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COVENANT UNIVERSITY ALPHA SEMESTER TUTORIAL KIT (VOL. 2) PROGRAMME: BIOCHEMISTRY 300 LEVEL DISCLAIMER The contents of this document are intended for practice and learning purposes at the undergraduate level. The materials are from different sources including the internet and the contributors do not in any way claim authorship or ownership of them. The materials are also not to be used for any commercial purpose. 1 LIST OF COURSES BCH311: Metabolism of Lipids BCH312: Enzymology BCH313: Metabolism of Amino Acids and Proteins BCH314: Analytical Biochemistry BCH315: Metabolism of Carbohydrates BCH316: Metabolism of Nucleic Acids BCH317: Food Biochemistry *Not included 2 BCH 311: METABOLISM OF LIPIDS (TUTORIAL QUESTIONS) Part 1 1. Explain the formation of lipid micelles, monolayers and bilayers. 2. 3. 4. 5. 6. Write on the similarities and differences in lipid micelles, monolayer and bilayers. Discuss the functions, structure and organization of biological membranes Describe the major classes of lipids, blood lipids and lipoproteins Write on lipoproteins and apolipoprotein and their implication on health and neurological conditions. Discuss the industrial and chemical applications of glyceraldehydes, Plasmalogens, sphingolipids, glycolipids, leucotrienes, prostaglandins, cerebrosides and thromboxanes. 7. 8. Write on the three (3) main families of lipids Draw the structures of cardiolipin, cholesterol, Phospholipids, Plasmalogens, sphingolipids, glycolipids, leucotrienes, prostaglandins and thromboxanes 9. Discuss the biosynthesis of phospholipids and sphingolipids Answers 1. Bilayer Spherical Micelle 3. Membrane fluidity: The interior of a lipid bilayer is normally highly fluid. In the liquid crystal state, hydrocarbon chains of phospholipids are disordered and in constant motion. At lower temperature, a membrane containing a single phospholipid type undergoes transition to a crystalline state in which fatty acid tails are fully extended, packing is highly ordered, & van der Waals interactions between adjacent chains are maximal. Kinks in fatty acid chains, due to cis double bonds, interfere with packing in the crystalline state, and lower the phase transition temperature. Cholesterol, an important constituent of cell membranes, has a rigid ring system and a short branched hydrocarbon tail HO Cholesterol 3 5. Lipoproteins differ in the ratio of protein to lipids, and in the particular apoproteins & lipids that they contain. They are classified based on their density: Chylomicron (largest; lowest in density due to high lipid/protein ratio; highest % weight triacylglycerols) VLDL (very low density lipoprotein; 2nd highest in triacylglycerols as % of weight) IDL (intermediate density lipoprotein) LDL (low density lipoprotein, highest in cholesteryl esters as % of weight) HDL (high density lipoprotein; highest in density due to high protein/lipid ratio) Apolipoprotein A-I (apoA-I) of human HDL, in the absence of lipid, is found consist of an Nterminal antiparallel 4-helix bundle and a C-terminal domain that is also a-helical a constituent of various lipoproteins, e.g. VLDL & HDL, a variant of apolipoprotein E, designated apoE4, is implicated in Alzheimer's disease and other neurological conditions. Having the apoE4 isoform is a major risk factor for Alzheimer's disease. Fragments of apoE4 are found to generate intracellular deposits resembling the neurofibrillary tangles seen in Alzheimer's disease. 8. cardiolipin - is an important inner mitochondrial membrane component = two PA’s esterified to 1 and 3 position of another glycerol. The only phosphoglyceride that is antigenic. plasmalogens - fatty acid at carbon 1 position is an ether instead of an ester linkage a) three classes - phosphatidalcholines, phosphatidal- ethanolamines, and phosphatidalserines b) myelin - has much ethanolamine plasmalogen c) heart muscle - has much choline plasmalogen d) platelet-activating factor (PAF) – strong biological mediator; causes platelet activation; increases pulmonary and airway edema in lungs; mediates hypersensitivity, acute inflammatory reactions, and anaphylactic shock; stimulates neutrophils and macrophages to produce superoxide radicals; binds to membrane receptors Sphingomyelins CH3 H3C + N O H2 C H2 C O CH3 P O O phosphocholine H2C sphingosine O fatty acid Sphingomyelin OH