excision-repair mechanisms for damaged bases: base excision repair, mismatch repair, and nucleotide excision repair.

Given the importance of mRNA as an information-carrying molecule, faulty pre-mRNAs and mRNAs must be eliminated – they are destroyed by nonsense-mediated decay or nonstop decay:
1. A pre-mRNA made from a mutant gene usually has an exon junction complex (EJC) in the wrong position. This error activates nonsense-mediated decay (NMD) and destroys the pre-mRNA before it can be used to make flawed proteins. There are at least two kinds of NMD: one requires the protein UPF2 and the other does not.
2. Nonstop decay is mRNA turnover mechanism that has none of the properties of normal mRNA turnover or of NMD. A multi-enzyme complex called the exosome is important for nonstop decay. The exosome is the site for binding of a specific adapter protein called Ski7p. Nonstop decay shares none of the enzymes required for nonsense-mediated decay.

Just as cells repair DNA, they must also maintain the proteome by managing damaged proteins. Heat stress denaturates proteins, causing weakening of polar bonds and exposure of hydrophobic groups. The cellular stress response (heat-shock response) protects organisms from damage resulting from environmental stressors such as heat, UV light, trace metals, and xenobiotics. Stress genes are activated to rapidly synthesize stress proteins, which are highly conserved in biological evolution and play similar roles in organisms from bacteria to humans. Normally, several constitutive stress proteins are present at low levels to function as molecular chaperones, so as to facilitate folding, assembly, and distribution of newly synthesized proteins. For the environmentally stressed cell, stress proteins protect and repair vulnerable protein targets, and play a role in the lysosomal and ubiquitin protein degradation pathways (for removal of unsalvageable proteins). Thus, the cellular stress response performs orchestrated induction of key proteins necessary for cellular protein repair and degradation systems.

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A

2007-12-31T23:58:00.000-08:00

o-o items o-o are in brief format :

o-o activator o-o active transport o-o adaptor protein o-o adenylyl cyclases o-o Akt o-o allele o-o alternative splicing o-o apoptosis o-o ATP synthase o-o autoinducer

Links to more detailed items on Companion sites:
AC : acidic amino acids : acidic and basic amino acids סּ actin ~ activator סּ active transport AD ~ adenine cytosine guanine thymine uracil bases ¤ adenoviruses ◊ adenylate cyclases סּ adhesion סּ adhesion - cytoskeleton ~ adhesion molecules AK ◊ Akt AL ~ alternative splicing ~ allele AM ~ amines ~ amino acids : amino acids - acidic : amino acids - acidic and basic: amino acids - basic : amino acids - polar : amino acids - non-polar ~ amphipathic § amplifier proteinsAN ф antibodies ф antigen ¤ amplification - genes § anchoring proteins AP ф APCs סּ apoptosis AT ◊ ATPases ~ ATPases AU ф autoimmunity

Molecules and Pathways φ Acetyl Co-Enzyme A ››› acetyl CoA pathway φ acetylcholine φ adenine φ adenosine ››› aerobic respiration φ alanine φ AMP ››› anabolism and catabolism ››› anaplerotic reactions φ arginine φ asparagine φ aspartic acid φ ATP

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active transport

2007-12-22T04:15:00.001-08:00

Active transport refers to the transport of hydrophilic macromolecules and ions across membranes, against chemical or concentration gradients, by membrane pumps that require expenditure of energy (most often in the form of ATP).

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

activator

2007-12-22T04:15:00.000-08:00

In molecular genetics, an activator is a DNA-binding protein that regulates one or more genes by increasing the rate of transcription.

In biochemistry, an activator is a substance that combines with an enzyme to increase its catalytic activity.

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

adaptor

2007-12-21T23:08:00.000-08:00

An adaptor protein links signaling components by acting as an accessory to the chief proteins of the signal transduction pathway. Adaptor proteins lack any intrinsic enzymatic activity, instead they mediate specific protein-protein interactions that drive the formation of protein complexes. The specificity of Toll-like receptor signaling occurs by means of adaptor proteins possessing Toll–interleukin 1 receptor (TIR) domains.

adenylyl cyclases

2007-12-21T19:01:00.000-08:00

Adenylyl cyclases (adenylate cyclases) are transmembrane enzymes that cross the membrane twelve times, and which convert ATP to the second-messenger cAMP (3',5' cyclic AMP) and pyrophosphate (Pi).

Adenylyl cyclases are coincidence detectors, meaning that they are only activated by several different signals occurring together – they are modulated by G-proteins, forskolin, Ca2+/calmodulin, and other class-specific substrates.

In cell physiology research, forskolin is a vasodilator drug that is employed to elevate cAMP levels. Forskolin activates adenylyl cyclase and resensitizes cell receptors. Calmodulin (CaM) is a small, versatile, acidic protein that binds Ca2+ second messenger through CaM's four EF-hand domains (motifs).

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

communing

2007-12-21T01:00:00.000-08:00

Associated science sites • Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Glossary • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Molecule • Molecular Biology • Molecular Paths • Neurosciences • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Taxonomy Phylogeny • Tissue • Virus • And some philosophy/general interest sites • A-Deistic • Adeistic • Black Out • cosmic • Eine Kleine Nattermusing • eMusings • eVolition • Galaria • Godborygmi • Godspell Follies • Gray Matters • MetaThoughts • Mimble Wimble • Naturalism • BLogodaedaly • palimpsest • Salient • Science of Evolution • Sechuam • Sintheist • Tabula Flexuosa • The Scarlet A • Weltschauung •

Akt

2007-12-14T16:59:00.000-08:00

Akt1 is 'thymoma viral proto-oncogene 1', a synonym for protein kinase B, and is a serine/threonine kinase that promotes cellular survival.

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

allele

2007-12-13T12:37:00.000-08:00

An allele is an alternate form of a gene at a particular location (locus) on a chromosome, and provides for genetic variability. Biological evolution involves an alteration in the intergenerational frequency of alleles in populations.

