Weak Forces - ี่www.lerson.sc.chula.ac.th

Transcription

LEGO Minifigures are trademarks of the LEGO Group. © 2005 The LEGO Group. STAR WARS and related properties are trademarks of Lucasfilm Ltd. © 2005 Lucasfilm Entertainment Company Ltd. or Lucasfilm Ltd. & ® or TM as indicated. All rights reserved.
Strong and Weak Forces
(May the Forces be with you!)
Lerson Tanasugarn, Ph.D.
Department of Biochemistry
Faculty of Science
[email protected]
2310332 Topic: Weak Forces (1 Hour)
• Instructor
• Lerson Tanasugarn, Ph.D. Klum 515, Faculty of Science,
02-218-5424, 080-963-8080 [email protected]
• Textbook
3rd Edition
4th Edition
5th Edition
6th Edition
• Nelson, D. L. & M. M. Cox (2009)
Lehninger Principles of Biochemistry,
5th Edition. NY:Worth Publishing.
• Web Site
• http://www.lerson.sc.chula.ac.th/
public/bc/2310332/2013.pdf
Copyright © 2009 by Lerson Tanasugarn. All rights reserved.
2
Chang (1981), p. 458.
Weak Forces vs Strong Force
• Strong forces == covalent bonding ->
average bond energy at 25 ℃ for a
single covalent bond ~ 400 kJ/mole
• Nature takes advantage of “weak
forces,” i.e. natural interactions that are
much weaker in magnitude than
conventional “covalent bonds”
• The large number of possible “sites”
that can participate in these weak
interactions could make the total bond
energy large enough to do useful things
(like folding a protein molecule and keep
it folded)
3
Weak Forces (Weak Interactions)
• Ionic bond (ionic interaction)
• Van der Waals interactions (dipole-dipole interaction)
• Permanent dipole - permanent dipole interaction
• Permanent dipole - induced dipole interaction
• Induced dipole - induced dipole interaction (London
dispersion force)
• Hydrogen bond
• Hydrophobic interaction
How strong?
intramolecular
intermolecular
Bond energies are on the order of <100 kJ•mole-1.
4
1. Ionic Bond
(Ionic Interaction, Salt Bridge, Ion Pair)
• Relatively strong interaction among the 4 weak
forces.
• Recall Coulomb Force between charges
• Different charges - attractive force
+
NH
• Same charge - repulsive force
3
COO
• From Physics II
• Point charges
• Vector summation after drawing a free-body diagram
• Principle of Superposition
+
NH
3
+
NH
3
5
http://www.funnyphotos.net.au/images/ static-electricity-hair-stand-on-end1.jpg
Coulomb’s Law of Electricity
Felectrical 21
Felectrical 12 ȓ12
+q2
+q1
ce
pa
free s
um)
u
c
a
v
(
r12
!
F electrical
2,1
1 q1 q2
=
r̂ N
2
4⇡✏0 r12
Felectrical 21 = force acting on charge q2 due to charge q1 in N
• ȓ (pronounced “r hat” or “r roof”)= unit vector pointing from charge q1 to charge q2
• q1, q2 = charges in Coulomb, C
• Basic: 1 C = 6.25 x 1018 elementary charges; 1 elementary charge = 1.602 x 10-19 C
• Old unit: 1 C = 2.998 x 109 esu (statcoulomb); 1 esu (statcoulomb) = 3.335 x 10-10 C
• Big unit: 1 Faraday, F = 1 mole of elementary charges = 6.023 x 1023 elementary
charges = 96,485.4 C
• The electric constant (vacuum permittivity or permittivity of free space),
C2
C
F
A2 s4
12
✏0 = 8.854 ⇥ 10
or
or
or
N m2
Vm
