- A-form DNA:
- A short, fat, right-handed form of the DNA double helix. This is a largely dehydrated form. Because the base pairs are pushed out from the axis, and tilted relative to the axis, this form can accommodate RNA, either in a DNA-RNA hybrid or an RNA-RNA double helix.
- Activation domain:
- That part of a transcription factor which is responsible for the increase in transcription observed on binding of the factor to the DNA control region of a particular gene.
- Adenine, guanine, cytosine, thymine:
- The four nitrogenous bases used to assemble DNA. Adenine and guanine are purines, consisting of two fused heterocyclic rings; cytosine and thymine are pyrimidines, consisting of one heterocyclic ring. In RNA, thymine is replaced by uracil.
- A polysaccharide complex extracted from algae found in sea water. The less purified form (called "agar") is added to liquid growth media, which is poured into petri dishes to form a semi-solid substrate for the growth of bacteria ("agar plates"). A more purified neutral gelling fraction of agar is "agarose," which is used to make gels for the separation of nucleic acid fragments
- Each gene has two copies, one copy on the maternal chromosome and one copy on the paternal chromosome. These two copies may differ from each other; each different version of the gene (each allele) may impart a different phenotype (trait).
- Allosteric change, conformational change:
- A reversible change in protein conformation (shape), generally in response to binding of a small effector molecule. For example, binding lactose causes the lac repressor to change shape so that it no longer binds to DNA.
- Alu sequences:
- A set of dispersed, related sequences, each about 300 bp long, in the human genome; a retrotransposon. The individual members have a characteristic Alu (restriction enzyme) cleavage site.
- Alternative splicing:
- The inclusion or exclusion of certain possible exons in the splicing reactions that determine the sequences included in the final mRNA product. This mechanism is utilized to generate a series of closely related protein isoforms, which differ by the inclusion or exclusion of a particular domain, such as a membrane binding domain. Alternative splicing can also be used to negate transcription, by introducing an exon with a stop codon that results in production of a non-functional protein. Alternative splicing can be directed by RNA-binding proteins that block utilization of a particular splice site, or by RNA-binding proteins that stimulate utilization of a weak splice site.
- Anneal, hybridize:
- To pair complementary strands of DNA to form a double helix. If one strand is labeled, it can identify the position of the second, unlabeled strand- for example, in filter hybridization, the labeled probe will hybridize to the unlabeled complementary DNA that is stuck to the filter.
- Toxins produced by many simple organisms such as bacteria, yeasts, and molds to fight soil bacteria with which they compete for nutrients. There are several mechanisms by which antibiotics act on bacteria. Tetracycline and chloramphenicol arrest cell growth by blocking protein synthesis, but do not kill the bacteria. Ampicillin is incorporated into the cell wall, blocking the formation of cross-linking structures that stabilize the wall. Kanamycin kills cells by binding to the ribosome and causing the misreading of mRNA during translation. (Drugs that do kill the cell can specifically be termed bactericides.) Genes that provide resistance to these and other antibiotics are commonly found on plasmids, and have been used as markers in vector constructs. Often the nomenclature "tetR" or "tetS" is used to indicate a cell that is tetracycline resistant or tetracycline sensitive.
- The sequence of three nucleotides in tRNA that recognizes an mRNA codon through complimentary base pairing.
- Radioactive substrates can be incorporated into biological molecules by synthesis, hybridization, or other means, either in the test tube, the intact cell, or even an intact plant/animal. That radioactivity can then be detected if the sample is placed next to a film or covered with photographic emulsion. This results in a pattern on the film or in the emulsion that corresponds to the position of the radioactivity within the specimen. The picture obtained is called an autoradiogram, or autorad for short.
- B-form DNA:
- Conformation of the Watson-Crick model in which the two strands of DNA form a right-handed double helix. This is the hydrated form, the predominant form in which DNA exists in the cell.
- A virus that infects bacteria (for example, T2, T4, λ); often shortened to "phage."
- Base pairing:
- The alignment of one of the bases (A, T, G, C) with another, as dictated by the optimization of hydrogen bond formation. In A, B, and Z DNA, A pairs with T and G pairs with C. Two polynucleotide strands, or regions thereof, in which all the nucleotides form such base pairs are said to be complementary in an antiparallel conformation. One strand runs 5’ → 3’ and the other strand runs 3’ → 5’. In achieving complementarity, each strand of DNA can serve as a template for synthesis of its partner strand -- the secret of inheritance.
- Base stacking:
- The positioning of one base pair approximately over another excludes water and contributes significantly to the stabilization of the double helix.
- Beta-galactosidase (β-gal):
- The enzyme encoded by the lactose operon which catalyzes the initial breakdown of β-galactosides into two separate sugars. This enzyme can be easily monitored using a substrate which, upon cleavage by the enzyme, turns blue; consequently, it is frequently used as a marker in cloning.
- Blunt ends:
- Ends of a DNA duplex in which both strands are broken at the same nucleotide position.
- C value:
- The total amount of DNA in a haploid genome.
- C value paradox:
- The apparent discrepancy between the amounts of DNA present per haploid genome and the amounts that can be inferred to be necessary to carry the information required to generate the organism, given its relative complexity. Mammals typically have 3000 times more DNA than E. coli, and newts and salamanders often have about 10 times more than mammals.
- A 7-methylguanosine residue that is posttranscriptionally added to the 5' end of a eukaryotic mRNA.
- cDNA (copy DNA):
- A double-stranded DNA molecule prepared in vitro by copying an mRNA molecule, starting with an oligo (dT) primer and using reverse transcriptase to copy the RNA into a DNA strand. The RNA component of the resulting RNA-DNA hybrid is then destroyed by alkali, and the DNA strand "copied back" by DNA polymerase, using the free 3' end as a primer. After using S1 nuclease (which cuts single strand DNA) to cut the loop at the end of the molecule, the resulting double strand DNA can be used for cloning and analysis.
- cDNA library:
- A collection of recombinant DNA molecules, used to transform an appropriate host cell type, containing cDNA copies of all of the mRNAs present in a given cell, tissue, or organism. A cDNA library is very selective, containing sequences for only those genes expressed (as mRNA) by the starting cells. Because the starting material is mRNA, no regulatory sequences are included.
- Cell extract:
- The starting material for attempts at enzyme purification. Generally cells are broken open (by grinding in a Waring blender or other homogenizer in buffer), and gross debri, including cell membranes, is removed either by filtration or low speed centrifugation. The soluble material left will contain many enzymes; the proteins can be fractionated by size separation, charge separation, and differences in affinity for different binding groups using column chromatography, among other techniques. If you have a good assay for the activity you are interested in, you should be able to purify the enzyme responsible.
- Chimeric DNA molecule:
- A DNA molecule containing two or more regions of different origin (for example, plasmid DNA from bacterium containing a fragment of human DNA); recombinant DNA.
- ChIP (Chromatin ImmunoPrecipitation):
- A technique to analyze the distribution of specific proteins or histone modifications across the genome. The chromatin is cross-linked, sheared to small fragments, and precipitated using antibodies specific for a given protein or histone variant. DNA from the fraction pulled down using a given antibody is then sequenced, and the sequences mapped back to the genome to generate the pattern of association.
