biophysics summary (1)
TRANSCRIPT
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Biophysics Exam
Chapter 2 Biothermodynamics
What is Biothermodynamics?
The studying of:
1. The states of equilibrium of material systems
2. The processes by which these equilibrium states are reached
3. The energetic aspects of physical and chemical processes in material systems
4. Direction and limits of developing spontaneous processes.
When thermodynamics deals with biological systems it is called Biothermodynamics.
The statement of the first law of Thermodynamics
U = Q+L
U: Internal energy
Q: Heat
L: Labour
A change in the internal energy of a closed thermodynamic system is equal to the difference
between the heat supplied to the system and the amount ofwork done by the system on its
surroundings.
What is a chemodynamic system?
In chemodynamic systems a part of the chemical energy is transformed to heat and another
part of it to mechanical work. The living organism is a chemodynamic system.
What are the types of isothermal coefficients?
Physical isothermal coefficients: which is the quantity of energy released by one gram of food
fully oxidized in oxygen atmosphere and where the end results are water and carbon dioxide.
Physiological isothermal coefficients: are expressing the quantity of energy released in
organism during the oxidation reaction of one gram food.
Practical isothermal coefficients: are also physiological coefficients but they take to account
the digestibility/absorption degree of food.
What is metabolic rate and basal metabolism?
Basal Metabolic Rate (BMR), and the closely related resting metabolic rate (RMR), is the
amount of daily energy expended by humans and animals at rest. Rest is defined as existing in
a neutrally temperate environment while in the post-absorptive state. In plants, different
considerations apply.
The release of energy in this state is sufficient only for the functioning of the vital organs,
the heart, lungs, nervous system, kidneys, liver, intestine, sex organs, muscles, and skin.
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Relation between thermodynamic probability and entropy
The thermodynamic probability of a state is defined as the number of micro states of the
system that corresponding to the given macro state.
The thermodynamic probability and entropy will increase if the organizing degree of
molecules is decreasing. ( S= entropy, = thermodynamic probability and they are related to
the entropy Sby S= kln , where kis Boltzmann's constant.
What is negative entropy?
Thermodynamic entropy is a measure of how organized or disorganized energy is present in a
system of atoms or molecules. An ordered system has less entropy than an disordered one.
The negentropy, also negative entropy or syntropy, of a living system is the entropy that itexports to keep its own entropy low; it lies at the intersection ofentropy and life.
How the second law of thermodynamics is applied to living organisms?
Trying to apply the second principle of thermodynamics at living organism, was found that
the validity is questioned, as they evolve to increase structural complexity and diversification
of structures, in which case the entropy will decrease.
Chapter 3 Water
Water in living organisms, distribution, roles and forms?
Water is the medium where multiple hydrolysis and enzymatic reactions take place (by
hydrogen ions) and it results as a final product of the condensing reactions and
biological oxidations.
It contributes in maintaining the constant temperature of organisms (by thermal
conductibility and vaporization heat, all very high).
It is the universal solvent in the interstitial (versttning: 1. Relating to, occurring in,
or affecting interstices.) and intracellular medium where it forms real or colloidal(versttning: A system in which finely divided particles, which are approximately 10
to 10,000 angstroms in size, are dispersed within a continuous medium in a manner
that prevents them from being filtered easily or settled rapidly.)solutions transported
by water
It is the transport medium between organs, using extra cellular circulating fluids
Its the medium necessary to eliminate products of catabolism out of the organism
(urine and transpiration) (versttning: the process of giving off or exhaling water
vapor through the skin or mucous membranes)
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The Nernst & Goldmans relation
In electrochemistry, the Nernst equation is an equation that can be used (in conjunction with
other information) to determine the equilibrium reduction potential of a half-cell in
an electrochemical cell. It can also be used to determine the total voltage (electromotive force)
for a full electrochemical cell. It is named after the German physical chemist who first
formulated it, Walther Nernst.
The GoldmanHodgkinKatz voltage equation, more commonly known as the Goldman
equation is used in cell membrane physiology to determine the equilibrium potential across acell's membrane taking into account all of the ions that are permeate through that membrane.