Conserved sequences sequences are unchanged over evolutionary time. Conserved sequences are often regulatory sequences that control biosynthesis or they are signal sequences that regulate maturation or direct molecules to specific intracellular sites.

»»» Basic mechanisms of evolution »» Biological Evolution »» Beyond Darwin and Neo-Darwinism Biological variation »» Conserved & Consensus ₪ gene regulation and biological evolution Gene Regulation in E.coli ₪ genetic variation Genotype Variability»» Mutation »» Deletion »» Duplication »» Frameshift »» Insertion »» Inversion »» Meiosis »» mispairing »» Mutation »» Population Genetics and Formulae »» Recombination »» Substitution »» Translocation »» The modern synthesis .

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

alternative splicing

2007-12-13T04:36:00.000-08:00

Alternative splicing is a closely regulated, variable adaptation of the constitutive RNA modification process of pre-mRNA splicing. Alternative splicing is a form of epigenetic mechanism that enables a single gene to give rise to multiple, differentially spliced versions of a protein, increasing complexity without a change in the genome.

₪ alternative exons ₪ alternative 3' splicing ₪ alternative 5' splicing ₪ cassette exons ₪ epigenetic mechanisms ₪ ESE ₪ ESS ₪ exon skipping ₪ gene regulation and biological evolution ₪ genetic variation ₪ intron retention ₪ ISE ₪ ISS ₪ micro RNA ₪ molecular switches

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

ATP synthase

2007-12-05T08:55:00.000-08:00

ATP synthase is an ATPase. It is the final enzyme of oxidative phosporylation, and is located in the inner mitochondrial membrane where it utilizes the potential energy generated by an electron transfer chain to phosphorylate ADP to ATP. The F1Fo ATP synthase is the commonest chemi-mechanical motor found in nature.

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

autoinducer

2007-12-04T04:09:00.000-08:00

In microbiology, autoinducers are signaling molecules in bacterial quorum sensing that regulate mRNA production for specific genes in response to population density. Autoinducer molecules, which include certain peptides and compounds known as homoserine lactones, can interact with specific repressor or enhancer sequences in DNA.

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

B

2007-11-30T23:59:00.000-08:00

o-o items o-o are in brief format :
o-o base excision repair o-o Bcl-2 o-o

Links to more detailed items on Companion sites:
ф B cells ~ base ~ bases/nucleobases adenine cytosine guanine thymine uracil + phosphate → nucleotides ~ base excision repair : basic amino acids : basic and acidic amino acids »»» Basic mechanisms of evolution § bifurcation proteins »» Biological Evolution »» Beyond Darwin and Neo-Darwinism »» Bottleneck »»

Molecules and Pathways ››› beta-oxidation

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Companion Sites : Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution • Cancer • Cell Biology • Chemistry of Life • Complex Systems • Cyanobacteria • Enzymes • Evo Devo • Immunology • Mechanisms of Evolution • Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites • Taxonomy Phylogeny • Virus • White Sites • Diagrams & Tables • Eubacteria & Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •

base excision repair

2007-11-24T17:35:00.000-08:00

Base excision repair (BER) is one form of DNA excision repair in which damaged bases or incorrect bases are excised and replaced through the action of specific enzymes. Other modes of DNA repair are mismatch repair and nucleotide excision repair.

The biochemical processes involved in BER are equivalent across species, so bacterial DNA repair functions can operate in eukaryotic cells, and vice versa.

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Companion Sites : Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life Ω Complex Systems ººº Cyanobacteria ◊ Enzymes ₪ Evo Devo Ơ Fat ф Immunology »» Mechanisms of Evolution ○ Molecular Biology ** Origin of Life ◘ Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ Sleep • Stromatolites † Taxonomy Phylogeny ۰۰ Virus • White Sites Diagrams & Tables æ Eubacteria & Archaea φ Molecule → Molecular Paths ››› Pathways ☼ Photosynthesis • Black Sites Ǒ Endosymbiosis ō Organics •

C

2007-11-01T00:59:00.000-07:00

o-o items o-o are in brief format :
o-o cadherins
o-o calmodulin
o-o cAMP-dependent protein kinase
o-o capping
o-o caspases
o-o catabolite gene activator protein
o-o cell adhesion
o-o cellular stress response
o-o chromatin
o-o chromosome
o-o cloroplast (plastid)
o-o cis-acting elements
o-o coding signal
o-o codon
o-o cognate
o-o coincidence detectors
o-o commensal (symbiont, symbiosis)
o-o constitutive
o-o CpG island
o-o cyclin-dependent kinases
o-o cytochrome c
o-o cytokines
o-o cytolysis

Links to more detailed items on Companion sites:
C- ¤ c-Fos ¤ c-Jun ¤ c-Myc CA ◊ cAMP-dependent protein kinase ~ CAMs ~ cadherins סּ cadherin- cytoskeleton ¤ Cancer ф cancer and immune system ф cancers of immune system ~ cap-dependent translation initiation ~ capping ¤ carcinogenesis סּ caspases ₪ cassette exons סּ catenins - cytoskeleton CD ф CD CE ~ cell adhesion molecules Cell Adhesion Molecules ₪ cell cycle סּ cell-cycle control סּ cell growth סּ cell membranes סּ cell motility ₪ cellular fate סּ cellular signal transduction Cell signaling סּ cellular stress response ~ cellular stress response ₪ cellular survival סּ centrioles CH סּ chemotaxis סּ chloroplast ~ chromosome items ~ chromosome סּ chromosomes CI סּ cilia ~ cis versus trans-acting factors CL ф clonal selection CO ~ codon ~ Cofactors, Coenzymes, Intermediates~ cofactor סּ communication ф complement system סּ concentration gradients »» Conjugation »» Conjugation »» Consensus »» Conjugation »» conserved »» Conserved & Consensus CY ◊ cyclin-dependent kinases ~ cyclin-dependent kinases ~ cytokines ~ cytokine receptors Cytokines - Immune סּ cytoplasm ~ cytosine adenine guanine thymine uracil bases סּ cytoskeleton .

