BIOLOGY

ORIGIN OF LIFE: PART 1

Nothing in biology makes sense except in the light of evolution(Theodosius dobzhansky)

It is not the strongest of the species that survives ,not the most intelligent that survives,it is the one most adaptable to change(Charles Darwin)

 Primitive earth and biomolecule formation

The conditions in primitive earth was very different from today. The oceans and continents had formed. However the surface of earth was exposed to a number of high energy phenomena. It was constantly bombarded by meteorites ,which may have contained biomolecules. There being no ozone layer the surface of earth was exposed to UV rays which hastened chemical reactions.Volcanic lava and underwater hot springs were sources of energy for chemical reactions. All these favoured rapid chemical reactions. The earth was formed four and half billion years ago. The atmosphere was reducing and contained methane ,carbon dioxide besides water. These underwent rapid reactions to produce sugars .amino acids , Hydrogen cyanide, and some nucleotides. Probably the entire earth at one time was covered by these biomolecules

  Rise of probionts

Due to the plentiful supply of biomolecules on earths surface it gave rise to a strong gradient favouring formation of some biomolecules which could utilize them. They were called Probionts. A single RNA polynucleotide even if formed by chance in this ocean of biomolecules could increase in number by complementary recognition of purines and pyrimidines. Though the process would be slow in the absence of proteins and enzyme catalysis ,due to their stability the RNA molecules would increase in geological time. They could have been helped in this by random amino acid polypeptides.

Rise of RNA world

Apart from complementary chain formation RNA molecules have catalytic properties also.Just like protein  molecules RNA molecules can fold and have secondary and tertiary structure through hydrogen bonding. This creates a 3dimensional active site within the molecule. It can increase the rate of a reaction if the reactant molecules have a 3dimensional configuration matching the active site.

   Primitive RNA molecules had varied random primary sequences of nucleotides. Eventually they gave rise to a number of active sites for catalysis of reactions.One of them was breakage and lysis of RNA nucleotides. This catalytic property allowed cooperation of a number of RNA molecules. RNA molecules triplet nucleotide sequences could be recognized by rRNA. A  complementary sequence of triplet nucleotides could be brought by a t RNA to the site to construct  a nascent RNA strand.The rRNA could ligate the triplet nucleotides and lengthen it.All this allowed replication of RNA strands faithfully.

   The cutting and ligation functions of RNA represents the basics of the RNA world of replicators.However the catalytic  properties of RNA is much less than that of proteins.There was eventually the rise of a protein catalytic world . The ribozymes of RNA world could carry out many metabolic functions. In this they were aided by NADH,ATP most of which are nucleotides.

Discovery of translation and protien synthesis

Initially the RNA world was geared up for replication of RNA.The tRNA used to bring triplets of nucleotides to rRNA had a tail in the molecule. This tail could reversibly   attach amino acids. Probably this attachment changed the configuration of entire tRNA and helped in delivering the nucleotides. Over a period of time two tRNA carrying two amino acids  lying side by side on the rRNA ,underwent a ligation reaction. This catalytic  function was acquired by the rRNA and even today it remains the same.With this new function the amino acids could be reliably chained to form polypeptides.

   Gradually the rRNA and tRNA cooperation became targeted to creating polypeptide chains rather than replicating RNA. This was the origin of translation. Now r RNAread a m RNA triplet and the t RNA functioned to bring an amino acid to it by complementary reading. Each tRNA became specific to read a different triplet nucleotide sequence. Also for a different triplet a specific amino acid was added by a tRNA This was the origin of the genetic code. 

  As translation was established specific mRNA served as template for polypeptides. In addition these polypeptides developed tertiary active sites. Some of them catalyzed rRNA and others tRNA function and made these reactions much faster.

Origin of cell membrane,energy transduction and metabolism

Today in prokaryotic cells the entire genetic machinery remans attached to inside of cell membrane This fact gives a hint to the relationship between them in protocells . The primitive membrane may have been wholly made of proteins as lipids were not readily present on the primitive earth. Later on lipid membrane may have arisen by incorporation of lipids as the protocell became better at synthesizing them through metabolism. The primitive membrane initially served as an anchor for RNA molecules as they replicated by cooperation among themselves.Later ,probably after incorporation of lipids it turned into a spherical shape . This brought the RNA machinery inside a protocell  still attached to  the cell membrane . 

        The chief advantage of a membrane bound cell would be that reactants and products of metabolic reactions would stay in proximity allowing predictable reactions. The major problem for the replicators would be now to access energy and nucleotides from outside the membrane. The newly acquired protein  catalysts would help in both.The cell membrane got incorporated by a protein  enzyme,ATP cyclase.This protein can pump hydrogen out of the cell and create a proton gradient across it.This energy of protons can be converted by other proteins catalysts like NADH and ATP by creating high energy covalent bonds. Ultimately these molecules supply energy to the chemical reactions of nucleotide and protein synthesis.

    The other problem of obtaining nucleotides and amino acids from outside the membrane was also solved by carrier proteins . These could bind to substrates reversibly outside and realease them inside the cell. Over a period of geological time the  natural synthesis of amino acids and nucleotides became less on the primitive earth. However the environment of earth still had various inorganic substrates such as carbon dioxide, methane,hydrogen cyanide,water,nitrogen. The enzymes now cooperated to form metabolic chains for chemical processing. Probably the earliest was the glycolysis chain .Here sugars transported across the membrane was broken down by a series of reactions to generate ATP for the cell. Thereafter synthetic reaction chains for nucleotides  and amino acids were invented.The protocell  could now get energy from sugars in the environment. The synthesis of nucleotides and amino acids was also independent of the environment

   However with changing environment the supply of sugars also diminished. This was a major challenge for the protocell. Fortunately photosynthesis arose where a series of enzymatic reactions could convert energy of sunlight first into a proton gradient Subsequently another reaction series synthesiszed sugars fromcarbon dioxide and water.

  Ack:A world from dust,organic and biological chemistry(Stephen stoker),An introduction to systems biology(Uri alon))The evolving universe and origin of life ,Thespark of life-Darwin and the primeval soup,Beginnings of cellular life,