Chemistry

From the early 19th to the current 21st century people have come to rely on electricity almost as much as much as the water they drink and the air they breathe. This relationship came about from the integration of electronic based technologies and a society that has growing increasing dependent on them for either education, entertainment and even a means of comfort, all of which has ensured that the society as most people know it today would cease to exist should electricity ever stop flowing into the gadgets that they use on a daily basis. With the current electricity crisis engulfing the U.S. society as most people know is in danger of ceasing to be. The luxuries and comforts taken for granted such as air-conditioning, televisions, private computers and internet access all of the comforts of home that society has prized so much has the potential of being lost to many individuals. As such what is presented here and now is a quandary of possibilities faced with facts, of potential versus actual truths and the an inevitability faced with mere potential. With the current need for electricity the U.S. government is planning to build a nuclear power plant only a few minutes away from this current location and as such due to the relative distance of the plant to this community it will be the first to benefit from a greatly enriched power grid (Macfarlane 2010). Luxuries and comforts that are endanger of disappearing will be reinstated and people will be able to get along with their lives in a similar fashion to the way things were years ago. Yet not everything is good news, with the creation of a nuclear power plant so close by what this community is faced with is the potential from possible radiation sickness, the probability that something may go wrong and the possibility of a nuclear explosion that would claim the lives of everyone around here (Meshkati 2007). With this in mind what must be considered is whether or not the benefits outweigh the costs and if possible wouldnt there be some other way to produce electricity for the country

Benefits and costs
Building a nuclear reactor is no easy matter for one thing the sheer costs of construction estimated at 6 -  8 billion dollars is no laughing matter not to mention the fact that the sheer amount of space needed for such a venture would virtually eliminate previous areas where people from surrounding communities may have used as recreation areas (Bilbao 2010). Not only that but the environmental costs in the form  of trees and forests clear for development as well as the nuclear waste in the form of spent nuclear fuel rods presents a clear and present danger for people in communities around the reactor. The Chernobyl nuclear plant disaster come to mind where a breached nuclear reactor and ill used cooling system resulting in a massive nuclear disaster which affected thousands of individuals, poisoned large swaths of land and made nuclear emergency generation synonymous with danger and death (Miller 2010). What must be considered though is that science learns from its mistakes and that the present versions of nuclear energy generation are far removed from that used in Chernobyl with high margins of safety and fewer possibilities for nuclear accidents from occurring (Berger 2010). Also one of the best aspects of constructing a nuclear power plant nearby is that of course initially provide construction jobs and create quick economic growth for the community due materials being sourced from local stores and depots. When the plant is finished it would also continue to provide jobs in the form of maintenance engineers, technicians, plant workers etc. Having a nuclear power plant nearby is boon for any community since with it comes the potential for prosperity. If radioactive wastes are an issue for community leaders none of it actually gets stored in the area surrounding the reactor itself instead a large container depot at Yucca mountain as been chosen as a site to hold the nuclear wastes accumulated from energy production till the spent nuclear fuel rods eventually cycle through their half life stages and become inert (House 2010).

Other alternatives to nuclear power
While it is true that their are other alternatives to nuclear power in the form of renewable energy resources such as wind,, solar, hydro and geothermal power most of these forms except for solar energy are location specific meaning that they only work in locations with the ideal environment needed for the technology to work properly (Lloyd-Evans 2010). Solar power on the other hand could work nearly everywhere however with the current level of technology solar power collectors would need a land area several times that used by a nuclear reactor in order to produce the same amount of energy and even though the source of the energy is free the initial costs would be just as heft as building a nuclear reactor. Nuclear reactors can be built almost anywhere with a large source of water needed as a coolant for the nuclear fission process (Bilbao 2010). On the other hand it must be noted that renewable sources of power do have their benefits as being a cleaner and much safer technology to use as compared to nuclear reactors not to mention the fact that their initial costs are usually quickly recouped from the relatively free source of energy. The thing is though renewable energy technologies are still in their infancy that while they are able to contribute to the energies sourced from power grids they are still unable to fully provide for the energy needs of the entire U.S. population. This is due to the fact that conventional electricity generating technologies such as coal, fuel and nuclear power plants are able to produce far more energy than the average renewal energy technology can provide at its current state. Not to mention the fact that in order for many viable renewable energy technologies to produce enough power there is an inherent need to create more units to gather it namely more wind turbines, more solar panels, more water turbines whereas with conventional energy producing plants there has been a need to produce only one structure without have to be overly concerned over the precise location in relation to the kind of energy resource that is being used.

