John Wise on Science and the Supernatural

 
John Wise is a Professor of Biology at Southern Methodist University in Dallas, Texas (USA). He writes on the campus website [Intelligent Design is not science: why this matters].

Because science gives us methods to accurately understand and manipulate the world we live in. Few people would dispute that our present scientific understanding of the physical world has led to a tremendously long list of advances in medicine, technology, engineering, the structure of the universe and the atom, and on and on. The list is nearly endless, but it does not include everything. Science can tell us only what is governed by natural forces. Miracles are extra-ordinary events; gods are super-natural beings.

Are there reasonable philosophical arguments that can be made for the existence of God? Certainly. Are there reasonable philosophical arguments that can be made that God does not exist? Yes. Is there scientific evidence that answers either of these great questions one way or another? None that holds up to close scrutiny. Collins has no more scientific evidence that God exists than Dawkins has that God does not. Their evidence is philosophical, not scientific. Philosophy can encompass these issues, science cannot.

Okay, let's examine that argument. Science deals with the natural world, that's fair enough. Religion deals with the supernatural world so it's outside of science. That's also a fair statement. The question is, is there such a thing as a "supernatural world" and how can we learn anything about it?

We can deal with the natural world and we can at least imagine that there's a supernatural world beyond the reach of science. But there's a whole lot of middle ground that's being excluded here. Any religious claim that impinges on the natural world is subject to scientific analysis. That includes claims of miracles.

The only kind of religion that can be completely outside of science is one that believes in a God who never meddles in human affairs. Because as soon as that meddling occurs—answering prayers, for example—we scientists can legitimately ask whether the meddling is detectable or not.

Miracles either exist or they don't. If they do then we should have evidence for miracles. If there's no evidence then you should not believe in them. If you believe in miracles in the absence of evidence for their existence, then your belief is in conflict with science.

Professor Wise says that science can't prove the non-existence of God. That's true. In fact, we can't prove the non-existence of many things. We can't prove, for example, that astrology is completely false in every single case. What we can do is to limit its probability to such a small number that it makes no sense to believe in astrology. That's the power of science.

Professor Wise goes on to describe Professor Behe's testimony at the Dover trial in 2005.

Listen further to the transcripts of these hearings - they are astounding. Professor Behe, star witness for the ID proponents and Discovery Institute senior fellow, gave a Discovery Institute-approved definition of scientific theory in his testimony. Unfortunately for both Dr. Behe and the Discovery Institute, Eric Rothschild, the brilliant lawyer for the parents, asked Dr. Behe, "But you are clear, under your definition, the definition that sweeps in Intelligent Design, astrology is also a scientific theory, correct?" And Dr. Behe answered, "Yes, that's correct."

Is this what America wants and needs? A definition of science that is so weak and neutered that astrology qualifies?

Of course we don't want such a science. We want a science that rejects astrology because there's no evidence for it. We don't want astrologers to try and escape scientific scrutiny by claiming that astrology is outside of science, do we? We don't want astrologers to claim that their horoscopes are "miracles" and therefore just as legitimate as science.

Why is it that we feel very comfortable rejecting the ridiculous claims of astrology but we have to make special excuses to protect religion from close scientific scrutiny?

[Hat Tip: The Panda's Thumb]

Becoming Canadian

 
Jeffrey Shallit, a long time opponent of intelligent design creationism, is an American citizen living in Canada. Why doesn't he become a Canadian citizen?
[Towards a Canadian Republic]

My answer has always been the same: I'll seriously consider becoming a citizen when Canada removes one citizenship requirement: that I swear allegiance to "Her Majesty the Queen Elizabeth the Second, Queen of Canada, her Heirs and Successors".

As an American who is proud of the republican tradition (small "r" in "republican", please), the citizenship requirement that one swear allegiance to a person seems unappealingly feudal to me. Paul McCartney famously observed that the current Queen is a pretty nice girl, but that doesn't mean I want to swear allegiance to her.

It seems like an innocent enough anachronism to me.

But the more important question is how does Professor Shallit feel about pledging allegiance to a "thing" as in ....

I pledge allegiance to the flag of the United States of America, and to the Republic, for which it stands, one nation under God, indivisible, with liberty and justice for all.

