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25.24: Glossary: G - Biology

25.24: Glossary: G - Biology



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25.24: Glossary: G

Biology Unit 1 2020

Words and terms that are common to the biology course.

Abiotic

Things in the environment that are non-living such as light, temperature, water, etc.

Adapt

1. (noun) Physical structures, functions or behaviours of an organism that help it survive.

2. (verb) The process of changing a structure, function or behaviour to increase the chance of survival.

Archaea

Single-celled organisms that appear to be very ancient and often live in extreme conditions such as hot springs. They are a separate group from bacteria and single-celled eukaryotes.

Adenosine triphosphate is a molecule that contains three phosphate molecules, each attached with more energy in the bond that n the one before. ATP acts as the battery of the cell, storing energy until it is needed.

Autotroph

An organism capable of synthesizing its own food from inorganic substances, using light or chemical energy. Green plants, algae, and certain bacteria are autotrophs.

Bacteria

Bacteria are simple, prokaryotic cells that lack a nucleus and membrane-bound organelles.

Biodiversity

The term given to the variety of life on Earth or in a specific environment. It is the variety within and between all species of plants, animals and micro-organisms and the ecosystems within which they live and interact.

Biology

Biology is the study of life and living organisms, including their structure, function, growth, evolution, distribution, and taxonomy.

Biotic

Living organisms in the environment or things that have come from living organisms such as dead material, waste products, etc.

Carbohydrate

A large group of organic compounds occurring in foods and living tissues and including sugars, starch, and cellulose. They contain hydrogen and oxygen in the same ratio as water (2:1) and typically can be broken down to release energy in the animal body.


Oxford Dictionary of Biochemistry and Molecular Biology (2 ed.)

‘the book is almost an encyclopedia. It is comprehensive, thorough, clear, and accurate’ - TIBS

The Oxford Dictionary of Biochemistry and Molecular Biology provides a comprehensive survey of modern biochemistry and molecular biology. Fully revised and updated, this new edition includes definitions of terms from the fields of Bioinformatics, Biophysics, Cell Biology, Chemistry, Genetics, Immunology, Mathematics, Microbiology, Pharmacology, Systems Biology, and Toxicology. Entries are short and informative, covering details of biochemical substances and the processes in which they are involved, methods and concepts in molecular biology, and definitions of biochemical symbols and abbreviations. Each entry is accessibly written, pointing out the pitfalls where terms are often confused and providing recommended nomenclature and alternative names.

Bibliographic Information

Authors

The editors are Richard Cammack of the Department of Biochemistry, King's College London, Teresa Atwood of the Faculty of Life Sciences, University of Manchester, Peter Campbell, deceased, Howard Parish of the School of Biochemistry and Molecular Biology, University of Leeds, Anthony Smith, Emeritus Reader in Biochemistry at University College London, Frank Vella of the Department of Biochemistry, University of Saskatchewan, and John Stirling, Department of Biochemistry, King's College London.


Biology Teaching Resources. The Desert Locust


Mating. The male locust mounts the back of the female, applies the tip of his abdomen to hers and passes sperms into her reproductive tract. The sperms are stored in a sperm sac in the female's abdomen, and as the eggs pass down the oviduct during laying, the sperms are released and so fertilize the eggs.

Eggs. After mating, the female lays her eggs in warm, moist sand following a rainy spell. She pushes her abdomen down into the sand, extending the membranes between the segments, and burrowing to a depth of 50 or 60 mm. In this burrow, 50 to 100 eggs are laid and mixed with a frothy fluid, which hardens slightly and may help to maintain an air supply round the eggs. In 10 to 20 days depending on temperature and moisture, the eggs hatch and the nymphs make their way to the surface and emerge as &lsquohoppers&rsquo (like miniature adults but wingless at this stage).

Swarming. If food is in adequate supply and the hoppers are not forced to crowd together when they emerge from the eggs, the locusts live their lives separately as do other grasshoppers. If, however, the hoppers are crowded together for one reason or another, they enter a gregarious phase of activity. The hoppers tend to keep together in a band and move forward together. The crowding effect also results in a change of colour from the normal green, buff or brown to a striking black and yellow (or orange) coloration. There are also structural differences from the solitary form. The bands of hoppers vary in size from hundreds to millions, covering a few square metres or several square kilometres, depending partly on the age of the hoppers and how many bands have combined. As hoppers, they migrate only a few kilometres each day, basking in the early morning sun until their body temperature rises to a level which allows them to move off and eat all the vegetation in their path. When the temperature drops at night they climb bushes and plant stems and remain immobile.

After the final ecdysis, the adult locusts take to the wing and after a few days of short flights set off on extensive migrations, settling at night and in the middle of the day when it is hottest. A medium-sized swarm may contain a thousand million locusts and cover an area of 20 square kilometres. Such a swarm will consume some 3000 tonnes of vegetation per day and so if a swarm lands on agricultural crops, the locusts will strip them of every vestige of leaf and edible stem.

The swarms may travel many hundreds of kilometres from their place of origin, e.g. from Africa to India, and the females will lay eggs during their journey, so leaving the nucleus of successive swarms within a few weeks.

Methods of control. The range of the adult locusts is so great that international cooperation is essential for effective control. A swarm may originate in India but cause devastating damage to crops in Africa. Sixty countries in Asia and Africa are threatened by swarms of the desert locust.

