G Proteins Are Signal Transducers

 
Many membrane receptors interact with a family of guanine nucleotide- binding proteins called G proteins. G proteins act as transducers, the agents that transmit external stimuli to effector enzymes. G proteins have GTPase activity; that is, they slowly catalyze hydrolysis of bound guanosine 5′-triphosphate (GTP, the guanine analog of ATP) to guanosine 5′-diphosphate (GDP). GDP was Monday's Molecule #27.

When GTP is bound to G protein it is active in signal transduction and when GDP is bound to G protein it is inactive. The cyclic activation and deactivation of G proteins is shown below. The G proteins involved in signaling by hormone receptors are peripheral membrane proteins located on the inner surface of the plasma membrane.

Each protein consists of an α, a β, and a γ subunit. The α and γ subunits are lipid-anchored membrane proteins; the α subunit is a fatty-acyl anchored protein, and the γ subunit is prenyl-anchored protein. The complex of G_αβγ and GDP is inactive.

When a hormone–receptor complex diffusing laterally in the membrane encounters and binds G_αβγ it induces the G protein to change to an active conformation. Bound GDP is rapidly exchanged for GTP, promoting the dissociation of G_α-GTP from G_βγ. Activated G_α-GTP then interacts with the effector enzyme. For example, it can stimulate adenylyl cyclase in regulating glycogen metabolism or in causing a sense of smell.

The GTPase activity of the G protein acts as a built-in timer since G proteins slowly catalyze the hydrolysis of GTP to GDP. When GTP is hydrolyzed the G_α-GDP complex reassociates with G_βγ and the G_αβγ-GDP complex is regenerated. G proteins have evolved into good switches but very poor catalysts, typically having a k_cat of only about 3 min^-1.

G proteins are found in dozens of signaling pathways, including the adenylyl cyclase and the inositol–phospholipid pathways. An effector enzyme can respond to stimulatory G proteins (G_s) or inhibitory G proteins (G_i). The α subunits of different G proteins are distinct, providing varying specificity, but the β and γ subunits are similar and often interchangeable. Humans have two dozen α proteins, five β proteins, and six γ proteins.

What Is an Aggregator?

 
There are probably some people who don't know what an aggregator is. It's a feed reader, or a program that reads the news feeds from your favorite web site. This is how you can keep up with the news on all the important blogs like Sandwalk!

I use the Goggle Reader that's featured in the following video by commoncraft. It will teach you all you need to know about Really Simple Syndication (RSS). There are other readers that are just as good but I like the web based readers 'cause I can access them from several different computers.

Click To Play

There are two types of Internet users, those that use RSS and those that don't. This video is for the people who could save time using RSS, but don't know where to start.

[Hat Tip: Shelley Batts who used to read blogs the old fashioned way.]

Darwin misconceptions in textbooks slammed in biology journal

 
"Darwin misconceptions in textbooks slammed in biology journal" is the title of an article posted by Denyse O'Leary on Post-Darwinist. Here's what she says,

British ID blog Truth in Science features a critique of Darwin hagiography and misconceptions promoted in textbooks, published by Brit prof Dr. Paul Rees in the Journal of Biological Education. The critique aims at inaccurate accounts of Charles Darwin "found in many A-Level textbooks", identifying seven common misconceptions in twelve popular textbooks published in 12 popular textboks over the last 35 years. The .pdf of the article is here. A suitable addition to examples of ridiculous hagiography in trade books and exhibitions.

Here's the link to the actual article by Raul A. Rees [The evolution of textbook misconceptions about Darwin]. Let's look at the seven misconceptions to see how they help Denyse and the Intelligent Design Creationists.

