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Showing posts with label Biochemistry. Show all posts
Showing posts with label Biochemistry. Show all posts

Friday, August 07, 2026

The evolution of metabolic enzymes in LUCA, Bacteria, and Archaea

The best scenario for the origin of life is that it first arose in hydrothermal vents deep in the ocean. The first catalysts of metabolic reactions were metals and later on simple organic molecules bound to metals. The substrates for all reactions were inorganic compounds such as H2, CO2, NH3, H2S and phosphate/phosphite.

Over time, the inorganic catalysts were gradually replaced by protein and RNA catalysts that often incorporated the metal ions into their active sites or used cofactors containing metal ions. There are about 400 basic metabolic reactions that are fundamental to life. Some enzyme catalysts are very ancient but others seem to be more recent.

Sunday, June 14, 2026

Do scientists at Amgen understand the human genome?

Amgen Inc. is a major pharmaceutical company based in Thousand Oaks, California (USA). [Wikipedia: Amgen] It was founded in 1980 to exploit developments in biotechnology, especially recombinant DNA technology. (Amgen is short for Applied Molecular Genetics.)

Like most pharmaceutical companies, Amgen produces promotional videos that are supposed to show how close they are to cutting edge science. Here's one that celebrates DNA Day and answers the question "What Is the Dark Genome? 98% of DNA explained." Are you impressed?

What Is the Dark Genome?

Monday, May 18, 2026

Anaerobic carbon fixation in ancient prokaryotes

Most of us were taught that plants are the main source of fixing carbon from carbon dioxide. Some of us even had to memorize the enzymes and reactions of the Calvin Cycle including the complicated reaction catalyzed by rubisco, the main CO2 fixing enzyme. [Fixing Carbon: the Rubisco Reaction].

We were led to believe that plants were the main source of sugars and other organic molecules but that's because undergraduate biochemistry education emphasizes human biochemistry. Photosynthesis and plants are only important because they are food. We were also taught, incorrectly, that photosynthesis is defined as a carbon-fixation process. [What is photosynthesis?]

It turns out that the Calvin Cycle isn't restricted to plants and it doesn't even require oxygen. Anaerobic bacteria also have a version of the Calvin Cycle and they are perfectly capable of fixing carbon without a major energy source like photosynthesis. [Carbon Dioxide Fixation in the Dark Ocean]

This makes sense since the earliest forms of life had to be able to turn inorganic molecules (e.g. CO2) into organic molecules so they had to be able to fix carbon. Current models of the origin of life are referred to as Metabolism First models because they postulate that life began with simple metabolic reactions that made organic molecules from inorganic molecules. One of the most important of these early reactions is the fixation of two molecules of CO2 into a two carbon compound (acetate).

Monday, May 11, 2026

The functions of human protein-coding genes

There are about 20,000 protein-coding genes in the human genome. We'd like to know what all these genes are doing but the only way to find out is to rely on experiments that explore the function of an individual protein.

This functional data has been collected and assembled in a large database called the Gene Ontology Resource (GO). Unfortunately, it only covers about one third of all human proteins.

Feuermann et al. (2025) developed a program to extend the coverage provided by direct annotation of human genes by making use of annotation records in related genes from other species. They constructed phylogenetic trees for 6,333 gene families representing a total of 17,079 human genes. This allowed them to deduce the functions of many more genes by taking advantage of GO annotations in homologous genes.

The "Venn diagram" (their words) illustrates the advantage of combining phylogenetic data with GO annotation. The yellow part represent the fraction of human proteins that have been directly annotated in the GO database while the brown and blue sections show how function can be inferred from a much larger set of proteins by looking at annotations in other species.

The results are not surprising. Most of the proteins are involved in basic metabolism such as cellular processes: (deep blue), cellular metabolism: (blue), and cell structure (cell structure: dark blue). Most of the genes families involved in these functions are derived from single genes that are also found in bacteria. The important point here is that the increase in number of genes in complex eukaryotes is mostly due to gene duplication and subspecialization.


Feuermann, M., Mi, H., Gaudet, P., Muruganujan, A., Lewis, S.E., Ebert, D., Mushayahama, T., Consortium, G.O. and Thomas, P.D. (2025) A compendium of human gene functions derived from evolutionary modelling. Nature 640:146-154. [doi: 10.1038/s41586-025-08592-0]

Saturday, May 09, 2026

Pervasive transcription = genes + noise

Most of the DNA in the human genome is transcribed at some point in development or in some cell type. This fact has been known since the late 1960s.

There are basically two types of transcripts. Functional transcripts mostly come from genes although there might be a few exceptions (e.g. enhancer RNAs). Non-functional transcripts can be produced by pseudogenes or from virus and transposon fossils. They can also due to transcriptional noise caused by spurious transcription.

Saturday, February 14, 2026

Protein concentration in bacteria is regulated primarily at the level of transcription initiation

The amount of a given protein in Escherichia coli depends on a number of factors such as the amount of mRNA and the rate of translation. The standard model of regulation is based on decades of study of individual genes and it reveals that the amount of protein is mostly dependent on the amount of mRNA that was translated. This, in turn, indicates that most regulation occurs at the level of transcription initiation.

