Associations of amphipathic molecules in aqueous solutions.

Ionic Mobilities in H2O at 25°C.

Mean lifetime of a hydronium ion is 10-12 s

This makes proton transfer reactions (acid base reactions) among the fastest in aqueous solutions.

Acid Base Chemistry

HA + H2O H3O+ + A-

Conjugate acid Conjugate base

K = [H3O+][A-]

[HA][H2O]

K = dissociation constant is a measure of the strength of an acid

[H2O] = 55.5M

Ka = K[H2O] = [H+][A-][HA] [H3O+] = [H+]

Water as an acid

H2O H+ + OH-

Conjugate acid Conjugate base

K = [H+][OH-]

[H2O]

Pure water contains equimolar hydroxide ions and protons

At 25ºC Kw = 10-14 M2

[H+] = [OH-] = 10-7 M

[H2O] = 55.5M

Kw = K[H2O] = [H+][OH-]

Henderson Hasselbach and pH

-log[H+]pH =

[H+] = Ka([HA]/A-])

pH = -log Ka + log ([A-]/[HA])

pH = pKa + log ([A-]/[HA])

Titration curve of a 1L solution of 1M H3PO4.

ThermodynamicsFirst Law

Energy is conserved

∆U = Ufinal - Uinitial = q - w

q = heat absorbedw = work done

∆U = 0 for any process that returns to its initial state

Exothermic processes release heat

Endothermic processes gain heat

H = U + PV

Enthalpy is defined as:

P = pressure (constant)∆V = volume (insignificant)∆H = ∆U + P∆V

∆H = ∆U = q - w

∆H = q

w often is zero in biological systems

q = heat transferred to/from the surroundings

Thermodynamics

Second LawEntropy increases

∆Suniverse > 0

Two bulbs of equal volumes connected by a stopcock.

N molecules of gas

2N equallyprobable ways of distributing them

WL =N!

L!(N-L)!

WL = number of different ways of placing L of the N molecules in the

left bulb

For any N the most probable state isL = N/2 (half the gas in the left bulb)

Probability = WL/2N

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

Pag

e 54

9 positions, 4 identical balls

W = 9•8•7•6•5•4•3•2•1 = 126(4•3•2•1)(5•4•3•2•1)

Only 4 out of 126 possible arrangements have 4 balls

touching each other

WL =N!

L!(N-L)!

WL = number of different ways of placing L of the N molecules in the

left bulb

S = kB ln W

In a system where energy does not change a spontaneous process has ∆S > 0

WL =N!

L!(N-L)!

W is approximately 107x1022 if the previous experiment uses a

mole of real gas

To make this more manageable entropy was “invented”

This does not mean that order cannot existIn 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 > 0

Free EnergyG = H - TS

∆G = ∆H - T∆S

∆G ≤ 0 for a spontaneous process

Exergonic ∆G < 0 SpontaneousEndergonic ∆G > 0 Must input energy

Variation of Reaction Spontaneity (Sign of ∆G) with the signs of ∆H and ∆S.

How do we drive endergonic processes?

Greek lettering scheme used to identify the atoms in the glutamyl and lysyl R groups.

An -amino acid

H C

COO-

NH3+

HS

Glycine - The Simplest -Amino Acid

Fischer Projection

Preferred representation

+H3N

C

C

O

O-

HSH

H C

COO-

NH3+

HS

L--alanine or(-)- -alanine

(S)--alanine

S = counterclockwise

Alanine

H C CH3

COO-

NH3+

-OOC NH3+

CH3

H(Z)

(W)

(Y)

(X)

H C

COO-

NH3+

CH3

+H3N

C

C

O

O-

CH3H

C

H C CH

COO-

NH3+

CH3

CH3

-valineL-(-)--valineS--valine

Valine

H C

COO-

NH3+

CH

CH3

CH3

-OOC NH3+

CH

H(Z)

(W)

(Y)

(X)

H3C CH3+H3N

C

C

O

O-

CHH

H3C

CH3

C

H C CH2

COO-

NH3+

CH

CH3

CH3

-leucineL--leucine(-) --leucineS--leucine

Leucine

H C

COO-

NH3+

CH2 CH

CH3

CH3 -OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

CH

H3C CH3

+H3N

C

C

O

O-

CH2H

CH

H3C

CH3

C

H C C

COO-

NH3+

CH2

CH3

H

CH3

Isoleucine2 chiral centers

(2S,3S)-isoleucine

CH C

-OOC

+H3N

CH2CH3

CH3

H

+H3N

C

C

O

O-

CH

H3C

H

CH2CH3

Isoleucine2 chiral centers

(2S,3S)-isoleucine

Both centers are S

-OOC NH3+

C

H(Z)

