Biochemistry

A.Y. 2019/2020
9
Max ECTS
80
Overall hours
SSD
BIO/10
Language
Italian
Learning objectives
The teaching aims to provide the educational elements related to living organisms, with particular attention to fundamental biochemical knowledge. Particular relevance is given to the understanding of the structure-function relationships of biological (macro)molecules and their interactions, the mechanism of action of some proteins and in particular of enzymes, the main metabolic pathways, highlighting the logic of organization, their regulation and interconnections.
Expected learning outcomes
At the end of the teaching class the student will be familiar with the nomenclature and structures of the main biological molecules and macromolecules. He/she will know the mechanisms of action of select proteins and have an analytical knowledge of the bases of enzyme kinetics and inhibition. Furthermore, the student will be expected to understand the energy and matter flows through metabolic cycles and their regulation, and have an in-depth knowledge of the main metabolic pathways that control the energy flow in the cell, the regulation and interconnection among the main metabolic pathways studied.
Learning these topics will be a fundamental element for the student to deal with the rest of the degree course with preparation and awareness. An aspect of considerable applicative importance is also the ability to identify in the panorama of the most modern methods of investigation those that are most suitable to answer the scientific questions that concern a modern active biologist.
Course syllabus and organization

A - L

Responsible
Lesson period
First semester
Course syllabus
- Bioelements, biomolecules and macromolecules. Water as the biological solvent. Role of weak interactions and pH in macromolecular structure and function.
- Nucleic acids: structure and physico-chemical properties of nucleotides , DNA and RNA.
- Proteins: Structure and properties of amino acids. The peptide bond. Polypeptides.
- Protein structure (primary, secondary, tertiary and quaternary structure; domains and motifs). Solution properties of proteins.
- An introduction to protein purification and structural characterization.
- Protein folding. Achievement of protein 3D structure: the folding process. -
- The basics of the biochemistry of DNA replication and transcription and Protein synthesis.
- Oxygen transport proteins: structure-function relations in myoglobin and hemoglobin.
- Enzymes: principles of enzyme catalysis; cofactors and coenzymes; Stereospecificity and stereochemical control of catalysis.
- Chemical kinetics and enzyme kinetics. Transition state theory. Steady-state kinetics and meaning of kinetic parameters. The Michaelis-Menten equation
- Inhibition and allosteric regulation of enzymes.
- Classification of biological reactions; reaction mechanisms of selected key enzymes.
- Energy changes in biological processes: free energy changes, chemical equilibria, relation between free energy change and oxidoreduction potential. Coupled reactions. Energy flux and high-energy compounds. ATP and metabolic role of phosphate transfer reactions.
- Metabolism: basic aspects of metabolic pathways and methods for their study.
- Glycolysis and fermentations. Gluconeogenesis. Glycogen metabolism and glycogen phosphorylase as an example of an allosterically and covalently regulated enzyme. Pentose phosphate shunt
- The pyruvate dehydrogenase complex.
- The Krebs cycle.
- The oxidative phosphorylation (electron transport chain and ATP synthesis)
- The basics of photosynthesis
- Fatty acid metabolism (beta oxidation and fatty acid biosynthesis)
- Amino acids synthesis and degradation (general principles), urea metabolism.
Prerequisites for admission
Students must be fully proficient (i.e. they are asked to have passed the respective first year exams) in General and inorganic chemistry and in Organic chemistry; Physical-chemistry; other courses in the first year provide additional useful cultural bases.
Teaching methods
Lectures will be issued interactively, using skemes and formulas on the blackboard together with PowerPoint slides, computer animations, molecular simulations and numerical exercises. Students will be strongly invited to attend lectures, participate actively in the discussions in order to improve his/her own critical capacities, rehearse the main concepts and learning the best way to communicate them. To facilitate all such activities, copies of the slides used for the lectures will be available through the Ariel platform, together with practical tests and examples from previous exam sessions.
Teaching Resources
The use of the latest edition of one of the following basic biochemistry textbooks is highly recommended:
- Appling, Antony-Cahill & Mathews: Biochimica, Molecole e Metabolismo (Pearson 2017)
- Nelson D.L. & Cox M.M. - Lehninger's Principles of Biochemistry, Worth Publishers / Zanichelli (2018)
- Voet D. & Voet, J.G. - Principles of Biochemistry, Wiley & Sons. / Zanichelli (2017)
- Mathews CK, Van Holde KE, Appling DR, Anthony-Cahill DR - Biochemistry- 4th Edition (2013) Pearson


