Biochemistry I
Semester 1st ()
Code MED_121
Hours Lectures, seminars and laboratory work 8 hours (per week)
Teachers
Description
1. INTRODUCTION TO BIOCHEMISTRY
Aqueous solutions of molecules and ions
Distinction between molecular and colloidal solutions.
Colligative properties of solutions (osmolarity)
Acids, bases, salts
Definitions, properties
Acids-bases titrations, equivalente point, neutral solution.
Water ionization, pΗ and Ionic strength of solutions
Buffer Solutions
Ηenderson-Hasselbalch equation
Preparation of buffer solutions
Solutions of chemical complexes
Definition and properties of Coordination compounds
Types of bonds of chemical complexes
Stability and instability constants
Biological significance of chemical complexes
2. STRUCTURE AND FUNCTION OF PROTEINS
Amino Acids and their properties
Peptides and Proteins
Importance of the nature of side chains of the amino acids in the properties of peptides and proteins.
Electrolytic behavior of proteins/ physicochemical properties
Amino acid and peptide bond stereochemistry
Determination of the amino acid sequence of proteins
Levels of organization of protein structure
Denaturation and denaturants. Importance of denaturation in protein’s biological activity
Protein purification methods
Structure-function relationships
3. NUCLEIC ACIDS AND FLOW OF THE GENETIC INFORMATION
Primary structure of nucleic acids
Sensitivity of nucleic acids primary structure to acids and bases
Secondary structure of nucleic acids (Α, Β and Ζ helices)
Tertiary structure of nucleic acids
DNA denaturation-rearrangement
Genes and genomes
Recombinant DNA technology
DNA sequencing
Bioinformatics
Homologous genes and phylogenetic trees
4. ENZYMES
General properties of enzymes
Enzymes classification
Coenzymes and prosthetic groups
Structure and biological significance of high-energy compounds (ATP, NADH, FADH2)
Kinetic analysis of enzymatic reactions (Activation energy)
Mechanisms of catalysis
Kinetics of first-order reactions
Inhibition of enzymatic reactions
Regulatory mechanisms of enzymatic function
Proteolytic activation of zymogens
Allosteric regulation of enzymes
5. STEREOCHEMISTRY OF BIOMOLECULES AND SUGARS
Enantiomeric and diastereomeric compounds
Stereoisomers D, L, R and S.
Molecular configurations
Chirality και and its biological applications
Cis-trans isomerization in molecules with double bonds
Simple monosaccharides, D- and L-Glyceraldehyde derivatives
Physicochemical properties
Ring structure of monosaccharides
Glycosidic bonds, oligosaccharides
Polysaccharides (starch, cellulose, agarose, cell wall polysaccharides, glycogen)
6. LIPIDS AND BIOLOGICAL MEMBRANES
Fatty acids, lipids and phospholipids
Composition and structure of membranes
Membrane fluidity and transport
Cell membrane receptors
7. MEMBRANE CHANELS AND PUMPS
Passive and active transport
Membrane transport proteins
Free energy transport and the Nerst potential equilibrium
Sodium-potassium pump (Να+/Κ+ΑΤΡase)
8. METABOLISM AND BIOENERGETICS
Constitutive thermodynamic equations (enthalpy, entropy, Gibbs free energy)
Characteristics of exergonic and endergonic reactions
Transformation of Gibbs free energy to transportation, mechanical and biosynthetic output
Effects of pH, temperature and ionic strength on the equilibrium constant
High-energy group transfer potential
Basic reactions of metabolic processes (redox, hydrolysis, carboxylation, decarboxylation, isomerisation)
Classification of reactions and reactants (mesomerism and resonance structures, nucleophilic and electrophilic attack, elimination reactions, tautomerization reactions).
LABORATORY CLASSES
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Becoming familiar with the laboratory space, introduction to health and safety regulations (use of chemical reagents, disposal, transfer of liquids). Learning the concepts of dilutions and preparation of simple aqueous solutions.
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Spectrophotometry. Theory and practical acquaintance with spectrophotometers. Determination of the optimal wavelength for paranitrophenol absorption, application of the Beer-Lambert law and determination of paranitrophenol concentration in an unknown sample.
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Kinetic study of the enzymatic activity of wheat acid phosphatase with para-nitro-phenol phosphate ester as the substrate. Study of reaction speed and determination of Vmax of KM and enzyme activity (U / L).
Scope
The course is an introduction to Biochemistry and to the fundamental reactions of metabolism that take place inside the cell. It includes the analysis of all basic aspects and methodology of Biochemistry in the study of the basic building blocks, their organization into macromolecules and their involvement in metabolic pathways and reactions that take place under normal and pathological conditions. The aim of the course is to understand the composition and complexity of the compounds participating in the main metabolic networks, and how these are altered and determined in different conditions, such as the change in enzymes activity or transport proteins.
Upon completion of the course the students should be able to:
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Understand the basic concepts of biochemistry and use the scientific literature to extract information in order to update their knowledge based on the latest scientific advances.
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Distinguish biomolecule classes, their structural organization and their intracellular localization and understand the importance of their homeostasis for human health.
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Understand the structure and function of enzymes, transport proteins and nucleic acids, as well as the genes coding them.
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Understand the basic motifs of the reactions taking place in a cell, as well as the importance of the enzymes that catalyze them and their potential as therapeutic targets.
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Recognize the importance of compounds that carry prosthetic groups or are responsible for the creation of redox potential and free radicals and how they relate to proper functioning of the human body, aging and disease
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Perform experiments in the form of laboratory exercises related to diagnosis and interpret their results
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Have the ability to collect and interpret relevant data within their knowledge field in order to make decisions on clinical and diagnostic issues as well as on wider scientific issues concerning scientific and ethical aspects
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Use the knowledge and understanding they have acquired in a way that shows a professional approach to their work or profession and have acquired the skills they typically demonstrate by developing and supporting arguments to solve problems within the field of biochemistry.
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Communicate information, ideas, problems and solutions to both qualified and non-specialized audiences.
Reading Material
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BergJ.M., TymoczkoJ.L. andStryerL. Biochemistry 8th edition, 2015 W.H. Freeman and Company.
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Devlin T.M.Textbook of Biochemistry with Clinical Correlations 7th Edition, Wiley-Liss.