Eurofins MWG Operon's Glossary of Biotechnical Terms
-#-
3’ End: See “3’ Terminus.”
3’ Terminus: the end of a polynucleotide
chain that has a 3’-hydroxyl group left unbound.
3’ Untranslated Region (UTR): the portion
of an mRNA from the 3’ end to the position of the last codon used in translation.
5’ End: See “5’ Terminus.”
5’ Terminus: the
end of polynucleotide chain that has a 5’-hydroxyl group left unbound.
-A-
A260/280: a ratio useful for measuring
impurities in solutions. For pure genomic DNA in solution, OD at 260 is twice what
it is at 280. Any increase in this ratio indicates the presence of impurities. For
oligos, A260 depends on the base composition since the extinction coefficients
for guanine and adenine are much higher than those of thymine and cytosine. For
highly purified oligos, the A260/280 ratio ranges from 1.4 to 2.2, depending
on the base composition.
Absorbance (A): the extent
to which a solution absorbs UV light, as measured in UV spectroscopy. This is useful
because the absorbance of a solution is directly proportional to the concentration
of that solution.
Absorbance Unit (AU): the unit of absorbance,
as used in UV spectroscopy.
Absorbance Units Full Scale (AUFS): a term
used in HPLC to describe the sensitivity of a detection system which measures UV
absorbance. In a typical HPLC system, a chart recorder pen moves across a moving
chart paper to record the absorbance. The pen will deflect to full scale when the
detector measures a previously specified absorbance.
Acetic Acid: a simple carboxylic acid. In its pure form it is
a strong acid and will cause burns to unprotected skin and eyes.
Acetic Anhydride: a simple acid anhydride. Acetic anhydride is
corrosive, flammable, and its vapor is irritating to the eyes and upper respiratory
tract. In oligonucleotide synthesis, acetic anhydride is part of the capping reaction.
Acetonitrile: an organic solvent. Acetonitrile is absorbed through
oral, dermal, or inhalation exposure and can pose a serious health risk. It is commonly
used as a solvent in oligonucleotide synthesis due to its lack of reactive groups.
Acetyl Group: an organic functional group consisting of a carbon
with both a methyl group and double bonded oxygen.
Acetylation: a reaction that introduces an acetyl functional
group into an organic compound. In oligonucleotide synthesis, acetylation is used
in the capping step.
Acid: any chemical compound that, when dissolved in water, produces
a solution with a pH lower than 7.
Acrylamide Gel: a polymer gel used in electrophoresis to measure
the size of DNA or protein. Acrylamide gels are especially useful for high resolution
separations of DNA.
Adenine (A): a purine
nucleobase. It is one of four nucleobases that comprise the nucleic acids DNA and
RNA. Adenine binds to thymine (DNA) or uracil (RNA).
Adenosine (A): a nucleoside. It is one
of four nucleosides that comprise RNA. Adenosine consists of adenine attached to
a ribose sugar.
Affine Gap: any maximal, consecutive
run of spaces in a single string of a given alignment in a similarity score. Gaps
help create alignments that better conform to underlying biological models and more
closely fit patterns that one expects to find in meaningful alignments. The idea
is to consider the number of continuous gaps and not only the number of spaces when
calculating an alignment. Affine gaps contain a component for gap insertion and
a component for gap extension, where the extension penalty is usually much lower
than the insertion penalty. This mimics biological reality as multiple gaps would
imply multiple mutations, but a single mutation can lead to a long gap quite easily.
Anion: an ion with a negative net charge.
Alkaline: a type of base formed as a carbonate, hydroxide or
other basic ionic salt from an alkali metal or alkali earth metal element.
Alkaline Phosphatase: See “Bacterial
Alkaline Phosphatase.”
Alkane: a hydrocarbon in which all carbons are connected by only
single bonds.
Alkyl Group (R): a hydrocarbon group
with only single bonds.
Allele: a number of alternate forms of a gene occupying a given
locus on a chromosome. For each gene, there are two alleles, one from each parent.
Alpha (α): the first letter in the
Greek alphabet. In chemistry it refers to the first member of a series of atoms
or residues.
α-Helix: the spiral structure of a double-stranded polypeptide
chain. This provides for maximal hydrogen bonding between the two chains. It is
a common secondary protein structure.
Alternative Splicing: process where exons can be retained in
the mature mRNA or targeted for removal in different combinations to create a diversity
of proteins encoded by one gene.
Amide: an organic functional group characterized by a carbonyl
group linked to a nitrogen atom.
Amine: an organic compound or functional group containing a nitrogen
atom. The substituents may be either hydrogen atoms or other functional groups.
Amino Acid: any molecule that contains both amine and carboxylic
acid functional groups. These are the building blocks of peptides or proteins. There
are 20 common amino acids. Except proline, all amino acids have the same general
structure differing only in their side groups.
For the structures of 20 common amino acids see Appendix C .
Amino Acid Sequence: the linear order of the amino acids in a
peptide or protein.
Amino Group: an organic functional group characteristically basic
in nature as it tends to accept protons. It is a primary amine group.
Amino Linker (L):
used to join a modifier to the oligonucleotide or to attach an oligonucleotide to
a surface. The group contains a primary amino group attached to a carbon chain of
specified length. The carbon chain helps to keep the amino group spatially separated
from the oligonucleotide.
Amino Terminal: the end of a polypeptide
chain that has a free amino group. It is often referred to as the N-terminal.
Ammonia: a gaseous compound. It is toxic and corrosive to some
materials. It has a characteristic pungent odor. In oligonucleotide synthesis, aqueous
ammonia is used in the deprotection process to hydrolyze the amide and ester bonds
connected to various protecting groups, this process is called ammonolysis.
Amphipathic: the property of a molecule which has both hydrophobic
and hydrophilic regions.
Amphoteric: a quality in which a molecule is able to act as either
an acid or a base.
Amplification: a process of increasing the number of copies of
a specific DNA or RNA fragment. It can be done in vivo or in vitro.
Angstrom (Å): a unit of length used
to describe atomic dimensions. 1Å = 1.0 × 10e-10m.
Annealing: a process of combining two complementary single stranded
nucleic acids to make a double stranded product.
Analog: a compound derived from another compound, often different
by only one element.
Anticodon: a sequence of three nucleotides in a tRNA molecule
that are complementary to the three-nucleotide codon on an mRNA molecule. The anticodon
is matched to a specific amino acid that is covalently attached to the tRNA molecule.
Antigen (Ag): a molecule, or part of a
molecule, that stimulates the immune system to produce antibodies. Most antigens
are proteins. To study antigens, it is often convenient to use synthetic peptides
to represent one part of an entire protein.
Antiparallel: a term used to describe double stranded DNA that
runs in opposite directions. One is 5’ to 3’ while the other is 3’
to 5’.
Antisense Strand: a strand of
DNA complimentary (reverse complement) to the sense strand. In a region of double
stranded DNA that contains a gene, only one of the two strands, the sense strand,
will contain the genetic information that will ultimately be translated into a protein
sequence. During transcription, the antisense strand serves as the template for
the synthesis of mRNA. It is also referred to as the non-coding.
Aptamer: an oligonucleotide that binds specifically to only one
specific target.
Aqueous: means “in water.” An aqueous solution
is one where the principal solvent is water.
Aromatic: molecules that contain one or more ring structures
and multiple double bonds arranged such that some of the electrons in the ring(s)
are free to move throughout the ring(s). This property causes these compounds to
have strong UV absorbance at wavelengths near 254 nm.
Arrayed Library: consists of individual primary recombinant clones,
hosted in phage, cosmid, YAC, or other vector, that are placed in two-dimensional
arrays in microtiter dishes. Each primary clone can be identified by the plate and
location (row and column) on that plate. Arrayed libraries of clones can be used
for many applications, including screening for a specific gene or genomic region
of interest.
Assay: a process of evaluating a particular
quality of something through experimentation.
Assembly: a process of putting sequenced fragments
of DNA into their correct chromosomal positions.
Attenuator: an RNA sequence that functions as a transcription
terminator.
Autoradiography: a technique that uses X-ray film to visualize
radioactively labeled molecules or fragments of molecules.
-B-
Back Mutation: See “Reverse
Mutation.”
Bacterial Alkaline Phosphatase:
an enzyme responsible for removing phosphate groups in the 5- and 3- positions from
many types of molecules, including nucleotides, proteins, and alkaloids. As the
name suggests, alkaline phosphatases are most effective in an alkaline environment.
In oligonucleotide synthesis, it can be attached to an oligonucleotide via a biotin
group for use as a non-radioactive probe.
Bacteriophage: a virus that infects
bacteria.
Band Shift Assay: See “Gel Shift Assay.”
Base: 1) (as used in chemistry) any chemical compound that, when
dissolved in water, produces a solution with a pH higher than 7. 2)
(as used in molecular biology) See “Nucleobase.”
Base Analog: a purine or pyrimidine base that differs slightly
in structure from the normal nitrogenous bases.
Base Pair (bp): two nucleotides on opposite
sides of a nucleic acid chain which are hydrogen bonded together. Adenine forms
a pair with thymine (DNA) or uracil (RNA); guanine with cytosine (DNA and RNA).
Base Composition Analysis: the analysis of the relative amounts
of each nucleobases in a DNA sample.
Basic Local Alignment Search Tool (BLAST):
a bioinformatics search tool used to compare biological sequences. A BLAST search
allows a particular sequence to be compared against sequences in a library or database
resulting in the identification of sequences similar to the original sequence.
Beer’s Law: a representation of the relationship between
absorbance and concentration: A = εcl, where A is the absorbance (AU), ε
is the molar extinction coefficient ( /M x cm), c is the concentration (M), and
l is the pathlength (cm).
