Post on 07-Apr-2018
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Physical chemistry of natural
selection
Jean-Louis Sikorav
EPFL October 9 2008
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Approaches of natural
selectionFormal (based on logic, mathematics,
geometry, genetics) such as Genetical
Theory of Natural Selection (RA Fisher). Thishas an underlying materialistic basis: The
physical chemistry of natural selection
Other (higher) levels exist: cell, unicellular
vs mult icellular organisms, species,populations
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Physical chemistry of natural
selection
How do we understand the high yields
and the high rates of biochemistry?
Partial answer: a relation between
efficiency and heterogeneity,
macroscopic or microscopic (chiralityand polarity).
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Macroscopic heterogeneity:
Homogeneous versusheterogeneous biochemistry
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Homogeneous and
heterogeneous chemistry
The field of chemistry is commonly divided into two parts,
namely homogeneous and heterogeneous chemistry.
Homogeneous chemistry deals with the study of chemicalprocesses taking place in the bulk of a homogeneous phase,
such as a gaseous, a liquid (a solution) or a solid phase.
Heterogeneous chemistry is concerned with the investigation
of chemical processes that involve more than one phase
(either more than one phase at the onset of the process or acoupling between the process and a phase transition/phase
separation).
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The birth of physical chemistry:
heterogeneity as a nuisance
(vant Hoff)
Les mlanges homognes, les mlanges gazeux et les
solutions jouent souvent un rle prpondrant dans les
phnomnes dquilibres chimiques (1898)
Ce sont les ractions dquilibre des mlanges homognes
qui prsentent le plus dintrt (1898)
Lhtrognit est une nuisance , quil est possibledliminer, par exemple par humectation des
parois (Etudes de dynamique chimique, 1884)
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Importance of solutions:Arrhenius, The Theory of Solutions, 1912
"The liquid state was already at that time (The Middle
Ages) found to be the most suitable condition forchemical reactions.
The experience of the alchemists was summed up
under the formula "the Substances do not act upon
each other unless they are dissolved" (corpora nonagunt nisi soluta).
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Homogeneous and
heterogeneous biochemistry
In a similar way one can define a homogeneous anda heterogeneous biochemistry.
The scope of homogeneous biochemistry can benarrowed down to the study of biochemical processestaking place in the bulk of a homogeneous aqueousphase (an aqueous solution).
The goal of this lecturewill be to define and to explorethe field of heterogeneous biochemistry, with anemphasis on the heterogeneous biochemistry ofnucleic acids.
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The two meanings of
homogeneous biochemistryExperimental meaning: the study of processes takingplace in the bulk of a water solution.
Theoretical meaning: that a water solution can be
described as a homogeneous mass, which is only truefor a limited range of length and temporal scales.According to this point of view, a water solution can bedescribed using scalar (directionless), extensivevariables, and this simplifies its description.
Our focus in this presentation will be on the
experimental meaning and on bulk, macroscopichomogeneity/heterogeneity.
(Microscopic heterogeneity: chirality and polarity)
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Outline of the presentation
1. Historical background.2. A case study in heterogeneous biochemistry: DNA
cyclization and renaturation.
3. General concepts.4. Conclusions.
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A search for the relevant
literature
A search for the exact terms heterogeneousbiochemistry in several bibliographical databases(Pub Med: 1950-present; Chemical Abstracts: 1907-present; Science Citation Index 1945-present)completed by an internet search (Google, Scirus) isnegative.
In contrast with the field of heterogeneouschemistry for which there exists a rich literature, the
field of heterogeneous biochemistry has apparentlynever been reviewed.
Why?
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Why?
First possibility:
No one has ever discussed the role of phaseheterogeneity in biochemistry. There is no referencebecause this is a completely new concept.
This conclusion is incorrect.
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A history of homogeneous and
heterogeneous biochemistry (1) What are the concepts required to define
homogeneous and heterogeneous biochemistry?
In addition to the concepts of chemistry and
physiological or biological chemistry (mid 19thcentury: Hoppe-Seyler and others), we need theconcepts of homogeneity and phase.
When were these concepts introduced?Homogeneity: very old (Anaxagoras: see the article
Atoms by Maxwell in the Encyclopedia Britannica )Phase and phase coexistence: Gibbs (1875)
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J. Willard Gibbs. On the equilibrium of heterogeneous
substances. Transaction of the Connecticut Academy,
(1875-1876) vol. 3, pp. 108-248.
