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.

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.

Monday's Molecule #237

Last week's molecules (above) [Monday's Molecule #236] were the stereoisomers of L-threonine (D-threonine, L-allotheronine, and D-allothreonine). Nobody got the right answer so there was no winner last week. I guess that one was too hard.

It's not going to get any easier. This week's molecules (right) are related. You need to give the common names of each one and the complete IUPAC names. You'll have to be very careful in identifying and naming each one of the stereoisomers.

Email your answer to me at: Monday's Molecule #237. The first one with the correct answer wins. I will only post the names of winners 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 email message.)

Monday's Molecule #56

 
Most students are busy at this time of year so I'm going to give you a break today. This is a very well-known molecule. You have to name it, giving me the common name and the correct systematic IUPAC name.

There's a direct connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the relevant Nobel Laureate(s). I don't think this one is very difficult.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidate for this week's reward because Sandwalk readers have not been very successful in recent weeks. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule (with the correct IUPAC name) and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! The molecule is ADP or 5-(6-aminopurin-9-yl)
-3,4-dihydroxy- oxolan-2-yl methoxy-hydroxy- phosphoryl oxyphosphonic acid. The Nobel Laureates are the men who worked out how ATP synthase makes ATP using ADP as a substrate. Alivia Day was the first person to get the right answers.

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Monday's Molecule #119: Winners

 
The molecule is arsphenamine or Salvarsan—also known as compound 606 or "magic bullet." It is the first synthetic drug developed specifically to treat syphilis. It was discovered in Paul Ehrlich's lab in 1909. Ehrlich had already receive the Nobel Prize for his pioneering work on antibodies.

The discovery of arsphenamine was the subject of a 1940 movie called Dr. Ehrlich's Magic Bullet starring Edward G. Robinson as Dr. Ehrlich.

This week's winner is Laura Gerth of the University of Notre Dame. She identified the molecule, the Nobel Laureate, and even got the correct name of the movie! Laura has already agreed to donate her free lunch to a starving undergraduate.

The undergraduate winner is Stefan Tarnawsky of the University of Toronto. He took time off yesterday when he should have been studying for this morning's final exam in Biochemistry! I hope he didn't regret it.

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This is a very famous molecule. There was even a Hollywood movie about it! Can you name it?

There is one Nobel Laureate who is most closely identified with this particular molecule, although it had nothing to do with the awarding of the Nobel Prize. You have to identify the Nobel Laureate and what the prize was really for.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are six ineligible candidates for this week's reward: Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, Shumona De of Dalhousie University, Maria Altshuler of the University of Toronto, Mike Fraser of Toronto, and Alex Ling of the University of Toronto.

The Canadians continue their total dominance of the rest of the world. That's as it should be.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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Monday's Molecule #91

 
Identify this molecule. You need to describe what you see as accurately as possible and name the species from which this protein was purified. I don't think any of you can do it without a hint but I've received complaints that the hint makes it too easy. We'll see how you do without a hint.¹

There's a direct connection between today's molecule and a Nobel Prize. I'm looking for the person(s) who discovered the significance of the molecule—not necessarily the structure.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is a fragment of bovine prion protein and the Nobel Laureate is Stanley Prusiner. Four people got it right but the winner is Haruhiko Ishii.

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1. OK, maybe one little hint ... this week's Nobel Laureate(s) on Sandwalk were inspired by this week's 2008 winners.

Monday's Molecule #129: Winner

 
The molecule is the Src protein tyrosine kinase from chicken (Gallus gallus). The scr gene is a proto-oncogene, meaning that is the normal version of an oncogene, or a cancer-causing gene. Mutant alleles of proto-oncogenes are responsible for many types of cancer.

A highly derived version of the normal src gene (v-src) is present in strains of the chicken Rous sarcoma virus discovered by Payton Rous in 1911. RSV causes cancer in chickens and it was the first cancer-causing virus to be identified.

It wasn't until the 1970's that the gene responsible for the cancer was identified and recognized as a derivative of a normal cellular gene involved in signal transduction and regulation of cell growth. Michael Bishop and Harold Varmus received the Nobel Prize for identifying the src gene as a proto-oncogene. They are this week's Nobel Laureates.

Many people got the right answer but the first one was Cody Cobb, soon to be a graduate student at Rutgers University in New Jersey. He will be joining me for lunch in a week or two.

