FUNDAMENTALS OF ENZYME STRUCTURE AND KINETICS IN BIOLOGICAL SYSTEMS - O. A. Naumenko - 2017

5 List of Exam Questions

1. Definition of enzymology as a science.

2. Nomenclature and Classification of Enzymes (6 main classes). Introduction/14.html">Principles of Enzyme naming. Provide an example.

3. METABOLISM/2.html">THE CONCEPT OF monomers and oligomers.

4. Primary, secondary, and Tertiary Structure of monomeric Proteins. Elements of Protein Secondary structure.

5. Structure of oligomeric enzymes. Homogeneous and heterogeneous oligomers. The concept of Isoenzymes.

6. Supramolecular Organization of enzymes. Multi-enzyme complexes. Multi-enzyme conjugates. Multi-enzyme assemblies.

7. The Concept of the prosthetic group in complex enzymes. Definitions of apoenzyme, cofactor, and coenzyme. Enzyme Cofactors (inorganic and organic) and their role in enzymatic activity.

8. Principles of the Spatial Organization of enzyme molecules. Forces Stabilizing the tertiary structure of proteins.

9. The concept of activation energy, enthalpy, and Entropy. The Role of Hydrogen Bonds in The formation of the native Structure of enzymes.

10. Physical conformation of the tertiary structure of enzymes.

11. The role of disulfide covalent bonds in the formation of protein tertiary structure.

12. The Mechanism of protein folding into tertiary conformation.

13. Levinthal's paradox and its resolution. Properties of the native protein conformation.

14. Stages of Protein folding. The hierarchical principle of folding.

15. Intracellular Regulation of the Spatial Structure formation in proteins. Two regulatory mechanisms: folding rate and Protection of the protein against non-specific aggregation.

16. The concept of chaperones and chaperonins. Their significance in the Formation of the tertiary structure of enzyme proteins.

17. Domains: Structural and functional characteristics. Evidence for the domain stage of protein folding. Properties of domains.

18. STRUCTURE OF THE Active Site of an enzyme. Single-component and two-component active sites. Organization of two-component active sites.

19. Formation of the enzyme active site. Characteristics of nucleophilic and electrophilic R-groups involved in the active site structure.

20. Localization of the enzyme active site. Environmental properties of the enzyme active site.

21. The concept of the enzyme-substrate complex. CHARACTERISTICS OF THE bonds involved in complex formation. The concept of the "chelate" complex.

22. Four main Mechanisms for the formation of chelate enzyme-substrate complexes in an aqueous solvent.

23. Stability of enzyme-Ligand complexes (estimation of Free energy of sorption). Factors reducing entropy during enzyme-ligand complex formation.

24. Contribution of hydrophobic interactions to the free energy of sorption during the formation of the enzyme-ligand complex.

25. Contribution of electrostatic and hydrogen bonds to the free energy of sorption during the formation of the enzyme-ligand complex.

26. Reasons for rate acceleration by enzymes.

27. The concept of complementarity between the enzyme and the substrate. Characteristics of binding energy during the formation of the enzyme-substrate complex. Forces stabilizing the enzyme-substrate complex.

28. Catalysis by Serine proteases. Characteristics of the enzyme-substrate complex in serine protease catalysis. The role of the Hydrogen bond in stabilizing the Transition State of the substrate in this type of catalysis.

29. The induced-fit theory of enzyme-substrate interaction. Thermodynamic essence of the theory (free energy of sorption).

30. The "strain" or "distortion" theory in the formation of the enzyme-substrate complex. Thermodynamic essence of the theory (free energy of sorption).

31. Definition of metabolism and its pathways. Types of regulatory mechanisms: intensive and extensive. The concept of constitutive and adaptive enzymes.

