Glossary of Scientific Terms

Find definitions and explanations of technical terms from science and philosophy.

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(a) In physiology: a process by which nutrients move from the lower digestive tract (small and large intestine or colon) into the blood stream to be utilized by the body.
(b) In spectroscopy: the interaction between atoms and radiation (light, X-rays, UV, infrared), where some of the energy of the radiation is absorbed by the electrons of the atoms, increasing their energy content. The loss of intensity of the radiation (e.g. reduced light intensity) can be measured and is an indicator of the structural state of the molecules that absorb the radiation.

Action Potential
A spontaneous self-propagating change in membrane potential that travels as a 'wave' along electrically excitable cell membranes found in neurons and muscle cells. Action potentials are triggered when the cell's membrane potential depolarizes (i.e. becomes more positive with respect to the internal side) beyond a threshold value of usually -40mV. Voltage sensitive ion channels (Na and K channels) open and close in fast succession causing first in influx of sodium ions (making the inside more positive = depolarization) followed by potassium efflux (making the outside more positive and inside more negative = hyperpolarization). The potassium efflux brings the membrane potential below the threshold and thus to rest. A new action potential can only be triggered with a new stimulus which comes from neurotransmitter activated ion channels at locations of synaptic interaction between neurons or neurons and muscle cells.

A process in biological evolution as the result of natural selection where a species becomes better adjusted to the living conditions of its environment (temperature, food sources, and predators). In adaptation, individuals that have the most offspring contribute more of their genetic makeup to the next generation. Beneficial traits are favored in this editing process and the next generation of a species or population (for instance a smaller geographical subset of a species) is better adapted to new environmental conditions that caused certain individuals to have fewer offspring. Thus genes that are not optimal for certain conditions will become rarer as a result. Adaptation, as evolution in general, is studied at the level of a population of interbreeding individuals.

Adult Stem Cell
A specialized cell that is needed for growth, wound healing and tissue regeneration. Adult stem cells are found in all tissues and organs of animals and plants.

The genetic variant of a gene. A gene can be found in different variants in a population, even in the same individual. Alleles are responsible for the different traits of certain characteristics, such as eye and hair color in animals, and flower and seed color in plants. Alleles are also responsible for genetic diseases.

Amino Acid
Building block of proteins and enzymes. Dietary proteins need to be broken into their amino acid components before they can be used by the body. Note that there are 20 amino acids found in proteins. Many nutritional lists describe only 18 occluding glutamine and asparagine. Their values are included in those reported for the acidic forms glutamate and aspartate.

Biosynthesis of molecules in cells and part of metabolism.

A molecule that protects cells from oxidative damage of oxygen and free radical molecules that are chemically unstable and cause random reactions damaging proteins, nucleic acids, and cell membranes. Examples of dietary antioxidants are vitamins C, E, and K, and diverse plant products such as lycopene, a nutraceutical found in tomatoes.

Refers to the lack of symmetry in molecular structures or functions. An important insight into the mechanism of biological structures is their aperiodic composition and distribution of atoms causing the extraordinary complexity of cells.

A prokaryotic form of life that forms a domain in the tree of life. There are three domains: bacteria, archaea, and eukarya. Bacteria are also prokaryotic organisms. Eukaryotes include animals, plants, fungi, and protozoan and have very different cell structures, bigger and with internal membrane bound structures (organelles). While bacteria and archaea look similar in structure, they have very different metabolic and genetic activity. One defining physiological characteristic of archaea is their ability to live in extreme environments. They are often called extremophiles and unlike bacteria and eukarya depend on either high salt, high or low temperature, high pressure, or high or low pH.

Atom (atomistic)
The smallest unit of matter as recognized by chemical properties of molecules. Atoms are composed of protons, neutrons and electrons. The latter provide all properties described by molecular interactions and chemical reactions that are essential processes in biology.

Short for Adenosine triphosphate, a nucleotide and universal energy currency for metabolism. Almost all caloric content of food is converted into ATP before it can be utilized for tissue growth, muscle work and other physiological processes.

The cell extension of a neuron (nerve cell) that carries an electrical signal to synapses which are secreting chemical signaling molecules called neurotransmitters to stimulate/inhibit receiving cells. Some axons in the peripheral nervous system connecting to muscle cells or connecting sensory neurons from the skin, eye, or internal organs to the central nervous system can be quite long (measure in centimeters; 1 inch = 2.54 cm) compared to the size of an average cell (measured in micrometers).

Single cell organisms and most prevalent form of life on Earth. Bacteria are also known as prokaryotes (together with archaea; formerly archaebacteria) referring to the single compartment inside the cell and missing a membrane delineated cell nucleus found in all eukaryotes. Examples are Escherichia coli (E.coli), Salmonella typhimurium (S. typhi), Mycobacterium tuberculosis (M. tuberculosis), or Helicobacter pylori (H. pylori).

Bad cholesterol
See Cholesterol, Lipoprotein.

The digestive juice released from liver (stored in gall bladder) into the digestive tract to help solubilize and absorb fat soluble nutrients. Bile contains bile acids, biochemical derivatives of cholesterol. Bile acids serve as intestinal detergents for the proper homogenization and uptake (absorption) of dietary lipids.

A property of molecules or chemicals that refers to their usefulness as food because they can be metabolized (metabolism) by organism.

The collective richness and variety of all forms of life - bacteria, archaea, eukarya and associated viruses.

The term bioelectricity refers to the use of charged molecules and elements (= ions) in biological systems. The movement and placement of charges has a great influence on molecular interactions between molecules and thus affects structure and function of proteins, DNA, and cell membranes. The latter are able to stabilize local charge separation in form of ion gradients which are a form of energy storage but also serve as information processing device (see action potential).

Biological value (of proteins)
The biological value of a protein refers to the how much of the nitrogen content of food is retained by the body. The biological value of proteins ranges from 50 to 100 percent and is a measure of how much dietary protein source can support growth. Animal proteins have biological values of 70 percent or higher, and plant proteins have biological values of 50 to 70.

A new filed in agriculture using recombinant DNA technology to introduce genes into plants or livestock for the purpose of expressing a drug or nutrient in quantities not found in nature. Biopharming may be used to produce antibodies in cow milk or hormones in plant leaves or seeds for easy harvesting. The plant or animal serves as a natural bioreactor and has become a genetically modified organism in the process.

Application in biology to manipulate the structure and function of biological systems into forms not found in nature. Often used to improve or facilitate cellular processes such as energy metabolism, gene transfer between unrelated species, or the engineering of enzymes for the large scale synthesis of drugs.

Biochemical name for sugar containing molecules including single sugar (monosaccharides) like glucose and galactose, but also polysaccharides (complex carbohydrates) like starch (poly-glucose), cellulose (plant fiber material, also poly-glucose with a different chemical bond structure linking glucose units than those found in starch/glycogen and enzymatically indigestible by humans), chitin (hard shells of insects), and more complex carbohydrate components part of lipids and proteins such as blood serum glycoproteins (antibodies and blood group determinants A, O, B, rhesus positive or negative). All microorganisms (bacteria, viruses) contain carbohydrate surfaces (glycolipids) being the major determinants of immunogenic reactions during infections.

The element that defines the chemical properties of all life. All molecules that contain carbon are known as organic molecules and studies by organic chemistry. Carbon is the third most common element in cells, after hydrogen and oxygen, which are the most common biological elements because they are found in water. Also water makes up to 70% of a cells weight, it is not an organic molecule, since it lacks carbon.

Calorie (Cal)
Chemical energy in foods is expressed in calories (Cal). The scientific definition of a calorie is the amount of energy needed to raise the temperature of 1 gram of water by one degree Celsius from 15° to 16° at atmospheric pressure. This is the true calorie, sometimes referred to as a "small calorie". A kilocalorie is equal to 1000 calories. In reference to food energy, the term "calorie" is actually a 1,000 calories or 1 kilocalorie. The USDA Nutrient Database for Standard Reference contains values for both kilocalories and kilojoules (1 kcal equals 4.184 kJ).

An element (capacitor) in an electrical circuit capable of separating charges and storing electrical energy. In cells, membranes have capacitor properties contributing to the storage of electrochemical energy (ion gradients).

