Nevertheless the truly novel feature of the DNA structure, as Watson and Crick put it in their paper, is the way that the DNA strands (“ribbons”)are held together. Erwin Chargaff’s paper chromatograhy techniques had revealed that DNA’s content consistently included almost equal amounts of adenine(A) and thymine(T). The same was true of guanine(G) and cytosine(C). Crick and Watson realized that A bonded T while G held on to C; these pairings come about because they produce the most possible number of hydrogen bonds between these so-called purine and pyramidine ”bases”(Figure 14).
Figure 14
In cell division, the DNA molecule is slowly unwound, exposing A,T,G and C. If the complementary bases are then supplied to each half of the helix, two identical copies will emerge. This is what happens during cell division when each cell must first replicate its 46 chromosomes to create 92 before becoming two cells (Figure 15).
Figure 15 By copying each complimentary strand, two copies of the original DNA molecule can be made.
How did DNA transmit information? Recall that all life forms use 20 amino acids to make their highly versatile proteins. If the code for an amino acid consisted of only a single base, there would be only 4 codes, one for each of A, T, G and C. If there were two bases in the code, there would be enough codes for only 42 amino acids. Three bases is the way to go: with 43 = 64 possibilities, there could be at least one code per amino acid, and there is also room for stop codes, to tell the protein-making process when to terminate a chain of amino acids.
i. RNA
The workhorse-molecules who assemble the amino acids into polypeptides don’t read the codes directly from DNA. From select parts of a gene, the codes are transcribed into a simpler “foreman”-molecule known as messenger RNA(mRNA). mRNA is single-stranded molecule using ribose as its sugar in its untwisted spine. Another difference between mRNA and DNA is that any type of RNA uses the pyrimidine base uracil(U) instead of thymine, but the difference (an H attached to its ring instead of CH3) is almost negligent because it still makes 2 hydrogen bonds with adenine. mRNA has complementary bases to those of the usable parts of DNA. For example, if the DNA code from a gene includes …TACGGCATG…, the mRNA assembled will have …AUGCCGUAC….
On the ribosomes, the foreman will sit there while workers fetch the appropriate amino acid. The workers are another form of RNA known as transfer RNA (tRNA) . Each carries a triplet(three bases) and its structure is such that it only bonds to one amino acid. For example, a tRNA with the triplet UAC will only pick up methionine (Met). The tRNA, with its Met will bond temporarily to the mRNA at the right spot where the complementary bases match AUG(Figure 16a).
A tRNA carrying another amino acid will not have the appropriate triplet, will not bond there to mRNA and will not be bringing the wrong ingredient for the recipe. A tRNA with GGC will be carrying the amino acid proline(Pro) to the CCG spot on mRNA. Enzymes will form a peptide bond between the two amino acids, linking them together (Figure 16b). The entire assemblage is slid over by the space of a triplet, the UAC tRNA will be released so it could keep working(Figure 16 c), while a third triplet from mRNA (UAC) will await an ATG tRNA carrying tyrosine (Tyr).(Figures 16d, e) This goes on until a STOP signal is reached and the final polypeptide is synthesized. There is no tRNA with the code complementary to a STOP signal.
The motion of mRNA is made possible by the ribosomes (purple structure in Figure 16)which are an association of proteins and a third type of RNA known as ribosomal RNA (rRNA). The larger subunit of the rRNA acts as an enzyme, speeding up the linkage of amino acids. Prior to the 1980s it was believed that only proteins could act as enzymes.
In the early 2000s the nucleotide base sequence of the small subunit RNA’s of many organisms was used as the basis of constructing an evolutionary tree (Figure 17). But this was still using a single gene as a source, so it had similar shortcomings to that of using cytochrome c as discussed in Chapter 12. A more comprehensive attempt was made in 2016, when a tree was based on the sequences of 16 different ribosomal proteins from the organisms being compared (Figure 18).
Figure 17. A phylogenetic tree based on the differences found in a single gene for a small ribosomal subunit, which is found in all organisms. Source: Charley_Lineweaver/publication/226915802
Figure 18. A phylogenetic tree based on the differences found in 15 different ribosomal proteins common to all organisms. Source: modified from Nature Microbiology volume1, Article number: 16048 (2016)
In certain viruses there is no DNA. That’s the case with ones causing the common cold, SARS, influenza, hepatitis C, Ebola and measles.For those, RNA is the only nucleic acid carrying genetic information. The same is true of a virus that does not infect people but attacks the papaya, now a target for genetic modification, to be discussed below in the next section. RNA viruses have much higher rates of mutations (changes in the genetic code) than DNA-organisms. For that reason, RNA-harboring viruses can only persist if their total number of genes is small. Their specialty is in reproducing quickly and moving on to new hosts, even new species. Due to these characteristics, natural selection has had a harder time preventing them from wiping out an entire population.
ii. Genetically modified plants, one tool among many.
Knowledge of the genetic code has given us rich insight into how life goes on while its individual carriers die. Have there been practical benefits? The papaya is a fruit native to Central America. It is a good source of vitamins C and A with an average of 61 mg and 950 IU, respectively per 100 grams of fruit and with about 2/3 of the fiber of an apple. It was the first genetically modified fruit to be grown for commercial production. It was developed in Hawaii not to tolerate herbicides or insects but to resist the papaya ringspot virus (PRSV), a type of RNA virus (Figure 19).
Figure 19. (a) The wilted leaves and (b) the ringspots on a papaya plant and fruit infected with PRSV. Source: Wikipedia Commons
The virus was brought to the island of Oahu by tagging along with a plant in the 1930s. It either mutated into a more virulent form or another strain was brought to the island. In any case, with the help of a few species of aphids who spread the new form of the virus, papaya cultivation areas were decimated from 246 hectares in 1956 to only 16 hectares in 1968. When a plant was infected at a young age, the virus stunted its growth and it did not yield fruit. If the virus struck a mature plant, it would start yielding poor quality fruit. Puna on the Big Island of Hawaii subsequently became the major production site, but PRSV caught up to them too, reducing papaya production from 56 000 pounds in 1992 to 36 000 in 1998.
After conventional strategies failed, the key to protecting papayas from ringspot in Hawaii was to include part of the genetic material of the PRSV within papaya-DNA. From the PRSV, they isolated the RNA sequence it used to make a protein coating for itself, one of 8 proteins from a single long polypeptide. That sequence was incorporated into a ring of DNA that had two other genes, one for tracking the protein and another for switching it on. Researchers tried to get it into a callus of papaya plant tissue and across their cell walls by coating tiny beads with the DNA ring and firing them inside using a gene gun. In 1992, they took these “vaccinated” plants along with control plants and infected them all with PRSV. After a short while they found a line of plants that had incorporated the protective gene; it was the only one thriving. When tested in agricultural fields in Waimanalo, Oahu, it also showed resistance to the virus. Eventually they developed two resistant varieties, Sunup, which has two copies of the protein coat gene per cell; and Rainbow, a crossing of Sunup with a yellow flesh variety, which contains only one gene per cell. In 1998 and 2010 two other transgenic papayas were developed to resist the virus.
After seeds from resistant plant were released to farmers in 1998, overall production which had declined by 64% in the previous 6 years, improved by 20% by 2002. To this date, non-transgenic papayas continue to be grown alongside the Rainbow variety in a ratio of about one to 4 for countries that have aversions towards genetically modified products. With Rainbow in the way, the aphids don’t reach other trees as easily. In a 2011 study, no allergens or nutritional losses were found among Rainbow fruits, and only about 1% of non-transgenic papaya trees had picked up genes from Rainbow. This is because the papayas grown commercially are mostly hermaphrodites whose pollen moves from the male to female flowers of the same tree.
Following Hawaii’s success, other countries developed PRSV-resistant transgenic papaya bases on their local strains. In the same manner that there is not a single cold virus, there are different strains of PRSV. In China and Taiwan, genetically modified papayas were failing in 2018. The transgenic plants hadshown resistance initially, but they were eventually overcome by the virus as its genes recombined.