Beta (β): the second letter in the Greek
alphabet. In chemistry it refers to the second member of a series of atoms or residues.
Beta Particle: a high-energy electron released from the nucleus
of an atom during radioactive decay. The ejected electron gives off its energy over
a path of a few millimeters by ionizing other atoms along its path. In biochemistry,
compounds are often labeled with beta emitters so they can be detected with photographic
film.
β-Cyanoethyl: an organic group consisting of a three carbon
alkane triple bonded to a nitrogen. In oligonucleotide synthesis this group is used
as a protecting group for the oxygen on the phosphorous group in a phosphoramidite.
β-Cyanoethyl Phosphoramidite Method: a well established
method for the chemical synthesis of DNA.
β-Sheet: an extended pleat-like structure of a polypeptide
chain. It is a common secondary protein structure.
Binding Site: a place on cellular DNA to which a protein can
bind.
Bioinformatics: a field of study drawing from mathematics, statistics,
computer science, chemistry, and biology to solve biological problems on a molecular
level.
Biotin: vitamin H or vitamin B1 (same thing). It is often used
to bind proteins to nucleic acids and nucleic acids to solid supports.
Blastocyst: a mammalian embryo ready to the implanted in the
wall of the womb.
Blotting: See “Northern Blot”
and “Southern Blot.”
Buffer: a solution that can interact with either hydrogen or
hydroxyl ions to minimize a change in pH.
-C-
Calorie (cal): a measurement of energy.
A calorie is the amount of energy necessary to raise 1mL of water by 1°C.
Cap: the altered end of mRNA. All eukaryotes have a cap at the
5' end of their messages. It is added post-transcriptionally, creating a mature
mRNA, and is not encoded in the DNA.
Capping Reaction: a step in oligonucleotide synthesis that involves
the acetylation of unreacted polymers to prevent further reactions. For more information
see Appendix C.
Carbon-14 (14C): See “Radioactive Label:
14C.”
Carbonyl Group: an organic functional group consisting of a carbon
atom connected to an oxygen atom via a double bond.
Carboxyl Group: an organic functional group, characteristically
acidic, consisting of a carbon atom connected to both an oxygen via a double bond
and a hydroxyl group.
Carboxyl Terminal: the end of a polypeptide
chain that has an unbound α-carboxyl group; often referred to as the C-terminal.
Carboxylic Acid: a molecule that contains a carboxyl group.
CAT Box: a sequence found in the 5' flanking region of certain
genes which is necessary for efficient expression. A transcription factor binds
to this site. It is also recognized as CCAAt Box, CAAT Box, as well as other variants.
Catalyst: a substance that can increase the rate of a chemical
reaction without being consumed.
Cation: an ion with a positive net charge.
Cell Culture: a technique used to grow cells outside an organism.
Central Dogma (of Molecular Biology): the organizing principle
of molecular biology: genetic information flows from DNA to RNA to protein.
Chaperone: a protein that binds to other polypeptides and promotes
their folding.
Chimaera: an organism with at least two genetically different
tissues resulting from mutation of or the insertion of foreign cells into an embryo.
This can be applied to DNA as well: DNA containing genetic information from
at least two sources.
Chromatin: the strands of DNA and proteins that make-up chromosomes.
Chromatography: varying techniques used to separate a mixture
of components as it travels through a stationary matrix.
Chromosome: a thread-like structure into which the hereditary
material of cells and viruses are associated. Chromosomes are made of DNA. In higher
organisms, only a small fraction of this DNA is believed to encode genetic information.
Chromosome Walking: a technique for cloning everything in the genome
around a known piece of DNA.
Clone: 1) (noun) either a bacterium carrying a cloned DNA or
the cloned DNA itself. 2) (verb) to produce copies of something.
Coding Sequence: the portion of a gene or mRNA which actually
codes for a protein.
Codon: a sequence of three nucleotides in mRNA which code for
the incorporation of a specific amino acid into the growing protein
Cohesive Ends: See “Sticky Ends.”
Cointegrate: an intermediate in the transposition of a DNA segment
where the starting point and ending point of the segment are covalently attached.
Colony: a group of contiguous cells growing on a solid surface
that are derived from a single ancestor.
Complimentary: having a molecular surface with specifically arranged
chemical groups that interact with chemical groups in the surface of another molecule.
Complementary DNA (cDNA): DNA synthesized
from a mature mRNA template. It is commonly used to clone eukaryotic genes in prokaryotes.
cDNA Clone: a piece of DNA copied from an mRNA. The term clone
indicates that this cDNA has been inserted into a plasmid or other vector in order
to propagate it.
cDNA Library: a clone-containting tube consisting of a mixture
of bacteria, where each bacteria carries a different plasmid. Inserted into the
plasmids are thousands of different pieces of cDNA copied from some source of mRNA.
The basic idea is that if you have a large enough number of different cDNAs carried
in those bacteria, there is a 99% probability that a cDNA copy of any given mRNA
exists somewhere in the tube. In order to find the one required a process called
screening is used.
Conserved Sequences: the sequences in DNA that are similar to
one another suggesting that they have not differentiated greatly from a common ancestor.
Often times, conserved sequences are left nonfunctional by substitutions in their
nucleotides or amino acids.
Contig: a series of overlapping or continuous sequence that defines
an uninterrupted section of a chromosome.
Controlled Pore Glass (CPG): a solid support
used in the chemical synthesis of DNA. For more information see Appendix C.
Coupling: the reaction in oligonucleotide synthesis that connects
two nucleotides. The 5’-hydroxyl group of one nucleotide reacts with the phosphoramidite
bearing the next base. For more information see Appendix C.
Covalent Bond: a strong chemical bond formed by the sharing of
electrons between atoms.
Crossing Over: See “Genetic Recombination.”
C-Terminal: See “Carboxyl Terminal.”
Cytidine (C): a nucleoside. It is one
of four nucleosides that comprise RNA. Cytidine consists of cytosine attached to
a ribose sugar.
Cytoplasm: the chemical compounds and structures in a cell excluding
the nucleus.
Cytosine (C): a pyrimidine nucleobase.
It is one of four nucleobases that comprise the nucleic acids DNA and RNA. Cytosine
binds to Guanine.
-D-
Dalton (Da): a unit
of weight equal to the weight of a single hydrogen atom.
De Novo: means “beginning again” in Latin.
Deamination: the enzymatic removal of amino groups from a molecule.
Degenerate Codons: two or more codons that code for the same
amino acid.
Deletion: an occurrence where a portion of a chromosome is missing.
Denaturation: the loss of the native configuration of a macromolecule
resulting from heat treatment, extreme pH changes, chemical treatment, or other
denaturing agents. For nucleic acids, denaturation specifically means the disruption
of base pairing making it single stranded.
Deoxyadenosine (dA): a nucleoside. It is one
of four nucleosides that comprise DNA. Deoxyadenosine consists of adenine attached
to a deoxyribose sugar.
Deoxycytidine (dC): a nucleoside. It is one
of four nucleosides that comprise DNA. Deoxycytidine consists of cytosine attached
to a deoxyribose sugar.
Deoxyguanosine (dG): a nucleoside. It is one
of four nucleosides that comprise DNA. Deoxyguanosine consists of guanine attached
to a deoxyribose sugar.
Deoxyribonuclease (DNase): a class of enzymes
which digest DNA by catalyzing hydrolysis.
Deoxyribonucleic Acid (DNA): a polymer of deoxyribonucleotides
linked by phosphodiester bonds. DNA contains genetic information.
DNA Chip: See “Microarray.”
DNA Polymerase I: the first enzyme found to catalyze the formation
of the 3’-5’ phosphodiester bonds of DNA. It also possesses 3’
to 5’ single strand proofreading and 5’ to 3’ double-strand exonuclease
activities.
DNA Polymorphism: a difference in
the DNA sequence between two individuals. DNA polymorphisms are used as markers
in genetic mapping studies. Within a population, when certain markers are shown
to be highly correlated with certain genetic traits, such markers are said to be
closely linked to the gene responsible for that trait.
DNA-RNA Hybrid: a double helix that consists of one chain of
DNA hydrogen bonded to a chain of RNA by means of complementary base pairs.
Deoxyribonucleotide: the structural units of DNA. Deoxyribonucleotides
consist of a nitrogenous base, a deoxyribose sugar, and one or more phosphates.
Deoxythymidine (dT): a nucleoside. It is one
of four nucleosides that comprise DNA. Deoxythymidine consists of thymine attached
to a deoxyribose sugar.
Deprotection: the removal of protecting groups. In oligonucleotide
synthesis, several protecting groups are attached to some of the side groups of
the polymer during synthesis to prevent side reactions. These must be removed at
the end of synthesis. For more information see Appendix C.
Detritylation: the removal of the protecting group from the 5’-hydroxyl
of a synthetic oligonucleotide. The group is usually a dimethoxytrityl group. These
groups are attached through an ether linkage that can be cleaved by acid. The group
that is released is colored and can be detected by its absorbance at 436 nm. For
more information see Appendix C.
Dichloroacetic Acid (DCA): a very strong organic
acid. It is toxic and causes severe burns when placed on unprotected skin. It is
the acid used in detritylation in oligonucleotide synthesis.
Dichloromethane (DCM): a common hydrophobic
organic solvent used in both chemical DNA synthesis and peptide synthesis. It is
toxic and has a low boiling point, but is not flammable. It is readily absorbed
through skin and can pass through rubber gloves. In oligonucleotide synthesis, it
is the solvent used during the automated detritylation step.
Dideoxy Sequencing: See “Sanger Sequencing.”
Dideoxynucleotide Triphosphate (ddNTP): nucleotides,
without the customary 3’-hydroxyl group on their deoxyribose sugar, connected
to three phosphates. After this is added to a chain, no other nucleotides can be
added.
