Molecular Biophysics Flashcards
(31 cards)
Explain the fundamental system of SI base units.
The base SI units are: A, cd (luminous intensity), s, Kg, m, mol and K. All other units (derived SI units) are made up from the 7 fundamental SI units. E.g unit of velocity = [m s-1]
List the subsidiary units.
atto - a - 10-18
femto - f - 10-15
pico - p - 10-12
nano - n - 10-9
micro - µ - 10-6
milli - m - 10-3
centi - c - 10-2
deci - d - 10-1
deca - da - 101
hecto - h - 102
kilo - K - 103
mega - M - 106
giga - G - 109
tera - T - 1012
petra - P - 1015
exa - E - 1018
Describe the different kinds of phase states of matter.
Matter can exist in various phases - phase is mostly dependent on temperature and pressure.
Plasma Phase: a plasma is created by heating a gas or subjecting it to a strong electromagnetic field. Plasma is electrically conductive. Like a gas, plasma does not have a definite shape or a definite volume unless enclosed in a container. Unlike gas, under the influence of a magnetic field, it may form structures such as filaments, beams and double layers.
Gaseous
• gas consists of large number of identical molecules with random velocities
• kinetic energy is energy of translation
• molecules don’t interact except brief elastic collisions with each other and container walls
• average distance between molecules greater than diameter
Liquid
• number of molecules per unit volume greater than in gaseous phase
• less compressible and volume changes with temperature lower than gases
• surface tension due to Van der Waals
Solid
• crystalline structure is feature of solids
• ions, atoms or molecules from lattice with special spatial arrangement
• components of lattice oscillate around equilibrium position and amplitude of vibrations is function of temperature
• supply of thermal energy increases amplitude of vibration and lattice may collapse at high temperatures
What are the four assumptions of an ideal gas?
Four assumptions for ideal gas model:
i) The gas consists of a large number of identical molecules moving with random velocities
ii) All kinetic energy of molecules is only energy of translation
iii) The molecules do NOT interact except for BRIEF elastic collisions with each other and the wall of the container
iv) The average distance between the molecules is much greater than their diameter
State the ideal gas law. What is the The Boltzmann constant?
Ideal Gas Law - the pressure and volume of an ideal gas is directly proportional to the number of moles, and temperature of the gas:
P v = n R T
where…
P = Pressure [Pa], v = Volume [m3], n = moles [mol], R = universal gas constant = 8.31 [JK-1mol-1], T = temp [K]
Avagadro’s constant NA = the number of constituent particles in one mole of a substance
= 6.022 x 1023 [mol-1]
The Boltzmann constant k = R / NA = 1.38 x 10-23 [JK-1]
Boyle’s Law - T is constant, an isothermal process takes place - P1V1 = P2V2
Gay-Lussac’s Law - P is constant, and isobaric process takes place - V1/T1 = V2/T2
Charles’ Law - V is constant, isochoric process takes place - P1/T1 = P2/T2
Adiabatic process - There is NO heat exchange with environment Q = 0, (fastest thermodynamic process)
Describe the Maxwell-Boltzmann distribution.
The Maxwell-Boltzmann distribution is a function that describes the distribution of velocities of molecules of an ideal gas. The distribution depends on the temperature of the system and the mass of the particle.
The higher the temperature the broader the form of the curve and the position of the peak is shifted to the higher velocities (the right).
What is meant by the kinetic theory of gases?
The kinetic theory describes a gas as a large number of submicroscopic particles (atoms or molecules), all in random motion. The rapidly moving particles constantly collide with each other and with the walls of the container.
Kinetic theory explains macroscopic properties of gases, such as pressure, temperature, viscosity, thermal conductivity, and volume, by considering their molecular composition and motion. The theory posits that gas pressure is due to the impacts, on the walls of a container, of molecules or atoms moving at different velocities.
Kinetic theory of Gases - The total energy Uk of translational motion of 1 mol of a single atom is given by the formula:
Uk = (3/2)RT - Temp. is related to kinetic energy. The spectra of a molecular system contains lines corresponding to excited vibration and rotation states of molecules. Since small energy differences correspond to the changes of these states, these lines can be observed in the infrared spectrum region.
What is the theorem of the equipartition of energy?
According to Maxwell’s theorem - each degree of freedom has an average energy = (½)kT
When thermal energy is supplied to a molecular system, it fuels vibrational and rotational motion.
