Monday's Molecule #241

Last week's molecule (above) [Monday's Molecule #240] is a derivative of 2′-deoxythymidine triphosphate that's used in DNA sequencing reactions. The derivative has a 3′-O-azidomethyl group so that when this nucleotide is incorporated into a growing chain it cannot be extended because the 3′ -OH group is blocked. This is a chain-termination derivative. The large group attached to the methyl group at the C5 position on the thymine base is a color compound (a fluor). When this nucleotide is incorporated it stops chain growth, makes the DNA visible, and indicates that there's a T in the last position. The winner is James Wagstaff.

Almost all of you are familiar with today's molecule (right) although I suspect that many of you don't recognize it right away. Name the molecule—the common name will do—and briefly describe its biochemical function.

Email your answer to me at: Monday's Molecule #241. 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 #240

Last week's molecule (right) [Monday's Molecule #239] was 2-carboxy-D-arabinitol 1-phosphate. It's an inhibitor of the enzyme ribulose 1,5-bisphosphate carboxylase-oxygenase, better known as Rubisco. That's the key enzyme responsible for CO₂ fixation in the Calvin cycle. Plants have to inhibit Rubisco during the night when the lack of sunlight prevents production of ATP and NADPH by photosynthesis. One of the ways they inhibit the enzyme is to produce 2-carboxy-D-arabinitol 1-phosphate at night. The winner is Piotr Gąsiorowski.

This week's molecule (below) is pretty complicated. I don't expect a complete name; just concentrate on getting the correct name of the core part of the molecule on the left. In addition to identifying the molecule, you need to explain what it is used for and, specifically, the purpose of the -N₃ group in the lower left corner of the molecule.

Email your answer to me at: Monday's Molecule #239. 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 #239

Last week's molecules (right) [Monday's Molecule #238] were correctly identified by Dean Bruce (again) who wrote ...

... it is 3-hydroxy-3-methylglutarate-CoA (HMG-CoA) synthetase. HMG-CoA appears to be the only molecule in the active sites of the illustration. Acetoacetyl-CoA and Acetyl-CoA in a Claisen condensation (of the beta-carbonyl of acetoacetyl-CoA) form HMG-CoA.

The mitochondrial one is the isoform involved in metabolic pathology. The disease is called "mitochondrial HMG-CoA synthetase-2 deficiency" in the Online Mendelian Inheritance of Man.

This week's molecule is an important regulatory molecule in some species. Identify it using the standard IUPAC nomenclature and describe the enzyme whose activity it regulates.

Email your answer to me at: Monday's Molecule #239. 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 #238

Last week's molecules (right) [Monday's Molecule #237] were α-D-glucopyranosyl-(1➝4)-β-D-glucopyranose, the β anomer of maltose and α-D-glucopyranosyl-(1➝6)-α-D-glucopyranose, the β anomer of isomaltose. The winner is Dean Bruce. A surprising number of people got it right.

This week's molecules (below) are related. They are cytoplasmic (PDB 2P8U left) and mitochondrial (PDB 2WYA right) versions of very important enzymes. The human versions are shown. Name the enzymes and the products bound in the active sites (complete common name of the product). Mutations in one of the genes coding for one of these enzymes cause a rare genetic disease. Which one? Why are there no known diseases associated with genetic defects in the gene for the other version of the enzyme?

Email your answer to me at: Monday's Molecule #238. 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 #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 #236

Last week's molecule [Monday's Molecule #235] was N-formylmethionyl-tRNA_f^Met (fMet-tRNA_f^Met). The polynucleotide has to be specifically identified as the initiator tRNA (tRNA_f^Met, in bacteria). The winner is Jon Binkley. As I expected, there were very few people who got the right answer—in fact, there was only one other correct answer.

This week's molecules (below) may look very familiar but don't be fooled. You'll have to be very careful in identifying and naming each one of the stereoisomers. (Use common names.)

Email your answer to me at: Monday's Molecule #236. 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 #235

Last week's molecule [Monday's Molecule #234] was insect juvenile hormone. The winners are Frank Schmidt and Raul Félix de Sousa (still an undergraduate?). They live in foreign countries so they won't be coming to lunch.

