6.14.2008

Hydroponics - Wikipedia, the free encyclopedia - Sent Using Google Toolbar

Hydroponics - Wikipedia, the free encyclopedia

Hydroponics

From Wikipedia, the free encyclopedia

Jump to: navigation, search
Plants grown in a hydroponics grow box made to look like a computer
Plants grown in a hydroponics grow box made to look like a computer
NASA researcher checking hydroponic onions with Bibb lettuce to his left and radishes to the right
NASA researcher checking hydroponic onions with Bibb lettuce to his left and radishes to the right
Example of Autotrophic Metabolism
Example of Autotrophic Metabolism [1]

Hydroponics (from the Greek words hydro (water) and ponos (labour)) is a method of growing plants using mineral nutrient solutions instead of soil. Terrestrial plants may be grown with their roots in the mineral nutrient solution only or in an inert medium, such as perlite, gravel or mineral wool. A variety of techniques exist.

Plant physiology researchers discovered in the 19th century that plants absorb essential mineral nutrients as inorganic ions in water. In natural conditions, soil acts as a mineral nutrient reservoir but the soil itself is not essential to plant growth. When the mineral nutrients in the soil dissolve in water, plant roots are able to absorb them. When the required mineral nutrients are introduced into a plant's water supply artificially, soil is no longer required for the plant to thrive. Almost any terrestrial plant will grow with hydroponics, but some will do better than others. It is also very easy to do; the activity is often undertaken by very young children with such plants as watercress. Hydroponics is also a standard technique in biology research and teaching.

Contents

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[edit] History

Ancient people such as the Babylonians and Aztecs used growing techniques where nutrients were obtained from sources other than soil.[citation needed] The mineral nutrient solutions used today for hydroponics were not developed until the 1800s.

The earliest published work on growing terrestrial plants without soil was the 1627 book, Sylva Sylvarum by Sir Francis Bacon, although he died in 1626. Water culture became a popular research technique after that. In 1699, John Woodward published his water culture experiments with spearmint. He found that plants in less-pure water sources grew better than plants in distilled water. Mineral nutrient solutions for soilless culture of plants were first perfected in the 1860s by the German botanists, Julius von Sachs and Wilhelm Knop. Growth of terrestrial plants without soil in mineral nutrient solutions was called solution culture. It quickly became a standard research and teaching technique and is still widely used today. Solution culture is now considered a type of hydroponics where there is no inert medium.

In 1929, Professor William Frederick Gericke of the University of California at Berkeley began publicly promoting that solution culture be used for agricultural crop production. He first termed it aquaculture but later found that aquaculture was already applied to culture of aquatic organisms. Gericke created a sensation by growing tomato and other plants to a remarkable size in his backyard in mineral nutrient solutions rather than soil. By analogy with the ancient Greek term for agriculture, geoponics, the science of cultivating the earth, Gericke introduced the term hydroponics in 1937 (although he asserts that the term was suggested by Dr. W. A. Setchell, of the University of California) for the culture of plants in water (from the Greek hydros, water, and ponos, labor).

Reports of Gericke's work and his claims that hydroponics would revolutionize plant agriculture prompted a huge number of requests for further information. Gericke refused to reveal his secrets claiming he had done the work at home on his own time. This refusal eventually resulted in his leaving the University of California. In 1940, he wrote the book, Complete Guide to Soilless Gardening.

Two other plant nutritionists at the University of California were asked to research Gericke's claims. Dennis R. Hoagland and Daniel I. Arnon wrote a classic 1938 agricultural bulletin, The Water Culture Method for Growing Plants Without Soil, debunking the exaggerated claims made about hydroponics. Hoagland and Arnon found that hydroponic crop yields were no better than crop yields with good quality soils. Crop yields were ultimately limited by factors other than mineral nutrients, especially light. This research, however, overlooked the fact that hydroponics has other advantages including the fact that the roots of the plant have constant access to oxygen and that the plants have access to as much or as little water as they need. This is important as one of the most common errors when growing is over- and under- watering; and hydroponics prevents this from occurring as large amounts of water can be made available to the plant and any water not used, drained away, recirculated, or actively aerated, eliminating anoxic conditions which drown root systems in soil. In soil, a grower needs to be very experienced to know exactly how much water to feed the plant. Too much and the plant will not be able to access oxygen; too little and the plant will lose the ability to transport nutrients, which are typically moved into the roots while in solution.