m
kg m3
2
1
9 Nm
= 8.988 ⇥ 10
4⇥ 0
C2
Copyright © 2009 by Lerson Tanasugarn.
All rights reserved.
6
Coulomb’s Electrostatic Law vs
Newton’s Law of Gravity
Fgravitational 21
Fgravitational 12 ȓ12
m2
m1
Felectrical 21
Felectrical 12 ȓ12
+q2
+q1
r12
!
F gravitational
21
=
!
m1 m2
r̂12 F electrical
G 2
r12
2
11 N m
G = 6.674 ⇥ 10
= 6.674 ⇥ 10
kg 2
mearth ⇡ 6.0 ⇥ 10 kg
24
r12
11
m3 kg
mmoon ⇡ 7.4 ⇥ 1022 kg
1
s
2
0
21
= 8.85 ⇥ 10
mproton ⇡ 1.673 ⇥ 10
27
12
• Astronomical scale --> gravitational force wins
• Molecular --> practical scale: electronic force wins
• Atomic scale --> nuclear force wins
1
'
⇥ 10
36⇥
9
1
= 8.988 ⇥ 109
4⇡✏0
kg
Example: 1. two positively-charged amino groups (mw~17) separated by 4 Å
2. earth and moon, each with 10 C of charge, 1
separated by, say, 400,000 km.
Fe
8.85 ⇥ 10
4⇥ 0 q1 q2
1 q1 q2
=
r̂12
2
4⇡✏0 r12
C2
N m2
N m2
C2
(1.602 ⇥ 10 19 )2
=
=(
)
= 4.21 ⇥ 1012
11
27
2
Fg
G m1 m2
6.67 ⇥ 10
(17 ⇥ 1.673 ⇥ 10 )
1
Fe
q1 q2
8.85 ⇥ 10
= 4⇡✏0
=(
Fg
G m1 m2
6.67 ⇥ 10
12
12
)
11
(10)2
= 2.99 ⇥ 10
(6.0 ⇥ 1024 )(7.4 ⇥ 1022 )
47
7
Dielectric Constant
(Relative Permittivity), εr
not in vacuum F
21
F12 ȓ12
+q1
+q2
!
1 q1 q2
F 2,1 =
r̂ N
2
4⇡✏ r12
In general,
r12
✏ = ✏r ✏0
where
Dielectric Constant tells us how many times the electric constant of the medium is relative to that of vacuum.
Liquid
!
1 q1 q2
more F 2,1 =
r̂
101
2
4⇡✏0 ✏r r12
78.5 general,
εr
Sulfuric acid
Water
H2SO4
H2O
Dimethylsulfoxide, DMSO
Glycero
CH3-SO-CH3
HO-CH2-CH2-OH-CH2-OH
Nitromethane
Ethylene glycol
CH3-NO2
HO-CH2-CH2-OH
38.6
37.7
Acetonitrile
Methanol
CH3-CN
CH3-OH
36.2
32.6
Ethanol
Acetone
Acetic acid (glacial)
Benzene
Diethylether
Carbondisulfide
CH3-CH2-OH
CH3-CO-CH3
CH3-COOH
C6H6
C2H5-O-C2H5
CS2
24.3
20.7
6.2
4.6
4.3
2.6
49
42.5
don’t forget
0
= 8.85 ⇥ 10
12
'
1
⇥ 10
36⇥
1
= 8.988 ⇥ 109
4⇡✏0
9
N
C2
N m2
N m2
C2
Non-polar environment like
that inside a folded protein.
8
|Felectrical|
Example:
+1
εr = 1
①
② εr = 4
③ εr = 80
|Felectrical|
+1
4Å
2
①
!
②
Felectrical
(8.988 ⇥ 109 NCm2 )(1.602 ⇥ 10
1 q1 q2
=
=
2
4⇡✏0 ✏r r
(4 ⇥ 10 10 m)2
Felectrical
(8.988 ⇥ 109 NCm2 )(1.602 ⇥ 10
1 q1 q2
=
=
4⇡✏0 ✏r r2
(4)(4 ⇥ 10 10 m)2
Felectrical
(8.988 ⇥ 109 NCm2 )(1.602 ⇥ 10
1 q1 q2
=
=
4⇡✏0 ✏r r2
(80)(4 ⇥ 10 10 m)2
2
!
③
2
19
C)2
19
19
C)2
C)2
= 1.442 ⇥ 10
9
N
= 3.61 ⇥ 10
10
N
= 1.80 ⇥ 10
11
N
Compare with the gravitational force between the two protons:
Fgravitational =
m1 m2
G 2 =
r
(6.674 ⇥ 10
2
(1.673 ⇥ 10 27 kg)2
11 N m
)
kg 2
(4 ⇥ 10 10 m)2
=
6.98 ⇥ 10
46
N
The electrical force is about 4x1035 times the gravitational force.
9
Example: pK of Glycine vs those of
Aspartic Acid and Glutamic Acid
α carboxy group
pK = 1.99
α carboxy group
pK = 2.35
α carboxy group
pK = 2.10
α amino group
pK = 9.90
α amino group
pK = 9.47
α amino group
pK = 9.78
Glycine
⊖
⨁
NH3
β carboxy group
pK = 3.90
Aspartic ⊖
acid
• pKα carboxy < pKβ carboxy < pKγ carboxy
γ carboxy group
pK = 4.07
⨁
NH3
⊖
Glutamic acid ⊖
• The closer a carboxyl group is to a positively charged amino group, the
easier it is for the proton to leave, hence the lower pKa.
