MedInTO Medicine and Surgery

Preparatory biochemistry

Preparatory biochemistry

Academic year 2018/2019

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

By the end of the course, the Student will know basic organic chemistry and molecular representation, the structural classification of basic biochemical molecules (sugars, lipids, enzymes, amino-acids). 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, amino-acids) 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 (56 hours), accompanied by exercises, made in the full class with the help of the blackboard, personal laptops or Ipads (provided by the Department) or online.

Learning assessment methods

The exam is based on a written test, taken on the Moodle platform. The test will include multiple-choice questions and exercises, 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.

An oral assessment may follow 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). The oral interview can both increase or decrease the initial grade.   

The maximum score for an all correct test will be of 33 points. 40% of the grading will be given for exercises and activities, divided into exercises in the form of a question with numeric answer and into multichoice questions. The maximum score for this part will be 12+2, with a minimum score to pass of 6 points. 60% of the grading will be credited to theoretical topics, in the form of multichoice questions, with a maximum score of 18+1, and a minimum score to pass of 12 points.

A score greater or equal to 18 is sufficient to pass the test (with the minimum grading on both parts satisfied).

Support activities

The following list of topics will be covered as a supporting teaching activity where the student will be able to connect the theoretical knowledge accumulated within the course to medical applications

• Hot and cold packs
• Sizes, rates and numbers in biochemistry
• Intravenous fluids
• Protein dialysis and hemodialysis
• Traditional and modern antacids
• The chemistry of kidney stones
• Alcohol metabolism and the breath analyzer
• Coumadin and the history of anticoagulants 
• The biochemistry of frying
• Protein folding related diseases

Program

GENERAL CHEMISTRY

• Short review of atoms, elements, molecules, compounds. Electron Configuration and the Aufbau Principle. Atomic and Molecular Orbitals. 
• The periodic table. Trends in the Periodic Table. Nomenclature of Inorganic Compounds. Characterization of s-, p-, d- and f- elements and their compounds
• Basics of thermochemistry. The Laws of Thermodynamics, Enthalpy, Entropy, Free Energy. 
• The chemical bonds. Features and classification of bonds in molecules, strong and weak forces
• Solutions, suspensions, colloids.
• Colligative properties.
• Chemical reactions: precipitation, oxidation-reduction, acid-base.
• Chemical kinetics: the speed of reactions: the rate equation, reaction mechanisms.
• Chemical equilibrium: the equilibrium constant, the law of mass action.
• Acids and bases: definitions, neutralization, titration and properties.
• Salts and buffers, pH, acidic properties of the blood.

ORGANIC CHEMISTRY

• Hydrocarbons: physical-chemical properties, nomenclature and general reaction mechanisms. Isomers.
• IUPAC nomenclature, physico-chemical properties and main reactions of: alkanes, alkenes, aromatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and derivatives, amines, amides

BIOLOGICAL MOLECULES

• Carbohydrates.

• The monosaccharides and derivatives: esters, acids, lactones, alditols, amino-sugars. Disaccharides. The O-glucoside and N-glucoside bonds
• Maltose, lactose, fructose, cellobiose
• Omo- and hetero-polysaccharides
• Glycogen storage diseases
• Glycoproteins
• Lipids.
• Fatty acids.
• Triglycerides.
• Glycerophospholipids and Sphingolipids.
• Role of cholesterol in membranes.
• Phospholipids and cell membranes.
• Enzymes
• features, cofactors and catalysis, catalytic site, classification
• enzyme kinetics, Michaelis-Menten’s equation
• inhibitors, kinetics and function
• allosteric enzymes
• catalytic mechanisms: the example of proteases
• overview of the regulatory strategies of enzymes

• Vitamins: a brief review of the classes and functions                      

PROTEINS

• Amino acids: structure and properties, proteinogenic and non-proteinogenic, modified amino-acids, titration curves, the peptide bond
• 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.
• Post-translational protein modifications.

1. P.Atkins, L. Jones, L. Laverman, Chemical principles: The quest for insight, McMillan Learning
2. H. S. Stoker. General, Organic & Biological chemistry, Cengage Learning -or- Mc Murry, Ballantine, Hoeger and Peterson, Fundamentals of General, Organic and Biological chemistry, Pearson
3. Biochemistry. Jeremy M Berg, John L Tymoczko, and Lubert Stryer. W. H. Freeman and Company- New York (from the 5th edition on). This book will also be largely used in the second-semester course "Biochemical and molecular basis of metabolism"

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