These two researchers developed several formulas for mineral nutrient solutions, known as Hoagland solutions. Modified Hoagland solutions are still used today.

One of the early successes of hydroponics occurred on Wake Island, a rocky atoll in the Pacific Ocean used as a refueling stop for Pan American Airlines. Hydroponics was used there in the 1930s to grow vegetables for the passengers. Hydroponics was a necessity on Wake Island because there was no soil, and it was prohibitively expensive to airlift in fresh vegetables.

In the 1960s, Allen Cooper of England developed the Nutrient Film Technique. The Land Pavilion at Walt Disney World's EPCOT Center opened in 1982 and prominently features a variety of hydroponic techniques. In recent decades, NASA has done extensive hydroponic research for their Controlled Ecological Life Support System or CELSS. Hydroponics intended to take place on Mars are using LED lighting to grow in different color spectrums with much less heat.

[edit] Origin

[edit] Soilless culture

Gericke originally defined hydroponics as crop growth in mineral nutrient solutions, with no solid medium for the roots. He objected in print to people who applied the term hydroponics to other types of soilless culture such as sand culture and gravel culture. The distinction between hydroponics and soilless culture of plants has often been blurred. Soilless culture is a broader term than hydroponics; it only requires that no soils with clay or silt are used. Note that sand is a type of soil yet sand culture is considered a type of soilless culture. Hydroponics is always soilless culture, but not all soilless culture is hydroponics. Many types of soilless culture do not use the mineral nutrient solutions required for hydroponics.

Billions of container plants are produced annually, including fruit, shade and ornamental trees, shrubs, forest seedlings, vegetable seedlings, bedding plants, herbaceous perennials and vines. Most container plants are produced in soilless media, representing soilless culture. However, most are not hydroponics because the soilless medium often provides some of the mineral nutrients via slow release fertilizers, cation exchange and decomposition of the organic medium itself. Most soilless media for container plants also contain organic materials such as peat or composted bark, which provide some nitrogen to the plant. Greenhouse growth of plants in peat bags is often termed hydroponics, but technically it is not because the medium provides some of the mineral nutrients. Peat has a high cation exchange capacity and must be amended with limestone to raise the pH value.

[edit] Techniques

The two main types of hydroponics are solution culture and medium culture. Solution culture does not use a solid medium for the roots, just the nutrient solution. The three main types of solution culture are static solution culture, continuous flow solution culture and aeroponics. The medium culture method has a solid medium for the roots and is named for the type of medium, e.g. sand culture, gravel culture or rockwool culture. There are two main variations for each medium, subirrigation and top irrigation. For all techniques, most hydroponic reservoirs are now built of plastic but other materials have been used including concrete, glass, metal, vegetable solids and wood. The containers should exclude light to prevent algae growth in the nutrient solution.

[edit] Static solution culture

In static solution culture, plants are grown in containers of nutrient solution, such as glass Mason jars (typically in-home applications), plastic buckets, tubs or tanks. The solution is usually gently aerated but may be unaerated. If unaerated, the solution level is kept low enough that enough roots are above the solution so they get adequate oxygen. A hole is cut in the lid of the reservoir for each plant. There can be one to many plants per reservoir. Reservoir size can be increased as plant size increases. A homemade system can be constructed from plastic food containers or glass canning jars with aeration provided by an aquarium pump, aquarium airline tubing and aquarium valves. Clear containers are covered with aluminium foil, butcher paper, black plastic or other material to exclude light, thus helping to eliminate the formation of algae. The nutrient solution is either changed on a schedule, such as once per week, or when the concentration drops below a certain level as determined with an electrical conductivity meter. Whenever the solution is depleted below a certain level, either water or fresh nutrient solution is added. A Mariotte's bottle can be used to automatically maintain the solution level. In raft solution culture, plants are placed in a sheet of buoyant plastic that is floated on the surface of the nutrient solution. That way, the solution level never drops below the roots.