- The packaged form of the DNA in a eukaryotic cell nucleus. This assembly is approximately equal parts DNA, histones, and non-histone chromosomal proteins. The basic fiber is a nucleosome array, with ~170 bp of DNA wrapped around a histone bead to make up the repeating subunit.
- Chromatin remodeling factor (SWI/SNF, NURF):
- A factor that can alter nucleosome structure, facilitating access for transcription factors and RNA polymerase, resulting in creation of HS sites and gene expression.
- Chromosome scaffold:
- The protein matrix though to anchor loops of DNA, subdividing the chromosome into separate topological domains; each domain is on the order of 30-100 kb. The major protein components of the scaffold are topoisomerase II and SCMII; both proteins are important in the process of condensing chromatin into metaphase chromosomes.
- Configuration describing two sites on the same molecule of DNA.
- Cleft palate:
- A birth defect that affects the roof of the mouth. It is an opening in the roof of the mouth which that can be found on one or both sides and may extend to the full length of the palate.
- Colony of genetically uniform cells derived from a single parent cell; also used (in plural) for a unique population of recombinant DNA molecules (for example, plasmid clones). Many plants can be propagated as clones (for example, by separating bulbs, starting a new plant from a cutting of the parent, etc.) starting from a group of parent cells (asexual reproduction).
- Cloned DNA:
- DNA that has been isolated, inserted into a plasmid or other vector, and used to transform a host cell. By growing up large amounts of the host cell, one can recover significant amounts of a single purified DNA molecule.
- Cloning site:
- A restriction site in a vector that is cut and becomes the site of insertion for the DNA fragment to be cloned. Usually one chooses a restriction site that is unique (i.e., that occurs only once in the vector) and that does not interfere with the origin of replication (ori) or with at least one marker. Sometimes a cloning site is designed so that one can easily screen for insertion of DNA at that site.
- The sequence of three nucleotides in DNA or RNA that specifies a particular amino acid.
- Refers (in biology) to the degree that a DNA, RNA or protein sequence is maintained with a different DNA, RNA or protein sequence.
- Cooperativity, cooperative binding:
- Property exhibited by some DNA binding proteins whereby interaction with the same or a different DNA binding protein increases the binding affinity of the complex.
- Plasmids that carry the phage lambda cos sites. The cos sites are the cohesive ends of the lambda genome, which allow it to circularize; DNA of 35-40 kb flanked by cos sites can be packaged in vitro in the phage coat. Infection of E. coli with this phage provides an efficient mechanism for getting the DNA into the bacterial cells.
- Cot curve:
- A graph plotting the amount of DNA in a hybridization mixture that remains single stranded as a function of the log of the product of DNA concentration (Co) and time of incubation (t) in a reassociation reaction. To obtain a Cot curve, DNA is sheared to ~400 bp fragments and heated to ~90°C to dissociate the two strands; the temperature is then dropped, and the re-association of the strands followed over time. The rate of reassociation depends on how many different sequences are present in the DNA sample (at a standard concentration of nucleotides/liter). When eukaryotic DNA is used, different kinetic classes of DNA are observed (repetitious, unique).
- De novo:
- Newly made.
- Degenerate code:
- A code in which more than one symbol has the same meaning. In the genetic code, several different codons can code for the same amino acid.
- Nucleotides lacking both the 2' and 3' hydroxyl groups normally found on ribose. Such nucleotides can be incorporated into the growing strand by DNA polymerase, but do not serve as a substrate for further nucleotide addition, resulting in the termination of synthesis.
- Differential gene expression:
- Pattern of gene expression in multi-cellular organisms, where each cell type shows a distinctive group of transcripts.
- DNA affinity chromatography:
- A procedure in which a protein is separated from a mixture of other proteins by its ability to bind specifically to a particular sequence of DNA, immobilized on a matrix for use in a separation column.
- DNA ligase:
- An enzyme that joins broken pieces of DNA by catalyzing the formation of a phosphodiester bond between the 5' phosphate end of a hydrogen-bonded nucleotide and the 3'- OH group of the adjacent nucleotide. Needed to join together the newly synthesized fragments of the lagging strand.
- DNA-binding domain:
- That part of a DNA-binding protein that can specifically bind to DNA. Several motifs that can bind to DNA have been characterized -- the helix-loop-helix proteins, leucine zipper proteins, zinc-finger proteins, etc. In almost all cases, the structure of the protein is designed so that a portion interacts with a specific sequence of DNA by binding in the major groove.
- DNA strand directionality:
- Single stranded DNA molecules have an inherent directionality that derives from their chemical structure. At one end of a strand there is a phosphate, labeled the 5' end, and at the other end, there is a hydroxyl group, labeled the 3' end.
- DNase I footprinting:
- A means of determining the exact binding site of a protein on a specific DNA fragment. When a protein-DNA complex is subject to partial digestion by DNase I, the bound protein will protect the DNA from cleavage at the site of the protein-DNA complex. Assuming that the DNA fragment is labeled at one end, the size (pattern) of the cleavage fragments can be determined by gel electrophoresis. A comparison of the cleavage fragments from a naked (pure) DNA sample and the protein-DNA complex will indicate the region of protein binding by the absence of cleavage fragments of that length.
- DNase I hypersensitive site or hypersensitive site (HS site):
- A region along the chromatin fiber that is nucleosome-free, and hence accessible to cleavage by DNase I or other nucleases. Such sites are found at the promoters and enhancers of active or inducible genes.
- Double helix:
- Two parallel strands wound around a common axis. If the strands have polarity, and one runs up while the other runs down, they are said to be antiparallel.
- A means to separate molecules in an electric field. DNA migration takes place through a gel matrix (agarose or polyacrylamide) that acts as a molecular sieve. Since DNA is negatively charged, when placed in an electric field, it is attracted toward the positive electrode.
- End labeling:
- The addition of a radioactively labeled group to one end (5' or 3') of a DNA strand.
- A class of enzymes that cleaves a nucleic acid chain to generate new ends. Different endonucleases will cut DNA or RNA, either single-stranded or double-stranded. An endonclease that cuts dsDNA at a defined sequence (generally 4 to 16 bp) is called a "restriction enzyme."
- A eukaryotic DNA sequence located some distance from the transcription start site, where an activator of transcription (protein) may bind.
- Environmental containment:
- Containment of an organism (such as a host cell) based on its requirements for survival and growth. Can be used as a safety precaution when growing recombinant DNA clones with potentially hazardous properties (for example, when cloning a gene encoding a neurotoxin).
- Inheritance of phenotypic differences that do not depend on changes in the DNA sequence. These can be changes in gene expression due to histone modifications with acetyl, methyl or other chemical groups. Alternatively, these may be due to changes in the pattern of DNA methylation or changes in the spatial organization of the chromatin in the nucleus.
- Epigenetic effects:
- Change in gene expression due to histone modifications with acetyl, methyl or other chemical groups. Genes are not typically expressed in chromatin that has methylated histone proteins. Genes tend to be expressed in chromatin that have acetylated histone proteins.
- Ethidium bromide:
- An intercalating chemical which is used to stain DNA; it is fluorescent under ultraviolet light. EtBr is a mutagen; use gloves when handling this material.