This week's molecule (right) is very common. You have to identify the entire molecule including the specific polynucleotide. Emphasis is on the word "specific"—there's only one possibility. I'm betting that there won't be very many correct answers for this one.

Email your answer to me at: Monday's Molecule #235. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #234

Last week's molecules [Monday's Molecule #233] were oxaloacetate, ethanol, lactate, alanine, and acetyl-CoA. All of them can be synthesized in a reaction using pyruvate as a substrate (two steps to make ethanol). All of them are precursors to pyruvate and hence glucose. The winner is Jean-Marc Neuhaus. I will be buying him four meals next time I visit Switzerland. I'm thinking it will be two raclettes and two fondues with lots of wine.

This week's molecule (left) is probably not very familiar to most of you so I don't anticipate many correct answers. You can use the common name. Email your answer to me at: Monday's Molecule #234. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #233

Last week's molecules [Monday's Molecule #232] were all-trans and 13-cis retinal. Retinal is the active protein donor/acceptor in bacteriorhodopsin. The all-trans form is shifted to the 13-cis form when a photon of light is absorbed. The retinal molecules are arranged within the membrane-bound bacteriorhodpsin in a way that binding and release of a proton results in transport from the cytoplasm to the exterior. The creation of a proton gradient drives ATP synthesis.

The winner is Philip Johnson from Switzerland.

This week's molecule (left) is actually a collection of molecules. Name all five molecules and tell me what they have in common from a biochemical perspective. Common names will do.

Email your answer to me at: Monday's Molecule #233. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #232

Monday's Molecule #231 [Monday's Molecule #231] was the Shine-Delgarno sequence found a few nucleotides upstream of the initiation codon in many bacterial mRNAs. It interacts (base pairs) with a sequence on the 3′ end of 16S RNA to help form the translation initiation complex. This means that bacteria can have polycistronic mRNAs (from operons) and internal translation initiation. The winners were Keith Conover and Nevraj Kejiou. That's two weeks in a row that an undergraduate from the University of Toronto has won. I will be taking them to lunch. I encourage undergraduates from far, far away to hurry up and send in an answer to this week's molecule!

This week's molecule (left) is covalently bound to the lysine side chain of a protein. It exists in two distinct configurations that can be interconverted by a well-known chemical reaction. Name the two different configurations (common names only) and explain the significance of the reaction.

Email your answer to me at: Monday's Molecule #232. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #231

Monday's Molecule #230 (Jan. 27, 2014) [Monday's Molecule #230] was 2-carboxy-3-ketoarabinitol 1,5-bisphosphate. It's an intermediate in the reaction catalyzed by ribulose 1,5-bisphosphate carboxylase-osygenase (Rubisco), the key enzyme in the Carvin cycle. This is the molecule created by adding CO₂ to the 2-carbon atom of ribulose 1,5-bisphosphate. The winners were Bill Gunn closely followed by the first correct answer from an undergraduate, Ariel Gershon. Ariel is a student at the University of Toronto so it looks like I'm going to have to buy a lunch.

This week's molecule (below) is a sequence. Name the sequence in red and briefly describe it's function.

Email your answer to me at: Monday's Molecule #231. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #230

Last week's molecule was cholesterol [Monday's Molecule #229]. The figure shows how the molecule would look in a lipid bilayer (membrane). The winner was Tommy Stuleanu.

This week's molecule (below) is going to be hard. I won't be surprised if nobody gets the right answer. It's a key intermediate in an extremely important reaction. You need to give the common name AND the the overall reaction. Name the enzyme as well.

Email your answer to me at: Monday's Molecule #230. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #229

Last week's molecule was NADP^⊕ or nicotinamide adenine dinucleotide phosphate. That was an easy one [Monday's Molecule #228 ]. The winner was Tom Mueller.

This week's molecule (below) is going to be a bit of a challenge because you can't see all of the hydrogen atoms. It's a very common molecule. All you have to do is supply the common name and NOT the IUPAC systematic name that correctly identifies the exact molecule shown in the image. However, if anyone wants to supply the systematic name, feel free to do so.