The description of the membrane through electrical equivalent circuits
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Chapter 5 Transport through membranes
Types of transport in cell membrane and the differences between them
Active transport is the movement of a substance against its concentration gradient (from low
to high concentration). In all cells, this is usually concerned with accumulating high
concentrations of molecules that the cell needs, such as ions, glucose, and amino acids. If the
process uses chemical energy, such as from adenosine triphosphate (ATP), it is
termed primary active transport. Secondary active transport involves the use ofan electrochemical gradient. Active transport uses energy, unlike passive transport, which
does not use any type of energy. Active transport is a good example of a process for which
cells require energy. Examples of active transport include the uptake of glucose in the
intestines in humans and the uptake of mineral ions into root hair cells of plants.
Primary active transport, also called direct active transport, directly uses energy to transport
molecules across a membrane.[1]
Most of the enzymes that perform this type of active transport are transmembrane ATPases. A
primary ATPase universal to all cellular life is the sodium-potassium pump, which helps to
maintain the cell potential. Other sources of energy for Primary active transport
areredox energy andphotonenergy (light). An example of primary active transport using
Redox energy is the mitochondrial electron transport chain that uses the reduction energy
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ofNADH to move protons across the inner mitochondrial membrane against their
concentration gradient. An example of primary active transport using light energy are the
proteins involved inphotosynthesisthat use the energy of photons to create a proton gradient
across thethylakoid membrane and also to create reduction power in the form ofNADPH.
In secondary active transport orco-transport, uses energy to transport molecules across a
membrane; however, in contrast toprimary active transport, there is no direct coupling
ofATP; instead, theelectrochemical potential difference created by pumping ions out of the
cell is used. [1]
The two main forms of this areantiport and symport.
Passive transport means moving biochemical and other atomic or molecular substances
across membranes. Unlike active transport, this process does not involve chemical energy,
because, unlike in an active transport, the transport across membrane is always coupled with
the growth ofentropy of the system. So passive transport is dependent on the permeability of
the cell membrane, which, in turn, is dependent on the organization and characteristics of themembrane lipids and proteins. The four main kinds of passive transport
are diffusion, facilitated diffusion, filtration and osmosis.
Diffusion describes the spread ofparticles through random motion from regions of
higherconcentration to regions of lower concentration. The time dependence of the statistical
distribution in space is given by thediffusion equation. The concept of diffusion is tied to that
ofmass transferdriven by a concentration gradient. Diffusion is invoked in the social sciences
to describe the spread of ideas.
Facilitated diffusion (also known as facilitated transport orpassive-mediated transport)
is a process ofpassive transport, facilitated by integral proteins. Facilitated diffusion is thespontaneous passage of molecules or ions across a biological membrane passing through
specific transmembrane integral proteins. The facilitated diffusion may occur either
acrossbiological membranesor through aqueous compartments of an organism.
Filtration is commonly the mechanical or physical operation which is used for the separation
of solids from fluids (liquids or gases) by interposing a medium through which only the fluid
can pass. Oversize solids in the fluid are retained, but the separation is not complete; solids
will be contaminated with some fluid and filtrate will contain fine particles (depending on the
pore size and filter thickness). Filtration is also used to describe somebiological processes,
especially in water treatment andsewage treatment in which undesirable constituents are
removed by adsorption into a biological film grown on or in the filter medium.
Osmosis is the movement ofsolvent molecules through a selectivelypermeable membrane
into a region of highersoluteconcentration, aiming to equalize the solute concentrations on
the two sides.[1][2][3]It may also be used to describe a physical process in which any solvent
moves, without input of energy,[4]across a semipermeable membrane (permeable to
thesolvent, but not the solute) separating two solutions of different concentrations.[5] Although osmosis does not require input of energy, it does use kinetic energy[6] and can be
made to do work.[7]
Chapter 6 Membrane potential
The causes of the resting potential
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The resting potential of a cell is the membrane potential that would be maintained if there
were no action potentials, synaptic potentials, or other active changes in the membrane
potential. In most cells the resting potential has a negative value, which by convention means
that there is excess negative charge inside compared to outside. The resting potential is mostly
determined by the concentrations of the ions in the fluids on both sides of the cell
membrane and the ion transport proteins that are in the cell membrane. How the
concentrations of ions and the membrane transport proteins influence the value of the resting
potential is outlined below.