The number of degrees of freedom (i) is dependent on the number of atoms in the molecule, where for:
a single atom of gas, i = 3
molecules composed of 2 atoms, i = 5
molecules composed of 3 or more atoms, i = 6
What is Bernoulli’s equation, and what does it describe?
Bernoulli’s equation is a formula for ‘the law of energy conservation for liquids’. It describes how the work done on a flowing liquid is equal to the change in its mechanical energy. Liquid flowing in a tube into a smaller cross-sectional area follows the equation:
P + (½)ρv² + hρg = constant
The sum of pressure and total mechanical energy of liquid per unit volume is constant everywhereina flowing tube. P = absolute pressure of the fluid. The term (½)ρv² is kinetic energy, while hρg is the potential energy of the fluid per unit volume. The pressure at the same depth at two places in a fluid at rest is the same.
Equation of continuity. What is an ideal fluid?
Idela fluids are incompressible and have no viscosity (they do not actually exist).
The equation of continuity holds that if a certain volume of an ideal liquid enters one ned of a tube per unit time, the same volume must leave the other end.
Q = ΔV / Δt
Q = flow rate [m3s-1]
Flow rate = cross-sectional area of the tube times the velocity of the fluid:
A1v1 = A2v2
The Law of Laplace
Leplace’s law describes the relation between the pressure difference (ΔP) across the surface of a closed circular membrane and its wall tensionT [Nm-1]
ΔP = T(1/R1 + 1/R2) Where R’s = membrane curvature at given points.
The greater the pressure change, the greater the tension in the wall of the membrane. Clinical relevance, small radii of capillaries are able to withstand reasonably high blood pressures.
For a sphere where R1=R2=R and thus ∆P = 2T/R
Gibb’s phase rule
Gibb’s Law: The degrees of freedom of a heterogenous system is determined by the number of phases that coexist together and by the number of independent portions that created the system.
It relates the number of components, phases and degrees of freedom of a dispersion system:
p + d = c + 2… where… p = phase, d = degrees of freedom, c = chemical component
A dispersion system has at leats two phases: dispersive portion (not contiunous) is dispersed within the dispersing medium (continuous).
Heterogeneous - a boundary exists between the dispersive portion and the dispersive medium (water and oil); if the refractive index of the two phases is different, then heterogenity in light transsion is observable.
Homogeneous - e.g sugar in water, single-phase system is optically homogenous. It may contain more than two portions. The dispersion portion is dispersed in the medium in the form of particles so small that they can’t be observed - hence optically homogenous. Law of Gibb’s relates no. of components, phases and degrees of freedom.
The number of degrees of freedom of a heterogeneous system is the number of independent variables defining the equilibrium state (pressure, temp, concentration) which can be individually changed without the changing number of phases. i.e when 2 phases are in equilibrium (gas and liquid) the system has 1 degree of freedom (either pressure of temp). however with 3 phases (sol, liq & gas) in equilibrium p = 3, there are 0 degrees of freedom - triple point
Phase Chart of Water.
Plot of pressure (y axis) against temperature (x axis) in which there are well defined areas corresponding to the solid, liquid, and gas phase. The areas are separated by lines of sublimation (a), fusion (b) and evaporation (c). Line of evaporation represents equilibrium between liquid and vapour phases and represents boiling points at a given pressure. This line ends at critical temperature. A vapour CANNOT be converted back into a liquid at a temp. higher than the critical one. The triple point represents the point where all three phases can exist in equilibrium.
What are Liquid crystals?
Liquid crystals (LCs) have properties between that of a liquid and solid. A liquid crystal may flow like a liquid, but its molecules may be oriented in a crystal-like way. Different types of liquid-crystal phases can be distinguished by their different optical properties (such as birefringence). When viewed under a microscope using a polarized light source, different liquid crystal phases will appear to have distinct textures. The contrasting areas in the textures correspond to domains where the liquid-crystal molecules are oriented in different directions. Within a domain, however, the molecules are well ordered. LC materials may not always be in a liquid-crystal phase (just as water may turn into ice or steam).
Liquid crystals can be divided into thermotropic, lyotropic and metallotropic phases. Thermotropic and lyotropic liquid crystals consist of organic molecules. Thermotropic LCs exhibit a phase transition into the liquid-crystal phase as temperature is changed. Lyotropic LCs exhibit phase transitions as a function of both temperature and concentration of the liquid-crystal molecules in a solvent (typically water). Metallotropic LCs are composed of both organic and inorganic molecules; their liquid-crystal transition depends not only on temperature and concentration, but also on the inorganic-organic composition ratio.
