Glyceraldehydre 3-phosphate

Glyceraldehyde 3-phosphate (G3P) is a 3 carbon metabolic intermediate.

An intermediate in both glycolysis and gluconeogenesis

G3P is formed from the following three reversible reactions:
- Fructose-1,6-bisphosphate, (F1,6BP) catalyzed by aldolase
- Dihydroxyacetone phosphate (DHAP), catalyzed by triose phosphate isomerase (TIM)
- 1,3-bisphosphoglycerate, (1,3BPG) catalyzed by glyceraldehyde 3-phosphate dehydrogenase This intermediate is also of some importance since this is how glycerol (as DHAP) enters the glycolytic and gluconeogenesis pathways. It is also known as GADP in these reactions.

An intermediate in photosynthesis

G3P is often referred to as 3-phosphoglyceraldehyde (PGAL) with respect to the product of photosynthetic carbon fixation during the Calvin cycle. During plant photosynthesis, two molecules of glycerate 3-phosphate (GP, but also known as 3-phosphoglycerate (PGA)) are produced by the first step of the light-independent reactions when ribulose 1,5-bisphosphate (RuBP) and carbon dioxide are catalysed by the rubisco enzyme. The GP is converted to PGAL using the energy in ATP and the reducing power of NADPH as part of the Calvin cycle. This returns ADP, Pi, and NADP+ to the light-dependent reactions of photosynthesis for their continued functioning. PGAL can then be converted to glucose. RuBP is regenerated for the Calvin cycle to continue. PGAL is generally considered the prime end-product of photosynthesis and it can be used as an immediate food nutrient, combined and rearranged to form monosaccharide sugars, such as glucose, which can be transported to other cells, or packaged for storage as insoluble polysaccharides such as starch. PGAL is related primarily to autotrophic nutrition.

Balance sheet

6 CO₂ + 6 RuBP (+ energy from 12 ATP and 12 NADPH) → 12 PGAL (3-carbon) 10 PGAL (+ energy from 6 ATP) → 6 RuBP (ie starting material regenerated) 2 PGAL → glucose (6-carbon). Category:Photosynthesis

Gluconeogenesis

Gluconeogenesis, ultimately, is the generation of glucose from noncarbohydrate sources like lactate, glycerol, and amino acids. Many 3 and 4-carbon substrates can enter the gluconeogenesis pathway. Lactate from anaerobic exercise in skeletal muscle is easily converted to pyruvate; this happens as part of the Cori cycle. However, the first designated substrate in the gluconeogenic pathway is pyruvate. The vast majority of gluconeogenesis takes place in the liver and, to a smaller extent, in the kidney. This process occurs during periods of starvation or intense exercise and is highly exergonic. Gluconeogenesis is NOT a reverse of glycolysis, the three irreversible steps in glycolysis are bypassed in gluconeogenesis. This is done to ensure that glycolysis and gluconeogenesis do not operate at the same time in the cell. The majority of the enzymes responsible for gluconeogenesis are found in the cytoplasm; the exception is pyruvate carboxylase which is located in the mitochondria. The rate of gluconeogenesis is ultimately controlled by the action of a key enzyme fructose 1,6-bisphosphatase. Most factors that regulate the activity of the gluconeogenesis pathway do so by inhibiting the activity of key enzymes. However, both acetyl CoA and citrate activate gluconeogenesis enzymes (pyruvate carboxylase and fructose 1,6-bisphosphatase, respectively). Oxaloacetate (an intermediate in the citric acid cycle) can also be used for gluconeogenesis. Amino acids, after their amino group has been removed, feed into parts of the citric acid cycle, and can thus generate glucose in this pathway. Most fatty acids cannot be turned into glucose unless the glyoxylate cycle is used, the exception being odd-chain fatty acids which can yield propionyl CoA, a precursor for oxaloacetate. Fatty acids are regularly broken down into the two carbon acetyl CoA, which becomes degraded in the citric acid cycle. In contrast glycerol, which is a part of all triacylglycerols, can be used in gluconeogenesis. Gluconeogenesis begins with the formation of oxaloacetate through carboxylation of pyruvate at the expense of one molecule of ATP. This reaction is catalyzed by pyruvate carboxylase. Oxaloacetate is then decarboxylated and simultaneously phosphorylated by phosphoenolpyruvate carboxykinase to produce phosphoenolpyruvate. One molecule of GTP is hydrolyzed to GDP in the course of this reaction. Both reactions take place in mitochondria. Oxaloacetate has to be transformed into malate in order to be transported out of the mitochondria. Typically, the last step of gluconeogenesis, is the formation of glucose 6-phosphate from fructose 6-phosphate by phosphoglucose isomerase. Free glucose is not generated automatically because glucose, unlike glucose 6-phosphate, tends to freely diffuse out of the cell. The reaction of actual glucose formation is carried out in the lumen of the endoplasmic reticulum. Here, glucose 6-phosphate is hydrolyzed by glucose-6-phosphatase, a regulated membrane-bound enzyme, to produce glucose. Glucose is then shuttled into cytosol by glucose transporters located in the membrane of the endoplasmic reticulum. Category:Metabolism

F1,6BP

fructose 1,6-bisphosphate

DHAP

DHAP (or Dihydroxyacetonephosphate) is a biochemical compound involved in many reactions, from the Calvin Cycle in plants to the ether-lipid biosynthesis process in Leishmania mexicana. In the Calvin Cycle, it is one of the products of the sixfold reduction of 1,3-Bisphosphoglycerate by NADPH. It is also used in the synthesis of Sedoheptulose 1,7-bisphosphate and Fructose 1,6-bisphosphate which are both used to reform Ribulose 5-Phosphate, the 'key' carbohydrate of the Calvin cycle. Dihydroxylacetone Phosphate is also the product of the dehydrogenation of L-Glycerol-3-Phosphate which is part of the entry of glycerol (sourced from triglycerides) into the glycolytic pathway.

1,3BPG

1,3-bisphosphogylcerate (1,3BPG), also known as PGAP. This 3-carbon molecule, is a metabolic intermediate in both glycolysis and the Calvin cycle in photosynthesis. PGAP is a transition stage between PGA and PGAL during the fixation/reduction of CO2. Category:Photosynthesis

Glycerol

Glycerol
Chemical name	Propane-1,2,3-triol
Chemical formula	C₃H₈O₃
Molecular mass	92.09 g/mol
Melting point	17.8 °C
Boiling point	297 °C
Density	1.261 g/cm³
Food energy	4.32 kcal/g
CAS number	56-81-5
SMILES	OCC(O)CO
SMILES

Glycerin, also known as glycerine and glycerol, and less commonly as 1,2,3-propanetriol, 1,2,3-trihydroxypropane, glyceritol, and glycyl alcohol is a colorless, odorless, hygroscopic, and sweet-tasting viscous liquid. Glycerin is a sugar alcohol and has three hydrophilic alcoholic hydroxyl groups (-OH) that are responsible for its solubility in water. Glycerin is prochiral. Glycerin is used in glycerin soap, in cosmetics and creams, in foods, in chemistry, and in glycerin Fog machine mist. Glycerin is produced from dihydroxyacetone phosphate (DHAP) by the enzyme glycerol three-phosphate dehydrogenase (Gpd p) in the mitochondrion of the eukaryotic cell during glycolysis.[http://aem.asm.org/cgi/content/full/68/9/4448?view=full&pmid=12200299]

Glycerin and triglycerides

glycolysis When referring to its function in living organisms, the term glycerol is preferred. Glycerol is an important component of triglycerides (i.e. fats and oils) and of phospholipids. Glycerol is a three-carbon substance that forms the backbone of fatty acids in fats.(1) When the body uses stored fat as a source of energy, glycerol and fatty acids are released into the bloodstream. The glycerol component can be converted to glucose by the liver and provides energy for cellular metabolism. A byproduct of saponification and transesterification to obtain biodiesel, this is produced by hydrolysis of three ester linkages and loss of three equivalents of fatty acid from fat or biological oil. Fats and oils are insoluble in water, because the OH groups of glycerin are replaced by ester groups. They are hydrophobic.

Glycerin and biodiesel

As a byproduct of biodiesel production, each of the OH sites in HO-CH₂-CH(-OH)-CH₂-OH is one of the three places where a fatty acid chain is broken off the triglyceride molecule. See: transesterification.