Let us first consider the energy of any homogeneous part of agiven mass, and its variation for any possible variation in thecomposition and state of this part. (By homogeneous is meant thatthe part of question is uniform throughout, not only in chemicalcomposition but also in physical state).
In considering the different homogeneous bodies which can beformed out of any set of component substances, it will beconvenient to have a term which shall refer solely to thecomposition and thermodynamic state of any such body withoutregard to its quantity or form. We may call such bodies as differ incomposition of state different phases of the matter considered,
regarding all bodies which differ only in quantity and form asdifferent examples of the same phase. Phases which can existtogether, the dividing surfaces being plane, in an equilibrium whichdoes not depend upon passive resistances to change, we shall callcoexistent.
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A new search for the relevant
literatureBooks on History of Chemistry and Biochemistry(Fruton, Florkin, Laszlo)
Old text books on chemistry (vant Hoff, Arrhenius)
and biochemistry (Enzymes: Bayliss, Haldane,Sumner)
JSTOR, Bibliothque Nationale de France (Gallica),
Web site of the Nobel Foundation
This search is not completed (language barrier).
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A history of homogeneous and
heterogeneous biochemistry (2) Any researcher having read Gibbs is able to discuss
the relevance of the ideas of homogeneity/heterogeneity and phase for biochemistry.
Who was the first scientist to do it? A difficult question, with often no simple answer
(see TS Kuhn, Historical Structure of ScientificDiscovery, Science, 1962).
The relevance of the ideas of homogeneity/heterogeneity and phases for biochemistry is alreadyclearly understood in the beginning of the 20thcentury.
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A history of homogeneous and
heterogeneous biochemistry (3)
Many of the most important processes of normal life occur inheterogeneous systemsSvante Arrhenius, Immunochemistry (1907). Chapter III. Velocity ofReaction. Heterogeneous systems, p.136.
Even a hasty consideration of the arrangements present in living cells issufficient to bring conviction that the physical and chemical systemsoperate under conditions very different from those of reactions takingplace between substances in true solutions. We become aware of thefact that there are numerous constituents of the cell which do not mixwith one another. In other words, the cell system is one of manyphases to use the expression introduced by Willard Gibbs.
W. M. Bayliss. The physiological importance of phase boundaries.Science (1915) vol. 42, pp. 509-518.
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A history of homogeneous and
heterogeneous biochemistry (4)
Wtrich, Nobel Lecture 2002:
"Nuclear magnetic resonance (NMR) spectroscopy is
unique among the methods available for three-dimensional structure determination of proteins andnucleic acids at atomic resolution, since the NMR datacan be recorded in solution. Considering that bodyfluids such as blood, stomach liquid and saliva are
protein solutions where these molecules perform their physiological functions, knowledge of the molecularstructures in solution is highly relevant.
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A history of homogeneous and
heterogeneous biochemistry (5)
A puzzling situation
The importance of the ideas of homogeneity/
heterogeneity and of phases for biology andbiochemistry is well understood in the beginning of the20th century. These ideas are not discussed afterWorld War II.
Question: What happened?
A plausible answer is that the discussion of these ideaswas premature at that time.
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States of matter
(macroscopic phases) in 1875
1 Solid state
2 Liquid state
3 Gaseous state
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States of matter today
(classical macroscopic phases)
1 Solid state
Amorphous (glass)
Crystalline
2 Fluid state
Isotropic
Anisotropic (mesomorphous, liquid crystals,
amphiphiles)
3 Gaseous state4 Polymers
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Phase transitions in biopolymers
helix-coil, coil-globule, coil-stretch,
adsorption, threading through a pore.
sol-gel, aggregation, liquid-crystalline
states.
Flory J. Pol. Sci. (1961), DiMarzio (1999)
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Biopolymers
Answer:
Our understanding that proteins and nucleic acids arepolymers is essentially posterior to World War II.
Early discussions concerning the polyphasic nature ofcells became associated with the obscure concept of acolloidal state of biological matter (Bayliss, Bancroftthe Phase Ruler ).
This contributed to discredit such generalconsiderations after 1945.