Most contemporary electronic displays use liquid crystals.
Water as a solvent, and general fun facts about water (H20)
The water molecule is dipole. The bond angle of water = 105° due to the 2 lone pairs of electrons that oxygen has. O-H bond = 100pm the hydrogen bond = 180pm. On the contrary to other liquids, whose density decreases with increasing temperature, the highest density of water is observed at around 4°c.
Water is a polar solvent due to its large dipole moment.
Aggregated water molecules form the hydrate sheath when ions are then no longer surrounded by their partners. E.g Na+ ion radius = 0.095nm but in solution = 0.24nm. Reaction between water and surface of hydrophilic substances results in bound water.
Water in blood, skeleton and muscles = 79%, 22% and 76%
1.0g of albumin binds 1.3g of water
relative permittivity of water roughly = 80
Dispersion systems and their classification
A Dispersion system has at least 2 parts to it:
dispersive portion - dispersed in the medium, not continuous
dispersive medium - continuous
-A dispersion system can be classified by various parameters:
A. Size of the particles → reciprocal value of particle diameter (m-1) is called the dispersion degree - very fine particles possess a high dispersion degree
B. According to phases of dispersive medium and dispersive portion. E.g…
Dispersive medium
Dispersive portion
Coarse dispersions
Colloidal dispersions
Analytical dispersions
Gaseous
Gaseous
-
-
Mixture of gases
Liquid
Rain, fog
Aerosols
Vapours of liquids
Solid
Dust, smoke
Aerosols
Vapours of solids
Liquid
Gaseous
Bubbles, foams
Foams
Solution of gasses in liquids
Liquid
Emulsions
Lyosols
Solutions of solids in liquids
Solid
Suspensions
Lyosols
Solid
Gaseous
Rigid foams, bubbles of gas in solids
Rigid foams
Gas dissolved in a solid
Liquid
Bubbles closed in solids
Rigid foams
Crystalline water
Solid
Rigid mixtures
Rigid sols
Rigid solutions, doped crystals
Several types:
- Monodispersed system*: dispersed particles are of the same size
- Polydispersed system*: dispersed particles are of various sizes
Based on specific size:
- Analytical dispersion*: dispersed portion particles are up to 1nm in diameter
- Colloidal dispersion*: 1 - 1000 nm
- Coarse dispersion*: 1 μm and greater
Properties of colloid particles
- Particle size is 1- 1000 nm
- There are 2 types of colloidal solutions: (lyophobic and lyophillic) dependent on behaviour with respect to their solvent.
- There are two types of colloidal particles:
- Macromolecules*: molecular polymers of smaller molecular components bound by chemical bounds (ex: proteins, carbohydrates, etc)
- Micelles*: clusters of particles without any chemical bonds.
Properties:
- Colloidal particles move in solution as individual particles.
- Movement is zigzagged –Brown motion due to repeated collisions with molecules of solvent
- Velocity of sedimentation due to gravity, v = 2(ρ−ρ0)gr2 ÷ 9η, ρ = density of particle and ρ0 density of liquid, r = radius of particle, η = coefficient of viscosity
- Permeability or impermeablility across membranes (used to separate colloidal particle from the analytical portion of the solution or the dispersing medium itself)
- Tyndal phenomenon: scattering of light rays that hit colloidal particles in a solution. The intesity of scattered light depends on the particle’s size. For monodispersed systems, (particles are of the same size) the intensity of scattered light can be used to estimate the conc. of the particles.
On the surface of colloidal particles lays a double layer of charged particles.
Dialysis
Dialysis is a process for removing waste and excess water from the blood and is used primarily as an artificial replacement for lost kidney function.
Dialysis works by the diffusion of solutes and ultrafiltration of fluid across a semi-permeable membrane. Diffusion is a property of substances in water; substances in water tend to move from an area of high concentration to an area of low concentration. Blood flows by one side of a semi-permeable membrane, and a dialysate, or special dialysis fluid, flows by the opposite side. A semipermeable membrane is a thin layer of material that contains holes of various sizes, or pores. Smaller solutes and fluid pass through the membrane, but the membrane blocks the passage of larger substances (for example, red blood cells, large proteins). This replicates the filtering process that occurs in the glomerulus of the kidneys.
