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1
Illinois Institute of Technology
  • PHYS 561
  • RADIATION BIOPHYSICSLecture 3Interaction of
    Photons with Matter Radiation ChemistryIntroduc
    tion to Biology
  • ANDREW HOWARD
  • 10 June 2014

2
Radiation interacts with matter
  • Well investigate the chemical changes that occur
    in matter, particularly soft tissue, when
    ionizing radiation impinges on it
  • But first we need to finish discussing the
    initial interactions themselves.

3
Outline of Session
  • Left over from chapter 5
  • Pair production
  • Bremsstrahlung
  • Charged particles matter
  • Interaction of photons with matter
  • Size scales and biological cells
  • Energy deposition at different physical scales
  • Neutrons
  • Chapter 6
  • Types of energy transfer from electrons
  • Free Radicals
  • Radiation Chemistry of water
  • Fricke dosimeter
  • Recombination, Restitution, Repair
  • Biology 101

4
Relevant references
  • Some significant references on photoelectric
    effect and the interactions of photons with
    biological tissue
  • 1. J.H. Hubbell (1977) Radiation Research 70
    58-81.
  • 2. J.H. Scofield (1973) Theoretical
    Photoionization Cross Sections from 1 to 1500
    keV, Report UCRL-51326, University of California
    Lawrence Livermore National Laboratory, National
    Technical Information Center, Springfield, VA
  • 3. A.M. Kellerer and H.H. Rossi (1971)
    Radiation Research 47 15-34
  • 4. H.H. Rossi (1959) Radiation Research 10
    522-531

5
Typos of the Day
  • Page 79, first paragraph under IMPORTANCE OF THE
    COMPTON PROCESS, 4th linewith attention the
    the with attention to the
  • Page 86, List of possibilities, 3Either M or
    m0 is at rest ?Both M and m0 are at rest
  • Page 87, 2nd paragraph, 1st lineThe four
    principle ? The four principal

6
Pair Production
  • ? ? e- e see fig. 4.7
  • Can happen if Eg gt 1.022 MeV 2 m0(e-)c2
  • Rapidly increasing cross-section gt 1.022 MeV
  • This is the predominant mode of interaction over
    a range from a bit above that value up to 5MeV
  • Stopping power/atom varies as Z2
  • Energy transferred is hn - 1.022 MeV

7
What pair production does
  • Scattering nucleus plays fairly passive role
  • not much momentum transferred to nucleus
  • but it does soak up some momentumotherwise we
    couldnt get it to happen at all
  • Generally the positron gets annihilated, giving
    off a pair of 0.511 MeV photons. These generally
    escape and are not part of the absorbed energy

8
BremsstrahlungRadiative Energy Loss
  • Braking radiationA fast electron loses energy
    to its environment in a nonspecific way due to
    Coulombic interaction with neighboring charged
    particles.
  • The static particles are much more massive than
    the electron, so they dont get accelerated
    nearly as much as the electron does but the
    electron does get accelerated.
  • What happens when an electron is accelerated? It
    has to radiate! This type of Coulombically-motivat
    ed radiation is Bremsstrahlung

9
Dependence of Bremsstrahlung on Z
  • High-Z elements have much higher cross sections
    for braking radiation for a given initial
    electron energy because the acceleration goes
    like Z
  • Higher electron energies produce more
    Bremsstrahlung than lower electron energies

10
Significance of Bremsstrahlung
  • Example in X-ray generators
  • 1.5418Å (8KeV) characteristic X-rays are produced
    in great quantity when we shoot fast electrons at
    a copper target L-to-K shell transition
    emissions
  • BUT we also get a lot of radiative transfer of
    energy from the electrons as they move past the
    copper atoms. This gives rise to Bremsstrahlung,
    which has no characteristic energies.
  • Thus the spectrum is like this