Dimethoxytrityl (DMT): a common protecting
group for the 5’ hydroxyl group on a nucleoside.
Diploid State: the chromosome
state in which each type of chromosome except the sex chromosomes is always represented
twice.
Dipole: a molecule with both a positively charged group and a
negatively charged group.
Disulfide Bond: the covalent bond between two sulfur atoms in
two different cysteine residues of a protein. It is important in determining secondary
and tertiary structure.
Dominant: an allele which exerts its phenotypic effect when present
either in homozygous or heterozygous form.
Dot Blot: a technique for measuring the amount of one specific
DNA or RNA in a complex mixture.
Downstream: the direction toward the 3’ end of a nucleotide
sequence.
Effector: a substance that causes a cellular response to
a stimulus.
Electronegativity: the propensity for of an atom to attract electrons
belonging to another atom when they form a bond.
Electrophile: an atom or molecule with an electron deficiency.
Electrophoresis: the movement of charged molecules in an electric
field. This is often used to separate mixtures of ions, proteins, or nucleic acids.
Electrophoretic Mobility Shift Assay (EMSA):
See “Gel Shift Assay.”
Endergonic Reaction: a reaction that is thermodynamically unfavorable
and will not occur spontaneously.
Endonuclease: an enzyme which digests nucleic acids starting
in the middle of the strand.
Endothermic Reaction: a reaction that requires heat to proceed.
Enhancer: a DNA sequence located apart from the gene it assists
in the expression of.
Ensembl: a bioinformatics project meant to produce and maintain
automatic annotation on certain eukaryotic genomes.
Enzyme: a protein molecule capable of catalyzing chemical reactions.
Enzyme Inhibitior: a molecule that binds to an enzyme, decreasing
its activity.
Eucaryote: an organism whose cells have nuclear membranes, membrane-ground
organelles, and 80S ribosomes. Eucaryotes are often referred to as higher organisms
and generally have much larger genomes than procaryotes.
European Molecular Biology Laboratories (EMBL):
a laboratory that maintains the EMBL database, one of the major public sequence
databases.
European Molecular Biology Network (EMBnet):
a collaborative network among scientists. The URL for EMBnet’s website is
www.embnet.org.
Exergonic Reaction: a reaction that is thermodynamically favorable
and will occur spontaneously.
Exon: portion of a genomic DNA sequence which will be represented
in the final, mature mRNA.
Exonuclease: an enzyme which digests nucleic acids starting at
one end.
Exothermic Reaction: a reaction that gives off heat.
Expressed Sequence Tag (EST): a small sequence
from an expressed gene that can be amplified by PCR. ESTs act as physical markers
for cloning and full length sequencing of the cDNAs of expressed genes. ESTs are
typically identified by purifying mRNAs converting to cDNAs, and then sequencing
a portion of the cDNA.
Extinction Coefficient: See “Molar Extinction
Coefficient.”
-F-
FASTA Format: FASTA format was developed by Bill Pearson,
it is one of the simplest formats for sequences. The basic format is as follows:
>sequence_id_1
;comments (optional)
gggattcccctatcgg
The identifier line always begins with a greater than sign (>), and is only one
line. The sequence begins on the next line. Any comments are on a new line preceded
by a semicolon (;). Multiple sequences can be maintained in the same file.
Fluorescent Label: a fluorescent group
introduced into a molecule to facilitate observation.
Formamide: a small organic molecule used in double-stranded DNA
denaturation. Formamide combines with the free amino groups of adenine and prevents
the formation of A-T base pairs.
Fractionate: to divide a mixture of compounds into the individual
components in order to evaluate them.
Frameshift Mutation: an insertion or deletion in the hereditary
DNA molecule that shifts the normal reading form for translation. This often leads
to nonfunctional protein products.
Functional Group: a covalently bonded group of atoms that behave
as a unit in chemical reactions.
-G-
Gamma (γ): the third letter in
the Greek alphabet. In chemistry it refers to the third member of a series of atoms
or residues.
Gap Penalty: the penalty applied to a similarity score for the
insertion, deletion, or extension of a gap. Gap penalties are usually subtracted
from a cumulative score being determined for the comparison of two or more sequences
via an optimization algorithm that attempts to maximize that score.
Gap: See “Affine Gap.”
Gel Mobility Shift Assay (GMSA): See “Gel Shift Assay.”
Gel Shift Assay: a
method by which one can determine whether a particular protein preparation contains
factors which bind to a particular DNA fragment. When a radiolabeled DNA fragment
is run on a gel, it shows a characteristic mobility. If it is first incubated with
a cellular extract of proteins or with purified protein, any protein-DNA complexes
will migrate slower than the naked DNA - a shifted band.
GenBank: a data bank of genetic sequences operated by a division
of the National Institutes of Health.
Gene: a unit of DNA which performs one function. Usually this
is equated with the production of one RNA or one protein. A gene contains coding
regions, introns, untranslated regions and control regions.
Gene Expression: 1) the conversion of information
from gene to protein via transcription and translation. 2) a measure
of the presence, amount, and timecourse of one or more gene products in a particular
cell or tissue. Expression studies are typically performed at the mRNA or protein
leveling order to determine the number, type, and level of genes that may be up-regulated
or down-regulated during a cellular process, in response to an external stimulus,
in sickness or in disease. Gene chips and proteomics now allow the study of expression
profiles of sets of genes or even entire genomes.
Gene Family: a subset of genes containing homologous sequences
that correlate with a common function.
Gene Regulatory Protein: a protein able to recognize and bind
to a specific sequence in DNA resulting in a change in gene expression.
Genetic Code: the set of nucleotide triplets, in DNA or mRNA,
coding for amino acids. For more information see Appendix C.
Genetic Information: the hereditary information contained in
chromosomal DNA or RNA.
Genetic Map: the arrangement of mutable sites on a chromosome
as deduced from genetic recombination experiments.
Genetic Recombination: the rearrangement
of genes on chromosomes resulting from the breakage and reassembling of segments
of homologous chromosomes.
Genome: the total DNA contained in each cell of an organism.
The genes comprising the genome include coding regions, 5' and 3' untranslated regions,
introns, 5' and 3' flanking DNA. Also present in the genome are structural segments
such as telomeric and centromeric DNA and replication origins, as well as intergenic
DNA.
Genomic DNA: DNA sequence typically obtained from mammalian or
other higher-order species, which include both intron and exon sequences, as well
as non-coding regulatory sequences such as promoter and enhancer sequences.
Genomic Blot: a type of Southern blot specifically used to analyze
a mixture of DNA fragments derived from total genomic DNA. When DNA has been digested
with restriction enzymes it produces a complex set of fragments ranging from tens
of bp to tens of thousands of bp. However, any specific gene will be reproducibly
found on only one or a few specific fragments. A million identical cells will produce
a million identical restriction fragments for any given gene, so probing a genomic
Southern with a gene-specific probe will produce a pattern of perhaps one or just
a few bands.
Genomic Clone: a piece of DNA taken from the genome of a cell
or animal, and spliced into a bacteriophage or other cloning vector.
Genomic Library: a tube containing a mixture of phages. Similar
in concept to a cDNA library, but differs in three major ways: 1) the library carries
pieces of genomic DNA, so it contains introns and flanking regions, as well as coding
and untranslated. 2) you need bacteriophage or cosmids because 3) the inserts are
5-40 kb long. Enough different phages must be present in the library so that any
given piece of DNA from the source genome has a 99% probability of being present.
Genomics: the study of the relationship between gene structure
and function.
Genotype: the genetic composition of an organism.
Glucocorticoid Response Element (GRE): a binding
site in a promoter to which the activated glucocorticoid receptor can bind. The
glucocorticoid receptor is essentially a transcription factor which is activated
only in the presence of glucocorticoids. The activated receptor will bind to a GRE
and transcription of the adjacent gene will be altered.
Glycoprotein: a polypeptide to which sugar residues are attached.
Guanine (G): a purine nucleobase. It is
one of four nucleobases that comprise the nucleic acids DNA and RNA. Guanine binds
to cytosine.
Guanosine (G): a nucleoside. It is one
of the four nucleosides that comprise RNA. Guanosine consists of guanine attached
to a ribose sugar.
-H-
Hairpin Loop: a region of double helix formed by the pairing
of two contiguous complementary stretches of bases on the same single DNA or RNA
strand.
Half-Life: a measure of the instability of a radioactive isotope.
The half-life is the amount of time required for half of the radioactive material
to breakdown.
Haploid State: the state of
a cell in which only one copy of each chromosome is present. Most human cells contain
46 chromosomes (23 pairs), but some cells, such as human sperm cell, are haploid
and contain only 23 chromosomes.
Helix: a spiral structure with a repeating pattern described
by two simultaneous operations: rotation and translation. It is the natural conformation
of many regular biological polymers.
Helix-Loop-Helix: a protein structural motif characteristic of
certain DNA-binding proteins.
Heterogeneous Nuclear RNA (hnRNA): refers
collectively to the variety of RNA found in the nucleus including primary transcripts,
partially processed RNA and snRNA. The term hnRNA is often used just for the unprocessed
primary transcripts.
Heterozygous: a cellular trait where the cell contains more than
one allele, usually two, for a particular gene.
High Pressure Liquid Chromatography (HPLC):
a method for separating chemical compounds. In this method a solvent, known as the
mobile phase, is pumped at high pressure through a column packed with a solid material,
known as the stationary phase. The sample to be purified is introduced to the system
via an injection valve. Components are retained on the column for differing periods
of time. Individual components will exit the column at different times and be detected
by UV spectroscopy. Fractions of the eluted solvent/compound mixture can be collected
if desired.
