Better Biochemistry at EB2013

I've been talking to a lot of people here at EB2013 in Boston. One of the main topics of conversation is education in biochemistry and molecular biology. Another is blogs and social media. Some of these new friends are going to be looking at Sandwalk so I've prepared a short list of links on teaching biochemistry.

You can get updates on new posts on Twitter [@larryonsandwalk], on Facebook [Laurence A. Moran], and on Google⁺ [Laurence A. Moran].

April 21, 2013
Judging the Quality of MOOCs

April 15, 2013
Monday's Molecule #202

April 15, 2013
Why Do We Do Science?

April 16, 2013
Where Do Organisms Get Their Energy?

March 18, 2013
Monday's Molecule #200

September 12, 2012
Does the Central Dogma Still Stand?

August 21, 2012
Designing a New Biochemistry Curriculum

August 7, 2012
Changing Ideas About The Origin Of Life

August 6, 2012
What Does "pH" Mean?

August 3, 2012
On the Evolution of New Enzymes: Completely Different Enzymes Can Catalyze Similar Reactions

July 20, 2012
Better Biochemistry: Good Enough Enzymes

July 13, 2012
Slip Slidin' Along - How DNA Binding Proteins Find Their Target

May 23, 2012
Better Biochemistry: The Perfect Enzyme

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Monday's Molecule #202

The last Monday's Molecule was the pyrrolysine, 23rd amino acid. The winner was Michael Florea [Monday's Molecule #201].

Today's molecule is an enzyme. Homologous enzymes are found in all species. They play an essential role in metabolism. The green part binds the substrate and the subsequent reaction reduces a bound FAD prosthetic group (yellow). Electrons are then passed to an FAD molecule in the purple part in the orientation shown on the left. Notice that the yellow FAD molecules are close together. (The two purple parts on the left should be joined but the connection can't be resolved in the structure.) This electron transfer results in a shift in conformation to the conformation of the purple structure shown on the right. Note that the FAD molecule has shifted to a less exposed position. The purple protein then dissociates and carries electrons to an membrane-bound enzyme that transfers electrons to ubiquinol (QH₂). Name the green protein and the purple protein.

This week I'm trying a new format in order to avoid moderating comments. Email your answers to me at: Monday's Molecule #202. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post mostly 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 email message.)

Monday's Molecule #201

The last Monday's Molecule was L-gulose and the winner was Bill Gunn. It was a special anniversary (#200) so I reposted my original Monday's Molecule from November 13, 2006 [Monday's Molecule #200]. I don't think it was any easier this year than it was seven years ago. That's a shame since biochemistry students should have had no problem getting the right answer if they understand the basic concept behind drawing structures of carbohydrates.

Let's see if you can do any better with the same molecule from November 20, 2006. It's a common molecule, although I think it's not taught in most introductory biochemistry courses. It's in most of the textbooks.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #200

This is the 200th Monday's Molecule. I started this series back on November 13, 2006. Today's molecule is a repeat of that first one. Let's see if readers in 2013 can do better than those in 2006! The last "Monday's Molecule" was puromycin [Monday's Molecule #199]. The winners were Bell Gunn and River Jiang. River needs to contact me by email to set up a lunch date. I'm going to try and treat all the previous winners this week so if I owe you a lunch you should get in touch right away to collect.

The mystery molecule is an aldohexose. There are 16 different aldohexoses. The structures and names of 8 of them are show below in order to help you out.

This is a tough one. You have to know several carbohydrate naming conventions and you have to understand Fischer projections. Good luck.



Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #199

The last "Monday's Molecule" was phycoerythrin [Monday's Molecule #198]. The winner was Piotr Gasiorowski.

This week's molecule can do some very bad things to certain cells. You just have to give the common name and briefly explain what it does and how it works.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #198

The last "Monday's Molecule" was 2R,3S-isocitre [Monday's Molecule #197]. The winner was Evey Salara. She's probably too far away to come for lunch.

This week's molecule is very strange looking but it serves a very important role in some species. What is the molecule, what species have it, and what does it do?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #197

The last "Monday's Molecule" was β-D-mannopyranose, shown in boat and chair configurations [Monday's Molecule #196]. The winners were Bill Chaney, Dima Klenchin, and Bill Gunn. Bill Gunn should contact me if he is within range of Toronto.

Students often find it very difficult to distinguish between various stereoisomers. For example, many of you thought that the last molecule was glucose. This week's molecule should present a real challenge for most of you. It's a common molecule, present in all cells and it has a common name by which it is identified in most textbooks. However, the common name isn't good enough because there are several different conformations. The conformation shown in the figure is the only one that's synthesized in the normal reaction. Name this molecule using whatever conventions you have to employ to identify it correctly. [Hydrogen atoms are omitted for clarity. You should be able to infer their positions.]

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #196

Last week's molecule was tetrahydrofolate, an essential cofactor in several reactions; notably the synthesis of thymidine. The winner was Jacob Troth [Monday's Molecule #195]. He should contact me by email.

This week's molecule is a very important molecule. I'm showing you two different conformations of the same molecule. You need to identify this molecule using its full and complete common name. I'm going to be strict about this, if you give me an ambiguous name you will not win.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #195

Last week's molecule was allantoin, the breakdown product of uric acid that's found in the urine of mammals. Other animals can degrade allantoin to more simple compounds but mammals have lost the genes for this pathway. The winners were Paul Clapham and Jacob Troth [Monday's Molecule #194]. They should contact me by email.