32. Classification of mechanisms regulating enzyme activity via the intensive pathway.

33. Types of inhibition. Competitive and uncompetitive inhibition.

34. Irreversible covalent modification (Limited proteolysis).

35. Reversible covalent modification. Regulation by covalent binding.

36. The concept of activators and inhibitors. Reversible and irreversible Enzyme Inhibition.

37. Mechanisms of ENZYME ACTIVITY REGULATION without covalent modification.

38. Concerted allosteric model of regulation.

39. Types of allosteric interactions (homotropic and heterotropic).

40. MECHANISMS OF ENZYME activity regulation without covalent modification.

41. Sequential allosteric model of regulation.

42. Regulation of enzyme Activity by specific ligands: the substrate and a specific effector.

43. Mechanisms of enzyme activity regulation without covalent modification.

44. Dissociative mechanism of regulation. The concept of protomers and chimerae. Two Types of protomer association into chimerae: isologous and heterologous. Their role in The regulation of enzyme activity.

45. Mechanisms of enzyme activity regulation without covalent modification. Adsorption mechanism of regulation. Its physiological significance and the localization of adsorbed enzyme forms on subcellular structures. The concept of metabolite compartmentalization at the membrane.

46. Three Main Mechanisms of adsorption regulation.

47. Significance of the adsorption mechanism of regulation. Metabolite compartmentalization.

48. Relay-race model of enzyme action.

49. Adsorptive regulatory mechanism, its significance, and the "relay-race model" of enzyme action.

50. Enzyme kinetics. Thermodynamic processes and their types.

51. Thermodynamic systems and their types.

52. First law of Thermodynamics.

53. Second law of thermodynamics.

54. Enthalpy and entropy.

55. Characteristic Functions in thermodynamics.

56. Chemical kinetics. Reaction order and Methods for its determination.

57. Michaelis-Menten Equation.

58. Limitations of Michaelis-Menten kinetics. Seven core postulates for applying the Michaelis-Menten equation.

59. Formation of the kinetically stable enzyme-substrate complex (justification of the first postulate).

60. Nature of the constant K in the Michaelis-Menten equation.

61. Approximate solution of the Michaelis-Menten equation for long reaction times (justification of the second postulate).

62. Metabolism and its functions, REGULATION OF METABOLISM. Catabolism and anabolism, and their interrelationship.

63. Sequence of metabolic processes and stages of ENERGY EXTRACTION FROM nutrients.

64. Pathways of oxygen consumption (Biological Oxidation). The concept of redox potential. Nernst equation.

65. The concept of tissue Respiration, its stages, and calculation of the respiratory quotient.

66. Components of the Cell/36.html">Respiratory Chain and types of substrate oxidation. The concept of complete and truncated respiratory chains.

67. Oxidative Phosphorylation. Definition. Mechanism. Stages.

68. Quantitative evaluation of oxidative phosphorylation

69. Tricarboxylic Acid Cycle. History of discovery. Sequence of reactions and characterization of enzymes.

70. Biological significance and regulation of The Tricarboxylic Acid Cycle.

Class="center">6 Test Question Bank

Section 1 General Principles of the Structural organization of enzyme proteins

1.1 According to modern international nomenclature, enzyme names include:

a) historical names;

b) names of enzymes based on the type of catalyzed reaction;

c) names of enzymes based on the substrate of the reaction;

d) according to The structure of the enzyme;

e) according to classes, subclasses, and sub-subclasses.

1.2 Structurally distinct and spatially separated regions of a protein molecule that possess a certain degree of structural autonomy are called:

a) subunits;

b) conjugates;

c) domains;

d) active sites.

1.3 The nomenclature (sequential numbering) of isoenzymes is based on:

a) the number of subunits;

b) molecular weight;

c) electrical mobility in catalysis;

d) chemical activity in catalysis.

1.4 Which enzymes catalyze isomerization reactions:

a) oxidoreductases;

b) ligases;

c) Hydrolases

d) isomerases.

1.5 Which enzymes catalyze the Cleavage of a substrate to form an unsaturated product:

a) oxidoreductases;

b) ligases;

c) hydrolases;

d) lyases;

d) transferases.

1.6 Which groups of enzymes are distinguished by the structure of their protein molecule:

a) monomorphic;

b) monomeric;

c) multienzyme;

d) oligomeric;

e) isomeric.

