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Glossary of Terms

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

A

Atom
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 particles (electrons).

Acquired 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.

AIDS-related Complex (ARC)
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".

Analogy (adj. Analogous)
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 similar functions).

Antibody
A substance (e.g. a virus or bacterium) that causes an immune system response.

Antigen
A substance that stimulates the production of antibodies.

AutoDock
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.

B

Bacteria (singular: Bacterium)
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.

Bioinformatics
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.

Biotechnology
The industrial use of living organisms or biological techniques developed through basic research.

C

Cell
The smallest membrane-bound biological unit capable of replication. Includes cooperative components of tissue or organs as well as homeostatic microorganisms.

Chromosomes
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.

Computational science
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.

Computer Modeling
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 disease.

Computer Simulation
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.

D

Data
Information organized for analysis

Database
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 sets.

Deoxyribonucleic Acid (DNA)
A nucleic acid having a very complicated structure and forming the main constituent of the chromosomes of living cells

Disease
A condition of an organism that impairs normal physiological function. Also see Infectious Disease.

Docking
A procedure where computer modeling is used to simulate interactions between molecules and the prospective efficacy of drug candidates.

E

Entropia Network
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 applications.

Enzymes
Proteins that act as catalysts, speeding the rate at which biochemical reactions proceed but not altering the direction or nature of the reactions.

F

Fomite
A pathogen contaminated object can transfer the pathogen to a host.

G

Gene
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.

Genbank
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/

H

HIV
see "Human Immunodeficiency Virus"

Homology (Homologous)
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 therefore vestigial.

Homology modeling
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.

Hormone
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.

Human Immunodeficiency Virus (HIV)
A retrovirus that causes immune system failure and debilitation. HIV is spread through direct contact with bodily fluids.

I

Immune System
The cells and tissues which are responsible for recognizing and attacking foreign microbes and substances in the body.

Immunoglobulin
An antibody protein that is generated in response to and will bind to a specific antigen.

Infectious Disease
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.

Internet
That thing you're surfing on.

J

Joining Segment
A small DNA segment that links genes to yield a functional gene encoding an immunoglobulin.

K

Karyocyte
General scientific term for any cell with a nucleus.

L

Ligand
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an 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.

M

Microorganism (microbe)
An organism (including viruses) too small to be seen with the naked eye.

Molecule
Two or more atoms joined together by chemical bonds.

N

Nucleic Acid
A large molecule composed of nucleotide subunits.

Nucleotides
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.

O

Organ
A group of tissues which work together as a single unit to perform a particular function within a multicellular organism.

P

Pathogen
A microbe or some type of other organism that can cause disease.

Protein
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, and antibodies.

Q

Quantum Speciation
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 a treatment.

R

Rational Drug Design
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.

Ribonucleic Acid (RNA)
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.

S

Sexually Transmitted Disease (STD)
A disease that is transmitted during sexual intercourse (anal, oral, or vaginal). HIV is often contracted through sexual intercourse.

Strain
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.

T

Tissue
A group of cells that perform the same or similar function within a multicellular organism.

U

UI RNA
A common type of small nuclear RNA that serves to splice and/or remove exons of messenger RNA.

V

Vestigial
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.

Virus
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 virus.

W

Wandering Macrophage
A macrophage that leaves the blood and migrates to infected tissue.

X

X Chromosome
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 female-determining.

X-ray Crystallography
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.

Y

Y Chromosome
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 chromosomes.

Z

Zymosis
Any infectious disease.

Many 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.