Molecules and Pathways ››› Calvin cycle ››› C-3 ››› C-4 ››› CAM φ cAMP
››› choline-folate-methionine φ Cofactors, Coenzymes, Intermediates •: Crassulacean Acid Metabolism φ cysteine φ cytosine φ C to T φ C to U

cadherins

2007-10-24T20:25:00.000-07:00

Cadherins are developmentally regulated, calcium-dependent homophilic cell-cell adhesion molecules (CAMs), through which cell-cell and cell-matrix interactions are mediated.[]im[]

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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cAMP-dependent protein kinase

2007-10-24T11:08:00.000-07:00

cAMP-dependent protein kinase (PKA) is a serine/threonine kinase with catalytic (protein phosphorylating) activity that is modulated by cAMP levels.

Specific protein kinases transfer a phosphate group from a donor such as ATP to amino acid acceptors in proteins, while protein phosphatases remove the phosphate groups that have been attached by protein kinases.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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capping

2007-10-24T08:08:00.000-07:00

Capping occurs shortly after initiation of transcription, and is a stage of RNA processing in which the 5’ end of the nascent pre-mRNA is capped with a 7-methyl guanosine nucleotide, 7-methylguanylate.

The 5' cap is retained in mature mRNAs. Capping is required to protect the RNA transcript from degradation. It plays an important role in mRNA transport to the cytoplasm and in the initiation of protein synthesis (translation).

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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catabolite gene activator protein

2007-10-24T04:59:00.000-07:00

A catabolite gene activator protein (im), also called catabolite gene activator, is a cAMP dependent RNA polymerase that up-regulates gene expression by binding the polymerase at or near the DNA to be transcribed (families).

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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cell adhesion

2007-10-20T12:59:00.000-07:00

Cell adhesion relies upon specialized transmembrane cellular adhesion molecules (CAMs) that usually extend from the intracellular space to the extracellular space where they may bind to other cell membranes or to the extracellular matrix.

CAMs include cadherins, focal adhesion kinase (FAK), members of the Ig superfamily, integrins, and selectins. Some signaling molecules act as adhesion receptors, and cluster in focal adhesions upon ligand binding. (Rho protein, Rho GTPase).

Cell Adhesion Molecules Second Messengers Cell signaling

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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cellular stress response

2007-10-20T00:05:00.000-07:00

The cellular stress response (heat-shock response) protects organisms from damage resulting from environmental stressors such as heat, UV light, trace metals, and xenobiotics.

Physical or chemical stress inactivates or down-regulates many genes, including many housekeeping genes, while up-regulating stress genes that perform orchestrated induction of key proteins necessary for cellular protein repair and degradation systems. Stress genes are highly conserved in biological evolution and play similar roles in organisms from bacteria to humans.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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chromatin

2007-10-17T06:09:00.001-07:00

Chromatin is the composite form of DNA in nuclear eukaryotic chromosomes in which long helical strands of DNA are wrapped around structural proteins called histones (diagram).

Chromatin occurs in two forms euchromatin and heterochromatin.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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chromosome

2007-10-17T06:09:00.000-07:00

A chromosome contains a long strand of deoxyribonucleic acid containing genes, regulatory sequences, and non-coding sequences of nucleotides, condensed around histone proteins as chromatin.[]im[]

The full chromosomal complement of a cell comprises the genome, which is the complete hereditary information of an organism contained within macromolecules of archival DNA.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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cis-acting elements

2007-10-16T05:58:00.000-07:00

Cis-acting elements are DNA sequences in the vicinity of the structural portion of a gene, which are required for gene expression.

Most often, signal elements act only on the intramolecular nucleotide sequence to which they are attached, and they are said to act "in cis".

Regulatory Proteins Sequences

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codon

2007-10-10T20:09:00.000-07:00

Triplets of DNA nucleotides arranged in sequence along DNA are transcribed into the codons of mRNA strands.[]im[]code[]

Each tri-nucleotide sequence in the DNA reading frame and its transcribed mRNA codon signals for the insertion of one amino acid into a polymerizing peptide chain. The sequence of codons in genes determines the sequence of amino acids inserted into peptide, polypeptide and protein chains (primary structure).

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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cognate

2007-10-10T17:10:00.000-07:00

The adjective 'cognate' signifies specificity of binding, as applied, for example, to antigen-antibody or protein-ligand or enzyme-substrate pairs.

commensal

2007-10-10T11:11:00.000-07:00

Commensal organisms (symbionts) benefit from living symbiotically within another organism while not harming the host organism.

constitutive

2007-10-10T10:05:00.000-07:00

In biology, constitutive refers to any molecule that is constantly produced or to any gene that is constantly expressed (without need for regulatory stimulation by regulatory proteins or transcription factors).

Also referred to as 'wild-type', such genes are to be contrasted with inducible genes, which are subject to up-and down-regulation. Molecules such as proteins and RNAs that are not constitutive have cellular levels that are regulated by protein degradation or RNA decay.

CpG island

2007-10-09T17:16:00.000-07:00

CpG islands are discrete clusters of nonmethylated CpG dinucleotide segments composed of large numbers of phosphodiester-linked cytosine "p" guanine nucleobases. CpG islands comprise about 1 to 2% of the mammalian genome (4, 7), and are located near or within approximately 40% of promoters in mammalian genes.

The formal definition of a CpG island is 'a region with at least 200 bp and with a GC percentage that is greater than 50% and with an observed/expected CpG ratio that is greater than 0.6.'

In a CpG island, a cytosine nucleotide occurs phosphodiester-bonded to a guanine nucleotide. The "p" in the CpG notation distinguishes a cytosine adjacent to a phosphodiester-linked guanine from a cytosine base paired to a guanine on a complementary strand.

