BIOCHEMISTRY

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Marie Dale T. Peralis
Department of Physical Sciences
College of Science
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Biochemistry
 deals with the chemical compounds and
processes occurring in organisms

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Syllabus
 Water
 Structure, function, and properties of amino acids
 The Three-Dimensional Structure of Protein
 Protein Purification and Characterization Techniques
 Enzymes
 Carbohydrates
 Lipids
 Nucleic Acid
 Genetic Information in the Cell

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Water
The Solvent for Biochemical Reactions

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Water: The Medium for Life
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The most abundant substance in living systems,

making up 70% or more of the weight of most
organisms.
Chemical reactions occur in aqueous medium

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6 Structure of Water

Molecular geometry: _______________

Polar or nonpolar? ________________

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7 Polar or Nonpolar?

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Properties of Water
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 High melting point

 High boiling point
 High heat of vaporization
 High Surface tension
 Maximum density is found in the liquid (not the solid)
state
 Solid form, ice, occupies more space than does the
liquid form, water

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9 Hydrogen Bonding
 A special type of intermolecular attraction between the hydrogen atom in
a polar bond (particularly H-F, H-O, and H-N) and nonbonding electron pair
on a nearby small electronegative ion or atom usually F, O, or N (in another
molecule).

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10 Hydrogen Bonding

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11 Hydrogen Bonding
Directionality of the hydrogen bond

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12 Ice
 Hexagonal Structure is
the most common crystal
form of water
 Hexagonal ice has lower
density than liquid water

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Importance of Hydrogen Bonds
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 Source of unique properties of water

 Protein structure
 DNA structure
 Binding of substrates to enzymes

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Water as a solvent
 Water is a good solvent for charged and polar substances
–amino acids
–carbohydrates
 Water is a poor solvent for nonpolar substances
–aromatic
–aliphatic
 Water dissolves many salts

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 Ionization of water
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 Pure Water Is Slightly Ionized
H2O ↽ H + +OH −
H + + H2O -> H3O+
2 H2O ↽ H3O+ + OH −
H+ [OH− ]
Keq=
[H2O]

[H2O] can be determined from water density, it is 55.5 M

The value for Keq, determined by electrical-conductivity measurements of pure water,
is 1.8 X10−16 M at 25 ⁰C
Keq.[H2O]= [H+][OH− ]
1.8 X10−16 [55.5]= [H + ][OH − ]= 1X 10−14
Ion product of water (Kw)
Kw= [H + ][OH − ]= 1X 10−14
The amount of H + or OH − in 1 L (liter) of pure water at 25°C is __________ mol 15
pH
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 defined as the negative logarithm of the hydrogen ion

concentration
pH = -log[𝐇 + ]
Kw= [H + ][OH − ] = 1X10−14
-log[H + ] + -log[OH − ] = −log(1X10−14 )
pH + pOH= 14
Whether we have pure water or an aqueous solution of dissolved
species, the following relation always holds at 25⁰C:
Acidic Solution: [H + ] > 1X10−7 M, pH__7.00
Basic Solution: [H + ] < 1X10−7 M, pH__7.00
Neutral Solution: [H + ] = 1X10−7 M, pH__7.00

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Problems
1. What is the pH of a 0.0235 M HCl solution?

2. What is the pOH of a 0.0235 M HCl solution?

3. What is the pH of a 6.50 x 10 −3 M KOH solution?

4. What is the pH of a 6.2 x 10 −5 M NaOH solution?

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 pKa
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 defined by the
equation
𝟏
pKa= log = -log Ka
𝐊𝐚

Since most of the acids

encountered in biochemistry
are weak acids (Ka is less than
1), they defined a more
convenient numerical measure
of acid strength.
Strong acid: large Ka, small pKa
Weak acid: small Ka, large pKa

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Buffer
19 Solution
 A solution of (a) a weak acid or base Henderson- Hasselbalch Equation
and (b) its salt
HA ↽ H + +A−
Example: [H+ ][A− ]
Ka=
1. Acetic acid (CH3COOH) and its salt [HA]
sodium acetate (CH3COONa) [HA]
[H + ] = Ka [A− ]
2. Ammonia (NH3) and its salt
ammonium chloride (NH4Cl) [HA]
-log [H + ] = -logKa - log [A− ]
 The solution has the ability to resist
changes in pH upon the addition of [HA]
pH= pKa - log [A− ]
small amounts of either acid or base.
[𝐀− ]
 Buffering capacity is greatest at pH = pH= pKa + log
pKa [𝐇𝐀]

 Buffering capacity is lost when the

pH differs from pKa by more than 1
pH unit
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20 Problems
1. A buffer is prepared containing 1.00 M acetic acid and 1.00 M sodium
acetate. What is its pH? Ka of acetic acid is 1.8 x 10¯5

2. A buffer is prepared containing 0.800 molar acetic acid and 1.00 molar
sodium acetate. What is its pH? Ka of acetic acid is 1.8 x 10¯5

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21Buffering against pH Changes in Biological
Systems
 In cells and tissues, phosphate and bicarbonate buffer
systems maintain intracellular and extracellular fluids at
their optimum (physiological) pH, which is usually close to
pH 7
 Enzyme-catalyzed reactions have optimal pH

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Biomolecules
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 All forms of life are ultimately based on the four biomolecules

• Proteins
• Carbohydrates
• Lipids
• Nucleic Acids
 These biomolecules are organic compounds
 All of these are polymers, except for lipids

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