The main method of control is by spreading poisoned bait, for example bran containing insecticide, in the path of the migrating bands of hoppers. The insecticide kills them by being eaten and by its contact with their bodies. Poisoned bait can be used only when the locality of the hoppers is known, and a careful watch must be kept over wide areas so that swarms are discovered as soon as possible after they emerge. The information is then sent to anti-locust centres, e.g. in Nairobi or London, and trucks and personnel are mobilized to take the bait to the appropriate location.

Other methods employed are to spray insecticides over swarms of hoppers or settled adults using aircraft or motor vehicles, or to spray the vegetation in the path of the hoppers. If the region of egg-laying is known, the vegetation in the area can be sprayed with an insecticide which kills the hoppers at their first meal. The danger with all spraying techniques is that the chemicals used may be poisonous to humans and other animals, particularly if used on food crops.

Two other species, the red locust and the migratory locust, have been held in check for many years by effective control measures, but the desert locust still constitutes a major threat. Constant vigilance and international cooperation are needed if crops are to be protected against this insect.

Currently it is being discussed whether the hazardous nature of the insecticides and the expense of spreading them is a cost effective way of controlling the desert locust. However, new and safer insecticides are being produced all the time and there is little doubt that farmers whose crops are threatened by locust plagues will want control measures to continue.

For illustrations to accompany this article see Insect Life-Cycles


25.24: Glossary: G - Biology

The Science of Biotechnology

Discovering and Developing Medicines

How Are Biotech Medicines Made?

A technique used for the separation of DNA, RNA or protein molecules by using an electric current applied to a gel matrix. The gel is the medium used to contain, then separate the target molecules. Electrophoresis refers to the use of electricity to move the molecules through the gel matrix. Placing the molecules in wells in the gel and applying an electric current moves the molecules through the matrix at different rates based on their size, charge and/or shape.

A length of DNA that codes for a particular protein or, in certain cases, a functional or structural RNA molecule.

Generally Regarded as Safe (GRAS)

A designation that a substance is considered safe by experts under the conditions of its intended use. Examples are CHO and NS0 cell lines that have GRAS status for therapeutic protein production.

Alteration of the genetic material of cells or organisms in order, for example, to make them capable of making new substances or performing new functions.


25.24: Glossary: G - Biology

Sanskrit Dictionary understands and transcodes देवनागर्-ई IAST, Harvard-Kyoto, SLP1, ITRANS. You can type in any of the Sanskrit transliteration systems you are familiar with and we will detect and convert it to IAST for the purpose of searching.

Using the Devanagari and IAST Keyboards

Click the icon to enable a popup keybord and you can toggle between देवनागरी and IAST characters. If you want a system software for typing easily in देवनागरी or IAST you can download our software called SanskritWriter

Wildcard Searches and Exact Matching

To replace many characters us * example śakt* will give all words starting with śakt. To replace an individual character use ? for example śakt?m will give all words that have something in place of the ?. By default our search system looks for words “containing” the search keyword. To do an exact match use “” example “śaktimat” will search for this exact phrase.

Type sandhi: and a phrase to search for the sandhi of the two words example.

sandhi:sam yoga will search for saṃyoga

Type root: and a word to do a root search only for the word. You can also use the √ symbol, this is easily typed by typing / in SanskritWriter software.

Credits

Original Monier-Williams data courtesy of Cologne Digital Sanskrit Lexion.


25.24: Glossary: G - Biology

Glossary of Scientific Terms

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

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Absorption
(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.

Adaptation
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.

Allele
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.

Anabolism
Biosynthesis of molecules in cells and part of metabolism.

Antioxidant
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.

Aperiodic
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.

Archaea
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.

ATP
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.

Axon
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).

Bacteria
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.

Bile
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.

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

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

Bioelectricity
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.

Biopharming
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.

Biotechnology
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.

Carbohydrates
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.

Carbon
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).

Capacitance
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).

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

Cell
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.

Cholesterol
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.

Chromosome
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.

Chyme
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
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
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).

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

Covalent
The chemical bond between atoms.

Crystal
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.

Cytoskeleton
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.

Depolarization
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.

Ecosystem
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.

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

Electrophysiology
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.

Element
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.

Entropy
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.

Enzyme
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).

Epigenetics
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).

Exon
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.

Fractal
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.

Gene
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.)

Genome
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.

Genotype
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
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.

Glucose
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.

Glycogen
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.

Glycolysis
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.

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

Hemoglobin
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.

Heterozygous
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.

Homeostasis
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.

Homozygous
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.

Hormones
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.

Hyperpolarization
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.

Hypothesis
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
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.

Insulin
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.

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

Ions
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.

Intron
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).

Joule
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).

Karyotype
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
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.

Lecithin
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).

Lipid
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.

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

Macronutrients
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.

Macroscopic
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.

Microarray
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.

Microflora
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.

Microscopic
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.

Molecule
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.

Nanotechnology
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.

Neurotransmitter
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).

Nucleus
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).

Nutraceuticals
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.

Nutrient
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.

Oligomer
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.

Organelle
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.

Organic
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.

Organism
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.

Ortholog
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).

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

Phenotype
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).