Theme: ABO Blood Types

 
ABO Blood Types (Feb. 21, 2007)

Glycoproteins (Feb. 20, 2007)

Genetics of ABO Blood Types (Feb. 23, 2007)

Human ABO Gene (Feb. 22, 2007)

Nobel Laureates: Carl Ferdinand Cori and Gerty Theresa Cori

The Nobel Prize in Physiology or Medicine 1947.

"for their discovery of the course of the catalytic conversion of glycogen"



Carl Ferdinand Cori (1896-1984) and Gerty Theresa Cori (1896-1957) won the Nobel Prize in 1947 for their work on understanding the synthesis and degradation of glycogen. Their major contribution was understanding the importance of phosphorylated intermediates, especially the "Cori ester" glucose-1-phosphate [Monday's Molecule #25].

Professor Carl Cori and Doctor Gerty Cori. During the past decade the scientific world has followed your work on glycogen and glucose metabolism with an interest that has gradually increased to admiration. Since the discovery of glycogen by Claude Bernard ninety years ago, we have been almost totally ignorant of how this important constituent of the body is formed and broken down. Your magnificent work has now elucidated in great detail the extremely complicated enzymatic mechanism involved in the reversible reactions between glucose and glycogen. Your synthesis of glycogen in the test tube is beyond doubt one of the most brilliant achievements in modern biochemistry. Your discovery of the hormonal regulation of the hexokinase reaction would seem to lead to a new conception of how hormones and enzymes cooperate.

In the name of the Caroline Institute I extend to you hearty congratulations on your outstanding contribution to biochemistry and physiology.

Cori and Cori are one of the few husband and wife teams to receive the Nobel Prize. They worked at Washington University in St. Louis, MO (USA).

Glycogen Degradation/Utilization

 
Glucose is stored as the intracellular polysaccharides starch and glycogen. Starch occurs mostly in plants. Glycogen is an important storage polysaccharide in bacteria, protists, fungi and animals. Glycogen is stored in large granules. In mammals, these granules are found in muscle and liver cells. In electron micrographs, liver glycogen appears as clusters of cytosolic granules with a diameter of 100 nm—much larger than ribosomes. The enzymes required for synthesis of glycogen are found in muscle and liver cells [Glycogen Synthesis]. Those same cells contain the enzymes for glycogen degradation.

The glucose residues of starch and glycogen are released from storage polymers through the action of enzymes called polysaccharide phosphorylases: starch phosphorylase (in plants) and glycogen phosphorylase (in many other organisms). These enzymes catalyze the removal of glucose residues from the ends of starch or glycogen. As the name implies, the enzymes catalyze phosphorolysis—cleavage of a bond by group transfer to an oxygen atom of phosphate. In contrast to hydrolysis (group transfer to water), phosphorolysis produces phosphate esters. Thus, the first product of polysaccharide breakdown is α-D-glucose 1-phosphate, not free glucose.


Glucose 1-phosphate is one of the precursors required for glycogen synthesis. It is the "Cori ester" [Monday's Molecule] discovered by Carl Cori and Gerty Cori [Nobel Laureates: Carl Cori and Gerty Cori]. The Cori's also discovered and characterized glycogen phosphorylase.

In order for glucose 1-phosphate to be used in other pathways it has to be converted to glucose 6-phosphate by the enzyme phosphoglucomutase. This is the same enzyme that's used in the synthesis of glycogen from glucose 6-phosphate.

Glucose 6-phosphate can be oxidzed by the glycolysis pathway to produce ATP. This is what happens in muscle cells. Glucose is stored as glycogen during times of rest but during exercise the glycogen is broken down to glucose 6-phosphate and glycolysis is activated. The resulting ATP is used in muscle activity.

Obviously, there has to be a balance between the synthesis and degradation of glycogen and this balance is maintained by regulating the activities of the biosynthesis and degradation enzymes. This regulation occurs at many levels. Regulation by hormones is one of the classic examples of a signal transduction pathway in mammals.

[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

Glycogen Synthesis

All cells are capable of making glucose. The pathways is called gluconeogenesis and the end product is not actually glucose but a phosphorylated intermediate called glucose-6-phosphate.