The needs of the many outweigh the needs of the few
When building a nuclear reactor in a certain location what must be taken into consideration is the fact that building one isnt just for the sake of the community itself but rather for the sake of the larger American community. With the current energy crisis affecting numerous states it isnt just a single community that is being affected but hundreds scatters all throughout the United States. What ac community must consider when allowing a nuclear reactor to be built close by is that they are not the only ones to benefit rather it the greater American populace that benefits as well. If the area surrounding the community presents one of the best places to build a nuclear reactor then the community should allow it to be built for the sake of the rest of the people living in the country. An old saying comes to mind with this particular situation the needs of the many outweigh the needs of the few with this in mind the community should look out for others who are suffering just as they have been by allowing the creation of a nuclear power plant that would alleviate their suffering and bring the good times back again.

Conclusion
Based on what has been stated in this paper so far it can be said that the creation of a nuclear power plant close to the community while bearing a certain amount of risk presents itself as a great opportunity for people within the area to have better jobs and to be able to uplift the current economic status of the area in a much more vibrant one. While it is true that there are alternative forms of energy that could be pursued due to the fact that a lot of them are location centric it would be far more viable to be able to create a nuclear power plant with a proven record of being able to work nearly everywhere than on a type of technology that has a certain degree of selectiveness.    

The properties of plastics are determined by the polymers that constitute the unit. Based on this, plastics can be modified into biodegradable products by varying the constituents synthetically. Their chemical structures vary due to the substituting polyesters in the polymer chain. Lets study about the chemical differences and structure of green plastics PHA and PLA. Amylose and Amylopectin are the major polymer components of starch. In the link structure, all identical chain points are connected to CH2OH group. The oxygen in the ring structure chain facilitates degradation when reacted with water. Any hybrid variety can be produced with two components renewable natural polymer (starch) and petroleum based synthetic polymer (PCL).

Polylactide (PLA) is a bioplastic basically made from starch, the basic building material. Here lactic acid (CH3CHOHCOOH) is produced through fermentation where microorganisms convert sugar feedstock into lactic acid. The lactic acid thus isolated is depolymerized to lactide and by Ring-opening polymerization with catalysts it is converted into Polylactide polymer of high molecular weight. Based on the particle size, the rate of biodegradability and transparency varies. They find use in soluble fibers, compose bags and renewable products.

Polyhydroxyalkanoates (PHA) polymers are produced naturally by microorganisms directly from sugar feedstock. The polymer is isolated, purified and processed. These components can be controlled by varying the ratio of sugar feedstock. Synthesized PHA is copolyester composed of 3-hydroxy fatty acids hydroxybuterate, hydroxyvalerate and hydroxyhexanoate. In all PHAs the hydroxyl substituted carbon atom is steriochemical -R configuration. Since they are composed of short chain and long chain length R groups, they are used for a variety of commercial applications.

This essay is a review paper on the article Insulin by Nanette M. Wachter. The author of the article Insulin deals briefly about the various aspects of Insulin, namely- history, source, structure, manufacturing process, metabolic function and the clinical importance.  The article is well structured, written in a concise, coherent and impressive manner. The Chemical structure of Insulin is given in a pictorial form for easy understanding. This article is useful for beginners of Biochemistry and for all laymen for getting a grasp of the subject.

This article gives important information about Insulin. It covers details like The discovery of Insulin, natural and commercial sources of Insulin, its Chemical structure, and Biological functions.  The article also deals briefly about the causes of different types of Diabetes and the importance of Insulin in combating Type 1 Diabetes. The different formulations and the mode of administering the insulin are also discussed.

Insulin is a Biochemical which controls the metabolism of Glucose in animals including humans. It is a hormone, and is classified as a protein. Structurally, it is a cyclic peptide, having 51 amino acids, arranged in two chains, A and B, and the chains are linked by two disulphide bridges formed out of the Cysteine amino acids of both the chains. It is produced by the beta cells of pancreas.

Role of Insulin in metabolism of Glucose
Insulin, released to the blood stream by pancreas at the instance of rise of blood glucose, binds to the Insulin receptors on the cell membrane releasing the glucose transporter protein to
the surface of the cell membrane then the glucose transporter protein carries the glucose

molecule to the interior of the cells, for further metabolism. Thus in the absence of Insulin, glucose cannot be transported to the cells and the cells will starve of glucose. Hence, the failure of pancreas to produce insulin results in development of Type 1 Diabetes. Prior to its discovery in 1920s by a team consisting Frederick Grant Benting, John James Richard Macleod and Charles Best, there was no remedy for people having Type 1 Diabetes and this deficiency disease, caused by auto immune disorder, resulted in fatality with in a few years of onset.

