General scheme of nutrient catabolism in the body. Phases of catabolism, energy effect of individual phases. General and specific pathways of catabolism. General principles of regulation of metabolic pathways Basic principles of organization of metabolism staging of convergence
The result of the design should be tables that correctly and efficiently represent objects and their relationships.
A relational database is considered correct (agreed) and effective if it has the following characteristics:
1) lack of redundancy;
2) consistency preventing data loss;
3) minimal use of NULL values.
Relational database schema data is a set of headers of relations included in the database and their links. The schema contains structural and semantic information.
A certain single pivot table, which presents all the necessary data about the subject area, is called universal attitude (general or global table).
Such a master table can be quite inefficient due to two major design flaws: redundancy and inconsistency. (Yes, NULL values...
…)
The use of a generic relation containing redundant data can give rise to three inconsistency problems called anomalies : insertion (inclusion), deletion and update (modification) anomalies.
The process of ordering, structuring the presented data is called normalization.
Disadvantages of a global table (built for all occasions):
- rigidity;
— unreliability (potential inconsistency);
- increased consumption of resources;
- bulkiness (redundancy).
Rigidity is understood as a mandatory modification of the table itself when the problem statement changes.
Redundancy- the need to store complete information, for example, the name of the company in each product record.
Potential inconsistency– the need to change the value of the attribute in all records, with a programming error, is expensive.
Turn-on anomaly- there can be no records about the supplier if he did not deliver any goods.
Deletion anomaly– when deleting all goods supplied by the supplier, his address is lost, etc.
Normalization is a design process to ensure the efficiency of data structures in a relational database. When designing, the data is divided into several related tables, subject to special normalization requirements.
Normalization- practically - this is a partition of a table into two or more, with the best properties when enabling, modifying and deleting data. The ultimate goal of normalization is to obtain a database design in which each fact appears in only one place, i.e. information redundancy is excluded. This is done not so much to save memory, but to eliminate the possible inconsistency (inconsistency) of the stored data.
The basis of the normalization process is the formal apparatus proposed by E. Codd in the framework of relational theory, called normalization of relations.
It should be noted that the normalization process has nothing to do with the physical location of the data. It is only about the user and global logical representation of data
The normalization process is based on the concept functional dependence attributes.
Definition of functional dependence (FZ).
A tribute IN tables functionally dependent on the attribute A the same table if and only if at any given point in time for each of the different values of the attribute A only one of the distinct attribute values must exist IN. Note that the attributes A And IN can be single or composite.
The assertion that IN functionally depends on A, means the same as A uniquely defines IN,T. e. if at some point in time the value is known A, then you can get the value IN.
Functional dependency is indicated by an arrow A ® IN.
The concept of a function is similar to the concept of a function in mathematics and reflects the semantic (semantic) relationship of the corresponding attributes of an entity.
There are the following types of functional dependencies: full, partial and transitive FL.
If a non-key attribute depends on the entire composite key and does not depend on its parts, then one speaks of a complete functional dependence of the attribute on the composite key.
If a non-key attribute depends only on part of the composite key, then the attribute is said to be partially functionally dependent on the composite key.
If attribute B depends on attribute A, and C depends on attribute B, but there is no inverse relationship, then attribute C is said to depend transitively on A.
Some FDs reflect relationships in the subject area under study, while others can be generated by the structure of illiterately formed relationships (tables). With incorrectly grouped relationships, some FDs may turn out to be undesirable due to the indicated anomalies that they cause when maintaining (updating) the database.
Lecture 7. Definitions and characteristics of normal forms 1NF, 2NF, 3NF, BCNF. The concept and types of denormalization.
Definition . A relation is in 1NF if any values of all attributes are atomic and there are no repeating groups in the relation.
Obviously, if an arbitrary relation satisfies the requirements of the relational model, it accordingly satisfies the definition of 1NF.
Definition . A relation is in 2NF if it conforms to 1NF and its non-key attributes completely dependent from the entire primary key.
Definition . A relation is in 3NF if it conforms to 2NF and has no transitive dependencies.
Definition . A relation is in BCNF if it conforms to 3NF and if and only if any functional dependency between its fields reduces to a complete functional dependency on a possible key.
Lecture 8. CASE database design technologies. Design using the entity-relationship method.
General principles of the organization of catabolism in the body
The source of free energy in heterotrophic organisms is the breakdown of nutrients, in other words, catabolic processes occurring in cells and tissues. Catabolism includes hundreds of chemical reactions, dozens of metabolic pathways. At the same time, a certain logic can be traced in the organization of catabolic processes.
The entire catabolism of nutrients in the body can be divided into three stages or, as they are commonly called, three phases. In the first phase, polymer molecules are split into monomers: proteins are split into amino acids, oligos and polysaccharides into monosaccharides and their derivatives, lipids into higher fatty acids, glycerol, amino alcohols, etc. It should be noted that we are talking not only about the breakdown of food components in the gastrointestinal a path, but also disintegration of biopolymers directly in cells. In this phase, there are no oxidative processes; hydrolysis and phosphorolysis predominate. The release of energy does not exceed 12% of its total content in nutrients, and all the energy is dissipated in the form of heat.
However, one important event occurs in this phase - a sharp decrease in the number of compounds that then enter the second phase of catabolism. Yes, with various food products millions of different proteins enter the gastrointestinal tract with products, and all of them are split up to 2025 amino acid monomers, and several hundred different lipids, when split, give one and a half dozen different higher fatty acids and alcohols; several hundred different oligosaccharides and polysaccharides during decay give, in turn, one and a half dozen monosaccharides and their derivatives. Thus, instead of millions of different compounds entering the first phase, about 50 compounds are formed at the exit from it.
In the second phase, these five dozen compounds undergo further cleavage, so that only five compounds remain at the exit from this phase: acetyl-CoA, succinyl-CoA, fumarate, oxaloacetate, and 2-oxoglutarate. Thus, the breakdown of nutrients that continues in the second phase is accompanied by an even greater unification of intermediate products. The catabolic processes that take place in the second phase are of a mixed nature, because it includes phosphorolysis, lyase cleavage, thiolysis, and oxidative reactions. In the second phase, up to 1/3 of all the energy contained in the nutrients is released, and part of it is accumulated. In this phase of catabolism, all nitrogen-containing end products of catabolism are formed, as well as part of CO2 and H2O.
The internal logic of such an organization of catabolic processes is that as the breakdown of nutrients deepens, the amount of intermediate metabolic products decreases. This principle of building catabolic processes is called the principle of convergence.
The metabolic pathways of the first and second phases of catabolism are usually individual for individual compounds or groups of structurally related substances of the same class. Therefore, the metabolic pathways of the first and second phases of catabolism are called specific catabolism pathways. At the same time, the metabolic processes of the third phase of catabolism are the same regardless of which compound is cleaved. In this regard, the metabolic pathways of the third phase are called general catabolism pathways.
The presence of common metabolic pathways in the third phase of catabolism, in which 2/3 of all free energy is released, increases the adaptive capabilities of living organisms, because makes it relatively easy to switch from one type of nutrient to another. The presence of common metabolic pathways in the third phase also makes it possible to reduce the amount of various enzymes required by cells and tissues for the processing of various nutrients. All this helps organisms in the struggle for survival and is the result of a long evolution of living organisms.
When studying metabolic processes, we will first of all consider the metabolic pathways of the third phase of catabolism: the Krebs tricarboxylic acid cycle and the chain of respiratory enzymes.
The source of free E in heterotrophic organisms is nutrient breakdown, in other words, catabolic processes occurring in cells and tissues. Catabolism includes hundreds of chem. reactions, dozens of metabolic pathways. At the same time, a certain logic can be traced in the organization of catabolic processes. All catabolism pet. substances in the body can be divided into three stages or, as it is commonly called, three phases.
In the first phase polymer molecules are split into monomers: proteins are split into amino acids, oligos and polysaccharides into monosaccharides and their derivatives, lipids into higher fatty acids, glycerol, amino alcohols, etc. There are no oxidative processes in this phase, hydrolysis and phosphorolysis predominate. All energy is dissipated as heat. In this phase, there is a sharp decrease in the number of compounds that then enter the second phase of catabolism. So, millions of different proteins enter the gastrointestinal tract with a variety of food products, and all of them are broken down to 20-25 AA.
