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.
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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.)

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

Saving Bigfoot

 
Mike Lake is the Canadian member of parliament for Edmonton-Mill Woods-Beaumont. He belongs to the Conservative Party of Stephen Harper.

Lake is 38 years old and has a bachelor of commerce degree from the University of Alberta. In other words, he is a university graduate.

Lake calls for bigfoot to be protected under Canada's Species at Risk Act [Bigfoot risks extinction, says Canadian MP]. It appears that Mike Lake has been persuaded to make a fool of himself by bigfoot "researcher" Todd Standing. This should not be a surprise since all Conservative MP's have already demonstrated a certain amount of detachment from reality.

Canadians will get a kick out of another press release [Bigfoot May Gain Protection by Canadian Parliament] where Mike Lake MP is identified as a member of the Canadian Mounted Police.

[Hat Tip: fellow Canadian James Hrynyshyn]

Gene Genie #6

 
Read the sixth edition of Gene Genie at Scienceroll [Gene Genie: a Famous Blog Carnival’s Sixth Issue]. There's lots of good science but if that doesn't tempt you then go for the videos on Mendel and genetics.

My contributions are the articles on the genes for The Human Genes for the Pyruvate Dehydrogenase Complex and Noncoding DNA and Junk DNA.

What's Your Abel Number?

 
Pharmacologists at the recent Experimental Biology meeting in Washington were excited about their Abel numbers [Six degrees of pharmacology]. The Abel number represents the number of links to John J. Abel, the founder of modern pharmacology. In this case the links have to be through authors on a publication.

I wonder who we could choose for biochemistry?

They Put Nicotine in Tim Hortons Coffee

 
Friday's Urban Legend: FALSE

Have you received an email message like this one?

Are you a Non- Smoker or Against smoking all together ?

Do you ever wonder why you have to have your coffee every morning?

** TIM HORTON'S SHOCKER **

A man from Arkansas came up to Canada for a visit only to find himself in the hospital after a couple of days. Doctor's told him that he had suffered of cardiac arrest. He was allergic to Nicotine. The man did not understand why that would of happened as he does not smoke knowing full well he was allergic to Nicotine. He told the doctor that he had not done anything different while he was on vacation other than having Tim Horton's coffee. The man then went back to Tim Horton's and asked what was in their coffee. Tim Horton's refuses to divulge that information. After threatening legal action, Tim Horton's finally admitted.....

*** THERE IS NICOTINE IN TIM HORTON'S COFFEE ***

A girl I know was on the patch to quit smoking. After a couple of days she was having chest pains & was rushed to the hospital. The doctor told her that she was on a Nicotine overload. She swore up & down that she had not been smoking. SHE WAS HAVING HER COFFEE EVERY MORNING.

Now imagine a women who quits smoking because she finds out that she is pregnant, but still likes to have her Tim Horton's once in a while.

THIS IS NOT A JOKE, PLEASE PASS THIS ALONG.... YOU MIGHT SEE THIS ON THE NEWS SOON.

Another version has "them" putting MSG in the coffee instead of nicotine. That's the version that I received this week from well-meaning, but not very skeptical, friends.

As usual, snoopes.com is on the case [Nicotine Non-Fit]. There is no nicotine in Tim Hortons coffee and there's no MSG either.

I'm a "Modernist"

 

You scored as Modernist. Modernism represents the thought that science and reason are all we need to carry on. Religion is unnecessary and any sort of spirituality halts progress. You believe everything has a rational explanation. 50% of Americans share your world-view. Modernist 100% Materialist 88% Existentialist 81% Postmodernist 44% Romanticist 38% Idealist 31% Cultural Creative 25% Fundamentalist 0% What is Your World View? created with QuizFarm.com

[Hat Tip: Shalini]

USA Is Number 2 in Health Care

 
Scientific American, that paragon of science writing, has an article on health care. It reports the results of a study done by a bunch of Canadians. They compare the health care systems in the USA and Canada and discover that We're Number Two: Canada Has as Good or Better Health Care than the U.S..

According to Woolhandler, by looking at already ill patients, the researchers eliminated any Canadian lifestyle advantage and just examined the degree to which the two systems affected patient deaths. (Mortality was the one kind of data they could extract from a disparate pool of 38 papers examining everything from kidney failure to rheumatoid arthritis.)

Overall, the results favored Canadians, who were 5 percent less likely than Americans to die in the course of treatment. Some disorders, such as kidney failure, favored Canadians more strongly than Americans, whereas others, such as hip fracture, had slightly better outcomes in the U.S. than in Canada. Of the 38 studies the authors surveyed, which were winnowed down from a pool of thousands, 14 favored Canada, five the U.S., and 19 yielded mixed results.

These studies are never conclusive. There will always be people who quibble about this or that and just as you might expect there is the obligatory complaint about wait times in Canada.

The point isn't so much whether Canada is better—although it is—the point is that Americans have just got to stop pretending that they have the best health care system in the world. At the very least it's time to admit that it's "one of the best." One thing is very clear, the American system may not be the best in the world but it's sure the most expensive.

The study's authors highlight the fact that per capita spending on health care is 89 percent higher in the U.S. than in Canada. "One thing that people generally know is that the administration costs are much higher in the U.S.," Groome notes. Indeed, one study by Woolhandler published in The New England Journal of Medicine in 2003 found that 31 percent of spending on health care in the U.S. went to administrative costs, whereas Canada spent only 17 percent on the same functions.