The resting potential depend on:
The type of the cell
Its functional status
Composition of the extra cellular environment
The action potential
Inphysiology, an action potential is a short-lasting event in which the electrical membrane
potential of a cell rapidly rises and falls, following a consistent trajectory. Action potentials
occur in several types ofanimal cells, calledexcitable cells, which includeneurons,muscle
cells, and endocrine cells, as well as in someplant cells .Action potentials are generated by
special types ofvoltage-gated ion channels embedded in a cell'splasma membrane. These
channels are shut when the membrane potential is near the resting potential of the cell, but
they rapidly begin to open if the membrane potential increases to a precisely defined threshold
value. When the channels open, they allow an inward flow ofsodium ions, which changes theelectrochemical gradient, which in turn produces a further rise in the membrane potential.
This then causes more channels to open, producing a greater electric current, and so on.
The action potential has 5 phases:
1. The resting potential ( few potassium channels are open), ( There is no NET
movement of K ions)
2. Threshold (As the depolarizing stimulus appear, few Na channels are open) , (When
Na ions enter the cell the membrane potential is less negative), ( When the threshold is
achieved the action potential is generated)
3. The rising phase ( the depolarization reaches the threshold potential), (additional
voltage-gated sodium channels are open), ( a high flow of Na ions enter the cell), (the
membrane voltage becomes positive)
4. The falling phase ( at the peak of the action potential, two processes occur
simultaneously ; many voltage- gated sodium channels begin to close and many more
potassium channels open), (the positive charge leaves the cell), (the membrane
potential begins to shift back to the resting potential), ( as the membrane potential
approaches the resting potential all voltage-gated potassium channels are open and
maximally activated)
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5. The recovery phase ( the membrane repolarizes below the resting potential because of
the number of the potassium channels that are open), ( the additional potassium
channels now close)
Each action potential is followed by a refractory period : 1. Absolute refractory period it
is impossible to evoke another action potential 2. Relative refractory period a stronger
than usual stimulus is required.
Chapter 7 Blood circulation + Chapter 8 Muscle contraction + Chapter 9 vision system
+ Chapter 10 Hearing system + Chapter 11 Respiration system
Poiseuille-Hagen's law
In fluid dynamics, the HagenPoiseuille equation is a physical law that gives
the pressure drop in a fluid flowing through a long cylindrical pipe. The assumptions of the
equation are that the flow is laminar viscous and incompressible.
The total flow D of a cylindrical tube is given by:
P: Pressure
R: Radius
L: Lenght
If radius diminishes with only 16%, the flow will diminish
to half of its initial value.
If radius diminishes with 50%, flow will be 16 times
lower.
Bernoulli's equation
In fluid dynamics, Bernoulli's principle states that for an inviscid flow, an increase in thespeed of the fluid occurs simultaneously with a decrease in pressure or a decrease in
the fluid's potential energy.
P: Pressure
Pv: is the fluid flow speedat a point on a streamlineP: Density
Laplace Law
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In physics, the YoungLaplace equation is a nonlinear partial differential equation thatdescribes the capillary pressure difference sustained across the interface between two static
fluids, such as water and air, due to the phenomenon ofsurface tension or wall tension,
although usage on the latter is only applicable if assuming that the wall is very thin.
P: Pressure, R: Radis F: Force
Chapter 8
The 4 mechanisms that produce motility
actine-myosine (interaction between these proteins producemotility - muscular contraction,
cytoplasmic current and amiboid movements) uses ATP energy
tubulin-dynein (flagella and cilla motion inside the eukaryotes cells, chromosomes motionduring cellular division, intra cytoplasm motions) uses ATP energy
flagellin (a contractile protein used in bacteria's motion; a complex rotational system) uses
ATP energy
spasmin (produces contraction based on calcium binding,same way as in poly-electrolytic
chain) uses ATP energy to pump calcium through active transport
V. Hill's law
F = loading force
v = shortening velocity
F0 = loading force in isometric contraction
a is a constant having approximately the same values for all types of muscles
(meaning that chemo-mechanical efficiency is similar for all types of muscles)
b is a constant that has a specific value for each type of muscle
Muscle Shortening Mechanism
In the absence of calcium ions, tropomyosin blocks access to the mysosin binding site
of actin
When calcium binds to troponin, the myosin has access to binding site on actin
Myosin hydolyzes ATP and undergoes a conformational change into a high-energy state.
