Book Review: “The Vital Question”

By Rich Feldenberg:

On this episode of Darwin’s Kidneys – first of 2016- I’ll be reviewing a book by Nick Lane called, “The Vital Question: Energy, Evolution, and the Origins of Complex Life”. This book attempts to tackle some of the toughest questions in biology today, such as how, and in what environments, life originated, how the complex eukaryotic cell evolved, how the cellular mechanisms to generate energy echo back to the days before biology, and why sexual reproduction is the way it is based constraints placed on us by our energy generating systems -the mitochondria. It is a lot of territory to cover, but Dr. Lane does an amazing job of bringing all these seemingly diverse themes together, synthesizing them into a coherent narrative that flows as easily from one topic to the next, as electrons flow down the mitochondrial respiratory chain (a central subject of the book).

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For those of you, who like me, love the topic of biological origins, this book will keep you engaged, and I had trouble putting it down, as I waiting for the next amazing revelation to be exposed. The early part of the book describes the common thread between the most essential metabolic activities of all living cells on earth -whether they are bacteria, archaea, or complex eukaryotes – and the natural geochemical activity of Alkaline Hydrothermal Vents. All life generates its energy by using proton gradients to drive the production of ATP (the energy currency of the cell). In all cells today, special pumps have evolved to pump protons (hydrogen ions) across a membrane. This creates a proton gradient (more protons on one side of the membrane than the other) which will naturally lead to those protons tending to diffuse back across the membrane. Cells use this proton gradient to run the protein ATP-synthase, to generate ATP, just like running water can be used to turn a water wheel to do work at a mill. In order to get the proton, it has to be separated from its electron, and that is done through a series of oxidation-reduction (redox) reactions, where the electron is transferred from one compound to another with each subsequent compound having a greater affinity for the electron than the last compound. It ends with the electron being transferred to oxygen (O2), which has the most affinity for the electron, converting the oxygen to water. The compounds where the electron is being transferred, are the respiratory transport chain of proteins. It is also found in plants as part of their photosynthesis machinery.

 

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This process mirrors a naturally occurring geological process found in Alkaline Hydrothermal Vents on the ocean floor. These vents are different from the “Black Smokers” that have been better popularized, as sites of chemosynthesis, where an ecology of organisms survive using the energy of the vent, and are not directly dependent on energy of the sun. The Alkaline Vents, on the other hand, are not quite so hot, but more importantly are composed of a matrix of mineral with thin walls that mimics a cell membrane. The vent fluid is more alkaline, with a pH of around 10, and the ocean water more acidic. It is thought that the ocean pH, 4.5 billion years ago might have been even more acidic that it is today with a pH of around 6. Since pH is a measure of the proton concentration, there is a natural proton gradient between vent fluid and ocean water separated by a thin mineral. The mineral also contains Iron-Sulfer complexes and other minerals that can act as redox centers, producing the electron transfer that we also still see today in our respiratory transport chain.

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Dr. Lane argues that this environment provides a very plausible explanation for how life originated and why all life uses the unusual proton gradient method to generate energy. His own research is, in part, using reactors to replicate the Alkaline Vent environment to study this theory further.
He goes on to discuss how life could then have evolved more effective cell membranes making wondering further from the vent location possible, as long as these simple organisms could begin to pump protons on their own, at this point. This movement into the new environment, and an existence independent of the Alkaline Vent, is where the split between bacteria and archaea probably occurred. He shows the evidence for this hypothesis.
A great deal of the rest of the book describes the evolution of the complex cell, by the synthesis of an archaea host cell, with a bacterial endosymbiont which went on to become the mitochondria. He also describes, in detail, the genetic evidence, as well as, that logical considerations, that suggest this occurred, it occurred only once, and how the other features of the complex cell -such as nuclear membrane developed.

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The book is beautifully written, but I will say some background in biology certain helps, but his writing is clear, entertaining, and well focused.
I just finished reading, “The Vital Question” this month, but it is now in my top 10 all time favorite science books. The last Nick Lane book I read was called, “Oxygen” and was equally good. It was also about the biochemistry of energy generation in organisms. I urge you to check out, “The Vital Question”, and let me know what you think.