The authors of a recent review study of PRSV-resistance point out that a single solution towards the virus is not the best approach. Genetically modified papayas are just one tool among many. For example, silver reflective plastic mulches have been shown to repel aphids from young papaya plants, which delayed and reduced transmission of the virus. In Brazil they had success controlling PRSV by clearing weeds and cucurbits, a source of aphids, from the periphery of papaya orchards.
Figure 20. Biologically, cadaverine is derived from lysine. Notice, by comparing the two structures, that substituting lysine’s COOH group with hydrogen creates cadaverine. The net loss resulting from taking away COOH and adding a H is the loss of CO2, hence the name decarboxylation. Lysine decarboxylase enzyme facilitates the feat.
Few people recognize the word amine, yet just about everyone has smelled one if they have come across a dead fish or a penis that has not been washed after it has secreted semen. Amines are organic compounds that have an amino group, NH2, attached to a hydrocarbon. They are, in a sense, organic analogues of ammonia and like ammonia, most are alkaline molecules and soluble in water. Fish aroma is a complicated blend of various compounds, but a dominant one is the amine known as trimethylamine. Along with many marine organisms, fish use a similar compound, trimethyl amine-N-oxide (TMAO), to protect against the adverse effects of temperature, salinity, hydrostatic pressure and the presence of urea. When fish or other marine organisms die, bacteria quickly reduce TMAO to trimethyl amine.Given that the latter is a base, it explains why the addition of lemon juice to fish improves the taste and eliminates some of the smell. Some Newfoundlanders keep a pot of vinegar on the stove on low heat while they fry fish to attenuate the stench in their homes.
Cadaverine is another amine with an unpleasant odor, as the etymology of the word suggests. It is partly responsible for the smell of semen and decomposing flesh. It is formed by the decarboxylation of the amino acid lysine (Figure 20), and if lysine metabolism is defective, elevated levels will appear in the urine of an affected individual. There is already cadaverine in semen when it is in the prostate gland, before it is mixed with sperm cells from the testes. However, since semen also contains amino acids, it is likely that semen lingering outside the body will contain more cadaverine as lysine is converted to cadaverine by bacteria. Some chemical engineers are looking into ways of getting bacteria to produce cadaverine on an industrial scale to replace petroleum-derived hexamethylenediamine(a.k.a. cadaverine). The latter is used with adipic acid to produce Nylon.
Several neurotransmitters to be explored in Chapter 8 on potassium are amines. They include the blood-pressure-raising noradrenaline, which also acts as one of the animal’s fight or flee hormones secreted by the adrenal gland. The other, adrenaline, increases blood pressure, accelerates the heart rate lets more air into the lungs. Dopamine and serotonin.
Nitric oxide
When a single atom of oxygen and a single nitrogen interact to form nitric oxide(NO), we get a molecule with an odd sum of valence electrons. The unpaired electron makes the molecule highly reactive. Yet the compound has shown up in a variety of places, some of them highly surprising.
Due to nitrogen’s low reactivity, it takes a large input of energy to create nitric oxide. Intense forest fires, lightning and internal combustion engines are all capable of providing enough energy. It’s for that reason that cars are equipped with catalytic converters which take nitric oxide, theprimary nitrogen oxide pollutant, and break it back down to its constituent elements. The converters are not perfect; for vehicles that burn gasoline, 2% of the nitrogen oxides escape unscathed. For diesel vehicles their converters are only 95% efficient. With its high reactivity, any nitric oxide that escapes initiates a cascade of reactions that can lead to photochemical smog. Its formation depends on light intensity, air movement, the initial concentration of nitric oxide (Figure 21).The smog itself is a mixture of NO2, ozone and a large variety of organic compounds.
Figure 21. Levels of nitric oxide(NO) spike during early morning rush hour. Their conversion to other compounds and the increase in sunlight intensity leads to a peak concentration of oxidants around noon. There’s another peak in NO2 during rush hour but the lack of light changes the chemistry and NO peaks at midnight from side reactions. Source: Pitts and Pitts Adv. Environ.Sci. Tech. 7. 75, 1977
In 1998 a Nobel Prize was awarded for the discovery that nitric oxide acts as signalling molecule in the cardiovascular system. It also helps control blood pressure and blood flow by dilating blood vessels. By the time the prize was awarded, other research had revealed that nitric oxide is also a major paracrine signaling molecule in the nervous and immune systems. A paracrine signal is a hormonal effect that works only in the vicinity of the cells that secrete it. That’s related to nitric oxide’s short half life of about 10 seconds. After getting their job done, the highly reactive molecules get converted to nitrite and nitrate. When white blood cells produce larger amounts of it, nitric oxide kill microbial invaders such as harmful species of bacteria and parasites. If the immune system overreacts with the release of too much nitric oxide, its ability to dilate blood vessels backfires, blood pressure drops, and sepsis and shock could set in.
But how is nitric oxide made in the body, and how does it work as a hormone? We will use blood vessels and penile erections as an example. The story begins when, due to arousal, a nerve cell’s acetylcholine, a neurotransmitter, locks in with the receptor of cells on the interior (endothelial cells) of blood vessels. This stimulates the enzymatic conversion of the amino acid arginine to citrulline, which is accompanied by the release of nitric oxide. The NO molecules diffuse out and get into neighboring smooth muscle cells. Unlike most hormones, nitric oxide can diffuse directly across cell membranes and do not interact with a receptor. Inside a muscle cell, each NO reacts with the iron bound to the active site of the enzyme guanyl cyclase, stimulating its activity. This in turn leads to the synthesis of another molecule, cyclic guanosine monophosphate (cGMP). The presence of cGMP eventually relaxes the muscle cell by removing phosphoryl group of the muscle protein myosin’s light chain. (We will explore how muscles work at the molecular level in the phosphorus chapter). This in turn dilates blood vessels and lets in more blood flow (Figure 22). Eventually the enzyme phosphodiesterase type 5 (PDE5) degrades cGMP and the penis goes “back to sleep”.
Figure 22. The interior surface of a blood vessel, where the smooth cells relax when CGMp is made. Source: D. Rosenbach, Wikipedia Commons
By serendipity, a drug, sildenafil (trade name Viagra), was discovered that artificially prolonged penile erections by inhibiting PDE5, indirectly accentuating the effects of NO. A more important drug that is also related to nitric oxide is nitroglycerin. Small amounts of the explosive (0.2 to 0.5 milligrams) are given to angina patients. The drug, named glyceryl trinitrate (GTN), is eventually metabolized to nitric oxide, which dilates blood vessels and relieves the painful attack. From the Nobel Prize site nobelprize.org, we have another and classic reminder that is there is not always a clear boundary between nature, biochemical theory and industry.
Alfred Nobel invented dynamite, a product in which the explosion-prone nitroglycerin is curbed by being absorbed in kieselguhr, a porous soil rich in shells of diatoms. When Nobel was taken ill with heart disease, his doctor prescribed nitroglycerin. Nobel refused to take it, knowing that it caused headache and ruling out that it could eliminate chest pain. In a letter, Nobel wrote: “It is ironical that I am now ordered by my physician to eat nitroglycerin.” It has been known since last century (1878) that the explosive, nitroglycerin, has beneficial effects against chest pain. However, it would take 100 years until it was clarified that nitroglycerin acts by releasing NO gas.
The main component of Earth’s atmosphere, nitrogen, prevents the rest (mostly oxygen) from being explosive. When lightning strikes, the essential elements nitrogen and oxygen get converted into nitrate which fertilizes plants. A related reaction occurs in internal combustion engines, except that the product is not nitrate but the pollutant nitrogen monoxide gas. As we shall see later, specialized bacteria also have the ability to convert otherwise fairly inert nitrogen gas into ammonium, which plants can use to make protein, nucleic acids and other important biomolecules.