Soon after its discovery, insulin was recovered from pancreas of cows and pigs for clinical use. Now human Insulin is produced by recombinant DNA Techniques. Current effort of mass production of human insulin is based on genetic engineering using bakers yeast having human genes.

In Type 2 Diabetic persons, though the pancreas produces Insulin, there is resistance in the tissues to insulin and hence glucose is not metabolized properly, resulting in Diabetes 2.

Insulin is a typical Bio chemical. It is found in living organisms (animal), and is synthesized by the beta cells of pancreas. The article deals with the Chemical structure, source, synthesis (natural and commercial), functions, and biochemical mechanism of its activity.

Though the article does not cover the subject extensively, nevertheless, it is informative. It deals with the relevant details connected to the deadly diseases  Diabetes. The details are given in an arranged, coherent and convincing manner. The data given are all useful and reliable.

The diagram of the structure of Insulin is very simple and easily understandable. We can
recommend this article to students (beginners) of Bio chemistry and to laymen for giving them a grasp of the basic knowledge about Diabetes and the relationship it has got with Insulin.

This week my contributions to the problem of global warming, and subsequently the size of my carbon footprint are the same as they are every week. My daily routine means that I am contributing a lot to the problem of global warming and adding to the levels of carbon dioxide, methane and chlorofluorocarbons in the atmosphere. I drive my car every day, to school and to the shops, to see friends and to run other errands. I burn fossil fuels when having a BBQ at home or with friends, and I use chlorofluorocarbons during my daily routine. In order to cut down these levels of use, I would have to change my lifestyle in a number of ways, for example I could take public transport instead or walk to locations that are close to my home, I could switch the products that I use that contain methane and chlorofluorocarbons.

My personal contributions towards air pollution from exhaust fumes and other particles are quite large. As noted previously the exhaust fumes from my car are adding to the air pollution problem. The possible actions that could be taken to lower these levels of contribution would be to change my car for a more environmentally friendly automobile such as the Toyota Prius. I could also decide to ration the use of my car, and use it on alternate days instead of every day of the week.

My personal contributions towards ozone depletion are also fairly large, and they include aerosol use from deodorants and other products that I use that come in a compressed can. Actions to reduce my own levels of contribution to the ozone depletion issue could involve switching to non aerosol based products or to check the products before purchase to ensure they contain no chlorofluorocarbons. Since the problem with the hole in the ozone layer, chlorofluorocarbons have been slowly phased out of most of the aerosol products around the world.

The contributions made to the LA smog problem are again quite big, and could be reduced in some ways. My use of a car, of aerosols, along with having BBQs are things that I do nearly every day, and are things I should try to stop. Rationing my use of these products would help to reduce emission levels.

There is a tree outside my parents house, which has been there since I can remember, and when I was a child I used to climb the tree regularly and play there with friends, we made a tree house and had a lot of fun in this tree when I was younger. I brought the tree a wheelbarrow of composted material from my parents recycled organic waste and spread this around the base of the tree, I then gave the tree a drink of water from the hosepipe and said thank you to it for the oxygen it provides as well as apologizing to the tree for the damage the human race are causing the planet and to many millions of other trees around the world. I felt sad doing this, because the tree outside my parents house is very lucky compared to some trees that are being destroyed for illegal logging, and fossil fuel consumption. I was not aware that this is common in many cultures, but I am not surprised to find out that it is, we in the western, modernized world have forgotten our roots and what made us into the race of people we are, and that we have only begun to destroy the world in this way during the last one hundred fifty years since the industrial revolution. I think it should be commonplace to do this in our culture, and it may make people more aware of the damage we are causing the planet as a race, and may help to combat global warming and the destruction of our forests. I think it would make a big difference to the mentality of people if they were made to say thank you to nature for what it has given us as a species, and I think this idea would help change our collective attitudes and make us more aware as people if we were to adopt this idea and make sure at an elementary school level students are taught to do this as a requirement for their biology classes.

Phosphorous is a major essential element found in abundance to forms of life for their activities. Other than in life activities, it is also important in diverse applications and so many other industries. In nature phosphorus is never found free. Because of its reactivity with air and other oxygen containing substances it occurs as bound to other elements mostly as inorganic phosphate in minerals. Phosphorus is the eleventh most abundant element on the surface of the earth. Some of the most popular and widely occurring ores are apatite, found in rock phosphate. Apatite is an impure tricalcium mineral. Others are phosphorite, phosphorate and some others.    

