1. Biological Nanomaterials NANO*4100 FALL 2014
Lectures: M W F 13:30 – 14:20 MacN 201
Instructor: John Dutcher
Office: MacN 451
Phone + phone mail : Ext
Web:
Course Website:

2. Objectives of the Course
Understand the principles of the quantitative biology approach
Understand the basic building blocks of biology and how they bind to form biological molecules
Understand different interactions between biological molecules and the principles underlying the self-assembly of aggregates of biological molecules and nanomaterials
Appreciate the diversity and complexity of self-assembled biological nanomaterials
Expand scientific writing skills to develop
effective communication

3. Literature Required Text: “CD” directory with review & research papers
Available in the “cd” directory at:
Supplementary Reading :
Various journals related to biological molecules, biological materials, nanomaterials (see the website for links)
Please learn how to use internet to look for papers and to find their full texts. You should be familiar with the following: Entrez (PubMed); ISI Web of Knowledge (Science Citation Index and Biological Abstracts); Chemical Abstracts; Scholars Portal (or ScienceDirect); HighWire Press; Annual Reviews; ACS Publications

4. Evaluation
Problem Assignments 30% Directed Reading Assignments 15% Marking of NANO*1000 Report 5% Midterm Test 20% Final Examination 30% ____________________________________ Total 100%

5. Course Topics
• introduction to quantitative biology - power of physical approach to biological systems • introduction to biomolecules and biological membranes - building blocks and interactions • lipids and self-assembly of lipid structures • macromolecules: polymers - random walks & diffusion • macromolecules: proteins & DNA - building blocks and higher order structure • self-assembly of macromolecules - copolymers, protein filaments, peptide-based self-assembly • biological machines - bacterial flagella, myosin & kinesin walking, Brownian ratchet • bionanocomposites - unique properties

6. Guest Instructors Rob Wickham (Physics): copolymers
Leonid Brown (Physics): proteins
Doug Fudge (MCB): protein filaments

7. Soft Materials liquid crystals surfactants colloids polymers
biopolymers
cells
foods

8. Soft Materials bonding between molecules is weak
comparable to thermal energy kBT ~ 1/40 eV
can have big changes to soft materials with
small changes in environment
temperature, pH, ionic strength, applied fields

9. Soft Materials hydrogels As-prepared Swollen in water Swollen in NaCl
solution
Dried
C. Chang et al. Euro Polym J 46, 92 (2010)

10. Soft Materials rubber elasticity Stretched Unstretched
T. Russell, Science 297, 964 (2002)

11. Soft Materials drug delivery
heat-triggered dox release from Temperature Sensitive
Liposome due to MRI-guided high intensity focused
ultrasound
Grull & Langereis, J Controlled Release 161, 317 (2012)

12. Large Range of Length Scales
properties depend on length scale of measurement
complex, hierarchical structure
processing is the key
[P. Ball, Made to Measure]

13. Physics Meets Biology bring together biology & physics to get
biological physics
sophisticated experimental tools
sophisticated models of biological systems
Quantitative Biology
quantitative data demand quantitative models

14. PSI Biological Physics Projects
bacterial biophysics
viscoelastic properties of bacterial cells
bacterial twitching motility
Min protein oscillations & patterns
biopolymers at surfaces & membranes
single molecule pulling of proteins on nano-curved surfaces
single molecule imaging of peptides in lipid matrix
field driven changes in conformation & orientation
enzymatic degradation of cellulose
imaging & kinetics of adsorption & degradation
polysaccharide nanoparticles
startup company

15. Quantitative Biology eight fundamental concepts provide toolbox
for interpreting biological data
simple harmonic oscillator
ideal gas & ideal solutions
Ising model
random walks, entropy & diffusion
Poisson-Boltzmann model of charges in solution
elastic theory of 1D rods & 2D sheets
Newtonian fluid model & Navier-Stokes equations
rate equation models of chemical kinetics
Adapted from
Phillips et al., Physical Biology of the Cell

