User:WillPugarth/sandbox

Introduction
This is my sandbox page. I am just learning how to edit my sandbox so that I can practice creating content and editing it. I am following along with the Training modules in Wikipedia. Hopefully it will be fairly straightforward!

Summary of the Five Pillars
Here is my explanation of the Five Pillars of Wikipedia, the Free Encyclopedia.

The Blue pillar refers to the inherent nature of Wikipedia as an encyclopedia and not a directory or an ad agency.

The Green pillar references the goal of Wikipedia to be neutral in perspective.

The Yellow pillar demonstrates the site's goal of having free content available to everyone.

The Orange pillar requires users to follow etiquette established by Wikipedia users.

The Red pillar defines the rule structure of Wikipedia as being "spirit" based and not extremely restrictive.

More Practice
Here's a bold text option: Bold

And here's a link to something: Pug and Hogarth

Italics are used for genes

Headlines are used on Wikipedia.

Summary of characteristics of target article
Wikipedia article quality is determined in several grades. The highest levels of quality are FA, GA, and A, However for our assignment, we will be attempting to take a "stub" class article and bring it up to B (or higher) level

In order for an article to be considered a "B" level article, it must have enough information to be relatively useful and be arrange so that the information is accessible. Further, ideally it would have sources cited and some amount of images/diagrams.

Improvements that could be made to such an article include improving style, upgrading graphics and illustrations, as well as adding content and more reputable and effective sources.

The advancement of biofuel systems
Recently, the idea that various organisms can be used to power or even produce necessary components has become a popular avenue in advancing biofuel systems. It is known that species of both bacteria and algae are capable of utilizing carbon fixation. Cyanobacteria, which can be made capable of producing FFAs for fuel industry purposes, possess genes that make them particularly resistant to FFA production cellular damage. In addition to cyanobacteria, algae have also been explored as a possible means to alternative fuel cells. In particular, green algae has been explored as a possible replacement for platinum in battery electrodes.

Introductory citations

 * http://ghr.nlm.nih.gov/glossary=transferase
 * http://www.britannica.com/EBchecked/topic/602553/transferase
 * http://www.uniprot.org/keywords/KW-0808
 * pfam.sanger.ac.uk/family/PF02458
 * http://www.ncbi.nlm.nih.gov/pubmed/8443790 (aldehyde transferases)
 * http://ghr.nlm.nih.gov/condition/succinyl-coa3-ketoacid-coa-transferase-deficiency (Ketone transferase)
 * http://www.reference.md/files/D019/mD019880.html (aldehyde-ketone transferases)
 * http://www.yeastgenome.org/cgi-bin/GO/goTerm.pl?goid=16765 (aryl or alkyl transferase, non methyl)
 * https://en.wikipedia.org/wiki/Elevated_transaminases (transaminases)
 * http://www.ncbi.nlm.nih.gov/pubmed/17158705 (phospotransferase)
 * http://toxsci.oxfordjournals.org/content/90/1/5.full (sulfotransferase)
 * http://www.brenda-enzymes.org/php/result_flat.php4?ecno=2.9.1.1 (selenium transferases)

Types of transferases

 * methyltransferase: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3705300/
 * acyltransferase: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762864/ (this one actually has a lot of information on several types of transferases)
 * glycosyl transferase: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3390697/

Structural Citations
Coming soon!

Biological Functions
How transferases work, examples:
 * Terminal transferases: http://www.vivo.colostate.edu/hbooks/genetics/biotech/enzymes/tt.html
 * find various other types of transferases and amalgamate them into descriptions: ie, "Some transferases . . ., while others . . . "
 * Some examples of important transferases and how they work, on a less specific level than the main articles for those compounds

Cofactor Citations
Coming Soon!

Inhibition Citations
Coming Soon!

Kinetics Citations

 * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC232864/ --> article on kinematics of CoA Transferase
 * http://www.sciencedirect.com/science/article/pii/000398617590003X --> another on the same enzyme

looks like this section will be on CoA Transferase in E.coli

Disease Citations
Diseases include:
 * CPT deficiency: http://mda.org/disease/metabolic-diseases-of-muscle/CPT-deficiency
 * smoking-related coronary artery disease: http://www.ncbi.nlm.nih.gov/pubmed/10729397 and http://www.ncbi.nlm.nih.gov/pubmed/15088107
 * In mouse Alzheimer's disease: http://www.jbc.org/content/early/2013/10/17/jbc.M113.503904.abstract

Biotech/Medicine Citations
Coming Soon!

