Reading Notes 1 – Flashcards
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| microbe |
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| an organism or virus too small to be seen with the unaided human eye. |
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| virus |
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| a non-cellular particle containing a genome that can replicated only inside a cell |
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| prokaryote |
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| an organism whose cell or cells lack a nucleus: includes both bacteria and archaea. |
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| eukaryote |
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| an organism whose cells contain a nucleus and is a member of the domain Eukarya. |
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| genome |
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| the complex genetic content of an organism. The sequence of all the nucleotides in a haploid set of chromosomes. |
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| metagenome |
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| the sum of genomes of a community of organisms. |
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| spontaneous generation |
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| the theory, much debated in the 19th century, that under current Earth conditions life can arise spontaneously from nonliving matter. |
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| fermentation |
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| the production of ATP via substrate-level phosphorylation, using organic compounds as both electron donors and electron acceptors. |
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| autoclave |
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| device that uses pressurized steam to sterilize material by raising the temperature above the boiling point of water at standard pressure. |
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| germ theory of disease |
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| the theory that many diseases are caused by microbes. |
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| chain of infection |
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| the serial passage of a pathogenic organism from an infected individual to an uninfected individual, thus transmitting disease. |
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| pure culture |
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| a culture containing only a single strain or species of microorganism. A large number of microorganisms all descended from a single individual. |
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| colony |
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| a visible cluster of microbes on a plate, all derived from a single founding microbe. |
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| petri dish |
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| a round dish with vertical walls covered by an inverted dish of slightly large diameter. The smaller dish can be filled with a substrate for growing microbes. |
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| Koch's postulates |
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| Four criteria that should be met for a microbe to designated the causative agent of an infectious disease. |
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| agar |
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| a polymer of galactose that is used as a gelling agent. |
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| immunity |
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| resistance to a specific disease. |
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| vaccination |
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| exposure of an individual to a weakened version of a microbe to provoke immunity and prevent development of disease upon reexposure. |
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| immunization |
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| the stimulation of an immune response by deliberate inoculation with a weakened pathogen, in hopes of providing immunity to disease caused by the pathogen. |
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| immune system |
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| an organism’s cellular defense system against pathogens. |
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| antiseptic |
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| chemical that kills microbes. |
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| aseptic |
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| free of microbes. |
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| antibiotic |
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| a molecule that can kill or inhibit the growth of selected microorganisms. |
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| polyphyletic |
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| having multiple evolutionary origins. |
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| monophyletic |
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| diverging from a common ancestor. |
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| virus |
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| a non-cellular particle containing a genome that can replicated only inside a cell. |
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| virion |
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| a virus particle. |
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| capsid |
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| the protein shell that surrounds a virion's nucleic acid. |
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| bacteriophage |
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| a virus that infects bacteria. |
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| plaque |
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| a cell-free zone on a lawn of bacterial cells caused by viral lysis. |
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| host range |
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| the species that can be infected by a given pathogen. |
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| cloning vectors |
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| a small genome that can carry specific genes for cloning. |
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| viriod |
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| an infectious naked nucleic acid |
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| reading frames |
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| the position in a nucleic acid sequences from which triplet codons encode amino acids. |
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| prion |
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| an infectious agent that causes propagation of misfolded host proteins; usually consists of a defective version of the host protein. |
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| supernova |
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| an exploding star that has used up most of the nuclei available for fusion reactions. |
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| biosphere |
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| the region containing the sum total of all life on Earth. |
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| greenhouse effect |
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| the trapping of solar radiation heat in the atmosphere by CO2. |
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| Hadean eon |
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| the first eon of Earth’s existence from 4.5 to 3.8 gigayears before the present. |
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| Archaean eon |
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| the second eon of Earth's existence. from 3.8 to 2.5 gigayears before the present. The earliest geological evidence for life dates to this eon. |
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| microfossils |
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| a microscopic fossil in which calcium carbonate deposits have filled in the form of ancient microbial cells. |
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| isotope ratio |
