Making Sense of Synthetic Biology
Synthetic biology is hot, and there’s plenty being written about this new cutting-edge technology. But reading about synbio can be challenging, since it involves a lot of specialized jargon and technical terminology. Here’s a list of some important terms that will help you understand what we’re talking about when discussing synbio technology.
Adenine – One of the four bases that make up DNA and RNA. Adenine pairs up with thymine (T) in DNA, or with uracil (U) in RNA.
Allele – One variation of a gene. For example, a gene that determines hair color can have several alleles for multiple hair colors.
Amino acid – The building block of proteins, which are essential to all life forms. There are twenty-two different amino acids, twenty of which are encoded by human genes and two are produced by other biological processes. These amino acids, also called residues, can be strung together in different combinations, each combination resulting in a unique protein.
Antibiotic – A chemical or biological substance that kills or inhibits the growth of bacteria.
Antibody – A protein that binds to a foreign substance such as a virus, leading to the elimination of the foreign invader as part of the immune system response.
Base – One of five chemical structures that can make up part of a nucleoside. The names of the bases are adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U). Adenine, cytosine, and guanine are used in both DNA and RNA whereas thymine is only used in DNA and uracil is its RNA counterpart.
Base pair – A specific pairing of bases that enable the helical structure of both DNA and RNA. Cytosine always pairs with guanine using three hydrogen bonds, and adenine with thymine (in DNA) or uracil (in RNA) with two hydrogen bonds
BioBricks – Standard synthetic DNA sequences of known structure and function that can be used as “Lego-like” building blocks. These can be combined in different ways to generate a specific form and function. When inserted into living organisms, BioBricks create new, or replicate existing, biological systems.
Biofuels – Sources of energy derived from biomass such as plants, algae and animal waste products. The use of biofuels could substantially reduce greenhouse gas emissions by recycling carbon dioxide from the air and replacing fossil fuels such as oil. Synthetic biology tools are often used to in the development of biofuels.
Biological part (or simply, part) – is a sequence of DNA that encodes for a biological function, for example promoters or protein coding sequences.
At its simplest, a basic part is a single functional unit that cannot be divided further into smaller functional units. Basic parts can be assembled together to make longer, more complex composite parts, which in turn can be assembled together to make devices that will operate in living cells.
Carbon cycle – The cycle in which carbon is exchanged between the soil, living organisms, water and air. It is key to sustaining life on earth. For more reading on the carbon cycle, visit this blog post.
Chassis – The cell or organism into which BioBricks are inserted, producing a new biological system.
Cloning – Molecular cloning is the process of inserting foreign DNA into a cell in order to create many copies of it and/or translate it into protein.
Codon – A sequence of three nucleotides that codes for a specific amino acid.
CRISPR/Cas9 – A naturally-occurring system that has recently been used as a synthetic biology tool to edit genes. This system allows for the precise inactivation or recoding of any gene through the insertion, deletion or substitution of nucleotide sequences.
Cytidine – One of the four bases that make up DNA and RNA. It consists of a cytosine base bound to a ribose (RNA) or deoxyribose (DNA) sugar.
Data storage – A term that refers to any method used to store and archive digital data. Synthetic DNA can be used to store digital data, which researchers predict would be error-free when recovered after up to 1 million years.
DNA (Deoxyribonucleic acid) – Natural polymer that functions as the unique storage of genetic information in the cell. In its native form, DNA exists as a double stranded helix but the two strands may also come apart and become single-stranded DNA.
DNA synthesis – A process for producing DNA from individual nucleotides in the laboratory. These DNA fragments can be used as gene parts or building blocks to assemble whole genes or libraries. They are also used ubiquitously throughout academia and industry to study biology and develop medical products, such as vaccines and diagnostic tests
Engineering Biology – another term used to refer to synthetic biology (See synthetic biology)
Enzyme – A type of protein that catalyzes chemical reactions such as the degradation of other proteins or the production of organic compounds.
Expression – The process by which genetic information stored in DNA is transformed into a cellular function. Expression is a-2 step process, first transcription of DNA into RNA, and second translation into protein. Examples of expression is the growth of hair and production of insulin to process sugar.
Food safety – The process for keeping food free of contamination and safe for consumption. The tools of synthetic biology are being used to help detect and prevent such contamination.
GMO (Genetically Modified Organism) – An organism created through the use of genetic engineering or synthetic biology. Examples include self-fertilizing plants, pest-resistant organisms and plants that have improved production yields.
Gene – The basic unit of heredity; a specific DNA sequence that codes for a protein or RNA required for the organism to develop and function.
Genome – The complete set of genetic information of an organism, stored in genes made of DNA (most often) or RNA (rare).
Gene editing – The ability to insert a beneficial sequence, replace a mutated sequence or remove a diseased sequence of DNA using systems such as CRISP/Cas9.
Gene regulation – The control of gene expression. This can be effected by turning the expression of genes on and off at specific times through modulation of both direct and indirect factors such as promoters and enhancers.
Genetic engineering – Direct human manipulation of an organism’s genetic material, to add new traits not already found in that organism, or to delete an unwanted disease gene.