- The class of organisms, composed of one or more cells, containing a membrane-enclosed nucleus and packaging its DNA with histones in a nucleosome array. Eukaryotic cells typically have complex organelles, such as mitochondria.
- An exon is a contiguous segment of a gene found both in the initial transcript and in the final product; the introns are those segments found in the initial transcript which are removed during processing, and so are not found in the finished product.
- An enzyme that cleaves nucleotides one at a time from the end of a polynucleotide chain. Particular exonucleases are specific for either the 5' or 3' end; some cut DNA or and some cut RNA. DNA polymerases can contain 3'-to-5' exonuclease activity; this allows these enzymes to excise the nucleotide that they just added if it base pairs incorrectly ("editing").
- Expression library:
- A collection of clones prepared using a cDNA inserted into an expression vector. Such a library can be screened by looking for expression of the desired protein product, using either a functional assay or an antibody-based assay.
- Expression vector:
- A cloning vector that is designed with the cloning site downstream of the appropriate signals for initiation of transcription and initiation of translation in the host cell type. This vector allows expression of the DNA inserted in the cloning site, and will result in synthesis of the protein encoded by that DNA, assuming that the coding fragment is in phase for correct translation.
- Fetal Alcohol Syndrome (FAS):
- Problems in growth and mental and physical health that may occur in a baby when a mother drinks alcohol during pregnancy.
- Frameshift mutation:
- A mutation that by inserting or deleting one or two bases changes the reading frame of the triplet code.
- Functional complementation:
- The identification of a cloned gene by virtue of the ability of the cloned DNA to rescue a cell (on transformation) having a mutation in that gene.
- Fusion protein:
- A protein that contains portions originally from two different proteins; produced by recombinant DNA techniques, in which a fragment coding for a portion of one protein is ligated (in frame) to a DNA fragment coding for a portion of another gene, and the whole used in an expression vector to produce the new protein.
- GC-rich region, CpG island:
- A region of 20-50 nucleotides, CG-rich, found about 100 bp upstream of the start site of a group of eukaryotic genes encoding mRNA, often genes encoding "housekeeping" functions, transcribed at a low rate by RNA polymerase II.
- Gel shift assay, electrophoretic mobility shift assay (EMSA):
- A means of detecting DNA-protein interactions. A complex between a fragment of DNA and a protein moves more slowly during gel electrophoresis than does the DNA fragment alone, resulting in a "shift" in the position of the DNA fragment.
- The entire nucleic acid sequence within a genome that is necessary and sufficient for the synthesis of a functional product. Usually that product is a polypeptide, but in some cases it is an RNA (i.e., tRNA, rRNA, miRNA, or other non-coding RNA).
- Gene expression:
- The process by which the information contained in some genes are used to synthesize a protein.
- Gene transcripts:
- Each gene is expressed as an RNA molecule called a transcript which indicates that the gene is being used in a certain place (cell, tissue or organ) at a specific developmental time (for example: adulthood, juvenile stage, or embryonic stage). Essentially the cell ‘writes’ a copy of the DNA in the form of RNA retaining the same order of nucleotides (A,G,C, or T) found in the DNA, but replacing ‘T’ with ‘U’.
- Genetic syndrome:
- A disease or disorder that has a group of identifying symptoms, whose cause is genetic.
- The entire genetic material of an organism. The haploid genome refers to one copy of each chromosome.
- Genomic library:
- A population of cells, each of which carries a recombinant DNA molecule with a genome fragment in a cloning vector. Ideally, all of the cloned DNA molecules together represent the entire genome of the test organism. Also called a gene bank, gene library, clone bank, etc. This term is sometimes also used to denote all of the recombinant vector molecules, each carrying a piece of the chromosomal DNA of the test organism, prior to the insertion of these molecules into a population of host cells. If you wish to clone a complete gene, including its upstream regulatory sequences and the entire region of the transcript (including introns), you must use a genomic library.
- The study of all the genes in an organism.
- A topoisomerase II capable of driving formation of negative supercoils; found only in prokaryotes.
- A helix is characterized as right-handed if it is turning clockwise as it moves away from you; if it turns counter-clockwise, it is left-handed.
- An enzyme that uses the energy of ATP hydrolysis to disrupt the hydrogen bonds that hold the two strands of DNA together, allowing the double helix to unwind.
- Helix-turn-helix protein (or helix-loop-helix protein):
- A protein having a ~20-amino acid motif that forms two α helices that cross at an angle of ~120°. This motif occurs frequently in DNA binding proteins, with one of the α helices (stabilized by the other) forming contacts with the DNA in the major groove.
- That portion of the chromatin that remains relatively condensed as the cell progresses from metaphase back to interphase. Heterochromatic regions tend to have a high content of repetitious DNA (satellite DNA, middle repetitious sequences), are gene-poor, show little or no transcriptional activity, and replicate late in S-phase. Blocks of heterochromatin are generally found around the centromeres and telomeres. Regions of the genome that contain the bulk of the genes are packaged in euchromatin. Euchromatic regions are thought to be packaged in the 30 nm chromatin fiber, with heterochromatic regions being further condensed.
- Not all the same, or containing different components.
- Histone acetyltransferase (HAT):
- An enzyme that modifies the histones, acetylating the lysine residues in the N-terminal tail and reducing the net charge of these basic regions. The modification is reversed by histone deacetylase (HDAC), which removes such acetyl groups from the histone tails. Histone acetylation is associated with gene activation, while histone deacetylation is associated with silencing. The activation domain of several of the positive regulatory proteins has been found to have HAT activity, while several repressors appear to act by binding to a HDA complex.
- The small, basic proteins used to package the DNA in chromatin. The core histones (H2A, H2B, H3, and H4) are highly conserved over evolution, while histone H1 is more variable.
- A birth defect of the brain, in which the front part of the brain fails to normally divide into the right and left hemispheres
- A gene found in one organism whose DNA sequence is similar to that of another organism and is believed to have originated from an ancestral single gene or common ancestor.
- Host-vector system:
- The combination of a particular plasmid, phage, or virus and the bacterium or other host cell into which it is inserted. It is essential that the host cell be transformed by the vector DNA at a reasonable frequency, and that the vector have an appropriate origin of replication to function in the host cell.
- In situ hybridization:
- Performed by denaturing the DNA of cells or tissue sections on a microscope slide, or in whole-mounts, so that a hybridization reaction is possible with an added single-stranded DNA probe. The probe is labeled so that the site of hybridization can be detected by autoradiography or other appropriate staining protocols.
- In vitro:
- Carried out in the test tube, with no intact cells present. We can label DNA in vitro by putting the DNA template and appropriate primers into a test tube with the DNA polymerase, labeled dNTPs, and appropriate buffers.
- In vivo:
- In life; carried out within an intact cell. In the Meselson/Stahl experiment, the DNA was labeled in vivo. 15N was added to the medium in which the cells were growing, and all DNA synthesis occured in the growing cells.
- Mating organisms with siblings over many generations to obtain a group of organisms called a ‘strain’ that are almost genetically identical.
- A 125 cm column with mesh baffles used to collect fruit flies that have a phenotypic response to alcohol vapor: the more sensitive the fly is to alcohol, the faster it will pass out and fall to the bottom of the column.