Phospholipid
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.

Phytochemicals
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.

Polymer
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.

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

Population
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.

Prokaryote
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.

Protein
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.

Proteome
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).

Pseudogene
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.

Qualia
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).

Quinone
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
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.

Ribosome
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.

RNA
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.

Sequence
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
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
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.

Species
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).

Splicing
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.

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

Statistics
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).

Stochastic
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.

Stomata
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.

Synapse
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
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).

Theory
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.

Thermodynamics
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).

Trait
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.

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

Triglycerides
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.

Uracil
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 Radia tion
Ultraviolet radiation, an invisible, high energy component of sunlight can cause skin damage including cancer.

Virus
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.

X-chromosome
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.

Xenobiotics
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.

Y-chromosome
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.

Zygote
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).


GeoMan's Glossary of Earth Science Terms

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

Absolute Date: An estimate of the true age of a mineral or rock based on the rate of decay of radioactive minerals.

Acre-foot: The volume of water required to cover one acre of land to a depth of one (1) foot. One acre-foot is equal to 325,851 gallons of water.

Active volcano: A volcano that is erupting or one that, while not erupting at the present, has erupted within (geologically) recent time and is considered likely to do so in the (geologically) near future.

Adiabatic rate : The rate of temperature change in the atmosphere due to the raising or lowering of an air mass. The "dry adiabatic rate" is 5.5 deg. F. per 1000 feet, while the "wet" rate is 3.5 deg. F. per 1000 feet.

Alluvium: A general term for clay, silt, sand, gravel or similar unconsolidated material deposited by a stream or other body of running water.

Andesite: Intermediate volcanic rocks containing 54 to 62 percent silica and moderate amounts of iron and magnesium. Andesite minerals commonly include plagioclase and hornblende, with lesser amounts of mica, pyroxene, and various accessory minerals. Andesites are aphanitic in texture and are usually medium dark in color. They occur with composite volcanic cones associated with convergent plate margins.

Aquifer: A water-bearing layer of rock or sediment capable of holding and transmitting fluid (such as water, gas, or oil).

Aquifer, Confined (or Artesian): An aquifer overlain by a non-permeable layer or layers, in which pressure will force water to rise above the aquifer.

Aquifer, Perched: An aquifer containing unconfined groundwater separated from an underlying body of groundwater by an unsaturated zone.

Aquifer, Principal: The aquifer or combination of related aquifers in a given area that is the important economic source of water to wells.

Aquifer, Secondary: Any aquifer that is not the main source of water to wells in a given area.

Aquifer, Unconfined (or Water Table): An aquifer in which the upper surface is the water table.

Aquiclude: An impermeable geologic formation or stratum which will not hold or transmit fluid.

Aquitard: A geologic formation or stratum that significantly retards fluid movement.

Artesian Well: A well in an aquifer where the groundwater is confined under pressure and the water level will rise above the top of the confined aquifer.

Artificial Recharge: The unnatural addition of surface waters to groundwater. Recharge could result from reservoirs, storage basins, leaky canals, direct injection of water into an aquifer, or by spreading water over a large land surface.

Ash: Fine particles of rock material ejected during an explosive volcanic eruption (commonly intermediate to felsic events). Ash may be either solid or molten when first erupted, and generally measures less than 0.10 inch in size (larger particles have other names).

Ashfall (subaerial): Volcanic ash that has fallen through the air. The resulting deposit is usually well sorted and exhibits a finely layered structure.

Ash flow: A turbulent mixture of gas and rock fragments, most of which are ash-sized particles, ejected violently from a crater or fissure. The mass of pyroclastics is normally of very high temperature and moves rapidly down the slopes, or even along a level surface.

Avalanche: A large mass of material falling or sliding rapidly due to the force of gravity. In many cases, water acts as a catalyst and/or lubricant. Avalanches often are classified by what is moving, such as a snow, ice, soil, or rock avalanche. A mixture of these materials is commonly called a debris flow.

Bedrock A general term for any consolidated rock.

Bentonite A clay material composed principally of the mineral montmorillonite. It has a great affinity for fresh water and when hydrated will increase its volume more than seven times. Water/bentoninte suspensions are essentially impermeable. Commonly used as a sealant for ponds.

Biostratigraphy: The study and classification of rocks and their history based on their fossil content.

Block: Angular chunk of solid rock ejected during a volcanic eruption.

Bomb: Fragments of molten or semi-molten rock, several inches to several feet in diameter, which are blown out during an explosive volcanic eruption. Because of their semi-plastic condition, bombs are often modified in shape during their flight or upon impact.

Breccia: Angular fragments of material, commonly formed by physical weathering processes or explosive volcanic activity.

Brittle-Ductile Transition Zone : The location at depth within the earth's crust where the temperature and pressure have risen to such a high level that directed stress results in plastic deformation as opposed to fracturing and faulting.

Calorie : A unit of heat energy. The amount of heat required to raise the temperature of 1 gram (cubic Centimeter) of water 1 degree Celsius. Also, the substance which gives food its flavor.

Chattermarks : Erosional features associated with alpine glaciers.

Cinder cone: A volcanic cone built entirely of loose fragmented material (pyroclastics.)

Collection : The accumulation of precipitation into surface and underground areas, including lakes, rivers, and aquifers.