Email your answer to me at: Monday's Molecule #229. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #228

Last week's molecule was arachidonate, one of the key intermediates in the synthesis of complex lipids, especially protaglandins in mammals [Monday's Molecule #227 ]. The winner is Bill Gunn.

This week's molecule (left) is an easy one for all of the undergraduates who are just beginning a new term. This is one of those molecules that everyone should recognize. Just be sure you pay attention to all the groups and the part in red. All you have to do is supply the common name and NOT the IUPAC systematic name that correctly identifies the exact molecule shown in the image. However, if anyone wants to supply the systematic name, feel free to do so.

Email your answer to me at: Monday's Molecule #228. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #227

Last week's molecule was the drug pantoprazole, a proton pump inhibitor used to treat excess stomach acid or acid reflux [Monday's Molecule #226 ]. The winner is Bill Gunn.

This week's molecule (left) is related to one from last April. That molecule, is one of the essential molecules in the human diet and today's molecule is the reason why. This is one of those molecules that everyone should recognize because it's a key metabolic precursor in a large number of species. This is one of those times when all you have to do is supply the common name (Merry Christmas!) and NOT the IUPAC systematic name that correctly identifies the exact molecule shown in the image. However, if anyone wants to supply the systemiac name, feel free to do so.

Email your answer to me at: Monday's Molecule #227. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #226

Last week's molecule was sucrose 6-phosphate or α-D-glucopyranosyl-(1→2)-β-D-fructofuranoside 6-phosphate [Monday's Molecule #225 ]. The winner is Jean-Marc Neuhaus (again). He appears to be the only Sandwalk reader who has a copy of my book!

Today's molecule (below) looks a bit strange. It should be obvious that this is not a "natural" molecule. What is it and what does it do? You don't need to give me a long systematic name. The common name will do quite nicely.

Email your answer to me at: Monday's Molecule #226. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #225

Last week's molecule was EF-Tu (elongation factor-thermo unstable). EF-Tu binds to all tRNA molecules in the cell and helps position them in the A-site of the ribosome-mRNA complex during protein synthesis. Its release is coupled to GTP hydrolysis. Eukaryotes contain homologous proteins with different names (e.g. EF-1α). The winner was Jon Nuelle from Texas. The undergraduate winner was Ariel Gershon for the second week in a row.

Today's molecule (below) is an intermediate in a very important pathway that's only found in some species. This is one of those times when you need to supply the common name AND the correct scientific name that specifies the exact molecule shown in the figure.

Email your answer to me at: Monday's Molecule #225. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #224

Last week's molecule was the second messenger, phosphatidylinositol 4,5-bisphosphate or PIP₂. The winner is Dean Bruce. The undergraduate winner is Ariel Gershon [Monday's Molecule #223].

Today's molecule is a protein (purple). It's one of the most abundant proteins in E. coli because it's bound to almost all tRNA molecules in the cell. Name the protein (complete name, not just initials).

Email your answer to me at: Monday's Molecule #224. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #223

Last week's molecule was a Holliday junction, one of the key intermediates in recombination. It's named after Robin Holliday who has since retired from science to concentrate on being a sculptor. He has produced several "biological" sculptures including "DNA Structure" (top) and "Cross Over" (bottom). The winner is Caroline Josefsson from British Columbia. The undergraduate winner is Andrew Wallace but since he lives in Australia, I suspect he won't be coming to lunch [Monday's Molecule #222].

Today's molecule (below) is not one of my favorite molecules for many reasons. However, it's pretty important in some species. Name the molecule, being as specific as you can without resorting to IUPAC rules. I need the most common name as well as a more detailed name.

Email your answer to me at: Monday's Molecule #223. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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 #222

Last week's molecule was D-serine. (Not L-serine.) The winner is undergraduate Zhimeng Yu [Monday's Molecule #221].

I was reminded of this week's molecule by a discussion we are having in an evolution forum and by a comment from a student who took a MOOC on genetics. Does it depict something that should be taught in every introductory genetics course? Is it something that should be discussed in an evolution course? You need to name the structure formed by the blue, gray, and black strands. It has a specific name.

Email your answer to me at: Monday's Molecule #222. I'll hold off posting your answers for at least 24 hours. The first one with the correct answer wins. I will only post the names of people with 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.)