Physical Chemistry from Ostwald to Pauling: TheMaking of a Science in America. John W. Servos(1991)
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The origins of homogeneous or
solution biochemistry
1. The controversy between Pasteur and Liebig, andits solution by Buchner in 1897.
2. An application of Occams razor or parsimonyprinciple.
3. A persistent belief that (bio)chemical reactions caneither only take place in the bulk of a solution, orare more efficient in solutions.
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The origins of homogeneous or
solution biochemistry (1)
1. A controversy on the nature of biological catalysts (nowcalled enzymes following Khne, 1876): according toPasteur les vrais ferments (enzymes) sont des tresorganiss (in other words the catalytic action requires the
presence of the entire living cell and cannot be observedwith soluble substances). This is not true according toLiebig and others (Berthelot). Pasteur has a strict holistic(vitalistic) attitude, while Liebig has a more pragmatic,reductionist approach.
In 1897 Buchner grinds yeast cells and presses them with ahydraulic press. The resulting (cell-free) press juice is ableto ferment sucrose.
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The origins of homogeneous or
solution biochemistry (2)
At the same time as Pasteur earned for himself undying fame by hisbrilliant exposition of the significance of living beings as the ultimatecause of such processes, he put a brake on the progress of science inthis field by the vitalistic concept of the actual course of fermentation.
Presentation Speech for The Nobel Prize in Chemistry 1907
Avec des tissus ou des cellules entires, il est souvent difficile, etparfois mme impossible, de faire pntrer certains composs travers la membrane de la cellule. Avec les extraits, au contraire, ildevient relativement ais dintervenir dans une raction Il nest pasexagr de dire que, depuis lors, lanalyse dextraits sans cellule
constitue la mthode principale des chimistes qui tudient les tresvivants. Ainsi sindividualise au dbut de ce sicle, une branchenouvelle de la chimie, la chimie biologique
Franois Jacob, La logique du vivant (1970)
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The origins of homogeneous or
solution biochemistry (3)
Enzymatic approach to the problem of DNA replication
Although we have in the Watson and Crick proposal a mechanical model ofreplication, we may at this point pose the question: "What is the chemicalmechanism by which this super molecule is built up in the cell?" Some sixtyyears ago the alcoholic fermentation of sugar by a yeast cell was a "vital"process inseparable from the living cell, but through the Buchner discovery of
fermentation in extracts and the march of enzymology during the first half of thiscentury, we understand fermentation by yeast as a, now familiar, sequence ofintegrated chemical reactions. Five years ago the synthesis of DNA was alsoregarded as a "vital" process. Some people considered it useful for biochemiststo examine the combustion chambers of the cell, but tampering with the verygenetic apparatus itself would surely produce nothing but disorder. Thesegloomy predictions were not justified then, nor are similar pessimistic attitudes
justified now with regard to the problems of cellular structure and specializedfunction which face us. High adventures in enzymology lie ahead and many ofthe explorers will come from the training fields of carbohydrate, fat, amino acidand nucleic acid enzymology.
Arthur Kornberg Nobel Lecture 1959
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The origins of homogeneous or
solution biochemistry (4)2. An application of Occams razor or parsimony
principle.
J. H. Northrop. Annu. Rev. Biochem. (1961), vol. 30
pp. 1-10.
An aqueous solution is a simpler system than a
multiphasic system (less components). Thetheoretical study of phenomena in (dilute) solutions
is also easier: one can often assume a
thermodynamic ideal behavior; the kinetic analysisof the phenomena is also facilitated.
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The origins of homogeneous or
solution biochemistry (5)3. An old and persistent beliefthat (bio)chemical reactionscan only take place in the bulk of a solution (or are moreefficient in solutions).
Corpora non agunt nisi soluta
Compounds do not act unless solubilized.
Water is the deus ex machina of alchemy, the wonderfulsolvent, the word solutio being used equally for a chemical
solution and for the solution of a problem.C.G. Jung Psychology and Alchemy
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The origins of homogeneous or
solution biochemistry (6)
The experiments of Buchner have played a central role in thefoundation of modern enzymology and metabolism.