11
Output X-ray Spectrum of a Copper Target
12
Overview of photon-medium interactions
  • Weve seen four mechanisms by which photons can
    transfer energy to a medium
  • Photoelectric effect (mostly below 1MeV)
  • Coherent scattering (mostly below 20 keV)
  • Compton scattering (peaks around 1MeV)
  • Pair production (starts _at_ 1.022 MeV dominates at
    high energy)
  • We can write the overall event cross-section
    asµtot ?PE ?coh ?Compton ?pair

13
What predominates where?
  • Cf. fig. 5.2(a),(b)
  • For lead, Compton falls off from 100 keV upward
    and pair production takes over 5MeV
  • These figures make the distinction between
    absorption and transfer as well

14
How do mixtures absorb?
  • Well come back to this later
  • Mixtures, including polyatomic compounds, absorb
    according to their individual atomic attenuation
    properties, weighted by their mole fraction

15
Attenuation Coefficients for Molecules (and
mixtures)
  • Calculate mole fraction fmi for each atom type i
    in a molecule or mixture
  • subject to Sifmi 1
  • Thats why we call these mole fractions
  • Recognize that, in a molecule, fmi is
    proportional to the product of the number of
    atoms of that type in the molecule, ni, and to
    the atomic weight of that atom, mifmi Qni
    mi(Q a constant to be determined)

16
Attenuation coefficients, concld
  • Thus Sifmi Si Qni mi 1 so Q (Si ni mi)-1
  • Then (s/r) for the compound will be(s/r)Tot
    Sifmi (s/r)i SiQni mi(s/r)i (Si ni mi)-1 Sini
    mi(s/r)i
  • This will, in fact, work even with mixtures of
    compounds, as long as you keep your mole
    fractions straight.

17
Calculating Mole Fractions and Attenuation
Coefficients
  • Example 1 Water (in book)
  • H2 n1 2, m1 1 O n2 1, m2 16
  • Q (Si ni mi)-1 (21 1 16)-1 1/18
  • Thus fH2 2/18, fO 16/18,
  • (s/r)Tot Sifmi(s/r)I (2/18)(0.1129cm2g-1)
    (16/18)(0.0570 cm2g -1) 0.0632 cm2g-1
  • Benzene (C6H6)
  • C6 n1 6, m1 12 H6 n2 6, m2 1
  • Q (61261) 1/78, fC6 72/78, fH6 6/78

18
Interaction of Charged Particles with Matter
  • See pages 84 85 in the text-
  • Provides solutions to the dynamical equations
    describing motion of a heavy charged particle
    past a stationary electron or (by relativity)
    motion of an electron past a stationary heavy
    particle F kze2/r2 along line MQ

Q
19
Interaction of e- With Heavy Charged Particle
  • Momentum imparted to electronat distance of
    closest approach

classical coherentscattering by e-
non relativistic
20
Interaction of Charged Particles with Matter
  • Recall diagram 5.3, p.84.
  • The crucial equation is for DE(b), the energy
    imparted to the light particle DE(b)
    z2r02m0c4M/(b2E)where E is the (nonrelativistic)
    kinetic energy of the moving particle (1/2)Mv2.
  • It increases with decreasing impact parameter b,
    which stands to reason
  • Energy imparted is inversely proportional to the
    kinetic energy E of the incoming heavy particle!

21
Why does this formula matter?
  • Rate of energy loss is inversely proportional to
    the energy of the incoming particle
  • So most of the energy is yielded up as the heavy
    particle approaches its resting state
  • There are some details weve skipped, but theyre
    readily available in other textbooks.

22
Relativity tells us this is important!
  • We usually think about the electron moving and
    the heavy nucleus being stationary, not the other
    way around. Why do we go through this derivation?
  • (a) This could actually happen as described
  • (b) Galilean (or Einsteinian!) relativity says
    this is equivalent to what happens if the
    electron is moving and the heavy particle is at
    rest. Thats the more typical situation but the
    analysis still works.
  • (c) If Mm0, i.e. an electron-electron
    interaction, then the assumption of minimal
    interactivity fails, but we still find that the
    energy transfer goes like 1/v2 or like 1/E.

