Biochemistry

Biochemistry

Biochemistry is the study of the chemical processes in living organisms. The word biochemistry comes from the Greek word a biochemeia, which means the chemistry of life. It deals with the structure and function of cellular components, such as proteins, carbohydrates, lipids, nucleic acids, and other biomolecules. Chemical biology aims to answer many questions arising from biochemistry by using tools developed within chemical synthesis. Although there are a vast number of different biomolecules, many are complex and large molecules called polymers that are composed of similar repeating subunits called monomers. Each class of polymeric biomolecule has a different set of subunit types. For example, a protein is a polymer made up of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, in particular the chemistry of enzymecatalyzed reactions. The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code DNA, RNA, protein synthesis, cell membrane transport, and signal transduction. This article only discusses terrestrial biochemistry carbon and waterbased, as all the life forms we know are on Earth. Since life forms alive today are hypothesized by most to have descended from the same common ancestor, they have similar biochemistries, even for matters that seem to be essentially arbitrary, such as handedness of various biomolecules. It is unknown whether alternative biochemistries are possible or practical.




Metabolism


Metabolism is the complete set of chemical reactions that occur in living cells. These processes are the basis of life, allowing cells to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism yields energy, an example being the breakdown of food in cellular respiration. Anabolism, on the other hand, uses this energy to construct components of cells such as proteins and nucleic acids. The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by a sequence of enzymes. Enzymes are crucial to metabolism because they allow cells to drive desirable but thermodynamically unfavorable reactions by coupling them to favorable ones. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells. The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The speed of metabolism, the metabolic rate, also influences how much food an organism will require. A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the set of chemical intermediates in the citric acid cycle are found universally, among living cells as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants. This shared metabolic structure is most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history. Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule amino acids, carbohydrates and lipids often called fats. As these molecules are vital for life, metabolism focuses on making these molecules, in the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food.
                                               Many important biochemicals can be joined together to make polymers such as DNA and proteins. These macromolecules are essential parts of all living organisms. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy starch, glycogen and structural components cellulose in plants, chitin in animals. The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.

Coenzymes

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These grouptransfer intermediates are called coenzymes. Each class of grouptransfer reaction is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously being made, consumed and then recycled. The most central coenzyme is adenosine triphosphate ATP, the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions.
                                               There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.ATP acts as a bridge between catabolism and anabolism, with catabolic reactions generating ATP and anabolic reactions consuming it. It also serves as a carrier of phosphate groups in phosphorylation reactions. A vitamin is an organic compound needed in small quantities that cannot be made in the cells. In human nutrition, most vitamins function as coenzymes after modification for example, all watersoluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.Nicotinamide adenine dinucleotide NADH, a derivative of vitamin B3 niacin, is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions. Inorganic elements play critical roles in metabolism some are abundant e.g. sodium and potassium while others function at minute concentrations. About 99% of mammals' mass are the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, oxygen and sulfur. The organic compounds proteins, lipids and carbohydrates contain the majority of the carbon and nitrogen and most of the oxygen and hydrogen is present as water. The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate, and the organic ion bicarbonate. The maintenance of precise gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerves and muscles, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cytosol.Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and Ttubules. The transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant. These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygencarrier proteins such as hemoglobin.These cofactors are bound tightly to a specific protein although enzyme cofactors can be modified during catalysis, cofactors always return to their original state after catalysis has taken place. The metal micronutrients are taken up into organisms by specific transporters and bound to storage proteins such as ferritin or metallothionein when not being used.
                                               Catabolism is the set of metabolic processes that release energy. These include breaking down and oxidising food molecules as well as reactions that trap the energy in sunlight. The purpose of these 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, with 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 sulphate. 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 electrontransfer 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 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 nicotina.

