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Lecture content
1) Introduction
2) Thermodynamics
3) Inter- and intra-molecular interactions
4) Diffusion
5) Transport processes
6) Biological Membranes
7) Bioenergetics
8) Neuron
9) Entropic forces
10) Selected biophysical methods
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Suggested reading
The Chemistry of Life Steven Rose. Penguin,
London 1999.
Physical Chemistry (5th edition). P.W. Atkins.
Oxford University Press, 1994.
http//biosci.umn.edu/biophys/OLTB
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What is Biophysics?

• Cellular mechanics membranes, DNA, proteins

• Molecular dynamics interactions that control
  gene expression

• Signal propagation neurons, sensory cells,
  chemotaxis

• Force generation muscle, cell motility

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Biophysics is the development and use of
instrumentation to study biological
macromolecules and processes

• Microscopy

• Spectroscopy

• Chromatography

• Micro manipulation/fluidics

• Simulation/Informatics

• Probes/Sensors

Biophysics is the science in which physical
concepts are used to explain biological phenomena
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The object ..........
Sequence Sequence of DNA and Proteins
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Structure 3D Structure of Proteins and other
biomolecules and molecular complexes
Interactions How molecules interact?
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Processes exists at many time scales ?
hierarchies of processes

• Macromolecules have a hierarchy of structures.

• Molecular machines have a hierarchy of states.

• Biological processes have a hierarchy of
  pathways.

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Length scale
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Energy
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The surface of the channel defines the volume
that is accessible to a probe of radius 0.14 nm,
about the size of a water molecule.
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Molecular Forces
A water molecule has one billion thermal
collisions with other molecules every second.
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Molecular Composition of Cells
Molecule of Total Cell Weight
Small Molecules (74 of Total Cell
Weight) ions and other inorganics 1.2 sugars
1 fatty acids 1 individual amino
acids 0.4 individual nucleotides 0.4 water
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Medium Big Molecules (26 of Total Cell
Weight) protein 15 RNA 6 DNA
1 lipids 2 polysaccharides 2
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Covalent bonds
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Selected numbers
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Conformation - surface outline or contour or 3-D
orientation of chemical groups that are free to
assume different positions in space without
breaking any bonds thanks to

• free rotation of atoms about a single chemical
  bond

• non-covalent forces hold atoms in spatial arrays

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DNA 1000 base pairs, 4 units (CATG) have ln4/ln2
2 bits to code each pair Itotal 2 bits 1000
base pairs 2000 bits average mass of (CATG)
307.5 amu average information 2/(2 307.5)
3.2510-3 bits amu-1
Protein 1000 amino acid residues, 20 amino acids
need ln20/ln2 4.32 4 bits to code each
residue Itotal 4 bits 1000 residues 4000
bits average mass of amino acid residue 118.9
amu average information 4.32/118.9 36.310-3
bits amu-1
There are 10 times more information per mass unit
in protein than DNA!
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For centuries, life was defined in the unit of
the whole organism...a cat, a bird, a human being.
Unlike atoms and simple molecules studied in
chemistry and physics, no two cells are identical.
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The Definition of Life rests in the Definition of
a Cell...
... self contained
... self assembling
... self adjusting
... self perpetuating
... isothermal mix of biomolecules,
... held in a 3-D conformation by weak
non-covalent forces,
... can extract raw materials free energy from
its surroundings,
... can catalyze reactions with specific
biocatalysts (enzymes), which it makes itself,
... shows great efficiency economy of metabolic
regulation,
... maintains a dynamic steady state far from
equilibrium,
... can self-replicate, using the linear
information, in the "molecule of life" DNA.
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Crowding !!!!
Biochemical reactions in living systems take
place in media containing 50400 mg/ml of
macromolecules.
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Experimentally observed crowding and confinement
effects on macromolecular reactions

• Stabilization of supercoiled conformations of
  DNA by PEG

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Biological Design
TENSEGRITY is a fundamental aspect of
SELF-ASSEMBLY - an architectural system,
mechanically stable, yet dynamic, where the
forces of tension and compression balance.
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The law of entropy can be temporarily blocked
(Life), but it can never be violated.
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Catabolic reaction - oxidation (removal) of e-s
from foodstuffs
1. Digestion of polymers (foods) into monomers
2. GLYCO-LYSIS
3. Oxidation CO2 NADH ? H2O
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The release of stored energy is coupled to
thermodynamically unfavorable reactions.
Metabolic reactions are violent events inside
cells, carefully controlled by ENZYMES
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Robustness the important task of the cell can
be completed even as conditions vary.
1. Various number of proteins per cell,
2. Different salinity, temperature and pH,
3. Nutrient level.
Engineering Cells for Robustness
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Cells Have Different Phases for Different
Functions