Freelance Traveller

by Robert O'Connor

From Building Blocks to Biomolecules

Simple molecules - for example sugars, amino acids and nucleotides (purine or pyrimidine [nitrogen-containing] bases joined to phosphated sugars) - can join together to form polymers.

Polymer formation is relatively easy to induce. Heating of dry organic compounds can lead to polymer formation, as can catalysis by a wide range of substances e.g. inorganic phosphates.

These compounds would initially be completely random in their structure. Polynucleotides can act as templates for further polymerisation reactions, e.g.:

where A = adenine, C = cytosine, G = guanine, U = uracil and * represent hydrogen bonds ('weak' areas of relative negative and positive charge).

A can only link weakly with U and C with G due to the shapes of the molecules and the distribution of charge.

This process, called complementary templating, is the basis of genetic information transcription in all terrestrial organisms.

Polynucleotide chains will adopt unique three-dimensional shapes depending on their sequence. Such molecules have been demonstrated to exert catalytic activity on other molecules and the ability to copy themselves.

With time, errors would arise in the copying process, leading to new molecules being produced. Given an initial set of conditions, a group of 'replicators' would have eventually dominated the environment. One presumes the fastest, most accurate and most stable replicators prevailed.

Nucleotides are limited however in the variety of reactions they can catalyse. The potential number of amino acid polymers - proteins - is much larger, simply because there are more amino acids to choose from. [Note that even though twenty amino acids and five nucleotides make up almost all of those found in Earthly life, the number of possible amino acids and nucleotides is almost endless].

The number of possible sugar polymers [carbohydrates] is larger still. Consider this: eleven chemically distinct compounds can be created from two molecules of glucose. The variety of potential compounds is one possible explanation of how superficially similar biologies can be incompatible with each other (q.v. 'Local Biochemistry', G:T 'First In', p.68 sidebar).

It is currently thought that nucleotides came first, then proteins, then carbohydrates and fats. Any sequence is possible; the evidence for the current  theory is circumstantial at best due to the distance of time, as evidence of life on Earth dates back over three billion years. Carbohydrates and fats are yet to be shown to be capable of intrinsic catalytic activity - but the science of biochemistry is still relatively young.

David Summers brought an interesting fact to my attention over on the Traveller Mailing List. Using certain types of fats, chemists have formed vesicles containing photoreactive iron compounds. When these salts capture light, a potential difference is created across the wall of the vesicle - a source of energy for early life.

Aside : Optical isomerism

Compounds can display optical isomerism - they rotate polarised light in different directions. The structural requirement is simple - a carbon atom linked to four different chemical groups.

Chemists group compounds into those that rotate polarised light clockwise (dextro, + or D isomers) or counterclockwise (laevo, - or L isomers).

In terrestrial life, all amino acids are L isomers. Almost all sugars are D isomers (gut membrane glucose transporters will accept L-glucose with 1% of the avidity of the D form - but most organisms can't do anything with L-glucose).

Where optical isomerism is possible, in time one form will dominate over another because to catalyse reactions with the other isomer requires more energy. This phenomenon is known as 'stereoselectivity'.

How did this situation arise?

One theory suggests that a small excess of one isomer, created by an abundance of circularly polarised light (common in star forming regions), and subsequent amplification by later chemical reactions, did the trick.

[If left alone for long enough, amino acids will revert to a mixture of both isomers (a so-called racemic mixture). This is the basis of a relatively new sample dating technique, since this process occurs at a known rate].

So with time and the right conditions, molecules capable of sophisticated stereoselective synthetic reactions are possible. 'Communities' of these chemicals represent the precursors to life as we know it. How are their energy needs met?

Metabolism : What does it mean to be an 'oxygen breather', anyway?

The sum total of the chemical reactions taking place in an organism is termed metabolism.

Reactions are of two broad types: catabolic, where energy is liberated in a series of small usable steps via the breakdown of complex molecules, and anabolic - the synthesis of complex molecules from simpler substrates, which costs energy.

In Earthly life, there are two important chemical reactions that illustrate both processes:

The (catabolic) aerobic breakdown of glucose (C₆H₁₂O₆ + 6O₂ -> 6CO₂ + 6H₂O + 3085kJ/mol glucose - 50% of the energy released is stored in the high energy phosphate bonds of 38 molecules of adenosine triphosphate, ATP ; the remainder is 'wasted' heat), and the reverse anabolic reaction, photosynthesis - this allowed the replenishment of organic molecules from atmospheric gases.

Photosynthesis is the reason why worlds have oxygen in their atmospheres. Oxygen is difficult to liberate from rocks, etc. without extensive violent geological activity.