Nitrogen extends the shelf life of foods in bags. To get pure nitrogen, it first needs to be liquefied. If you haven’t experienced liquid nitrogen, it is something to behold. If you pour some out of a Dewar flask into a styrofoam container, it makes the container squeak in a way that gives you goose bumps. If you pour hot water on liquid nitrogen, within a dense cloud, what flies back at you is a showering cascade of icy particles. Or you can use it to make ice cream quickly. Ice cream needs small crystals to be smooth and enough trapped air to lower its density. Instead of churning it, a volume of liquid nitrogen equal to half of the volume of ice cream ingredients can be poured over them. While stirring the mixture, an equal amount of the –200 oC -liquid can be added until the ice cream hardens and stops fogging. The quick cooling caused by liquid nitrogen guarantees the formation of small crystals and as the liquid turns to gas, bubbles of nitrogen are sure to be trapped within the ice cream.
In a Youtube comment thread, a student pointed out that his teacher had looked at him as if he was crazy when he had asked how they could extract oxygen from the air. Of course, the video he later found demonstrated how it’s perfectly feasible in a high school lab by using liquid nitrogen. You just get air to liquefy in a test tube by placing it in liquid nitrogen; wait a little and keep testing the gas above the liquid with a glowing splint until it relights. The key to the mystery is that the liquification point of a mixture of gases with different boiling points is between the boiling points of the pure gases. The boiling point of pure oxygen, O2, is -182 °C and the boiling point of nitrogen, N2, is lower at -196 °C. If air is cooled at atmospheric pressure, air will completely liquefy at -194 °C , 2 °C above nitrogen’s boiling point. Not only does oxygen have the higher boiling point and thus will boil off after nitrogen, it is more dense than liquid nitrogen: 1141 kg/m3 for oxygen versus 808.5 kg/m3. So, an oxygen rich liquid at the bottom of the test tube remains closer to the cold Dewar flask and oxygen gets less exposed to the warmer air.
Nitrous oxide (N2O)
Nitrous oxide,or laughing gas, was a recreational drug long before being used as an anesthetic. Industrially it’s made from the controlled melting of potentially explosive ammonium nitrate. Mainly two different reactions occur between 190 and 250 °C. One produces laughing gas and water; the 2nd produces nitric acid and ammonia. After condensation, three different scrubbers are used to purify N2O.
Although its concentration in the atmosphere is 1250 times smaller than carbon dioxide’s, nitrous oxide has a greenhouse gas warming potential that’s 310 times stronger. In nature it forms as a byproduct from the bacterial denitrification of nitrate and as a byproduct from the microbial oxidation of ammonia, reasons for using fertilizer judiciously.
Nitrate ion (NO3−)
Often with the help of mycorrhizae, plants can absorb nitrogen from the soil either in the form of nitrate (NO3−) or ammonium (NH4+). Which one predominates around their roots depends on soil conditions. Either ion is used in the biosynthesis of a variety of life essential molecules. Interestingly, to use nitrate, plants first convert it to ammonium. The ammonium is attached to glutamate (1 amino group) to make glutamine (2 amino groups). Then the latter is converted into 2 glutamates, one of which goes back to the cycle while the other gets converted to different amino acids.
Nitrate is the most common form of nitrogen running off from terrestrial ecosystems to rivers, lakes and oceans. Excess levels of nitrates in water can create conditions that make it difficult for some aquatic organisms to survive by causing algal blooms. The nitrate ion is found in ammonium nitrate commercial fertilizer, which can also be a dangerous explosive since the compound contains both an oxidizing and reducing agent.
Nitrite ion (NO2−)
Nitrite, like nitrate, is part of the natural nitrogen cycle. In plants it is an intermediate between nitrate and ammonium. In soils the story is more complicated. Nitrite could form from the oxidation of ammonia that’s added to soils from animal waste. This is carried out not only by bacteria but by Archaea. Once formed nitrite can either be further oxidized to nitrate and absorbed by roots.But in anaerobic conditions, it could be reduced ultimately to nitrogen gas by denitrifying bacteria which consume carbon in the process.This means that the essential element is removed from the soil through the action of these microorganisms. This lowers agricultural output, but it is a desirable process in wastewater because it reduces the amount of nitrate that flows into waterways.
It’ s not a good idea to drink water from wells that have high levels of nitrite. The ion causes hemoglobin in the blood to change to methemoglobin by assisting the oxidation of hemoglobin’s Fe2+ to Fe3+. Methemoglobin reduces the amount of oxygen that can be carried in the blood. Excess nitrites in food can also lead to the formation of nitrosamines, which are probable carcinogens. Legal limits for the addition of nitrates and nitrites have been set by several countries and the European Union.
I hope that Health and Welfare Canada guidelines for certain additives are a bit more stringent than they have to be to help compensate for possible loose play on the part of some companies in the food industry. When I was a student and shortly after I graduated, I analyzed fat content, dextrose and nitrite levels in hot dogs and other meat products for a well-known company. I’m not naming the company because for all I know they may have mended their ways. Also, I never gathered evidence that the whole industry was or is guilty of the things that I witnessed.
Nitrite (NO2–) is added in small quantities to preserve and to color many cold cuts and hot dogs. At the time, acceptable limits for NO2– ranged for 100 to 150 ppm (mg of nitrite per kg of meat), depending on the product. But levels frequently surpassed the guidelines by 25 to 50%. At first, I questioned my own analyses, but they were confirmed by my supervisor. The head of the lab said he would look into it at the production end, but weeks later the problem persisted. In general, we were instructed not to carry out the analyses in duplicate, unless an anomalous result surfaced.
We had learned in the statistical math section of analytical chemistry that tests of the sort should be carried out in triplicate. One day an inspector from Health and Welfare Canada came into the lab, and I told him about the problem. He told me he was just a summer replacement with only a background in CEGEP (a junior college) health sciences, and so that he could not really understand what I was saying. Later that summer, I was switched to the night shift, and I was alone in the lab. Digging into records from the previous two years, I found that other technicians had also been routinely finding high levels of nitrite (exceeding guidelines) in two specific products.
At the time nitrite an important preservative had already been associated with cancer in rats, but the “traditional” consensus was that the possibility of a similar occurrence in humans was only slightly elevated because of the concurrent addition of erythorbate and/or ascorbic acid. This supposedly prevented the formation of nitrosamines in the stomach’s acidic environment, the actual compounds with carcinogenic connections in animals. But I also saw the pale color of the hot dog mixture prior to nitrite addition, and it would not have been so pale if the ingredients weren’t such a mishmash of intestines and other meat “scraps”.
Most of the public was unaware that what they were really tasting in hot dogs was not the meat but the strong spices, salt and sugars. Our analyses revealed that the fraction of dextrose in hot dogs (close to 10%) was routinely greater than that of protein, placing the product somewhere on a spectrum between meat and candy. (Currently, according to USDA analyses, things are better from that perspective. The ratio of protein to sugar in a 100-gram sample ranges from 6 to 10 grams of protein to 1 gram of sugar. Yet fresh meat or fish has triple the amount of protein.) Their ham was also adulterated with water, which then facilitated the growth of bacteria, thus increasing the need for nitrite additives. Even today processed ham is still diluted, slicing the protein level to half of what is found in fresh, lean pork loin, according to USDA analyses.
When working there, I was strongly tempted to become a whistle-blower and to go public with what I thought were outrageous company practices from both a health and scientific standpoint. But relatives and friends were not supportive, and I was too wimpy to act alone. Aside from writing this piece, I have told my story to hundreds of students in my career, and since those analyses, I don’t think I’ve eaten more than a couple of meat-hot dogs in the last three decades.
A Journal of the National Cancer Institute study in 2005 found a link between processed meats and pancreatic cancer. In recent years, many companies have used celery extract, which is rich in nitrites as a way of deceiving consumers into thinking they are buying a healthy alternative. A 2019 study in the International Journal of Cancer confirmed again that there’s an increased risk associated with consumption of processed meat and colorectal cancer, but no increased risk when the meat was traditionally processed without nitrites.