The part of metabolism responsible for degradation of nutrients and energy extraction for the benefit of ATP production.

Smallest unit of life (single cell organism or bacteria) or unit of higher organisms, i.e., multicellular organisms. Cells are surrounded by a cell membrane (and cell wall in bacteria and plants = a membrane plus some chemically more stable structures, often mixtures of proteins and polysaccharides) and contain all necessary elements to sustain life; proteins, nucleic acids, lipids, minerals, and a diverse class of metabolites. Cells of higher organisms (known as eukaryotes) are subdivided into subcellular compartments called organelles such as the mitochondrion, the cell nucleus, the endoplasmatic reticulum, the Golgi apparatus and many smaller organelles with highly specialized functions. While all these organelles are found in animal cells, plant cells in addition contain a central vacuole that controls pressure to stabilize the cell and chloroplasts, the site of photosynthesis or light depended biosynthesis of sugars (carbohydrates).

Cellular automaton
A program the applies a simple rule of what to do repeatedly. Depending on the rule of what to do next, the pattern or behavior generated can look (i) repetitive, simple, and symmetric, (ii) nested (fractal), (iii) random and without any symmetry or repetition whatsoever, or (iv) complex with local patterns but overall broken symmetry (see also complexity).

Channel (Ion Channel)
A membrane protein that allows the passive flow of ions across a cell membrane. Ion channels are usually selective for a specific ion type (e.g. Na, or K, or Cl, or Ca) and or either open or closed. These are two structural states of the protein and the change from the open to the closed state (gating) is regulated by the cell. Several regulatory mechanisms have been described including voltage-gating, ligand-gating, heat, and mechano-sensation (touch sensitive). Channels are a category of transporters.

Important lipid found only in animals. Cholesterol is important as cell membrane component, but also serves as a biosynthetic precursor for steroid hormones (e.g. sex hormones) and the active gall bladder ingredients bile acids (= detergents). The human liver can synthesize all the necessary levels of cholesterol and will reduce its own synthesis if cholesterol is taken in during a meal (only from animal sources). 'Bad' and 'Good' cholesterol refers to special transport particles of lipids in our blood serum called lipoprotein particles. The low density form or LDL is high in cholesterol and chronically high concentration of LDL in blood results in insoluble deposits that can clog arteries and restrict blood flow contributing to heart problems.

The physical unit of genetic material in a cell. Prokaryotes have usually one large circular chromosome and one or more small circular extra-chromosomal DNA (plasmids). Eukaryotic cells have often several to several dozen chromosomes. Humans have 46 chromosomes comprising two sets of 23 chromosomes. Each set constitutes the complete human Genome carrying approximately 35,000 genes. Each chromosome carries between 1,000 to 2,000 genes. Eukaryotic chromosomes are linear, long DNA molecules tightly packed with proteins that control their structure and activities of genes.

Digested content of the stomach released for further digestion in the small intestine.

Clone, cloning
A clone is a genetic copy of a parent cell or organism. Cloning is the process of producing a genetically identical offspring or copy. Cloning is a natural process that underlies asexual reproduction that include the binary fission of prokaryotic cells (bacteria and archaea) and mitotic cell division of eukaryotic cells. Mitosis occurs continuously in the human body due to growth and tissue repair (wound healing) and maintenance (skin regeneration, hair growth). Cloning can also refer to the technical process of duplicating genetic material in the laboratory, for instance through the polymerase chain reaction (PCR).

Co-Enzymes or Co-Factors
Non-protein substances necessary for the function of some enzymes. Essential coenzymes are also known as vitamins.

Code (genetic)
The genetic code is the information needed to translate a nucleic acid (gene) sequence into an amino acid (protein) sequence. The code consists of triplet structures called codons such as UUG meaning two uracil and one guanine base along the messenger RNA template. This codon is recognized through base pairing by an anti-codon (triplet) on a transfer RNA. The transfer RNA is a specialized small ribonucleic acid that identifies genetic sequences on messenger RNAs (with the help of ribosomes) and carries one specific amino acid. An amino acid always matches one particular anti-codon. There are twenty amino acids to choose from for protein synthesis, and a total of 64 triplet codons (four bases in triplet sequence = 4x4x4 combinations). Thus there are 64 codons to match 20 amino acids, which means that some amino acids are coded by more than one codon. Which codons are responsible for which amino acid is evolutionarily conserved and most organisms have the same code or translation table. There are some alternate assignments found in mitochondrial genomes, viral genomes and some bacterial genomes. Yet, the fact that most organisms, bacteria, archaea and eukarya use the same genetic code explains the ability for recombinant DNA technology, i.e., to cut and past genetic elements from one organism into an other organism, since the assign amino acids to the same codons. Thus a human gene can be expressed in bacteria or yeast or jelly fish, and jelly fish genes can be expressed in bacteria, plants, fungi, animals and protists. There are almost limitless combinations possible. Read more about genetic codes at the National Center for Biotechnology Information and see the standard genetic code for humans and most organisms.

Cognitive, cognition
Cognition refers to the physical recognition of external stimuli that lead to conscious experiences.

Complexity is the measure of the number and strength of interactions of its components. The components are organized not in a linear chain, but a network with specific connectivity, branches and loops. Network components affect each other through their interactions (molecular interactions). Complexity in biology is the result of dynamic interactions that follow each other in time and with both forward and feedback loops. Because of loops, the output of a network will affect a future input, thus continuously adjusting the physical output value of the system. Biological networks have evolved as stable systems. Stability means that biological systems are in homeostatic equilibrium, with information constantly flowing through the system and the output kept within a narrow range.

Conductance refers to the flow of ions (charges molecules and elements and measured in 'Siemens') such as sodium, potassium, and chloride and is the proportionality factor relating current to a voltage difference. In electricity theory conductance is the inverse of the resistance as defined by Ohm's law V = RI, where V is the voltage, R the resistance, and I the current).

The totality of all neuronal connection in the brain of an animal.

The chemical bond between atoms.

In biology refers to large, regular assembly of macromolecules such as proteins and nucleic acids. It is possible to isolate and purify proteins or DNA in large quantity and let them crystallize in saturated solution. These protein or DNA crystals contain millions of regularly aligned units that allow the determination of the electron distribution from X-ray diffraction studies. Since atoms are distinguished by their specific numbers of electrons, their distribution allows an analysis of the atomic composition of proteins or DNA. This electron distribution is then used to calculate the so called high resolution structure of molecules.

A fibrous network made of proteins that contributes to the structure and internal organization of eukaryotic cells. The cytoskeleton is found in the cytoplasm of cells and has three major fiber types: microfilaments made of actin protein, intermediate filaments made of various kinds of proteins (e.g. keratin), and microtubules made of tubulin. The three fiber types serve different functions; actin filaments are often associated to changes in cell size and structure, contractility such as in muscle cells, and cell division, growth and motility. Microtubules are major filaments for internal transport and movement of chromosomes and organelles during cell division. Intermediate filaments contribute to flexibility, elasticity, and stiffness of cells and tissues.

Darwinian fitness
The true measure of evolutionary change of an organism. Darwinian fitness refers to the numerical advantage of having offspring. The individual with the most offspring has the higher fitness. The reasons can be chance or natural selection and are not important to measure fitness. It is often equated with survival of the fittest, which is often meant to be the strongest or best adapted individual. However, this interpretation is wrong, if it does not explain why a certain individual has the most offspring. Overall, the genetic variation of the individuals with the most offspring will dominate the gene pool of a population. The change in genetic variability in a population from generation to generation is the true measure of (micro-)evolution.

Degree of freedom
A degree of freedom accounts for an independent variable in a system. Independent variables allow for changes within a system. For instance, the movement of two atoms in a gas is independent of each other assigning the distance between two atoms one degree of freedom. Two atoms covalently linked together within a molecule (a chemical bond) are also described by the same degree of freedom, also their movements are usually coupled. While this is true for the movement of the entire molecule, the length of the chemical bond is not static, but vibrates at very short time ranges measured in femto seconds to pico seconds (one trillionth to one billionth of a second). How many degrees of freedom a system has depends on the number of components and their interactions.

A process of changing the membrane potential from negative to more positive values. The sign of the potential refers to the inside of the cell. Depolarization causes action potentials in neurons and muscle cells. (See also hyperpolarization; op.). Depolarization is the result of inward currents carried by Na+ and Ca++ ions.

