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Introduction of Biochemistry and importance of H2O
By: Asheesh Kumar Pandey
Pancreatic cell section
Universal features of living cells
Phylogeny of the three domains of life
Introduce by Carl Woese in 1977 on the basis of 16SrRNA
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)
Very polar
Oxygen is highly electronegativeH-bond donor and acceptorHigh b.p., m.p., heat of vaporization,
surface tension
Properties of water
Water dissolves polar compounds
solvation shellor
hydration shell
Water
Hydrogen bonding in
ice
Hydrogen Bonding of Water
Crystal lattice of ice
One H2O molecule canassociate with 4
other H20 molecules
•Ice: 4 H-bonds per water molecule
•Water: 2.3 H-bonds per water molecule
Biologically important hydrogen bonds
Relative Bond Strengths
Bond type kJ/moleH3C-CH3 88H-H 104Ionic 40 to 200H-bond 2 - 20Hydrophobic interaction 3 -10van der Waals 0.4 - 4
non-covalent interactions
Directionality of the hydrogen bond
Water as a solvent
Non-polar substances are insoluble in water
Many lipids are amphipathic
How detergents work?
Amphipathic compounds in aqueous solution
Dispersion of lipids in water
Release of ordered water is energetically favorable
Ionization of Water
Ionization of water
pH Scale Devised by Sorenson (1902) [H+] can range from 1M and 1 X 10-14M using a log scale simplifies notation pH = -log [H+]Neutral pH = 7.0
Conjugate acid-base pairs consist of a proton donor and a proton acceptor
Titration curve of acetic acid
[OH-] [H+] Keq = [H2O]
Kw = [OH-] [H+] = 10-14 M2
Pure H2O : [H+] = [OH-] = 10-7 MpH = - log [H+] = -log (10-7) = 7If [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
H2O OH- + H+
Equilibriumconstant = = 1.8 x 10-16 M
Ion productof water
=
H2O
Ionization of WaterH20 + H20 H3O+ + OH-
Keq= [H+] [OH-] [H2O]
H20 H+ + OH-Keq=1.8 X 10-16M
[H2O] = 55.5 M[H2O] Keq = [H+] [OH-]
(1.8 X 10-16M)(55.5 M ) = [H+] [OH-]1.0 X 10-14 M2 = [H+] [OH-] = Kw
If [H+]=[OH-] then [H+] = 1.0 X 10-7
Acid/conjugate base pairs HA + H2O A- + H3O+ HA A- + H+HA = acid ( donates H+)(Bronstad Acid)A- = Conjugate base (accepts H+)(Bronstad Base)
Ka = [H+][A-] [HA]
Ka & pKa value describe tendency to loose H+
large Ka = stronger acidsmall Ka = weaker acid
pKa = - log Ka
pKa values determined by titration
Phosphate has three ionizable H+ and three
pKas
Buffers
Buffers are aqueous systems that resist changes in pH when small amounts of a strong acid or base are added.
A buffered system consist of a weak acid and its conjugate base.
The most effective buffering occurs at the region of minimum slope on a titration curve
(i.e. around the pKa).Buffers are effective at pHs that are within
+/-1 pH unit of the pKa
Henderson-Hasselbach Equation1) Ka = [H+][A-] [HA]
2) [H+] = Ka [HA] [A-]3) -log[H+] = -log Ka -log [HA] [A-]
4) -log[H+] = -log Ka +log [A-] [HA]
5) pH = pKa +log [A-] [HA]
HA = weak acid
A- = Conjugate base
* H-H equation describes the relationship between pH, pKa and buffer concentration
Relationship between pH and pKa
pH = pKa when:
The molar concentration of acid and conjugate base are equal
[H2PO4-] = [HPO42-]
pH = pKa = 6.8
Henderson – Hasselbalch equation
Physiological pHThe 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 H2CO3 H+ + HCO3- pKa = 6.1(acid) (hydrated (bicarbonate CO2) base)
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
Case where 10% acetate ion 90% acetic acid
pH = pKa + log10 [0.1 ] ¯¯¯¯¯¯¯¯¯¯ [0.9]
pH = 4.76 + (-0.95)pH = 3.81
pH = pKa + log10 [0.5 ] ¯¯¯¯¯¯¯¯¯¯ [0.5]
pH = 4.76 + 0pH = 4.76 = pKa
Case where 50% acetate ion 50% acetic acid
pH = pKa + log10 [0.9 ] ¯¯¯¯¯¯¯¯¯¯ [0.1]
pH = 4.76 + 0.95pH = 5.71
Case where 90% acetate ion 10% acetic acid
pH = pKa + log10 [0.99 ] ¯¯¯¯¯¯¯¯¯¯ [0.01]
pH = 4.76 + 2.00pH = 6.76
pH = pKa + log10 [0.01 ] ¯¯¯¯¯¯¯¯¯ [0.99]
pH = 4.76 - 2.00pH = 2.76
Cases when buffering fails
Weak Acids and Bases Equilibria
•Strong acids / bases – disassociate completely•Weak acids / bases – disassociate only partially•Enzyme activity sensitive to pH• weak acid/bases play important role in protein structure/function
LEHNINGER PRINCIPLES OF BIOCHEMISTRY
Sixth Edition
David L. Nelson and Michael M. Cox
© 2013 W. H. Freeman and Company
CHAPTER 1The Foundations of Biochemistry
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