Defenders of nitrite in processed meats like to point out that lettuce and spinach can also have elevated levels of nitrate(which can be converted into nitrite). There are two problems with their argument:
(1) Not all samples have concentrations comparable to nitrite levels. If the lettuce and spinach is not grown with fresh manure or with synthetic fertilizer, the nitrate levels plummet. For example, I measured about 250 ppm, relatively low for lettuce.
(2) More importantly it’s nitrosamines that form from nitrites that are the cancer-suspect agents. And nitrosamines form when nitrites are in contact with protein, which vegetables are low in.
It’s important to keep in mind the following: It’s from the World Health Organization:
No, processed meat has been classified in the same category as causes of cancer such as tobacco smoking and asbestos (IARC Group 1, carcinogenic to humans), but this does NOT mean that they are all equally dangerous. The IARC classifications describe the strength of the scientific evidence about an agent being a cause of cancer, rather than assessing the level of risk.
In other words eating processed meat on a regular basis will elevate risk for certain cancers but not to the same degree as smoking everyday or as working in an asbestos mine. For example, in the United States, approximately 3.5% of all cancer deaths are attributable to drinking alcohol whereas smoking is responsible for 30%. The extra danger posed by tobacco smoke is highlighted by the fact that 2/3 of Americans drink alcohol and only 11% smoke ( although the rate was higher, and many older victims of cancer gave up smoking too late. ) Processed meat consumption, although a group 1 carcinogen, is responsible for 0.7% of all cancers. And it’s usually colon cancer, which has a much higher survival rate than lung cancer or the cancers caused by alcohol.
Ammonium ion (NH4+)
Ammonium ion forms when an acid is added to ammonia. Smelling salts, which consist of ammonium carbonate, can be used to arouse consciousness, but a chemistry teacher should not use them on students who sleep in class. Breaking my own rule, I have discovered, however, that some people are far more sensitive to the smell of ammonia than others.
Most people have walked over ammonium, NH4+, without realizing it. When I was a teenager, my father would sooner believe that I was an incompetent lawn mower than even entertain the possibility that I was motivated to preserve what he considered weeds, those suburban symbols of lassitude and irresponsibility.
Ammoniojarosite (NH4)Fe3+(SO4)2(OH)6 is a mineral with ammonium ion. 20% of the global nitrogen pool is tied up in rock, even though many of the nitrogen minerals are obscure ones like this hydrothermal one.
If I’d see a patch of flowering clover or the tiny star-like flowers of stitchwort (Stellaria), I felt compelled to mow around them, come back to the patches with lawn clippers to cut protruding blades of grass and try to make the weeds as inconspicuous as possible, hoping to sneak my conservation effort past my father’s critical eye. But it never worked. Even though I tried to point out that stitchwort was rich in vitamin C, in his eyes there was a place for everything, and only grass should be grown in lawns.
I discovered that one of my father’s many kindred spirits lives on my street. A few nights ago, while walking my dog, I noticed he was destroying an attractive patch of black medic from his lawn that bordered the sidewalk.
Medic foliage and flowers. Picture by author.
With the friendliest tone I could manage, I asked him, “Did you know that plant is a member of the legume family, and it makes its own fertilizer?”
“Yes, but it’s not nice,” he replied.
I sensed it was hopeless, but my compulsion to explain science obliged me to continue. “The nitrogen from the air gets converted to useful ammonium by a helpful bacterium in that plant’s roots,” I said.
“Yes, but it’s not nice,” he repeated, still friendly.
For the sake of neighborly relations, now seemed like a good time to let go, so I smiled and concluded, “Oh well…it’s your property.” And I thought, “One man’s weed is another man’s science.”
Unable to spark a street discussion of the intricacies of black medic, I turn once again to the laptop keyboard. Medicago lupilina, is a member of the pea family (Leguminosae or Fabaceae). A close look at the cluster of yellow flowers reveals a set of miniature pea-like flowers. The bases, sepals and stamens are fused together into a cup-like structure, and you have to lift the cup and have exceptional closeup eyesight to see its reproductive parts.
Figure 1. The Rhizobium containing nodules of black medic. Picture by author.
A key ecological feature of this family is the nitrogen-fixing ability shared by most of its 18 to 20 thousand members. It happens through a symbiotic association with Rhizobium, which infect legume roots and form nodules(Figure 1), where in exchange for sugars, the bacteria use an anaerobic reaction to convert diatomic nitrogen into ammonium ion (NH4+). In the reaction, the nitrogen is “fixed”, because plants cannot convert relatively inert N2 into needed amino acids, but ammonium will do the trick. But free nitrogen gas has an oxidation number of zero, and it gets converted into NH4+ , whose nitrogen atom has an oxidation number of (-3). This reduction process would not occur if the common oxidizer in air, oxygen, would come into contact with the nitrogen-fixing enzymes.
Figure 2. Root cells of legumes deliver oxygen to a bacterium thanks to leghemoglobin.
But the problem is that the natural form of nitrogen fixation has something in common with the industrial version (Haber Process): it is an energy-demanding reaction, and what better way is there to release energy from sugars than through cellular respiration, which needs oxygen?
The bacteria get around this dilemma by making use of leghemoglobin(LEG), a pigment similar in structure to our hemoglobin but with a higher affinity for oxygen (Figure 2). In the diagram, notice that the pigment is in the nodule, outside of the bacterial cell wall, away from the enzyme complex (NC).
The small amount of oxygen is then delivered to the bacteria’s respiratory chain (RC), allowing several ATP molecules to be fed into the enzyme complex, where the reducing agent, NADH, converts the nitrogen into ammonium. The latter is released in aqueous form into the host cell , where it is converted into glutamine, asparagine and urea derivatives of the general form, R-CO-NH-CO NH2, where R can be a different hydrocarbon group.
Seeds from black medic are black. Picture by author.
These products are then transported to the rest of the plant through the xylem (not with sugars, which are distributed by the phloem), and with the abundance of these protein-building blocks, it is not surprising that the seeds of the black, ripe pods of black medic, like those of beans, lentils and other legumes, are rich in proteins.
Compared to other plants, legumes seem to be more sensitive to increases in carbon dioxide levels. Some species produce bigger seeds when the atmosphere is CO2-enriched, and in general, at least in soybeans, extra carbon facilitates the fixation of nitrogen, provided that there are no other stresses such as limited nutrient availability or drought.
I guess that’s another reason why my neighbor was digging up his black medic—better get to it before climate change amplifies his problem.
Ammonia (NH3 )
Ammonia is a gas with an unforgettable pungent odor. Most people first encounter with ammonia when they use a glass cleaner, which contains a very small amount of ammonia and a concoction of fragrance products. The combination of the small concentration and fragrances, one of which includes a compound from orange peels, makes the ammonia undetectable by the nose. Ammonia’s concentration is diluted by water and other ingredients. For example, Windex®Original Glass Cleaner contains ammonia along with four other cleaning agents and surfactants, two of which are also shampoo ingredients, and its characteristic sky-blue dye.
In water you find both ammonia and ammonium ion. Ammonia and ammonium do not have the same chemical properties. Ammonium is only 1/50th as toxic to aquatic life as ammonia itself. How much you have of each is determined by pH and temperature. Why? The answer to this question leads us to one of the key basic concepts of chemistry: equilibrium.
Each ammonia molecule in water bonds to at least three other molecules, but this arrangement also breaks up into ammonium and hydroxide ions. If the system is at equilibrium, the rate of break up is the same as the rate at which the ions combine to give you back the ammonia-water arrangement.
NH3(g) + nH2O(l)⇌
NH3.nH2O(aq) ⇌
NH4+(aq) + OH–(aq) + (n-1)H2O
Undissolved gas and water
Dissolved ammonia gas
Ions from gas and water in solution
Lowering pH increases the concentration of H+. These ions consume the hydroxide ion(OH–), slowing the rate at which they could revert to the ammonia form. At a lower pH we find more NH4+ and less dissolved NH3. As for temperature, since heat is released when ammonia dissolves in water, raising temperature gives the reverse reaction the edge and decreases solubility. At a near-neutral pH of 6.8 and at 18oC, the ratio of ammonium to ammonia is 367 to 1, so there tends to be a lot more of the less toxic species.
