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Glossary of Terms
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This is the tiniest particle of matter that retains the chemical properties
of an element; atoms are typically composed of neutral subatomic particles
(neutrons), positively-charged particles (protons) and negatively-charged
Immunodeficiency Syndrome (AIDS)
An epidemic disease caused by an infection by human immunodeficiency virus
(HIV-1), a retrovirus that causes immune
system failure and debilitation and is often accompanied by cancers
and secondary infections such as but not limited to tuberculosis. AIDS
is spread through direct contact with bodily fluids.
A set of symptoms, such as lymph node enlargement, fever, loss of weight,
diarrhea, and minor opportunistic diseases associated with a weakened
immune system, which indicates
a less severe form of infection by the HIV
virus than AIDS itself. In some cases
this is diagnosed as a precursor to AIDS. Also known as "AIDS-related
condition" or "AIDS-related syndrome".
Two anatomical structures or behavioral traits within different and
unrelated organisms which perform the same functions in each organism
but which did not originate from an ancestral structure or trait that
the organisms' ancestors had in common. Instead, the structures or traits
arose separately and then later evolved to perform the same function (or
A substance (e.g. a virus or bacterium)
that causes an immune system response.
A substance that stimulates the production of antibodies.
Three separate programs used to generate and simulate molecular interactions:
AutoDock performs the docking of the ligand
to a set of grids describing the target protein;
AutoGrid pre-calculates these grids; and AutoTors sets up which bonds
will treated as rotatable in the ligand.
Unicellular prokaryotic organisms that reproduce by cell division;
usually have cell walls; can be shaped like spheres, rods or spirals;
and can be found in virtually any environment.
The computerized annotation of genomic and biological information and
data (databases), and the transformation and manipulation of these data
through the use of software tools to produce more sophisticated understanding
about biological and medical processes. Bioinformatics is emerging as
an area of dramatic growth due to its anticipated impact on the health
sciences, medicine, and biotech industrial applications. It is also being
targeted as an exciting disciplinary area for new university degree programs.
The industrial use of living organisms or biological techniques developed
through basic research.
The smallest membrane-bound biological unit capable of replication. Includes
cooperative components of tissue or organs as well as homeostatic microorganisms.
The self-replicating genetic structures of cells containing the cellular
DNA that bears in its nucleotide sequence the linear array of genes. In
prokaryotes, chromosomal DNA is circular, and the entire genome is carried
on one chromosome. Eukaryotic genomes consist of a number of chromosomes
whose DNA is associated with different kinds of proteins.
Scientific investigation based on the use of computational simulations
(see next glossary item) that codify understanding of some natural phenomenon,
particularly one that can't be studied in a laboratory setting such as
cosmological phenomena. Such work can include learning more about a particular
chemical interaction in the human body (such as how molecules dock with
other as in this project), predicting the most likely path of a hurricane,
or designing materials to have particular characteristics under certain
circumstances such as stiffness, flexibility, or durability. Often described
as the "third mode" of science in additional to laboratory and theoretical
work. Often used in tandem with observational science to validate codes.
For example, observed data can be used as input parameters to a code,
then the code's output compared with observed data taken at a later time
step in the course of a natural event, such as in the progression of a
hurricane or an earthquake. This process, then, is used to verify-or,
more commonly, correct-the accuracy of the code to that it can be applied
with greater certainty to predict the course of such events in the future.
The construction of patterns using raw data to simulate an object or the
interaction of objects using a computer. In the case of Bioinformatics,
computer modeling is used to determine the size, shape, and interaction
of certain compounds in order to develop treatments associated to a specific
A software program that runs on any size computer that attempts to simulate
some phenomenon based on a scientist's conceptual and mathematical understanding
of the phenomenon. The scientist's conceptual understanding is reduced
to an algorithmic or mathematical logic, which is then programmed in one
of many programming languages (Fortran, C, C++, etc.) and compiled to
produce a binary code that runs on a computer. Also, the act of running
such a code on a computer.
Information organized for analysis
A collection of data arranged for ease of retrieval by a computer. Data
can also be stored in a manner where it is easily compared to existing
A nucleic acid having a very complicated
structure and forming the main constituent of the chromosomes of living
A condition of an organism that impairs normal physiological function.
Also see Infectious Disease.
A procedure where computer modeling
is used to simulate interactions between molecules
and the prospective efficacy of drug candidates.
The network of PCs on the Internet linked by Entropia 2000 that is used
as a virtual high-performance supercomputer to run demanding computations
supporting scientific investigation, philanthropic causes, and commercial
Proteins that act as catalysts, speeding the rate at which biochemical
reactions proceed but not altering the direction or nature of the reactions.
A pathogen contaminated object can transfer the pathogen to a host.
The fundamental physical and functional unit of heredity. A gene is an
ordered sequence of nucleotides located in a particular position on a
particular chromosome that encodes a specific functional product.
