Definitions

©2002 Timothy Paustian, University of Wisconsin-Madison
Pi

Biological shorthand for inorganic phosphate (PO4-3

Anabolism

Synthesis of complex molecules from simpler ones to form cell structures, this requires energy and often reducing power.

Antiparrallel

When two similar objects line up to one another, but point in opposite directions.

A diagram of antiparralell DNA

This is most often used in biology to refer to the topology of nucleic acid strands. The direction of DNA strands is determined by their 5' phosphate to 3' hydroyl linkages. The strands are said to be antiparrallel because the 5' to 3' linkages point in opposite directions.

auxotroph

A strain the requires one or more organic growth factors (like amino acids, nucleotides, or vitamins) that are not needed by the wild-type strain

Catabolism

How complex molecules are broken down into smaller, simpler, molecules with the release of energy and reducing power (electrons). This definition is simplistic-not all energy generating processes in bacteria involve the break down of larger molecules.

Commensalism

an association between two organisms wherein one organism may benefit but neither is harmed (Lat. com = together; mensa = table; "sharing the same table").

complementation

A complementation analysis asks if two putative alleles, when in the same cell and acting independently, can supply all functions necessary for a wild-type phenotype. Complementation is therefore a test of function.

conditional mutant

A mutant that it is known to display its mutant phenotype only under certain conditions. A particular condition where the mutant phenotype is evident is termed non-permissive, while the wild-type phenotype is observed when conditions are permissive. The typical examples are either cold-sensitive or temperature-sensitive mutants. These are mutants that display their mutant phenotype (in a recognizable fashion) only at low or high temperatures, respectively.

Dalton

A dalton (or atomic mass unit) is a unit of measure for atoms. The dalton is formally defined as 1/12 the weight of a carbon atom and is roughly equal to the weight of one proton. One dalton weighs 1.066 x 10 -24 grams. It is a convenient way of representing the weight of atoms and molecules.

Determinants of Virulence

The genetic, biochemical, and structural features of a pathogen that enable it to inflict damage on a host. The relationships between host and parasite are dynamic, since each modifies the activities and functions of the other. The outcome of host-parasite interaction depends on the pathogenicity of the parasite and the relative degree of resistance or susceptibility of the host.

EMP

The Emden Meyerhoff Parnas Pathway is a series of reactions for oxidizing glucose to pyruvate and many bacteria, animals and plants employ this pathway in their catabolism. Two net ATP and 2 NADH2 are generated. See Fermentation for more information.

Enzymes

Proteins that catalyze (speed up) chemical reactions. They do this by lowering the activation energy needed to get a reaction to go forward. Enzymes do not make chemical reactions more or less favorable.

ETLP

Electron Tranport Level Phosphorylation. High energy electrons are removed from the catabolic substrate and given to electron carriers (often NAD or FAD). These carriers eventually transfer their electrons to other electron carriers on proteins located in the membrane of the cell. The electrons then pass through a series of carriers (many of them proteins) each time loosing a portion of their energy. The energy extracted from the electrons is used to pump protons across the membrane. This charge separation can be thought of as a battery that can do work. The proton potential can be used to synthesize ATP using the enzyme ATPase. The electrons eventually end up on a terminal electron acceptor which can be, O2, NO3-2, SO4-2, CO2 or an organic molecule.

ETS

Electron Transport System. A membrane system that uses high energy electrons to pump ions (ususally protons) across a membrane. This separation in charge can then perform work

Extracellular Enzymes

Enzymes that are secreted by the cell into the outside environment. Often these enzymes will have a special string of amino acids at the begining of the protein (a leader peptide) that signal to the translation machinery that this protein belongs outside the cell.

Fermentation

Energy yielding process whereby organic molecules serve as both electron donors and electron acceptors

genotype

The DNA sequence of an organism. Often this refers to a mutant whose altered genotype results in a altered phenotype. However an altered genotype does not neccessarily mean an altered phenotype!

helper phage

A normal wild-type version of the phage, which grows along with a specialized phage and supplies whatever functions are necessary for generating phage particles.

Host

An organism that harbors and provides habitat or nourishment for another organism (Lat. hospes = receiver of guests).

Hydrogen Bond

A non-covalent bond between two adjacent atoms. One atom will be starved for electrons while the other has excess. By associating together, they share the electrons and this results in a more favorable structure.

Hydrophilic

Water loving. Compounds of this type are attracted to water. Normally they are either charged or have polar side groups that attract water to them.

Hydrophobic

Water hating. Compounds of this type are repelled from water. Hydrophobic molecules have no charge and repell water. Wax and vegetable oil are hydrophobic, they will not mix with water and are repelled by it.

Insertion Sequences

Mobile genetic elements that are known to encode only functions involved in insertion events. This is to be contrasted with transposons (Tn) that are mobile genetic elements containing additional detectable genes in addition and unrelated to insertion functions (for example, drug resistance).

leaky mutant

The mutant displays a much less distinct phenotype compared to wild type. Normally this occurs because the mutation damages the function of the gene, but does not destroy it. Under the growth conditions used, the mutant is able to grow, but it's growth is not very distinct from wild type.

linkage

the frequency with which two sites (a site can either be the site of a mutation or the site of the wild-type version of the mutation) on a piece of DNA are co-inherited using a particular gene transfer system

Metabolism

The sum total of all reactions which occur in a cell. Metabolism consists of two types of processes catabolism and anabolism.

mutant

A strain that has an altered growth property relative to wild type

mutation

A change in the sequence of DNA from what is found in the wild type irrespective of the resulting phenotype. A strain carrying such a change is termed a mutant.