Guanosine – One of the four bases that make up DNA and RNA. It consists of a guanine base bound to a ribose (RNA) or deoxyribose (DNA) sugar.
iGEM – A foundation dedicated to advancement of synthetic biology through education and competition. In its annual worldwide competition, college and high school level participants use standard parts and their own design to build new biological systems. To learn more about the 2015 Giant Jamboree at iGEM, please visit our blog.
mRNA (Messenger RNA) – Single-stranded copy of a gene that codes for a specific protein. DNA is transcribed through the action of RNA polymerases generating the pre-mRNA. This sequence then undergoes splicing to eliminate the non-protein coding regions called introns thus generating the mature RNA.
Mutagen – A physical or chemical agent that causes a change in the DNA sequence of an organism. Examples of mutagens are some chemicals in cigarette smoke and the sun.
Mutagenesis – The process by which a mutation is induced in a stable manner. It can occur spontaneously due to errors in DNA replication, as a result of exposure to mutagens, or through experimental manipulation in the laboratory.
Mutagenesis library – A collection of DNA oligonucleotides that can be used to create a group of gene variations, and is used for drug development.
Mutation – Change in a gene that occurs randomly or in response to radiation or chemical mutagens. Alternatively, using the synthesis of DNA, specific mutations can be designed on purpose by researchers for precise and controlled experimentation.
Nanobiology – A branch of biology that deals with biological interactions at a very small (nano) scale, often involving structures that are only millionths of an inch in size.
Nitrogen fixation – A process by which atmospheric nitrogen is converted by some plants into compounds such as ammonia and urea that are required for growth. To read more about the importance of nitrogen fixation, visit our blog post.
Nucleoside – Nucleosides consist of a ribose (or deoxyribose) sugar linked to a base. They are strung together to form DNA and RNA, with a phosphate group linking each nucleoside to the next.
Nucleotide – Nucleoside containing a phosphate group bound to the sugar, and making up the basic building blocks of life.
Oligonucleotide (oligo) – A short DNA or RNA polymer that is usually less than 100 nucleotides in length. It is often man-made (synthetic DNA or RNA).
Pathway – In biology, a pathway describes a series of actions between molecules that can lead to a change in a cell and/or a product such as sugar, protein, fat or organic molecules. A pathway is usually encoded as a string of genes in a long fragment of DNA.
PCR (Polymerase Chain Reaction) – A thermal cycling process for amplifying very small amounts of nucleic acid by several orders of magnitude through the action of polymerases.
Petrochemical – A chemical compound derived from petroleum.
Petroleum – A liquid mixture of compounds composed of hydrogen and carbon (hydrocarbons) found in certain rock strata and derived from the remains of ancient animals and plants. It can be refined to produce starting materials for the production of chemicals (petrochemicals), as well as fuels such as gasoline and kerosene.
Protein – A biological polymer made of amino acids strung together in a specific sequence.
Reaction – A chemical or biological process that results in rearrangement of the molecular structure of a substance to produce a new substance.
Reagent – A substance or mixture used in chemical and biological reactions in the laboratory.
Recombinant DNA – Synthetic DNA molecules that can consist of genetic information from multiple sources, creating genes that would not otherwise be found in the organism. The construction of recombinant DNA is one of the techniques used in synthetic biology.
Ribosome – A cellular structure made up of RNA and proteins that is responsible for translating the information coded in an mRNA into protein.
RNA (Ribonucleic Acid) – A long polymer made up of four ribonucleotide building blocks. RNA is similar to DNA, but is usually single-stranded.
Sequence – The specific order in which amino acids, deoxynucleotides, and ribonucleotides are strung together to form a specific protein, DNA or RNA, respectively.
Sequencing – Process by which scientists determine the specific order of base pairs within DNA, RNA, or protein.
Silicon – A metalloid with highly conductive properties enabling efficient heat transfer. This physical property when applied to the DNA synthesis process, such as in Twist Bioscience’s proprietary synthesis platform, allows for a tighter control over the chemical reactions required, improving yield and synthesis uniformity.
Sustainability – The ability of ecosystems to endure on the Earth. Synthetic biology provides a means of improving sustainability by reducing the use of fossil fuels, decreasing land and pesticide usage through improved agriculture, and advancing healthcare.
Synthetic Biology – is an interdisciplinary field of study combining molecular biology, biotechnology, evolutionary biology, systems biology, biophysics, computer engineering, and genetic engineering. Research in this area typically results in the redesign of existing organisms for useful purposes, using new and interchangeable biological parts. Also known as synbio or more recently, engineering biology.
Synthetic DNA – DNA generated using synthetic biology tools rather than extracted from a living organism. The resulting synthetic DNA can be created in exactly the same sequence as the DNA from a living organism. Synthetic DNA cannot create new organisms (even microscopic ones) from scratch, but can be used to add beneficial character traits to a plant (self-fertilizing, drought tolerant) or engineer new drugs or vaccines like artemisinin for malaria.
Thymidine – One of the four bases that make up DNA. It consists of a thymine base bound to a deoxyribose sugar.
Transcription – Copying genetic information stored in DNA into RNA so that the information can be used to encode protein.
Translation – Synthesizing protein from genetic information encoded in an mRNA copy of a gene using a ribosome.
Uridine – One of the four nucleosides that make up RNA. It consists of a uracil base bound to a ribose sugar.
Vaccine – A substance (antigen) that stimulates the immune system to produce antibodies to one or several diseases and thus provides immunity to them.