H C CH NH CH C R HC (CH2 )12 CH 4 1) backbone is sphingosine 2) fatty acid forms amide linkage with amino group of sphingosine = a ceramide (this is also a precursor for glycolipids) 3) esterification of carbon 1 of ceramide by phosphorylcholine = sphingomyelin important component of myelin in nerves function in membrane structure, anchoring proteins in the cell membrane, signal transduction across membranes, bile composition, lipoprotein particles 9. A cerebroside is a sphingolipid (ceramide) with a monosaccharide such as glucose or galactose as polar head group. A ganglioside is a ceramide with a polar head group that is a complex oligosaccharide, including the acidic sugar derivative sialic acid. 5 Cerebrosides and gangliosides, collectively called glycosphingolipids, are commonly found in the outer leaflet of the plasma membrane bilayer, with their sugar chains extending out from the cell surface CH2OH O OH H OH H H H OH O H H2C OH O cerebroside with -galactose head group H C CH NH CH C R HC (CH2 )12 CH3 Part 2 1. Mention the role of the following in digestion of lipids (a) Pancreatic lipases (b) Phospholipases (c) Cholesterol esterases. 2. (a) Describe the β- oxidation of (i) odd chain fatty acid (ii) unsaturated fatty acids (b) Write short notes on the biochemical role of the following (i) peroxisomal βoxidation (ii)α- oxidation (iii) ω- oxidation (iv) Regulation of ketogenesis (v)Release of fatty acids from adipose tissue. 3. What is the role of bile acids in lipid digestion? Mention two examples of bile salts. 4. How are lipids digested? 5. Mention the main classes of lipoproteins. 6. How are lipids transported? 7. What are ketone bodies? Mention the types of ketone bodies. ANSWERS 1. These enzymes play a role in the digestion of lipids in the small intestine, lipases break down triacylglycerols, phospholipases breakdown phospholipids while cholesterol esterases break down cholesterol esters. 3. Bile acids help to break lipids into small micelles thereby increasing the surface area available for lipases to act. 5. Chylomicrons, Very low density lipoproteins (VLDL), Intermediate density lipoproteins (IDL), Low density lipoproteins (LDL), High density lipoproteins (HDL). Ketone bodies are alternative sources of fuel Example s are acetone, acetoacetic acid and βhydroxylbutyrate Part 3 1. Describe the biosynthesis of fatty acid starting from acetyl coA 6 2. Write on the biosynthesis of a named saturated fatty acid 3. Describe the biosynthesis of a named unsaturated fatty acid 4. Describe the biosynthesis of a named essential fatty acid 5. Explain the cholesterol metabolism and the effect on health 7 BCH 312: ENZYMOLOGY (TUTORIAL QUESTIONS) 1. What are enzymes? What is the importance of enzymes for living beings? Enzymes are proteins that are catalysts of chemical reactions. Enzymes are catalysts that are non-consumable substances that reduce the activation energy necessary for a chemical reaction to occur. Enzymes are highly specific to the reactions they catalyze. They are of vital importance for life because most chemical reactions of the cells and tissues are catalyzed by enzymes. Without enzymatic action those reactions would not occur or would not happen in the required speed for the biological processes in which they participate. 2. What is meant by substrates of enzymatic reactions? Substrates are reagent molecules upon which enzymes act. The enzyme has spatial binding sites for the attachment of its substrate. These sites are called activation centers of the enzyme. Substrates bind to thesescenters forming the enzymesubstrate complex. 3. What are the main theoretical models that try to explain the formation of the enzyme-substrate complex? There are two main models that explain the formation of the enzyme-substrate complex: the lock and key model and the induced fit model. In the lock and key model the enzyme has a region with specific spatial conformation for the binding of the substrate. In the induced fit model the binding of the substrate induces a change in the spatial configuration of the enzyme for the substrate to fit. 4. On what structural level of the enzyme (primary, secondary, tertiary or quaternary) does the enzyme-substrate interaction depend? The substrate binds to the enzyme in the activation centers. These are specific three-dimensional sites and thus they depend on the protein tertiary and quaternary structures. The primary and secondary structures, however, condition the other structures and so they are equally important. 