[edit] Continuous flow solution culture

In continuous flow solution culture the nutrient solution constantly flows past the roots. It is much harder to automate than the static solution culture because sampling and adjustments to degree and nutrient concentrations can be made in a large storage tank that serves potentially thousands of plants. A popular variation is the nutrient film technique or NFT whereby a very shallow stream of water containing all the dissolved nutrients required for plant growth is recirculated past the bare roots of plants in a watertight gully, also known as channels. Ideally, the depth of the recirculating stream should be very shallow, little more than a film of water, hence the name 'nutrient film'. This ensures that the thick root mat, which develops in the bottom of the channel, has an upper surface which, although moist, is in the air. Subsequently, there is an abundant supply of oxygen to the roots of the plants. A properly designed NFT system is based on using the right channel slope, the right flow rate and the right channel length. The main advantage of the NFT system over other forms of hydroponics is that the plant roots are exposed to adequate supplies of water, oxygen and nutrients. In all other forms of production there is a conflict between the supply of these requirements, since excessive or deficient amounts of one results in an imbalance of one or both of the others. NFT, because of its design, provides a system where all three requirements for healthy plant growth can be met at the same time, providing the simple concept of NFT is always remembered and practised. The result of these advantages is that higher yields of high quality produce are obtained over an extended period of cropping. A downside of NFT is that it has very little buffering against interruptions in the flow e.g. power outages, but overall, it is probably one of the more productive techniques.

The same design characteristics apply to all conventional NFT systems. While slopes along channels of 1:100 have been recommended, in practice it is difficult to build a base for channels that is sufficiently true to enable nutrient films to flow without ponding in locally depressed areas. Consequently, it is recommended that slopes of 1:30 to 1:40 are used. This allows for minor irregularities in the surface but, even with these slopes, ponding and waterlogging may occur. The slope may be provided by the floor, or benches or racks may hold the channels and provide the required slope. Both methods are used and depend on local requirements, often determined by the site and crop requirements.

As a general guide, flow rates for each gully should be 1 litre per minute. At planting, rates may be half this and the upper limit of 2L/min appears about the maximum. Flow rates beyond these extremes are often associated with nutritional problems. Depressed growth rates of many crops have been observed when channels exceed 12 metres in length. On rapidly growing crops, tests have indicated that, while oxygen levels remain adequate, nitrogen may be depleted over the length of the gully. Consequently, channel length should not exceed 10-15 metres. In situations where this is not possible, the reductions in growth can be eliminated by placing another nutrient feed half way along the gully and reducing flow rates to 1L/min through each outlet.

[edit] Aeroponics

Main article: Aeroponics

Aeroponics is defined as a system where roots are continuously or discontinuously in an environment saturated with fine drops (a mist or aerosol) of nutrient solution. The method requires no substrate and entails growing plants with their roots suspended in a deep air or growth chamber with the roots periodically wetted with a fine mist of atomized nutrients. Excellent aeration is the main advantage of aeroponics.

Aeroponic techniques have proved very successful for propagation, but have yet to prove themselves on a commercial scale. Aeroponics is also widely used in laboratory studies of plant physiology. Aeroponic techniques have been given special attention from NASA since a mist is easier to handle than a liquid in a zero gravity environment.

[edit] Passive subirrigation

Main article: Passive hydroponics

Passive subirrigation, also known as passive hydroponics or semi-hydroponics, is a method where plants are grown in an inert porous medium that transports water and fertilizer to the roots by capillary action from a separate reservoir as necessary, reducing labor and providing a constant supply of water to the roots. In the simplest method, the pot sits in a shallow solution of fertilizer and water or on a capillary mat saturated with nutrient solution. The various hydroponic media available, such as expanded clay and coconut husk, contain more air space than more traditional potting mixes, delivering increased oxygen to the roots, which is important in epiphytic plants such as orchids and bromeliads, whose roots are exposed to the air in nature. Additional advantages of passive hydroponics are the reduction of root rot and the additional ambient humidity provided through evaporation.

[edit] Ebb and flow / Flood and drain subirrigation

Main article: Ebb and flow

In its simplest form, there is a tray above a reservoir of nutrient solution. The tray is either filled with growing medium (clay granules being the most common) and planted directly, or pots of medium stand in the tray. At regular intervals, a simple timer causes a pump to fill the upper tray with nutrient solution, after which the solution drains back down into the reservoir. This keeps the medium regularly flushed with nutrients and air.

[edit] Top irrigation

In top irrigation, nutrient solution is periodically applied to the medium surface. This may be done manually once per day in large containers of some media, such as sand. Usually, it is automated with a pump, timer and drip irrigation tubing to deliver nutrient solution as frequently as 5 to 10 minutes every hour.

