A

A band - The broad region that corresponds to the length of the thick filaments.

Abdominal cavity -  The body cavity in mammals that primarily houses parts of the digestive, excretory, and reproductive systems. It is separated from the more cranial thoracic cavity by the diaphragm.

Absorption spectra - a plot of the amount of light absorbed by a purified compound dissolved in solution against the wavelength of visible light   (web)

Acetyl Coenzyme A - the initial compound entering the Krebs Cycle; formed by the breakdown of pyruvate via pyruvate dehydrogenase in the matrix of mitochondria  (web)

Acetylcholine - common neurotransmitters, especially of neuro-muscular junction; binds to post-synaptic receptor, alters permeability to cation allowing depolarization or hyper-polarization of PSM. (web)

Acrosome - organelle-like part at tip of sperm cell, containing acrosomal filaments (MT's) and hydrolytic enzymes that facilitate penetration of egg cell during fertilization (web)

Actin - One of the most common neurotransmitters; functions by binding to receptors and altering the permeability of the postsynaptic membrane to specific ions, either depolarizing or hyperpolarizing the membrane.

A site - One of three binding sites for tRNA during translation, it holds the tRNA carrying the next amino acid to be added to the polypeptide chain; A stands for aminoacyl-tRNA site.

Aminoacyl-tRNA - an energy activated form of an amino acid, used in protein synthesis, consisting of an amino acid linked via a high energy phosphodiester bond to the 3'OH group of the terminal adenine of a tRNA molecule.

Anticodon - sequence of 3 nucleotides in a tRNA molecule that is complimentary to the mRNA codon. During protein synthesis, base pairing between an anticodon and a codon aligns the aminoacyl-tRNA for addition of its amino acid to the growing polypeptide.

Antisense RNA - An RNA molecule with sequence complementarity to a specific RNA transcript of mRNA, whose binding prevents processing of the transcript or translation of the mRNA.

Autoradiography - is the detection of radioactive isotopes on X-ray film. In autoradiography the specimen is the source of the radiation. The emissions of the isotopes form a latent image on the film which produces a final image upon development.

B

Bacterial Artificial Chromosome (BAC) - A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on the naturally occurring F-factor plasmid found in the bacterium E. coli.

C

5'-Cap - a post-transcriptional modification of mRNA in which 7-methylguanosine (m7-GDP, or m7-Gpp) is added to the 5' end of a mRNA molecule. This capping of the 5'-end with G happens in a reverse nucleotide fashion, thus the 5' end functionally becomes a 3' end.  Initiation factors recognize capped mRNAs during the early phases of translation, or protein synthesis.

cDNA (complementary DNA) - a double-stranded DNA molecule copied from isolated mRNAs by the enzyme reverse transcriptase and therefore lacks the introns present in nuclear (genomic) DNA. Sequencing of cDNA permits the amino acid sequence of the encoded protein to be deciphered.  The expression of cDNAs in recombinant cells can be used to produce large quantities of proteins in vitro. mRNA is converted into DNA (copy DNA, cDNA) by annealing oligo-dT to the 3' poly-A tail that occurs on all eucaryotic mRNA. After the dTs bind to the As, the enzyme reverse transcriptase" is used to read the RNA into DNA (to isolate mRNA's)   (to synthesize cDNA) (web site of research protocols for cDNA)

Cistron - a genetic unit (sequence of DNA nucleotides) that codes for a single polypeptide; an older term of bacterial genetics that is equivalent to the term "gene".

Clone - a population of genetically identical cells or DNA molecules all descended from a single progenitor. Also used to describe viruses or organisms that are genetically identical and descended from a single cell.

Cloning vector - An autonomously replicating genetic element used to carry a cDNA or a fragment of genomic DNA into a host cell for the purpose of copying (cloning) that genetic element.  Commonly used cloning vectors include bacterial plasmids and modified bacteriophage DNAs.

Coacervate - A coacervate is simply a liposome with enzymes in the lipid bilayer and inside.