Comet : An object which circles the sun in a non-circular orbit. Commonly made up of a large mass of rock debris and ice. Basically, a giant snockball from space.

Composite volcano: A steep volcanic cone built by both lava flows and pyroclastic eruptions.

Condensation : The change of state of water from the vapor to the liquid phase. Results in liberation of 80 calories per cubic centimeter.

Connate water : Water included in the groundwater which is derrived from the rock itself, as opposed to water which has percolated down from the surface.

Continental crust: Solid, outer layers of the earth, including the rocks of the continents.

Continental drift: The theory that horizontal movement of the earth's surface causes slow, relative movements of the continents toward or away from one another.

Continental shelf : Portions of the continental land masses covered by sea water. Extend varying distances outward from the exposed continental margins. Usually, the continental shelf will be wider along a passive continental margin, and narrower along an active margin.

Crater: A steep-sided, usually circular depression formed by either explosion or collapse at a volcanic vent.

Debris avalanche: A flow of unsorted masses of rock and other material downslope under the influence of gravity. Water is commonly involved as a catalyst and/or lubricant. For example: a rapid mass movement that included fragmented cold and hot volcanic rock, water, snow, glacial ice, trees and other debris, and hot pyroclastic material was associated with the May 18, 1980 eruption of Mt. St. Helens. Most of the deposits in the upper valley of the North Fork Toutle River and in the vicinity of Spirit Lake are from the debris avalanche resulting from the eruption.

Density : A measure of how tightly packed the atoms of a substance are. Measured in grams per cubic centimeter. Varies by the mineral or substance. For example, gold has a high density, while quartz has a low density. See also "specific gravity."

Detachment plane: The surface along which a landslide disconnects from its original position.

Dew point : The temperature (elevation) where adiabatic cooling results in the initiation of condensation of water vapor into cloud droplets.

Di-polar: The arrangement of the hydrogen atoms of a water molecule at 105 deg. across the oxygen results in a slight electrical charge to the molecule. It also results in water molecules looking like Mickey Mouse instead of Alfred E. Newman.

Dome: A steep-sided mass of viscous (doughy) lava extruded from a volcanic vent, often circular in plane view and spiny, rounded, or flat on top. Its surface is often rough and blocky as a result of fragmentation of the cooler, outer crust during growth of the dome.

Dormant volcano: This term is used to describe a volcano which is presently inactive but which may erupt again. The major volcanic cones of the Cascade Mountains (in Washington, Oregon, and California) are believed to be dormant rather than extinct.

Drift (glacial) : General term for material deposited by a glacier.

Erosion : The movement of weathered material downslope under the influence of gravity. Water acts as a catalyst and as a lubricant. Some common types of erosion includes landslides, rockfalls, creep, etc. Erosion takes weathered material and puts it in a river so it can be transported to the beach (see Strickler's 3rd Law of GeoFantasy).

Erratic (glacial) : Large rocks or other debris deposited by a glacier, usually in an area far removed from its source. Commonly used to indicate a big chunk of debris which is clearly out of place and shouldn't even be where it is.

Eruption: The process by which solid, liquid, and gaseous materials are ejected into the earth's atmosphere and onto the earth's surface by volcanic activity. Eruptions range from the quiet overflow of liquid rock to the tremendously violent expulsion of pyroclastics.

Eruption cloud: The column of gases, ash, and larger rock fragments rising from a crater or other vent. If it is of sufficient volume and velocity, this gaseous column may reach many miles into the stratosphere, where high winds will carry it long distances.

Eruptive vent: The opening through which volcanic material is emitted.

Evaporation : The change of state of water from the liquid to vapor phase. Requires the addition of 80 calories per cubic centimeter.

Evapotranspiration : Water used by plants and animals and subsequently returned directly to the atmosphere.

Evolution : The theory that living organisms mutate and change, generally from simple to increasingly complex forms.

Extinct volcano: A volcano that is not presently erupting and is not likely to do so for a very long time in the future.

Firn : The intermediate "granular" stage which occurs during the conversion of snow to glacial ice.

Fissures: Elongated fractures or cracks on the slopes of a volcano. Fissure eruptions typically produce liquid flows, but pyroclastics may also be ejected.

Flank eruption: An eruption from the side of a volcano (in contrast to a summit eruption.)

Fossil : Evidence of past life on earth. Can include the preserved hard and soft parts of plants and animals, tracks and burrows, whole organisms preserved intact in amber or tar, and fossilized dung. ANY evidence of life constitutes a fossil.

Floodplain : The low relief lands bordering a stream or river, common to the mature and old age stages of stream development. Floodplains store excess water in times of high water, and excess sediments in times of low water. Beware of building your dream house on a floodplain - they tend to get rather wet at irregular intervals.

Fumarole: A vent or opening through which issue steam, hydrogen sulfide, or other gases. The craters of many dormant volcanoes contain active fumaroles.

Geothermal energy: Energy derived from the internal heat of the earth.

Geothermal power: Power generated by using the heat energy of the earth.

Glacial ice : Naturally occurring ice which exhibits internal plastic flow and deformation.

Glacial abrasion : A copmmon mechanical weathering process where rock and debris frozen into the sides and bottom of a glacier act like sandpaper and wear down the bedrock the glacier is mocing across.