Designer foods
Foods that are enriched with nutraceuticals, antioxidants, and secondary metabolites to improve the physical performance of the body.

Diffusion coefficient D
The diffusion coefficient D describes the relationship between a concentration gradient DC/Dx and the flow of matter per unit area (flux rate J)

DNA (see also RNA)
Short for Deoxy-Ribonucleic Acid; makes up the genetic component of each cell. DNA is a linear polymer of four building blocks called nucleotides. Nucleotides are distinguished by their base structures known as adenine (A), guanine (G), thymine (T), and cytosine (C). The structure of DNA is the double helix and in all organisms contains only two forms of base pair combinations  -  AT (TA) and GC (CG)  -  which determine and control the accurate copying of the nucleotide sequence during cell division or protein biosynthesis.

Driving Force
A terminology used in thermodynamics expressing the availability of energy to 'drive' a process such as mechanical work or chemical synthesis. Driving forces exist where a potential gradient exist. A potential gradient can be in form of a temperature gradient causing heat to flow, an electrical gradient causing electrons or ions to flow, or a concentration gradient causing diffusion.

A specific characteristic biological system in a location or area with a unique mix of living organisms and physical consistency such as minerals, soil and air.

Subatomic particle carrying a negative electric charge in atoms or molecules.

The technique of recording and stimulating currents and voltages across cell membranes using microelectrodes. Electrodes can be used to measure membrane potentials and inject currents. The latter charges the membrane and changes the membrane potentials. If the recorded voltage change is fed back to the stimulating electrode, the current can be adjusted such that the measured membrane potential stays constant. This is called the 'voltage-clamp' technique and has largely been responsible to elucidate the mechanism underlying the electrical phenomena of neurons and muscle tissue.

An atom with a unique number of protons (atomic number). There are 102 different elements and some additional synthetic elements that are not found in nature. Elements have different physical and chemical properties and can be combined to molecules (two or more atoms linked through covalent bonds). The elements are listed according to atomic number and chemical properties in the periodic table.

Embryonic Stem Cell
The pluripotent stem cells in animals at the very early embryonic development. They have the potential to grow into a complete adult organism.

The energy form of a system that relates to its internal state of disorder. High entropy levels are disordered states, low entropy levels are characteristic of ordered states.

A protein (complex) that catalyzes a chemical reaction as part of a cell's metabolism. While many chemical reactions proceed spontaneously (although many don't), enzymes can increase the rate of these reactions by a thousand to a million fold. In addition to speeding up chemical reactions, enzymes are particularly good at selecting the correct molecules (substrate specificity) that can be used for a chemical reaction (e.g. extracting energy for the growth of an organism).

The study of the inheritance and regulation of gene expression that is independent of the DNA sequence of an organism, but depends on the structural modification of chromosome regions. These modifications can alter the phenotype without having to change the genotype proper.

Equilibrium (chemical)
At equilibrium, the state of a system does not change over time, although internal fluctuation may exist. Thermodynamically, the equilibrium is the physical state of a system that has the lowest total energy content. To lower the energy content, a system may give up energy in form of heat or work or entropy, and usually it is a combination of all three. The laws of thermodynamic dictate that the total amount of energy cannot be changed and whatever energy in a system is lost, is taken up by the surroundings (the first law). The second law dictates that at equilibrium the entropy portion of the energy content of a system must be at its maximum. Interestingly, life is characterized by avoiding equilibrium states and minimizing entropy. This is used as an explanation of how life can maintain highly organized structures (minimal entropy) at the expense of the environment, whose entropy or disorder increases. Importantly, the energy content of a system and its surroundings are interdependent and the equilibrium state of a system can be changed by changing the internal composition or external conditions (e.g. rising temperature). This shift from one equilibrium (state 1) to a second equilibrium (state 2) is often characterized as chemical equilibrium describing the relationship between two states of a system that exist under slightly different conditions. Mathematically, the equilibrium can be described with the equilibrium constant where both states are equally probable. This constant allows the quantification of system properties such as the binding of a drug to its receptor protein.

Essential amino acid or fatty acid
An amino acid or fatty acid that cannot be synthesized by our own cells and need to be part of our diet to stay healthy.

Eukaryotes, Eukarya
Organisms with large cells and internal membrane bound structures called organelles. The defining organelle is the nucleus. Eukaryotes differ from prokaryotes. The latter have no nucleus or any organelle, usually a single naked chromosome (eukarya have several inside the nucleus) and are either bacteria or archaea.

Evolution, theory of
The theory of evolution as initially formulated by Charles Darwin in 1859 is the central theory of biology. All processes that enable life are the result of the process of evolution over a period estimated to be more than 3 billion years. The mechanism of evolution are mutation and natural selection. These two processes result in changes at the genetic (mutation) and physiological level (selection of function). 

An exon is a stretch of protein coding sequence in eukaryotic genes. Exons are interrupted by intron or intervening sequences. Introns are cut out at the mRNA level and the exons spliced together to form a complete, uninterrupted coding sequence. This matured mRNA is recognized by ribosomes and used as a template to synthesize a corresponding amino acid sequence or protein (see also intron).

Fatty acids
Most common form of lipids found in all cells. Come in saturated (reduced) and unsaturated (oxidized) form and are a component of phospholipids and fats.

Fitness (Darwinian fitness)
The true measure of evolutionary change of an organism. Darwinian fitness refers to the numerical advantage of having offspring. The individual with the most offspring has the higher fitness. The reasons can be chance or natural selection and are not important to measure fitness. It is often equated with survival of the fittest, which is often meant to be the strongest or best adapted individual. However, this interpretation is wrong, if it does not explain why a certain individual has the most offspring. Overall, the genetic variation of the individuals with the most offspring will dominate the gene pool of a population. The change in genetic variability in a population from generation to generation is the true measure of (micro-)evolution.

Fluid mosaic membrane
The fluid mosaic model of cell membranes describes the structural and dynamical organization of biological membranes. It is composed of phospholipids that form large planar bilayers. In-between phospholipids exist membrane proteins and the alternating composition of phospholipids and proteins found in membranes has been compared to a mosaic structure. In addition, both components are not fixed in space but can freely move within the plane of the membrane. This 'fluidity' similar to the fluid or liquid state of water if it is nor frozen is essential for the proper function of proteins in membranes.

Foot and Mouth disease
All species of cloven-hoofed animals are susceptible to FMD, including domestic livestock and wild ungulates such as buffalo, antelope and warthogs. Clinical signs are essentially similar in all species although the severity may vary considerably. The principal signs are pyrexia followed by vesicle formation in the mouth and feet resulting in salivation and lameness (click here for more information.)
The disease is caused by a virus and is highly contagious but not dangerous to man.

A nested pattern that shows the same symmetry/geometry at any scale a pattern is looked at. It is an example of an infinite pattern in both larger and smaller dimensions. Fractals are geometrical abstractions and sometimes used to explain complexity in living organisms, also the comparison does not hold up on closer inspection. As abstractions, they are thought to continue into infinity, even the infinitely small, although physicists believe that there is a material limit to the what constitutes the smallest dimension. As for complex biological organisms, their structure is hierarchical with higher levels having emergent structures and properties not found at the lower levels. Thus it is not a true fractal.

Functional foods
See designer foods, nutraceuticals.

A gene is an hereditary unit of an organism that cannot be partitioned any further into smaller units; it is made of DNA. Functionally, a gene consists of regulatory and coding sequences. The regulatory sequences allow a cell to control when and how a gene is expressed its gene product (= RNA or protein) encoded by the coding sequence is synthesized. Often, gene products are only functional as groups (protein complexes) that require the expression of more than one gene (heteromeric complexes) or of a single gene in high copy numbers (homomeric complexes). As of September 2012, the human genome contains a reported 18,451 RNA genes, 11,224 pseudogenes, and 20,687 protein coding genes. Of the latter, an average of 6.3 splice variants per gene have been found, and protein coding gene sequences cover 2.94% of the whole genome, with protein coding exon sequences covering only 1.22% of the genome.