23
Final steps in absorption
  • Lets think about a high-energy photon entering a
    biological medium
  • It undergoes a modest number of scattering events
    that give rise to energetic (keV - MeV) electrons
  • These energetic electrons will themselves only
    affect the medium once they have transferred
    energy to other electrons in 10-50 eV packets
  • Four mechanisms for doing that(a) Delta
    rays (c) Bremsstrahlung in motion(b)
    Photoelectric (d) Direct collision

24
Delta rays
  • We expect that each individual event transfers a
    small amount of momentum, so the incoming
    electron doesnt change direction all that much
  • There are exceptions these are delta rays.
  • The delta ray is the common name for a
    secondary electron that itself has enough energy
    to ionize other things
  • The ionization events caused by the delta ray can
    produce electrons that have energies up to half
    of that of the primary electron
  • So some delta rays will even produce tertiary
    electrons that are themselves delta rays!

25
Photoelectric processes
  • If the primary photon is absorbed by an atom, a K
    or L-shell atomic electron is ejected
  • This makes an outer-shell electron hop in to fill
    the inner-shell vacancy, giving rise to an output
    photon with an energy equal to the difference in
    shell energies
  • The photon has to undergo ordinary scattering
    (probably Compton) in order to transfer energy
  • This process is most likely in high-Z media, for
    which the capture cross section is measurable

26
Bremsstrahlung with movement
  • Caused by Coulombic interaction of an emitted
    electron with nucleus
  • Incoming electron decelerates a little due to
    these interactions
  • This is not like the 1/E-dependent process we
    just described, because not much happens to the
    target in this instance
  • Loss due to Bremsstrahlung is important for
    incoming electrons above 10MeV in lead or 100 MeV
    in water that corresponds to almost 200 times
    the rest energy of the electron

27
Direct collisions
  • Extreme form of Bremsstrahlung electron stops
    and gives up all its kinetic energy to the
    absorber
  • Rare but can be measured

e-
28
Dose a definitional reminder
  • Remember that dose is about deposition (or
    absorption) of energy per unit mass, while kerma
    is about transfer of energy per unit mass
  • So energy that escapes the neighborhood of the
    initial event may not count in the dose in that
    region, but rather will count in the dose of some
    other region
  • Kerma, by contrast happens at the moment of
    impact
  • So kerma can be lower or higher than dose
    depending on circumstances

29
Dose and Kerma
  • See Fig. 5.5 in text.
  • Because secondary events extend farther into
    tissue (or other) than the initial deposited
    radiation, dose extends farther into the interior
    than kerma.

30
Photons interacting with matter
  • We mentioned at the beginning of the lecture that
    the interaction of a high-energy photon with a
    chunk of matter involves
  • Photoelectric effect
  • Coherent scatter
  • Compton scatter
  • Pair production

31
Compton Scattering, Revisited
  • The most important of these processes for hn gt
    100 KeV is Compton scatter, especially if the
    matter is water or tissue
  • See fig. 5.2(B) in the text to see whyµab/r
    (Compton) predominates above 100KeV

32
Compton Processes in Tissue
  • Biological soft tissue is predominantly made up
    of H, C, N, O, and a little P and S. So
    attenuation of photons is dominated by those
    light elements (Z ? 16)

33
Dose
  • Remember Dose energy deposited per unit mass.
  • What is the meaningful size scale for a mammalian
    cell?
  • Well need to know this to estimate dose on a
    cell.
  • size scales ?5mm
  • r ? 1 g/cm3 for water or
    soft tissue
  • mass of (5mm)3 ? r (5 10-4cm)3 ? r
  • 125 10-12cm3 ? 1g/cm3
  • 125 10-12g 1.25 10-13kg

34
Energy Absorbed in a Cell
  • Suppose N Joules of energy are deposited in a 70
    kg human. Nominally the dose is N/70 Gy.
  • How much energy is deposited in a single (5µm)3
    cell? (N/70)Gy 10-13 kg (N/70)10-13 J
    (1.310-15)N J (1.310-15)N/1.60910-19 J
    8500N eV. So its a lot of energy!
  • Is the Bethe-Blocke continuous slowing-down
    approximation applicable here? No! Too much
    energy is being stopped per cell for it to be
    applicable. But we try to use it anyway.