Glacial quarrying (plucking) : A common mechanical weathering process in alpine glaciated terrain where glacial ice frozen into cracks in the bedrock literally "pluck" rock material from the valley floor.

Glacial polish : Polished bedrock surfaces left behind after melting of glacial ice. The polishing is probably due to very fine grained rock flour carried at the base of the ice.

Graben: An elongate crustal block that is relatively depressed (downdropped) between two fault systems.

Groundwater : Water stored beneath the surface in open pore spaces and fractures in rock.

Heat transfer: Movement of heat from one place to another.

Horizontal blast: An explosive eruption in which the resultant cloud of hot ash and other material moves laterally rather than upward.

Hot-spot volcanoes: volcanoes related to a persistent heat source in the mantle.

Hydrologic cycle: The transfer of water between numerous temporary storage reservoirs. These include the ocean, rivers and streams, glacial ice, beer cans, dogs and cats, groundwater, and the atmosphere.

Hydrothermal reservoir: An underground zone of porous rock containing hot water.

Langley : The unit of solar energy relating to the amount which reaches a specific area of the earth's surface. In general, more "langleys" reach the surface of the earth at the equator than at the poles.

Lapilli: Literally, "little stones" round to angular rock fragments measuring 1/10 inch to 2-1/2 inches in diameter, which may be ejected in either a solid or molten state.

Lava: Magma which has reached the surface through a volcanic eruption. The term is most commonly applied to streams of liquid rock that flow from a crater or fissure. It also refers to cooled and solidified igneous rock.

Lava Flow: An outpouring of lava onto the surface from a vent or fissure. Also, a solidified tongue-like or sheet-like body formed by outpouring lava.

Lava tube: A tunnel formed when the surface of a mafic lava flow cools and solidifies, while the still-molten interior flows through and drains away. These can insulate the flow and allow it to travel great distances.

Leeward : The side facing away from the wind. When speaking of a mountain range, these areas are generally hotter and drier than on the windward side.

Loess : Very fine-grained sediments deposited by wind action. Commonly associated with the margins of continental ice sheets. Large expanses of loess from the recent ice age are in large part responsible for the bountiful corn and wheat fields of the American Midwest.

Magma chamber: The subterranean cavity containing magma. When a conduit is opened to the surface, a volcanic eruption is possible.

Mantle: The zone of the earth below the crust and above the core.

Magnitude: A numerical expression of the amount of energy released by an earthquake, determined by measuring earthquake waves on standardized recording instruments (seismographs.) The number scale for magnitude is a modified logarithmic value, rather than arithmetic, and the numbers get real big, real fast a magnitude 9 earthquake, for example, is 33 times greater than a magnitude 8 earthquake, 1089 times greater than a magnitude 7 earthquake, 35937 times greater than a magnitude 6 earthquake, and so on. The short version? Small quakes don't really do much to relieve stress in the crust.

Marker horizon (or bed) : A distinctive horizon which is used for regional correlation of lithology. A good marker horizon is distinctive, widespread, and represents a relatively short period of geologic time. For example, ash from a volcanic eruption, debris from a meteorite impact, etc. It is GeoMan's opinion that humans will represent one of the earth's finest marker horizons in the geologic record of the future. Our effect on the surface is certainly distinctive and widespread, and, at the rate we are going, it is likely that our species will have a relatively short lifespan (speaking in terms of geologic time, of course).

Metamorphic : From the Greek "meta" (change) and "morph" (form). Commonly occurs to rocks which are subjected to increased heat and/or pressure. Also applies to the conversion of snow into glacial ice.

Mineral : A naturally occurring, inorganic, crystalline solid with a definite internal structure and chemical composition.

Moraine : General term for material deposited beneath, along the sides, and/or at the terminus of a glacier. Also, what we get here in Oregon during the fall, winter, and spring. See also till.

Mudflow: A flowage of water-saturated earth material possessing a high degree of fluidity during movement. A less-saturated flowing mass is often called a debris flow. A mudflow originating on the flank of a volcano is properly called a lahar.

Nuée ardente: A French term applied to a highly heated mass of gas-charge ash which is expelled with explosive force down the mountainside. Common to intermediate volcanoes. Can be quite deadly. Also known as a "glowing avalanche."

Oceanic crust: The earth's crust where it underlies oceans.

Phreatic eruption (explosion): An explosive volcanic eruption caused when water and heated volcanic rocks interact to produce a violent expulsion of steam and pulverized rocks. Magma is not involved.

Pillow lava: Interconnected, sack-like bodies of lava that form underwater.

Plastic deformation (or flow) : Permanent bending or folding of rock (or ice) as a result of directed pressure. In rock, usually occurs below the Brittle-Ductile Transition Zone, and is commonly associated with metamorphism.

Plate tectonics: The theory that the earth's crust is broken into about fragments (plates,) which move in relation to one another, shifting continents, forming new ocean crust, and causing volcanic eruptions.

Plug: Solidified lava that fills the conduit of a volcano. Plugs (also called volcanic necks) are usually more resistant to erosion than the material making up the surrounding cone, and may remain standing as a solitary pinnacle when the rest of the original structure has eroded away.