Unlike CpG sites in the coding region of a gene, bases within CpG islands are unmethylated if the promoted genes are expressed. Most CpG islands are associated with genes or recognition sites for restriction enzmes. This includes all genes that are ubiquitously expressed (housekeeping genes) plus many genes with a tissue-restricted pattern of expression. Many human and mouse major histocompatibility locus (MHC) genes contain CpG-rich regions (64), yet only the β-chain genes for class II MHC have CpG-rich regions [r].

Promoters are normally located at the upstream edge of the CpG island, such that one or more of the 5′ exons of the gene generally fall within the island region. Although most CpG islands are nonmethylated in all tissues, a small proportion of islands become methylated during development [s]. 82% of all Not 1 sites are found in CpG islands.

Toll-like receptors, a type of innate immune system pattern-recognition receptor, recognize and ligate unmethylated CpGs as a subclass of pathogen-associated molecular pattern (PAMP)

cyclin-dependent kinases

2007-10-02T21:12:00.000-07:00

Cyclin-dependent kinases (CDKs) are a subclass of serine/threonine protein kinases that play a role in regulation of transcription and mRNA processing, and in regulation of the cell cycle. Specific protein kinases transfer a phosphate group from a donor such as ATP to amino acid acceptors in proteins, while protein phosphatases remove the phosphate groups that have been attached by protein kinases.

The activity of cyclin-dependent kinases is modulated by binding to cyclins, which are proteins so-named because their levels vary periodically during the cell cycle. The binding of cyclins to cyclin-dependent kinases regulates CDK activity, selecting the proteins to be phosphorylated. Although levels of CDK-molecules are constant during the cell cycle, their activities vary because of the regulatory function of the cyclins. Thus, periodic protein degradation is an important general control mechanism of the cell cycle.

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cytolysis

2007-10-02T04:09:00.001-07:00

Cytolysis (cell lysis) results when the plasma membrane is ruptured, resulting in osmosis-induced swelling and ultimately cell death.

cytokines

2007-10-02T04:09:00.000-07:00

Cytokines are small proteins that regulate and mediate immunity, inflammation, and hemotopoiesis.

Cytokines are secreted de novo in response to immune stimuli, and usually act briefly, locally, at very low concentrations (the exception being endocrine action at distant cells). Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, often tyrosine kinases, to alter cellular activity (gene expression).

Table Immune Cytokines.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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D

2007-09-30T23:59:00.000-07:00

o-o DNA ligase o-o double strand breaks o-o

Links to more detailed items on Companion sites:
~ DAG ~ DAGKs ~ damage repair items ~ decay ~ decay items סּ death of cells סּ death receptor »» Deletion ф dendritic cells ~ diacylglycerol ~ diacyl glycerol kinase ₪ differentiation & embryogenesis ~ DNA ~ DNA damage by ROS ~ DNA repair ~ DNA polymerases ~ DNA ligase ~ DNA mutation and alkylation ~ double strand breaks »» Duplication »»

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DNA ligase

2007-09-11T23:12:00.000-07:00

DNA ligases splint together strands of DNA by ligating (bonding) the 3'-OH and 5'-phosphate terminals of DNA. There are four DNA ligases in mammals: I-IV.

DNA ligases function in both DNA repair and replication, and are employed as research tools in recombination experiments.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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double strand breaks

2007-09-10T03:55:00.000-07:00

DNA double-strand breaks (DSBs) are potentially lethal, recombinogenic lesions that can be induced by exposure to external DNA damaging agents such as ionizing radiation or by endogenous events such as collapsed replication forks.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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E

2007-08-31T23:59:00.000-07:00

o-o items o-o are in brief format :
o-o endogenous
o-o enhancer
o-o evolution
o-o exogenous

Links to more detailed items on Companion Sites :
סּ ECM ǒ endosymbiosis - secondary ǒ endosymbiosis SET ₪ embryogenesis & differentiation סּ endoplasmic reticulum סּ endosomes ǒ Endosymbiotic transfers (SET) † Endosymbiotic transfer events (SET) ǒ endosymbiosis - history of ideas re SET ~ energy items סּ energy transducers ~ enhancer ~ enzymes items ~ enzyme ^ Eocyte Archaea Tree ф eosinophils ~ epigenetics ₪ epigenetic mechanisms »» Epistasis ~ ERKs ₪ ESE ₪ ESS ¤ estrogen receptors ^ Eubacteria taxonomy סּ eukaryotes, eukaryotic ǒ evidence for serial endosymbiosis α Evidence Found for Origin of Genes ₪ Evo Devo ~ evolution items »» Evolution - biological ₪ evolution and gene regulation ₪ evolution and genetic variation α evolution and organogenesis α Evolutionary Distance Analysis & Maximum Parsimony Analysis √ evolutionary hotspots in genome ~ exon ₪ exons - cassette ₪ exon skipping סּ exosome ǒ Experimental evidence for Endosymbiosis סּ extracellular matrix

Molecules & Pathways φ epinephrine

endogenous vs exogenous

2007-08-11T20:09:00.000-07:00

Endogenous substances or agents arise within the cell, tissue, or organism body. Conversely, exogenous substances or agents arise outside the cell, tissue, or organism.

enhancer

2007-08-11T16:56:00.000-07:00

An enhancer is a short DNA sequence that increases the level of expression of another gene. Specific trans-acting, transcription factors bind to the enhancer to bring about the increase in transcription rate – recruiting the preinitiation complex proteins, or stabilizing the preinitiation complex.

The enhancer segment may be situated upstream or downstream of the enhanced gene and, due to looping of the DNA strands, there may be a separation of several thousand base pairs between the enhancer and initiator gene (start site). However, the enhancer and its regulated gene are located on the same chromosome (cis). The orientation of enhancers is not fixed – that is, the enhancer’s sequence may be reversed without altering its function.