[edit] Deep water culture

Main article: Deep water culture

The hydroponic method of plant production by means of suspending the plant roots in a solution of nutrient rich, oxygenated water. Traditional methods favor the use of plastic buckets and large containers with the plant contained in a net pot suspended from the centre of the lid and the roots suspended in the nutrient solution.


[edit] Media

One of the most obvious decisions hydroponicists have to make is which medium they should use. Different media are appropriate for different growing techniques.

[edit] Diahydro

Diahydro is a natural sedimentary rock medium that consists of the fossilized remains of diatoms. Diahydro is extremely high in Silica (87-94%), an essential component for the growth of plants and strengthening of cell walls.

[edit] Expanded clay

Hydroton brand expanded clay pebbles.
Hydroton brand expanded clay pebbles.

Also known under the trademarks 'Hydroton' or LECA (light expanded clay aggregate), these small, round baked spheres of clay are inert and are suitable for hydroponic systems in which all nutrients are carefully controlled in water solution. The clay pellet is also inert, pH neutral and do not contain any nutrient value.

The clay is formed into round pellets and fired in rotary kilns at 1200°C. This causes the clay to expand, like popcorn, and become porous. It is light in weight, and does not compact over time. Shape of individual pellet can be irregular or uniform depending on brand and manufacturing process. The manufacturers consider expanded clay to be an ecologically sustainable and re-usable growing medium because of its ability to be cleaned and sterilized, typically by washing in solutions of white vinegar, chlorine bleach or hydrogen peroxide (H2O2), and rinsing completely.

Another viewpoint is clay pebbles are best not re-used even when they are cleaned due to root growth which may enter the medium. Breaking open a clay pebble after a crop has been grown will reveal this. However, this view is generally not widely shared.

[edit] Rockwool

Rockwool is probably the most widely used medium in hydroponics. Made from basalt rock it is heat-treated at high temperatures then spun back together like candy floss. It comes in lots of different forms including cubes, blocks, slabs and granulated or flock.

Rockwool is an excellent inert substrate for both 'free drainage' and recirculating systems. In free drainage or run-to-waste systems, the chance of disease spread is greatly lessened. Rockwool is also lightweight and self-contained, which allows plants to be grown at different densities in different stages - young plants can be grown to an advanced stage in a small area before being planted out into the main growing area, thus improving crop turnaround. Its light weight also permits setting up to be quick and inexpensive. Because it is light and rigid it eliminates back-breaking work in preparation and planting and gives substantial labor-saving costs. Rockwool is noted for providing a favourable root environment, thus minimizing plant stress. Root temperature can also be controlled, thus giving substantial energy savings. Rockwool initially causes an increase in pH level. You must adjust the pH level of the nutrient solution to counteract this. A pH level of 5.5-6.5 should suffice to create a suitable pH.

The disadvantages of rockwool are few. Although relatively inexpensive, because of its bulk, transport costs to remote regions can be prohibitive. However, the fact that it can be used several times over will reduce the growers overall costs. Before handling, gloves and long shirt sleeves should be worn to prevent minor skin irritation. This can also be lessened by wetting the rockwool before handling. When this medium is dry, care needs to be taken so as not to inhale any particles; inhaling such particles may carry a health risk.

[edit] Coir

Coco peat, also known as coir or coco, is the leftover material after the fibres have been removed from the outermost shell (bolster) of the coconut. It took 10 centuries to make this waste a viable plant substrate. The first description of the coco process dates from the 11th century and was recorded by Arabian traders. In 1290, Marco Polo described the process of extracting fibres from coconuts. For centuries, this process remained unchanged. Coco peat was a waste product from factories that used coco fibre as a raw material for making sailing ropes, chair seats and mattress fillings.

Coco is a 100% natural grow and flowering medium, which has proven its value across years and years. Coco is not only a high quality product, but also an environmentally friendly product[citation needed]. For many years the raw material was considered waste material, and enormous useless "Coco Mountains" appeared in the landscapes of countries like Sri Lanka and India. By developing a special biological composting process this "waste" transformed into a high quality product. This innovation was, and still is, an important contributor to the local economy of India and Sri Lanka. This and the unique growth characteristics ensure coco is the medium of the moment and the future.

The coco substrate is an environmentally friendly product. No energy wasteful production methods are used during the production of this long-lasting cultivation medium. Coconut fibres are obtained from the coconuts' husks which are a natural product that can be harvested throughout the year. Coir comes in bags and in slabs.