It's now possible to look simultaneously at the characteristics of large numbers of protein-coding genes to see whether this generality holds. That's what Balakrishan et al. (2022) reported in a Science paper a few years ago. They looked at the characteristics of 1900 protein-coding genes in E. coli to see how protein concentration was regulated.

Thursday, December 11, 2025

How many regulatory sites in the human genome?

The current best model of the human genome is that only 10% is functional and 90% is junk. This model was first developed over half a century ago (see Junk DNA). From the very beginning, the model recognized that regulatory sequences would make up a significant proportion of the functional elements but early suggestions that most of the repetitive DNA would turn out to be involved in regulation were rejected.

As more and more data accumulated on regulatory sequences, it became apparent that most regulatory sequences of pol II (RNA polymerase II) genes could be found in relatively short regions of DNA just upstream of the transcription start site. It also became apparent that for each transcription factor there were thousands of transcription factor binding sites even though only a small number were actually involved in genuine gene regulation.1

Tuesday, April 01, 2025

Structure of the mitochondrial respirasome (electron transport complexes)

The membranes of bacterial cells and mitochondria contain a series of complexes that catalyze the oxidation of NADH. A lengthy electron transport chain leads eventually to the reduction of oxygen to water. Electrons lose energy as they pass down the chain and this is coupled to the transport of protons (H+) from one side of the membrane to the other. This proton gradient is used to drive ATP synthesis by the ATP synthase complex. The mechanism of making ATP is chemiosmosis but the pathway is often called oxidative phosphorylation or respiration.

The discovery of chemiosmosis (Chemiosmotic Theory) is one the few examples of a genuine paradigm shift. It is largely due to the work of Peter Mitchell [Ode to Peter Mitchell].

Saturday, February 15, 2025

Junk DNA is gradually making its way into mainstream textbooks

The idea that most of the human genome is junk originated more that 50 years ago. Since then, evidence in support of this concept has steadily accumulated but it has been stongly resisted by most biochemists and molecular biologists. Opposition is even stronger among scientists in other fields and in the general public thanks to a steady stream of anti-junk articles in the popular press.

Much of this opposition to junk DNA stems from a massive publiciy campaign launched by ENCODE researchers and the leading science journals back in 2012.

It's likely that most of the controversy over junk DNA is related to differing views on evolution and the power of natural selection. Most people think that natural selection is very powerful so that modern species must be extremely well-adapted to their present environment. They tend to believe that complexity is simply a reflection of sophisticated fine-tuning and this must apply to the human genome. According to this view, the presence of huge amounts of DNA with an unknown function is just a temporary situation and in the next few years most of this 'dark matter' will turn out to have a function. It has to have a function otherwise natural selection would have eliminated it.

Tuesday, February 04, 2025

What is photosynthesis?

A recent commentary in Nature prompts me to revisit an old bugaboo. The commentary discusses some recent work on CO2 fixation in plants [A genetic switch drove photosynthesis in plants1]. It begins with,

Photosynthesis, which uses energy from the Sun and carbon dioxide from the atmosphere to create carbohydrates, might be the most influential set of biochemical reactions on the planet.

Here's the problem. That's not a very good definition of photosynthesis. I discuss a much better definition in a post from seven years ago: Scientists confused about photosynthesis. A better definition is that photosynthesis is the process by which light energy is captured and converted to chemical energy. The direct products of photosynthesis are ATP and reducing equivalents such as NADPH. These cofactors are used to drive all sorts of reactions in the cell including DNA synthesis, protein synthesis, lipid synthesis, and carbohydrate synthesis.

This is very obvious when you examine photosynthetic bacteria but, unfortunately, photosynthesis was initially studied in large plants where much of the chemical energy produced by photosynthesis is used to fix CO2 and make carbohydrates. This led to the widespread belief that photosynthesis is all about making carbohydrates.

1. I'm using the title from the printed version of the journal. The web version has a different title. (I don't know why.)

Monday, November 18, 2024

Monday's Molecule #246

Today's molecule is complicated and you may not recognize it right away from the 3D structure. It was discovered in the middle of the last century and has proven to be very useful.

You can use whatever tricks you want to identify today's molecule. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #246. 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 coffee and donut at Tim Hortons if you are ever in Toronto or Mississauga (Ontario, Canada).

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.)

In order to win you must give your correct name. Anonymous and pseudoanonymous players can't win.

Comments are closed for at least 24 hours.

UPDATE:The molecule is doxycline, a tetracycline class of broad-spectrum antibiotic. The winner is Chris Dicus. I don't know where Chris is located but I'm pretty sure it's not near me so I'll have to wait unitil he visits Toronto to collect his double-double and chocolage dip donut.

