Tuesday, 7 December 2010

Digestion of Dietary Carbohydrates

Dietary carbohydrate from which humans gain energy enter the body in complex forms, such as disaccharides and the polymers starch (amylose and amylopectin) and glycogen. The polymer cellulose is also consumed but not digested. The first step in the metabolism of digestible carbohydrate is the conversion of the higher polymers to simpler, soluble forms that can be transported across the intestinal wall and delivered to the tissues. The breakdown of polymeric sugars begins in the mouth. Saliva has a slightly acidic pH of 6.8 and contains lingual amylase that begins the digestion of carbohydrates. The action of lingual amylase is limited to the area of the mouth and the esophagus; it is virtually inactivated by the much stronger acid pH of the stomach. Once the food has arrived in the stomach, acid hydrolysis contributes to its degradation; specific gastric proteases and lipases aid this process for proteins and fats, respectively. The mixture of gastric secretions, saliva, and food, known collectively as chyme, moves to the small intestine.

The main polymeric-carbohydrate digesting enzyme of the small intestine is α-amylase. This enzyme is secreted by the pancreas and has the same activity as salivary amylase, producing disaccharides and trisaccharides. The latter are converted to monosaccharides by intestinal saccharidases, including maltases that hydrolyze di- and trisaccharides, and the more specific disaccharidases, sucrase, lactase, and trehalase. The net result is the almost complete conversion of digestible carbohydrate to its constituent monosaccharides. The resultant glucose and other simple carbohydrates are transported across the intestinal wall to the hepatic portal vein and then to liver parenchymal cells and other tissues. There they are converted to fatty acids, amino acids, and glycogen, or else oxidized by the various catabolic pathways of cells.

Oxidation of glucose is known as glycolysis.Glucose is oxidized to either lactate or pyruvate. Under aerobic conditions, the dominant product in most tissues is pyruvate and the pathway is known as aerobic glycolysis. When oxygen is depleted, as for instance during prolonged vigorous exercise, the dominant glycolytic product in many tissues is lactate and the process is known as anaerobic glycolysis.

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The Energy Derived from Glucose Oxidation

Aerobic glycolysis of glucose to pyruvate, requires two equivalents of ATP to activate the process, with the subsequent production of four equivalents of ATP and two equivalents of NADH. Thus, conversion of one mole of glucose to two moles of pyruvate is accompanied by the net production of two moles each of ATP and NADH.

Glucose + 2 ADP + 2 NAD⁺ + 2 P_i ——> 2 Pyruvate + 2 ATP + 2 NADH + 2 H⁺

The NADH generated during glycolysis is used to fuel mitochondrial ATP synthesis via oxidative phosphorylation, producing either two or three equivalents of ATP depending upon whether the glycerol phosphate shuttle or the malate-aspartate shuttle is used to transport the electrons from cytoplasmic NADH into the mitochondria.

The malate-aspartate shuttle is the principal mechanism for the movement of reducing equivalents (in the form of NADH) from the cytoplasm to the mitochondria. The glycolytic pathway is a primary source of NADH. Within the mitochodria the electrons of NADH can be coupled to ATP production during the process of oxidative phosphorylation. The electrons are "carried" into the mitochondria in the form of malate. Cytoplasmic malate dehydrogenase (MDH) reduces oxaloacetate (OAA) to malate while oxidizing NADH to NAD⁺. Malate then enters the mitochondria where the reverse reaction is carried out by mitochondrial MDH. Movement of mitochondrial OAA to the cytoplasm to maintain this cycle requires it be transaminated to aspartate (Asp, D) with the amino group being donated by glutamate (Glu, E). The Asp then leaves the mitochondria and enters the cytoplasm. The deamination of glutamate generates α-ketoglutarate (α-KG) which leaves the mitochondria for the cytoplasm. All the participants in the cycle are present in the proper cellular compartment for the shuttle to function due to concentration dependent movement. When the energy level of the cell rises the rate of mitochondrial oxidation of NADH to NAD⁺ declines and therefore, the shuttle slows. G3PDH is glyceraldehyde-3-phosphate dehydrogenase.