Glucose-6-phosphate (G6P) serves as the precursor for synthesis of many other compounds such as the ribose sugars needed in making DNA and RNA. The only organisms that make free glucose are multicellular organisms, such as animals, that secrete it into the circulatory system so it can be taken up and used by other cells (Glucose-6-phosphate cannot diffuse across the membrane so it's retained within cells.)

In times of plenty, G6P may not be needed in further biosynthesis reactions so cells have evolved a way of storing, or banking, excess glucose. The stored glucose molecules can then be retrieved when times get tough. Think of bacteria growing in the ocean, for example. There may be times when an abundant supply of CO₂ combined with a surplus of inorganic energy sources (e.g., H₂S) allows for synthesis of lots of G6P. These cells can store the excess G6P by making glycogen—a polymer of glucose residues.

Glycogen consists of long chains of glucose molecules joined end-to-end through their carbon atoms at the 1 and 4 positions. The chains can have many branches. Completed chains can have up to 6000 glucose residues making glycogen one of the largest molecules in living cells.

The advantage of converting G6P to glycogen is that it avoids the concentration effects of having too many small molecules floating around inside the cell. By compacting all these molecules into a single large polymer the cell is able to form large granules of stored sugar (see photo above).

The first step in the synthesis of glycogen is the conversion of glucose-6-phosphate to glucose-1-phosphate by the action of an enzyme called phosphoglucomutase. (Mutases are enzymes that rearrange functional groups, in this case moving a phosphate from the 6 position of glucose to the 1 position.) The glycogen synthesis reaction requires adding new molecules that will be connected to the chain through their #1 carbon atoms so this preliminary reaction is required in order to "activate" the right end of the glucose residue.
Glucose-1-phosphate is the "Cori ester" [Monday's Molecule #25] that was discovered by Carl Cori and Gerty Cori while they were working out this pathway [Nobel Laureates: Carl Cori and Gerty Cori].

The next step is the conversion of glucose-1-phosphate to the real activated sugar, UDP-glucose. The enzyme is UDP-glucose pyrophosphorylase and the UDP-glucose product is similar to many other compound that are activated by attaching a nucleotide. In some bacteria, the activated sugar is ADP-glucose but the enzyme is the same as that found in eukaryotes. ADP-glucose is the activated sugar in plants, as well. In plants the storage molecules are starch, not glycogen, but the difference is small (starch has fewer branches).

Glycogen synthesis is a polymerization reaction where glucose units in the form of UDP-glucose are added one at a time to a growing polysaccharide chain. The reaction is catalyzed by glycogen synthase.



[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

Mendel's Garden #14

 

Mendel's Garden #14 has been posted on Epigenetic News.

Nobel Laureate: Walther Hermann Nernst

 

The Nobel Prize in Chemistry 1920.

"in recognition of his work in thermochemistry"

Walther Hermann Nernst won the Nobel Prize in 1920 for his work in understanding the energy of reactions. The main work is summarized in the presentation speech,

Before Nernst began his actual thermochemical work in 1906, the position was as follows. Through the law of the conservation of energy, the first fundamental law of the theory of heat, it was possible on the one hand to calculate the change in the evolution of heat with the temperature. This is due to the fact that this change is equal to the difference between the specific heats of the original and the newly-formed substances, that is to say, the amount of heat required to raise their temperature from 0° to 1° C. According to van't Hoff, one could on the other hand calculate the change in chemical equilibrium, and consequently the relationship with temperature, if one knew the point of equilibrium at one given temperature as well as the heat of reaction.

The big problem, however, that of calculating the chemical affinity or the chemical equilibrium from thermochemical data, was still unsolved.

With the aid of his co-workers Nernst was able through extremely valuable experimental research to obtain a most remarkable result concerning the change in specific heats at low temperatures.

That is to say, it was shown that at relatively low temperatures specific heats begin to drop rapidly, and if extreme experimental measures such as freezing with liquid hydrogen are used to achieve temperatures approaching absolute zero, i.e. in the region of -273° C, they fall almost to zero.

This means that at these low temperatures the difference between the specific heats of various substances comes even closer to zero, and thus that the heat of reaction for solid and liquid substances practically becomes independent of temperature at very low temperatures.

