180
R. Fausto and N. Kuş
used these inexpensive molecular materials as pieces to build up their own bodies
and machinery, from controlling and defense systems to structural and reproductive
devices. Proteins are made from simple building blocks, the amino acids, which
can be produced from non-biomorphic materials under certain circumstances,
and that are believed to have been initially formed that way on the Earth. Amino
acids also play a critical role in the systems of command of the living beings,
as neurotransmitters. the main components of the nucleic acids are relatively
simple heterocyclic molecules, belonging to the purine and pyrimidine families,
which are the most widely-distributed kind of nitrogen-containing heterocycles in
nature [1]. Purines are also significant components in a number of other important
biomolecules, such as adenosine- and guanosine- 5’-triphosphates (AtP, gtP),
cyclic adenosine monophosphate, nicotinamide-adenine dinucleotide (NAd
+
/
NAdh) and coenzyme A, for example, which are main actors in the fundamental
bioprocesses of energy production, intracellular signal transduction, biosynthesis
and ribonucleic acid (RNA) transcription. Pyrimidine phosphates participate in
the biosynthesis of several molecules too. the life-related purines and pyrimidines
can also be obtained from non-biological materials. the parent purine was first
synthesized in 1899 from uric acid [2], and purines can nowadays be obtained in
the laboratory from formamide [3], the simplest amide. Pyrimidines can also be
prepared in the laboratory from very simple molecules, e.g., by reacting amides
with carbonitriles under electrophilic activation of the amide [4]. though the
chemistry and biological functioning of proteins and nucleic acids cannot be
described by the sum of those of their building blocks, the detailed understanding
of the relevant properties of these latter constitutes a fundamental piece of information for improving our understanding of the complex systems and of their way
of working.
Along evolution, biological systems had also to develop molecular machinery
for recognition of molecules (and other biological systems) that might be either
beneficial or dangerous. these recognition systems, such as most of the biological
processing and signaling devices (enzymes, prions, nucleic acids, neurotransmitters, hormones, etc), take as essential information at the molecular level the spatial
forms of the molecules. Small modifications in a molecule, produced by substituting one of its atoms by a different one or by changing the spatial arrangement of the
atoms in the molecule (conformational changes), can lead to dramatic changes in
its function or be responsible for the activation of a complex biological process. For
example, methylated versions of the major pyrimidine nucleic acid bases (cytosine,
thymine, uracil), which can also occur as minor forms in these latter biomolecules,
appear to have regulatory functions rather than participating directly in the coding
and transcription processes [5]. on the other hand, the importance of molecular conformation in biochemistry is well-recognized. Conformations largely determine, for
instance, catalytic mechanisms in enzymes, antifreeze cryoprotectants efficiency
and membrane properties, and are the basis of the general phenomenon of molecular recognition. Conformational changes are key events in the vision process [6], in
the control of membrane permeability and molecular transport in cells [7], and in
R. Fausto and N. Kuş
used these inexpensive molecular materials as pieces to build up their own bodies
and machinery, from controlling and defense systems to structural and reproductive
devices. Proteins are made from simple building blocks, the amino acids, which
can be produced from non-biomorphic materials under certain circumstances,
and that are believed to have been initially formed that way on the Earth. Amino
acids also play a critical role in the systems of command of the living beings,
as neurotransmitters. the main components of the nucleic acids are relatively
simple heterocyclic molecules, belonging to the purine and pyrimidine families,
which are the most widely-distributed kind of nitrogen-containing heterocycles in
nature [1]. Purines are also significant components in a number of other important
biomolecules, such as adenosine- and guanosine- 5’-triphosphates (AtP, gtP),
cyclic adenosine monophosphate, nicotinamide-adenine dinucleotide (NAd
+
/
NAdh) and coenzyme A, for example, which are main actors in the fundamental
bioprocesses of energy production, intracellular signal transduction, biosynthesis
and ribonucleic acid (RNA) transcription. Pyrimidine phosphates participate in
the biosynthesis of several molecules too. the life-related purines and pyrimidines
can also be obtained from non-biological materials. the parent purine was first
synthesized in 1899 from uric acid [2], and purines can nowadays be obtained in
the laboratory from formamide [3], the simplest amide. Pyrimidines can also be
prepared in the laboratory from very simple molecules, e.g., by reacting amides
with carbonitriles under electrophilic activation of the amide [4]. though the
chemistry and biological functioning of proteins and nucleic acids cannot be
described by the sum of those of their building blocks, the detailed understanding
of the relevant properties of these latter constitutes a fundamental piece of information for improving our understanding of the complex systems and of their way
of working.
Along evolution, biological systems had also to develop molecular machinery
for recognition of molecules (and other biological systems) that might be either
beneficial or dangerous. these recognition systems, such as most of the biological
processing and signaling devices (enzymes, prions, nucleic acids, neurotransmitters, hormones, etc), take as essential information at the molecular level the spatial
forms of the molecules. Small modifications in a molecule, produced by substituting one of its atoms by a different one or by changing the spatial arrangement of the
atoms in the molecule (conformational changes), can lead to dramatic changes in
its function or be responsible for the activation of a complex biological process. For
example, methylated versions of the major pyrimidine nucleic acid bases (cytosine,
thymine, uracil), which can also occur as minor forms in these latter biomolecules,
appear to have regulatory functions rather than participating directly in the coding
and transcription processes [5]. on the other hand, the importance of molecular conformation in biochemistry is well-recognized. Conformations largely determine, for
instance, catalytic mechanisms in enzymes, antifreeze cryoprotectants efficiency
and membrane properties, and are the basis of the general phenomenon of molecular recognition. Conformational changes are key events in the vision process [6], in
the control of membrane permeability and molecular transport in cells [7], and in