Codon (triplet) - a sequence of 3 nucleotides in DNA or mRNA that specify a particular amino acid during translation. There are 64 possible codons based upon a 4 letter genetic alphabet (A, T, C, G), 61 which spell amino acids and 3 which specify stops (no amino acid).

D

Degenerate code - in reference to the genetic code, having more than one codon    (triplet sequence) specifying a particular amino acid.

DNA Fingerprint - or a DNA profile, is a restriction fragment electrophoretic pattern made from biological samples. DNA is extracted and cut into segments using restriction enzymes and are separated by electrophoresis. The segments are radioactively tagged to produce a visual pattern known as an autoradiograph, or "DNA fingerprint, on X-ray film. DNA fingerprints are used, especially in law enforcement, to identify suspects from hair, blood, semen, or other biological materials found at the scene of a violent crime. It depends on the fact that no two people, save identical twins, have exactly the same DNA sequence, and that although only limited segments of a person's DNA are scrutinized in the procedure, those segments will be statistically unique.

DNA library - a collection of cloned DNA molecules consisting of fragment pieces of the entire genome (genomic library) or of DNA copies of all the mRNAs produced by a cell type (cDNA library) inserted into a suitable cloning vector.

Downstream - for a gene: toward the direction the RNA polymerase moves, which is toward the 5' end of the DNA template strand.  By conventions, the +1 position is the 1st transcribed nucleotide, others are +2, etc...

E

Elongation factor (EFs)- one of a group of regulatory proteins required for translation of mRNA.

Enhancer sequence - a regulatory eucaryotic DNA sequence (rarely found in procaryotes) that is often located a good distance upstream and the gene it controls.  The binding of enhancer proteins to these sequences helps regulate the rate of transcription of its associated gene.

Epitope - Epitope tagging is used for the detection and purification of expressed proteins. Unique amino acid sequences (tags) fused to the N-terminal or C-terminal of an expressed protein.  An expressed protein in one made by insertion of a nucleotide sequence into a plasmid that is then inserted into a cell. Epitope tags make it easier for antibody detection and do not cause structural or functional perturbations. The original FLAG sequence asp-tyr-lys-asp-asp-asp-asp-lys is recognized by 2 monclonal antibodies.

Exon - gene segments of a eucaryotic gene (or its primary transcript) that eventually reaches the cytoplasm as part of a mature (processed) mRNA.

Expression vector - a modified plasmid molecule or virus that carries a gene piece or cDNA into a suitable host cell and when there directs the synthesis of its encoded protein.

F

Fibroblast - the principal non-motile cells of connective tissue; fibroblasts are large, flat, elongated (spindle-shaped) cells possessing processes extending out from the ends of the cell body. Fibroblasts produce tropocollagen, which is the forerunner of collagen, and ground substance, an amorphous, gel-like matrix that fills the spaces between cells and fibers in connective tissue.

G

Galaxy - any of the systems of stars and interstellar matter that make up the Cosmos. Many such assemblages are so enormous that they contain hundreds of billions of stars. The Galaxy contains three main structural components: (1) a thin flat disk of stars, gas, and dust, (2) a spheroidal central bulge containing only stars, and (3) a quasi-spherical halo of old stars.

Genomic Library - a set of thousands of DNA fragments (from one type of endonuclease cutting) from an organism's whole genome, each fragment carried on a plasmid molecule, or in a phage particle, or other cloning vector.

H

Helicase - an enzyme that moves along a DNA molecule and helps separate (unwind) the two helical strands.

The Human Genome Project (HGP), composed of the DOE and NIH Human Genome Programs, is the national coordinated effort to characterize all human genetic material by determining the complete sequence of the DNA in the human genome. The ultimate goal is to discover the sequence of all human genes.

Hybridization - association of 2 complementary polynucleotide strands to form a double stranded molecule. Depending on the complementarity 2 DNA, 2 RNA, or 1 DNA & 1 RNA strand can be paired. This technique is used to measure the degree of complementarity between related species.

