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Chemistry Wonder World: Thirty VIP inorganic and organic chemical molecules & compounds to know and understand

© Donald Reinhardt, October 23, 2013

The world of chemistry is filled with important and less important chemical compounds. This list and grouping of thirty (30) important compounds will frame the bigger picture of the important compounds of the chemical world and show you why they are so important.

Glucose, the most common 6-carbon sugar. Diagram Credit: Pub Med, NIH

Thirty (30) chemical compounds as a foundation for your chemical thinking

Inorganic chemistry is the chemistry that is not carbon based – H2O, NaCl, CaCO3, KNO3 are just a few simple examples of inorganic compounds. The chemistry of carbon compounds is termed organic chemistry and here we find carbon is associated with the elements such as hydrogen, oxygen and nitrogen and other elements to form unique compounds. So, let’s explore 30 important inorganic and organic compounds.

1. Oxygen gas found in the atmosphere (O2) 
Oxygen gas is two atoms of oxygen joined by a covalent bond. Remember that 21% of the atmosphere is oxygen gas. That is the second largest percentage of a gas in the earth’s atmosphere. Nitrogen gas (N2) at 78% accounts for a major portion of the atmosphere.

Oxygen is necessary for the life many types of organisms (aerobes or aerobic organisms) and certainly for our unique and important lives. There are organisms than can survive without oxygen – these organisms are called anaerobes. Most anaerobic life is small and microscopic and includes a large number of different kinds of bacteria. Therefore, most life on our planet depends on oxygen for its existence.

2. Nitrogen gas (N2)
Here we see two atoms of nitrogen are joined by a covalent bond. In normal air 78% of planet earth’s atmosphere is N2.

Nitrogen can be fixed from the air and converted into NO2-(nitrites) and NO3- (nitrates). For example, lightning causes some N2 to be converted into NO2- .

The NO2- and the NO3- (ions of nitrite and nitrate respectively) can be taken up and into (assimilated) by living organisms (microbes, plants and animals). When inside the organism these ions and compounds are converted into important nitrogen-containing carbon compounds such as amino acids, nitrogen bases and nucleic acids (RNA and DNA).

3. Hydrogen gas (H2) and 4. Helium Gas (He2) 
These two gasses are the substance of the sun and the stars. Our sun, which warms this earth and generates energy for photosynthesis in plants, is a gigantic mass of hydrogen and helium. These two basic gasses, hydrogen and helium, are the stuff of fusion reactions that generate the enormous light and heat which make planet earth what it is – a thriving, living planet filled with a diversity of life.
5. H2O – water is dihydrogen oxide
Water is essential for all life on planet earth. A large proportion of the body mass (about 70% on average) of all living organisms is water. Water is a distinctive compound with very important properties and is explained in more detail here
Carbon dioxide (CO2)
CO2 gas is fully oxidized carbon. CO2 is the result of the complete oxidation of carbon compounds and pure carbon itself. So, if we burn coal (C) with O2 we get C + O2 à CO2. Carbon dioxide has covalent, double bonds, i.e., 2 sets of paired or shared electrons for each oxygen atom joined to the carbon.

In humans, when we burn carbon compounds such as sugar in our bodies we see the following type reaction: C6H12O6 (glucose) + 6O2 ------=> 6CO2 + 6H2O.

Notice in the above formula that the number of atoms on the left and right side of the equation are equal and accounted for in number – this is a balanced chemical reaction. This is a reaction that affirms correctly and accurately that the law of conservation of matter is true for in the equation given above – no matter, no atoms were created or destroyed, we see that every atom is accounted for numerically. That is the correct way to balance chemical reactions. It is the same when an accountant balances the business financial books or a personal checkbook is balanced for money received and money spent.

7. Carbon monoxide (CO) is formed from the incomplete combustion of carbon. It has a triple, unsaturated covalent bond.
CO is dangerous to humans since it binds more strongly to hemoglobin than it does to oxygen. CO can cause death by molecular asphyxiation, i.e., the oxygen cannot bind to hemoglobin because the CO is occupying that specific location where oxygen normally binds and this bound CO does not release readily from the normal O2 binding site on the hemoglobin molecule. Think of a seat occupied by someone else and you cannot sit there unless they leave – if CO is in that position (it occupies the site in a distinctive molecular way), then the O2 cannot link to and occupy that site.
8. Carbonic acid (H2CO3)
When CO2 is bubbled into water (H2O), it forms carbonic acid which is H2CO3. Imagine blowing out CO2 through a straw or CO2 being produced by an animal swimming in water. The CO2 reacts with water as follows: H2O + CO2---=> H2CO3 (carbonic acid).

Carbonic acid under pressure will release CO2 when the pressure is dropped. This causes bubbles in soft drinks (pop, soda) and bubbly wines like champagnes to escape when the cap is removed. All this is the result of carbonation.

Sodastream” is the newest commercial example of a carbonation device which converts water and syrup into a flavorful soda pop.

9. Bicarbonate (HCO3-)

When carbonic acid ionizes in solution it forms or yields upon ionization one proton (H+) and bicarbonate, HCO3- . HCO3- serves as a buffer in the human body and many other animals.

