Antigen: A toxin or other foreign substance which induces an immune response in the body, especially the production of antibodies.
Base Pairs: The bonded nucleotides that form the DNA strand. Depending on the species of bacteria, the restriction enzyme will be specialized to recognize and cut different sequences of base pairs.
Chimera: In genetics and molecular biology, a chimera is a single DNA sequence originating from multiple transcripts or parent sequences. Chimeras are generally considered a contaminant, as a chimera can be interpreted as a novel sequence while it is in fact an artifact.
Complementary DNA (cDNA): Single strand DNA that is complementary to RNA or DNA that’s been synthesized from mRNA, in a lab, by reverse transcriptase.
DNA or Deoxyribonucleic Acid: A nucleic acid (one of two such acids found in nature) that serves to store genetic information about an organism in a way that can be transmitted to subsequent generations. The other nucleic acid is RNA, or ribonucleic acid. DNA carries the genetic code for every single protein your body makes and thus acts as a template for the entirety of you. A string of DNA that codes for a single protein product is called a gene. DNA consists of very long polymers of monomeric units called nucleotides, which contain three distinct regions and come in four distinct flavors in DNA, thanks to variances in the structure of one of these three regions.
DNA sits in the cytoplasm of the cell, as prokaryotes lack nuclei. In eukaryotic cells, DNA sits in the nucleus. Here, it is broken into chromosomes. Humans have 46 distinct chromosomes with 23 from each parent. These 23 different chromosomes are all distinct on physical appearance under a microscope, so they can be numbered 1 through 22 and then X or Y for the sex chromosome. Corresponding chromosomes from different parents (e.g., chromosome 11 from your mother and chromosome 11 from your father) are called homologous chromosomes. DNA provides fundamental and distinctive characteristics or qualities of someone or something, especially when regarded as unchangeable, but can be changed with gene editing or genetic engineering, thus forming the original organism into a chimera.
Exogenous DNA: Originates outside the organism. The introduction of exogenous DNA into a cell is called transformation or transfection in cells. This can take place artificially or naturally. Methods of artificial transfection include: Chemical methods; including calcium phosphate precipitation DEAE–dextran complex and lipid mediated transfer; Physical methods, including electroporation, micro-injection and biolistic particle delivery (gene gun); Using recombinant, lab manipulated viruses as vectors
Gene: A segment of Deoxyribonucleic Acid (DNA) is inside every cell of all organisms that carries the genetic code for assembling a particular protein product. Genes determine what organisms (animals, plants, fungi and bacteria) are and what they are destined to develop into. While the behavior of genes is influenced by environmental factors (e.g., nutrition) and by other genes, the composition of your genetic material dictates almost everything about you; visible and unseen. The size of your body is a result of your genes. Your response to microbial invaders, allergens and other external agents are also part of your genes.
Gene Editing: The discovery in the 1960s of restriction endonucleases, also known as restriction enzymes, led to a breakthrough in gene editing. These enzymes cut DNA at specific locations in the chain of base pairs. In plain terms, this involves snipping a strand of host DNA using special enzymes, inserting the new gene into the gap created by the snipping and attaching the DNA at both ends of the gene to the host DNA. The first instance of modern genetic modification was in 1973, when Herbert Boyer and Stanley Cohen transferred a gene from one strain of bacteria into another; the gene coded for antibiotic resistance. The following year, scientists created the first genetically modified animal, when Rudolf Jaenisch and Beatrice Mintz successfully inserted foreign DNA into mouse embryos. Scientists began applying genetic engineering to a wide field of organisms for a burgeoning number of new technologies.
