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Dr. Akepati S. Reddy School of Energy and Environment Thapar University Patiala (PUNJAB) 147001 INDIA
Metabolic Diversity
1. Chemoheterotrophs: Energy source: Organic compounds. Carbon source: Organic compounds.
Examples: Most bacteria, all protozoans, all fungi, and all animals.
2. Chemoautotrophs: Energy source: Inorganic compounds (H2S, NH3, S, H2, Fe2+, etc.) Carbon source: Carbon dioxide.
Examples: Iron, sulfur, hydrogen, and nitrifying bacteria.
Metabolism
Refers to the thousands of chemical reactions occurring in living organisms and characteristic of all organisms except viruses Subdivided into catabolism and anabolism Anabolism process of biosynthesis of complex organic molecules & structures from simpler ones involves consumption of energy often involve dehydration synthesis Catabolism degradative chemical process involves break down of larger molecules into smaller ones involves release energy often involve hydrolysis processes Catabolic reactions provide the energy needed for driving anabolic reactions energy from catabolic reactions is stored as ATP and used to drive anabolic reactions catabolic reactions are often coupled to ATP synthesis while anabolic reactions to ATP hydrolysis anabolic catabolic reactions are linked by ATP Metabolic pathways Highly evolved intracellular series of metabolic reactions, each catalyzed by enzymes may be linear, branched or cyclic (starting molecule is generated at the end of the pathway to initiate another turn of the cycle)
Bioenergetics
Enzymes
Enzymes are proteins with molecular weight ranging from a few thousands to over one million daltons Some enzymes (conjugated enzymes or holo-enzymes) contain non-protein part (cofactor) Cofactors can be organic molecules (coenzymes) or an inorganic molecules Enzyme cofactors may have metal ions (iron, magnesium, copper, manganese, zinc, cobalt, magnesium, calcium, etc.) Coenzymes are generally carriers of other molecules or ions Some of the coenzymes are derived from vitamins (NAD and NADP from niacin, FAD from riboflavin, coenzyme A from pantothenic acid) Enzyme naming Many enzymes are named by adding suffix ase substrate name (sucrase) or reaction taking place (dehydrogenase and phosphotase) or the group to which the enzyme belongs procedes the suffix some enzymes have traditional names
Enzymes (contd..)
Enzymes can be grouped on the basis of the type reactions they catalyse (oxidoreductases, hydrolases, ligases, etc.) Enzymes can be divided into the following classes Oxidoreductases Transferases (functional groups are transferred) Hydrolases (breaking bodns by adding water) Lyases (remove groups of atmos without hydrolysis) Isomerases (rearrange atmos within a molecule) Ligases (joins two molecules ATP hydrolysis provides the energy needed) Catalyze chemical reactions of metabolism Speed up the reactions upto 10 billion times Turnover number of substrate molecules range is 1 50,000/sec. Speeds up the reactions through decreasing the energy of activation without increasing temperature and pressure Temperature, pressure, substrate concentration, pH and several other factors influence the enzyme activity or reaction rate
Enzymes (contd..)
Enzyme specificity Can be best explained by Lock and Key theory Can be substrate specific (lypase for lipids, urease for urea, protease for proteins and sucrase for sucrose) Can be specific in terms of the products into which the accepted substrates are converted Substrates are molecules entering the enzymatically catalyzed reactions Products are what the substrates are enzymatically converted into Enzyme activity Enzymes have 3-D structure and one or more active sites where chemical reactions occur 3-D structure is essential for the enzyme activity Denaturation that usually involve breakage of hydrogen bonds and other non-covalent bonds results in loss of 3-D structure Excessive heat and excessive pH can cause denaturation and loss of 3-D structure Susceptible to chemical and physical changes (many chemicals destroy enzymes)
Enzymes (contd..)