The HCO3- can react with OH-(hydroxyl group, basic group) to form water H2O and CO3= (carbonate): HCO3- +OH- -----> H2O + CO3=.

Buffering occurs with bicarbonate.

When there is an excess of HCO3- and H+, the reaction is driven in the opposite direction to form carbonic acid. Thus, bicarbonate can serve to neutralize or keep pH balanced. The HCO3- can react with an excess of H+ (acid ions) and prevent acidification or the lowering of pH. When (OH) - hydroxyl ions are in abundance, then the HCO3- can react with the basic OH- groups (which can cause alkalinization). The buffering reaction is as follows: HCO3- + OH ----=> HOH + CO3=

If sodium is present in the solution, we can get sodium bicarbonate or baking soda: Na+ and HCO3- may react to yield NaHCO3 (baking soda).

10. Carbonate (CO3=) is a double-negatively-charged (divalent) atom. The charge is negative so it is a minus 2 (-2) and it is usually written as CO3= to represent the charged ionic group. Carbonate can react with a variety of metals to form various types of carbonates  compounds. Examples: MgCO3 and CaCO3 are carbonates of magnesium and calcium respectively. 
11. Calcium carbonate (CaCO3) is an important compound found in shells of snails, mollusks (clams, oysters, mussels) – the sea-shelled animals of the world are protected by their hard shells.
Calcium carbonate is also found in limestone caves and forms those ornate and beautiful chemical formations known as stalactites and stalagmites.
Calcium carbonate is formed when calcium (Ca++) in solution reacts with CO3= (carbonate, double negative ions) to yield CaCO3.

To summarize: Ca++ and CO3-- can react together to yield----=> CaCO3

12. Calcium phosphate is the compound of bones and teeth. The ions (charged atoms) are Ca++ (divalent positive calcium) and PO4--- (trivalent negative phosphate) which react in proper and exact proportions to yield Ca3 (PO4)2.

13. AmmoniaNH3 is an important source of nitrogen for many microbes, plants and animals. Ammonia is produced during metabolism and during the breakdown and decomposition of living organisms which have died. Ammonia can react with water to form a solution of ammonium hydroxide as follows: NH3 + HOH -----=  NH4OH.

Nitrogen is essential for living organisms and may be obtained in the form of ammonia, NO2- or NO3- or the very compounds themselves (we will see these later) which are needed (amino acids and nitrogen bases). Plants use ammonia, nitrites and nitrates and urea to make and assemble amino acids and nucleic acids.

Amino acids are needed to make protein compounds.

Nitrogen bases are needed to make DNA and RNA.

14. Glycerol (glycerin) – a polyalcohol that is the backbone of fats (solid at room temperature) and oils (liquid at room temperature). Up to three fatty acids (saturated or unsaturated) can attach to glycerol by an esterification reaction).

15. Fatty Acids – these are usually long carbon chains (16 to 20 carbons long) with many hydrogen atoms attached to the chain and with a carboxylic acid (-COOH) group at the end of the chain.

16. Lipids (fats and oils).
Lipids are composed of the elements C, H, an O – the same elements found in carbohydrates – carbon, hydrogen and oxygen.

Oils are composed of glycerol with unsaturated carbon chain fatty acids and fats are glycerol with fully-saturated fatty acid chains.

Both fats and oils are composed of glycerol (the tri- or poly- alcohol) with attached trios of fatty acids. The alcohol (R-OH) and acid (R-COOH) react to form an ester bond (R-COO-R).
Glycerol (left side, is a polyalcohol) with 3 fatty acids in ester bond linkage. This is a triglyceride molecule. Photo Credit: Wikipedia Commons.
Pictured above you will find ester bonds at the region of the OH and COOH reaction site. Notice again that is glycerol is a polyalcohol, it has three hydroxyl groups (-OH) attached to the carbon. When three fatty acids react with the three OH groups on glycerol they form an ester bond.

Also remember this: Whenever fats and oils are broken down by enzymes, they typically yield glycerol and fatty acids.

Typically oils have a double bond in one or more places in the fatty acid chains. The double bond indicates a state unsaturated of the carbon chain, i.e., oleic acid and linoleic acid are two examples of unsaturated fatty acids.

17. Urea – CO (NH2)2 is a major waste product of protein and nucleic acid metabolism in animals. The urea can be assimilated by plants such as grasses and used for metabolism and growth and the synthesis of proteins and nucleic acids. There are patches of greener grass where an animal has deposited waste – those areas have been naturally-fertilized and those nutrients, particularly the nitrogen in urea, stimulate plant growth.

It is important to remember that urea produced during nitrogen metabolism is toxic (harmful to the well-being of a living organism) internally. This toxic urea must be removed and this urea is typically filtered by healthy kidneys and passed as urine (urine is an appropriate name, don’t you think so?).

If too much urea accumulates an animal can die of uremic poisoning. In humans, kidney failure or disease (nephritis) can cause urea to accumulate and result in death.

18. Amino acids –these compounds have two important features – all amino acids have an amino group (-NH2) and a carboxylic acid group (-COOH).

