Monday's Molecule #`165

Name this molecule. You don't need the full IUPAC name but you do need to be specific since there are several different molecules with very similar structures. You also have to tell us why this molecule is important in biochemistry.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The Molecule is kanamycin C (not A or B). It binds to the small subunit of the prokaryotic ribosome and inhibits translation. It is/was widely used in cloning experiments since there are several plasmids with kanamycin resistance alleles. I posted all three of the responses that recognized kanamycin but only one named this variant as kanamycin C. That person didn't mention that this was a translation inhibitor so there are no winners this week.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout
April 10: no winner

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Monday's Molecule #164

 

What is this structure and what is its significance? You don't need to come up with a chemical name but you do need to be as specific as possible.

Don't forget to tell us why this structure exists.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is the cap structure on the 5′ end of eukaryotic mRNAs. It's actually a CAP 2 structure with methyl groups at the 2′ positions of the last two nucleotides but that terminology seems to be outdated so I won't insist that you specify. (Thanks to Bill Chaney for getting it right.) The winner is Sean Ridout. (Please contact me by email.)

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner
March 26: John Runnels, Raul A. Félix de Sousa
April 2: Sean Ridout

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Monday's Molecule #163

 

You blew it last week because you didn't follow instructions. It's not going to get any easier. This week you have to identify the molecule using TWO different common names AND name the Nobel Prize winner most closely associated with this molecule.

Remember, you need THREE answers or you can't win!

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answers wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is Vitamin B12, also known as cobalamin. The Nobel Laureate is Dorothy Crowfoot Hodgkin. This week's winners are John Runnels and Raul A. Félix de Sousa. Contact me by email to set up a time.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner

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Monday's Molecule #162

 

The last few challenges have been too easy so I'm going to make this week's molecule a bit more difficult. Not only do you have to identify the molecule but you also have to identify each of the four residues that are sugar derivatives. What is the molecule in blue and what are the other three sugary-looking residues?

Be sure to give a complete unambiguous name—that means getting the stereochemistry correct.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch. I'll be setting up a lunch for this Thursday so expect an email message. If I owe you a lunch, it wouldn't hurt to remind me in case I forget you.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is ganglioside G_M2. The residues are N-acetyl-α-neuraminic acid (blue), N-acetyl-β-D-galactosamide, β-D-galactose, and β-D-glucose (left to right). You were asked to be specific in naming the sugar residues. Several people got the molecule correct but nobody named the sugar residues in a completely unambiguous manner, although the correct names are implied in the formal name of the molecule. There is no winner this week.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj
March 12: Bill Chaney, Raul A. Félix de Sousa
March 19: no winner

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Monday's Molecule #161

 

Some species make this molecule for a very special reason. Identify the molecule using the common name and the IUPAC name. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. The winner will be treated to a free lunch with a famous Nobel Laureate, or with me if the Nobel Laureate isn't available.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisible for 24 hours. Comments are now open.

UPDATE: The molecule is taurocholate (2-{[(3α,5β,7α,12α)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}ethanesulfonate). Taurocholate is a bile salt in mammals. This week's winners are Bill Chaney and Raul A. Félix de Sousa.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody
March 5: Albi Celaj

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Monday's Molecule #160

 

This is a very important molecule for some species. It's important to me, for example, because I worked with it in an undergraduate research project forty-nine many years ago.

UPDATE: The original structure was missing a methyl group at the bottom right. This has now been corrected.

Identify the molecule—the common name will do but make sure you get it right because there are quite a few similar molecules. You must also say why it's important for some species.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

Comments are invisable for 24 hours. Comments are now open.

UPDATE: The molecule is a gibberellin-like molecule. It was intended to be gibberellin GA1 but I left off a methyl group. This is similar to Monday's Molecule #102 (gibberellin GA3). Defects in one of the genes for gibberellin GA1 synthesis gave rise to the tall/short phenotype studied by Gregor Mendel [Mendel's Stem Length Gene (Le)]. Gibberellin GA1 was one of the molecules synthesized by Elias James Corey, winner of the Nobel Prize in Chemistry 1990. The winner this week is Albi Celaj.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi
Feb. 13: Joseph C. Somody

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Monday's Molecule #159

 

This is a very important molecule for many reasons. Versions of it are found in all living species. Its function is essential in most (all?) species.

Pieces of this molecule are found in many viruses. The molecule also plays a prominent role in the debate about junk DNA.

Identify the molecule—the common name will do. You don't have to specify the species but anyone who does will get an honorable mention if the winner doesn't. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch. I'm about to leave for Los Angeles for a couple of weeks but I promise to organize lunch dates as soon as I get back at the end of February.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: It's 7SL RNA from humans. The winner is Joseph C. Somody.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan
Feb. 7: Thomas Ferraro, Charles Motraghi

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Monday's Molecule #158

 

This molecule is responsible for one of the distinguishing features of an entire group of species. Sadly, most undergraduates have never heard of this molecule and they never study the fundamental process that it represents. In my experience, about 90% of all introductory biochemistry courses skip the relevant chapter(s) in the textbooks. There's no reasonable excuse for that omission. It's just bad teaching.