⨁
NH3
⊖
10
Ionic Interaction
Summary
Force
Energy
where
1 q1 q2
F =
4⇡✏0 ✏r r2
N
1 q1 q2
U=
4⇡✏0 ✏r r
VJ
1
= 8.988 ⇥ 109
4⇡✏0
+
NH3
N m2
C2
+
NH
3
COO-
+
NH
3
• Salt bridge, ion pair
11
Example:
-1
1. εr = 4
2. εr = 80
+1
4Å
two point charges 4Å apart in a medium with dielectric constant = 4
F =
1 q1 q2
4⇡✏0 ✏r r 2
U=
1 q1 q2
4⇡✏0 ✏r r
=
=
19
C)2
9 N m2 (1.602⇥10
(8.988 ⇥ 10 C 2 ) (4⇥10 10 m)2
=
19
C)2
9 N m2 (1.602⇥10
(8.988⇥10 C 2 ) (4⇥10 10 m)
= ( 5.767 ⇥ 10
22
kJ)(6.023 ⇥ 1023
1
mole )
1.442 ⇥ 10
=
= 347
5.767⇥10
9
N
22
kJ
kJ/mole
• This strong interaction diminishes quickly to 4.34 kJ/mole in water
(εr=80).
• The free energy of solvation of 2 separate ions roughly equals the
free energy of formation of the unsolvated pairs. Therefore, the ion
pair contributes little towards the stability of macromolecules.
12
Protonation-Deprotonation
The Henderson-Hasselbalch Equation
HA ⌦ H + + A
[H + ][A ]
Ka =
[HA]
log Ka = log [H + ]
proton dissociation from an acid
write out the equilibrium constant
log [A ] + log [HA]
pKa = pH log [A ] + log [HA]
pH = pKa + log [A ] log [HA]
[A ]
pH = pKa + log
[HA]
“pH equals pK plus the log of conjugate base to (free) acid”
• For now, take pKa as a constant for a given chemical species.
• The difference between pH and pKa is related to the logarithm of
the degree of dissociation of the acid.
13
Carboxyl Group Dissociation
Amino Group Dissociation
N H3+ ⌦ H + + N H2
C
B
1.00
[N H2 ]
Dissociation [N H ] + [N H + ]
2
3
Dissociation
[A ]
[A ] + [HA]
COOH ⌦ H + + COO
COO- wins
0.75
A
0.50
50% dissociation
0.25
COOH wins
0.00
0 E
D
4
pKa=3.00
8
12
16
pH
1.00
NH2 wins
0.75
50% dissociation
0.50
0.25
NH3+ wins
0.00
0
4
8
12
16
pH
pKa=9.00
• Suppose the pKa of a particular carboxyl group was 3.00.
• Suppose the pKa of a particular amino group was 9.00.
14
Isoelectric Point (pI)
and Isoionic Point
If pH<2
~ little charge on COOH
+1 charge on NH3+
Net charge approaches 1
α carboxy group
pK = 2.35
α amino group
pK = 9.78
Glycine
At pH 6.07 [=(2.35+9.78)/2]
Total positive charges = total negative charges
Net charge =0
If pH>10
~ little charge on NH2
-1 charge on COONet charge approaches -1
IUPAC Compendium of Chemical Terminology, 2nd Edition (1997)
• Isoelectric Point, pI [or pH(I)] is the pH value at which the net electric
charge of an elementary entity is zero. [i.e., all adsorbed ions are
taken into account - This is the term biochemists use for amino
acids and proteins such as in the above scenario. - LT ]
• Isoionic Point is the pH value at which the net electric charge of an
elementary entity in pure water equals zero.
15
Salting-In
&
Salting-Out
• Vertical axis = solubility of proteins
• Good solubility of proteins above ionic strength ~ 0.1
• Solubility decreases @ ionic strength >1, esp. (NH4)2 SO4
• Different proteins ppt @ different ionic strengths
16
Explanation of Salting-in & Salting-Out
(NH4)2SO4 is often used:
• good solubility in water
• high ionic strength due to -2
charges on the sulfate group