Purification

Like biodiesel by-product, the purification of the lower glycerin phase involves: neutralisation, separation of unreacted methanol, dilution with wash liquid stream coming from methylester washing, splitting of soaps and final concentration up to 80%. Partially refined glycerin can be delivered as such to specialized distillers. Feedstock pre-treatment and upgrading of glycerin to pharmaceutical grade (>99.7%) can be optionally implemented within the biodiesel factory itself. When used in food, care should be taken to use only pure vegetable glycerin that is specifically labeled for use in food. "External use only" warnings should be heeded.

Applications

Drugs

- Used in medical and pharmaceutical preparations, mainly as a means of improving smoothness, providing lubrication and as a humectant. Also may be used to lower intracranial and intraocular pressures.
- Laxative suppositories, cough syrups, elixirs and expectorants.

Personal care

- Serves as an emollient, humectant, solvent and lubricant in personal care products
- Competes with sorbitol although glycerin has better taste and higher solubility.
- Toothpaste, mouthwashes, skin care products, hair care products and soaps :: Glycerin is a component of glycerin soap, which is made from denatured alcohol, glycerin, sodium castorate (from castor), sodium cocoate, sodium tallowate, sucrose, water and parfum (fragrance). Sometimes one adds sodium laureth sulfate. This kind of soap is used by people with sensitive, easily irritated skin because it prevents skin dryness with its moisturizing properties. When used as an emollient, glycerin should never be applied undiluted to the skin. The same powerful hygroscopic property that draws moisture out of the air to moisten the skin will draw moisture out of the skin if the glycerin is too concentrated. A minimum of two or three parts water should be added to one part glycerin.

Foods and beverages

- Serves as humectant, solvent and sweetener, may help preserve foods.
- Solvent for flavors (such as vanilla) and food coloring.
- Humectant and softening agent in candy, cakes and casings for meats and cheeses.
- Manufacture of mono- and di-glycerides for use as emulsifiers
- Used in manufacture of polyglycerol esters going into shortenings and margarine.
- Used as filler in low-fat food products (i.e., cookies). Glycerin has approximately 27 food calories per teaspoon and is 60% as sweet as table sugar. Although it has about the same food energy as table sugar, it does not raise blood sugar levels, nor does it feed the bacteria that form plaques and cause dental cavities. Glycerin should not be consumed undiluted, as unhydrated glycerin will draw water from tissues, causing blistering in the mouth and gastric distress.

Polyether polyols

- One of the major raw materials for the manufacture of polyols for flexible foams, and to a lesser extent rigid polyurethane foams
- Glycerin is the initiator to which propylene oxide/ethylene oxide is added

Alkyd resins (plastics) and cellophane

- Used in surface coatings and paints
- Used as a softener and plasticizer to impart flexibility, pliability and toughness
- Uses include meat casings, collagen casings (medical applications)and nonmeat packaging
- Plasticizer in cellophane.

Absolute alcohol

- There is an absolute alcohol production process by dehydration using glycerin.

Other applications

- Manufacture of paper as a plasticizer, Nitroglycerin, humectant and lubricant
- Humectant for pet foods to retain moisture and enhance palatability
- Used in lubricating, sizing and softening of yarn and fabric
- Used in de-/anti-icing fluids, as in vitrification of blood cells for storage in liquid nitrogen
- Patent applications have been filed for detergent softeners and surfactants based on glycerin (i.e., alkyl glyceryl ethers) instead of quaternary ammonium compounds.
- A way to preserve leaves is to submerge them in a solution of glycerin and water. :: Use a mixture of one part glycerin to two parts water. Place the mixture in a flat pan, and totally submerge the leaves in a single layer in the liquid. You'll have to weigh them down to keep them submerged. In two to six days, they should have absorbed the liquid and be soft and pliable. Remove them from the pan and wipe off all the liquid with a soft cloth. Done correctly, the leaves will remain soft and pliable indefinitely.
- Can be added to solutions of water and soap to increase that solution's ability to generate soap bubbles that will last a long time.
- Use as antifreeze in cryogenic process.
- Used in fog machine fluids See also: oleochemicals.

External links

- [http://www.pioneerthinking.com/glycerin.html What is Glycerin?]
- [http://www.ccnphawaii.com/glossary.htm Glossary for the Modern Soap Maker]
- [http://www.gal.es Glycerin soap]
- [http://journeytoforever.org/biofuel_library/Mariller.html Absolute alcohol using glycerin]
- [http://www.compchemwiki.org/index.php?title=Glycerol Computational Chemistry Wiki]

Sources

1. http://www.health.gov/dietaryguidelines/dga2005/report/HTML/G1_Glossary.htm ---- Glycerine is also the title of a single from the album Sixteen Stone by the band Bush. Category:Alcohols Category:Food additives Category:Personal lubricants Category:Household chemicals Category:Cosmetic chemicals Category:Solvents Category:Laxatives ja:グリセリン

Glycolysis

Glycolysis is a series of biochemical reactions by which a molecule of glucose (Glc) is oxidized to two molecules of pyruvic acid (Pyr). The word glycolysis is from Greek glyk meaning sweet and lysis meaning dissolving. It is the initial process of many pathways of carbohydrate catabolism, and serves two principal functions: generation of high-energy molecules(ATP and NADH), and production of a variety of six- or three-carbon intermediate metabolites which may be removed at various steps in the process for other intracellular purposes (such as nucleotide biosynthesis). Glycolysis is one of the most universal metabolic processes known, and occurs (with variations) in many types of cells in nearly all types of organisms. Glycolysis alone produces less energy per glucose molecule than complete aerobic oxidation and so flux through the pathway is greater in anaerobic conditions (i.e. in the absence of oxygen). The most common and well-known type of glycolysis is the Embden-Meyerhof pathway, initially elucidated by Gustav Embden and Otto Meyerhof. The term can be taken to include alternative pathways, such as the Entner-Doudoroff Pathway. However, glycolysis will be used here as a synonym for the Embden-Meyerhof pathway.

Overview

The overall reaction of glycolysis is: :Glc + 2 NAD⁺ + 2 ADP + 2 P_i → 2 NADH + 2 Pyr + 2 ATP + 2 H₂O + 2 H⁺ So, for simple fermentations, the metabolism of 1 molecule of glucose has a net yield of 2 molecules of ATP. Cells performing respiration synthesize much more ATP but this is not considered part of glycolysis proper, although these aerobic reactions do use the product of glycolysis. Eukaryotic aerobic respiration produces an additional 34 molecules (approximately) of ATP for each glucose molecule oxidized. Unlike most of the molecules of ATP produced via aerobic respiration, those of glycolysis are produced by substrate-level phosphorylation. In eukaryotes glycolysis takes place within the cytosol of the cell. Some of the glycolytic reactions are conserved in the Calvin cycle that functions inside the chloroplast. This is consistent with the fact that glycolysis is highly conserved in evolution, being common to nearly all living organisms. This suggests great antiquity; it may have originated with the first prokaryotes, 3.5 billion years ago or more.

Pathway

Sequence of reactions

Preparatory phase

The first five steps are regarded as a preparatory phase since they actually consume energy as the glucose is converted to two three-carbon sugars phosphates (G3P). The bold abbreviations in the two tables correspond to the nomenclature used in the diagram.

Pay-off phase

The second half of glycolysis is known as the pay-off phase characterised by a net gain of the energy rich molecules ATP and NADH. Since glucose leads to two triose sugars in the preparatory phase each reaction in the pay-off phase occurs twice per glucose molecule. This yields 2NADH and 4ATP, leading to a net gain of 2NADH and 2ATP from the gylcolytic pathway per glucose. prokaryote

Entry of sugars

The first step in glycolysis is phosphorylation of Glc by a family of enzymes called HKs to form G6P. In the liver an isozyme of hexokinase called GCK is used, which differs primarily in regulatory properties. This reaction consumes 1 ATP, but the energy is well spent - it keeps [Glc]_{i_{low as to allow continuous entry of Glc through its plasma membrane transporters; prevents Glc leakage out - the cell lacks such transporters for G6P; activates Glc preparing it for the next metabolic changes.

G6P is then rearranged into F6P by GPI. Fru can also enter the glycolytic pathway via phosphorylation at this point.

Control of flux
The flux through the glycolytic pathway must be adjusted in response to conditions both inside and outside the cell. The rate is regulated to meet two major cellular needs: (1) the production of ATP, and (2) the provision of building blocks for biosynthetic reactions. In glycolysis, the reactions catalyzed by hexokinase, phosphofructokinase, and pyruvate kinase are effectively irreversible. In metabolic pathways, such enzymes are potential sites of control and these three enzymes all serve this purpose in glycolysis.