Homologous: 1) two or more biological species,
systems or molecules that share a common evolutionary ancestor. 2)
two or more gene or protein sequences that share a significant degree of similarity,
typically measured by the amount of identity that they share along their lengths.
Genes or gene products that share significant similarity might also share similar
ancestry or function.
Homozygous: a cellular trait where the cell contains only one
allele for a particular gene.
Host Strain: the bacterium used to harbor a plasmid.
Hybridization: the reaction by which the pairing of complementary
strands of nucleic acid occurs. DNA is usually double-stranded, and when the strands
are separated they will re-hybridize under the appropriate conditions. Hybrids can
form between DNA-DNA, DNA-RNA or RNA-RNA. They can form between a short strand and
a long strand containing a region complementary to the short one. Imperfect hybrids
can also form, but the more imperfect they are, the less stable they will be.
Hydrogen Bond: a weak, attractive force between a hydrogen atom
that is attached to an electronegative atom and another electronegative atom.
Hydrolase: an enzyme that catalyzes hydrolysis reactions.
Hydrolysis: a chemical reaction between a molecule and water
where the molecule is split into two parts. One part of the split molecule gains
the hydrogen from the water molecule; the other part gains the hydroxyl group. This
reaction can be catalyzed by either an acid or a base. In oligonucleotide synthesis
hydrolysis is used in the final deprotection step to remove protecting groups attached
through ester or amide bonds.
Hydrophilic: means “water loving.” This pertains
to molecules that readily associate with and dissolve in H2O. Hydrophilic molecules
are polar and tend to be insoluble in organic solvents.
Hydrophobic: means “water fearing.”
This is used to describe molecules that are poorly soluble in water, if at
all. Hydrophobic molecules are non-polar and tend to be soluble in organic solvents.
Hydroxyl Group: an organic functional group consisting of an
oxygen and hydrogen connected by a single bond from the oxygen.
-I-
In Silico: (in computational biology) the use of computers
to simulate, process or analyze a biological experiment.
In Situ: means “in place” in Latin. This refers to
experiments done in their natural environment.
In Situ Hybridization: a variation of the DNA/RNA hybridization
procedure in which the denatured DNA is actually in the cell and is then exposed
to RNA or DNA extracted from another source.
In Vitro: means “in glass” in Latin. This refers
to experiments done in a cell-free system. The term is sometimes modified to include
the growth of cells from multicellular organisms under cell culture conditions.
In Vivo: means “in life” in Latin. This refers to
experiments done in a system such that the organism remains intact either at the
cellular level, for bacteria, or at the level of the whole organism, for animals.
Initiation: the first step in polypeptide synthesis when the
ribosome attaches to the mRNA at the initiation codon.
Initiation Codon: the site to
which the ribosome attaches to the mRNA to assure that the ribosome reads the correct
reading frame.
Inosine (I): an unusual nucleoside found
in some RNA molecules. It is best known for its occurrence in the anticodon region
of some tRNA molecules where it may wobble.
Insert: one type of DNA in a complete plasmid clone. In a complete
plasmid clone, there are two types of DNA - the vector sequences and the insert.
The insert is the piece of DNA with which studies are concerned.
Insoluble: unable to be dissolved in a particular liquid.
Intergenic: means between two genes. Intergenic DNA is the DNA
found between two genes. The term is often used to mean non-functional DNA or at
least DNA with no known importance to the two genes flanking it. Alternatively,
one might speak of the intergenic distance between two genes as the number of base
pairs from the polyA site of the first gene to the cap site of the second.
Intervening Sequence: See “Intron.”
Intron: portion of genomic DNA, found between
coding sequences, which is transcribed and present in the primary transcript, but
is later spliced out. As a result, introns are not present in the mature mRNA.
Inversion: the result when a fragment of a chromosome breaks
off and then is reintegrated in reverse order.
Ion-Exchange Chromatography: a purification technique where the
varying ionic charges of proteins or molecules are used to separate them.
Ionic Bond: the attractive force between two or more atoms with
opposite charges.
Isotope: any of multiple forms of an element, all with the same
number of protons, but with differing numbers of neutrons.
-K-
Kilo-Base (kb): a unit of length equal
to one thousand nucleotides.
Kinase: 1) an enzyme that catalyzes the transfer
of a phosphate group from ATP to something else. 2) (in molecular
biology) the transfer onto DNA of a radiolabeled phosphate group. This would be
done in order to use the resultant DNA as a probe.
Knock-Out Experiment: a technique for deleting, mutating or otherwise
inactivating a gene in an organism. This laborious method involves transfecting
a crippled gene into cultured embryonic stem cells, searching through the thousands
of resulting clones for one in which the crippled gene exactly replaced the normal
one, and inserting that cell back into a blastocyst. The resulting organism will
be a chimaera, but its germ cells will carry the deleted gene. A few rounds of careful
breeding can then produce progeny in which both copies of the gene are inactivated.
-L-
Label: See “Radioactive Label”
or “Fluorescent Label.”
Lagging Strand: the DNA strand that is synthesized in the opposite
direction of the replication fork during replication.
Leading Strand: the DNA strand that is synthesized in the same
direction of the replication fork during replication.
Leucine Zipper: a pattern found in certain proteins in which
leucine residues are evenly spaced through an α-helical region, such that
they would end up on the same face of the helix. Dimers can form between two such
proteins. The leucine zipper is important in the function of transcription factors
and related proteins.
Library: a tube carrying a mixture of thousands of different
clones, bacteria or phages. Each clone carries an insert, the cloned DNA.
Ligand: a molecule, with a complimentary structure, that can
bind to a receptor.
Ligase: an enzyme which can link pieces of DNA together. The
pieces must have compatible ends: either both blunt or both sticky.
Ligation: the process of splicing two pieces of DNA together.
In practice, a pool of DNA fragments is treated with ligase in the presence of ATP.
All possible splicing products are produced. Generally, only some of these products
are useful and the investigator must have some way of selecting the desirable ones.
Linkage Group: two or more genes on the same chromosome that
are inherited as a group.
Linker: a small piece of synthetic double-stranded DNA which
contains something useful such as a restriction site. A linker might be ligated
onto the end of another piece of DNA to provide a desired restriction site.
Locus: the position of a gene on a chromosome.
Lyophilize: to freeze-dry; rapid freezing followed by dehydration
under high vacuum.
Lysis: the bursting of a cell through the destruction of its
cell membrane.
-M-
Macromolecule: a molecule with a molecular weight ranging
from a few thousand to hundreds of millions of Daltons.
Marker: 1) (Molecular Weight Size Marker) a
piece of DNA of known size, or a mixture of pieces with known size, used on electrophoresis
gels to determine the size of unknown DNA by comparison. 2) (Genetic
marker) a known site on the chromosome.
Melting: (with respect to DNA) the denaturation of double-stranded
DNA into two single strands by the application of heat. Denaturation breaks the
hydrogen bonds holding the double-stranded DNA together.
Melting Point (Tm): the temperature
at which a particular double-stranded nucleic acid melts. Technically, this is defined
as the temperature at which 50% of the strands are in double-stranded form and 50%
are single-stranded. A primer has a specific Tm because it is assumed that it will
find an opposite strand of appropriate character.
Message: See “Messenger RNA.”
Messenger RNA (mRNA): RNA that serves as a
template for protein synthesis. The term mRNA is used only for a mature transcript
with a polyA tail and with all introns removed, rather than the primary transcript
in the nucleus. An mRNA will have a 5' untranslated region, a coding region, a 3'
untranslated region and usually a polyA tail. Typically about 2% of the total cellular
RNA is mRNA.
Methyl Group: a non-polar chemical group consisting of a carbon
and three hydrogens.
Methylene Chloride: See “Dichloromethane.”
Microarray: a small glass or silicon
chip with oligonucleotides or cDNA covalently attached in an indicated pattern of
rows and columns. Thousands of genes or genomic sequences can be represented on
a single chip providing a high-throughput parallel method of probing gene expression,
genotype, or gene function.
Micron (μm): a unit of length convenient
for describing cellular dimensions. A micron is a micrometer and is equal to 10e-6m.
Micro RNA (miRNA): a single stranded RNA gene, typically 21-23
nucleotides long, that is transcribed from DNA, but is not translated into protein,
rather miRNAs are thought to regulate the expression of other genes.
Microsatellite: See “Simple Sequence
Repeat.”
Missense Mutation: a mutation that changes a codon coding for
one amino acid to a codon corresponding to another amino acid.
Mixed Bases: the resulting mixture of residues when, in oligonucleotide
synthesis, a mixture of two or more different nucleotide monomers are added during
the coupling step. Such mixtures are usually requested when a researcher is designing
an oligonucleotide probe to a degenerate sequence.
Model Organism: an animal, exhibiting typical characteristics
of a human disease or illness, which is used in a laboratory.
Molar Absorptivity: See “Molar Extinction
Coefficient.”
Molar Extinction Coefficient (ε): a
constant that indicates the extent to which a given molecule in solution absorbs
light of a given wavelength. Its units are AU/ [Molarity × cm].
Molarity (M): a measure of concentration.
Molarity is equivalent to moles of solute per liters of solution.
Mole (mol): a measure of amount. One mole
of a substance is equal to 6.02 x 10e23 molecules of that particular substance.
Molecular Weight (MW): the weight
of one mole of a particular substance.
Monocistronic mRNA: an mRNA that can only be translated into
one protein.
Monomer: the basic subunit from which polymers are made.
Multiple Cloning Site (MCS): a short segment
of DNA containing many, generally twenty or more, restriction sites. This is especially
useful in the creation of genetically modified organisms by allowing DNA segments
to be inserted in the MCS region.
