A. Organic law governs chemical compounds of carbon that are intrinsic to the study of biochemistry. Planet Earth, the Solar System and the enveloping circulatory Oort Cloud comets that reach halfway to the next star (Comet 1:7), were formed approximately 4.6 billion years ago. Simple fermenting one-celled life forms first became present on Planet Earth 3.5 billion years ago. Life may have been photosynthetic as early as 3.1 billion years ago, but geological evidence about the oxidation state of sedimentary iron deposits indicates that the atmosphere only became oxidizing around 1.8 to 1.4 billion years ago. O₂released as a byproduct of photosynthesis gradually changed the atmosphere from oxygen reducing to what we know today with 20% free oxygen. Multi-celled life forms dependent upon the energy surplus that only O₂respiration could provide made an appearance roughly between 1000 and 700 million years ago setting the pattern for later evolution of higher organisms reliant upon symbiotic relationship combusting the O₂ produced by photosynthetic plants (Principles 21-11:888).

1. The American Chemical Society (ACS) has maintained a register of chemical compounds mentioned in the literature since 1965. By the end of 1982 there were 5.9 million different chemical substances in the register (Principles 21:821). Of these, 90% were compounds based on a carbon backbone, the remaining 600,000 were divided between alloys and inorganic compounds. So many carbon compounds exist because carbon links well with hydrogen and can link with itself as no other element can, to make straight chains and branched chains with each carbon atom bonding with as many as four bonds. Chains made by the repetition of subunits are called polymers, and the repeated unit is called a monomer (Principles 21-1:822). Double bonds are also a distinguishing feature of high energy yielding carbon molecules known as unsaturated that can be converted to a single bond known as saturated by adding an atom at each end of the bond (Principles 21-1:824).

Art. 102 Atoms

A. An atom consists of a positively charged nucleus, surrounded by one or more negatively charged particles called electrons. The positive charges equal the negative charges, so the atom has no overall charge; it is electrically neutral. Similar to the solar system or a comet, much of an atom’s mass is in its nucleus (Principles 1-1:2). The nucleus contains both protons and neutrons that haven nearly equal masses, but differ in charge. A neutron has no charge, whereas a proton has a positive charge that exactly balances the negative charge on an electron. The atomic mass unit (amu) is defined as exactly one-twelfth the mass of a carbon atom that has six protons and six neutrons in its nucleus. With this scale protons (1.00728 amu) and neutrons (1.00887 amu) have masses that are close to, but not precisely, 1 amu each and electrons (0.000549 amu). The mass of an electron is only 1/1836 the mass of the lightest nucleus, hydrogen. There are 6.022 x 10²³ amu in 1 gram, this number is known as Avogradro’s number (Principles 1-1:3).

1. The number of protons in the nucleus of an atom is known as the atomic number listed above the Element in the periodic table. It is the same as the number of electrons around the nucleus. The mass number of an atom is an integer equal to the total number of heavy particles; protons and neutrons in amu (Principles 1-1:3).

2. Although all atoms of an element have the same number of protons, the atoms may differ in the number of neutrons they have. Differing atoms of the same element are called isotopes. Isotopes are indicated by adding the number of neutrons and protons to the atomic number reflecting the total of number of neutrons and varying number of protons in superscript before the Element, ie ³⁵Cl or ³⁷Cl. Isotopes that have more protons than the atomic number are radioactive as the result of instability causing the element to break down until it reaches (Principles 1-2:4).

Art. 103 Molecules

A. The formation of molecules from fundamental particles occurs when atoms are close enough for their electrons to interact and form covalent bonds. Two or more atoms held together by chemical bonds are known as molecules. Bonds based on electron sharing are known as covalent bonds. Molecular diagrams represent the covalent, electron sharing bond with a straight line (Principles 1-3:9). The molecular formula tells how many atoms of each element are in the molecule. The sum of the atomic weights of all the atoms in a molecule is its molecular weight. For example the molecular weight of water is ( H 2 X 1.0080 amu = 2.0160 ) + O 15.9994 amu = 18.0154 amu (Principles 1-3:10). In practice chemists weigh their materials in grams, not in atomic mass units. To scale up from the molecular level to laboratory level the mole is used. A mole of a substance is a weight, in grams equal to that substance’s molecular weight expressed in atomic mass units. The term gram-atom applied to a mole atoms is no longer widely used (Principles 1-5:15).

