introduction - people.unica.it · • introduction, program and reference textbooks • a few...
TRANSCRIPT
![Page 1: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/1.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Introduction
1
![Page 2: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/2.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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
2
![Page 3: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/3.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Outline
• Introduction, program and reference textbooks
3
![Page 4: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/4.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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
=2016&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=2016&mostra_percorsi=S
4
![Page 5: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/5.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Reference textbooxs Phillips et al., Physical Biology of the Cell, 2nd Edition
(2013), Garland Science Editor
5
• 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
![Page 6: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/6.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Reference textbooxs Philip Nelson, Biological Physics, Updated 1st Edition (2008),
Editor W. H. Freeman & Company
6
• 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
![Page 7: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/7.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Outline
• Introduction, program and reference textbooks
• A few definition and facts
7
![Page 8: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/8.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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
8
![Page 9: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/9.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Some general facts of Life • In contrast to inert materials, living
entities are made-up by several macromolecules, which are large,
structurally complex (often built by repeating blocks) and flexible entities.
• Four main macromolecules: nucleic acids, proteins, carbohydrates, lipids.
• Few organic atoms form constitutive blocks (covalently bound) of virtually all
macromolecules of life:
9
Nucleic acid
Lipid Carbohydrate
Protein
Atom C O N H S P
% 10.7 25.7 2.4 60.5 0.13 0.17
![Page 10: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/10.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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, signal transduction, 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…
10
![Page 11: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/11.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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
11
![Page 12: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/12.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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…)
12
![Page 13: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/13.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Models in physics • Physics set-up models to describe Nature’s behavior.
• Models work because hierarchical arrangement of Nature into levels, corresponding to processes occurring at different length scales.
• Different strategies to model processes of interest at any given length scale.
13
![Page 14: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/14.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Models in physics • Physics set-up models to describe Nature’s behavior.
• Models work because hierarchical arrangement of Nature into levels, corresponding to processes occurring at different length scales.
• Different strategies to model processes of interest at any given length scale.
14
Goal of biological physics
To understand how life emerges from fundamental physical and chemical interactions at different
ranges of space and time
![Page 15: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/15.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features • Same object can be modeled in a number of different ways.
– Depends on set of properties thought to be essential to describe process/system under study.
• Models usually complementary to each other.
– Emphasize different aspects of same object or process.
• No single representation or model of any system can give a full understanding of behavior of living cells!
– Each provides quantitative insights into some aspects of life.
– All together different models give a more realistic description than each of them, taken alone, does.
15
![Page 16: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/16.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
16
Models of DNA
![Page 17: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/17.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
17
Models of
Protein
Models of
Water
![Page 18: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/18.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
18
Models of Membranes
![Page 19: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/19.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
19
Models of a bacterium: E. coli
![Page 20: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/20.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
20
Modeling Mitochondria
Electron micrograph Cryo-electron microscopy
From experimental data…
![Page 21: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/21.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
21
Modeling Mitochondria
…to cartoon models of structure and functions
![Page 22: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/22.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
22
Modeling Mitochondria
…to cartoon models of structure and functions
![Page 23: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/23.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Modeling to catch key features
23
…to cartoon models of structure and functions
Don’t forget…
Each of these cartoons (and models) is the results of decades of efforts aiming to conceptualize a
usually large number of experimental evidences!!!
Modeling Mitochondria
![Page 24: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/24.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Quantitative models Despite giving key glimpses on process/system being modeled, usually cartoons fail to reproduce details of experimental data.
They are not quantitative
Indeed…models needs mathematics to pretend being quantitative (i.e. to reproduce numbers and trends).
24
![Page 25: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/25.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Some key physics laws in biology …just a few (broad) are sufficient to rigorously interpret many
(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
25
![Page 26: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/26.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
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).
26
![Page 27: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/27.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Key rules of thumb in biology
27
![Page 28: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/28.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
Key rules of thumb in biology
More numbers at the BioNumbers website: http://bionumbers.hms.harvard.edu
28
![Page 29: Introduction - people.unica.it · • Introduction, program and reference textbooks • A few definition and facts • Modeling of biological systems: – Models in space and time:](https://reader033.vdocument.in/reader033/viewer/2022043017/5f39dc59b375e453114346dd/html5/thumbnails/29.jpg)
Biophysics Course held at Physics Department, University of Cagliari, Italy. Academic Year: 2016/2017. Dr. Attilio Vittorio Vargiu PLEASE NOTE! This material is meant just as a guide, it does not substitute the books suggested for the Course.
References
• Books • Phillips, chap. 1
• Online resources • http://www.life.illinois.edu/crofts/bioph354/
29