Many inhibitors affect enzyme activity Competitive inhibition inhibitor competes for the active sites on enzyme with the substrate Non-competitive inhibition inhibitor binds to an allosteric site and alters the active site configuration of the enzyme Feedback inhibition enzyme activity is inhibited by the end product (A enzyme-1 B enzyme-2 C enzyme-3 D) here enzyme-1 may be inhibited by product D Feedback inhibition regulates ATP, amino acid, numcleotide and vitamin synthesis Mechanism of enzyme action Substrate specifically binds to the active site on the surface of the enzyme and as a consequence enzyme-substrate complex is formed can result in change of structure of the enzyme Substrate is transformed into product by Rearrangement of existing atoms Breakdown of substrate molecules Combining with other substrate molecules Resultant products do not fit the active site and thus are released and the enzyme site becomes free for complexing with other substrate molecules
Factors that Affect Enzyme Activity: pH, Temperature, and Substrate Concentration
Competitive inhibitor: inhibitor binds to the active site and obstruct access of substrate to the active site Non-competitive inhibitor (by regulatory molecule): temporarily changes enzyme and alters its relative affinity for the substrate Non-competitive inhibitor (by enzyme poison): permanently changes enzyme and renders it non-functional
Oxidation-Reduction (Redox)
Catabolism
Aerobic and anaerobic respiration and fermentation
Aerobic respiration
includes glycolysis, transition reaction, Krebs cycle and electron transport system oxygen is electron acceptor
Anaerobic respiration
includes glycolysis, transition reaction, Krebs cycle and electron transport system not oxygen but nitrate or sulfate or carbon dioxide is electron acceptor
Fermentation
Oxygen not required Krebs cycle and electron transport system are missing Pyruvic acid or derivatives of pyruvic acid oxidize the NADH+H to form fermentation end products
Catabolism (contd..)
Catabolism of carbohydrates
Maltose glucose glycolysis Sucrose glucose and fructose both into glycolysis Lactose glucose and galactose galactose into a compound of glycolysis through a series of transformations Starch glucose - glycolysis
Catabolism of proteins amino acids into compounds of glycolysis and krebs cycle through deamination
deamination of alanine produce pyruvic acid Deamination of aspartic acid produces oxaloacetic acid Deamination of glutamic acid produces alphaketoglutaric acid
Catabolism of fats
Fats glycerol and fatty acids glycerol to dihydroxyacetone phosphate (glycolysis) Fatty acids beta oxidation into acetyle CoA krebs cycle
Anabolism: Photosynthesis
Photoelectric effect (forcing electrons out from materials) and pigments Particle properties of light cause it Each substance has critical wavelength (maximum wavelength of light that creates photoelectric effect) Pigment is any substance that absorbs light
every pigment has a characteristic light absorption spectrum color of the pigment is from the non-absorption but reflection of a specific wavelength light (in the visible region) by it
A process by which plants, some bacteria and some protists use light energy to produce sugar is photosynthesis Also occurs in microorganisms having pigments (purple and green sulfur bacteria, cyanobacteria and algae) Activities of green pigment (chlorophyll) are responsible and water and carbon dioxide are used and oxygen is released Includes two phases use of light energy to synthesize ATP and NADPH (energy fixing or light reactions) use these energy molecules to formulate carbohydrate molecules (carbon fixing or dark reactions)
Purple sulfur bacteria uses compounds like hydrogen sulfide in place of water and emits elemental sulfur In some eukaryotes and primitive photosynthetic bacteria cyclic photophosphorilation occurs and has only photosystem-1
Only ATP can be synthesized by this Occurs when additional ATP is required or when there is no NADP+, cyclic electron flow occurs
In halobacteria (facultative aerobes) there is bacteriorhodopsin (a complex of purple pigment and membrane protein) which is also capable of ATPsynthesis
In halobacteria (facultative aerobes) there is bacteriorhodopsin (a complex of purple pigment and membrane protein) which is also capable of ATP synthesis Photoautotrophs using H2S in place of water and releasing sulfur in place of oxygen Phtoheterotrophs using organic carbon in place of carbon dioxide Chemolithoautotrophs using the bond energy of inorganic compounds in place of light energy
Remaining carbon skeletons enter carbohydrate metabolic pathways Generation of energy from carbon skeletons from amino acid degradation. Genetic disorders resulting from defects in amino acid metabolism. Amino acids can serve as precusor for many other biologically important and active compounds.
Sequence of steps involved are 1. Binding of Acetyl CoA to cys site and Malonyl CoA to pant site of the enzyme complex 2. Condensation reaction involving decarboxilation of malonyl moity and attachment of the moity present on the cys site to the moity present on the pant site 3. Reduction of ketone group of the chain into hydroxyl group, dehydration to yield transient double bond and reduction of the resultant double bond to obtain saturated chain 4. Transfer of the growing saturated chain from pant site to cys site 5. Binding of malonyl CoA on pant site of the enzyme complex continuation from step-3 (loop of steps 2 to 5) 6. Release of the saturated fatty acid from the pant site once the length reaches 16-C