Plug dome: The steep-sided, rounded mound formed when viscous lava wells up into a crater and is too stiff to flow away. It piles up as a dome-shaped mass, often completely filling the vent from which it emerged.

Pluton: A large igneous intrusion formed at great depth in the crust.

Potential energy (gravitational) : The stored energy of a substance. Water has a lot of this if there is an elevation difference. Potential energy can be converted to kinetic energy if the water (or other substance) is allowed to move.

Precipitation : Any condensed water falling from the atmosphere to the surface of the earth. Common types include rain, snow, sleet, and hail.

Problem : A situation which is generally uncomfortable, or otherwise undesirable. I always seem to have several - how about you?

Pumice: Light-colored, frothy volcanic rock, usually of dacite or rhyolite composition, formed by the expansion of gas in erupting lava. Commonly seen as lumps or fragments of pea-size and larger, but can also occur abundantly as ash-sized particles.

Pyroclastic: Pertaining to fragmented (clastic) rock material formed by a volcanic explosion or ejection from a volcanic vent.

Pyroclastic flow: Lateral flowage of a turbulent mixture of hot gases (�°C) and unsorted pyroclastic material (volcanic fragments, crystals, ash, pumice, and glass shards) that can move at high speed (100 miles an hour or more). Also known as a "glowing avalanche" or "nueé ardente."

Ridge, Oceanic: A major submarine mountain range. Commonly the sites of crustal rifting and plate separation, and the eruption of mafic basaltic lavas.

Rift system: The oceanic ridges formed where tectonic plates are separating and a new crust is being created also, their on-land counterparts like the East African Rift.

Ring of Fire: The regions of mountain-building earthquakes and volcanoes which surround the Pacific Ocean.

Rock flour : Finely ground rock material, usually associated with glaciers (or faults). Can be mixed with water and formed into loaves which, when baked for 45 minutes at 350°, are totally unedible.

Sea level : The top of the ocean, where the water meets the atmosphere. It's not necessarily level!

Sediment : Rock debris commonly produced by mechanical or chemical weathering processes.

Seismograph: An instrument that records seismic waves that is, vibrations of the earth. Used to record and measure earthquakes.

Shearing: The motion of surfaces sliding past one another.

Shield volcano: A gently sloping volcano in the shape of a flattened dome, built almost exclusively of mafic lava flows. The Hawaiian Islands are a good example.

Silica: A chemical combination of silicon and oxygen.

Sniceball: A snowball which has been stored in the freezer for several months (or more). Useful for surprising unwelcome visitors during the spring and summer months.

Snirtball: A combination of snow and dirt. Snirtballs are produced by accident when the total snowfall on bare ground is less than 0.537 inches.

Snockball: A combination of snow and rock: generally an innocent-looking snowball with a dense, rocky core. Snockballs are always premeditated, and are not known to occur naturally on earth. Giant snockballs from space (also called comets) may be responsible to the initial introduction of water onto our planet.

Snowball: A spherical accumulation of water in the crystalline form.

Snowline : The lower limit of any year's permanent snowfall. Separates the Zone of Accumulation from the Zone of Ablation.

Solid state : In metamorphism, indicates the change of mineral identity without melting. All ion migration occurs while the rock (or pre-glacial ice) is still solid.

Specific gravity : A measure of how tightly packed the atoms of a substance are. Varies by the mineral or substance. Example, gold has a high specific gravity, while quartz has a low specific gravity. See also "density."

Spines: Horn-like projections formed upon a lava dome.

Spring : The time between winter and summer.

Spring : A surface flow of groundwater which occurs any time the water table intersects the surface.

Stratovolcano: A volcano composed of both lava flows and pyroclastic material. Also called "Composite" volcanoes. Common at convergent boundaries. Excellent examples in the U.S. include Mt. St. Helens, Mt. Shasta, and the other peaks of the Cascade Range of California, Oregon, and Washington.

Striations (glacial) : Grooves eroded into bedrock by rock debris frozen into the base of a glacier.

Strike-slip fault: A nearly vertical fault with side-slipping displacement.

Subduction zone: The zone of convergence of two tectonic plates, one of which usually overrides the other.

Sublimation : The direct change from the solid to the vapor phase (without passing through the liquid phase). Commonly occurs in ice and snow fields on sunny days above the snowline.

Till (glacial) : General term for material deposited by a glacier. See also moraine.

Tsunami: A great sea wave produced by a submarine earthquake, volcanic eruption, or large landslide. Commonly (but erroneously) called a "tidal wave," tsunamis can cause great damage due to flooding of low coastal areas.

Tuff: Rock formed of pyroclastic material.

Vent: The opening at the earth's surface through which volcanic materials reach the surface.

Vesicular basalt: Holes and other openings in basaltic flow which are the result of trapped gas bubbles. Vesicles are often filled at a later date with a wide variety of materials, including, quartz, agate, zeolites, and many other minerals.

Viscosity: A measure of resistance to flow in a liquid (molasses in January has high viscosity while molasses in August has lower viscosity).

Volcanic Neck: Solidified lava that fills the conduit of a volcano. Volcanic necks (also called plugs) are usually more resistant to erosion than the material making up the surrounding cone, and may remain standing as a solitary pinnacle when the rest of the original structure has eroded away.

Vulcan: Roman God of fire and the forge, after whom volcanoes are named.