Identify the molecule—the common name will do. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is phycocyanobilin the light absorbing pigment in cyanobacteria (and some other species). This blue pigment is found in large structures called phycobilosomes and it is the reason why cyanobacteria were called blue-green algae. The winners are Thomas Ferraro and Charles Motraghi (undergraduate).

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller
Jan. 30: Peter Monaghan

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Monday's Molecule #157

 

You need to pay close attention in order to identify this molecule correctly.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is L-sedoheptulose 1,7-bisphosphate or L-altro-hept-2-ulose 1,7-bisphosphate. The D isomer is part of the pentose phosphate cycle and the Calvin cycle. The winner is Peter Monaghan.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin
Jan. 23: David Schuller

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Monday's Molecule #156

 

This is one of the most important molecules on Earth. Without it we wouldn't be around and neither would most species. The revised structure is shown here. The one shown in the textbooks is wrong and this includes my own recently published edition of Principles of Biochemistry. Oops!

You need to identify the molecule, including the part with the white carbon atoms. You also need to specify how this molecule differs from the one shown in most textbooks.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is the iron-sulfur-molydenum cluster with bound homocitrate. The central atom was thought to be nitrogen but recent work has shown that it is most likely carbon. The cluster is in the active site of bacterial nitrogenase, an enzyme responsible for fixing atmospheric nitrogen and converting it to ammonia. This is a key part of the nitrogen cycle. The winner is David J. Schuller. I don't know if he will come for lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody
Jan. 9: Dima Klenchin

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Congratulations Vip!

 

Here's Vipulan Vigneswaran with his fabulous Biochemistry textbook that he won by contributing to Monday's Molecule [And the Winner Is ...]. Vip is studying Chemistry at the University of Toronto.

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Monday's Molecule #155

 

We're going to talk about the evolution of this molecule in my class tomorrow. It's a good examples for illustrating some basic principles of molecular evolution.

You need to identify the exact molecule, including the species. Here's a hint: ANKSKGIVWN.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The winner is Dima Klenchin who was the first to identify the molecule as cytochrome c from tuna (Thunnus alalunga). The figure is from the PDB file 3CYT. This PDB file supercedes 1CYT which was reportedly from another species of tuna.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney
Dec. 19: Joseph C. Somody

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Monday's Molecule #154

 

Today's molecule is a bit more complicated than some of the others. You have to identify the molecule (common name only) and describe (briefly) its function. Can you name the precursor?

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment. This is your last chance to enter the Christmas draw for a free textbook!

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is thyrotropin-releasing hormone. It's derived from a long precursor protein containing multiple repeats of the tripeptide Glu-His-Pro.

The winner is Joseph C. Somody.

I'll announce the undergraduate winner of my textbook on Christmas day.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)
Dec. 12: Bill Chaney

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Monday's Molecule #153

 

Today's¹ molecule has a special significance for me since I "accidentally" purified the enzyme that catalyzes the last step in its synthesis. That was one of my first successful experiments as a graduate student (1969).

This is a complex molecule so I'm not going to insist on the IUPAC name. You can supply a common name as long as it is unambiguous (be careful!). This time it's not sufficient to just give me the name of the molecule. You also have to briefly explain what it does and where you can find it, including the "species." The functional explanation has to be a biochemical explanation.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

After today, you have only one more chance to win an autographed book.

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE:The molecule is β-D-glucopyranosyl-5-hydroxymethylcytosine. This is a modified base found in T4 bacteriophage and its relatives. The modification is required to protect phage DNA from E. coli host restriction endonucleases.

The winner is Bill Chaney.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger
Dec. 5: 凌嘉誠 (Alex Ling)

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1. Yes, I know it's Wednesday. I was too busy on Monday to post a molecule.

Monday's Molecule #152

 

This is a simple molecule so I'm going to insist on the IUPAC name as well as the common name. This time it's not sufficient to just give me the name of the molecule. You also have to briefly explain what it does and why it's important to some humans. The functional explanation has to be a biochemical explanation, not a physiological one.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

Winners will have to contact me by email to arrange a lunch date.

UPDATE: The molecule is chlorothiazide of hydrochlorothiazide or 6-chloro-1,1-dioxo-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide. It's a drug commonly used to treat high blood pressure. Chlorothiazide belongs to a class of drugs that function as diuretics—they decrease blood volume by preventing reabsorption of water from the urine.

