MedInTO Medicine and Surgery

Preparatory biochemistry and molecular biology

Preparatory biochemistry and molecular biology

Academic year 2017/2018

Sommario del corso

• Course objectives
• Results of learning outcomes
• Course delivery
• Learning assessment methods
• Support activities
• Program
• Suggested textbooks and readings
• Teaching tools

Course objectives

The syllabus aims to provide the  knowledge  required to undertake  the second semester course   "Biochemical and molecular basis of metabolism". In particular  it will provide essential concepts on  the nature of chemical bonds and chemical reactions,   the role of catalysts in advancing the chemical reactions, as well as  the role of electron transfer (oxidation - reduction) as the key step for  energy extraction  from nutrients. Moreover, the structure and classification of sugars, lipids, amino acids,  proteins and nucleic acids will be learned during the course. The catalytic role of enzymatic proteins and its  regulation will be proposed as a central topic for the future understanding of  metabolism.

This kind of basic knowledge is essential not only for the following courses in metabolic biochemistry and molecular biology, but also for a number of courses concerning both basic and applied biology and for many medical and clinical courses in the MD programme. Basic organic chemistry and biochemistry knowledge is essential for future MDs.  

Results of learning outcomes

At the end of the course, the Student will know basics of organic chemistry and molecular representation, and know the structural classification of basic biochemical molecules (sugars, lipids, aminoacids, nucleotides). They will also have introductory knowledge on the structure of proteins and molecular representation models, together with a basic knowledge of biochemical catalysis and macromolecular interaction principles.

The Student will have a clear understanding of how form and function of molecules are inextricably linked and how basic chemistry can explain the life of cells. On this framework the student will develop a true curiosity for the specific reactions that make up metabolism and make cells complex functional entities. The Student will be able to draw simple biochemical molecules (monosaccharides, fatty acids, aminoacids, nucleotides) and to recognize more complex molecules in the most common molecular representation formalisms.

Course delivery

Core activities consist of lectures given to the full class (64 hours), accompanied by exercises, made in the full class with the help of personal laptops + Ipads (provided by the Department).

Exercises consists in chemical formula drawing with the help of JME implemented in Moodle, molecular structure models, using JSMol in Moodle, and problem solving exercises + quizzes for testing comprehension. 14 hours of class exercises will be accompanied by on-line activities throughout the course. Classroom activities and selected on-line activities will be evaluated and will make part of the final evaluation (up to 7/30 points).

Learning assessment methods

The exam is based on a test, which is normally administered on the Moodle platform. The test will include multiple-choice questions, exercises and open questions, covering all the topics in the syllabus. Specific questions will be dedicated to verify the acquisition of a global and integrated vision of the topics. Exercises will test acquired abilities, such as interpreting a database screenshot or genome browser image. The test will give a score of up to 25/30 points. Participation in the practical classroom activities, as well as on-line complements, will be evaluated to up to 7/30 points at the exam. An oral  discussion may  follow  this test whenever the teachers or the students request to do so (for example in order  to clarify and discuss specific topics of the written exam, or in general to increase  the overall quality of the learning assessment ). Oral interview can modify the final score up to +/- 4 points.  

Support activities

A number of optional activities are offered on the Moodle Platform (http://medicina.i-learn.unito.it/) concerning further exercises on molecular structures, virtual visits to sites reporting molecular structures, and video or pages on specific aspects of the course, with no grading.

Program

GENERAL CHEMISTRY

• Short  review of  atoms, elements, molecules, compounds.

• The periodic table.

• Basics of thermochemistry.

• The chemical bonds.

• Features and classification of bonds in molecules. .

• Chemical reactions of precipitation, oxidation-reduction, acid-base.

• The oxidation number.

• Solutions, suspensions, colloids.

• Colligative properties.

• The speed of reactions: the rate equation, reaction mechanisms.

• Chemical equilibrium: the equilibrium constant, law of mass action.

• Acids and bases: definitions and equilibria in solutions of acids and bases.

• Salts and and buffers.

ORGANIC CHEMISTRY

• Hydrocarbons: physical-chemical properties, nomenclature and general reaction mechanisms. Isomers.

• Nomenclature, physical and chemical properties of and main reactions of: alkanes, alkenes, aromatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and derivatives, amines, amides.

PROPAEDEUTIC BIOCHEMISTRY

• Carbohydrates.

• The monosaccharides and derivatives: esters, acids, lactones, alditols, aminosugars. Disaccharides. The O-glucoside and N-glucoside bonds.

• Maltose, lactose, fructose, cellobiose.

• Omopolisaccarides and heteropolysaccarides.

• Glycogen storage diseases

• Glycoproteins.

• The Lipids. Fatty acids. Triglycerides.

• Glycerophospholipids and  Sphingolipids.

• Role of cholesterol in membranes.

• Phospholipids and cell membranes.

• Amino acids: structure and properties, proteic and non proteic

• modified aminoacids, titration curves, the peptidic bond.

Biochemical catalysis

• Enzyme kinetics: What is an enzyme? Katalysis in serine-proteases.

• Michaelis' equation, Vmax and Michaelis' constant.

• Effect of enzyme concentration on reaction speed.

• Kinetic analysis using v/[S] curve.

• Lineweaver-Burk, Eadie-Hofstee and Hanes methods for kinetic enzyme analysis.

• Reversible and irreversible inhibitors.

• Competitive, noncompetitive and competitive inhibitors.

• Product inhibition.

• Substrate driven inhibition. Inhibition constant (Ki).

• Multi-substrate reactions.

• Kinetic mechanisms (ordered sequential, random sequential, Ping-pong). Substrate concentration effects.

• Product and substrate inhibition.

• Kinetic parameters: Definitions.

• Allosteric enzymes characteristics.

• Allosteric mechanism.

Propaedeutic MOLECULAR BIOLOGY

• Protein structure: primary structure.

• Secondary structure components.

• Introduction to tertiary and quaternary protein structure.

• Domain organization in tertiary structure.

• Globins: Tertiary and quaternary structure.

• Functional characteristics of myoglobin and hemoglobin.

• Hemoglobin: O2/CO2 kinetics, Perutz model, mutations and functional implications.

• Immunoglobulins structure.

• Post-translational protein modifications.

• Protein turnover.

• Structures and functional meaning of protein protein-interactions (SH3, Coiled-coils, SH2).

• Protein:nucleic acid interactions. tRNA structure in aminoacyl-tRNA-synthetase recognition. Aminoacid charge selectivity.

• Catalysis by RNA: nucleoside-derived cofactors, ribozymes

F.A Bettelheim, W.H. Brown, M.K. Campbell, S.O. Farrell. Introduction to General, Organic, and Biochemistry.

Stryer, Biochemistry.

• Teaching materials
• Exams and finals
• Go to Moodle
• Visit the forums