Weathering (surface) : "Making little ones out of big ones." Waethering includes the processes which mechanically and chemically break down the mountains into little pieces, so they can be eroded and transported to the beach (see Strickler's 3rd Law of GeoFantasy).

Well : A hole dug into the ground in the attempt to intersect water or other subsurface fluids.

Windward : The side facing into the wind. When speaking of a mountain range, these areas are generally cooler and wetter than on the leeward side.


The way Reverse Dictionary works is pretty simple. It simply looks through tonnes of dictionary definitions and grabs the ones that most closely match your search query. For example, if you type something like "longing for a time in the past", then the engine will return "nostalgia". The engine has indexed several million definitions so far, and at this stage it's starting to give consistently good results (though it may return weird results sometimes). It acts a lot like a thesaurus except that it allows you to search with a definition, rather than a single word. So in a sense, this tool is a "search engine for words", or a sentence to word converter.

I made this tool after working on Related Words which is a very similar tool, except it uses a bunch of algorithms and multiple databases to find similar words to a search query. That project is closer to a thesaurus in the sense that it returns synonyms for a word (or short phrase) query, but it also returns many broadly related words that aren't included in thesauri. So this project, Reverse Dictionary, is meant to go hand-in-hand with Related Words to act as a word-finding and brainstorming toolset. For those interested, I also developed Describing Words which helps you find adjectives and interesting descriptors for things (e.g. waves, sunsets, trees, etc.).

In case you didn't notice, you can click on words in the search results and you'll be presented with the definition of that word (if available). The definitions are sourced from the famous and open-source WordNet database, so a huge thanks to the many contributors for creating such an awesome free resource.

Special thanks to the contributors of the open-source code that was used in this project: Elastic Search, @HubSpot, WordNet, and @mongodb.

Please note that Reverse Dictionary uses third party scripts (such as Google Analytics and advertisements) which use cookies. To learn more, see the privacy policy.


System Examples

What is a system and what are the examples? A system is a structure composed of related components that serve in a group to give the final output.

The Solar System

The solar system is the system in the universe where the Earth belongs. The mass of the solar system is found mainly in the sun followed by Jupiter. All planets of the solar system orbit in definite paths similar to discs. The solar system does not only contain the sun and planets but also small rocks, especially those found between Jupiter and Mars (called the asteroid belt). Let’s take a closer look at the Earth’s systems.

Earth systems

The Earth has four main types of systems: (1) geosphere (land system), (2) hydrosphere (water system), (3) atmosphere (air system), and (4) biosphere (life system). The geosphere represents the land and rocks. It forms the external surface and internal structure of the earth, which is made of rocks and minerals. The hydrosphere represents all the water present on the Earth’s surface including salty and freshwater. The major portion of the hydrosphere is saline water (96.5%), which some animals and humans cannot drink if not processed. About three-quarters of the freshwater on earth is found in the form of ice and water vapor while the remaining portion is present in rivers and lakes. The atmosphere is a mixture of gases including oxygen, nitrogen, and to a lesser extent water vapor, hydrogen, ozone, carbon dioxide, and argon. The atmosphere is essential for the existence of life. The atmospheric gases provide protection from the harmful ultraviolet rays of the sun. It also keeps the temperature of the earth in a range suitable for life. Thus, it contributes to the survival of life on Earth.

The biosphere is the living part of the Earth. It includes all living organisms — from unicellular bacteria, archaea, and protists, to multicellular fungi, plants, and animals. The geosphere, hydrosphere, and atmosphere provide an ecosystem to various life forms on Earth.

Earth’s systems are integrated together. They are overlapping so if one system is affected it affects other systems as well. For example, when air (atmosphere) is saturated with water particles (hydrosphere), it rains on the surface of the earth (geosphere).

Raining or snowing may promote erosion of rocks where large rocks are broken down into smaller ones. Consequently, the shape of these large rocks or mountains is changed.

On a larger scale, the interconnection between the Earth’s systems may cause natural phenomenons, such as tsunamis, volcanic eruptions, changes in the chemistry of some oceans, and alterations in the components of the atmosphere. The microbial diversity of the soil may also be altered through time. Human activities, in particular, impact the Earth systems. Burning fossil fuels, for example, causes greenhouse gases (carbon dioxide) to get trapped in the atmosphere. This contributes to global warming and climate change. Improper disposal of wastes has also been the primary factor of pollutions. Read: Pollution in Freshwater Ecosystems – Biology Online Tutorials

Ecological systems

Ecological systems or ecosystems are systems consisting of biotic and abiotic components that function together as a unit. Biotic components are the living organisms whereas the abiotic components include all the non-living components in a system. These living and non-living components are connected together by energy flows and nutrient cycles.

Energy obtained from the sun enters the ecosystem through photosynthesis performed by different plants and algae. Animals feed on plants or on each other. Animals contribute to the flow of energy throughout the system. Moreover, they affect the number of plants and microbes in the system. Decomposers break down dead matter releasing its content in a simpler form in the soil and atmosphere to be used again by plants and microbes.