1. Darwin was the first to propound the theory of evolution by natural selection. Rees argues that natural selection was discovered by others before Darwin, and not just Wallace. This is rather silly, in my opinion. I don't take issue with textbooks that say Darwin discovered the theory of natural selction.
2. Darwin created the concept of "survival of the fittest". The term was coined by Herbert Spencer in 1864—five years after the first edition of Origin of Sepcies. If textbooks actually state flat out that Darwin made up the term then they need to be changed. Very few do this.
3. Darwin travelled around the world on HMS Beagle and published On the Origin of Species on his return to England. Rees doesn't actually give any examples of this misconception. Instead he laments the fact that most textbooks don't emphasize the long delay (23 years) between returning to England and publishing On the Origin of Species. It would be nice if the textbooks got this right.
4. Darwin was an observant naturalist and made careful collections of specimens during his voyage. Rees wants to make the point that Darwin didn't recognize the evidence for natural selection in the material he collected on the Beagle voyage. This isn't very important but it would be nice if the textbooks placed more emphasis on the theory and recognized that it didn't just fall out of the data.
5. Darwin recognized the evolutionary significance of the adaptations shown by the Galapagos finches. It's not true that the Galapagos finches played an important role in developing the theory of natural selection. In fact, Darwin didn't appreciate the signficance until Gould pointed it out in 1837 and even then it took a while for Darwin to start using the finches as evidence for selection.
6. Darwin first heard that Alfred Russel Wallace had independently formulated a theory of evolution when he received a letter from him in 1858. This is essentiall correct. Rees wants textbooks to point out that the two had corresponded for several years.
7. Darwin and Wallace jointly presented papers on their ideas at a meeting of the Linnean Society in London in 1858. Wallace was in the Far East and Darwin was at home burying his son. It would be wrong for textbooks to state that they were both present at the meeting where their papers were read. Rees quotes from two textbooks published in 1984 and 1987 that imply otherwise. Tempest in a teapot.

How do these "misconceptions" affect evolution? Not at all. The IDiots would like to think that all criticism of Charles Darwin and his ideas represent evidence against evolutionary biology. They are fixated on Darwinism and events that happened 148 years ago when On the Origin of Species was first published.

Denyse O'Leary and her creationist friends seem incapable of understanding that modern evolutionary biology has moved far beyond anything that Darwin could have imagined. He is rightly credited with founding modern evolutionary biology but the scientific facts of evolution do not depend on any of the seven "misconceptions" that Paul A. Rees raises.

---

Rees, P.A. (2007) The evolution of textbook misconceptions about Darwin. J. Biol. Education 41: 53-55 [PDF]

American Society for Microbiology in Toronto

 
The American Society for Microbiology is meeting in Toronto this week. There are several bloggers and blog readers in town and we'll be getting together over the next few days. Email me at "sandwalk at "bioinfo dot med dot utoronto dot ca" if you'd like to join us.

Tara Smith did not have a great first day. Hopefully today will be better. Jonathan Badger had a much better first day. He even met a scientifically literate Canadian customs agent. (Let's not tell him that many custom agents are university students employed for the summer.) John Logsdon is landing right now but he hasn't announced it on his blog (yet).

Monday's Molecule #27

 
Today's molecule is an easy one. The trivial name will do since it's very well known but if you can supply the correct chemical name that would be good.

As usual, there's a connection between Monday's molecule and this Wednesday's Nobel Laureate(s). This one is very straightforward. 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 collected the prize. There are no ineligible candidates for this Wednesday's reward.

Comments will be blocked for 24 hours. Comments are now open.

Queen Victoria Day

 

Today is Victoria Day in Ontario. It's the day we celebrate Queen Victoria's birthday (she was actually born on May 24, 1819). In 2007 it's just a good excuse for a holiday.

Gene Genie #7

 
The 7th version of Gene Genie has been posted at Gene Sherpas.

Christianity Today Poll

 
Vote here.



[Hat Tip: Friendly Atheist]

Methodological Naturalism

UPDATE: This post no longer reflects my opinion on this subject. I now believe that science is not bound by methodological naturalism. Science as a way of knowing is free to investigate claims of the supernatural. [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism].