Most biological chemistry or biochemistry is understood and
taught today as an aqueous solution biochemistry.See the textbooks of Jencks, Fersht, Stryer, Lehninger. Thisis especially true for the study of nucleic acids (Cantor andSchimmel, Bloomfield, Crothers and Tinoco)
An important exception concerns membrane biochemistry.See P. B. Mitchell (Nature, 1961; J. Gen. Microbiol. 1962;Nobel lecture 1978, Eur.J. Biochem. 1979).
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Case studies
1. DNA cyclization2. DNA renaturationin homogeneous and heterogeneous systems
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DNA cyclization in homogeneous and
heterogeneous systems
Bacteriophage DNA: 50,000 base pair long double-stranded DNA (dsDNA), terminated by 12 base long
single-stranded (ssDNA) complementary (cohesive)ends.
Linear in the head of the bacteriophage.
Becomes circular in a few minutes after its injection inEscherichia coli.
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E. coli
Cyclization
in a few
minutes
Cyclization
in a few
hours
0,05 m
1 m
1 m
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DNA cyclization in homogeneous systems
(Wang & Davidson 1966-1968)
Cyclization of the random coil form of phage DNA(in water, in the presence of monovalent salts).
L
C orL + L
L2
Cyclization and multimerization are competingreactions. One must use dilute chain concentrations(typically 5 g/ml or lower) to have a high yield of
circles.The rate of the reaction is too slow (4.6 10-5 s-1 inthe presence of 2M NaCl 25 C ) to account for therapidity of the reaction in vivo.
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DNA cyclization in homogeneous systems
(Wang & Davidson 1966-1968)
Measurement of the cyclization probability by comparingwith a bimolecular reaction:
1/2 left L + 1/2 right LL
J factor (for Jacobson-Stockmayer) or effectiveconcentration of about 6 10-10 M.
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Cyclization of globular DNA
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Cyclization of globular DNA
in the presence of a condensing agent
(spermidine 3+
) Using extremely dilute solutions (50 ng/ml) because
of the presence of a fast (diffusion controlled)aggregation (a phase separation) process. (Rugli Ziegler)
Fast collapse of the chain (on the millisecond timescale) for1.5 mM spermidine. Final state: a toroidalstate, an intramolecular liquid crystal.
Very fast rates (1.4-2 s-1 at 1.5 mM spermidine)involving collapsed chains. Compatible with in vivorates of cyclization.
Jary & Sikorav. Biochemistry. 1999. 38:3323-3327.
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0
100
200
300
400
0,1 1 10 100 1000
0,1 1 10 100
1 m 0,1 m
Electron
microscopy
coil globule
Sedimentation
Cyclization rateCspd
3+
Cspd3+
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Cyclization of globular DNA
in the presence of a condensing agent
(spermidine 3+
)Measurement of the cyclization probability bycomparing with a bimolecular reaction:
L + O
LO
O: a 12base longoligonucleotide complementary tothe right cohesive end of DNA.
Jfactor of about 6 10-6 M in the presence of 1.5 mMspermidine (105 larger than in the random coil state).
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2. Thermal DNA renaturation
(homogeneous)
Using dilute or very dilute
solut ions (below the
overlap concentration C*)
Bimolecular reaction:
k2rates in M-1 s-1
Thermal renaturation takes place in the bulk of
an aqueous solution in the presence of
monovalent salts and belongs to homogeneousbiochemistry.
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Coupling renaturation with aggregation
Sikorav and Church (1991)
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DNA renaturation in the presence of
a condensing agent (spermine 4+)
25000 fold faster than thermal renaturation at room temperaturefor short chains. Rates are more compatible with a diffusion-controlled process (Smoluchowski).
Addition of the condensing agent (e.g. spermine) to a verydilute solution of denatured DNA chains. Renaturation takesplace at the same time as an aggregation process:simultaneous attraction of the like and of the complementarystrands. The aggregated state is anisotropic.
Sikorav & Church. J Mol Biol. 1991, 222:1085-108.Pelta, Livolant & Sikorav. J Biol Chem. 1996, 271:5656-62.
Chaperon & Sikorav. Biopolymers. 1998, 46:195-200.
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P.E.R.T ( Phenol Emulsion Reassociation Technique)
(Kohne et al., Biochemistry, 1977)
DNA renaturation in a two-phase system:
PERT
Water + Salt+ denatured
DNA
Phenol
Continuous and vigorous shaking
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Hypotheses
The reaction involves a transient adsorption of ssDNAchains at the water-phenol interface
DNA renaturation takes place at the water-phenol interfaceGoldar & Sikorav. Eur. Phys. J. E. 2004, 14:211239.