In the second phase these five dozen compounds undergo further cleavage, so that only five compounds remain at the exit from this phase: acetyl CoA, succinyl CoA, fumarate, oxalo acetate and 2 oxoglutarate. Thus, the breakdown of nutrients that continues in the second phase is accompanied by an even greater unification of intermediate products. The catabolic processes that take place in the second phase are of a mixed nature, because it includes phosphorolysis, lyase cleavage, thiolysis, and oxidative reactions. In this phase of catabolism, all nitrogen-containing end products of catabolism are formed, as well as part of CO2 and H2O. The organization of catabolic processes lies in the fact that as the breakdown of nutrients deepens, the amount of intermediate metabolic products decreases. This principle of building catabolic processes is called the principle of convergence. The metabolic pathways of the first and second phases of catabolism are usually individual for individual compounds or groups of structurally related substances of the same class. Therefore, the metabolic pathways of the first and second phases of catabolism are called specific catabolism pathways. At the same time, the metabolic processes of the third phase of catabolism are the same regardless of which compound is cleaved.
As a result, metabolic pathways third phase called the general pathways of catabolism. The presence of common metabolic pathways in the third phase of catabolism, in which 2/3 of all free energy is released, increases the adaptive capabilities of living organisms, because makes it relatively easy to switch from one type of nutrient to another. The presence of common metabolic pathways in the third phase also makes it possible to reduce the amount of various enzymes required by cells and tissues for the processing of various nutrients. All this helps organisms in the struggle for survival and is the result of a long evolution of living organisms. Pathways of the third phase of catabolism: the Krebs tricarboxylic acid cycle and the respiratory enzyme chain
Option 1
1. Write an equation of thermodynamics that reflects the relationship between changes in free energy (G) and the total energy of the system (E). Answer:
2. Specify what two types of energy the cell can use to do work. Answer : To perform work, a cell can use either the energy of chemical bonds of macroergs, or the energy of transmembrane electrochemical gradients.
3. Indicate the amount of free energy released when 1 mole of thioether bonds are broken in compounds of the acyl-CoA type under standard conditions . Answer : 8.0 kcal/M.
4. Specify the value of the caloric coefficient for fats. Answer : 9.3 kcal/g.
5. Specify what is called "basic exchange". Answer : The level of energy consumption for maintaining the life of the body.
6. Indicate the level of "basal metabolic rate" for a person of average weight, expressed in kcal / day. Answer: Approximately 1800 to cal.
7. Name 5 ways to break chemical bonds in compounds that are most widely used in biological systems. Answer: Hydrolysis, phosphorolysis, thiolysis, lipase cleavage, oxidation.
8. Name three main classes of compounds coming from the first phase of catabolism to the second phase. Answer: Monosaccharides, higher fatty acids, amino acids.
9. Indicate which way of splitting chemical bonds prevails in the third phase of catabolism. Answer : Oxidation.
10. Explain what the term "convergent principle of organization of catabolism" means in the body. Answer :
11. Explain what advantages the convergent principle of organizing catabolism in his body gives a person. Answer:
12. Write, using the structural formulas of metabolites, the oxidation reaction of isocitrate in the Krebs cycle, indicating all the compounds involved in the reaction. Answer
13. Indicate how the direction of the flow of metabolites in the Krebs tricarboxylic acid cycle is controlled .Answer: Thermodynamic control - due to the inclusion of two reactions in the metabolic pathway, accompanied by a large loss of free energy.
14. Specify 2 possible ways to replenish the pool of intermediate metabolites of the Krebs cycle. Answer: a) Their entry from the second phase of catabolism, b) The reaction of pyruvate carboxylation.
15. Indicate in which cell structure the chains of respiratory enzymes are localized. Answer : In the inner membrane of mitochondria.
16. Draw a diagram describing the functioning of the intermediate electron carriers that are part of the IV complex of the main respiratory chain. Answer:
17. Define the term "oxidative phosphorylation". Answer : Synthesis of ATP using the energy released in the process of biological oxidation
18. Specify the role of protein F | in the mechanism of oxidative phosphorylation in the chain of respiratory enzymes according to Mitchell. Answer : ProteinF | due to protons moving along the electrochemical gradient, catalyzes the formation of ATP nz ADP and inorganic phosphate.
19. Specify the mechanism of action of compounds that cause uncoupling of oxidation and phosphorylation in mitochondria. Answer : These compounds act as proton carriers across the inner mitochondrial membrane, bypassing the ATP synthesis system.
20.Specify 2 possible causes development of hypoxic hypoenergetic states. Answer : Any 2 options out of 4 possible: a) lack of oxygen in the environment; b) violation of the respiratory system; c) circulatory disorders; d) impaired ability of blood hemoglobin to carry oxygen.
21. Give 2 examples of compounds, in the neutralization of which the microsomal oxidation system takes part. Answer : 2 any examples of aromatic carbocycles (anthracene, benzanthracene, naphthacene, 3,4-benzpyrene, methylcholanthrene).
22. Explain the mechanism of the protective action of antioxidants such as vitamin E or carotene. Answer : These compounds accept an extra electron from the superoxide anion radical, forming a less reactive structure due to the redistribution of the electron density along the system of conjugated double bonds present in their structure.
Option 2
1. Explain why for chemical processes occurring in cells, the change in the enthalpy of the system (H) is almost equal to the change in the total energy of the system (E).
Answer: In biological systems, there are no changes in temperature or pressure during chemical reactions..
2. Indicate which chemical reactions from the point of view of thermodynamics can proceed spontaneously. Answer : Only exergonic chemical reactions can proceed spontaneously.
3. Give 2 examples of macroergic compounds from the class of thioethers. Answer: Any two specific acyl-CoAs
Answer: 10.3 kcal/M.
5. Specify what changes occur with nutrients in the first phase of catabolism. Answer : Breakdown of polymers into monomers.
6. Indicate what part of the total energy of nutrients is released in the second phase of cataoolism. Answer : 1/3 of all energy.
7. Indicate what end products of metabolism are formed in the third phase of catabolism. Answer : Water, carbon dioxide.
8. Write a general scheme of monooxygenase reactions occurring in cells. Answer: SH2 + O2 +KOH 2 ->S-OH+ Ko oxidized + H 2 O
Answer:
10. Write, using the structural formulas of metabolites, the oxidation reaction of succinate in the Krebs cycle, indicating all the compounds involved in the reaction. Answer:
11. Write the total equation of the Krebs tricarboxylic acid cycle. Answer: Acetyl-CoA + ZNAD + + FAD + GDP~P + 2H: O-> CO 2 - ZNADH + H + + FADH 2 + GTP
12. Indicate 2 compounds that are allosteric activators of regulatory enzymes of the Krebs cycle. Answer: ADP.AMF.
13. Define the metabolic pathway known as "the main chain of mitochondrial respiratory enzymes". Answer: Metabolic pathway for the transport of protons and electrons with NADH+H 2 to oxygen.
14. Name the intermediate carriers of the main respiratory chain, capable of accepting hydrogen atoms or electrons from external sources. Answer: Co.Q, cytochrome C.
15. Indicate how much free energy is released under standard conditions during the oxidation of 1 mol of NADH + H" with the formation of 1 mol of H 2 O. Answer : -52.6 kcal/M.
16. Explain what is called uncoupling of oxidation and phosphorylation. Answer: Violation of the relationship between the processes of oxidation and phosphorylation with the conversion of released free energy into heat.
17. Explain the meaning of the term "hypoenergetic state". Answer: Lack of energy in the cell.
18. Name 2 cytochromes involved in oxidative processes localized in the membranes of the endoplasmic reticulum. Answer: Cytochromeb5, cytochromeP 450 .
19. Give a diagram of the electron carrier chain with the participation of cytochrome P 450, functioning in the membranes of the endoplasmic reticulum. Answer: fuck you
20. Name 2 compounds whose biosynthesis involves the microsomal oxidation system. Answer: Adrenaline (norepinephrine). steroid hormones.
21. Indicate 2 possible sources of peroxide anion-radical formation in tissues. Answer :
Option 3
1. Give an explanation of the term "free energy of the system". Answer: Free energy - part of the total energy of the system, due to which work can be done.