Gene Therapy: Human gene therapy seeks to modify or manipulate the expression of a gene or to alter the biological properties of living cells for therapeutic use in those with a defective gene. In someone with a defective gene, a copy of the working gene can be introduced into that person’s cells so that the required protein can be made using foreign DNA. Then decide where in the target DNA that gene will go. A vector must be found for transfer into the recipient organism. A vector is a piece of DNA, often from bacteria or yeast, in which the gene can be inserted. Also needed is an appropriate restriction endonucleases–an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. These enzymes can be cut short (4-8 bases) so that other lengths of DNA can be inserted in their place. The target and vector DNA are finally blended in the presence of DNA ligase, an enzyme that links them together to produce recombinant DNA.
Genetically Modification (GMO): The process of altering an organism’s genotype, the sum of its individual genes, and hence its genetic “blueprint” is known as genetic modification or genetic engineering. Genetic modification is any process by which genes are manipulated, changed, deleted or adjusted in order to amplify, change or adjust a certain characteristic of an organism. It is the manipulation of traits at the cellular level. In plain terms, this involves snipping a strand of host DNA using special enzymes, inserting the new gene into the gap created by the snipping and attaching the DNA at both ends of the gene to the host DNA.
Genetic Engineering: The deliberate modification of the characteristics of an organism by manipulating its genetic material. The ability to change, modify or engineer genes in specific ways would therefore introduce the option of being able to create exquisitely tailored organisms, including humans using given combinations of DNA known to contain certain genes. It happens in a laboratory instead of by selective breeding, since genes are copied and moved from one piece of DNA to another, or from one organism’s cell to another organism’s DNA. This relies on a ring of DNA called a plasmid. Plasmids are present in bacterial and yeast cells, and are separate from chromosomes. Although both contain DNA, plasmids are typically not necessary for the cell to survive. While bacterial chromosomes contain thousands of genes, plasmids contain only as many genes as you would count on one hand. This makes them much simpler to manipulate and analyze.
Genome: The material used to store genetic information in the nuclei or mitochondria of cells; either DNA or RNA. The genome includes both the genes–the coding region, and non-coding DNA, as well as mitochondrial DNA and chloroplast DNA. The study of genes is called genomics.
Messenger RNA (mRNA): A single strand RNA molecule that is complementary to one of the DNA strands. It is found within all forms of cellular life, and it has been described as a sister molecule to DNA. mRNA is an RNA version of the gene that leaves the cell nucleus and moves to the cytoplasm where proteins are made. During protein synthesis, an organelle called ribosome moves along the mRNA, reades its base sequence and uses the genetic code to translate each 3-base triplet or codon into its corresponding amino acid.
Molecular Biology: The molecular basis of biological activity between the various systems of a cell, including the interactions between the different types of DNA, RNA and proteins and their biosynthesis, and studies how these interactions are regulated.
Polymerase: An enzyme that synthesizes long chain polymers or nucleic acid. DNA and RNA polymerase are used to assemble DNA and RNA molecules, respectively, by copying a DNA template strand using base-pairing interactions or RNA by half ladder replication.
Provirus is a virus genome that integrates into the DNA of the host cell. This can be a stage of virus replication, or a state that persists over longer periods of time as either an inactive viral infection or an endogenous viral element. In inactive viral infections the virus will not replicate except in replication of its host cell that can last over many host cell generations. Endogenous viruses are always in a state of provirus. When a non-endogenous virus invades a cell, the RNA of the retrovirus is reverse-transcribed into DNA by reverse transcriptase, then inserted into a host genome by integrase. A provirus does not directly make new DNA copies of itself white integrated into a host genome in this way. Instead it is passively replicated along with the host genome and passed on to the original cell’s offspring.
All descendants will also have provirus in their genome. This is known as the lysogenic cycle, a viral reproduction. The lytic cycle involves the reproduction of viruses using a host cell to manufacture more viruses; the viruses then burst out of the cell. The lysogenic cycle involves the incorporation of the viral genome into the host cell genome, infecting it from within. Integration can result in a latent infection or a productive infection. In a productive infection, the provirus is transcribed into mRNA which directly produces new virus, which in turn will infect other cells via the lytic cycle.