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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evolution

2007-08-04T09:03:00.000-07:00

Evolution, in a vernacular sense, is a process by which something passes by degrees to a different stage (particularly to a more advanced or mature stage).

Evolution is also used to represent, or misrepresent (too often!) biological evolution or the body of scientific theories that seek to explain the observable fact of biological evolution. In the broadest sense, biological evolution refers to the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms. More specifically, biological evolution has come to be defined according to alteration in genotype. Because the regulation and timing of gene expression determines phenotype, it is simplistic to demand a 1:1 correspondence between genotype and phenotype.

Scientists observing biological evolution first sought to explain observed morphological changes over time – phenotypic evidence of changes in body structure found in the fossil record. Since the advent of modern molecular genetics, biological evolution has come to be understood as a change in genotype – a genetic alteration in the intergenerational frequency of alleles in populations. The modern synthesis has moved understanding beyond Darwinism and Neo-Darwinism, and simple taxonomies are being superceded by phylogenetic analyses.

A α Analyses of physiological evolutionary response ∩∩∩ Ancient stromatolite reefs ¿ Answers to Creationist Nonsense † Archaea Eocyte Tree B † Bacterial taxonomy α Before the Beginning ¿ Biological evolution »»» Basic mechanisms of evolution »» Biological Evolution »» Beyond Darwin and Neo-Darwinism »» Bottleneck C † Cambrian explosion »» Conjugation »» Conserved & Consensus ¿ Creationism vs Evolution α CHONSP and RNA world »» Conjugation »» Conserved & Consensus D α Darwin α Darwin in the Galapagos »» Deletion α DNA evolutionary connections √ directional epistasis »» Duplication √ duplications of gene & genome E † Endosymbiotic transfer events »» Epistasis α Evidence Found for Origin of Genes α evolution and organogenesis α Evolutionary Distance Analysis & Maximum Parsimony Analysis √ evolutionary hotspots in genome F »» formulae »» Founder effect »» Frameshift G »» Gene flow »» Genetic drift »» genetics »» genome and proteome H † History of taxonomic concepts »» Horizontal Gene Transfer I ¿ Illogical Deceit Theory »» Important features of the genome and proteome »» Insertion »» Inversion L √ lateral gene transfer ¿ Logic & Science α LUCA M √ Maximum Likelihood method »» Meiosis »» Mendel's Laws α MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes α Miller-Urey & Beyond α Minimal Genome α Minimal Molecules »» mispairing »» Missense Mutation ∩∩∩ Modern stromatolites – living fossils »» modern synthesis »» Molecular Genetics α mtDNA α Multi-Level Selection »» Mutation N »» Natural selection »» Non-disjunction »» Nonsense Mutation O ¿ On the teaching of Pseudoscience α optimization P »» Persistence of functional gene duplicates »» Phyletic gradualism √ Phylogenetic trees »» point mutation »» Population Genetics and Formulae α Primordial Soup : Theories »» proteome and genome »» Punctuated equilibria R\¿ Recapitulating recapitulation »» Recombination ¿ Reducible complexity α RNA world ~ RNA world S »» selection »» single nucleotide polymorphism »» SNP »» Speciation ∩∩∩ Stromatolite fossils √ supertrees »» synthesis T † Taxonomy »» The modern synthesis α Timeline of Life α Top Down & Bottom Up α Tree of Life α Tree of Life or Fuzzy Bush of Life »» Transduction »» Transformation »» transition »» Translocation »» transversion W α Why I'm Happy I Evolved - New York Times .

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Gray Sites α Abiogenesis & Evolution √ Algorithms of Evolution • Cancer • Cell Biology ~ Chemistry of Life • Cyanobacteria • Enzymes ₪ Evo Devo • Immunology »» Mechanisms of Evolution • Molecular Biology • Origin of Life • Paleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ∩∩∩ Stromatolites † Taxonomy Phylogeny • Virus • White Sites • Diagrams & Tables • Eubacteria & Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •

F

2007-07-31T23:59:00.000-07:00

o-o items o-o are in brief format :
o-o FADD o-o FAS gene o-o FasL
o-o fibronectin
o-o forskolin

Links to more detailed items on Companion sites:

: FADD : FAS gene ○ FAS gene »» formulae in population genetics »» Founder effect »» Frameshift

Alphabetic links to Glossary items:
◦ A ◦ B ◦ C ◦ D ◦ E ◦ F ◦ G ◦ H ◦ I ◦ J ◦ K ◦ L ◦ M ◦ N ◦ O ◦ P ◦ Q ◦ R ◦ S ◦ T ◦ U ◦ V ◦ W ◦ X ◦ Y ◦ Z ◦

Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life • Cyanobacteria ◊ Enzymes • Evo Devo ф Immunology »» Mechanisms of Evolution ○ Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites ^ Taxonomy Phylogeny • Virus • White Sites Diagrams & Tables • Eubacteria & Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •

fibronectin

2007-07-16T22:06:00.000-07:00

Fibronectin is a high molecular weight glycoprotein integrin-binding ligand that also binds to components of the extracellular matrix (collagen, fibrin, heparin).

The various isoforms of fibronectin are all the product of a single, alternatively spliced gene and comprise three types of repeated varying length internal regions (I, II and III) with or without disulfide bonds.

A soluble, disulfide-bonded form of fibronectin circulates in the blood plasma, and fibronectin participates in wound healing.