2. State why endergonic reactions cannot proceed spontaneously. Answer : Endergonic reactions require an external source of energy.
3. Indicate the amount of free energy released when 1 mole of ATP pyrophosphate bonds are broken under standard conditions. Answer : 7.3 kcal/mol.
4. Indicate the amount of free energy released when a macroergic bond is broken in 1 mole of creatine phosphate under standard conditions. Answer: 10.3 kcal/M.
5. Indicate the value of a person's daily protein requirement, expressed in g/kg of body weight (WHO standard). Answer : 1 g/kg.
6. Indicate the value of the caloric coefficient for proteins during their breakdown in the human body Answer : 4.1 kcal/g.
7. Indicate what part of the total energy consumption of a person is covered by the breakdown of proteins. Answer: 15%.
8. Define the concept of catabolism. Answer : The total breakdown of nutrients in the body.
9. Explain why the metabolic pathways of the first and second phases of catabolism are called specific catabolism pathways. Answer: In these phases of catabolism, each compound or group of structurally related compounds is degraded using different metabolic pathways.
10. Explain what the term "convergent principle of organization of catabolism" means in the body. Answer: As the breakdown of nutrients deepens, the number of intermediate products decreases.
11. Explain what advantages the convergent principle of organizing catabolism in his body gives a person. Answer : A). Ease of transition from one type of nutrient to another. b). Reducing the number of enzymes at the final stage of catabolism.
12. Indicate 5 features that distinguish between the oxidation processes taking place in biological objects and the oxidation processes taking place in an abiogenic environment. Answer: a) "Mild" conditions in which the process takes place, b) The participation of enzymes, c) Oxidation proceeds mainly by dehydrogenation, d) The process is multi-stage, e) The intensity of the process is regulated in conjunction answer in relation to the energy needs of the cell.
13. Write, using the structural formulas of metabolites, the overall reaction of the transformation of 2-oxoglutarate. in succinyl-CoA, indicating all compounds involved in the reaction Answer :
14. Name 2 reactions that are points of thermodynamic control of the direction of metabolite flow in the Krebs cycle. Answer : a) Citrate synthase reaction b) 2-oxoglutarate dehydrogenase reaction.
15. Indicate 3 compounds in the structure of which energy is accumulated, released during the oxidation of acetyl residues in the Krebs cycle. Answer : NADH + H +, FADH 2, GTP.
16. Name 2 intermediate acceptors of hydrogen atoms that supply protons and electrons to the chain of respiratory enzymes. Answer: NADH + H + , FADH 2
17. Draw a diagram describing the functioning of the intermediate carriers of protons and electrons that are part of the 1st complex of the main respiratory chain. Answer :
18. Give a formula that can be used to calculate the amount of free energy released during electron transfer, if the values of the redox potentials of the initial and final points of the electron transport chain are known. Answer : G" = - nXFx E".
19. Indicate the essence of the second stage of the transformation of the energy released in the chain of respiratory enzymes into the energy of macroergic bonds of ATP within the framework of the chemo-osmotic concept of conjugation proposed by Mitchell. Answer : The energy of the transmembrane proton electrochemical gradient is usedfor the formation of a macroergic bond of ATP.
20. Give 3 examples of compounds that uncouple the processes of oxidation and phosphorylation in mitochondria. Answer : Polychlorophenols, polynitrophenols, acetylsalicylic acid.
21. Indicate which method of compounds oxidation is realized mainly in the course of microsomal oxidation processes. Answer : oxygenation.
22. Name 3 functions of microsomal oxidation. Answer : a) Participation in the catabolism of various compounds. b) Participation in the biosynthesis of compounds necessary for the body, c) Detoxification.
23. Specify 3 possible ways inactivation of the superoxide anion radical. Answer : a) Donation of an extra electron to cytochrome C. b) Donation of an extra electron to an antioxidant compound (such as vitamin E, carotene, etc.) c) Inactivation during the superoxide dismutase reaction.
24. Indicate 2 possible sources of peroxide anion-radical formation in tissues. Answer: a) Formed in aerobic dehydrogenation reactions b) Formed in superoxide dismutase reaction.
25. Indicate 3 possible ways to inactivate the peroxide anion-radical in cells. Answer : a) During the reaction catalysed by catalase, b) During the reaction catalyzed by glutathione peroxidase. c) During the reaction catalyzed by peroxidase
26. Specify the role of microsomal oxidation processes in chemical carcinogenesis. Answer: During the neutralization of polycyclic aromatic hydrocarbons, their epoxides are formed, which have mutagenic activity.
Option 4
1. Give an equation that describes the I law of thermodynamics in a form acceptable for describing the thermodynamics of living objects Answer: ∆EsnstemyN+∆Eenvironment = 0.
2. Explain what is called the energy conjugation of chemical reactions. Answer: The use of free energy released during an exergonic reaction to carry out an endergonic reaction.
3. Indicate the type of macroergic chemical bond in compounds of the class of nucleoside polyphosphates. Answer: Phosphoanhydride or pyrophosphate bond.
4. Indicate the level of daily energy consumption of a person engaged in mental work. Answer : 2500 - 3000 kcal / day.
5. Indicate what part of the total energy of nutrients is released in the first phase of catabolism. Answer: until 3%.
6. Specify what 5 ways of breaking the chemical bonds of nutrients are used in the second phase of catabolism. Answer : hydrolysis, phosphorolysis, thiolysis, lyase cleavage, oxidation.
7. Indicate 3 compounds whose macroergic bonds accumulate the energy released in the third phase of catabolism. Answer : ATP, GTP, succinyl-CoA.
8. Write the general scheme of the aerobic dehydrogenation reaction. Answer: SH2+ O2 ->Soxidized+H2 O2
9. Write, using the structural formulas of metabolites, the oxidation reaction of malate of the Krebs cycle, indicating all the compounds involved in it. Answer:
10. Indicate, due to the action of which two main factors, the intensity of the flow of metabolites in the Krebs cycle is regulated. Answer: a) Change in the activity of regulatory enzymes b) The concentration of oxaloacetate and acetyl-CoA.
11. Name the enzymes of the Krebs cycle, the activity of which is inhibited by the allosteric mechanism by high concentrations of ATP. Answer: Citrate synthase, isocitrate dehydrogenase.
12. Name the compound that is the final electron acceptor in the chain of respiratory enzymes. Answer : Oxygen.
13. Draw a diagram describing the functioning of the intermediate electron carriers that are part of complex III of the main respiratory chain. Answer:
14. Specify the value of the redox potential difference between the beginning and the end of the main respiratory chain. Answer: 1, 14v
15. Indicate the essence of the first stage of the transformation of the energy released in the chain of respiratory enzymes into the energy of macroergic bonds of ATP within the framework of the chemiosmotic concept
conjugation proposed by Mitchell, Answer: The free energy released during the operation of the chain of respiratory enzymes is used to form a proton electrochemical gradient relative to the inner membrane of mitochondria.
16. Indicate the role of the F 0 protein in the mechanism of oxidative phosphorylation in the chain of respiratory enzymes according to Mitchell. Answer: ProteinF 0 ensures the flow of protons along the electrochemical gradient to the active centerthe enzyme ATP synthetase.
17. Give 2 examples of compounds that inhibit the work of complex IV of the main chain of respiratory enzymes. Answer: Cyanide, carbon monoxide.
18. Indicate 2 possible reasons for the development of hypoxic hypoenergetic conditions. Answer: Any 2 options out of 4 possible: a) lack of oxygen in the environment; b) violation of the respiratory system; c) circulatory disorders; d) impaired ability of blood hemoglobin to carry oxygen.
Option 5
1. Give an equation that describes the second law of thermodynamics in a form suitable for describing the thermodynamics of residential buildings. Answer : DSsystems+ DSenvironments > 0.
2. Indicate the condition under which two energetically coupled reactions can proceed spontaneously. Answer : Two energetically conjugated reactions can proceed spontaneously if the total change in free energy is negative
3. Give 2 examples of macroergic compounds from the class of nucleoside polyphosphates. Answer: Any 2 of the following: ATP, GTP, CTP, UTP or their biphosphate analogs
4. Name 2 nitrogen-containing end products of protein catabolism in the human body. Answer : Any two of the following: ammonia, urea, creatinine.
