book

energy, which is utilized in the chemical reactions leading to the synthesis of
carbohydrates. The biochemistry is extremely complex and is surveyed in the
specialized literature. The general equation is represented as follows:

As a result of photosynthesis molecular oxygen (O₂) is released into
the atmosphere raising gradually its content up to 21% in our day.
The accumulation of oxygen in the atmosphere has become the
prerequisite for the augmentation of the variety of living forms —
photosynthesizing bacteria, blue-green algae, fungi, plants and animals.
Only the first “earth inhabitans” — the anaerobic bacteria — have proved
suppressed by the increase of oxygen. Some of them have been wiped out
forever, some have adapted themselves as facultative anaerobes, and
others have found their ecological niche and have continued up to the
present day so as to “testify” to the far-off past when life has emerged and
started to develop.
The primary products (mainly glucose), formed in the light stage of
photosynthesis as result of a number of successive redox processes during
the dark stage, are converted into different sugar derivatives with the
release of energy used for meeting the energy needs of the cells and for
the synthesis of organic compounds, and in the end they are degraded to
CO₂ and H₂O. This problem can be generally presented in the following
manner:

Upon comparison of the two summed up equations of the process of
photosynthesis (assimilation) and the one of respiration (dissimilation) we
can be easily convinced that the law of preservation and conversion of
energy is strictly observed. This shows that living matter exists and
develops in the framework of the general laws for preservation and
alteration of inorganic matter, from which it has originated.
It can be stated with a great dose of certainty that photosynthesis has
not emerged at once and spontaneously in one living cell or organism but it
has gone a long evolutionary way. This assumption is based on the diversity
of the living forms capable of photosynthesis and the differences in the
mechanisms which they resort to for its accomplishment. A lot of them have
been treated in detail in the “Biochemistry” by A. Lehninger (1976).
Not only eukaryotes (higher plants, unicellular and multicellular algae,
euglens, dinoflagellates, etc.) are endowed with the capacity for
photosynthesis, but also some prokaryotes (blue-green algae, green and
purple bacteria) can do it. The purple bacteria are obligatory anaerobes.
They inhabit the soil and bottom of water basins (swamps, lakes, seas and
oceans) that are rich in hydrogen sulphide, sulphates and native sulphur. It
is accepted that one of the donors of electrons for the reduction of CO₂ in

The difference between the anaerobic degradation of sugars, i.e. the
fermentations (wittily called by Pasteur “life without oxygen”), and
respiration, which is only possible in the presence of oxygen shows that
oxygen has joined at a later stage when its content in the atmosphere has
risen. This is a clear and very convincing proof in support of the concept of
the earth origin and development of cells, since they have been in
dependence of its absence and later its presence in the earth atmosphere.

Figure 1–8. Scheme of anaerobic and aerobic degradation of sugars.

Due to the exhaustion of organic matter supplies (as are the conjectures
of some authors) or because of the increased metabolic capacities of the cells
as a result of the acquisition of new mechanisms and genetic changes, some
of the cells have reached up to photosynthesis. This has been a turning point
in the evolution of life on Earth and has unleashed a variety of forms of
unicellular and multicellular organisms. This process has become the main
source of organic substances both for the photosynthesizing organisms
themselves as well as for the non-photosynthesizing heterotrophs which have
adapted to their utilization as ready products.
The discovery of photosynthesis represents a fascinating story. It has
begun with the classical experiments of the English chemist J. Priestley
(1772—77) on the recovery of the air composition through the release of
oxygen by plants. Priestley has proved experimentally that a mouse if placed
under a glass lid can only survive in the presence of a green plant exposed to
light. At the same time Ingen-Housz (1779) has discovered that for the
accomplishment of this process the presence of sunlight is crucial and
Senebier (1782) has supplemented it with the participation of CO₂ from the air.
Further studies on photosynthesis have been carried out of a great number of
authors who cannot be mentioned in this short presentation of the problem for
brevity.
Undoubtedly photosynthesis is a biochemical mechanism that has
emerged later, by which organic compounds are synthesized from H₂O and
CO₂ at the expense of solar energy. Sun rays falling onto chlorophyll
molecules excite electrons which upon passing to a lower energy level release