Today, Nernst is known for his other contributions to thermodynamics. In biochemistry he is responsible for the Nernst equation that relates standard reduction potentials and Gibbs free energy.

The Nernst Equation

 
In standard oxidation-reduction reactions you can usually tell whether a given compound will donate or receive electrons by looking at the standard reduction potential (ΔE°ʹ) [Oxidation-Reduction Reactions]. This is a big step toward understanding how electrons flow in biochemical reactions but we would like to know more about the energy of oxidation-reduction reactions since they are the fundamental energy-producing reactions in the cell.

The standard reduction potential for the transfer of electrons from one molecular species to another is related to the standard Gibbs free energy change (ΔG°ʹ) for the oxidation-reduction reaction by the equation

where n is the number of electrons transferred and ℱ (F) is Faraday’s constant (96.48 kJ V^-1 mol^-1). ΔE°ʹ is defined as the difference in volts between the standard reduction potential of the electron-acceptor system and that of the electron-donor system. The Δ (delta) symbol indicates a change or a difference between two values.

You may recall that electrons tend to flow from half-reactions with a more negative standard reduction potential to those with a more positive one. For example, in the pyruvate dehydrogenase reaction electrons flow from pyruvate (E°' = -0.48 V) to NAD⁺ (E°' = -0.32 V). We can calculate the change in standard reduction potentials; it's equal to +0.16 V [-0.32 - (-0.48) = +0.16].

Now we can calculate a standard Gibbs free energy change (ΔG°ʹ) for the electron transfer part of the pyruvate dehydrogenase reaction. Two electrons are transferred from pyruvate to NAD⁺ so the standard Gibbs free energy change is -31 kJ mol^-1 [-2(96.48)(0.16)]. This turns out to be a significant amount of energy that could be captured by the NADH molecule but you have to keep in mind that this is a standard Gibbs free energy change and conditions inside the cell are far from standard. The biggest difference is that standard Gibbs free energy changes are computed with equal concentrations of reactants and products at a concentration of 1M—about a thousand times higher than the concentrations inside the cell where, in addition, the concentrations of reactants and products are not equal.

Fortunately, we have a way of adjusting the values of the Gibbs free energy change and the change in the standard reduction potential to account for the actual concentrations inside the cell. The standard Gibbs free energy change is related to the equilibrium constant of a reaction K_eq by the equation

Just as the actual Gibbs free energy change for a reaction is related to the standard Gibbs free energy change by this equation, an observed difference in reduction potentials (ΔE) is related to the difference in the standard reduction potentials (ΔE°') by the Nernst equation.

By combining equations for ΔG°ʹ we get
For a reaction involving the oxidation and reduction of two molecules, A and B,
the Nernst equation is
where [A_ox] is the concentration of oxidized A inside the cell. The Nernst equation tells us the actual difference in reduction potential (ΔE) and not the artificial standard change in reduction potential (ΔE°ʹ).

At 298 K (25° C), this equation reduces to
where Q represents the ratio of the actual concentrations of reduced and oxidized species. To calculate the electromotive force of a reaction under nonstandard conditions, use the Nernst equation and substitute the actual concentrations of reactants and products. Keep in mind that a positive E value indicates that an oxidation-reduction reaction will have a negative value for the standard Gibbs free energy change.

The Nernst equation is very famous but it's actually not very useful. The problem is that many of the oxidation-reduction reactions take place within an enzyme complex such as the pyruvate dehydrogenase complex. The concentrations of the reactants and products are difficult to calculate under such conditions. That's why we usually use the standard reduction potentials instead of the actual reduction potentials, keeping in mind that these are only approximations of what goes on inside the cell.

Let's see what happens when we calculate the standard Gibbs free energy change for the reaction where NADH donates electrons to oxygen. Oxygen serves as an electron sink for getting rid of excess electrons [Oxidation-Reduction Reactions].

NAD⁺ is reduced to NADH in coupled reactions where electrons are transferred from a metabolite (e.g., pyruvate) to NAD⁺. The reduced form of the coenzyme (NADH) becomes a source of electrons in other oxidation-reduction reactions. The Gibbs free energy changes associated with the overall oxidation-reduction reaction under standard conditions can be calculated from the standard reduction potentials of the two half-reactions using the equations above.