Possible Outline

 * 1) the history and background for transferases;
 * 2) kinds of transferases
 * 3) the general structure of transferases;
 * 4) how transferases work;
 * 5) the energy considerations of transferases;
 * 6) any cofactors, coenzymes, etc.;
 * 7) How are transferases controlled/regulated;
 * 8) Any diseases transferase is involved in;
 * 9) Biotech/industrial/medical research uses relating to transferase

Possible Images
Need to find or make an image including the transferase equation currently given in the text Also need to add images relating to any examples given

--WillPugarth (talk) 19:45, 21 October 2013 (UTC) I'm not sure what you want,but here are some images we can use:
 * http://upload.wikimedia.org/wikipedia/commons/c/ce/Galactose-1-phosphate_uridylyltransferase_1GUP.png
 * http://upload.wikimedia.org/wikipedia/commons/c/cc/1400x1048_pdh_regulation.png
 * http://upload.wikimedia.org/wikipedia/commons/6/6d/Phe_Tyr.png
 * http://upload.wikimedia.org/wikipedia/commons/0/0b/Tryptophan_metabolism.png

Do you think you would want an image for each type? Do you want specific reactions or just images of the transferases themselves? Adimart1 (talk) 02:32, 28 October 2013 (UTC)
 * These are fantastic! We probably want one molecule example for the header image, and the rest can be reactions. But what you added here should be more than enough. Then we can just write up sections that explain the reactions when it is time to revise the sections related to the images you found.  These will save us a lot of time and help us to bulk up the article. --WillPugarth (talk) 04:11, 29 October 2013 (UTC)
 * Glad you like them. I'm not much of a writer, but I am a really good researcher. Adimart1 (talk) 04:35, 29 October 2013 (UTC)

EC Table
Here is a possible table I have been working on for the EC section. It just needs to be filled in:

--WillPugarth (talk) 07:35, 18 November 2013 (UTC)

Previous format:

Transferases are classified into these subclasses:
 * EC 2.1 includes enzymes that transfer single-carbon groups (e.g. methyltransferases, formyltransferases, carboxytransferases, and amidotransferases)
 * EC 2.2 includes enzymes that transfer aldehyde or ketone groups
 * EC 2.3 includes enzymes that transfer acyl groups (acyltransferases) or acyl groups that become alkyl groups during the transfer
 * EC 2.4 includes enzymes that transfer glycosyl groups glycosyltransferases, as well as hexosyltransferases and pentosyltransferases
 * EC 2.5 includes enzymes that transfer alkyl or aryl groups, other than methyl groups
 * EC 2.6 includes enzymes that transfer nitrogenous groups (e.g. transaminase, amidinotransferases, and oximinotransferases)
 * EC 2.7 includes enzymes that transfer phosphorus-containing groups (e.g.phosphotransferase), and is further subdivided based on what type of group acts as the acceptor (e.g. alcohol, carboxyl, etc.) and activity (e.g. polymerase and kinase)
 * EC 2.8 includes enzymes that transfer sulfur-containing groups (e.g. sulfurtransferase and sulfotransferase)
 * EC 2.9 includes enzymes that transfer selenium-containing groups (selenotransferases)
 * EC 2.10 includes enzymes that transfer molybdenum or tungsten-containing groups (e.g. molybdenumtransferases and tungstentransferases)

New images
Images and formula for Galactose-1-phosphate uridyltransferase

EC 2.1: single carbon transferases
EC 2.1 includes enzymes that transfer single-carbon groups. This category consists of methyl-, hydroxymethyl-, formyl-, carboxy-, carbamoyl-, and amidotransferases.  Carbamoyltransferases, as an example, transfer a carbamoyl group from one molecule to another.  Carbamoyl groups follow the formula NH2CO . In ATCase such a transfer is written as Carbamyl phosphate + L-aspertate $$\rightarrow$$ L-carbamyl aspartate + phosphate , or graphically:



EC 2.2: aldehyde and ketone transferases
EC 2.2 includes enzymes that transfer aldehyde or ketone groups. This category consists of various transketolases and transaldolases.  transaldolase, the namesake of aldehyde transferases, is an important part of the pentose phosphate pathway.  The reaction it catalyzes consists of a transfer of a dihydroxyacetone functional group to G3P. The reaction is as follows: sedoheptulose 7-phosphate + glyceraldehyde 3-phosphate $$\rightleftharpoons$$ erythrose 4-phosphate + fructose 6-phosphate 



EC 2.3: acyl transferases
EC 2.3 includes enzymes that transfer acyl groups or acyl groups that become alkyl groups during the process of being transferred. Further, this category also differentiates between amino-acyl and non-amino-acyl groups. Peptidyl transferase is a ribozyme that facilitates formation of peptide bonds during translation. As an aminoacyltransferase, it catalyzes the following reaction: peptidyl-tRNAA + aminoacyl-tRNAB $$\rightleftharpoons$$ tRNAA + peptidyl aminoacyl-tRNAB.

EC 2.4: glycosyl, hexosyl, and pentosyl transferases
EC 2.4 includes enzymes that transfer glycosyl groups, as well as those that transfer hexose and pentose. Glycosyltransferase is a subcategory of transferase that is involved in biosynthesis of disaccharides and polysaccharides through transfer of monosaccharides to other molecules. An example of a prominent glycosyltransferase is lactose synthase which is a dimer possessing two protein subunits. Its primary action is to produce lactose from glucose and UDP-glucose. This occurs via the following pathway: UDP-α-D-glucose + D-glucose $$\rightleftharpoons$$ UDP + lactose.