- Initiation, elongation, termination (process of RNA synthesis):
- RNA polymerase will initiate at defined sites, beginning synthesis of an RNA molecule without any requirement for a primer. The enzyme is completely processive, and will proceed to elongate the growing RNA molecule, incorporating nucleotides to produce an RNA complimentary to the DNA template strand. Termination (cessation of strand synthesis, and dissociation of the RNA polymerase from the DNA template) in prokaryotes occurs either in response to a stem-loop signal or a rho protein signal in the nascent RNA.
- A weak consensus sequence [PyPyAN(T/A)PyPyPy] found with the A at +1 that serves as a recognition sequence for RNA polymerase II,
- Klenow fragment:
- A proteolytic fragment of DNA polymerase I that lacks the domain with the 5'-to-3' exonuclease activity, but still has the 5'-to-3' polymerase activity and the 3'-to-5' exonuclease activity. This fragment of the polymerase can therefore synthesize DNA, and can edit its work, but it cannot chew up a fragment of DNA from the 5' end.
- A technique used by developmental biologists in which a gene is deliberately made non-functional through genetic engineering.
- Lac operon:
- An operon is a prokaryotic genetic unit that consists of several genes, usually with related functions, transcribed as a single mRNA molecule. The lac operon includes the genes for ϐ-galactosidase, lactose permease, and thiogalactoside transacetylase.
- Leading strand:
- The daughter strand of newly replicated DNA synthesized continuously from one RNA primer, moving in the same direction as the growing fork. The lagging strand is synthesized in fragments of ~1000 bases (Okazaki fragments), using a new RNA primer for each fragment, in the direction away from the movement of the replication fork.
- A collection of cloned DNA fragments -- for example, a "cDNA library" or a "genomic library." Alternatively, this could be a collection of small molecules to be tested in a given assay.
- The formation of a phosphodiester bond to link two adjacent bases separated by a nick in one strand of a double helix of DNA. Staggered or sticky ends that have hybridized can be joined covalently by ligase. The term is also applied to covalent joining of blunt-end double-stranded DNA (blunt-end ligation). The enzymes which do this are called ligases.
- A short, chemically synthesized double-stranded oligonucleotide which contains the target site for a restriction enzyme. Linkers may be added to the ends of a DNA fragment prepared by cleavage with some other enzyme (or by random shearing) during construction of a desired recombinant DNA.
- Lipid biosynthesis
- Making fats in an organism or cell. Synthesizing certain fats is important for energy storage and for generating structures such as the cellular membranes.
- Locomotor activity:
- The ability of an organism to move. Flies, for example, commonly walk upward in the container in which they are placed. Normally, flies also tend to jump around, sometimes falling down and immediately scrambling back up: even if they fall on their backs, they can quickly flip over to walk upward.
- Major groove:
- The groove on a DNA double helix onto which the glycosidic bonds of a base pair (the bonds connecting the bases with the sugars) form an angle greater than 180°.
- Melting, dissociation, denaturation:
- The conversion of double stranded DNA into single stranded DNA by raising the temperature or changing the pH.
- Melting temperature, Tm:
- The midpoint of a melting reaction; the temperature at which half of the DNA in a sample has dissociated into single strands as a result of an increase in temperature. Under standard buffer conditions, most DNA melts between 70° and 80°C.
- Middle repetitious DNA:
- Sequences present in the genome in 10-100,000 copies. This group includes sequences coding for functional RNAs, such as rRNA and tRNA, and some proteins, such as the histones. Most middle repetitious DNA is of unknown function (LINES, SINES, Alu sequences, VNTRs, microsatellites, etc.).
- An imaginary line drawn vertically from the middle of the face and body forming two equal halves.
- Minor groove:
- Groove on a DNA double helix onto which the glycosidic bonds of a base pair form an angle less than 180°.
- A protein or substance that is present in embryonic tissues that induces developmental processes via a concentration gradient.
- mRNA (messenger RNA):
- A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA; directs the polymerization of amino acids (on the ribosome) to form a polypeptide with the sequence dictated by the ordered codons.
- Networks (in the context of networks of genes):
- An interlinked system of many genes that are all important for working together to complete a bodily process such as alcohol metabolism, or acting out an aggressive behavior.
- Neural tube defect:
- Failure of the spinal cord (spina bifida) or brain (anacephaly) to close during early development of the developing fetus.
- Specialized cells of the nervous system that convey information through electrical and chemical signals.
- The chemical messengers of the nervous system.
- Next-gen sequencing:
- Any of several techniques that sequence DNA by synthesis, but read out the sequence information during nucleotide incorporation, eliminating the need to size-separate the products. These techniques can generate sequence from thousands of DNA fragments at a time, reducing the cost significantly.
- Northern blotting:
- The procedure for transferring denatured RNA from an agarose gel to a nitrocellulose filter where it can be hybridized with a complementary nucleic acid. Named by analogy to the Southern blot.
- A cartilage-containing structure found in all embryonic animals whose function is to support the body. Some adult animals, i.e. the vertebrates, lose the notochord during development.
- A small molecule made up of either a purine or pyrimidine base linked to a pentose (sugar), generally either ribose or deoxyribose.
- The repeating subunit of the 100A chromatin fiber, having ca. 200 bp of DNA, the octamer of core histones (two each of H2A, H2B, H3 and H4), and one molecule of H1. Ca. 147 bp of DNA are wound around the histone core in 1.67 left-handed turns; the remaining DNA, the linker, connects to the next nucleosome. H1 is associated with the DNA where it enters and exits from association with the core, and may also contact the linker DNA. The core particle (made up of the histone octamer and 147 bp DNA), which has been crystallized, is a compact disc of ca. 100 A diameter and a thickness of 50 A.
- A nucleoside linked to one or more phosphate groups via an ester bond with the pentose. DNA and RNA are polymers of nucleotides, linked through the 5' and 3' carbons of the sugar.
- Null allele:
- No functional RNA or protein expressed from the gene. Often the function of a gene can be defined by what trait(s) (phenotype(s)) are manifest in the organism when the gene transcript and/or protein is missing.
- Null Hypothesis
- The null hypothesis generally corresponds to what we expect will happen if nothing "interesting" is happening. If you flip a coin many times, and generally get roughly 50% heads and 50% tails, this is consistent with the null hypothesis that the coin is fair. If you flip a coin many times and get 99% heads, the coin may be unfair, and hence you may have cause to reject the null hypothesis that it is fair.
- Olfactory memory:
- Using the odors in the environment to trigger memory. Often the strongest memories are generated with odors. For example, if you smell apple pie, you may think of a time when you ate pie with friends or family. If you are a fly, you may smell alcohol and it triggers memories of behaviors such as feeding and courtship (to lay your eggs in a food-rich environment so your offspring are well-fed and survive).
- A DNA sequence close to the start site of a gene that acts by binding a repressor.
- Origin of replication (ori):
- The sequence of DNA at which replication is initiated.
- A gene that has similar sequence in each species in which it is found because of a common ancestor between the species during evolutionary time. For example, the alcohol dehydrogenase and Malic Enzyme 1 genes are similar in both Drosophila melanogaster and Homo sapiens. Normally, orthologous genes have the same function in each species in which they are found; therefore, studying the function of a gene in a model organism can provide good evidence for the function of the orthologous gene in humans.
