Chapter II

CHAPTER II
2.1 Metabolism
The living cell is the site of tremendous biochemical activity called metabolism. This is the process of chemical and physical change which goes on continually in the living organism. Build-up of new tissue, replacement of old tissue, conversion of food to energy, disposal of waste materials, reproduction - all the activities that we characterize as "life. "This building up and tearing down takes place in the face of an apparent paradox. The greatest majority of these biochemical reactions do not take place spontaneously. Enzyme is a substance that can accelerate a chemical reaction in the body but it does not follow to react. Hence, enzyme is also called biocatalyst.
Metabolism includes only the chemical changes that occur within the tissue cells of the body. It does not include changes to any other substances, such as foodstuffs going through the digestive tract. The body needs many nutrients to function optimally. A slight deficiency of even one vitamin can slow down metabolism and cause chaos throughout the body. The body builds thousands of enzymes to drive the metabolism in the direction dictated by activity and nutrition. So, if you generally train several hours a day, you had better make sure that your diet contains the nutrients it needs to fuel its many metabolic pathways.
Metabolism, whether anabolism or catabolism is called also enzymatic reaction because the changes happen in those two process always use an enzyme. One of the functions of enzyme in those two process is to accelerate the happening of a chemical reaction.
2.2 Enzyme
Enzyme is a subtance that can accelerate a chemical reaction in the body but it does not follow to react. Hence, enzyme is is called biocatalyst.
The phenomenon of catalysis makes possible biochemical reactions necessary for all life processes. Catalysis is defined as the acceleration of a chemical reaction by some substance which itself undergoes no permanent chemical change. The catalysts of biochemical reactions are enzymes and are responsible for bringing about almost all of the chemical reactions in living organisms. Without enzymes, these reactions take place at a rate far too slow for the pace of metabolism. The oxidation of a fatty acid to carbon dioxide and water is not a gentle process in a test tube - extremes of pH, high temperatures and corrosive chemicals are required. Yet in the body, such a reaction takes place smoothly and rapidly within a narrow range of pH and temperature. In the laboratory, the average protein must be boiled for about 24 hours in a 20% HCl solution to achieve a complete breakdown. In the body, the breakdown takes place in four hours or less under conditions of mild physiological temperature and pH. It is through attempts at understanding more about enzyme catalysts - what they are, what they do, and how they do it - that many advances in medicine and the life sciences have been brought about.
2.2.1 The Composition of Enzyme
Chemically, enzyme is made up of two parts, those are protein part and non-protein part. Protein part is called apoenzyme, while non-protein part is called prosthetic group. Apoenzyme and prosthetic group are a unit called holoenzyme.
- Apoenzyme that is made up of protein compound has thermolabile property. Thermolabile means that it is not heat-resistant. This causes the work of an enzyme is influenced by the temperature.
- Prosthetic groups are active groups. Prosthetic groups are distinguished into two, namely:
1) Cofactor, that is prosthetic groups that come from anorganic molecules such as iron, cooper and zinc.
2) Coenzyme, that is prosthetic groups that come from complex organic molecules, such as NADH, FADH, coenzyme-A, and vitamin-B.
2.2.2 Chemical Nature of Enzymes
All known enzymes are proteins. They are high molecular weight compounds made up principally of chains of amino acids linked together by peptide bonds. Enzymes can be denatured and precipitated with salts, solvents and other reagents. They have
molecular weights ranging from 10,000 to 2,000,000.
Many enzymes require the presence of other compounds - cofactors - before their catalytic activity can be exerted. This entire active complex is referred to as the holoenzyme; i.e., apoenzyme (protein portion) plus the cofactor (coenzyme, prosthetic group or metal ionactivator) is called the holoenzyme.
Apoenzyme + Cofactor = Holoenzyme
According to Holum, the cofactor may be:
1. A coenzyme - a non-protein organic substance which is dialyzable, thermostable and loosely attached to the protein part.
2. A prosthetic group - an organic substance which is dialyzable and thermostable which is firmly attached to the protein or apoenzyme portion.
3. A metal-ion-activator - these include K+, Fe++, Fe+++, Cu++, Co++, Zn++, Mn++, Mg++, Ca++, and Mo+++.
2.2.3 Specificity of Enzymes
One of the properties of enzymes that makes them so important as diagnostic and research tools is the specificity they exhibit relative to the reactions they catalyze. A few enzymes exhibit absolute specificity; that is, they will catalyze only one particular reaction. Other enzymes will be specific for a particular type of chemical bond or functional group. In general, there are four distinct types of specificity:
1. Absolute specificity - the enzyme will catalyze only one reaction.
2. Group specificity - the enzyme will act only on molecules that have specific functional groups, such as amino, phosphate and methyl groups.
3. Linkage specificity - the enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure.
4. Stereochemical specificity - the enzyme will act on a particular steric or optical isomer. Though enzymes exhibit great degrees of specificity, cofactors may serve many apoenzymes. For example, nicotinamide adenine dinucleotide (NAD) is a coenzyme for a great number of dehydrogenase reactions in which it acts as a hydrogen acceptor. Among them are the alcohol dehydrogenase, malate dehydrogenase and lactate dehydrogenase reactions.
2.2.4 Characteristic of Enzyme
Characteristic of enzyme are as follows:
a. It is biocatalytic in property, meaning enzyme can accelerate a reaction without it reacts.
b. Enzyme is a protein so it has properties like protein, for example it can coagulate at a high temperature.
c. Works specifically, meaning one kind of an enzyme can only influence one reaction and not influence other reaction.
d. It can be used repeatedly because it does not undergo change when reaction happens except if the enzyme is broken then it must be replaced.
e. It can be broken by heat (thermolabile) because enzyme is a kind of protein. Commonly enzyme is broken at temperature above 500C. The broken of enzyme is called denaturation. If enzyme as been broken, the enzyme cannot work anymore eventhough at normal temperature.
f. It is required in a little amount because enzyme only functions as reaction accelerator, without follows in reaction. One enzyme molecule can work frequently as long as the enzyme is not broken.
g. It is reversible in working, meaning an enzyme can work to decompose a compound to be other compounds or compose those compounds to be the initial compounds. For example: substance (substrate) A is decomposed by an enzyme to be substances B and C, on the contrary substance B can be reacted again by substance C by that enzyme to form substance B.
Its chemicaky reaction can be written as follows:

Substance A substance B + substance C

h. Works inside cell (endoenzyme) or outside cell ectoenzyme.



2.2.5 Working Method of Enzyme
Molecules always move and collide to one another. If a substrate molecule collide a right enzyme molecule, that substrate will stick to enzyme and it causes the happening of a reaction that ends by formation of a product molecule. The place of substrate molecule to stick in enzyme is called active site.
There is also a theory that explains about the working method of enzyme, namely lock and key theory and induced fit theory.
a. Lock and Key Theory
Enzyme has active site. This active site of enzyme has certain form that is suitable only for one kind of substrate therefore enzyme is considered as lock, on the contrary substrate is considered like key because they can bond correctly in active site of enzyme (lock).
Based on the case, then enzyme works specifically. If enzyme is broken because the influence of temperature or pH, the form of active site of enzyme will change causing substrate is not suitable anymore for that enzyme,
b. Induced Fit Theory
The theory states that the active site of an enzyme is more flexible in fitting substance’s structure meaning that the active site can change its form based on the form which is appropriate to its substrate.