The glycerol phosphate shuttle is a secondary mechanism for the transport of electrons from cytosolic NADH to mitochondrial carriers of the oxidative phosphorylation pathway. The primary cytoplasmic NADH electron shuttle is the malate-aspartate shuttle. Two enzymes are involved in this shuttle. One is the cytosolic version of the enzyme glycerol-3-phosphate dehydrogenase (glycerol-3-PDH) which has as one substrate, NADH. The second is is the mitochondrial form of the enzyme which has as one of its' substrates, FAD⁺. The net result is that there is a continual conversion of the glycolytic intermediate, DHAP and glycerol-3-phosphate with the concomitant transfer of the electrons from reduced cytosolic NADH to mitochondrial oxidized FAD⁺. Since the electrons from mitochondrial FADH₂ feed into the oxidative phosphorylation pathway at coenzyme Q (as opposed to NADH-ubiquinone oxidoreductase [complex I]) only 2 moles of ATP will be generated from glycolysis. G3PDH is glyceraldehyde-3-phoshate dehydrogenase.

The net yield from the oxidation of 1 mole of glucose to 2 moles of pyruvate is, therefore, either 6 or 8 moles of ATP. Complete oxidation of the 2 moles of pyruvate, through the TCA cycle, yields an additional 30 moles of ATP; the total yield, therefore being either 36 or 38 moles of ATP from the complete oxidation of 1 mole of glucose to CO₂and H₂O.

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The Individual Reactions of Glycolysis

The pathway of glycolysis can be seen as consisting of 2 separate phases. The first is the chemical priming phase requiring energy in the form of ATP, and the second is considered the energy-yielding phase. In the first phase, 2 equivalents of ATP are used to convert glucose to fructose 1,6-bisphosphate (F1,6BP). In the second phase F1,6BP is degraded to pyruvate, with the production of 4 equivalents of ATP and 2 equivalents of NADH.

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 K_m 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 K_m 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 K_m 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 K_m 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 (ΔG^0' = +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 ofinherited non-spherocytic anemia.

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Anaerobic Glycolysis

Under aerobic conditions, pyruvate in most cells is further metabolized via the TCA cycle. Under anaerobic conditions and in erythrocytes under aerobic conditions, pyruvate is converted to lactate by the enzyme lactate dehydrogenase (LDH), and the lactate is transported out of the cell into the circulation. The conversion of pyruvate to lactate, under anaerobic conditions, provides the cell with a mechanism for the oxidation of NADH (produced during the G3PDH reaction) to NAD⁺ which occurs during the LDH catalyzed reaction. This reduction is required since NAD⁺ is a necessary substrate for G3PDH, without which glycolysis will cease. Normally, during aerobic glycolysis the electrons of cytoplasmic NADH are transferred to mitochondrial carriers of the oxidative phosphorylation pathway generating a continuous pool of cytoplasmic NAD⁺.

Aerobic glycolysis generates substantially more ATP per mole of glucose oxidized than does anaerobic glycolysis. The utility of anaerobic glycolysis, to a muscle cell when it needs large amounts of energy, stems from the fact that the rate of ATP production from glycolysis is approximately 100X faster than from oxidative phosphorylation. During exertion muscle cells do not need to energize anabolic reaction pathways. The requirement is to generate the maximum amount of ATP, for muscle contraction, in the shortest time frame. This is why muscle cells derive almost all of the ATP consumed during exertion from anaerobic glycolysis.

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Regulation of Glycolysis

The reactions catalyzed by hexokinase, PFK-1 and PK all proceed with a relatively large free energy decrease. These non-equilibrium reactions of glycolysis would be ideal candidates for regulation of the flux through glycolysis. Indeed, in vitro studies have shown all three enzymes to be allosterically controlled.