Figure 3. An overview of the industrial setup in making ammonia from hydrogen and nitrogen, the so-called Haber Process. Source: Wikipedia Improving the Haber Process
i. The Haber Process Ammonia is the product of the Haber-Bosch Process(Figure 3) which converts hydrogen and nitrogen gases into NH3.Ammonia can then be oxidized to nitric acid, a source of nitrates for fertilizer. There’s little doubt that there have been more positive benefits from the Haber-Bosch Process than drawbacks. Using air’s major component as its major raw ingredient, it has provided one of the three essential elements to agriculture. It has provided more food to a world whose population has gone from 1.75 billion in 1910, when Haber’s tabletop process was scaled up industrially, to 7.7 billion in 2019. It is easy to underappreciate the efforts it took up to “scale up” the original setup. In his Nobel-accepting speech, Bosch mentions that making the system as efficient as industry could make it at the time and finding the right catalysts took close to 20 000 experiments! They had to start with small compressors that could not run more than 12 hours without disturbances, and they developed their own 2200 kW one that operated for 6 months without interruption. The process as it stands now is our way of mimicking nitrogen fixation by microorganisms like Azotobacter, Nostoc and Rhizobium. But whereas the living versions have had millions of years to fine-tune them, we have had far less time to make necessary adjustments.
Figure 4 Rice and corn consume the most nitrogen fertilizer in the United States Source: Earth Syst. Sci. Data, 10, 969–984, 2018
What adjustments would be desirable? Notice in the diagram that the source of hydrogen gas is methane. Extraction of methane through hydraulic fracking has environmental consequences, but assuming those can be minimized, the carbon in methane ends up combining with the oxygen in steam to create carbon monoxide and eventually carbon dioxide. Canada’s largest maker of fertilizer, Nutrien, makes nitrogen, phosphorus and potash fertilizer. The majority of their direct carbon emissions come from their use of the Haber-Bosch process. According to their own website, annually they emit 11 million metric tons of CO2, which is about 40% of emissions by all light vehicles in Canada. A carbon capture process would be a welcome addition. An alternative would be to use a means of producing hydrogen that does not rely on methane. An example would be hydroelectric or geothermal powered hydrolysis to be explored in Chapter 4.
The Haber process is very energy-intensive because of the high temperatures and pressures employed. Currently a potassium-doped iron catalyst is used to accelerate the reaction. There is a need for more intensive research to find other iron catalysts that can produce ammonia at lower temperatures.
According to a study by Cassman and his colleagues, only 18% to 49% of the fertilizer nitrogen applied is taken up by crops, while the remainder is lost by runoff, leaching and volatilization or immobilized in the soil organic matter. Those cannot be all inevitable losses. The use of stabilized nitrogen fertilizer can help. Examples of such fertilizer include less soluble forms and compounds equipped with protective coatings to slow the release of nitrogen. There is also a urea-containing product that is mixed with dual inhibitors. One additive slows down the conversion to ammonia, which can be lost to the atmosphere where it can contribute to air pollution. The other inhibits the microbial conversion of ammonium to nitrate, which binds less to soil particles and is more prone to runoff and is subject to denitrification.
The practice of fertigation involves synchronizing watering and fertilization. This reduces the amount of fertilizer and water needed without sacrificing production and cuts down on the emissions of the greenhouse gas N2O. Haber-Bosch production can also be cut if less farmers relied exclusively on synthetic fertilizer. Supplementary sources could include compost manure, compost, fermentation residues from biogas production, crop residues and treated leftovers from food production.
There are also non-technical factors to consider. Fertilizers are not only produced to “feed the world”; production is also boosted to overfeed a growing minority, given the current world epidemic in overweight people and type 2 diabetes. Corn and rice demand the most nitrogen fertilizer among all U.S. crops(Figure 4). Yet the bulk of corn production is for animal feed. Soy, a good alternative source of protein, demands a tiny fraction of nitrogen fertilizer because it fixes its own nitrogen thanks to Rhizobium bacteria. If more people ate less meat and more soy, fertilizer consumption would be cut dramatically. A move in the wrong direction would be to mimic Japan, where the share of rice in feedstuff for pigs has risen from 10 percent to 30 percent. Elsewhere it is also being considered as an alternative elsewhere, and yet rice is even more nitrogen-intensive than corn.
ii. The excretion of ammonia
Ammonia is naturally found in varying amounts in human sweat and reacts with HOCl in pools to produce a variety of chloramines, which give pools their characteristic smell, irritate eyes and sensitive lungs of asthmatics. Urea from a cat’s litter or from any mammal’s pee will eventually decompose into pungent ammonia.
Can animals directly “pee out” ammonia, the way we sweat some out? Given that animals start their lives as eggs and embryos and given the toxicity of ammonia, the answer to that question depends a lot on their immediate environment.
Eggs of freshwater fish and some amphibians have constant access to fresh water. Those animals excrete much of their nitrogenous waste as ammonia.
If there’s less access to freshwater for the embryo, even though it requires an investment of energy, it is imperative to produce urea, which is less toxic than ammonia and does not have to be diluted as much. All mammals, sharks and many marine animals produce urea.
Urea is however water-soluble. If the embryo develops within an egg with a hard shell, excretion of urea would poison the food supply. The solution here is to produce uric acid which does not dissolve in water. Birds and reptiles excrete uric acid.
Amino acids and proteins
Table 1 The structure of 20 amino acids
All proteins from all species of life are made from only the 20 amino acids listed in Table 1. In fact, the basic unit of all amino acids is a tetrahedral carbon with four different groups: a nitrogen-containing amino group (NH2), a hydrogen atom, a carboxylic group (COOH) and a variable R group, drawn in pink in Table1. These groups will prove to be important in determining the shape and properties of the protein.Some can attract important cofactor ions, as we shall soon explore in this and other chapters. Whenever there are four different groups on a tetrahedral carbon, unless there is a plane of symmetry running through the molecule, the molecule will be chiral. A chiral molecule is related to its mirror-image-molecule like a left-hand glove is to a right-hand one: they are not interchangeable, not superimposable. Life only uses L-amino acids and glycine to make proteins. Glycine’s carbon is not chiral because it has a second hydrogen as its R group.
Figure 5. L-alanine is the amino acid incorporated into proteins. Its non-superimposable mirror image is not used. In the picture below, the model of L-alanine is the one held by the left hand that is being reflected in the mirror.
What exactly is an L-amino acid? Look at the chiral carbon of L-alanine (Figure 5), the simplest of the chiral amino acids, with the CH3 group pointing away from you. Imagine that the bond between the chiral C and CH3 is an axis. Rotate the molecule from the H to NH2 to COOH groups. Notice that you have moved them clockwise. All L-amino acids are like that. Now look at D-alanine in figure 2. If we follow the same rules, we will be moving the groups counterclockwise. None of the D-amino acids are used to make proteins. The D and L versions are mirror images of one another, but no matter how you flip one, if you try to place it over the other, there will always be two groups that do not match in the 3-dimensional space they occupy.
Proteins form by bonding amino acids to one another into a chain called a polypeptide. In organisms whose cells have nuclei(eukaryotes), the average protein has about 360 amino acids. The amino acids that are chosen and the sequence that they are placed in when the polypeptide is assembled determines the properties and role served by the protein. The roles are quite diverse,ranging from structural, such as keratin in hair, feathers and horns; to hormonal, such as follicle-stimulating hormone and insulin; to enzymatic, such as the digestive catalysts and other facilitators of biological reactions; to regulatory, such as the ones that influence which DNA regions are expressed; to antibodies. To gain some insight into how such diverse molecules can all be created from the same 20 amino acids, we will take a closer look at the chemistry of amino acids.
i. How polypeptides are made
Figure 6. At physiological pHs, amino acids exist as dipolar ions formed when the basic amino group picks up the acidic hydrogen from the carboxylic group.