2.2.6 Factors Affecting Enzyme Activity
Knowledge of basic enzyme kinetic theory is important in enzyme analysis in order both to understand the basic enzymatic mechanism and to select a method for enzyme analysis. The conditions selected to measure the activity of an enzyme would not be the same as those selected to measure the concentration of its substrate. Several factors affect the rate at which enzymatic reactions proceed - temperature, pH, enzyme concentration, substrate concentration, and the presence of any inhibitors or activators.
a. Temperature
It has been explained before that enzyme is made up of proteins, its thermolabile (it is broken by heat). Enzyme will undergo denaturation at temperature above 500C. Enzyme commonly works optimally at temperature of 300C – 400C or at the body temperature, while at a low temperature (00C or below) enzyme will be non active, but it is not broken if its temperature return to the normal, the enzyme can work again. Like most chemical reactions, the rate of an enzyme-catalyzed reaction increases as the temperature is raised. A ten degree Centigrade rise in temperature will increase the activity of most enzymes by 50 to 100%. Variations in reaction temperature as small as 1 or 2 degrees may introduce changes of 10 to 20% in the results. In the case of enzymatic reactions, this is complicated by the fact that many enzymes are adversely affected by high temperatures. The reaction rate increases with temperature to a maximum level, then
Abruptly declines with further increase of temperature. Because most animal enzymes rapidly become denatured at temperatures above 40•C, most enzyme determinations are carried out somewhat below that temperature.
Over a period of time, enzymes will be deactivated at even moderate temperatures. Storage of enzymes at 5•C or below is generally the most suitable. Some enzymes lose their activity when frozen.
b. pH (Acidity Degree)
The work of enzyme is influenced by pH because of pH changes it will cause the change of key amino acid at the active site of enzyme so inhibit the active site to join with substrate. The optimum pH required for the work of enzyme varies depending on the kind of enzyme but enzyme commonly will work optimally at neutral pH.
Extremely high or low pH values generally result in complete loss of activity for most enzymes. pH is also a factor in the stability of enzymes. As with activity, for each enzyme there is also a region of pH optimal stability. In addition to temperature and pH there are other factors, such as ionic strength, which can affect the enzymatic reaction. Each of these physical and chemical parameters must be considered and optimized in order for an enzymatic reaction to be accurate and reproducible.
c. Concentration
A reaction will work optimally if concentration of enzyme and substrate are in equilibrium. If concentration of substrate is more than concentration of enzyme, reaction will take place slowly even there are substances which are not catalyzed, on the contrary if concentration of enzyme is more than concentration of substrate reaction will take place rapidly because the more enzyme added in a reaction then the faster that reaction happens.
Enzyme Concentration
In order to study the effect of increasing the enzyme concentration upon the reaction rate, the substrate must be present in an excess amount; i.e., the reaction must be independent of the substrate concentration. Any change in the amount of product formed over a specified period of time will be dependent upon the level of enzyme present.
The amount of enzyme present in a reaction is measured by the activity it catalyzes. The relationship between activity and concentration is affected by many factors such as temperature, pH, etc. An enzyme assay must be designed so that the observed activity is proportional to the amount of enzyme present in order that the enzyme concentration is the only limiting factor. It is satisfied only when the reaction is zero order.
To measure enzyme activity ideally, the measurements must be made in that portion of the curve where the reaction is zero order. A reaction is most likely to be zero order initially since substrate concentration is then highest. To be certain that a reaction is zero order multiple measurements of product (or substrate) concentration must be made.
Substrate Concentration
It has been shown experimentally that if the amount of the enzyme is kept constant and the substrate concentration is then gradually increased, the reaction velocity will increase until it reaches a maximum. A small Km indicates that the enzyme requires only a small amount of substrate to become saturated. Hence, the maximum velocity is reached at relatively low substrate concentrations. A large Km indicates the need for high substrate concentrations to achieve maximum reaction velocity. The substrate with the lowest Km upon which the enzyme acts as a catalyst is frequently assumed to be enzyme's natural substrate, though this is not true for all enzymes.
d. Inhibitor
The works of enzyme can be retarded by inhibitor. If inhibitor is added into mixture of enzyme and substrate, the will reaction speed will decrease. Inhibitor works by making a bond with enzyme forming enzyme-inhibitor complex. There is also an enzyme-inhibitor complexes which is still able to bond with substrate., but some are not able to make bond wit substrate. Enzyme inhibitors are substances which alter the catalytic action of the enzyme and consequently slow down, or in some cases, stop catalysis. There are three common types of enzyme inhibition - competitive, non-competitive and substrate inhibition. Most theories concerning inhibition mechanisms are based on the existence of the enzyme substrate complex ES. As mentioned earlier, the existence of temporary ES structures has been verified in the laboratory.
Some inhibitors are reversible in property and some are irreversible.
1. Reversible Inhibitor
Reversible inhibitor are distinguished into two, namely competitive inhibitor and noncompetitive inhibitor.
- Competitive Inhibitor
Competitive inhibitor retards the work of enzyme by placing the active site of enzyme. The structure of inhibitor is similar to the structure of substrate, so this inhibitor competes with substrate to make bond with the active site of enzyme. If inhibitor is firstly bonded with the active site of enzyme, the substrate cannot make bond anymore with the active site of enzyme.
Competitive inhibition occurs when the substrate and a substance resembling the substrate are both added to the enzyme. A theory called the "lock-key theory" of enzyme catalysts can be used to explain why inhibition occurs. The lock and key theory utilizes the concept of an "active site." The concept holds that one particular portion of the enzyme surface has a strong affinity for the substrate. The substrate is held in such a way that its conversion to the reaction products is more favorable. If we consider the enzyme as the lock and the substrate, the key is inserted in the lock, is turned, and the door is opened and the reaction proceeds. However, when an inhibitor which resembles the substrate is present, it will compete with the substrate for the position in the enzyme lock. When the inhibitor wins, it gains the lock position but is unable to open the lock. Hence, the observed reaction is slowed down because some of the available enzyme sites are occupied by the inhibitor. If a dissimilar substance which does not fit the site is present, the enzyme rejects it, accepts the substrate, and the reaction proceeds normally.
Blockage done by inhibitor is reversible and can be removed by adding the concentration of substrate. Example of competitive inhibitor is oxalocinnate. This inhibitor competes with substrate that is oxalicinnate to make bond with cinnate dehydrogenase enzyme.
- Noncompetitive Inhibitor
Noncompetitive inhibitor commonly is chemical compound that is not similar to substrate and bonds at a site besides the active site of an enzyme. The bond between enzyme and inhibitor causes the change of enzyme shape so the active site of enzyme is not suitable anymore for its substrate.
Non-competitive inhibitors are considered to be substances which when added to the enzyme alter the enzyme in a way that it cannot accept the substrate. Substrate inhibition will sometimes occur when excessive amounts of substrate are present. Additional amounts of substrate added to the reaction mixture after this point actually decrease the reaction rate. This is thought to be due to the fact that there are so many substrate molecules competing for the active sites on the enzyme surfaces that they block the sites and prevent any other substrate molecules from occupying them. This causes the reaction rate to drop since all of the enzyme present is not being used.
Blockage done by inhibitor is reversible but cannot be removed by adding concentration of substrate. Example of noncompetitive inhibitor is penicillin antibiotic that retards the work of enzyme that makes up cell wall of bacteria.
2. Irreversible Inhibitor
Irreversible inhibitor bonds with the active site of enzyme strongly, so it cannot be escaped. The presence of this inhibitor causes enzyme is not active and cannot be active as do before. Example of the inhibitor is diisopropylfluorophosphate. That retards the works of acetylcholine – esterase enzyme.

2.2.7 Nomenclature and Grouping
Enzyme is named based on its substrate and given by suffix “ase”. For example its substrate is amylum, then the name of its enzyme is amylase. Amyum is changed by amylase enzyme to be maltose.
Several others are follows
a. Enzyme that changes maltose to be glucose is maltase.
b. Enzyme that changes lipid to be fatty acid and glycerol is lipase.
c. Enzyme that changes protein to be amino acid is protease.

Except for some of the originally studied enzymes such as pepsin, rennin, and trypsin, most enzyme names end in "ase". The International Union of Biochemistry (I.U.B.) initiated standards of enzyme nomenclature which recommend that enzyme names indicate both the substrate acted upon and the type of reaction catalyzed. Under this system, the enzyme uricase is called urate: O2 oxidoreductase, while the enzyme glutamic oxaloacetic transaminase (GOT) is called L-aspartate: 2-oxoglutarate aminotransferase.
Enzymes can be classified by the kind of chemical reaction catalyzed.
I.Addition or removal of water
A. Hydrolases - these include esterases, carbohydrases, nucleases, deaminases,
amidases, and proteases
B. Hydrases such as fumarase, enolase, aconitase and carbonic anhydrase
II. Transfer of electrons
A. Oxidases
B. Dehydrogenases
III. Transfer of a radical
A. Transglycosidases - of monosaccharides
B. Transphosphorylases and phosphomutases - of a phosphate group
C. Transaminases - of amino group
D. Transmethylases - of a methyl group
E. Transacetylases - of an acetyl group
IV. Splitting or forming a C-C bond
A. Desmolases
V. Changing geometry or structure of a molecule
A. Isomerases
VI. Joining two molecules through hydrolysis of pyrophosphate bond in ATP other tri-phosphate
A. Ligases

Enzyme nomenclature is separated into two, namely by means of systematic method and trivial method. Systematic nomenclature is based on the reaction which happens. For example the reaction of ATP + glucose ADP + glucose 6-phosphate then the enzyme is ATP: glucose 6-phosphatase.
Trivial nomenclature is short nomenclature of an enzyme. For example the name of enzyme for the reaction above is hexokinase.
Based on the phenomenon that happens in a reaction, enzyme is grouped into two groups, namely hydrolase and desmolase.
- Hydrolase enzyme is enzyme that change any substrate to be final product if into that reaction water is added or in that reaction water is found.
For examples are protease, lipase and carboxylase.
- Desmolase enzyme is enzyme that can break the bond of C-C and C-N.

For example dehydrogenase, transminase, carboxilase, catalase, and peroxidase.

2.3 CATABOLISM
Catabolism (Greek kata = downward + ballein = to throw) is the set of metabolic pathways that break down molecules into smaller units and release energy.[1] In catabolism, large molecules such as polysaccharides, lipids, nucleic acids and proteins are broken down into smaller units such as monosaccharides, fatty acids, nucleotides and amino acids, respectively. As molecules such as polysaccharides, proteins and nucleic acids are made from long chains of these small monomer units (mono = one + mer = part), the large molecules are called polymers (poly = many).
Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidising food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules being used as a source of energy in organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

Cells use the monomers released from breaking down polymers to either construct new polymer molecules, or degrade the monomers further to simple waste products, releasing energy. Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia, and urea. The creation of these wastes is usually an oxidation process involving a release of chemical free energy, some of which is lost as heat, but the rest of which is used to drive the synthesis of adenosine triphosphate (ATP). This molecule acts as a way for the cell to transfer the energy released by catabolism to the energy-requiring reactions that make up anabolism. Catabolism therefore provides the chemical energy necessary for the maintenance and growth of cells. Examples of catabolic processes include glycolysis, the citric acid cycle, the breakdown of muscle protein in order to use amino acids as substrates for gluconeogenesis and breakdown of fat in adipose tissue to fatty acids.