~ adhesion molecules סּ cytoskeleton ~ integrins ~

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution • Cell Biology • Chemistry of Life • Cyanobacteria • Enzymes • Evo Devo • Immunology • Mechanisms of Evolution • Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites • Taxonomy Phylogeny • Virus • White Sites • Diagrams & Tables • Eubacteria & Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •

G

2007-06-30T23:59:00.000-07:00

o-o items o-o are in brief format :
o-o GTPases o-o

Companion site items :
¤ gene amplification »» Gene flow ~ gene regulation ₪ gene regulation and biological evolution ~ genes »» genetics »» Genetic drift ~ Genetics Molecular Introduction »» Genetics Population Formulae ₪ genetic variation »» genome and proteome »» genome and proteome ~ genome items ~ genome ~ genetic repair - targetted סּ Golgi apparatus סּ GPCRs סּ GPCR families ф granulocytes ~ growth factors ◊ GTPases ~ guanine adenine cytosine thymine uracil bases

Molecules and Pathways φ GABA φ GDP φ glutamic acid φ glutamine φ glycine ››› glycogenolysis ››› glycolysis ››› glyoxylate cycle φ GMP φ GTP φ guanine

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Gray Sites • Abiogenesis & Evolution • Algorithms of Evolution ¤ Cancer סּ Cell Biology ~ Chemistry of Life • Cyanobacteria ◊ Enzymes • Evo Devo ф Immunology »» Mechanisms of Evolution ○ Molecular Biology • Origin of Life • Paleogeology • Refuting ID • Serial Endosymbiosis • Stromatolites ^ Taxonomy Phylogeny • Virus • White Sites Diagrams & Tables • Eubacteria & Archaea • Molecule • Molecular Paths • Pathways • Photosynthesis • Black Sites • Endosymbiosis • Organics •

GTPases

2007-06-05T08:56:00.000-07:00

GTPases hydrolyze GTP to GDP + Pi in the highly conserved domains of G-proteins, which are associated with GPCRs (also called guanine nucleotide-binding protein-coupled receptors, G-protein coupled receptors, serpentine receptors, 7TM receptors, or heptahelical receptors).

Glossary : A . B . C . D . E . F . G . H . I . J . K . L . M . N . O . P . Q . R . S . T . U . V . W . X . Y . Z .

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H

2007-05-31T23:59:00.000-07:00

o-o items o-o are in brief format :
o-o homeostasis o-o homology o-o

¤ HBV ~ helicases ф hemotopoiesis ~ heterochromatin ~ heterocyclic ¤ HIV ф HIV/AIDs ¤ HTLV-I ~ hnRNP ₪ homeobox genes ₪ homeodomain »» Horizontal Gene Transfer ~ hormones ¤ HPV ф humoral immunity ~ hydrogen bond ~ hydrophilic ~ hydrophobic

Molecules & Pathways φ histidine ››› HMG-CoA-reductase pathway ››› 3-hydroxypropionate cycle

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homeostasis

2007-05-10T11:36:00.000-07:00

Homeostasis pertains to the balanced, optimized physio-chemical functioning toward which regulatory mechanisms of cells and organisms have evolved.

Homeostasis is classified as strong, weak, or structural homeostasis.

Related detailed items on Companion Sites :
סּ active transport סּ apoptosis ₪ cell cycle סּ cell-cycle control סּ cell growth ₪ cellular fate סּ cell membranes סּ cell motility סּ cellular stress response ₪ cellular survival סּ chemotaxis ₪ differentiation & embryogenesis סּ communication סּ concentration gradients סּ cytoplasm סּ cytoskeleton סּ death of cells סּ death receptor סּ ECM סּ endosomes סּ energy transducers ₪ epigenetic mechanisms סּ exosome סּ extracellular matrix סּ ion channels סּ lysosome סּ microtubules ¤ mitogens ₪ molecular switches סּ peroxisome סּ phagocytosis סּ physiological function סּ pinocytosis סּ protein degradation סּ proteasome סּ pumps סּ receptor proteins סּ receptor-mediated endocytosis ₪ regulation ₪ signaling סּ signaling gradients ~ signaling items ¤ signaling molecules סּ signal transduction סּ transport סּ two-component systems סּ vacuole סּ vesicle

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homology

2007-05-10T11:09:00.000-07:00

Homology refers to common ancestry of two or more genes or gene products that have evolved from the same feature in the last common ancestor of the species. When applied to nucleotide or protein sequences, homology refers specifically to this relationship due to descent from a common ancestral sequence.

Homologous features are derived through the same evolutionary or phylogenetic origin, yet do not necessarily share the same function or structure. Homologous genes share an arbitrary threshold level of similarity determined by alignment of matching bases. Such homology is an important organizing principle for genomic studies because structural and functional similarities tend to change together along the structure of homology relationships. It may be difficult to determine that genes share a common ancestor when their structure has been modified through descent. Functional genes often display homology across species because evolutionary tinkering that destroys essential functions could be detrimental to the survival of the organism, and hence to transmission of the altered gene.

Homology is a qualitative term (+/-), while similarity is the corresponding quantitative term in that we refer to degrees of similarity. Homology is distinguished from homoplasy, which refers to the similarity between structures that is due to common ancestry. In cladistics, both homology and homoplasy are determined a posteriori with reference to a particular phylogeny that maximizes homology and minimizes homoplasy. The amount of homology between species may be used to determine evolutionary relationships and degrees of divergence.

Homeobox genes provide an example of functional conservation that is misapplied by creationists in a misbegotten attempt to refute biological evolution. Hox genes control early development and necessarily show high degrees of homology across species.

I

2007-04-30T23:59:00.000-07:00

o-o items o-o are in brief format :
0-0 intracellular translocation 0-0 intracellular transport 0-0

Links to more detailed items on Companion sites:
ф immune cytokines ¤ immune evasion ~ immunoglobulins »» Important features of the genome and proteome ф inflammatory response : inositol : inositol phospholipids : InsP3 : IP3 : »» Insertion ~ insulator ~ integrins ~ Intermediates, Coenzymes, Cofactors ~ internal ribosomal entry site ~ internal ribosomal entry ~ intron ₪ intron retention ~ IRES »» Inversion ₪ ISE ₪ ISS סּ ion channels ¤ irradiation

Molecules & Pathways φ isoleucine

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J

2007-04-01T00:59:00.000-07:00

o-o items o-o are in brief format :
o-o o-o join signal

Links to more detailed items on Companion sites:
: Jun : JNK

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join coding signal

2007-03-10T21:09:00.000-08:00

Coding join refers to the segment of DNA at the newly formed junction in VDJ recombination.