Hydrogen Ion Pump [H+] - a membrane bound protein that transports hydrogen ions against a concentration gradient and creates a positive charge on one side of a membrane.

I

Initiation factor (IF) - one of a group of regulatory proteins that promote the proper association of the ribosome and the mRNA at the start of protein synthesis.

Initiator codon - a eucaryotic promoter triplet sequence where RNA polymerase II binds and specifies the point where the initiation of transcription occurs.

Intron - a part of a primary transcript (hnRNA), or the DNA encoding it, that is spliced out during RNA processing and whose sequence is not included in the mature functional mRNA that ends up in the cytoplasm.

J

Jacob, Francois - study of the mechanisms responsible for the transfer of genetic information as well as the regulatory pathways which, in the bacterial cell, adjust the activity and synthesis of macromolecules (web).

K

L

Label - a radioactive atom, or fluorescent chemical group, incorporated into a molecule in order to spatially locate that molecule or follow it through a reaction or purification scheme.

Ligase - an enzyme that links together the 3' end of one nucleic acid strand with the 5' end of another, thereby forming a continuous strand.

Liposome - Liposomes are also droplets that form but differ in the respect that the ingredients include certain lipids.  Hence, liposomes have a lipid bilayer separating proteins from the environment.  Liposomes behave dynamically by engulfing smaller liposomes then splitting into two smaller liposomes. Combining Liposomes and Enzymes: creates the ability for the liposome to absorb a substrate and "spit out" a transformed product acted upon by the enzymes in the lipid bilayer. A coacervate is simply a liposome with enzymes in the lipid bilayer and inside.

Leucine Zipper - a motif of dimeric eucaryotic transcription factors characterized by a C-terminal coiled-coil dimerization domain and an N-terminal DNA binding domain.

M

Motif - in proteins, a structural unit exhibiting a particular 3D architecture that is found in a group of proteins and is often associated with a specific protein function.

Mutation -  a permanent, hereditable change in the nucleotide sequence of the DNA of a chromosome, usually in a single gene that may lead to a change in the function of a protein.

N

Northern blot - a technique for detecting specific RNAs separated by gel electrophoresis by hybridizing a labeled DNA probe to the RNAs.

O

Oncogene - a gene whose product protein is involved in either transforming cells in tissue culture or in inducing cancer in animals.  Most oncogenes are mutant forms of  normal genes (proto-oncogenes) in the control of cell growth or division.

Operator - a short DNA sequence in bacterial or viral genomes that bind a repressor protein and control the transcription of an adjacent gene.

Operon - in bacterial DNA, a cluster of contiguous genes transcribed from one promoter that gives rise to a single polycistronic mRNA.

P

PCR [polymerase chain reaction] - a technique, created by Kerry Mullis, for amplifying a specific DNA segment via a series of multiple cycles of DNA synthesis from short oligonucleotide primers followed by brief heat treatment to separate the complementary strands, and repeats, etc...

Plasmid - small, circular extrachromosomal DNA molecule capable of autonomous replication within a cell; a commonly used cloning vector.

Point Mutation - a change of a single nucleotide (or a few nucleotides) in DNA, often in a region coding for a protein that may result in the formation of a codon specifying a different amino acid or stop codon, or a shift in the normal reading frame.

Poly-A - a linear strand of 20 to 200+ adenines added to the 3' end of a processed mRNA by the enzyme Poly(A) Polymerase.  There is no complementary sequence of T's in the parental DNA that the mRNA is copied from. Functions to protect mRNA.

Primary Transcript [hnRNA] - an initial RNA molecule produced in the nucleus from the direct copying of a gene DNA template, that contains Introns and Exons.  Many primary transcripts undergo RNA processing (cuts up to smaller pieces) to form molecularly active RNA pieces.

Primase - a specialized RNA polymerase enzyme that synthesizes short stretches of RNA, complimentary to the sense strand of replicating DNA, to be used as primer molecules in DNA replication.

Primer - a short piece of RNA containing a 3'-OH end that bases pairs with a complimentary template strand  and functions as the starting point for the addition of new DNA nucleotides to the growing DNA strand.

