A Central Dogma Molecular Biology Glossary

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 autoradio-
                graphy 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.

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.

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 DNA molecules copied from a mRNA 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 recomb-
                inant cells can be used to produce large quantities of proteins in vitro.

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).

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.

Domain - an independently folding region of a protein with a specific structural of functions role;
           one domain may be an enzyme active site, while another a receptor region. Different exons
           code for the different domains of a protein. 

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...

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.

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.

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. 

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

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

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.

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.

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

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.

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

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.

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 (genes) 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 140C.
                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 70C 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 semipermeable 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.

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 electro-
                phoresing 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.

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.

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.

Tumor Suppressor Gene - a gene whose protein products inhibit cell division, thereby
                preventing uncontrolled cell growth (cancer).

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...

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-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.

 

 

 

 

 
copyright c2001
Charles Mallery,
  Department of Biology,
University of Miami, Coral Gables, FL 33124
Last Update - 11 Nov 2001