Associations of amphipathic molecules in aqueous solutions.

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Associations of amphipathic molecules in aqueous
solutions.
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Ionic Mobilities in H2O at 25C.
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Mean lifetime of a hydronium ion is 10-12 s
This makes proton transfer reactions (acid base
reactions) among the fastest in aqueous solutions.
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Acid Base Chemistry
Conjugate acid
Conjugate base
HA H2O
H3O A-
H3OA-
K
H2O 55.5M
HAH2O
HA-
Ka KH2O
H3O H
HA
K dissociation constant is a measure of the
strength of an acid
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Water as an acid
Conjugate acid
Conjugate base
H2O
H OH-
HOH-
K
H2O 55.5M
H2O
Kw KH2O
HOH-
Pure water contains equimolar hydroxide ions and
protons At 25ºC Kw 10-14 M2 H OH- 10-7
M
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Henderson Hasselbach and pH
pH
-logH
H
Ka(HA/A-)
pH
-log Ka log (A-/HA)
pH
pKa log (A-/HA)
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Titration curve of a 1L solution of 1M H3PO4.
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Thermodynamics
First Law Energy is conserved
?U Ufinal - Uinitial q - w
q heat absorbed w work done
?U 0 for any process that returns to its
initial state
Exothermic processes release heat Endothermic
processes gain heat
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Enthalpy is defined as
H U PV
P pressure (constant) ?V volume
(insignificant)
?H ?U P?V
w often is zero in biological systems
?H ?U q - w
?H q
q heat transferred to/from the surroundings
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Thermodynamics
Second Law Entropy increases
?Suniverse gt 0
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2N equally probable ways of distributing them
N molecules of gas
Two bulbs of equal volumes connected by a
stopcock.
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WL number of different ways of placing L of the
N molecules in the left bulb
N!
WL
L!(N-L)!
Probability WL/2N
For any N the most probable state is L N/2
(half the gas in the left bulb)
If N 1023 the probability that the of
molecules in the left and right bulbs differ by 1
molecule is 10 billion in 10-434
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WL number of different ways of placing L of the
N molecules in the left bulb
N!
WL
L!(N-L)!
9 positions, 4 identical balls
W 987654321 126
(4321)(54321)
Only 4 out of 126 possible arrangements have 4
balls touching each other
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N!
W is approximately 107x1022 if the previous
experiment uses a mole of real gas
WL
L!(N-L)!
To make this more manageable entropy was
invented
S kB ln W
In a system where energy does not change a
spontaneous process has ?S gt 0
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This does not mean that order cannot exist In a
localized system. It means that order can only
exist at the expense of surrounding
systems. Biology gains order by disordering the
nutrients that it consumes.
?Ssystem ?Ssurroundings ?Suniverse gt 0
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Free Energy
G H - TS
?G ?H - T?S
?G 0 for a spontaneous process
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Exergonic ?G lt 0 Spontaneous Endergonic ?G gt
0 Must input energy
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Variation of Reaction Spontaneity (Sign of ?G)
with the signs of ?H and ?S.
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How do we drive endergonic processes?
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Greek lettering scheme used to identify the atoms
in the glutamyl and lysyl R groups.
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An a-amino acid
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a
a
a
a
Fischer Projection
Preferred representation
Glycine - The Simplest a-Amino Acid
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L-a-alanine or (-)- a -alanine
Alanine
a
a
Ca
a
b
(S)-a-alanine
S counterclockwise
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a-valine L-(-)-a-valine S-a-valine
Valine
g1
b
a
g2
a
Ca
a
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a -leucine L-a-leucine (-) -a-leucine S-a-leucine
d1
Leucine
b
a
g
d2
a
Ca
a
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Isoleucine2 chiral centers(2S,3S)-isoleucine
g2
d1
a
b
g1
a
a
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Isoleucine2 chiral centers(2S,3S)-isoleucine
Ca
Cb
Both centers are S
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Methionine is non-polar but S-atom is reactive
a-methionine L-methionine (-)-a-methionine S-methi
onine
b
g
e
d
a
a
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Methionine is non-polar but S-atom is reactive
a-methionine L-methionine (-)-a-methionine S-methi
onine
a
Ca
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Proline is a cyclic imino acid
a-proline L-proline (-)-a-proline S-proline
b
a
g
e
d
a