Probe - a sequence defined RNA or DNA fragment/piece, that is made radioactive or chemically labeled (for ease of tracking) that is used to detect native specific nucleic acid sequences by hybridizing with these pieces.

Promoter - a unique DNA sequence [-TATAAAA-] that determines the point where RNA polymerase binds to initiate transcription.     TATA box - a highly conserved sequence in the promoter of many eucaryotes where the transcription-initiation complex assembles.

Proteinoids - Proteinoids are protein-like molecules formed inorganically from amino acids. Some theories of abiogenesis propose that proteinoids were a precursor to the first living cells.  The inorganic polymerization of amino acids into proteins through the formation of peptide bonds was thought to occur only at temperatures over 140°C. However, the U. Miami biochemist, S. W. Fox, discovered that phosphoric acid acted as a catalyst for this reaction. He was able to form protein-like chains from a mixture of 18 common amino acids at only 70°C in the presence of phosphoric acid, and dubbed these protein-like chains protenoids.

Protobionts - Protobionts are excitable, metabolically active, inaccurately reproducing protein clusters.  These clusters form when their protein parts are mixed with cold water:  they self-assemble into microspheres.  Protobionts also can release voltage like a neuron because some protobionts store energy through a similar method of membrane potential as organelles.  If coated with a impermeable membrane, a protobiont will swell and contract osmotically when in solutions of differing salt concentrations.  The protobiont shares its weak catabolic capabilities with the liposome.

Proto-oncogene - a normal cellular gene that encodes a protein usually involved in the regulation of cell growth or division and that may be mutated into a cancer promoting oncogene.

Pulse Chase Experiment - a type of experiment in which a radioactive isotope (14C, 32P, 3H) is added to a cell for a brief period of time (the pulse) and then is replaced  with an excess amount of the unlabeled form of the same isotope (the chase). These types of experiments are used to detect inside an actively metabolizing cell the cellular location of the isotopic molecule or to follow its metabolic fate over time.

Q

R

Radiocarbon (C-14) dating - method of age determination that depends upon the decay of isotope of 14carbon to nitrogen. Carbon-14 has a half-life of 5,730 years, thus from the time of death of a living system the amount of 14C is reduced by half every 5,730 years, thus the ability to date.

Reading Frame - The sequence of nucleotide triplets (codons) that run from a specific start codon in a mRNA to a stop codon. Many mRNA's can be translated into many different polypeptides by being read in two different reading frames.

Recombinant DNA - any DNA molecule formed by the joining of DNA fragments from two different sources. Commonly made artificially by cutting DNA molecules with restriction enzymes and then joining the resulting DNA fragments from the different sources with DNA ligase.

Reductionism - Reductionism is the belief that complex phenomena can be "reduced" to simpler physical processes, which themselves can in theory be reduced to the simplest level of physical explanation, where elementary particles interact according to the laws of physics. Thus Reductionism is a view that asserts that entities of a given kind are collections or combinations of entities of a simpler or more basic kind.

Replicase - A type of RNA polymerase which uses RNA molecules as a template for making new RNA molecules (in a process which works exactly the same as the replication of DNA molecules).   Synonym: RNA replicase.

Restriction Endonuclease - any enzyme that recognizes and cleaves a specific short DNA sequence, the restriction site, in double stranded DNA molecules. These enzymes are native to bacteria where they serve to prevent phage DNA infection.

Restriction Fragment Length Polymorphism (RFLP) - sequence differences on the two homologous chromosomes which results in a different band pattern of the DNA fragments made from treating the DNA with a restriction enzyme. Useful in genetic testing.

Restriction Map - a type of physical "map" of the banding pattern seen in gel electropherograms made from treating chromosomal DNA with restriction enzymes and then electrophoresing the fragments... a kind of "fingerprint" of the DNA fragments.

Restriction Site - a specific, and unique, sequence of nucleotides on a DNA strand that is recognized as a "cut site" by a restriction endonuclease enzyme.

