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 Radiation
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).
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