There are many signals that control catabolism. Most of the known signals are hormones and the molecules involved in metabolism itself. Endocrinologists have traditionally classified many of the hormones as anabolic or catabolic, depending on which part of metabolism they stimulate. The "classic" catabolic hormones known since the early 20th century are cortisol, glucagon, and adrenaline (and other catecholamines). In recent decades, many more hormones with at least some catabolic effects have been discovered, including cytokines, orexin and hypocretin (a hormone pair), and melatonin.

2.3.1 Purposes of Catabolism

- To release energy which can be used to generate ATP from ADP and phosphate.
- To release electrons which serve as "reducing power."
- Also to provide some of the "building blocks" for biosynthesis.

2.3.2 Types of Catabolic Pathways

Catabolic pathways create energy for the cell. In catabolism the goal is to take energy out of what is gathered and store it in energy carriers (ATP) and electron carriers like NAD and Flavin-Adenine Dinucleotide (FAD). This energy and reducing power fuels growth, repair and movement. In this section we will discuss generally the two major ways of living on this planet phototrophy and chemotrophy.

Phototrophs

Phototrophs take light from the sun and convert it directly into biochemical energy and reducing power. This is a complex, multi-protein process that always requires a membrane bound system. Energy is generated by photophosphorylation. Cell material is often built from CO2. Note that photosynthesis is not the private domain of plants; photosynthetic bacteria are common.

Dependent Chemotrophs

These chemotrophs depend on phototrophs, either directly or indirectly, to make complex organic molecules that they can oxidize and generate energy from. Energy is generated by substrate level phosphorylation (SLP) or by electron transport level phosphorylation (ETLP). They also often use these same organic molecules (or breakdown products from catabolizing them) as building blocks for more cells.

Independent Chemotrophs

Recently scientists have discovered microbes living deep in the sea on the ocean floor near areas of sea floor spreading. In these areas lava erupts into the ocean and eventually forms hydrothermal vents. The vents pump out hot sea water loaded with minerals. Microbes living here do not depend on plants or the sun at all to live, but generate their energy by oxidizing reduced chemicals in the vent plumes and build their cell material from CO2. In fact the reactions that they use to make cell material from CO2 are identical to those used by phototrophs. Follow the link to learn more about hydrothermal vents. There are also independent chemotrophs living in terrestrial environments.

Energy Generation

Catabolism is all about running reactions to make energy for the cell. Despite the great diversity of life, all organisms on this planet generate their energy using one of three processes.

Substrate level Phosphorylation (SLP)- Synthesis of ATP from ADP directly coupled to the breakdown of high energy organic substrates. A high energy phosphate molecule is transferred from the substrate being catabolized to ADP forming ATP.

Oxidative or Electron Transport Level Phosphorylation (ETLP) - High energy electrons are removed from the catabolic substrate and given to electron carriers (often NAD or FAD). These carriers eventually transfer their electrons to an electron transport chain which synthesizes ATP using the enzyme ATPase. Eventually the electrons combine with O2 (or some other terminal electron accepter) and H+ to form H20.

Photophosphorylation - The conversion of light energy in the form of photons to high energy electrons. These electrons then pass through an analogous electron transport chain as describe under ETLP, eventually resulting in the formation of ATP.

2.3.3 Types of Catabolic Process
There are three kind of catabolic process, namely

2.3.3.1 Catabolism of Carbohydrate
In each living cell, metabolic process happen, one of them is catabolism. Catabolic process that will be discussed is catabolism of carbohydrate that happens in a cell, which is cellular respiration.
Respiration is one of the imperative functions of the body that are of crucial importance for all the living organisms be it human being, or the microscopic bacteria. In general the process of respiration serves two basic purposes in living organisms, the first one being disposal of electrons generated during catabolism and the second one being production of ATP. The respiration machinery is located in cell membranes of prokaryotes whereas it is placed in the inner membranes of mitochondria for eukaryotes. Respiration requires a terminal electron acceptor. Simply put, the respiration process, which uses oxygen as its terminal electron acceptor, is called aerobic respiration and the one, which uses terminal electron acceptors other than oxygen, is called anaerobic respiration. Based on its need to oxygen, respiration is separated into two, namely aerobic respiration and anaerobic respiration.
- Aerobic Respiration
Aerobic respiration is the process that takes place in presence of oxygen. Aerobic respiration is the metabolic process that involves break down of fuel molecules to obtain bio-chemical energy and has oxygen as the terminal electron acceptor. Fuel molecules commonly used by cells in aerobic respiration are glucose, amino acids and fatty acids.. The process of obtaining energy in aerobic respiration can be represented in the following equation:

Glucose + Oxygen →Energy + Carbon dioxide + Water

The aerobic respiration is a high energy yielding process. During the process of aerobic respiration as many as 38 molecules of ATP are produced for every molecule of glucose that is utilized. Thus aerobic respiration process breaks down a single glucose molecule to yield 38 units of the energy storing ATP molecules.
Aerobic respiration involves oxygen as hydrogen acceptor. Hydrogen released in oxidation process must join with oxygen to form H2O.
- Anaerobic Respiration
Anaerobic respiration is respiratory process that does not need oxygen. This kind of respiration can happen in free air, but its respiratory process does not use O2 found in air.
The term anaerobic means without air and hence anaerobic respiration refers to the special type of respiration, which takes place without oxygen. Anaerobic respiration is the process of oxidation of molecules in the absence of oxygen, which results in production of energy in the form of ATP or adenosine tri-phosphate. Anaerobic respiration is synonymous with fermentation especially when the glycolytic pathway of energy production is functional in a particular cell. The process of anaerobic respiration for production of energy can occur in either of the ways represented below:

Glucose (Broken down to) →Energy (ATP) + Ethanol + Carbon dioxide (CO2)
Glucose (Broken down to) →Energy (ATP) + Lactic acid
The process of anaerobic respiration is relatively less energy yielding as compared to the aerobic respiration process. During the alcoholic fermentation or the anaerobic respiration (represented in the first equation) two molecules of ATP (energy) are produced. for every molecule of glucose used in the reaction. Similarly for the lactate fermentation (represented in the second equation) 2 molecules of ATP are produced for every molecule of glucose used. Thus anaerobic respiration breaks down one glucose molecule to obtain two units of the energy storing ATP molecules.

Microbes are capable of using all sorts of other terminal electron accepters besides oxygen. Below we talk about a few examples of anaerobic respiration. The one thing that they all have in common is the use of an electron transport system in a membrane and the synthesis of ATP via ATP synthase. In both nitrate reduction and sulfate reduction there are two types of pathways, assimilatory and dissimilatory. Assimilatory pathways are methods for taking a nutrient in the soil, moving it into the cell and using it for biosynthesis of macromolecules. Dissimilatory pathways use the substrate as a place to dump electrons and generate energy. Here we examine dissimilatory pathways. Assimilatory pathways will be explained in the context of cell biosynthesis.

Nitrate reduction

Some microbes are capable of using nitrate as their terminal electron accepter. The ETS used is somewhat similar to aerobic respiration, but the terminal electron transport protein donates its electrons to nitrate instead of oxygen. Nitrate reduction in some species (the best studied being E. coli) is a two electron transfer where nitrate is reduced to nitrite. Electrons flow through the quinone pool and the cytochrome b/c1 complex and then nitrate reductase resulting in the transport of protons across the membrane as discussed earlier for aerobic respiration.

N03- + 2e- + 2H+arrow pictureN02-+ H20

This reaction is not particularly efficient. Nitrate does not as willingly accept electrons when compared to oxygen and the potential energy gain from reducing nitrate is less. If microbes have a choice, they will use oxygen instead of nitrate, but in environments where oxygen is limiting and nitrate is plentiful, nitrate reduction takes place.

Denitrification

Nitrite, the product of nitrate reduction, is still a highly oxidized molecule and can accept up to six more electrons before being fully reduced to nitrogen gas. Microbes exist (Paracoccus species, Pseudomonas stutzeri, Pseudomonas aeruginosa, and Rhodobacter sphaeroides are a few examples) that are able to reduce nitrate all the way to nitrogen gas. The process is carefully regulated by the microbe since some of the products of the reduction of nitrate to nitrogen gas are toxic to metabolism. This may explain the large number of genes involved in the process and the limited number of bacteria that are capable of denitrification. Below is the chemical equation for the reduction of nitrate to N2.