There are 21 naturally-occurring amino acids that are used to make thousands of different kinds of proteins.

19. Proteins – Proteins contains the elements C, H, O, N and S. Proteins are used for structural and functional reasons.
Hair, skin and nails are all made of keratin protein. Did you know that a turtle shell is also keratin protein? Yes, turtle shells are keratin protein.

There are many thousands of different proteins and these different proteins include: enzymes, cell membrane components, and signal peptides (small proteins made up of a few amino acids).

Examples of enzymes are pepsin and trypsin. Enzymes are specialized protein compounds which speed up reactions without being used up in the reaction.  Enzymes are catalysts – they speed up reactions and do that task over and over again very quickly. Some enzymes even digest and breakdown other proteins and enzymes.
There are also important peptide (small protein) hormones which instruct cells to behave or perform in certain ways. For example, insulin is a protein hormone that promotes the passage of glucose across cell membranes and into cells.

20. Glucose (C6H12O6) - a 6-carbon sugar produced by green plants during photosynthesis and converted into starch for long term storage in certain types of plants (potatoes). All carbohydrates contain C, H and O elements.

21, Acetic acid – (CH3COOH)                                 
This is a two-carbon organic acid. Note that acetic acid is a weak acid when compared to HCl, HNO3 and H2SO4 (hydrochloric, nitric and sulfuric acids). These inorganic acids are each very strong, mineral (non-carbon-based) acids.
Acetic acid is also known as vinegar and it is produced during glucose metabolism when pyruvate is decarboxylated.                                                                                             Acetic acid is an end-product of the incomplete oxidation of glucose. Acetic acid is an organic acid with a pH of about 2 to 3 depending upon its concentration.
Finally, if acetic acid is anaerobically fermented it is converted to common alcohol (CH3CH2OH) also known as ethanol. Ethanol is fermented in tanks from corn sugars and used as a fuel additive for gasoline.
22. Pyruvic acid (CH3COCOOH) is a three-carbon organic acid . This organic acid is produced during the metabolism of glucose by the process called glycolysis.
When pyruvic acid is reduced (fermented), it is converted into lactic acid. If pyruvate is decarboxylated (CO2 is removed by an enzyme) it is converted into acetic acid.
23. Lactic Acid (CH3CHOHCOOH) – is an important product of fermentation formed by the reduction and hydrogenation of pyruvic acid (see above).
 Lactic acid is produced in yogurt and lactic acid is responsible for the sour taste of yogurt. Sugar or artificial sweeteners are added to mask the sour taste of yogurt. Yogurt as a whole and the microbes in yogurt are considered a healthy natural food.

Lactic acid is also produced in muscle deprived of oxygen (i.e., anaerobic conditions prevail temporarily) and is responsible for muscle fatigue.

24. Ethanol (CH3CH2OH) is basic and common alcohol produced by fermentation (an anaerobic process) of glucose. Ethanol is the alcohol found in beers, wines and whiskies.

Yeasts are the main microorganisms which are able to metabolize sugar (glucose and fructose) in the absence of oxygen and convert these sugars into ethanol.

25. Ribose – a five-carbon sugar that forms part of the backbone of RNA (ribonucleic acid). The sugar ribose is chemical bonded with the nitrogen bases: adenine, uracil, guanine and cytosine. There are three major types of RNA known: transfer RNA (t-RNA), messenger RNA (m-RNA) and ribosomal RNA (r-RNA).

26. Deoxyribose –this is ribose sugar with one less oxygen atom. Deoxyribose can link with adenine, thymine, guanine and cytosine to form long, chains of nucleotides which form the famous double-helix discovered by Watson and Crick in 1951. DNA molecules contain the genetic codes of life for living organisms.

27. Nitrogen bases – there are a total of 5 nitrogen bases: adenine, thymine, guanine, cytosine and uracil. These are important for the manufacture and structure of RNA and DNA.

28. DNA - Deoxyribonucleic acid is the major information and instruction manual for living organisms. DNA is the code of life – it contains the necessary and complete information for the architecture and functioning of an organism or life form. 
The nucleic acids, DNA and RNA each have the elements C, H. O. N. P in their structure.
Deoxyribonucleic acid contains dexoyribose linked covalently with the four specific nitrogen bases. There is a regular adenine and thymine paired hydrogen-bonded cross-linkage and guanine and cytosine paired cross-linkage. Remember A binds to T and G binds to C, i.e. A-T and G-C hydrogen-bonding crosslinks the base pairings.
29. RNA - ribonucleic acid
The 3 types of ribonucleic acids are:
  1. m-RNA, messenger RNA, the information molecules (m-RNA) for protein structure obtained via transcription from DNA.
  2. r-RNA, ribosomal RNA which combines with different proteins to form distinct structures called ribosomes to which m-RNA sticks and is read.
  3. t-RNA (aka: s-RNA), transfer or soluble RNA, which are unique carriers of the specific amino acids which are brought to the m-RNA attached to the ribosomes for assembly into peptides and proteins.

30. Hormone compounds– special types of compounds that stimulate cells, tissues and organs in ways that promotes adaptation, regulation of functions and survival of the living organism that has those hormones.