Signal join refers to the segment of DNA that has been excised out by the RAG enzymes and
repair enzymes in VDJ recombination.

K

2007-02-28T23:59:00.000-08:00

o-o items o-o are in brief format :
Companion site items :

ф killer T cells

Molecules & Pathways ››› Krebs cycle

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L

2007-01-31T23:59:00.000-08:00

o-o items o-o are in brief format :
o-o ligand
o-o ligation

Companion site items :
ф leukocytes ф lymphocytes ф lymphoid system ф lymphokines סּ lysosome

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ligand

2007-01-16T17:57:00.000-08:00

A ligand is any molecule, atom, or ion that specifically and reversibly binds to a protein, inducing a conformational change in the protein.

Common examples include neurotransmitters or signaling molecules that bind to receptor proteins and DNA (as a ligand) bound to protein transcription factors.

ligation

2007-01-16T17:56:00.000-08:00

In biology, ligation is the joining or binding of two molecules or a ligand to a receptor protein – two strands of RNA spliced, or two strands of DNA ligated by a DNA ligase; an antigen ligated to a CD on a leukocyte.

M

2006-12-31T23:59:00.000-08:00

o-o items o-o are in brief format :

Companion site items :
ф macrophages סּ macula adherens (desmosome) ¤ malignant transformation ◊ MAPKs √ Math & Biology √ Maximum Likelihood method סּ meiosis »» Meiosis ◊ MEK »» Mendel's Laws § messenger proteins ¤ metastasis סּ microfilaments סּ microtubules ₪ micro RNA »» mispairing »» Missense Mutation ¤ mitogens ф MHC סּ microtubules סּ migration ф migration ~ miRNAs α MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes ~ mismatch repair ¤ mitogens סּ mitosis סּ mitochondria, mitochondrion »» modern synthesis ∩∩∩ Modern stromatolites – living fossils »» Molecular Genetics ₪ molecular switches ф monocytes סּ motility ◊ MPF α mtDNA ◊ mTOR ~ mRNA ¤ mutagens α mtDNA α Multi-Level Selection ¤ mutations »» Mutation √ mutation - duplications of gene & genome ¤ MYC .

Molecules & Pathways φ methionine ››› methylerythritol phosphate pathway

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N

2006-11-30T23:59:00.000-08:00

o-o items o-o are in brief format :
o-o neontology o-o

Companion site items :
»» Natural selection ¤ neoplasia ¤ neoplastic mutations סּ neuronal interconnections ~ neurotransmitters ф neutrophils סּ Nitric Oxide »» Non-disjunction ¤ non-mutagenic carcinogens : non-polar amino acids »» Nonsense Mutation ~ nonsense-mediated decay ~ nonstop decay סּ nuclear membrane סּ nuclear pore ~ nuclear speckles ~ nucleic acids ~ nucleobases/bases adenine cytosine guanine thymine uracil + phosphate → nucleotides ~ nucleosome ~ nucleotide ~ nucleotide excision repair סּ nuclear membrane סּ nuclear pore סּ nucleolus סּ nucleus סּ

Molecules & Pathways φ NADH : NAD+ : NADPH : NADP+ φ N-formylmethionine φ Nicotinamide adenine dinucleotide ››› nitrogen assimilation ☼ noncyclic photophosphorylation ☼ Nonoxygenic photosynthesis φ norepinephrine φ

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neontology

2006-11-20T09:10:00.000-08:00

Neontology is a branch of biology that emphasizes the study of modern biota (living or recent organisms) rather than fossilized organisms (paleontology).

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O

2006-10-31T23:59:00.000-08:00

o-o items o-o are in brief format :
o-o operons
o-o opsonins
o-o opsonization

Companion site items :
~ Okazaki fragments ¤ oncogenes ~ open reading frame ~ oxidative stress and DNA damage ~ oxoG repair

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operons

2006-10-09T19:06:00.000-07:00

In prokaryotes, operons are defined as groups of genes transcribed under the control of a single operator gene.

The operon comprises a functionally integrated genetic unit for the control of gene expression in bacteria. The operon comprises one or more genes together with an adjacent* promoter (activator or repressor) and an operator that controls expression through interaction with a regulator protein.

Control of prokaryotic gene expression is brought about by control of the rate of transcriptional initiation by two DNA promoter sequence elements. Regulatory accessory proteins alter the activity of RNA polymerase at a given promoter by affecting the ability of RNA polymerase to recognize start-sites. These regulatory proteins can act both positively (activators) and negatively (repressors).

In bacteria, regulons comprise several operons, and are global regulatory systems that participate in pleiotropic regulatory domains.

(* in eukaryotes, a regulon is defined as a group of non-contiguous genes)

opsonization

2006-10-09T05:09:00.000-07:00

Opsonins bind to target antigens, marking their carrier for phagocytosis. Opsonin molecules include IgG antibodies and components of the complement system (C3b, C4b, and iC3b).

Phagocytic cells express opsonin-binding receptors, and opsonization promotes phagocytosis in addition to inducing increasing the expression of complement receptors on phagocytes.

