- •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
3. Prolamins and glutelins.
Prolamins are proteins of vegetative origin. They contain 20-25% of glutamic acid and 10-15% of proline. They are dissoluble in 60-80% ethanol water solution while all other simple proteins in these conditions usually form sediment.
Glutelins are simple proteins. They are contained in seeds of gramen, in green parts of plants. They are characterized by high amount of glutamic acid and lysine. They are dissoluble in dilute solutions of alkalis. Glutelins are reserve proteins.
1.6.2. Conjugative proteins
Conjugated proteins are two-component proteins which consist of simple protein and non-protein component (prosthetic group).
1. Chromoproteins (from Gr. chroma - color) consist of simple protein and the pigmented non-protein component bound to it. We distinguish hemoproteins and flavoproteins. They participate in such processes as breath, transport of oxygen and carbon dioxide, redox reactions, light- and colour perception, etc.
The group of hemoproteins include hemoglobin, myoglobin, cytochromes, catalase, peroxidases. All of them contain ferriporphyrin, but vary in protein structure, and carry out various biological functions. Specific distinctions of hemoglobin are caused by globin.
Let's consider hemoglobin structure. It is a blood protein. Non-protein component of hemoglobin is the heme (fig. 5). It’s a pigment giving blood its red color. The basis of its structure is the protoporphyrin IX. In the heme centre the atom of iron is bounded to two atoms of nitrogen covalently and with two others by coordination bonds.
A heme is "wrapped up" by one polypeptide chain. In a molecule of hemoglobin of an adult person НbА there are four polypeptide chains which together form the protein part of a molecule - globin. Two α-chains contain 141 amino-acid residues, two β-chains – 146 (fig. 6).
Fig. 5. Heme Fig. 6. Hemoglobin
In blood of an adult person there is also hemoglobin НbА2 (2α, 2δ chains, 2,5%) and НbA3 (less than 1%, differs by structure of -chains).
There is fetal hemoglobin HbF, consisting of 2 α- and 2 γ-chains. Hemoglobin F possesses the increased affinity to oxygen and allows rather small volume of blood of a fetus to carry out oxygen-bearing functions more effectively. Blood of the newborn contains up to 80% HbF, by the end of the 1st year of life it is almost entirely changed to НbА.
Diseases of hemoglobins (more than 200) are called hemoglobinoses.
1. Hemoglobinopathy, at the basis of which hereditary structural change of any chain of normal hemoglobin. In blood of a human about 150 various types of mutant hemoglobins are found.
Abnormal hemoglobins differ in physical and chemical properties (electrophoretic mobility, solubility, isoelectric point, affinity to oxygen).
Classical example of hemoglobinopathy is sickle-cell anemia. It widely spread in the countries of South America, Africa and South East Asia. Chemical defect is reduced to glutamic acid changing in 6th position from the N-end to valine in β-chains of a molecule of hemoglobin (HbS). It is the result of a mutation in DNA molecule. The HbS solubility and affinity to oxygen are reduced. Erythrocytes in the conditions of low partial pressure of oxygen take the form of a sickle. HbS after oxygen return in tissues turns in low solubility desoxiform and drops out into sediment in the form of spindle-shaped crystals. They distort a cell and lead to a hemolysis. The heterozygous form of anomaly proceeds asymptomatically or is accompanied by an easy hemolytic anemia. Homozygous individuals from the first months of life have the heavy form of sickle-cell anemia. Disease proceeds sharply, and children often die in an early age.
2. Thalassemia is a group of diseases with hereditary infringement of synthesis of one of globin chains. We distinguish α- and β-thalassemia. Hemoglobinopathy Н is one of the variants of -thalassemia. It manifests in hemolytic anemia, the precipitation of hemoglobin H, enlarged spleen, severe osteal changes.
3. Iron-deficient anemia is infringement of synthesis of hemoglobin owing to deficiency of iron. Principal causes are blood loss and lack of nutrition rich with heme - meat and fish.
Hemoglobin derivatives
Oxyhemoglobin HbO2. Molecular oxygen is joined to each heme of Hb by means of iron coordination bonds. Binding of each molecule of oxygen facilitates binding of the subsequent. This allosteric dependence has received the name Bohr effect. Oxyhemoglobin, getting to tissues, loses oxygen, becoming deoxyhemoglobin.
Carbhemoglobin HbCO2 is hemoglobin bond with carbon dioxide. It is unstable and quickly dissociates in pulmonary capillars detaching СО2.
Carboxyhemoglobin HbCO is a product of the addition of carbon monoxide to hemoglobin. Hemoglobin has high affinity to CO and is strong bound with it. Hemoglobin loses ability to bind oxygen, and here comes death from suffocation.