Phosphorous is a polyvalent non-metal grouped in the nitrogen group of the periodic table of the chemical elements. Elemental phosphorous exists in white and red forms. Whit phosphorous reacts with air to glow due a phenomenon called phosphorescence (a kind of chemiluminiscence). With an atomic number of 15 and denoted by the chemical symbol P, phosphorous is used by all plants. In P-deficient soils it is given as phosphate fertilizers. Algae thriving on soils and water bodies are due to eutrophication (1) and indicate high phosphate levels. In biological systems phosphorous in a dynamic state both as free as unique inorganic phosphate (Pi) andor as bound in mostly organic forms such as with nucleotides and ATPADP and many other molecules.

The major use of phosphates is as agricultural fertilizers. Phosphorous has no synthetic source and is dependent upon mining only and is used and wasted as never earlier. Therefore there is warning signal of the impending shortage of phosphate very soon as early as in the next three decades phosphate sources. There is an international urge to look for alternate sources as well recycling of the used phosphates. In the either situations the critical requirement is that of a reliable cheap and a rapid technique for determination of phosphorous.

The analytical chemistry of phosphorus is very important in many fields, for example, medical and clinical science, agriculture, metallurgy and environmental science. Moreover, in recent years large quantities of phosphate have been used in beverages, detergents, fertilizers6 and also in sugar industries.
Phosphorus is designated as an important plant nutrient and as a result comprises a significant part of agricultural fertilizers and phosphate production has sharply risen in the past half a century. However, phosphorus-based compounds typically have a low solubility. The issue of phosphorus determination has attracted considerable academic research. Pardo et al (2) outline the growth in phosphate concentrations in water and attribute this to increased eutrophication. Environmental problems created by phosphorus and many other inorganic and organic pollutants have generated a great interest in improving methods for accurate and rapid qualitative and quantitative determination of phosphorus.

Definition
In water phosphorous can exist in different forms. The total phosphorus concentration denotes the aggregate of the percentages of these of these percentages. According to Pardo et al (2), labile phosphorus, phosphorus is usually linked with aluminium, iron and manganese oxides and hydroxides. In contrast, phosphorus is often linked with calcium, both in organic and residual phosphorus with calcium, organic phosphorus and residual phosphorus. The aggregation of labile phosphorus and phosphorus connected to AlFeMn oxyhydrates is referred to as non-apatite inorganic phosphorus (NAIP) and calcium associated phosphorus is also named apatite phosphorus (AP). These forms of phosphorus are the most important fractions and this paper will limit its scope to determining these forms of phosphorus.

The need and Contexts for Phosphorus Analysis 
In such diverse situations the need for phosphorus analysis is only underestimated and understated in policy matters. The complexity and diversity of the needs are so very wide that a generalized approach may never be possible. There are the environmental issues concerning, water, air, soils and mineral sites. The quantity ranges required for analysis in such situations would be in milligrams or grams. On the other hand in a biological context would be in milligrams or much less. In clinical researches the accuracy and quantities would be much finer. In a purely analytical sense a different strategy would be required for very high purity detection by more sophisticated and expensive methods but for a high precision

Thesis Statement
The purpose of this paper is to demonstrate some commonly used laboratory techniques employed to classify the percentage of phosphorus present and its concentration. Various techniques of differing complexity exist to achieve this outcome and the paper will classify the best methods that provide precise means of detecting phosphorus using modern chemical experimental equipment.

Literature Review
Various phosphate determination procedures have been developed for a long time and used reported (3). Some of the popularly used methods are titrometry, complexogravimetry, colorimetry, atomic absorption spectroscopy, flow injection analysis, HPLC and spectrophotometry methods. Spectrophotometry uses molybdovanadate and ammonium molybdate are most commonly used. In ammonium molybdate spectrophotometric method, different reductants have been employed such as tin(II) chloride, ascorbic acid and 1-amino-2-naphthol-4-sulfonic acid.

Spectroscopy methods are popular because of the sensitivity of the method and ease of converting organic phosphorous into a blue colored complex by several reducing agents. These methods or modifications are based on the original report by Bell, R. D. and Doisy (5). Many modifications of this original method are available (e.g., 4, 6, later 7, 8 and many more). Some of the most recent methods based on this principle but with modifications are 9, 12,12a, 12b, 12c and many more.