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Today's molecule is very famous so you aren't going to get any hints other than the fact it's from the species Gallus gallus

You need to name the molecule, identify its function, and explain why it is so famous. That will lead you to one or more Nobel Laureates whose Nobel Prize was directly related to this protein and, more importantly, its gene.

The first person to identify the molecule and the Nobel Laureate(s), wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of the University of Toronto, Jason Oakley of the University of Toronto, Bill Chaney of the University of Nebraska, Ian Clarke of New England Biolabs Canada in Pickering ON, Canada. Dima Klenchin of the University of Wisconsin at Madison, Dara Gilbert of the University of Waterloo, and Anne Johnson of Ryerson University.

I have an extra free lunch for a deserving undergraduate so I'm going to continue to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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The figure is from Williams et al. (1997).

Williams, J.C., Weijland, A., Gonfloni, S., Thompson, A., Courtneidge, S.A., Superti-Furga, G., Wierenga, R.K. (1997) The 2.35 A crystal structure of the inactivated form of chicken Src: a dynamic molecule with multiple regulatory interactions. J. Mol. Biol. 274:757-75. [PubMed] [doi:10.1006/jmbi.1997.1426]

Monday's Molecule #139

 
The molecule is 4-sulfonamide-2',4'-diaminobenzol or "Prontosil," a potent antibiotic. Gerhard Domagk received the Nobel Prize for developing Prontosil as a treatment against bacterial infections.

The overall winner is Markus-Frederik Bohn of the Lehrstuhl für Biotechnik in Erlangen, Germany. The undergraduate winner is Jason Oakley a biochemistry student at the University of Toronto.

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Name this molecule. The common name will do. Briefly describe what it does.

There's a Nobel Prize directly connected to this molecule. If you can name the molecule then you can find the Nobel Laureate(s).

The first person to identify the molecule and name the Nobel Laureate(s) wins a free lunch. Previous winners are ineligible for six weeks from the time they first won the prize.

There are only four ineligible candidates for this week's reward: Philip Johnson of the University of Toronto, Ben Morgan of the University of North Carolina at Chapel Hill, Frank Schmidt of the University of Missouri and Joshua Johnson of Victoria University in Australia.

Frank and Joshua have agreed to donate their free lunch to an undergraduate. Consequently, I have an extra free lunch for a deserving undergraduate so I'm going to award an additional prize to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch. If you can't make it for lunch then please consider donating it to someone who can in the next round.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule(s) and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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Monday's Molecule #87

 
This could be difficult so I'll give you a few clues. This molecule is secreted and it's function is to degrade nucleic acid. I want the name of the molecule and also a brief description of the image you see on the left. What is it showing?

There's a indirect connection between the image of today's molecule and a Nobel Prize. We are looking for the single person most responsible for the particular kind of image you see here.

The first person to correctly identify the molecule and name the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: This week's winner is Dima Klenchin of the University of Wisconsin. The molecule is bovine ribonuclease and the image depicts the different conformations of the molecle in solution as solved by NMR. The Nobel Laureate is Kurt Wüthrich. Congratulations Dima!

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Monday's Molecule #59

 

This is an example of a very common molecule found in every cell. It's obviously not a chemical structure but a diagram of something else. You have to give us the common name of this thing and identify the species. You'll be pleased to know that I don't need the systematic IUPAC name for this one.

There's a direct connection between this molecule, the species, and Wednesday's Nobel Laureate. As a matter of fact, the diagram above is from the acceptance speech of the Nobel Laureate. Your task is to figure out the significance of today's molecule and identify the Nobel Laureate who studied it.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate. Previous winners are ineligible for one month from the time they first collected the prize. There are two ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: We have a winner! Alex Knoll wins a free lunch at the Faculty CLub whenever he's in Toronto. The molecule is the ribosomal RNA transcription unit from Tetrahymena thermophila and the Nobel Laureate is Tom Cech who studied the self-spicing reaction of the ribosomal RNA precursor.

The good news is that every one of the people who responded got it right. The bad news is that there were only eight of you.

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Monday's Molecule #117: Winners

 
UPDATE: The molecule is yellow fever virus.

The Nobel Laureate is Max Theiler.

This week's winner is Maria Altshuler of the University of Toronto.