- Oxidation-reduction pathway (in the context of cell biology)
- A process that occurs in the "energy factories" of the cell: the mitochondria. Specifically, a series of reactions occurs in the mitochondrial membrane in which electrons are passed from protein to protein; this process eventually produces stored cellular energy (in the form of ATP or NADH). As the proteins lose electrons they are said to be oxidized; as they gain electrons, they are said to be reduced. Some chemistry instructors use the following mnemonic device: LEO the lion goes GER, where LEO = losing electrons oxidation and GER = gaining electrons reduction.
- Partial digestion:
- Cleaving DNA with a nuclease (for example, a restriction enzyme) under conditions of concentration, time, etc. so that the reaction does not go to completion. Some, rather than all, of the restriction sites for that particular enzyme will be cut, so that in a population of molecules, fragments of different sizes will be produced.
- Phosphodiester bonds:
- Covalent bonds in which two hydroxyl groups form ester linkages to the same phosphate group; joins successive nucleotides in RNA or DNA.
- Physical containment:
- Use of sterile techniques, clean hoods, clean rooms (with filtered air, limited access, etc.) to prevent the spread of an organism.
- The distance along the helix axis required for one full turn of the DNA.
- A small circular DNA molecule which carries genetic elements permitting its autonomous extra-chromosomal replication in bacteria or other single-cell organisms. A plasmid can be used as a recombinant DNA vector, to propagate foreign DNA in a bacterial cell. In addition to the essential origin for replication, plasmids generally carry a variety of marker genes, enabling easy identification of cells harboring the recombinant DNA.
- Poly (A) tail:
- The segment of adenylate residues that is posttranscriptionally added to the 3' end of eukaryotic mRNA. About 250 nucleotides of (A) are added by poly (A) polymerase following cleavage of the newly synthesized RNA about 20 nucleotides downstream of an AAUAAA signal sequence.
- A synthetic polymer that can be cast into semi-solid gels for the separation of molecules by electrohoresis. Appropriate polyacrylamide gels can be used to separate DNA fragments at base pair resolution, and are used for DNA sequencing. Caution: in its unpolymerized form, acrylamide is a neurotoxin.
- A short stretch of DNA containing several unique restriction enzyme sites. Useful for cloning.
- Polymerase chain reaction (PCR):
- A method for amplifying a specific DNA segment from a complex mixture in vitro, using short oligonucleotide primers, that exploits certain features of DNA replication.
- Primary transcript:
- The immediate product of transcription, which is often modified before becoming fully functional.
- A short (typically 20 bases) oligonucleotide with a free 3' hydroxyl group that base pairs with a complimentary template strand and functions as the starting point for addition of nucleotides by DNA polymerase to copy the template strand.
- Prior expectation:
- Statistical term for what we expect to happen, or what we believe to be true.
- A defined nucleic acid segment that can be used to identify specific DNA (or RNA) molecules bearing the complementary sequence, through hybridization (Watson-Crick base pairing). The probe is usually labeled with radioactivity (32P), with a fluorescent dye tag, or by some other means to allow its specific detection. The term is sometimes used to describe a specific antibody, used to detect a protein on a Western blot, or used to screen an expression library. A degenerate probe is a collection of DNA molecules synthesized to correspond to a particular amino acid sequence, including all of the possible alternatives resulting from the degeneracy of the genetic code.
- Single-cell organisms that lack a true membrane-limited nucleus and other organelles. This class includes the eubacteria and archaea. These organisms often have a genome made up of one circular DNA molecule; they do not use histones to package their DNA.
- The DNA sequence that binds RNA polymerase, leading to initiation of transcription.
- Protein aggregate:
- A large cluster of a specific protein(s).
- Pulse-chase experiment:
- An experiment in which a synthetic system (often, an intact cell) is supplied with a labeled precursor, followed shortly thereafter by a wash and transfer to medium with unlabeled precursor. This allows one to follow the incorporation of the label into the molecule being synthesized, and to determine the stability and/or destination of the product.
- Reassociation, renaturation, hybridization:
- The conversion of single stranded DNA into double stranded DNA by lowering the temperature or shifting the pH. "Reassociation" or "renaturation" is usually used when referring to the reaction in solution, whereas "hybridization" is usually used when one component of the reaction is fixed, on a slide (as in "in situ hybridization") or on a filter (as in "filter hybridization").
- Recombinant DNA:
- See chimeric DNA.
- The process of producing two DNA molecules from one. In semi-conservative replication, the two strands of the parent helix separate, and DNA polymerase synthesizes a new daughter strand off of each parental strand, following the rules of base pairing (A-T and G-C).
- Replication fork (growing fork):
- The point at which the two strands of DNA are separated to allow replication of each strand.
- Reporter gene:
- A gene that produces a product that is easily monitored, such as ϐ-galactosidease or Green Flourescent Protein. The protein coding region of such a gene is frequently spliced to the regulatory regions of other genes, to provide a convenient assay of the time and tissue specificity of expression dictated by those regulatory regions.
- A protein which, by binding to an operator sequence, prevents transcription of a gene.
- Restriction enzymes (restriction endonucleases):
- Enzymes produced by bacterial cells which recognize specific short sequences of (usually) unmethylated DNA and cleave the duplex. The recognition sites, of four to eight base pairs, are usually symmetric. The ends generated may be either "blunt" or "sticky" depending on the enzyme. Many bacteria contain one or more restriction enzymes, which serve to protect them from foreign DNA. A given restriction enzyme will generate a defined set of DNA fragments (restriction fragments) from substrate DNA by cleavage at the restriction site where it occurs in that DNA.
- Restriction map:
- A linear array of sites on DNA cleaved by various restriction enzymes. The restriction map of a plasmid is circular.
- Reverse transcriptase:
- An enzyme that catalyzes the synthesis of a strand of DNA using an RNA template. Some viruses have an RNA genome, but must produce double stranded DNA as part of their replication cycle. These viruses are called retroviruses; the group includes many RNA tumor viruses, and HIV is a retrovirus. This enzyme adds a new dimension to the "central dogma," as it causes information to flow from RNA to DNA.
- RFLP (restriction fragment length polymorphism):
- Inherited differences in DNA sequences (polymorphisms) among members of a species, leading to variation in the sites of cleavage by restriction enzymes, and hence to variation in the size of the fragments generated.
- An RNA molecule that has catalytic activity. Ribozymes include the self-splicing rRNA precursor in Tetrahymena (splices RNA), the snRNAs in spliceosomes (splices RNA), the RNA component of RNase P (cuts RNA), and the RNA in ribosomes (catalyzes peptide bond formation).
- RNA interference (RNAi):
- A group of mechanisms using small RNA molecules to silence gene expression, and hence protein production, in a cell or organism. RNAi probably originated as a defense against invading retrotransposons and DNA transposons. Silencing can be accomplished either post-transcriptionally (PTGS) by targeting an mRNA for degradation, or at the transcriptional level (TGS), by promoting heterochromatin formation.