Ecosystems are influenced by several internal and external factors. Internal factors are exemplified by shading, decomposition, and species present in the system. External factors, in turn, are exemplified by the various materials that form the soil and the atmosphere. For instance, climate affects the structure of an ecosystem by influencing the temperature and the extent of rainfall. It will therefore be a limiting factor as to which organisms can thrive and survive. It determines the availability of energy and water in an ecosystem. As such, it would have also an effect on photosynthesis and, subsequently, on the energy flow within the ecosystem.

Apart from climate, another important factor is the materials with which the soil is formed as they will determine the abundance, and therefore, the availability, of minerals and nutrients. The abundance or shortage of one element of an ecosystem affects the other elements. For example, the availability of nutrients in an aquatic ecosystem affects the production of algae. Thus, it consequently affects the abundance of animals that use algae for nutrition.

Figure 3 The components of the ecosystem are interconnected. See how human activities, such as dumping industrial effluents, fishing, and irrigation, leads to the pollution that disrupts the ecosystem. In this case, the population of fish fauna is depleted due to water pollution. Credit Nilesh Heda – diagram, CC BY-SA 3.0.

Biological systems

Biological systems (definition) are systems that are made up of different biological structures called organs. Organs differ in their actions and structures according to the desired outcome of each system. Examples of biological systems are the respiratory system, digestive system, and circulatory system. The human body consists of the following systems:

    – responsible for one of the vital functions in any living organism, breathing, and gas exchange. The respiratory system consists of the two lungs which are the main respiratory organs, the pharynx, the larynx, bronchi, and the diaphragm. – intakes, digests, absorbs food and nutrients. It breaks down the complex food material into simpler molecules by which the body can benefit from in its different metabolic actions as well as obtaining energy. Moreover, it is responsible for the excretion of wastes. The digestive system is made up of salivary glands (secrete saliva for digestion), esophagus, stomach (stores and digests food), liver, gallbladder (secretes bile responsible for the digestion and breaking down of fats), pancreas (secretes the pancreatic juice), intestines (where most food materials are digested), rectum and anus (responsible for excretion of wastes). – delivers blood containing water, nutrients, and oxygen to all body organs and tissues. Also, it is responsible for collecting wastes from peripheral cells and transporting them to specialized excretory organs. It also contributes to maintaining body temperature and pH. The circulatory system is vital to all other body systems. It is made up of the heart that pumps the blood throughout the whole body, blood, and blood vessels. – responsible for urine excretion and balancing electrolytes and fluids in the body. It consists of the two kidneys, ureters, the bladder, and the urethra. – responsible for the protection and structural support of the body as well as the production of different blood cells from the bone marrow. The skeletal system includes bones, ligaments, tendons, and cartilages. – one of the most essential systems of the body as it controls the homeostasis, growth, and metabolism functions of the body through communicating with different parts of the body via the action of different hormones, such as thyroxin, corticoids, sex hormones, and other hormones secreted from endocrine glands including the adrenal gland, thyroid gland, and parathyroid glands. – responsible for transferring lymph between the blood and tissues. It includes the vessels, tonsils, thymus, spleen, lymph nodes, and lymph. The lymphatic system has an immune function so it protects the body against invading pathogens and foreign bodies. – sends signals through nerves to all body cells and collects information from peripheral nerves when they are exposed to different stimuli to be processed in the brain. It is composed of the brain, spinal cord, and peripheral nerves. – responsible for gamete formation and reproduction. It includes the sex organs of males and females.

Classification systems

In a general sense, a system pertains to a group of related or interdependent unified components of a whole. Another biologically-relevant concept is the classification system. A classification system is a system for classifying organisms. It is a collection of procedures, characteristics, and definitions used to classify and/or identify, living things. As proposed by Carl Woese, living things are classified into three major domains: the Archaea, the Eubacteria (true bacteria), and the Eucarya (Eukarya). Below the domain are other major taxonomic ranks. These taxonomic ranks are kingdom, phyla, class, order, family, genus, and species. The branch of biology that studies the naming, arranging, classifying, and describing organisms into groups and levels is taxonomy.

Both Domains Archaea and Eubacteria include prokaryotic organisms. They differ, however, in their genes and certain metabolic pathways. In essence, archaea although similarly prokaryotic as the bacteria possess genes that indicate that they are more closely related to eukaryotes than bacteria.

Eukaryotes are organisms that belong to Domain Eucarya. Unlike prokaryotes, the eukaryotes have a nucleus and other organelles, such as mitochondria, Gogi apparatus, and endoplasmic reticulum, inside the cell. Within Domain Eucarya, the organisms are further classified into these groups: protists, fungi, plants, and animals.

Protists are unicellular organisms although some of them may appear multicellular because they form colonies. Protozoans, algae, slime molds, and water molds belong to this group. Fungi are mostly multicellular organisms. They occur as filaments (hyphae) that form structures called a mycelium. They are saprophytic and nonphotosynthetic. Mushrooms, mildews, and puffballs are examples of fungi. Yeasts are also fungi but they are single-celled organisms. Plants are autotrophic eukaryotes. They possess chlorophyll (green pigment) that enable them to capture and use light energy for food production (photosynthesis). Animals are heterotrophic eukaryotes. They are multicellular organisms that rely on other organisms for nutrients as they do not have the ability to produce their own food as plants do. Humans belong to the animal group. Below is an example of human taxonomy.

Figure 4: Taxonomy of Human


Watch the video: Genetics glossary (August 2022).