introduction -...

Dispense del Corso di Biofisica, Dipartimento di Fisica, Università di Cagliari. A.A.: 2015/2016 Docente: Dott. Attilio Vittorio Vargiu NB: Queste dispense non sostituiscono il materiale didattico suggerito a piè del programma!

Introduction

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Outline

•  Introduction, program and reference textbooks

•  A few definition and facts

•  Modeling of biological systems:

–  Models in space and time: from molecules to the cell

–  Quantitative models

–  Mathematizing biology

–  Essential physics & biology to know

–  A few rules of thumb

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Outline


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Program of the Course The program is available at the following links

in Italian:

https://webstudenti.unica.it/esse3/Guide/PaginaADErogata.do;jsessionid=324CBC945F4B8ED7068BE5FCFC8

B9CCD?ad_er_id=2015*N0*N0*S1*19968*19133&ANNO_ACCADEMICO

=2015&mostra_percorsi=S

or in English:

https://webstudenti.unica.it/esse3/Guide/PaginaADErogata.do;jsessionid=324CBC945F4B8ED7068BE5FCFC8

B9CCD?cod_lingua=eng&ad_er_id=2015*N0*N0*S1*19968*19133&ANN

O_ACCADEMICO=2015&mostra_percorsi=S

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Reference textbooxs Phillips et al., Physical Biology of the Cell, 2nd Edition

(2013), Garland Science Editor

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•  Comprehensive and updated book on physical biology.

•  Access to multimedia and raw data, hints to solution of problems, etc. at:

http://microsite.garlandscience.com/pboc2/home.html


Reference textbooxs Philip Nelson, Biological Physics, Updated 1st Edition (2008),

Editor W. H. Freeman & Company

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•  Clear and exhaustive book on physical phenomena dictating behaviors of

biological systems.

•  New can be found here: http://www.macmillanhighered.com/Catalog/product/biologicalphysics-

firstedition-nelson

•  Free (old, uncorrected) pdf found here: http://maths.dur.ac.uk/users/

kasper.peeters/pdf/nelson_free.pdf


Outline



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Physical Biology Why physical biology?

Biology, as any other scientific discipline which aims to be quantitative, also needs quantitative data and models to greet them and make

reliable predictions.

Physical biology is a relatively new branch of life sciences, born to satisfy in a notch with the three following needs:

•  The need for quantitative data in biology

•  The need for quantitative interpretative models

•  The need for quantitative predictions by models

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Some general facts of Life

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•  In contrast to inert materials, living entities are made-up also

by several (four main ones) macromolecules, which are large, structurally complex (often built

by repeating blocks) and flexible entities.


Some general facts of Life

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Nucleic acid

Lipid Carbohydrate

Protein

•  In contrast to inert materials, living entities are made-up also

by several (four main ones) macromolecules, which are large, structurally complex (often built



Some general facts of Life •  In contrast to inert materials,

living entities are made-up also by several (four main ones)

macromolecules, which are large, structurally complex (often built


•  Only a few organic atoms are the constitutive blocks (covalently

bound) of virtually all macromolecules of life. They are: C, O, N, H, S, P with percentages

of 10.7, 25.7, 2.4, 60.5, 0.13 and 0.17% respectively.

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Nucleic acid

Lipid Carbohydrate

Protein


Some general facts of Life Different macromolecules perform different functions

•  Proteins structural elements, reaction catalysts, motors, etc…

•  Lipids barrier between cells and external world, compartmentalization into organelles, etc…

•  Nucleic acids memory and operating instructions allowing for building of new blocks and cell replication.

•  Carbohydrates energy storage, structural elements (e.g. cell walls), modify properties of external membranes, etc…

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Outline



•  Modeling of biological systems:

–  Models in space and time: from molecules to the cell

–  Quantitative models

–  Mathematizing biology

–  Essential physics & biology to know

–  A few rules of thumb

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Models of life Requires two main ingredients:

1. A series of experimental facts, grounds on which the model is built:

–  Building blocks of cells are proteins, nucleic acids, fatty acids, etc

–  Membranes of different kinds are responsible for compartmentalization

–  Cells are characterized by temporal cycles

–  …

–  Identify essential features in order to simplify abstraction level

2. A set of physical/chemical principles:

–  Biological processes and systems must obey laws of physics and chemistry (statistical mechanics, thermodynamics, conservation laws, etc…)

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Models in physics •  Physics set-up models to describe Nature’s behavior.

•  Models work because Nature is hierarchically arranged into levels corresponding to processes occurring at different length scales.

•  Different strategies are most successful to model processes of interest at any given length scale.

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Models in physics •  Physics set-up models to describe Nature’s behavior.

•  Models work because Nature is hierarchically arranged into levels corresponding to processes occurring at different length scales.

•  Different strategies are most successful to model processes of interest at any given length scale.

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Goal of biological physics

To understand how life emerges from fundamental physical and chemical interactions at different

ranges of space and time


Modeling to catch key features

•  The same object can be modeled in a number of different ways depending on the set of properties which is thought to be essential to

describe the process/system under study.

•  Models are usually complementary to each other, as they emphasize different aspects of the same object or process.

•  No representation or model of any system can give a full understanding of the behavior of living cells.

•  Each of them provides quantitative insights into some aspects of life.

•  All together different models give a more realistic description than each of them, taken alone, does.

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DNA



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Protein Water



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Membranes



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E. coli



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Mitochondria

Electron micrograph Cryo-electron microscopy

From experimental data…



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Mitochondria

…to cartoon models of structure and functions



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Mitochondria




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Mitochondria


Don’t forget…

Each of these cartoons (and models) is the results of decades of efforts at conceptualizing a usually

large number of experimental evidences!!!


Quantitative models Despite giving key glimpses on the process/system being modeled,

usually cartoons fail to reproduce details of experimental data (that is they are not quantitative).

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Indeed…models needs mathematics to pretend being quantitative (i.e. to reproduce numbers and trends).

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Some key physics laws in biology …just a few (broad) are sufficient to rigorously interpret many (but not

all of course) kinds of quantitative biological data…

•  Harmonic oscillator

•  Ideal gas/solution

•  Two-state systems and Ising statistical model

•  Random walks, entropy, macromolecular structure

•  Poisson-Boltzmann equation

•  Elastic theory of continuum materials

•  Newtonian fluids and Navier-Stokes equation

•  Diffusion and random walks

•  Rate equation models of chemical kinetics

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Some key biological foundations

•  All living organisms are related through descent from a common ancestor through evolution by natural selection (theory of evolution).

•  DNA is the carrier of genetic information (genetics and the nature of inheritance).

•  All living organisms are made up of cells (cell theory).

•  A few shared macromolecular assemblies implement similar functions in different organisms (unity of biochemistry).

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Key rules of thumb in biology

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Key rules of thumb in biology

More numbers at the BioNumbers website: http://bionumbers.hms.harvard.edu

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References

•  Books •  Phillips, chap. 1

•  Online resources •  http://www.life.illinois.edu/crofts/bioph354/

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