One of the oldest methods most popularly used method was described by Fiske and Subbarow (4). They used the reduction of phosphomolybdic acid by hydroquinone suggested earlier by Bell and Daisy (5) modified later by Briggs (6), many later modifications) for blood and urine analysis for phosphorus. This method has stayed so long with many modifications (see 7, 8 chen et al brenblaum, and many more). Both the two earlier papers differed. In the Briggs procedure during the synthesis of phosphomolybdic acid and its subsequent reduction by hydroquinone, the concentration of the latter was reduced to 150th of that suggested by Bell and Daisy (51920). But this alteration was not without its weaknesses such as despite the prolonged treatment with hydroquinone from 5 min in Bell and Daisy to 30 min by Briggs(6), the intensity of the blue color is not as much as seen in the earlier procedure. The basic principle of the process is the conversion of phosphate to phosphomolybdic acid followed by its reduction by sulphuric acid to result in a blue substance. Among the various reducing substances Fiske and Subbarow (4) found the use of 1, 2, 6- aminonaphthol sulphonic acid to be superior and this produced very encouraging results. This substance acts rapidly in excess of equimolar quantities of the sulfonic acid and also giving accurate results in short time.  
Fiske and Subbarow (4) conjectured the possibility of interfering substances during extraction of phosphorus from organic substances and also the eventualities of the formation other interfering compounds in the earlier processes. He analyzed various reducing substances which were available.

In the standard method for phosphorus analysis only phosphate, called the reactive phosphate is measured. The reason is that what is actually measured is phosphomolybdate which is the product of molybdate reaction itself. In other words phosphorus which is available for reactions for further analysis is called the reactive phosphorus. In many samples phosphorus may not be available in that form. Therefore the samples have to be treated with other process such as digestionextraction, filtration, purification and so on before the concentrations can be determined through the colorimetric methods. Different phosphorus species (are distinguished from each other empirically by filtration), and then a series of digestions that selectively convert phosphorus to phosphate. After the digestion phosphate is measured. Reactive phosphate is then determined in each digest

For total phosphorus determination sample is digested to convert all phosphorus compounds to phosphate. The digest is filtered and phosphate is then measured, usually by molybdenum blue. The most widely used method is that of Fiske and Subbarow with many modifications. The modifications are in the extraction procedures or chemicals and also the use of reducing agent. The modifications can also be large interferences by heavy metals such as arsenic.

Molybdate ascorbate method is one of the most widely used procedures. As and recommended by American Public Health Association (9) there are following basic steps are described
Digestion This is to facilitate availability of phosphorous bound in organic forms as orthophosphate. Perchloric acid digestion is very strong and requires long time and is therefore suggested for difficult water samples with heavy sediments. Digestion of some samples is also facilitated by UV light treatment along with persulfate oxidation in an automated digestion-determination by flow injection method. The Nitric acid-Sulfuric acid is generally suggested for most samples.

Colorimetric Method As mentioned above the basic principle are using blue complexes with molybdate for reading color reading in a colorimeterspectrophotometer. The choice of the exact method to be used depends upon the expected range of concentrations in the samples. For very small quantities ranging   between 0.01 to 6 mg PL ascorbic acid or the stannous chloride suggested by Murphy and Riley (8) method is the choice. For lower ranges than this, an extraction step has to be incorporated to remove the interfering substances.  The popularity of the ascorbic acid method has been great enough for developing an automated method and its availability presently.

For routine analysis in the range of 1 to 20 mg PL, vanadomolybdophosphoric acid method is most useful choice.

Comparison of Efficacy of Methods There are few research reports which provide a comparative analysis of the efficiency of on method with another. Chamberlain and Shapiro (10) compared the phosphorus concentrations of 13 water samples as determined by several chemical procedures. After employing the algal biomass assay, they found that there were appreciable differences among these methods. They attributed arsenic interference as the reason and not the phosphate hydrolysis compounds. The reason for this is that arsenate forms the same blue color as phosphate but arsenic concentrations as much as 100 gL do not interfere. They therefore recommend the use of arsenate insensitive extraction procedure. But it is not known if the arsenic concentrations are higher.  

It has to be pointed out that pH strongly affects the color of molybdate blue complex. While arsenic is serious interfering substance barium, lead and silver form precipitate as phosphates easily but the effects were not very significant. Similar observations have been mentioned for silica.