Genetic information
Refers to the information content of genes or genomes and is organized in sequences of nucleotides, structures of genes, and arrangement of genes within genomes. Genetic information is the information that is inherited from generation to generation and can be accessed by the cellular machinery with the help of proteins to synthesize all necessary components for the growth maintenance of an organism.

Genetic code
The genetic code is the information needed to translate a nucleic acid (gene) sequence into an amino acid (protein) sequence. The code consists of triplet structures called codons such as UUG meaning two uracil and one guanine base along the messenger RNA template. This codon is recognized through base pairing by an anti-codon (triplet) on a transfer RNA. The transfer RNA is a specialized small ribonucleic acid that identifies genetic sequences on messenger RNAs (with the help of ribosomes) and carries one specific amino acid. An amino acid always matches one particular anti-codon. There are twenty amino acids to choose from for protein synthesis, and a total of 64 triplet codons (four bases in triplet sequence = 4x4x4 combinations). Thus there are 64 codons to match 20 amino acids, which means that some amino acids are coded by more than one codon. Which codons are responsible for which amino acid is evolutionarily conserved and most organisms have the same code or translation table. There are some alternate assignments found in mitochondrial genomes, viral genomes and some bacterial genomes. Yet, the fact that most organisms, bacteria, archaea and eukarya use the same genetic code explains the ability for recombinant DNA technology, i.e., to cut and past genetic elements from one organism into an other organism, since the assign amino acids to the same codons. Thus a human gene can be expressed in bacteria or yeast or jelly fish, and jelly fish genes can be expressed in bacteria, plants, fungi, animals and protists. There are almost limitless combinations possible. Read more about genetic codes at the National Center for Biotechnology Information and see the standard genetic code for humans and most organisms.   (Note: genetic code is often used inappropriately in the news media when in fact the topic is the genome or genetic information of an organism.)

The genome denotes the full set of genes or genetic information of an organism. It included both coding and non-coding sequences and is physically partitioned into chromosomes. The importance of coding sequences is for protein synthesis and RNA synthesis, while non-coding sequences contain regulatory sequences, sequences of old, inactive genes, repeat sequences that allow recombination of genetic information (DNA pieces) from different chromosomes, locations, or even foreign DNA that is introduces by microbial or viral infection. Many non-coding sequences are transposable elements meaning that they can copy and insert themselves at many different sites within chromosomes. These rearrangement of physical location of DNA strands affects number, location, and sequence of genes coding for proteins and RNA and thus are vital for generating mutations important for evolutionary fitness of an organism. The human genome has been found to contain only 5% coding sequences (genes that make proteins), while half of all non-coding portions are made of transposable elements reminiscent of viral DNA. This similarity between human and viral DNA indicates that human evolution cannot be thought of as independent but is closely related to the evolution of viruses. The modern existence of pathogenic viruses is an indication of the importance of this co-evolution that likely has helped humans to maintain a heterogeneous gene pool important for rapid adaptation to environmental changes.

The genetic description of an organism; often only one or two genes out of thousands are of interest in a genetic comparison between individuals or the analysis of genealogical traits, family history etc..  The genotype is the genetic information underlying a phenotype, the exterior expression of characteristics or traits (e.g. eye color). Most phenotypes that are really physical or functional attributes of an organism are multi factorial, meaning that several genes contribute to its expression. Even at the level of cellular mechanism and metabolism, phenotypes (e.g. photosynthesis) are multi factorial because of the particular composition of enzymes as protein complexes, where individual proteins are coded for by different genes. Photosynthesis, for example, is the concerted action of dozens of proteins (genes) with copy numbers in the hundreds to enable a simple chemical equation:  carbon dioxide + water =  sugar. In fact this simple overall equation is really performed in many different subsets of reactions.

Genotyping is the process of comparing various strains of microorganisms including viruses and bacteria to distinguish pathogenic from non-pathogenic strains (infectious versus non-infectious types). The technique used for genotyping are DNA microarrays.

The major carbohydrate in starch and fruit sugar. The latter is also known as sucrose and contains fructose with every glucose molecule.

Glycemic index
A measure of how rapidly glucose of various forms of carbohydrates are absorbed into the blood circulation.

The major complex carbohydrate in animal cells made of glucose. Glycogen is for animals what starch is for plants. Although glycogen is an important long term storage of energy in muscle and liver cells, it is of little nutritional significance, because most glycogen in muscle spontaneously degrades during slaughtering. Thus meats, except liver, have little or no carbohydrate content.

A metabolic pathway found in all organisms. This pathway consists of ten chemical reactions catalyzed by proteins (enzymes) and is responsible for the degradation and synthesis of carbohydrates. Glycolysis does not depend on the presence of oxygen and is able to provide the cell with the universal energy currency called ATP, short for adenosine triophosphate. This pathway can degrade glucose only partially and will produce waste products such as lactate (in mammalian muscle causing sour muscle under anaerobic exercise conditions) or ethanol in microorganisms (used for fermentation of wine or beer). In the presence of oxygen, no waste products are formed and instead further degraded to carbon dioxide and water. The latter processes are known as Krebs cycle and oxidative phosphorylation.

A type of dietary fiber made up glucose and many other types of sugars and differs from cellulose, which only contains glucose.

A protein that binds and transports molecular oxygen in animals. It is a tetrameric protein (a protein with four subunits) where each subunit binds one heme, a co-factor responsible for oxygen binding. Oxygen binding on individual subunits shows positive cooperativity, a form of interaction between subunits where binding of oxygen to the heme in one subunit increases the strength of binding of oxygen to hemes in all other subunits.

Identifies the two alleles of a diploid organism as being different from each other. If both alleles are genetically identical, the cell or organism is homozygous. Often, one of the two alleles is the dominant, the other the recessive allele. If a dominant allele is present, one copy is enough to establish the corresponding phenotype (e.g. dark eye color). The recessive allele for light eye color cannot be expressed, until two copies of the allele (homozygous) are present.

Histone (protein)
A family of proteins forming organizing complexes to structure chromosomal DNA in eukaryotic cells. Histone modification by acetylation and methylation has been shown to affect large scale changes in chromosome packing affecting the ability of cells to 'read' genes. The more packed, the less access the cell has to genes. This large scale modification is part of epigenetic control of gene expression, i.e., the making of proteins from DNA code.

In biology used to describe a condition where an organism maintains a stable structure where in fact a constant flux of molecules occurs. Although many organisms can live for years, all cellular components like proteins, membranes, sugars, and nucleic acids are constantly recycled while never compromising the integrity of the organism as a whole. This turnover processes can be characterized by specific half-life values that for most proteins, membranes, and RNA (but not DNA structures) are measured in hours. In a more narrow sense homeostasis refers to the maintenance of water and salt concentration in cells.

Identifies the two alleles of a gene in a diploid organisms as being identical to each other. In heterozygous individuals, the two alleles are different versions of the gene.

Messenger substances synthesized in the body and secreted by the endocrine glands. Hormones regulate the digestive system, growth, hunger, thirst, blood glucose and cholesterol levels, fat burning and storage, absorption and excretion, internal clocks such as day and night cycles, menstrual cycles, and sex drive.

Hydrogenated fats (partially)
Partially hydrogenated fats are a the result of chemical addition of hydrogen units to polyunsaturated fatty acids. If hydrogenation is not complete, the process renders trans-fats (as compared to cis-fats found commonly by natural processes). The reason for hydrogenation is to gain optimal texture of fats and oils in processed foods. Trans-fats have been associated to increases in bad cholesterol (LDLs), but fully hydrogenated fats do not contain trans-fats and are not associated to clinical symptoms of heart disease.

Hydrophobic (op. hydrophilic)
Means water insoluble and refers to non-polar properties as opposed to polar properties of water. Water soluble, or hydrophilic, molecules do not easily mix with hydrophobic molecules or solutions. Oil is a hydrophobic substance and mixtures of oily and watery molecules tend to minimize their contact surface. Thus the observed separation of oil from water when left standing. However, oil can be partially mixed with water when shaking a container vigorously indicating that the separation or mixing of molecules is determined by the energy of molecular interaction. The energy to overcome these molecular interactions can be provided by mechanical force (shaking) or high temperature.  The latter is a well known observation; salts, sugars, and fats normally mix better in hot than cold water, and hot water is better in removing stains form dishes or cloths.