In a comment on The Neville Chamberlain Atheists thread "slc" repeats a claim that he/she has been making for several months. I started to reply on that thread but the comment grew too long so I'm making it into a separate posting.
"slc" says,

As I have commented on this and other blogs, Prof. Morans' position, along with Myers and Dawkins is that philosophical naturalism is science and therefore science == atheism.

Indeed, I've seen you make that claim several dozen times. I'm glad it makes you happy.
For the record, I am an atheist so naturally I'm a philosophical naturalist. (Duh!) But I do not claim that good science requires philosophical naturalism. I claim that methodological naturalism is a requirement.
Most of my arguments [e.g. Theistic Evolution: The Fallacy of the Middle Ground] are based on the idea that methodological naturalism is the foundation of science and that, therefore, science is effectively atheistic in practice. I've been trying to show that methodological naturalism all by itself is capable of highlighting all of the important conflicts between science and religion. In my opinion, it's simply not true that the only conflicts that arise are when you make the leap to philosophical naturalism.
In this sense—and this sense only—I'm defending the concept of non-overlapping magisteria (NOMA) promoted by Stephen Jay Gould. As long as religion sticks to it's proper domain (magisterium) and stays out of science then it's okay (e.g., I have no problem with Deism and most versions of Buddhism). The problem is that most believers want to violate the rules of methodological naturalism and still be praised for being good scientists. One of the ways they rationalize this obvious conflict is to try and equate methodological naturalism with philosophical naturalism. They claim that it's okay to allow a little bit of religion into science because science is not the same as atheism. We see an example of that in "slc"'s attempt to dismiss what many of us are saying about the conflict between science and religion.

The Neville Chamberlain Atheists

There seem to be a lot of people who don't understand the origin of the term "Neville Chamberlain School of Evolutionists." I've seen it attributed to PZ Myers and even to me.

For the record, it comes from The God Delusion and I'm going to quote from the Dawkins' book below. But before doing that I want to acknowledge that I don't like the term very much even though I used it several times last Fall. I think it does an injustice to Neville Chamberlain. Lately I've been referring to this group as just appeasers but now I prefer to use "accommodationist" to describe them.

If you recognize yourself in the description below and want to offer up a term that fits with your position then please make a comment and we'll see if we can reach an agreement about what to call you.

Another prominent luminary of what we might call the Neville Chamberlain school of evolutionists is the philosopher Michael Ruse. Ruse has been an effective fighter against creationism, both on paper and in court. He claims to be an atheist, but his article in Playboy takes the view that

we who love science must realize that the enemy of our enemies is our friend. Too often evolutionists spend time insulting would-be allies. This is especially true of secular evolutionists. Atheists spend more time running down sympathetic Christians than they do countering creationists. When John Paul II wrote a letter endorsing Darwinism, Richard Dawkins's response was simply that the pope was a hypocrite, that he could not be genuine about science and that Dawkins himself simply preferred an honest fundamentalist.

From a purely tactical viewpoint, I can see the superficial appeal of Ruse's comparison with the fight against Hitler: "Winston Churchill and Franklin Roosevelt did not like Stalin and communism. But in fighting Hitler they realized that they had to work with the Soviet Union. Evolutionists of all kinds must likewise work together to fight creationism." But I finally come down on the side of my colleague the Chicago geneticist Jerry Coyne, who wrote that Ruse

fails to grasp the real nature of the conflict. It's not just about evolution versus creationism. To scientists like Dawkins and Wilson [E.O. Wilson, the celebrated Harvard biologist], the real war is between rationalism and superstition. Science is but one form of rationalism, while religion is the most common form of superstition. Creationism is just a symptom of what they see as the greatest enemy:religion. While religion can exist without creationism, creationism cannot exist without religion.

Dawkins agrees with Coyne, and so do PZ Myers, me, and many others. The real battle is between rationalism and superstition and that's why we have to point out the superstitious beliefs of Theistic Evolutionists just like we point out the superstitious beliefs of Intelligent Design Creationists.