Mutagen: a physical or chemical agent that increases the frequency
of mutation. Some examples are radiation, heat, and alkylating agents.
Mutagenesis: the course of mutation in a cell or organism.
Mutation: an inheritable change in a chromosome.
-N-
National Center for Biotechnology
Information (NCBI): a branch of the National Institute of Health (NIH).
It houses the genome sequencing data in GenBank.
Native Conformation: the biologically active form of a macromolecule.
Nick Translation: a method for incorporating radioactive isotopes
into a piece of DNA. The DNA is randomly nicked with DNase. Starting from those
nicks DNA polymerase I digests and then replaces a stretch of DNA. Radiolabeled
precursor nucleotide triphosphates can then be incorporated.
Nitrogenous Base: See “Nucleobase.”
Non-coding Strand: See “Antisense Strand.”
Nonsense Codon: a codon that does not specify any amino acid.
Nonsense codons have the function of terminating the polypeptide chain.
Nonsense Mutation: a mutation that converts a codon specifying
some amino acid into a nonsense codon.
Northern Blot: a technique for analyzing
mixtures of RNA, whereby the presence and approximate size of one particular type
of RNA can be ascertained.
N-Terminal: See “Amino Terminal.”
Nuclear Run-On: a method used to estimate the relative rate of
transcription of a given gene. This technique is based on the assumption that a
highly-transcribed gene should have more molecules of RNA polymerase bound to it
than the same gene in a less-active state will. If properly prepared, isolated nuclei
will continue to transcribe genes and incorporate 32P into RNA, but only
in those transcripts that were in progress at the time the nuclei were isolated.
Once the polymerase molecules complete the transcript they have in progress, they
should not be able to re-initiate transcription. Then the amount of radiolabel incorporated
into a specific type of mRNA is theoretically proportional to the number of RNA
polymerase complexes present on that gene at the time of isolation.
Nuclease: an enzyme that degrades nucleic acids. A nuclease can
be DNA-specific (a DNase), RNA-specific (RNase) or non-specific. It may act only
on single stranded nucleic acids, only on double-stranded nucleic acids, or it may
be non-specific with respect to strandedness. A nuclease may degrade only from an
end (an exonuclease) or may be able to start in the middle of a strand (an endonuclease).
To further complicate matters, many enzymes have multiple functions.
Nuclease Protection Assay: See "RNase Protection
Assay."
Nucleic Acid: polymers made up of nucleotides. In living organisms
nucleic acid is based on one of two sugars: ribose (RNA) or deoxyribose (DNA).
Nucleobase: one of the purines or the
pyrimidines found in nucleic acids. The nucleobases are where the hydrogen bonds
are formed causing the double helix structure.
Nucleophile: an atom or molecule that is electron-rich.
Nucleoside: a purine or pyrimidine nucleobase covalently bonded
to a pentose.
Nucleotide (nt): 1) the monomeric
unit from which DNA or RNA are built. Each nucleotide has three components: a nitrogenous
base, a pentose, and a phosphate. 2) the size of a nucleic acid
strand in terms of the number of nucleotides in its chain. So “nt” can
be a measure of chain length.
Nucleus: an organelle containing chromosomes found in eukaryote
cells.
-O-
Oligo: a common term for oligonucleotide.
Oligonucleotide: a short DNA molecule, usually synthetic, consisting
of several linked nucleotides (typically between 10 and 100) covalently attached
by phosphodiester bonds.
Oncogene: a gene in a tumor virus or in cancerous cells which,
when transferred into other cells, can cause transformation. Note that only certain
cells are susceptible to transformation by any one oncogene. Functional oncogenes
are not present in normal cells. The prefix "v-" indicates that a gene
is derived from a virus and is generally an oncogene.
Open Reading Frame (ORF): any region of DNA
or RNA where a protein could be encoded. There must be a string of nucleotides in
which one of the three reading frames has no stop codons.
Operator: a chromosomal region capable of interacting with a
specific repressor, thereby controlling the functioning of an adjacent operon.
Eurofins MWG Operon: a unit of transcription consisting of structural genes,
a promoter, an operator, and a regulatory gene.
Optical Density (OD): a measurement of absorbance
which has become a common measurement for oligonucleotides. The OD is often measured
at the maximum absorbance for DNA, 260nm.
Origin of Replication (ORI): the nucleotide
sequence in DNA where replication is initiated.
Orthologs: the genes in different organisms that are related
to each other by sequence or function.
Oxidation: the reaction in oligonucleotide synthesis that changes
the phosphorous group to a phosphate group. For more information see Appendix C.
Oxidation-Reduction Reaction: a chemical reaction that involves
an electron transfer from one molecule to another. The molecule that losses electrons
is oxidized, while the molecule that gains electrons is reduced.
-P-
Palindrome: a region of DNA with a symmetrical arrangement
of bases occurring about a single point such that the base sequence on either side
of that point are identical if the strands are both read in the same direction.
For example, 5’ATTCTT3’ whose complementary sequence is 3’AAGAAT5’.
Partial Denaturation: the partial unwinding of the double helix.
Those regions that remain intact last are probably GC-rich since G-C base pairs
are held together by three hydrogen bonds making them more stable than A-T base
pairs which are held together by two hydrogen bonds.
Pathogen: anything capable of causing infection or disease in
a cell or organism.
Peptide: a polymer of amino acids connected with peptide bonds.
Peptide Bond: an amide linkage between the α-amino group
of one amino acid and the α-carboxyl group of another.
pH: a term used to describe the relative acidity of an aqueous
solution. It is equal to the negative base 10 logarithm of the hydrogen ion concentration
(pH = -log[H+]). A pH value of less than 3 is considered strongly acidic; from 3
to 6 moderately acidic; 6 to 8 is near neutral; 8 to 11 is moderately basic;
greater than 11 is strongly basic.
Phage: See “Bacteriophage.”
Phagemid: a type of plasmid which carries within its sequence
a bacteriophage replication origin. When the host bacterium is infected with phage
the phagemid is replicated along with the phage DNA and packaged into phage capsids.
Phenotype: the physical characteristics of an organism.
Phosphodiester Bond: a linkage containing a phosphate group covalently
bonded to two other molecules through ester bonds.
Phosphoramidite: the monomer building block most commonly used
in the chemical synthesis of DNA. The standard monomer contains a deoxynucleoside,
a 5’-dimethoxytrityl group, a 3’-phosphite group, a di-isopropylamino
group attached to the pyhosphorus, and a β-cyanoethyl group attached to the
phosphite oxygen.
Phosphorothioate: a modified phosphodiester bond with one of
the oxygen atoms in the phosphate group replaced with a sulfur atom.
Phosphorus-32 (32P): See “Radioactive Label:
32P.”
Pitch: the number of base pairs per turn of the double helix.
Plasmid: a circular piece of DNA present in bacteria or isolated
from bacteria. Plasmids may have other DNA inserted by the investigator. A bacterium
carrying a plasmid and replicating a million-fold will produce a million identical
copies of that plasmid.
Polarity: the uneven distribution of electrons in a molecule.
Nonpolar compounds, which are hydrophobic, have a more even distribution than polar
compounds, which are hydrophilic.
PolyA Tail: a stretch of adenine residues (typically 50-200)
added to the 3' end of an mRNA after it is transcribed from a gene. These polyA
tails increase mRNA stability and allow for the isolation of mRNA from cells by
PCR amplification using polyT primers. Note that not all mRNAs have a polyA tail.
Polyacrylamide Gel Electrophoresis (PAGE): a
method of molecular separation which relies on the differential migration rates
of molecules through a polyacrylamide matrix upon application of an electrical potential.
Polyadenylation: the addition of a polyA tail to mRNA during
the RNA processing set.
Polyadenylation Site: a site on the 3’ end of the mRNA
that signals the addition of a polyA tail during the RNA processing step and before
the mRNa migrates to the cytoplasm.
Polylinker: See “Multiple Cloning Site.”
Polymer: a regular, covalently bonded arrangement of chemical
subunits that is produced by repetitive application of one or a few chemical reactions.
Polymerase: an enzyme which links individual nucleotides together
into a long strand using another strand as a template. There are two general types
of polymerases: DNA polymerases and RNA polymerases. Within these two classes there
are numerous sub-types of polymerases. These depend on what type of nucleic acid
functions as the template and what type of nucleic acid is formed.
Polymerase Chain Reaction (PCR): a technique
for replicating a specific piece of DNA in vitro, even in the presence
of excess non-specific DNA. Primers are added to initiate the copying of
each strand, along with nucleotides and Taq polymerase. By cycling the temperature,
the target DNA is repetitively denatured and copied. A single copy of the target
DNA, even if mixed in with other undesirable DNA, can be amplified to obtain billions
of replicates.
PCR is the basis for a number of extremely important methods in molecular biology.
It can be used to detect and measure vanishingly small amounts of DNA and to create
customized pieces of DNA. It has been applied to clinical diagnosis and therapy,
to forensics and to vast numbers of research applications.
Polymorphism: See “DNA Polymorphism.”
Polynucleotide: a linear sequence of nucleotides in which the
3’ position of the sugar of one nucleotide is linked through a phosphate group
to the 5’ position on the sugar of the adjacent nucleotide.
Polypeptide: a long chain of amino acids linked by peptide bonds.
Post-Transcriptional Regulation: any process occurring after
transcription which affects the amount of protein a gene produces. This includes
RNA processing efficiency, RNA stability, translation efficiency, and protein stability.
Post-Translational Processing: reactions which alter a protein's
covalent structure such as phosphorylation, glycosylation and proteolytic cleavage.
Post-Translational Regulation: any process occurring after translation
which affects the amount of protein produced from a gene. This is often just a buzz-word
for regulation of the stability of the protein. The more stable a protein is, the
more it will accumulate.