5. Indicate what methods of breaking the chemical bonds of nutrients are used in the first phase of catabolism. Answer : Hydrolysis, phosphorolysis.
6. Name 4 end products of metabolism formed in the second phase of catabolism. Answer : 4 compounds from the following: water, carbon dioxide, ammonia, urea, creatinine, uric acid.
7. Explain why the metabolic pathways of the third phase of catabolism are called general pathways of catabolism. Answer: These metabolic pathways are the same for the breakdown of any nutrient.
8. Write one of the options for the general scheme of dioxygenase reactions occurring in cells. Answer : One of the options: a) R-CH=CH-R 2 +ABOUT 2 ->R1-C(O)H + R-C(O)H(aldehydes) b) SH2+ O2 -> HO-S-OH-> S=0 + H2ABOUT
9. Using the structural formulas of the metabolites, write the reaction for the synthesis of citrate in the Krebs cycle, indicating all the compounds involved in the reaction. Answer :
10. Name 4 regulatory enzymes involved in the catalysis of partial reactions of the Krebs cycle. Answer : Citrate synthase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase complex, succinate dehydrogenase.
11. Indicate 2 possible ways to replenish the pool of intermediate metabolites of the Krebs cycle. Answer : a) Their entry from the second phase of catabolism, b) The reaction of pyruvate carboxylation.
12. Indicate in which compartment of the cell the metabolone of the tricarboxylic acid cycle is localized. Answer : in the mitochondrial matrix.
13. Give the names of the IV enzyme complex from the composition of the main respiratory chain of mitochondria. Answer : Cytochrome C- oxidase complex
14. Write a summary equation describing the work of the main chain of respiratory enzymes. Answer: NADH + H "+ 1 / 2O 2 -> OVER + +H 2 O
15. Explain why electrons and protons from a number of oxidizable substrates, such as glutamate, isocitrate, malate, etc., are transferred to NAD + . Answer : The redox potentials of these compounds are less than those of NADH+H + , so electrons from these compounds can be transferred to NAD + along the redox potential gradient.
16. Give the scheme of oxidative phosphorylation reactions at the substrate level, which take place in the tricarboxylic acid cycle. Answer
17. Give an example of a compound that inhibits the work of complex III of the main chain of respiratory enzymes. Answer : Antimycin.
18. Indicate in which cell structures the processes of microsomal oxidation are predominantly localized. Answer : in the membranes of the endoplasmic reticulum.
19. Indicate 3 possible sources of formation of superoxide anion-radical in cells. Answer: a) When H is oxidizedbVMetHb. 6) One-electron oxidationKoQH 2 transfer of an electron to an oxygen molecule c) In the case of one-electron oxidation of reduced flavins. (Other options are possible).
20. Write the peroxide neutralization reaction catalyzed by glutathione peroxidase. Answer: H 2 O 2 + 2 Gl-SH -> Gl-S- S-Gl + 2 H 2 O
Option 6
1. Write an equation that can be used to calculate the change in the level of free energy in the course of one or another chemical reaction under standard conditions.
Answer : ∆ G =- 2.303xRxTxlgKequilibrium
2. Give a general scheme of energy conjugation of two chemical reactions running in parallel in living objects Answer :
3. Specify the biological role of macroergic compounds. Answer : Accumulation of free energy released during exergonic reactions and providing energy for endergonic reactions.
4. Indicate what part of the total nutrient energy is released in the third phase
catabolism. Answer : 2/3 .
5. Name 5 compounds that enter the Krebs tricarboxylic acid cycle from the second phase of catabolism. Answer : Acetyl-CoA, oxaloacetate, 2-oxoglutarate, fumarate, succinyl-CoA.
6. Specify 3 ways of oxidation of compounds used in cells. Answer : Dehydrogenation, oxygenation, removal of electrons.
7. Specify 4 functions of biological oxidation in the body. Answer : a) Energy function. b) Plastic function, c) Detoxification, d) Generation of recovery potentials.
8. List 3 functions of the Krebs tricarboxylic acid cycle. Answer : Energy, plastic, integration.
9. Name the enzymes of the Krebs cycle, the activity of which is inhibited by the allosteric mechanism by high concentrations of ATP. Answer : Citrate synthase, isocitrate dehydrogenase.
10. Name 3 intermediates of the Krebs cycle used as starting substrates for biosyntheses. Answer : Oxaloacetate, 2-oxoglutarate, succinyl-CoA
11. Give the names of the III enzyme complex from the composition of the main respiratory chain of mitochondria. Answer :Co.QH 2 ,cytochrome C-oxidoreductase complex
12. Explain why electrons and protons during the oxidation of a number of substrates, such as succinate, 3-phosphoglycerol, etc., are transferred not to NAD +, but through flavoproteins to KoQ. Answer : The values of the redox potentials of these compounds are higher than those of NADH +H + , but less thanKoq,therefore, electrons from these compounds can be transferred along the redox potential gradient only toKoQ.
13. Define the term "oxidative phosphorylation in the chain of respiratory enzymes". Answer : Synthesis of ATP due to the energy released during the movement of electrons along the chain of respiratory enzymes.
14. Indicate the role of the F 0 protein in the mechanism of oxidative phosphorylation in the chain of respiratory enzymes according to Mitchell. Answer : ProteinF 0 ensures the flow of protons along the electrochemical gradient intoactive centerenzyme ATP synthetase.
15. Give a classification of hypoenergetic states based on the cause of their occurrence. Answer : a) Alimentary. 6).Hypoxic. c) Histotoxic. G). Combined.
16. Give a diagram of the electron carrier chain with the participation of cytochrome P 450, functioning in the membranes of the endoplasmic reticulum. Answer :
17. Give the equation for the reaction catalyzed by the enzyme superoxide dismutase.
Answer : O 2- + 0 2- + 2H + -> H 2 O 2 + O 2
Option 7
1. Explain why living objects cannot use thermal energy to do work. Answer : INbiological systems do not have a temperature gradient.
2. Indicate by what principle chemical bonds in certain compounds are macroergic bonds. Answer: The free energy of breaking such a bond must exceed 5 kcal/mol (equivalently: > 21 kJ/M).
3. Name 4 classes of macroergic compounds. Answer: Any 4 of the following: nucleoside polyphosphates, carbonyl phosphates, thioethers. guanidine phosphates, aminoacyladenylates, aminoacyl-tRNA.
4. Indicate the value of a person's daily requirement for lipids, expressed in g/kg of body weight. Answer : 1.5 g/kg.
5. Specify the value of the caloric factor for carbohydrates. Answer : 4.1 kcal/g.
6. Indicate what part of the total energy expenditure of a person is covered by the breakdown of lipids. Answer : 30%.
7. Specify the biological role of the first phase of catabolism. Answer : A sharp decrease in the number of individual compounds entering the second phase.
8. Name 2 metabolic pathways related to the third phase of catabolism. Answer : The Krebs tricarboxylic acid cycle, the main chain of respiratory enzymes.
9. Write a general scheme of anaerobic dehydrogenation reactions. Answer: SH 2 + X -> Soxidized + XH 2
10. Define the metabolic pathway known as the Krebs tricarboxylic acid cycle. Answer : A cyclic pathway of mutual transformations of di- and tricarboxylic acids, during which the acetyl residue is oxidized to two CO2 molecules.
11. Describe, using structural formulas, the transition of citrate to isocitrate, indicating all participants in the process. Answer :
12. Specify the enzymes of the Krebs cycle, the activity of which is allosterically inhibited by high concentrations of NADH+H + . Answer : Citrate synthase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase complex.
13. Write the reaction for the synthesis of oxaloacetic acid from pyruvate, indicating all the participants in the process. Answer :CH 2 -CO-COOH+ CO 2 + ATP -> COOH-CH 2 -CO-COOH + ADP + F.
14. Give a general scheme of the main respiratory chain of mitochondria. Answer :
15. Give the names of 1 enzyme complex from the composition of the main respiratory chain of mitochondria. Answer : NADH + H + ,KoQ- oxidoreductase complex.
16. Indicate the reason (driving force) forcing electrons to move along the carrier system of the main respiratory chain. Answer : The difference in redox potential between compounds at the beginning and at the end of the respiratory transport chain.