Some types of coir are very high in sodium (salt) due to the nature of coconut palms growing on island environments and being processed in the salt air. Quality coir has not been sterilized or heat treated and so retains its natural sponge-like qualities as well as the natural, beneficial trichoderma fungi which has been scientifically shown[citation needed] to combat root rot and other diseases.[citation needed] Trichoderma is also well-known for promoting root growth.[citation needed]

This substrate combines the tolerant, organic nature of soil with the precision of rockwool. Due to the special characteristics of the substrate the nutrient doesn't have a grow and flower variant, there is just one unique formulation for both growth and blooming phase. Due to the unique buffering capability of the coir substrate, and its sponge-like structure, the nutrients needed to ensure high yields are stored in the coco. This means that the plant itself can regulate the amount and timing of its nutrient intake.

Coconut fibres have sufficient capillary action to retain enough water and nutrients. This means that the plant can go for longer periods with-out water, which could happen if a feeding pump was to break down for example.

Quality coir can be used a number of times and makes an excellent soil improver after use.

[edit] Perlite

Perlite is a volcanic rock that has been superheated into very lightweight expanded glass pebbles. It is used loose or in plastic sleeves immersed in the water. It is also used in potting soil mixes to decrease soil density. Perlite has similar properties and uses to vermiculite but generally holds more air and less water. If not contained, it can float if flood and drain feeding is used.

[edit] Vermiculite

Like perlite, vermiculite is another mineral that has been superheated until it has expanded into light pebbles. Vermiculite holds more water than perlite and has a natural "wicking" property that can draw water and nutrients in a passive hydroponic system. If too much water and not enough air surrounds the plants roots, it's possible to gradually lower the medium's water-retention capability by mixing in increasing quantities of perlite.

[edit] Sand

Sand is cheap and easily available. However, it is heavy, it does not always drain well, and it must be sterilized between use.

[edit] Gravel

The same type that is used in aquariums, though any small gravel can be used, provided it is washed first. Indeed, plants growing in a typical traditional gravel filter bed, with water circulated using electric powerhead pumps, are in effect being grown using gravel hydroponics. Gravel is inexpensive, easy to keep clean, drains well and won't become waterlogged. However, it is also heavy, and if the system doesn't provide continuous water, the plant roots may dry out.

[edit] Brick Shards

Brick shards have similar properties to gravel. They have the added disadvantages of possibly altering the pH and requiring extra cleaning before reuse.

[edit] Polystyrene packing peanuts

Polystyrene packing peanuts are inexpensive, readily available, and have excellent drainage. However, they can be too lightweight for some uses. They are mainly used in closed tube systems. Note that polystyrene peanuts must be used; biodegradable packing peanuts will decompose into a sludge. Plants may absorb styrene and pass it to their consumers; this is a possible health risk.

[edit] Nutrient solutions

Plant nutrients are dissolved in the water used in hydroponics and are mostly in inorganic and ionic form. Primary among the dissolved cations (positively-charged ions) are Ca2+ (calcium), Mg2+ (magnesium), and K+ (potassium); the major nutrient anions in nutrient solutions are NO3 (nitrate), SO42− (sulfate), and H2PO4 (phosphate).

Numerous 'recipes' for hydroponic solutions are available. Many use different combinations of chemicals to reach similar total final compositions. Commonly-used chemicals for the macronutrients include potassium nitrate, calcium nitrate, potassium phosphate, and magnesium sulfate. Various micronutrients are typically added to hydroponic solutions to supply essential elements; among them are Fe (iron), Mn (manganese), Cu (copper), Zn (zinc), B (boron), Cl (chlorine), and Ni (nickel). Chelating agents are sometimes used to keep Fe soluble. Many variations of the nutrient solutions used by Arnon and Hoagland (see above) have been styled 'modified Hoagland solutions' and are widely used.

Plants will change the composition of the nutrient solutions upon contact by depleting specific nutrients more rapidly than others, removing water from the solution, and altering the pH by excretion of either acidity or alkalinity. Care is required not to allow salt concentrations to become too high, nutrients to become too depleted, or pH to wander far from the desired value.

[edit] Commercial

A miniature garden using hydroponics and aeroponics.
A miniature garden using hydroponics and aeroponics.

