Introduction to Biochemistry

Chemical Bonds and Reactivity

Prof. Dr. Özlem Dalmızrak

Department of Medical Biochemistry
Faculty of Medicine
Near East University
Biochemistry is the study of chemistry of life. Biochemistry
describes the structure, organization, and functions of living
matter in molecular terms
• What are the chemical structures of the components of living
matter?
• How do the interactions of these components give rise to
organized supramolecular structures, cells, multicellular
tissues, and organisms?
• How are the chemical reactions controlled inside living cells?
• How does living matter extract energy from its surroundings
in order to remain alive?
• How does an organism store and transmit the information it
needs to grow and reproduce itself accurately?
• What chemical changes accompany the reproduction, growth,
development, aging, and death of cells and organisms?
Distinguishing features of living organisms:
• A high degree of chemical complexity and microscopic
organization.
• Systems for extracting, transforming and using energy from
the environment.
• Defined functions for each of an organism’s components and
regulated interactions among them.
• Mechanism for sensing and responding to alterations in their
surroundings.
• A capacity for precise self-replication and self-assembly.
• A capacity to change over time by gradual evolution.
Cells are the Structural and Functional Units of All
Living Organisms
Eukaryotes-Prokaryotes
Organisms can be classified according to how they obtain the
energy and carbon they need for synthesizing cellular
material.
Bacterial cells
Monomeric Units of Complex Macromolecules
Molecular Organization of Cell
Essential Elements for life and health
 Three-Dimentional Structure of Molecules
Stereochemistry: Arrangement of the molecule’s constituent
atoms in three-dimentional space.
A carbon containing compound commonly exist as stereoisomers
(Molecules with the same chemical bonds but different
configuration).

Perspective form
Ball-and-stick model

Structure of amino acid alanine

Space-filling model
Configuration is conferred by the presence of either (1) double
bonds, around which there is no freedom of rotation or (2) chiral
centers, around which substituent groups are arranged in a
specific orientation.

Geometric isomers
(cis-trans isomers)
Number of stereoisomers: 2n n = Number of chiral carbon
• Stereoisomers are the mirror images of each other are called
enantiomers.
Pairs of stereoisomers that are not mirror images of each
other are called diastereomers.
Conformation: The position of atoms in space that can
be changed by rotation about single bonds, without
breaking any bonds.
Interactions between Biomolecules are Stereospecific

Three-dimentional structures of biomolecules: Configuration and

conformation
• Enzyme-substrate
• Antigen-antibody
• Hormone-receptor
In living organisms, chiral molecules are usually present in only
one of their chiral forms. Amino acids – L isomers, glucose – D
isomers.
 Physical Foundations
• Living cells and organisms must perform work to stay alive and
to reproduce themselves.
• The synthetic reactions that occur within cells require the
input of energy.
• Living organisms exist in dynamic steady state, never at
equilibrium with their surroundings.
• Organisms transform energy and matter from their
surroundings.
System: All the constituent reactants and products and
solvent that contains them and immediate atmosphere in
short everything within a defined region of space (Isolated /
Closed / Open Systems).
Universe: The system and surroundings together constituent
the universe
• If the system exchanges neither energy nor matter
with its surroundings , it is isolated.

• If the system exchanges energy but not matter with

its surroundings, it is a closed system.

• If it exchanges both energy and matter with its

surrounding, it is an open system.

A living organism is an open system

Cellular energy conversions=Thermodynamic

The first law of thermodynamics explains

the principle of the conservation of the
energy: in any physical or chemical change,
the total amount of energy in the universe
remain constant, although the form of the
energy may change.
The second law of thermodynamics:
The total entropy of the universe is
continually increasing.
 Entropy (Randomness / Disorder)
C6H12O6 + 6O2 → 6CO2 + 6H2O

Whenever a chemical reaction results in an increase in the

number of molecules-or when a solid substance is converted into
liquid or gaseous products, which allow more freedom or
molecular movement than solids-molecular disorder, and thus
entropy, increases.
Entropy change: S
Free-energy content: G
Enthalpy: H, the number and kinds of bonds
Absolute temperature: T (in Kelvin)
The definition of free energy is G = H – TS
Free energy change G = H – T S
IF G IS NEGATIVE, A PROCESS TENDS TO OCCUR SPONTANEOUSLY.
Energy requiring reactions are called endergonic.
Energy releasing reactions are called exergonic.

Aminoacids → Protein
ATP → AMP + P-P (or ADP + P)
Major Chemical Bonds and
Functional Groups
in Biological Molecules
 Formation and Stabilization of Biological
Molecules
Major biological molecules are macromolecules with very high
molecular weight.

Macromolecules are stabilized by various types of chemical

bonds:

1. Non-covalent interactions

2. Covalent bonds
 Non-Covalent Interactions-1

Strength of
interaction

1. Charge-Charge + - -NH3+ -OOC- 1/r

2. Charge-Dipole q+ q- + H 2O +H
3N- 1/r2

3. Dipole-Dipole q+ q- q+ q- H 2O H 2O 1/r3

4.Charge-Induced -NH3+
dipole
q+ q- + - + 1/r4

5.Dipole-Induced q+ q- q+ q- H 2O - + 1/r5
dipole
 Non-Covalent Interactions-2

6. Dispersion
q+ q- - +
1/r6
q- q+ + -

7. Van der Waals interactions:

a. Attraction
b. Repulsion 1/r12

8. Hydrogen bonds
q- q+ C=O H-N

Acceptor donor
Covalent Bonds
The chemistry of living organisms is organized around
carbon.
 Geometry of carbon bonding

Tetrahedral structure

Covalently linked carbon atoms in biomolecules can form linear

chains, branched chains and cyclic structures.
Common functional groups in biomolecules

C = NH

Imino
 O
Phenol R OH R S OH
O
Sulpho
O O
Pyrophosphate R P O P OH
OH OH
 Ether Bonds

R-OH + HO-R’ R O R’ + H2O

Glycosidic Bonds

a) O-Glycosidic Bonds

b) N-Glycosidic Bonds

R-NH2 + HO-R’ R NH R’ + H2O

R-OH + HO-R* R O R* + H2O
 Ester Bonds

O O
R-C-OH + HO-R’ R-C-O-R’ + H2O

O O
R-OH + HO-P-O- R-O-P-O- + H2O
O- O-
 Thioester Bond

O O
R-SH + HO-C-R’ R-S-C-R’ + H2O

Amide Bond

H O O
+
R- N-H + HO-C-R’ R-N-C-R’ + H2O
H H
Dehydrogenation of amines, via the formation of an imine,
results in deamination:

HH
-2H + H2O
R-C-N-H R-C=NH R- C=O + NH3
R’ R’ R’
H H
-2H + H2O
R-C-N-H R-C=NH R- C=O + NH3
H H H
Dehydrogenation of aldehyde hydrate produces carboxylic acids:

O H
-2H
R-C-H + H2O R-C-OH R-C= O
OH OH
Hemiacetal and Hemiketal Formation
Despite the presence of reactive group in biological molecules,
rarely spontaneous reactions take place.

All of the chemical reactions are catalyzed by biocatalysts,

enzymes.
 Further Reading

1. Lehninger Principles of Biochemistry

2. Harper’s Illustrated Biochemistry