96023 - Cell Physical Chemistry and Quantitative Biology

Learning outcomes

At the end of the course, the students know i) the physical-chemical principles governing the processes of energy transformations, diffusion and the kinetics of those processes in cells; ii) physical-chemical quantitative methods and approaches to study the cell biology. It includes making accurate measurements to test a predefined hypothesis and comparing the obtained experimental data with theoretical model predictions. The student is able to use calculation and experimental tools for the quantitative description of cellular processes.

Course contents

Cell Physical Chemistry and Cell Biology by the Numbers

The Geography of the Cells:

Their structures, the molecules that populate them and how they vary over time.

1. Size and Geometry.
   Cells, organelles, cellular building blocks, viruses. Visualizing cells and cell components, an excursus on state-of-the-art techniques
2. Molecular census of the cells: concentrations and absolute numbers.
3. Forces and Energies.
   Biology meets Physical Chemistry: First and second thermodynamic principles. Free energy and free energy in (bio)chemical reactions, equilibrium. Entropy and Entropy rules in the cell.
   Energetic currency, Forces, Energetic-budget in the cell.
4. States of matter. Phase diagrams and phase transitions. Systems with more than one phase or components. Chemical potentials. Properties of solutions with two components. Colligative properties. Focus on DNA, proteins and biological membranes.
5. Rates and Durations. Time scales for small molecules, Central dogma, Other Cellular processes, Cells life cycle. Chemical kinetics: reaction rate, order and molecularity. Enzymatic catalysis. Cellular dynamics and diffusion processes in the cell.
6. Hints on Functional imaging of living cells and biosensors.

Basic of Bio-Statistics

How to deal with quantitative data:

Basics of statistics and probability with applications to experimental data. Data analysis and plotting.

Theory and exercises.

Laboratory practice:

Practices on: i) DNA phase transition; ii) Determining the rates and kinetics of a biochemical reaction; iii) Quantitative physical-chemistry measurement of metabolic activity of cells.

Readings/Bibliography

Lecture notes and slides

Papers from scientific literature

Ron Milo, Rob Phillips. “Cell Biology by the numbers”. 1^st Ed. 2015

Whitlock, Schluter. "The Analysis of Biological Data". 2nd 2015 or 3rd Edition

Rob Phillips, Jane Kondev, Julie Theriot "Physical Biology of the Cell". 2nd Ed. 2012

P.W. Atkins, J. De Paula, Physical Chemistry for the Life Sciences, 2nd Edition

 

Teaching methods

The course consists in 32 hours of lectures. The course also comprises 12 hours of numerical exercises and 15 hours of laboratory practice.

As concerns the teaching methods of this course unit, all students must attend Module 1, 2 [https://www.unibo.it/en/services-and-opportunities/health-and-assistance/health-and-safety/online-course-on-health-and-safety-in-study-and-internship-areas] online, while Module 3 on health and safety is to be attended in class or on Microsoft Teams according to the modality chosen by the teacher. Information about Module 3 attendance schedule is available on the website of your degree program.

Assessment methods

The exams is written and oral. The written part consists of numerical exercises similar to those solved during the course. The oral exam (which can be taken after passing the written part) will ascertain the comprehension of the theoretical part of the course and of the laboratory practicals. A written report on the laboratory practice is also required.

Teaching tools

Videoprojector, laboratories, PC, online IOL platform.

Office hours

See the website of Stefania Rapino