Use a decoupling scheme to studyindependently adsorption and renaturation
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Adsorption of ssDNA3'
5'32P
NaCl + 10 mM Tris
+ 1 mM EDTA
Phnol satur en tris
Vigorous andcontinuous shaking
Centrifugation
1 min
Quantify the radioactivity
in the aqueous and the organic phases
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Partitioning of ssDNA as a
function of NaCl. I(dsDNA partitions entirely in the aqueous
phase in these conditions)
0,0 0,5 1,0 1,5 2,0 2,5 3,0
0
20
40
60
80
100
Partitionde118-(%)
CNaCl
(M)
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Adsorption of ssDNA at the
water (+ 0.85 M NaCl)-phenol
interface II
0 20 40 60 80 100 120
0
1
2
3
4
5
6
7
hauteur(cm)
Nombre de coups
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Reversibility of the adsorption
0,0 0,2 0,4 0,6 0,8 1,0
0,0
0,2
0,4
0,6
0,8
1,0
Fraction
de
118+d
ans
la
phase
aqueuse
CNaCl
(M)
Reversible adsorption at lowsaltIrreversible adsorption at highsalt
No desorption at 0.85M NaCl
The hysteresis is due to a
different partitioning of NaCl inthe two phases
0,0 0,5 1,0 1,5 2,0 2,5 3,0
1,00
1,02
1,04
1,06
1,08
1,10
1,12
1,14
1,16
(
g.cm-3)
CNaCl
(M)
TE*1 satur en phnolPhnol satur en Tris
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Desorption by the complementary
strand at 0.85 M Na Cl (1)
Agitation continueet vigoureuse
La phaseaqueuse est
prleve
On ajoute une phaseaqueuse avec la mmeconcentation en NaClet du brin complmentaire des concentrationsvaries
Agitation continue
et vigoureuse
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Desorption by the complementary
strand at 0.85 M Na Cl (2)
0 4 8 12 16 20
0
10
20
30
40
50
60
70
80
0,0 0,5 1,0 1,5 2,0 2,5 3,0 3,5 4,0 4,5
0
10
20
30
40
50
60
70
CssDNA
(ng.ml-1
)
D
sorptionde118-(%)
D
sorptionde118-(%)
CssDNA
(ng.ml-1
)
The desorbed material isdoubled-stranded
A stoichiometric process
An interfacial reaction
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Renaturation without shaking
(1)
( ) ( ) ( )003
2
1
1ln2
32 ttt
D
D
V
R
R
tdsDNA
d
d
s
dsDNA
+
+
=
Two possible paths:
1-2-3 Eley Rideal 1-2-2-3 Langmuir-
Hinshelwood
1
2
3 1'
2'2"
Phnol
Phase aqueuse
R t ti ith t h ki
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Renaturation without shaking
(2)
0 20 40 60 80 100 120
0
15
30
45
60
75
90
0
15
30
45
60
75
90
118-adsorb(%)
(Temps)1/2
(s1/2
)
ADNrenatur(%)
0 2000 4000 6000 8000 10000 12000 14000 1600010
15
20
25
30
35
40
ADNrenatur(%)
temps (s)
+
1ln2
1
2
R
R
D
s
d
(cm2.s-1)
( )0t
dsDNA
Parameters t0
(s)
values 1.7 10-10 3.5 10-12 3390 58.5 0.28 2 10-3
D2d ~ 3.6 10-9 6 10-10 cm2.s-1
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Renaturation without shaking
(3)
SURFACE DIFFUSION VERSUS BULK DIFFUSION:
Here D2d (~ 3.6 10-9 6 10-10 cm2.s-1) is 60 timessmaller than D3d (~ 2.4 10
-7 9.6 10-9).
In other systems (diffusion of dsDNA on mica) D2d is106 times smaller than D3d (Guthold et al. Biophys. J.
77, 2284-2294, 1999).
