Glossary and Overviews

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.

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .

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.

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .

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 •

▲ Top ▲

| 0 Guide-Glossary

A

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

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .

| 0 Guide-Glossary

active transport

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).

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

activator

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.

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

adaptor

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.

| 0 Guide-Glossary

adenylyl cyclases

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).

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

communing

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 •

| 0 Guide-Glossary

Akt

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

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

allele

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 .

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

alternative splicing

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

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

ATP synthase

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.

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary

autoinducer

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.

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 ◦ o-o animation index o-o diagram index o-o image index o-o micrograph index o-o table index o-o sem/tem index o-o video index .


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 •

| 0 Guide-Glossary