Biological chemistry I
BIO-212
This file is part of the content downloaded from Biological chemistry I.
Biological Chemistry I
Lecturers
Aleksandar Antanasijevic Matteo Dal Peraro
Language
English
Summary
Biochemistry is a key discipline in the Life Sciences. Biological
Chemistry I and II are two tightly interconnected courses that aims to
understand in molecular terms the processes that make life possible.Content
In this course we will learn the properties of biological macromolecules at the atomic level in order to understand their function within the cell. We will dissect therefore the basics of macromolecular structure and how it translates into functional molecular mechanisms. Among the major types of biological macromolecules, including nucleic acids, proteins, lipids and carbohydrates, we will put a major emphasis on proteins - the workhorses of cells. The content of the course will touch the following topics:
- Building blocks: Sugars, lipids, amino acids, oligonucleotides
- Protein structural organization, folding
- Analysis and visualization of proteins
- Protein expression and purification
- Protein structure determination by experimental and computational methods
- Thermodynamics and kinetics of biomolecules
- Methods to measure protein-protein and protein-ligand interactions
- Enzymatic catalysis and reaction mechanisms
Keywords
proteins, lipids, carbohydrates, nucleic acids, structural biology, biochemistry, enzymes, experimental and computational methods, protein folding, biophysics
Teaching methods
- Lectures
- Exercise session accompanying each lecture
- Execises session on bioinformatics and proteins structure visualization tools
Expected student activities
- Attending to classes
- Attendance to exercise
- Class participation
Assessment methods
- written exam - the exam will be an "open book" exam and what this means is that you are allowed to bring all the materials provided during the semester (slides, exercises, solutions), but not the recommended book (The Molecules of Life).
Teaching assistants
- Kiruthika Kumar – kiruthika.kumar@epfl.ch
- Alissa Agerova – alissa.agerova@epfl.ch
- Fernando Meireles – fernando.meireles@epfl.ch
- Evgenia Elizarova – evgenia.elizarova@epfl.ch
- Camilla DiGiulio - camilla.digiulio@epfl.ch
- Arthur Samurkas - arthur.samurkas@epfl.ch
- Yangyang Miao - yangyang.miao@epfl.ch
- Edoardo Cavani - edoardo.cavani@epfl.ch
Bibliography
and other various resources indicated during lectures.
- Lecture 1 - Molecular interactions, Nucleic acids (updated with solutions) (File)
- Lecture 1 - Exercises (File)
- Lecture 1 - Exercise Solutions (File)
- Lecture 2 - Nucleic acids and Lipids (File)
- Lecture 2 - Exercises (File)
- Lecture 2 - Exercise Solutions (File)
- Lecture 3 - Introduction to Carbohydrates and Proteins (File)
- Lecture 3 - Exercises (File)
- Lecture 3 - Exercise Solutions (File)
- Lecture 4 - Protein Folding and Thermodynamics (updated) (File)
- Lecture 4 - Exercises (File)
- Lecture 4 - Solutions (File)
- Lecture 5 - Introduction to Structural Biology (File)
- Lecture 5 - Exercises (File)
- Lecture 5 - Exercise solutions (File)
- Lecture 6 - Protein structure prediction and design (updated) (File)
- Lecture 6 - Visualisation practical (File)
- Lecture 6 - Visualisation practical solutions (File)
- info on BLAST (File)
- ran.pse (File)
- elec_density.pse (File)
- Lecture 7 - AlphaFold and PeSTo practical (File)
- Lecture 7 - AlphaFold and PeSTo practical - Solutions (File)
- 2V3M_B.pdb (File)
- Lecture 7 - Protein Design practical (File)
- Lecture 7 - Protein Design practical - Solutions (File)
- Lecture 8 - Exercises (File)
- Lecture 8 - Exercises with Solutions (File)
- Lecture 8 - Production and Purification of Biomolecules (File)
- Lecture 9 - Exercises - Updated (File)
- Lecture 9 - Exercises and solutions - Updated (File)
- Lecture 9 - Introduction to Biophysical Methods (File)
- Lecture 10 - Molecular mechanics, Boltzmann distribution, entropy (File)
- Lecture 10 - ExercisesSession (File)
- Lecture 10 - Solution of exercises (File)
- Extra material : Derivation of Boltzmann distribution (File)
- Lecture 11 - Chemical potential and molecular binding (updated) (File)
- Lecture 11 - Exercises (File)
- Lecture 11 - Solutions (updated) (File)
- Lecture 12 - Measuring Biomolecular Interactions (File)
- Lecture 12 - Exercises (File)
- Lecture 12 - Exercises and Solutions (File)
- Lecture 13 - Kinetics and Catalysis (File)
- Lecture 13 - Exercises and solutions (File)
- Lecture 13 - Exercises (File)
Lecture 14
- Lecture 14 - Biomolecule Engineering (File)
- BIO212 - Exam from 2023 (File)
- BIO212 - Exam from 2023 Answers (File)