RNA World hypothesis

Amongst the four basic biomolecules are the proteins and the nucleic acids: DNA, RNA: that play a vital role in the biochemistry of a cell. DNA is the storage of information that encrypts for RNA which is then translated into proteins: the work horses of the cells. Yet in both transcription and regulation of gene expression processes, DNA requires the aid of various proteins ^(I). This fascinating interaction in between these three bio molecules leave abiogenists with the question ‘Which of these molecules appeared first in the primordial soup 3 billion years ago, to form the first life form or the common ancestor from which all typical cells nowadays are believed to have evolved from?’ ^(II) RNA world hypothesis is one of the possible explanations which was first suggested by Francis Crick, Carl Woose, Leslie Orgel (1968) ^(III) ; yet the term “RNA world” was introduced by Walter Gilbert in 1986^(IV).

As predicted if RNA is the first to appear, it should demonstrate properties of all these three molecules. With the discovery of catalytic RNA or the ribozymes it was proven possible that RNA can perform enzymatic activities like proteins. (Thomas R. Cech 1980)^(V) Also varieties like the hammerhead ribozyme which has the ability to perform self cleavage, would have contributed in inventing new nucleotide sequences that might have created diversity within the RNA world. ^(VI) Ribozymes and riboswitches would have contributed in gene regulation instead of proteins. ^(VII) Ribozymes act as auto catalysts of self replication which makes it possible for RNA to create more copies of its own sequence just as DNA. If we consider the building blocks of the nucleic acids they differ only in two ways; either due to the presence of the 2’OH in the sugar molecule or due to the presence the base thymine or uracil. Other than that the chemical composition is likely to be similar which would give RNA the ability to store information like DNA. Also in the Fisher-Tropsch experiment it was found that only adenine, guanine, cytosine and uracil could be produced under the conditions of the pre biotic atmosphere. Creation of thymine wasn’t expected because it required methilization of uracil which wasn’t possible at that time. ^(VIII)

How was DNA and proteins first created? rRNA, one of the major components of the ribosomes, is always involved in the assortment of amino acids in order to form peptide linkages to create proteins. In the same manner it may have begun protein synthesis. With reverse transcriptase cDNA can be produced; and still the central dogma of molecular biology is secured. (Francis Crick 1958)^(IX) Likewise during evolution DNA would have formed.

Then the question comes; why was RNA replaced by proteins in catalytic tasks while DNA became the dominant molecule of heredity? The vast chemical diversity among the amino acids due to different functional groups, allow proteins to step ahead of RNA in reactivity properties. Higher reactivity provides more advantages for a catalyst and thereby proteins may have evolved to be the biocatalysts. The RNA molecule is destabilized by base induced deprotonization of the 2’OH in the ribose sugar component of the nucleotides. As it will not occur in the deoxyribose in DNA, it’s considered prior to RNA in stability. Therefore flow of information via DNA is favoured in highly organized species. ^(X) But still the idea of RNA world remains a hypothesis as it has to compete with other suggestions such as ‘Iron- Sulfer world hypothesis’, which are also put forward to explain the origin of life.

References:

