The Science of Existence – Chemistry Synopsis

Chemistry Synopsis


▫ Matter is anything that occupies space and has mass.

▫ The atom is a basic unit of matter, comprising a nucleus and electrons. An atomic nucleus typically comprises protons and neutrons.

Only the simplest form of hydrogen, with a single proton, can have a nucleus without neutrons. Protons on their own repulse each other. So, any stable atom with multiple protons also has neutrons. Neutrons are necessary to hold atomic nuclei together.

▫ Matter involves a hierarchy of combinations. Subatomic particles form atoms. Atoms form molecules. Molecules combine to form a vast variety of compounds.

▫ From atoms up, electrical properties provide guidance for the energetic transactions (reactions) of building up more complex macromolecules or breaking them down.

▫ Electrons swirl about atomic nuclei in an orbital cloud, equalizing the positive charge of protons via the negative charge possessed by electrons. Electron clouds self-organize into layers (shells) which generally differentiate by energy levels. Shell layering is an hd dynamic.

▫ The Zen of matter is emptiness. An atom’s electron cloud whorls far above its nucleus. An atom is 99.99+% space.


▫ Chemistry is the study of matter and the changes which substances undergo. Chemistry is extensively entangled with other fields of study, notably physics. The disciplines concerned with life rely heavily on biochemistry: the application of chemistry to biological processes.

▫ Molecules are the functional unit of chemistry, the basic building block of matter in an everyday sense.

▫ Seeking stability in the electrical charge created by the outer shell of an electron cloud, atoms combine into molecules by forming covalent bonds.

The internal vibrations of molecules drive the structural transformations that underpin chemistry and cellular function. ~ Indian American physical chemist Ara Apkarian et al

▫ The energy to effect chemical reactions may be meager. Slight differences at the subatomic level influence the dynamics of molecular transformation. Chemical butterfly effects are common.

▫ Chemical reactions are promoted by catalysts which lower the activation energy required for a reaction to occur. Without catalysts, chemical reactions would be much harder to come by.

Yet reactions readily occur where they should not. According to the classical laws of chemistry, the vast expanses of interstellar space are too frigidly forbidding for organic molecules to form. Via quantum tunneling – a term that labels but does not explain – prodigious amounts of alcohol and other organic compounds are formed in space.

▫ Radiation arises from energy fluctuations, which are pervasive throughout the universe. Electromagnetic radiation emits photonic wave energy. Particulate radiation arises from atomic decay. Radiation is an hd process initiated by quantum tunneling, where a subatomic particle escapes 4d confines.

▫ Molecular geometry characterizes molecules by the positions of their constituent atoms in space. Many molecular properties are affected by shape. The vibrational qualities of atoms also greatly affect their chemistry, but little is known of this.

▫ Water is a unique molecule, with unusual chemical and quantum properties. H2O behaves like H3.6O in its fluid atomic bonding, but a single snapshot of a water molecule appears as H1.5O.

Though molecularly stable and supposedly electrically neutral, water is an ionizing agent, and so is a universal solvent. Water acts as a catalyst in many biochemical reactions.

Water is one of the few chemical compounds that exists alternately as a gas, liquid, or solid within the temperature range of ordinary life. Water enacts an intricate quantum dance to transition from one state to another.

Water may selectively exist in multiple phases simultaneously. This occurs at the surface of water, in the nanometer interface between air and H2O.

All of life depends on water. The Earth’s hydrological cycle (water cycle) is a primary biospheric cycle. Polluted water ravages life.

▫ pH is a measure of aqueous acidity. Pure water is neutral (pH = 7). Acids have a pH < 7, while bases have a ▫ 7 pH.

Neutralization is the process of an aqueous solution approaching neutral pH. This is largely accomplished by proton transfer, not just deionization.

Organic Chemistry

▫ Carbon is the life’s chemical king, owing to its self-chaining and flexible compounding with other elements.

Nitrogen is queen, as it provides a scaffold for amino acids and thus acts as a key constituent in proteins and nucleic acids (RNA, DNA). Unlike carbon’s easy bonding, naturally trivalent nitrogen is not so easily swayed into molecular configurations. So, whereas carbon happily plays its part, nitrogen reluctantly joins in. Yet this perfectly explains why these 2 elements play their respective roles so well.

Carbon’s pliability makes it ideal for readily constructing complex compounds and effecting transformations. Nitrogen’s inherent stability renders it as the best chemical basis for storing information.

▫ Oxygen also plays a key role in life, though as a chemical wild card: biochemistry’s joker. Oxygen is highly reactive, hence a fabulous fuel source, if abundantly available. But oxygen, because of its reactive nature, requires special handling, and so is not well-suited as a fuel for the more simply structured life.

Abundant oxygen was not available for early life. The planet transformers that would turn into plants relied instead upon then-abundant CO2 and H2O, along with sunlight as a catalyst, to create energy-rich sugar, with extra oxygen and water left over. Their success oxygenated the atmosphere.

▫ Both carbon and nitrogen are critical in the cycles by which the planet precariously supports life. Befitting the element’s respective characters, Earth’s carbon cycle is readily altered, while the nitrogen cycle is more reluctantly swayed.

Balance in the carbon cycle is one of abundance, most notably the level of atmospheric CO2, while the nitrogen cycle spins on its scarcity in bioavailability. Planetary imbalance in either of the carbon or nitrogen cycles portends serious consequences to all life on Earth.

▫ Plants have long held a central regulatory role in the carbon cycle, and thus climate control. The fate of all animals, from air to food to habitat, has always depended upon plants.

▫ Life is entangled at the molecular level. The environment that biomolecules live in determines their levels of activity and rates of interactions.


▫ Proteins are living macromolecules of varying complexity. They are the workhorse molecule of life, participating in virtually every process that takes place within cells, as well as acting as messengers between cells.

Protein folding is essential to proper functionality. Misfolded proteins – prions – can cause debilitating diseases.

A protein is a complex polymer built up from chains of polypeptide molecules. A polypeptide is formed from numerous peptides. A peptide is a short polymer of amino acid monomers linked by peptide bonds.

▫ An amino acid is a compound of simple functional groups. The key elements of the amino acid functional groups are carbon, hydrogen, oxygen, and nitrogen.

▫ The active site of a protein is where substrates bind and undergo chemical reactions. The active site is not the only place affecting protein functioning. Protein activity can be regulated by an enzyme or other effector molecule binding at a protein’s allosteric site: a site that is not the active site.

▫ An enzyme is a protein that acts as a catalyst in reactions involving proteins or other organic substrates. Every biochemical reaction is promoted by a specific enzyme, though some enzymes learn specificity rather than being produced with an intended specificity.