- •Federal Agency of Education tambov state university named after g.R. Derzhavin
- •Biochemistry (part I)
- •Tambov 2012
- •I. Theoretical part The subject Of biological chemistry
- •1. Chemistry of proteins
- •1.1. Methods of exctraction and purification of proteins
- •1.2. Functions of proteins
- •1.3. Amino-acid composition of proteins
- •1.4. The structural organization of proteins
- •1.5. Physical and chemical properties of proteins
- •1.6. Classification of proteins
- •1.6.1. Simple proteins
- •1. Albumins and globulins.
- •2. Protamines and histones.
- •3. Prolamins and glutelins.
- •1.6.2. Conjugative proteins
- •1. Proteins containing non-heme iron.
- •Nucleic acids
- •The structure of nucleic acids
- •Test Questions
- •2. Enzymes
- •2.1. The chemical nature of enzymes
- •2.2. The mechanism of enzymes action
- •2.3. Kinetics of enzymatic reactions
- •2.4. Enzyme properties
- •2.5. Regulation of enzyme activity
- •1. Control of the enzyme amount.
- •2. Control of enzyme activity.
- •2.1. The influence of activators and inhibitors on the enzymes.
- •2.3. Chemical modification of the enzyme.
- •2.4. Allosteric regulation.
- •2.6. Classification and nomenclature of enzymes
- •2.7. Enzymes in medicine
- •Test Questions
- •3. Vitamins
- •3.1. Fat soluble vitamins
- •3.2. Water soluble vitamins
- •Vitamin-like substances
- •Test Questions
- •4. Basic principles of biomembranes’ organisation
- •4.1. Structure and functions of membranes
- •1. Phospholipids (90%) - glycerophospholipids and sphingophospholipids:
- •4.2. Transport of substances across membranes
- •2. Facilitated diffusion
- •Test Questions
- •5. Transmembrane transduction of the hormonal signal
- •Test Questions
- •6. Introduction to metabolism
- •6.1. Stages of catabolism
- •III. A common catabolic pathway.
- •6.2. Bioenergetics
- •6.3. Organization and operation of the respiratory chain
- •6.4. Uncoupling of oxidation from phosphorylation
- •6.5. Generation of free radicals in cells
- •6.6. Reactions of the common catabolic pathway
- •6.6.1. Oxidative decarboxylation of pyruvate
- •6.6.2. Citric acid cycle
- •7. Carbohydrate metabolism
- •7.1. Digestion of carbohydrates
- •7.2. Glycogen metabolism
- •7.3. Glycolysis
- •7.4. The inclusion of fructose and galactose
- •In glycolysis
- •7.5. The shuttle mechanisms
- •7.6. Cori cycle
- •7.7. Alcoholic fermentation
- •C6h12o6 → 2 ch3chohcooh
- •7.8. Pentose phosphate pathway (hexose monophosphate shunt)
- •7.9. Gluconeogenesis
- •Synthesis of glucose from the pyruvic acid.
- •Fructose bisphosphatase
- •Glucose-6-phosphatase
- •7.10. Regulation of carbohydrate metabolism
- •Glucose → glucose-6-phosphate.
- •Pyruvate → oxaloacetate → phosphoenolpyruvate
- •7.11. Violations of carbohydrate metabolism
- •Violation of hydrolysis and absorption of carbohydrates
- •Violations of the intermediate metabolism of carbohydrates
- •Quiz Questions
- •II. Laboratory practice Laboratory work 1. The analysis of amino acids and proteins
- •1. Qualitative analysis of amino acid mixtures by thing layer chromatography method.
- •2. Colour reaction of proteins.
- •2.1. Millon’s reaction.
- •2.2. Ninhydrin’s reaction.
- •3. Reactions of precipitation of proteins.
- •3.1. Precipitation of proteins with salts of heavy metals.
- •3.3. Precipitation of proteins with the help of concentrated mineral acids.
- •3.4. Precipitation of proteins by organic acids.
- •Test questions
- •Laboratory work 2. Conjugated proteins: glycoproteins and phosphoproteins
- •1. Phosphoproteins.
- •1.1. Proof of protein component’s present in the casein hydrolyzate.
- •1.2. Proof of phosphoric acid’s presence in the casein hydrolyzate.
- •1.3. Determination of the isoelectric point of casein.
- •2.4. Proof of carbohydrate’s presence in the egg albumin.
- •Test questions
- •Laboratory work 3. Conjugated proteins: nucleoproteins and chromoproteins
- •1. Nucleoproteins
- •1.1. Isolation of deoxyribonucleoproteins from the spleen.
- •1.2. Reaction with diphenylamine.
- •2. Chromoproteins.
- •2.1. Benzidine test for hemin group of hemoglobin.
- •Test questions
- •Laboratory work 4. Enzymes
- •1. Detection of peroxidase in potatoes.
- •2. Detection of pepsin in the gastric juice.