The head group of myosin binds to actin forming a crossbridge between the thick and
thin filaments
The energy stored by myosin is released => ADP and inorganic phosphate dissociate frommyosin. The resulting relaxation of the myosin molecule entails rotation of the
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globular head (=> longitudinal sliding of the filaments)
it's like a rowboat movement
The Purkinje effect
is the tendency for the peak luminance sensitivity of the human eye to shift toward the blue
end of the color spectrum at low illumination levels. This effect introduces a difference in
color contrast under different levels of illumination. For instance, in
bright sunlight, geranium flowers appear bright red against the dull green of their leaves, or
adjacent blue flowers, but in the same scene viewed at dusk, the contrast is reversed, with the
red petals appearing a dark red or black, and the leaves and blue petals appearing relatively
bright.
Defects of eyes
Presbyopia the ability to accommodate is reduced (due to the loss of elasticity of the
crystalline lens)
Astigmatism due to defects of sphericity of the transparent Cornea
Myopia near-sightedness. F is in front of retina because eye is too long or power is too
high
Hyperopia far-sightedness. F is behind retina because eye is too short or power is too low
Fick's law applied to gases
Fick's laws of diffusion describe diffusion and can be used to solve for the diffusion
coefficient,D.
s represents the solubility coefficient of gases in liquid
Dalton's law of partial pressures
In chemistry and physics, Dalton's law (also called Dalton's law of partial pressures) states
that the total pressure exerted by a gaseous mixture is equal to the sum of the partial
pressures of each individual component in a gas mixture.
the barometric (atmospheric) pressurepB is
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Structure of the eye
The three optic mediums of the eye are:
1. the aqueous humour (n=1.336) fills the anterior compartment of the eye which is limited
towards the air by transparent cornea and towards the eye by iris
2. the crystalline (nav=1.406) is a biconvex, asymmetric lens. It is an elastic tissue composed
of thin lens. The shape of the crystalline may vary due to ciliary muscles that surround it.
3. the vitreous humour (n=1.336) is limited in the posterior part by the retina (which contains
the photosensitive cells).
OBS: The chemical composition of the two liquids is
different, but optically, both behave the same.
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The frequency range for sounds.
Sound = mechanical longitudinal wave that provoke the auditive sensation
The sound is characterized by:
amplitude: the maximal value of elongation
frequency: the number of periods in time unit (16-20000Hz)
the propagation (propagation betyder: 3.Physics The act or process of propagating,
especially the process by which a disturbance, such as the motion of electromagnetic or sound
waves, is transmitted through a medium such as air or water.) speed
the intensity - represents the quantity of transported energy that passes in a second through
the unit of perpendicular surface on the direction of wave propagation. The mechanical waveswith frequency smaller that 16Hz = Infrasounds The mechanical waves with frequency
greater that 20kHz = ultrasounds
The Law of the threshold
For a sound to be able to produce an auditive sensation, its intensity must overpass a certain
minimal intensity, called the threshold intensity,that varies according to the frequency of the
sounds. The sounds with the frequency between 1000-5000Hz have the smallest threshold -
this is the frequency field of current speech. The graphical representation of the threshold ofsound with the frequency is called audiogram.
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The Law of Weber-Fechner
If the intensity of the excitant stimulus increases in geometric progression, then the intensity
of the sensation produced by it increases in arithmetical (Arithmetical betyder: 2. Changingaccording to an arithmetic progression: The increase in the food supply is arithmetic. )
progression
Intensity of sound
For the measurement of the intensity of a sound, two relative units have been introduced:
The Bel - measures the relative intensity of a sound towards another sound taken as
reference, of the same frequency
A decibel is the tenth part of a bel
The audibility area is between 0-140dB
The Phon - a sound has the relative intensity of one phon if it is 10 times more intense than
the sound with the frequency equal to 1000Hz and with the intensity equal to the minimalperceivable threshold
The choice of the frequency of the standard sound at 1.000Hz is justified by the fact that for
this frequency there are no age fluctuations of the sensitivity of human hearing
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Chapter 12 Radiation
Nuclear radiation, types and characteristics
The main characteristics of nuclear radiation is that through interaction with the substance
they produce, directly or indirectly, the ionization of this.