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References:
1. The Vital Question, by Nick Lane

2. Nick Lane webpage.

3. Darwin’s Kidney Article on Molecular Fossils (EMMAs).

4. Article on the necessity of a new word, Mesign, to help differentiate between something purposefully designed and something that has the false appearance of design being evolved by natural selection.

EMMA knows the secrets of your past – but will she tell?:

How molecular relics in your cells tell the story of our common origins.
By Rich Feldenberg

In “Emma”, Jane Austin’s classic Novel, Emma Woodworth is described as handsome, clever, and rich. She takes to matchmaking, perhaps overestimating her abilities, and in doing so a variety of humorous and near disastrous calamities ensue. Of course, all ends well for Emma and her friends in the Novel. In this article we will examine a different sort of EMMA, but there may be some analogy to be found that even the brilliant Ms. Austin could not have foreseen. EMMAs is my acronym for Evolutionarily Modified Molecular Artifacts. I have used it in place of what has previously been referred to by some as molecular fossils. Fossil has the implication of something long dead, now extinct, and not seen in the world for many ages. Besides not being precisely what is meant by molecular fossil, when used by molecular biologists or astrobiologists, molecular fossil already has another meaning when referring to molecular or chemical remnants of past life. EMMAs may be a more appropriate term since it refers to molecular parts of still living systems that still display some resemblance to their more ancient and primitive forms. In this article we’ll explore a few examples of EMMAs and see what they can tell us about our distant past and the origin of life on earth. Austin’s Emma says “seldom, very seldom does complete truth belong to any human disclosure; seldom can it happen that something is not a little disguised or a little mistaken”. It is the nature of Evolutionarily Modified Molecular Artifacts, that their true nature is more than a little disguised and has traditionally been more than just a little mistaken. Lets look at the evidence that these living artifacts may give us a glimpse at a truth about our distant past, where we came from, and our common origins with our fellow living inhabitants on planet earth.

There are a number of critical biological molecules that are common to all life forms on earth today, and that have some unusual properties suggesting a common origin arising from more primitive precursor molecules. With this in mind, we’ll look at the common molecule ATP and the coenzymes NAD, and Acetyl Coenzyme-A, and finally the catalytic site of the protein synthesizing ribosome, which is perhaps the most fundamental molecular machine of any living cell. We’ll see that these examples also hint at a previous and now lost stage of life known as the RNA world, that preceded the Last Universal Common Ancestor (LUCA) of all living things on our planet today. To continue to stretch our Jane Austin analogy just a little further, we might imagine that the RNA world played matchmaker, in world long lost in deep time, and successfully paired DNA and protein, the two major biomolecules of life in our modern world. EMMAs demonstrate the remnants of that world before the matchmaking. Over evolutionary time they have been mesigned in their original forms, and re-mesigned into their current disguised forms. Like children who can not imagine a world before they were born, or before their parents existed, we too have a difficult time looking past the DNA/protein paradigm and into the RNA world.

Just like any good Austin Novel there are many interesting and complex characters. Some of the important players in our story of life on earth include molecules that contain pieces of ribonucleic acids (RNA). The first we’ll meet a key character known as adenine triphosphate (ATP). We will then be introduced to several of the coenzymes – small organic molecules that are necessary for the function of larger enzyme complexes. An finally we’ll become acquainted with one of the classic characters on life’s busy stage, the active site of the ribosome, which catalyzes one of the most fundamental reaction of the cell – the peptide bond to build protein. As stated above, each one of these molecules contains an RNA component, even though none of them are used to store or transfer genetic information. They are all involved in important biochemical reactions that have traditionally been thought to be performed only by protein enzymes. As we will see, the catalytic site of the ribosome relies on RNA exclusively to catalyze it’s fundamental reaction, and is therefore a ribozyme (RNA enzyme). These examples, and many others that we won’t describe today, appear to provide evidence of a long lost RNA world, with protein eventually evolving around the RNA core to assist and improve its biochemical efficiency.

First let’s look at the simple ATP molecule, which is well known to serve as the energy currency of the cell. It functions to power chemical reactions by transferring energy from its high energy phosphate bonds. It contains the base adenine, bound to the pentose sugar ribose. Ribose is the same sugar used in RNA (ribonucleic acid). The sugar ribose differs from the sugar deoxyribose (the sugar of DNA) only in the presence of a hydroxyl (OH) group at the 2-prime carbon. DNA does not contain this 2-prime hydroxyl group.