N03-arrow pictureN02-arrow picture NO arrow picture N2Oarrow picture N2

The advantage for the cell of carrying out a complete reduction of nitrate is two fold. The nitrate ETS serves as a place to oxidize NADH and free it to be used in catabolism of more substrate. Denitrification take eight electrons from metabolism and adds them to nitrate to form N2 versus just two for nitrate reduction alone. Also, donation of electrons from NADH through the cytochrome b/c1 complex and eventually to nitrous oxide (N2O) reductase provides another opportunity to pump protons across the membrane. The figure below presents a schematic of the spacial arrangement of the denitrification enzymes in the membrane

Nitrate reduction has been extensively studied in bacteria due to its significance in the global nitrogen cycle. Denitrification removes nitrate, an accessible nitrogen source for plants, from the soil and converts it to N2 a much less tractable source of nitrogen that most plants cannot use. This decreases soil fertility making farming more expensive. Intermediates of denitrification, nitrous oxide and nitric oxide, are gases and will sometimes escape the cell before being completely reduced. These compounds, when in the atmosphere, contribute to the greenhouse effect and exacerbate global warming. The use of high nitrate fertilizers in modern agriculture makes matters worse. For more information, there is an extensive review of denitrification available on line.
Sulfate reduction

The disimilatory reduction of sulfate seems to be a strictly anaerobic process as all the microbes capable of carrying it out only grow in environments devoid of oxygen. Sulfate (SO4-2 is reduced to sulfide (S-2), typically in the form of hydrogen sulfide (H2S). Eight electrons are add to sulfate to make sulfide

acetate + SO4-2 + 3H+ + arrow picture 2CO2 + H2S + 2H2O

The electron potential and energy yield for sulfate reduction is much lower than for nitrate or oxygen. However, there is still enough energy to allow the synthesis of ATP when the catabolic substrate used results in the formation of NADH or FADH. Substrates for sulfate reducers range from hydrogen gas to aromatic compounds such as benzoate. The most commonly utilized are acetate, lactate and other small organic acids (lactate, malate, pyruvate and ethanol are some examples). These compounds are prevalent in anaerobic environments where anaerobic catabolism of complex organic polymers such as cellulose and starch is taking place.

Biochemistry of sulfate reducers

Sulfate reducers take these growth substrates and metabolize them to acetate. The reducing power generated travels down an electron transport chain eventually reducing sulfate to hydrogen sulfide and generating energy using ATP synthase.

Lactate (in blue) is oxidized to acetate (in red) and the electrons remove eventually end up reducing sulfate (in blue) to sulfide (in red). Note that the energy gained in the process by SLP - converting acetyl phosphate to acetate - is used up to activate sulfate in the first step of sulfate reduction. Energy for metabolism is only generated via an electron transport chain.

Recent work in bioremediation of anaerobic sediments has resulted in the isolation of many novel sulfate reducing species capable of metabolizing environmentally intractable compounds including TNT, PCP and benzoate. It is becoming apparent that this group of bacterias are very important in recycling carbon to CO2 as part of the global carbon cycle in anaerobic environments. For a look at some recent research on sulfate reducing bacteria, check out the "Journal of Bacteriology"
Carbonate reduction
Several groups of microbes are capable of using carbonate (CO2) as a terminal electron accepter. Carbonate is a poor choice to leave your electrons with due to its low reduction potential and energy yields from CO2 reduction are low. However, carbonate is one of the most common anions in nature and its ready availability makes it a tempting target.

Several groups of microbes have evolved mechanisms to take advantage of carbonate. The most important group among these is the methanogens. Methanogens are Archaea and comprise one phylogenetic group that is very closely related. Methanogenesis seems to be highly conserved and have deeps roots in the phylogenetic tree of life. It must have evolve early on and practitioners of methanogenesis cannot mess with the genes too much, lest they die.

HC03- + 4H2 + H+ arrow picture CH4 + 3H2O

Methanogens use compounds that contain very high energy electrons as their electron donors and in the process convert CO2 to methane (CH4). Above is shown the use of hydrogen as the source of electrons. They are the only group of microbes that produce a hydrocarbon as major end product of their metabolism.

Another group of carbonate reducing microbes are the homoacetogens. They utilize hydrogen as the electron source and use it to reduce CO2 to acetic acid.

HC03- + 4H2 + H+ arrow picture CH3-COO- + 4H2O

Before we leave anaerobic respiration I want to emphasize several points

* Anaerobic respiration is a common occurrence. Microbes that carry out this process are common in the environment and their activities greatly influence the global cycling of elements.
* With the exception of methanogenesis these catabolic capabilities are not associated with any phylogenetic group, but are found scattered among the various groups of bacteria.
* All of these processes are less efficient that oxidative phosphorylation. This may explain why aerobic organisms dominate the earth. That and the toxic effects of oxygen.
* All types of respiration investigated so far involve a membrane system, the generation of a ion gradient and the formation of ATP via ATP synthase.
Cellular respiration is divided into four phases, namely :




a. Glycolisis

Glycolisis is a series conversion reaction of glucose molecules to be pyruvic acid by producing NADH and ATP that happen both by aerobic and anaerobic processes, there are enzymatic activities, ADP, and ATP. ADP and ATP function to displace phosphate from one molecule to another. The explanation from of the scheme is as follows. Briefly, glycolisis process can be illustrated in the following scheme.

Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose, C6H12O6, into pyruvate, C3H6O3-. The free energy released in this process is used to form the high energy compounds, ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

Glycolysis is a sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate is a source of the glycerol that combines with fatty acids to form fat.

Glycolysis is thought to be the archetype of a universal metabolic pathway. It occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways.

The most common type of glycolysis is the Embden-Meyerhof pathway, which was first discovered by Gustav Embden and Otto Meyerhof. Glycolysis also refers to other pathways, such as the Entner–Doudoroff pathway. However, the discussion here will be limited to the Embden-Meyerhof pathway.

Reaction of Glycolisis

Pathway of glycolysis from glucose to pyruvate. Substrates and products are in blue, enzymes are in green. The two high energy intermediates whose oxidations are coupled to ATP synthesis are shown in red (1,3-bisphosphoglycerate and phosphoenolpyruvate). Place mouse over intermediate names to see chemical structures.

The Hexokinase Reaction:

The ATP-dependent phosphorylation of glucose to form glucose 6-phosphate (G6P)is the first reaction of glycolysis, and is catalyzed by tissue-specific isoenzymes known as hexokinases. The phosphorylation accomplishes two goals: First, the hexokinase reaction converts nonionic glucose into an anion that is trapped in the cell, since cells lack transport systems for phosphorylated sugars. Second, the otherwise biologically inert glucose becomes activated into a labile form capable of being further metabolized.

Four mammalian isozymes of hexokinase are known (Types I–IV), with the Type IV isozyme often referred to as glucokinase. Glucokinase is the form of the enzyme found in hepatocytes and pancreatic β-cells. The high Km of glucokinase for glucose means that this enzyme is saturated only at very high concentrations of substrate. Saturation curves comparing hexokinase and glucokinase

Comparison of the activities of hexokinase and glucokinase. The Km for hexokinase is significantly lower (0.1mM) than that of glucokinase (10mM). This difference ensures that non-hepatic tissues (which contain hexokinase) rapidly and efficiently trap blood glucose within their cells by converting it to glucose-6-phosphate. One major function of the liver is to deliver glucose to the blood and this in ensured by having a glucose phosphorylating enzyme (glucokinase) whose Km for glucose is sufficiently higher that the normal circulating concentration of glucose (5mM).

This feature of hepatic glucokinase allows the liver to buffer blood glucose. After meals, when postprandial blood glucose levels are high, liver glucokinase is significantly active, which causes the liver preferentially to trap and to store circulating glucose. When blood glucose falls to very low levels, tissues such as liver and kidney, which contain glucokinases but are not highly dependent on glucose, do not continue to use the meager glucose supplies that remain available. At the same time, tissues such as the brain, which are critically dependent on glucose, continue to scavenge blood glucose using their low Km hexokinases, and as a consequence their viability is protected. Under various conditions of glucose deficiency, such as long periods between meals, the liver is stimulated to supply the blood with glucose through the pathway of gluconeogenesis. The levels of glucose produced during gluconeogenesis are insufficient to activate glucokinase, allowing the glucose to pass out of hepatocytes and into the blood.

The regulation of hexokinase and glucokinase activities is also different. Hexokinases I, II, and III are allosterically inhibited by product (G6P) accumulation, whereas glucokinases are not. The latter further insures liver accumulation of glucose stores during times of glucose excess, while favoring peripheral glucose utilization when glucose is required to supply energy to peripheral tissues.

Phosphohexose Isomerase:

The second reaction of glycolysis is an isomerization, in which G6P is converted to fructose 6-phosphate (F6P). The enzyme catalyzing this reaction is phosphohexose isomerase (also known as phosphoglucose isomerase). The reaction is freely reversible at normal cellular concentrations of the two hexose phosphates and thus catalyzes this interconversion during glycolytic carbon flow and during gluconeogenesis.

6-Phosphofructo-1-Kinase (Phosphofructokinase-1, PFK-1):

The next reaction of glycolysis involves the utilization of a second ATP to convert F6P to fructose 1,6-bisphosphate (F1,6BP). This reaction is catalyzed by 6-phosphofructo-1-kinase, better known as phosphofructokinase-1 or PFK-1. This reaction is not readily reversible because of its large positive free energy (ΔG0' = +5.4 kcal/mol) in the reverse direction. Nevertheless, fructose units readily flow in the reverse (gluconeogenic) direction because of the ubiquitous presence of the hydrolytic enzyme, fructose-1,6-bisphosphatase (F-1,6-BPase).

The presence of these two enzymes in the same cell compartment provides an example of a metabolic futile cycle, which if unregulated would rapidly deplete cell energy stores. However, the activity of these two enzymes is so highly regulated that PFK-1 is considered to be the rate-limiting enzyme of glycolysis and F-1,6-BPase is considered to be the rate-limiting enzyme in gluconeogenesis.