- RNA polymerase:
- The enzyme capable of synthesizing a strand of RNA by adding successive ribonucleotides (rNTPs) in the order dictated by a template strand of DNA. Synthesis is in the 5' to the 3' direction by adding rNTPs base-paired sequentially with nucleotides in the template strand. The basic biochemical reaction catalyzed is:
(rNMP)n + rNTP ----> (rNMP)n+1 + PPiwhere rNMP is the growing chain of monophosphate ribonucleosides and rNTP is any of the four ribonucleoside 5'-triphosphates. Note that the enzyme requires a DNA template, but unlike DNA polymerase, it can start de novo, and does not require a primer. Prokaryotes have one RNA polymerase, while eukaryotes typically have three different enzymes, producing rRNA, mRNA, and small RNAs such as tRNA, respectively.
- RNA polymerases I, II, and III:
- The eukaryotic enzymes capable of synthesizing a strand of RNA by adding successive ribonucleotides in the order dictated by a template strand of DNA; see general description of RNA polymerases above. In eukaryotes there are three distinct RNA polymerases which differ in some of their subunits (although other subunits are common to all three); the three enzymes can be separated by column chromatography, and show different sensitivity to α-amanitin. RNA pol I transcribes the rRNA genes; RNA pol II transcribes the genes encoding proteins; and RNA pol III transcribes the genes for tRNAs, 5S RNA, and some additional small RNAs.
- rRNA (ribosomal RNA):
- RNA molecules that are components of the ribosome. rRNA forms the structural scaffold for assembly of the ribosome, and plays a critical role in catalyzing peptide bond formation.
- S1 nuclease:
- An enzyme that specifically degrades single stranded DNA. It is used to cut the loop found at the end of the DNA molecule produced in generating cDNA from mRNA.
- Sanger sequencing:
- Sequencing DNA by copying the template strand into a new strand of DNA in the presence of small amounts of dideoxy nucleotides (ddNTP) tagged with a colored label. Incorporation of a ddNTP stops further synthesis, creating a fragment of defined size tagged as to the base incorporated. Separation of these fragments by size allows one to read out the sequence of the DNA. Named for Fred Sanger, who received a Nobel prize for developing this technique.
- Satellite DNA, simple sequence DNA:
- Highly repetitious DNA; generally based on a short sequence (7-20 nucleotides) repeated up to a million times in the haploid genome. Usually found in heterochromatic regions, often associated with the centromere. The name comes from the fact that this DNA frequently has a composition, and hence a buoyant density, different from the average for the genome, and hence forms a "satellite," distinct from the main band of DNA in a density gradient.
- Screening a library:
- To search through a collection of clones to find one that contains the recombinant DNA of interest. Techniques for screening vary widely, depending on the information available concerning the desired gene. If a homologous DNA probe is available, or if a synthetic (degenerate) probe can be prepared based on the known protein sequence, the screen is generally carried out by filter hybridization.
- Selfish DNA:
- A name sometimes used to refer to DNA within a genome which has no observable function that would benefit the organism. There is a continuing debate as to whether such DNA is "garbage" (which the organism would benefit by getting rid of it if it could) or "junk" (which is of potential use to the organism in an evolutionary sense). In some cases we now have evidence that remnants of transposable elements have become regulatory signals for a specific gene network, suggesting that the latter is the case.
- Sequence identity:
- Regions (DNA, RNA, or protein) of similarity between two or more sequences. This could imply structural, functional or evolutionary relatedness between the sequences.
- Shuttle vector:
- A single plasmid that carries origins of replication for two different species, and hence can replicate in either. It usually also carries selectable genetic markers for each species. In this way, a single vector can be used to manipulate a gene in E. coli, and express the product in yeast, for example.
- Sigma factor (σ):
- The polypeptide subunit of prokaryotic RNA polymerase responsible for identification and specific binding to the promoter. Sigma factor plays a critical role in establishing the open complex required for transcription of double-stranded DNA.
- Single nucleotide polymorphism (SNP):
- When comparing the DNA between two or more individuals, there is one nucleotide (A,T,G, or C) that differs in association with a phenotype or trait. A SNP in an exon will affect the amino acid sequence, whereas SNPs in introns may impact levels of protein production. If there is less alcohol dehydrogenase protein, for example, in the cells of a person or fly then a smaller amount of alcohol would be toxic -- the individual would be "sensitive" to alcohol.
- Snapback DNA:
- A region of DNA having an inverse repeat such that a single strand can form a double helix by looping back and base pairing with itself, generating a "hairpin" or "stem-loop" structure.
- Small nuclear RNAs, which function as the catalysts in the spliceosome, bringing together the 5' and 3' splice sites and facilitating the transesterification reactions that result in splicing.
- Southern blotting:
- The procedure for transferring denatured DNA from an agarose gel to a nitrocellulose filter where it can be hybridized with a complementary nucleic acid. Named for Ed Southern, a Scotsman who invented the procedure.
- Splice sites:
- The 5' and 3' boundaries between an intron and the flanking exons, joined during the process of RNA splicing.
- A 50S to 60S particle containing proteins, snRNAs, and pre-mRNA; it catalyzes the splicing reactions that remove introns, converting the primary transcript into a mature mRNA.
- The usually ribonucleoprotein-catalyzed process by which introns are removed and exons are joined to produce a mature, functional RNA from a primary transcript. Some RNAs are self-splicing.
- Start site, initiation site:
- The nucleotide at which transcription starts; +1
- Sticky ends:
- Complementary single strands of DNA that protrude from opposite ends of a duplex or from the ends of different duplex molecules. Can be generated by some restriction enzymes that make staggered cuts in duplex DNA.
- Stop codon or termination codon:
- A codon that specifies the termination of peptide synthesis; sometimes called "nonsense codons," since they do not specify any amino acid.
- Tertiary structure (i.e., the coiling in space) of a double-stranded circular DNA molecule. Superhelical coils are introduces to relieve the strain when the helix is either underwound or overwound, since the double helix itself is stable in the B-form of one twist per 10 base pairs. A right-handed supercoil is negative.
- Tandem array:
- The same sequence, immediately repeated multiple times. Genes encoding rRNA and the histones are usually in tandem arrays. Repetitious sequences that are NOT in a tandem array are referred to as "dispersed."
- Taq DNA polymerase:
- DNA polymerase from the organism Thermus aquaticus, which resists denaturation at high temperatures and is able to synthesize DNA at temperatures up to 72°C.
- TATA box:
- A consensus sequence TATA(A/T)A found about 25 bp upstream from the start site of a group of eukaryotic genes encoding mRNA, often those that can be transcribed at a high rate. The TATA box binds the TATA box binding protein (TBP), a subunit of TFIID, initiating the process of RNA polymerase II assembly at the promoter in vitro, and plays a key role as a recognition sequence for RNA polymerase II in vivo.
- An enzyme made up of RNA and protein that adds a repeating sequence (one deoxyribonucleotide at a time) to the 3' end of the double helix in a eukaryotic chromosome. Because the telomerase uses its own RNA as the template for this reaction, and synthesizes a strand of DNA, it can be categorized as a reverse transcriptase.
- 30 nm chromatin fiber:
- The next level of packaging of the chromatin fiber above the 100 A “beads on a string” configuration, thought to be a solenoid with ca. six nucleosomes per turn. Available evidence suggests that the nucleosomes are oriented such that the DNA strands are parallel to the fiber axis, and arranged such that linker DNA and histone H1 are on the inside of the fiber. Many details of this structure are as yet unknown.