A large database and data repository of nucleic
acid and protein sequences at
the National Library of Medicine (USA). http://www.ncbi.nlm.nih.gov/
see "Human Immunodeficiency Virus"
Two anatomical structures or behavioral traits within different organisms
which originated from a structure or trait of their common ancestral organism.
The structures or traits in their current forms may not necessarily perform
the same functions in each organism, nor perform the functions it did
in the common ancestor. They may even have become completely unused and
The computational study of proteins
based on comparing the degree of similarity between their amino acid sequences.
As the degree of similarity rises, so too does the likelihood of the proteins
sharing a similar three-dimensional structure, and, therefore, similar
function. Commonly used in a situation in which a scientist is trying
to determine more about an unfamiliar protein by comparing it against
a protein with known structure and function.
A biochemical substance that is produced by a specific cell or tissue
and causes a change or activity in a cell or tissue located elsewhere
in an organism.
Immunodeficiency Virus (HIV)
A retrovirus that causes immune system failure and debilitation. HIV is
spread through direct contact with bodily fluids.
The cells and tissues which are responsible for recognizing and attacking
foreign microbes and substances in the body.
An antibody protein that is generated in response to and will bind to
a specific antigen.
Any of many diseases or illnesses (caused by bacteria
or viruses) that can be transmitted
from person to person or from organism to organism. For instance, the
common cold and AIDS are infectious diseases,
whereas illnesses such as diabetes and gout are not.
That thing you're surfing on.
A small DNA segment that links genes
to yield a functional gene encoding an
General scientific term for any cell
with a nucleus.
A molecule that binds to another molecule, used especially to refer to
a small molecule that binds specifically to a larger molecule, e.g.,
antigen binding to an antibody
or a hormone binding to a receptor.
In the case of drug design, a ligand is a candidate drug molecule.
An organism (including viruses) too small to be seen with the naked eye.
Two or more atoms joined together by chemical bonds.
A large molecule composed of nucleotide
Subunit of DNA or RNA
consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine
in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule,
and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands
of nucleotides are linked to form a DNA or RNA molecule.
A group of tissues which work together
as a single unit to perform a particular function within a multicellular
A microbe or some type of other
organism that can cause disease.
A large molecule composed of one
or more chains of amino acids in a specific order. This order is determined
by the base sequence of nucleotides in the gene coding for the protein.
Proteins are required for the structure, function, and regulation of the
body's cells, tissues, and organs, and each protein has unique functions.
Examples are hormones, enzymes,
The rapid evolution of a new species from a small population that is partially
or totally isolated from the parent population; usually involves a few
mutations that have a large impact on the organisms' observable physical
traits. Many viruses (such as AIDS)
perform this type of speciation, which increases the difficulty of finding
Structure-based drug design that relies heavily upon computer modeling
to modify an existing drug or design a new drug which will interact specifically
with a selected molecular target important in disease progression.
A compound having a complicated, single-strand structure found in the
nucleus, cytoplasm, and ribosome's of all living cells and functioning
in the synthesis of proteins.
Transmitted Disease (STD)
A disease that is transmitted during
sexual intercourse (anal, oral, or vaginal). HIV
is often contracted through sexual intercourse.
A population of cells that are descended
from one single cell. Can also refer to a virus
that has descended from a particular type of a specific virus.
A group of cells that perform the same
or similar function within a multicellular organism.
A common type of small nuclear RNA that serves to splice and/or remove
exons of messenger RNA.
Refers to an organ or part which is greatly reduced from the original
ancestral form and is no longer functional. An example of this would be
the human appendix.
A noncellular biological entity that can reproduce only within a host
cell. Viruses consist of nucleic acid covered by protein;
some animal viruses are also surrounded by membrane. Inside the infected
cell, the virus uses the synthetic capability of the host to produce progeny
A macrophage that leaves the blood and migrates to infected tissue.
A sex chromosome found in certain animals where the male is the heterogametic
sex. In the XY set of sex chromosomes, the female has two X chromosomes
and the male has only one (and usually also a Y
chromosome). In plants which use the XY system, this chromosome is
A technique of determining a molecule's
three-dimensional structure by analyzing the x-ray diffraction patterns
of crystals made up of the molecule in question.
A sex chromosome where the male
is the heterogametic sex. The Y chromosome causes the individual to become
male in most mammal species and carries few other genes besides those
dictating sperm development and triggering appropriate hormonal output.
It is part of the XY set of sex chromosomes, where the male has only one
X chromosome and usually a Y chromosome, and the female has two X
Any infectious disease.
of the terms used in this glossary have been colleted from BioTech Resources
Web Project at the University of Texas Institute for Cellular and Molecular
Biology. For a more comprehensive list and a searchable database of terms,
go to http://biotech.icmb.utexas.edu.