- •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
6.4. Uncoupling of oxidation from phosphorylation
Uncouplers are lipophilic substances that can accept protons, and carry them through the inner mitochondrial membrane, but not passing its proton channel.
Natural uncouplers are products of peroxidation of lipid, fatty acids with a long chain, and high doses of thyroid hormones.
Artificial uncouplers are dinitrophenol, ether, derivatives of vitamin K, anesthetics, antibiotics (gramicidin, valinomycin)
Consider the example of uncoupling mechanism in dinitrophenol. It easily diffuses across the mitochondrial membrane in both ionized and a non-ionized forms and can carry hydrogen ions across the membrane. Therefore, 2,4-dinitrophenol destroys ΔpH of mitochondrial membrane. Oxygen consumption and substrate oxidation are continuing, but ATP synthesis is impossible. Since the energy of oxidation in uncoupling is dissipated in the form of heat, the uncouplers increase body temperature (pyrogenic action).
There is a particular tissue, specialized in heat production by uncoupling of respiration from oxidative phosphorylation. This is brown adipose tissue. It has such name because of a large number of mitochondria (they are brown). About 10% of all proteins of these mitochondria accounts for the so-called uncoupling protein. Brown adipose tissue is involved in maintaining body temperature.
Biological oxidation which is not accompanied with the storage of energy is called the free (uncoupling) oxidation. It accounts for 5-10% of oxygen entering the body. It is out of mitochondria, mostly in the endoplasmic reticulum, so sometimes this process is called microsomal oxidation (microsomes are fragments of ER).
One of the functions of free oxidation is transformation of natural or unnatural substrates, called xenobiotics.
Free oxidation takes place with the participation of oxygenases. Oxygenases are enzymes of oxidoreductases class; they catalyze the oxidation of substrates by including one oxygen atom (monooxygenases) or two oxygen atoms (dioxygenases) in their molecules.
Oxygenases work in the multienzymatic complex, embedded in the membrane. Multienzymatic complex consists of 3 components: flavin dehydrogenases, iron-sulfur protein, cytochrome P450.
Cytochrome P450 is a group of enzymes related to hemoproteins. Cytochrome P450 system participates in the oxidation of both endogenous (steroids, bile acids, unsaturated fatty acids) and exogenous substances which are called xenobiotics (xeno - incompatible, bios - life), for example, medicines, poisons and drugs.
Oxygen and reduced respiratory carriers (usually NADPH) are also involved in reactions of free oxidation. Cytochrome P-450 is an electron acceptor.
RH + O2 + NADPH + H+ ROH + NADP+ + H2O
Hydroxylation of xenobiotic makes it more soluble, facilitates the following destruction and elimination from the body.
6.5. Generation of free radicals in cells
Reactive oxygen species (ROS) are compounds in which oxygen has an unpaired electron.
ROS are formed in the following cases: when the conditions of the respiratory chain action are changed (e.g., during hypoxia); under UV rays; during the interaction of oxygen with metal ions of variable valence (iron); during the spontaneous oxidation of some substances; during the participation of the enzymes xanthine oxidase or NADPH oxidase. Under these conditions, a superoxide anion of oxygen О2 is formed, then hydrogen peroxide Н2О2 and hydroxyl radical HO. Reactive oxygen species are causing lipid peroxidation. It is a process leading to severe damage of membranes, proteins and DNA damage.
Inactivation of reactive oxygen species in cells is under the influence of the antioxidant system. It consists of several antioxidant enzymes and low molecular antioxidants (vitamin C, glutathione, vitamin E, etc.).
Superoxide dismutase (SOD) converts superoxide anion of oxygen into hydrogen peroxide Н2О2:
2 O2-.+ 2Н+ H2O2 + O2.
Catalase is hemin enzyme, containing Fe3+. It catalyzes the reaction of hydrogen peroxide splitting. In this reaction water and oxygen are formed:
2 H2O2 O2 + 2H2О.
The highest catalase activity in the body is typical of the liver. There is a lot of catalase in erythrocytes. There it protects the heme of hemoglobin from oxidation.
Peroxidase is hemin enzyme which reduces hydrogen peroxide to water, while another substance is oxidized.
2 H2O2 2H2О + RO2.
Peroxidase is able to split other peroxides, converting them to alcohols. Peroxidase activity is found in the liver, kidneys, and neutrophilic leukocytes.
Antioxidants are biologically active substances that interact with free radicals and prevent the process of free radical oxidation of organic substances in the body.
Vitamins which have antioxidant properties are C, E, A, P. Glutathione, taurine (2-aminoetansulfonic acid), dipeptide carnosine are also reveal antioxidant properties.
Complete suppression of peroxide processes in the tissues seems inappropriate. Free radicals induce apoptosis and are involved in the formation of cellular immunity, stimulate phospholipases, thereby participating in the synthesis of eicosanoids.
However, the enhanced generation of free radicals accompanies pathological conditions (Parkinson's disease, Alzheimer's disease) and the process of biological aging.