• I. Garette, R., Grisham, C. (2003). Nucleotides and nucleic acids. 3^rd ed: Biochemistry (328). USA: Brooks- Cole publications
• II. Horten, H.R., Moran, L.A., Scrimgeour, K.G., Rawn, J.D.(2008). Introduction to biochemistry. 4^th ed: Principles of Biochemistry (114). USA: Pearson publications
• III. Cox, M.M., Nelson, D.L., (2008). RNA metabolism. 5^th ed: Leninger: Principles of Biochemistry (1057). NY: Freeman and company.
• IV. Gilbert, W. (1986, Feb.). The RNA world. Nature, (618):319
• V. Cox, M.M., Nelson, D.L., (2008). RNA Metabolism. 5^th ed: Leninger: Principles of Biochemistry (1033-4). NY: Freeman and company.
• VI. Voet, D., Voet, J.G., Pratt, C.W., (2008). DNA structure and interaction with proteins. 3^rd ed: Principles of Biochemistry (870). NJ: Wiley & sons, inc.
• VII. Cox, M.M., Nelson, D.L., (2008). Regulation of gene expression. 5^th ed: Leninger: Principles of Biochemistry (1133). NY: Freeman and company.
• VIII. Murey, R.K., Granner, D.K., Mayes, P.A., Rodwell, V.W. (2003). Metabolism of purines and pirimidines. 26^th ed: Harper’s Illustrated Biochemistry (301-2). USA: McGraw Hill Companies.
• IX. Berg, G.M., Tymoczko, J.L., Stryer, L. Exploring genes. 5^th ed: Biochemistry(258)
• X. Voet, D., Voet, J.G., Pratt, C.W., (2008). DNA structure and interaction with proteins. 3^rd ed: Principles of Biochemistry (871). NJ: Wiley & sons, inc.
• Exploring Life's Origin
• The RNA World
  

The Big Bang- 3

Origin of stars.

By the time the universe was 200 million years old and its temperature had dropped so fast that it was around -220⁰C. (H atoms bond together to form H₂ molecules now.) When the early universe emerged from the Big Bang it was uneven. It contained cracks which were filled in with swelling clouds of dust and gases such as H₂ to form nebulae. Let's see what nebulae are; A huge cloud of gases and dust in the intergalactic space is called a nebula. There are various types of nebulae such as;

• Ring Nebula

• Reflection Nebula

• Emission Nebula
  

• Planetary Nebula
  

• Stellar Nursery

These stellar nurseries give birth to proto stars. As these huge dusty gaseous clouds pull over together due to gravitational forces the clouds shrink and make a proto star. The temperature rises when the rate of collision increases as the clouds get denser. The contraction stops when the pressure is equal to the gravitational pull. Then it has two options: one is to become a brown dwarf star if the temperature needed to accelerate nuclear fusion is not reached. If it does, nuclear fusion would start over in the core. H₂ is the most abundant of all gases, so two ionized H⁺ s { Due high temperature of the core, H₂ molecules would be ionized to H⁺/ protons} would fuse together to form He. With the emission of the heat and radiation (energy) from the nucleosynthesis (nucleosynthesis: the process by which nuclei of chemical elements are formed) a star is born.

The formation of the alpha particle

(H) 4 p⁺ → 4 He²⁺ + 2e⁺ + energy( E=mC²)

This process of burning hydrogen is known as the main sequence. A star occasionally spends 90% of its life time in main sequence. When the primary burning of H₂ is over the star reaches its older age.

The duration of the death of the star depends on the initial mass of the star. Larger stars have more fuel, but they have to burn it faster in order to maintain equilibrium. Because thermonuclear fusion occurs at a faster rate in massive stars all of their fuel is used during a comparatively shorter period of time. This means that bigger is not better with respect to how long a star will live. A smaller star has less fuel, but its rate of fusion is not as fast. Therefore, smaller stars live longer than larger stars because their rate of fuel consumption is not as rapid.

When a star has used up all its H₂ then He comes to picture. As most of the H₂ is used up there’s not enough pressure to balance the gravitational force and the core starts shrinks again. When the star regains enough pressure to start fusion of He atoms production of carbon and other light elements begin. Once ignited, helium burns much hotter than hydrogen. The additional heat pushes the outer layer of the star out much further than it used to be, making the star much larger.

3 ⁴He → ¹²C + energy

With the entire He gone the lower mass stars (<.5 Solar Mass) can’t get C atoms to fuse together. They exit creating explosions called planetary nebulae and collapse into white dwarf stars.