Regulation of hexokinase, however, is not the major control point in glycolysis. This is due to the fact that large amounts of G6P are derived from the breakdown of glycogen (the predominant mechanism of carbohydrate entry into glycolysis in skeletal muscle) and, therefore, the hexokinase reaction is not necessary. Regulation of PK is important for reversing glycolysis when ATP is high in order to activate gluconeogenesis. As such this enzyme catalyzed reaction is not a major control point in glycolysis. The rate limiting step in glycolysis is the reaction catalyzed by PFK-1.

PFK-1 is a tetrameric enzyme that exist in two conformational states termed R and T that are in equilibrium. ATP is both a substrate and an allosteric inhibitor of PFK-1. Each subunit has two ATP binding sites, a substrate site and an inhibitor site. The substrate site binds ATP equally well when the tetramer is in either conformation. The inhibitor site binds ATP essentially only when the enzyme is in the T state. F6P is the other substrate for PFK-1 and it also binds preferentially to the R state enzyme. At high concentrations of ATP, the inhibitor site becomes occupied and shifting the equilibrium of PFK-1 conformation to that of the T state decreasing PFK-1's ability to bind F6P. The inhibition of PFK-1 by ATP is overcome by AMP which binds to the R state of the enzyme and, therefore, stabilizes the conformation of the enzyme capable of binding F6P. The most important allosteric regulator of both glycolysis and gluconeogenesis is fructose 2,6-bisphosphate, F2,6BP, which is not an intermediate in glycolysis or in gluconeogenesis.

Regulation of glycolysis and gluconeogenesis by fructose 2,6-bisphosphate (F2,6BP). The major sites for regulation of glycolysis and gluconeogenesis are the phosphofructokinase-1 (PFK-1) and fructose-1,6-bisphosphatase (F-1,6-BPase) catalyzed reactions. PFK-2 is the kinase activity and F-2,6-BPase is the phosphatase activity of the bi-functional regulatory enzyme, phosphofructokinase-2/fructose-2,6-bisphosphatase. PKA is cAMP-dependent protein kinase which phosphorylates PFK-2/F-2,6-BPase turning on the phosphatase activity. (+ve) and (-ve) refer to positive and negative activities, respectively.

The synthesis of F2,6BP is catalyzed by the bifunctional enzyme phosphofructokinase-2/fructose-2,6-bisphosphatase (PFK-2/F-2,6-BPase). In the nonphosphorylated form the enzyme is known as PFK-2 and serves to catalyze the synthesis of F2,6BP by phosphorylating fructose 6-phosphate. The result is that the activity of PFK-1 is greatly stimulated and the activity of F-1,6-BPase is greatly inhibited.

Under conditions where PFK-2 is active, fructose flow through the PFK-1/F-1,6-BPase reactions takes place in the glycolytic direction, with a net production of F1,6BP. When the bifunctional enzyme is phosphorylated it no longer exhibits kinase activity, but a new active site hydrolyzes F2,6BP to F6P and inorganic phosphate. The metabolic result of the phosphorylation of the bifunctional enzyme is that allosteric stimulation of PFK-1 ceases, allosteric inhibition of F-1,6-BPase is eliminated, and net flow of fructose through these two enzymes is gluconeogenic, producing F6P and eventually glucose.

The interconversion of the bifunctional enzyme is catalyzed by cAMP-dependent protein kinase (PKA), which in turn is regulated by circulating peptide hormones. When blood glucose levels drop, pancreatic insulin production falls, glucagon secretion is stimulated, and circulating glucagon is highly increased. Hormones such as glucagon bind to plasma membrane receptors on liver cells, activating membrane-localized adenylate cyclase leading to an increase in the conversion of ATP to cAMP (see diagram below). cAMP binds to the regulatory subunits of PKA, leading to release and activation of the catalytic subunits. PKA phosphorylates numerous enzymes, including the bifunctional PFK-2/F-2,6-BPase. Under these conditions the liver stops consuming glucose and becomes metabolically gluconeogenic, producing glucose to reestablish normoglycemia.