Different types are Alpha () radiation consists of a fast movinghelium-4 (4
He) nucleus and is stopped by a sheet of paper. Beta () radiation, consisting ofelectrons, is
halted by an aluminium plate. Gamma () radiation, consisting of energeticphotons, iseventually absorbed as it penetrates a dense material.
The law of radioactive disintegration
Activity, half time and the counting speed
The interaction of the radiations with substance
The radiation may interact with
The electron
The nucleus
The coulombian field
In collision process we may have:
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Absorbation
Inelastic scattering
Elastic scattering of gamma photon
The attenuation of radiation
In physics,attenuation (in some contexts also called extinction) is the gradual loss in intensity of anykind offlux through a medium. For instance, sunlight is attenuated by dark glasses,X-raysareattenuated by lead, and lightand sound are attenuated by water.
Finns inte s mycket mer
The biological action of radiation:
- Through direct action: the effect is due to the unmediated action of radiations with sensible
elements of the biological system
- Through indirect action: nuclear radiations ionise water and the ionized radicals act
upon the different molecules from the living substance
- Through distance action: new relations are formed between the irradiated parts and
the unirradiated ones
Biological effects:
- Somatic effects appear at the irradiated individual
- Genetic effects appear at the offspring
For same energy absorbed in the tissue, the particles with higher linear
ionization (protons, helions) produce stroner biological effects than the particles
with smaller linear ionization (electrons)
Relative biological effectiveness (RBE):
RBE of radiation given towards normal tissue is defined through the ratio
between the energy absorbed by the tissue at its irradiation with standard
radiation and the energy absorbed by the tissue at the irradiation with the given
radiation to produce the same biological, qualitative and quantitative effect.
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The energy dose (absorbed dose):
Absorbed dose (D), is the ratio between energy W transferred by the radiations
to a volume from the irradiated material and mass (m) of the respective volume
Formeln fr detta r D = W delat med m
Units: Gray (1GY=1J/kg) or rad (1rad=100erg/g)
The biological dose:
B = RBE x D
Units: rem (-rad) or Sv (Sievert) (-Gy)
Irradiation sources of the body (Natural, Sanitary, Technical and Variousirradiations):
Natural irradiation: Is due to the so called radiation background, that containscosmical radiations, the radiations of the radioactive substances from the earths
surface, from the drinking water, from the building materials, etc.
0,5 mrem/day or 200mrem/year
Sanitary irradiation: is due to the use of roentgen radiations for diagnosis andtreatment
- Lung radiography 0,5 2 rem
- Dental radiography 2-15 rem
- Fluoroscopical examination 5 60rem
- Treatment for malignant tumours 3000 7000 rem
Technical irradiation or artificial irradiation:Is due to the sources of nuclear radiations created by man after 1940 (radioactive
sources, accelerators of particles and nuclear reactors used in laboratories forresearch purpose, industry, agriculture, medicine.
Various irradiations:Wich come from different sources, starting the tv screens, of measuring devices
and phosphorescent watches and ending with detection systems from the airports
or in advertising purposes.
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Classification of territory and population from the point of view ofirradiation risk:
For the point of view of the irradiation risk, the territory of a country is dividedin:
- Controlled areas include the spaces of nuclear units, in wich there is therisk for professional irradiation
- Supervised areas include the areas next to the controlled areas
- Unsupervised areas the rest of the countrys territory
From the same point of view, the population of a country is divided in:
- Professionally irradiated staff(the one who works in controlled areas)
- Unprofessionally irradiated staff(the one who works in supervisedareas
- The rest of the population (from unsupervised areas)
The norms of radioprotection:
Professionally irradiated staff: Whole body 5rem/year = 50mSv/year, (Hands,legs 75rem/year = 750mSv/year
Unprofessionally irradiated staff: Whole body 1.5rem/year = 15mSv/year,
(Hands, legs 7.5rem/year = 75mSv/year
For the rest of the population: Whole body 0.5rem/year = 5mSv/year, inget fr
hander ftter.