16. Quantitative Biology simple harmonic oscillator
Phillips et al., Physical Biology of the Cell

17. Quantitative Biology different levels of modeling
beyond the spherical cow
membrane
DNA
Phillips et al., Physical Biology of the Cell

18. Rules of Thumb
Phillips et al., Physical Biology of the Cell

19. Rules of Thumb
Phillips et al., Physical Biology of the Cell

20. Random Walks
Drunkard’s walk
Courtesy of George
Gamow

21. Random Walk – Common Theme
random walk is a recurring concept in course
helps with seemingly unrelated problems
diffusion of molecules, cells & nanomachines
polymer conformation
protein conformation
compact random walk
other non-obvious implementations
packing of chromosomes in nuclei
looping of DNA fragments
DNA melting
molecular motors

22. Polymer Conformation a N = 1000 Gaussian random walk (b) self-avoiding
Random coils are loosely-packed structures b

23. Self-Similarity of a Polymer Molecule

24. Swimming of Bacteria

25. Contribution of Physical Science to Biology Is Hard to Overestimate
RGS9-1
from Ridge et al.
PDE
X-ray
NMR
-1.5
+1.5
ppm (1H)
-5.5
+5.5
ppm (13C)
Gt/i1
ESR EM
Made it to here after first lecture F12

26. Case Study of Bacteriorhodopsin - Contribution of Physical Methods
7 transmembrane
helices
light-driven ion pump
Youtube video on bacteriorhodopsin
from Alberts et al.
from Luecke et al.

27. Case Study of Bacteriorhodopsin - Contribution of Physical Methods
UV/Vis spectroscopy - kinetics and thermodynamics of the photocycle, orientation of the chromophore (LD)
Raman spectroscopy - configuration of the retinal chromophore and its changes in the photocycle
FTIR spectroscopy - conformational changes of the protein and its chromophore in the photocycle, protonation changes of carboxylic acids
NMR spectroscopy - structure of protein fragments, orientation of the chromophore, dynamics of certain residues
ESR spectroscopy - protein topology, conformational changes
Electron, Neutron, X-ray diffraction - structure of the protein and its intermediates, location of water molecules
Atomic force microscopy - single molecule imaging & spectroscopy
Quantum chemistry/Molecular Dynamics - properties of the chromophore and its binding site

28. Cells Many different kinds of cells Prokaryotic cells
Relatively simple membrane structure
Few internal membranes
Eukaryotic cells
Plant cells
Plasma membrane inside
the cell wall
Internal chloroplasts
Animal cells
Plasma membrane
Nuclear membrane

29. Dynamics of Cells Youtube video on the Inner Life of the Cell
Swimming bacteria (Howard Berg)
Youtube video on the Inner Life of the Cell
from Biovisions Harvard
Pilus retraction
(Howard Berg)

30. Biological Membranes Major functions of cell membranes:
To separate interior and exterior of the cell
To maintain concentration gradients of various ions, which serve both as sources of energy and as a basis for excitability
To house functionally important protein complexes such as energy-producing machines, transporters, enzymes, and receptors
From Lodish et al

31. Biological Membranes
Cryo-electron microscopy reveals detailed structure
C. crescentus
Intestinal epithelial cells
Photoreceptors in rod cell
Mitochondrian surrounded
by endoplasmic reticulum
Phillips
S. aureus septum
V. Matias, U of Guelph
PhD thesis

32. Major Components of a Membrane
from Luecke et al.
Dalton: unified atomic mass unit (amu), 1 g/mol, mass of one nucleon
Lipid
Bilayer
Membrane
Proteins
Characteristic molecular weights
Lipids: kDa
Proteins: kDa
Other components: carbohydrates, water, ions

33. Fluid Mosaic Model
Singer & Nicolson, Science (1972)
From Cooper

34. Evolution of Membrane Models
Singer & Nicolson (1972)
Sackmann (1995)
Israelachvili (1978)
Phillips, Physical Biology of the Cell

35. Restrictions to Free Diffusion of Membrane Proteins
A – lipid microdomains
B, C – cytoskeleton
D – protein association
from Vereb et al.