- •3. Hydrolysis of starch by α-amylase.
- •4. Specificity of amylase and sucrase enzymes action.
- •Test questions
- •Laboratory work 5. Identifying the activity of enzymes
- •1. The influence of activators and inhibitors upon activity of enzymes.
- •1. The influence of activators and inhibitors upon α-amylase.
- •1.2. Inhibitory effect of chloride ions on dehydrogenase complex of potatoes.
- •2. Identifying the activity of α-amylase according to Wolgemut.
- •Test questions
- •Inhibitor calimine
- •Laboratory work 6. Vitamins
- •Vitamin a (vitamin a, retinol)
- •Vitamin d (calciferol)
- •3.1. Reaction with concentrated nitric acid.
- •3.2. Reaction with ferric chloride (III).
- •9.2. Reaction with methylene-blue.
- •Test questions
- •Laboratory work 7. Oxidoreductases. Common catabolic pathway
- •1. Comparison of redox-potentials of riboflavin and methylene blue.
- •2. Identifying of catalase activity according to a.N. Bach and а.I. Oparin.
- •Test questions
- •Laboratory work 8. Carbohydrate metabolism
- •2.1. Trommer’s test with copper hydroxide.
- •2.2. Discovery of fructosuria by Selivanov’s test.
- •2.3. Enzymatic method of semi-quantitative identification of glucose in urine with the help of "GlucoPhan" test strip.
- •Test questions
- •References
III. A common catabolic pathway.
Acetyl-CoA undergoes oxidation in the cycle of di- and tricarboxylic acids (Krebs cycle). Oxidation is accompanied by the formation of reduced forms of NADH + H+ and FADH2. These are the primary donors of hydrogen for the electron transport chain. Reactions of the common catabolic pathway occur in the matrix of mitochondria. Reduced coenzymes transfer hydrogen directly to the components of the respiratory chain which are located in the inner membrane of mitochondria, where ATP is produced. There is a transfer of electrons from reduced nucleotides to oxygen (through the respiratory chain). It is accompanied by the formation of water. This electron transport is associated with ATP synthesis during oxidative phosphorylation. At this stage, 2/3 energy of nutrients are released.
Thus, after the formation of pyruvic acid further path of breakdown of substances to CO2 and H2O occurs identically in the common catabolic pathway.
Metabolites of the common catabolic pathway are precursors in the synthesis of a number of substances in the body. For example, pyruvate is a precursor for glucose and acetyl-CoA is a precursor for fatty acids.
6.2. Bioenergetics
Metabolism is divided into two categories: catabolism and anabolism. One of the main functions of catabolism is receiving chemical energy contained in nutrients and the usage of this energy to provide necessary functions.
The energy of oxidized substances is used mainly for the synthesis of ATP from ADP. ATP is the universal source of energy in the body.
If the energy released during the hydrolysis reaction of the substance, exceeds 30 kJ/mole, the hydrolysable bond is called a high-energy (energy-rich) bond. The energy of ATP hydrolysis is about 50 kJ/mole. In formula the energy-rich bond is denoted by ~ (tilde).
Types of energy-rich compounds: pyrophosphates (ATP), phosphoguanidines (creatine phosphate), acyl phosphate (1,3 bisphosphoglycerate), enol phosphates (phosphoenol pyruvate), thiol esters (acetyl-CoA).
Cell energy supply can occur in anaerobic conditions:
C6H12O6 = 2 C3H6O3 + 65 kJ/mole
One way of ATP synthesis from ADP is substrate level phosphorylation. It is ATP formation at the expense of other high-energy compound:
1,3-bisphosphoglycerate 3-phosphoglycerate
The use of oxygen by cells opens the possibility for a more complete Tissue respiration is a set of oxidation reactions of substrates in living cells, accompanied by the consumption of molecular oxygen and leading to the releasing of carbon dioxide and water and formation of biological energy.
For the first time the essence of breath was explained by Antoine Laurent Lavoisier (1777); he drew attention to the similarity between the combustion of organic substances outside the body and the respiration of animals. In the body, oxidation occurs at relatively low temperature in the presence of water, and its velocity is regulated by metabolism.
Let’s consider the reaction of glucose oxidation:
In the body, this process is multistage. Carbon is converted into carbon dioxide by the oxygen of the oxidized substance and the oxygen of water. This reaction involves hydrogen acceptors, which carry hydrogen on oxygen. Oxygen is used for the synthesis of water from the hydrogen of oxidized substrates.
The other substances are oxidized in the same way. Kidneys, brain, liver are characterized by the highest rate of tissue respiration; and the skin, muscles (at rest) - the smallest one.
The main way of ATP synthesis from ADP is oxidative phosphorylation. This is the synthesis of ATP from ADP and inorganic phosphate, which occurs due to the energy released by oxidation of organic substances in the process of cellular respiration. It is coupling of respiration and phosphorylation.
ADP + H3PO4 + energy ATP + H2O