ATP is produced by the metabolic processes of glycolysis, the Kreb’s cycle, oxidative respiration, and by light powered photosynthesis, but is used in a multitude of reactions to provide the energy necessary to drive those reactions in the desired direction. Why should it be necessary that this energy storage molecule is a nucleotide? Could this be a hint that it’s important role began at a time when RNA played a much more central role in biology than it does today? Is the adenine now just a left over of the original mesign?

ATP – the energy currency of the cell.

Let me now introduce you to the charming NAD. Nicotinamide Adenine Dinucleotide(NAD) is a coenzyme that is composed of two ribose containing nucleotides linked together by a diphosphate connector. One of the nucleotides is adenine, just like that found in RNA, and the other nucleotide contains the non-RNA base nicotinamide. Being a dinucleotide, again should make us appreciate this coenzyme’s primitive origins.

Nicotinamide Adenine Dinucleotide (NAD)
The Adenine base is on the bottom half and the Nicotinamide is on the top half.

Nicotinamide is converted from nicotinic acid to its amide form. Nicotinic acid is also known as the vitamin niacin. The name was changed to niacin due the concern that people would confuse the nicotinic acid with nicotine and falsely believe that nicotine had nutritional health benefits. Nicotinic acid and nicotine are chemically distinct molecules, although they both share a pyridine ring structure- which is an aromatic heterocyclic ring with nitrogen at position 1 (see below). Both nicotinic acid and nicotine have their own distinct biological effects. Of course, nicotine is produced by the tobacco plant, but is not produced by animal cells. Nicotinic acid is found in all living cells, whether they are animal, plant, or single celled bacteria.

Chemical similarities between Nicotinamide (part of NAD) on the left, Nicotinic acid (Niacin) in the middle, and Nicotine (harmful carcinogen) on the right.

Nicotinamide Adenine Dinucleotide (NAD) is necessary for the operations of a wide variety of enzymes in all cells. The NAD molecule can be in either an oxidized form (NAD+) or a reduced form (NADH), and is therefore an important component of many oxidation-reduction reactions in the cell. It can transport electrons in its NADH form, or take them away in its NAD+ form. Since cell metabolism is, in large part, the process of extracting energy from biomolecules like sugars and fatty acids – in other words oxidizing these molecules in a slow and controlled way – NAD is important for the function of many enzymes found along these these metabolic pathways in the cytosol and mitochondria in eukaryotic cells. In the mitochondria NADH becomes oxidized, as electrons flow down the electron transport chain. The resulting H+ (proton) is pumped across the cellular membrane, creating a proton electrochemical gradient, which then is used to produce ATP – to be used to power other non-spontaneously occurring chemical reactions.

Ball and Stick chemical model of NAD

The coenzyme known as Acetyl-CoenzymeA , like NAD, also contains the nucleotide adenine. Connected to it is a molecule with a thiol group (SH) at its end. This molecule participates in important chemical reactions that require the transfer of an acetyl group (a methyl bonded to a carbonyl – see below).

         acetyl group

Many steps in key chemical pathways involve acetyl transfers to build or break down molecules. The sulfur group in Coenzyme A can chemically attack the acetyl group of another molecule, remove it from that molecule, and thereby take it for use in a multitude of biochemical reactions. In the process Coenzyme A becomes Acetyl Coenzyme A, and can be recycled back to Coenzyme A once it released the acetyl group at the right time and place. It is an important part of enzymes involved in glycolysis and the Krebs cycle – both chains of reactions that break down glucose to create ATP. Gene expression can also be regulated by acetylation of histone protein, telling the cell which genes to transcribe and which need to remain silent in a given cell type. It is also used to create the neurotransmitter acetyl-choline from choline.

Conenzyme A. To become Acetyl-Coenzyme A, an acetyl functional group is attached to the thiol group at the far left end of the molecule. In this way, Acetyl-Coenzyme A can transport a carbon atom to be used in other chemical reactions.

