Some organic chemistry, simplified

Types of elements used in life

  • the four elements HCNO comprise 95% of living matter
  • these elements are relatively abundant in the universe (recall stellar nucleosynthesis), therefore the basic composition of life is not itself a barrier
  • these elements have chemical properties which make them advantageous for use in life
  • carbon can form four bonds
  • carbon bonds with CNO are fairly strong
    • C-N, C=N, C-O, C=O
  • oxygen readily reacts with carbon
  • both O and N exist as gases in the atmosphere which allows them to cycle through the environment (in solid and liquid form)
  • the abundance of "other" elements in life (e.g., calcium (Ca), phosphorus (P)) resembles the abundance in sea water; this observation suggests that life arose in the oceans
  • these elements are used in small proportions and serve very specific functions, e.g., zinc (Zn) in insulin and iron (Fe) in hemoglobin, copper (Cu) in hemocyanin.
    • indicative of a complex interaction between life and the environment

Molecular Structures

  • life (1) stores and (2) transmits genetic information using polymers
  • a polymer is a molecule consisting of the repeated pattern of a small unit, where the units are called monomers
    • example: A-A-A-A-A-A-A is a polymer of the "A" monomer
    • example: A-B-B-A-B-A-B is a (generalized) polymer, and both A and B are monomers
  • amino acids are the monomers used to construct polymers called proteins
  • these polymers store and transmit information by varying (1) the elemental composition and (2) the structure (or shape) of the molecule
  • shape
    • the shape of a polymer can aid (speed up) chemical reactions that would otherwise occur slowly
    • these aids are called catalysts
    • in life processes, catalysts are called enzymes
  • life shows a high degree of selectivity in the compounds it uses and in the shape of those compounds, for example:
    • only 20 amino acids are commonly used out of the infinitely many possible
    • Biochemists describe the shape of many molecules using "handedness", or "chirality". It described two molecules that are identical, except that one is the mirror image of the other. Therefore, the two molecules cannot superimpose upon one another exactly (try it using your left and right hands).

      One chirality is named left handed, and one is right handed. Biochemistry on Earth uses left handed or L-amino acids and right handed or D-sugars. The chiral organic molecules that have been detected in space so far have been 50% left and 50% right handed. These two observations mildly suggest that all life on Earth has a common origin, and that extraterrestrial organic molecules are not biological.

      Chirality in molecules seems like a small thing, but in fact it is vitally important. A popular example is that of the artificial sweetener, aspartame. The right handed version tastes sweet, but the left handed version tastes bitter.

Reproduction at the molecular level

  • reproduction relies upon DNA and RNA polymers
    • DNA = deoxyribonucleic acid
    • RNA = ribonucleic acid
    • DNA and RNA are not directly involved in the reproductive process, rather, they act as intermediaries
  • DNA (1) stores genetic information and (2) oversees the construction of proteins
  • genetic information tells the next generation how to grow, reproduce and carry on with life activities
  • DNA is in the shape of a twisted ladder, called a double helix, whereas RNA is a one-sided or single strand molecule
  • the backbone of the ladder is made up of monomers called nucleotides
  • a nucleotide is a molecule containing:
    • sugar (ribose or deoxyribose) + phosphate (PO4) + base
    • "base" as opposed to an "acid"
  • there are four bases:
    • adenine (A)
    • guanine (G)
    • cytosine (C)
    • thymine (T)
  • There is a fifth base called uracil (U) that is used instead of thymine by RNA. Other bases are possible, but they are not used on Earth. Maybe they don't work as well, or maybe A,G,C,and T/U were "good enough".
  • the rungs of DNA are made of two bases, called a base pair
  • the base pairs cannot link randomly, rather, only A-T and G-C pairs are possible, called complementary base pairing
  • DNA carries information via the order of bases along its length