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| the ratio of amounts of two different isotopes of an element. May serve as a biosignature if the ratio between certain isotopes of a given element is altered by biological activity. |
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| banded ion formation (BIFs) |
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| a geological formation consisting of layers of oxidized iron, which indicates formation under oxygen-rich conditions. |
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| abiotically |
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| produced without living organisms; occurring in the absence of life |
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| RNA world |
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| a model of early life in which RNA perfomed all the information and catalytic roles of today’s DNA and proteins. |
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| prebiotic soup |
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| a model for the origin of life based on the abiotic formation of fundamental biomolecules and cell structures such as membranes out of a “soup” of nutrients present on early Earth. |
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| metabolist model |
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| a model of early life in which the central components of intermediary metabolism arose from self-sustaining chemical reactions based on inorganic chemicals. |
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| ribozymes |
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| an RNA capable of enzymatic reactions. |
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| panspermia |
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| the hypothesis that life-forms originated elsewhere and “seeded” life on Earth. |
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| clades/monophyletic group |
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| a group of organisms that includes an ancestral species and all of its descendents. |
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| reductive evolution |
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| the loss of mutation of DNA encoding unselected traits. |
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| molecular clock |
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| the use of DNA or RNA sequence information to measure the time of divergence among different species. |
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| small subunit rRNA (SSU rRNA) |
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| in bacteria, 16S rRNA. A ribosomal RNA found in the small subunit of the ribosome. Its gene is often sequenced for phylogenetic comparisons. |
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| phylogenic tree |
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| a diagram depicting estimates of the relative amounts of evolutionary divergence among different species. |
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| root of a tree |
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| the earliest common ancestor of all members of a phylogenetic tree. |
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| horizontal gene transfer |
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| the passage of genes from one cell into another mature cell. |
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| vertical gene transfer |
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| gene transfer from parent to offspring through reproduction. |
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| genomic islands |
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| a region of DNA sequence whose properties indicate that it has been transferred from another genome. Usually comprises a set of genes with shared function, such as pathogenicity or symbiosis support. |
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| pan-genome |
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| all the genes possessed by all individual members of species. |
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| core genome |
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| a set of genes shared by a group of related bacterial strains, showing stable inheritance. |
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| taxonomy |
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| the description of distinct life-forms and their organization into different categories. |
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| classification |
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| the recognition of different forms of life and their placement into different categories. |
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| nomenclature |
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| the naming of different taxonomic groups of organisms. |
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| identification |
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| the recognition of the class of a microbe isolated in pure culture. |
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| species |
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| a single, specific type of organisms designated by a genus and species name. |
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| genus name |
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| the Latin name assigned to the taxonomic rank consisting of closely related species. |
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| species name |
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| the scientific name of a specific type of organism; presented following the genus names as in Escherichia (genus) coli (species). |
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| isolate |
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| a microbe that has been obtained from a specific location and grown in pure culture. |
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| candidate species |
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| a newly described microbial isolate that may become accepted as an official species. |
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| metagenomics |
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| the study of community genomes, or metagenomes. |
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| dichotomous key |
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| a tool for identifying organisms, in which a series of yes/no decisions successively narrows down the possible categories of species. |
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| probabilistic indicator |
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| a means of quickly identifying microbes in the clinical setting, based on a battery of biochemical tests performed simultaneously on an isolated strain. |
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| symbiosis |
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| the intimate association of two unrelated species. |
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| mutualism |
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| a symbiotic relationship in which both partners benefit. |
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| parasitism |
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| a symbiotic relationship un which one member benefits and the other is harmed. |
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| coevolution |
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| the evolution of two species in response to one another. |
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| endosymbiosis |
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| an intimate association between different species in which one partner population grows within the body of another organism. |
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| endosymbiont |
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| an organism that lives as a symbiont inside another organism. |
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| symbiogenesis |
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| an evolutionary process by which two or more species become intimately associated. |
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| biosignatures |
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| a chemical indicator of life. |
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| terraforming |
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| the idea transforming the environment of another planted to make it suitable for life from Earth. |