35
Track structure
  • We draw different kinds of conclusions depending
    on the size range we think about
  • The smaller the target, the bigger the
    fluctuations in dose that we have to recognize
  • So deliver of 1 cGy to a large volume could mean
    were delivering anywhere between 0 and 103 Gy to
    a single chromatin fiber
  • We can attempt to account for this in various
    ways Rossi does it in terms of EY/d

36
Can LET tell us what we want?
  • Envision variations in dose in terms of the
    individual values of E/m for small m these may
    differ from the bulk dose by many orders of
    magnitude
  • Rossi defines E/m for these small masses as the
    local energy density, Z
  • Remember that LET is dEL/dl, where l is the
    length along the track of the ionization source.
  • This might give us a handle on the effectiveness
    of a given bulk dose in causing damage, or it
    might not.
  • Rossi uses LET in fudging his values, as well
    now discuss.

37
Rossis alternative
  • He makes some assumptions
  • Particles and their secondaries deposit over
    spherical volumes of specific size
  • Source and its secondaries can deposit an energy
    Ey within the sphere
  • We call each deposition an event
  • Event size Y is defined as Ey/d, where d is the
    sphere diameter
  • The hope is that for idealized tracks, Y will be
    a constant independent of d

38
How this is used
  • Rossi fudges the real spheres by looking at
    experimental systems involving spherical
    ionization chambers containing low-pressure
    gases
  • These become surrogates for tiny
    tissue-equivalent spheres
  • Then he plots Y as the independent axis and the
    energy loss D(Y), corrected for LET distribution
  • See fig. 5.6 for 1.5 µm spheres the largest
    D(Y) values occur around 70 keV/µm for protons

39
Local energy density
  • Tissues have densities close to 1 g cm-3 103 kg
    m-3
  • Alpen shows you that the amount of locally
    deposited energy?Z 30.6 d-2 J kg-1
  • So for high LET and small d, this can be as high
    as 10.9 Gy for reasonable values of Y
  • For high LET radiation lots of events produce Z0
    and a few give us very big values
  • For low LET is more boring the distributions are
    Gaussian and centered on the absorbed dose
  • General conclusion high-LET radiation is harder
    to predict results at the single-cell level

40
Demonstration That Events Dont Interact Much
  • Spurs are 400 nm apart
  • 1 nm 10-9 m
  • 400 nm 0.4 mm
  • Hydrogen radical diffusion (see below)
  • 8 ? 10-5cm2s-1 diffusion constant for H
  • Typical lifetime ? 10-6s
  • Typical diffusion distance 180 nm
  • This is smaller than the distance between spurs!

41
Mozumder Magee
  • 1 MeV typical electron Portion of
    energy deposited
  • Spurs 6 - 100 eV 65
  • Blobs 100 - 500 eV 15
  • Tracks 500 - 5000 eV 20

42
Blobs, Spurs, and TracksDistribution is
Energy-Dependent
  • Mozumder Magee short tracks dominate at low
    primary electron energy spurs more important at
    high energy

43
Neutrons
  • Neutrons are produced as byproducts of various
    reactions and are therefore moderately
    significant as portions of human or environmental
    exposure
  • We can learn things from neutron studies that
    will help us in understanding the ways that ions
    and other heavy particles interact with tissue