There are several different ways to regulate the activity of an enzyme. An immediate form of control is feedback via allosteric effectors or by covalent modification. Alternatively the amounts of these important enzymes can vary due to transcriptional regulation.
hexokinase
Phosphofructokinase-1
Phosphofructokinase is an important control point in the glycolytic pathway since it is immediately down stream of the entry points for hexose sugars.

High levels of ATP inhibit the PFK enzyme by lowering its affinity for F6P. ATP causes this control by binding to a specific regulatory site that is distinct from the catalytic site. This is a good example of allosteric control. AMP can reverse the inhibitory effect of ATP. A consequence is that PFK is tightly controlled by the ratio of ATP/AMP in the cell. This makes sense since these molecules are direct indicators of the energy charge in the cell.

Since glycolysis is also a source of carbon skeletons for biosynthesis a negative feedback control to glycolysis from the carbon skeleton pool is useful. Citrate is an example of a metabolite that regulates phosphofructokinase by enhancing the inhibitory effect of ATP. Citrate is an early intermediate in the citric acid cycle and a high level means that biosynthetic precursors are abundant.

Low pH also inhibits phosphofructokinase activity and prevents the excessive rise of lactic acid during anaerobic conditions that could otherwise cause a drop in blood pH (acidosis).

Lastly fructose 2,6-bisphosphate (F2,6BP) is a potent activator of phosphofructokinase (PFK-1) that is synthesised when F6P is phosphorylated by a second phosphofructokinase (PFK2). This second enzyme is inactive when cAMP is high and links the regulation of glycolysis to hormone activity in the body. Both glucagon and adrenalin cause high levels of cAMP in the liver. The result is lower levels of liver fructose 2,6-bisphosphate such that gluconeogenesis (glycolysis in reverse) is favored. This is consistent with the role of the liver in such situations since the response of the liver to these hormones is to releases glucose to the blood.
Pyruvate kinase
Energy pay-off
Each molecule of GADP is then oxidized by a molecule of NAD⁺ in the presence of GAP, forming 1,3-bisphosphoglycerate. In the next step, PGK generates a molecule of ATP while forming 3-phosphoglycerate. At this step glycolysis has reached the break-even point: 2 molecules of ATP were consumed, and 2 new molecules have been synthesized. This step, one of the two substrate-level phosphorylation steps, requires ADP; thus, when the cell has plenty of ATP (and little ADP) this reaction does not occur. Because ATP decays relatively quickly when it is not metabolized, this is an important regulatory point in the glycolytic pathway.
PGAM then forms 2-phosphoglycerate; ENO then forms phosphoenolpyruvate; and another substrate-level phosphorylation then forms a molecule of Pyr and a molecule of ATP by means of the enzyme PK. This serves as an additional regulatory step.

After the formation of F1,6bP, many of the reactions are energetically unfavorable. The only reactions that are favorable are the 2 substrate-level phosphorylation steps that result in the formation of ATP. These two reactions pull the glycolytic pathway to completion.

Follow up
The ultimate fate of pyruvate and NADH produced in glycolysis depends upon the organism and the conditions, most notably the presence or absence of oxygen and other external electron acceptors.

In aerobic organisms, pyruvate typically enters the mitochondria where it is fully oxidized to carbon dioxide and water by pyruvate decarboylase and the set of enzymes of the citric acid cycle (also known as the TCA or Krebs cycle). The products of pyruvate are sequentially dehydrogenated as they pass through the cycle conserving the hydrogen equivalents via the reduction of NAD^{+^{to NADH . NADH is ultimately oxidized by an electron transport chain using oxygen as final electron acceptor to produce a large amount of ATP via the action of the ATP synthase complex, a process known as oxidative phosphorylation. A small amount of ATP is also produced by substrate-level phosphorylation during the TCA cycle.

Although human metabolism is primarily aerobic, under hypoxic (or partially anaerobic) conditions, for example in overworked muscles that are starved of oxygen or in infarcted heart muscle cells, pyruvate is converted to the waste product lactate. This and similar reactions are known as fermentation and they are a solution to maintain the metabolic flux through glycolysis in response to an anaerobic or severely hypoxic environment.

Although fermentation does not produce much energy, it is critical for an anaerobic or hypoxic cell since it regenerates NAD^{+^{that is required for glycolysis to proceed. This is important for normal cellular function as glycolysis is the only source of ATP in anaerobic or severely hypoxic conditions.

There are several types of fermentation where pyruvate and NADH are anaerobically metabolized to yield any of a variety of products with an organic molecule acting as the final hydrogen acceptor. For example, the bacteria involved in making yogurt simply reduce pyruvate to lactic acid, whereas yeast produces ethanol and carbon dioxide. Anaerobic bacteria are capable of using a wide variety of compounds, other than oxygen, as terminal electron acceptors in respiration: nitrogenous compounds (such as nitrates and nitrites), sulphur compounds (such as sulphates, sulphites, sulphur dioxide, and elemental sulphur), carbon dioxide, iron compounds, manganese compounds, cobalt compounds, and uranium compounds.
Intermediates for other pathways
This article concentrates on the catabolic role of glycolysis with regard to converting potential chemical energy to usable chemical energy during the oxidation of glucose to pyruvate. Many of the metabolites in the glycolytic pathway are also used by anabolic pathways, consequently, flux through the pathway is also critical to maintain a supply carbon skeletons for biosynthesis.

From an energy perspective, NADH is either recycled to NAD+ during anaerobic conditions, to maintain the flux through the glycolytic pathway, or used during aerobic conditions to produce more ATP by oxidative phosphorylation. From an anabolic metabolism perspective, the NADH has a role to drive synthetic reactions. It does this directly or indirectly by reducing the pool of NADP+ in the cell to NADPH, which is another important reducing agent for biosynthetic pathways in a cell.

High aerobic glycolysis
During anaerobic conditions glycolysis is the cellular mechanism to obtain ATP, by fermentation. However, in mammalian cells glycolysis is coupled with aerobic respiration. In the presence of oxygen, mitochondria take up pyruvate, the end-product of glycolysis, and further oxidize it into CO₂ and water. Consequently the flux through the glycolytic pathway is lower during aerobic conditions since the full oxidation of one molecule of pyruvate (equivalent to one-half molecule of glucose) can lead to 18 times more ATP. Malignant rapidly-growing tumor cells, however, have glycolytic rates which are up to 200 times higher than their normal tissues of origin despite the ample availability of oxygen. A classical view to explain the high gylcolytic rate in these cells is that it is probably due to the local depletion of oxygen within the tumor. Nevertheless, there is also strong experimental evidence that attributes these high aerobic glycolytic rates to an overexpressed form of mitochondrially-bound hexokinase responsible for driving the high glycolytic activity when oxygen is not necessarily depleted.This phenomenon was first described in 1930 by Otto Warburg and hence it is referred to as the Warburg Effect. This has a current important medical application as aerobic glycolysis by malignant tumors is utilized clinically to diagnose and monitor treatment responses of cancers by imaging uptake of 2-¹⁸F-2-deoxyglucose (a radioactive modified hexokinase substrate) with positron emission tomography (PET) , .

Alternative nomenclature
Some of the metabolites in glycolysis have alternative names and nomenclature. In part, this is beacuse some are common to other pathways, such as the Calvin cycle.

See also

- Gluconeogenesis

- Citric acid cycle (Krebs cycle)

- Anaerobic respiration

- Cellular respiration

- Anaerobic glycolysis

External links

- [http://nist.rcsb.org/pdb/molecules/pdb50_1.html The Glycolytic enzymes in Glycolysis: Protein Data Bank]

- [http://www.wdv.com/CellWorld/Biochemistry/Glycolytic Glycolytic cycle with animations]

- [http://www.biochemweb.org/metabolism.shtml Metabolism, Cellular Respiration and Photosynthesis - The Virtual Library of Biochemistry and Cell Biology]

- [http://www2.ufp.pt/~pedros/bq/glycolysis.htm The chemical logic behind glycolysis]

References

- Stryer, Lubert (1987). Biochemistry. W.H. Freeman. ISBN 0-7167-1920-7
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Category:Cellular respiration
Category:Metabolism
Category:Biochemistry

ko:해당작용

ja:解糖系

Gluconeogenesis
Gluconeogenesis, ultimately, is the generation of glucose from noncarbohydrate sources like lactate, glycerol, and amino acids. Many 3 and 4-carbon substrates can enter the gluconeogenesis pathway. Lactate from anaerobic exercise in skeletal muscle is easily converted to pyruvate; this happens as part of the Cori cycle. However, the first designated substrate in the gluconeogenic pathway is pyruvate. The vast majority of gluconeogenesis takes place in the liver and, to a smaller extent, in the kidney. This process occurs during periods of starvation or intense exercise and is highly exergonic.

