David L. Nelson and Michael M. Cox
LEHNINGER
PRINCIPLES OF BIOCHEMISTRY
Sixth Edition
CHAPTER 1
The Foundations of Biochemistry
© 2013 W. H. Freeman and Company
Pancreatic cell section
Universal features of living cells
Phylogeny of the three domains of life
Classification of Organisms
Several functional groups in a single biomolecule
Complementary fit between a
macromolecule and a small
molecule
Stereoisomers have different effects in humans
Many drugs are racemic mixtures
Energy
Transformations in
Living Organisms
The major carrier of chemical
energy in all cells is adenosine
triphosphate (ATP)
David L. Nelson and Michael M. Cox
LEHNINGER
PRINCIPLES OF BIOCHEMISTRY
Sixth Edition
CHAPTER 2
Water
© 2013 W. H. Freeman and Company
Water
Hydrogen
bonding in
ice
Common hydrogen bonds
in biological systems
Biologically important hydrogen bonds
Directionality of the hydrogen bond
Water as a solvent
Amphipathic compounds in aqueous solution
Dispersion of lipids
in water
Release of ordered water
is energetically favorable
Ionization of
water
Conjugate acid-base pairs consist of a proton donor and a proton acceptor
Titration curve of acetic acid
H2O
H2O
Equilibrium
= Keq =
constant
Ion product
of water
=
OH- + H+
[OH-] [H+]
= 1.8 x 10-16 M
[H2O]
Kw = [OH-] [H+] = 10-14 M2
Pure H2O : [H+] = [OH-] = 10-7 M
pH = - log [H+] = -log (10-7) = 7
If [H+] > 10-7 M then pH < 7 (acidic)
If [H+] < 10-7 M then pH > 7 (basic)
Blood: [H+] = 4 x 10-8 M
Blood pH = 7.4
Acids and Bases
Acid (HA) - something that has a proton and is willing to give it up.
Base (A-) - something that has a place to put a proton
HA
H + + A-
HA + H2O
H 3O+ + A-
Strong acids completely dissolve in H2O (H+Cl-).
Weak acids don’t completely dissolve in H2O.
[A-] [H+]
K=
O
[HA]
H2PO4(acid)
O
HPO42- + H+
(base)
P
OH
Ka =
[HPO42-] [H+]
[H2PO4-]
pKa = - log (Ka) = 6.82
= 1.51 x 10-7 M
OH
Relationship between pH and pKa
Henderson – Hasselbalch equation
pH = pKa when:
The molar concentration of acid and conjugate base are equal
[H2PO4-] = [HPO42-]
pH = pKa = 6.8
Physiological pH
The pH in the human body needs to remain ~7. Enzyme catalysis,
protein-protein interactions, receptor binding, and other biological
processes are very sensitive to pH.
pH balance of the blood is maintained using a CO2 - bicarbonate buffer.
CO2 + H2O
(acid)
H2CO3
(hydrated
CO2)
H+ + HCO3-
(bicarbonate
base)
pKa = 6.1
There is more than 10-fold more base (HCO3-) than acid (CO2)
so pH > pK (pH= 7.4)
CO2 is exhaled by the lungs H+ + HCO3-
CO2 + H2O
Breathing rate controls CO2
CO2 balance is controlled by the lungs, HCO3- by the kidneys