44
Neutrons Elastic Scatter
  • Important up to 14 MeV range

Energy imparted to nucleus

average over angles
45
How to average cos2q
  • Addition formula for cosine
  • cos(AB) cosAcosB - sinAsinB
  • For ABq, cos(2q) cos2q - sin2q
  • Furthermore cos2q sin2q 1 so
  • cos2q cos2q - (1 - cos2q) 2cos2q - 1
  • Therefore cos2? (1 cos2q) / 2
  • This gives us the tools we need to integrate
    cos2q over an interval.
  • In general ltf(x)gt over an interval (a,b) is

46
ltcos2qgt, continued
47
Significance in Elastic Scatter
  • Recall we said that for any value of q, the
    energy transferred to the target nucleus, Et,
    isEt En (4MaMn)cos2q / (Ma Mn)2
  • So the average energy imparted to the target
    nucleus is
  • ltEtgt En (4MaMn) / (Ma Mn)2 ltcos2qgt
  • We just spent three pages proving ltcos2qgt1/2
  • Thus ltEtgt 2EnMaMn / (Ma Mn)2

48
Inelastic Scatter
  • Increasingly important at higher neutron energies



49
Neutrons Other Mechanisms
  • (III) Nonelastic (75 MeV)
  • 12C n ? 9Be a gt KE 1.75 MeV
  • (IV) Neutron Capture
  • 14N n ? 14C p
  • 1H n ? 2H ? 2.2 MeV
  • (V) Spallation Nucleus fragments!
  • Need very high-energy neutrons ( gt 100 MeV)


50
Free RadicalsDefinitions and Illustrations
  • A free radical is defined as a molecular species
    containing an unpaired electron. It may be
    charged or uncharged.
  • Most biological free radicals, with the
    significant exception of superoxide (O2- ), are
    uncharged.
  • OH- Hydroxide ion (9 protons, 10 electrons)
  • OH Hydroxyl radical (9 protons, 9 electrons)

Moses Gomberg Characterized the triphenylmethyl
radical in 1900
51
Reactivity of free radicals
  • Free radicals are reactive because the unpaired
    electrons tend to seek out targets, either other
    unpaired electronsH H ? H2 or other
    acceptors of unpaired electrons.
  • Reactivities vary considerably depending on
    presence or absence of stabilizing influences,
    such as channels through which the unpaired
    electron can be delocalized
  • In the absence of those channels, free radicals
    tend to recombine in picoseconds
  • With those channels, they can last seconds or
    longer, even at room temperature

52
Radical Stability
  • This has nothing to do with political psychology
    -)
  • Highly unstable free radicals tend not to stay
    around long enough for ordinary spectroscopic
    methods to detect.
  • Radicals where the unpaired electron can be
    highly delocalized last long enough to detect.
  • Triphenylmethyl radical

C
H
C
H
53
Cartoons of Electron Distributions in ions,
molecules, and radicals
  • Hydroxyl radical(8 paired e-, 1 unpaired e-, 9
    p)
  • Hydroxide ion(10 paired e-, 9 p)
  • Molecular oxygen(16 paired e-, 16 p)
  • Superoxide ionic radical(16 paired e-, 1
    unpaired e-, 16 p)

H

O




H

O




O
O






O
O





54
10-16 - 10-12 s Scale Events and After
  • e-fast H2O ? H2O e- e-fast
  • e-fast H2O ? e-fast H2O ? H OH

Ionization
(lt100 eV)
H2O
H OH
H2O-
nH2O
Solvated aqueous hydrated
(10-4s)
e-aq
Acid
Activation
H ? H2
H
10-11s
H, OH, e-aq O ? O2 O2-, H2O2
H2O
55
Radiation Chemistry of Water
  • Since biological tissue is mostly water, were
    very interested in the products produced when
    water absorbs ionizing radiation
  • The reactive species formed out of water are
    responsible for a large fraction of the
    biological activities of radiation
  • Ordinary ions (H, OH-, H3O) are among these
    species, as is hydrogen peroxide (H2O2)
  • So are free radicals H, OH, O2-, HO2
  • We often discuss the solvated electron, eaq-.