Some of you are only interested in the American struggle to keep Intelligent Design out of the schools—a serious tactical error, as far as I'm concerned. In that battle you may see the Pope as an ally. That's fine. You can be accommodationists if it suits you in order to win that fight. But don't assume that your fight is my fight. That's where you make a mistake in criticizing my position and that of Dawkins etc.

Glycogen Storage Diseases

Type 0: Hypoglycemia due to lack of glycogen synthase [OMIM 240600, OMIM 138571]

Glycogen synthase is the enzyme required for glycogen synthesis [Glycogen Synthesis]. There are two forms of the enzyme; liver and muscle. The muscle form is found in many different tissues but the liver version of the enzyme is only found in liver cells. Mutations in the gene for the liver enzyme (GTS2) cause glycogen storage disease type 0.

The disease is usually recognized in infants who have very low blood sugar (hypoglycemia) after a short fast. The low sugar is due to the fact that there's no store of glycogen in the liver. In normal cases, the liver stores glucose as glycogen right after a meal then breaks it down as blood glucose is depleted. In the absence of liver glycogen synthase the maintenance of blood sugar levels is impaired.

Here's what OMIM has to say about typical cases.

Gitzelmann et al. (1996) described 3 children with liver glycogen synthase deficiency from 2 German families and compared the observations with the previously published 3 families comprising 8 patients. The 2 index cases presented with morning fatigue, had ketotic hypoglycemia when fasting which rapidly disappeared after eating, and hepatic glycogen deficiency with absent or very low hepatic glycogen synthase activity. Metabolic profiles comprising glucose, lactate, alanine, and ketones in blood were typical for hepatic glycogen synthase deficiency. Symptoms were rapidly relieved and chemical signs corrected by introducing frequent protein-rich meals and nighttime feedings of suspensions of uncooked corn starch. The discovery of oligosymptomatic and asymptomatic sibs suggested that there are persons with undiagnosed hepatic glycogen synthase deficiency. Gitzelmann et al. (1996) stated that the disorder should be sought in children who, before the first meal of the day, present with drowsiness, lack of attention, pallor, uncoordinated eye movements, disorientation, or convulsions, and who have hypoglycemia and acetone in the urine.

Type I: Von Gierke's Disease: Deficiency in glucose 6-phosphatase [Ia OMIM 232200, Ib OMIM 602671, Ib OMIM 232220, Ic OMIM #232240]

The synthesis of glucose (gluconeogenesis) in the liver ends with glucose 6-phosphate. It can be stored as glycogen in the liver for use later on or it can be converted to glucose. Glucose is then secreted into the blood stream where it can be taken up by muscle cells. The cycling of glucose between muscle and liver is called the Cori Cycle.

One of the key enzymes is glucose 6-phosphatase. This is the enzyme that removes the phosphate group from glucose 6-phosphate to make free glucose. In mammals, this enzyme is located in the membranes of the endoplasmic reticulum. The enzyme is part of a complex that includes a glucose 6-phosphate transporter (G6PT) and a phosphate transporter. G6PT moves glucose 6-phosphate from the cytosol to the interior of the ER where it is hydrolyzed to glucose and inorganic phosphate. Phosphate is returned to the cytosol and glucose is transported to the cell surface (and the bloodstream) via the secretory pathway.

The other enzymes required for gluconeogenesis are found, at least in small amounts, in many mammalian tissues. By contrast, glucose 6-phosphatase is found only in cells from the liver, kidneys, and small intestine, so only these tissues can synthesize free glucose. Cells of tissues that lack glucose 6-phosphatase retain glucose 6-phosphate for internal carbohydrate metabolism.

Defects in glucose 6-phosphatase affect mostly liver and kidneys where stored glycogen can accumulate to high levels due to the fact that it can't be broken down to free glucose for secretion into the blood stream. Glycogen storage disease Ia results from mutations in the catalytic subunit of glucose 6-phosphatase (G6PC gene) while Ib and Ic are caused by mutations in the transporter subunits.