The two main types of dialysis, hemodialysis and peritoneal dialysis.
Hemodialysis removes wastes and water by circulating blood outside the body through an external filter, called a dialyzer, that contains a semipermeable membrane. The blood flows in one direction and the dialysate flows in the opposite. The counter-current flow of the blood and dialysate maximizes the concentration gradient of solutes between the blood and dialysate, which helps to remove more urea and creatinine from the blood.
In peritoneal dialysis, wastes and water are removed from the blood inside the body using the peritoneum as a natural semipermeable membrane. Wastes and excess water move from the blood, across the peritoneal membrane, and into a special dialysis solution, called dialysate, in the abdominal cavity.
Principle of electrophoresis
- Electrophoresis is a technique used to separate and sometimes purify macromolecules - especially proteins and nucleic acids - that differ in size, charge or conformation.
- It is one of the most widely used techniques in biochemistry and molecular biology.
- When a charged molecule is placed in an electric field, it migrates toward either the positive (anode) or negative (cathode) pole according to its mass: charge ratio.
- The migration velocity is proportional to the strength of the electrical field & the charge of the molecule, and inversely proportional to its mass.
In contrast to proteins, which can have either a net positive or net negative charge, nucleic acids always have a negative charge due to their phosphate backbone, and migrate towards the cathode.
What is meant by electrokinetic (Zeta) potential?
The zeta potential is a key indicator of the stability of colloidal dispersions.
Zeta potential is the potential difference between the dispersion medium and the stationary layer of fluid attached to the dispersed particle.
Zeta potential [mV] : Stability behavior of the colloid
from 0 to ±5, Rapid coagulation or flocculation
from ±10 to ±30 Incipient instability
from ±30 to ±40 Moderate stability
from ±40 to ±60 Good stability
more than ±61 Excellent stability
What is meant by transport phenomena?
Transport phenomena are related to the motion of molecules and interaction between molecules causing the net movement of physical quantities.
- viscosity is the transport of momentum
- conduction of heat is the transport of energy
- diffusion is the transport of molecules.
-In order for transport of any of these things to occur, an appropriate gradient must exist.
Ex: concentration, temperature, or velocity gradient.
Viscosity
- Viscosity is a measure of the internal friction of a fluid between adjacent layers of liquid molecules as they slide past each other.
- The ideal fluid has 0 viscosity.
Fluids that have small values of viscosity move more readily and behave more like ideal fluids.
- In a cylindrical tube of radius r, a velocity gradient exists with the velocity vectors oriented in a parabolic fashion.
- Tangent tension (σ):* the force of internal friction F results in tangent tension. It is proportional to the vector of the velocity gradient (S).
Unit is the Pascal (N/m2)
σ = F/S σ = n ∆v
∆r
- Dynamic viscosity:* the proportionality coefficient n (unit is Pa.s)
- Kinetic viscosity*: the dynamic velocity (n) / density (p)(unit is m2.s-1)
- Newtonian liquids*: have a tangent tension proportional to the velocity gradient
ex: single component liquids and analytical solutions - Non-Newtonian liquids*: have a tangent tension that is not proportional to the velocity gradient
ex: colloidal particles, suspensions, and emulsions
Factors that influence viscosity:
- Temperature → Since the motion of particles depends on temp so does viscosity.
~In liquids, viscosity decreases with increasing temp
~In gases, viscosity increases with increasing temp
- Concentration of suspended particles (c) → The greater the conc. of suspended particles, the greater the viscosity. i.e. higher hematocrit raises the viscosity of blood
Ns= n(1+kc)
*The highest Velocity Vmax is in the center of the tube.
Velocity decreases with increasing distance from the center of the tube until it reaches 0 at the walls of the tube.
Viscosity measurement
- the measurement of viscosity of solutions is important for determining the molar weight, especially for macromolecular substances of higher viscosity.
- Uses the equation for flow rate Q (Hagen-Poiseulles Law (2.26))
- Ostwald viscosimeter:*
The liquid measured is soaked from the wide pipe into the narrow one and the given volume flows back. The time it takes to flow back is measured.
- Body viscosimeter:* applies Stoke‘s law
- -* a spherical body is let to fall down in the given liquid and the time of its fall (or the rise of the gas bubble ) is measured
- The internal friction force F for a sphere of the radius r moving in a medium of viscosity n at velocity v is given by:
Stokes law: F= 6πnrv