Early in life's history, it is presumed that energy requirements were met by the anaerobic degradation of glucose (glycolysis) as it forms the "backbone" of most contemporary organisms' metabolic pathways: glucose -> lactic acid + 2 ATP

The capability to use oxygen came later when it became more abundant. Aerobic respiration [the citric acid or Krebs cycle and the electron
transport chain] is based entirely within mitochondria, which are symbiotic bacteria which merged with our distant ancestors early in the story of life.

Chloroplasts, the organelles of photosynthesis, also appear to be endosymbionts.

Some Alternative Systems

Hypothetical central metabolic pathways take the following general form:

'biomolecule' + 'reactant' <-> 'breakdown products' + energy

Melting and boiling points are in degrees Celsius at one atmosphere ambient pressure, unless otherwise stated.

* Carbon dioxide sublimes, turning directly from solid to gas at one atmosphere pressure. The melting point given is under multiple atmospheres pressure (about 4).

** These compounds are very stable, having melting and boiling points in the hundreds of degrees.

*** melting and boiling points increase with increasing chain length. Compounds less than 5 carbons long are gases at 15 °C ; compounds less than 16 carbons long are liquids at this temperature.

The choice of available compounds for surface life's metabolism will be limited by temperature and surface gravity, as discussed in Part 1. Worlds with hydrogen atmospheres will be gas or sub-giants or far flung outer zone bodies.

The forward (left -> right) reaction is equivalent to the breakdown of glucose; the reverse, photosynthesis.

In general terms, reactions analogous to glucose breakdown should:

• cause the 'biomolecule' to lose electrons (oxidation)
• cause the 'reactant' to gain electrons (reduction)
• lead to the release of energy from bond rearrangements.

The ammonia -> nitric acid and hydrogen sulphide -> sulphuric acid systems do not fulfil the criteria above, in that the reactant substances are oxidised, not reduced; but energy production is reasonable. Exotic or corrosive atmosphere worlds could be populated with organisms that run on such systems.

The coming of cells : the importance of membranes

To maintain large amounts of complicated machinery in a stable environment, the machinery should be enclosed.

Cells can be seen as complex chemical plants. Membranes develop to let nutrients in, wastes out and to keep interconnected machinery in close proximity.

Cell membranes are made up primarily of phospholipids : molecules with a charged end and an uncharged one. Fats form droplets in water; phospholipids form vesicles with a bilayer of phospholipid molecules separating inside and outside.

where 0 represents the charged (hydrophilic) end, = the hydrophobic portions.

Keeping cellular machinery and metabolic intermediates charged prevents them from leaving the cell, as they can't easily cross the hydrophobic portion of the membrane. [Uncharged compounds with reasonable solubility in both media can cross easily - e.g. oxygen and carbon dioxide]. As cells become more complex, internal membranes arise to divide the cell into compartments or organelles.

Some notable examples include:

• the nucleus, where genetic information is stored, transcribed and repaired
• the endoplasmic reticulum, where protein and lipid synthesis is performed, as well as many miscellaneous reactions (e.g. breakdown of foreign compounds)
• the Golgi apparatus, which adds carbohydrate chains to proteins
• vesicles which serve storage, secretory and degradative functions (lysosomes and peroxisomes as examples of the last category).

Multicellularity : the grand experiment

Most terrestrial life is made up of single celled organisms without nuclei (prokaryotes or bacteria). Depending on which estimates you read, most of the Earth's biomass could actually be subsurface bacteria.

Why do multicellular organisms exist at all? There must be some benefits from specialisation e.g. easier to maintain a certain environment (temperature, acidity, solute concentration) and the ability to better make use of available resources (e.g. a tree vs. a blue-green alga or cyanobacterium harnessing sunlight). Avoiding predators, catching prey, increased tissue efficiency, and better adaptation to hostile environments are other possible benefits.

With the advent of different organisms, different ecological niches arose - and yet more creatures appeared to inhabit these new environments.

The process probably had its beginnings in colonial organisms, single-celled forms which grouped together because they could feed more efficiently. Examples include myxobacteria (which 'hunt in packs' and form 'fruiting bodies' when resources run low), and green algae e.g. Gonium sp. which aggregate in groups of 4, 8, 16 or 32 cells. Volvox sp. can have more than 50,000 cells linked together to form a hollow sphere. There is some division of labour within these colonies, with a small population of cells serving a reproductive function.

From these humble beginnings, things became very complicated as organisms adapted to meet the challenges of varied and varying environments.

Next part: Scaling Laws and Physiology