2
2


2
a
Ca

2
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Large non-polararomatic
a-phenylalanine L-phenylalanine (-)-a-phenylalanin
e S-phenylalanine
e1
d1
b
a
a
g
z1
d2
e2
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Large and non-polar
a-phenylalanine L-phenylalanine (-)-a-phenylalanin
e S-phenylalanine
Ca
a
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Large and non-polar
a-tryptophan L-tryptophan (-)-a-tryptophan S-trypt
ophan
a
z3
e3
h2
d2
b
e2
a
z2
g
d1
e1
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Large and non-polar
a-tryptophan L-tryptophan (-)-a-tryptophan S-trypt
ophan
Ca
a
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a-tyrosine L-tyrosine (-)-a-tyrosine S-tyrosine
Uncharged Polar Amino Acids
a
d1
e1
b
a
g
z1
h

d2
e2
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a-tyrosine L-tyrosine (-)-a-tyrosine S-tyrosine
Uncharged Polar Amino Acids
Ca
a
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Uncharged Polar Amino Acids
a-serine L-serine (-)-a-serine S-serine
a
a
g
b

Ca
a
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Uncharged Polar Amino Acids - cysteine is often
charged
a-cysteine L-cysteine (-)-a-cysteine R-cysteine
b
g
a
Ca

a
a
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Uncharged Polar Amino Acids
a-asparagine L-asparagine (-)-a-asparagine S-aspar
agine
a
d1
b
a
g

d2
Ca
a
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a-glutamine L-glutamine (-)-a-glutamine S-glutamin
e
Uncharged Polar Amino Acids
e1
b
a
g
d
a

e2
Ca
a
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Threonine has 2 chiral centers(2S,3R)-threonine
b
a
g2
g1
a
a
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Threonine has 2 chiral centers(2S,3R)-threonine
Ca
Cb
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Charged amino acids
a-arginine L-arginine (-)-a-arginine S-arginine
h2
a
b
g
z
a
d
e

h1
a
Ca
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a-lysine L-lysine (-)-a-lysine S-lysine
Charged amino acids
g
z
a
b
d
e
a

a
Ca
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a-histidine L-histidine (-)-a-histidine S-histidin
e
Charged amino acids
d1
e1
b
a
g
a

e2
d2
a
Ca
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Charged amino acids
a-glutamate L-glutamate (-)-a-glutamate S-glutamat
e
e1
a
b
g
a
d

e2
Ca
a
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a-aspartate L-aspartate (-)-a-aspartate S-aspartat
e
Charged amino acids
d1
b
a
g
a

d2
a
Ca
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Alanine Ala A Cysteine Cys C Glycine Gly G Histidi
ne His H Isoleucine Ile I Leucine Leu L Methionine
Met M Proline Pro P Serine Ser S Threonine Thr
T Valine Val V
Arginine Arg R Asparagine Asn N Aspartate Asp D Gl
utamate Glu E Glutamine Gln Q Lysine Lys K Phenyl
alanine Phe F Tryptophan Trp W Tyrosine Tyr Y
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Non-standard encoded amino acids
Selenocysteine Sec, U
a

Pyrrolysine Pyl, O
a

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Amino acids bear structural similarity to each
other
Asparate
Glutamate
d1
e1
b
b
g
a
a
g
d


d2
e2
Asparagine
Glutamine
d1
e1
b
a
g
b
a
g
d

d2

e2
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Amino acids bear structural similarity to each
other
Cysteine
Selenocysteine
b
g
a
a


Threonine
Serine
b
a
a
g
b
g2

g1
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Amino acids bear structural similarity to each
other
Tyrosine
d1
e1
b
a
g
z1
h

d2
e2
Phenylalanine
e1
d1
b
a
g
z1
d2
e2
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Amino acids bear structural similarity to each
other
Histidine
Histidine
Arginine
Asparagine
Histidine
Histidine
Arginine
Glutamine
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Amino acids bear structural similarity to each
other
Histidine
Tryptophan
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Amino acids bear structural similarity to each
other
Phenylalanine Tyrosine
Phenylalanine Leucine
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• Glutamate, glycine
• neurotransmitters
• D-serine
• neurotransmitter
• S-adenosylmethionine
• methyl transfer

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Non-peptide amino acids
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Titration curve of glycine.
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These values are the pKas of the free amino
acids in aqueous solution. As we shall see later
an aqueous solution may not represent reality
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These values are the pKas of the free amino
acids in aqueous solution. As we shall see later
an aqueous solution may not represent reality
Hydrophobic pocket