Molecular biophysics Flashcards
SI units
All other units are based upon 7 base units • Mass (kg) • Current (A) • Time (s) • Temp (K) • Amount of substance (mole) • Length (m) • Luminous intensity (Cd)
Magnitudes of unit
- 1015 = P (peta) 10-18 = a (atto)
- 1012 = T 10-15 = f (femto)
- 109 = G 10-12 = p (pico)
- 106 = M 10-9 = n
- 103 = k 10-6 = μ
- 102 = h 10-3 = m
- 101 = d 10-2 = c
- 100 = 1 10-1 = d
Phases of matter
-Matter can exist in a various phases (its phase is mainly dependent on temperature and pressure)
Gas – atoms or molecules move around rapidly and are far apart from each other. Only very weak intermolecular forces exist between the particles. Gases are easily compressible.
Liquid –atoms or molecules are held together closely, liquids have definite volumes and are not easily compressible, can move and take the shape of their container
Solid –attractive forces between atoms are strong, particles can only vibrate around a fixed position. The kinetic energy of solids is in the form of vibrational energy
Plasma
*gases and liquids are in a state of continuous irregular (thermal motion) while the thermal motion of solids is limited to vibration and rotation of the bonds between atoms
State equation of ideal gas
There are 4 assumptions of an ideal gas
(i) consists of large number of identical molecules moving with random velocities
(ii) all kinetic energy is in the form of translational energy
(iii) molecules do not interact expect during brief elastic collisions with their container and themselves
(iv) average distance between molecules is greater than their diameter
*Ideal gas law: the pressure and volume of an ideal gas is directly proportional to the # of moles (n), and the temperature of the gas
P V = n R T
P=pressure, V= volume, n= number of moles in a gas, R= universal gas constant, T=temperature
Gas constant R= 8.31 J/ mol-1 K-1
Avogadro’s number (N): the number of atoms/molecles in one mole N = 8.31 J/mol/kelvin
-If we denote N (total # of atoms/molecules) instead, (N = n x Na ) and we use Boltzmann‘s constant k = R/Na, then pV =NkT
*The state equation of an ideal gas holds for real gases at low pressure and high temperature. In this case, interaction between molecules is minimal and can be ignored.
Boyles Law:
For isothermal processes
-The volume of a gas is inversely proportional to its pressure
PV=constant P1V1 = P2V2
*as pressure increases, volume decreases and vice versa
Charles Law:
For isobaric processes
-The volume of a gas is directly proportional to its temperature
V/T= constant V1/T1 =V2/T2
- as temperature increases, volume increases and vice versa
- pressure and temperature are related in the same way
Bernouilli equation, equation of continuity
Bernoulli equation
• Work done on a flowing fluid is equal to the change of its mechanical energy:
p + ½ρv2 + hρg = const
• Sum of pressure and total mechanical energy of liquid per unit volume is constant everywhere in a flow tube. ½ρv2 represents kinetic energy, and hρg the potential energy of the fluid per unit volume
• Pressure at same depth at two places in a fluid at rest is the same
Equation of continuity
A1v1 = A2v2
Law of Laplace
Describes the relation between the pressure difference (ΔP) across the surface of a closed membrane and the wall tension T (N.m-1).