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Today's "molecule" is fairly complex for a "molecule" but not quite as complex as a living cell. You have to identify the particular type of "molecule" that's shown here but it will be too hard to do that without some clues. One of the clues is the connection to a Nobel Laureate. The other one is cleverly hidden in the bottom part of this posting.

The first person to identify the "molecule" and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Dima Klenchin from the university of Wisconsin, Alex Ling from the University of Toronto, Bill Chaney of the University of Nebraska, Elvis Cela from the University of Toronto, Peter Horwich from Dalhousie University, Devin Trudeau from the University of Toronto, and Shumona De of Dalhousie University

Dima and Bill have donated their free lunch to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

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

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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 #102

 
Name this molecule. Your task is to identify the molecule and give it a biochemically accurate name (the IUPAC name would be perfect, but it's not required). A Nobel Laureate is associated with this molecule, and similar molecules, because the prize was awarded, in part, for synthesizing them in the laboratory.

The first one to correctly identify the molecule and name the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are three ineligible candidates for this week's reward: Alex Ling of the University of Toronto, Timothy Evans of the University of Pennsylvania, and John Bothwell of the Marine Biological Association of the UK in Plymouth, UK. John, Dale, and a previous winner (Ms. Sandwalk) have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Alex got the first one.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is gibberellin A3 (GA3), a plant hormone. The Nobel Laureate is Elias Corey. The winner is, once again, Dima Klenchin of the University of Wisconsin. Congratulations Dima.

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Monday's Molecule #99

 
Name this molecule. This time we need the common name and the systematic (IUPAC) name. A Nobel Prize was awarded for discovering how this molecule is related to your ability to remember its name and recognize the structure.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are four ineligible candidates for this week's reward: Dima Klenchin of the University of Wisconsin, Dale Hoyt from Athens, Georgia, Ms. Sandwalk from Mississauga, Ontario, Canada and Alex Ling of the University of Toronto. Dale and Ms. Sandwalk have offered to donate the free lunch to a deserving undergraduate so the first two undergraduates to win and collect a free lunch can also invite a friend. Alex gets the first one.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the "molecule" and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

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

UPDATE: The molecule is cyclic AMP (cAMP) or (1S,6R,8R,9R) -8-(6-aminopurin-9-yl) -3-hydroxy-3-oxo-2,4, 7-trioxa- 3λ5-phosphabicyclo [4.3.0]nonan-9-ol. The Noble Laureate is Eric Kandel. Several people guessed the molecule and Kandel but they added a second Nobel Laureate—one that I had already covered (usually Paul Greengard). Only one person picked up on the clue about memory and named Kandel alone. Congratulations to Timothy Evans of the Dept. of Neuroscience, University of Pennsylvania.

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Monday's Molecule #60

 
I'm a little pressed for time today 'cause my mid-term test is tomorrow. This is a molecule for all you hard-core biochemists out there.

You have to give me the common name of this molecule and explain what it's used for. You'll be pleased to know that I don't need the systematic IUPAC name for this one.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who worked with it.

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward.¹ The prize is a free lunch at the Faculty Club.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate. Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: The winner is Mike Fraser who correctly guessed that this is the tert-butyloxycarbonyl derivative of valine, also known as Boc-valine. The Boc group acts as a carboxy-terminal blocking group in the chemical synthesis of proteins. The most common peptide synthesizers are the solid phase peptide synthesizers originally developed by Bruce Merrifield. Merrifield received the Nobel Prize in 1984.

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1. Here's an interesting bit of trivia. How many ScienceBlog^TM authors have won the free lunch? How many have guessed the correct answer even though they weren't the first to do so? The answers might surprise you.

Monday's Molecule #125

 
This is the tentative structure of a very important molecule. It's "tentative" because the exact structure hasn't been fully worked out and because the "molecule" is heterogeneous—it's actually a mixture of several similar molecules.

Identify this molecule by giving its common name and the organism(s) from which it is derived. This particular molecule is part of a much larger complex that was first identified over 100 years ago. The person who discovered that large complex received a Nobel Prize. Identify the Nobel Laureate.

The first person to identify the molecule and the Nobel Laureate, wins a free lunch at the Faculty Club. Previous winners are ineligible for six weeks from the time they first won the prize. Please note the change in the length of time you are ineligible. The idea is to give more more people a chance to win.