56
Fricke Dosimeter
  • Bookkeeping tool for aqueous radical
    chemistry,based on Fe2 ? Fe3
    e- ferrous ferric
  • Sequence of reactionsH O2 ? HO2 (i.e.
    H-OO)HO2 Fe2 ?HO2- Fe3 HO2- H ?
    H2O2OH Fe2 ? Fe3 OH-H2O2 Fe2 ? Fe3
    OH- OH
  • In absence of O2 H H2O ? OH H2

57
Fricke Dosimeter bookkeeping
  • Each hydrogen radical H causes the oxidation of
    three molecules of ferrous ion
  • H2O2 produced by radiolysis will oxidize two
    ferrous ions one directly, one indirectly.
  • A radiolytically-produced OH radical gives rise
    to one more oxidation
  • Therefore at acidic pH in the presence of
    oxygen,G(Fe3) 2G(H2O2) 3G(H) G(OH)

58
Definition of Yield
  • G Yield ? Number of events produced per 100 eV
    energy deposition
  • Were often interested in dG(E)/dE
  • Yield is either dimensionless or has dimensions
    of (energy)-1 depending on your perspective
  • Fricke dosimeter provides a way of measuring
    yield

59
Fricke bookkeeping
  • Results on p. 112 for 60Co photonsG(H)
    3.65G(H2O2) 0.75G(OH) 3.15
  • We then apply formula 6.8 to determine G(Fe3)
  • Recall that under appropriate conditionsG(Fe3)
    3 G(H) 2 G(H2O2) G(OH) 3 3.65
    2 0.75 3.15 15.6
  • Under anaerobic conditions eqn. 6.9 applies
    G(Fe3) G(H) G(OH) 2G(H2O2) 8.3

60
Interactions of Energetic Electrons With
Biological Tissue
biol response
  • Direct
  • e-fast DNA ? DNAbrokene-fast
  • e-fast Protein ? Proteinbrokene-fast
  • Indirect Action
  • H2O e-fast
  • e-fast H2O
  • H2O e-H2Oe-fast

log - linear dose - response
further radical chemistry
61
Direct Action the model
  • Direct action of radiation on a species says that
    a single hit of radiation onto a molecule damages
    it. Then if N is the number of undamaged
    molecules after irradiation with dose D, we
    expect the change in N, DN, with a small increase
    DD in dose is proportional to N and to DD.

Radiation in


N0 Total moleculesN Undamaged
molecules
62
Physical model and mathematics
  • Let N number of undamaged molecules after
    irradiation with dose D. Then dN ? N dD.
  • More radiation dose implies more response
  • More undamaged molecules implies more damage.

f
A ? A e-or other chemistry
63
Why should the damage be log-linear?
  • The relationship dN ? N dD can be rewritten dN
    -kN dD, where k inactivation constant.
  • Then dN / N -kdD. Integrating both sides,
  • ln N -kD C. Raising e to a power on both
    sides,
  • elnN e(-kD C) e-kD eC. Defining eC N0,
  • N N0e-kD
  • Thus the physical meaning (boundary condition) of
    N0is that it is the number of entities present
    in the case where the dose is 0.

64
Significance of the inactivation constant
  • Inactivation constant, k, is in dimensions of
    inverse dose (e.g. units of Gy-1) and is the
    reciprocal of the dose required to reduce the
    number of undamaged molecules down to 1/e times
    the original count.
  • N N0e-kD if Di 1/k, then
  • N(Di) N0e-kDi N0e-k/k N0e-1 N0/e
  • We could define a half-inactivation dose D1/2,
    analogous to the half-life of an emitter
  • For D D1/2, NN0/2 N0e-kD1/2, ln1/2 -kD1/2
  • Thus -ln2 -kD1/2,so D1/2 (ln 2)/ k 0.693 /
    k

65
Indirect action of radiation
  • Initial absorption of radiative energy gives rise
    to secondary chemical events
  • Specifically, in biological tissue
  • R H2O ? H2O (R radiation)H2O biological
    macromolecules ?damaged biological
    macromolecules
  • The species H2O may be a free radical or an
    ion, but its certainly an activated species
    derived from water.
  • Effects are usually temperature-dependent,
    because they depend on diffusion of the reactive
    species to the biological macromolecule.

