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Docente
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GRGURINA INGEBORG
(programma)
BACHELOR DEGREE IN BIOINFORMATICS
COURSE OF BIOCHEMISTRY 1
Prof. Ingeborg Grgurina
(2018-2019)
INTRODUCTION TO PROTEINS
Basic Concepts of Thermodynamics and Kinetics. Enthalpy, the First Law of Thermodynamics. Entropy, the Second Law of Thermodynamics. Free Energy and Useful Work. Chemical Reaction Rates and the Effects of Catalysts. Transition States and Reaction Rates. (4 hours)
The Primary Level of Protein Structure. Structure, Stereochemistry and Acid-Base Properties of Amino Acids. The Peptide Bond. The Three-Dimensional Structure of Proteins.
Secondary Structure. Regular Ways to Fold the Polypeptide Chain. α-Helices and β-Sheets. Ramachandran Plots.
Tertiary Structure. Globular Proteins. Functional Diversity. The Interactions Stabilizing the Tertiary Structure: Charge–Charge Interactions, Internal Hydrogen Bonds Van der Waals Interactions, The Hydrophobic Effect, Disulfide Bonds. The Thermodynamics of Folding. Dynamics of Globular Protein Structure. Protein Misfolding and Disease. Prediction of Protein Secondary and Tertiary Structure. Collagen: Example of a Fibrous Protein (4 hours).
Quaternary Structure of Proteins. Multisubunit Proteins: Hemoglobin, Structure and Function. Oxygen Transport from Lungs to Tissues: Protein Conformational Change Enhances Function. The Oxygen-Binding Sites in Myoglobin and Hemoglobin. Analysis of Oxygen Binding by Myoglobin. The Role of Conformational Change in Oxygen Transport. Cooperative Binding and Allostery. Models for the Allosteric Change in Hemoglobin. Changes in Hemoglobin Structure Accompanying Oxygen Binding. Allosteric Effectors of Hemoglobin. The Bohr Effect. Hemoglobin Variants and Their Inheritance: Genetic Diseases (Sickle Cell Disease).
Antibody Structure and Function. The Adaptive Immune Response. The Structure of Antibodies. Antibody-Antigen Interactions. Shape and Charge Complementarity Interactions. Production of monoclonal antibodies. Production of antibodies which can recognize small molecules.( 6 hours).
ENZYMES AS BIOLOGICAL CATALYSTS
The Diversity of Enzyme Function. Reaction Rates, Rate Constants, and Reaction Order. Transition State Theory Applied to Enzymatic Catalysis. Mechanisms for Achieving Rate Acceleration: Principles and Examples (Serine Proteases). Models for Substrate Binding and Catalysis. Michaelis-Menten Kinetics. Interpreting KM, kcat and kcat/KM. Enzyme Inhibition. Competitive, Uncompetitive and Mixed Inhibition. Irreversible Inhibition. The Regulation of Enzyme Activity. Substrate-level Control. Feedback Control. Allosteric Enzymes. Covalent Modifications. (6 hours).
METABOLISM (20 hours)
Introduction
Overview and Chemical Logic of Metabolism. Catabolic and Anabolic Pathways. Distinct Pathways for Biosynthesis and Degradation. Compartmentation. ATP as a Free Energy Currency. Major Metabolic Control Mechanisms. Control of Enzyme Levels, Control of Enzyme Activity, Hormonal Regulation.
Experimental Analysis of Metabolism. Levels of Organization at Which Metabolism is Studied (Whole Organisms, Organs, Whole Cells, Cell-free Systems, Purified Components, Metabolic Probes. Metabolomics: Experimental Approaches and Fields of Application.
Carbohydrate Metabolism
Glycolysis. Chemical Strategy of Glycolysis. Reactions Leading from Glucose to Pyruvate. The Energy Investment Phase and Energy Generation Phase. Main Control Points. Regulation of Phosphofructokinase. Relation of Glycolysis to Other Pathways.
Metabolic Fates of Pyruvate. Lactate Metabolism. Ethanol Metabolism. Acetyl-CoA Formation: Pyruvate Dehydrogenase Complex.
The Pentose Phosphate Pathway. Oxidative and Nonoxidative Phase.
Gluconeogenesis: Reactions and Relation to Glycolysis. Coordinated Regulation of Glycolysis and Gluconeogenesis.
Glycogen: Structure and Function: Reactions Involved in the Breakdown and Biosynthesis of Glycogen. Coordinated Regulation of Glycogen Metabolism.
Lipids Metabolism
Triacylglycerol and Fatty Acid Metabolism: Degradation and Biosynthesis. Fatty acid oxidation: Fatty Acid Activation and Transport into Mitochondria. The β-Oxidation Pathway. Fatty Acid Biosynthesis by Multifunctional Proteins. Formation and Degradation of Triacylglycerols.
Citric Acid Cycle
Chemical Strategy, Reactions and Energetics of the Citric Acid Cycle.
Malfunctions of the Citric Acid Cycle as a Cause of Human Disease. Anaplerotic Sequences.
Electron Transport, Oxidative Phosphorylation
Free Energy Changes in Biological Oxidation. Mitochondrial Transport Systems. Respiratory Complexes, Electron Carriers in the Respiratory Chain. Chemioosmotic Coupling. The Structure of Mitochondrial ATP-Synthase Enzyme and Mechanism of ATP Synthesis.
Amino Acid Metabolism
Degradation and Biosynthesis of Amino Acids: Selected Examples. Transamination Reactions, Glutamate Dehydrogenase. Urea Cycle.
Problems and Exercices, Examples of metabolomic studies. (The role of metabolomic profiling in the identification of metabolic alterations in disease, of the metabolic pathways involved and in the detection of disease-specific biomarkers.) Analytical aspects (isotope labelling, protein purification, immunochemical techniques).
 TEXTBOOK
BIOCHEMISTRY: CONCEPTS AND CONNECTIONS, Global Edition
Dean R. Appling, Spencer J. Anthony-Cahill, Christopher K. Mathews,
ISBN-13: 9781292112008
2016 • Pearson •
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