There are nine ineligible candidates for this week's reward: Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., Michael Clarkson of Waltham MA (USA), Òscar Reig of Barcelona, Maria Altshuler of the University of Toronto, Mike Fraser of the University of Toronto, and Jaseon Oakley of the University of Toronto.

Mike has saved Canadians from embarrassment.

I still have one extra free lunch donated by a previous winner to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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[Image Credit: The structure of Mycobacterium tuberculosis lipoarabinomannan (LAM) by Achim Treumann and Steve Homans.]

Monday's Molecule #49

 
Today's molecule is very simple. You don't get any credit for just naming the molecule.

There's an indirect connection between this molecule and Wednesday's Nobel Laureate(s). Let's see who knows and loves biochemistry!

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. This way I may select multiple winners if several people get it right. This one is easy. Get your response in quickly.

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

UPDATE: The molecule is polyphosphate. We have a winner!

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Monday's Molecule #122

 
Today's molecule is a drug as well as a biological molecule that's found in some species. You need to supply the common name and the correct IUPAC name for this molecule. The stereochemistry isn't shown in the figure but you have to specify it in your answer.

As a drug, this molecule is used to treat a common but life-threatening condition. Identify that condition and name the Nobel Laureate who first described and characterized it.

The first person to identify the molecule and the Nobel Laureate wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first won the prize.

There are seven ineligible candidates for this week's reward: Mike Fraser of Toronto, Alex Ling of the University of Toronto, Laura Gerth of the University of Notre Dame, Stefan Tarnawsky of the University of Toronto, Dima Klenchin of the University of Wisconsin, Madison, Adam Santoro of the University of Toronto., and Michael Clarkson of Waltham MA (USA).

The Canadians are still ahead in the competition between Canadians the rest of the world but their recent dominance is coming to an end. I want to thank all those smart Canadians who have been holding back in order to give the rest of the world a chance.

I still have one extra free lunch donated by a previous winner (Michael Clarkson) to a deserving undergraduate so I'm going to continue to award an additional free lunch to the first undergraduate student who can accept it. Please indicate in your email message whether you are an undergraduate and whether you can make it for lunch.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Prizes so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow.

Comments will be blocked for 24 hours.

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Fixing Carbon: the Rubisco Reaction

Life as we know it is based on carbon. All organisms need to have a source of carbon in order to grow and multiply. Animals, such as humans, get their carbon from eating other living things but there are many other species that can assimilate carbon directly from inorganic sources. This process is known as carbon fixation.

In most cases, carbon is derived from carbon dioxide in the atmosphere or dissolved in water. There are dozens of different chemical reactions in which carbon dioxide is taken up and attached to another organic molecule. Humans can do this to limited extent but not enough to support all of our carbon needs. Bacteria, protists, plants and fungi are much better at efficiently incorporating carbon from carbon dioxide.

The reactions of carbon fixation are often expensive because they require an input of energy to drive the assimilation of the newly-fixed carbon into metabolic pathways that are operating inside the cell. Photosynthetic organisms often have an abundant supply of energy so they can take up large amounts of carbon to make organic molecules. In fact, the association between carbon fixation and photosynthesis is so obvious that it's often assumed that the processes are directly coupled.

They aren't. There are many non-photosynthetic species that can efficiently fix carbon from carbon dioxide and there are many organisms that can carry out photosynthesis but they don't fix huge amounts of carbon using the standard pathways.

Nevertheless, there is one major carbon-fixing pathway that is present in most photosynthesizing bacteria, protists, fungi, and especially plants. It's called the Calvin Cycle after its discoverer Melvin Calvin (see photo) [Nobel Laureate 1961]. In modern biochemistry courses we discuss this pathway in the photosynthesis chapter but it's no longer considered to be part of photosynthesis. Photosynthesis ends with the light-driven synthesis of the energy molecules ATP and NADPH.

The first step in this pathway is the most important; it's the step where a carbon dioxide molecule is attached to a five carbon compound and the resulting 6-carbon intermediate is split into two 3-carbon molecules. The 3-carbon molecules then enter various metabolic pathways, including a pathway that recreates the 5-carbon precursor—hence the name "cycle."