Carbohydrate

Carbohydrate - Wikipedia, the free encyclopedia

Carbohydrates

Carbohydrates are the main energy source for the human body. Chemically, carbohydrates are organic molecules in which carbon, hydrogen, and oxygen bond together in the ratio: C_x(H₂O)_y, where x and y are whole numbers that differ depending on the specific carbohydrate to which we are referring. Animals (including humans) break down carbohydrates during the process ofmetabolism to release energy. For example, the chemical metabolism of thesugar glucose is shown below:

C₆H₁₂O₆ + 6 O₂

6 CO₂ + 6 H₂O + energy

Animals obtain carbohydrates by eating foods that contain them, for example potatoes, rice, breads, and so on. These carbohydrates are manufactured by plants during the process of photosynthesis. Plants harvest energy from sunlight to run the reaction just described in reverse:

6 CO₂ + 6 H₂O + energy (from sunlight)

C₆H₁₂O₆ + 6 O₂

A potato, for example, is primarily a chemical storage system containing glucose molecules manufactured during photosynthesis. In a potato, however, those glucose molecules are bound together in a long chain. As it turns out, there are two types of carbohydrates, the simple sugars and those carbohydrates that are made of long chains of sugars - the complex carbohydrates.

Simple sugars

All carbohydrates are made up of units of sugar (also called saccharide units). Carbohydrates that contain only one sugar unit (monosaccharides) or two sugar units (disaccharides) are referred to as simple sugars. Simple sugars are sweet in taste and are broken down quickly in the body to release energy. Two of the most common monosaccharides are glucose and fructose. Glucose is the primary form of sugar stored in the human body for energy. Fructose is the main sugar found in most fruits. Both glucose and fructose have the same chemical formula (C₆H₁₂O₆); however, they have different structures, as shown (note: the carbon atoms that sit in the "corners" of the rings are not labeled):


Glucose	Fructose

Disaccharides have two sugar units bonded together. For example, common table sugar is sucrose, a disaccharide that consists of a glucose unit bonded to a fructose unit:

Sucrose

Complex carbohydrates

Complex carbohydrates are polymers of the simple sugars. In other words, the complex carbohydrates are long chains of simple sugar units bonded together (for this reason the complex carbohydrates are often referred to as polysaccharides). The potato we discussed earlier actually contains the complex carbohydrate starch. Starch is a polymer of the monosaccharide glucose:

Starch
(n is the number of repeating glucose units and ranges in the 1,000's)

Starch is the principal polysaccharide used by plants to store glucose for later use as energy. Plants often store starch in seeds or other specialized organs; for example, common sources of starch include rice, beans, wheat, corn, potatoes, and so on. When humans eat starch, an enzyme that occurs in saliva and in the intestines called amylase breaks the bonds between the repeating glucose units, thus allowing the sugar to be absorbed into the bloodstream. Once absorbed into the bloodstream, the human body distributes glucose to the areas where it is needed for energy or stores it as its own special polymer - glycogen. Glycogen, another polymer of glucose, is the polysaccharide used by animals to store energy. Excess glucose is bonded together to form glycogen molecules, which the animal stores in the liver and muscle tissue as an "instant" source of energy. Both starch and glycogen are polymers of glucose; however, starch is a long, straight chain of glucose units, whereas glycogen is a branched chain of glucose units, as seen in the illustrations linked below:

The Starch Molecule • The Glycogen Molecule

Another important polysaccharide is cellulose. Cellulose is yet a thirdpolymer of the monosaccharide glucose. Cellulose differs from starch and glycogen because the glucose units form a two-dimensional structure, withhydrogen bonds holding together nearby polymers, thus giving the moleculeadded stability. Cellulose, also known as plant fiber, cannot be digested by human beings, therefore cellulose passes through the digestive tract without being absorbed into the body. Some animals, such as cows and termites, contain bacteria in their digestive tract that help them to digest cellulose. Cellulose is a relatively stiff material, and in plants it is used as a structural molecule to add support to the leaves, stem, and other plant parts. Despite the fact that it cannot be used as an energy source in most animals, cellulose fiber is essential in the diet because it helps exercise the digestive track and keep it clean and healthy

Biochemistry General

What is Biochemistry?