Retrovirus - a eucaryotic virus containing an RNA genome that replicates in cells by first making a DNA copy of its RNA. The proviral DNA is inserted into cellular chromosomal DNA, and gives rise to further genomic RNA, as well as the mRNAs for the viral proteins.

Reverse Transcriptase - an enzyme found in retroviruses that catalyze synthesis of a double-stranded DNA from a single-stranded RNA template.

Ribozyme - an RNA molecule with catalytic (enzyme-like) activity.

RNA Processing - the various chemical modifications that occur to many, but not all, primary transcripts (hnRNA) to produce functional, mature RNA molecules.

RNA Splicing - a process that results in the removal of introns and the joining together of exons in mRNAs; also called the template strand.

S

Sense Strand - the strand of the two DNA strands that is read and copied into a functional RNA product molecule.

Southern Blot - a technique for detecting specific DNA sequences separated by gel electrophoresis via hybridization to a previously radioactively labeled nucleic acid probe.

Splicesome - a large (about same size as a ribosome) ribonucleoprotein complex (made of RNA & protein) that cuts up a primary transcript to assemble the exons into a mature functional mRNA.

Supercoils - DNA regions in which the DNA helix is twisted back upon itself several times.

Suppressor Mutation - a mutation that reverses the phenotype of a previous mutation.

Svedberg Unit (70s) - A unit equal to 10-13 second used for expressing sedimentation coefficients of macromolecules. Symbol S. Named for Theodor Svedberg, Swedish chemist, 1884-1971, inventor of the ultracentrifuge and winner of the Nobel prize for chemistry in 1926 for his work on disperse systems.

T

TATA box - a highly conserved sequence in the promoter of many eucaryotes where the transcription-initiation complex assembles.

Telomere - the end region of a eucaryotic chromosome that contains telomeric sequences that are replicated in a special process and thus counteracting the tendency of a chromosome to become shorter during each round of replication.

Termination Factor - one of several proteins that act to terminate protein synthesis by recognizing a STOP codon in mRNA and causing the release of the ribosomal subunits.

Toposiomerase - a class of enzymes that control the number an topology of supercoils in DNA. Type I toposiomerase cut one DNA strand, rotate it about the other, and reseal the cut ends. Type II topoisomerases cut and reseal both DNA strands.

Transcription Factor - proteins required to initiate or regulate transcription in eucaryotic cells. They participate in the formation of initiation complexes near the initiator codon.

Transcription Unit - a DNA region bounded by a start codon and a termination codon that is transcribed into a primary transcript;  a gene.

Transformation - a permanent, hereditable change in a cell that results from the uptake and incorporation of "foreign" DNA into the host cell's genome.

Transgene - a cloned gene that is introduced and incorporated into a plant or animal and is subsequently passed along to successive generations.

Transposon - a relatively long mobile DNA piece, in procaryotes and eucaryotes, that moves within the structure of the genome, by a mechanism involving DNA synthesis and transposition.

U

Universe  the whole cosmic system of matter and energy of which the Earth is a part. in astronomy, the entire physical universe consisting of all objects and phenomena observed or postulated.

Upstream - the direction of a DNA molecule opposite tot he direction that the RNA polymerase normally moves during transcription. By convention, nucleotide upstream from the initiator codon are designated -1, -2, etc...

V

W

Western Blot - a technique for detecting specific proteins separated by gel electrophoresis                 by tagging them with labeled antibodies.

Wild Type - the normal, nonmutant form of the phenotype of gene.

X

X-ray Crystallography - a technique for determining the 3D structure of macromolecules (especially proteins and nucleic acids) by passing x-rays through a crystal of the purified macromolecule and analyzing the diffraction pattern that result.

Y

Z

Zinc-finger - a conserved DNA-binding motif composed of protein domains folded around a zinc ion that is present in several eucaryotic transcription factors.

copyright c2007   Charles Mallery,  Department of Biology, University of Miami, Coral Gables, FL 33124   Last Update - December 21, 2006