5. What is the activation center of an enzyme? Is it the key or the lock of the lock and key model? The activation center is a region of the enzyme produced by its spatial conformation to which the substrate binds. In the lock and key model the activation center is the lock and the substrate is the key. 6. What happens to a denatured enzyme regarding its functionality? How can that result be explained with the help of the lock and key model? 8 According to the lock and key model the enzyme functionality depends entirely on the integrity of the activation center, a molecular region with specific spatial characteristics. After the denaturation the spatial conformation of the protein is modified, the activation center is destroyed and the enzyme loses its catalytic activity. 7. What are the main factors that alter the speed of enzymatic reactions? The main factors that change the speed of enzymatic reactions are temperature, pH and substrate concentration (quantity). 8. What are enzyme cofactors? Some enzymes need other associated molecules to work. These moleculesare called enzyme cofactors and they can be, for example, organic ions like mineral salts, or organic molecules. Inactive enzymes which are not bound to their cofactors are called apoenzymes. Active enzymes bound to their cofactors are called holoenzymes. 9. What is the relationship between vitamins and enzyme cofactors? Many vitamins are enzyme cofactors that cannot be synthesized by the organism and must be obtained from the diet. 10. State five characteristics of enzymes • • • • • 11. 12. 13. 14. 15. They They type They They They are mostly proteins in nature are highly specific for the reactants or substrates they act on and catalyze only one of chemical reaction. increase reaction rates by decreasing the activation energy do not change or alter the equilibrium of the chemical reaction. are not changed by the reaction they catalyze. With a relevant example, discuss briefly on irreversible inhibition Using the steady state assumption, derive the mathematical expression in enzyme kinetics Write briefly on two factors that affect enzyme activity Differentiate the following parameters; Km, Kcat, Kspecificity Differentiate between uncompetitive inhibition and non competitive inhibition 9 BCH 313: METABOLISM OF AMINO ACIDS AND PROTEINS (TUTORIAL QUESTIONS) 1. Classify amino acids based on charge, polarity and side chains - Glycine is aliphatic, non polar and uncharged - Alanine is aliphatic, non polar and uncharged - Valine is aliphatic, non polar and uncharged - Leucine is aliphatic branched-chain, non polar and uncharged - Isoleucine is aliphatic branched-chain, non polar and uncharged - Proline is aliphatic , non polar and uncharged - Phenylalanine is aromatic, non polar and uncharged - Methionine is sulphur-containing, non polar and uncharged - Tryptophan is aromatic, non polar and uncharged - Tyrosine is aromatic, Polar and uncharged - Serine is hydroxy, Polar and uncharged - Threonine is hydroxyl, Polar and uncharged - Cystine is sulfur-containing, Polar and uncharged - Asparagine is amide, Polar and uncharged - Glutamine is amide, Polar and uncharged - Arginine is basic, Polar and positively charged - Histidine is basic, Polar and positively charged - Lycine is basic, Polar and positively charged - Glutamic acid is acidic, Polar and negatively charged - Aspartic acid is acidic, Polar and negatively charged 2. Draw the structures of two named examples of Aromatic amino acids 3. Draw the structures of two named examples of Basic amino acids 4. Draw the structures of two named examples of Acidic amino acids 10 5. Discuss the role of amino acids in protein structure determination and function Protein structure is generated by 4 levels of structure – primary, secondary, tertiary and quartenary. The four levels are generated by interactions between constituent amino acids Primary structure is the linear sequence of all the amino acids joined by peptide bonds between their free amino and carboxyl groups. Primary structure is determined by Peptide and disulfide bonds. Amino acid side chains (R groups) do not contribute. Secondary structure Involves local folding of the primary structure (polypeptide chain) into