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Adsorption with vortexing (1)
Competition between diffusion andconvection
Increase of the interfacial area
0 20 40 60 80 100 120
50
55
60
65
70
75
80
85
90
95
100
2400 rpm1800 rpm1400 rpm1200 rpm1000 rpm
118-adsorb(%)
Temps(s)
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Renaturation with vortexing (2)
2400 rpm
k2 ~ 4.2 1010 M-1.s-1
0 5 10 15 20 25 30
0
10
20
30
40
50
60
70
ADNrenatur(%)
Temps(s)
0 5 10 15 20 25 30
1
2
3
1/fss
temps (s)
PERT is an interfacial reactionReaction takes place during thecoalescence of phenol droplets
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Comparing PERT with other systemsNucleic acid Reaction medium Temperature k2
(M-1s-1)
Reference
Intact Phage 7 DNA
(39.9 kb)
0.1 mM buffer, pH 8
40 mM NaCl
25 C 4 104 Studier (1969)
Intact Phage 7 DNA(39.9 kb)
0.1 mM buffer, pH 8
60 mM NaCl
35 C 6 105 Studier (1969)
Intact Phage 7 DNA
(39.9 kb)
0.1 mM buffer, pH 8
0.5 M NaCl
65 C 1.2 108 Studier (1969)
Phage T4 DNA (168.9 kb)~ 16 kb long
fragments
20 mM buffer, pH 7.610 mM KCl
40 mM MgSO4gP32 (in excess over DNA)
37 C 1 108 Alberts and Frey (1970)
Intact Phage DNA
(48.5 kb)
10 mM buffer, pH 5.5
10 mM NaCl
10 mM MgCl2Eco SSB (1.2-fold excess over
DNA)
37 C 1.6 107 Christiansen and Baldwin (1977)
Intact Phage DNA
(48.5 kb)
10 mM buffer, pH 5.2
20 mM NaClEco SSB (10-fold excess over
DNA)2 mM spermine
37 C 3.4 108 Christiansen and Baldwin (1977)
118 bp DNA fragment from
phage X 174
10 mM Tris HCl1 mM EDTA
0.46 mM spermine
25 C 1.4 109 Chaperon and Sikorav (1998)
124 bp DNA fragment from
pSV2gpt
50 mM NaCl
1 mM CTAB
68 C 6 109 Pontius and Berg (1991)
E. coli DNA 0.5 g / ml PERT, 2 M LiSCN 22-24 C 4.2 1010 Kohne et al. 1977
118 bp DNA fragment from
phage X 174
PERT, 0.85 M NaCl 22-24 C 4.2 1010 This work
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Comparison with other systems
involving surface diffusion processes
Role of a reduction of dimensionality in biologicalprocesses: Adam and Delbrck (1968).
Computation of mean time of diffusion (i) to a small targetof diametera within a large diffusion space ofdimensionality iand diameterb: the reduction of
dimensionality can greatly speed up diffusion processes.
Related to a Langmuir-Hinshelwood mechanism! Importance of a liquid-like structure of the interface for
polymer diffusion ( Rouse dynamics (Maier and Rdler,1999) versus solid friction (Guthold et al., 1999)
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Summary on PERT
PERT is an interfacial reaction ssDNA is adsorbed and mobile The rate of PERT is governed by the rate of
vortexing and exceeds a three-dimensional diffusion-
controlled rate.
Use of a heterogeneous reaction medium
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Summary on cyclization and
renaturation experiments (1)
Standard conditions for the study of DNA correspondto homogeneous conditions (actually dilute aqueoussolutions).
In these conditions DNA-DNA interactions arerepulsive (for dsDNA or for similar ssDNA).
The kinetics are slow. The effective concentrations are low One cannot explain the cyclization ofDNA invivo.
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Summary on cyclization and
renaturation experiments (2) In these heterogeneous systems, there is a coupling of thereaction to a phase change:
Collapse; isotropic-liquid crystalline; aggregation (withcondensing agents).
Adsorption at a liquid-liquid interface in PERT
Condensed states of nucleic acids as in vivo; rates ofcyclization compatible with in vivo rates.
Fast kinetics + high effective concentration + low
activation energies: in common with catalysts. Relevant forthe study of the origin of life and for applied biochemistry
(improving hybridization techniques).
