MedInTO Medicine and Surgery

Preparatory Biochemistry

Preparatory Biochemistry

Academic year 2023/2024

Sommario del corso

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

Course objectives

The course will provide the basis for the understanding of the biochemical and molecular mechanisms of cellular and organism homeostasis. It will explore the correlation between the molecular structures and interactions and the cellular and organ functions and it will illustrate the deep molecular rationale for the action of drugs. 

These general objectives will be carried out by focusing on the deep mechanistic understanding of the chemical interactions between atoms and molecules. To this aim particular attention is devoted to the ability to solve problems and exercises in the context of both chemistry and biochemistry. 

The course will review all the essential concepts on 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 their regulation will be proposed as a central topic for the future understanding of metabolism.

The course will provide the necessary connections between general chemistry problems and medically relevant counterparts in order for students to acquire the correct motivation and understanding of the relevance of the proposed topics.

This kind of basic knowledge and its connection to medicine 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. 

Results of learning outcomes

By the end of the course, the student will be able to describe mechanistically how chemical reactions occur from energetic considerations, kinetic and equilibrium points of view. The student will be able to understand and apply the concepts of acid and base behaviour to biochemically/medically relevant problems. The student will be familiar with a number of medically related problems with important chemical connections.

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). The student will have developed the ability to recognize and draw simple biochemical molecules (monosaccharides, fatty acids, amino acids) and to recognize more complex molecules in the most common molecular representation formalisms, by identifying the most important functional groups.

Students 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.

Ultimately the student will have a clear understanding of how the 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. 

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 haemoglobin.
• Post-translational protein modifications.

Course delivery

Core activities consist of lectures given face-to-face to the full class. According to the learning objectives, in-class activities will be held with the help of online tools and software.

Lectures will be accompanied by exercises, made in the full class with the help of a blackboard.

Lectures' keynote slides, exercise handbook and all other learning material will be made available through the Moodle page of the course.

Particular attention will be devoted to the possibility of interacting directly with the teachers, through either dedicated sessions or other tools such as forums, chats, etc. We expect feedback from the students in order to make these moments effective and useful.

Some of the activities will be delivered as e-learning autonomous activities. Students will be instructed on how to proceed in a timely manner.

Students should remember that the only and official channel to receive information is Moodle's website. For obvious reasons, it is of paramount importance that you regularly check the learning material and the discussions and that you either request or give feedback when needed. Please note that notices will be sent via institutional email to you, which is also the only account that should be used in order to communicate with the teachers. Once you connect to the Moodle website indicated, you should be able to enrol in the course without any password, you need to have a working Unito account though. If you have trouble signing in please contact the teachers directly. Enrollment on Moodle is mandatory for the reasons described above.

Learning assessment methods

The exam is based on a written test, taken on the Moodle platform, in class.  The test will include multiple-choice questions and exercises, covering all the topics in the syllabus. Specific questions will be dedicated to verifying the acquisition of a global and integrated vision of the topics. The test is organized into separate sections with different overall aims.

A first written test is aimed at verifying the student’s basic knowledge. This will include molecules that students need to be able to recognize/draw, notions that represent the core knowledge of basic chemistry and biochemistry (examples: recognize simple sugars, chemical reactions, the definition of chemical bonds, pH, concentrations). This part of the test will follow a pass/not pass logic that will affect the whole exam. 10 out of 12 questions must be answered correctly in order to pass with a time of 15 minutes for the whole test. Students can administer their time as they wish, but no navigation of the test is allowed in this part, i.e. once the question is answered it is not possible to go back.

A second part of the test is instead formed by exercises and multiple-choice questions that involve more reasoning and a deeper understanding of the teaching material. This is a standard quiz with the usual questions and exercises. It will allow free navigation and it will allow a maximum score of 17 points, thereby having 10 of the first part plus 17 for maximum 27 points. A minimum score of 18 is necessary to pass the test.  

The oral discussion will be performed upon Student's or Professor's specific request, for example in order to clarify and discuss specific topics of the test, or to improve the grade. Oral interview can increase the written test grade to up to 6 points. It is of course possible that the oral will decrease the score.

Practical advice:

pre-enrol on the moodle exam platform as directed by the teachers, self enrolment will be open, please do that the day before the exam

Everybody in principle can listen to other people’s oral assessments. 

You will know your final score by the end of your own written test or oral assessment, you will then have to decide whether you accept it (irreversible decision) or not.

During the test you are allowed to check only the PDF with the math formulae and the periodic table, should you need it. (https://medicina.i-learn.unito.it/pluginfile.php/65861/mod_resource/content/0/formulae_to_be_known.pdf and https://medicina.i-learn.unito.it/pluginfile.php/51589/mod_resource/content/0/periodic-table_color.pdf )

The exam will be delivered through the specific moodle platform hosted on this website for everyone, where detailed instructions are posted and up to date.

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

As described, the course learning material will be uploaded during the course of the lectures on the Moodle's course website. However, it is recommended that the students complement the matierial with textbooks for completeness. These are the adopted textbooks:

1. H. S. Stoker, General, organic and biological chemistry, Cengage Learning, ISBN 9781285853918 (students can benefit from a 30% discount when purchasing their copies through our online store https://www.cengage.uk/; Discount code to use: ALG22BACKTOUNIVERSITY30 --The code will be valid from September 5^th until December 5^th and can be applied to either the print or eBook versions)
2. Biochemistry. Jeremy M. Berg, Lubert Stryer, John Tymoczko, Gregory Gatto, Macmillan Learning (from the 5th edition on). This book will also be largely used in the second-semester course Biochemical and molecular basis of metabolism.

Notes

Students with DSA or disabilities are kindly requested to take note of the reception services and support services offered by the University of Turin, and in particular of the procedures required for exam support.

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