A. Biochemistry is concerned with structural chemistry. It seeks to determine the structures of molecules found in living systems in order to understand structure-function relationships.

B. Biochemistry is concerned with chemical change, this is reflected in the stu dy of metabolic pathways

C. Biochemistry is concerned with information which has accumulated through evolution and is preserved in DNA (or sometimes RNA). These nucleic acid sequences code for amino acid sequences, which result in folded proteins. These proteins are often catalysts (enzymes) and some of them are regulated (able to sense the chemical state inside the cell and, in some cases, the outside)

History of biochemistry:

(Proteins - enzymes)
1828 Wohler --> synthesized a biological compound (urea) from ammonium cyanate (an inorganic chemical)! NH4⁺ NCO^-

1897 the Buchner brothers (Eduard and Hans) demonstrated that alcoholic fermentation could occur in a cell-free extract.

1926 J.B. Sumner demonstrated that an enzyme (urease) was a protein and could be crystallized (indicative of fixed molecular structure and purity)

set stage for Perutz and Kendrew's work on X-ray structure of myoglobin and hemoglobin

Nucleic acid polymers (DNA and RNA)

Another series of discoveries surrounding nucleic acids: Miescher; Mendel; Avery, McCarty, and McLeod; Watson and Crick; Hershey and Chase

Distinguishing Characteristics of Living Systems

a. They are complex, that is they are highly organized (cell - nucleus - chromosome - nucleosomes - DNA base pairs - bases). This organization has physical chemical implications.

b. They are capable of self-replication (biochemistry comes from genetics)

c. They can transform energy. Energy is required to create order (G = H -TS)

Implications of Chemistry for Biology

a. There is an underlying simplicity in the molecular organization of cells (similar proteins are found in E. coli and in humans).

b. All living forms have a "common ancestor" (evolution). Biochemists seek a "logical" molecular path upward.

c. Identity (phenotype) of organism is determined by its set of nucleic acids (genotype) and proteins (gene products) and the regulation of their expression (interaction with the environment).

d. There is a molecular economy in living systems; some molecules appear to have an advantage over many others and are used repeatedly (ATP).

Scope and importance of Biochemistry.

Biochemistry refers to the study of the various chemical processes that goes on inside the body of a living organism. A large number of students are opting for this branch of study because of the wide range of job opportunities that this subject presents.

Students can obtain PhD, M.Sc. and even degree certificates in this subject to get a successful career in Biochemistry. The students who have high marks in Plus II level and had Physics, Chemistry and Biology as their optional subjects can go for a degree course in Biochemistry.

A large number of colleges in India offer a B.Sc. degree in Biochemistry. The students who opt for Biochemistry as their main subject can choose subjects like Chemistry, Botany, Zoology and Industrial Microbiology as the subsidiary subjects. Some of the colleges even allow their students to study Biotechnology as the main subject and Biochemistry as the subsidiary subject. The students who have Zoology or Botany as their main subject can also select Biochemistry as their subsidiary subject for a course of B.Sc. degree.

The students can also go for a course in Biochemistry for their M.Sc., M.Phil or Ph.D. degree. The students who score high marks in their B.Sc. degree course in Biochemistry, Zoology, Botany, Biotechnology, etc. can opt for a M.Sc. in Biochemistry and only the students who score greater than 55% in their M.Sc. course can go for an M.Phil or Ph.D. programs that are offered at a limited number of colleges.