The initial reaction is shown in the schematic below where each ball represents a carbon atom. The substrate for the reaction is the 5-carbon compound with the green balls and the blue ball represents the carbon atom in carbon dioxide (CO₂). As you can see, the reaction takes place in two steps. The first step is the actual fixation reaction; it creates a 6-carbon molecule with the incorporated carbon atom from CO₂. In the second step this 6-carbon molecule is cleaved producing two 3-carbon molecules.


The 5-carbon substrate is called ribulose 1,5-bisphosphate [Monday's Molecule #34]. It's related to the ribose in ribonucleic acid (RNA) except that it's the keto form of ribose and it has two phosphate groups attached to the 1 and 5 positions. The final products are called 3-phosphoglycerate. They are common intermediates in many metabolic pathways.

Here's the complete reaction. The enzyme that catalyzes this reaction is the most abundant enzyme on the entire planet. It's called ribulose 1,5-bisphosphate carboxylase-oxygenase, or Rubisco for short.

Mechanism of Rubisco-catalyzed carboxylation of ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate. A proton is abstracted from C-3 of ribulose 1,5 -bisphosphate to create a 2,3 -enediolate intermediate. The nucleophilic enediolate attacks producing 2-carboxy-3-ketoarabinitol 1,5 -bisphosphate, which is hydrated to an unstable gem diol intermediate. The C-2-C-3 bond of the intermediate is immediately cleaved, generating a carbanion and one molecule of 3-phosphoglycerate. Stereospecific protonation of the carbanion yields a second molecule of 3-phosphoglycerate. This step completes the carbon fixation stage of the Calvin cycle—two molecules of 3-phosphoglycerate are formed from CO₂ and the five-carbon sugar ribulose 1,5-bisphosphate.

©Laurence A. Moran and Pearson Prentice Hall 2007

Monday's Molecule #69

 
This colorful molecule plays an important role in regulating carbohydrate metabolism, among other things. Your task for today is to identify the molecule. Be as specific as possible (what species?).

Identify the Nobel Laureate(s) who was/were awarded a Nobel Prize for discovering fundamental properties of this molecule without knowing the sequence or the structure. [Hint: The award was very controversial in the home country of the Nobel Laureate(s).]

Here's part of the PDB file to help you.

SEQRES 1 A 191 PHE PRO THR ILE PRO LEU SER ARG LEU PHE GLN ASN ALA
SEQRES 2 A 191 MET LEU ARG ALA HIS ARG LEU HIS GLN LEU ALA PHE ASP
SEQRES 3 A 191 THR TYR GLU GLU PHE GLU GLU ALA TYR ILE PRO LYS GLU
SEQRES 4 A 191 GLN LYS TYR SER PHE LEU GLN ALA PRO GLN ALA SER LEU
SEQRES 5 A 191 CYS PHE SER GLU SER ILE PRO THR PRO SER ASN ARG GLU
SEQRES 6 A 191 GLN ALA GLN GLN LYS SER ASN LEU GLN LEU LEU ARG ILE
SEQRES 7 A 191 SER LEU LEU LEU ILE GLN SER TRP LEU GLU PRO VAL GLY
SEQRES 8 A 191 PHE LEU ARG SER VAL PHE ALA ASN SER LEU VAL TYR GLY
SEQRES 9 A 191 ALA SER ASP SER ASP VAL TYR ASP LEU LEU LYS ASP LEU
SEQRES 10 A 191 GLU GLU GLY ILE GLN THR LEU MET GLY ARG LEU GLU ASP
SEQRES 11 A 191 GLY SER PRO ARG THR GLY GLN ALA PHE LYS GLN THR TYR
SEQRES 12 A 191 ALA LYS PHE ASP ALA ASN SER HIS ASN ASP ASP ALA LEU
SEQRES 13 A 191 LEU LYS ASN TYR GLY LEU LEU TYR CYS PHE ARG LYS ASP
SEQRES 14 A 191 MET ASP LYS VAL GLU THR PHE LEU ARG ILE VAL GLN CYS
SEQRES 15 A 191 ARG SER VAL GLU GLY SER CYS GLY PHE

The first person to correctly identify the specific molecule and name the Nobel Laureate(s) wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There is only one ineligible candidates for this week's reward.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureates so you might want to check the list of previous Sandwalk postings.

Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

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

UPDATE: This week's winner is David Schuller of Cornell University (again). He correctly identified the molecule as human growth hormone and the Nobel Laureate is Bernardo Houssay (1947). Thanks to all the others who sent in their guesses.

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