36. Hydration of a Lipid Bilayer (MD Simulation)
from Popot and Engelman

37. Membrane Proteins and Lipids Are Often Linked with Carbohydrates (glycoproteins and glycolipids)
From Lodish et al

38. Building a Lipid Molecule
Start with fat
Long chain hydrocarbon
Different numbers of
carbons with either
Single bonds (saturated)
Double bonds (unsaturated)
Convert hydrocarbon chain to fatty acid by attaching
carboxyl (-COOH) group at end
Fatty acids are fundamental building block of lipids
2 to 36 carbons long, with most common between 14 & 22
Usually even number of carbons
most fatty acid chains are unsaturated
single double bond most common, up to 6 double bonds
e.g. oleic acid
e.g. DHA (docosahexaenoic acid)

39. Building a Lipid Molecule
fatty acids rarely found free in cell
chemical linking to hydrophobic group, e.g. glycerol, produces
non-polar lipid
di-acylglycerol has 2 fatty acids
Key lipid in signaling pathways
tri-acylglycerol is typical storage fat
can replace one of the fatty acids with a polar group
polar lipid or glycero-phospholipid
hydrophobic tail & hydrophilic head
e.g. PC, PE, PG, PI
PC: phosphatidylcholine or lecithin
PE: phosphatidylethanolamine
PG: phosphatidylglycerol
PI: phosphatidylinositol
neutral
charged

40. Building a Lipid Molecule
polar
hydrophobic
Fatty acid myristic acid (14:0)
Oleic acid (18:1)
DHA (22:6)
Di-acylglycerol of myristic acid
Tri-acylglycerol of stearic acid
(triglyceride)
glycerol
From Mouritsen

41. Building a Lipid Molecule
polar
hydrophobic
glycerol
DMPC lipid:
di-acylglycerol &
phosphatidylcholine
phosphate
choline
lysolipid
Phosphatic acid
From Mouritsen

42. Phospholipids: Structure Overview
Amphipathic Nature!
Polar, Hydrophilic
Non-Polar, Hydrophobic
Variable
From Renninger
Typical Phospholipid

43. Major Phospholipids
From Alberts et al
choline
phosphate
glycerol

44. Major Phospholipids From Mouritsen
Made it to here after second lecture F12
From Mouritsen

45. Major Phospholipids
From Mouritsen

46. Glyco(sphingo)lipids
From Alberts et al

47. Cholesterol “Stiffens” Fluid Membranes
From Alberts et al

48. Lipid Rafts
From Dykstra et al

49. Phase Transitions in Lipid Layers
Can use differential scanning calorimetry (DSC)
Heat sample and reference (material similar to sample
but not does have phase transition in the region of interest)
at identical rate
e.g. sample is lipid + solvent, reference is solvent
At phase transition, more heat must be applied to the sample
to maintain the linear increase in temperature with time
The excess or differential heat supplied to the sample is
recorded as a function of temperature
The sensitivity depends on the sample size, but also on scan rate
At a phase transition, get a peak
Tm: peak position (phase transition temperature)
DT1/2: FWHM of peak
DH: area under the peak (enthalpy of transition)
DS = DH/Tm: entropy of transition

50. Differential Scanning Calorimetry
variation of excess specific heat with temperature for
two-state, endothermic process

51. Differential Scanning Calorimetry

52. Differential Scanning Calorimetry

53. Differential Scanning Calorimetry
DSC curves of distearoyl PC
(DSPC) layers as a function
of water content C
Peak at 62 deg C
Chapman et al., Chem. Phys. Lipids (1967)