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General concepts
Merits and limitations of homogeneous biochemistry. Economics of heterogeneity
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Limitations of homogeneous
or solution biochemistry
The interior of a cell or a virus cannot bedescribed using the concepts of a bulk
homogeneous aqueous solutions:1) Numerous constituents do not mix with one another
(hydrophobic effect; phase separation of thenucleoid from the bacterial cytoplasm).
2) A bulk system is unbounded, in contrast with cellsor viruses.
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Limitations of homogeneous
or solution biochemistry
It excludes the physiology of gaseous
compounds (including respiration), membrane
biology.It excludes the study of biological solid states
(e.g. gels, biomineralization, spores (anhydrobiosis).
It severely limits the study of biologicalmorphology and morphogenesis.
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Homogeneous or solution
biochemistry
- Allows a study of the structure and of the
dynamics of individual biomolecules, in an highly
artificial environment.
- Allows mostly the study of specific interactions
between biomolecules.
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Intermolecular forces in
physics and in biochemistryIn (statistical) physics the focus is often on generic
interactions such as attraction/repulsion, interactions
between like objects or between incompatible ones.
In biochemistry the focus is on specific interactionsbased complementary recognition (Pauling): lock and
key of Fischer (enzymes), ligand (drug)-receptor
magic bullet of Ehrlich, antigen-antibody, base-pairing in nucleic acids.
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Many bodies interactions in
Physics/Biochemistry Interactions between
like structures
Role of repulsive stericeffects/entropic forces:depletion, confinement
Universality
Interactions betweencomplementary
structures Role of attractive forces
Specificity
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Beyond homogeneous
biochemistry: the importance
liquid crystals and surfaces
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States of matter:
4) Mesomorphous states (Friedel) or
Liquid crystalsAn intermediate state of matter between liquid and solidstates. It often involves strongly elongated (anisotropic)molecules: either small organic molecules (for instanceamphiphilic compounds that constitute biological
membranes) or long rods (synthetic polypeptides, DNA,viruses).
Ordering through an anisotropic attraction (Maier andSaupe 1958)
Ordering through steric repulsion only for long rods orsemi-flexible polymers (Onsager 1949, Flory 1956, Khokhlovand Semenov 1982).
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Biological
importance of liquid crystals
Liquid crystals possess internal structures lacking in
liquids, and directional properties not found in gelsThe oriented molecules in liquid crystals furnish in ideal
medium for catalytic action, particularly of the complex
type needed to account for growth and reproduction.
J. D. Bernal Trans. Farad. Soc. (1933) vol. 29, p. 1082.
Examples: membrane enzymology; cyclization and
renaturation of condensed DNA.
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The importance of surfaces
and interfaces in vivo
The compartmentalized organisation of the cell (nucleus,cytoplasm) involves the presence of boundaries(interfaces).
A particular biochemical process often occurs at aspecific location and its product crosses the interfacebetween two compartments.
More than half of the proteins present in the cell areassociated with membranes
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Surface science of DNA:
Douarche et al (2008)
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Economics of heterogeneity
(1)
Increasing the yield or the rate of a reaction through
a decrease of the solubility of the reactant(s):
1) vant Hoff and the
vant Hoff-Dimroth relation
2) Smoluchowskis theory of diffusion-controlledreaction/aggregation
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Economics of heterogeneity (2)
3) The continuous transfer of the product of a reactionto a different phase can be used to displace achemical equilibrium (a common practice in chemicalengineering).
4) The reduction of dimensionality of the reactivesystem can be used to speed up diffusion processes:connection between the Langmuir-Hinshelwoodmechanism and the work of Adam and Delbrck.
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Conclusions (1)
1) History of homogeneous and heterogeneous biochemistry: acomplex story, spanning over 100 years and involving physics
(phase equilibria and phase changes), chemistry and
biochemistry.
2) Todays enzymology and biochemistry are mostly focused onhomogeneous systems, especially for nucleic acids
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Conclusions (2)
The need for a heterogeneous biochemistry:
1) It is necessary to develop experimentally heterogeneoussystems in vitro to model living organisms.
2) It is necessary to take into account both macroscopic andmicroscopic heterogeneity to describe living organisms
3) Heterogeneous systems can be used to improve theefficiency of some reactions (renaturation and cyclization).
4) To permit a unification of the points of view of physicists
(van der Waals, Landau, Wilson) and of biochemists(Fischer, Ehrlich, Pauling).