A mechanism by which a membrane potential is made more negative inside with respect to the outside of the cell. Hyperpolarization causes neurons and muscle cells to be electrically silent (see action potentials) and stabilize at a resting potential. Hyperpolarization is the result of moving positive charges from in to out of a cell which is usually the result of K+ ions moving out, but can also be achieved by moving Cl- ions into the cell.

A testable scientific idea that can be proved right or wrong with experiments. A hypothesis is a formulation of a question that lends itself to a prediction. This prediction can be verified or falsified. A question can only be use as scientific hypothesis, if their is an experimental approach or observational study that can be designed to check the outcome of a prediction.

Immunology is the science of molecular self-defense of organisms against infections. It deals with the immune system, a complex organ that produces both cells and proteins involved in detecting and destroying foreign molecules and microorganisms (the 'non-self'). It is most elaborate in mammals. The immune cells are white blood cells, originate from the bone marrow and mature in the lymph system. Some of these cells produce antibodies (proteins) that circulate in the blood as a result of a detected infection. These antibodies can be produced for a very long time after the initial infection and are the basis of immunity against further infection by the same microorganism (e.g. flu vaccine). If the microorganism mutates, as if often the case, immunity is no longer given and a new response must be provided by the immune system. In order to avoid costly development of antibodies, the innate immune system provides a broad and less specific protection against a large class of pathogens. Sometimes, the immune system overreacts and destroys cells of the body (the 'self'). The result is an autoimmune disease. Common autoimmune diseases are arthritis, lupus, and type I or juvenile diabetes. There are no known cures for autoimmune disease except for immune system suppressant and pain relievers.

A protein hormone that regulates the use of glucose after a carbohydrate rich meal stimulating the degradation of glucose to extract energy and the storage of excess glucose in glycogen or metabolic conversion to fatty acids and cholesterol.

Compounds that do not contain carbon, such as minerals and water. Inorganic is not synonymous with synthetic as is some times erroneously suggested.

Positively or negatively charged molecules due to an unequal number of protons (+) and electrons (-), mostly one, two, or three. Salts are composed of pairs of ions that readily dissolve in water. Important metal ions in cells are sodium, potassium, calcium, magnesium, zinc and iron. The positively charged metal ions are always found with an equal number of negatively charged counter ions like chloride or phosphate.

An intron in genetics is a part of a gene, which is excised at the level of the transcript. An intron sequence is a non-coding sequence, meaning it is not translated or used to make a protein. Introns interrupt exons, the protein coding parts of genes. When introns are excised, the exons are spliced together forming a contiguous coding sequence that will be read by the ribosomes and translated into a protein. Introns are found mostly in eukaryotic genes, in some archaea genes and very rarely in bacterial genomes (see also exon).

The modern unit in physics for energy. Is used in place of calorie. 1 cal equals 4.184 J.

Junction (Cell-)
A protein based structure that connects two adjacent cells. Junctions are used for contact formation and communication. Common junctions in animal systems are tight junctions, gap junctions, desmosomes and hemidesmosome (connects a cell to the extra-cellular matrix to form stable connective tissue).


The number and ordering of eukaryotic chromosomes according to size and appearance. The karyotype of an organism is a conserved feature and any changes in number and size of chromosomes are mutations that cause severe diseases and birth defects and are commonly lethal. The importance of chromosome structure is found in the spatial organization of genes on chromosomes, which has been found to be influencing when genes can be expressed, i.e., used to make a protein or functional RNA (see also 'epigenetics').

Kinetics is the science of measuring changes, of assessing rates of movements and flow. In biology, kinetics is concerned with enzyme kinetics, the rate of how proteins help catalyze a chemical reactions. Another application of kinetics is the rate of flow of molecules in solution by diffusion or in an energy field (such as charges in an electric field, or mass in a gravitational field). Flux rates of molecules across biological membranes are also studied by kinetics.

A major component of cell membranes containing equal amounts of saturated and monounsaturated fatty acids, phosphate, and choline. Lecithin is a member of the lipid group called phospholipids. Its biochemical name is phosphatidylcholine (PC).

A lipid is a water insoluble (hydrophobic) substance and is the name of a large class of structurally and functionally diverse molecules. Important lipids include fatty acids (saturated and unsaturated), they are a component of phospholipids and fats
- phospholipids, main component of biological membranes composed of glycerol phosphate backbone, fatty acid substituents, and hydrophobic headgroups
- sterols, cholesterol derived membrane components, (sex) hormones, and bile salts (intestinal detergents)

Lipoprotein particle
These are protein based carriers of triglycerides (fats) and cholesterol in the blood circulation. The low-density lipoprotein particle LDL is also known as 'bad cholesterol' as it is the major carrier of blood plasma cholesterol and high levels of LDL particles are associated to increased risk of heart disease.

Large molecules in biological systems namely proteins, nucleic acids, and polysaccharides.

Also called caloric nutrients including proteins, carbohydrates, and fats. Some definitions include water and alcohol. The term is used by gardeners and in agriculture referring to common minerals needed for proper plant growth.

Used in science to describe large scale processes like the temperature, volume, pressure,and energy of a system characterizing the behavior of a very large number of molecules. The macroscopic values tend to be predictable and represent the average behavior of a system. They give no detailed information about the behavior of individual molecules or units of a system.

Membrane (cell membrane; phospholipid bilayer)
A planar structure surrounding cells and organelles within eukaryotic cells (e.g. membranes of cell nucleus of mitochondrion) separating aqueous compartments which carry out different metabolic processes. Cell membranes are electrical insulators but permeable to hydrophobic molecules such as steroidal hormones and small gases (carbon dioxide, molecular oxygen, nitric oxide). All other water soluble and charged molecules depend on the presence of membrane proteins which provide transport pathways across the phospholipid bilayer.

Metabolism, metabolic
The totality of all chemical processes in cells and all living organisms. Metabolism is the chemistry of energy extraction from nutrients and the biosynthesis of the building blocks of life (amino acids, sugars, lipids). A process by which absorbed nutrients are converted to chemical energy and building blocks for vital processes or cellular structures. Metabolism regulates the rate at which you burn Calories.

A microarray is an experimental platform used to study the presence or activity of a full set of genes or proteins found in a cell or organism. When studying the presence of genes, the microarray (DNA microarray) is used for genotyping, i.e., assessing the full genetic complement of an organism as compared to a closely related organism.

The bacterial colonies found in the large intestine. These bacteria are important for proper digestion and fecal excretion of waste products. Micronutrients
Vitamins or Minerals that are needed in daily amounts up to a few milligrams.

The description of the behavior of individual molecules (at the molecular level). The behavior of an individual molecule may be very different from other identical molecules. In systems with a very large number of identical molecules, these individual deviations are negligible and contribute to the noise (random fluctuation) of a property of this system. The decay of a radioactive material is a good example of such an internal fluctuation. While the decay of isotopes can be predicted for a large clump of radioactive material (e.g. its half-life time, which is a macroscopic property), the actual time point of decay of an individual isotope cannot be predicted with accuracy and is random. However, we can assign a probability that it will decay within a certain amount of time (similar arguments can be made for individuals who have risk factors indicating the chance of developing a disease like cancer or a heart attack).

Molecular Biology
The science of studying the genetic composition and mechanism of living organisms at the molecular level. It historically refers to the understanding and manipulation of genes (DNA). The molecular studies of all other organic molecules like proteins, fats, and carbohydrates is called biochemistry.

A chemically unique aggregate of at least two atoms (see also elements).  The atoms are linked to each other by chemical (covalent) bonds. All matter is made up of molecules. Free atoms are rarely found but are important in the form of salts or metal ions in water.

Mutation, mutant
Mutations are changes in the nucleotide sequence of the genome (affecting genes) and the resulting changes in the amino acid sequence of proteins. The amino acid sequence of proteins determines their structure and function, the latter being subject to natural selection. Mutation occur in different forms, from single nucleotide mutations to insertions and deletions of longer sequences as well as gene duplications, deletions and chromosomal rearrangements in higher organisms.