Primary Structure: the linear sequence of units in a polymer.
Primary Transcript: an RNA molecule that has not undergone any
modification after its synthesis yet.
Primer: a small oligonucleotide (anywhere from 6 to 50 nt long)
used in DNA synthesis. A primer sticks to the template and is used to initiate the
replication. Primers are necessary for DNA sequencing and PCR.
Primer Extension: a method used to figure out how far upstream
from a fixed site the start of an mRNA is. First, the original part is sequenced
and the coding strand is determined. Next, an oligonucleotide complementary to the
5'-most region of the coding strand is made. This primer is hybridized to mRNA and
reverse transcriptase is added to copy the mRNA from the primer out to the 5' end.
The size of the resulting DNA fragment shows how far away from the 5' end your primer
is.
Priming Site: a portion of a large DNA molecule which is complementary
to a DNA or RNA primer. The priming site is the point at which DNA polymerization
is initiated.
Probe: a fragment of DNA or RNA which is labeled in some way
and is used to hybridize with the nucleic acid which is being investigated. A probe
can be radioactively labeled or tagged with another functional group. It can be
either cloned DNA or a synthetic DNA strand. Probes are used for Real Time PCR experiments
and for hybridization experiments such as microarrays.
Processing: 1) the reactions occurring in the
nucleus that convert the primary RNA transcripts into a mature mRNA. Processing
reactions include capping, splicing, and polyadenylation. 2) refers
to the processing of the protein product including proteolytic cleavages, glycosylation,
etc.
Progesterone Response Element (PRE): a binding
site in a promoter to which the activated progesterone receptor can bind. The progesterone
receptor is essentially a transcription factor which is activated only in the presence
of progesterone. The activated receptor will bind to a PRE, and transcription of
the adjacent gene will be altered.
Prokaryote: a simple unicellular organism with no nuclear membrane
or membrane-bound organelles.
Promoter: a DNA sequence that enables a gene to be transcribed;
the first few hundred nucleotides of DNA upstream of a gene which control the transcription
of that gene. The promoter is part of the 5' flanking DNA. It is not transcribed
into RNA, but without the promoter, the gene is not functional. With regards to
the size of the region encompassed, the promoter of a gene starts with the nucleotide
immediately upstream from the cap site and includes binding sites for one or more
transcription factors which can not work if moved farther away from the gene.
Proofreading: the correction of errors in the synthesis of a
polymer through removal of incorrect monomers after they have been added.
Protein: a macromolecule composed of a characteristic chain of
amino acids linked by peptide bonds.
Protein Family: a set of proteins that share a common evolutionary
origin reflected by their related functions, similarities in sequence, or similar
primary, secondary, or tertiary structure.
Protoplasm: the entire contents of a cell.
Proto-Oncogene: a gene present in a normal cell which carries
out a normal cellular function but which can become an oncogene under certain circumstances.
The prefix "c-" indicates a cellular gene and is generally used for proto-oncogenes.
Pseudogene: a sequence, homologous to functional genes, riddled
with mutations rendering it nonfunctional.
Pulsed Field Gel Electrophoresis (PFGE):
a gel technique which allows size-separation of very large fragments of DNA
(in the range of hundreds of kb to thousands of kb). As in other gel electrophoresis
techniques, populations of molecules migrate through the gel, at a speed related
to their size, producing discrete bands. Unlike normal electrophoresis in which
DNA fragments greater than a certain size are forced to migrate at the same rate
through the gel, in PFGE the electrophoretic voltage is applied alternately along
two perpendicular axes forcing even the larger DNA fragments to separate by size.
Purine: a nitrogenous base found in nucleotides and nucleic acids.
Important purine derivatives include adenine and guanine.
Pyridine: a simple heterocyclic aromatic organic compound structurally
related to benzene. Pyridine is used in the oxidation step of oligonucleotide synthesis.
Pyrimidine: a nitrogenous base found in nucleotides and nucleic
acids. Important pyrimidine derivatives include cytosine, thymine, and uracil.
-Q-
Quaternary Protein Structure: the three-dimensional organization
of a protein that consists of more than one polypeptide chain.
Query: a DNA, RNA, or protein sequence used to search a sequence
database in order to identify homology or analogs from which the function of the
query sequence may be deduced.
-R-
Radioactive Isotope: an isotope that emits streams of energetic
particles as its unstable atoms decay.
Radioactive Label: a radioactive isotope
introduced into a molecule to facilitate observation.
3H: a radioactive isotope of hydrogen that emits
weak beta particles and has a half-life of 12.5 years.
14C: a radioactive carbon isotope that emits
weak beta particles and has a half-life of approximately 5700 years.
32P: a radioactive isotope of phosphorous that
emits strong beta particles and has a half-life of 14.3 days.
35S: a radioactive isotope of sulfur that emits
beta particles and has a half-life of 87 days.
Random Primed Synthesis: a method for producing radioactive copies
of a DNA clone. It is first denatured then a mixture of all possible 6-mer oligonucleotides
is hybridized to that template. Those oligos will act as primers for the synthesis
of labeled strands by DNA polymerase in the presence of radiolabeled precursors.
Reading Frame: the order in which a particular grouping of nucleotides
are read. When mRNA is translated by the cell the nucleotides are read three at
a time. By starting at different positions, the groupings of three that are produced,
the reading frames, can be entirely different. The one with an initiation codon
is the one used.
Real-Time PCR: a polymerase chain reaction technique used to
both quantify and amplify a specific DNA segment at the same time. This procedure
is similar to normal polymerase chain reaction techniques only with the addition
of regular quantification after each round of amplification,
Receptor: any substance that can bind to a specific molecular.
This binding often results in uptake or signal transduction.
Recessive: an allele which exerts its phenotypic effect only
when present in homozygous form; otherwise it is masked by the dominant allele.
Recombinant DNA: molecules containing DNA sequences, derived
from more than one source.
Recombination: the appearance in the offspring of traits that
were not found together in either of the parents.
Redundancy: the presence of more than one identical sequence.
In bioinformatics, the term is used with reference to the sequences in a sequence
database. If a database is described as being redundant, more than one identical
sequence may be found.
Regulatory Gene: a gene whose primary function is to control
the rate of synthesis of the products of another gene.
Renaturation: the return of a protein or nucleic acid from a
denatured state to its native configuration.
Repeat Sequence: a repeated simple sequence in a genome. These
may be short repeats, just a few nt long, or they may range up to a few hundred
nt long. The function of these elements is often unknown. They are useful markers
for familial relationships and have been used in paternity testing, forensic science
and in the identification of human remains.
Replicating Fork: the Y-shaped region of a chromosome that is
a growing point in DNA replication.
Replication: the copying of genetic material.
Replication Origin: See “Origin of Replication.”
Repressor: a regulatory gene protein that binds to DNA and prevents
transcription.
Residue: the part of a monomer molecule which resides in a polymer
molecule once the polymer is formed. The properties of a residue are usually similar,
but not identical, to the free monomer.
Response Element: a portion of a gene which must be present in
order for that gene to respond to some hormone or other stimulus. Response elements
are binding sites for transcription factors. Certain transcription factors are activated
by stimuli such as hormones or heat shock. A gene may respond to the presence of
that hormone because the gene has in its promoter region a binding site for hormone-activated
transcription factor.
Restriction: (with respect to DNA) to cut DNA with a restriction
enzyme.
Restriction Enzyme: a class of enzymes, generally isolated from
bacteria, which are able to recognize and cut specific sequences in DNA. Bacteria
produce restriction enzymes for protection against invasion by foreign DNA such
as phages. The bacteria's own DNA is modified in such a way as to prevent it from
being clipped. There are more than six hundred known restriction enzymes.
Restriction Fragment: the piece of DNA released after restriction
digestion of plasmids or genomic DNA. A plasmid can be digested isolating one particular
restriction fragment. The term also describes the fragments detected on a genomic
blot which carry the gene of interest.
Restriction Fragment Length Polymorphism (RFLP):
restriction enzymes which give a pattern difference between two individuals.
Although two individuals of the same species have almost identical genomes, they
will always differ at a few nucleotides. Some of these differences will produce
or remove new restriction sites causing the banding pattern seen on a genomic Southern
to be affected. The less related the individuals, the more divergent their DNA sequences
are and the more likely you are to find a RFLP. The acronym is pronounced "riflip".
Restriction Map: a depiction of the locations within a stretch
of known DNA where restriction enzymes will cut.
The map usually indicates the approximate length of the entire piece, as well as
the position within the piece at which designated enzymes will cut. (The map shown
is of a plasmid, and the two ends are joined together with about 25 nt between the
EcoRI and HindIII sites.)
Restriction Site: a sequence where a specific restriction enzyme
will cut the DNA.
Reverse Mutation: a heritable
change in a mutant gene that restores the original nucleotide sequence.
Reverse Transcriptase (RT): an enzyme which
will make a DNA copy of an RNA template, a DNA-dependant RNA polymerase. RT is used
to make cDNA by isolating polyadenylated mRNA, providing oligo-dT as a primer, and
adding nucleotide triphosphates and RT to copy the RNA into cDNA.
Reverse Transcriptase Polymerase Chain Reaction (RT-PCR):
a two phase procedure used for replicating a specific piece of RNA. The
RNA is first converted to DNA via reverse transcriptase. Then it is replicated using
standard PCR.
Ribonuclease (RNase): an enzyme which degrades
RNA by cleaving the phosphodiester bond. It is ubiquitous in living organisms and
is exceptionally stable. The prevention of RNase activity is the primary problem
in handling RNA.