Gluconeogenesis is NOT a reverse of glycolysis, the three irreversible steps in glycolysis are bypassed in gluconeogenesis. This is done to ensure that glycolysis and gluconeogenesis do not operate at the same time in the cell. The majority of the enzymes responsible for gluconeogenesis are found in the cytoplasm; the exception is pyruvate carboxylase which is located in the mitochondria. The rate of gluconeogenesis is ultimately controlled by the action of a key enzyme fructose 1,6-bisphosphatase. Most factors that regulate the activity of the gluconeogenesis pathway do so by inhibiting the activity of key enzymes. However, both acetyl CoA and citrate activate gluconeogenesis enzymes (pyruvate carboxylase and fructose 1,6-bisphosphatase, respectively).

Oxaloacetate (an intermediate in the citric acid cycle) can also be used for gluconeogenesis. Amino acids, after their amino group has been removed, feed into parts of the citric acid cycle, and can thus generate glucose in this pathway.

Most fatty acids cannot be turned into glucose unless the glyoxylate cycle is used, the exception being odd-chain fatty acids which can yield propionyl CoA, a precursor for oxaloacetate. Fatty acids are regularly broken down into the two carbon acetyl CoA, which becomes degraded in the citric acid cycle. In contrast glycerol, which is a part of all triacylglycerols, can be used in gluconeogenesis.

Gluconeogenesis begins with the formation of oxaloacetate through carboxylation of pyruvate at the expense of one molecule of ATP. This reaction is catalyzed by pyruvate carboxylase. Oxaloacetate is then decarboxylated and simultaneously phosphorylated by phosphoenolpyruvate carboxykinase to produce phosphoenolpyruvate. One molecule of GTP is hydrolyzed to GDP in the course of this reaction. Both reactions take place in mitochondria. Oxaloacetate has to be transformed into malate in order to be transported out of the mitochondria.

Typically, the last step of gluconeogenesis, is the formation of glucose 6-phosphate from fructose 6-phosphate by phosphoglucose isomerase. Free glucose is not generated automatically because glucose, unlike glucose 6-phosphate, tends to freely diffuse out of the cell. The reaction of actual glucose formation is carried out in the lumen of the endoplasmic reticulum. Here, glucose 6-phosphate is hydrolyzed by glucose-6-phosphatase, a regulated membrane-bound enzyme, to produce glucose. Glucose is then shuttled into cytosol by glucose transporters located in the membrane of the endoplasmic reticulum.

Category:Metabolism

Photosynthesis

Photosynthesis is an important biochemical process in which plants, algae, and some bacteria harness the energy of sunlight to produce food. Ultimately, nearly all living things depend on energy produced from photosynthesis for their nourishment, making it vital to life on Earth. It is also responsible for producing the oxygen that makes up a large portion of the Earth's atmosphere. Organisms that produce energy through photosynthesis are called photoautotrophs.

Plant photosynthesis

Plants are photoautotrophs, which means they are able to synthesize food directly from inorganic compounds using light energy, instead of eating other organisms or relying on material derived from them. This is distinct from chemoautotrophs that do not depend on light energy, but use energy from inorganic compounds.

The energy for photosynthesis ultimately comes from absorbed photons and involves a reducing agent, which is water in the case of plants, releasing oxygen as a waste product. The light energy is converted to chemical energy, in the form of ATP and NADPH, using the light-dependent reactions and is then available for carbon fixation. Most notably plants use the chemical energy to fix carbon dioxide into carbohydrates and other organic compounds through light-independent reactions. The overall equation for photosynthesis in green plants is:

:n CO₂ + 2n H₂O + light energy → (CH₂O)_n + n O₂ + n H₂O

Where n is defined according to the structure of the resulting carbohydrate. However, hexose sugars and starch are the primary products, so the following generalised equation is often used to represent photosynthesis:

:6 CO₂ + 12 H₂O + light energy → C₆H₁₂O₆ + 6 O₂ + 6 H₂O

More specifically, photosynthetic reactions usually produces an intermediate product, which is then converted to the final hexose carbohydrate products. These carbohydrate products are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis or as a fuel in cellular respiration. The latter not only occurs in plants, but also in animals when the energy from plants get passed through a food chain. In general outline, cellular respiration is the opposite of photosynthesis: glucose and other compounds are oxidised to produce carbon dioxide, water, and chemical energy. However, both processes actually take place through a different sequence of reactions and in different cellular compartments.

food chain
Plants capture light primarily using the pigment chlorophyll, which is the reason that most plants have a green color. The function of chlorophyll is often supported by other accessory pigments such as carotenoids and xanthophylls. Both chlorophyll and accessory pigments are contained in organelles (compartments within the cell) called chloroplasts. Although all cells in the green parts of a plant have chloroplasts, most of the energy is captured in the leaves. The cells in the interior tissues of a leaf, called the mesophyll, contain about half a million chloroplasts for every square millimeter of leaf. The surface of the leaf is uniformly coated with a water-resistant, waxy cuticle, that protects the leaf from excessive evaporation of water as well as decreasing the absorption of ultraviolet or blue light to reduce heating. The transparent, colourless epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.

Photosynthesis in algae and bacteria

Algae range from multicellular forms like kelp to microscopic, single-celled organisms. Although they are not as complex as land plants, photosynthesis takes place biochemically the same way. Light is absorbed by chlorophyll, although various accessory pigments to give them a wide variety of colours, located inside chloroplasts. All algae produce oxygen, and many are autotrophic. However, some are heterotrophic, relying on materials produced by other organisms.

Photosynthetic bacteria do not have chloroplasts. Instead, photosynthesis takes place directly within the cell. The cyanobacteria contain chlorophyll and oxygen, in the same way that chloroplasts do, in fact chloroplasts are now considered to have evolved from cyanobacteria by endosymbiosis. The other photosynthetic bacteria have a variety of different pigments, called bacteriochlorophylls, and do not produce oxygen.

Molecular production
Light-dependent reaction

bacteriochlorophyll
bacteriochlorophyll
The products of the light dependent reactions are ATP from photophosphorylation and NADPH from photoreduction. Both are then utilized as an energy source for the light-independent reactions.
Z scheme
In plants, the light-dependent reactions occur in the thylakoid membranes of the chloroplasts and use light energy to sythesize ATP and NADPH. The photons are captured in the antenna complexes of photosystem I and II by chlorophyll and accessory pigments (see diagram at right). When a chorophyll a molecule at a photosystems reaction center absorbs energy, an electron is excited and transferred to an electron-acceptor molecule through a process called Photoinduced charge separation. These electrons are shuttled through an electron transport chain that initially functions to generate a chemiosmotic potential across the membrane, the so called Z-scheme shown in the diagram. An ATP synthase enzyme uses the chemiosmotic potential to make ATP during photophosphorylation while NADPH is a product of the terminal redox reaction in the Z-scheme.

Water photolysis
The NADPH is the main reducing agent in chloroplasts, providing a source of energetic electrons to other reactions. Its production leaves chlorophyll with a deficit of electrons (oxidized), which must be obtained from some other reducing agent. The excited electrons lost from chlorophyll in photosystem I are replaced from the electron transport chain by plastocyanin. However, since photosystem II includes the first steps of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. This role is played by water during a reaction known as photolysis and results in water being split to give electrons, oxygen and hydrogen ions. Photosystem II is the only known biological enzyme that carries out this oxidation of water. Initially, the hydrogen ions from photolysis contribute to the chemiosmotic potential but eventually they combine with the hydrogen carrier molecule NADP⁺ to form NADPH. Oxygen is a waste product of photosynthesis but it has a vital role for all organisms that use it for cellular respiration.

Oxygen and photosynthesis
With respect to oxygen and photosynthesis, there are two important concepts.

- Plant and algal cells also use oxygen for cellular respiration, although they have a net output of oxygen since much more is produced during photosynthesis.

- Oxygen is a product of the photolysis reaction not the fixation of carbon dioxide during the light-independent reactions. Consequently, the source of oxygen during photosynthesis is water, NOT carbon dioxide.

Bacterial variations
The second concept was first proposed by Cornelis Bernadus van Neil in the 1930s, who studied photosynthetic bacteria. Aside from the cyanobacteria, bacteria only have one photosystem and use reducing agents other than water. They get electrons from a variety of different inorganic chemicals including sulfide or hydrogen, so for most of these bacteria oxygen is not produced.