There are vast employment opportunities for the students of Biochemistry as they can be absorbed in a number of Research Institutions. They can also work as faculty in the colleges that offer a course in Biochemistry. The students of Biochemistry can also work as Scientists, research officers, research associates, chemical examiners, etc.Scope and importance of Biochemistry.

Bio chemistry

AU biochemistry syllabus..

BIOCHEMISTRY

Scope and importance of Biochemistry.

Carbohydrates: Classification, chemistry and properties of monosaccharides

(Ribose, Glucose, Fructose), disaccharides (maltose, lactose, sucrose) and

polysaccharides (homopolysaccharides and heteropolysaccharides). Metabolism of

carbohydrates : Glycolysis, TCA cycle, electron transport and oxidative

phosphorylation, HMP shunt pathway, Glycogenesis and Glycogenolysis.

Proteins and amino acids: Classification and properties of aminoacids and

proteins, peptide bond, chemical synthesis of peptides and Solid-phase peptide

synthesis. Structural organization of proteins: primary, secondary, tertiary and

quaternary structure of proteins, denaturation of proteins.

Lipids: Classification, structure and physiological functions of triglycerides,

fattyacids, phospholipids, cerebrosides, gangliosides and cholestrol. Digestion and

absorption of fats, biosynthesis and degradation of fattyacids and triglycerides.

Nucleic acids: Structure and properties of purines and pyrimidine bases,

nucleosides, nucleotides, cellular localization, isolation and estimation of nucleic

acids. Types of nucleicacids, double helical structure of DNA, types of RNA.

Biosynthesis and catabolism of purines and pyramidines.

Enzymes: Introduction, nomenclature and classification of enzymes, kinetic

properties of enzymes, factors affecting enzyme action, coenzymes. Enzyme

inhibition- competitive, non-competitive and uncompetitive inhibitions.

Porphyrins: Chemistry of haemoglobin and chlorophyll; syntheis of heme and

chlorophyll andheme catabolism.

Vitamins and harmones: definition, classification, chemistry, source, functions

and deficiency of vitamins. Out lines of harmones and their functions.

Text Books:

1. Fundamentals of Biochemistry – J.L.Jain, S.Chand & company Ltd, New

Delhi.

2. Principles of Biochemistry- Lehninger, Nelson and Cox

CBS Publications.

Overview and Brief History

Overview and Brief History of biotechnology

Biotechnology seems to be leading a sudden new biological revolution. It has brought us to the brink of a world of "engineered" products that are based in the natural world rather than on chemical and industrial processes.

Biotechnology has been described as "Janus-faced." This implies that there are two sides. On one, techniques allow DNA to be manipulated to move genes from one organism to another. On the other, it involves relatively new technologies whose consequences are untested and should be met with caution. The term "biotechnology" was coined in 1919 by Karl Ereky, an Hungarian engineer. At that time, the term meant all the lines of work by which products are produced from raw materials with the aid of living organisms. Ereky envisioned a biochemical age similar to the stone and iron ages.

A common misconception among teachers is the thought that biotechnology includes only DNA and genetic engineering. To keep students abreast of current knowledge, teachers sometimes have emphasized the techniques of DNA science as the "end-and-all" of biotechnology. This trend has also led to a misunderstanding in the general population. Biotechnology is NOT new. Man has been manipulating living things to solve problems and improve his way of life for millennia. Early agriculture concentrated on producing food. Plants and animals were selectively bred, and microorganisms were used to make food items such as beverages, cheese, and bread.

The late eighteenth century and the beginning of the nineteenth century saw the advent of vaccinations, crop rotation involving leguminous crops, and animal drawn machinery. The end of the nineteenth century was a milestone of biology. Microorganisms were discovered, Mendel's work on genetics was accomplished, and institutes for investigating fermentation and other microbial processes were established by Koch, Pasteur, and Lister.