• slightly acidic solution is
close to pI of many proteins
• reasonably priced (not an
expensive salt)
• Salting-in: salt helps water to form hydrate shell
• Salting-out: salt and ionizable groups on protein
compete for a limited number of polar water molecuels
17
Gel
http://www.hormel.com/images/ glossary/g/gelatin_jello.jpg
http://www.gmap-gelatin.com/ pics/gummybears.GIF
• Meshwork of polymer
absorbing solvent (water)
• Cross link or not
• Many kinds of gel
• Protein gel
• Carbohydrate gel
• Organic gel
http://www.fell2earth.com/content.php?cid=1210
18
Carbohydrate Gel: Carrageenans
Chondrus crispus seaweed!
http://www.cybercolloids.net/library/
carrageenan/chondrus-crispus.jpg
Source: Rees (1972) in Glicksman (1982).
http://www.rsaum.co.uk/ weblog/archives/colour/
Detection of the thermal coil-to-double helix conformational transition of Κ Carrageenan, using the technique of circular dichroism
http://academic.brooklyn.cuny.edu/ chem/maggie/res/papers/ac00_2~3.htm
Hot aqueous solution - - - random coil polymer!
On cooling!
- - - double helices form!
! Iota Carrageenan - intermediate sulfate contents, elastic gel, good freeze-thaw!
! Kappa Carrageenan - gels in potassium ion. Calcium ions make the gel brittle. Syneresis is likely, especially when combined with locust bean gum to produce a strong gel. About 70% of world carrageenan production.!
!Lambda carrageenan - highly sulfated, does not gel - mouth feel & creamy sensation
19
Carbohydrate Gel: Agar
http://www.bulkfoods.com/ agar_agar.htm
• Complex mixture of 2-3 polysaccharides with the
same backbone structure but with variable degrees
of charged groups
• Agarose = alternate b(1Ý3) D-galactose and a(1Ý4)
3,6-anhydro-L-galactose units
• Gels at 32-39°C on cooling and melts at >85°C with
brittle, crunchy texture
• Use locust bean gum as plasticizer
20
Carbohydrate Gel: Alginates
http://www.bulkfoods.com/agar_agar.htm
Source: Glicksman (1982)
Linear copolymer of D-mannuronic and L-guluronic acids
Salt Bridges
21
Chitosan Gel
http://www.igb.fraunhofer.de/WWW/GF/Biokatalyse/en/GFBK_221_Chitosan.en.html
• Chitin-chitosan from crustacean shells
• Deacetylation of chitin to produce chitosan
• Positively charge, pK around 6.2-6.7
22
Carbopol, an organic gel
• carbopol usually comes as white powder
• carbopol initially dissolved in water is not
viscous at all
• What should we do to make it gel?
• What can we do to turn the gel into a
watery substance again?
http://www.traderscity.com/board/products-1/offers-tosell-and-export-1/carbomer-carbopol-203010/
http://www.pharmainfo.net/reviews/carbopol-and-its-pharmaceutical-significance-review
23
Chitosan + Carbopol --> ?
• Can we predict in advance what is going to happen?
• chitosan (pK around 6.5)
• carbopol (pK around 3.8)
• At pH in between (e.g. 5)
• Chitosan is positively charged
• Carbopol is negatively charged
• What will the two oppositely charged polymers do
to each other?
24
Ion & Dipole
+
!"
F = qE
!"
F = qE
+
l
!"
F = −qE
-
Net charge = +1
Moves to the right