Others, such as the halophiles (an Archeae) produced so called purple membranes where the bacteriorhodopsin could harvest light and produce energy. The purple membranes was one of the first to be used to demonstrate the chemiosmotic theory: light hit the membranes and the pH of the solution that contained the purple membranes dropped as protons were pumping out of the membrane.

Light-independent reaction

The fixation of carbon dioxide is a light-independent process in which carbon dioxide combines with a five-carbon sugar, ribulose bisphosphate (RuBP), to give two molecules of a three-carbon compound, glycerate 3-phosphate (GP). This compound is also sometimes known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehye 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate (a three-carbon sugar). This is the point at which carbohydrates are produced during photosynthesis. Some of the triose phosphates condense to form hexose phosphates, sucrose, starch and cellulose or are converted to acetylcoenzyme A to make amino acids and lipids. Others go on to regenerate RuBP so the process can continue (see Calvin Cycle).

Discovery
Although some of the steps in photosynthesis are still not completely understood, the overall photosynthetic equation has been known since the 1800s.

Jan van Helmont began the research of the process in the mid-1600s when he carefully measured the mass of the soil used by a plant and the mass of the plant as it grew. After noticing that the soil mass changed very little, he hypothesized that the mass of the growing plant must come from the water, the only substance he added to the potted plant. This was a partially accurate hypothesis - much of the gained mass also comes from carbon dioxide as well as water. However, this was a signalling point to the idea that the bulk of a plant's biomass comes from the inputs of photosynthesis, not the soil itself.

Joseph Priestley, a chemist and minister, discovered that when he isolated a volume of air under an inverted jar, and burned a candle in it, the candle would burn out very quickly, much before it ran out of wax. He further discovered that a mouse could similarly "injure" air. He then showed that the air that had been "injured" by the candle and the mouse could be restored by a plant.

In 1778, Jan Ingenhousz, court physician to the Austrian Empress, repeated Priestley's experiments. He discovered that it was the influence of sun and light on the plant that could cause it to rescue a mouse in a matter of hours.

In 1796, Jean Senebier, a French pastor, showed that CO₂ was the "fixed" or "injured" air and that it was taken up by plants in photosynthesis. Soon afterwards, Nicolas-Théodore de Saussure showed that the increase in mass of the plant as it grows could not be due only to uptake of CO₂, but also to the incorporation of water. Thus the basic reaction by which photosynthesis is used to produce food (such as glucose) was outlined.

Modern scientists built on the foundation of knowledge from those scientists centuries ago and were able to discover many things.

Cornelius Van Niel made key discoveries explaining the chemistry of photosynthesis. By studying purple sulfur bacteria and green bacteria he was the first scientist to demonstrate that photosynthesis is a light-dependent redox reaction, in which hydrogen reduces carbon dioxide.

Further experiments to prove that the oxygen developed during the photosynthesis of green plants came from water, were performed by Robert Hill in 1937 and 1939. He showed that isolated chloroplasts give off oxygen in the presence of unnatural reducing agents like iron oxalate, ferricyanide or benzoquinone after exposure to light. The Hill reaction is as follows:

:2 H₂O + 2 A + (light, chloroplasts) → 2 AH₂ + O₂

where A is the electron acceptor. Therefore, in light the electron acceptor is reduced and oxygen is evolved.

Samuel Ruben and Martin Camen used radioactive isotopes to determine that the oxygen liberated in photosynthesis came from the water.

Melvin Calvin and his partner Benson were able to puzzle out each stage in the dark or light-independent phase of photosynthesis, known as the Calvin Cycle.

A Nobel Prize winning scientist, Rudolph A. Marcus, was able to discover the function and significance of the electron transport chain.

Bioenergetics of Photosynthesis

Photosynthesis is a physiological phenomenon that coverts solar energy into photochemical energy. This physiological phenomenon may be described thermodynamically in terms of changes in energy, entropy and free energy. The energetics of photosynthesis, driven by light, causes a change in entropy that in turn yields a usable source of energy for the plant.

The following equation summarizes the products and reactants of photosynthesis in the typical green photosynthesizing plant:

CO₂ + H₂O → O₂ + (CH₂O) + 112 kcal/mol CO₂

On earth, there are two sources of free energy: light energy from the sun, and terrestrial sources, including volcanoes, hot springs and radioactivity of certain elements. The biochemical value of electromagnetic radiation has led plants to use the free energy from the sun in particular. Visible light, which is used specifically by green plants to photosynthesize, may result in the formation of electronically excited states of certain substances called pigments (Gregory). For example, Chl a is a pigment which acts as a catalyst, converting solar energy into photochemical energy that is necessary for photosynthesis (Govindjee).

With the presence of solar energy, the plant has a usable source of energy, which is termed the free energy (F) of the system. However, thermal energy is not completely interconvertible, which means that the character of the solar energy may lead to the limited convertibility of it into forms that may be used by the plant. This relates back to the work of Josiah Willard Gibbs: the change in free energy (ΔF) is related to both the change in entropy (ΔS) and the change in enthalpy (ΔH) of the system (Rabinowitch).

Gibbs energy equation: ΔF = ΔH – TΔS

Past experiments have shown that the total energy produced by photosynthesis is 112 kcal/mol. However in the experiment, the free energy due to light was 120 kcal/mol. An overall loss of 8 kcal/mol was due to entropy, as described by Gibbs equation (Gonindjee). In other words, since the usable energy of the system is related directly to the entropy and temperature of the system, a smaller amount of thermal energy is available for conversion into usable forms of energy (including mechanical and chemical) when entropy is great (Rabinowitch). This concept relates back to the second law of thermodynamics in that an increase in entropy is needed to convert light energy into energy suitable for the plant.

Overall, in conjunction with the oxidation-reduction reaction nature of the photosynthesis equation, and the interrelationships between entropy and enthalpy, energy in a usable form will be produced by the photosynthesizing green plant.

References

Govindjee. Bioenergetics of Photosynthesis. New York: Academic Press, 1975.

Gregory, R.P.F. Biochemistry of Photosynthesis. Belfast: Universities Press, 1971.

Rabinowitch, Eugene and Govindjee. Photosynthesis. New York: John Wiley & Sons, Inc., 1969.

Factors affecting photosynthesis

There are three main factors affecting photosynthesis and several corollary factors. The three main are:

- Light irradiance and wavelength

- Carbon dioxide concentration

- Temperature

Light Intensity (Irradiance), Wavelength and Temperature

In the early 1900s F.F. Blackman investigated the effects of light intensity (irradiance) and temperature on the rate of photosynthesis. At constant temperature the rate of photosynthesis varies with irradiance, initially increasing as the irradiance increases. However at higher irradiance this relationship no longer holds and the rate of photosynthesis reaches a plateau. The effect on the rate of photosynthesis of varying the temperature at constant irradiance can be seen in image to the left. At high irradiance the rate of photosynthesis increases as the temperature is increased over a limited range. At low irradiance, increasing the temperature has little effect on the rate of photosynthesis. These two experiments illustrate vital points: firstly, from research it is known that photochemical reactions are not generally affected by temperature. However, these experiments clearly show that temperature affects the rate of photosynthesis, so there must be two sets of reactions in the full process of photosynthesis. These are of course the light-dependent 'photochemical' stage and the light-independent, temperature-dependent stage. Secondly, Blackman's experiments illustrate the concept of limiting factors. Another limiting factor is the wavelength of light. Cyanobacteria which reside several metres underwater cannot recieve the correct wavelengths required to cause photoinduced charge seperation in conventional photosynthetic pigments. To combat this problem a series of proteins with different flourescent pigments surround the reaction centre. This unit is called a phycobilisome.

Carbon Dioxide

An increase in the carbon dioxide concentration increases the rate at which carbon is incorporated into carbohydrate in the light-independent reaction and so the rate of photosynthesis generally increases until limited by another factor. Carbon dioxide helps increase the rate of photosynthesis. This is because rubisco, the enzyme fixing the carbon dioxide in the light-dependent reactions, has affinity for both carbon dioxide and oxygen. Thus, an increase in the concentration of carbon dioxide increases the probability of rubisco fixing carbon dioxide instead of oxygen. This allows the plant to be more productive since the fixation of oxygen requires photorespiration to remove glycolate a product of rubisco's oxygenase activity. Photorespiration is bad for a plant since it actually releases carbon dioxide and uses energy in the process.

