1.1.2 Origin of Catalytic Activity of Enzymes
Living organisms are essentially systems of chemical reactions catalyzed by
enzymes that synthesized in protein synthesis system according with genetic information of cell. In addition to enzymatic function, biological functions of proteins are
antibodies of immune systems and receptors of cellular signaling. There are 20 species of amino acids in living organism on the earth. General structure of amino acid
is composed of amino moiety, carboxyl moiety and one of 20 different side chains
for each amino acid. And these amino acids are classified into basic (histidine,
lysine, arginine), acidic and their amide (aspartate, glutamate, asparagine, glutamine), aliphatic (glycine, alanine, valine, leucine, isoleucine), hydroxyl or sulfurcontaining (serine, cysteine, cystine, threonine, methionine), cyclic (proline) and
aromatic (phenylalanine, tyrosine, tryptophan) amino acids. And they are polymerized by peptide bond between amino and carboxyl moieties. Gibbs free energy (ΔG)
of peptide bond formation is ΔG 0 '¼ 8–20 kJ/mol (1.9–4.8 kcal/mol). For formation
of peptides in biosynthesis of protein, amino acid is activated as amino acyl-tRNA.
On the other hand, heating of amino acids mixture polymerizes amino acids to result
generation of in thermal polymer in vitro. Catalytic function of enzyme is one of
important function of proteins which are polymerized structure of amino acids. And
the thermal polymer of amino acids and the polymer shows small but significant
catalytic activities such as hydrolysis, decarboxylation, aminization, deamination
and redox reaction. Acidic, basic, hydroxyl and sulfur-containing amino acids are
required for these catalytic activities, and these amino acids are arranged in active
site of enzyme (Table 1.3). For example, active site of trypsin is composed of His57,
Asp102 and Ser195, and other parts of amino acids play a role of arranging these
amino acids in right position of active site. Living organism on the earth is essentially a system of regulated chemical reactions catalyzed by enzymes. Catalytic role
is performed by enzyme and its genetic information is stored in nucleic acid (DNA).
1.1.3 Development of Genetic Information and RNA World
There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA) which are polymers of nucleotides. Nucleotide is composed of nucleic
acid base, sugar (deoxyribose or ribose) and phosphate (mono- di- or tri-phosphate).
There are adenine, thymine, guanine and cytosine for DNA, and uridine instead of
thymidine for RNA. Nucleotides of triphosphate (ATP, TTP, GTP and CTP) are
high energy biomolecules used in cells. Hydrolysis of nucleotide triphosphate
releases ΔG 0 '¼À7.3 kcal/mol as Gibbs free energy, and used in various biological
functions (Fig. 1.2). So, it is possible for nucleotide triphosphates to polymerize by
use of own energy. Watson-Crick base pair is most important rule for gene replication. Double strand of DNA is formed by complementary structure of base pairs
between adenine and thymine (A-T) and between guanine and cytosine (G-C)
(Fig. 1.3). Two hydrogen bonds connect between adenine and thymine at distance
4
1 Physics in the Origin of Life
Living organisms are essentially systems of chemical reactions catalyzed by
enzymes that synthesized in protein synthesis system according with genetic information of cell. In addition to enzymatic function, biological functions of proteins are
antibodies of immune systems and receptors of cellular signaling. There are 20 species of amino acids in living organism on the earth. General structure of amino acid
is composed of amino moiety, carboxyl moiety and one of 20 different side chains
for each amino acid. And these amino acids are classified into basic (histidine,
lysine, arginine), acidic and their amide (aspartate, glutamate, asparagine, glutamine), aliphatic (glycine, alanine, valine, leucine, isoleucine), hydroxyl or sulfurcontaining (serine, cysteine, cystine, threonine, methionine), cyclic (proline) and
aromatic (phenylalanine, tyrosine, tryptophan) amino acids. And they are polymerized by peptide bond between amino and carboxyl moieties. Gibbs free energy (ΔG)
of peptide bond formation is ΔG 0 '¼ 8–20 kJ/mol (1.9–4.8 kcal/mol). For formation
of peptides in biosynthesis of protein, amino acid is activated as amino acyl-tRNA.
On the other hand, heating of amino acids mixture polymerizes amino acids to result
generation of in thermal polymer in vitro. Catalytic function of enzyme is one of
important function of proteins which are polymerized structure of amino acids. And
the thermal polymer of amino acids and the polymer shows small but significant
catalytic activities such as hydrolysis, decarboxylation, aminization, deamination
and redox reaction. Acidic, basic, hydroxyl and sulfur-containing amino acids are
required for these catalytic activities, and these amino acids are arranged in active
site of enzyme (Table 1.3). For example, active site of trypsin is composed of His57,
Asp102 and Ser195, and other parts of amino acids play a role of arranging these
amino acids in right position of active site. Living organism on the earth is essentially a system of regulated chemical reactions catalyzed by enzymes. Catalytic role
is performed by enzyme and its genetic information is stored in nucleic acid (DNA).
1.1.3 Development of Genetic Information and RNA World
There are two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA) which are polymers of nucleotides. Nucleotide is composed of nucleic
acid base, sugar (deoxyribose or ribose) and phosphate (mono- di- or tri-phosphate).
There are adenine, thymine, guanine and cytosine for DNA, and uridine instead of
thymidine for RNA. Nucleotides of triphosphate (ATP, TTP, GTP and CTP) are
high energy biomolecules used in cells. Hydrolysis of nucleotide triphosphate
releases ΔG 0 '¼À7.3 kcal/mol as Gibbs free energy, and used in various biological
functions (Fig. 1.2). So, it is possible for nucleotide triphosphates to polymerize by
use of own energy. Watson-Crick base pair is most important rule for gene replication. Double strand of DNA is formed by complementary structure of base pairs
between adenine and thymine (A-T) and between guanine and cytosine (G-C)
(Fig. 1.3). Two hydrogen bonds connect between adenine and thymine at distance
4
1 Physics in the Origin of Life