As an example, let’s consider the reaction where NADH is oxidized and molecular oxygen is reduced. This represents the available free energy change during membrane-associated electron transport. This free energy is recovered in the form of ATP synthesis.

The two half-reactions from a table of standard reduction potentials are,

and
Since the NAD⁺ half-reaction has the more negative standard reduction potential, NADH is the electron donor and oxygen is the electron acceptor. The net reaction is
and the change in standard reduction potential is

Using the equations described above we get

What this tells us is that a great deal of energy can be released when electrons are passed from NADH to oxygen provided the conditions inside the cell resemble those for the standard reduction potentials (they do). The standard Gibbs free energy change for the formation of ATP from ADP + P_i is -32 kJ mol^-1 (the actual free-energy change is greater under the conditions of the living cell, it's about -45 kJ mol^-1). This strongly suggests that the energy released during the oxidation of NADH under cellular conditions is sufficient to drive the formation of several molecules of ATP. Actual measurements reveal that the oxidation of NADH can be connected to formation of 2.5 molecules of ATP giving us confidence that the theory behind oxidation-reduction reactions is sound.

[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

A Rational Canadian Speaks Out

 
Dan Gardner wrote a column in the Ottawa Citizen [Those fanatical atheists]. He makes so much sense I'm just going to quote several paragraphs and let everyone see what every rational person should be saying. This is the effect Richard Dawkins is having and I think it's about time.

Then there's the problem on the other side -- among the atheists such as Richard Dawkins who have been labelled "fanatics." Now, it is absolutely true that Dawkins' tone is often as charming as fingernails dragged slowly down a chalkboard. But just what is the core of Dawkins' radical message?

Well, it goes something like this: If you claim that something is true, I will examine the evidence which supports your claim; if you have no evidence, I will not accept that what you say is true and I will think you a foolish and gullible person for believing it so.

That's it. That's the whole, crazy, fanatical package.

When the Pope says that a few words and some hand-waving causes a cracker to transform into the flesh of a 2,000-year-old man, Dawkins and his fellow travellers say, well, prove it. It should be simple. Swab the Host and do a DNA analysis. If you don't, we will give your claim no more respect than we give to those who say they see the future in crystal balls or bend spoons with their minds or become werewolves at each full moon.

And for this, it is Dawkins, not the Pope, who is labelled the unreasonable fanatic on par with faith-saturated madmen who sacrifice children to an invisible spirit.

This is completely contrary to how we live the rest of our lives. We demand proof of even trivial claims ("John was the main creative force behind Sergeant Pepper") and we dismiss those who make such claims without proof. We are still more demanding when claims are made on matters that are at least temporarily important ("Saddam Hussein has weapons of mass destruction" being a notorious example).

So isn't it odd that when claims are made about matters as important as the nature of existence and our place in it we suddenly drop all expectation of proof and we respect those who make and believe claims without the slightest evidence? Why is it perfectly reasonable to roll my eyes when someone makes the bald assertion that Ringo was the greatest Beatle but it is "fundamentalist" and "fanatical" to say that, absent evidence, it is absurd to believe Muhammad was not lying or hallucinating when he claimed to have long chats with God?

[Hat Tip: PZ Myers]

Oxidation-Reduction Reactions

 
Biochemical reactions are just a complicated form of organic chemistry. Living organisms have evolved enzymes that make these reactions go faster but the underlying chemistry is unchanged.

Cells are constantly having to deal with the problem of shuffling electrons and channeling them to the right place. You might be familiar with the classic fuel metabolism example of glycolysis where the breakdown of glucose to CO₂ releases electrons. When a reaction results in the loss of electrons it's called an oxidation reaction. When electrons are gained it's a reduction reaction. Oxidations and reductions always go together since electrons are passed from one molecule to another.


Loss of Electrons is Oxidation (LEO)


Gain of Electrons is Reduction (GER)


LEO says GER


Oxidation Is Loss of electrons (OIL)


Reduction Is Gain of electrons (RIG)


OIL RIG

During glycolysis, the electrons that are released have to be deposited in some sort of electron sink and expelled as waste. If a cell couldn't get rid of its electrons it would build up a huge negative charge.