The major problem is hypoglycemia (low glucose) and lactic acidemia due to inefficient conversion of lactic acid to free glucose. These can be fatal but nowadays the symptoms are treated by feeding carbohydrates at regular intervals throughout the day and though a gut tube at night. This is an autosomal recessive disease.

Type II (Pompe Disease): Deficiency of α-glucosidase [OMIM #232300, OMIM 606800]

Glycogen granules are taken up by lysosomes where they are broken down by a pathway that's different from the normal glycogen degradation pathway. One of the key lysosomal enzymes is α1,4-glucosidase. Mutations in the gene for this enzyme cause glycogen storage disease type II.

This is a very severe form of the disease. Although glycogen breakdown in lysosomes is relatively minor in terms of overall glycogen metabolism, the inability to process glycogen granules leads to their accumulation in lysosomes and consequent disruption of many important lysosomal functions. This disruption takes place in all cells and all tissues.

In the classic cases, infants are inactive and hypertonic with enlarged hearts. Death usually occurs before the first year, usually from heart failure. An adult onset version is known. It usually begins with respiratory difficulties and often ends in death from ruptures of the arteries or respiratory failure.

Type III: (Cori Disease): Defects in glycogen debranching enzyme [OMIM 232400, OMIM 610860]

The glycogen debranching enzyme is required for the complete mobilization of glucose from glycogen. The standard glycogen phosphorylase enzyme will lop off glucose residues until it come to within for residues of a branch point in the glycogen chain. This produces a truncated glycogen molecule known as limit dextrin.

Further degradation of glycogen requires the activity of the debranching enzyme which actually has two separate activities: a glucanotransferase activity that transfers glucose residues from the end of one branch to the end of another, and a glucosidase activity that chops off the last glucose residue on a branch. The gene is the AGL gene (amylo-1,6-glucosidase, 4-α -glucanotransferase) in humans and the GDE gene (glycogen debranching enzyme) in many other species.

There are several subtypes of type III glycogen storage disease. They all result from mutations in the AGL gene. The most common type is IIIa where debranching activity is missing in both liver and muscle cells [see The Cori Cycle]. Patients have muscle weakness and liver problems similar to those in von Gierke's Disease (type I) but the symptoms are milder and not usually life threatening.

In type IIIb the deficiency in debranching enzyme is only detectable in liver. This is probably due to lower production of functional enzyme that only affects liver cells where more debranching enzyme is needed than in muscle cells.

Types IIIc and IIId are quite rare. They only affect the glucanotransferase activity (IIIc) or the glucosidase activity (IIId).

Type IV (Anderson Disease): Deficiency in glycogen branching enzyme [OMIM #232500, OMIM 607839]

Glycogen storage disease IV is caused by a deficiency of glycogen branching enzyme (amylo-(1,4 → 1,6)-transglycosylase). This is the enzyme that adds new branches for glycogen during synthesis. A deficiency in this enzyme results in reduced ability to store glucose residues in glycogen.(This is the enzyme responsible for the wrinkled pea phenotype that Gregor Mendel studied. [ Biochemist Gregor Mendel Studied Starch Synthesis.)

The disease is severe according to OMIM.

Glycogen storage disease type IV is a clinically heterogeneous disorder. The typical 'classic' hepatic presentation is liver disease of childhood, progressing to lethal cirrhosis. The neuromuscular presentation of GSD IV is distinguished by age at onset into 4 groups: perinatal, presenting as fetal akinesia deformation sequence (FADS) and perinatal death; congenital, with hypotonia, neuronal involvement, and death in early infancy; childhood, with myopathy or cardiomyopathy; and adult, with isolated myopathy or adult polyglucosan body disease (Bruno et al., 2004). The enzyme deficiency results in tissue accumulation of abnormal glycogen with fewer branching points and longer outer branches, resembling an amylopectin-like structure, also known as polyglucosan (Tay et al., 2004).

