Saturday, December 31, 2016

Water is Life Part 2: Respiration

Note: This program first aired on December 31, 2016. 

There has been a lot of talk lately about the fact that water is life. We spoke last week about the biochemical reality of that concept, and looked at how water is involved in photosynthesis on a molecular level. Water is key to the reaction that allows plants to transform the energy of the sun from non storable electromagnetic radiation to storable chemical energy. The other great biochemical reaction that life depends on is respiration, the liberation of energy from chemical bonds. And once again, as in photosynthesis, water isn’t the main focus of the chemical reaction, but an extremely useful and in fact necessary bystander, without which the reaction could not occur. The star of the respiration show, the final product that is the real reason for the reaction to occur is called ATP (or adenosine triphosphate), a high energy, unstable molecule that does a good job of temporarily holding on to the chemical energy liberated from the glucose molecule, for a matter of seconds to minutes. Everything that happens in respiration supports the formation of ATP, one way or another.

Typically we think of the respiration reaction as combining glucose and oxygen gas to yield carbon dioxide and water. In reality, we combine glucose, oxygen gas and water to yield carbon dioxide and even more water. We put some water in on the reactant side, and get even more water out on the product side.

Respiration, particularly the aerobic or oxygen using kind we are talking about today, is, just like photosynthesis, a fabulously complicated process with many mind numbing intermediate molecules. The first part of the process, glycolysis, has 10 sub reactions all of its own, just to turn a 6 carbon glucose molecule into two 3 carbon molecules. Those three carbon molecules, get further processed into two 2 carbon molecules, and then enter something you may remember from school, the Citric Acid cycle, or Kreb’s cycle, which uses a series of organic acids to further process the  two carbon molecules to their ultimate fate, being turned into carbon dioxide gas. And all along the way, at key steps, electrons are getting moved around, electrons that started in the glucose molecule. Electrons that originally came from water molecules back in the photosynthesis reaction that formed the glucose.

If you are thinking ahead, you can see where this is going. Water plays several roles in respiration. The first is that it is the solvent in which all of these other chemicals are dissolved. Without water, these reactions would have no matrix within which to take place. Secondly, water plays a supporting chemical role in the citric acid cycle, stepping in as a reactant. Water also allows for the initiation of respiration by hydrolyzing or breaking down starch and other more complex carbohydrates into individual glucose molecules. Thirdly, and probably most importantly, water gets formed as a result of all of those electrons getting passed around. 

As the electrons get moved from one intermediate carrier molecule to another, conditions inside the cell get set up for the generation of ATP, which remember is the ultimate goal of respiration. Once the stage is set for the ATP generation, virtually all of the useful energy has been wrung from the electrons, and the last hand off, to what we call the terminal electron acceptor, releases the last of the energy. The terminal electron acceptor is oxygen (that is why you need to breathe air with oxygen in it). Oxygen on its own though, with an extra couple of electrons, is what we call a free radical, an unstable and potentially destructive molecule. The destructive power is based on the imbalance of the electrostatic forces in the atom. To counter this, the oxygen quickly joins some hydrogen ions that are available in the cell, and forms water, and the products of respiration are complete. If water wasn’t formed as a result of respiration, we would be left with a free radical form of oxygen which can be destructive to the cell. So once again, the Oscar for best supporting chemical in a biological reaction goes to: water.


As if often the case, any college level Biology text book should cover this in sufficient detail. I use Freeman et al, Biological Science 6th ed. Pearson Higher Ed

From this article in Pharmacology Review:

Saturday, December 24, 2016

Water is Life Part 1: Photosynthesis

Note: This program first aired December 24, 2016.

There has been a lot of talk lately about the fact that water is life. That means a great many things to a great many people. To the fishing communities here on the coast of Maine, water provides a living, a work place, a source of income and food. On a hot summer day water provides relief, a place to cool your body. For many people the water is life idea is a spiritual endeavor; water represents the blood of the earth, traveling across the body of the earth, bringing sustenance. Even those recreationalists less spiritually aligned recognize water as a means of direct immersive contact with the natural world. We all understand intuitively that water is life, but few of us understand exactly why. But talk to a biologist, or a chemist, and you will learn that “water is life” has literal concrete molecular meaning. 

Water has a specific and intimate role in the most basic biological reactions, playing a key part in both photosynthesis and aerobic respiration.  I’ve talked about photosynthesis before on the show, but it is hard to overemphasize the importance of this reaction to the fact that we are all here. It is the means by which all of the energy our bodies use becomes accessible to us; our bodies can’t use light energy, but we can use the chemical energy stored in organic molecules created by plants and transferred up the food web. Virtually our entire economy is based on photosynthesis*, and until a couple of hundred years ago that was all “current photosynthesis”. The advent of the industrial age brought a reliance on fossil fuels, but the “fossil” in fossil fuels is photosynthesis. All the chemical energy stored in oil, gas and coal originated exactly the same way as the energy in your bowl of Wheaties-through an intricate set of biological reactions that move electrons up and down and from atom to atom and result in a final product that has higher potential energy than the original ingredients. Photosynthesis pushes energy up hill. We rely on it utterly. And it relies on water.

The kind of photosynthesis we are talking about, oxygenic photosynthesis is the kind you learned about in school, when you learned that plants can take carbon dioxide and water in the presence of sunlight and make glucose and oxygen. A specific group of bacteria, called cyanobacteria (also known as blue green algae, but this is a misnomer as they are not algae) and certain members of the eukaryotes, a group of organisms that includes us and pretty much everything else you would picture as alive are the organisms that can perform oxygenic photosynthesis. There are other forms of photosynthesis, but they don’t make oxygen, and more importantly for the story today, they don’t use water.