(W)

(Y)

(X)

H3CH2C

CH3H

C CH3

CHCH3

H(Z)

(W)(Y)

(X)

C

C

H C

COO-

NH3+

CH2 CH2 S CH3

Methionine is non-polar but S-atom is reactive

CH

-OOC

+H3N

CH2 CH2 S CH3

-methionineL-methionine(-)--methionineS-methionine

Methionine is non-polar but S-atom is reactive -methionine

L-methionine(-)--methionineS-methionine

+H3N

C

C

O

O-

CH2H CH2 S CH3

-OOC NH3+

CH2CH2SCH3

H(Z)

(W)

(Y)

(X)

C

Proline is a cyclic imino acid-prolineL-proline(-)--prolineS-proline

CH

-OOC

N

H2C

CH2

CH2H

H C

COO-

HNCH2

CH2

CH2

-OOCHN

H2C

H(Z)

(W)

(Y)

(X)

CH2

CH2NH

C

C

O

O-

CH2H

CH2

H2C

C

2

+

2 +

2+

2+

Large non-polararomatic-phenylalanine

L-phenylalanine(-)--phenylalanineS-phenylalanine

CH

-OOC

+H3N

CH2

H C

COO-

NH3+

CH2

Large and non-polar-phenylalanineL-phenylalanine(-)--phenylalanineS-phenylalanine

+H3N

C

C

O

O-

CH2H

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

C

Large and non-polar

CH

-OOC

+H3N

CH2

NH

3

3

-tryptophanL-tryptophan(-)--tryptophanS-tryptophan

H C

COO-

NH3+

CH2

NH

Large and non-polar-tryptophanL-tryptophan(-)--tryptophanS-tryptophan

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

HN

+H3N

C

C

O

O-

CH2H

HN

C

Uncharged Polar Amino Acids

-tyrosineL-tyrosine(-)--tyrosineS-tyrosine

CH

-OOC

NH3

CH2 OH

H C

COO-

NH3+

CH2 OH

+


-tyrosineL-tyrosine(-)--tyrosineS-tyrosine

+H3N

C

C

O

O-

CH2H

OH -OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

OH

C


CH

-OOC

NH3

CH2 OH

-serineL-serine(-)--serineS-serine

H C

COO-

NH3+

CH2 OH

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

OH+H3N

C

C

O

O-

CH2H

OH

C

+

Uncharged Polar Amino Acids - cysteine is often charged

CH

-OOC

NH3

CH2 SH

-cysteineL-cysteine(-)--cysteineR-cysteine

-OOC NH3

+

CH2

H(Z)

(W)(Y)

(X)

SHH C

COO-

NH3+

CH2 SH

+H3N

C

C

O

O-

CH2H

SH

C

+


-asparagineL-asparagine(-)--asparagineS-asparagine

CH

-OOC

NH3

CH2 C

O

NH2

H C

COO-

NH3+

CH2 C

O

NH2

+H3N

C

C

O

O-

CH2H

C

O

NH2

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

C

ONH2

C

+


-glutamineL-glutamine(-)--glutamineS-glutamine

CH

-OOC

NH3

CH2 CH2 C

O

NH2

H C

COO-

NH3+

CH2 CH2 C

O

NH2

+H3N

C

C

O

O-

CH2H

C

O

NH2

H2C

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

C

ONH2

CH2

C

+

Threonine has 2 chiral centers

(2S,3R)-threonine

CH C

-OOC

+H3N

CH3

H

OH

H C

-OOC

NH3+

C CH3

H

OH

+H3N

C

C

O

O-

CH

H

OH

CH3

Threonine has 2 chiral centers

(2S,3R)-threonine

-OOC NH3+

C

H(Z)

(W)

(Y)

(X)

CH3

HHO

C CH3

OH

H(Z)

(W)

(Y)

(X)

C

C

Charged amino acids

CH

-OOC

NH3

CH2 CH2 CH2 NH C

NH2

NH2+

-arginineL-arginine(-)--arginineS-arginine

H C

-OOC

NH3+

CH2 CH2 CH2 NH

NH2+

NH2

-OOC NH3+

H2C

H(Z)(W)

(Y)

(X)