EC 2.5: alkyl and aryl transferases
EC 2.5 includes enzymes that transfer alkyl or aryl groups, but does not include methyl groups. This is in contrast to functional groups that become alkyl groups when transferred, as those are included in EC 2.3. EC 2.5 currently only possesses one sub-class: Alkyl and aryl transferases. Cysteine synthase, for example, catalyzes the formation of acetic acids and cysteine from O3-acetyl-L-serine and hydrogen sulfide: O3-acetyl-L-serine + H2S $$\rightleftharpoons$$ L-cysteine + acetate.

EC 2.6: nitrogenous transferases
The grouping consistent with transfer of nitrogenous groups is EC 2.6. This includes enzymes like transaminase (also known as "aminotransferase"), and a very small number of oximinotransferases and other nitrogen group transferring enzymes. EC 2.6 previously included amidinotransferase but it has since been reclassified as a subcategory of EC 2.1 (single-carbon transferring enzymes). In the case of aspartate transaminase, which can act on tyrosine, phenylalanine, and tryptophan, it reversibly transfers an amino group from one molecule to the other.

The reaction, for example, follows the following reaction: L-aspartate +2-oxoglutarate $$\rightleftharpoons$$ oxaloacetate + L-glutamate.



EC 2.7: phosphorus transferases
While EC 2.7 includes enzymes that transfer phosphorus-containing groups, it also includes nuclotidyl transferases as well. Sub-category phosphotransferase is divided up in categories based on the type of group that accepts the transfer.(CITE EC2 Intro) Groups that are classified as phosphate acceptors include: alcohols, carboxy groups, nitrogenous groups, and phosphate groups. (CITE EC2 list) Further constituents of this subclass of transferases are various kinases. A prominent kinase is cyclin-dependent kinase (or CDK), which comprises a sub-family of protein kinases. As their name implies, CDKs are heavily dependent on specific cyclin molecules for activation. Once combined, the CDK-cyclin complex is capable of enacting its function within the cell cycle.

The reaction catalyzed by CDK is as follows: ATP + a target protein $$\rightarrow$$ ADP + a phosphoprotein.

EC 2.8: sulfur transferases


Transfer of sulfur-containing groups is covered by EC 2.8 and is subdivided into the subcategories of sulfurtransferases, sulfotransferases, and CoA-transferases, as well as enzymes that transfer alkylthio groups. A specific group of sulfotransferases are those that use PAPS as a sulfate group donor. Within this group is alcohol sulfotransferase which has a broad targeting capacity. Due to this, alcohol sulfotransferase is also known by several other names including "hydroxysteroid sulfotransferase," "steroid sulfokinase," and "estrogen sulfotransferase." Decreases in its activity has been linked to human liver disease. This transferase acts via the following reaction: 3'-phosphoadenylyl sulfate + an alcohol $$\rightleftharpoons$$ adenosine 3',5'bisphosphate + an alkyl sulfate.

EC 2.9: selenium transferases
EC 2.9 includes enzymes that transfer selenium-containing groups. This category only contains two transferases, and thus is one of the smallest categories of transferase. Selenocysteine synthase, whcih was first added to the classification system in 1999, converts seryl-tRNA(Sec UCA) into selenocysteyl-tRNA(Sec UCA).

EC 2.10: metal transferases
The category of EC 2.10 includes enzymes that transfer molybdenum or tungsten-containing groups. However as of 2011, only one enzyme has been added: molybdopterin molybdotransferase. This enzyme is a component of MoCo biosynthesis in Escherichia coli. The reaction it catalyzes is as follows:

--WillPugarth (talk) 00:49, 25 November 2013 (UTC)

History additions
1930s Transamination, or the transfer of an amine (or NH2) group from an amino acid to a keto acid by an aminotransferase (also known as a "transaminase"), was first noted in 1930 by D. M. Needham, after observing the disappearance of glutamic acid added to pigeon breast muscle. This observance was later verified by the discovery of its reaction mechanism by Braunstein and Kritzmann in 1937. Their analysis showed that this reversible reaction could be applied to other tissues. This assertion was validated by Schoenheimer's work with radioisotopes as tracers in 1937. This in turn would pave the way for the possibility that similar transfers were a primary means of producing most amino acids via amino transfer.

Cofactors
transaminase uses puridoxal phosphate (B6) as a cofactor

Mechanisms
Relation of structures between hydrolases and transferases

links at:
 * https://en.wikibooks.org/wiki/Structural_Biochemistry/Specific_Enzymes_and_Catalytic_Mechanisms/Enzyme_Classification
 * http://www.sciencedirect.com/science/article/pii/S0144861700002496

Recent developments
Classification of transferases continues to this day, with new ones being discovered frequently. An example of this is Pipe, a sulfotransferase involved in the dorsal-ventral patterning of Drosophilia. Initially, the exact mechanism of Pipe was unknown, due to a lack of information on its substrate. Research into Pipe's catalytic activity eliminated the likelihood of it being a heparan sulfate glycosaminoglycan. Further research has shown that Pipe targets the ovarian structures for sulfation. Pipe is currently classified as a Drosophilia heparan sulfate 2-O-sulfotransferase.