P

2006-09-30T23:59:00.000-07:00

o-o items o-o are in brief format
o-o PCD
o-o phylogenetics
o-o plasmid
o-o plastid
o-o pleiotropic
o-o polyphenic gene
o-o proto-oncogene
o-o pseudogenes

Companion site items :
p53 PA ф pattern-recognition receptors PD: PDGF receptor ◊ PDK1 ◊ PDK1 PE ~ peptide סּ peroxisome »» Persistence of functional gene duplicates PH ф phagocyte סּ phagocytosis ◊ phosphatases : phosphatidic acid, PA : phosphatidylinositol : phosphatidylinositol phosphates, PIPs ◊ phosphodiesterases ¨ phospholipases : phospholipase A2 : phospholipase C family : phospolipase C-γ סּ phosphotransfer-mediated signaling pathways ◊ phosphorylases ››› phosphorylation ~ phospolipid סּ photosynthesis »» Phyletic gradualism ^ Phylogenetics סּ physiological function PI ◊ PIKK ◊ PI3K : PI3K ARF : PI3K cancer : PI3K Kit : PI3K signaling ~ PIPs PL סּ plant cell PK ◊ PKA ◊ PKB ◊ PKCs PO »» point mutation : polar amino acids ~ polyadenylation ~ polypeptide : polyphosphoinositides »» Population Genetics and Formulae PR~ preinitiation complex ~ pre-mRNA ~ pre-mRNA splicing ~ promoters ~ proteome »» proteome and genome סּ prokaryotes, prokaryotic ¤ proliferation : prostaglandins סּ protein degradation סּ proteasome ◊ protein kinases סּ Protein Kinase Signaling Networks ~ proteins ~ protein tyrosine kinases ¤ proto-oncogenes PT ◊ PTEN ~ PTKs PU »» Punctuated equilibria סּ pumps סּ

Molecules and Pathways φ phenylalanine ☼ Photosynthesis Overview ☼ Photophosphorylation φ proline φ purine pyrimidine φ pyruvate ››› pyruvate dehydrogenase reaction

Microbiology • Phosphorylation switches • Photosynthetic bacteria • Prokaryote Genetics & Biochemistry • Prokaryote Physiology & Communication

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PCD

2006-09-22T20:59:00.000-07:00

Programmed cell death (PCD) or cellular death-by-suicide is part of normal development, and is termed apoptosis. PCD is a part of normal cell turnover and tissue homeostasis, and it plays a significant role in embryogenesis, induction and maintenance of immune tolerance, development of the nervous system, and atrophy of endocrine-dependent tissue.

Signals from tumor suppressors such as APC, CBFA2T3, FAS gene, Hsp90, MDM2, p53, PTEN, TP53, Wnt prevent the uncontrolled proliferation characteristic of cancers by inducing apoptosis.

PCD is initiated via the death receptor pathway or the mitochondrial pathway, which lead to the activation of an initiator caspase, which in turn initiates a proteolytic cascade, ultimately leading to apoptotic cell death. Death receptors include the TNF-R (tumour necrosis factor receptors) and Fas receptor families (FADD). Activation of death receptors by binding of ligands such as TNF-α and CD-95L (FasL) leads to caspase-8 activity. Players in the mitochondrial pathway include members of the Bcl-2 family, which regulate the release, through the mitochondrial PT pore, of pro-apoptotic substances such as AIF, Endonuclease G, Smac/DIABLO and cytochrome C. Mitochondrial efflux of cytochrome-c drives generation of the apoptosome (apoptotic body) in the cytoplasm, which in turn leads to caspase-9 activity.

Apoptosis (PCD) exhibits characteristic morphological changes, and is distinct from necrosis.

Џ Flash animation Џ ICAD-CAD animation Џ

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plasmid

2006-09-13T23:05:00.000-07:00

Plasmids are small circular, extrachromosomal, mobile genetic elements that can be transmitted from one bacterium to another through the pili during conjugation.

Plasmids are not to be confused with plastids, which are chloroplasts – cellular, membrane- bounded organelles containing photosynthetic and/or acessory pigments in their internal (thylakoid) membranes. The plastid is the site of photosynthesis in eukaryotic cells, and is the site of the Calvin cycle just as the mitochondrion is the site of oxidative phosphorylation.

pleiotropic

2006-09-13T19:16:00.000-07:00

In pleiotropy a single gene is associated with more than one phenotype for an organism. A pleiotropic gene is also termed polyphenic gene.

Pleiotropic effects result from environmental, regulatory, and epigenetic phenomena that result in complex transcriptional responses involving multiple genes and regulons. (A regulon is defined as a group of transcriptional units or operons that are coordinately controlled by a regulator. Bacteria have operons, which are protein-encoding gene clusters.)

Examples of pleiotropic mechanisms:
● the cyclic-AMP concentration in a cell can produce a variety of effects because the cAMP second messenger controls protein kinases that affect a variety of proteins.
● TNFR cluster of differentiation, CD30 binding by CD30L mediates pleiotropic effects, including cellular proliferation, activation, differentiation, and apoptosis..

phylogenetics

2006-09-10T01:12:00.000-07:00

Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.

Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.

Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.

Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.

Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.

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proto-oncogene

2006-09-07T09:04:00.000-07:00

Proto-oncogenes participate in a variety of normal cellular functions, but have the potential to tranform into cellular oncogenes when damaged.

Proto-oncogenes normally function in the various signal transduction cascades that regulate cell growth, proliferation and differentiation. Cellular proto-oncogenes resident in transforming retroviruses are designated as c- (cellular origin) as opposed to v- (retroviral origin). Oncogenes are malignantly transformed proto-oncogenes. Table Oncogenes Proto-oncogenes.

¤ c-Fos ¤ c-Jun ¤ c-Myc ¤ c-Sis ¤ c-Src ¤ Ras ¤ Rb ¤ Src ¤ v-Src ¤

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pseudogenes

2006-09-06T19:03:00.000-07:00

Pseudogenes are non-functional relatives of known functional genes, which have lost protein-coding ability or are no longer expressed in the cell.

Pseudogenes may have some gene-like features, such as promoters, CpG islands, and splice sites, yet are nonfunctional in that they lack protein-coding ability. This loss of gene function results from stop codons, frameshifts, lack of transcriptional capacity, or from an inability to function as an RNA (as with rRNA pseudogenes).