I suspect there are many European countries with health care systems that are just as good as the one in America. I suspect that Japan, New Zealand, and Australia have good health care as well. I've never seen any data that shows that the quality of health care in America is better than everywhere else in the world. It seems to be one of those myths of American superiority that has no basis in fact. The myth prevents Americans from joining the rest of the civilized world and adopting socialized medicine.

Seven Warning Signs of Bogus Science

 
One of my readers (thanks Allyson) has directed me to an article on the Seven Warning Signs of Bogus Science. Most of them are familiar to skeptics but they deserve to be more widely publicized. Here are seven ways to recognize a kook.

1. The discoverer pitches the claim directly to the media.
2. The discoverer says that a powerful establishment is trying to suppress his or her work.
3. The scientific effect involved is always at the very limit of detection.
4. Evidence for a discovery is anecdotal.
5. The discoverer says a belief is credible because it has endured for centuries.
6. The discoverer has worked in isolation.
7. The discoverer must propose new laws of nature to explain an observation.

I'd like to add an eight criterion to this list.

8. The discoverer does not critically evaluate contrary evidence.

Science Blogs

 
The latest issue of Cell has an opinion piece on science blogs by Laura Bonetta. Laure did her homework. She interviewd many of us and distilled the results into a pretty good summary of what science blogging is all about [Scientists Enter the Blogosphere].

I'm pleased that she quoted me on the trade-off between writing a blog and the amount of time it takes away from doing other things.

Moran, at age 60, is somewhat unique among bloggers. Most bloggers, regardless of what they write about, tend to be younger. According to the Pew Internet and American Life Project more than half of all bloggers in the United States are under the age of 30. “Most of my colleagues think what I do is strange. Partly, that's because they are not into the technology. I happen to have grown up with the Internet and understand its culture,” says Moran. “I think the younger people who are blogging now are likely to be doing it when they are 60.”

The age barrier is not the only thing keeping more scientists from blogging. The biggest impediment is probably lack of time. According to most bloggers, posts can take 30 minutes to a couple of hours to research and compose. That may not seem like much, except that a critical factor for a blog's success is that posts are updated frequently, ideally at least once a day. “If I ever stop doing this, it is because of time commitment,” says Moran.

This is an important point. I don't know how some of my blogger friends can keep on posting several things every day. It takes me hours to write up a scientific posting. I just can't do it every day.

On the other hand, it takes me only a few minutes to post an opinion piece. Perhaps that's why those postings are more common, even on science blogs. Here's the conundrum. Does a science blog need to have controversial opinion pieces in order to attract enough readers to make the science postings worthwhile? I think the answer is yes.

Undegraduate Research Experience

 
The following press release appeared on EurekAlert [Students benefit from undergraduate research opportunities].

Students benefit from undergraduate research opportunities

Many pursue advanced degrees in science, technology, engineering and mathematics

Undergraduate students who participate in hands-on research are more likely to pursue advanced degrees and careers in science, technology, engineering and mathematics (STEM) fields, according to a new study.

The study's authors state that National Science Foundation (NSF) and other entities' efforts to encourage representation of underrepresented groups in STEM fields appear to be effective.

For example, students who entered 2-year colleges were as likely as those who entered 4-year colleges or universities to participate in research. And undergraduate researchers were more likely than non-researchers to pursue a doctorate.

"This study indicates that carefully designed undergraduate research experiences motivate students," said Myles Boylan, program director for NSF's Course, Curriculum and Laboratory Improvement Program in the Divisions of Undergraduate Education and Graduate Education. "Students consider their research experiences to be effective previews of doing STEM graduate work as well as good learning experiences."

Many of the talks and discussions at the recent Experimental Biology meeting in Washington focused on the value of the undergraduate research experience. There were a lot of talks noting the correlation between students who went on to graduate school and students who did an undergraduate research project. Most assumed that it was the undergraduate research experience that motivated students to apply to graduate school.

I'm a little disappointed in these claims. As a scientist, I'm well aware of the fact that a correlation does not prove a cause. In my school, the undergraduates know that you have to do an undergraduate research project in order to enhance your chances of getting into graduate school. Thus, students who are motivated to go to graduate school will choose to do an undergraduate reseach project. I'm not sure that the undergraduate research experience is what motivates students to apply to graduate school or whether it is the motivation to go to graduate school that causes students to choose an undergraduate research project.

In my experience, the undergraduate research project is a fourth (senior) year phenomenon. Usually the application to graduate school has to be sent in before Christmas and the GRE's have to be written long before that. To me this suggests that the motivation precedes the research experience but then I'm just a scientist. What do I know about these things?

Don't get me wrong, I think research experience is a wonderful thing. My concern is that its value is being hyped at the expense of other ways of acquiring knowledge and motivating students to pursue a career in science.

At the meeting, I attended ten different talks on undergraduate research. There wasn't a single talk about how to improve the teaching of basic concepts and principles in biochemistry and molecular biology. Is this a problem? You bet. Several of the speakers revealed some misunderstanding of those very concepts and principles. This leads me to suspect that they are concentrating too much on the "doing" of science and not enough on the understanding.

Where Was I Yesterday? (3)

 

Where Was I Yesterday? (2)