The winner is 凌嘉誠 (Alex Ling). His answer emphasizes the role of the drug in inhibiting carbonic anhydrase and that's a valid property. However, the most important immediate effect is probably the inhibition of the Na⁺/Cl^- transporter in the kidneys. As far as I can tell the effects of the drug at the molecular level are not as clear-cut as one would like. The decrease in blood volume appears to be temporary and the long-term effect in lowering blood pressure is probabably due to some unknown effect on veins and arteries.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
Nov. 28: Philip Rodger

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Monday's Molecule #151

 

This is a very complicated molecule so I'm not going to ask for the IUPAC name. You can win with the common name but be sure to get it right!

This molecule has played a very important role in elucidating some basic concepts in molecular biology but its structure is rarely shown in 21st century biochemistry textbooks.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: The molecule is rifampicin, an inhibitor of bacterial RNA polymerase. The winner is Philip Rodger. Congratulations Philip, please send me an email message so we can arrange lunch.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran
Nov. 21: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)

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Monday's Molecule #150

 

Today's molecule has a common name but this time I'll need the complete IUPAC name. There is considerable controversy over whether this molecule actually exists in most cells.

Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: This one was more difficult than I expected. The molecule is oxalosuccinate or 1-oxopropane-1,2,3-tricarboxylate. I posted all the answers that used this IUPAC name or 1-oxopropane-1,2,3-tricarboxylic acid. This is clearly not the acid form of the molecule but that didn't make you ineligible to win the prize.

Oxalosuccinate is thought to be a transient intermediate in the reaction catalyzed by isocitrate dehydrogenase (citric acid cycle) but this is only a hypothesis—the intermediate has never been detected.

The molecule contains a chiral carbon atom (C3 of oxalosuccinate and C2 of oxopropane). I was expecting all answers to specifically identify the [2S] or [3S] stereoisomer, especially since we had recently discussed stereoisomers on this blog. "Cyau" was the only one to get this correct (on her second try) but she is not eligible because she didn't identify herself.

RaulFelix was the first person to name the molecule as 1-oxopropane-1,2,3-tricarboxylate and she would be the winner if I knew her real name. That means Vipulan Vigneswaran is this week's winner, beating out Joseph Somody by less that one minute.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley
Nov. 15: Thomas Ferraro, Vipulan Vigneswaran

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Monday's Molecule #149

 

Today's molecule is one member of a large class. Give me the complete, unambiguous, name of this molecule to win a free lunch. Post your answer in the comments. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post correct answers to avoid embarrassment.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.) Every undergraduate who posts a correct answer will have their names entered in a Christmas draw. The winner gets a free autographed copy of my book! (One entry per week. If you post a correct answer every week you will have ten chances to win.)

Some past winners are from distant lands so their chances of taking up my offer of a free lunch are slim. (That's why I can afford to do this!)

Name the molecule shown in the figure. Remember that your name has to be unambiguous. The best way to do this is to use the full IUPAC name but usually there are traditional names that will do. In this case there's a trivial name and that will suffice.

In order to win you must post your correct name. Anonymous and pseudoanonymous commenters can't win the free lunch.

UPDATE: Several people got this one right. The molecule is prostaglandin H2. The winner is Thomas Ferraro. The undergraduate winner is "Vip" = Vipulan Vigneswaran.

Winners
Nov. 2009: Jason Oakley, Alex Ling
Oct. 17: Bill Chaney, Roger Fan
Oct. 24: DK
Oct. 31: Joseph C. Somody
Nov. 7: Jason Oakley

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Better Biochemistry: Fischer Projections

Biochemistry is a three-dimensional subject but most of us aren't comfortable thinking in three dimensions. For example, we often have difficulty envisaging how a three-dimensional substrate binds to a three-dimensional enzyme.

The problem is exacerbated because we usually teach in two dimensions for simplicity—especially in textbooks.¹ There are certain rules that have to be followed when displaying a three-dimensional object on a two-dimensional page. This is especially true for metabolites where the stereochemistry is crucial. One of these rules is called the Fischer projection.²

Most students (and faculty) don't understand the relationship between a two-dimensional Fischer projection and the three-dimensional molecule it's supposed to represent. This is unfortunate because it means they don't really understand the three-dimensional conformation of metabolites.

Let's look at a simple three-carbon compound—glyceraldehyde. There are two different versions of glyceraldehyde: D-glyceraldehyde and L-glyceraldehyde. The two different molecules cannot be superimposed, that's why you know that they are different molecules. Enzymes can tell the difference; that's why D-glyceraldehyde is a common metabolite and L-glyceraldehyde is rarely found in cells.

Professor or Hobo?

 

Can you tell the difference between a Professor and a hobo? Joseph Somody has posted a quiz. Check it out: Professor or Hobo?.

Joseph is the undergraduate winner of Monday's Molecule #147. I'll be having lunch with him on Wednesday. If you have any other pictures of professors or hobos, you could post a link in the comments and I'll be sure to pass them long. (Joseph will probably read them anyway.)

I'm thinking we could do a similar quiz for students—something along the lines of "university student or not?" There are plenty of pictures on facebook that professors could use.

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