No rotation
Net charge = -1
Moves to the left
No rotation
!"
F = −qE
-
Net charge = 0
No translational movement
Rotates clockwise
Dipole Moment, µ = ql
esuicm
25
Unit of Dipole Moment
1 debye = 1x10 −18 esuicm
(
= 1x10
−18
C ⎞⎛ 1 m ⎞
⎛ 1
esuicm ⎜
⎝ 3x10 9 esu ⎟⎠ ⎜⎝ 100 cm ⎟⎠
= 3.33x10 −30 Cim
)
http://en.wikipedia.org/ wiki/Peter_Debye
• In honor of Peter Joseph William Debye, a German scientist who
studied dipole moment in the early 1900s and won a Nobel
Prize in 1936
• For example, if a +1 and a -1 charges are separated by a
distance of 1 Å Dipole Moment = (4.80x10-10)(10-8) esu•cm = 4.80 debye
• Note: For convenience, biochemists rarely use Coulomb•m as a
unit for dipoles. We routinely use “debye,” which we define in
the cgs sytem as 1x10-18 esu•cm.
26
Zwitterion Nature of Amino acids
http://en.wikipedia.org/wiki/Zwitterion
• What evidence do we have to support the
zwitterion nature of amino acids?
27
Jeffries Wyman (1936)
+H
-+H N -[Glycine] -COON
-[CH
]
-COO
3
2n
3
n
Polyglycine oligopeptide
Wyman, J. (1936) Chem. Rev. 19:213, cited in Gabler, R. (1978) Electrical Interactions in Molecular Biophysics. NY:Academic Press.
• Recall that • Dielectric constant is related to dipole moment
• dipole moment = product of charge and separation, D=ql
• n = # of carbon atoms b/t the amino and the carboxyl groups
28
Dunning and Shutt (1938)
• Between pH 4.5 and 7.5 -> zwitterion
• Beyond this range, dipole
is gone, so is D
Dunning, W. J. and W. J. Shutt (1938) Trans. Faraday
Soc. 34:479, cited in Gabler, R. (1978) Electrical
Interactions in Molecular Biophysics. NY:Academic Press.
∂D
µ = 10
∂c
Semiempirical estimate
of dipole moment from
dielectric constant
29
2. Dipole-Dipole Interaction (van der Waals Interaction)
α = polarizability
D = dielectric constant
-1
kJ•mol I = first ionization potential
µ = dipole moment
r = separation
• Dipole-dipole interaction: c=o c=o 2 µ A2 µ B2 1
Energy = −
3 D 2 r 6 kt
• Ion-induced dipole:
1 α e2
Energy = −
2 Dr 4
• Dipole-induced dipole:
2αµ 2
Energy = −
0.4<U<4
Na+ C6H6 0.4<U<4 kJ•mol-1 c=o H3C- (Debye, 1920) 0.4<U<4 kJ•mol-1 D2r 6
• London dispersion force: -CH3 H3C- (London, 1930) Energy
= − 3
I A I B α Aα B
2 IA + IB r6
4<U<40 kJ•mol-1
Weak interaction but significantly stabilize protein
structure
30
Magnitude of van der Waals
• Example: two c=o groups each with dipole moment of 4.2x10-30 C•m (1.3 debye) in head-to tail arrangement (c=o c=o) distance r=5 Å in a medium with dielectric constant = 4 => attractive energy -9.3 kJ•mol-1(-2.2 kcal•mol-1)!
• In alpha helix: many pairs in the same direction, low
dielectric constant inside protein
31
Example: Ab combining site
Lysozyme
[Voet & Voet (1995) p. 1217]
32
Nonbonding Interaction in Molecular
Mechanics
• Molecular Mechanics (MM) is a technique to find a
quick estimate of the relative energy associated with a
molecule. In MM, energies have no absolute meaning.
• Etotal = Er + Eθ + Eφ + Enb + [special terms]
• Er <= bond stretching
= Σ Kr (r-r0)2
• Eθ <= bond angle bending