Oxygen is the electron sink in mammalian fuel metabolism. A molecule of oxygen takes up electrons and combines with protons to make water. The easiest way to see this is to draw the molecules as Lewis structures showing the valence electrons (Pushing Electrons).

There are sixteen electron on each side of this equation for the reduction of molecular oxygen. Remember, reduction is a gain of electrons. This is a half-reaction, there is no corresponding oxidation that provides the electrons so this isn't a valid oxidation-reduction reaction. It just shows the reduction part.

None of the reactions of glycolysis result in the direct reduction of molecular oxygen. In all cases, the release of electrons when glucose is broken down to CO₂ is coupled to temporary electron storage in various coenzymes. We have already encountered several of these electron storage molecules such as ubiquinone, FMN & FAD, and NADPH.

We discussed a simple electron transport chain where electrons were passed from pyruvate to NAD⁺ in the pyruvate dehydrogenase reaction. This is a classic oxidation-reduction reaction.

How do we know which direction electron are going to flow? For example, if ubiquinone is reduced to ubiquinol by acquiring two electrons then where do the electrons come from? Can NADH pass electrons to ubiquinone or does ubiquinol pass its two electrons to NAD⁺? And where does FAD⁺ fit? Can it receive electrons from NADH?

The answer is related to the reduction potential of the various electron carriers. In order to understand reduction potentials we need to learn a little inorganic chemistry.

The reduction potential of a reducing agent is a measure of its thermodynamic reactivity. Reduction potential can be measured in electrochemical cells. An example of a simple inorganic oxidation-reduction reaction is the transfer of a pair of electrons from a zinc atom (Zn) to a copper ion (Cu²⁺) as shown below. When a pair of electrons is removed from zinc it leaves a zinc ion that's deficient in two negative charges (Zn²⁺). These electrons can be taken up by a copper ion (Cu²⁺) resulting in a copper atom (Cu) with no charge.

This reaction can be carried out in two separate solutions that divide the overall reaction into two half-reactions. At the zinc electrode, two electrons are given up by each zinc atom that reacts (the reducing agent). The electrons flow through a wire to the copper electrode, where they reduce Cu2+ (the oxidizing agent) to metallic copper. A salt bridge, consisting of a tube with a porous partition filled with electrolyte, preserves electrical neutrality by providing an aqueous path for the flow of nonreactive counterions between the two solutions. The flow of ions and the flow of electons are separated in an electrochemical cell. Electron flow (i.e., electric energy) can be measured using a voltmeter.
The direction of the current through the circuit in the figure indicates that Zn is more easily oxidized than Cu (i.e., Zn is a stronger reducing agent than Cu). The reading on the voltmeter represents a potential difference—the difference between the reduction potential of the reaction on the left and that on the right. The measured potential difference is the electromotive force.

It is useful to have a reference standard for measurements of reduction potentials just as in measurements of Gibbs free energy changes. For reduction potentials, the reference is not simply a set of reaction conditions but a reference half-reaction to which all other half-reactions can be compared. The reference half-reaction is the reduction of H+ to hydrogen gas (H2). The reduction potential of this half-reaction under standard conditions (E̊) is arbitrarily set at 0.0 V. The standard reduction potential of any other half-reaction is measured with an oxidation-reduction coupled reaction in which the reference half-cell contains a solution of 1M H+ and 1 atm H2(gaseous), and the sample half-cell contains 1 M each of the oxidized and reduced species of the substance whose reduction potential is to be determined. Under standard conditions for biological measurements, the hydrogen ion concentration in the sample half-cell is (pH 7.0). The voltmeter across the oxidation-reduction couple measures the electromotive force, or the difference in the reduction potential, between the reference and sample half-reactions. Since the standard reduction potential of the reference half-reaction is 0.0 V, the measured potential is that of the sample half-reaction.
The table below gives the standard reduction potentials at pH 7.0 (E̊́) of some important biological half-reactions. Electrons flow spontaneously from the more readily oxidized substance (the one with the more negative reduction potential) to the more readily reduced substance (the one with the more positive reduction potential). Therefore, more negative potentials are assigned to reaction systems that have a greater tendency to donate electrons (i.e., systems that tend to oxidize most easily).

