COURSE CONTENT
Introduction. Biochemical processes in the living cell. Hierarchy of molecular organization in the cell. The four types of cellular macromolecules. Non-covalent interactions (ionic, van der Waals, hydrogen bonds).
Protein Structure. Properties of amino acids. The peptide bond. Simple and conjugated proteins. Levels of protein structure. Primary protein structure is determined by the nucleotide sequence of the gene. Methods for determining primary protein structure. Ramachandran plot. Secondary structures: ?-helix, ?-sheet, collagen helix, ?-turn. Tertiary structure. Globular and non-globular proteins. Quaternary structure of oligomeric proteins.
Protein Folding and Native Conformation. The amino acid sequence determines conformation. Stabilization of the native structure. Protein folding. Denaturation and renaturation of proteins.
Experimental Approaches to Proteins. Obtaining protein extract. Methods of protein isolation based on charge and size. Affinity chromatography. Determination of protein mass. Quantification and localization of proteins using antibodies. Determination of 3D protein structure. Automated protein synthesis.
Myoglobin and Hemoglobin. Spatial structure of myoglobin; oxygen binding to myoglobin. Tetrameric structure of hemoglobin. Hemoglobin as an allosteric protein; cooperative oxygen binding. Bohr effect. Binding of CO? and bisphosphoglycerate. Fetal and embryonic hemoglobin. Genetic diseases: sickle cell anemia and hemoglobin S, other hemoglobinopathies; thalassemias.
Basic Bioinformatics Methods in Protein and Nucleic Acid Analysis. Sequence alignment of amino acids and nucleotides, sequence database searches. Phylogenetic trees.
Introduction to Enzymes. Basic concepts of enzyme catalysis; enzyme efficiency and specificity; stereospecificity; kinetics of enzyme-catalyzed reactions (Michaelis-Menten model); inhibition; allosteric enzymes. Effect of inhibitors on enzyme kinetics. Allosteric enzymes do not follow Michaelis-Menten kinetics.
Enzyme Mechanism of Action ? Examples (lysozyme, serine proteases, alcohol dehydrogenase).
Regulation of Enzyme Activity. Enzymes with catalytic and regulatory subunits. Allosteric enzymes (e.g., aspartate transcarbamoylase). Regulation of enzyme activity via post-translational modifications (e.g., phosphorylation). Enzyme activation through proteolytic cleavage (chymotrypsinogen, trypsinogen). Cascade regulation: blood clotting factors and hemophilia.
Protein Degradation: Ubiquitination and degradation in the proteasome.
Structure and Biological Role of Carbohydrates. Polysaccharides. Disaccharides. Monosaccharides. Proteoglycans and glycoproteins. Protein glycosylation and the sugar code.
Structure and Dynamics of Biological Membranes. Types of lipids and proteins that make up membranes. Lipid bilayer and its properties; functions of membrane proteins; membrane asymmetry. Membrane reconstitution. Membrane potentials. Membrane permeability and transport. Signal transduction.
Basic Scheme of Metabolism. Catabolism and anabolism. Three stages of catabolic metabolism and energy production. Structure and function of ATP, major electron carriers, vitamins and coenzymes. Energy expenditure and fundamental features of biosynthetic reactions.
Carbohydrate Metabolism. Glycolysis: reactions of glucose breakdown to pyruvate. Reaction mechanisms. Gluconeogenesis: synthesis of glucose from non-carbohydrate precursors. Pentose phosphate pathway: generation of NADPH and pentose phosphates, transaldolase and transketolase reactions.
Polysaccharide Degradation and Biosynthesis. Reaction steps in glycogen breakdown; energy release. Glycogen synthesis and energy expenditure. Reaction mechanisms and regulation. Principles of metabolic regulation: glucose and glycogen.
LEARNING OUTCOMES
Explain the basic elements of protein structure, relate the interdependence of various structural levels, and demonstrate understanding of the relationship between protein structure and function.
Conclude that all cellular reactions are catalyzed by enzymes and show understanding of enzyme catalytic mechanisms.
Distinguish between different modes of enzyme activity regulation (from simple inhibition, through allosteric regulation and post-translational modification, to proteolytic degradation), relate them to each other and to the regulation of metabolic pathways and the physiological state of the cell.
Explain the structure and function of cellular membranes, describe the structures of their basic components, and compare different mechanisms of membrane transport.
Explain the biological role of carbohydrates and polysaccharides. Represent the structures of key examples and write reactions by which these compounds are synthesized and degraded in the cell.
Demonstrate understanding of general metabolic principles. Compare catabolic and biosynthetic glucose metabolism, distinguish reciprocal pathways, and describe their shared regulation.
Interpret organism- or tissue-specific features of metabolic pathway regulation and prevalence (e.g., bacteria, plants, mammals; liver, muscle, brain).
REQUIRED LITERATURE
D. L. Nelson and M. M. Cox: Lehninger Principles of Biochemistry, 8th ed., Macmillan Learning, 2021
SUPPLEMENTARY LITERATURE
J. Berg, G. Gatto Jr., J. Hines, J. L. Tymoczko, L. Stryer: Biochemistry, 10th ed., Macmillan Learning, 2023
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Lehninger Principles of Biochemistry, 8th ed, D. L. Nelson and M. M. Cox:, Macmillan Learning, 2021.
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Biochemistry, 10th ed, J. Berg, G. Gatto Jr., J. Hines, J. L. Tymoczko, L. Stryer, Macmillan Learning, 2023.
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