• Eφ <= bond torsion = Σ Kθ (θ-θ0)2
= Σ Kφ [1+cos(nφ-φ0)]
• Enb <= nonbonding interaction
• K = force constants for bonds, angle, and dihedral angle r0, θ0, φ0 = equilibrium distance, angle, phase angle n = periodicity of the Fourier term
33
Lennard-Jones 6-12 Potential
Potential
0
-0.1
-0.2
-0.3
0.5 1.0 1.5
12
6
⎡
0.39 nm
σ⎞
σ⎞ ⎤
⎛
⎛
Distance (nm) VLJ = 4 ε ⎢⎜ ⎟ − ⎜ ⎟ ⎥
⎝
⎠
⎝
⎠
r
r
⎢
⎥⎦
⎣
Example: water
http://polymer.bu.edu/Wasser/robert/work/node8.html
σ = 0.3165555 nm
ε = 0.6501696 kJ/mol
"
"
When r is large, the 6th power term dominates =>
induced dipole-induced dipole interaction (London
dispersion/ van der Waals)
When r is small, the 12th power term dominates ->
collision of electron clouds
34
Polyacrylamide Gel
Polyacrylamide gel: a hydrogel consisting of nonionic polymer that is cross-linked by methylenebisacrylamide.
Stryer ©
(1988)
Biochemistry
3rd ed.All rights reserved.
Copyright
2009 by
Lerson Tanasugarn.
35
Shrinkage of Polyacrylamide Gel
van der Walls
Miscible organic solvent
e.g. acetone or ethanol
In H2O
Donnan Equilibrium
Rubber elasticity
• Tanaka’s Model of Gel Contraction
• Control variable can be temperature, etc.
36
Expansion of acrylamide- acrylic acid copolymer
• Acrylamide --(hydrolysis)--> acrylic acid catalyzed by N,N,N’,N’-tetramethylethylenediamine (TEMED) Pickling of acrylamide gel in TEMED for about 3 weeks.
• Carboxyl group, COO-, are substantially deprotinated at around neutral pH, giving
rise to negative charges on the molecules.
TEMED
3 weeks
polyacrylamide
low pH
low dielectric constant
acrylamide-acrylic acid copolymer
37
3. Hydrogen Bonding
H!
2.1!
Li
Be
B
C
N
O
F!
1.0 1.5
2.0 2.5 3.0 3.5 4.0!
Na
Al
Mg
0.9 1.2
K
Ca
Ti
Mn
Fe
0.8 1.0
1.3
1.5 1.6 1.6 1.5
1.8
Rb
Y
Zr
1.2
0.8 1.0
Cs
Ba La-Lu
V
Nb
Cr
Ra
0.7 0.9
S
Cl!
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br!
1.9 1.9 1.9 1.6 1.6 1.8 2.0 2.4 2.8!
Tc
Ru
1.4 1.6 1.8
1.9
2.2 2.2 2.2 1.9 1.7 1.7 1.8 1.9 2.1 2.5!
Hf
Re
Os
1.9
2.2 2.2 2.2 2.4 1.9 1.8 1.9 1.9 2.0 2.2!
Ta
Mo
W
0.7 0.9 1-1.2 1.3 1.5 1.7
Fr
P
1.5 1.8 2.1 2.5 3.0!
Sc
Sr
Si
Ac
Th
1.1
1.3 1.4 1.4 1.4-1.3
Pa
U
Rh
Ir
Pd
Pt
Ag
Au
Cd
Hg
In
Tl
Sn
Pb
Sb
Bi
Te
Po
I!
At!
Np-No!
• H between two electronegative atoms e.g. >C=O…H-N- (…2Å, -1Å) In alpha-helix (2.7 to 3.1Å) Angle: linear is strongest
• Bond energy (4 to 40 kJ•mol-1) is about 20 kJ•mol-1 in
water and from 12 to 30 kJ•mol-1 in protein
(depending on angle and dielectric constant)
Internal H-bonds almost do not stabilize proteins but provide a structural basis for protein folding pattern.
38
H-bond Example 1: Protein a-helix & b-pleated sheet
[Voet & Voet (1995), p. 146 and 150.
In a-helix, H bonds are almost parallel to the helix length. The O-N distance is about 3 Å
Antiparallel β-sheet
39
H-bond Example 2: Carbohydrate
• H-bonds within the
same layer and
between two adjacent
layers help stabilize
cellulose in plant cell
walls.
[Voet & Voet (1995) p. 261]
40
H-bond Example 3: Nucleic Acid
[Voet & Voet (1995) pp. 852 and 854]
l
l
