Chemistry of Life

Chemical elements forming life were synthesized in the interior of stars. Their relative content in different forms of inanimate and living matter is represented in Table 1. The main life elements (hydrogen, carbon, nitrogen, and oxygen - from the first and second periods of Mendeleev's table) are also most common in space. The concentration of heavy elements is much higher in living matter. Sulfur and phosphorus are from the third period; as the first four elements, they can form multiple bonds. Apart from the common elements, life uses rare ones for special aims.

An extremely important substance for life is water. It is a universal medium for almost all chemical processes of life. According to the expression of R. Dubois, ''life is animated water.''

It is improbable that carbon can be substituted by silicon, and water by ammonia in some extraterrestrial forms of life, as it is described in science fiction. Siliceous polymers are unstable in solutions, and oxide of silicon is solid and inert substance.

The basis of life is formed by organic polymers. There are proteins, nucleic acids, carbohydrates, and lipids. All living beings use the same kinds of macromolecules; it is an illustration of commonalties of life. Polymers convey such life functions as metabolism, genetic inheritance, growth and reproduction, energy storage, and conversion.

'Metabolism' is a circular process of extracting, converting, and storing energy from nutrients. It is a complex network of chemical reactions, such as group transfer and oxidation-reduction reactions, dehydration, carboncarbon bonding, etc. Groups of reactions form 'catabolism' (the oxidative degradation of molecules) and 'anabolism' (the reductive synthesis of molecules), maintaining metabolic 'homeostasis' (a steady state of organism).

Two key groups of macromolecules are nucleic acids ('legislative body' - storage and development of information) and proteins ('executive body' - metabolism and maintenance of nucleic acids).

In ordinary chemistry, reactions proceed as a result of heat motion. In biochemistry, proteins, called enzymes, evolve catalytic chemical reactions, proceeding in a very specific and efficient way. They have special active centers, geometrically stimulating proximity of algoristic molecules and their interaction. Under the influence of enzymes, reactions can run in conditions of low temperature, although usually they proceed under high temperature only: outside of organism, lipids and carbohydrates oxidize under the temperature 400-500 °C; synthesis of ammonia from molecular nitrogen proceeds under the temperature 500 °C and pressure 300-350 atm.

Enzymes catalyze every biological process of life, but proteins also play other roles in living organism. They form physical basis of tissues (collagen), transporting (hemoglobin), protecting (immunoglobulin), regulatory (hormones) agents. In human organism, there are more than 5 million different proteins.

Proteins are the result of polymerization of amino acids: from several dozens to many hundreds. Amino acids are connected by covalent peptide bonds and form the primary structure. The primary thread is packed in the spatial secondary and tertiary structures by hydrogen bonds. Several proteins (protomers) can form quaternary structure (oligomer). There are 20 different amino acids in proteins of living organisms.

Nucleic acids have two forms in living organisms: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). They are polymers of nucleotides, made up of the nitrogen bases: two purines (adenine and guanine) and two pyrimidines (thymine in DNA or uracil in RNA and cytosine). RNA has a spiral primary structure and more complex secondary ones. DNA forms a double helix from two complementary macromolecules.

Table 1 Content of different elements in inanimate and living matter

Content (% per weight)

Chemical elements Solar matter Atmosphere Ocean Earth's crust Soil Plants Animals

Hydrogen (H)

72

10.7

1.6

3.1

10.0

11.0

Helium (He)

27

Oxygen (O)

0.28

20.97

85.8

56.2

66.8

70.0

65.0

Carbon (C)

0.12

0.01

1.2

18.0

19.0

Nitrogen (N)

0.05

78.08

0.26

0.06

0.9

3.0

Magnesium (Mg)

0.01

0.13

1.46

0.37

0.08

0.05

Silicon (Si)

0.01

23.05

19.41

0.35

0.24

Sulfur (S)

0.01

0.09

0.24

0.05

0.14

0.18

Iron (Fe)

0.01

3.63

2.24

0.02

0.02

Aluminum (Al)

6.3

4.18

0.01

Natrium (Na)

1.03

1.95

0.37

0.03

0.05

Potassium (K)

0.04

1.95

0.8

0.03

0.02

Calcium (Ca)

0.04

2.58

0.81

0.03

0.03

Chlorine (Cl)

1.93

0.02

0.01

0.01

0.02

The hereditary role of nucleic acids became clear in 1944, when the transfer of hereditary characters was discovered. A triplet of nucleotides ('codon') in DNA or RNA codes amino acid. The hereditary code was deciphered by J. D. Watson and F. Crick in 1953. Sixty-four different triplets code 20 amino acids in accordance with some rules. Human genome includes about 3.3 x 109 pairs of nucleotides.

One of the most important processes in living organisms is a cyclic process of joint replication of DNA and proteins: nucleic acids store information about structure of enzymes, which, in their turn, catalyze replication of DNA.