Due to its arid climate, Israel has developed advanced hydroponic technology. They have marketed their system to Nicaragua, which uses it to produce more than one million pounds of peppers annually for sale abroad, including the United States.

The largest commercial hydroponics facility in the world is Eurofresh Farms in Willcox, Arizona, which sold 125 million pounds of tomatoes in 2005.[2] Eurofresh has 256 acres under glass and represents about a third of the commercial hydroponic greenhouse area in the U.S. [3] Eurofresh does not consider their tomatoes organic, but they are pesticide-free. They are grown in rockwool with top irrigation.

Some commercial installations use no pesticides or herbicides, preferring integrated pest management techniques. There is often a price premium willingly paid by consumers for produce which is labeled "organic". Some states in the USA require soil as an essential to obtain organic certification. There are also overlapping and somewhat contradictory rules established by the US Federal Government, so some food grown with hydroponics can be certified organic.

Hydroponics also saves an incredible amount of water; it uses as little as 1/20 the amount as a regular farm to produce the same amount of food. The water table can be impacted by the water use and run-off of chemicals from farms, but hydroponics may minimize impact as well as having the advantage that water use and water returns are easier to measure. This can save the farmer money by allowing reduced water use and the ability to measure consequences to the land around a farm.

The environment in a hydroponics greenhouse is tightly controlled for maximum efficiency and this new mindset is called Soil-less/Controlled Environment Agriculture (S/CEA). With this growers can make ultra-premium foods anywhere in the world, regardless of temperature and growing seasons. Growers monitor the temperature, humidity, and pH level constantly.

Hydroponics have been used to enhance vegetables to provide more nutritional value. A hydroponic farmer in Virginia has developed a calcium and potassium enriched head of lettuce, scheduled to be widely available in April 2007. Grocers in test markets have said that the lettuce sells "very well", and the farmers claim that their hydroponic lettuce uses 90% less water than traditional soil farming.[4]

[edit] Scientific literature

Scientific literature on hydroponics can be found in various journals, including Annals of Botany, New Phytologist, Plant and Soil and Plant Physiology.

[edit] Advancements

With pest problems reduced, and nutrients constantly fed to the roots, productivity in hydroponics is high, plant growth being limited by the low levels of carbon dioxide in the atmosphere, or limited light. To increase yield further, some sealed greenhouses inject carbon dioxide into their environment to help growth (CO2 enrichment), or add lights to lengthen the day, control vegetative growth etc.[citation needed]

[edit] See also

[edit] References

  1. ^ Winterborne J, 2005. Hydroponics - Indoor Horticulture [1]
  2. ^ Kenney, Brad P. 2006. Success under glass. American Vegetable Grower. May, pages 12-13.[2]
  3. ^ Sorenson, Dan. 2006. Hydroponic tomatoes. Arizona Daily Star [3]
  4. ^ Murphy, Katie. 2006. Farm Grows Hydroponic Lettuce. Observer Online [4]

[edit] External links

6.09.2008

Phosphorylation - Wikipedia, the free encyclopedia

Phosphorylation - Wikipedia, the free encyclopedia

Phosphorylation

From Wikipedia, the free encyclopedia

Jump to: navigation, search
A phosphorylated serine residue
A phosphorylated serine residue

Phosphorylation is the addition of a phosphate (PO4) group to a protein molecule or a small molecule. It can also be thought of as the introduction of a phosphate group into an organic molecule. Its prominent role in biochemistry is the subject of a very large body of research (as of February 2008, the Medline database returns nearly 148,000 articles on the subject, largely on protein phosphorylation).

Contents

[hide]

[edit] Protein phosphorylation

[edit] History

In 1906, Phoebus A. Levene at the Rockefeller Institute for Medical Research identified phosphate in the protein Vitellin (phosvitin),[1] and by 1933 had detected phosphoserine in Casein, with Fritz Lipmann.[2] However, it took another 20 years before Eugene P. Kennedy described the first 'enzymatic phosphorylation of proteins'.[3]

[edit] Function

Reversible phosphorylation of proteins is an important regulatory mechanism that occurs in both prokaryotic and eukaryotic organisms.[4][5][6][7] Enzymes called kinases (phosphorylation) and phosphatases (dephosphorylation) are involved in this process. Many enzymes and receptors are switched "on" or "off" by phosphorylation and dephosphorylation. Reversible phosphorylation results in a conformational change in the structure in many enzymes and receptors, causing them to become activated or deactivated. Phosphorylation usually occurs on serine, threonine, and tyrosine residues in eukaryotic proteins. In addition, phosphorylation occurs on the basic amino acid residues histidine or arginine or lysine in prokaryotic proteins[4][5]. The addition of a phosphate (PO4) molecule to a polar R group of an amino acid residue can turn a hydrophobic portion of a protein into a polar and extremely hydrophilic portion of molecule. In this way it can introduce a conformational change in the structure of the protein via interaction with other hydrophobic and hydrophilic residues in the protein.