This week's molecule is a ubiquitous and essential molecule in all species. Give the common name but be sure you don't confuse it with other, very similar, molecules.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #194

Last week's molecule was N-(2-aminoethyl)glycine, a molecule that has been used to build artificial DNA molecules. The winner was Michael Rasmussen [Monday's Molecule #193].

This week's molecule is a real pisser. You'll have to give the complete, unambiguous, formal name AND explain why we don't make it.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #193

Last week's molecule was capsaicin, the molecule responsible for the "hot" sensation of chili peppers. There were two winners: Seth Kasowitz and Bill Gunn [Monday's Molecule #192].

This week's molecule is featured in an article that I will (hopefully) blog about in the next few days. There's a common name of sorts but you will need to supply the correct IUPAC name to win the free lunch.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #192

Last week's molecule was photosystem I (PSI). Mikkel Rasmussen was the only one to get it right [Monday's Molecule #191].

I thought of this week's molecule while I was in Los Angeles last week. We got to sample some excellent examples of cuisine that's hard to find in Toronto. You need to supply the common name AND the formal IUPAC name.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #191

Last week's molecule was L-dopa. The winner was Raul A. Félix de Sousa (again, but this time only by four minutes!) [Monday's Molecule #190].

This week's molecule is much more complicated and it's also much more important. You need to identify this complex making sure you distinguish it from other similar complexes. You don't need to name the exact species but you should have some idea of which organisms have this complex and which ones don't. There's not enough room in the comments for the complete IUPAC name!

You'll get special bonus points (and the expensive lunch in the dining room instead of the pub) for explaining how an irreducibly complex structure like this could have evolved.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #190

Last week's molecule was carnitine (3-hydroxy-4-(trimethylazaniumyl)butanoate) or carnitine. The winner was Raúl Mancera [Monday's Molecule #189].

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #189

Last week's molecules were cis Δ⁹-octadecanic acid (oleic acid) and trans Δ⁹-octadecanic acid (elaidic acid). Last week's winner was John Runnels. He should email me.

Name this week's molecule. Be sure to give an unambiguous name—it can be the common name or the IUPAC name. Why is this molecule important in some species?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #188

Last week's molecule was N-formylmethionyl-tRNA_f^Met [Monday's Molecule #188]. Only three people came close. The winner was Mikkel Rasmussen.

Name these molecules. One of them has a well-known common name that you have to include in your answer. The other one also has a common name but you don't have to find it. You have to give the complete formal names of each molecule. Do you know the significance of these two molecules?

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #187

Last week's molecule was the core nucleosome complex [Monday's Molecule #186] and nobody who was eligible for a win got it! That's quite shocking. Here's an easy one for today.

Name this molecule, including the name of the "R" group. You'll have to guess but there's really only one possibility in living cells. Don't forget, I need the full name of the most likely molecule given the partial structure that you see.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #186

Last week's molecules were the four common nuleosides in DNA [Monday's Molecule #185]. The winner was Matt Talarico.

This week I'm asking you to identify a complex structure made up of eight different components (top) plus one other (bottom). Name the structure making sure to be as specific as possible, Name the none components.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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.)

Monday's Molecule #185

Last week's molecule was warfarin, a rat poison with another role [Monday's Molecule #184]. The winner was Matt McFarlane.

This week we're in the middle of the ENCODE/junk DNA controversy. A dispute that reveals a serious lack of knowledge of fundamental concepts in biochemistry. I'm going to go back to basics today and ask you to name these four molecules. Be careful, I'm going to insist that you use the correct unambiguous names. Name them in order from upper left to upper right to lower left then lower right.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

Comments are now open.

UPDATE: The molecules are deoxyadenosine, deoxyguanosine, deoxycytidine, deoxythymidine. This week's winner is Matt Talarico. Matt should 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
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane
Aug. 20: Stephen Spiro
Aug. 27: Raul A. Félix de Sousa
Sept. 3: Matt McFarlane
Sept. 10: Matt Talarico

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Monday's Molecule #184

Last week's molecule was raltitrexid, an anti-cancer drug [Monday's Molecule #183]. The winner was Raul A. Félix de Sousa. Raul has won ten times since I restarted Monday's Molecule last November.

This week's molecule is another strange-looking molecule with a very specific purpose. Identify the molecule and its role in mammals.

Post your answers as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly 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. Please try and beat the regular winners. Most of them live far away and I'll never get to take them to lunch. This makes me sad.

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

UPDATE: The molecule is warfarin or Coumadin®, a rat poison and an anticoagulant. It's a competitive inhibitor of vitamin K reductase and this blocks blood clotting. The winner is Matt McFarlane, one of the few people who can actually collect a free lunch. 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
April 9: no winner
April 16: Raul A. Félix de Sousa
April 23: Dima Klenchin, Deena Allan
April 30: Sean Ridout
May 7: Matt McFarlane
May 14: no winner
May 21: no winner
May 29: Mike Hamilton, Dmitri Tchigvintsev
June 4: Bill Chaney, Matt McFarlane
June 18: Raul A. Félix de Sousa
June 25: Raul A. Félix de Sousa
July 2: Raul A. Félix de Sousa
July 16: Sean Ridout, William Grecia
July 23: Raul A. Félix de Sousa
July 30: Bill Chaney and Raul A. Félix de Sousa
Aug. 7: Raul A. Félix de Sousa
Aug. 13: Matt McFarlane
Aug. 20: Stephen Spiro
Aug. 27: Raul A. Félix de Sousa
Sept. 3: Matt McFarlane

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