A technology that creates small materials at the scale of molecules by manipulating single atoms. The name nano comes from the size of molecules which is measured in nanometers - or one billionth of a meter (0.000000001 meter). The dimension of single atoms is ten fold smaller. The molecular processes of life, particularly the activity of proteins (enzymes) and the self-organizing behavior of many biological molecules has greatly inspired nanotechnology and molecular motors (i.e. protein complexes) could be considered the result of natures nanotechnology.

Natural selection
The process described by Darwin's theory of evolution that favors certain genotypes and disfavors others. This process is entirely guided by the interaction of an organism with its environment. See also adaptation.

A chemical substance released from neurons in synapses that binds to corresponding receptors on nearby cell surfaces (post synaptic membrane) causing a physiological stimulus in form of a membrane current (triggering action potentials) or second messenger cascade activating channels, pumps, kinases, or proteases. The molecular mechanisms of activation are similar to those of hormones.

Nucleic acid
The collective name for DNA and RNA molecules found in every cell. The genetic component of cells (DNA, RNA polymers), but also important for cellular energy metabolism, signaling, and protein biosynthesis (RNA, single nucleotides).

An organelle in eukaryotic cells. It forms a membrane compartment containing most of the genetic material (DNA and RNA) of a eukaryotic cell (residual extra-nuclear genes are found in mitochondria and chloroplasts). A double membrane envelope separates the genetic material (chromosomes) from the cytoplasmic compartment. Nuclear pores allow for the exchange of proteins and RNA, but not chromosomes, during gene regulation and expression. The nuclear compartment separates the processes of transcription (messenger RNA formation) from translation (protein biosynthesis).

Chemicals that have beneficial effects (pharmacological effects) on our physiology if taken in appropriate amounts with food. Plants are the major source of nutraceuticals also known as phytochemicals. Plants produce those molecules for self-defense or to attract insects and animals to facilitate pollen distribution. For the latter purpose, they often are colorants while tasting bitter to ward of animals.

Molecules that can be used by cells or living organism to extract energy through metabolic processes. Although nutrients are often sought off only as energy providers, they can also be used as molecular building block for the biosynthesis of cellular structures.

A short polymer with two to fifteen or twenty subunits. There is no cosensus of what the upper limit of units constitutes a oligmer, rather than an polymer. For carbohydrates and nucleic acids, an oligosaccharide (oligonucleotide) has up to 10 or 15 units, while longer polymeres are referred to as polysaccharides and nucleic acids, respectively. For proteins the term 'peptide' is up for short polymers up to 50 amino acids, while the terms polypeptides or proteins are synonymous for longer polymers.

Subcellular structure in eukaryotic cells (e.g. plants and animals) providing specialized function within cells. Organelles are separated from each other and the cytoplasm of the cell by membranes.

Compounds that contain carbon, such as vitamins, carbohydrates, proteins and fats, but not minerals. Organic is a chemical term designating compounds containing a carbon skeleton plus hydrogens, oxygen, and in smaller and variable amounts nitrogen, phosphorus, or sulfur.

The individual member of a species; can be a single cell or a multicellular organism. Organisms are the biological unit of reproduction and while cells of single cell organism are autonomous (bacteria, archaea), individual cells of multicellular organisms (fungi, plants, animals) are not.

The term ortholog is used to indicate an evolutionary related gene existing in two or more different organism. Orthologous genes have a high degree of similarity or sequence identity (see similarity). Orthology is a important way of assessing an organisms evolutionary history. For instance, some two thirds or all human genes have orthologs in the fruit fly Drosophila melanogaster. Humans share 99% of their genes with chimpanzee. Thus the degree of orthology correlates with the evolutionary relatedness between organisms (see also paralogs).

The net movement of water across membranes from a region of low solute (high water) concentration to a region of high solute (low water) concentration. Organisms are usually in osmotic equilibrium, meaning that the water concentration across compartment boundaries are the same, i.e., there is no water gradient. Oganisms usually regulate water flow (osmosis) by disturbing this equilibrium through active transport of solutes such as ions across membranes.

Paralog refers to genes of high similarity within the same organism. Paralogous genes thus are members of a gene or protein family with similar sequence, structure and function (see also ortholog).

Partition coefficient K
The partition coefficient most often refers to the oil-water or air-water partition coefficient expressing the concentration ratio of a solute in a two-phasic system (e.g. oil and water). After thoroughly mixing an oil-water solution with a particular solute (an amino acid, lipid, hormone, gas etc.) the concentration of the solute are measured in each phase after the system comes to rest and the oil (gas) phase is well separated from the water phase. The ratio thus is an expression of the relative solubility of a molecule in oil vs water quantifying its hydrophobicity, or its ability to be soluble in oil. The oil-water partition coefficient of molecules is a good indicator if a molecule can easily diffuse across cell membranes or not. The more soluble it is in oil, the better its permeation across membranes. However, very high oil solubility is also an indicator of small molecules to function as general anesthetics, because they tend to stick in cell membranes rather than diffuse across it, thus altering the composition and physical properties of membranes and some of its proteins. If membrane solubility affects neuronal membranes, a loss of sensation or consciousness can be the result.

Pharmacogenomics extends the study of pharmacology to modern genetics. Knowing the full genetic complement of the human genome, the development and testing of drugs can be assessed at a global molecular level and can also take into account genetic differences between individuals, e.g., can assess the drug efficacy one patient at a time. Basing pharmacology on genomics thus will eventually allow to match drugs with patients that actually respond well to them, and avoid giving medication to patients that do not respond at all or have side effects.

Pharmacology is the study of drugs and their interactions with the human body (or test animal). A branch of medicine.

The characteristic of a species or individual of a species that is inherited from generation to generation. Each phenotype is the result of a genotype, i.e., the genetic information stored in DNA. Most phenotypes are morphological, i.e., they describe a particular structure, size, texture, or color of an organism or part of an organism. Examples are the shape and arrangement of leaves of plants, or the legs, wings, and body segmentation of insects. These morphological phenotypes are the bases of most taxonomic classification of an organism, i.e., the organization of the evolutionary relationship among all life on Earth thought to originate from a single ancestral cell type. Phenotypes can also be functional characteristics and can best be thought of as hereditary diseases or metabolic processes (photosynthesis, skin color pigmentation).

Main lipid component of cell membranes. Phospholipids are a heterogeneous type of molecule composed of glycerol, phosphate, two fatty acid residues, and 'headgroups' with different chemical properties. The organization of phospholipids in cell membranes is known as phospholipid bilayer where the fatty acid residues face the center of the membrane (hydrophobic or water insoluble) and the headgroups forming the surface of the membrane. As such, bilayers separate water filled compartments and provide an electrically insulating barrier between these two compartments. This barrier is overcome by the placement of membrane proteins penetrating the fatty acid core of the membrane and forming channels and transport pathways for metabolites. The latter are usually water soluble and/or charged and would not diffuse across cell membranes without the help of these transport proteins.

Plant molecules with beneficial effects for our physiology such as antioxidant properties. They are also known as nutraceuticals or and are found in designer foods.

A string of units covalently linked together either in linear form or with branching points. A macromolecule made of two or more units. The units can be identical forming a homo-polymer. Glycogen and starch, the glucose storage particles in animals and plants are examples of homopolymers. Polymers can be made of strings of different units. Proteins are made of 20 different amino acids, DNA and RNA are made of 4 different types of nucleotides. These polymers are called hetero-polymers Many polysaccharides are heteropolymers and found on cell surfaces where they serve as protective layer and receptors.

Polymerase (DNA, RNA)
An enzyme complex responsible for the synthesis of nucleic acids. DNA polymerase synthesizes DNA strands, RNA polymerase synthesizes RNA strands. Usually meanst to indicate DNA replication (DNA polymerase) and transcription (RNA polymerase). Polymerases can be further distinguished by the template nulceic acid they are using. For instance, reverse transcriptase of HIV is a DNA polymerase using an RNA template.

Sugars or carbohydrates made up of more than one sugar unit (monosaccharide). See 'carbohydrates' for more information.

The totality of a closely related number of individual organisms that belong to the same species and live in the same geographical area and interact with each other through sexual (or asexual for bacteria) reproduction.

Prebiotic (life)
Prebiotic refers to the state of matter before life existed, but was conducive to the formation of life (the origin of life). The prebiotic 'soup' is the mixture of organic molecules in bodies of water that are thought to have spontaneous, self-assembly property for the first formation of an organic complex with self-replicating qualities.