α-helix; ß-pleated sheets. Secondary structure is created by H- bonds formed b/w amino (H) and carboxyl (O) of peptide bonds and disulfide bonds. The amino Side chains (R groups) do not play any role in secondary structure Tertiary structure involves non-covalent interactions b/w side chain (R groups) that are far apart in the primary structure. Major Non-covalent interactions include H-bonds, ionic, van der waal, hydrophobic depending on the R group. Hydrophilic, polar and charged amino acids are usually located on the surface of protein. Hydrophobic , non polar uncharged amino acids are usually located within the protein. Charged, ionized amino acids are located on the surface and stabilized by water. Quaternary structure involves non- covalent interactions (ionic, H, hydrophobic) b/w R groups of amino acids on polypeptide chains 6. Describe the role of covalent and non covalent bonds in protein structure 7. Briefly explain the role of the ubiquitin/26S proteasome in degrading cellular proteins to amino acids? Proteins selected for degradation by the ubiquitin-proteasome mechanism are first covalently attached to ubiquitin, a small, globular protein. Ubiquitination of the target substrate occurs through linkage of the α-carboxyl glycine of ubiquitin to a lysine ε-amino group on the protein substrate by a three-step, enzyme-catalyzed process. The consecutive addition of ubiquitin moieties generates a polyubiquitin chain. Proteins tagged with ubiquitin are then recognized byproteasome. The proteasome cuts the target protein into fragments that are then further degraded to amino acids, which enter the amino acid pool. 8. Discuss the metabolism of creatine and Creatinine 9. Explain the regulation of Creatinine metabolism Formation of guanidinoacetate by AGAT is the rate limiting step of Creatinine biosynthesis. Control is by feedback repression of AGAT by Creatinine (i.e inhibition by end product). Other metabolites that can inhibit AGAT include cyclocreatine, Nacetimidoylsarcosine and N-ethyl-guanidinoacetate. Hormones such as growth, thyroxine and sex hormones regulate AGAT 10. With the aid of a well labelled diagram, describe the urea cycle 11 11. Describe three main steps which nitrogen gets removed from circulation. Where is the nitrogen taken? Nitrogen is taken to the liver by three main ways. 1. Transamination: amino group transferred to alpha-ketogluterate to make glutamate. In muscle, N --> alanine Normally low [ECF] but damage to tissue will make [transferases] increase 2. Oxidative de-amination (Glutamate Dehydrogenase). Amino group released as ammonia from glutamate in liver and kidney producing alpha-ketogluterate 3. Transport of ammonia to the liver. Pyruvate is made into alanine (ammonia cannot transport itself). 12. Differentiate glucogenic versus ketogenic amino acids 13. . Name the amino acids that are both Glucogenic and Ketogenic Isoleucine Phenylalanine Threonine Tryptophan Tyrosine 14. Which Glucogenic amino acids are precursors for Pyruvate? 15. Which Ketogenic amino acid are precursors for Acetoacetate? Phenylalanine Phenylalanine Tyrosine 16. How do amino acids enter and leave the amino acid pool? 17. Discuss the toxicity of ammonia. Every amino acid contains at least one amino group. Therefore every amino acid degradation pathway has a key step where the amino group is removed. In short amino acid catabolism generates ammonia. Brain tissue is very sensitive to ammonia. Ammonia intoxication produces a comatose state. Cells get rid of excess ammonia by the reductive amination of α−ketoglutarate to form glutamate by glutamate dehydrogenase and the conversion of glutamate into glutamine by glutamine synthetase. Both of these enzymes are found in high concentrations in the brain. A high concentration of ammonia shifts the equilibrium of these two reactions towards glutamine. Glutamine synthetase use ATP to activate glutamate for amination to form glutamine. The result is high concentrations of ammonia deplete cells of 12 ATP. ATP is essential for brain function. (Increased synthesis of glutamate from αketoglutarate leads to α-ketoglutarate depletion in CNS cells, resulting in TCA cycle inhibition and ATP decrease.) α-Ketoglutarate + NH4+ + NAD(P)H ⇆ Glutamate + NAD(P)+ Glutamate + NH4+ +ATP ⇆ Glutamine + ADP + Pi Glutamate is a neurotransmitter. Glutamate is also the precursor for γ-aminobutyrate (GABA) which is another important neurotransmitter. High concentrations of ammonia deplete the concentration of glutamate which produces a similar decrease of GABA which impairs brain function. 