Corollary Factors

- Amount of water

- Leaf morphology

- Leaf nitrogen content

- Molecular Carriers such as NADP and FAD

In Detail

Metabolic pathways involved in photosynthesis:

- Light-dependent reaction

- Light-independent reaction

See also

- Artificial photosynthesis

- Calvin Cycle

External links

- [http://www.biochemweb.org/metabolism.shtml Metabolism, Cellular Respiration and Photosynthesis - The Virtual Library of Biochemistry and Cell Biology]

- [http://www.chemsoc.org/networks/learnnet/cfb/Photosynthesis.htm Overall examination of Photosynthesis at an intermediate level]

- [http://www.life.uiuc.edu/govindjee/photosynBook.html Overall Energetics of Photosynthesis]

Category:Biochemistry
Category:Botany

Category:Metabolism
Category:Agronomy

ko:광합성

ms:Fotosintesis

ja:光合成

simple:Photosynthesis

th:การสังเคราะห์ด้วยแสง

Carbon fixation
Carbon fixation is a process found in autotrophs, usually driven by photosynthesis, whereby carbon dioxide is converted into organic compounds. In plants, there are three types:

- C₃ - plant that uses the Calvin Cycle for the initial steps that incorporate CO₂ into organic matter, forming a 3-carbon compound as the 1^st stable intermediate.

- C₄ - plant that prefaces the Calvin Cycle with reactions that incorporate CO₂ into 4-carbon compound. This pathway is found mostly in hot regions with intense sunlight.

- CAM - plant that uses Crassulacean acid metabolism as an adaptation for arid conditions. CO₂ entering the stomata during the night is converted into organic acids, which release CO₂ for the Calvin Cycle during the day, when the stomata is closed.
Category:PhotosynthesisCategory:Metabolism

ja:炭素固定

Calvin cycle
The Calvin cycle (or Calvin-Benson cycle) is a series of biochemical reactions that takes place in the chloroplasts of photosynthetic organisms. It was discovered by Melvin Calvin and Andew Benson at the University of California, Berkeley. James Bassham also made important contributions to elucidating this pathway. It is one of the light-independent reactions and occurs in the stroma.

During photosynthesis, light energy is used to generate chemical free energy, stored in ATP and NADPH. The light-independent Calvin ("dark") cycle uses the energy from short-lived electronically-excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals which feed on it). This set of reactions is also called carbon fixation. The key enzyme of the cycle is called RuBisCO. In the following equations, the chemical species (phosphates and carboxylic acids) exist in equilibria among their various ionized states as governed by the pH.

The sum of reactions in the Calvin cycle is the following:
:6 CO₂ + 12 NADPH + 12 H₂O + 18 ATP → C₆H₁₂O₆ + 12 NADP⁺ + 18 ADP + 18 P_i

- The steps in the Calvin cycle are:

- RuBisCO reacts with CO₂, creating a 3-carbon compound, PGA.

- One ATP from the light reactions is used, producing an ADP and a P_i (inorganic phosphate).

- An NADPH from the light reactions combines with an H⁺ and becomes NADP⁺.

- PGAL, a 3-carbon compound, is produced, which stores free energy.

- Another ATP is consumed, yielding an ADP and a P_i.

- RuBP is produced, which is a 5-carbon compound.

At high temperatures, RuBisCO will react with O₂ instead of CO₂ in photorespiration, an apparently-puzzling process, since it seems to throw away captured energy. However it may be a mechanism for preventing overload during periods of high light flux. C4 plants use the enzyme PEP initially, which has a higher affinity for CO₂. The process first makes a 4-carbon intermediate compound; hence the name C4 plants.

CAM plants keep their stomata (on the underside of the leaf) closed during the day, which conserves water but prevents photosynthesis, which requires CO₂ to pass by gas exchange through these openings. Evaporation through the upper side of a leaf is prevented by a layer of wax.

References

Bassham JA (2003) Mapping the carbon reduction cycle: a personal retrospective. Photosynthesis Research, volume 76, pages 25-52 (see: ).

Calvin cycle

ja:カルビン - ベンソン回路

Photosynthesis

Photosynthesis is an important biochemical process in which plants, algae, and some bacteria harness the energy of sunlight to produce food. Ultimately, nearly all living things depend on energy produced from photosynthesis for their nourishment, making it vital to life on Earth. It is also responsible for producing the oxygen that makes up a large portion of the Earth's atmosphere. Organisms that produce energy through photosynthesis are called photoautotrophs.

Plant photosynthesis

Plants are photoautotrophs, which means they are able to synthesize food directly from inorganic compounds using light energy, instead of eating other organisms or relying on material derived from them. This is distinct from chemoautotrophs that do not depend on light energy, but use energy from inorganic compounds.

The energy for photosynthesis ultimately comes from absorbed photons and involves a reducing agent, which is water in the case of plants, releasing oxygen as a waste product. The light energy is converted to chemical energy, in the form of ATP and NADPH, using the light-dependent reactions and is then available for carbon fixation. Most notably plants use the chemical energy to fix carbon dioxide into carbohydrates and other organic compounds through light-independent reactions. The overall equation for photosynthesis in green plants is:

:n CO₂ + 2n H₂O + light energy → (CH₂O)_n + n O₂ + n H₂O

Where n is defined according to the structure of the resulting carbohydrate. However, hexose sugars and starch are the primary products, so the following generalised equation is often used to represent photosynthesis:

:6 CO₂ + 12 H₂O + light energy → C₆H₁₂O₆ + 6 O₂ + 6 H₂O

More specifically, photosynthetic reactions usually produces an intermediate product, which is then converted to the final hexose carbohydrate products. These carbohydrate products are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis or as a fuel in cellular respiration. The latter not only occurs in plants, but also in animals when the energy from plants get passed through a food chain. In general outline, cellular respiration is the opposite of photosynthesis: glucose and other compounds are oxidised to produce carbon dioxide, water, and chemical energy. However, both processes actually take place through a different sequence of reactions and in different cellular compartments.

food chain
Plants capture light primarily using the pigment chlorophyll, which is the reason that most plants have a green color. The function of chlorophyll is often supported by other accessory pigments such as carotenoids and xanthophylls. Both chlorophyll and accessory pigments are contained in organelles (compartments within the cell) called chloroplasts. Although all cells in the green parts of a plant have chloroplasts, most of the energy is captured in the leaves. The cells in the interior tissues of a leaf, called the mesophyll, contain about half a million chloroplasts for every square millimeter of leaf. The surface of the leaf is uniformly coated with a water-resistant, waxy cuticle, that protects the leaf from excessive evaporation of water as well as decreasing the absorption of ultraviolet or blue light to reduce heating. The transparent, colourless epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.

Photosynthesis in algae and bacteria

Algae range from multicellular forms like kelp to microscopic, single-celled organisms. Although they are not as complex as land plants, photosynthesis takes place biochemically the same way. Light is absorbed by chlorophyll, although various accessory pigments to give them a wide variety of colours, located inside chloroplasts. All algae produce oxygen, and many are autotrophic. However, some are heterotrophic, relying on materials produced by other organisms.

Photosynthetic bacteria do not have chloroplasts. Instead, photosynthesis takes place directly within the cell. The cyanobacteria contain chlorophyll and oxygen, in the same way that chloroplasts do, in fact chloroplasts are now considered to have evolved from cyanobacteria by endosymbiosis. The other photosynthetic bacteria have a variety of different pigments, called bacteriochlorophylls, and do not produce oxygen.

Molecular production
Light-dependent reaction

bacteriochlorophyll
bacteriochlorophyll
The products of the light dependent reactions are ATP from photophosphorylation and NADPH from photoreduction. Both are then utilized as an energy source for the light-independent reactions.
Z scheme
In plants, the light-dependent reactions occur in the thylakoid membranes of the chloroplasts and use light energy to sythesize ATP and NADPH. The photons are captured in the antenna complexes of photosystem I and II by chlorophyll and accessory pigments (see diagram at right). When a chorophyll a molecule at a photosystems reaction center absorbs energy, an electron is excited and transferred to an electron-acceptor molecule through a process called Photoinduced charge separation. These electrons are shuttled through an electron transport chain that initially functions to generate a chemiosmotic potential across the membrane, the so called Z-scheme shown in the diagram. An ATP synthase enzyme uses the chemiosmotic potential to make ATP during photophosphorylation while NADPH is a product of the terminal redox reaction in the Z-scheme.