At pHs found in the cytoplasm of the cell where proteins are made, amino acids exist as dipolar ions (di = two; polar = of opposite charge). For example, glycine’s acidic hydrogen(H+) from its COOH group will be picked up by the amino group, which is basic because of its unbonded pair of electrons. As a result of all this, glycine in the cell looks like the structure on the right-hand side of Figure 6.
Figure 7 How one amino acid molecule reacts with another: the first step’s mechanism
Chemically, how does this molecule bond to another one like alanine and take the baby-step towards becoming a polypeptide? The NH3+ group must first lose its hydrogen to another amino acid’s COO– group. This will make an electron pair from the nitrogen atom available and active again. It can then “attack” the carbon on the carboxylic group. The carbon is prone to receiving the amino group’s electrons because the oxygens on the carbon tend to pull electrons away from it (Figure 7).
Since the fourth bond is now made between carbon and the incoming nitrogen, a pair of electrons from one of the C=O bonds moves to oxygen, leaving it with a negative charge, one that’s balanced by the positive one developed by the nitrogen.
Figure 8. A rearrangement of electrons expels a water molecule. The dipeptide will be ready for another round once the proton is transferred away from the NH3+ group.
As shown in Figure 8, the charges developed are only temporary. As the double bond on the carbon is restored a pair of electrons flows towards the OH group where a pair of electrons snatches the hydrogen from the nitrogen, restoring its lone pair and eliminating the positive charge. Water is formed along with a peptide bond, shown in blue. Each time another amino acid is joined to the growing peptide chain, a molecule of water is produced. The formation of water during an organism’s protein synthesis compensates for the loss of water involved in the reverse reaction—the digestion of protein. Foreign proteins from the plants and/or animal tissue we ingest have to be digested into amino acids for purposes of distribution throughout our bodies, and when they reach their destination, they can be assembled into human protein. New protein is continuously needed for growth and/or to replace whatever was lost from the death of cells.
Figure 9. Three-dimensional shapes of common proteins. From RCSB Protein Data Bank.
But a protein molecule is not the long chain of amino acid beads that can be imagined from the assembly we have so far described. They look more like the images shown in Figure 9 obtained from RCSB’s Protein Data Bank.
ii.
How do they assume such shapes as shown in Figure 9? A polypeptide is part of the primary structure of a protein. Along the long chain of a polypeptide there can be attractions within the molecule, specifically between the partially negative oxygen of a C=O group and the partially positive H of an N-H group. These hydrogen bonds give the protein either an a-helical or b-pleated sheet form. (Figure 10).
What determines how one form is chosen over another? Close to a vertex of a twisting loop of the a-helix, there will be two chiral carbons, from two different amino acids. Each of these amino acids, which bonded in forming part of the polypeptide, has its own R group. The distance between these chiral carbons is only 1.5 Å. If that R- group is too bulky and can be easily rotated towards a neighboring R , as it is in proline, it will prevent the formation of the helical structure.
On the other hand, the separation between beta sheets is 3.5 Å. With much more space in between, beta sheets are much more likely to form when polypeptide sequences are richer in bulky R groups. Silk is an example of a protein that is almost entirely in the form of beta sheets. Examples of proteins that consist of a-helixes include hair, muscle’s myosin, myoglobin (70% helical), skin’s epidermis and blood clots’ fibrin (discussed in Chapter 9).
iii. Tertiary and quaternary structures of proteins
There are amino acids whose R groups attract water(hydrophilic), for example glutamic acid and aspartic acid. There are other amino acids whose R groups are hydrophobic, meaning that they are more strongly attracted to lipid substances. A part of a polypeptide chain may be suited less to form a-helixes and more suited to form less organized loops in which hydrophilic and/or hydrophilic groups attract their own kind. In addition, a “disulfide bridge” can be formed when the sulfur atoms of two distant cysteine amino acid-residues bond. Figure 11 reveals such interactions for part of the chymotrypsin enzyme, which digests proteins.
Figure 11 Different types links between peptide chains
The sum of these interactions will lead to a tertiary structure for the protein, leading to a globular appearance. The tertiary globular structure of enzymes is crucial for their function. The grooves in the 3D structure of the enzymes are the parking zones for the molecules whose reactions enzyme facilitate.Figure 12 reveals a complete and far more accurate model of the active form of bovine chymotrypsin. The colored molecule reveals the location of the enzyme’s active site.
Figure 12. A model of the active form of chymotrypsin. The colored molecule represents the active site of the digestive enzyme. The gold-colored coil at the bottom left is the a-helix. Source: proteopedia.org/wiki/index.php/Chymotrypsin
Some biochemists feel that the fourth level of organization(quaternary) is arbitrary. It describes molecules like hemoglobin that consists of at least two polypeptides (hemoglobin has four, two of each type, each connected to a heme) that interact with each other. Some authors restrict the definition to those that bond polypeptides to each other with intermolecular bonds and not covalent bonds like disulfide bridges.
The most important molecules of life that use nitrogen are the nucleic acids. Having no notion of genetic molecules and while ignoring the fact that children also resemble their mothers, spermists of the 17th century imagined that the sperm cell harbored a homunculus, a miniature person. Misconceptions about sperm to this day are reflected in the expression “a man plants his seed in a woman during reproduction”. It makes use of a weak plant analogy. A seed has a full set of a plant’s chromosomes, which are separate bundles of nucleic acids and protein. A man’s sperm does not have the 46 chromosomes that come in similar pairs in an embryo. Sperm is more akin to pollen, which also has only half of the total amount of genetic material. When eggs or sperm are produced in their respective sex, only one of each chromosome pairs is selected. In making a human egg or a sperm only 23 are chosen, which implies that any given cell is only one of 223 or one of almost 8.4 million possibilities. The body cells of an orange tree have only 9 pairs of chromosomes, so each tree can produce eggs or pollen with 29 or 512 different sets of DNA. When the human female egg is fertilized by a sperm in the womb and the two different and unique sets of 23 chromosomes join to produce 46, it’s only then that we have a “seed”.
Figure 14. The strands of DNA are held together by hydrogen bonds. The optimal number of hydrogen bonds are made when adenine pairs with thymine, forming two H-bonds and guanine forms three with cytosine. Source: Madeline Price Ball, Wikipedia
The DNA molecule is more beautiful and more organized than any protein molecule of the previous section. Using X-ray diffraction data from Rosalind Franklin who realized the molecule’s backbone had to be on the outside, James Watson and Francis Crick proposed their double helix model in a paper in Nature on April 25, 1953. They included the drawing shown in Figure 13, where the twisting “ribbons” consist of repeating units of a phosphate linked to a sugar (deoxyribose). Each phosphate in the ribbon-backbone has let go of its H+, which is why DNA is an acid. In his personal account of the discovery, Watson reveals how he was motivated to outcompete Linus Pauling, who was most people’s best bet to unravel DNA’s structure before anyone else. But Pauling’s model involved a careless error that had overlooked DNA’s acidity.
Figure 13. DNA’s double helix, from Watson and Crick’s model in Nature.
The simplest of all elements is essential to life, whose compounds so frequently bond hydrogen to carbon, oxygen and nitrogen to make an astounding variety of compounds ranging from protein to water. Even when it stands on its own, deprived of an electron, it serves key roles as an acid.
It exists as an odorless diatomic gas at room temperature. You will probably smell something if you drop some mossy zinc into hydrochloric acid. The metal will lose electrons to the “naked protons” that are in solution. Now “dressed” and bonded, hydrogen gas bubbles are ready to come out. But what you’re smelling is not the hydrogen but some of the excess HCl froth that vaporized from the heat.
More potential deception awaits. If you fill a party balloon with hydrogen gas and ignite it, there is an orange to red glow during the spectacularly loud explosion. It is odd because no such color appears if you collect and ignite the same gas obtained from reacting hydrochloric acid with zinc. One immediately suspects that the balloon fabric has something to do with it, but further investigations reveal that’s not the correct explanation. As revealed in a Periodic Table video from the University of Nottingham, after initially getting it wrong in a previous video, they point out that gases don’t mix instantaneously. Not all of the hydrogen in an exploding balloon is consumed by oxygen. The color comes from the incandescence of the excess hydrogen, thanks to the heat of reaction. There are two ways to verify this alternate explanation:
(1) Use a high-speed camera to record the explosion. This captured image reveals that the fragments of the balloon are nowhere near the orange glow and therefore cannot be contributing to the glow(Figure 1).