heterotrophic behaviour. The higher on the evolutionary ladder, the more
complex metabolic pathways are found including new enzymes, cycles, etc.
The view that is prevailing in our day is that the first live organisms on
Earth were the methane-producing anaerobic bacteria also called archaic.
Some of the characteristics give grounds for that: a) typical autotrophs
which satisfy their needs from water, inorganic sources and CO₂ from the
atmosphere; b) they do not possess any biological means for protection
from atmospheric oxygen (O₂); c) they grow in a wide range of extreme
conditions such as temperatures over 90°C; d) they differ from the other
bacteria in the strongly “conservative” 16S ribosomal RNA (rRNA), which
shows that their evolution has followed a path of their own differing from
that of the others (Woese, Fox, 1977); e) they convert organic matter into
CH₄ and CO₂ (Abbanat et al., 1989).
At this early stage of cell evolution have also emerged cyanobacteria
known as blue-green algae (Chyanophyta). These organisms have the
capacity to fix CO₂ and N₂ from the atmosphere thus synthesizing more
complex compounds. Since the CO₂ and N₂ molecules are very stable and
a great amount of energy is needed for their conversion into a useful
metabolite form, chemical reactions have been greatly elaborated with the
inclusion of new enzymes, pigments and phases of the processes.
Nitrogen fixation capacity preserved in some bacteria and blue-green
algae is an interesting biological phenomenon which if implemented in
genetic engineering for eventual changes in the genome of higher
organisms could lead to a rise in yields from important crops. Besides the
classical type of nitrogen fixation characterized with tuber-formation,
associative nitrogen fixation also provokes great interest. In it the effect is
generated by the interaction of the nitrogen fixing microorganisms living in
the soil with the root rhisosphere of plants.
Accepting the anaerobic methanogenic bacteria as the first “inhabitants”
of the Earth renders an answer to two essential questions having a direct
relevance to the origin of life: 1) the atmosphere of the Earth in the early times
has been devoid of oxygen or its content has only been limited to insignificant
quantities; 2) the first organisms have been developing in the absence of
oxygen utilizing inorganic substances from the environment and CO₂ from the
atmosphere reduced by hydrogen for the synthesis of the organic substances
needed. That is why glycolysis in anaerobic conditions which is a chain of
chemical reactions effectuating carbohydrate degradation in the absence of
oxygen can be regarded as the most ancient metabolic pathway.
It must be noted that even in our day glycolysis is taking place in all
living cells, but the mechanisms have become two. The already mentioned
anaerobic one results in fermentation products (methane, alcohols or lactic
acid) and the other one — aerobic (with the participation of oxygen) where
carbohydrates (sugars) are degraded to CO₂ and H2O (Fig. 1–8).

deviations testify to the viewpoint that it has evolved from a simpler form
(when it has been encoding a smaller number of amino acids) to a more
complex one imposed by the evolution of living systems.
Based on the assumption for a smaller number of amino acids needed
for the ancient proteins and the one of the possibility for protein synthesis
without the participation of nucleic acids O. Ivanov (1989 b) has grounded
the idea expressed later also by other authors (Juckes, Osawa, 1990)
about the existence of a more ancient, simpler genetic code corresponding
to a smaller number of amino acids (the two first bases of the codon are
valid). Davydov (1989) has launched the idea for the existence of a reverse
genetic code i.e. a dependency between the structural and chemical
properties of the amino acids and the corresponding codons.
The publication of Kolyassnikov (1993), in which on the grounds of his
tetrameric model of water has suggested the hypothesis that water has
served as matrix for the polymerization of amino acids and nucleic acids,
has arisen a great deal of discussion. This idea of his is very attractive but it
needs serious proofs.
The exceptions pointed out give grounds for the conclusion that the
genetic code is not universal and has undergone an evolution from a simpler
to a more complex mechanism. The accumulation of more data and facts in
that respect would help to make clear the third “white spot” in biology.

Metabolism
The term metabolism (Greek: metabolé — change) denotes the exchange
of substances in living systems. This problem will be treated with the
intention of giving its development in retrospect and by no means
attempting to fully cover it, so as to mark the evolutionary path from the
cells since their emergence, trace their further development and their
incorporation into the more complex multicellular organisms.
In order to throw light on the issue a short review of the well-known facts
is needed. All cells are divided basically into two groups: autotrophic cells,
which can synthesize the organic compounds necessary for their functions
from inorganic substances and water using CO₂ from the atmosphere, and
heterotrophic ones, which are in no capacity to assimilate CO₂ and satisfy
their needs with organic products synthesized by other organisms.
Depending on the source of energy they are phototrophic — such using
solar light and chemotrophic — which use the energy derived from redox
processes. Besides, the cells are also divided into anaerobic, in which
metabolic processes take place in the absence of oxygen and aerobic, in
which they are accomplished with the participation of oxygen. Some of them
are obligatory anaerobes and respectively aerobes while others are
facultative ones, since they can exist both in absence and in presence of
oxygen. Metabolic adaptability is observed even in higher plants where the
cells containing chlorophyll are autotrophic and the ones of the roots show a

was obtained thus disclosing the first triplet (UUU). After that the codons for a
number of amino acids were established: AAA — for lysine, CCC — for
proline, etc. In this way the path leading to the in vitro synthesis of amino
acids, polypeptide chains (proteins) and genes (Khorana, 1979) has been
widely opened. Since these studies are strictly in the domain of molecular
biology they will not be discussed in detail.
As to the “age” of the genetic code it was determined by Eigen et al.
(1989) to not more than 3.8 (±0.6) billions of years, i.e. approximately the age
of the Earth, supposing the self-generation of life, if not transferred from the
outside world. The thesis supporting the extraterrestrial origin of the genetic
code is backed by F. Crick as shown in Section 1. 5.
The genetic code is assumed universal though it was basically
worked out on the well-known bacterium Escherichia coli. It must be
noted that it has attracted researchers attention mainly by posing three
great questions: 1) when has it arisen?; 2) is it universal?; 3) has it
undergone evolutionary changes or not?

T. Jukes (1973, 1990) considered the possibilities for an evolution of the
genetic code from a preceding form and has reported some exceptions to the
universal genetic code. They were initially established in mitochondria, then in
the nuclear codons of bacteria, yeasts, ciliated protozoa and algae. These

reproduction of living systems, since without them the peptides thus formed
would have been exhausted and/or eventually hydrolized.
The clarification of these issues is a necessary condition for
overcoming the second “white spot” in biology. Decisive roles in that can be
played by quantum chemistry and molecular biology.
What has been said up to this point shows that the argument about what
has arisen earlier — proteins or nucleic acids — is not meaningless. It is
difficult to conceive a scenario in which they have simultaneously come on the
scene at the time of a siutable structural organization, and as a result from
their interactions life has emerged. Such an approach makes the evolutionary
process meaningless. It is even more difficult to accept the dominant pioneer
role of nucleic acids that is imposed by some authors. Eigen (1973) is quite
right stating that there can be no “function”, if there is no “information”. But this
“information” is not necessarily due to be in the form of nucleic acid
macromolecules (Fox, 1975). As Bernal (1969) has very well put it “the picture
of a solitary DNA-molecule on the Ocean shore giving rise to the entire
ensuing life is less plausible than the one of Adam and Eve in the garden of
Eden”.
Is the Genetic Code Universal and Invariable?
The idea implying the existence of a genetic code has cropped up in 1953
immediately after the discovery of the spatial structure of DNA and its
determination as the sole bearer of genetic information. The necessity of
elucidating the question how the hereditary information incorporated in it is
transferred to the protein molecules enhanced interest in that field.
According to present day views the genetic code is the order of the
arrangement of the bases (respectively the nucleotides) in nucleic acids (see
Fig. 2–37 A, B) which determines the amino acid sequences in protein
molecules. Since amino acids building proteins amount to 20 and the bases
to 4, the first two variants of singlet and diplet codes were unacceptable. The
well-known physicist and mathematician G. Gamov (1954) has forwarded the
initial pattern of the triplet model of the genetic code in which one amino acid
is coded for by three nucleotides called triplets or codons. In that case
(4³=64) the number of the participating amino acids is exceeded. That is why
it was accepted that to each amino acid correspond several triplets which is
known as degeneration of code and some of the triplets not encoding
amino acids were named non-sense or stop-codons.
The discovery of the genetic code is a great achievement in biology
finalized by the composition of the code dictionary in 1965 (Table 2). A great
number of scientists have devoted their efforts to the study of the genetic
code such as the world famous F. Crick, A. Kornberg, S. Brenner, M.
Nirenberg, G. Khorana, S. Ochoa, etc. Its practical decipherment was begun
by the classic work of Nirenberg and Matthaei (1961) when an artificial
protein (polyphenylalanine) consisting of only one amino acid (phenylalanine)

