Standard Biological Parts

Today, I began looking at the standard biological parts used in the process of synthesising DNA. Here are their definitions:


Promoters
A promoter deals with preparing the DNA for transcription and assisting with the process. Transcription is the process of turning DNA into RNA (which is itself later turned into proteins).

In the DNA sequence, the Promoter is typically located near the gene it regulates. The enzyme that is responsible for synthesizing RNA from the DNA, Ribonucleic Polymerase (RNAP) needs somewhere on the DNA strand to bind to so that it can perform its job. This is where the Promoter comes in, providing a secure binding site for the RNAP as well as proteins called transcription factors that help recruit RNAP.

Once bound, a complicated process of synthesis begins, resulting in different types of RNA, dependent on what the gene encodes for (mRNA for genes that encode proteins).



Ribosome Binding Site
The Ribosome Binding Site (RBS) is a sequence found in mRNA that is bound by the ribosome when initiating protein translation.

The mRNA is produced from DNA in the process known as transcription, described above. The Ribosome Binding Site is then bound by a Ribosome. A Ribosome is a component of cells that uses the mRNA as a template for the correct sequence of amino acids. Transfer RNA (tRNA) molecules which are RNA molecules which are bound to a specific amino acid are brought in and mapped to the mRNA sequence. The Ribosome then adds the tRNA's amino acid to the growing peptide chain which is a chain of amino acids.

The polypeptide is later folded into a 3D structure to form a protein.

Protein Domains
Protein domains are logical sections of a protein sequence. Each Protein domain can evolve, function and exist, separate from the rest of the protein chain.

The Protein Domain is a 3D structure and can be thought of as a functioning protein that can join with other Protein Domains to form a larger Protein, with a new function. Because they are self-stable, domains can be swapped by Genetic Engineering between one protein and another.

Because of their nature, Protein Domains play an important role in evolution.

Pyruvate Kinase, a protein from 3 domains

Protein Coding Sequences
Protein coding sequences are DNA sequences that are transcribed into mRNA and in which the corresponding mRNA molecules are translated into a polypeptide chain. Every three nucleotides, termed a codon, in a protein coding sequence encodes 1 amino acid in the polypeptide chain.

Translational Units
Translational units are composed of a ribosome binding site and a protein coding sequence.

Since Translational Units are composed of an RBS and a Protein Coding Sequence, they can be thought of as composite components. Translational units begin with the RBS, the site of ribosome binding and translational initiation, and end with a stop codon, the site of translational termination.


Terminators
A Terminator is a DNA sequence that causes RNA Polymerase to cease Transcription. This sequence marks the end of the gene and signals to the RNAP to release the newly made RNA molecule.

Plasmids
A plasmid is a DNA molecule that is separate from and can replicate independently of the Chromosomal DNA. They are double stranded and typically circular. Plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state.

Plasmids are imporant in Genetic Engineering where they are called 'Vectors'. They are used to multiply or to express a gene within a host cell. Plasmids are inserted into the host cell typically via transformation which are then cloned to proliferate the cells with the added genes.



Primer
A Primer is a short, single strand of DNA that serves as the starting point for DNA replication. A Primer is required because the enzymes that catalyze replication, called DNA polymerases, can only add new nucleotides to an existing strand of DNA.