So what role does water play in this most fundamental biological process? There are actually two key roles, Water goes into the photosynthetic reaction and gets deconstructed for parts. The oxygen gas generated as a byproduct of this reaction, the oxygen that changed the composition of the atmosphere and enabled all of the life we see around us is the O in H2O. Take apart a couple of water molecules and you have two oxygen atoms, that bond to each other to create the diatomic oxygen gas we know, love and depend on.  But photosynthesis isn’t trying to create oxygen, it is trying to turn electromagnetic energy into storable chemical energy, and to do that it needs some electrons. Electrons are the currency of non nuclear atomic energetics. The light energy that gets absorbed by chlorophyll serves to excite electrons, and the net result of the first part of photosynthesis is that a special chlorophyll molecule called the reaction center loses some of these excited electrons as they are passed on to other molecules in the photosystem.  That is its job, to absorb sunlight and pass that energy along to the rest of the system in the form of electrons. To keep doing its job though, the reaction center chlorophyll needs electrons to replace the ones it gave away. Where does it get those replacement parts? You know it already—it gets them from water. That is the reason water is required for photosynthesis, and therefore life—its electrons.

Getting electrons from water isn’t easy to do. Oxygen is an incredibly greedy atom and is loath to relinquish any electrons, chemists call that being strongly electronegative. The only things that can get electrons away from a water molecule are an even more strongly electronegative reaction center chlorophyll molecule, and some very clever enzymes.

So there you have it, water is life, because water is the source of the electrons that provide the medium by which the sun’s energy gets turned into chemical energy, and as a handy byproduct also happens to provide the world with the oxygen it needs. What we need that oxygen, and yet more water for, we’ll talk about next week.


As if often the case, any college level Biology text book should cover this in sufficient detail. I use Freeman et al, Biological Science 6th ed. Pearson Higher Ed

Saturday, December 3, 2016

Right Whales and Ship Strikes

Note: This program first aired on December 3, 2016.

If you wanted to design an ocean animal that is perfectly constructed to get hit by ships, what characteristics would you include? It should probably be big, and slow moving. Make it dark so it is hard to see. If it is a mammal, it will need to spend time at the surface, so it can breath. It should have to spend long amounts of time feeding on very small food items, again, often at the surface, at night. Make it easily stressed by noise, which decreases its ability to communicate with others of its kind. Put its range right near shore, in major shipping lanes near highly populated areas.

This isn’t just a hypothetical exercise, this animal actually exists. It is called the Eubalaena glacialis, North Atlantic Right Whale, and it is one of the most endangered large whales in the world.

Many people have heard the story of the Right Whale, so called because they were the “right” whale to hunt especially in the early days of whaling. As a species evolved to feed in relatively shallow productive water of the continental shelf, they stay close to shore, which made them accessible to land based hunters in small boats. They could be brought to shore and processed on land, and were an important part of the land based whaling industry, before the more ocean going sperm whale was discovered and chased all over the global ocean on multi year whaling expeditions. Right whales also have enough blubber, or body fat, to lower their overall density enough that they will float when killed, again, making them easier to manage from a small boat. It is hard to know how many Right Whales were around before commercial whaling began, but they received internationally recognized protection starting in 1935, after having been harvested consistently in the northwest Atlantic since the 1500’s, and most likely earlier in European waters. Researchers estimate that there were less than 100 North Atlantic Right whales left in the western Atlantic in 1935. Since that time the population has rebounded, but very very slowly. The most current published population estimate puts the number around 476 individuals, based on direct observation.  Though they are no longer hunted, they are still highly endangered.

Why are they still endangered? If we return to our list of characteristics of our vulnerable ocean animal, we can start to see why. They like to hang out where we spend most of our time in the ocean too. They fish where we fish. They travel where we travel. The two big reasons that Right whales die as a result of human activity are 1. They get tangled in fishing gear and 2. They get struck by ships.

The fishing gear entanglement issue is complicated, and unfortunately seems to be a fact of life for North Atlantic Right Whales. Researchers have observed that 83% of these whales have scarring consistent with entanglement, and around half show signs of multiple entanglements. Changes to fishing gear are a start at preventing this problem, but there is further work to do.

On the ship strike side, and because I work at a maritime college I focus more on this end of things, some very positive strides have been taken. In areas where these whales are known to congregate at certain times of the year, speed limits have been imposed for vessels over 65 feet. These zones are called seasonal management areas or SMAs and came into effect in 2008. Compliance on the part of industry has slowly but surely increased since that time. Speed makes a huge difference. If a whale is struck by a ship traveling at 20 knots, mortality is 100%. When ship speed is reduced to 9 knots, mortality is around 20%. And it has had an impact. Before 2008, 87% of the ship strike mortality occurred within or just outside the SMAs, because that is where most of the whales were. Since these slow zones were established, all of the documented ship strike mortality events, averaging 1 per year, occurred outside of the SMAs. So just getting ships to slow down where the concentration of whales is highest has worked to decrease our impact on this population. Not that we should stop and pat ourselves on the back, there is certainly more to do. These whales continue to face the threats of ship strike outside of the SMAs, entanglement in fishing gear, increased stress from noise pollution, and the likelihood of a genetic bottle neck stemming from such low population numbers in the early 20th century. We’ll learn more about what is being done on a future show.


There is a ton of info out there on these whales, including many federal websites, due to the federal regulations stemming from the protections encumbered by the Endangered Species Act.

The study that documented the positive impact of the speed reduction zones: