Plant

Biochemistry
Saeed A. Abro

C
H
O
N

What is Biochemistry?
Biochemistry is an experimental science
which deals with the structure, composition,
properties and metabolism of molecules of
cell.

Biomolecul
es
Proteins
Carbohydrate
s
Nucleic
Lipids
Acids

Composition of cell
composition
%Molecular
Atomic composition
15

12

15 5

10
3
80

20

60
50

Hydrogen Oxygen
Carbon
Water
Proteins Nucliec acids
Nitrogen
P,S,Mg,Mn,Se etc
Carbohydrates Lipids

Some basics

Bonds
Carbon
Functional groups
Linkages

Bonds

A force to held atoms in

molecules

Covalent
Hydrogen

Covalent Bonds
A principle force that holds atoms
together by sharing electrons
Length 0.15 0.20 nm
Strength 83 K cal/mol
to break C-C

At physiologically
relevant temperature
dont break
Can rotate, stretch,
bent but do not break

H-O-

Can be single C-C,

double C=C and triple

Electron sharing
Equal sharing as in C-C and C-H
bonds (non-polar)
Unequal sharing as in O-H bonds
(polar)
Electronegativity = greediness of an

atom for electrons

-

104.5o

Hydrogen Bond
A bond generated through a slight
electrostatic charge (+) of H atom
bonded to O or N and (-) O or N to the H
Week bonds i.e. the energy of
bond dissociation is about 23
kJ/mol as compared to 470 KJ/mol
of O-H and 348 KJ/mol C-C covalent
bond.
It is 10% covalent due to
overlapping of orbitals and 90%
electrostatic.
At room temperature the thermal
energy of aqueous solution is same
magnitude as required to break
hydrogen bonds.

Hydrogen Bond

Common
bonds in
systems

hydrogen
biological

Some
biologically
important hydrogen bonds

Carbon
Organic
Molecules
Inorganic

Carbon bonded to
hydrogen
Carbon not bonded
to hydrogen directly

Chemistry of life is based on CARBON because all the

biomolecules are made of carbon except water

Carbon bonding

A carbon atom has four

electrons
in
its
outermost
energy level.
Thus it can form four covalent
bonds to other elements.
the
biologically
significant
property is its formation of
single, double and triple bonds
with carbon atoms.
Due to this property carbon
makes
skeleton
of
macromolecules
in
different
forms.

Carbon bonding

Four bonds project from nucleus to four apices of a tetrahedron.

Thus it is tetrahedral in configuration.
The angle is 109.5 and average bond length is 0.154 nm.
There is free rotation around each single bond unless a large or
charged groups are attached to each carbon atom.
Double bonds are shorter (0.134 nm) and rigid thus show very
limited rotation.

Functional groups

Functional group is a
set of atoms that give
specific properties to
the compound.

Monomers

Smaller molecules of molecular

weight of 100 to 500 Daltons.
Universal
Common amino acids, nucleotides,
sugars and their phosphorylated
derivatives, and mono-, di-, and
tricarboxylic acids.
molecules are polar or charged,
water soluble,
and present in micromolar to
millimolar concentrations.
PRIMARY METABOLITES

Characteristic to vascular
plants.
Specific to certain cells or
organisms.
Play specific roles
Examples are: morphine,
quinine,
nicotine,
and
caffeine etc.
SECONDARY
METABOLITES

Biomolecules are polymers

Polymers of monomers
Large molecules with molecular weights > 5000 Daltons
Smaller polymers are oligomers.
The polymers are synthesized by condensation reactions by the use of energy.
Similarly the polymers are broken down into monomers by hydrolysis.
The monomers are joined together by specific covalent bonds called LINKAGES.

Linkages

Glycosidic

Ester
Peptide

Disulfid
e

Phosphodiester

Polymer 3-D structure

Polymer 3-D structure is described by configuration and confirmation

Stereochemistry ..stereoisomers (molecules with same chemistry
but different configuration).
Three ways to show configuration.. Perspective diagram, ball and
stick and space fill model.

Polymer 3-D structure

Configuration is conferred by the presence of

Double bond around which there is no freedom of

rotation
Chiral centers

Geometric or cis, trans isomers

Chirality

When a tetrahedral carbon is bonded to four different groups is

called asymmetric
Asymmetric carbons are Chiral centers
Asymmetric carbon can have two configurations ..isomers.
A molecule with only one chiral carbon can have two
stereoisomers;
when two or more (n) chiral carbons are present, there can be
2n stereoisomers.
Stereoisomers that are mirror images of each other are called
enantiomers
Pairs of stereoisomers that are not mirror images of each other
are called diastereomers

Further readings