54. Lipid Layer Ordering Short range order described by
a: chains are disordered (melted)
Trans-gauche isomerization
Rapid diffusion (translation & rotation)
b: chains stiff, oriented parallel to each other, perpendicular to
bilayer plane
b’: chains tilted with respect to bilayer normal
c: crystalline phase (Lc is lamellar but crystalline within the plane)
Long range order described by
L: 1D lamellar T: 3D tetragonal
P: 2D rectangular R: rhombohedral
H: 2D hexagonal Q: cubic

55. Lipid Layer Ordering

56. Lipid Phase Diagram Phase diagram for PC/water systems
Blume, Acta ThermChimActa (1991)

57. Lipid Phase Transition
Gel to liquid crystal phase transition involves
Cooperative melting of hydrocarbon chains
Introduces large number of trans-gauche
isomerizations
Introduces kinks and jogs into chains
Large increase in lateral diffusion rate of lipids in plane of
bilayer
Small increase in volume
Large increase in area per polar head
Decrease in bilayer thickness
Observed not only in model systems but also in whole cells

58. Lipid Phase Transitions
Can investigate changes in transition temps with chain length, etc.
Blume, Acta ThermChimActa (1991)

59. Lipid Phase Transitions
Dependence of DH and Tm
on position of double bond
in PCs with chain length of
18 carbons
Nature can control Tm by
placement of double bond
Blume, Acta ThermChimActa (1991)

60. Influence of Polar Head Group
PEs have a higher Tm than PCs
smaller headgroup for PE
hydrogen bonding of PE
protonated amino group with adjacent negatively charged phosphate group
note effect of pH
increase pH to 12 to deprotonate PE headgroup
Tm decreases from 63oC to 41oC for DPPE PG
negatively charged
in high ionic strength solvent, charges are shielded
at neutral pH, Tm, DH and DS for PGs are similar to those for PCs PS
at neutral pH, 2 negative charges and 1 positive charge
Tm influenced by pH and ionic strength

61. Lipid Monolayers Not a bilayer, but…
Well defined geometry with which to study the intermolecular
interactions between lipids and between lipids & proteins
Create a so-called Langmuir monolayer by spreading amphiphilic
molecules at the air-water interface using a Langmuir trough
Movable barriers allow the control of the surface area A which
causes a change in the surface pressure p
This allows measurement of the p-A isotherm, which has
characteristic shape for each type of molecule and provides
information about the orientation and packing of the molecules

62. Langmuir Trough Schematic of Langmuir trough
Norde, Colloids and Interfaces in Life Sciences (2003)

63. Surface Pressure-Area Isotherm
G: gas; LE: liquid expanded; LC: liquid condensed; S: solid
Norde, Colloids and Interfaces in Life Sciences (2003)

64. Phase Coexistence Brewster angle microscopy of monolayers showing the
Coexistence of LC (light) and LE (dark) phases
Norde, Colloids and Interfaces in Life Sciences (2003)

65. Compressibility
slope of p-A isotherm is measure of isothermal compressibility
monolayer in gas state is highly compressible but it is less in more
condensed states

66. Phase Coexistence Orientations of amphiphilic molecules
for the various phases
on the pressure-area
isotherms
Norde, Colloids and Interfaces in Life Sciences (2003)

67. Temperature Dependence of p-A Isotherms
as temperature increases
pressure at onset of LE → LC transition increases
corresponding value of am decreases
coexistence region decreases
Norde, Colloids and Interfaces in Life Sciences (2003)

68. Temperature Dependence of p-A Isotherms
p-A isotherms for DPPC at different temperatures
Albrecht et al., J. Phys. (Paris) (1978)

69. Langmuir-Blodgett Film Formation
formation of Y-type Langmuir-Blodgett film
transfer rates of ~1 mm/s
Norde, Colloids and Interfaces in Life Sciences (2003)

70. Langmuir-Blodgett Film Formation
X-type transfer
Z-type transfer
can also use Langmuir-Schaefer deposition
horizontal touch of substrate on monolayer
Norde, Colloids and Interfaces in Life Sciences (2003)