17. Define the term "oxidative phosphorylation at the substrate level". Answer : Synthesis of ATP using the energy released during the oxidation of a particular compound.
18. Give 2 examples of compounds that inhibit the work of 1 complex of the main chain of respiratory enzymes. Answer : Rotenone, sodium amytal.
19. Specify 2 possible reasons for the development of histotoxic hypoenergetic conditions. Answer : a) Blocking the work of the chain of respiratory enzymes, b) Uncoupling of oxidation and phosphorylation.
20. Name 2 compounds whose catabolism involves the microsomal oxidation system. Answer : Tryptophan, phenylalanine.
Introduction to Metabolism (Biochemistry)
Metabolism or metabolism is a set of chemical reactions in the body that provide it with the substances and energy necessary for life. The process of metabolism, accompanied by the formation of simpler compounds from complex ones, is referred to as catabolism. The process that goes in the opposite direction and ultimately leads to the formation of a complex product from relatively simpler ones is anabolism. Anabolic processes are accompanied by energy consumption, catabolic processes are accompanied by release.
Anabolism and catabolism are not simple reaction reversals. Anabolic pathways must be different from the catabolism pathways of at least one of the enzymatic reactions in order to be regulated independently, and by controlling the activity of these enzymes, the overall rate of decay and synthesis of substances is regulated. Enzymes that determine the speed of the entire process as a whole are called key.
Moreover, the path along which the catabolism of a particular molecule proceeds may be unsuitable for its synthesis for energy reasons. For example, the breakdown of glucose to pyruvate in the liver is a process consisting of 11 successive stages catalyzed by specific enzymes. It would seem that the synthesis of glucose from pyruvate should be a simple reversal of all these enzymatic steps of its breakdown. At first glance, this way seems both the most natural and the most economical. However, in reality, the biosynthesis of glucose (gluconeogenesis) in the liver proceeds differently. It includes only 8 of the 11 enzymatic steps involved in its breakdown, and the 3 missing steps are replaced in it by a completely different set of enzymatic reactions that are unique to this biosynthetic pathway. In addition, the reactions of catabolism and anabolism are often separated by membranes and occur in different cell compartments.
Table 8.1. Compartmentalization of some metabolic pathways in the hepatocyte
|
Compartment |
metabolic pathways |
|---|---|
|
Cytosol |
Glycolysis, many reactions of gluconeogenesis, amino acid activation, fatty acid synthesis |
|
plasma membrane |
Energy dependent transport systems |
|
DNA replication, synthesis of various types of RNA |
|
|
Ribosomes |
protein synthesis |
|
Lysosomes |
Isolation of hydrolytic enzymes |
|
Golgi complex |
Formation of the plasma membrane and secretory vesicles |
|
Microsomes |
Localization of catalase and amino acid oxidases |
|
Endoplasmic reticulum |
Lipid synthesis |
|
Mitochondria |
Tricarboxylic acid cycle, tissue respiration chain, fatty acid oxidation, oxidative phosphorylation |
Metabolism performs 4 functions:
1. supplying the body with chemical energy obtained from the breakdown of energy-rich food substances;
2. the transformation of nutrients into building blocks, which are used in the cell for the biosynthesis of macromolecules;
3. assembly of macromolecular (biopolymers) and supramolecular structures of a living organism, plastic and energy maintenance of its structure;
4. synthesis and destruction of those biomolecules that are necessary for the performance of specific functions of the cell and organism.
A metabolic pathway is a sequence of chemical transformations of a particular substance in the body. The intermediate products formed during the transformation process are called metabolites, and the last compound of the metabolic pathway is the final product. An example of a metabolic pathway is glycolysis, the synthesis of cholesterol.
A metabolic cycle is such a metabolic pathway, one of the end products of which is identical to one of the compounds involved in this process. The most important metabolic cycles in the human body are the tricarboxylic acid cycle (Krebs cycle) and the ornithine urea cycle.
Almost all metabolic reactions are ultimately interconnected, since the product of one enzymatic reaction serves as a substrate for another, which in this process plays the role of the next step. Thus, metabolism can be represented as an extremely complex network of enzymatic reactions. If the flow of nutrients in any one part of this network is reduced or disrupted, then changes in another part of the network can occur in response in order for this first change to be somehow balanced or compensated. Moreover, both catabolic and anabolic reactions are adjusted in such a way that they proceed in the most economical way, that is, with the least expenditure of energy and substances. For example, the oxidation of nutrients in a cell occurs at a rate just sufficient to satisfy its energy needs at the moment.
Specific and general pathways of catabolism
There are three stages in catabolism:
1. Polymers are converted into monomers (proteins into amino acids, carbohydrates into monosaccharides, lipids into glycerol and fatty acids). The chemical energy is dissipated in the form of heat.
2. Monomers are converted into common products, the vast majority into acetyl-CoA. Chemical energy is partly dissipated in the form of heat, partly accumulated in the form of reduced coenzyme forms (NADH, FADH2), and partly stored in macroergic bonds of ATP (substrate phosphorylation).
The 1st and 2nd stages of catabolism refer to specific pathways that are unique to the metabolism of proteins, lipids and carbohydrates.
3. The final stage catabolism, is reduced to the oxidation of acetyl-CoA to CO 2 and H 2 O in the reactions of the tricarboxylic acid cycle (Krebs cycle) - the general path of catabolism. Oxidative reactions of the general path of catabolism are associated with a chain of tissue respiration. At the same time, energy (40–45%) is stored in the form of ATP (oxidative phosphorylation).
As a result of specific and general pathways of catabolism, biopolymers (proteins, carbohydrates, lipids) break down to CO 2 , H 2 O and NH 3 , which are the main end products of catabolism.
Metabolites in normal and pathological conditions
Hundreds of metabolites are formed every second in a living cell. However, their concentrations are maintained at a certain level, which is a specific biochemical constant or reference value. In diseases, there is a change in the concentration of metabolites, which is the basis of biochemical laboratory diagnostics. Normal metabolites include glucose, urea, cholesterol, total serum protein, and a number of others. The output of the concentration of these substances beyond the limits of physiological norms (increase or decrease) indicates a violation of their metabolism in the body. Moreover, a number of substances in the body of a healthy person are found only in certain biological fluids, which is due to the specifics of their metabolism. For example, serum proteins do not normally pass through the kidney filter and are therefore not found in the urine. But with inflammation of the kidneys (glomerulonephritis), proteins (primarily albumins) penetrate the glomerular capsule, appear in the urine - proteinuria and are interpreted as pathological components of urine.
Pathological metabolites are myeloma proteins (Bence-Jones proteins), paraproteins in Waldenström's macroglobulinemia, the accumulation of abnormal glycogen in glycogenosis, various fractions of complex lipids in sphingolipidoses, etc. They are found only in diseases and are not characteristic of a healthy body.
Levels of study of metabolism
Levels of study of metabolism:
1. The whole organism.
2. Isolated organs (perfused).
3. Sections of tissues.
4. Cell cultures.
5. Tissue homogenates.
6. Isolated cell organelles.
7. Molecular level (purified enzymes, receptors, etc.).
Quite often, radioactive isotopes (3 H, 32 P, 14 C, 35 S, 18 O) are used to study metabolism, which mark substances introduced into the body. You can then follow the cellular localization of these substances, determine the half-life and their metabolic pathways.
Rice. 8.1. Diagram of specific and general pathways of catabolism
Chapter 9
The cell is a biological system, which is based on membrane structures that separate the cell from external environment, which form its compartments (compartments), as well as ensure the intake and removal of metabolites, the perception and transmission of signals, and are the structural organizers of metabolic pathways.
The coordinated functioning of membrane systems - receptors, enzymes, transport mechanisms helps maintain cell homeostasis and at the same time quickly respond to changes in the external environment.
Membranes are non-covalent supramolecular structures. The proteins and lipids in them are held together by a variety of non-covalent interactions (cooperative in nature).
The main functions of membranes include:
1. separation of the cell from the environment and the formation of intracellular compartments (compartments);
2. control and regulation of the transport of a huge variety of substances through membranes (selective permeability);
3. participation in providing intercellular interactions;
4. perception and signal transmission inside the cell (reception);
5. localization of enzymes;
6. energy-transforming function.