(Not to be confused with prebiotics, non-digestible food components that benefit gut bacteria).

Primary structure
The primary structure of a protein is the sequence of its amino acid components.

A single-celled form of life without internal membrane bound organelles known as a nucleus, a distinctive sub-cellular structure found in the larger eukaryotic cells. Prokayrotes are thought to be the oldest (primitive) forms of life on earth predating the eukaryotes. Earliest accounts of prokaryotic cell like structure date ancestral forms as anywhere from 2.2 to 3.4 billion years old. Prokaryotes have been found to form two major groups (domains) of life, the archaea and bacteria (eubacteria) that differ in genetic and biochemical structures such as the composition of the cell wall and membrane lipids, as well as chromosome organziation.

Proteins are macromolecules made from twenty different types of amino acids. Proteins constitute the active component of cells . Proteins function as enzyme in metabolism, transporters and receptors in cell membranes, hormones, antibodies, and help read, translate, and replicate the genetic information. 

The proteome is the full set of proteins found at any given time in a cell or organisms. Proteins are the machinery of life and thus knowing all the proteins used by an organism tells about the metabolism and physiology of this organism. The proteome can change during the life cycle of an organisms and often proteins active during development are different from those used in adulthood (see also transcriptome).

A non-functional copy or fragment of a gene originating through gene duplication followed by disruption, deletion or transposition of fragments
. As of September 2012, there are a reported 11,224 pseudogenes in the human genome, and 20,687 protein coding genes.

A property of self, of experiencing the environment such as colors, tastes, or pain. The qualia refers to a part of consciousness that is different from the physical nature of the stimulus that provokes it. For example, in describing a color - red, blue, or green - we talk about a qualia of an object. The physical existence of a color is a quantum mechanical state that emits energy in from of electromagnetic radiation that is decoded by our sensory organs - the eye and the visual cortex in the brain as red, blue, or green. We have no a priori knowledge if these colors exists independent of us. We can only assert that the radiation has a certain energy who's quanta (the single photon) can elicit quantum mechanical effect in the retinal cell layer of our eyes.

Quantum Mechanics
The physical theory of the composition and behavior of atoms and subatomic particles; explains the duality of light as wave and particle, the existence of chemical bonds, and radioactivity.

Quaternary Structure
The highest level of organization within a protein complex that describes the number of subunits (individual polypeptide chains) and their interactions. It thus describes the organization of protein complexes as dimers (two subunits), trimers (three subunits), tetramers (four subunits) and so on. The lower levels are tertiary structure (of each subunit or individual polypeptide), the secondary structure (local regular repeats in polypeptide folding) and primary structure (sequence).

An enzymatic cofactor that plays an important role in photosynthesis and respiration. More specifically, it is part of the electron transport chain in mitochondria and chloroplast membranes.

Quorum sensing
A molecular signaling mechanism used by bacteria under stress (such as lack of nutrients) to start forming a protective biofilm..

Recessive trait
The quality of a gene or allele regarding its ability to express a phenotype. A recessive allele can only express its phenotype if both copies in a diploid organisms are identical. Often, a recessive allele is matched with a dominant allele, which overrides the activity of the recessive one. In this case, the effect of the gene cannot be seen, but it can still be inherited. These are important considerations in genetic diseases that are often caused by defective copies of a gene (allele) that cause the disease only, if both copies of the gene are defective (homozygous for the recessive allele). Heterozygous individuals with a healthy allele do not suffer the disease but are carriers. Examples of recessive genetic diseases are cystic fibrosis and hypercholesterolemia.

Redundancy in biology is an important hallmark of the complexity and robustness of life. Redundancy usually means that different parts of a cell or organism can carry out the same function. This way, a defective part is not damaging to the cell. Redundancy also allows evolution of diversity, because a particular structure may mutate (change) and adopt a new function. The loss of the old function is taken over by another part of the cell or organism.

Replication, of DNA
The replication of DNA is a fundamental process during cell division that provides the two daughter cells (offspring) with identical sets of genes. The replication requires the temporary separation of the DNA double helix into single strand forms where each of the two strands serves as a molecular template for the synthesis of one new complementary strand to form two new double helical copies of the original DNA. The accuracy of replication is based on the specific molecular interaction between two of the four existing nucleotides (A adenine; T thymine; G guanine; C cytosine) to form only AT or GC base pairs. Any other pairing can cause mutations in the daughter DNA, a process that occurs very rarely, and is one of the processes leading to genetic diversity of life.

The cellular particles made of protein and RNA subunits that catalyze the synthesis of proteins along a messenger RNA (mRNA) template. This process is called translation that converts a nucleic acid genetic code into an amino acid sequence. The result are proteins (enzymes) with each having a specific structure and function carrying out a particular metabolic reaction in a cell.

Ribonucleic acid, the most common form of nucleic acid used for storage of chemical energy, processing genetic information from genes (DNA) via messenger RNA (mRNA) into proteins. RNA is one of the most ancient form of molecular structures with enzymatic activity. As a matter of fact, protein biosynthesis is entirely controlled by RNA molecules including mRNA (genetic information), transfer RNA (tRNA) for translating the DNA code into amino acid code, and ribosomal RNA (rRNA) that provide the enzymatic linkage (chemical bond formation) of amino acids into proteins. The use of RNA probably precedes the use of proteins and most modern genomes (except for some viruses) are made of DNA instead of RNA but can only be read by proteins. DNA is the more chemically stable of the two forms of nucleic acids.

Secondary structure
Short repetitive stuctural elements in protein chains (polypeptides) that form helices (alpha helix), extended sheets (beta sheets) or random coils.

The linear arrangement of building blocks in biological macromolecules like DNA, RNA, protein and polysaccharides. DNA and RNA macromolecules are linear polymers of nucleotides. Proteins are linear polymers of amino acids. Polysaccharides are linear and branched polymers of monosaccharides (sugars). While the sequence of RNA and proteins are encoded for by the nucleotide sequence in DNA (the genes and genomes), polysaccharides which play important roles in physiology are not encoded for by genetic information, but rather by the spatial and temporal activity of enzymes that synthesize these polysaccharides. 

Similarity in biology refers to the relatedness of nucleic acid and amino acid sequences and protein structures. Similarity can be expressed in percent identity referring to the percentage of building blocks in any two or more sequences found in the same string or pattern. Similarity is used to infer homology, a term in evolutionary biology that indicates a common ancestry between sequences or structures, i.e., to modern genes or proteins, albeit not identical but highly similar (~72%) are evolutionarily related and have diverged and accumulated changes independently from each other after a speciation event. Similarities around 25% identity or lower can no longer indicate an evolutionary relationship.

Speciation is the process of forming two new species from a common ancestor species. Speciation is the central process of macroevolution, the evolution of novel forms.

A group of organisms (individuals) that can interbreed and reproduce with each other. Used to distinguish sexually reproducing organisms into groups. Individuals from two different species cannot have offspring. They are said to be reproductively isolated. The biologist Ernst Mayr formulated this definition of a species advancing our understanding of the mechanism of evolution of higher organisms. For microbes, the species definition does not properly apply, because they do not reproduce sexually, but have an efficient mechanism to exchange genetic material even between evolutionarily distant forms. This exchange of genes is known as horizontal gene transfer. Unlike sexual reproduction, it usually involves only a fraction of an organisms genome that is being transferred and is a mechanisms of increasing genetic variability among microorganisms that does not depend on cellular reproduction (cell division).

A process during protein synthesis where the mRNA cuts out the intron sequences and strings together the exon (coding) sequences derived from a DNA template during transcription. Usually, eukaryotic genes consist of several exons/introns and sometimes not all exons are used in the final mature RNA. Ultimately, a single gene can be spliced into more than one mature mRNA producing splice variants. Splice variants give rise to proteins with different size and functionality.

The major complex carbohydrate of caloric value from plant products. Starch is a polymer made of thousands of glucose units.

The mathematical procedure to describe probabilities and the random or non-random distribution of matter or occurrence of events.