Our true hero is the ribosome, the site of protein synthesis, and common to all modern cell types, although, the molecular structure differs enough between prokaryotes (single celled organisms like bacteria and archaea) and eukaryotes (more sophisticated cell types like that seen in animal or plant cells) that these differences can be exploited by certain antibiotics which target prokaryotic ribosomes, but leave the eukaryotic ribosomes unharmed. Even the mitochondria found in animal and plant cells have their own ribosomes that resemble prokaryotic ribosomes more than eukaryotic ribosome found in the cytoplasm of those same cells. The production of protein is perhaps the most primitive and basic metabolic function of all living cells. It came as a huge surprise to scientists when they learned that the active site of the ribosome (where the peptide bonding reaction takes place – the peptidyl transferase reaction) is composed only of RNA and no protein at all. Additional structural studies have confirmed that it is the RNA that catalyzes this basic cell reaction.

This would seem to support the notion that RNA played the major role in the biochemistry of the most primitive life forms. Ribosomes today are complex molecules, made of multiple components, some of which are ribosomal RNA and other parts are protein – it is therefore a ribonucleoprotein. The protein portions seem to assist the ribosome in doing its job more efficiently.

The examples given above reveal the important role that RNA molecules play in cellular biochemistry. The fact that some of the basic process of life rely on these RNA containing molecules lends support for the RNA world hypothesis. Except for the ribosome where the actual catalytic site is still a ribozyme, the other examples don’t use the RNA portion for the vital catalytic role, but may possibly have done so in the distant past. The presence of the RNA still retained in the coenzyme may offer proof that it is a molecular fossil – or as I prefer an Evolutionarily Modified Molecular Artifact (EMMA). To paraphrase Jane Austin, when referring to the RNA that lays hidden at the core of many of our most rudimentary metabolic processes, which may have served a grander role in a far distant past, and which now has relinquished it’s primary role for one of a more modest, behind the scenes assistant, “The sweetest and best of all molecules, faultless in spite of all her faults”. In future articles we can examine some other examples of EMMAs, such as additional types or ribozymes and riboswitches.

References:

1. Article on Mesign in Nature (also linked to within this article):
http://darwinskidneys-science.com/2015/07/08/another-clever-mesign-brought-to-you-by-mother-nature/

2. Nicotinamide Adenine Dinucleotide (NAD) Wiki article.
https://en.m.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide

3. Acetyl Coenzyme A Wikipedia article.
https://en.m.wikipedia.org/wiki/Acetyl-CoA

4. “The RNA World” Gesteland, Cech, and Atkins. Second Edition, Cold Spring Harbor Laboratory Press. 1999.

5. “Molecular Biology of the Gene” Watson, Hopkins, Roberts, Steitz, Weiner. Fourth Edition, 1987.

6. Life as we don’t know it.   “Musings on the Biochemistry of Saturn’s Moon Titan”.

Musings on the biochemistry on Saturn’s moon Titan. Part I

Part I: what makes potential life on Titan such a challenge?
By Rich Feldenberg

As we have been repeatedly surprised by the discoveries made by our robotic explorers over the last few decades, it is certainly clear that our solar system is much more interesting and diverse than we ever previously imagined. There appears to be at least several objects among our cosmic neighbors that show promise as potential habits for life outside of Earth. Some of the prime real estate in this respect would be Mars, Jupiter’s moon Europa, and Saturn’s moon Enceladus. Both Europa and Enceladus show evidence of having liquid water, vast oceans in fact, beneath their frozen crust, and Mars most likely had liquid water on its surface billions of years ago, and perhaps still has liquid water somewhere below the surface. Even Venus may have been covered in water in it’s early history only to evaporate it’s oceans away due to an out of control green house effect. In addition to these, there are other candidates moons and even dwarf planets, that may be home to liquid water beneath a frozen surface, and therefore also a potential abode for living things.

