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Biochemical and Molecular Basis of Metabolism

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Biochemical and Molecular Basis of Metabolism

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Academic year 2023/2024

Course ID
SCB0314
Teachers
Michele De Bortoli (Coordinator)
Santina Cutrupi
Marco Arese
Ymera Pignochino
Giulio Ferrero
Year
1st year
Teaching period
Second semester
Type
Basic
Credits/Recognition
11 (120 hours of lectures, 60 hours of exercises)
Course disciplinary sector (SSD)
BIO/10 - biochemistry
BIO/11 - molecular biology
INF/01 - informatics
Delivery
Formal authority
Language
English
Attendance
Mandatory
Type of examination
Written and oral
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Sommario del corso

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Course objectives

The program aims to introduce students to the biochemical basis necessary to deal effectively with medical problems. In particular, the production of energy and its use represents the core of the program as a paradigmatic example to understand life at a mechanistic level. The key concepts understudy will focus on how complex molecules that are found in living organisms create structures, carry out chemical reactions, and store and use the information to generate the remarkable properties of living organisms. Metabolism is also a key level in which a myriad of interactions between molecules illustrate the concepts of living cells and organisms as complex systems.

Biomedical knowledge is increasingly organized today in databases and knowledge repositories, spanning from genomics to metabolomics and pharmacogenomics. Consequently, the awareness of the biomedical data available and basic bioinformatic tools to deal with data is an absolute requirement in any Medicine curriculum, in order to guarantee the ability to access certified, robust and constantly adjourned information. This will be spent in many other courses in the following years.    

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Results of learning outcomes

At the end of the course, the student will have an in-depth knowledge of the chemical processes that extract energy from cells. Moreover, the student will mature the ability to observe biological phenomena and think of them as the result of complex interactions between single molecules. As a future MD, the student will be eager to search for disease-causing errors within this network of interactions and think of drugs as agents that can restore the physiological status.   

In addition, the Student will be able to obtain basic information on genes and proteins and how they are interacting at a network level, by interrogating the most common genomic and biomedical databases. This ability will be gained through tutored and autonomous bioinformatic activities in the computer room.

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Program

  • Metabolic Biochemistry
  • Metabolism:
    • Introduction to mechanisms of regulation of metabolic pathways;
    • The metabolome.
  • The metabolism of carbohydrates:
    • Glycolysis;
    • The metabolism of glycogen in the liver and muscles;
    • The citric acid cycle;
    • Electron transport, oxidative phosphorylation and regulation of ATP production;
    • Pentose phosphates;
    • Gluconeogenesis;
    • Digestion of carbohydrates;
    • Utilization of galactose, fructose, mannose;
    • Genetic diseases related to carbohydrate metabolism;
    • Regulation of carbohydrate metabolism by hormones and transcriptional circuits
  • Lipid metabolism:
    • The oxidation of fatty acids;
    • Biosynthesis of fatty acids;
    • Biosynthesis of phospholipids;
    • Biosynthesis of cholesterol and bile acids;
    • Prostanoids;
    • Regulation of lipid metabolism by hormones and transcriptional circuits;
    • The production and the effects of oxygen radicals.
  • Nucleic acid metabolism:
    • Purine biosynthesis;
    • Pyrimidine biosynthesis;
    • Purine catabolism;
    • Pyrimidine catabolism;
    • Genetic diseases related to nucleotide metabolism;
    • Regulation of nucleotide metabolism.
  • Protein metabolism:
    • The anabolic pathways of nitrogen;
    • Nitrogen fixation;
    • The synthesis of glutamate, glutamine, carbamoyl phosphate;
    • Paradigmatic examples of synthesis of amino acids: alanine, aspartate, cysteine, tyrosine;
    • The urea cycle;
    • The metabolism of heme.
  • Integration of metabolism:
    • Overview of metabolism connections and separation in the body;
    • The metabolism during stress, aerobic and anaerobic activity;
    • Metabolism of alcohol.
  • Special Topics Biochemistry
    • Biochemistry of the central nervous system

 

