Biophysical Methods Flashcards
What does EM radiation and its interactions give rise to?
The interaction gives rise to:
A) Absorption - results from transitions from a lower to a higher energy level; e.g. IR, UV/vis
B) Emission - results from transitions from a higher to a lower energy level, e.g. Fluorescence
C) Scattering/ diffraction - results from oscillations indicted in the scatterer by EM radiation
What are the properties of waves?
- Waves have amplitude A; velocity c; wavelength λ frequency n; phase φ; (n=c/λ)
- EM radiation corresponds to 2 waves, at right angles to one another - the E (electric) wave and the M(H) (magnetic) wave - travelling with velocity c
- Polarisation - can be related to the direction of the E waves (M is always 90 degrees to E). Can be unpolarised (E waves have equal intensity in all directions), partially polarised or plane polarised.
- Interference - waves can add (constructive; same phase) or subtract (destructive; out of phase so waves cancel out)
Conversion between scales equations
E=hv (h is Planck constant, 6.63x10-34Js, v is velocity) - converts wavelength to energy
C=λv (velocity of EM radiation of wavelength λ)
V=c/λ (Hz or s-1)
E(energy/atom)=hv/atom (J)
E (energy/mol) = E X avogadros no (6x10 23) (kJ/mol)
V’ (wave number) = 1/λ (used in IR spectroscopy)
Molecules in cells have…
- Concentration
- Structure {f(X,y,z)} e.g atomic orbitals, conformation, assembly
- Dynamics E.g. Thermal motion, diffusion etc.
- Energy (related to structure and dynamics)
Structure - methods to obtain
For molecular structure need atomic resolution (
Dynamics
- Molecular movement - diffusion/membrane transport, ‘waggling’ motion, EPR, fluorescence etc
- Speed of reactions, e.g. Photo cycles in bR
Energetic a
Ligand binding - can measure Kd by monitoring [P] [PL] [L] by fluorescence, NMR, ITC etc. Can also infer from k1 and k-1
DNA melting - UV absorbance vs temperature; Keq = [SS]/[DD]; ΔG=-RTlnKeq; Keq=1 at Tm.
Energy
- Energy is quantised: ground and excited states
- Molecules in a system are distributed among energy levels according to the Boltzmann law: n{u1}/n{g}=exp(-ΔΕ/RT)
- Application of a angelic field Bo splits the energy levels of a system with spin (I) into 2I +1 levels.
Energy of different molecular processes
- Molecular processes have different energy:
i) Electronic transitions approx. 10^5 J/mol
ii) molecular vibrations approx. 10^4 J/mol
iii) Nuclear spin flips approx. 10^3 J/mol - The energy of different molecular processes corresponds to different parts of the EM spectrum.
- Wavelength corresponds to energy.
- The population distribution among energy levesl is very different for different techniques e.g for nuclear spin/NMR the population is u and g are nearly equal while in UV/Vis the population is essentially all in the ground state.
- Note: the greater the population difference the greater the sensitivity.
What is scattering and what does it depend on?
- Scattering results from oscillations induced by applied EM radiation, followed by re-emission at the same wavelength.
- The extent of oscilaltion depends on sample properties, e.g. electron polarisability and scattering cross section.
- Scatterers behave like dirven oscillators
- In a solution the scattering depends on the number of scatterers (concentration) and their size (RG*)
- Scattering can give infomration about the shape of particles in soluation and their motion.
Angular dependence of scattering
- When wavelength>radius of gyration, Raleigh scattering is isotropic (same in all angles).
- When WL is approx RG or WL
What are the 3 main classes of scattering experiment?
1) Measure turbidity - ‘absorbance’
2) Measure I (intensity of scattered light) as a function of MW and theta. e.g. MALS, SAXS/SANS, diffraction.
3) Measure I as a function of wavelength (or v), e.g. DLS and Raman
Multi Angle Light Scattering(MALS)
- The intensity of light scattering informs about molecular weight.
- Measures scattering at several fixed angles.
- With SEC and refractive index detection (SEC-MALS) it can provide accurate molecular weights.
- The amount of scattering depends on size and concentration of protein.
SAXS and SANS
- The angular dependence of scattering gives more detailed information about shape when WLRg requirement of many biological systems, so they are the main sources used.
- Experiments are known as Small Angle X-ray Scattering (SAXS) and Small Angle Neutron Scattering (SANS).
SAXS plot
- Usually plot is lnI vs Q(/nm)
- At large angles the plot gives information about particle shape.
- At small angles, a Guinier plot (lnI vs Qsquared) is linear and givers information about MW (I intercept) and Rg (slope).
- lnI vs Q plots can be converted to P(r) [probability of distance] vs r plot with a Fourier transform. This MAY define a unique molecular shape.
X-rays and neutrons
- X-rays are scattered by electrons while neutrons are scattered by nuclei. The response depends on the scattering cross section, B.
- For X-rays, B increases directly with number of electrons in atom.
- For neutrons, B can be very different for different isotopes; e.g. H is negative while D is positive.
- What this means is that scattered waves from H and D are 180˚ out of phase.
- Can give more info about particle shape than MALS because of their shorter wavelength.
SANS - contrast matching
- Because H and D scatter with opposite ‘sign’, a large range of solvent scattering cross sections can be achieved by changing the H2O/D2O ratios. We can therefore match the solvent background to various macromolecular components in a solution.
- The plot of Scattering length density vs %D2O shows the variation in scattering for different H2O/D2O ratios, for solvent, lipids, proteins, and DNA (different lines). The contrast is matched where the lines cross.
Dynamic Light Scattering
- Static scatterers emit at frequency Vin but if the scatterer moves then the scattered llight is ‘spread by the Doppler effect.
- The faster the movement, the broader the spectrum.
- Can calculte the diffusion rate (D) from the width of the Raleigh line.
- Diffusion coefficicents (D) measured by DLS give information on sample size, aggregation etc.
- DLS instruments are relatively cheap and easy to use.
What is the Doppler effect?
Frequency depends on whether scattere approaches or recedes from observer.
What is refraction?
Refraction is the bending of light when it enters a medium.
Can be described by n=Co/C
When do evanescent waves form?
- Evanescent waves are formed when EM waves undergo total internal reflection at an interface.
- Evanescent means tending to vanish; the intensity of an evanescent wave decays exponentially with distance from the interface.
How does Surface Plasmon Resonance (SPR) work?
- A sensor technique that utilizes a surface plasmon - an oscillation of electrons in a thin metal film such as gold.
- The SP can interact (resonate) with an evanscent wave in a way that is very sensntive to the properties of the medium near the metal surface.
- Light is shone on a prism such that TIRF occurs.
- Light incident at a particular angle (θspr) generates plasmon resonance on a metal film, causing a minimum in the reflected intensity.
- Changes in refractiv eindex near the metal index cause θspr to change.
SPR to show binding
- The binding of prey moelcules to bait molecules increases the refractive index of the surface layer.
- This alters the resonance angle for plasmon induction, which can be measured by a detector.
When does total internal reflection (TIRF) occur?
TIRF occurs when a light ray passes from a higher to a lower refractive index and the angle of incidence is greater than a ‘critical’ angle.