Aldolase:
Aldolase catalyses the hydrolysis of F1,6BP into two 3-carbon products: dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). The aldolase reaction proceeds readily in the reverse direction, being utilized for both glycolysis and gluconeogenesis.

Triose Phosphate Isomerase:

The two products of the aldolase reaction equilibrate readily in a reaction catalyzed by triose phosphate isomerase. Succeeding reactions of glycolysis utilize G3P as a substrate; thus, the aldolase reaction is pulled in the glycolytic direction by mass action principals.

Glyceraldehyde-3-Phosphate Dehydrogenase:

The second phase of glucose catabolism features the energy-yielding glycolytic reactions that produce ATP and NADH. In the first of these reactions, glyceraldehyde-3-P dehydrogenase (G3PDH) catalyzes the NAD+-dependent oxidation of G3P to 1,3-bisphosphoglycerate (1,3BPG) and NADH. The G3PDH reaction is reversible, and the same enzyme catalyzes the reverse reaction during gluconeogenesis.

Phosphoglycerate Kinase:

The high-energy phosphate of 1,3-BPG is used to form ATP and 3-phosphoglycerate (3PG) by the enzyme phosphoglycerate kinase. Note that this is the only reaction of glycolysis or gluconeogenesis that involves ATP and yet is reversible under normal cell conditions. Associated with the phosphoglycerate kinase pathway is an important reaction of erythrocytes, the formation of 2,3-bisphosphoglycerate, 2,3BPG (see Figure below) by the enzyme bisphosphoglycerate mutase. 2,3BPG is an important regulator of hemoglobin's affinity for oxygen. Note that 2,3-bisphosphoglycerate phosphatase degrades 2,3BPG to 3-phosphoglycerate, a normal intermediate of glycolysis. The 2,3BPG shunt thus operates with the expenditure of 1 equivalent of ATP per triose passed through the shunt. The process is not reversible under physiological conditions.

Pathway for 2,3-bisphosphoglycerate synthesis in erythrocytes

The pathway for 2,3-bisphosphoglycerate (2,3-BPG) synthesis within erythrocytes. Synthesis of 2,3-BPG represents a major reaction pathway for the consumption of glucose in erythrocytes. The synthesis of 2,3-BPG in erythrocytes is critical for controlling hemoglobin affinity for oxygen. Note that when glucose is oxidized by this pathway the erythrocyte loses the ability to gain 2 moles of ATP from glycolytic oxidation of 1,3-BPG to 3-phosphoglycerate via the phosphoglycerate kinase reaction.

Phosphoglycerate Mutase and Enolase:

The remaining reactions of glycolysis are aimed at converting the relatively low energy phosphoacyl-ester of 3PG to a high-energy form and harvesting the phosphate as ATP. The 3PG is first converted to 2PG by phosphoglycerate mutase and the 2PG conversion to phosphoenoylpyruvate (PEP) is catalyzed by enolase.

Pyruvate Kinase

The final reaction of aerobic glycolysis is catalyzed by the highly regulated enzyme pyruvate kinase (PK). In this strongly exergonic reaction, the high-energy phosphate of PEP is conserved as ATP. The loss of phosphate by PEP leads to the production of pyruvate in an unstable enol form, which spontaneously tautomerizes to the more stable, keto form of pyruvate. This reaction contributes a large proportion of the free energy of hydrolysis of PEP.

There are two distinct genes encoding PK activity. One is located on chromosome 1 and encodes the liver and erythrocyte PK proteins (identified as the PKLR gene) and the other is located on chromosome 15 and encodes the muscle PK proteins (identified as the PKM gene). The muscle PKM gene directs the synthesis of two isoforms of muscle PK termed PK-M1 and PK-M2. Deficiencies in the PKLR gene are the cause of the most common form of inherited non-spherocytic anemia.

Oksidative Decarboxilation
Pyruvic acid produced by glycolisis process will be oxidized and removed its 1 carbon atom (carbon is removed in the form of CO2) so it produces 2 carbonized fragments called acetylene group and changes NAD+ to be NADH. The reaction is complex, involving 3 phases of intermediary reaction.
In the end of reaction, acetylene group joins with cofactor of coenzyme A (CoA) forming acetylene-CoA. This Acetylene-CoA then enters Krebs’s cycle.

Krebs’s Cycle
Krebs’s Cycle happens in mitochondria matrix that involves 9 series of reactions. The reaction is started by the entering at acetylene-CoA into Krebs’s cycle. Besides, in this cycle the releasing of 2 CO2 molecules and 8 electrons happens.
The citric acid cycle is also called the Krebs cycle, after Hans Krebs, who first proposed its cyclic nature. The Krebs' cycle reactions take place in the matrix of the mitochondria. Some of the final steps of intermediate metabolism take place there as well. For example, in the matrix as well as the cytoplasm, glutamate (the amino acid glutamic acid) loses its amino group and is oxidized to alpha-ketoglutarate.
Most texts and lecture courses start with glycolysis, then proceed to describe Krebs' cycle as the "next step" in metabolism of sugars. Unfortunately, such a presentation may leave students with the impression that metabolites follow a linear progression through glycolysis to acetyl-coenzyme A to citric acid, through the Krebs intermediates to oxaloacetate, which is then coupled to the two carbons of another acteyl-coenzyme A to regenerate citric acid. Even in biochemistry texts, chapters on Krebs' cycle may start with a picture showing only pyruvate as the starting point.

This figure is what sticks in the minds of most introductory level students, and it isn't complete at all. First, it isn't just glycolysis that leads to the generation of acetyl coenzyme A. Carbohydrates, fats, and proteins are all nutrients, and in fact fatty acid metabolism results in the generation of acetyl coenzyme A as well.
Second, the 'starting point' for Krebs' cycle need not be acetyl-coenzyme A at all. In fact, it really isn't appropriate to refer to a cycle as having a starting point (e.g., where does a circle start?). Amino acids and odd-chain fatty acids can be metabolized into Krebs intermediates, and enter at several points.
Finally, intermediates can be 'siphoned off' for use in biosynthetic pathways. They must be replaced in order to maintain energy balance, however the fate of a Krebs intermediate is not necessarily to cycle through the enzymes until it is completely oxidized to carbon dioxide and water.
Since cycle intermediates can be incorporated into both anabolic and catabolic pathways, the cycle is really amphibolic, not just catabolic.

Glutamate to alpha-ketoglutarate

The conservation of energy by Krebs reactions can be illustrated by looking at the fate of glutamic acid, or glutamate. There are, in fact, several Krebs reactions that conserve the energy of oxidation of substrates. Glutamate enters the intermembrane space through the porins. A transport mechanism in the inner membrane called the glutamate-aspartate exchange carrier takes the glutamate molecule into the matrix.
The enzyme complex known as glutamate dehydrogenase binds the glutamate molecule, a molecule of oxidized nicotine adenine dinucleotide (NAD), and a water molecule. Off comes the amino group, and glutamate is partially oxidized to alpha-ketoglutarate, which you should recognize as a Krebs intermediate. In vivo, the alpha-ketoglutarate would be further oxidized to succinyl-coenzyme A by alpha-ketoglutarate dehydrogenase, then the succinyl-coenzyme A would be oxidized to succinate, etc. However, remember the amphibolic nature of Krebs cycle - substrates may be utilized for biosynthesis rather than undergoing further oxidations. In addition, limitations on Krebs cycle in isolated mitochondria must be considered.
The oxidation of organic compounds releases free energy. This energy would be wasted as heat, except the enzyme also catalyzes the reduction of the NAD. The enzyme is designed so that the reaction cannot take place unless all of the reactants are present. Free energy from the partial oxidation of glutamate is used to reduce the NAD. The result is a molecule of NADH, which retains in its structure some of the free energy lost by the glutamate.
Glutamate dehydrogenase catalyzes a reaction in which the energy from an exothermic reaction is used to power an endothermic reaction. Therefore it performs what we call a coupled reaction. The second law of thermodynamics, paraphrased, states that some of the useful energy in any system is converted to useless energy during any process. That is, any spontaneous process causes the entropy of the universe to increase. In coupled reactions, only some of the free energy is conserved in the form of a reduced product. The remainder is released as heat.

NADH is an energy carrier. After release from glutamate dehydrogenase it can be used to power other reactions. It can also bind a specific enzyme on the mitochondria inner membrane, transferring some of its free energy to the electron transport system. In mitochondria, this is the principle role of NADH.

Succinate to fumarate

An important substrate in our studies of mitochondria function is succinic acid (succinate). When succinate is brought into or generated in the mitochondria matrix in sufficient quantity, succinate molecules bind the enzyme complex called succinate dehydrogenase. The succinate dehydrogenase complex is also known as complex II of the electron transport system, thus the oxidation of succinate to fumarate is the only Krebs reaction that takes place on the inner membrane itself, as opposed to the other reactions that are catalyzed by soluble enzymes. The energy carrier flavin adenine dinucleotide (FAD) is also a part of the succinate dehydrogenase complex.

Because the enzyme and FAD are both part of the same complex, the only step needed to initiate succinate oxidation is the binding of succinate to the enzyme. Even in severely compomised mitochondria succinate supported respiration can usually be accomplished, as long as fragments of the inner membrane remain.