The membranes are asymmetric in structural and functional respects (carbohydrates are always localized on the outside and they are not on the inside of the membrane). These are dynamic structures: the proteins and lipids that make up them can move in the plane of the membrane (lateral diffusion). However, there is also a transition of proteins and lipids from one side of the membrane to the other (transverse diffusion, flip-flop), which occurs extremely slowly. The mobility and fluidity of membranes depend on its composition: the ratio of saturated and unsaturated fatty acids, as well as cholesterol. The lower the membrane fluidity, the higher the saturation of fatty acids in phospholipids and the higher the cholesterol content. In addition, membranes are characterized by self-assembly.
General properties cell membranes:
1. easily permeable to water and neutral lipophilic compounds;
2. less permeable to polar substances (sugars, amides);
3. poorly permeable to small ions (Na + , Cl - etc.);
4. characterized by high electrical resistance;
5. asymmetry;
6. can spontaneously restore integrity;
7. liquidity.
Chemical composition of membranes.
The membranes are composed of lipid and protein molecules, the relative amount of which varies widely in different membranes. Carbohydrates are contained in the form of glycoproteins, glycolipids and make up 0.5% -10% of the membrane substances. According to the fluid mosaic model of the membrane structure (Sanger and Nicholson, 1972), the basis of the membrane is a lipid bilayer, in the formation of which phospholipids and glycolipids participate. The lipid bilayer is formed by two rows of lipids, the hydrophobic radicals of which are hidden inside, and the hydrophilic groups are turned outward and are in contact with the aqueous medium. Protein molecules are, as it were, dissolved in the lipid bilayer and relatively freely "float in the lipid sea in the form of icebergs on which glycocalyx trees grow."
membrane lipids.
Membrane lipids are amphiphilic molecules, i.e. the molecule contains both hydrophilic groups (polar heads) and aliphatic radicals (hydrophobic tails), which spontaneously form a bilayer in which the lipid tails face each other. The thickness of one lipid layer is 2.5 nm, of which 1 nm falls on the head and 1.5 nm on the tail. There are three main types of lipids in membranes: phospholipids, glycolipids, and cholesterol. The average cholesterol/phospholipid molar ratio is 0.3-0.4, but in the plasma membrane this ratio is much higher (0.8-0.9). The presence of cholesterol in membranes reduces the mobility of fatty acids, reduces the lateral diffusion of lipids and proteins.
Phospholipids can be divided into glycerophospholipids and sphingophospholipids. The most common membrane glycerophospholipids are phosphatidylcholines and phosphatidylethanolamines. Each glycerophospholipid, such as phosphatidylcholine, is represented by several dozen phosphatidylcholines that differ from each other in the structure of fatty acid residues.
Glycerophospholipids account for 2–8% of all membrane phospholipids. The most common are phosphatidylinositols.
Specific phospholipids of the inner mitochondrial membrane, cardiolipins (diphosphatide glycerols), built on the basis of glycerol and two phosphatidic acid residues, account for about 22% of all mitochondrial membrane phospholipids.
in myelin sheath nerve cells sphingomyelins are contained in significant quantities.
Membrane glycolipids are represented by cerebrosides and gangliosides, in which the hydrophobic part is represented by ceramide. The hydrophilic group - a carbohydrate residue - is attached by a glycosidic bond to the hydroxyl group of the first carbon atom of ceramide. In significant quantities, glycolipids are found in the membranes of brain cells, epithelium and erythrocytes. Gangliosides of erythrocytes of different individuals differ in the structure of oligosaccharide chains and exhibit antigenic properties.
Cholesterol is present in all membranes of animal cells. Its molecule consists of a rigid hydrophobic core and a flexible hydrocarbon chain, the only hydroxyl group is the polar head.
Functions of membrane lipids.
Phospho- and glycolipids of membranes, in addition to participating in the formation of the lipid bilayer, perform a number of other functions. Membrane lipids form an environment for the functioning of membrane proteins, which adopt a native conformation in it.
Some membrane lipids are precursors of second messengers in the transmission of hormonal signals. So phosphatidylinositol diphosphate under the action of phospholipase C is hydrolyzed to diacylglycerol and inositol triphosphate, which are second messengers of hormones.
A number of lipids are involved in the fixation of anchored proteins. An example of an anchored protein is acetylcholinesterase, which is fixed on the postsynaptic membrane to phosphatitylinositol.
Membrane proteins.
Membrane proteins are responsible for the functional activity of membranes and account for 30 to 70% of them. Membrane proteins differ in their position in the membrane. They can penetrate deeply into the lipid bilayer or even permeate it - integral proteins, different ways attach to the membrane - surface proteins, or covalently contact with it - anchored proteins. Surface proteins are almost always glycosylated. Oligosaccharide residues protect the protein from proteolysis and are involved in ligand recognition and adhesion.
Proteins localized in the membrane perform structural and specific functions:
1. transport;
2. enzymatic;
3. receptor;
4. antigenic.
Mechanisms of membrane transport of substances
There are several ways of transporting substances through the membrane:
1. Simple diffusion- this is the transfer of small neutral molecules along the concentration gradient without the expenditure of energy and carriers. The easiest way to pass by simple diffusion through the lipid membrane is small non-polar molecules, such as O 2, steroids, thyroid hormones. Small polar uncharged molecules - CO 2 , NH 3 , H 2 O, ethanol and urea - also diffuse at a sufficient rate. Diffusion of glycerol is much slower, and glucose is practically unable to pass through the membrane on its own. For all charged molecules, regardless of size, the lipid membrane is impermeable.
2. Facilitated diffusion- transfer of a substance along a concentration gradient without energy expenditure, but with a carrier. characteristic of water-soluble substances. Facilitated diffusion differs from simple diffusion by a higher transfer rate and the ability to saturate. There are two types of facilitated diffusion:
Transport through special channels formed in transmembrane proteins (for example, cation-selective channels);
With the help of translocase proteins that interact with a specific ligand, they ensure its diffusion along a concentration gradient (ping-pong) (transfer of glucose into erythrocytes using the GLUT-1 carrier protein).
Kinetically, the transfer of substances by facilitated diffusion resembles an enzymatic reaction. For translocases, there is a saturating concentration of the ligand, at which all the binding sites of the protein with the ligand are occupied, and the proteins work with maximum speed. Therefore, the rate of transport of substances by facilitated diffusion depends not only on the concentration gradient of the transported substance, but also on the number of carrier backs in the membrane.
Simple and facilitated diffusion refers to passive transport, as it occurs without energy consumption.
3. Active transport- transport of a substance against a concentration gradient (uncharged particles) or an electrochemical gradient (for charged particles), requiring energy, most often ATP. There are two types of it: primary active transport uses the energy of ATP or redox potential and is carried out with the help of transport ATPases. The most common in the plasma membrane of human cells are Na +, K + - ATP-ase, Ca 2+ -ATP-ase, H + -ATP-ase.
In secondary active transport, an ion gradient is used, created on the membrane due to the operation of the primary active transport system (glucose absorption by intestinal cells and reabsorption of glucose and amino acids from primary urine by kidney cells, carried out when Na + ions move along the concentration gradient).
Transfer of macromolecules across the membrane. Transport proteins ensure the transport of polar molecules across the cell membrane small size, but they cannot transport macromolecules such as proteins, nucleic acids, polysaccharides, or individual particles.
The mechanisms by which cells can take up such substances or remove them from the cell are different from the mechanisms by which ions and polar compounds are transported.
1. Endocytosis. This is the transfer of a substance from the environment into the cell along with part of the plasma membrane. Through endocytosis (phagocytosis), cells can absorb large particles such as viruses, bacteria, or cell fragments. The absorption of liquid and substances dissolved in it with the help of small bubbles is called pinocytosis.
2. Exocytosis. Macromolecules, such as plasma proteins, peptide hormones, digestive enzymes, are synthesized in cells and then secreted into the extracellular space or blood. But the membrane is not permeable to such macromolecules or complexes; their secretion occurs by exocytosis. The body has both regulated and unregulated pathways of exocytosis. Unregulated secretion is characterized by continuous synthesis of secreted proteins. An example is the synthesis and secretion of collagen by fibroblasts to form the extracellular matrix.