- Enzymes that change the linking number of DNA. Topo I ("swivelase" or "nicking-closing enzyme") changes the linking number by 1; topo II changes the linking number by 2. Both are abundant enzymes that can relax supercoiled DNA. Topo I is used extensively during transcription; topo II is essential for replication/cytokinesis. Prokaryotes (but not eukaryotes) have a topo II ("gyrase") that can drive formation of negative supercoils.
- Configuration of two sites which are present on two different DNA molecules (compare to cis). A trans-acting regulatory factor is generally a protein, coded for on a different DNA molecule, which can bind to a specific cis-regulatory element affecting gene expression.
- The process of copying one strand of a DNA double helix, creating a complimentary strand of RNA; carried out by RNA polymerase.
- Transcription control regions:
- Segments of DNA within the genome that have an impact on the expression of a gene.
- Transcription factor:
- A protein that promotes or inhibits the transcription of a gene by binding to DNA sequences at or near the gene or by interacting with other proteins that do so.
- Permanent, heritable alteration in a cell resulting from the uptake of a foreign DNA.
- Transforming principle:
- The agent responsible for genetic transformation, i.e., for the acquisition of a new genetic trait; DNA.
- Transgenic organism:
- An organism that contains one or more genes (DNA) from a different organism, stably integrated into the genome.
- Translational study
- Research in a model organisms such as flies or worms that can be applied directly to human conditions. These studies allow scientists to discover what gene variation(s) such as alleles or SNPs are responsible for certain human illnesses including cancer and alcoholism. It is unethical to experiment on humans; therefore, it essential to use model organisms to make medical advances.
- Transposable genetic element:
- A general term for a genetic element that can insert into a chromosome, exit and relocate; includes insertion sequences, DNA transposons, retrotransposons, some phages, and controlling elements. Much of the middle repetitious DNA in eukaryotic genomes is made up of remnants of transposable elements.
- The enzyme that recognized a particular transposon and allows it to insert into or jump our of the host genome. The insertion of a transposon generally inactivates a gene; hence transposons can be used like a mutagen. The mutated gene now contains a known DNA sequence (the transposon), facilitating cloning. This approach to identifying a gene based on phenotype, and recovering its DNA, is called transposon tagging.
- A DNA sequence able to insert itself at a new location in the genome (generally without any sequence relationship to the target site). This DNA generally codes for only one protein, the enzyme (transposase) that accomplishes the insertion (or excision) of the transposon.
- tRNA (transfer RNA):
- Small (ca. 75 bp) L-shaped RNA molecules that deliver specific amino acids, which have been covalently linked to the tRNA's 3' ends, to ribosomes according to the sequence of a bound mRNA. The proper tRNA is selected through the complementary base pairing of its three-nucleotide anticodon with the mRNA's codon, and its amino acid group is transferred to the growing polypeptide.
- Unique DNA:
- Sequences found only once in the genome. Most sequences that code for proteins are unique.
- UnTranslated Region. The 5’ and 3’ ends of a mRNA molecule are typically not translated, and are referred to as the 5’ UTR or the 3’ UTR.
- Vector (or cloning vector):
- A plasmid, phage, or other DNA that is used to maintain and propagate inserted foreign DNA in a host cell for the purpose of producing more copies or a protein product.
- Western blot:
- The procedure for transferring proteins from an agarose or acrylamide gel to a nitrocellulose filter where a specific protein can be detected by using an antibody. [Antibodies are proteins that will recognize and bind to a biological structure (often another protein) with high specificity; antibodies are produced by certain cells of our immune system in response to the presence of a foreign protein/virus/cell.]
- Yeast artificial chromosome (YAC):
- A cloning vector which can accept a large insert of foreign DNA (100-800 kb) and can be propagated as a chromosome in yeast. In addition to the cloning site, the YAC contains selectable markers, as well as the yeast ars (autonomous replication sequence- origin for replication) and centromere. The telomeres in the construct were originally from Tetrahymena. YACs are useful for cloning large genomes.
- Z-form DNA:
- Alternative left-handed form of the DNA double helix which retains Watson-Crick base pairing, but has a zig-zag sugar-phosphate backbone. Z-DNA can exist transiently in cells, and may promote recombination.
A cell of the immune system, which circulates through the blood, bone marrow, and spleen, and plays an important role in antimicrobial defense.
A gelatinous substance used to grow, or culture, microorganisms. Agar provides the microorganisms a surface to grow on and contains nutrients.
A protein in the immune system that recognizes a specific target, or antigen, on a foreign molecule, allowing these two structures to bind together with precision.
A chromosome for which there is an equal number of copies in males and females -- that is, a chromosome that is not a sex chromosome.
A protein which, by binding to an operator sequence, promotes transcription of a gene.
The "genetic code" in a DNA molecule is written in four bases -- adenine (A), cytosine (C), guanine (G) and thymine (T) -- that are arrayed along each strand of the twisted, two-stranded molecule (the famous "double helix"). Each base is chemically tuned to pair, via hydrogen bonds, with a corresponding base on the opposite strand -- A with T, G with C. The size of an organism's genome is usually given by the number of base pairs.
A technique for analyzing interactions of proteins with DNA, consisting of chromosomal immunoprecipitation, followed by massively parallel DNA sequencing.
The combination of DNA and proteins found in the nucleus of a cell, which makes up chromosomes. Chromatin helps fold DNA so it will fit into the cell and is involved in both gene expression and DNA replication.
A structure of coiled DNA and proteins that organizes the genetic material in the cell's nucleus.
The scientific term for cells becoming more specialized throughout development.
DNA encodes the genetic blueprint of an organsim. This genetic material is composed of deoxyribonucleotides -- individual units combining a sugar, a base, and a phosphate group -- that each have different chemical properties, and are referred to by the different base names adenine (A), cytosine (C), guanine (G) and thymine (T). Combinations of these bases "spell out" the code of a given gene.
Proteins with a specific or general affinity for DNA.
The process of determining the specific order of nucleotide bases in a DNA molecule.
Biological molecules (mainly proteins) that catalyze, or increase the rate of, a chemical reaction
The study of changes in gene expression resulting from mechanisms other than changes in the underlying DNA sequence.
The class of organisms, composed of one or more cells, containing a membrane-enclosed nucleus and packaging its DNA with histones in a nucleosome array. Eukaryotic cells typically have complex organelles, such as mitochondria.
An exon is a contiguous segment of a gene found both in the initial transcript and in the final product; the introns are those segments found in the initial transcript which are removed during processing, and so are not found in the finished product.
In molecular biology, a gene is the molecular unit of inheritance for a single function or phenotype -- or, more precisely, the full sequence of bases within a section of the genome that is necessary and sufficient for the synthesis of a functional product. Usually that product is a polypeptide (a section of a protein), but in some cases it is an RNA molecule.
The full complement of genetic information recorded in the chromosomal DNA (or, for some organisms, RNA).
Within a genome sequencing project, annotation is the process of identifying biologically relevant elements within the genome sequence (e.g., genes), and adding information to the sequence on how those elements function.
The specific genetic encoding, or allele of a gene, that leads to an observable characteristic in an organism.