Electron Transpor
Electron transfer is principal phase of cellular respiration. In this phase packaging of energy from glucose to be ATP. Electron transfer happens inside the membrane of mitochondria. The electron transport chain is also called the ETC. An enzyme called ATP synthase catalyzes a reaction to generate ATP. The structure of this enzyme and its underlying genetic code is remarkably conserved in all known forms of life.
ATP synthase is powered by a transmembrane electrochemical potential gradient usually[citation needed] in the form of a proton gradient. The function of the electron transport chain is to produce this gradient. In all living organisms, a series of redox reactions is used to produce a transmembrane electrochemical potential gradient.
Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The underlying force driving these reactions is the Gibbs free energy of the reactants and products. The Gibbs free energy is the energy available ("free") to do work. Any reaction that decreases the overall Gibbs free energy of a system will proceed spontaneously.
The transfer of electrons from a high-energy molecule (the donor) to a lower-energy molecule (the acceptor) can be spatially separated into a series of intermediate redox reactions. This is an electron transport chain.
The fact that a reaction is thermodynamically possible does not mean that it will actually occur; for example, a mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an activation energy or to lower the intrinsic activation energy of the system, in order to make most biochemical reactions proceed at a useful rate. Living systems use complex macromolecular structures (enzymes) to lower the activation energies of biochemical reactions.
It is possible to couple a thermodynamically favorable reaction (a transition from a high-energy state to a lower-energy state) to a thermodynamically unfavorable reaction (such as a separation of charges, or the creation of an osmotic gradient), in such a way that the overall free energy of the system decreases (making it thermodynamically possible), while useful work is done at the same time. Biological macromolecules that catalyze a thermodynamically unfavorable reaction if and only if a thermodynamically favorable reaction occurs simultaneously underlie all known forms of life.
Electron transport chains capture energy in the form of a transmembrane electrochemical potential gradient. This energy can then be harnessed to do useful work. The gradient can be used to transport molecules across membranes. It can be used to do mechanical work, such as rotating bacterial flagella, and also to produce ATP, a high-energy molecule which can go on to power other cellular reactions.
A small amount of ATP is available from substrate-level phosphorylation (for example, in glycolysis). Some organisms can obtain ATP exclusively by fermentation. In most organisms, however, the majority of ATP is generated by electron transport chains.
An electron transport chain couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer of H+ ions across a membrane, through a set of mediating biochemical reactions. These H+ ions are used to produce adenosine triphosphate (ATP), the main energy intermediate in living organisms, as they move back across the membrane. Electron transport chains are used for extracting energy from sunlight (photosynthesis) and from redox reactions such as the oxidation of sugars (respiration).
In chloroplasts, light drives the conversion of water to oxygen and NADP+ to NADPH and a transfer of H+ ions. NADPH is used as an electron donor for carbon fixation. In mitochondria, it is the conversion of oxygen to water, NADH to NAD+ and succinate to fumarate that drives the transfer of H+ ions. While some bacteria have electron transport chains similar to those in chloroplasts or mitochondria, other bacteria use different electron donors and acceptors. Both the respiratory and photosynthetic electron transport chains are major sites of premature electron leakage to oxygen, thus being major sites of superoxide production and drivers of oxidative stress.
Mitochondrial redox carriers
Complex I (NADH dehydrogenase, also called NADH:ubiquinone oxidoreductase; EC 1.6.5.3) removes two electrons from NADH and transfers them to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH2) is free to diffuse within the membrane. At the same time, Complex I moves four protons (H+) across the membrane, producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of main sites of production of a harmful free radical called superoxide.
The pathway of electrons occurs as follows:
NADH is oxidized to NAD+, reducing Flavin mononucleotide to FMNH2 in one two-electron step. The next electron carrier is a Fe-S cluster, which can only accept one electron at a time to reduce the ferric ion into a ferrous ion. In a convenient manner, FMNH2 can be oxidized in only two one-electron steps, through a semiquinone intermediate. The electron thus travels from the FMNH2 to the Fe-S cluster, then from the Fe-S cluster to the oxidized Q to give the free-radical (semiquinone) form of Q. This happens again to reduce the semiquinone form to the ubiquinol form, QH2. During this process, four protons are translocated across the inner mitochondrial membrane, from the matrix to the intermembrane space. This creates a proton gradient that will be later used to generate ATP through oxidative phosphorylation.
Complex II (succinate dehydrogenase; EC 1.3.5.1) is not a proton pump. It serves to funnel additional electrons into the quinone pool (Q) by removing electrons from succinate and transferring them (via FAD) to Q. Complex II consists of four protein subunits: SDHA,SDHB,SDHC, and SDHD. Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also funnel electrons into Q (via FAD), again without producing a proton gradient.
Complex III (cytochrome bc1 complex; EC 1.10.2.2) removes in a stepwise fashion two electrons from QH2 at the QO site and sequentially transfers them to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons are sequentially passed across the protein to the Qi site where quinone part of ubiquinone is reduced to quinol. A proton gradient is formed because it takes 2 quinol (4H+4e-) oxidations at the Qo site to form one quinol (2H+2e-) at the Qi site. (in total 6 protons: 2 protons reduce quinone to quinol and 4 protons are released from 2 ubiquinol). The bc1 complex does NOT 'pump' protons, it helps build the proton gradient by an asymmetric absorption/release of protons.
When electron transfer is hindered (by a high membrane potential, point mutations or respiratory inhibitors such as antimycin A), Complex III may leak electrons to oxygen resulting in the formation of superoxide, a highly-toxic species, which is thought to contribute to the pathology of a number of diseases, including aging.
Complex IV (cytochrome c oxidase; EC 1.9.3.1) removes four electrons from four molecules of cytochrome c and transfers them to molecular oxygen (O2), producing two molecules of water (H2O). At the same time, it moves four protons across the membrane, producing a proton gradient.

2.3.3.2 Catabolism of Fats (Lipids)
Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the actyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups, in animals and fungi all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway.
Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products.These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other steroids such as cholesterol and ergosterol.
Up until this point you might think sugars are the only substrates that bacteria can grow on. Nothing could be farther from the truth. Bacteria are able to grow on all sorts of substrates and in this section we cover how fats are catabolized.
Bacteria are capable of growth on fatty acids and lipids. Lipids are part of the membranes of living organisms and if available (usually because the organism that was using them dies) can be used as a food source. Lipids are large molecules and cannot be transported across the membrane. Class of extracellular enzyme calls lipase responsible for the breakdown of lipids. Lipases attack the bond between the glycerol molecule oxygen and the fatty acid. Phospholipids are attacked by phospholipases. There are four classes of phospholipases given different names depending upon the bond they cleave. Phospholipases are not particular about their substrate and will attack a glycerol ester linkage containing any length fatty acid attached to it. The result of this digestion is a hydrophillic head molecule, glycerol and fatty acids of various chain lengths. The head can be one of several small organic molecules that are funneled into the TCA cycle by one or two reactions that we won't cover here. Glycerol is converted into 3-Phosphoglycerate (depending upon the action of phospholipase C or phospholipase D) and eventually pyruvate via glycolysis. This leaves the fatty acids to deal with.
Fatty acids are degraded by a four step process called b-oxidation. The fatty acid is first activated by the addition of Coenzyme-A to the end. This activation requires energy in the form of ATP, but is only performed once per fatty acid degraded. The b carbon (see figure) is then oxidized from CH2 to C=O (a ketone) by three reactions. (This is where the pathway gets its name.) The oxidized b group is now susceptible to attack. An enzyme called b-ketothiolase splits the fatty acid into acetyl-CoA and adds another Coenzyme-A to the previously oxidized b group on the fatty acid.
The fatty acid is now two carbons shorter and an Acetyl-CoA has been generated which can be fed into the TCA cycle. The smaller fatty acid moves through the b-oxidation pathway again, producing another Acetyl-CoA and shrinking by 2 carbons. By performing successive rounds of beta oxidation on a fatty acid, it is possible to convert it completely to Acetyl-CoA. The perceptive reader might notice that for fatty acids with odd numbers of carbons, the final reaction will yield acetyl-CoA and Coenzyme-A hooked to a three carbon fatty acid (propionyl-CoA). Propionyl-CoA is handled differently by different bacteria. In E. coli it is converted into pyruvate.
When comparing catabolism of fats and sugars two points jump out.
Reuse of components - Whenever possible, the cell will reuse a carrier, cofactor or enzyme. For example in fatty acid breakdown, Coenzyme-A plays a major role and the electron carriers FAD and NAD are used.
Funneling - Cells also try to reuse common pathways. A given substrate will be converted into a common metabolite and then funneled into an already existing pathway. Fatty acids are broken down into Acetyl-Coenzyme-A and this is fed into the TCA cycle.

2.3.3.3 Catabolism of Proteins and Amino Acids
Remember that proteins are polymers. They are large and just like lipids need to be broken down into smaller pieces before being transported into the cell. A class of extracellular enzymes called proteases break down proteins into peptides (short polymers of amino acids). There are many different proteases synthesized by cells and each of them have a different specificity. The ones used in catabolism tend to be nonspecific and attack many different peptide bonds between amino acids.
The small peptides produced can then be transported into the cell where they are further degraded into amino acids. Several of the amino acids are structurally so similar to important intermediates in the TCA cycle and other major metabolic pathways that it is a simple matter to convert them into "central metabolites". In most cases this involves removal of the amino group (deamination). Below is listed some deaminations and the products produced.