The energy per H-bond is rather weak, about 5 kJ•mol-1 !
The stability to the DNA Molecule comes from the cooperative nature of H-bond formation.
41
Carbohydrate Gels: Pectin
1,4-linked a-D-galacturonic acid, containing other sugars and methoxy modifications
Top: H-bonding!
Bottom: Ca++ for methoxy pectin
Regular pectin form gels at acid pH with high sugar!
Low methoxyl pectin - similar to alginate(require divalent cation) can be formed without sugar over a wide pH range
42
H-bond disruptors
NH2+
O
H2N-C-NH2
H2N-C-NH2
Guanidinium ion
Urea
• Urea and guanidinium ion (Gu+) in the
concentration range 5 to 10 M are the most
commonly used protein denaturants.
• They disrupt hydrogen bonds.
43
Breaking Up Hydrogen Bonds
• Heat = vibration e.g. boiled eggwhite
• Chemicals, e.g. • 6M guanidinium ion
• 9M urea, e.g. nail removal
http://www.gather.com/viewArticle.action?
articleId=281474977680328
http://www.mediorta.com/how-to-treat-nail-fungus/ http://www.nail-fungus-help.com/nail-fungus-pictures.php
http://www.fotosearch.com/UNE419/u13480552/
http://www.drblakeshealingsole.com/2010/10/toe-nail-fungus-carmol-40-urea.html
44
Polyvinylalcohol + Borate
http://www.sci-experiments.com/slime/slime.html
• How many hydrogen bonds are shown in the
above diagram?
45
4. Hydrophobic Interaction
• This interaction is different from all other weak forces
in that it does not involve two atomic centers.
• Nonpolar substances spontaneously minimize their
contact with water.
• Large and negative ΔG for transferring HC from water
to nonpolar solvents is entropy-driven
• Positive ΔH (endothermic) for all aliphatic compounds,
athermic for all aromatic compounds
• Entropy is large and negative
• Entropy of what?
46
Example
Recall that ΔG = ΔH - TΔS
Transferring a hydrocarbon ΔH!!
-TΔS! !
ΔG from water to hydrocarbon! kJ•mol-1 kJ•mol-1 ! kJ•mol-1 CH4 in H2O! ! -> C6H6! 11.7! !
CH4 in H2O! ! -> CCl4! 10.5! !
C2H6 in H2O! ! -> C6H6! 9.2! !
C2H4 in H2O! ! -> C6H6! 6.7! !
C2H2 in H2O! ! -> C6H6! 0.8! !
C6H6 in H2O! ! -> C6H6! 0.0! !
C6H5CH3 in H2O!->! C6H6
0.0! !
Transfer from water to HC
Positive or Zero
enthalpy
-22.6!
-22.6!
-25.1!
-18.8!
-8.8!
-17.2!
-20.0!
Positive Entropy
!
!
!
!
!
!
!
-10.9!
-12.1!
-15.9!
-12.1!
-8.0!
-17.2!
-20.0
Negative Gibbs free energy
47
Water Cage
Ordered structure of water molecules surrounding a nonpolar solute particle
[Voet & Voet (1995) p. 177-8]
The aggregation of nonpolar solute reduces the number of solute particles and therefore minimizes the ordered structure of water. Therefore, entropy is increased, leading to large negative -TΔS.
48
Consequences
ordered water
ordered water
New disordered water
New ordered water
• R1(H2O)n + R2(H2O)n -> R1R2 (H2O)m + 2nH2O
• R1 reacts with R2 in aqueous solution and liberates the
ordered water molecules originally surrounding R1 and
R2. That means entropy increase, which drives ΔG
down to a negative level.
49
Hydropathy
Protein! Side Chain!Hydropathy
• Aggregation of nonpolar molecules
minimizes the surface area and the entropy loss of the system