  • Metabolisms as molecular networks:
    • Basics of graph theory;
    • Circuits and Networks;
    • Metabolic networks;
    • Interaction between macromolecules: protein-protein, protein-DNA, protein-RNA, RNA-RNA;
    • Methods to assess molecular interactions;
    • Analysis of protein-DNA interaction and chromatin accessibility on a global scale.
  • Genomic Regulation:
    • Genome expression, regulation and control in development, homeostasis and disease;
    • Global analysis of gene structure and expression;
    • Epigenetic control of the genome;
    • Networks of transcriptional and post-transcriptional control of gene expression;
    • MicroRNA, lncRNA and their role in the circuits controlling acute, damped, homeostatic and cyclic responses; other roles of lncRNAs.
  • Functional genomics
    • The genome projects and their functional significance: ENCODE, GWAS, TCGA, 1000 Genomes and others;
    • Biological databases; primary and secondary databases; knowledge databases;
    • Reference database for medicine; OMIM, TCGA, and other databases of interest;
    • Tools for network and pathway analysis and visualization.
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Course delivery

Teaching is organized in both lectures and active learning parts. Lectures will accomplish for a total of 122 hours. For each Lecture package (6-8 hours), and accompanying active learning part will be accomplished both in the classrooms and online, based on the Moodle platform. Simple molecular design and modelling are performed online using JME and JSMol. Introductory use of biological databases is exercised using the NCBI and ENSEMBL websites. Knowledge databases as NCBI Gene, Gene Ontology, GEO, are used to recover information on specific components of simple metabolic pathways. Network and pathway analytical tools as those offered in KEGG, Wikipathways, REACTOME, are used to describe examples. Finally, specific examples of metabolic pathway alterations are explored using OMIM, TCGA and other phenotype-genotype databases.

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Learning assessment methods

  • moodle multichoice quiz
  • open questions
  • oral examination

Note:

For obvious reasons, depending on the number of participating students, the exam sessions could last up to three  days, in order to examine all students.   Students should be taking that into account in their planning. 

  • The quiz will evaluate the complete knowledge with respect to BMBM program
  • 50 closed questions. Time: 1h
  • The open questions will be done in the “traditional” approach: use of pen and paper to answer the questions; the materials will be provided at exam time. One question will be focused on metabolic reactions and, one question on molecular biology mechanisms. Time: 10 min.
  • Pass to interview: >18/30. The result of this test will be communicated as pass/non-pass only, without a score 
  • Only students that pass the written part are admitted to the oral examination 

Biochemistry. Two questions randomly extracted from a pool of open questions. Discussion time: 15 min

Molecular Biology. Two questions randomly extracted from a pool of open questions. Discussion time: 15 min

Final grading is the weighted average of the marks according to credits of each discipline

Final mark is expressed as a value out of 30 points.

If final mark is ≥18/30, BMBM exam is passed.

If final mark is <18/30, BMBM exam is failed. All parts  of the exam must reattempt in next sessions. 

If your final mark is 30/30, the outstanding results of all exam parts and active participation in the lessons will be honored “cum Laude". 

NOTE: GRADES  MUST BE EITHER ACCEPTED OR REFUSED IMMEDIATELY AFTER COMMUNICATION BY THE TEACHERS.  ABSENCE OR SILENCE OF THE STUDENT AT THAT MOMENT  WILL BE INTERPRETED AS A REFUSAL,  AND THE EXAM WILL BE CONSIDERED FAILED. 

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Support activities

A number of optional activities are available on the Moodle Platform (Moodle site), concerning further exercises on molecular structures, and verification quizzes at the end of each part (or Chapter).

Suggested readings and bibliography



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Book
Title:  
Biochemistry, 5th Ed.
Year of publication:  
2002
Publisher:  
W. H. Freeman
Author:  
Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert
ISBN  
Permalink:  
Required:  
Yes


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Book
Title:  
Lehninger Principles of Biochemistry
Year of publication:  
2008
Publisher:  
W.H. Freeman
Author:  
Nelson, David L.; Cox, Michael M.
ISBN  
Permalink:  
Required:  
Yes
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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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Teaching Modules

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