Allarino (12) compared three methods of Mehlich (12a, Olsen and Bray for estimating available P on Iowa calcareous soils or across soils of varying soil pH. Their results demonstrate that the Olsen and the Mehlich-3 methods are more reliable tools than the Bray-P1 method for estimating available P on Iowa calcareous soils or across soils varying in soil pH. Because these methods seem to have similar ability to the Bray-P1 for estimating available P on neutral and slightly acid soils the results suggest that either the Olsen or Mehlich-3 methods would be much better than the Bray-P 1 test when a single soil-test for P is used for routine analysis of Iowa soils. It is noteworthy, however that there was a small proportion of calcareous soils in which estimations of available P by any of the three methods were unsatisfactory. Further research is being conducted to explain these results.

The Mehlich-3 extractant proposed as a universal extractant is an attractive method for routine soil testing because of its reliability for neutral or slightly acid soils. But there is a lack of information on correlations and crop-responses of the phosphorus concentrations.

Future 
With the phosphorus availability becoming bleak there is a stronger growing need for a widely test for phosphorus analysis including the extractiondigestion procedure.

Interfering substances have been unpredictable and therefore difficult to anticipate the diversity and ranges of available concentrations. This is particularly important because of the urgency of the environmental contamination problems. Different elemental and their compounds together only confound and confuse the prospects and situation of analytical approaches. While many techniques are available they are all confined to laboratories that are well equipped and manned by trained technical experts.

A field level portable phosphorus test method for rapid analysis is very necessary.

There is no standardized comparison of all the tests available presently. The diversity of soils, waters and organic samples for analysis is wide enough to warrant at least some tests. In the case of phosphorus one possibility for improving laboratory efficiency would be to use a single extractant for multiple purposes

Preservation of food is very important because it aims at preventing microbial spoilage of food products and growth of food borne pathogens. There are a number of methods used to preserve food and among them is radiation. Preserving food by radiation means ionizing radiation also known as irradiation. The process involves exposing food to ionizing radiation that destroys microorganisms, insects, bacteria or virus that might be present in food. The method works through processing of food with ionizing radiation by gamma rays, high-energy electrons or x-rays from accelerators (Tomoda, 2006). Treatment of food through this process has certain effects which include killing insect pests, molds, bacteria, inducing sterility and reducing spoiling or ripening of fruits. The technology of food preservation by radiation is compared with cold pasteurization because the food products are not heated. Food preservation by radiation is applicable in preserving food of high initial quality, as it is not always effective against viruses.

Radiation process is unrelated to nuclear energy although it uses radiation emitted from radioactive nuclides produced in nuclear reactors. Food irradiation is one of the best applications of atomic energy in food preservation since development of canning. It is an alternative to fumigants which are being phased out because of their negative effects to human health and environment. Preserving food by radiation is more advantageous than using other food preservation methods because it does not lead to loss of quality, oduor, flavour or texture (Ann, 2008). Radiation is used to preserve almost all types of foodstuffs as long as they are of initial high quality. Radiation processing is used for anti-infestation of food grains inhibit sprouting in potatoes, onions, ginger or yam, and prevention of microbial contamination of species. In addition, food preservation by radiation extends shelf life under certain conditions of storage including overcoming of quarantine barriers in international trade.

The structure and function of the protein product of a cDNA sequence isolated from Haemonchus contortus was predicted using computational tools.  The 951-base pair cDNA sequence generated a 317-amino acid residue polypeptide that was characterized with tandem helices, as well as threads and coils.  Tertiary protein structure prediction indicated that the protein traversed the cell membrane, with both N- and C-terminal located within the cytoplasm of the cell.  BLAST analysis of the translated sequence showed that the predicted polypeptide was highly homologous to serinethreonine phosphatases of other invertebrate species.  The predicted protein sequence harbored two conserved domains, namely specific to that of metallophosphatases and the serinethreonine phosphatases.  Computational analysis facilitates in the design of molecular manipulations that could target specific amino acids for the inactivation of the protein.  The predicted protein product could therefore be involved in the regulation of cellular processes such as cell cycle progression, cell differentiation and cell migration.

INTRODUCTION

Majority of the biological processes in a cell are governed by the reactions involving the phosphorylation and dephosphorylation of proteins. These molecular switches regulate the expression of genes, as well as the progression of the cell cycle.  In addition, cellular differentiation is also controlled by the transfer of phosphate groups to or from a specific protein (Liu et al 2008).  Other cellular processes that are influenced by protein phosphorylation include programmed cell death, cellular transformation and transmission.
Phosphatases are the main proteins involved in the transfer of phosphate groups to or from a specific protein substrate (Davare et al 2000).  Biochemical investigations have resulted in the identification of a number of phosphatases, with parallel sub-classification schemes based on their functional capacity.  Phosphatases could be further grouped according to their specificity to specific substrates (Pais et al 2009).  As such, there are therefore serinethreonine phosphatases, as well as tyrosine phosphatases.  Interestingly, there are certain phosphatases that confer dual specificity, wherein the enzyme has the capability of using both serinethreonine and tyrosine as its substrate (Bakan et al 2008).