Mutualism

A mutually beneficial association between two organisms (both organisms benefit from the association together).

Nonpolar

Electrons are shared equally among atoms with the molecule having equally distributed charge. Non polar molecules attract other non-polar molecules and repell water.

Parasitism

a relationship between two organisms in which one organism lives at the expense of the other and may cause damage or harm to it (Gr. para = besides; sitos = grain; "besides grain" or parasite = "fellow guest". In ancient Greece a parasite was a "professional dinner guest").

Pathogen

An organism that is able to inflict damage on a host. Parasites which are able to bring about damage or harm to a host are pathogens.

Pathogenicity

Referring to a parasites ability to inflict damage (produce disease) on a host. The term virulence is usually regarded as a quantitative term used to indicate the relative degree of pathogenicity of a specific parasite.

Peptidoglycan

A thick rigid layer that is found in both G+ and G- cells. It composed of a overlapping lattice of 2 sugars that are crosslinked by amino acid bridges. The exact molecular makeup of these layers is species specific.

phenotype

The growth properties of a strain.

Photon

Specific packets of electromagnetic energy. They have no mass but do have momentum. Photosynthetic organisms capture the momentum of a photon and translate it into biological energy.

Photophosphorylation

The conversion of light energy in the form of photons to high energy electrons. These electrons then pass through an analogous electron transport chain as describe under ETLP, eventually resulting in the formation of ATP.

plasmid

A replicon, or replicating piece of DNA, that is stably inherited in an extrachromosomal state.

Pleomorphic

Having no defined shape. Bacterial cells that have no cell wall will often be pleomorphic. However, there are also microbes with cells walls that have this property and the growth state of the microbe sometimes influences this.

Polar

Two covalently attached atoms where one atom pulls the electrons towards itself. That side of the molecule thus accumulates more electrons and will be attacted to other polar molecules, such as water.

Polymer

A typically large molecule that is made from a small number of repeating parts. Two examples are DNA and proteins. DNA is made up of the 4 bases, adenine, thymine, guanine, and cytosine. Protiens contain the 20 amino acids.

Polysome

A group of ribosomes that line up on a mRNA that is actively being transcribed. The ribosomes move down the mRNA, translating the mRNA into protein.These structures are common in eubacteria, but are not seen in eukaryotes.

Proton

A hydrogen atom contains one proton and one electron. It is the lightest of the elements. Removal of the electron from hydrogen leaves one proton and a net positive charge. Biologist often refer to the hydrongen ion (H+) as a proton .

Proton Motive Force

The force created by the acumulation of hydrogen ions on one side of a cell membrane and not the other. This concentration gradient is created by the utilization of energy sources such as glucose, inorganic iron, lactate, or the sun. Once established the proton motive force can perform work, such as generating ATP, rotating flagella, or pumping compounds across the membrane.

prototroph

A strain that can derive all carbon requirements from the principal carbon source plus needed growth factors required for all strains of the species.

recombinant

The product strain (the genotypically altered recipient) of a recombinational event is often referred to as a recombinant.

repeat

Two streches of DNA that have an identical or nearly identical sequences. Repeats can be either inverted; the direction of the repeated sequences point toward one another or direct; the direction of the sequence is parallel to one another

replicon

A piece of DNA capable of copying itself and maintaining a stable presence inside a cell. This definition encompasses both chromosomes and plasmids.

  • Respiration

    The oxidation of a source of energy by removal of electrons and donation to an inorganic terminal electron acceptor. The path the electrons follow from source to acceptor usually involves a membrane bound system that creates a proton gradient. This proton gradient can do work and is used to create ATP.

    reversion

    The return of a mutant to a wild-type phenotype. This does not neccessarily mean a return to the wild-type genotype.

    SLP

    Synthesis of ATP from ADP directly coupled to the breakdown of high energy organic substrates. A high energy phosphate molecule is transferred from the substrate being catabolized to ADP forming ATP.

    suppressors

    the class of second-site mutations that, in the presence of the original mutation, modify the original phenotype of the strain to be enough like that of wild-type to be scored as such.

    Symbiosis

    An association between two organisms that live together (Gr. sum = together; bios = life; "living together").

    tight mutant

    A tight mutant displays its non-wild-type phenotype distinctly and clearly under the growth conditions used.

    transducing fragment

    A fragment of host DNA that is moved by a bacterial virus.

  • transducing particle

    A phage (bacterial virus head) containing mistakenly packaged host DNA. This particle can be used to move DNA from one strain to another.

    transposon

    A mobile genetic element containing additional genes unrelated to transposition functions.

    wild-type

    An arbitrarily chosen benchmark strain used in genetic analysis of a species. This strain is assumed to have the "normal" set of genes and enzymes.


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