1.7 A homogeneous oligomer consists of:

a) identical subunits;

b) different subunits;

c) identical domains;

d) different domains;

1.8 An oligomer consisting of four subunits of two types can have:

a) 2 isomers;

b) 6 isomers;

c) 4 isomers;

d) 5 isomers.

1.9 Regions of hydrophobic amino acid residues located on the hydrophilic shell of an enzyme play the role of (single-choice):

a) an inhibitor;

b) an activator;

c) a substrate-binding site;

d) a product-binding site.

1.10 During the folding process, a protein-enzyme tends to minimize the interface area in order to (single-choice):

a) increase entropy losses;

b) decrease entropy losses;

c) increase enthalpy;

d) decrease enthalpy.

1.11 The First stage of enzyme protein folding involves:

a) Formation of oligomers;

b) Formation of primary structure Polypeptides;

c) Formation of secondary structure elements;

d) Formation of protein supersecondary structure elements.

Section 2 GENERAL ISSUES IN Kinetics and Thermodynamics of Enzymatic Reactions

2.1 The set of bodies or substances involved in the exchange of matter or energy with each other and the environment is called

a) an open thermodynamic system

b) a closed thermodynamic system

c) an isolated thermodynamic system

d) None of the above

2.2 Intensive properties of a thermodynamic system include

a) Temperature

b) pressure

c) weight

d) volume

2.3 Characteristics of a reversible thermodynamic process in a thermodynamic system include

a) The work done on the system is maximal

b) The work done on the system is minimal

c) The work done by the system itself is minimal

d) The work done by the system itself is maximal

2.4 Endothermic reactions in a thermodynamic system are accompanied by

a) an increase in enthalpy

b) a decrease in enthalpy

в) - dH

г) + dH

2.5 If the value of dS in a thermodynamic system increases, this means

a) an increase in the ordering of substance molecules

б) a decrease in the ordering of substance molecules

в) an increase in the rotational degrees of freedom of molecules

г) a decrease in the rotational degrees of freedom of molecules

2.6 The Laws of Thermodynamics can be applied to

а) open thermodynamic systems

б) closed thermodynamic systems

в) isolated thermodynamic systems

г) none of the above

2.7 Extensive properties of a thermodynamic system include

а) temperature

б) pressure

в) weight

г) volume

2.8 Features of a non-equilibrium thermodynamic process in a system include

а) the work done on the system is maximal

б) the work done on the system is minimal

в) the work done by the system itself is minimal

г) the work done by the system itself is maximal

2.9 Exothermic reactions in a thermodynamic system are accompanied by

а) an increase in enthalpy

b) by a decrease in enthalpy

c) - dH

d) + dH

2.10 If the dS value in a thermodynamic system decreases, this indicates

a) an increase in the ordering of the substance molecules

b) a decrease in the ordering of the substance molecules

c) an increase in the degrees of freedom of rotational motion of the molecules

d) a decrease in the degrees of freedom of rotational motion of the molecules

2.11 From a physical standpoint, the order of a chemical reaction is determined by

a) The sequence of interaction of the reacting substances

b) the number of simultaneously reacting substances

c) the number of interacting molecules of the reacting substances

d) the number of interacting moles of the reacting substances

e) the number of interacting moles of the reacting substances

2.12 If 1 molecule of a substance participates in a chemical reaction, the reaction order is

a) zero

b) monomolecular

c) bimolecular

d) tetramolecular

2.13 The rate of an enzymatic reaction with respect to Enzyme Concentration

a) does not depend

b) depends directly (linearly)

c) depends non-linearly

d) depends inversely (linearly)

2.14 A sign of the stationary state of a chemical enzymatic reaction is

a) constant reaction rate

b) constant concentration of reacting substances

c) The ratio of The change in reaction rate to the change in reaction time is equal to "zero"

d) all of the above

2.15 The rate of an enzymatic reaction is determined by

a) enzyme activity in units of activity

b) the turnover number of the reaction per unit time

c) specific activity

d) none of the above