Textbooks, reading material and complementary teaching material
Copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano (http://ariel.ctu.unimi.it). By no means these materials replace the lectures or a textbook. The material is made available only to registered students of the Degree Course in Biological Sciences and should not be distributed to others.
Assessment methods and Criteria
Students will reach a basic knowledge on the structure and composition of biological molecules and macromolecules, on their mechanisms in the context of a series of selected cell metabolic pathways. Moreover, students must be proficient with the energetics of biochemistry, with the associated thermodynamics and kinetic processes. The final exam consists of a written test, of about 12 open questions, covering the whole program developed over the course. Students will be offered (recommended for those that regularly attend the lectures) the possibility to split the full exam into two partial tests (at half and at the end of the course) that will have equal weights (50%) for the composition of the final scores.
BIO/10 - BIOCHEMISTRY - University credits: 9
Practicals: 16 hours
Lessons: 64 hours
Professor: Bolognesi Martino

M - Z

Lesson period
First semester
Course syllabus
- Bioelements, biomolecules and macromolecules. Water as the biological solvent. Role of weak interactions and pH in macromolecular structure and function.
- Nucleic acids: structure and physico-chemical properties of nucleotides , DNA and RNA.
- Proteins: Structure and properties of amino acids. The peptide bond. Polypeptides.
- Protein structure (primary, secondary, tertiary and quaternary structure; domains and motifs). Solution properties of proteins.
- An introduction to protein purification and structural characterization.
- Protein folding. Achievement of protein 3D structure: the folding process. -
- The basics of the biochemistry of DNA replication and transcription and Protein synthesis.
- Oxygen transport proteins: structure-function relations in myoglobin and hemoglobin.
- Enzymes: principles of enzyme catalysis; cofactors and coenzymes; Stereospecificity and stereochemical control of catalysis.
- Chemical kinetics and enzyme kinetics. Transition state theory. Steady-state kinetics and meaning of kinetic parameters. The Michaelis-Menten equation
- Inhibition and allosteric regulation of enzymes.
- Classification of biological reactions; reaction mechanisms of selected key enzymes.
- Energy changes in biological processes: free energy changes, chemical equilibria, relation between free energy change and oxidoreduction potential. Coupled reactions. Energy flux and high-energy compounds. ATP and metabolic role of phosphate transfer reactions.
- Metabolism: basic aspects of metabolic pathways and methods for their study.
- Glycolysis and fermentations. Gluconeogenesis. Glycogen metabolism and glycogen phosphorylase as an example of an allosterically and covalently regulated enzyme. Pentose phosphate shunt
- The pyruvate dehydrogenase complex.
- The Krebs cycle.
- The oxidative phosphorylation (electron transport chain and ATP synthesis)
- The basics of photosynthesis
- Fatty acid metabolism (beta oxidation and fatty acid biosynthesis)
- Amino acids synthesis and degradation (general principles), urea metabolism.
The formal lectures will be complemented by classroom sessions of problem solving, use of animations and molecular graphics and common discussions.
Prerequisites for admission
Students must be proficient in General and inorganic chemistry and in Organic chemistry and Physical-chemistry; the materials covered by first year classes provide additional useful cultural bases.
Teaching methods
The class will be based on classroom lectures supported by PowerPoint slides, computer animations, molecular simulations and numerical exercises. Students are strongly encouraged to attend lectures, actively participate in the discussions in order to improve his/her own critical skills, assimilate the main concepts and learn how to communicate them using the suitable technical vocabulary.
To facilitate all such activities, copies of the slides used for the lectures will be available through the Ariel platform, together with numerical problems and examples of previous exam papers (http://mavanonicb.ariel.ctu.unimi.it). The class will be taught in Italian with short summaries in English at the beginning/end of lectures.
Teaching Resources
The use of the latest edition of one of the following basic biochemistry textbooks is highly recommended:
- Nelson D.L. & Cox M.M. - Lehninger's Principles of Biochemistry, Worth Publishers/Zanichelli (2018)
- Voet D. & Voet, J.G. - Biochemistry, Wiley & Sons (latest edition).
- Mathews CK, Van Holde KE, Appling DR, Anthony-Cahill DR - Biochemistry- 4th Edition (2013) Pearson
- Appling, Antony-Cahill & Mathews: Biochimica, Molecole e Metabolismo (Pearson 2017)


Copies of the slides projected in the classroom as well as other materials will be made available through the course website on the ARIEL platform of the University of Milano (http://ariel.ctu.unimi.it). By no means these materials substitute for the lectures or a textbook. The material is made available only to registered students of the Degree Course in Biological Sciences and should not be distributed to others.
Assessment methods and Criteria
The final exam will consist of a written test, of about 12 open questions and numerical problems, covering the whole program developed during the class. Students will be offered the possibility to split the full exam into two partial tests (half-way through the class and at the end) that will have approximately equal weight towards the final grade. Such split test is highly recommended to students attending classes regularly.
BIO/10 - BIOCHEMISTRY - University credits: 9
Practicals: 16 hours
Lessons: 64 hours
Professor(s)
Reception:
Monday through Friday - previously setting the proper time
Dept. of BioSciences - Building C, 5th floor
Reception:
Monday, 1 pm -2 pm
Protein Biochemistry Unit, DSBB, Via Celoria 26, 5C