Regulated secretion is characterized by the storage of molecules prepared for export in transport vesicles. With the help of regulated secretion, the release of digestive enzymes, as well as the secretion of hormones and neurotransmitters.
Chapter 10 biological oxidation
From the point of view of thermodynamics, living organisms are open systems. An exchange of energy is possible between the system and the environment, which occurs in accordance with the laws of thermodynamics. Each organic compound that enters the body has a certain amount of energy (E). Some of this energy can be used to do useful work. Such energy is called free energy (G). The direction of a chemical reaction is determined by the DG value. If this value is negative, then the reaction proceeds spontaneously. Such reactions are called exergonic. If DG is positive, then the reaction will proceed only when free energy comes from outside - these are endergonic reactions. In biological systems, thermodynamically unfavorable endergonic reactions can proceed only at the expense of the energy of exergonic reactions. Such reactions are called energetically coupled.
The most important function of many biological membranes is the transformation of one form of energy into another. Membranes with such functions are called energy-converting. Any membrane that performs an energy function is capable of converting the chemical energy of oxidized substrates or ATP into electrical energy, namely, into a transmembrane electric potential difference (DY) or into the energy of a difference in the concentrations of substances contained in solutions separated by a membrane, and vice versa. Among the energy-converting membranes having highest value, we can name the inner membrane of mitochondria, the outer cytoplasmic membrane, the membranes of lysosomes and the Golgi complex, the sarcoplasmic reticulum. The outer membrane of the mitochondria and the nuclear membrane cannot convert one form of energy into another.
Energy conversion in a living cell is described by the following general scheme:
Energy resources → ΔμI → work
where ΔμI is the transmembrane difference of the electrochemical potentials of the ion I. Consequently, the processes of energy utilization and performance of work due to it are coupled through the formation and use of ΔμI. Therefore, this ion can be called a conjugating ion. The main conjugating ion in the eukaryotic cell is H + , and accordingly ΔμH + is the main convertible form of energy storage. The second most important conjugating ion is Na + (ΔμNa +). While Ca 2+ , K + and Cl - are not used to do any work.
Biological oxidation is the process of dehydrogenation of a substrate with the help of intermediate hydrogen carriers and its final acceptor. If oxygen acts as the final acceptor, the process is called aerobic oxidation or tissue respiration, if the final acceptor is not oxygen - anaerobic oxidation. Anaerobic oxidation is of limited importance in the human body. The main function of biological oxidation is to provide the cell with energy in an accessible form.
Tissue respiration is the process of hydrogen oxidation with oxygen to water by the enzymes of the tissue respiration chain. It proceeds according to the following scheme:
A substance is oxidized if it donates electrons or simultaneously electrons and protons (hydrogen atoms), or attaches oxygen. The ability of a molecule to donate electrons to another molecule is determined by the redox potential (redox potential). Any compound can only donate electrons to a substance with a higher redox potential. An oxidizing agent and a reducing agent always form a conjugated pair.
There are 2 types of oxidizable substrates:
1. Pyridine-dependent - alcohol or aldehyde - isocitrate, α-ketoglutarate, pyruvate, malate, glutamate, β-hydroxyacyl-CoA, β-hydroxybutyrate - NAD-dependent dehydrogenases participate in their dehydrogenation.
2. flavin-dependent - are derivatives of hydrocarbons - succinate, acyl-CoA, glycerol-3-phosphate, choline - when dehydrogenated, they transfer hydrogen to FAD-dependent dehydrogenases.
The tissue respiration chain is a sequence of carriers of hydrogen protons (H+) and electrons from an oxidized substrate to oxygen localized on the inner membrane of mitochondria.
Rice. 10.1. Scheme of the CTD
CTD components:
1. NAD-dependent dehydrogenases dehydrate pyridine-dependent substrates and accept 2ē and one H + .
2. FAD (FMN) - dependent dehydrogenases accept 2 hydrogen atoms (2H + and 2ē). FMN-dependent dehydrogenase only dehydrates NADH, while FAD dehydrogenases oxidize flavin-dependent substrates.
3. Fat-soluble carrier ubiquinone (coenzyme Q, CoQ) - freely moves along the mitochondrial membrane and accepts two hydrogen atoms and turns into CoQH 2 (reduced form - ubiquinol).
4. Cytochrome system - transfers only electrons. Cytochromes are iron-containing proteins whose prosthetic group resembles heme in structure. In contrast to heme, the iron atom in cytochrome can reversibly change from two to the trivalent state (Fe 3+ + ē → Fe 2+). This ensures the participation of cytochrome in electron transport. Cytochromes act in ascending order of their redox potential and are located in the respiratory chain as follows: b-c 1 -c-a-a 3. The last two work in association as one enzyme, cytochrome oxidase aa 3 . Cytochrome oxidase consists of 6 subunits (2 - cytochrome a and 4 - cytochrome a 3). In cytochrome a 3, in addition to iron, there are copper atoms and it transfers electrons directly to oxygen. In this case, the oxygen atom becomes negatively charged and acquires the ability to interact with protons to form metabolic water.
Iron-sulfur proteins (FeS) contain non-heme iron and are involved in redox processes proceeding by a one-electron mechanism and are associated with flavoproteins and cytochrome b.
Structural organization of the tissue respiration chain
The components of the respiratory chain in the inner membrane of micochondria form complexes:
1. Complex I (NADH-CoQH 2 -reductase) - accepts electrons from mitochondrial NADH and transports them to CoQ. Protons are transported into the intermembrane space. FMN and iron-sulfur proteins are intermediate acceptors and carriers of protons and electrons. Complex I separates the flow of electrons and protons.
2. Complex II - succinate - KoQ - reductase - includes FAD-dependent dehydrogenases and iron-sulfur proteins. It transports electrons and protons from flavin-dependent substrates to ubiquinone, with the formation of an intermediate FADH 2 .
Ubiquinone easily moves across the membrane and transfers electrons to complex III.
3. Complex III - CoQH 2 - cytochrome c - reductase - contains cytochromes b and c 1, as well as iron-sulfur proteins. The functioning of CoQ with complex III leads to separation of the flow of protons and electrons: protons from the matrix are pumped into the intermembrane space of mitochondria, and electrons are transported further along the CTD.
4. Complex IV - cytochrome a - cytochrome oxidase - contains cytochrome oxidase and transports electrons to oxygen from the intermediate carrier of cytochrome c, which is a mobile component of the chain.
There are 2 types of CTD:
1. Complete chain - pyridine-dependent substrates enter it and betray hydrogen atoms to NAD-dependent dehydrogenases
2. Incomplete (shortened or reduced) CTD in which hydrogen atoms are transferred from FAD-dependent substrates, bypassing the first complex.
Oxidative phosphorylation of ATP
Oxidative phosphorylation is the process of ATP formation, coupled with the transport of electrons along the tissue respiration chain from the oxidized substrate to oxygen. Electrons always tend to move from electronegative to electropositive systems, so their transport through the CTD is accompanied by a decrease in free energy. In the respiratory chain, at each stage, the decrease in free energy occurs in steps. In this case, three sections can be distinguished in which the electron transfer is accompanied by a relatively large decrease in the free energy. These steps are able to provide energy for the synthesis of ATP, since the amount of free energy released is approximately equal to the energy required for the synthesis of ATP from ADP and phosphate.
To explain the mechanisms of conjugation of respiration and phosphorylation, a number of hypotheses have been put forward.
Mechanochemical or conformational (Green-Boyer).
During the transfer of protons and electrons, the conformation of enzyme proteins changes. They go into a new, energy-rich conformational state, and then, when they return to their original conformation, give energy for the synthesis of ATP.
Hypothesis of chemical conjugation (Lipman).
"Coupling" substances are involved in the conjugation of respiration and phosphorylation. They accept protons and electrons and interact with H 3 RO 4 . At the moment of donation of protons and electrons, the bond with phosphate becomes macroergic and the phosphate group is transferred to ADP with the formation of ATP by substrate phosphorylation. The hypothesis is logical, but "coupling" substances have not yet been isolated.