Water photolysis
The NADPH is the main reducing agent in chloroplasts, providing a source of energetic electrons to other reactions. Its production leaves chlorophyll with a deficit of electrons (oxidized), which must be obtained from some other reducing agent. The excited electrons lost from chlorophyll in photosystem I are replaced from the electron transport chain by plastocyanin. However, since photosystem II includes the first steps of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. This role is played by water during a reaction known as photolysis and results in water being split to give electrons, oxygen and hydrogen ions. Photosystem II is the only known biological enzyme that carries out this oxidation of water. Initially, the hydrogen ions from photolysis contribute to the chemiosmotic potential but eventually they combine with the hydrogen carrier molecule NADP⁺ to form NADPH. Oxygen is a waste product of photosynthesis but it has a vital role for all organisms that use it for cellular respiration.

Oxygen and photosynthesis
With respect to oxygen and photosynthesis, there are two important concepts.

- Plant and algal cells also use oxygen for cellular respiration, although they have a net output of oxygen since much more is produced during photosynthesis.

- Oxygen is a product of the photolysis reaction not the fixation of carbon dioxide during the light-independent reactions. Consequently, the source of oxygen during photosynthesis is water, NOT carbon dioxide.

Bacterial variations
The second concept was first proposed by Cornelis Bernadus van Neil in the 1930s, who studied photosynthetic bacteria. Aside from the cyanobacteria, bacteria only have one photosystem and use reducing agents other than water. They get electrons from a variety of different inorganic chemicals including sulfide or hydrogen, so for most of these bacteria oxygen is not produced.

Others, such as the halophiles (an Archeae) produced so called purple membranes where the bacteriorhodopsin could harvest light and produce energy. The purple membranes was one of the first to be used to demonstrate the chemiosmotic theory: light hit the membranes and the pH of the solution that contained the purple membranes dropped as protons were pumping out of the membrane.

Light-independent reaction

The fixation of carbon dioxide is a light-independent process in which carbon dioxide combines with a five-carbon sugar, ribulose bisphosphate (RuBP), to give two molecules of a three-carbon compound, glycerate 3-phosphate (GP). This compound is also sometimes known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehye 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate (a three-carbon sugar). This is the point at which carbohydrates are produced during photosynthesis. Some of the triose phosphates condense to form hexose phosphates, sucrose, starch and cellulose or are converted to acetylcoenzyme A to make amino acids and lipids. Others go on to regenerate RuBP so the process can continue (see Calvin Cycle).

Discovery
Although some of the steps in photosynthesis are still not completely understood, the overall photosynthetic equation has been known since the 1800s.

Jan van Helmont began the research of the process in the mid-1600s when he carefully measured the mass of the soil used by a plant and the mass of the plant as it grew. After noticing that the soil mass changed very little, he hypothesized that the mass of the growing plant must come from the water, the only substance he added to the potted plant. This was a partially accurate hypothesis - much of the gained mass also comes from carbon dioxide as well as water. However, this was a signalling point to the idea that the bulk of a plant's biomass comes from the inputs of photosynthesis, not the soil itself.

Joseph Priestley, a chemist and minister, discovered that when he isolated a volume of air under an inverted jar, and burned a candle in it, the candle would burn out very quickly, much before it ran out of wax. He further discovered that a mouse could similarly "injure" air. He then showed that the air that had been "injured" by the candle and the mouse could be restored by a plant.

In 1778, Jan Ingenhousz, court physician to the Austrian Empress, repeated Priestley's experiments. He discovered that it was the influence of sun and light on the plant that could cause it to rescue a mouse in a matter of hours.

In 1796, Jean Senebier, a French pastor, showed that CO₂ was the "fixed" or "injured" air and that it was taken up by plants in photosynthesis. Soon afterwards, Nicolas-Théodore de Saussure showed that the increase in mass of the plant as it grows could not be due only to uptake of CO₂, but also to the incorporation of water. Thus the basic reaction by which photosynthesis is used to produce food (such as glucose) was outlined.

Modern scientists built on the foundation of knowledge from those scientists centuries ago and were able to discover many things.

Cornelius Van Niel made key discoveries explaining the chemistry of photosynthesis. By studying purple sulfur bacteria and green bacteria he was the first scientist to demonstrate that photosynthesis is a light-dependent redox reaction, in which hydrogen reduces carbon dioxide.

Further experiments to prove that the oxygen developed during the photosynthesis of green plants came from water, were performed by Robert Hill in 1937 and 1939. He showed that isolated chloroplasts give off oxygen in the presence of unnatural reducing agents like iron oxalate, ferricyanide or benzoquinone after exposure to light. The Hill reaction is as follows:

:2 H₂O + 2 A + (light, chloroplasts) → 2 AH₂ + O₂

where A is the electron acceptor. Therefore, in light the electron acceptor is reduced and oxygen is evolved.

Samuel Ruben and Martin Camen used radioactive isotopes to determine that the oxygen liberated in photosynthesis came from the water.

Melvin Calvin and his partner Benson were able to puzzle out each stage in the dark or light-independent phase of photosynthesis, known as the Calvin Cycle.

A Nobel Prize winning scientist, Rudolph A. Marcus, was able to discover the function and significance of the electron transport chain.

Bioenergetics of Photosynthesis

Photosynthesis is a physiological phenomenon that coverts solar energy into photochemical energy. This physiological phenomenon may be described thermodynamically in terms of changes in energy, entropy and free energy. The energetics of photosynthesis, driven by light, causes a change in entropy that in turn yields a usable source of energy for the plant.

The following equation summarizes the products and reactants of photosynthesis in the typical green photosynthesizing plant:

CO₂ + H₂O → O₂ + (CH₂O) + 112 kcal/mol CO₂

On earth, there are two sources of free energy: light energy from the sun, and terrestrial sources, including volcanoes, hot springs and radioactivity of certain elements. The biochemical value of electromagnetic radiation has led plants to use the free energy from the sun in particular. Visible light, which is used specifically by green plants to photosynthesize, may result in the formation of electronically excited states of certain substances called pigments (Gregory). For example, Chl a is a pigment which acts as a catalyst, converting solar energy into photochemical energy that is necessary for photosynthesis (Govindjee).

With the presence of solar energy, the plant has a usable source of energy, which is termed the free energy (F) of the system. However, thermal energy is not completely interconvertible, which means that the character of the solar energy may lead to the limited convertibility of it into forms that may be used by the plant. This relates back to the work of Josiah Willard Gibbs: the change in free energy (ΔF) is related to both the change in entropy (ΔS) and the change in enthalpy (ΔH) of the system (Rabinowitch).

Gibbs energy equation: ΔF = ΔH – TΔS

Past experiments have shown that the total energy produced by photosynthesis is 112 kcal/mol. However in the experiment, the free energy due to light was 120 kcal/mol. An overall loss of 8 kcal/mol was due to entropy, as described by Gibbs equation (Gonindjee). In other words, since the usable energy of the system is related directly to the entropy and temperature of the system, a smaller amount of thermal energy is available for conversion into usable forms of energy (including mechanical and chemical) when entropy is great (Rabinowitch). This concept relates back to the second law of thermodynamics in that an increase in entropy is needed to convert light energy into energy suitable for the plant.

Overall, in conjunction with the oxidation-reduction reaction nature of the photosynthesis equation, and the interrelationships between entropy and enthalpy, energy in a usable form will be produced by the photosynthesizing green plant.

References

Govindjee. Bioenergetics of Photosynthesis. New York: Academic Press, 1975.

Gregory, R.P.F. Biochemistry of Photosynthesis. Belfast: Universities Press, 1971.

Rabinowitch, Eugene and Govindjee. Photosynthesis. New York: John Wiley & Sons, Inc., 1969.

Factors affecting photosynthesis

There are three main factors affecting photosynthesis and several corollary factors. The three main are:

- Light irradiance and wavelength

- Carbon dioxide concentration

- Temperature

Light Intensity (Irradiance), Wavelength and Temperature

In the early 1900s F.F. Blackman investigated the effects of light intensity (irradiance) and temperature on the rate of photosynthesis. At constant temperature the rate of photosynthesis varies with irradiance, initially increasing as the irradiance increases. However at higher irradiance this relationship no longer holds and the rate of photosynthesis reaches a plateau. The effect on the rate of photosynthesis of varying the temperature at constant irradiance can be seen in image to the left. At high irradiance the rate of photosynthesis increases as the temperature is increased over a limited range. At low irradiance, increasing the temperature has little effect on the rate of photosynthesis. These two experiments illustrate vital points: firstly, from research it is known that photochemical reactions are not generally affected by temperature. However, these experiments clearly show that temperature affects the rate of photosynthesis, so there must be two sets of reactions in the full process of photosynthesis. These are of course the light-dependent 'photochemical' stage and the light-independent, temperature-dependent stage. Secondly, Blackman's experiments illustrate the concept of limiting factors. Another limiting factor is the wavelength of light. Cyanobacteria which reside several metres underwater cannot recieve the correct wavelengths required to cause photoinduced charge seperation in conventional photosynthetic pigments. To combat this problem a series of proteins with different flourescent pigments surround the reaction centre. This unit is called a phycobilisome.

