Introduction of Biochemistry

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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