Biotechnology at the beginning of the twentieth century began to bring industry and agriculture together. During World War I, fermentation processes were developed that produced acetone from starch and paint solvents for the rapidly growing automobile industry. Work in the 1930s was geared toward using surplus agricultural products to supply industry instead of imports or petrochemicals. The advent of World War II brought the manufacture of penicillin. The biotechnical focus moved to pharmaceuticals. The "cold war" years were dominated by work with microorganisms in preparation for biological warfare, as well as antibiotics and fermentation processes.

Biotechnology is currently being used in many areas including agriculture, bioremediation, food processing, and energy production. DNA fingerprinting is becoming a common practice in forensics. Similar techniques were used recently to identify the bones of the last Czar of Russia and several members of his family. Production of insulin and other medicines is accomplished through cloning of vectors that now carry the chosen gene. Immunoassays are used not only in medicine for drug level and pregnancy testing, but also by farmers to aid in detection of unsafe levels of pesticides, herbicides, and toxins on crops and in animal products. These assays also provide rapid field tests for industrial chemicals in ground water, sediment, and soil. In agriculture, genetic engineering is being used to produce plants that are resistant to insects, weeds, and plant diseases.

A current agricultural controversy involves the tomato. A recent article in the New Yorker magazine compared the discovery of the edible tomato that came about by early biotechnology with the new "Flavr-Savr" tomato brought about through modern techniques. In the very near future, you will be given the opportunity to bite into the Flavr-Savr tomato, the first food created by the use of recombinant DNA technology ever to go on sale.

What will you think as you raise the tomato to your mouth? Will you hesitate? This moment may be for you as it was for Robert Gibbon Johnson in 1820 on the steps of the courthouse in Salem, New Jersey. Prior to this moment, the tomato was widely believed to be poisonous. As a large crowd watched, Johnson consumed two tomatoes and changed forever the human-tomato relationship. Since that time, man has sought to produce the supermarket tomato with that "backyard flavor." Americans also want that tomato available year-round.

New biotechnological techniques have permitted scientists to manipulate desired traits. Prior to the advancement of the methods of recombinant DNA, scientists were limited to the techniques of their time - cross-pollination, selective breeding, pesticides, and herbicides. Today's biotechnology has its "roots" in chemistry, physics, and biology . The explosion in techniques has resulted in three major branches of biotechnology: genetic engineering, diagnostic techniques, and cell/tissue techniques.

Where Did Biotechnology Begin?

Bio technology begins....

With the Basics

Certain practices that we would now classify as applications of biotechnology have been in use since man's earliest days. Nearly 10,000 years ago, our ancestors were producing wine, beer, and bread by using fermentation, a natural process in which the biological activity of one-celled organisms plays a critical role.

In fermentation, microorganisms such as bacteria, yeasts, and molds are mixed with ingredients that provide them with food. As they digest this food, the organisms produce two critical by-products, carbon dioxide gas and alcohol.

In beer making, yeast cells break down starch and sugar (present in cereal grains) to form alcohol; the froth, or head, of the beer results from the carbon dioxide gas that the cells produce. In simple terms, the living cells rearrange chemical elements to form new products that they need to live and reproduce. By happy coincidence, in the process of doing so they help make a popular beverage.

Bread baking is also dependent on the action of yeast cells. The bread dough contains nutrients that these cells digest for their own sustenance. The digestion process generates alcohol (which contributes to that wonderful aroma of baking bread) and carbon dioxide gas (which makes the dough rise and forms the honeycomb texture of the baked loaf).

Discovery of the fermentation process allowed early peoples to produce foods by allowing live organisms to act on other ingredients. But our ancestors also found that, by manipulating the conditions under which the fermentation took place, they could improve both the quality and the yield of the ingredients themselves.

Crop Improvement

Although plant science is a relatively modern discipline, its fundamental techniques have been applied throughout human history. When early man went through the crucial transition from nomadic hunter to settled farmer, cultivated crops became vital for survival. These primitive farmers, although ignorant of the natural principles at work, found that they could increase the yield and improve the taste of crops by selecting seeds from particularly desirable plants.

