Team:Aachen/Glossary
Glossary
During iGEM we have got into the habit of using special scientific terms of the “language” of synthetic biology which are not self-explanatory. But for those who do not have a biological background or want to explore an unfamiliar area, a glossary of all these terms is shown below.
Non canonical amino acid
In biochemistry, non-canonical, non-coded, non-proteinogenic, or "unnatural" amino acids are those not naturally encoded or found in the genetic code of any organisms. Naturally, an organism could encode for 20 amino acids.
4,5-dimethoxy-2-nitrobenzylserine (DMNBS)
Serine with O-nitrobenzyl protection group, a non-canonical amino acid (“caged” serine).
Ortho-nitrobenzyl tyrosine (ONBY)
Tyrosine with O-nitrobenzyl protection group, a non-canonical amino acid (“Caged” tyrosine).
They are used in the process of photo-caging with its corresponding orthogonal tRNA/synthetase pair.
Aminoacyl tRNA synthetase
An aminoacyl tRNA synthetase (aaRS) is an enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalysing the esterification of a specific amino acid or its precursor to one of all its compatible equivalent tRNAs to form an aminoacyl-tRNA.
BioBrick
BioBrick standard biological parts are DNA sequences of defined structure and function; These building blocks are used to design and assemble larger synthetic biological circuits from individual parts and combinations of parts with defined functions, which would then be incorporated into living cells such as Escherichia coli cells to construct new biological systems. They represent an effort to introduce the engineering principles of abstraction and standardization into synthetic biology. Examples of BioBrick parts include promoters, ribosomal binding sites (RBS), coding sequences and terminators.
Codon optimization
The vast majority of amino acids are encoded by multiple codons, which means that there are multiple tRNAs that carry any given amino acid. Of any group of "redundant" tRNAs, one is usually much more abundant. Codon optimization is switching the codons used in a transgene without changing the amino acid that it encodes for -- this typically dramatically increases the abundance of the protein, which is encoded by the codon optimized gene; because it replaces “rare” with abundant codons.
Codon
A sequence of three adjacent nucleotides that corresponds to a specific amino acid during protein synthesis. There is at least one tRNA for any codon, and sometimes multiple codons translate into the same amino acid. Many tRNAs are compatible with several codons.
Subtilisin E
Subtilisin is a non-specific, extracellular alkaline serine protease (a protein-digesting enzyme) initially obtained from Bacillus subtilis. It catalyzes the hydrolysis of proteins and peptide amides
Molecular Cloning
Cutting a piece of DNA (restriction digestion) from one organism and inserting it into a vector (ligation) where it can be replicated by a host organism
Dephosphorylation
The process by which phosphate groups are removed from a molecule by an enzyme called phosphatase. Removal of phosphate groups from a DNA fragment can prevent self-ligation.
Site-directed mutagenesis (SDM)
A molecular biology method to create specific, targeted changes (Mutations) in double stranded plasmid DNA. There are many reasons to make specific DNA alterations (insertions, deletions and substitutions), including:
- To study changes in protein activity that occur due to the change in DNA sequence.
- To select or screen for mutations that have a desired property at the DNA, RNA or protein level.
- To insert or remove restriction sites or tags.
Proteolytic Activity
The process of hydrolysis of proteins into simpler, soluble substances (polypeptides or amino acids) by the action of enzymes (Proteases)
E. coli (Escherichia coli)
Escherichia coli (abbreviated as E.coli) are bacteria found in the environment, foods, and intestines of people and animals. It is used extensively in recombinant DNA research because it has been genetically well characterised which makes them desirable organisms for the researchers to work with.
Enzyme
Proteins that catalyze any complex reaction are called enzymes. They are highly specific on where and under which conditions they react (temperature, pH) and are biodegradable.
Some of the commonly used enzymes in laboratory includes:
- Restriction enzymes - also known as molecular scissors, which are used to cleave DNA at a targeted site).
- Ligase - enzymes which are used to fuse two ends of DNA.
- DNA Polymerase – An enzyme which assembles the nucleotides to create a DNA molecules.
- Protease – Enzymes which breaks down proteins (In our case, Subtilisin E).
- Rennet - an enzyme that acts on milk proteins to form curd
- Lactase – enzyme used in ice cream production.
- Trypsin – removes hair from leather products.