There are currently a number of serinethreonine phosphatases that have been identified, with each type classified according to their mechanism of action and dependence on cofactors (Golden et al 2008).  To date, the largest group is the protein phosphatase (PP) family, which is comprised of 7 subfamilies.  It has been reported that majority of the phosphorylation activities within the cell are performed by serinethreonine phosphatases PP1 and PP2A (Adams et al 2005).  Another group of protein phosphatases is characterized by its dependence on metal ions (PPMs).

The advent of computational techniques has allowed researchers to study macromolecules using a different approach, mainly involving sequence analysis and prediction strategies.  Such novel method has been applied to almost every area of biomedical research, from basic biological processes to drug discovery.  In the field of biochemistry, computational methods have facilitated in protein structure and function predictions, which could subsequently lead to the discovery of protein targets for molecular therapeutics.  However, it should be understood that the quality and reliability of data generated by bioinformatics tools are dependent on human reasoning and thus the researcher still controls the direction and progression of the computational analysis.
This report will focus on the computational prediction of the structure and function of a complementary deoxyribonucleic acid (cDNA) sequence that was isolated from the strongylid nematode, Haemonchus contortus.  This species commonly thrives as a parasite in small ruminant vertebrate species.  This study will initially predict various levels of protein configurations based on the cDNA sequence of interest.

Furthermore, this investigation will attempt to determine putative functional sites within the predicted protein, in order to infer possible roles of the protein product in the cell.  We hypothesize that the protein product of Hc-STP-1 carries specific amino sequence motifs that serve as binding sites for other proteins of the cell.  In addition, the putative protein of Hc-STP-1 may have active sites the influence the rate of binding with other cellular proteins.  Candidate interacting proteins will also be presented in this study, alongside prospective approaches for inhibition and enhancement of phosphorylation reactions within the cell.

RESULTS

Translation of the 951-base pair cDNA sequence of serinethreonine phosphatase-1 derived from Haemonchus contortus (Hc-STP-1) using BLASTX 2.2.23 (Altschul 1997) generated a primary polypeptide chain of approximately 317 amino acids in length (Figure 1).  Secondary protein structure prediction of the translated primary polypeptide chain using PSIPRED (Yang et al 2010) resulted the identification of regions that showed specific configurations (Figure 2).  Majority of the secondary protein configuration were observed to have high levels of confidence in prediction, as indicated in the blue bars above the predicted secondary protein structures.

The secondary protein configuration was mainly composed of helices that were distributed across the entire stretch of the polypeptide chain.  A total of 12 helices were found in the predicted secondary protein structure, with varying lengths ranging from 4 to 17 amino acids in length.  In addition, there were 13 strands that were distributed across the entire stretch of the polypeptide chain.  The length of the strands also varied, yet were relatively shorter as compared to that of the helices, ranging from 2 to 6 residues in length.  The remaining regions of the secondary polypeptide structure were predicted to follow a coiled configuration.

One peculiar feature of the predicted secondary structure was that amino acid residues 121 to 160 was largely predicted as three tandem coils with very short coils of 1-3 residues in between.  More specifically, two of the three coils located at residues 140 to 160 only had one amino acid residue in between and this is located at residue 152.  It is possible that this region of the polypeptide chain may be directed towards further conformational changes that may influence its interaction with other substrates.

Prediction of the tertiary structure of Hc-STP-1 using MEMSAT-SVM (Nugent 2010) resulted in a protein structure that traversed the cell membrane (Figure 3).  Both N- and C-
terminals of the protein were located within the cytoplasm of the cell.  Two major helical segments traverse the cell membrane, the first helix starts at residue 93 and runs through to residue 108.  The second helix runs from residue 147 to 162.  Amino acid residues 109 to 146 are located at the extracellular side of the cell membrane.