Oxidative phosphorylation

Oxidative phosphorylation is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate ATP. Although the many forms of life on Earth utilize a range of different nutrients, almost all carry out oxidative phosphorylation to produce ATP, the molecule that supplies energy to metabolism. This pathway is probably so pervasive because it is a highly efficient way of storing energy, compared to alternative fermentation processes such as glycolysis. During oxidative phosphorylation, electrons are transferred from electron donors to electron acceptors such as oxygen, in a redox reaction. This redox step releases energy, which is captured in the form of ATP. In eukaryotes these redox reactions are carried out by a series of protein complexes within mitochondria, whereas in prokaryotes, these proteins are located in the cells' inner membranes. These linked sets of enzymes are called electron transport chains. In eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors. The energy released as electrons flow through this electron transport chain is used to transport protons across the inner mitochondrial membrane, in a process called chemiosmosis. This generates potential energy in the form of a pH gradient and an electrical
                                               potential across this membrane. This store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase. This enzyme uses this energy to generate ATP from adenosine diphosphate ADP, in a phosphorylation reaction. Unusually, the ATP synthase works by the proton flow driving the rotation of part of the enzyme it is a rotary mechanical motor. Although oxidative phosphorylation is a vital part of metabolism, it produces reactive oxygen species such as free radicals that damage cells and contribute to ageing and disease. The enzymes carrying out this metabolic pathway are also the target of many drugs and poisons that inhibit their activities. Oxidative phosphorylation works by using energyreleasing chemical reactions to drive energyrequiring reactions the two sets of reactions are said to be coupled, as one cannot occur without the other. The flow of electrons through the electron transport chain, from electron donors such as NADH to electron acceptors such as oxygen, is an exergonic process it releases energy while the synthesis of ATP is an endergonic process that requires an input of energy. Both the electron transport chain and the ATP synthase are embedded in a membrane, and energy is transferred from one enzyme to the other by a flow of protons across this membrane, in a process called chemiosmosis. In practice, this is like a simple electric circuit, with a current of protons being driven from the negative Nside of the membrane to the positive Pside by the protonpumping enzymes of the electron transport chain. These enzymes are like a battery, as they perform work to drive current through the circuit. The movement of protons creates an electrochemical gradient across the membrane, which is often called the protonmotive force. This gradient has two components a difference in proton concentration a pH gradient and a difference in electric potential, with the Nside having a negative charge. The energy is stored largely as the difference of electric potentials in mitochondria, but as a pH gradient in chloroplasts. ATP synthase releases this stored energy by completing the circuit and allowing protons to flow down the electrochemical gradient, back to the Nside of the membrane. This enzyme is like an electric motor as it uses the protonmotive force to drive the rotation of part of its structure and couples this motion to the synthesis of ATP. The amount of energy released by oxidative phosphorylation is high, compared with the amount produced by anaerobic fermentation. Glycolysis only produces 2 ATP molecules, but 26 ATPs are produced by the oxidative phosphorylation of the 10 NADH and 2 succinate molecules that are made by converting one molecule of glucose to carbon dioxide and water. This ATP yield is the theoretical maximum value in practice some protons leak across the membrane, lowering the yield of ATP.

Geomicrobiology

Geomicrobiology is a subset of the scientific discipline microbiology. The field of geomicrobiology concerns the role of microbe and microbial processes in geological and geochemical processes. The field is especially important when dealing with microorganisms in aquifers and public drinking water supplies.Another area of investigation in geomicrobiology is the study of extremophile organisms, the microorganisms that thrive in environments normally considered hostile. Such environments may include extremely hot hot springs or midocean ridge black smoker environments, extremely saline environments, or even space environments such as Martian soil or comets.Recent observations and research in hypersaline lagoon environments in Brazil and Australia have shown that anaerobic sulfatereducing bacteria may be directly involved in the formation of dolomite. This suggests the alteration and replacement of limestone sediments by dolomitization in ancient rocks was possibly aided by ancestors to these anaerobic bacteria. Some bacteria use metal ions as their energy source. They convert or chemically reduce the dissolved metal ions from one electrical state to another. This reduction releases energy for the bacteria's use, and, as a side product, serves to concentrate the metals into what ultimately become ore deposits. Certain iron, uranium and even gold ores are thought to have formed as the result of microbe action.Microbes are being studied and used to degrade organic and even nuclear waste pollution see Deinococcus radiodurans and assist in environmental cleanup. It should be stressed however that microorganisms can not decrease the total radioactivity of nuclear waste.An application of geomicrobiology is bioleaching, the use of microbes to extract metals from mine waste. is the study of microorganisms, which are unicellular or cellcluster microscopic organisms.
                                               This includes eukaryotes such as fungi and protists, and prokaryotes such as bacteria and certain algae. Viruses, though not strictly classed as living organisms, are also studied. Microbiology is a broad term which includes many branches like virology, mycology, parasitology and others. A person who specializes in the area of microbiology is called a microbiologist. Although much is now known in the field of microbiology, advances are being made regularly. We have probably only studied about 1% of all of the microbes on Earth. Thus, despite the fact that over three hundred years have passed since the discovery of microbes, the field of microbiology could be said to be in its infancy relative to other biological disciplines such as zoology, botany and entomology. The existence of microorganisms was hypothesized during the late Middle Ages but they were not observed or proven until the invention of the microscope in the 17th century. In The Canon of Medicine 1020, Abu Ali ibn Sina Avicenna stated that bodily secretion is contaminated by foul foreign earthly bodies before being infected, but he did not view them as primary causes of disease. When the Black Death bubonic plague reached alAndalus in the 14th century, Ibn Khatima and Ibn alKhatib hypothesized that infectious diseases are caused by microorganisms which enter the human body. Bacteria were first observed by Anton van Leeuwenhoek in 1676 using a singlelens microscope of his own design. The name bacterium was introduced much later, by Ehrenberg in 1828, meaning small stick. While van Leeuwenhoek is often cited as the first microbiologist, the first recorded microbiological observation, that of the fruiting bodies of molds, was made earlier in 1665 by Robert Hooke. The field of bacteriology later a subdiscipline of microbiology is generally considered to have been founded by Ferdinand Cohn 1828–1898, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria. Pasteur 1822–1895 and Robert Koch 1843–1910 were contemporaries of Cohn’s and are often considered to be the founders of medical microbiology. Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science. Pasteur also designed methods for food preservation pasteurization and vaccines against several diseases such as anthrax, fowl cholera and rabies. Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms.
                                               He developed a series of criteria that have become known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis. While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the work of Martinus Beijerinck 1851–1931 and Sergei Winogradsky 1856–1953, the founders of general microbiology an older term encompassing aspects of microbial physiology, diversity and ecology, that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology the discovery of viruses and the development of enrichment culture techniques. While his work on the Tobacco Mosaic Virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes. He was responsible for the first isolation and description of both nitrifying and nitrogenfixing bacteria.