Farmers long ago noted that they could improve each succeeding year's harvest by using seed from only the best plants of the current crop. Plants that, for example, gave the highest yield, stayed the healthiest during periods of drought or disease, or were easiest to harvest tended to produce future generations with these same characteristics. Through several years of careful seed selection, farmers could maintain and strengthen such desirable traits.

The possibilities for improving plants expanded as a result of Gregor Mendel's investigations in the mid-1860s of hereditary traits in peas. Once the genetic basis of heredity was understood, the benefits of cross-breeding, or hybridization, became apparent: plants with different desirable traits could be used to cultivate a later generation that combined these characteristics.

An understanding of the scientific principles behind fermentation and crop improvement practices has come only in the last hundred years. But the early, crude techniques, even without the benefit of sophisticated laboratories and automated equipment, were a true practice of biotechnology guiding natural processes to improve man's physical and economic well-being.

Harnessing Microbes for Health

Every student of chemistry knows the shape of a Buchner funnel, but they may be unaware that the distinguished German scientist it was named after made the vital discovery (in 1897) that enzymes extracted from yeast are effective in converting sugar into alcohol. Major outbreaks of disease in overcrowded industrial cities led eventually to the introduction, in the early years of the present century, of large-scale sewage purification systems based on microbial activity. By this time it had proved possible to generate certain key industrial chemicals (glycerol, acetone, and butanol) using bacteria.

Another major beneficial legacy of early 20th century biotechnology was the discovery by Alexander Fleming (in 1928) of penicillin, an antibiotic derived from the mold Penicillium. Large-scale production of penicillin was achieved in the 1940s. However, the revolution in understanding the chemical basis of cell function that stemmed from the post-war emergence of molecular biology was still to come. It was this exciting phase of bioscience that led to the recent explosive development of biotechnology.

What is Biotechnology?

what bio technology is ??/

Biotechnology in one form or another has flourished since prehistoric times. When the first human beings realized that they could plant their own crops and breed their own animals, they learned to use biotechnology. The discovery that fruit juices fermented into wine, or that milk could be converted into cheese or yogurt, or that beer could be made by fermenting solutions of malt and hops began the study of biotechnology. When the first bakers found that they could make a soft, spongy bread rather than a firm, thin cracker, they were acting as fledgling biotechnologists. The first animal breeders, realizing that different physical traits could be either magnified or lost by mating appropriate pairs of animals, engaged in the manipulations of biotechnology.

What then is biotechnology? The term brings to mind many different things. Some think of developing new types of animals. Others dream of almost unlimited sources of human therapeutic drugs. Still others envision the possibility of growing crops that are more nutritious and naturally pest-resistant to feed a rapidly growing world population. This question elicits almost as many first-thought responses as there are people to whom the question can be posed.

In its purest form, the term "biotechnology" refers to the use of living organisms or their products to modify human health and the human environment. Prehistoric biotechnologists did this as they used yeast cells to raise bread dough and to ferment alcoholic beverages, and bacterial cells to make cheeses and yogurts and as they bred their strong, productive animals to make even stronger and more productive offspring.

Throughout human history, we have learned a great deal about the different organisms that our ancestors used so effectively. The marked increase in our understanding of these organisms and their cell products gains us the ability to control the many functions of various cells and organisms. Using the techniques of gene splicing and recombinant DNA technology, we can now actually combine the genetic elements of two or more living cells. Functioning lengths of DNA can be taken from one organism and placed into the cells of another organism. As a result, for example, we can cause bacterial cells to produce human molecules. Cows can produce more milk for the same amount of feed. And we can synthesize therapeutic molecules that have never before existed.

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Tuesday, 7 December 2010

Pentose Phosphate Pathway

glycolysis

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Glucose + 2 ADP + 2 NAD⁺ + 2 P_i ——> 2 Pyruvate + 2 ATP + 2 NADH + 2 H⁺