Massive stars (> 3 Solar masses) utilize carbon burning. It was Sir Fred Hoyle who determined that stars acted like nuclear reactants producing elements heavier than H and He. Fusion reactions inside these stars release enormous amounts of energy and heat which force more atoms to fuse and create new heavier elements one after the other. Three He nuclei combine to create C, two carbon nuclei fuse to form Mg, Mg formed Ne and so on. This continues until silicon finally fuses to form iron. And the process is called stellar nucleosynthesis.

Iron is a very special atom because ⁵⁶Fe has the most stable nucleus of all. Within the nucleus there are energy levels, it’s considered stable when the no of protons and neutrons are equal inside the nucleus and they are tightly bound together so that the extreme temperatures within the stars couldn’t get it to fuse together to form newer elements. Production of elements would shut down when they reach iron.

²H⁺ + ⁴He²⁺ → other elements { ¹²C, ¹⁶O, ²⁰Ne, ⁵⁶Fe} All are multiples of He

Still some of the vital elements were missing; elements that are heavier than Fe. A higher mass core in medium mass stars would create neutron stars while bursting into supernovas. When the giants stars, which had already made the lighter elements, run out of fuel their cores collapse on themselves creating incredible amount of energy in enormous explosions called supernovas. These are so powerful that they are able to fuse elements heavier than iron. This is called explosive nucleosynthesis. This is the point where most heavy elements such as uranium origin.

Basically stars can be categorized as below:

• First generation stars: Mostly red dwarf stars which are still in the main sequence burning its primary H and He. They consist of only H and He (perhaps Li) as elements.

• Second generation stars: giant and super giant stars which consist of lighter elements from C to Fe. Our sun is a second generation star.

• Third generation stars: The stars which undergo supernova explosions and later turn into either neutron stars or black holes. Most blue giants are in this category.

Together these elements formed smaller bodies which orbit around the sun that later developed into planets and asteroids.

Earth is the next post to come :) TC

The Big Bang- 2

Have you ever thought where all these atoms which are the building blocks of almost everything come from? All these are results of the Big Bang: the left over excess matter after the antimatter (positrons/ anti protons)and the matter annihilated. This is what happens when matter and anti matter particles collide on to each other.

The result of the annihilation of the electron and positron creates gamma ray photons or at higher energies other particles:

e⁻ + e⁺ → γ

During a low-energy collision, proton-anti proton annihilation usually produces a collection of pions or related light mesons. High-energy particle colliders, like the tevtrons, sometimes collide protons with anti protons at very high energy and these collisions can produce a long list of heavy particles.

(Source- Wikipedia)

At this stage the universe was 0.7 billion years old and consisted of subatomic particles smashing into each other due to the high temperature the universe held. Then as time passed by the expanding cosmos cooled sufficiently enough for the protons and the neutrons to bind together with the help of the nuclear forces to form the first atomic nuclei H and He.

p +n → ²H⁺ nucleus (deuterium)

2p +2n → ⁴He²⁺ nucleus (alpha particle)

But still there weren’t proper atoms with missing electrons because the heat and the energy of the hot baby universe provided the electrons great amount of kinetic energy that it could not exist stably bonded to the nuclei. It took nearly 3.8 million years after the big bang to reach the temperature suitable to the creation of complete atoms. From the beginning the universe was in total darkness where light was trapped inside a thick fog of fast moving electrons. The drop down in temperature reduced the energy of the electrons and slowed them down, finally ready be bonded to create the firet atoms. This was called the Big Bang nucleosynthesis. As the dense fog was reduced with the decreasing number of unbound electrons light was released. Overtime this burst of light dimmed and cooled losing energy to become microwaves. This faint microwave radiation was picked up by Prof. Arno Penzias and Robert Wilson in 1963 which marked the critical moment of origin of the first atoms.

But the world we live in nowadays consist of more than 100 elements. Without the other elements there’s no chance for us to exist, not even planets and galaxies. To form the others the H and the He atoms had to fuse together somehow. But how exactly? To do this stars came in to picture.

See you in the next post with stars.