Molecular Biology, Medicinal Chemistry and Computer Science for Pharmaceutical Applications

LUCIANO DE SIO

The Fundamentals of Biophysics course provides students with basic biophysics knowledge aligned with the latest scientific and technological developments in modern medicine. The goal is to understand the fundamental principles of biophysics that underlie biomedical phenomena and new spectroscopic methodologies, while promoting an interdisciplinary perspective that integrates physical laws and concepts as applied to biology and medicine.
The course is organized into the following modules:
Part I (6 hours) – Fundamentals of physics: electric and magnetic fields, electromagnetic waves, geometric optics. Molecular interactions: covalent bonding, electrostatic, and van der Waals interactions.
Part II (6 hours) – Thermodynamics applied to biological systems: internal energy, free energy, reaction kinetics, energy associated with electromagnetic radiation.
Part III (12 hours) – Biological polymers: structure and function of nucleic acids (DNA, RNA) and proteins; protein folding mechanisms.
Part IV (6 hours) – Energy in living systems: energy metabolism, photosynthesis, ATP production. Study of biomembranes, nerve signal transmission, memory function, biomechanics, and hearing.
Part V (10 hours) – Techniques and methodologies: introduction to X-ray diffraction, electron microscopy, optical microscopy, and UV-Vis spectroscopy.
Part VI (8 hours) – Nanomaterials for drug delivery: plasmonic and organic nanoparticles, nanoparticle functionalization, photosensitive nanoparticles, and controlled drug release mechanisms.

At the end of this course, the student should be able to apply physics's main laws to understand biological systems.

Basic math skills (algebra, Euclidean geometry, and basic trigonometric functions).

Part I (6 hours) Electric/Magnetic field, electromagnetic waves, ray optics. Molecular interactions, ranging from covalent bonding to electrostatic and van-der-Waals interactions.
Part II (6 hours) Thermodynamics, Internal energy, Free energy, Rates of Reaction, Radiation Energy
Part III (12 hours) Biological Polymers: Nucleic acids (DNA, RNA), Proteins, Protein Folding
Part IV (6 hours) Biological energy: The energy of living systems is energy consumption, photosynthesis, and ATP production. Biomembranes, nerve signals, memory function, biomechanics, hearing.
Part V (10 hours) Some techniques and methods: X-ray diffraction, Scanning Tunneling Microscopy, Scanning Emission Microscopy, Transmission Emission microscopy, Optical Microscopy, and UV-Vis spectroscopy.
Part VI (8 hours) Nanomaterials for drug delivery: plasmonic nanoparticles, organic nanoparticles, nanoparticles functionalization, stimuli-responsive nanoparticles, examples of drug release.

Biophysics: An Introduction, Rodney M.J. Cotterill, John Wiley & Sons, LTD

Fundamentals of Physics: David Halliday, Robert Resnick, Jearl Walker John Wiley & Sons

The course occurs with lectures where students have required continuous interaction by favoring questions on the topics discussed during the lesson.

Attendance is not mandatory, although it is strongly suggested. However, students with an attendance >68% can present a research project instead of a standard written exam. The formal written exam consists in solving ten problems related to the topics of the course.

To be admitted to the oral exam, students must pass the written exam with a score of 18/30

Written exam: Research project (if the attendance is >68%)

Written exam: 10 problems (if the attendance is < 68%)

Describe a helpful spectroscopic technique to characterize a biological polymer.

• Lesson 1
  
  
  Electric and magnetic fields
  
  
  Electromagnetic waves: generation, propagation, and basic properties
  
  
  Connection between fields and biological matter


• Lesson 2
  
  
  Geometrical optics
  
  
  Reflection, refraction, and Snell’s law
  
  
  Optical systems and their applications in microscopy and vision


• Lesson 3
  
  
  Molecular interactions: covalent bonding, electrostatic and van der Waals forces
  
  
  Hydrogen bonding and molecular recognition in biological systems


• Lesson 4
  
  
  Fundamentals of thermodynamics
  
  
  Internal energy and energy transfer in biological systems


• Lesson 5
  
  
  Free energy and spontaneity of processes
  
  
  Relation between energy, equilibrium, and reaction direction


• Lesson 6
  
  
  Reaction kinetics and rate laws
  
  
  Activation energy and catalysis
  
  
  Energy of electromagnetic radiation and its biological effects


• Lesson 7
  
  
  Introduction to biological macromolecules
  
  
  Structure and properties of nucleic acids


• Lesson 8
  
  
  DNA: molecular structure, double helix, and base pairing
  
  
  DNA replication and repair mechanisms


• Lesson 9
  
  
  RNA: transcription, translation, and regulatory functions
  
  
  Structural differences between RNA and DNA


• Lesson 10
  
  
  Proteins: amino acids, peptide bonds, and primary structure
  
  
  Forces stabilizing secondary structures (α-helix, β-sheet)


• Lesson 11
  
  
  Tertiary and quaternary protein structure
  
  
  Protein folding and misfolding (e.g., prions, Alzheimer’s)


• Lesson 12
  
  
  Relationship between structure and function in biomolecules
  
  
  Experimental techniques for studying macromolecules


• Lesson 13
  
  
  Energy in living systems: energy flow and consumption
  
  
  ATP as the energy currency of the cell


• Lesson 14
  
  
  Photosynthesis and bioenergetics
  
  
  Electron transport chain and oxidative phosphorylation


• Lesson 15
  
  
  Biomembranes: structure, transport mechanisms, and membrane potential
  
  
  Nerve signals, memory function, biomechanics, and hearing


• Lesson 16
  
  
  Introduction to structural and optical characterization methods
  
  
  Interaction of radiation with matter


• Lesson 17
  
  
  X-ray diffraction: principles and applications in crystallography
  
  
  Determination of molecular structure


• Lesson 18
  
  
  Electron microscopy: TEM and SEM
  
  
  Resolution limits and biological sample preparation


• Lesson 19
  
  
  Optical microscopy and advanced imaging (fluorescence, confocal)
  
  
  Spectroscopy fundamentals


• Lesson 20
  
  
  UV-Visible spectroscopy
  
  
  Quantitative analysis of biomolecules (proteins, nucleic acids)


• Lesson 21
  
  
  Introduction to nanomaterials and nanomedicine
  
  
  Overview of drug delivery strategies


• Lesson 22
  
  
  Plasmonic nanoparticles: optical properties and photothermal effects
  
  
  Organic nanoparticles: liposomes and polymeric systems


• Lesson 23
  
  
  Surface functionalization of nanoparticles
  
  
  Targeting mechanisms and biocompatibility


• Lesson 24
  
  
  Photosensitive nanoparticles and light-controlled drug release
  
  
  Case studies: nanomedicine for cancer therapy and biosensing