Figure 1. Exploding balloon fragments don’t color the flame orange.Source: captures from Periodic Videos: Hydrogen; University of Nottingham
(2) Mix approximately one volume of oxygen with two hydrogens in the balloon before igniting it. This stoichiometric ratio ensures that a lot less hydrogen will remain after ignition. I tried it, and sure enough, we saw very little color. I also tried to rent a high-speed camera, found it to be prohibitively expensive, so let’s rely on Nottingham’s budget and my captures of their video of hydrogen burning when the ratio is 2:1 (Figure 2a and 2b). Interestingly, the stage 2 of the Saturn V rockets that were part of the Apollo missions used a 3: 1 ratio, given that the stoichiometric ratio would be too explosive.
Figure 2a When a hydrogen balloon explodes, the orange color only appears in the balloon in which hydrogen is not mixed with oxygen.Although most hydrogen reacts with O2 in the air, some H2 is left in excess and incandesces.
Figure 2b The subtleties of the exploding hydrogen balloon in the form of a visual, albeit nerdy, poem by the author.
Industrially, hydrogen is already important, and it may become even more so if it will be used as a hybrid fuel to complement electric batteries. It’s a precursor to ammonia and methanol which are needed for fertilizers and polymers, respectively. Hydrogen’s ability to bond to oxygen comes in handy when refining certain metal ores. I recall my experience with using it in an analytical setting at a copper refinery. Copper’s ability to conduct decreases significantly in the presence of oxygen impurities. To verify that the product was indeed at least 99.95% pure, (I honestly recall 99.7% from the 1980s; so I state the current standard in case it has changed, or if my memory deceives me) I would pre-weigh several samples of copper powder in specialized tubes, slide them into tight-fitting holes of a furnace and connect the tubes to a hydrogen gas dispenser. Since at high temperatures, the gas would react with any of the oxygen in the copper to create escaping steam, the tubes would weigh slightly less after they baked for while. A ratio of the new mass to the original would reveal the purity. I also recall inadvertently starting a fire from a loosely inserted tube, but we put it out without any injuries or significant damage to the lab.
Most hydrogen is currently made by steam-methane reforming. Methane reacts with ~800 ºC steam under 300–2500 kPa of pressure in the presence of a nickel catalyst to produce hydrogen, carbon monoxide, and a relatively small amount of carbon dioxide. The carbon monoxide and excess steam are then reacted, again in a catalyst’s presence, to produce carbon dioxide and more hydrogen.
In the transition away from exclusive fossil fuel dependence, hydroelectricity or geothermal energy can be used to electrolyze water into hydrogen and oxygen. The latter reaction has nevertheless a lot of potential for a sustainable economy. Since oxygen reacts with hydrogen to produce only water, hydrogen becomes a desirable fuel if it is generated in a green, economical fashion. After previous attempts by other companies stuttered, ON Power (Orka náttúrunnar) in Iceland started producing hydrogen again in2018. They use an electrolyzer which can make enough hydrogen for all of Iceland’s hydrogen-powered cars and five hydrogen-powered buses. They were in service at the end of 2019. The turbines used to generate the electricity required to dissociate water are powered by Iceland’s abundant geothermal energy. As the project becomes scaled up, it should become profitable. In 2023, a Swiss company expressed interest in using Iceland’s green hydrogen to produce methane. Recall that hydrogen is also required for the fertilizer-producing Haber-Bocsh process, but currently it is derived from a fossil fuel. Geothermal electrolyzer have a much lower carbon footprint when producing hydrogen compared to deriving it from methane, whose carbon is wasted.
Water (H2O)
Rain, geysers, icebergs, rivers, oceans and clouds all have water, H2O, as their main component. Yet they all seem so different, that on the surface it seems reductionist to associate them all with the same compound. That only happens because we forget (or perhaps never had a chance to learn) that a formula can only summarize the ratio of atoms of its bonded elements. It doesn’t reveal the shape of the molecule, how the atoms get along, its varying density or how it responds to light and heat. Water’s unusual properties, which are consistent in at least this universe, are not only the reason icebergs float and seem different from rain but are also why water is the fluid of life.
To explain water’s properties, let’s delve into a combination of crude and refined abstractions. If you take a simplistic view of what supposedly happens when two hydrogen atoms, each with 1 electron, approach an oxygen atom with 6 of its 8 electrons in its outer energy level (“shell”), it seems like it should be a match made in heaven. Given that there is room for 2 electrons in the first energy level and 8 electrons in the second, a novice could naively but understandably imagine two possibilities: (1) an electron (negatively charged) leaves each hydrogen atom rendering them both positive, while the oxygen accepts the pair and acquires a charge of -2. Then the charged atoms stick together. Or, (2) one electron from each hydrogen is perfectly shared with an electron from oxygen to form two bonding pairs, keeping the molecule together.
Neither possibility is correct. Why? For one thing, electrons aren’t solid, little particles; they have wave-like properties. Unoccupied energy levels are not like empty beds waiting to be filled; they get more varied as the atom gets bigger. The combination of those two realities means that for any given atom, the best we could do is calculate three dimensional zones (“orbitals”) of where electrons are most likely to be. And each time atoms combine to form molecules, new orbitals arise with new limited and discrete energy levels.
Figure 3a. There is an almost tetrahedral angle between the oxygen atoms in the Mickey-Mouse shape of the water molecule.
Figure 3b. In water, the two lone pairs on oxygen along with the two bonds with hydrogen form an almost tetrahedral angle . The actual angle is reduced by the bulkier lone pairs of electrons.
Returning to the specific example of the water molecule, the combination of all total orbital contributions leads to areas of high electron density between oxygen and hydrogen atoms. That’s the current view of molecular bonds. But we haven’t gone full circle and come back to possibility number 2. The “sharing” is far from perfect. Partly due to oxygen’s greater number of protons and the difference in hydrogen’s and oxygen’s original orbitals, at any given moment, the electrons in the molecule can be thought of being closer to oxygen than hydrogen. This leaves a partial negative charge on the oxygen atom and a partial positive charge on the hydrogen atom. Equally important, the arrangement of the 3 atoms is not linear. With oxygen at the vertex, there’s an angle of about 104.45º (Figure 3a). It’s not a coincidence that the angle is close to the tetrahedral angle of 109.5o. Given that in addition to two bonding pairs, there also two lone pairs attached to the oxygen atom, there is an almost tetrahedral arrangement between the four groups, again to get as far from one another as possible (Figure 3b). The two non-bonding pairs, however, take up more room than the bonding pairs decreasing the angle between the latter. If it sounds like a rationalization, consider that the ammonia (NH3) molecule has only one non-bonding pair of electrons as one of nitrogen’s four groups to accommodate. With one less bulky “zone” than H2O, each H-N-H angle is 107o, even closer to the tetrahedral angle.
What then does this have to do with floating icebergs? If you pour vegetable oil into the slots of an ice cube maker, wait for it to freeze and then drop a cube into a glass of liquid vegetable oil, it sinks to the bottom. That implies that the arrangement of oil molecules in the oil-ice-cube is such that the molecules are more densely packed than in the liquid state. For any given volume of oil-ice, there will be more matter packed, exerting a greater force due to gravity. That’s what drives the oil-ice cube down. And it stays at the bottom of the glass until it melts, since the dense cluster can support the more loosely arranged liquid molecules. Oil is not the exception. Most solids are denser than their liquid states. But water-ice floats on water. Why?