Green Fluorescent Protein (GFP)
A protein first isolated from the jellyfish Aequorea victoria that exhibits bright green fluorescence when exposed to ultraviolet blue light. The GFP gene can be introduced into organisms and used by scientists to "see" gene expression.
An organism containing both male and female reproductive organs within the same individual.
The small, basic proteins used to package the DNA in chromatin. The core histones (H2A, H2B, H3, and H4) are highly conserved over evolution, while histone H1 is more variable.
Histone Code Hypothesis
The hypothesis that combinations of chemical modifications to histone proteins in the chromatin form a complex, separate mechanism for regulating transcription and, thus, gene expression.
An enzyme that removes acetyl groups from the ends of histone proteins.
A gene found in an organism that shares an ancestral sequence with that of another organism. Homologs are often identified based on the retention of shared genetic or protein-level identities between two different species that share a common evolutionary history.
High-Occupancy Target (HOT) Region
Genomic regions where 15 or more independent transcription factors bind.
The process of isolating and concentrating a specific protein of interest by trapping an antibody that binds to that protein, using any of a number of lab techniques.
The intermediate developmental stages that an insect (such as Drosophila) undergoes between molts until it reaches sexual maturity.
The full complement of metabolites -- small molecules produced by cellular or organismal metabolism -- that characterize a cell, cell population, tissue, or organism.
Post-transcriptional regulators that bind to complementary sequences on target messenger RNAs, usually leading to gene silencing.
A non-human species used in experimental biology to study biological processes that might illuminate workings of the same processes in other organisms, for which the same experiments might be infeasible or unethical.
Molting, or ecdysis, is the periodic shedding of the outer skeleton, or exoskeleton, that accompanies the growth of most arthropods, including insects.
The form and structure of an organism.
Next-Generation Sequencing (NGS)
A family of techniques for DNA sequencing that rely on massively parallel processing of many millions of DNA fragments, followed by analysis and re-assembly of those fragments using computer techniques.
A unit of length equal to one billionth of a meter.
The basic unit of DNA packaging, consisting of DNA wound around histones.
The null hypothesis generally corresponds to what we expect if nothing "interesting" is happening. If you flip a coin many times, and generally get roughly 50% heads and 50% tails, that is consistent with the null hypothesis that the coin is fair. If you flip a coin many times and get 99% heads, the coin may be unfair, and hence you may have cause to reject the null hypothesis that it is fair.
A gene that has similar sequence in each species in which it's found because the species have a common ancestor during evolutionary time. For example, the alcohol dehydrogenase and Malic Enzyme 1 genes are similar in both Drosophila melanogaster and Homo sapiens. Normally, orthologous genes have the same function in each species in which they are found; therefore, studying the function of a gene in a model organism can provide good evidence for the function of the orthologous gene in humans
A shallow cylindrical dish, made of glass or plastic, used to grow, or culture, cells, bacteria, and other microorganisms.
The observable characteristics or traits of an organism, resulting from the interaction of the expression of the organism's genes with the influence of environmental factors.
A type of nonverbal communication, usually a chemical or hormone secreted by an animal, which often influences the behavior of other members of the same species. Pheromones are used to establish territory and attract mates.
Giant chromosomes formed by some cells that undergo multiple rounds of DNA replication without actual cell division. The salivary glands of Drosophila contain examples of such chromosomes. Their size makes them especially convenient for work in the lab.
Any of a variety of additional changes to a protein after translation that can modify its behavior and thus affect in gene expression.
A scientific term for offspring.
The class of single-cell organisms, including the eubacteria and archaea, that lack a true membrane-limited nucleus and other organelles.
Biological compounds made up of one or more polypeptides (a chain of amino acids) typically folded into a 3-D form. The sequence of amino acids in a protein is defined by the sequence of a gene.
A variety of processes used to isolate a particular protein from a biological tissue or culture, and thereby to allow the further characterization of the protein's structure and function.
The full complement of proteins expressed by a genome, cell, tissue, or organism.
A protein which, by binding to an operator sequence, prevents transcription of a gene.
A genome sequence assembled from the experimentally obtained sequences of a number of individuals in a species, designed to serve as a representative example of the "typical" gene sequence of that species.
Segments of DNA where transcription factors bind preferentially.
An enzyme that uses RNA as a template to transcribe single-stranded DNA -- thereby reversing the more familiar information flow from DNA to RNA. In addition to its use in the lab, RT has been extensively studied in retroviruses (particularly HIV) that have an RNA genome but must produce double-stranded DNA that becomes integrated into the host cell genome as part of their replication cycle.
The complex molecules that catalyze protein synthesis within the cell.
RNA is composed of nucleotides, just like DNA -- three major differences between the two: (1) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (2) RNA has the nucleobase uracil, while DNA contains thymine; (3) unlike DNA, most RNA molecules are single-stranded.
RNA Interference (RNAi)
The silencing or reduction of RNA expression (which generally correspondes to protein production) for a given gene in a cell or organism. It occurs as a natural process within living cells, but is also a powerful technique for studies of gene expression in the lab.
RNA Polymerase I, II, and III
Enzymes in eukaryotic cells that manage the synthesis of a strand of RNA based on the sequence encoded in the DNA.
A high-throughput technique for sequencing an organism's "transcriptome" -- the RNA transcribed from the genome under investigation.
The sequence of a small fragment of DNA, obtained as part of a high-throughput sequencing experiment.
A pair of chromosomes, usually designated X or Y, in the germ cells of most animals and some plants, that combine to determine the sex and sex-linked characteristics of an individual.
Small Interfering RNA (siRNA)
Short, 20-to-25-nucleotide, double-stranded RNA fragments that interfere with the expression of a specific gene.
Single-nucleotide polymorphism (SNP)
A difference in a single base pair in a given gene sequence, between two or more individuals, or between an individual and a reference genome, that is associated with a difference in phenotype or expressed trait.
The state of equilibrium or inactivity, analogous to hibernation.
During transcription, a DNA sequence is read by RNA polymerase and a complementary RNA copy of the DNA sequence is created.
A consensus sequence, TATA(A/T)A, found about 25 base pairs upstream from the start site of a group of eukaryotic genes encoding messenger RNA -- often those that can be transcribed at a high rate. The TATA box binds the TATA box binding protein (TBP), a subunit of TFIID, initiating the process of RNA polymerase II assembly at the promoter in vitro, and plays a key role as a recognition sequence for RNA polymerase II in eukaryotic organisms.
A protein that binds to a DNA sequence and controls (increases or decreases) the rate of transcription (the flow of genetic information from DNA to RNA).
The full complement of RNA molecules produced in a given cell or cell population.
Transcription Preinitiation Complex
A group of proteins necessary for the start of protein transcription in eukaryotic organisms.
The process in which RNA, produced during transcription, is decoded to produce an amino acid chain (polypeptide) that will then fold into an active protein.
Slang term for the domain of classic lab experiments handling actual and analyzing actual biological materials, as opposed to experiments and work performed using computer analysis.
This is the typical or most common form, appearance, or strain of an organism that exists in the wild, as opposed to the lab. It can also refer to the normal, non-mutated form of a gene that's common in nature.
The earliest developmental stage of the embryo, occurring when two gamete cells are joined by means of sexual reproduction.