66
Dose-response for indirect action
  • Unlike the direct-action case, we cant write
    down a simple mathematical model for whats going
    to happen. The dose-response curve may be
    log-linear, but it doesnt have to be

ln(Surviving Fraction)
Dose
67
Interaction of energetic electrons with
biological tissue
  • Direct actione-fast DNA ? DNAbroken e-fast
    (log-linear)e-fast protein ? proteinbroken
    e-fast (log-linear)dN/dD -kD Nundamaged
    N0e-kD
  • Indirect action H2O e-faste-fast
    H2O further radical chemistry
    H2O. e-H2O e-fast(water molecules)
    (biomolecules) ? (biomolecules) radical water
    products

68
Radical Fates/Damaged Biomolecule Fates
  • Recombination A B ? A - B (timescale
    10-11s)
  • Generally A B i.e. A A ? A - A
  • Restitution Non catalyzed regeneration of
    non-radical species (microsecond timescale)
  • A X ? A X
  • Repair Catalyzed regeneration of undamaged
    species
  • A E R ? Amod E R where E is enzyme
    (ms-sec)

biol
biol molecule
out
diffuseable
biol
biol
69
Fundamentals of Biology for the Radiation
Biophysicist
  • It would be presumptuous of me to try to
    summarize all of biology in half of one lecture
  • Ill therefore content myself with pointing out a
    few fundamentals that will be relevant to our
    studies of the interactions between ionizing
    radiation and biological tissue
  • As an endpoint, were primarily concerned with
    the effects of radiation on vertebrate,
    especially human, tissues but we do need to have
    some feel for how radiation affects bacteria and
    yeast as well

70
What is life?
  • That was the title of a series of lectures given
    by Erwin Schrödinger in Dublin in 1943
  • His focus was on articulating how quantum physics
    could help to explain the organizational
    principles found in organisms
  • But we can kidnap that name to focus on what we
    actually do want to do, which is differentiate
    living organisms from non-living entities

71
What are living organisms?
  • Entities capable of
  • Reproduction
  • Energy processing
  • Adaptation to changes in environment
  • Capable of local decreases in entropy

72
Based on that definition,what is alive?
  • On this basis, conventional life from archaea and
    eubacteria up through elephants and redwood trees
    are living
  • Viruses are a borderline case prions highly
    questionable

73
Organisms are made up of cells
  • Cells are somewhat self-contained objects within
    which chemical reactions and reproduction can
    occur
  • Every cell interacts with its environment
  • Cells are surrounded by a differentially
    permeable boundary called a cell membrane
  • Sizes of cells vary but theyre generally between
    1 and 10 micrometers on a side

74
Highest-level taxonomic distinctions
  • Most fundamental distinction is made on the basis
    of whether the organisms cells have nuclei
  • Eukaryotic cells have nuclei
  • Prokaryotic (archaeal and eubacterial) cells
    dont
  • Eubacteria are simple, generally unicellular,
    organisms lacking nuclei
  • Archaea are like that too, but they appear to
    derive from a separate evolutionary history many
    are extremophiles

75
Eukaryotes
  • These organisms have nuclei and generally have
    other definable organelles as well mitochondria,
    endoplasmic reticulum, Golgi apparatus, vacuoles,
    chloroplasts,
  • Often but not always multicellular
  • Yeast, e.g. Saccharomyces, is a unicellular
    eukaryote
  • Some organisms are complex but unicellular

