- •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
4.2. Transport of substances across membranes
Uniport is transport of a substance in one direction depending on the gradient of concentration.
Symport is transport of two substances in one direction through one carrier.
Antiport is movement of two substances in different directions through a single carrier.
Symport and antiport are cotransport systems.
Passive transport:
1. Simple (passive) diffusion. Small neutral molecules such as Н2О, СО2, О2, NH3, urea, ethanol, hydrophobic organic compounds with low molecular mass (steroid hormones, benzene) diffuse through the membrane without the involvement of specific mechanisms. Transfer of substances is carried by the concentration gradient and at a low rate.
2. Facilitated diffusion
Lipid bilayer is almost impermeable for larger polar molecules (glucose, amino acids), as well as for ions, as its interior is hydrophobic. These substances are transported across the membrane on the gradient of concentration, but with the participation of membrane proteins.
2a. Transfer through ion channels. Transmembrane transport of several ions (Са2+, Na+, K+, C1−) occurs through ion channels. These are intrinsic proteins of membrane. They form a transmembrane hydrophilic (water-filled) channel. The selectivity of channels to ions is determined by the presence of specific center in protein canal for ion linking. Channels can be either closed or open. Signal to change the state of the channel may be a hormone or other signaling molecule. The example of controlled channels is Ca-channels.
2b. Transfer by transmembrane carrier protein (translocase). Each substance or group of similar substances has its own carrier. Transferred substance joins to the translocase. Then carrier changes its conformation. The substance is released from the other side of the membrane. Since there is no hydrophobic barrier, this mechanism is called facilitated diffusion. Example is facilitated diffusion (uniport) of glucose in erythrocytes with GLUT-1. Molecule of glucose links to translocase on the outer surface of the plasma membrane. Conformational change occurs, and the center of the carrier, occupied by glucose, is open inside the cell. As a result of conformational changes a carrier loses affinity for glucose, and the molecule is released in the cell cytosol. Separation of glucose causes a conformational change of the carrier protein, and it returns to the original conformation.
Passive transport does not require energy.
Fig. 16. a - types of transport, b - passive and active transport:
1 - passive diffusion, 2 - diffusion through the channel, 3 - diffusion through the carrier, 4 - the active transport, 5 - secondary-active transport.
Active transport of substances occurs against the concentration gradient and it is associated with the supply of metabolic energy. In this way, there is transfer of many mineral ions from the extracellular fluid into the cell or in the opposite direction, the transfer of amino acids from the intestinal lumen into the cells of the intestine, transport of glucose from the primary urine through the kidney tubules cells in the blood. The main source of energy for active transport is ATP. Therefore, as a rule, these systems are ATPases.
The example is Na+,K+-pump. There is an integral plasma membrane protein sodium-potassium ATPase. It moves potassium ions into the cell, and sodium ions from the cell.
ATPase attaches inside of the membrane three Na+ ions. These ions alter the conformation of the active site of ATPase, and it hydrolyzes one molecule of ATP and attaches phosphate. The released energy is used to change the conformation of ATPase, after which three sodium ions are on the outer side of the membrane, and the phosphate ion is replaced by 2 K+ ions from the outside. Then, the carrier conformation changes to the original, and K+ ions are inside membrane. Here, K+ ions are split off, and the carrier is again ready for use.
The work of Na+,K+-pump creates not only the difference in concentration, but difference in charges. On the outer side of the membrane a positive charge is created, and negative charge is inside. It is necessary for the nerve impulse transmittion.
Secondary active transport. It is cotransport system. The gradient of a substance is used to transport the other. Carrier in this case has specific binding sites for both substances. The substance is transported against its concentration gradient by symport or antiport. Symport and antiport can occur due to the energy of the concentration gradient of Na+ ions, produced by Na+,K+-pump. In this way there is, for example, amino acid absorption from the intestine and the glucose from the primary urine and intestines.
An example of secondary-active symport is transport of glucose and sodium ions, secondary-active antiport - Ca, Na-active transport.
The secondary active transport has probably the greatest value for transfer of carbohydrates, amino acids and other metabolites in comparison with other mechanisms.
There are special mechanisms for the transport of proteins, polysaccharides, and nucleic acids through the membrane. These are endocytosis (phagocytosis and pinocytosis) and exocytosis.
Violation of the transport functions is due to more than 20 “transport diseases”, including renal glucosuria, cystinuria, malabsorption of glucose, galactose, and vitamin B12.