1. Molecules, whether organic or inorganic, are slightly “sticky” as the result of forces, caused by momentary fluctuations in electron distributions around the atoms, are known as van der Waals attraction (after Dutch physicist Johannes van der Walls). The attraction between molecules is responsible for the existence of three states of matter at different temperatures - solids, liquids, and gases – and is regulated by the laws of Thermodynamics (Principles 1-4:12).

a. The solid state is close packed crystalline lattice of molecules.

b. The liquid state occurs if the temperature rises above the melting point increasing molecular vibration with enough energy to cause the molecular crystal to break up and the molecules are free to slide past each other, although they are still touching.

c. The gaseous state occurs at the boiling point when so much energy is given that they overcome the van der Waals attraction and travel in independent molecular trajectories through space (Principles 1-4:13).

2. The second law of thermodynamics states, any process taking place in a closed system causes disorder, entropy, of the system as a whole to increase (Principles 21-11:876).

Art. 104 Photosynthesis

A. Green plant photosynthesis is the reverse of that of the combustion of glucose. Water is split apart as the source of hydrogen atoms to reduce CO₂to glucose, and the unwanted oxygen gas is released into the atmosphere.

6CO₂+ 6H₂O C₈H₁₂O₆+ 6O₂ΔG° = +2870kJ

1. The energy for this process come from sunlight. Green plant synthesis can be divided into two separate processes the photo reactions and the synthesis reactions or as they are more commonly known light and dark reactions (Principles 21-11:888).

a. In the light reaction the light absorbing elements are molecules of chlorophyll comprised of a conjugated ring of carbon atoms with delocalized elections surrounding a magnesium atom the light energy using H₂O as the reducing agent.

light

NADP + H₂Oenergy NADPH + H +1/2O₂

b. The dark reactions are known as the Calvin-Benson cycle. In dark reactions, CO₂is reduced to glucose using hydrogen atoms from stored NADPH. The synthesis of glucose requires only 226kJ of energy and the reaction between ATP and H₂O produces 548 kJ of energy giving the process a net spontaneous drive of 322kJ. The dark reactions are as follows (Principles 21-11:887);

6CO₂ + 12NADPH + 12H⁺C₆H₁₂O₆+ 6H₂O + 12NADP⁺ ΔG° = +226kJ

18ATP + 18H₂O 18ADP +18P_i ΔG° = -548 kJ

Art. 105 Aerobic respiration

The degradation of high-energy fuels and the extraction of their energy is called metabolism (Principles 21-11:878). Aerobic respiration yields 19 times more energy per gram of food (mole of glucose) than anaerobic fermentation. The respiratory chain is three step process whereby hydrogen atoms and electrons from NADH and FADH are passed along a series of flavin-containing proteins and cytochromes until they ultimately reduce O₂ into H₂O in a three step process that synthesizes adenosine triphosphate (ATP). In the first stage known as glycolosis ATP is built from adenine, ribose (a five-carbon sugar) and three linked phosphate groups. In the second and most complex stage known as the citric acid cycle is also called the tricarboxylic acid (TCA) cycle and the Krebs cycle. Two carbons enter the citric acid cycle as acetyl CoA and two carbons leave as CO₂. In the course of the cycle, four oxidation-reduction reactions take place to yield reduction potential in the form of three molecules of NADH and one molecule of FADH₂. A high energy phosphate bond (GTP) is also formed. In the third stage known as oxidative phosphoralization the terminal phosphate group in ATP can be hydolyzed with the addition of OH^- and H⁺to yield phosphate and adenosine diphosphate (ADP). ADP can be decomposed even further to produce another phosphate group and adonosine monosphosphate (AMP). Finally, the last phosphate group can be removed to adenosine. ATP is formed from ADP and inorganic phosphate in a reaction coupled to the oxidation of glyceraldehyde phosphate to phosphoglyceric acid. The first two cleavage liberate 30.5 kJ mol^-1 of free energy each, whereas the third cleavage liberates only 8kJ^-1(Principles 21-11:880). Every time a molcule of glucose is degraded biochemically to two molecules of pyruvate, eight molecules of ATP are formed from 8ADP resulting in the storage of 8 x 30.5 = 244 kJ mol^-1 of free energy as ATP (Principles 21-11:881)

Dickerson, Richard E.; Gray, Harry B; Darensbourg, Marcetta Y.; Darensbourg, Donald J. Chemical Principles (Fourth Edition) The Benhamin/Cummings Publishing Company, Inc. 2727 Sand Hill Road; Menlo Park California 94025. 1984

Sagan, Carl; Druyan, Ann. Comet. Random House. New York. 1985