It's important to note the direction of all these reactions is written in the form of a reduction or gain of electrons. That's not important when it comes to determining the direction of electron flow. For example, note that the reduction of acetyl-CoA to pyruvate is at the top of the list (E̊́= -0.48 V). This is the reaction catalyzed by pyruvate dehydrogenase. Electrons released by the oxidation of pyruvate will flow to any half reaction that has a higher (less negative) standard reduction potential. In this case the electrons end up in NADH (E̊́ = -0.32 V).

The reduction of oxygen is way down at the bottom of the list. That's why it's an effective electron sink for gettng rid of electrons.

Now we'd like to know something about the thermodynamics of these electron transport reactions so we can find out how much energy is available to do useful work. This will lead us to the Nobel Laureate for April 25th.

[©Laurence A. Moran. Some of the text is from Principles of Biochemistry 4th ed. ©Pearson/Prentice Hall]

Pushing Electrons

 
Biochemistry, as the name implies, is concerned with the chemistry of life. The chemistry part is mostly organic chemistry and organic chemistry is mostly about pushing electrons.

Covalent bonds are formed when the nuclei of two atoms share a pair of electrons. The "bond" is actually a cloud of electrons orbiting the two nuclei. The atoms are held together because neither one is stable without the shared electrons. The reactions in organic chemistry and biochemistry can be thought of as simple rearrangements of electrons to form new covalent bonds and break apart old ones. In this sense it's all about pushing electrons from one location to another.

The best way to think about covalent bonds is to visualize the electrons in the other shell of atoms. Those are the ones that participated in bonding. The outer shell electrons are often referred to as the valence electrons. The first shell of electrons can only hold two electrons. Hydrogen atoms have a single electron so in order to form a stable compound they have to combine with something that supplies an electron that can be shared. The simplest of these compounds is a molecule of hydrogen (H₂).

When two atoms of hydrogen combine to form H₂ both atoms succeed in filling their outer shells with two electron by sharing electrons. The shared pair of electrons is the covalent bond. The type of structures shown in the equation are called Lewis Structures. The dots represent electrons in the outer shell of the atom.

The inner electron shell can only hold two electrons but all other shells can accommodate eight electrons. The atomic number of oxygen is 8, which means that it has two electrons in the inner shell and only six in the outer shell. It needs to combine with two other atoms in order to get enough electrons to fill the outer shell.
In this example, oxygen with six electrons in the valence shell is combining with two hydrogen atoms to form water (H₂O). By sharing electrons both the hydrogen atoms and the oxygen atom will complete their outer shells of electrons—hydrogen with two electrons and oxygen with eight.

Sometimes atoms can share more than a pair of electrons. For example, when two atoms of oxygen combine to form the oxygen molecule (O₂) there are four electrons shared between the two atoms. This results in a double bond between them.
Carbon has an atomic number of 6, which means that it has two electrons in the inner shell and only four electrons in the outer shell. Carbon can combine with four other atoms to fill up its outer shell with eight electrons. This ability to combine with several different atoms is one of the reasons why carbon is such a versatile atom. The structure of ethanol (CH₃CH₂OH, left) illustrates this versatility. Note that each atom has a complete outer shell of electrons and that each carbon atom is covalently bonded to four other atoms.

Biochemical reactions are a lot more complicated but once you understand the concept of electron pushing it becomes relatively easy to make sense of the reaction mechanisms seen in textbooks. The only additional information you need is the knowledge that some atoms can carry an extra electron and this makes them a negatively charged ion (e.g., — O^-). Some stable atoms are missing an electron in their outer shell so this makes them a positively charged ion (e.g., — N⁺).

In many cases a proton (H⁺) is released from a compound leaving its electron behind. This proton has to combine with an atom that already has a pair of electrons in its outer shell (e.g., a base B:). Here's an example of the reaction mechanism for aldolase, one of the enzymes in the gluconeogenesis/glycolysis pathway.
The outline of the enzyme is shown in blue. One of the key concepts in biochemistry is that enzymes speed up reactions, in part, by supplying and storing electrons. In this case an electron withdrawing group (X) pulls electrons from oxygen and this weakens the carbon-oxygen double bond (keto group). Carbon #2, in turn, pulls an electron from carbon #3 weakening the C3-C4 bond that will be broken. (Aldolase cleaves a six-carbon compound into two three-carbon compounds as shown here. It also preforms the reverse reaction where two three-carbon compounds are combined to form a six-carbon compound.)