76
Reproduction
  • We included this in our definition of life
  • Unicellular organisms generally reproduce by
    fission, but not inevitably there are
    cooperative (sexual) events that occur even among
    bacteria
  • Multicellular organisms undergo mitosis at the
    cellular level but they also have a level of
    organization wherein an entire organism can be
    engendered via combinations of meiosis, mitosis,
    and growth

77
Eukaryotic organelles
  • Nucleus site of replication and
    transcriptioncontains DNA in various levels of
    organization
  • Mitochondrion site of most catabolic
    (energy-producing) reactions, which typically
    yield ATP
  • Endoplasmic reticulum vehicle for lipid
    synthesis and protein processing
  • Golgi apparatus vehicle for trafficking
  • Cytoskeleton stiff proteinaceous organizers
  • Vacuoles sacs containing fluids
  • Chloroplasts sites of photosynthesis

78
How do we study biological systems?
  • Observations of ecosystems
  • Direct observations of whole organisms
  • Recognition of tissue-tissue interactions
  • Delineation of tissue types
  • Recognition of cell-cell interactions
  • Delineation of cell types
  • Characterization of molecular events in a cell
    and in the extracellular matrix
  • Understanding of the underlying physics that
    enables those molecular events to occur

79
Biological activity depends on chemistry
  • Thats a commonplace now, but it wasnt fully
    recognized until sometime in the nineteenth
    century
  • It applies to chemical transformations within
    cells, but it also applies to extracellular
    systems and macroscopic movements, such as muscle
    contraction
  • Understanding the energetics (does the activity
    require or release energy) and the kinetics (how
    does one overcome an activation barrier) is
    critical to understanding biochemical processes

80
Biological reactions are catalyzed
  • A catalyst is an entity that participates in a
    reaction but is ultimately returned to its
    original state after the reaction completes
  • Therefore a catalyst influences kinetics but not
    equilibrium
  • Biological catalysts are called enzymes
  • Enzymes have three fundamental properties
  • They are catalytic
  • They are specific
  • They can be regulated

81
Most, but not all, enzymes are proteins
  • Note that many proteins arent enzymes
  • The recognition that enzymes are proteins arose
    in the 1920s and 1930s
  • By the 1970s it became clear that certain RNA
    molecules are catalytic
  • Some RNA-catalyzed reactions, notably the
    creation of new protein molecules, are central to
    biological function

82
DNA is the vehicle for heritance
  • Deoxyribonucleic acid is a polymer found in all
    organisms and many viruses
  • Building blocks phosphodeoxyribose
    backbone,N-containing side-groups called nucleic
    acid bases
  • DNA contains information enabling parent cell or
    organism to produce nearly-identical offspring
  • Differences arise from
  • Mutations
  • Recombination
  • Sexual segregation of chromosomes
  • Epigenetic effects

83
Central dogma, modern form
  • DNA becomes replicated prior to each cell
    division
  • Double-stranded DNA uncoils
  • Fresh copy of each strand created and coiled up
  • DNA is transcribed into various forms of RNA
  • Gene transcribed when RNA is called for
  • One strand of DNA provides template
  • Messenger RNA is translated at ribosome
  • mRNA sequence defines amino acid sequence of
    resulting protein
  • Protein then folds, either spontaneously or not

84
DNA replication is protected against error
  • Inherent error rate might be one base
    substitution in 104 or 105 replicated bases
  • Error correction within DNA polymerase drops that
    to about 1 in 107
  • Further error correction (repair) by external
    enzymes drops it to about 1 in 109

85
Why is that relevant?
  • In the human genome, 1 in 109 is still several
    surviving base substitutions in each replication!
  • Most substitutions are harmful most arent fatal
  • Exposure to ionizing radiation and certain
    chemical mutagens, particularly at certain stages
    in the cell cycle, can significantly increase the
    error rate
  • Human genetic conditions that hinder DNA repair
    substantially increase radiation sensitivity
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