• Protein Folding
• Hydrophobicity Hydrophilicity Hydropathy
• Kyte-Doolittle scale for amino acids ---->
Ile! 4.5 Val! 4.2 Leu! 3.8 Phe! 2.8 Cys! 2.5 Met! 1.9 Ala! 1.8 Gly! -0.4 Thr! -0.7 Ser! -0.8 Trp! -0.9 Tyr! -1.3 Pro! -1.6 His! -3.2 Glu! -3.5 Gln! -3.5 Asp!-3.5 Asn!-3.5 Lys! -3.9 Arg!-4.5
50
Sickle-cell
Hemoglobin
Intermolecular Contact
Glu β6 -> Val β6
[Geis, from Voet & Voet (1995) p. 238]
220 Å dia. Fiber layer repeat = 64 Å twist repeat = 350 Å
Deoxy HbS spilling out of a ruptured erythrocyte [Joseph, R., from Voet & Voet (1995) p. 237]
51
Mad Cow Disease
www.eskimo.com/ ~nickz/bse/madcow.html
Reuter, www.mad-cow.org/00/ may00_last_news.html
Web.mit.edu/newsoffice/tt/ 2002/oct30/prions.html
• PrPc misfolds into the deadly PrPsc (helix->sheet) which
induces more conversion. PrPsc is routed into the cytosol
and kills the neuron even at low concentrations.
• Example of shift in the delicate balance of weak forces.
52
Hydrophobic Sand
http://www.profbunsen.com.au/shop/ item/hydrophobic-sand-magic-sand
http://www.scientificsonline.com/ space-sand-9658.html
https://www.wardsci.com/store/catalog/ product.jsp?catalog_number=6569400
• What would happen if you poured some sand that
is coated with a hydrophobic substance into water?
53
Summary of Bondings
Bond Energy kJ•mol-1
!
200 -800 !
!
!
!
• Covalent bond!!
No simple expression for energy!
-C-C-!
• Ion-ion interation (salt bridge)!
-kqAqB/Dr!
!
-NH4+ -COO-!!
40 -400 • Ion-dipole interaction!
-eµ/Dr2!
!
!
Na+(H2O)n! !
4 - 40 • Dipole-dipole interaction:!
!
!
c=oc=o!!
• -(2/3) (µA2 µB2)/D2r6(1/kT)
!
!
0.4 -
4
• Dipole-induced dipole interaction: c=oH3C-
-2αµ2/D2r6![α = polarizability]!
0.4 -
4 • Ion-induced dipole interaction:! !
-(1/2)αe2/Dr4 0.4 -
4 Na+C6H6
!
-CH3 H3C-!
4 - 40 • London dispersion force:! !
-(3/2){IAIB/(IA+IB)}(αAαB/r6) [α = polarizability, I = first ionization potential]!
!
• Hydrogen bond:! !
Hydrophobic interaction:!
!
!
!
!
>C=O … H-N<!
4 - 40 hydrocarbons Copyright © 2009 by Lerson Tanasugarn.
All rights reserved.
54
Protein Folding
Domains are folded first.
H-bonds help in getting the correct configuration.
Van der Waals as well as hydrophobic interactions help stabilizing the structure.
[Voet & Voet (1995) p. 195]
55
Protein Denaturation
Physical Agent
Interaction
heat
pH
detergent
water soluble organic substances such as aliphatic
alcohols and ketones
?
- ionic
- dipole-dipole
- hydrogen bond
- hydrophobic
?
chaotropic agents I-, ClO4-, SCN-, Li+, Mg2+, Ca2+, Ba2+ guanidinium ion, urea
56
www.theufos.com/images/ Extraterrestrial_Being.jpg
The End
57

Weak Forces - ี่www.lerson.sc.chula.ac.th

Transcription

Similar documents

King Koil - Chez-Del

Anniversary Promotion

essie·gel la palette de couleurs - Haar

Product information

Sure Gel MSDS

TALIKA Launches NEW Feet Therapy Socks

lO - Dr Frank Lipman

Wichita, KAN. – Gel II® is adding implements to your professional

Xintex: Geltex

Antiquing Gel Instructions

CHEM1902/4 2014-N-6 November 2014 • Boric acid, B(OH) 3, is a