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.
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 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 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.