RNase Protection Assay: a sensitive
method to determine the amount of a specific mRNA present in a complex mixture of
mRNA and/or the sizes of exons which comprise the mRNA of interest. A radioactive
DNA or RNA probe is allowed to hybridize with a sample of mRNA, after which the
mixture is digested with a single-strand specific nuclease. Only the probe which
is hybridized to the specific mRNA will escape the nuclease treatment, and can be
detected on a gel. The amount of radioactivity which was protected from nuclease
is proportional to the amount of mRNA to which it hybridized. If the probe included
both introns and exons only the exons will be protected from the nuclease and their
sizes can be ascertained on the gel.
Ribonucleic Acid (RNA): a polymer of ribonucleotides
linked by phosphodiester bonds.
RNA Interference (RNAi): using double-stranded
RNA to silence the expression of a particular gene. The double-stranded RNA, known
as siRNA, interferes with expression of any mRNA having a similar sequence via fragmentation
of the mRNA.
RNA Splicing: removal of introns from a primary transcript.
Ribonucleotide: structural units of RNA. Ribonucleotides consist
of a nitrogenous base, a ribose sugar, and one or more phosphates.
Riboprobe: a strand of RNA synthesized in vitro, usually
radiolabeled, and used as a probe for hybridization reactions. An RNA probe can
be synthesized at very high specific activity, is single stranded (so as not to
self anneal), and can be used for very sensitive detection of DNA or RNA.
Ribose: a five carbon sugar which serves as a common structural
component of RNA.
Ribosomal DNA (rDNA): the DNA sequences encoding
rRNA.
Ribosomal RNA (rRNA): any of several RNAs
which become part of the ribosome and are involved in translating mRNA and synthesizing
proteins.
Ribosome: a cellular particle which is involved in the translation
of mRNAs to make proteins. Ribosomes are complexed consisting of rRNA and several
proteins.
Ribozyme: an RNA molecule that acts as a catalyst in cellular
reactions.
-S-
S1 End Mapping: a technique to determine where the end of
an RNA transcript lies with respect to its template DNA gene.
S1 Nuclease: an enzyme which digests only single-stranded nucleic
acids.
Sanger Sequencing: the most common
method used to determine the nucleotide sequence of a strand of DNA. The unknown
sequence must have a known sequence located upstream of it. An oligonucleotide primer
which is complementary to the know sequence is annealed to this strand. A mixture
of dNTP’s, DNA polymerase, and a labeling compound are used to extend the
primer through the unknown sequence. A small amount of one dideoxynucleotide triphosphate
is also placed in the reaction mixture. This dideoxy compound causes chain termination
at some sites where cytidine would otherwise be added. By running the resulting
mixture of chain termination products on gel electrophoresis, or capillary electrophoresis,
and visualizing those bands with an optical device which detects the incorporated
fluorophores a pattern called a sequencing ladder can be seen. Four such reactions
are run and four ladders are produced on the same gel in four separate lanes. The
unknown DNA sequence can be determined simply by canning the gel from one end to
the other, calling out the name of the lane at each position which has a termination
band.
Satellite DNA: regions of highly repetitive DNA from a eukaryotic
chromosome, identifiable by its unusual nucleotide composition. These are not transcribed
and its function is not clear.
Screening: to select and isolate individual clones out of the
mixture of clones from a library.
Screening by Antibody: a screening option if the bacteria and
plasmid are designed to express proteins from the cDNA inserts. The principle is
similar to that of screening by hybridization, in that you lift replica filters
from bacterial plates, but then you use the antibody to show which colony expresses
the desired protein.
Screening by Hybridization: a screening option which involves
spreading the mixture of bacteria out on a dozen or so agar plates to grow several
tens of thousands of isolated colonies. Membranes are laid onto each plate and some
of the bacteria from each colony stick producing replicas of each colony in their
original growth position. The membranes are lifted and the adherent bacteria are
lysed, then hybridized to a radioactive piece of alpha DNA. When X-ray film is laid
on the filter only colonies carrying alpha sequences will light up. Their position
on the membranes show where they grew on the original plates, so you now can go
back to the original plate, where the remnants of the colonies are still alive,
pick the colony off the plate and grow it up. You now have an unlimited source of
alpha cDNA.
Secondary Bond: See “Weak Interactions.”
Secondary Structure: the conformation of the units in the backbone
of a polymer. This includes any interchain and intrachain bonds.
Selectivity: (as used in bioinformatics) the significance threshold
for reporting database sequence matches in similarity search algorithms.
Sense Strand: a strand of DNA that can be translated exactly
as the mRNA sequence can. In a region of double stranded DNA that contains a gene
only one of the two strands, the sense strand, will contain the genetic information
that will ultimately be translated into a protein sequence. Note that when the RNA
is transcribed from this sequence, the antisense strand is used as the template
for RNA polymerization. After all, the RNA must base-pair with its template strand,
so the process of transcription produces the complement of the anti-sense strand.
It is also referred to as the coding strand by some and in some rare cases sense
and antisense are given opposites definitions than what are given here.
Sensitivity: (as used in bioinformatics) the comprehensiveness
of a similarity search algorithm. At the user’s discretion, the speed
of most similarity search programs can be sacrificed in exchange for greater sensitivity
with an emphasis on detecting lower scoring matches.
Sequence: 1) (noun) the structure of a DNA molecule
in terms of the sequence of bases it contains. 2) (verb) to determine
the structure of a piece of DNA with regards to the sequence of nucleotides it contains.
Sequence Tagged Site (STS): a unique sequence
from a known chromosomal location that can be amplified by PCR. STSs are physical
markers for genomic mapping and cloning.
Shotgun Cloning: the practice of randomly clipping a larger DNA
fragment into various smaller pieces, cloning everything, and then studying the
resulting individual clones to figure out what happened.
Shotgun Sequencing: a way of determining the sequence of a large
DNA fragment. The large fragment is shotgun cloned, and then each of the resulting
subclones is sequenced. By finding out where the subclones overlap, the sequence
of the larger piece becomes apparent. Note that some of the regions will get sequenced
several times just by chance.
Similarity Search: a search based on the detection of significant
extended sequence similarity to a protein of know structure or of a sequence pattern
characteristic of a protein family in an attempt to predict the structure and function
of a newly sequenced gene. Statistical methods can also be used but are less
powerful and more generalized. These are based on the derivation of structural preference
values for single residues, pairs of residues, short oligopeptides, or short sequence
patterns. The transfer of structure/function information to a potentially homologous
protein is straightforward when the sequence similarity is high and extended in
length, but the assessment of the structural significance of a sequence similarity
can be difficult when sequence similarity is weak or restricted to a short region.
Simple Sequence Repeat (SSR): a repeat
in a sequence. It might be a homopolymer ('...TTTTTTT...'), a dinucleotide repeat
('....CACACACACACACA.....'), trinucleotide repeat ('....AGTAGTAGTAGTAGT...'), etc.
Due to polymerase slip, during DNA replication there is a slight chance these repeat
sequences may become altered; copies of the repeat unit can be created or removed.
Consequently, the exact number of repeat units may differ between unrelated individuals.
Considering all the known microsatellite markers, no two individuals are identical.
This is the basis for forensic DNA identification and for testing of familial relationships.
Single Nucleotide Polymorphism (SNP): a position
in a genomic DNA sequence that varies from one individual to another. It is thought
that the primary source of genetic difference between any two humans is due to the
presence of single nucleotide polymorphisms in their DNA. Furthermore, these SNPs
can be extremely useful in genetic mapping to follow inheritance of specific segments
of DNA in a lineage. SNP-typing is the process of determining the exact nucleotide
at positions known to be polymorphic.
Site-Directed Mutagenesis: a technique used to alter a gene in
a particular way causing it to produce a protein with a specifically modified amino
acid sequence.
Slot Blot: a technique similar to a dot blot, but the analyte
is put onto the membrane using a slot-shaped template. The template produces a consistently
shaped spot, thus decreasing errors and improving the accuracy of the analysis.
Small Inhibitory RNA (siRNA): small double-stranded
RNAs that can interfere with expression of any mRNA with a similar sequence.
Small Nuclear RNA (snRNA): RNA that forms
complexes with proteins to form snRNPs. It is involved in RNA splicing, polyadenylation
reactions, other functions.
Small Nuclear Ribonucleoprotein (snRNP): particles which are
complexes between small nuclear RNAs and proteins. They are involved in RNA splicing
and polyadenylation reactions. The abbreviation is pronounced "snerps."
Soluble: able to be dissolved in a particular liquid.
Solute: a substance dissolved in another substance.
Solution Hybridization: a method closely related to RNase protection.
Solution hybridization is designed to measure the levels of a specific mRNA species
in a complex population of RNA. An excess of radioactive probe is allowed to hybridize
to the RNA, then single-strand specific nuclease is used to destroy the remaining
unhybridized probe and RNA. The protected probe is separated from the degraded fragments,
and the amount of radioactivity in it is proportional to the amount of mRNA in the
sample which was capable of hybridization. This can be a very sensitive detection
method.
Solvent: a liquid able to dissolve other substances.
Somatic Mutation: a mutation occurring in any cell that is not
destined to become a germ cell.
Southern Blot: a technique for analyzing
mixtures of DNA whereby the presence and approximate size of one or more particular
fragments of DNA can be ascertained. This is done by hybridization of the fragments
to labeled probes.
Spectrophotometer: an instrument used to measure the amount of
light absorbed by a solution at a specific wavelength.
Split Gene: a gene with at least one an intervening sequence.
Spontaneous Mutations: mutations that occur randomly with no
known cause.
Stable Transfection: a form of transfection experiment designed
to produce permanent lines of cultured cells with a new gene inserted into their
genome. Usually this is done by linking the desired gene with a gene which confers
resistance to a toxin. Upon putting the toxin into the culture medium only those
cells which incorporate the resistance gene will survive.