of authors. Some of them find it unacceptable (Miller, Orgel, 1974; Orgel,
1987) while others point out the advantages of RNA molecules in their
metabolism and reproduction due to catalytic and autocatalytic properties
(Pace, Marsh, 1985; Zaug, Cech, 1986; Cech, 1987) that have been
foreseen by Woese (1967, 1968), Crick (1968), Orgel (1968), Sulston, Orgel
(1971). This has given grounds to Alberts (1986), Lazcano (1986) and Gilbert
(1986) to assume that there has never existed a prebiotic translation
synthesis of proteins and their reproduction and metabolism have been
dependent on the catalytic abilities of RNA molecules. Gilbert has forwarded
the “RNA World” as a possibility.
On the basis of a large number of studies — the proving of the central
role of the different RNA molecules in protein biosynthesis (Crick, 1968,
and others) which has led to the postulation that this process can be carried
out in the absence of DNA but is impossible without RNA (Spirin, 1986), the
existence of biological replicative systems such as the ones in the viroids
(Diener, 1982) and viruses (Reanney, 1982) that are using single or twostranded RNA molecules, the enzyme reduction role of ribonucleotides in
the synthesis of the deoxyribonucleotides (Sprengel, Follmann, 1981;
Lammers, Follmann, 1983) — a large number of authors have
independently expressed their view that RNA has preceded DNA as
genetic material and has played a great role in the biological processes at
the early stages of cell evolution (Lazcano, 1986, 1998).
These facts have led to the alteration of the postulated Central
dogma in biology established after 1953 with the Watson and Crick model
of DNA — DNA → RNA → protein into DNA RNA → protein. A twoway arrow has been placed.
Despite the great achievements of biology the opinion of many authors
(Alberts et al., 1986; Oró et al., 1990 and others), which is shared by the
author of the book, is that it is still quite unclear how exactly protein
biosynthesis takes place. This is especially true for the initial stages of the
existence of living systems when they did not have at their disposal the
complex mechanisms of synthesis and reproduction that have emerged later
and have established themselves in the evolutionary process at the cell and
organism level. This problem will be treated again in Chapter 2, Section 2. 7
(Proteins).
Since by now there is no clear and convincing scheme about the ways
and mechanisms by which the abiotic formation of the monomers was
effectuated through the “lucky combination” of the atoms and their conversion
into polymers as well as there are no data about the exact timing of the
emergence of replication and translation in the biological systems, the problem
of the origin of life remains still unclear. Most justly Oró et al. (1990) conceive
the origins of replication and translation as “two major unsolved problems”.
According to the authors these mechanisms are of crucial importance to the

Figure 1–7. “PRION” supplement to the Central dogma in 
biology (After Kordyum, 1990). 

The “mad cow disease” has proved to be a condition of this kind and has been
registered for the first time in 1985. The fears arisen from its wide spreading in the
world and the link between it and its human equivalent — the Creutzfeldt—
Jakob’s syndrome first described in 1920, made the EU (European Union) introduce
on March 25th 1996 a ban on the imports of meat and later on meat products from
such animals used as supplement toanimal feed.
What is essential in the case of prions i.e. the infectious proteins is that
they self-reproduce in a manner — distinct from the normal pathway encoded
by DNA or RNA, which is unknown for the present. Judging from the
descriptions in the literature on the etiology of the diseases caused by them
— their rapid accumulation in the brain of the diseased animals as long
strands, their resistance to UV-irradiations and proteinases, the failure to
induce an immune response and in some cases lack of antibody
production, their highly lethal impact (up to 100 %) as well as the non-mandatory
presence of the prion itself or its gene for initiation of synthesis,
it can be conjectured that these are “remains” from the primeval (ancient)
long-stranded proteins that are implicated in the studies of Ivanov (1978 a—c).
Most probably the discussions on this key problem will go on since it has
bearing on the mechanisms involved in the pre-cell evolution. In a review
article Weissmann (1991), after acknowledging the availability of convincing
proofs that the transmitter of the encephalopathies, scrapie including is a
modified normal prion in the host devoid of nucleic acids of any kind,
undertakes an attempt to reconcile the supporters of the purely protein nature
of prions and the ones looking for obligatorily participating nucleic acid as a
cause for their self-reproduction. He has forwarded a model of his own in
which the two extreme hypothesis are combined — “pure protein” and a
“nucleoprotein”.
In his book De Duve (1991) “Blueprint of a Cell: The Nature and Origin
of Life” has launched the idea that chemical evolution has led to the
creation of a protometabolism, catalyzed by oligopeptides formed prior to
the emergence of the replication and translation mechanisms. This idea of
his was subjected to severe criticism by Cavalier-Smith (1991).
The expressed opinion that primeval replication mechanisms have
existed in polypeptides (see again Dose, 1974; Fox, Dose, 1977; Dyson,
1982; Kauffmann, 1986) has encountered serious objections from a number

