Difference between revisions of "Help:Parts"

Revision as of 19:24, 7 February 2012

What are biological parts

A biological part (or simply, part) is a sequence of DNA that encodes for a biological function, like a promoter or protein coding region. 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. The Registry organizes these parts by their type/function, which means that you can browse for a part that is specific to your needs.

Why use Registry parts

The Registry Catalog

If you wanted to build a traditional electronic device you would first pick up the specific electronic components that you would need (transistors, switches, LEDs, etc). When you go to an electronics store or website you'll find that these electronic components are organized by their function, specification, and requirements. This makes the process of creating your electronic device easier and faster. You don't have to manufacture the components from scratch, and there is already a wealth of information about each part, telling you how they work and how to use them.

The Registry offers this same advantage: you can browse the Registry's catalog of parts to find a promoter, ribosome binding site, protein coding region, and terminator to build a simple biological device to generate a protein.

Documentation & Testing

The BioBrick Standard

Once you've found the parts you want, the second advantage to Registry is that these parts are easily assembled. The "standard" in standard parts will define how those parts will be assembled together by the engineer. A standard, like the BioBrick, ensures compatibility between parts, allowing them to be assembled together creating new longer and more complex parts, while still maintaining the structural elements of the standard. This idempotent characteristic means that any newly composed part will adhere to its standard without need for manipulation, and can be used in future assemblies without issue.

<Too much info? - Parts belonging to the BioBrick standard are flanked on both ends with standard sequences, referred to as a prefix and suffix. The prefix and suffix contain restriction sites, which when used with specific restriction enzymes (cutting) and DNA ligase (connecting), allows parts to be assembled together forming a new part. See the standards help page for more information.>

What types of parts are there

You can check out the help pages for the different Registry part types below. You can browse through the part types on the part catalog.

<ADD> Info on part symbols

	Promoters: A promoter is a DNA sequence that tends to recruit transcriptional machinery and lead to transcription of the downstream DNA sequence.
	Ribosome Binding Sites: A ribosome binding site (RBS) is an RNA sequence found in mRNA to which ribosomes can bind and initiate translation.
	Protein domains: Protein domains are portions of proteins cloned in frame with other proteins domains to make up a protein coding sequence. Some protein domains might change the protein's location, alter its degradation rate, target the protein for cleavage, or enable it to be readily purified.
	Protein coding sequences: Protein coding sequences encode the amino acid sequence of a particular protein. Note that some protein coding sequences only encode a protein domain or half a protein. Others encode a full-length protein from start codon to stop codon. Coding sequences for gene expression reporters such as LacZ and GFP are also included here.
	Translational units: Translational units are composed of a ribosome binding site and a protein coding sequence. They begin at the site of translational initiation, the RBS, and end at the site of translational termination, the stop codon.
	Terminators: A terminator is an RNA sequence that usually occurs at the end of a gene or operon mRNA and causes transcription to stop.
	DNA: DNA parts provide functionality to the DNA itself. DNA parts include cloning sites, scars, primer binding sites, spacers, recombination sites, conjugative tranfer elements, transposons, origami, and aptamers.
	Plasmid backbones: A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. A plasmid backbone is defined as the plasmid sequence beginning with the BioBrick suffix, including the replication origin and antibiotic resistance marker, and ending with the BioBrick prefix.
	Plasmids: A plasmid is a circular, double-stranded DNA molecules typically containing a few thousand base pairs that replicate within the cell independently of the chromosomal DNA. If you're looking for a plasmid or vector to propagate or assemble plasmid backbones, please see the set of plasmid backbones. There are a few parts in the Registry that are only available as circular plasmids, not as parts in a plasmid backbone, you can find them here. Note that these plasmids largely do not conform to the BioBrick standard.
	Primers: A primer is a short single-stranded DNA sequences used as a starting point for PCR amplification or sequencing. Although primers are not actually available via the Registry distribution, we include commonly used primer sequences here.
	Composite parts: Composite parts are combinations of of two or more BioBrick parts.

What else do I need to know

1. Plasmid Backbones act as the packaging for your parts
2. Standards
3. Assembly is how you'll put your parts together to make more complex ones.

How do I...

locate parts

get parts

use parts

add parts

construct parts

send parts