A basic residue in the protein (B) removes a proton from the -OH (hydroxyl) group to form a B-H covalent bond. This leaves an additional electron on the oxygen and it combines with one left on C4 to from a double bond. The red arrows show the movement of electrons in these reaction mechanisms.

The key point here is that biochemical reactions are just like those of all chemical reactions. They involve the movement of electrons to break and form covalent bonds.

Canada's Secret Spy Coin

 
According to the US Defense Department, Canada is planting coins containing secret radio transmitters on US Defense contractors travelling in Canada ['Poppy quarter' behind spy coin alert]. The coins are the 2004 commemorative quarters issued to remember those who died in Canada's wars. The coins have a red poppy in the center [In Flanders Fields].

Here's what the Associated Press article says,

WASHINGTON - An odd-looking Canadian quarter with a bright red flower was the culprit behind a false espionage warning from the Defense Department about mysterious coins with radio frequency transmitters, The Associated Press has learned.
ADVERTISEMENT

The harmless "poppy quarter" was so unfamiliar to suspicious U.S. Army contractors traveling in Canada that they filed confidential espionage accounts about them. The worried contractors described the coins as "filled with something man-made that looked like nano-technology," according to once-classified U.S. government reports and e-mails obtained by the AP.

I can see why the contractors were confused. American coins and paper money are so boring they probably thought every country had boring money.

Actually it's all a ruse to direct the contractors' attention away from the real source of the radio transmitters. They're in Tim Hortons coffee.

[Hat Tip: Mustafa Mond, FCD]

Theme: The Three Domain Hypothesis

 
This is a series of postings that describe the Three Domain Hypothesis. The Three Domain Hypothesis is the idea that life is divided into three domains—bacteria, archaebacteria, and eukaryotes—and that the archaebacteria and eukaryotes share a common ancestor. An example of this tree of life is shown on the Dept. of Energy (USA) Joint Genome Initiative website [JGI Microbial Genomes] (left).

The hypothesis was promoted by Carl Woese in the 1980's but the pure form has now been abandoned and replaced with a “net of life” concept of early evolution as shown in the figure below. This figure is taken from Ford Doolittle's Scientific American article "Uprooting the Tree of Life" (February 2000). © Scientific American




The Three Domain Hypothesis (part 1) (Nov. 17, 2006 )

The Three Domain Hypothesis (part 2) (Nov. 22, 2006)

The Three Domain Hypothesis (part 3) (Nov. 26, 2006)

The Three Domain Hypothesis (part 4) (Nov. 29, 2006)

The Three Domain Hypothesis (part 5) (Dec. 8, 2006)

The Three Domain Hypothesis (part 6) Carl Woese (Dec. 31, 2006)

Now the IDiots Don't Get Evolution (Feb. 14, 2007)

The Web of Life (March 15, 2007)

Is "Prokaryote" a Useful Term? (October 4, 2007)

Celebrating the Three Domain Hypothesis (October 18, 2007)

The Tree of Life (May 22, 2008)

Sequence Alignment (June 22, 2008)

On the Origin of Eukaryotes (December 27, 2008)

The Tree of Life (July 29, 2009)

Perspectives on the Tree of Life: Ford Doolittle (July 30, 2009)

Perspectives on the Tree of Life: Day One (July 31, 2009)

Perspectives on the Tree of Life: Day Two (August 1, 2009)

Perspectrives of the Tree of Life: Day Three (August 7, 2009)

Monday's Molecule #25

 
Name this molecule. We need the exact name since it's pretty easy to guess one of the trivial names.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate(s). This one is dead easy—at least it will seem that way once you recognize the Nobel Prize winner(s). The reward (free lunch) goes to the person who correctly identifies both the molecule and the Nobel Laureate(s). (Previous free lunch winners are ineligible for one month from the time they first won. There is only one ineligible candidate for this Wednesday's reward.)

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