Amino Acid Reaction Product
glutamate oxidative deamination 2-oxoglutarate
aspartate oxidative deamination oxaloacetate
alanine oxidative deamination pyruvate
serine deamination pyruvate
valine oxidative deamination 2-oxoisovalerate
leucine oxidative deamination 2-oxoisocaproate
Whereas 2-oxoglutarate, oxaloacetate and pyruvate are central metabolites and can be easily metabolized, 2-oxoisovalerate and 2-oxoisocaproate are not and must be handled by specific catabolic pathways. Eventually these pathways lead into glycolysis or the TCA cycle.
The specific catabolic products produced depend upon the amino acid and it is not useful to study all twenty pathways. The general pattern to understand is that proteins are broken into amino acids by proteases. The amino acids are attacked by various pathways that then feed into the TCA cycle to generate energy.
A general pathway for the catabolism of proteins and amino acids. Specific pathways for every amino acid are not shown. The ability to grow on a certain amino acid as sole carbon and energy source is specific to the strain of bacteria and not every bacteria is going to be capable of growth on an amino acid.
2.4 ANABOLISM
Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. Firstly, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.
Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.
The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.
In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves energy being stored as a proton concentration gradient and this proton motive force then driving ATP synthesis. The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres or rhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.
In plants, algae, and cyanobateria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle which is discussed below, or recycled for further ATP generation.
2.4.1 Photosynthesis
Photosynthesis (from the Greek φώτο- [photo-], "light," and σύνθεσις [synthesis], "putting together.", "composition") is a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of Bacteria, but not in Archaea. Photosynthetic organisms are called photoautotrophs, since it allows them to create their own food. In plants, algae and cyanobacteria photosynthesis uses carbon dioxide and water, releasing oxygen as a waste product. Photosynthesis is vital for life on Earth. As well as maintaining the normal level of oxygen in the atmosphere, nearly all life either depends on it directly as a source of energy, or indirectly as the ultimate source of the energy in their food (the exceptions are chemoautotrophs that live in rocks or around deep sea hydrothermal vents). The amount of energy trapped by photosynthesis is immense, approximately 100 terawatts: which is about six times larger than the power consumption of human civilization. As well as energy, photosynthesis is also the source of the carbon in all the organic compounds within organisms' bodies. In all, photosynthetic organisms convert around 100,000,000,000 tones of carbon into biomass per year.
Although photosynthesis can happen in different ways in different species, some features are always the same. For example, the process always begins when energy from light is absorbed by proteins called photosynthetic reaction centers that contain chlorophylls. In plants, these proteins are held inside organelles called chloroplasts, while in bacteria they are embedded in the plasma membrane. Some of the light energy gathered by chlorophylls is stored in the form of adenosine triphosphate (ATP). The rest of the energy is used to remove electrons from a substance such as water. These electrons are then used in the reactions that turn carbon dioxide into organic compounds. In plants, algae and cyanobacteria this is done by a sequence of reactions called the Calvin cycle, but different sets of reactions are found in some bacteria, such as the reverse Krebs cycle in Chlorobium. Many photosynthetic organisms have adaptations that concentrate or store carbon dioxide. This helps reduce a wasteful process called photorespiration that can consume part of the sugar produced during photosynthesis.
Photosynthesis is the process of converting light energy to chemical energy and storing it in the bonds of sugar. This process occurs in plants and some algae (Kingdom Protista). Plants need only light energy, CO2, and H2O to make sugar. The process of photosynthesis takes place in the chloroplasts, specifically using chlorophyll, the green pigment involved in photosynthesis.
Photosynthesis takes place primarily in plant leaves, and little to none occurs in stems, etc. The parts of a typical leaf include the upper and lower epidermis, the mesophyll, the vascular bundle(s) (veins), and the stomates. The upper and lower epidermal cells do not have chloroplasts, thus photosynthesis does not occur there. They serve primarily as protection for the rest of the leaf. The stomates are holes which occur primarily in the lower epidermis and are for air exchange: they let CO2 in and O2 out. The vascular bundles or veins in a leaf are part of the plant's transportation system, moving water and nutrients around the plant as needed. The mesophyll cells have chloroplasts and this is where photosynthesis occurs.
As you hopefully recall, the parts of a chloroplast include the outer and inner membranes, intermembrane space, stroma, and thylakoids stacked in grana. The chlorophyll is built into the membranes of the thylakoids.
Chlorophyll looks green because it absorbs red and blue light, making these colors unavailable to be seen by our eyes. It is the green light which is NOT absorbed that finally reaches our eyes, making chlorophyll appear green. However, it is the energy from the red and blue light that are absorbed that is, thereby, able to be used to do photosynthesis. The green light we can see is not/cannot be absorbed by the plant, and thus cannot be used to do photosynthesis.
The overall chemical reaction involved in photosynthesis is: 6CO2 + 6H2O (+ light energy) C6H12O6 + 6O2. This is the source of the O2 we breathe, and thus, a significant factor in the concerns about deforestation
There are two parts to photosynthesis:
The Light Reaction
The light reaction happens in the thylakoid membrane and converts light energy to chemical energy. This chemical reaction must, therefore, take place in the light. Chlorophyll and several other pigments such as beta-carotene are organized in clusters in the thylakoid membrane and are involved in the light reaction. Each of these differently-colored pigments can absorb a slightly different color of light and pass its energy to the central chlorphyll molecule to do photosynthesis. The central part of the chemical structure of a chlorophyll molecule is a porphyrin ring, which consists of several fused rings of carbon and nitrogen with a magnesium ion in the center.
In the light reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, allowing the start of a flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient across the chloroplast membrane; its dissipation is used by ATP synthase for the concomitant synthesis of ATP. The chlorophyll molecule regains the lost electron from a water molecule through a process called photolysis, which releases a dioxygen (O2) molecule. The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is:

2 H2O + 2 NADP+ + 2 ADP + 2 Pi + light → 2 NADPH + 2 H+ + 2 ATP + O2

Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.
In plants, light-dependent reactions occur in the thylakoid membranes of the chloroplasts and use light energy to synthesize ATP and NADPH. The light-dependent reaction has two forms: cyclic and non-cyclic. In the non-cyclic reaction, the photons are captured in the light-harvesting antenna complexes of photosystem II by chlorophyll and other accessory pigments (see diagram at right). When a chlorophyll molecule at the core of the photosystem II reaction center obtains sufficient excitation energy from the adjacent antenna pigments, an electron is transferred to the primary electron-acceptor molecule, Pheophytin, through a process called photoinduced charge separation. These electrons are shuttled through an electron transport chain, the so called Z-scheme shown in the diagram, that initially functions to generate a chemiosmotic potential across the membrane. An ATP synthase enzyme uses the chemiosmotic potential to make ATP during photophosphorylation, whereas NADPH is a product of the terminal redox reaction in the Z-scheme. The electron enters the Photosystem I molecule. The electron is excited due to the light absorbed by the photosystem. A second electron carrier accepts the electron, which again is passed down lowering energies of electron acceptors. The energy created by the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. The electron is used to reduce the co-enzyme NADP, which has functions in the light-independent reaction. The cyclic reaction is similar to that of the non-cyclic, but differs in the form that it generates only ATP, and no reduced NADP (NADPH) is created. The cyclic reaction takes place only at photosystem I. Once the electron is displaced from the photosystem, the electron is passed down the electron acceptor molecules and returns back to photosystem I, from where it was emitted, hence the name cyclic reaction.
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. The source of electrons in green-plant and cyanobacterial photosynthesis is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions; the electron yielded in each step is transferred to a redox-active tyrosine residue that then reduces the photoxidized paired-chlorophyll a species called P680 that serves as the primary (light-driven) electron donor in the photosystem II reaction center. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion; this oxygen-evolving complex binds two water molecules and stores the four oxidizing equivalents that are required to drive the water-oxidizing reaction. Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use oxygen for cellular respiration, including photosynthetic organisms.
In this reaction, sunlight functions as physical energy source absorbed by chlorophyll and changed to be chemical energy in the form of ATP. The change of physical energy to be chemical energy happens gradually through electron transfer. Electron transfer is called phosphorilation.
In oxidative phosphorylation, the electrons removed from food molecules in pathways such as the citric acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane. These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane.
Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate - turning it into ATP.
Phosphorilation is separated into two namely
- Cyclic phosphorilation
In a cyclic phosphorilation, electron released by chlorophyll will return to chlorophyll. Besides, in this process ATP is produced.
Chlorophyll functions as the recipient of physical energy and electron donor. In the beginning of light reaction, chlorophyll struck by sunlight will release one of of its elections that contains a high energy. This electron is then received by the first electron recipient, that is flavin mononucleotide (FMN). Then this electron moves to cytochrome enzymatic system that functions as the recipient of the second electron. In cytochromatic, enzyme system the electron moves from one electron recipient to another. Finally, electrons go out quits from cytochromatic enzyme system and received by ionized chlorophyll (KL+) so that ionized chlorophyll they are changes to be normal chlorophyll.
In every electron transfer the releasing energy of electron happens gradually. This releases energy is received by adenosine diphosphate (ADP) to form adenosine triphosphate.
- Noncyclic phosphorilation
In noncyclic phosphorilation, the electron released by chlorophyll does not return to chlorophyll. In this process, besides ATP, NADPH2 is also produced.
In noncyclic phosphorilation, photolysis produces ionization of water so hydrogen ion (H+) and hydroxyl (OH-) are formed. Two H+ ions are received by NADP and by addition of electrons from chlorophyll, NADP changes to be NADPH2. NADPH2 then will be used in the dark reaction. Meanwhile two OH- ions will join to form water and oxygen by releasing electrons.
The Dark Reaction
The dark reaction takes place in the stroma within the chloroplast, and converts CO2 to sugar. This reaction doesn't directly need light in order to occur, but it does need the products of the light reaction (ATP and another chemical called NADPH). The dark reaction involves a cycle called the Calvin cycle in which CO2 and energy from ATP are used to form sugar. Actually, notice that the first product of photosynthesis is a three-carbon compound called glyceraldehyde 3-phosphate. Almost immediately, two of these join to form a glucose molecule.
In the Light-independent or dark reactions the enzyme RuBisCO captures CO2 from the atmosphere and in a process that requires the newly formed NADPH, called the Calvin-Benson Cycle, releases three-carbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is:
3 CO2 + 9 ATP + 6 NADPH + 6 H+ → C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O
To be more specific, carbon fixation produces an intermediate product, which is then converted to the final carbohydrate products. The carbon skeletons produced by photosynthesis 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 occurs not only in plants but also in animals when the energy from plants gets passed through a food chain.
The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-bisphosphate (RuBP), to yield two molecules of a three-carbon compound, glycerate 3-phosphate (GP), also known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehyde 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate. Triose is a 3-carbon sugar (see carbohydrates). Most (5 out of 6 molecules) of the G3P produced is used to regenerate RuBP so the process can continue (see Calvin-Benson cycle). The 1 out of 6 molecules of the triose phosphates not "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.
Most plants put CO2 directly into the Calvin cycle. Thus the first stable organic compound formed is the glyceraldehyde 3-phosphate. Since that molecule contains three carbon atoms, these plants are called C3 plants. For all plants, hot summer weather increases the amount of water that evaporates from the plant. Plants lessen the amount of water that evaporates by keeping their stomates closed during hot, dry weather. Unfortunately, this means that once the CO2 in their leaves reaches a low level, they must stop doing photosynthesis. Even if there is a tiny bit of CO2 left, the enzymes used to grab it and put it into the Calvin cycle just don't have enough CO2 to use. Typically the grass in our yards just turns brown and goes dormant. Some plants like crabgrass, corn, and sugar cane have a special modification to conserve water. These plants capture CO2 in a different way: they do an extra step first, before doing the Calvin cycle. These plants have a special enzyme that can work better, even at very low CO2 levels, to grab CO2 and turn it first into oxaloacetate, which contains four carbons. Thus, these plants are called C4 plants. The CO2 is then released from the oxaloacetate and put into the Calvin cycle. This is why crabgrass can stay green and keep growing when all the rest of your grass is dried up and brown.
There is yet another strategy to cope with very hot, dry, desert weather and conserve water. Some plants (for example, cacti and pineapple) that live in extremely hot, dry areas like deserts, can only safely open their stomates at night when the weather is cool. Thus, there is no chance for them to get the CO2 needed for the dark reaction during the daytime. At night when they can open their stomates and take in CO2, these plants incorporate the CO2 into various organic compounds to store it. In the daytime, when the light reaction is occurring and ATP is available (but the stomates must remain closed), they take the CO2 from these organic compounds and put it into the Calvin cycle. These plants are called CAM plants, which stands for crassulacean acid metabolism after the plant family, Crassulaceae (which includes the garden plant Sedum) where this process was first discovered.
Chemosynthesis
Chemosynthesis is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate), ferrous iron (FeII) or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility.
In chemosynthesis CO2 as source of carbon and water is also used. The difference of chemosynthesis and photosynthesis is its energy source. If in photosynthesis the energy source is light, in chemosynthesis the energy source is a chemical substances from products of inorganic compound obtained from its environment.
Metabolic Disorders and Conditions
Several of the hormones of the endocrine system are involved in controlling the rate and direction of metabolism. Thyroxine, a hormone produced and released by the thyroid gland, plays a key role in determining how fast or slow the chemical reactions of metabolism proceed in a person's body.
Another gland, the pancreas secretes hormones that help determine whether the body's main metabolic activity at a particular time will be anabolic or catabolic. For example, after eating a meal, usually more anabolic activity occurs because eating increases the level of glucose — the body's most important fuel — in the blood. The pancreas senses this increased level of glucose and releases the hormone insulin, which signals cells to increase their anabolic activities.
Metabolism is a complicated chemical process, so it's not surprising that many people think of it in its simplest sense: as something that influences how easily our bodies gain or lose weight. That's where calories come in. A calorie is a unit that measures how much energy a particular food provides to the body. A chocolate bar has more calories than an apple, so it provides the body with more energy — and sometimes that can be too much of a good thing. Just as a car stores gas in the gas tank until it is needed to fuel the engine, the body stores calories — primarily as fat. If you overfill a car's gas tank, it spills over onto the pavement. Likewise, if a person eats too many calories, they "spill over" in the form of excess body fat.
The number of calories someone burns in a day is affected by how much that person exercises, the amount of fat and muscle in his or her body, and the person's basal metabolic rate (or BMR). BMR is a measure of the rate at which a person's body "burns" energy, in the form of calories, while at rest. The BMR can play a role in someone's tendency to gain weight. For example, a person with a low BMR (who therefore burns fewer calories while at rest or sleeping) will tend to gain more pounds of body fat over time, compared with a similar-sized person with an average BMR who eats the same amount of food and gets the same amount of exercise.
G6PD deficiency. Glucose-6-phosphate dehydrogenase, or G6PD, is just one of the many enzymes that play a role in cell metabolism. G6PD is produced by red blood cells and helps the body metabolize carbohydrates. Without enough normal G6PD to help red blood cells handle certain harmful substances, red blood cells can be damaged or destroyed, leading to a condition known as hemolytic anemia. In a process called hemolysis, red blood cells are destroyed prematurely, and the bone marrow (the soft, spongy part of the bone that produces new blood cells) may not be able to keep up with the body's need to produce more new red blood cells. Kids with G6PD deficiency may be pale and tired and have a rapid heartbeat and breathing. They may also have an enlarged spleen or jaundice — a yellowing of the skin and eyes. G6PD deficiency is usually treated by discontinuing medications or treating the illness or infection causing the stress on the red blood cells.
Galactosemia. Babies born with this inborn error of metabolism do not have enough of the enzyme that breaks down the sugar in milk called galactose. This enzyme is produced in the liver. If the liver doesn't produce enough of this enzyme, galactose builds up in the blood and can cause serious health problems. Symptoms usually occur within the first days of life and include vomiting, swollen liver, and jaundice. If galactosemia is not diagnosed and treated quickly, it can cause liver, eye, kidney, and brain damage.
Hyperthyroidism. Hyperthyroidism is caused by an overactive thyroid gland. The thyroid releases too much of the hormone thyroxine, which increases the person's basal metabolic rate (BMR). It causes symptoms such as weight loss, increased heart rate and blood pressure, protruding eyes, and a swelling in the neck from an enlarged thyroid (goiter). The disease may be controlled with medications or through surgery or radiation treatments.
Hypothyroidism. Hypothyroidism is caused by an absent or underactive thyroid gland and it results from a developmental problem or a destructive disease of the thyroid. The thyroid releases too little of the hormone thyroxine, so a person's basal metabolic rate (BMR) is low. In infants and young children who don't get treatment, this condition can result in stunted growth and mental retardation. Hypothyroidism slows body processes and causes fatigue, slow heart rate, excessive weight gain, and constipation. Kids and teens with this condition can be treated with oral thyroid hormone to achieve normal levels in the body.

Phenylketonuria. Also known as PKU, this condition occurs in infants due to a defect in the enzyme that breaks down the amino acid phenylalanine. This amino acid is necessary for normal growth in infants and children and for normal protein production. However, if too much of it builds up in the body, brain tissue is affected and mental retardation occurs. Early diagnosis and dietary restriction of the amino acid can prevent or lessen the severity of these complications.
Type 1 diabetes mellitus. Type 1 diabetes occurs when the pancreas doesn't produce and secrete enough insulin. Symptoms of this disease include excessive thirst and urination, hunger, and weight loss. Over the long term, the disease can cause kidney problems, pain due to nerve damage, blindness, and heart and blood vessel disease. Kids and teens with type 1 diabetes need to receive regular injections of insulin and control blood sugar levels to reduce the risk of developing problems from diabetes.
Type 2 diabetes. Type 2 diabetes happens when the body can't respond normally to insulin. The symptoms of this disorder are similar to those of type 1 diabetes. Many kids who develop type 2 diabetes are overweight, and this is thought to play a role in their decreased responsiveness to insulin. Some can be treated successfully with dietary changes, exercise, and oral medication, but insulin injections are necessary in other cases. Controlling blood sugar levels reduces the risk of developing the same kinds of long-term health problems that occur with type 1 diabetes.
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