The densities of ice and snow, as varied as they can be, are always less than that of liquid. That’s a consequence of the partial charges on the oxygen and hydrogen atoms and of the angle between them. The higher density of electrons around the oxygen atom symbolized by ”δ – ” and the lower density around hydrogen ( δ +) is why water is known as a polar molecule. It implies not that it’s a relative of the polar bear but that any given molecule of water will be attracted to another water molecule. Each time water molecules bond, their overall energy decreases while their orderliness increases. Whether liquid water becomes ice might seem to be controlled entirely by temperature. After all, if the molecules are too agitated, they will not slow down enough to feel each others’ attraction. They will remain in the liquid state.
But if you wonder why freezing eventually happens at one specific freezing point and if you want to know what kind of shape the molecules will adopt in the frozen state, those properties are controlled not only by (1) temperature but by (2) how much energy is released upon freezing, which is influenced by the difference in the type and number of bonds between the frozen and liquid states (3) the difference in the orderly arrangements between states. Those factors lead to a hexagonal arrangement, the most common one for solid H2O found in natural ice and snowflakes. For any molecule A(Figure 4), one of its hydrogens is attracted to an oxygen atom from molecule B while the other is attracted to an oxygen from molecule C. From the molecule A’s oxygen’s point of view, it is attracted to a hydrogen from molecule D and to one from molecule E. In short, each molecule is bonded to four other ones, making so-called hydrogen bonds. With the approximate tetrahedral angle of 104. 5º in three dimensions, it creates a hexagonal structure.Note that Molecule A is making 4 hydrogen bonds (highlighted in yellow) with neighbors. The bonds are responsible for the toughness of ice.
There is a lot of empty space between molecules (although it’s greatly exaggerated in the diagram). This is what lowers the density of snow and ice. In nature, there isn’t often perfect continuity within the network. Air and liquid water could slip in, leading to a wide range of densities, but if solid H2O is present, the mixture will be less dense than its completely liquid counterpart. In the absence of significant amounts of salt or other solutes, and in the presence of a small number other impurities whose role we shall soon explain, liquid water molecules come closer together until about 4 ºC. Between that temperature and 0ºC, they begin to move apart again slightly, getting ready for the hexagonal arrangement. In other words, water reaches its maximum density at 4 ºC. Why does that matter to life?
In colder areas where lakes and parts of seas freeze over winter, if the water kept getting denser past 4 ºC, the colder water would sink, exposing the warmer water to the cold air above the surface of the body of water. Eventually the entire lake or shallow part of the sea would freeze. But if the warmer 4 ºC is at the bottom, then the colder layer of water at the surface will eventually freeze and insulate the rest of the water and its organisms, preventing them from freezing.
Why are impurities needed for freezing to occur? In fact, they are needed in the formation of clouds, regardless of whether they are ice-filled cirrus or water-droplet-filled stratus clouds. To start the orderly arrangement, the molecules need to be attracted to more than just themselves, so the crystal must be seeded by an impurity that can attract the initial molecules. Without any “seeds” even as temperatures drop below the freezing point, water will keep getting colder without forming ice. Similarly, water vapour needs a surface or impurity to condense into liquid. The technical term for cloud seeds is cloud condensation nuclei (CCN). Sulfates and other sulfur compounds from the sea can make up such nuclei but size rather than composition seems to rule how effective they can be.
Clouds are aerosols, tiny impurities coated by tiny droplets of ice or water, all suspended in air. When crystals and droplets coalesce, their weight drives them towards earth. They parachute down, continuously slowed by air until they reach a terminal velocity. If the weather has been dry, enough to stress bacteria in the soil, they form resistant spores. Their coats are coated with dimethyl-9-decalol, also known as geosmin, an organic alcohol. If a hard rain splashes down on a dry soil, water coats the spores and the force of the rain bounces the little spheres into the air. This geosmin-containing aerosol is associated with the smell of rain..
It is a good thing that rain, oceans and rivers are not pure H2O; life depends on their lack of purity. Water’s ability to dissolve a wide variety of substances means that rivers can deliver essential ions to algae, the basis of the food chain in aqueous ecosystems, and bicarbonate ion which helps buffer seawater against pH changes. Blood, essentially the river that runs through our vessels, carries soluble ions, nutrients, wastes and hormones. Why are all these soluble in water? Again, its polarity allows it to draw ions away from crystals of salt (NaCl), for example, when they are still undissolved, and then keeps them in solution by surrounding positive(sodium) ions with the δ – face of several molecules and the negative(chloride) ions with the δ + face(Figure5). Other molecules like sugar also have a polar nature, and water dissolves them by a similar mechanism, except that there are hydrogen bonds between water and solvated sugar molecules.
Figure 5. Top figure: space-filling model of a sodium chloride crystal. A 2- dimensional cross section of ions in aqueous solution. This arrangement where ions are shielded from each other by water molecules is important. For ions with a less optimal charge-to-size- ratio, the “blanketing” of the ions by water is less common, and less of the substance will dissolve. Diagram by author.
To provide support, to keep poisons out of rivers, it’s also important for the planet and its organisms that everything does not dissolve in water. Bones could not never me formed if its mineral dissolved in water. Technically when we point out “does not dissolve” we really mean “not dissolve substantially” because at least a minute amount of just about any mineral can enter solution. Similar factors to those that control changes of state influence a substance’s solubility. An increase in temperature usually, but not necessarily, increases solubility. For a substance to be very soluble water’s attractions must be able to overcome the charges between bound atoms in the crystal and, equally important, there must be a favorable arrangement of water molecules around the ions of the crystal. For example, if ammonium, sodium or any of its alkali family members is bonded to carbonate, an ion needed to make seashells, the compound will readily dissolve in water and not serve the purpose. What do organisms use instead? Anything else would do so they chose from the next most readily available positive ions in the sea, magnesium and calcium. Since at 25oC, magnesium carbonate’s solubility in pure water is 0.22g/L but calcium carbonate’s (CaCO3) is only 0.006g/L, organisms opted for calcium, which has other advantages over magnesium for metabolism.
More than once, I intended to prepare hard boiled eggs for my kids in the morning, placed water in a pot but forgot the egg. If I remembered within 30 seconds or so, it was still safe to place my hand in the water, but it was a bad idea to touch the pot itself. Metals warm up faster than water does—that’s what a low specific heat implies. Specific heat is a characteristic property that measures how much energy it takes to raise the temperature of 1 gram of a material by 1 oC. The higher the c value is, the more difficult it is to warm up that substance. By the same token, substances with high specific heats also lose their heat with difficulty, while metals cool off with ease.
The high specific heat capacity of water helps slow the rate at which air changes temperature, which is why temperature changes between seasons is gradual, especially near large lakes or the ocean. Water is the reason why Toronto is milder than Montreal.
Both sea breezes in the day and land breezes at night are initiated by the fact that water warms more slowly than land in the day’s sunshine and then takes longer to cool at night. If we take the day as an example there is more of a buoyancy effect for air parcels above the warmer land. As it rises the extra molecules temporarily exert a higher pressure than what is found laterally, at the same altitude above the cooler sea. But as the higher pressure moves the air across to an area above the sea, it increases the pressure near the surface of the sea and lowers the pressure above the surface of the land. Wind then blows from sea to land.
It’s the reason that the Gulf stream can retain the heat of water heated in the Caribbean and carry it towards London, England, a city with an average temperature of 7 ºC, even though its latitude is six degrees more North than that of Montreal, whose average January- temperature is only -9 ºC.
If water’s specific heat was lower than it is, life would not be possible. The rate of evaporation would be too high, and it would be too difficult for the evolutionary precursors of cells to maintain homeostasis. Why is water special? The reason it is difficult to raise water’s temperature can again be explained by the hydrogen bonds that exist between molecules of water. To overcome this attraction, energy is needed. The bonds between the water molecules are like the links between the wagons of a train. Just like it is difficult to get a big train to reach a high speed, it takes a lot of energy to warm up water. Once the train is moving, it is difficult to stop. Similarly, it is difficult to cool water. Of course, in the liquid state, the links are not as fixed as those of train links. As molecules rotate, they constantly break and reform H-bonds, but their overall effect is to maintain attractions within the group.
Sciences in the Mural of Life 