One such example of the regulatory role that phosphorylation plays is the p53 tumor suppressor protein. The p53 protein is heavily regulated[8] and contains more than 18 different phosphorylation sites. Activation of p53 can lead to cell cycle arrest, which can be reversed under some circumstances, or apoptotic cell death[9] This activity occurs only in situations wherein the cell is damaged or physiology is disturbed in normal healthy individuals.

Upon the deactivating signal, the protein becomes dephosphorylated again and stops working. This is the mechanism in many forms of signal transduction, for example the way in which incoming light is processed in the light-sensitive cells of the retina.

Regulatory roles of phosphorylation include

  • Mediates enzyme inhibition
    • phosphorylation of the enzyme GSK-3 by AKT (Protein kinase B) as part of the insulin signaling pathway.[10]
    • phosphorylation of src tyrosine kinase (pronounced "sarc") by C-terminal Src kinase (Csk) induces a conformational change in the enzyme, resulting in a fold in the structure, which masks its kinase domain, and is thus shut "off".[11]
  • Important in protein degradation.
    • In the late 1990s, it was recognized that phosphorylation of some proteins causes them to be degraded by the ATP-dependent ubiquitin/proteasome pathway. These target proteins become substrates for particular E3 ubiquitin ligases only when they are phosphorylated.

[edit] Signaling networks

Elucidating complex signaling pathway phosphorylation events can be difficult. In a cellular signaling pathways, a protein A phosphorylates protein B, and B phosphorylates C. However, in another signaling pathway, protein D phosphorylates A, or phosphorylates protein C. Global approaches such as phosphoproteomics the study of phosphorylated proteins, which is a sub-branch of proteomics combined with mass spectrometry-based proteomics, have been utilised to identify and quantify dynamic changes in phosphorylated proteins over time. These techniques are becoming increasingly important for the systematic analysis of complex phosphorylation networks.[13] They have been successfully used to identify dynamic changes in the phosphorylation status of more than 6000 sites after stimulation with epidermal growth factor.[13][14]

[edit] Protein phosphorylation sites

There are thousands of distinct phosphorylation sites in a given cell since: 1) There are thousands of different kinds of proteins in any particular cell (such as a lymphocyte). 2) It is estimated that 1/10th to 1/2 of proteins are phosphorylated (in some cellular state). 3) Phosphorylation often occurs on multiple distinct sites on a given protein.

Since phosphorylation of any site on a given protein can change the function or localization of that protein, understanding the "state" of a cell requires knowing the phosphorylation state of its proteins. For example, if amino acid Serine-473 ("S473") in the protein AKT is phosphorylated, AKT is, in general, functionally active as a kinase. If not, it is an inactive kinase.

[edit] Types of phosphorylation

See also kinases for more details on the different types of phosphorylation

Within a protein, phosphorylation can occur on several amino acids. Phosphorylation on serine is the most common, followed by threonine. Tyrosine phosphorylation is relatively rare. However, since tyrosine phosphorylated proteins are relatively easy to purify using antibodies, tyrosine phosphorylation sites are relatively well understood. Histidine and aspartate phosphorylation occurs in prokaryotes as part of two-component signaling and in some cases in eukaryotes in some signal transduction pathways[1].

[edit] Detection and characterization

Antibodies can be used as powerful tools to detect whether a protein is phosphorylated at a particular site. Antibodies bind to and detect phosphorylation-induced conformational changes in the protein. Such antibodies are called phospho-specific antibodies; hundreds of such antibodies are now available. They are becoming critical reagents both for basic research and for clinical diagnosis.