Carbon Dioxide

An increase in the carbon dioxide concentration increases the rate at which carbon is incorporated into carbohydrate in the light-independent reaction and so the rate of photosynthesis generally increases until limited by another factor. Carbon dioxide helps increase the rate of photosynthesis. This is because rubisco, the enzyme fixing the carbon dioxide in the light-dependent reactions, has affinity for both carbon dioxide and oxygen. Thus, an increase in the concentration of carbon dioxide increases the probability of rubisco fixing carbon dioxide instead of oxygen. This allows the plant to be more productive since the fixation of oxygen requires photorespiration to remove glycolate a product of rubisco's oxygenase activity. Photorespiration is bad for a plant since it actually releases carbon dioxide and uses energy in the process.

Corollary Factors

- Amount of water

- Leaf morphology

- Leaf nitrogen content

- Molecular Carriers such as NADP and FAD

In Detail

Metabolic pathways involved in photosynthesis:

- Light-dependent reaction

- Light-independent reaction

See also

- Artificial photosynthesis

- Calvin Cycle

External links

- [http://www.biochemweb.org/metabolism.shtml Metabolism, Cellular Respiration and Photosynthesis - The Virtual Library of Biochemistry and Cell Biology]

- [http://www.chemsoc.org/networks/learnnet/cfb/Photosynthesis.htm Overall examination of Photosynthesis at an intermediate level]

- [http://www.life.uiuc.edu/govindjee/photosynBook.html Overall Energetics of Photosynthesis]

Category:Biochemistry
Category:Botany

Category:Metabolism
Category:Agronomy

ko:광합성

ms:Fotosintesis

ja:光合成

simple:Photosynthesis

th:การสังเคราะห์ด้วยแสง

Glycerate 3-phosphateGlycerate 3-phosphate (GP) or 3-phosphoglycerate (3PG).

This 3-carbon molecule is a metabolic intermediate in both glycolysis and the Calvin cycle. This chemical is often termed PGA when referring to the Calvin cycle.

Category:Photosynthesis

Light-independent reaction

In photosynthesis, the light-independent reactions (also somewhat misleadingly called the dark reactions) are chemical reactions that convert carbon dioxide and other compounds into glucose. These reactions, unlike the light-dependent reactions, do not need light to occur (hence dark reactions). These reactions take the products of the light-dependent reactions and perform further chemical processes on them. The light-independent reactions are two: carbon fixation and the Calvin cycle.

In CAM plants, carbon fixation actually does take place at night.

Carbon fixation

CAM
The carbon fixation reaction is the first step of the light-independent reactions. Carbon from carbon dioxide is "fixed" into a larger carbohydrate. Three pathways (processes) exist for this reaction to occur: C3 carbon fixation (the most common), C4 carbon fixation, and CAM (Crassulacean Acid Metabolism). C3 fixation occurs as the first step of the Calvin cycle in all plants. C4 plants first fix carbon dioxide into malate, which is then used to supply carbon dioxide in the middle of the night to the Calvin cycle. CAM plants perform a similar process.

Calvin cycle
The Calvin cycle takes carbon dioxide and converts it to glucose, which the plant uses for energy.

External links

- [http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm The Biochemistry of the Calvin Cycle at Rensselaer Polytechnic Institute]

Category:Photosynthesis
Category:Metabolism

Carbon dioxide

Carbon dioxide is an atmospheric gas comprised of one carbon and two oxygen atoms. A very widely known chemical compound, it is frequently called by its formula CO₂. In its solid state, it is commonly known as dry ice.

Carbon dioxide derives from multiple sources including volcanic outgassing, the combustion of organic matter and respiration processes of living aerobic organisms. It is also produced by various microorganisms from fermentation and cellular respiration. Plants utilize carbon dioxide during photosynthesis, using both the carbon and the oxygen to construct carbohydrates. In addition, plants also release oxygen to the atmosphere, which is subsequently used for respiration by heterotrophic organisms, forming a cycle. It is present in the Earth's atmosphere at a low concentration and acts as a greenhouse gas. It is a major component of the carbon cycle.

Chemical and physical properties
Carbon dioxide is a colorless gas which, when inhaled at high concentrations (a dangerous activity because of the associated asphyxiation risk), produces a sour taste in the mouth and a stinging sensation in the nose and throat. These effects result from the gas dissolving in the mucous membranes and saliva, forming a weak solution of carbonic acid.

Its density at 25 °C is 1.98 kg m⁻³, about 1.5 times that of air. The carbon dioxide molecule (O=C=O) contains two double bonds and has a linear shape. It has no electrical dipole. As it is fully oxidized, it is not very reactive and, in particular, not flammable.

At temperatures below −78 °C, carbon dioxide condenses into a white solid called dry ice. Liquid carbon dioxide forms only at pressures above 5.1 atm; at atmospheric pressure, it passes directly between the gaseous and solid phases in a process called sublimation.

Water will absorb its own volume of carbon dioxide, and more than this under pressure. About 1% of the dissolved carbon dioxide turns into carbonic acid. The carbonic acid in turn dissociates partly to form bicarbonate and carbonate ions.

Test For Carbon Dioxide.
When a lighted splint is inserted into a test tube containing carbon dioxide, the flame is immediately extinguished, as carbon dioxide does not support combustion. (Certain fire extinguishers contain carbon dioxide to extinguish the flame). To further confirm that the gas is carbon dioxide, the gas may be bubbled into calcium hydroxide solution. The calcium hydroxide turns milky because of the formation of calcium carbonate.

Uses
Liquid and solid carbon dioxide are important refrigerants, especially in the food industry, where they are employed during the transportation and storage of ice cream and other frozen foods.

Carbon dioxide is used to produce carbonated soft drinks and soda water. Traditionally, the carbonation in beer and sparkling wine comes about through natural fermentation, but some manufacturers carbonate these beverages artificially.

The leavening agents used in baking produce carbon dioxide to cause dough to rise. Baker's yeast produces carbon dioxide by fermentation within the dough, while chemical leaveners such as baking powder and baking soda release carbon dioxide when heated or exposed to acids.

Carbon dioxide is often used as an inexpensive, nonflammable pressurized gas. Life jackets often contain canisters of pressured carbon dioxide for quick inflation. Steel capsules are also sold as supplies of compressed gas for airguns, paintball markers, for inflating bicycle tires, and for making seltzer. Rapid vaporization of liquid CO₂ is used for blasting in coal mines.

Carbon dioxide extinguishes flames, and some fire extinguishers, especially those designed for electrical fires, contain liquid carbon dioxide under pressure. Carbon dioxide also finds use as an atmosphere for welding, although in the welding arc, it reacts to oxidize most metals. Use in the automotive industry is common despite significant evidence that welds made in carbon dioxide are brittler than those made in more inert atmospheres, and that such weld joints deteriorate over time because of the formation of carbonic acid. It is used as a welding gas primarily because it is much less expensive than more inert gases such as argon or helium.

Liquid carbon dioxide is a good solvent for many organic compounds, and is used to remove caffeine from coffee. It has begun to attract attention in the pharmaceutical and other chemical processing industries as a less toxic alternative to more traditional solvents such as organochlorides. (See green chemistry.)

Plants require carbon dioxide to conduct photosynthesis, and greenhouses may enrich their atmospheres with additional CO₂ to boost plant growth. It has been proposed that carbon dioxide from power generation be bubbled into ponds to grow algae that could then be converted into biodiesel fuel. High levels of carbon dioxide in the atmosphere effectively exterminate many pests. Greenhouses will raise the level of CO₂ to 10,000 ppm (1%) for several hours to eliminate pests such as whitefly, spider mites, and others.

In medicine, up to 5% carbon dioxide is added to pure oxygen for stimulation of breathing after apnea and to stabilize the O₂/CO₂ balance in blood.

A common type of industrial gas laser, the carbon dioxide laser, uses carbon dioxide as a medium.

Carbon dioxide is commonly injected into or adjacent to producing oil wells. It will act as both a pressurizing agent and, when dissolved into the underground crude oil, will significantly reduce its viscosity, enabling the oil to flow more rapidly through the earth to the removal well. In mature oil fields, extensive pipe networks are used to carry the carbon dioxide to the injection points.

Dry Ice
Dry ice is a genericized trademark for solid ("frozen")}}}}}}