Water and Biomolecule

Water and Biomolecule

Introduction; Basic Chemistry

Electron in the Bond

outside layer Length and angle
Octet rule Single, double
Hibridisation
 From Atoms to Biological Molecules
The atomic composition
Chemical properties of living organism is more
Periodical Table complex than others
H
CNO

Life prefers lighter atoms Atomic

(1) More abundant on Earth sizes
(2) Stronger bonding between small atoms
1H 6C 7N 8O
sp3
1s 2s 2p
Electrons on
the outer shell H C N O
The tetrahedral structure
sp3 of carbon orbital has rigid
steric strain which makes
Components of the early
atmosphere
H2 CH4 NH3 H2O the basic building unit of
protein conformation

Juang RH (2004) BCbasics

 Energy of Chemical Bonds in Cells
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53

Room Temperature ATP Hydrolysis Covalent bond Glucose Oxidation

0.1 1 10 100

Secondary bond kcal/mole

Van der Waal force 0.1 kcal/mole

Hydrophobic bond 1 kcal/mole

Hydrogen bond 1 kcal/mole

Ionic bond 3 kcal/mole

Covalent bond 90 kcal/mole

Juang RH (2004) BCbasics

Water and Biomolecule

Hidrogen Bond
 Hydrogen Bond (H-Bond)

The linearity is important for a perfect H-bond

+
N H O
Weaker H-bond
O

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58
Water and Biomolecule

Water
Water and Biomolecule

Other Molecule
Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87
Water as solvent: Ionic Bond Is Not Stable in Water Solution

+ + -
-
Solvation
O +
H
-

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115
C - +
- H N
+H
+

O + - -
-
+
+

+?-
- + - -
-+ + + - - - + + + -
- - +
+
+
+
- - + - +
+ -
-+ + - -+ + - -

But enzyme forms stable binding with its substrate in water

Bond Energy in Water Might Be Different

Bond length In vacuum Water solution

Covalent bond 0.15 nm 90 90
Ionic bond 0.25 nm 80 3
Hydrogen bond 0.30 nm 4 1
Van der Waal force 0.35 nm 0.1 0.1

kcal/mole

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57
 Affinity between Two Molecules

Like
Dissolves
Like
Molecules having similar polarity will attract each other

Polar Polar
Nonpolar Nonpolar

Juang RH (2004) BCbasics

Water and Biomolecule

Henderson-Hasselbalch Equation
Water and Biomolecule
Water and Biomolecule

pH and Dissociation
Contoh : Hitunglah pH dari
buffer yang terdiri dari [tris]
= 0.025 M dan [trisH+] =
0.075 M, dengan pKa = 8.08
untuk trisH+.

pH = pKa + log [deprotonated]/[protonated]

pH = 8.08 + log (0.025/0.075)

pH = 7.6
Water and Biomolecule

Aplication : Titration curve

Water and Biomolecule

Change in Amino Acid charge

Change in charge and activity

Water and Biomolecule

Carbonat dissociation in blood

 Functional Group
Components of the early
atmosphere H2 CH4 NH3 H2O
Review the structure of water
C-C
Organic compound - +
COOH
lp lp
C -d
C
Electro- NH2
negativity
R CH3 O
O 3.5
N 3.0 Functional group Permanent
+d dipole
C 2.5 If atoms in a functional group
have notable difference in High polarity
H 2.1 High dielectric constant
electronegativity, then this
functional group will express H-bond formation
high polarity and will be pH influence
highly active

Juang RH (2004) BCbasics

Water and Biomolecule

Functional Group
Water and Biomolecule

Example : Important Molecule

Water and Biomolecule

Why biochemically reactive ?

Water and Biomolecule

Active nucleophilic
Water and Biomolecule

Other
Water and Biomolecule

Peptide elongation
Water and Biomolecule

Peptide hydrolisis
Water and Biomolecule
Water and Biomolecule
Water and Biomolecule

Building Blocks of macromolecule

Water and Biomolecule
Water and Biomolecule
Water and Biomolecule

Sub-unit are linked to each other

Macromolecule
subunits are linked
by removing water
dehydration
condensation
Subunits are broken
apart by adding
water to a bond
hydrolysis
Water and Biomolecule

Important macromolecule and their subunits

Lipid Glycerol and Fattybacids

Carbohydraet Glucose
Nucleic acids Base, sugar and
Protein phosphate
Asam amino
Water and Biomolecule

6 Lipids in Cell
Water and Biomolecule
Water and Biomolecule

Fatty Acid
Amphipathic
Several
polar
groups
Saturated
No
double
bonds
Unsaturated
Double
bonds
Water and Biomolecule

Triglyceride
Subunits
Glycerol
3 fatty acids

Linked through
condensation
Water and Biomolecule

Phospholipids

Subunits : Glycerol, 2 fatty acids and Head with phosphate group

Linked by condensation reactions
Water and Biomolecule

Phospholipids in Membranes

Amphipathic structure causes formation of a bilayer

Charged groups associate with water
Hydrophobic tails clump together
Water and Biomolecule

Protein embedded in the membrane

(transmembrane)
Water and Biomolecule

Polyssacharide Formation
2 sugars link to form
disaccharide
Several sugars
oligosaccharide
Long chains of sugars
polysaccharide
Linked through
dehydration
condensation to form
polysaccharides
Molecule for energy
stored
Water and Biomolecule

Carbohydrates and Structure

Cellulose
Structural support
for plant cells
Glucose
polysaccharide with
bonds in straight
orientation
Chitin
Exoskeleton of
arthropods
Modified sugars in
chains
Water and Biomolecule

Complex Carbohydrates
Water and Biomolecule

Glycoproteins and Glycolipids

Glycoproteins have short chains of
sugars attached to proteins
Glycolipids have short chains of
sugars attached to lipids
Both found on the exterior surface of
cells
Important in cell signaling
Water and Biomolecule

Nucleic Acids
Structure
Subunits
nucleotides
3 building blocks
for each
nucleotide:
Sugar
Phosphate
Nitrogenous
base
Water and Biomolecule

Component
Nitrogenous Base
Pyrimidines, single
ring
Purines, 2 rings
Differ in functional
groups attached to
the rings
5 carbon sugars
Ribose in RNA
Deoxyribose in DNA
Phosphate groups link
nucleotides together
Water and Biomolecule

Formation of Nucleic Acids

Linked by
dehydration
condensation
Bond is called a
phosphodiester
linkage
Water and Biomolecule

Nucleic Acid Structure

Water and Biomolecule

DNA Structure
Water and Biomolecule

Amino Acids
Subunits of
polypeptides
20 different
types
Structure:
Amino group
Carboxyl (acid)
group
R groups differ
Water and Biomolecule
Water and Biomolecule

Formation of Polypeptides
Linked by
dehydration
condensation
Bonds are
peptide bonds
Functions
Structure
and support
Transport
molecules
Perform
chemical
reactions
as enzymes
Water and Biomolecule
Water and Biomolecule