Methemoglobin MtHb is the hemoglobin form in which heme iron is in a trivalent state. It is not capable to carry oxygen. It is formed of free hemoglobin under the influence of various oxidants, and in an organism - after some poisonings.
Methemoglobinemia is an appearance of methemoglobin in blood. There are hereditary and acquired methemoglobinemia. Hereditary evolves as a result of presence of abnormal hemoglobins. Among the acquired can be toxic methemoglobinemia of exogenous parentage, arising under the influence of some chemicals (nitrates, nitrites, aniline, some medical products), and endogenous, owing to infringement of production and adsorptions of nitrates during enterocolitis. With significant methemoglobinemia there is an anoxemia (hypoxia).
Method of qualitative test of various derivatives of hemoglobin is research of their absorption spectrums.
Myoglobin is a globular protein which reserves in muscles molecular oxygen and transfers it to the oxidative systems of cells. It consists of one polypeptide chain. As well as in hemoglobin, the active centre of a molecule binding O2, is the heme. Myoglobin defines the color of muscles.
Chromoproteins are also catalase, peroxidase, cytochromes enzymes.
Flavoproteins are the chromoproteins, which prosthetic groups are presented by derivatives of isoalloxasine - flavine mononucleotide (FMN) and flavine adenine dinucleotide (FAD). Flavoproteins are a part of some oxidoreductases - enzymes catalyzing redox reactions in a cell.
2. Lipoproteins consist of protein and the prosthetic group presented by any lipid (neutral fats, free fatty acids, phospholipids, derivatives of cholesterol). Lipoproteins are widely spread and also carry out various biological functions. Representatives of lipoproteins are protein of lungs tissue, lipovitellin of an egg yolk etc.
Lipoproteins are present in free state (mainly in blood plasma). Lipoproteins of blood serum contain hydrophobic lipid nuclei surrounded with polar lipids and a cover of proteins, called apoproteins. They provide transport of water insoluble lipids.
The lipids covalently bound with protein, serve as an anchor with the help of which proteins are attached to the membrane. These are structured lipoproteins (lipids of cells membranes, myelin sheath of nerve fibers).
3. Phosphoproteins are conjugative proteins into which composition as a non-protein component the phosphoric acid enters and is attached to a polypeptide chain by an ester bond through the residues of serine or threonine. The ionic bonding is also possible.
Phosphoproteins include caseinogens of milk, egg white ovalbumin, a number of enzymes such as RNA polymerase. A large number of phosphoproteins found in cells of the CNS.
Phosphoproteins are a valuable source of energy and plastic material in the process of embryogenesis and postnatal growth and development, participate in the regulation of nuclear activity of the cell, ion transport and oxidative processes in mitochondria.
4. Glycoproteins are conjugative proteins that contain, in addition to a simple protein or peptide, linear or branched geterooligosaccharide chains containing from 2 to 15 residues of hexose, pentose and the terminal carbohydrate (N-acetylgalactosamine or others). Carbohydrate component is connected to the protein by covalent bonds – N-glycoside and O-glycoside.
Glycoproteins are proteins of blood plasma (except albumin), certain enzymes, saliva mucin, proteins of cartilage and bone tissues. Glycoproteins are important structural component of cell membranes. They provide a cell adhesion, molecular and cellular recognition. Carbohydrate components in addition to the informative function increase the stability of the molecules, to which they belong, to various chemical or physical treatments, and protect them from the action of proteases.
Erythrocyte membrane glycoproteins determine the blood group in humans. The typical glycoproteins include interferons, immunoglobulins.
Interferons - inhibitors of reproduction of many types of viruses. They are formed in the cell in response to the invasion of viruses’ nucleic acids. Interferons are proteins thought to be essential not only as protective against viral infection, but also of tumors.
Immunoglobulins, or antibodies are protective proteins. They neutralize entering the body foreign substances of any chemical nature - antigens. There are three major classes of immunoglobulins: IgG, IgA, IgM; minor classes of immunoglobulins of human plasma are referred to as IgD and IgE. Immunoglobulins of different classes differ in molecular weight, the concentration in the blood, biological properties.
At rheumatic arthritis abnormal antibodies are synthesized with an unusually short sugar chains, which causes stimulation of the immune system against the organism.
Proteoglycans are complexes of proteins and glycosaminoglycans. Carbohydrate in these compounds is the main part of the molecule (95%). Typical glycosaminoglycan is hyaluronic acid. Its main function in the connective tissue is binding of water. Heparin involved in the regulation of blood coagulation.
5. Metalloproteins, in addition to protein, contain ions of a single metal or several metals.