CH2

H2C

NH

C

NH2+

NH2

+H3N

C

C

O

O-

CH2H

CH2

CH2

NH

C

NH2+

H2N

C

+

Charged amino acids

CH

-OOC

NH3

CH2 CH2 CH2 CH2 NH3+

-lysineL-lysine(-)--lysineS-lysine

H C

-OOC

NH3+

CH2 CH2 CH2 CH2 NH3+

+H3N

C

C

O

O-

CH2H

CH2

CH2

CH2

NH3+

-OOC NH3+

H2C

H(Z)(W)

(Y)

(X)

CH2

CH2

CH2

NH3+

C

+

Charged amino acids

-histidineL-histidine(-)--histidineS-histidine

CH

-OOC

NH3

CH2

N

HN

H

+

H C

-OOC

NH3+

CH2

NH+

HN

+H3N

C

C

O

O-

CH2H

NH+HN

-OOC NH3+

H2C

H(Z)(W)

(Y)

(X)

NH+

HN

C

+

Charged amino acids

-glutamateL-glutamate(-)--glutamateS-glutamate

CH

-OOC

NH3

CH2 CH2 C

O

O-

H C

COO-

NH3+

CH2 C

O

O-

CH2

+H3N

C

C

O

O-

CH2H

C

O

O-

H2C

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

C

OO-

CH2

C

+

Charged amino acids

-aspartateL-aspartate(-)--aspartateS-aspartate

CH

-OOC

NH3

CH2 C

O

O-

+H3N

C

C

O

O-

CH2H

C

O

O-

-OOC NH3+

CH2

H(Z)

(W)

(Y)

(X)

C

OO-

H C

COO-

NH3+

CH2 C

O

O-

C

+

Alanine Ala ACysteine Cys CGlycine Gly GHistidine His HIsoleucine Ile ILeucine Leu LMethionine Met MProline Pro PSerine Ser SThreonine Thr TValine Val V

Arginine Arg RAsparagine Asn NAspartate Asp DGlutamate Glu EGlutamine Gln QLysine Lys KPhenylalanine Phe FTryptophan Trp WTyrosine Tyr Y

Non-standard encoded amino acids

CH

-OOC

NH3

CH2 SeH SelenocysteineSec, U

PyrrolysinePyl, O

+

+

CH

-OOC

NH3

CH2 CH2 CH2 CH2

HN

O

N

CH3

Amino acids bear structural similarity to each other

CH

-OOC

NH3

CH2 C

O

O-

CH

-OOC

NH3

CH2 CH2 C

O

O-

CH

-OOC

NH3

CH2 CH2 C

O

NH2

CH

-OOC

NH3

CH2 C

O

NH2

Asparate

Asparagine

Glutamate

Glutamine

+

+

+

+


Cysteine Selenocysteine

Serine

CH

-OOC

NH3

CH2 SH

CH

-OOC

NH3

CH2 SeH

CH

-OOC

NH3

CH2 OH

CH C

-OOC

+H3N

CH3

H

OH

Threonine

+ +

+


Tyrosine

Phenylalanine

CH

-OOC

NH3

CH2 OH

CH

-OOC

+H3N

CH2

+


Histidine

CH2

N+

N

H

HAsparagine

Glutamine

ArginineCH2

O

HN

H

CH2N

H

HO

Histidine

CH2

N+

N

H

H

CH2N

N

H

H

H

NH2+

Histidine

CH2

N+

N

H

H

CH2+H2N

H

Histidine

CH2

N+

N

H

HArginine


Histidine

Tryptophan

CH2

N+

N

H

H

CH2N

H


CH2CH2

OH PhenylalanineTyrosine

CH2

PhenylalanineLeucine

CH2

CH3H3C

• Glutamate, glycine– neurotransmitters

• D-serine– neurotransmitter

• S-adenosylmethionine– methyl transfer CH

-OOC

NH3+

CH2 CH2 S CH3

N

N

NN

H2N

O

OH

OH

H

H

H

H

Pag

e 77

Non-peptide amino acids

Titration curve of glycine.

These values are the pKa’s of the free amino acids in aqueous solution. As we shall see later an aqueous

solution may not represent reality

+H3N

C

C

O

O-

CH2H

NNH

C

O

-O

CH2OH

These values are the pKa’s of the free amino acids in aqueous solution. As we shall see later an aqueous

solution may not represent reality

C

O

OH

Hydrophobic pocket

Associations of amphipathic molecules in aqueous solutions.

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