Chemiosmotic hypothesis by Peter Mitchell (1961)
The main postulates of this theory:
1. the inner membrane of mitochondria is impermeable to H + and OH − ions;
2. due to the energy of electron transport through complexes I, III and IV of the respiratory chain, protons are pumped out of the matrix;
3. the electrochemical potential arising on the membrane is an intermediate form of energy storage;
4. The return of protons to the mitochondrial matrix through the proton channel of ATP synthase is the energy supplier for ATP synthesis according to the scheme
ADP + H 3 RO 4 → ATP + H 2 O
Evidence for the chemioosmotic theory:
1. there is an H + gradient on the inner membrane and it can be measured;
2. the creation of an H + gradient in mitochondria is accompanied by the synthesis of ATP;
3. ionophores (uncouplers) that destroy the proton gradient and inhibit the synthesis of ATP;
4. inhibitors that block the transport of protons through the proton channels of ATP synthase inhibit the synthesis of ATP.
The structure of ATP synthase
ATP synthase is an integral protein of the inner membrane of mitochondria. It is located in close proximity to the respiratory chain and is referred to as complex V. ATP synthase consists of 2 subunits, referred to as F 0 and F 1 . The hydrophobic F0 complex is immersed in the inner mitochondrial membrane and consists of several protomers that form a channel through which protons are transferred to the matrix. The F 1 subunit protrudes into the mitochondrial matrix and consists of 9 protomers. Moreover, three of them bind the F 0 and F 1 subunits, forming a kind of leg and are sensitive to oligomycin.
The essence of the chemioosmotic theory: due to the energy of electron transfer along the CTD, protons move through the inner mitochondrial membrane into the intermembrane space, where an electrochemical potential (ΔμH +) is created, which leads to a conformational rearrangement of the ATP synthase active center, as a result of which the reverse transport of protons becomes possible through the proton channels of ATP synthase. When the protons return back, the electrochemical potential is transformed into the energy of the macroergic bond of ATP. The resulting ATP, with the help of the translocase carrier protein, moves to the cytosol of the cell, and in return ADP and Fn enter the matrix.
The phosphorylation coefficient (P/O) is the number of inorganic phosphate atoms included in ATP molecules, calculated per one atom of absorbed oxygen used.
Phosphorylation sites are sites in the respiratory chain where the energy of electron transport is used to generate a proton gradient, and then stored in the form of ATP during phosphorylation:
1. 1 point - between pyridine-dependent and flavin-dependent dehydrogenases; 2 point - between cytochromes b and c 1; 3 point - between cytochromes a and a 3.
2. Consequently, during the oxidation of NAD-dependent substrates, the P/O coefficient is 3, since electrons from NADH are transported with the participation of all CTD complexes. Oxidation of FAD-dependent substrates bypasses complex I of the respiratory chain and P/O is 2.
Energy metabolism disorders
All living cells constantly need ATP for various activities. Violation of any stage of metabolism, leading to the cessation of ATP synthesis, is fatal to the cell. Tissues with high energy requirements (CNS, myocardium, kidneys, skeletal muscles and liver) are the most vulnerable. Conditions in which ATP synthesis is reduced are combined by the term "hypoenergetic". The causes of these conditions can be divided into two groups:
Alimentary - starvation and hypovitaminosis B2 and PP - there is a violation of the supply of oxidizable substrates in the CTD or the synthesis of coenzymes.
Hypoxic - occur when there is a violation of the delivery or utilization of oxygen in the cell.
CTD regulation.
It is carried out with the help of respiratory control.
Respiratory control is the regulation of the rate of electron transfer along the respiratory chain by the ratio of ATP/ADP. The lower this ratio, the more intense respiration and the more actively ATP is synthesized. If ATP is not used, and its concentration in the cell increases, then the flow of electrons to oxygen stops. Accumulation of ADP increases substrate oxidation and oxygen uptake. The respiratory control mechanism is characterized by high precision and has importance, because as a result of its action, the rate of ATP synthesis corresponds to the energy needs of the cell. There are no reserves of ATP in the cell. The relative concentrations of ATP/ADP in tissues vary within narrow limits, while the energy consumption of a cell can vary by dozens of times.
American biochemist D. Chance proposed to consider 5 states of mitochondria, in which the rate of their respiration is limited by certain factors:
1. Lack of SH 2 and ADP - the rate of respiration is very low.
2. Lack of SH 2 in the presence of ADP - the speed is limited.
3. There is SH 2 and ADP - respiration is very active (it is limited only by the speed of transport of ions through the membrane).
4. Lack of ADP in the presence of SH 2 - breathing is inhibited (state of respiratory control).
5. Lack of oxygen, in the presence of SH 2 and ADP - a state of anaerobiosis.
Mitochondria in a resting cell are in state 4, in which the rate of respiration is determined by the amount of ADP. During intensive work, they can be in state 3 (the possibilities of the respiratory chain are exhausted) or 5 (lack of oxygen) - hypoxia.
CTD inhibitors are medications, which block the transfer of electrons through the CTD. These include: barbiturates (amytal), which block the transport of electrons through complex I of the respiratory chain, the antibiotic antimycin blocks the oxidation of cytochrome b; carbon monoxide and cyanides inhibit cytochrome oxidase and block the transport of electrons to oxygen.
Inhibitors of oxidative phosphorylation (oligomycin) are substances that block the transport of H + through the proton channel of ATP synthase.
Uncouplers of oxidative phosphorylation (ionophores) are substances that suppress oxidative phosphorylation without affecting the process of electron transfer through CTD. The mechanism of action of uncouplers is that they are fat-soluble (lipophilic) substances and have the ability to bind protons and transfer them through the inner mitochondrial membrane to the matrix, bypassing the proton channel of ATP synthase. The energy released in this process is dissipated in the form of heat.
Artificial uncouplers - dinitrophenol, vitamin K derivatives (dicumarol), some antibiotics (valinomycin).
Natural uncouplers are products of lipid peroxidation, long chain fatty acids, large doses of iodine-containing thyroid hormones, thermogenin proteins.
The thermoregulatory function of tissue respiration is based on the uncoupling of respiration and phosphorylation. The mitochondria of brown adipose tissue produce more heat, since the thermogenin protein present in them uncouples oxidation and phosphorylation. It is essential in maintaining the body temperature of newborns.
Regulation of the rate of reactions in a particular metabolic pathway is often accomplished by changing the rate of one or perhaps two key reactions catalyzed by "regulatory enzymes". Some physicochemical factors that control the rate of an enzymatic reaction, such as substrate concentration (see Chapter 9), are of paramount importance in regulating the overall rate of formation of a product of a given metabolic pathway. At the same time, other factors that affect the activity of enzymes, such as temperature and pH, are constant in warm-blooded animals and practically do not matter for the regulation of the rate of metabolic processes. (Note, however, the change in pH along the gastrointestinal tract and its effect on digestion; see chapter 53.)
Equilibrium and non-equilibrium reactions
When equilibrium is reached, the forward and reverse reactions proceed at the same rate, and hence the product and substrate concentrations remain constant. Many metabolic reactions take place under such conditions, that is, they are "equilibrium".
Under stationary conditions in vivo, the reaction proceeding from left to right is possible due to the continuous supply of the substrate and the constant removal of product D. Such a pathway could function, but there would be little opportunity to regulate its rate by changing the activity of the enzyme, since an increase in activity would only lead to faster balance.
In fact, in the metabolic pathway, as a rule, there are one or more reactions of a "non-equilibrium" type, the concentrations of reactants of which are far from equilibrium. When the reaction proceeds in an equilibrium state, free energy is dissipated in the form of heat, and the reaction turns out to be practically irreversible.
In this way, the flow of reactants goes in a certain direction, but without a control system, it will be depleted. The concentrations of enzymes that catalyze nonequilibrium reactions are usually low, and the activity of enzymes is regulated by special mechanisms; these mechanisms operate on the principle of a "one-way" valve and allow you to control the rate of product formation.
The rate-determining reaction of the metabolic pathway
The rate-determining reaction is the first reaction of the metabolic pathway whose enzyme is saturated with the substrate. It can be defined as a "non-equilibrium" reaction, characterized by a value significantly less than the normal concentration of the substrate. The first reaction of glycolysis, catalyzed by hexokinase (Figure 22.2), is an example of such a rate-determining reaction.