Everything we know about life on earth points to the importance of water in the origin and maintenance of life. If we find life on any of these worlds it will probably be “life as we know it”, in the sense of having a similar biochemistry to earth life with a dependance on liquid water. In fact, it would probably be a consequence of being water based that would contribute to the close similarities in molecules like DNA and proteins, that would most likely be present on a watery world. There may certainly be some important and interesting differences, such as using a different genetic code to specify amino acids, perhaps having a different chirality (i.e. Right handed amino acids instead of left handed ones), and possibly having a different set and number of amino acids, but the basics of DNA to code and store information and proteins made of amino acids to carry out metabolism, will likely look like a odd version of what we have here on earth. But, there may be one place in our solar system where the potential for “life as we don’t know it”, also has the potential to exist. That place is Saturn’s moon Titan.

Titan is unique in the solar system in a number of important respects. For a moon its quite big, being the second largest moon in the solar system – only Jupiter’s moon Ganymede is larger. Titan has twice the diameter of earth’s moon. If it was in orbit around the sun instead of Saturn, it might be considered a planet unto itself. It is also the only moon with a thick atmosphere, as dense as the atmosphere down here on earth. Like Earth, the atmosphere on Titan is primarily nitrogen, but unlike earth there is no oxygen to breath. But perhaps the most remarkable thing about Titan is that there is liquid on it’s surface. Besides Titan, only the earth is known to have a large volume of surface liquid today. As we said before, Mars probably had liquid water on it’s surface billions of years ago that has since evaporated away. Of course, the earth has vast oceans of liquid water, but the liquid on Titan is not water, it’s liquid methane. There are lakes of methane, and evidence for rain and rivers of the stuff! We think that liquid is necessary for the chemistry of life to take place. In solids the molecules are too fixed to react much and gases are usually to dispersed for reactions to have a high chance of occurring, and are difficult to contain. A major difference between Earth and Titan, however, is that Titan is cold – really cold. The surface temperature on Titan is -179.2 degrees celsius or -291 degrees fahrenheit. Now that’s pretty darn cold, and Titan would be even colder if not for the greenhouse effect of methane in its atmosphere. It’s both the extreme cold and the fact that methane is the liquid we have to deal with, that makes any type of biochemistry onTitan so challenging to consider.

Water has properties that make it an ideal solvent to dissolve the molecules of life into solution. Could liquid methane serve a similar role on the frozen moon Titan? What would it take for life to find a way to use methane as a solvent for the molecules of “life as we don’t know it”? Let’s look at some of the possibilities for a methane dependent life form that lives in the conditions present on Titan. We will stick, as much as possible, to the rules of organic chemistry, but Warning, wild speculation ahead.

Let’s first look at the major differences between water and methane as your choice of solvent. Every school child knows that water is H2O – made up of two hydrogen atoms covalently bonded to an oxygen atom. It is not a linear molecule, however, but has a bent shape. This creates an electric dipole moment in the molecule, meaning that one side of the molecule is partially negatively charged (the oxygen in this case), and the other end, facing the hydrogens, has a partial positive charge. The electric dipole moment can be measured and it’s value is placed in units of the debye (D), with water having an electric dipole moment of 1.85D. It is this dipole, combined with the fact that oxygen and hydrogen are extremely common throughout the cosmos, that makes water such and interesting, useful, and seemingly indispensable substance. Most organic molecules are electrically neutral – they have no formal charge – but many of the functional groups in the organic molecules do have an uneven distribution of electron sharing, creating a partial charge separation in the chemical bonds between certain atoms. For example, in the carboxyl group there is a partial negative charge on the oxygen and a partial positive charge on the carbon. This means that the carbon can act like an electrophile (attracted to electron rich atoms) and reacts with a partially negative charged molecule, and a nucleophile (attracted to an electron poor atom) will tend to react with the carbon. The reactions due to these kinds of attractive forces are called polar interactions, and it is these types of interactions that create interesting chemistry, and life is all about interesting chemistry.

Water can form hydrogen bonds with other water molecules, as in the figure above. Because of waters dipole properties it will interact strongly with other molecules that contain polar covalent bonds, and this allows them to be soluble in a watery solution. This is energetically favorable for polar molecules, because even though they cause the hydrogen bonds of the water matrix to break as they take up space in the solution (energetically unfavorable), they then form polar bonds with the water to replace the broken bonds (energetically stable)- so in a sense, no harm done. This allows the polar molecules to be soluble in water solution, and this is what you want for your biomolecules if you’re a life form – soluble molecules, not ones that precipitate out of solution. Water helps to stabilize polar molecules and is very important for maintaining the proper shape and structure of important biomolecules like DNA and proteins.