Cholesterol

Cholesterol is a sterol a combination steroid and alcohol, a lipid found in the cell membranes of all body tissues, and is transported in the blood plasma of all animals. Because cholesterol is synthesized by all eukaryotes, trace amounts of cholesterol are also found in membranes of plants and fungi.The name originates from the Greek chole bile and stereos solid, and the chemical suffix ol for an alcohol, as researchers first identified cholesterol in solid form in gallstones by François Poulletier de la Salle in 1769. However, it is only in 1815 that chemist Eugène Chevreul named the compound cholesterine.Most of the cholesterol is synthesized by the body and some has dietary origin. Cholesterol is more abundant in tissues which either synthesize more or have more abundant denselypacked membranes, for example, the liver, spinal cord, brain, and atheromata arterial plaques. Cholesterol plays a central role in many biochemical processes, but is best known for the association of cardiovascular disease with various lipoprotein cholesterol transport patterns and high levels of cholesterol in the blood. Cholesterol is insoluble in blood, but is transported in the circulatory system bound to one of the varieties of lipoprotein, spherical particles which have an exterior composed mainly of watersoluble proteins.In recent years, the term bad cholesterol has been used to refer to cholesterol contained in LDL lowdensity lipoprotein which, according to the lipid hypothesis, is thought to have harmful actions, and good cholesterol to refer to cholesterol contained in HDL highdensity lipoprotein, thought to have beneficial actions. Cholesterol is required to build and maintain cell membranes it regulates membrane fluidity over a wider range of temperatures. The hydroxyl group on cholesterol interacts with the phosphate head of the membrane, while the bulky steroid and the hydrocarbon chain is embedded in the membrane. Some research indicates that cholesterol may act as an antioxidant.
                                               Cholesterol also aids in the manufacture of bile which is stored in the gallbladder and helps digest fats, and is also important for the metabolism of fat soluble vitamins, including vitamins A, D, E and K. It is the major precursor for the synthesis of vitamin D and of the various steroid hormones which include cortisol and aldosterone in the adrenal glands, and the sex hormones progesterone, the various estrogens, testosterone, and derivatives. Recently, cholesterol has also been implicated in cell signalling processes, where it has been suggested that it forms lipid rafts in the plasma membrane. It also reduces the permeability of the plasma membrane to hydrogen ions protons and sodium ions.Cholesterol is essential for the structure and function of invaginated caveolae and clathrincoated pits, including the caveolaedependent endocytosis and clathrindependent endocytosis. The role of cholesterol in caveolaedependent and clathrindependent endocytosis can be investigated by using methyl beta cyclodextrin MßCD to remove cholesterol from the plasma membrane.Cholesterol is required in the membrane of mammalian cells for normal cellular function, and is either synthesized in the endoplasmic reticulum, or derived from the diet, in which case it is delivered by the bloodstream in lowdensity lipoproteins. These are taken into the cell by receptormediated endocytosis in clathrincoated pits, and then hydrolysed in lysosomes. Cholesterol is primarily synthesized from acetyl CoA through the HMGCoA reductase pathway in many cells and tissues. About 20 – 25% of total daily production ~1 g/day occurs in the liver other sites of higher synthesis rates include the intestines, adrenal glands and reproductive organs. For a person of about 150 pounds 68 kg, typical total body content is about 35 g, typical daily internal production is about 1 g and typical daily dietary intake is 200 to 300 mg in the United States and societies adopting its dietary patterns. Of the cholesterol input to the intestines via bile production, 9297% is reabsorbed in the intestines and recycled via enterohepatic circulation.Konrad Bloch and Feodor Lynen shared the Nobel Prize in Physiology or Medicine in 1964 for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism.

Carbohydrate

Monosaccharides are classified according to three different characteristics the placement of its carbonyl group, the number of carbon atoms it contains, and its chiral handedness. If the carbonyl group is an aldehyde, the monosaccharide is an aldose if the carbonyl group is a ketone, the monosaccharide is a ketose. Monosaccharides with three carbon atoms are called trioses, those with four are called tetroses, five are called pentoses, six are hexoses, and so on. These two systems of classification are often combined. For example, glucose is an aldohexose a sixcarbon aldehyde, ribose is an aldopentose a fivecarbon aldehyde, and fructose is a ketohexose a sixcarbon ketone.Each carbon atom bearing a hydroxyl group OH, with the exception of the first and last carbons, are asymmetric, making them stereocenters with two possible configurations each R or S. Because of this asymmetry, a number of isomers may exist for any given monosaccharide formula. The aldohexose Dglucose, for example, has the formula C·H2O6, of which all but two of its six carbons atoms are stereogenic, making Dglucose one of 24 = 16 possible stereoisomers. In the case of glyceraldehyde, an aldotriose, there is one pair of possible stereoisomers, which are enantiomers and epimers. 1,3dihydroxyacetone, the ketose corresponding to the aldose glyceraldehye, is a symmetric molecule with no stereocenters.
                                               The assignment of D or L is made according to the orientation of the asymmetric carbon furthest from the carbonyl group in a standard Fischer projection if the hydroxyl group is on the right the molecule is a D sugar, otherwise it is an L sugar. Because D sugars are biologically far more common, the D is often omitted.Pyran and furan, after which the pyranose and furanose rings forms of monosaccharides are named. Pyran and furan, after which the pyranose and furanose rings forms of monosaccharides are named. The aldehyde or ketone group of a straightchain monosaccharide will react reversibly with a hydroxyl group on a different carbon atom to form a hemiacetal or hemiketal, forming a heterocyclic ring with an oxygen bridge between two carbon atoms. Rings with five and six atoms are called furanose and pyranose forms, respectively, and exist in equilibrium with the straightchain form.During the conversion from straightchain form to cyclic form, the carbon atom containing the carbonyl oxygen, called the anomeric carbon, becomes a chiral center with two possible configurations the oxygen atom may take a position either above or below the plane of the ring. The resulting possible pair of stereoisomers are called anomers.
                                               In the 1945, anomer, the OH substituent on the anomeric carbon rests on the opposite side trans of the ring from the CH2OH side branch. The alternative form, in which the CH2OH substituent and the anomeric hydroxyl are on the same side cis of the plane of the ring, is called the β anomer. Because the ring and straightchain forms readily interconvert, both anomers exist in equilibrium.Monosaccharides are the major source of fuel for metabolism, being used both as an energy source glucose being the most important in nature and in biosynthesis. When monosaccharides are not needed by cells they are quickly converted into another form, such as polysaccharides.Two joined monosaccharides are called disaccharides and represent the simplest polysaccharides. Examples include sucrose and lactose. They are composed of two monosaccharide units bound together by a covalent bond known as a glycosidic linkage formed via a dehydration reaction, resulting in the loss of a hydrogen atom from one monosaccharide and a hydroxyl group from the other. The formula of unmodified disaccharides is C12H22O11. Although there are numerous kinds of disaccharides, a handful of disaccharides are particularly notable.
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