RNA/Ribonucleic Acid: A nucleic acid present in all living cells. Its principal role is to act as a messenger carrying instructions from DNA for controlling the synthesis of proteins, although in some viruses RNA rather than DNA carries the genetic information.
Recombinant DNA (rDNA): Is made by combining DNA from two or more sources. Recombinant DNA molecules are DNA molecules formed by a laboratory process of genetic recombination to bring together genetic material from multiple sources, creating sequences which would not otherwise be found in the genome, such as molecular cloning. Recombinant DNA is the general name for a piece of DNA that has been created by combining at least 2 strands. The process depends on the ability of cut and re-joined DNA molecules at points identified by specific sequences of nucleotide bases, or restriction sites. Different techniques are required if the goal is to introduce the new DNA into the cell of an organism that is not bacteria, One of these is a gene gun, which blasts very tiny particles of heavy-metal elements coated with the recombinant DNA at plant or animal tissue. Two other techniques require harnessing the power of infectious disease processes. Scientists remove the disease-causing genes from the plasmid responsible for the disease-inducing plasmid. They replace those genes with whatever genes they want to transfer into the organism so that it will become “infected” with the desirable DNA. If the DNA source was a different species, the new plasmid is called recombinant DNA, or a chimera. Once the plasmid is reintroduced into the bacterial cell, the new genes are expressed as if the bacterium had always possessed that genetic makeup. As the bacterium replicates and multiplies, the gene will also be copied.
Retroviral Vectors: A portion of DNA containing certain genes is put into special kinds of viruses, which then transport the genetic material into the cells of another organism. This material is incorporated into the host genome so that they can be expressed along with the rest of the DNA in that organism.
Retrovirus: A type of virus that uses RNA as its genetic material. After infecting a cell, the virus uses an enzyme called reverse transcriptase to convert its RNA into DNA. The retrovirus then integrates its viral DNA into the DNA of the host cell, which allows the retrovirus to replicate. Retroviruses are RNA viruses which reverse transcribe their RNA genomes into DNA’ the DNA is then integrated into the host genome, where it serves as a template for the synthesis of new RNA genomes. Retroviruses may enter the host cell either by direct fusion or by fusion after internalization using the endocytic route. Fusion results in the release of viral nucleoprotein core particles into the cytoplasm. This is followed by a poorly understood uncoating step and the formation of the reverse transcript=tion process. While significant progress has been made in understanding the general nuclear entry mechanisms used by viruses, much remains to be done. It is evident that different viruses use different host nuclear import pathways, and viral genomes gain access to the nucleus of their host cells not only by using the cellular nuclear import machinery but also components of other cellular pathways, such as components of the apoptotic machinery.
Reverse Transcription of RNA to DNA: Is used to generate complementary DNA (cDNA) from an RNA template, the process of reverse transcription. Reverse Transcriptase are used by retroviruses to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes, and by some non-retroviruses. (pg 54)
Transfection: The process of deliberately introducing purified nucleic acids into eukaryotic cells. It may also refer to other methods and cell types though other terms are preferred. Transfection involves the opening of transient pores or holes in the cell membrane to allow uptake of material. Transfection can be carried out by calcium phosphate and electroporation, by cell squeezing or by mixing cationic lipids with material to produce liposomes that fuse with the cell membrane and deposit their cargo inside. Transfection can result in unexpected morphologies and abnormalities in the target cells–how DNA of the nucleus is changed: Transfection
Viral or Plasmid Vectors: The introduction of a gene into a phage (a virus that infects bacteria or their prokaryotic relatives) or a plasmid vector, then place the modified plasmid or phage into other cells to introduce the new gene. The use of such vectors can amplify an existing characteristic instead of creating a new one. A viral vector can be used to transfer DNA into a plant or animal cell. The disease-causing genes are removed and replaced with the desired genes, which may include marker genes to signal that the transfer occurred.