Type V (McArdle Disease): Deficiency of muscle glycogen phosphorylase [OMIM 23600, OMIM 608455]

Glycogen phosphorylase is the enzyme that degrades glycogen [Glycogen Degadation]. Deficiencies in the muscle form of the enzyme lead to severe muscle cramps. Patients are not able to perfom strenuous exercise. The lack of muscle glycogen phosphorylase prevents breakdown of glycogen in muscle and consequent lack of glucose to fuel ATP production via glycolysis. One of the characteristic symptoms is an absence of blood lactate since muscle cells are unable to convert glycogen to glucose and then to lactate.

Muscle tissue breaks down due to lack of ATP leading to general weakness, especially in adults. The disease is not fatal; in fact, it is relatively harmless as long as patients avoid exercise.

Type VI (Hers Disease): Deficiency in liver phosphorylase [OMIM 23700]

Deficiencies of the liver form of glycogen phosphorylase are not as harmful as deficiencies of the muscle version (type V). The disease is inherited as an autosomal recessive and it's due to mutations in the gene for the liver form of glycogen phosphorylase.

The symptoms are mild compared to other forms of glycogen storage disease, giving rise to enlarged liver with mild hypoglycemia, mild ketosis, and retarded growth.

Type VII (Tarui Disease): Muscle phosphofructokinase deficiency [OMIM #232800, OMIM 610681]

According to OMIM,

Glycogen storage disease VII is an autosomal recessive metabolic disorder characterized clinically by exercise intolerance, muscle cramping, exertional myopathy, and compensated hemolysis. Myoglobinuria may also occur. The deficiency of the muscle isoform of PFK results in a total and partial loss of muscle and red cell PFK activity, respectively. Raben and Sherman (1995) noted that not all patients with GSD VII seek medical care because in some cases it is a relatively mild disorder.

Muscle phosphofructokinase (PFKM) is an enzyme required for glycolysis. When glycolysis is blocked in muscle cells glycogen cannot be broken down and there is no abundant supply of ATP available for muscle activity.

Type IXa (X-linked liver glycogenosis): Deficiency of liver phosphorylase kinase [OMIM 306000

Phosphorylase kinase is the enzyme that phosphorylates glycogen phosphorylase in order to regulate its activity [Regulating Glycogen Metabolism]. Defects in the phosphorylase kinase gene (PHK) cause glycogenstorage disease type IXa&mdash a very mild form of the disease according to OMIM.

Deficiency of liver phosphorylase kinase (PHK; ATP:phosphotransferase; EC 2.7.1.38) produces one of the mildest of the glycogenoses of man. The clinical symptoms include hepatomegaly, growth retardation, elevation of glutamate-pyruvate transaminase and glutamate-oxaloacetate transaminase, hypercholesterolemia, hypertriglyceridemia, and fasting hyperketosis (Schimke et al., 1973; Willems et al., 1990). With age, these clinical and biochemical abnormalities gradually disappear and most adult patients are asymptomatic.

Phosphorylase kinase consists of α, β, γ, and δ sunbuits each of which is encoded by specific genes. Defects in the α subunit gene (PHKA) are what causes glycogen storage disease type IXa. There are two different genes for α subunits on the X chromosome: one for the liver specific version of the enzyme (PHA2) and one for the muscle specific version of the enzyme (PHA1). Mutations in either one cause the disease, which is why it is called an X-linked glycogen storage disease.

99 Years and Counting

At this time next year, the Department of Biochemistry at the University of Toronto will be celebrating its 100th anniversary with a symposium and a party. Everyone is invited!

Our department was the first biochemistry department in Canada and one of the first in the world [Biochemistry at the University of Toronto - A Short History]. Readers are invited to submit examples of older biochemistry departments if you can find them

The first chair of the department, Archibald Byron Macallum, was appointed in 1907 for the 1907-08 academic year. We've decided to celebrate at the end of the 2007-2008 academic year.

Former students, staff, faculty, post-docs and anyone else who has ever been associated with the department will meet here for several days in May 2008. We expect to play host to guests from every biochemistry department in Canada and from many other places throughout the rest of the world.

