Biochemistry I

Semester 1st ()

Code MED_121

Hours Lectures, seminars and laboratory work 8 hours (per week)

Teachers

• STATHOPOULOS CONSTANTINOS (Professor)
• DINOS GEORGE (Professor)

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

1. 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.

2. 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.

3. 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 V_max of K_M 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:

1. 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.

2. Distinguish biomolecule classes, their structural organization and their intracellular localization and understand the importance of their homeostasis for human health.

3. Understand the structure and function of enzymes, transport proteins and nucleic acids, as well as the genes coding them.

4. 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.

5. 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

6. Perform experiments in the form of laboratory exercises related to diagnosis and interpret their results

7. 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

8. 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.

9. Communicate information, ideas, problems and solutions to both qualified and non-specialized audiences.

Reading Material

1. BergJ.M., TymoczkoJ.L. andStryerL. Biochemistry 8^th edition, 2015 W.H. Freeman and Company.

2. Devlin T.M.Textbook of Biochemistry with Clinical Correlations 7th Edition, Wiley-Liss.