Manufacture of proteins

  • DNA also contains all the information needed for manufacturing proteins
  • DNA uses three adjacent bases as a single unit called a base-triplet or a codon to encode how proteins are manufactured (three of ACGT, e.g., "AAC")
  • each amino acid bonds to a single base-triplet, and the sequence of base-triplets determines the sequence of amino acid monomers, which as a unit determines the type of protein that is manufactured
  • in other words, the base-triplets determine which amino acid is placed in a protein
  • a base-triplet can have any of the 4 bases, for a total of 4x4x4 = 64 distinct amino acids that can be encoded
  • life uses only 20 amino acids
  • the remaining (extra) base-triplets are used for redundancy and three are used as a "stop" command, to identify one terminus of the protein
  • DNA directs the manufacture of proteins that use between 100-500 triplets of bases
  • Sequences that are significant to the organism are called genes. When first discovered, it was thought that a gene is a portion of the DNA molecule that directs the manufacture of a single protein - the phrase "one gene, one protein" became a popular mnemonic device. Today we know that this is not strictly true, in that there are single proteins that are manufactured by genes acting together.
  • by splitting down the middle, DNA replicates itself "exactly" due to the unique pairing ability of the nucleotide bases, A-T and G-C
  • DNA serves as the blueprint for protein synthesis
  • DNA forms RNA, which is a "working copy" of the gene or protein it wishes to produce
  • the RNA is recognized by a ribosome, which translates the RNA message into a protein using the base triplets, the ribosome is therefore the actual site of protein synthesis
  • a ribosome is not a molecule but a granule (i.e., a clump of molecules) that serves a similar function in cells that organs do in animals
  • RNA replaces thymine (T) with uracil (U) in its structure

RNA World Theory

  • RNA resembles a single strand of DNA, i.e., a "half ladder" (DNA split down the middle)
  • RNA can catalyze itself, or act as its own enzyme in reproduction (DNA can't because it is normally wound up.)
  • researchers think that RNA came first in our evolutionary sequence, the RNA world theory
  • a branch of current research explores the formation of RNA

Mutation

  • sometimes there is a change in the sequence of nucleotide bases, a mutation
  • causes -
    • high energy photons
    • high energy particles (cosmic ray particles)
    • chemical agents (mutagens)
    • error in the DNA copying mechanism - somewhat rare
  • the error causes an incorrect amino acid to be entered into a protein
  • there are two basic types of mutation, a point mutation and a frameshift mutation
  • a point mutation is the substitution of one nucleotide for another, whereas a frameshift mutation is the addition or deletion of a nucleotide, setting everything after that out of sync.
  • in either case, the sequence of base pairs is changed but the molecule remains intact, allowing the construction of a different protein
  • many mutations are neutral, but some will harm or help the organism
  • "help" means "more successful in reproduction"
  • over time, favourable mutations will dominate the genetic material of a species, a process called natural selection

How can all this complexity arise out of random reactions?

  • Problem: The Second Law of Thermodynamics states that the total disorder (called "entropy") of any closed system must increase with time, but Earth seems to have done the opposite.
  • Earth is not a closed system. It is receiving energy from the Sun. The entropy of the Solar System as a whole is increasing.
  • In a random set of complex molecules the ones that will proliferate will be, by definition, the self replicating ones, while the others will fall by the wayside.
  • It is possible to get ordered motion out of disordered motions. Consider the rachet or this system:

    Thermal motion (random motion due to the presence of heat) jiggles the surface every which way, but with no net direction. A molecule resting in one of the grooves will get thrown up with a 50% chance of going either left or right a bit before it falls back to the shaking surface. If it goes right, it lands in the next groove and rolls to the bottom. If it goes left, it lands in the same groove and rolls right back to where it started! Only the right jumps have a permanent effect, and the molecule receives a mean rightward velocity from random pushes.

Miller-Urey experiments

  • these experiments, named after the original researchers who performed them, try to recreate the conditions of Earth's very early history
  • they take an enclosed mixture of methane, ammonia, hydrogen, and water gases and provide it with a source of energy, like heat or electrical discharges
  • the gases are cycled through liquid water
  • after a short time, there is the production of many organic molecules including amino acids
  • more carefully controlled conditions show the production of sugars
  • There has been no production of DNA or RNA (yet?). Current experiments suggest that the holdup is the ribose molecule, which appears to be tough to produce. Maybe the first life used a protein backbone to hold its base pairs and then produced ribose later, the so-called PNA world theory.
  • the production of long polymers may depend upon the specific environment
    • for example, clays might be important since they are composed of fine grains with large surface areas
    • organic molecules readily stick to these grain surfaces
    • the grain surface might be stable enough to help potential monomers to come together to form long chains
    • the monomers are free-floating initially, probably in water
    • in fact, shallow, warm and still water might be the best environment
    • this type of environment is provided by tide pools
  • so we have come full-circle, both starting and finishing with some mention of the significance of water