RNA has some abilities to self-catalyze, and there is idea about 'RNA world' as one of the first steps of the life formation. The self-replication is not very reliable (1-10% of mistakes), and it is an explanation of forming modern catalytic replication (much less than 10_9% of mistakes), but natural selection of RNA could take place.

There are many other organic substances, extremely important for life: carbohydrates, lipids, adenosinepho-sphates, etc. Theories about 'sugar model' by A. Weber in 1997 or 'lipid world' by D. Segre in 2001 reflect the base role of these substances for life functioning. It is necessary to emphasize the fundamental role of the energetic molecules well-known as adenosinetripho-sphate (ATP). The beginning of cyclic reproduction of RNA or the system proteins DNA needed energy. A process of ATP synthesis, probably, preceded these cycles; from this point of view, ATP can be considered as the first molecule of life.

Organisms can produce most of the necessary chemical substances, although there are several dozens of them which should come from outside. All substances, especially proteins, are constantly destroying and synthesizing, renewing their composition.

Level of Cell

The next level of the life organization is a cell. Excluding some primitive forms, such as viruses, living matter is divided into separate cells. As an object of concentration of all coordinated chemical reactions of life, the cell must be big enough to be independent of fluctuations of the heat motion.

The simplest structure corresponds to prokaryotic cells. It contains only absolutely necessary parts -membrane, DNA, and cytoplasm - where chemical processes of protein synthesis (in special particles -'ribosomes'), energy production, respiration, reproduction, and others are arranged. This type of cells is used by bacteria, archaea, cyanobacteria, actinomycete, and others. Some parasitic forms of prokaryotes such as Mycoplasma, Chlamydiae, and Rickettsia lost certain cellular mechanisms.

The eukaryotic cells are much larger (10-100 times). They contain multiple internal 'organelles', including the 'nucleus' (storage of hereditary information), the 'mitochondria' and, in plant cells, 'chloroplasts' (energy transformation), 'lysosomes' (digestion), 'kinetosomes' (movement), 'cytoplasmic reticulum' (redistribution of chemical substances). The cell structure is represented in Figure 1.

Eukaryotes are the result of symbiosis: chloroplasts are progeny of cyanobacteria, mitochondria descend from bacteria, etc. Mitochondria, chloroplasts, and kinetosomes have their own DNA and can reproduce partly independently (using proteins, synthesizing by the cell). Coding of proteins in mitochondria is different from nuclear one. But all processes in cell are coordinated - it is a united complex system.

The cell is separated from the environment by membrane; its internal space is also divided by membranes into compartments. The fluid mosaic model of membrane defines a phospholipid bilayer with hydrophilic part from the outside and hydrophobic layer inside. Membrane proteins float in the phospholipids and control exchange of matter with the environment.

Chemical synthesis in the cell is a complex process with multiple feedbacks. Proteins are synthesized permanently, but only from active sections of DNA. Some sections can be repressed by special regulatory proteins, histones; to be active, they must be 'derepressed'. For starting synthesis, a special 'inductor' has to interact

11 10

11 10

Figure 1 The cell structure (1, the nucleus; 2, DNA; 3, nucleolus; 4, membrane; 5, cytoplasm; 6, lysosome; 7, mitochondrion; 8, cytoplasmic reticulum; 9, centriole; 10, pinocytic vesicle; 11, plasmid).

Figure 1 The cell structure (1, the nucleus; 2, DNA; 3, nucleolus; 4, membrane; 5, cytoplasm; 6, lysosome; 7, mitochondrion; 8, cytoplasmic reticulum; 9, centriole; 10, pinocytic vesicle; 11, plasmid).

with corresponding DNA section. Inductors and dere-pressors play information role (metabolites or hormones).

Information about protein structure is copied ('tran-scripted') to iRNA molecules and transported to cytoplasm, where it is processed by ribosomes. The ribo-somes move along iRNA and read the information, synthesizing simultaneously the protein from amino acids transported by tRNA molecules.

A post-transcription and post-ribosome regulation of protein activity can take place. Under the influence of enzymes, proteins can be chemically transformed: for example, proline is oxidized to oxyproline. Other enzymes, 'allosteric effectors' (hormones, adenosine monophosphate (AMP), etc.), can change tertiary structure of proteins, influencing on their active centers. Finally, such agents as 'inhibitors' can temporarily deactivate enzymes.

The presence of the number of ways of regulation gives a possibility to establish a complex and reliable 'cybernetic structure' of the chemical synthesis process in the cell. In a typical cell, there are more than 1000 systems of control for production of different enzymes. They are in permanent interaction. The simplest way is to use the reaction product as a repressor of own synthesis, or its substratum can play the role of its inductor; but often the scheme is much more complex.

For all single-celled organisms (and somatic cells of multicellular organisms), 'asexual reproduction' is typical. Simple cell division involves duplicating the genetic material and separating into the two ensuing daughter cells. The process is called 'mitosis' for eukaryotic cells, and 'binary fission' for prokaryotic cells.

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