18. Which one of the following compounds does not supply atoms for the synthesis of the purine ring system? 19. What is the role of folate in the synthesis of biomolecules Tetrahydrofolate (THF) functions as co-enzyme that transfer C-1 units in amino acids and biomolecules synthesis. Most reactions require NADPH/NADH, they maintain redox status and the substrates for methylation reactions 20. Describe the synthesis of alanine and aspartate showing the starting materials and the enzymes involved 13 DEPARTMENT OF BIOLOGICAL SCIENCES BCH 314: ANALYTICAL BIOCHEMISTRY (TUTORIAL QUESTIONS) 1. Discuss exhaustively the mechanical property of fluids that confers on them the tendency to resist flow. 2. Using a standard viscometric technique and instrumentation, analyze the viscosity of engine oil. 3. Describe how you would analyze the sample in an Eppendorf tube containing DNA fragments that have been digested with restriction enzymes. 4. Explore the theory of electrophoresis and extensively discuss the preferred analytical technique for the separation of Escherichia coli proteins. 5. Discuss the underlying principle of chromatography. 6. Explore all available terms in chromatography and discuss ten different types of application of this method in separating components of samples. 7. In the process of DNA double helix elucidation, Rosalind Franklin and Maurice Wilkins employed a technique to analyze DNA fibers that gave a clue to end result used by Watson and Crick. What is this powerful method and discuss this extensively. 8. Review the underlying principle of X-ray diffraction and discuss five application of the method. 9. Define isotopy and relate this to radiolabeling. 10. Present in detail five research experiments that employed techniques of radiolabeling in the process of structural elucidation in biosystems. 14 BCH 315: METABOLISM OF CARBOHYDRATES (TUTORIAL QUESTIONS) Part 1 1. Write on the importance of uronic acids 2. Write extensively on the different classes of carbohydrates. 3. Discuss the chemistry and reactions involved in the degradation of the following i. Disaccharides ii. oligosaccharides iii. storage polysaccharides 4. Succinctly describe how dietary fibers help in the management of diseases 5. Structural polysaccharides are the most abundant carbohydrates on earth. Write on the structure, function and applications of any five (5) in this group. 6. Give two (2) examples of oligosaccharides found in legumes and cereals 7. 8. 9. 10. 11. Example of sugar alcohol prepared commercially to make diabetic soft drink is ……. Manitol and ducitol are alcohols derived from ---- and ---Give two (2) examples of complex carbohydrates What are dietary fibers? Give examples Describe fully the Glycolytic pathway and tricarboxylic acid (TCA) cycle 12. Explain the Electron transport and oxidative phosphorylation 13. Describe the following pathways in full a) Glyoxylate cycle b) phosphogluconate c) ascorbic acid d) glucuronate Answers 1. URONIC ACIDS – formed when terminal CH2OH group of a mono sugar is oxidised – Important acids in animals – D-glucuronic acid and its epimer L-iduronic acid – In liver cells glucuronic acid combines with steroids, certain drugs, and bilirubin to improve water solubility therby helping the removal of waste products from the body – These acids are abundant in the connective tissue carbohydrate components. 2. Monosaccharides are colorless, crystalline solids, soluble in water but insoluble in nonpolar solvents. One of the carbon atoms is double-bonded to an oxygen atom to form a carbonyl group; each of the other carbon atoms has a hydroxyl group. Carbohydrates with an aldehyde (-CHO) functional group are called aldoses e.g. glyceraldehyde (CH2OH-CHOH-CHO). Those with a keto group (-C=O) are ketoses e.g.dihydroxyacetone (CH2OH-C=O-CH2OH) . They are classified according to the number of carbon atoms they contain 15 Dissacharides LACTOSE Lactose: (milk sugar) disaccharide found in milk; composed of one molecule of galactose and glucose linked through beta(1,4) glycosidic linkage; because of the hemiacetal group of the glucose component, lactose is a reducing sugar common table sugar: cane sugar or beet sugar produced in the leaves and stems of plants; it is a disaccharide containing both alfa-glucose and beta-fructose residues linked by alfa,beta(1,2)glycosidic bond. Oligosaccharides are small polymers often found attached to polypeptides in glycoproteins and some glycolipids. 