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INTRODUCTION

The use of microcomputers will certainly become an integral part of the biochemistry curriculum.Computational biochemistry is the new interdisciplinary subject that applies computer technology to solve biochemical problems and to manage and analyze biochemical information.

1.1. BIOCHEMISTRY: STUDIES OF LIFE AT THE MOLECULAR LEVEL

All the living organisms share many common attributes, such as the capability to extract energy from nutrients, the power to respond to changes in their environ- ments, and the ability to grow, to differentiate, and to reproduce. Biochemistry is the study of life at the molecular level(Garrett and Grisham, 1999; Mathews and van Holde, 1996; Voet and Voet, 1995; Stryer, 1995; Zubay, 1998). It investigates the phenomena of life by using physical and chemical methods dealing with(a) the structures of biological compounds(biomolecules),(b) biomolecular transformations and functions,(c) changes accompanying these transformations,(d) their control mechanisms, and(e) impacts arising from these activities.

The distinct feature of biochemistry is that it uses the principles and language of one science, chemistry, to explain the other science, biology at the molecular level. Biochemistry can be divided into three principal areas:(1) Structural biochemistry focuses on the structural chemistry of the components of living matter and the relationship between chemical structure and biological function.(2) Dynamic bio- chemistry deals with the totality of chemical reactions known as metabolic processes that occur in living systems and their regulations.(3) Information biochemistry is

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An Introduction to Computational Biochemistry.C. Stan Tsai
Copyright\ue000 2002 by Wiley-Liss, Inc.
ISBN: 0-471-40120-X
Figure 1.1.Representative organizations of biochemical components. Three component

areas of biochemistry\u2014 structural, dynamic, and information biochemistry\u2014 are repre- sented as organizations in space (dimensions of biomolecules and assemblies), time (rates of typical biochemical processes), and number (number of nucleotides in bioinformatic materials).

concerned with the chemistry of processes and substances that store and transmit biological information(Figure 1.1). The third area is also the province of molecular genetics, a \ufb01eld that seeks to understand heredity and the expression of genetic information in molecular terms.

Among biomolecules, water is the most common compound in living organisms, accounting for at least 70% of the weight of most cells, because water is both the major solvent of organisms and a reagent in many biochemical reactions. Most complex biomolecules are composed of only a few chemical elements. In fact, over 97% of the weight of most organisms is due to six elements(% in human): oxygen

(62.81%), carbon (19.37%), hydrogen (9.31%), nitrogen (5.14%), phosphorus
(0.63%), and sulfur (0.64%). In addition to covalent bonds (3000< 150 kJ/mol for
single bonds) that hold molecules together, a number of weaker chemical forces
(ranging from 4 to 30 kJ/mol)acting between molecules are responsible for many of
the important properties of biomolecules. Among these noncovalent interactions
(Table 1.1)are van der Waals forces, hydrogen bonds, ionic bonds/electrostatic
interactions, and hydrophobic interactions.
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INTRODUCTION
TABLE 1.1. Energy Contribution and Distance of Noncovalent Interactions in Biomolecules
Chemical
Energy
Distance
Force
Description
(kJ/mol)
(nm)
Remark
Van der Waals Induced electronic
0.4\u2014 4.0
0.2
The limit of approach is
interactions
interactions between
determined by the sum of
closely approaching
theirvdW radii and related
atoms/molecules.
to the separation (r) of the
two atoms byr\\ue000.
Hydrogen
Formed between a
12\u2014 38
0.15\u20140.30 Proportional to the polarity of
bonds
covalently bonded
the donor and acceptor,
hydrogen atom and
stable enough to provide
an electronegative atom
signi\ufb01cant binding energy,
that serves as the
but suf\ufb01ciently weak to allow
hydrogen bond acceptor.
rapid dissociation.
Ionic bonds
Attractive forces between
:20
0.25
Depending on the polarity of
oppositely charged
the interacting charged
groups in aqueous
species and related to
solutions.
qG qH /DrGH.
Hydrophobic
Tendency of nonpolar
:25
\u2014
Proportional to buried surface
interactions
groups or molecules to
area for the transfer of small
stick together in
molecules to hydrophobic
aqueous solutions.

solvents, the energy of
transfer is 80\u2014 100 kJ/mol/\u00c5\ue001
that becomes buried.

All biomolecules are ultimately derived from very simple, low-molecular-weight
precursors(M.W.: 30< 15), such as CO\ue001, H\ue001O, and NH\ue002, obtained from the
environment. These precursors are converted by living matter via series of metabolic
intermediates(M.W.: 150< 100), such as acetate,\ue000-keto acids, carbamyl phos-

pahate etc., into the building-block biomoleucles(M.W.:300< 150) such as glucose, amino acids, fatty acids and mononucleotides. They are then linked to each other covalently in a speci\ufb01c manner to formbiomacromolecules(M.W.: 10\ue003< 10\ue004) or biopolymers. The unique chemistry of living systems results in large part from the remarkable and diverse properties of biomacromolecules. Macromolecules from each of the four major classes(e.g., polysaccharides, lipid bilayers, proteins, nucleic acids) may act individually in a speci\ufb01c cellular process, whereas others associate with one another to form supramolecular structures(particle weight9 10\ue000) such as proteo- some, ribosomes, and chromosomes. All of these structures are involved in important cellular processes. The supramolecular complexes/systems are further assembled into organelles of eukaryotic cells and other types of structures. These organelles and substructures are enveloped by cell membrane into intracellular structures to form cells that are the fundamental units of living organisms. Viruses are supramolecular complexes of nucleic acids(either DNA or RNA) encapsulated in a protein coat and, in some instances, surrounded by a membrane envelope. Viruses infecting bacteria are called bacteriophages.

The cell is the basic unit of life and is the setting for most biochemical phenomena. The two classes of cell, eukaryotic and prokaryotic, differ in several respects but most fundamentally in that a eukaryotic cell has a nucleus and a

BIOCHEMISTRY: STUDIES OF LIFE AT THE MOLECULAR LEVEL
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