The BLASTX results also provided similarity searches in the protein database of GenBank.  The translated sequence of Hc-STP-1 was found to be highly similar (90 to 95 sequence identity) to four serinethreonine phosphatase enzymes of Trichostrongylus virtrinus.  The GenBank entries are as follows embCAM84506.1, embCAM84505.1, embCAM84509.1 and embCAM84507.1.  The protein alignments shown in Figures 4 through 7 indicate where similarities were evident, as well as where differences were observed.  Gaps were inserted within the query sequence in order to attain a global alignment of the query and the database protein.

Identification of conserved domains within the polypeptide sequence indicated that the product of Hc-STP-1 contained sequence motifs that conferred regulatory functions in relation to the cell cycle.  In addition, the polypeptide sequence also showed motifs associated with the synthesis of specific proteins that were responsible for the normal physiology of the cell.  Given the high similarity of the translated Hc-STP-1 sequence with identified proteins in the database, it is highly likely that the protein product of the cDNA query would function as a phosphatase.

DISCUSSION

The employment of bioinformatics tools has facilitated in the prediction of protein structure and function of the cDNA sequence of Hc-STP-1.  From a 951-base pair DNA sequence isolated from Haemonchus contortus, a 317-amino acid residue polypeptide chain was predicted from the BLASTX translation feature.  Further prediction analysis has generated the secondary configuration of the protein of interest.  Bioinformatics has allowed the identification of identification of amino acid segments that would configure into coils, thread or sheets.  Such prediction is mainly based on the combination of amino acids that are present within a defined polypeptide length.

The presence of helices within a secondary protein configuration allows the macromolecule to achieve a condensed state as it progresses to its final tertiary or quaternary structure.  In addition, the strands within the secondary protein configuration allow interactions between other amino acids within the protein sequence.  The strands also allow interactions between two different proteins, as these structures are capable of arranging themselves in a parallel orientation between each other.

Secondary protein structure prediction has determined that the polypeptide chain is predominantly composed of helices.  The region of the polypeptide chain that was covered with helices was also observed in the predicted tertiary structure.  It should be understood that in order for a protein to exist within the cell membrane and at the same time attain its normal physiological function, it is essential that this specific region exist as a helix.  Such configuration has been predicted in the tertiary structure of the Hc-STP-1 protein.  The helical structure facilitates in the protection of polar amino acids within the inner side of the helix.  On the other hand, the amino acids that have non-polar R groups are positioned in the outer side of the helical structure.  This polarity preserves the protein and thus maintains its protein functionality, as it exists within the bipolar plasma membrane of the cell.

Sequence alignments using the predicted protein of Hc-STP-1 showed that the sequence was highly homologous to other identified serinethreonine phosphatases.  The protein alignments serve as tools in quantifying the exert of similarity of a pair of protein sequences and this also allows the identification of blocks of amino acid sequence that have been conserved across different taxa.  There are two major types of conserved domains that have been detected in the predicted protein of cDNA Hc-STP-1.
Metallophosphatases (MPPs) are considered as a superfamily of enzymes that have the inherent capacity to interact with metal ions.  Such interactions with managanese or zinc ions assist in the caging of specific polar amino acids such as histidine and asparagine.  The most common metallophosphatases include exonucleases, phosphoprotein phosphatases and sphingomyelinases.  This conserved region is composed of a beta-pleated sheet that is positioned between two metal-dependent active sites that are localized to the C-terminal side of protein region.  The metallophosphatase domain facilitates in the coordinated interaction with metal ions within the cell s environment.

Another conserved domain that has been identified within the predicted polypeptide of the cDNA Hc-STP-1 is that of the serinethreonine phosphatase.  This domain is capable of transferring a phosphate group from one site to another in the presence of either the serine or threonine amino acid residue in its active site.  The presence of these conserved domains allows the design of future protein manipulations that could deactivate the protein.  More importantly, the prediction of the structure and function of the cDNA sequence allows researchers to design molecular treatments that could target such proteins, especially when they are found to be highly active or over-expressed.  Certain medical conditions, such as cancer and metabolic syndromes, are commonly characterized with active expression of proteins that regulate major cellular processes such as cell division and differentiation.  The prediction of the structure and function of a cDNA sequence through the use of bioinformatics tools will facilitate in future investigations that would want to address methods in regulating such biological pathways.

CONCLUSION

Computational analysis has predicted that the protein product of the cDNA Hc-STP-1 is a serinethreonine phosphatase that is very similar to paralogous sequences in other species.  The predicted protein is a 317-amino acid polypeptide that contains coils, threads and helices.  The protein has been predicted to traverse the cell membrane, with both N- and C-terminal located within the cytoplasm of the cell.  Molecular targets can be designed to regulate the activity of the predicted protein within the cell.