Nobel Laureate: Eduard Buchner

 
The Nobel Prize in Chemistry 1907.

"for his biochemical researches and his discovery of cell-free fermentation"



Eduard Buchner (1860-1917) won the Nobel Prize in 1907 for discovering that cell free extracts of yeast could convert sugar to ethanol. This was one of the greatest discoveries in biology [Fermentation: Synthesis of Ethanol]. The presentation speech outlines the importance of the discovery so I'll quote a large part of it below. This speech was never actually delivered because the award ceremony had to be cancelled due to the death of King Oscar II just two days earlier.

... it has been found possible to lift the veil which hitherto covered the phenomena of organic life. Thus a very large number of substances, which at the time in question it was assumed could only be formed by living organisms, can now be prepared synthetically. When, however, it is a matter of the inner course during the formation and conversion of these substances in living beings, we have to admit that our knowledge is still very far from complete. To be sure, it is no longer said that the living being is governed by a special "life force", but very often we have to make do even today with another expression which, in its actual meaning, does not differ very much from the first. It is frequently said now that this or that process should be regarded as a "life phenomenon" or "life expression" in certain cells. Regrettably we have to recognize that in this we are to a great extent merely providing a word instead of a deeper insight. It is certainly true that the frontier territories in which chemical research is now struggling to penetrate the complicated, mystic phenomena of life have in many respects advanced far beyond where it stood in 1813. Meanwhile, it still remains a fact that we owe considerable unconditional recognition to a work which in this field has taken experimental chemical research a sure step farther.

This is applicable to the work which is now the subject of the Prize award.

In a few words I shall try to explain to you what it is about.

For a long time chemists have been paying great attention to the phenomena which we now call fermentation. Under this name we include a number of chemical processes which occur in living beings and for which they are of the greatest importance. Usually these are decomposition processes in which compound substances are split under the influence of agents which we call ferments. These ferments act, so to speak, by their mere presence. Without being themselves transformed, they cause certain definite changes in other substances, the effect of each ferment being limited to a certain substance or a certain group of substances. It is an important property of ferments that, precisely under such circumstances as obtain in living beings, they exert a powerful action, whilst under others they frequently and easily become ineffective. Since, on the other hand, by means of other chemical aids, chemical processes can be brought about which appear similar to the actions of the ferments-several examples of which are available-it often happens that for this purpose agents are necessary whose nature makes them quite foreign to, and often incompatible with, conditions in living beings.

In very recent times, particularly, the advancement of our knowledge has made it probable that there are processes which are fermentative to a particularly high degree, which bring about the conversion of substances in living beings and which thus control this condition of life. Just as chemical science has during the past century acquired an extensive knowledge of the composition and structure of organic substances, so a thorough knowledge of the nature and action of ferments is now essential, in order that this science may be in a position to master the laws of the formation and dissociation of substances within the organism.

Meanwhile, we know these ferments up to now only by the effects they produce. Their inner nature and the constitution of their substance are still unknown to us. It is to be hoped, however, that a solution to this puzzle may be the subject of a future Nobel Prize.

A number of fermentations have been readily observable. This relates, for example, to the ferments which occur in dissolved state in the secretions which are discharged into the digestive system and exert such a great influence there. It has thus been possible to gain very considerable experimental experience concerning these fermentations.

Another group of fermentations, however, had been seen to occur only in the presence of living cells. To this group belonged, among others, the decomposition of sugar into alcohol and carbon dioxide, under the action of ordinary yeast. The connection between this fermentation and the presence of live yeast cells appeared so irresolvable that this fermentation process was regarded as an "expression of life" by the cells. This process thus appeared to be inaccessible to more detailed research.

Through Pasteur this view was accepted and generally adopted in scientific circles.