16 Glycolysis glucose Glycolysis ATP Hexokinase ADP glucose-6-phosphate Phosphoglucose Isomerase fructose-6-phosphate ATP Phosphofructokinase ADP fructose-1,6-bisphosphate Aldolase glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate Triosephosphate Isomerase Glycolysis continued glyceraldehyde-3-phosphate NAD+ + Pi Glyceraldehyde-3-phosphate + Dehydrogenase NADH + H 1,3-bisphosphoglycerate ADP Phosphoglycerate Kinase ATP 3-phosphoglycerate Phosphoglycerate Mutase 2-phosphoglycerate Enolase H2O phosphoenolpyruvate ADP Pyruvate Kinase ATP pyruvate 17 The pentose phosphate pathway. The Nonoxidative Steps of the Pentose Phosphate Pathway Four Ways to Combine the Reactions of Glycolysis and Pentose Phosphate Vitamin C is also a highly effective antioxidant - it can absorb free oxygen radicals. Even in small amounts vitamin C can protect indispensable molecules in the body, such as proteins, lipids, carbohydrates, and nucleic acids (DNA and RNA) from damage by free radicals 18 Part 2 1. With the aid of a diagrammatic illustration, describe the gluconeogenesis pathway. 2. Discuss gluconeogenesis. 3. Discuss photosynthesis. 4. Discuss how CAM and C4 plants prevent photorespiration. 5. Using a diagrammatic illustration, explain the pathways involved in glycogen metabolism. 6. How is carbohydrate metabolism regulated? Discuss elaborately. 7. Write short essays on any FOUR (4) disorders of carbohydrate metabolism. 19 BCH 316: METABOLISM OF NUCLEIC ACIDS (TUTORIAL QUESTIONS) 1. Discuss in detail the double helical structure of eukaryotic genetic material according Watson and Crick’s model; highlighting the specific nucleotides that comprise the molecular structure. 2. Describe all available methods for isolating DNA OR RNA 3. Discuss two (2) metabolic disorders each of purine and pyrimidine catabolism. 4. Critically review the regulation of nucleic acids metabolism with specific highlight on structure and mechanism of the regulatory enzymes. 5. Discuss in detail the complete degradation of purine nucleotides with special highlights on specific end products in diverse classes of animals. 6. No DNA, no protein. Justify and/or argue this statement. 7. Compare and contrast de novo biosynthesis of purine nucleotides in rat liver hepatocytes and Escherichia coli. 8. How are thymidylate and cytidylate synthesized in biological systems? Eplore both de novo and salvage pathways. 9. Critically review the structure and activity of the Aspartate transcarbamoylase (ATCase). 10. Discuss the importance of phosphoribosyl transferases (PRTs) in both de novo and salvage pathways of nucleotides anabolism. 11. Lesch nyhan syndrome: Discuss its cause, consequence and containment. 12. Discuss the catabolism of purine nucleotides in a bony fish. 13. Differentiate between DNA degradation and denaturation. 14. What is Gout? 15. Discuss a clinical anomaly associated with pyrimidine biosynthesis. 16. How is purine nucleotide biosynthesis regulated? 17. How is pyrimidine nucleotide biosynthesis regulated? 20 18. Write briefly on severe combined immunodeficiency syndrome. 19. How does the cell regulate the synthesis of deoxyribonucleotides? 20. State the source, type, and function of five nucleases 21 DEPARTMENT OF BIOLOGICAL SCIENCES BCH 317: FOOD BIOCHEMISTRY (TUTORIAL QUESTIONS) 1. Storage can be defined as …………. The art of keeping the quality of agricultural materials and preventing them from deterioration for specific period of time, beyond their normal shelf life 2. The term shelf-life meant …………………… The minimum period for a product to be stored optimally 3. Spoilage is any loss in ………. as well as ……………….. of products. Quantity and quality 4. a. b. c. d. e. Suggest the various classes of foods Grains/Cereals/ pulses Fruits/ vegetables Beverages e.g coffee, cocao Oil seeds Root & Tuber crops 5. The art of keeping the quality of stored products without appreciable deteriorations for up to 12 months is referred to as ……………. Medium term storage 6. List the various ways of drying. a. b. c. d. e. Conventional drying Vacuum drying Osmotic drying Solar drying Fossil fuel drying 22