Non-polar molecules, on the other hand, really don’t do well in water and they will not go into solution. The non-polar molecules also break the waters hydrogen bonds since they have to fit in the water matrix, but since they are non-polar they can not replace those bonds, and so remain energetically unfavorable. They will tend to form a separate layer from water and stick together to minimize their interaction with water molecules. For this reason, the non-polar molecules are called hydrophobic, which means water fearing or water hating.

Water is also great at dissolving important salts in solution, like sodium chloride (NaCl) for example. The polar nature of water will break the ionic bonds between the sodium atom and the chloride atom apart, and the sodium will be surrounded by a sphere of water with it’s partially negative oxygen atoms facing it, while the chloride will be surrounded by a sphere of water with it’s partially positive hydrogen atoms facing it. Inorganic ions from salts like sodium chloride, potassium chloride, calcium phosphate, magnesium sulfate, and others are vital to the workings of enzymes and stabilizing biomolecules. Would these ions be able to exist in a non-polar methane sea?

Unlike most organic molecules, one group that is non-polar and water hating are the hydrocarbons. Methane is the simplest hydrocarbon, having just one carbon atom covalently bonded to four hydrogens. There is no dipole moment in the methane molecule. Carbon and hydrogen both have approximately the same amount of pull for the electrons. Even if that weren’t so, the symmetrical tetrahedral shape of methane would still cause the polar bonds to cancel each other out. Hydrocarbons with long chains of carbons are also non-polar. Propane is a hydrocarbon with 3 carbons and 8 hydrogens, and octane is one with 8 carbons and 18 hydrogens. Methane is the major liquid on Titan, with some ethane (2 carbons) thrown in for good measure. Hydrocarbons don’t undergo polar reactions. That’s one reason that they can remain liquid at such low temperatures where other organics would freeze solid – they interact so weakly that it is difficult to get them to interact enough that they become solid. These non-polar molecules do have their own very weak interactions, however. They are subject to non-polar forces called Van der Waals forces. These results from a weak induced dipole, as one molecule gets close to another. Say you have a mixture of methane molecules. There is no permanent dipole, but when the hydrogen of one methane gets too close to the hydrogen of another methane the electron of the first will repel the electron of the second one, and that creates a tiny fleeting attraction between the two molecules. It becomes more pronounced at very low temperatures where the heat energy of motion is not too great. At temperatures that we find comfortable, these minuscule interactions are easily overwhelmed by all the thermal motion. If you have very long hydrocarbons, or other non-polar molecules, then the combined Van der Waals forces acting along the different parts of the molecule can make the effect more significant. This would possibly be a very important force in any Titan life form. On Earth, Van der Waals forces certainly have their important places, and can be important in many DNA-protein interactions and some protein-protein interactions, but many of the interactions between biomolecules rely on polar chemistry to create covalent bonds, and this might be difficult to achieve for a living thing on Titan.

In part II of this article we will examine two possible solutions for Titan biochemistry – What I’m calling The Non-Polar liquid solution (NPLS) versus the Polar-Non-Aqueous liquid (PNAL) solution, or the NPLS vs PNAL. By solution, the meaning can equally double as referring to either a mixture of a liquid with another substance or an answer to a problem – either works fine.

References:
1. Titan: Wikipedia; https://en.m.wikipedia.org/wiki/Titan_(moon)

2. Freezing and Melting Points of some common liquids:
http://www.engineeringtoolbox.com/freezing-points-liquids-d_1261.html

3. “Selected values for electric dipole moments for molecules in the gas phase”, United States Department of Commerce; http://www.nist.gov/data/nsrds/NSRDS-NBS-10.pdf

4. Organic Chemistry; John E. McMurry, 8th edition. ISBN-13: 978-0840054449

5. Also see my article on Silicon Based Life forms (another variety of life as we don’t know it):
In this case it would presumably be water dependent but not based on carbon.
“Why the Horta would not have looked like a rock monster”;
http://darwinskidneys-science.com/2015/06/18/why-the-horta-would-not-have-looked-like-a-rock-monster/