Example of posttranslational modification detected on a 2D gel (spot boundaries delimited by analysis software, identification by mass spectrometry, P46462 is the protein ID in Expasy)
Example of posttranslational modification detected on a 2D gel (spot boundaries delimited by analysis software, identification by mass spectrometry, P46462 is the protein ID in Expasy)

PTM (Posttranslational Modification) isoforms are easily detected on 2D gels. Indeed, phosphorylation replaces neutral hydroxyl groups on serines, threonines, or tyrosines with negatively-charged phosphates with pKs near 1.2 and 6.5. Thus, below pH 5.5, phosphates add a single negative charge; near pH 6.5, they add 1.5 negative charges; above pH 7.5, they add 2 negative charges. The relative amount of each isoform can also easily and rapidly be determined from staining intensity on 2D gels.

A detailed characterization of the sites of phosphorylation is very difficult, and the quantitation of protein phosphorylation by mass spectrometry requires isotopic internal standard approaches (Gerber et al., 2003). A relative quantitation can be obtained with a variety of differential isotope labeling technologies (Gygi et al., 2002, Goshe et al., 2003).

[edit] Other kinds

ATP, the "high-energy" exchange medium in the cell, is synthesized in the mitochondrion by addition of a third phosphate group to ADP in a process referred to as oxidative phosphorylation. ATP is also synthesized by substrate-level phosphorylation during glycolysis. ATP is synthesized at the expense of solar energy by photophosphorylation in the chloroplasts of plant cells.

Phosphorylation of sugars is often the first stage of their catabolism. It allows cells to accumulate sugars because the phosphate group prevents the molecules from diffusing back across their transporter.

[edit] External links

[edit] References

  1. ^ P.A. Levene and C.L. Alsberg, The cleavage products of vitellin, J. Biol. Chem. 2 (1906), pp. 127–133.
  2. ^ F.A. Lipmann and P.A. Levene, Serinephosphoric acid obtained on hydrolysis of vitellinic acid, J. Biol. Chem. 98 (1932), pp. 109–114.
  3. ^ G. Burnett and E.P. Kennedy, The enzymatic phosphorylation of proteins, J. Biol. Chem. 211 (1954), pp. 969–980.
  4. ^ a b A.J. Cozzon (1988) Protein phosphorylation in prokaryotes Ann. Rev. Microbiol. 42:97-125
  5. ^ a b J.B. Stock, A.J. Ninfa and A.M. Stock (1989) Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol. Rev., p. 450-490
  6. ^ C. Chang and R.C. Stewart (1998) The Two-Component System. Plant Physiol. 117: 723-731
  7. ^ D. Barford, A.K. Das and MP. Egloff. (1998) The Structure and mechanism of protein phosphatases: Insights into Catalysis and Regulation Annu Rev Biophys Biomol Struct. Vol. 27: 133-164
  8. ^ M. Ashcroft, M.H.G. Kubbutat, and K.H. Vousden (1999). Regulation of p53 Function and Stability by Phosphorylation. Mol Cell Biol Mar;19(3):1751-8.
  9. ^ S. Bates, and K. H. Vousden. (1996). p53 in signalling checkpoint arrest or apoptosis. Curr. Opin. Genet. Dev. 6:1-7.
  10. ^ P.C. van Weeren, K.M. de Bruyn, A.M. de Vries-Smits, J. Van Lint, B.M. Burgering. (1998). "Essential role for protein kinase B (PKB) in insulin-induced glycogen synthase kinase 3 inactivation. Characterization of dominant-negative mutant of PKB. J Biol Chem 22;273(21):13150-6.
  11. ^ Cole, P.A., Shen, K., Qiao, Y., and Wang, D. (2003) Protein tyrosine kinases Src and Csk: A tail's tale, Curr. Opin. Chem., Biol. 7:580-585.
  12. ^ Babior, B.M., (1999). NADPH oxidase: an update. Blood 93, pp. 1464–1476
  13. ^ a b J.V. Olsen, B.Blagoev, F. Gnad, B. Macek, C. Kumar, P. Mortensen, and M. Mann. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 3;127(3):635-48.
  14. ^ Y. Li-Rong , H.J. Issaq and T.D. Veenstra. (2007) Phosphoproteomics for the discovery of kinases as cancer biomarkers and drug targets. Proteomics Clin. Appl. 1, 1042–1057
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Protein primary structure and posttranslational modifications
General
N terminus
C terminus
Lysine
Cysteine
Serine/Threonine
Tyrosine
Asparagine
Aspartate
Glutamine
Glutamate
Arginine
Proline