Steady-state (equilibrium)
A process in biochemistry that refers to situations of high activity even though the overall structure and composition of cells seems not to change. Steady state processes are used to explain metabolic homeostasis. The flow of water molecules in a river or free flowing traffic are examples of steady state processes where the overall movement of water molecules (cars) does not appear to change, although the composition of particular molecules (cars) is constantly changing.

Stem Cell
Stem cells are specialized cells of animals and plants that have the ability to grow and divide by mitosis. Cell division results in self-regeneration as well as differentiation. This means that stem cells can maintain their characteristic as stem cells (self-regeneration), but also change into a different cell type (differentiation).

A stochastic event is based on random behavior. The occurrence of individual events cannot be predicted, although measuring the distribution of all observations usually follows a predictable pattern. These patterns can be described by statistical means. An example is the decay of radio active material, where a clump of matter has a measurable and thus predictable half-life time. It is impossible, however, to mark an individual atom and predict when it will decay and emit radiation. The latter process is a stochastic event.

The pore openings underneath plant leaves that can open and close according to the metabolic needs of the plant. They are the ports for exchange of oxygen and carbon dioxide gas for photosynthesis, but also release excess water into the air. This process of water loss maintains a steady flow of water and minerals from the roots to the leaves. To minimize the water loss, many plants regulate the duration and time of day when stomatas are open.

Structure, high-resolution
The high resolution structure of a molecule refers to its atomic organization in three-dimensional space. It is either obtained from analysis of diffraction patterns of high energy radiation (X-rays, electron waves) or nuclear magnetic resonance spectra (NMR). Structural information has an important place in biological studies at the molecular level, because structures can be used to elucidate the detailed mechanism of a chemical reaction, a biological binding events such as hormone signaling or immunological defenses, or nutrient transport (absorption) across intestinal epithelial cell layers and cell membranes. The structural analysis of DNA in 1953 has helped understand the mechanism of replication of genetic information during reproduction as well as the mechanism of genetic encoding, reading (transcription), and synthesis (translation)of amino acid sequences in proteins and enzymes.

Subunit (protein)
A polypeptide or protein unit that interacts with other protein units in a protein complex. Each subunit is an independently made protein (coded for by a gene). Subunits can be identical or different forming homomeric and heteromeric protein complexes, respectively. An example of a heteromeric protein complex is the hemoglobin that consists of two alpha globin subunits and two beta globin subunits. An example of a homomeric protein is the aquaporin, a homotetrameric protein made up of four identical polypeptide units.

The synapse is a specialized portion of a neuron or nerve cell that is used for cell to cell communication with other neurons and muscle cells. The chemical synapse contains packaged neurotransmitters that can be released upon an electrical signal (action potential) reaching the synapse from the dendrites and cell body of the neuron, where action potentials originate (where synapses of other neurons interact with the signaling cell). A neuron can have multiple synapses, often with different signaling properties being excitatory or inhibitory synapses. Multiple synapses signaling to a receiving neuron or muscle can strengthen a stimulus or inhibition by activating some or all of the synapses through addition of signaling strength. In addition to chemical synapses, electrical synapses are propagating an action potential signal without a neurotransmitter, but directly by coupling membranes of adjacent cells using gap junctions. The feature of both chemical and electrical synapses allows the signal to propagate unidirectional. The signal cannot reverse. However, feedback signals between the signaling and receiving cell to strengthen or weaken the synaptic interaction, a process called synaptic plasticity.

Taxonomy is the classification of organisms according to their evolutionary relationship. Taxonomic groups are organized in a hierarchical fashion from the most inclusive domains of life (archaea, bacteria, eukarya, viridae) to the lowest most specific species description (e.g. Homo sapiens).

Teleological (teleology)
A way of arguing that natural systems have a way to look forward to improve their own situation. Teleological arguments are often found in evolutionary literature such as '... a plant becomes tastier in order to gratify the animal's needs and desires....' (see Pollan, 2008, In Defense of Food, p.102). Of course, plants to not plan on being tastier, but this 'tastiness' is the result of animals preferring this particular flavor increasing the seedling's chance to grow and have its own offspring.

Tertiary Structure
The structure of an invididual protein chain (polypeptide) indicating the folding of the backbone (helical, extended, looping).

A scientific theory is an established and experimentally verified fact or collection of facts about the world. Unlike the everyday use of the word theory, it is not an unproved idea, or just some theoretical speculation. The latter meaning of a 'theory' in science is called a hypothesis.

The physical theory of heat and energy distribution in the universe. The two important laws of thermodynamics state that the total energy of the universe is constant and energy can neither be made nor destroyed, and that the distribution of energy in the universe over time proceeds from a state of order to a state of disorder (entropy increase).

The physical or metabolic phenotype of an organism such as red flower color and length of stem in plants and black fur or pink eye in mice. See also phenotype and genotype.

Transcript, transcriptome
A transcript is an RNA copy of a DNA template, i.e., a ribonucleic acid copy of a gene. Transcripts are also known as messenger RNA and are the mediator between the gene and a protein product. The transcriptome is a term used to indicate the total set of transcripts found at any given time in a cell or organisms. The idea is that the presence of mRNA in a cell indicates the use of a gene. The type and number of active genes is an indicator of the actual metabolic and physiological state of a cell.

A membrane protein that functions as an ion channel, solute transporter, facilitator or pump to move molecules across cell membranes.

The constituent of fat composed of glycerol and three fatty acids. Most triglycerides are obtained from food as fats or synthesized by the liver and stored in liver and fat cells (adipocytes). Triglycerides are one of three major sources of metabolic fuel (the other sources are carbohydrates and proteins) providing energy for the physiological processes of the body.

Uncertainty Principle (Heisenberg's)
A necessary consequence of the quantum mechanical description of matter. Unlike in classical mechanics where the position of a large object in time and space (including its speed) can exactly be described and predicted based on measurements (Newton's laws of gravity, actio and reactio), the position and speed of individual subatomic particles like electrons, and thus the behavior of individual molecular interaction, can neither be measured nor predicted with certainty, yet perfectly described by statistical methods when studied in large numbers.

A pyrimidine base and one of four nitrogenous bases found in ribonucleic acid (RNA). It is part of UTP, the triphosphorylated nucleotide. The other three bases found in RNA are adenine, guanine, and cytosine.

UV Radiation
Ultraviolet radiation, an invisible, high energy component of sunlight can cause skin damage including cancer.

Smallest of all organisms and often not considered alive because they strictly depend on a cellular host organism (bacteria, plant, animal) to reproduce. Viruses have no metabolism of their own and depend on passive carriers to transport them around. Viruses are infectious particles with a DNA or RNA based small genome that can control the cellular mechanism of infected cells prompting the host cell to synthesize new viruses. Infections often cause mild to severe symptoms, yet some viruses do not cause any harm or not in all host organisms (called carriers). Because they have no metabolic activity they are not susceptible to antibiotics and most drugs, unless a drug can interfere during the infection and viral replication stages. Outside cells, viruses are passive and are easily destroyed by chemical intervention.

Visual cortex
One of five regions of the cerebrum processing visual information in animal brains.

Wild Type (wt)
The wild type (wt) is a term referring to the natural genetic form of an organism. A wild type is distinguished from a mutant form (an organism with a genetic mutation). Usually, the distinction between wild type and mutant is based on a single mutation. It should be noted, that within a population of an organism, there is no such thing as a wild type. The term, however, is useful for geneticists because it allows a simple definition of a standard or control condition.

One of two sex chromosomes in higher organisms that defines the gender of the adult. In almost all sexually reproducing organisms, the X-chromosome defines female characteristics.

Molecules entering an organism that has no physiological function and is not found in an organism if not taken up by eating, breathing, or injury. The term xenobiotics is used to describe a foreign particle or molecule that is potentially dangerous or toxic.

One of two sex chromosomes in higher organisms that defines the gender of the adult. In almost all sexually reproducing organisms, the Y-chromosome defines male characteristics.

Zebra fish
The Zebra fish is one of many model organisms used in biomedical research to understand development of higher organisms, the functioning of nervous systems, and fundamental aspects of physiology and the cause of diseases.

A zygote is a fertilized egg containing two sets of chromosomes, one from the egg (oocyte) and one form the sperm. The zygote is a single cell and the result of a fusion between two gametes, an egg (female) and one sperm cell (male).

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