The unforgettable service done by Pasteur is that he showed that there are living organisms which are the originators of putrefaction and fermentation and of a number of processes which are of very great significance. Pasteur, who was distinguished not only by the genius of his ideas but also by an eminent talent as an experimenter, also tried - particularly as regards ordinary alcohol fermentation - to investigate the intrinsic interrelationship in this process. In particular he tried to answer the question whether the fermentation of alcohol was due primarily to a ferment produced by the yeast cells, in which case this ferment must be separated from them and be able to work independently of the presence of live yeast cells. His experiments, however, like those of others, concerning the occurrence of such a soluble ferment gave a negative result. Pasteur's view was thus considered to be confirmed, namely that the chemical process in alcoholic fermentation was a life expression by the yeast cells, and was thus inextricably linked with their life. This view prevailed for several decades.

At the same time as Pasteur earned for himself undying fame by his brilliant exposition of the significance of living beings as the ultimate cause of such processes, he put a brake on the progress of science in this field by the vitalistic concept of the actual course of fermentation. So long as fermentation was regarded as an "expression of life", and hence a phenomenon inseparable from life, there was little hope of being able to penetrate more deeply into the question of its course. It should be noted that this was of all the greater importance as it concerned not only alcoholic fermentation but a large group of important processes.

Under these circumstances it can easily be understood that a great sensation was created when E. Buchner, after many years' work, succeeded in showing that alcoholic fermentation could be produced from the juices expressed from yeast cells, free from live cells. He demonstrated incontrovertibly that this fermentation was due to a ferment produced by the yeast cells, from which it can be separated. Fermentation is not a direct expression of life by yeast cells; the cells can be killed and destroyed, while the ferment remains.

By Buchner's work, the fermentation mentioned and various other processes analogous to it have been freed from the shackles which previously held them and which prevented any progress in research. Now, no special difficulty is encountered in obtaining from yeast cells and various other cells an ample amount of powerfully active cell substance which is free from live cells. Numerous clarifying investigations into its properties have also been made, partly by Buchner himself and partly by others. Hitherto inaccessible territories have now been brought into the field of chemical research, and vast new prospects have now been opened up to chemical science.

Fermentation: Synthesis of Ethanol

 
Monday's Molecule #26 was actually three molecules: pyruvate, acetaldehyde, and ethanol. They're part of the pathway from sugar to ethanol.

In the first part of the pathway glucose is converted to pyruvate by the standard reactions of glycolysis. In the presence of oxygen the end product, pyruvate, will be oxidized to acetyl-CoA and CO₂ by pyruvate dehydrogenase. Acetyl-CoA will enter the citric acid cycle to complete the oxidation of glucose. There are several other fates of pyruvate including the conversion to lactate or ethanol. Both of these pathways take place in the absence of oxygen. They are called fermentation pathways.

The ability of yeast to ferment grapes and other fruits has been known for several millenia. Yeast cells can take the sugar from fruit (or grain) and convert it to pyruvate. If you mix yeast and fruit in a container that doesn't have much oxygen then the yeast cells will obligingly produce ethanol, a compound that has proven to be useful in the human diet. Yeast also produces CO₂ under these conditions and shown in the pathway above.

Today we know all about the enzymes that carry out these reactions but one hundred years ago things were less clear. It wasn't certain that fermentation could occur outside of living cells.

In one of the major conceptual advances in biology, Eduard Buchner (in 1897) was able to ferment sugar using a cell free extract of yeast. The reason why this was such an important discovery is that it removed all doubt about vitalism and the possibility that life was some special property outside of chemistry. Buchner showed that the production of ethanol from sugar was just a series of chemical reactions that did not need a living cell. This led directly to the discovery of enzymes and the elucidation of their properties. In a very real sense Buchner is the father of biochemistry [Nobel Laureate: Eduard Buchner].

Marks Are Posted!

 
The grades for my biochemsitry course have just been released to the students. I've already got several email messages from students who are complaining about their marks. One student got "only" 84% and wants to know how to petition for more marks. One student failed the final exam and ended up with a C- for a final grade. She thinks this is unfair.

Sigh. Why do we have to go through this every year? Is it just my students or does eveyone have this problem?