- •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
1.2. Functions of proteins
Catalytic function. The majority of enzymes known as biological catalists, are proteins. Now, some thousand enzymes are described.
Transport function. Respiratory function of blood, in particular oxygen transfer, is carried out by molecules of hemoglobin protein of erythrocytes. Albumins of blood serum take part in transport of lipids.
Protective function. In response to bacteria, toxins, viruses or alien proteins entering in organism protective proteins-antibodies are synthesized (immune defenses). A number of proteins of blood plasma are capable to coagulation that protects from wounds blood loss (physical protection).
Hormonal function. A series of hormones is presented by proteins or polypeptides, for example, pancreas hormone - insulin.
Structural function. In complex with lipids proteins participate in the formation of biomembranes of cells. Cytoskeleton structural proteins provide shape of cells and many organoids. Structural proteins are collagen in connective tissue, keratin in hair, nails, skin, elastin in a vascular wall, etc.
Nutrient (reserve) function. Proteins of egg (ovalbumins) are a source of nutrition for the fetus. The basic protein of milk (casein) also carries out nutrient function.
Receptor function. Protein receptors can be integrated into the cell membrane or in the cytoplasm. The receptor accepts a signal which is often a chemical substance.
Contractile (motor) function. Contractile function is inherent to muscular proteins (actin and myosin), to proteins of cytoskeleton and that provides discrepancy of chromosomes in the course of mitosis.
Other important functions of proteins - ability to sustain oncotic pressure in cells and blood, the buffer properties sustaining physiological рН value of internal environment, etc.
1.3. Amino-acid composition of proteins
To establish the amino-acid composition of proteins we use a combination of acid (НС1), alkaline (Ba (OH)2) and, less often, enzyme hydrolysis or one of them. It is known that in hydrolysis of pure protein, free from admixings, 20 various amino acids are released.
The amino acids which are part of proteins, are a-amino acids. All of them belong to an L-number, and the size and optical rotation sign depend on the nature of radicals of amino acids and the value of рН solution. In human proteins D-amino-acids are not found, however they are found in cellular wall of bacteria, as part of some antibiotics (actinomycins).
Amino acids classified on the base of the chemical nature of radical R which does not participate in peptide bond formation. Modern rational classification of amino acids is based on polarity of radicals.
There are: 1) non-polar (hydrophobic); 2) polar (hydrophilic); 3) aromatic (mostly non-polar), 4) negatively charged and 5) positively charged amino acids.
In some proteins derivatives of amino acids are found. In the protein of connective tissue collagen there are hydroxyproline and hydroxylysine. Diiodotyrosine is the basis of structure of thyroid gland hormones.
Oxylysine Oxyproline Diiodotyrosine
Amino acids possess one universal property. They have an amphoteric character (from Gr. amphoteros - bilateral). In рН interval from 4,0 to 9,0 almost all amino acids exist mainly in the form of zwitterions (bipolar ions). The value of IEP of amino acid is calculated by the formula:
For monoaminodicarboxylic acids рI is calculated as a half-sum of values рК - and -carboxylic groups, for diaminodicarboxylic acids - as a half-sum of values рК - and -amino groups.
There are nonessential amino acids which can be synthesised in a human body, and essential which are not formed in the organism and should be received from food.
Essential amino acids or indispensable amino acids are an amino acids that cannot be synthesized de novo by the organism, and therefore must be supplied in the diet. They are: valine, leucine, isoleucine, lysine, methionine, threonine, indole amino-propionic acid, phenyl alanine.
Non-essential amino acids are those that are produced within the human body. These include: glycine, lactamic acid, asparagine, aspartate, glutamine, glutamate, proline, serine.
Conditionally essential amino acids can be synthesised in the organism from other amino acids: arginine (from citrulline), thyrosin (from phenyl alanine), cysteine (from serine), histidine (with the assistance of glutamine).
The amount of various amino acids in proteins is unequal. For discovering in biological objects and quantitative definition of amino acids we use the reaction with ninhydrin.