Starting Codon: See “Initiation Codon.”
Stem Cell: a relatively undifferentiated cell that can continue
to divide indefinitely producing cells which can develop to be more specialized.
Sticky Ends: complementary single stranded
tails projecting from otherwise double-helical nucleic acid molecules.
Stop Codon: See “Termination Codon.”
Stringency: a term used to describe the conditions of hybridization.
By varying the conditions, especially salt concentration and temperature, a given
probe sequence may be allowed to hybridize only with its exact complement (high
stringency), or with any somewhat related sequences (relaxed or low stringency).
Increasing the temperature or decreasing the salt concentration will tend to increase
the selectivity of a hybridization reaction, consequently raising the stringency.
Structural Gene: a gene that codes for a protein or RNA molecule.
Sub-Cloning: a method of producing unlimited copies of only part
of a piece of DNA. This involves starting with several million copies of the original,
cutting with restriction enzymes, and purifying the desired fragment out of the
mixture. That fragment can then be inserted into a new piece for replication.
Substrate: a reactant bound by an enzyme.
Sulfer-35 (35S): See “Radioactive Label:
35S.”
Supercoiled: a DNA molecule that is twisted upon itself.
Synteny: any conservation of gene order along the chromosomes
of different species.
-T-
Tandem Repeats: where a sequence repeats itself continually.
Taq Polymerase: a DNA polymerase that is very stable at high
temperatures. It was isolated from the bacterium Thermophilis aquaticus.
It is used in PCR procedures and high temperature sequencing.
TATA box: a sequence found in the promoter of many genes. Deletion
of this site causes a marked reduction in transcription and gives rise to heterogeneous
transcription initiation sites.
Telomere: a stretch of repeated sequences forming a cap at the
end of a chromosome. This is found at the ends of eukaryotic chromosomes.
Termination Codon: a condon whose
function is to stop polypeptide assembly.
Template: the macromolecular mold for the synthesis of another
macromolecule.
Template Strand: a strand of nucleic acid used to synthesize
a complementary strand.
Tertiary Protein Structure: the three-dimensional folding of
the polypeptide chains that characterize a protein in its native state.
Tetrazole: a weak acid used to catalyze the amidite coupling
step in oligonucleotide synthesis.
Thymine (T): a pyrimidine nucleobase. It
is one of four nucleobases that comprise the nucleic acid DNA. Thymine binds to
Adenine.
TIGR: the Institute for Genomic Research, a non-profit genomics
research institute that sequences the genomes of important model organisms.
Tissue-Specific Expression: the gene function which is restricted
to a particular tissue or cell type. Tissue specific expression is usually the result
of an enhancer which is activated only in the proper cell type.
Topoisomerase: an enzyme capable of unwinding DNA from a supercoiled
state. This unwinding is necessary for replication and transcription.
Transcription: the process of copying DNA to produce an RNA transcript.
This is the first step in the expression of any gene. The resulting RNA, if it codes
for a protein, will be spliced, polyadenylated, transported to the cytoplasm, and
by the process of translation will produce the desired protein molecule.
Transcription Factor: a protein which is required to initiate
the transcription of genes. These usually bind to DNA as part of their function
but not necessarily. A transcription factor may be general or tissue-specific. Its
activity may be constitutive or may depend on the presence of some stimulus.
Transcription Unit: a segment of DNA onto which a primary transcript
is transcribed.
Transduction: the transfer of bacterial genes from one bacterium
to another by a bacteriophage particle.
Transfection: a method by which experimental DNA may be put into
a cultured mammalian cell. Such experiments are usually performed using cloned DNA
containing coding sequences and control regions in order to test whether the DNA
will be expressed. Since the cloned DNA may have been extensively modified this
procedure is often used to test whether a particular modification affects the function
of a gene.
Transfer RNA (tRNA): one of a class of rather
small RNAs used by the cell to carry amino acids to the ribosome which builds proteins
using mRNA as a guide.
Transformation: 1) (with respect to bacteria) the process by
which a bacteria acquires a plasmid and becomes antibiotic resistant. This term
most commonly refers to a bench procedure performed by the investigator which introduces
experimental plasmids into bacteria. 2) (with respect to cultured
cells) a change in cell morphology and behavior which is generally related to carcinogenesis.
Transformed cells tend to exhibit characteristics known collectively as the transformed
phenotype. There are different degrees of transformation, and cells may exhibit
only a subset of these characteristics.
Transgenic Animal: a laboratory animal which carries experimentally
introduced DNA. The procedure used to make a transgenic animal involves the injection
of DNA into a fertilized embryo at the pro-nuclear stage. The DNA is generally cloned
and may be experimentally altered. It will become incorporated into the genome of
the embryo. That embryo is implanted into a foster mother who gives birth to the
animal carrying the new gene. Various experiments are then carried out to test the
functionality of the inserted DNA.
Transient Transfection: when DNA is transfected into cultured
cells where it is able to stay for about 2-3 days. After that it will be lost. During
those 2-3 days the DNA is functional and any functional genes it contains will be
expressed. Investigators take advantage of this transient expression period to test
gene function.
Translation: the process of decoding a strand of mRNA thereby
producing a protein based on the code. This process requires ribosomes to perform
the synthesis and tRNA to bring in the amino acids. Sometimes people speak of translating
the DNA or RNA when they are merely reading the nucleotide sequence and predicting
from it the sequence of the encoded protein.
Translocation: when all or part of one chromosome becomes attached
to another chromosome.
Transposable Element: segment of DNA
able to move from one site in a genome to another site.
Transposition: the movement of segments of DNA from one site
on in a genome to another site. This movement often effects gene expression.
Transposon: See “Transposable Element.”
Tritium (3H): See “Radioactive Label: 3H.”
-U-
Ultraviolet (UV) Light: electromagnetic
radiation with a wavelength ranging from 1-380nm.
UV Shadowing: a technique used to visualize DNA on a gel. The
gel is placed between a fluorescent surface and a UV lamp. The surface will glow
uniformly, except below the DNA bands which absorb the UV light and cast a shadow.
It is often used to purify oligonucleotides with PAGE.
UV Spectroscopy: a method of determining the concentration of
substances in a solution by measuring the extent to which a beam of ultraviolet
light is absorbed by that solution. The measurement may be done with UV light of
one or a handful of discrete UV wavelengths or the wavelength may be varied throughout
a range to yield a continuous profile of measurements known as a UV spectrum.
Unidentified Reading Frame (URF): an open reading
frame encoding a protein with an unknown function.
UniGene: a database of unique genes, segregated by organism,
at NCBI.
Upstream: the direction toward the 5’ end of a nucleotide
sequence.
Uracil (U): a pyrimidine nucleobase. It
is one of four nucleobases that comprise the nucleic acid RNA. Uracil binds to adenine.
Uridine (U): a nucleoside. It is one of
four nucleosides that comprise RNA. Uridine consists of uracil attached to a ribose
sugar.
-V-
Van der Waals Force: a weak attractive force acting over
very short distances, resulting from attraction of induce dipoles that holds together
two molecules or two different parts of the same molecule.
Vector: one type of DNA in a complete plasmid clone. In a complete
plasmid clone there are two types of DNA: the vector sequences and the insert. The
vector sequences are those regions necessary for propagation, antibiotic resistance,
and all the functions necessary for useful cloning.
Virus: a particle consisting of nucleic acid enclosed in a protein
coat and capable of replicating within a host cell and spreading from cell to cell.
A virus often causes a disease.
-W-
Wavelength (λ): the distance
between two points in the same spot on adjacent waves. Different wavelengths of
light have different properties, effecting substances differently.
Weak Interaction: a force between atoms
that is less strong than the force involved in a covalent bond. This includes ionic
bonds, hydrogen bonds and Van der Waals forces.
Western Blot: a technique used for analyzing a mixture of proteins
to show the presence, size, and abundance of one particular type of protein.
Wobble: 1) (noun) a degenerate position in a
nucleotide sequence inferred from a known peptide sequence. When an oligonucleotide
is synthesized to represent such a degenerate sequence, mixed bases are used at
degenerate sites to represent all possible bases which could occur at each site.
2) (verb) Ability of the third base in the tRNA anticodon to hydrogen
bond with any of the two or three bases at the 3’ end codon. Thus a single
tRNA species can recognize several different codons.
-X-
X-Ray Crystallography: a technique used to deduce the structure
of proteins. X-rays are shot at the protein. The electrons in the protein scatter
the radiation. The pattern of the scattered radiation is related to the structure
of the protein.
-Z-
[Top of Page]
Appendix A: Abbreviations and Acronyms
[Top of Page]
Appendix B: Metric Prefixes
|
Power
|
Prefix
|
Symbol
|
|
24
|
yotta
|
Y
|
|
21
|
zeta
|
Z
|
|
18
|
exa
|
E
|
|
15
|
peta
|
P
|
|
12
|
tera
|
T
|
|
9
|
giga
|
G
|
|
6
|
mega
|
M
|
|
3
|
kilo
|
k
|
|
2
|
hecto
|
h
|
|
1
|
deca
|
da
|
|
-1
|
deci
|
d
|
|
-2
|
centi
|
c
|
|
-3
|
milli
|
m
|
|
-6
|
micro
|
μ
|
|
-9
|
nano
|
n
|
|
-12
|
pico
|
p
|
|
-15
|
femto
|
f
|
|
-18
|
atto
|
a
|
|
-21
|
zepto
|
z
|
|
-24
|
yocto
|
y
|
The Genetic Code
The Genetic Code: This representation of the genetic code is read from the
center (5’) towards the outer edge (3’). The mRNA triplet code
for the amino acid is shown on the periphery.
•Terminator Codons
☐Initiation Codons