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Before we continue on to the subject of macromolecules, it is necessary to clarify the way the molecules become organized and how energy is used to drive the system to a non-equilibrium state as mentioned in topic 1.
When energy (such as in a photon) is pumped into a chemical system, the energy partitions into thermal and electronic components. The thermal component makes the molecules move faster, and the electronic component increases the number of "high-energy" electronic states. Both energy components will foster molecular organization: the faster the molecules vibrate, rotate, and translate, and the more of them that are in electronic states above ground level, the higher is the probability that the molecules will interact and the more work can be done in organizing them. However, there is a limit to that. At very high energy levels all chemical bonds become inherently unstable, the molecular structures eventually fall to pieces. It draws the line to the energy input; it is impossible to make a macro- molecule in one run from scratch. It has to be made by supplying the required energy little by little. The aggregates (such as DNA or protein) are created by joining the units one at a time. This way each step of molecular synthesis could be driven by a separate and tolerable energy input.Living organisms store photon energy in chemical form, and then trickle it down molecular chains to the individual molecular bonding sites. The energy flux that organizes all living matter on our planet is so channeled as to first pump CO2 and H in the atmosphere and water up to the level of
|carbohydrate, namely glucose, and then to drop the level gradually from that reservoir back to the ground again. This gradient drives nearly all work in the biomass, not just the making of macromolecules. The smallest unit for this chemical (energy) currency is stored in the third phosphate bond of the ATP. |
The flow starts with the capture of photons by certain molecules, such as the chlorophyll of plants and similar pigments of microorganisms according to the photosynthesis reaction:
6CO2 + 6H2O + energy C6H12O6 + 6O2
Respiration runs in the reversed direction. While the energy input is carried by photons in photosynthesis, the energy output in respiration is distributed among a maximum of 38 ATPs.The photon energy is stored in the covalent bonds3 of glucose -- about 6 quanta of photon in one glucose molecules. From this reservoir, energy then flows along various pathways, nursing everything, all organization and all work. The chemical energy chains that nurse macromolecular organization commonly use ATP as their final link. Each package contains an energy of 7.3 kilocal per mole (~ 0.3 ev/ATP4). It is given off at the sites of amalgamation of the molecular building blocks -- one package for each site with spatial precision to where it is needed.
(See "ATP synthase" for the production of ATP.)
The following chemical formula shows a simple case of molecular synthesis. The 7.3 kilocalorie package of ATP is fed into the site of elongation, the last member of the carbon chain. NH2 is added to the glutamate using the energy from the hydrolysis of ATP (into ADP and Pi, the phosphate). The glutamine becomes an energized molecular system stably links a NH2 group to the chain.
Since aerobic respiration (energy-producing process with air) requires oxygen, the energy carrier ATP cannot be manufactured in the absence of this substance. The aerobic cells and organism will soon expire because the metabolism2 will stop without energy supply. The energized covalent bonds would break down due to a variety of causes such as thermal agitation, chemical corrosion, biological degradation, and damage by radiations. In addition, water would tends to hydrolysis many of the organic compounds. Eventually, the organism would return to dust (the basic chemical components) just like an old house crumbling down to ruin.The rate of energy comsumption for all orgamisms from whale to single cell seems to follow a simple 3/4 power-law of the body mass (see "Metabolic Rate and Kleiber's Law" in the appendix for detail).
2Metabolism is the sum of all chemical activities occurring inside a living cell. Metabolic cycle (pathway) begins with a particular reactant and terminate with an end product.
3The bonding energy for the various chemical bonds are roughly in the ratio - Van der Waals : Hydrogen Bonds : Covalent Bonds = 1 : 10 : 100. Formation of hydrogen bonds releases 3 - 10 kcal/mole (~ 0.1 - 0.4 ev). Hydrogen bonds are found between only a few elements of the periodic table. The most common are those in which H connects two atoms from the group F, O, N, and, less commonly, Cl. The hydrogen bond in water has the configuration: H-O-H(+)...(-)O=H2. Covalent bonds are created with sharing electrons in between two atomic nuclei. A stable configuration can be achieved by sharing up to three pairs of electrons. Van der Waals forces are the intermolecular attractions produced by temporary dipoles (shifting of electrons).
4The ev is an energy unit called electron volt. It is defined as the energy acquired by a particle of one electronic charge e, accelerated through a potential difference of 1 volt. Approximately 1 ev ~ 1.6 x 10-19 joule. Photosynthesis peaks at a wavelength of around 700 nm (red light), which carries an energy of about 5 ev.