synthesis with the proto-ribosomes must have arisen in exchange with the
heterotrophic pre-cell formation of primary proteinoids”.
Of certain interest are the studies of Ch. Ivanov and O. Ivanov (1973—
93) on the possibility of proteolytic shortening of the long-chain ancient
proteins (built from a smaller number of amino acids bound on the basis of
preference towards structurally and functionally similar amino acid, as a result
of which short-chain proteins or fragments are obtained that are able to
combine among themselves until reaching functional sufficiency) to have
played an important role at the earliest stages of protein evolution. Thus, the
tendency in the molecular evolution of proteins from the ordinary amino acids
(gly, ala, pro, arg, val, leu, asp, glu, ser, thr) to the specialized ones (asn, gln,
lys, his, ile, met, cys, phe, tyr, trp) was revealed (Ivanov, 1989 a, 1993).
Recently, the problem and respectively the discussions on prions has
provoked considerable interest. The term was suggested by S. Prusiner
(1982) for designating the transmitter of the scrapie disease (proteinaceous
infectious particles) that has inflicted heavy damages on sheep and goat
flocks around the world and Scotland in particular. Based on studies of his
as well as on data of other researchers, the author implies two possible
models of the agent’s structure: a minute nucleic acid thickly wrapped in a
protein capsule, or a protein free of nucleic acids i.e. an infectious protein.
In his view this protein acts as an inductor or a matrix for its own synthesis.
It is now accepted that prions or the infectious proteins are the cause of
certain typical diseases such as Creutzfeldt—Jakob’s and the Gerstmann—
Sträussler—Scheinker’s syndromes in man and some encephalopathies in
animals characterized with a high lethality rate. Sometimes they develop very
rapidly and death comes within several months.
In a disputable article Kordyum (1990) after analyzing the data from
investigations on prions motivates his proposal, that as a supplement to
the widely-known type the genetic coding in the form of primary sequence
of nucleic acids there exists another form of biological information transfer
which is the spatial structure of proteins capable of self-reproduction (Fig.
1–7). “It is found — states the author — that pure protein molecules
without the presence of nucleic acids are capable in some way to ensure
in the cell their own multiplication, accumulation and realization of the
pathological process and have the capacity when invading a healthy
organism to carry out this cycle from the beginning”. According to his data
there are six typically prion-induced disorders known by now, but he
admits that their diversity might be greater. The presence of prions in
yeasts and their wide spread in nature is supported by other authors
(Vogel, 1996; Patino et al., 1996).

Besides, as it will be shown later they are the main constituents of
chromatin in the chromosomes — bearers of heredity and instrument for
distributing genetic material in cell divisions.
In the Prologue of the Russian translation of the remarkable book
“Molecular Biology of the Cell” Alberts et al. (1986) have noted: ”When the
dominating role of DNA has already been established, the feeling cropped up
that upon understanding the structure and function of nucleic acids we have
comprehended the essence of the living state and that the greatest mysteries
of biology have been unveiled… This view is not however shared by us”.
The stated by the authors of the book conforms with the existing
understanding of the exceptional intricacy of life whose “secrets” are so deeply
encryptioned that is impossible for many of them to be yet deciphered. In the
search of ways and approaches for their disclosure only two issues that are of
vital importance for the “white spots” erasure will be considered.

Can Proteins Self-Reproduce?
Let the posing of this question not raise alarm. Its importance lies mainly in
the initial stages of biological evolution. Some authors tend to leave it
without the due consideration, while others would state their outright
dissent. Being raised in the same categorical manner in the
above-mentioned book of Eigen (1973) it has got a negative answer. And yet, at
the end of his conclusion the author has remarked: “As far as proteins in
their being self-reproductive molecules display advantages as well as
shortcomings this problem ought to be surveyed in a greater detail”.
The slightly open door left by Eigen lets in those who share an opinion
differing from the one imposed by the so-called Central dogma in biology
that has postulated the dominant role of nucleic acids in protein synthesis.
For example, the easy obtaining of amino acids and their polymerization in
conditions resembling the prebiological ones existing on the Earth has led
some researchers (Dose, 1974; Fox, Dose, 1977; Dyson, 1982; Kauffman,
1986) to the idea that primitive replication mechanisms have existed in
polypeptides.
In another article Fox (1975) forwards the following scenario for the
initial steps of the primary living systems: “At the initial stage the question is
posed in the following manner: which information molecule has cropped up
first? It is not obligatory for the macromolecule to be a nucleic acid in order
to be an information one. Experiments at high temperatures give an answer
to this question: proteinoids (not proteins) are primary since as such
polymers they have possessed a high inner orderliness and catalytic
activities as well. The proto-cell formed by such a polymer would have been
capable of self-reproduction at the pre-cell level. Proto-nucleic acids have
emerged at a second stage. They have bound to the basic proto-proteins
(proteinoids) thus forming proto-ribosomes. At the third stage proteins and
nucleic acids have been formed approximately at the same time. Protein