ΔP = T (1/R1+1/R2)
where R1 and R2 are the main radii of the membrane curvature at the given point. For a cylindrical form of the membrane, one of the radii is infinitely large and thus ΔPcylinder = T/R, for a sphere R1=R2=R and thus P = 2T/R
Gibbs phase rule, phase chart of water
Dispersion system consists of dispersive portion dispersed within dispersive medium
• Heterogeneous system; boundary between portion and medium e.g. oil in water
• Homogeneous system; no boundary
Relates the number of components (c), phases (p) and degrees of freedom (d)
p + d = c + 2
d of heterogeneous system is number of independent variables (pressure, temp, conc); when p = 3 no variable can be changed as equilibrium would be lost, this is the triple point (no degree of freedom)
An increase in pressure results in a decrease of melting point temperature, i.e. at a given temperature ice can be made to melt by the application of pressure
Three phase equilibrium lines intersect at the triple point; at this pressure and temperature the three phases can coexist in equilibrium
Water as a solvent
- water is a dipole
- polar solvent with good solvent power
- bond angle is 105°
- water molecules interconnected by hydrogen bonds in liquid and solid phases
- substantial component of all body liquids and organs and represent dispersion medium for macromolecules, molecules, and ions in cells and enables their interactions
Dispersion systems and their classifications
Classification:
• Size of particles
1. Analytical dispersion 1μm
• Phase of dispersive medium
• Phase of dispersive portion
Analytical dispersions
• homogeneous
• dispersion portion is ions, molecules or atoms
• gas + gas
− Dalton’s law p = p1 + p2 + …
− Amagad’s law v = v1 + v2 + …
• liquid + gas
− Henry’s law states that the amount of a gas dissolved in a liquid is directly proportional to the partial pressure of the gas above the liquid when the gas and liquid do not chemically react
• liquid + liquid
− homogeneous analytical dispersion possible (not heterogeneous)
• solid + liquid
− solid dissociates into ions and organic compounds with polar groups
− solubility of solid increases with increasing temperature
− solidification of solid phase should appear on cooling
Colloidal dispersions
• highest biological importance
• lyophobic and lyophillic according to behaviour with solvent
• macromolecules (with chemical bonds) or micelles (particles without chemical bonds) form colloidal particles
• thermal motion of liquid molecules disturbs sedimentation process but after certain time interval sedimentation equilibrium is reached
• sedimentation rate depends on temperature (centrifugation accelerates sedimentation)
• permeability or impermeability of colloidal particles through membranes allows for separation from analytical portion of solution or dispersion medium
• measurement of intensity of scattered light can be applied for estimation of concentration (dependent on particle size)
Properties of colloid particles
• double layer of charged particles on surface distinguishing them from other dispersions
• arranged by electrolytical dissociation or by adsorption of an ion
− e.g. micelles of AgI (insoluble in water) prepared by missing KI with AgNO3 → K+ I- Ag+ NO3-
− excess of AgNO3 ∴overall production of AgI which coagulates with some AgI micelles remaining in solution. They attract the Ag+ ions, which then attract the NO3- ions forming a double layer
• adsorption forces and electrostatic forces with decrease with squared distance
• electric double layer gives colloidal particles an electrokinetic potential
Principle of electrophoresis, electrokinetic potential
Electrophoresis
• technique used to separate and sometimes purify macromolecules (especially proteins and nucleic acids) that differ in size, charge or conformation
• one of the most widely-used techniques in biochemistry and molecular biology
• when charged molecules are placed in an electric field, they migrate toward either the positive (anode) or negative (cathode) pole according to their charge
• proteins have either a net positive or net negative charge, whilst nucleic acids have a consistent negative charge imparted by their phosphate backbone, and migrate toward the anode
• relative movement of the charged macromolecule depends on mass: charge.
Electrokinetic potential
• potential across the interface of all solids and liquids
• specifically, potential across the diffuse layer of ions surrounding a charged colloidal particle, which is largely responsible for colloidal stability
Transport Phenomena
• related to motion of molecules and processes of interactions of molecules
• transport of some physical quantities occurs
− viscosity is transport of momentum
− conduction of heat is transport of energy
− diffusion is transport of molecules
• necessary condition for transport is presence of appertaining gradient of flow velocity, temperature or concentration
Viscosity and its Measurement
Fluids contain internal friction between adjacent layers (molecules) of liquids as they move past each other
Highest velocity vmax in centre of tube. Velocity equals zero just at the wall of the tube.
Kinetic Velocity
• dynamic velocity (Pa.s) divided by density (kg.m-3)
• v = η/ρ
Tangent tension σ (Pa)
• σ = η(Δv/Δr)
Hagen-Poiseuille’s law, flow rate Q (m3.s-1)
• increase of radius by 19% results in twofold increased flow rate
• Q = (πR4ΔP)/(8ηL)
Flow resistance Rf (Pa.s.m-3)
• Rf = ΔP/Q
• ratio of pressure drop to flow rate
Stokes law
• at constant velocity, the driving and frictional forces differ only in sign, and velocity is proportional to driving force
• Fr = 6πηrv
• Reynolds number Re defined by 2ρvavR/η. Re3000 flow is turbulent and some energy dissipated as sound (principle used in measuring blood pressure)
Diffusion, 1st law of Fick
Diffusion
• net transport of molecules from high concentration to low concentration
• primary mechanism in body for absorbing and distributing substances required by living cells
• release of by products of cellular function (e.g. CO2) also proceeds by diffusion
• density of diffusion flux, n/Aτ (mol.m-2.s-1) is proportional to concentration gradien:
1st Law of Fick
• n/Aτ = -D Δc/Δx (D = diffusion coefficient, m2.s-1)
• -ve sign indicates that direction of flux in opposite direction to concentration gradient