-->

Winners

#145, Oct. 17, 2011: Bill Chaney, Roger Fan
#146, Oct. 24, 2011: DK
#147, Oct. 31, 2011: Joseph C. Somody
#148, Nov. 7, 2011: Jason Oakley
#149, Nov. 15, 2011: Thomas Ferraro, Vipulan Vigneswaran
#150, Nov. 21, 2011: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
#151, Nov. 28, 2011: Philip Rodger
#152, Dec. 5, 2011: 凌嘉誠 (Alex Ling)
#153, Dec. 12, 2011: Bill Chaney
#154, Dec. 19, 2011: Joseph C. Somody
#155, Jan. 9, 2012: Dima Klenchin
#156, Jan. 23, 2012: David Schuller
#157, Jan. 30, 2012: Peter Monaghan
#158, Feb. 7, 2012: Thomas Ferraro, Charles Motraghi
#159, Feb. 13, 2012: Joseph C. Somody
#160, March 5, 2012: Albi Celaj
#161, March 12, 2012: Bill Chaney, Raul A. Félix de Sousa
#162, March 19, 2012: no winner
#163, March 26, 2012: John Runnels, Raul A. Félix de Sousa
#164, April 2, 2012: Sean Ridout
#165, April 9, 2012: no winner
#166, April 16, 2012: Raul A. Félix de Sousa
#167, April 23, 2012: Dima Klenchin, Deena Allan
#168, April 30, 2012: Sean Ridout
#169, May 7, 2012: Matt McFarlane
#170, May 14, 2012: no winner
#171, May 21, 2012: no winner
#172, May 29, 2012: Mike Hamilton, Dmitri Tchigvintsev
#173, June 4, 2012: Bill Chaney, Matt McFarlane
#174, June 18, 2012: Raul A. Félix de Sousa
#175, June 25, 2012: Raul A. Félix de Sousa
#176, July 2, 2012: Raul A. Félix de Sousa
#177, July 16, 2012: Sean Ridout, William Grecia
#178, July 23, 2012: Raul A. Félix de Sousa
#179, July 30, 2012: Bill Chaney and Raul A. Félix de Sousa
#180, Aug. 7, 2012: Raul A. Félix de Sousa
#181, Aug. 13, 2012: Matt McFarlane
#182, Aug. 20, 2012: Stephen Spiro
#183, Aug. 27, 2012: Raul A. Félix de Sousa
#184, Sept. 3, 2012: Matt McFarlane
#185, Sept. 10, 2012: Matt Talarico
#186, Sept. 17, 2012: no winner
#187, Sept. 24, 2012: Mikkel Rasmussen
#188, Oct. 1, 2012: John Runnels
#189, Oct. 8, 2012: Raúl Mancera
#190, Oct. 15, 2012: Raul A. Félix de Sousa
#191, Oct. 22, 2012: Mikkel Rasmussen
#192, Nov. 12, 2012: Seth Kasowitz, Bill Gunn
#193, Nov. 19, 2012: Michael Rasmussen
#194, Dec. 4, 2012: Paul Clapham, Jacob Toth
#195, Dec. 10, 2012: Jacob Toth
#196, Dec. 17, 2012: Bill Chaney, Dima Klenchin, Bill Gunn
#197, Jan. 14, 2013: Evey Salara
#198, Jan. 21, 2013: Piotr Gasiorowski
#199, March 11, 2013: Bill Gunn, River Jiang
#200, March 18, 2013: Bill Gunn
#201, April 8, 2013: Michael Florea
#202, April 15, 2013: no winner
#203, April 29, 2013: Anders Ernberg
#204, May 6, 2013: Alex Ling, Michael Florea
#205, May 13, 2013: Bill Chaney
#206, June 24, 2013: Michael Florea
#207, July 2, 2013: Matt McFarlane
#208, July 8, 2013: no winner
#209, July 15, 2013: Rosie Redfield, Thuc Quyen Huynh
#210, July 22, 2013: Jacob Toth
#211, July 29, 2013: Alex Ling, Matt McFarlane
#212, August 5, 2013: Brian Shewchuk
#213, Sept. 2, 2013: no winner
#214, Sept. 9, 2013: Bill Chaney
#215, Sept. 16, 2013: Zhimeng Yu
#216, Sept. 23, 2013: Mark Sturtevant, Jacob Toth
#217, Sept. 30, 2013: Susan Heaphy
#218, Oct. 7, 2013: Piotr Gasiorowski, Jacob Troth
#219, Oct. 14, 2013: Jean-Marc Neuhaus
#220, Oct. 21, 2013: Jean-Marc Neuhaus
#221, Oct. 28, 2013: Zhimeng Yu
#222, Nov. 10, 2013: Caroline Josefsson, Andrew Wallace
#223, Nov. 18, 2013: Dean Bruce, Ariel Gershon
#224, Nov. 25, 2013: Jon Nuelle, Ariel Gershon
#225, Dec. 2, 2013: Jean-Marc Neuhaus
#226, Dec. 9, 2013: Bill Gunn
#227, Dec. 16, 2013: Piotr Gasiorowski
#228, Jan. 13, 2014: Tom Mueller
#229, Jan. 20, 2014: Tommy Stuleanu
#230, Jan. 27, 2014: Bill Gunn, Ariel Gershon
#231; March 3, 2014: Keith Conover, Nevraj Kejiou
#232, March 10, 2014: Philip Johnson
#233, March 17, 2014: Jean-Marc Neuhaus
#234, March 24, 2014: Frank Schmidt, Raul Félix de Sousa
#235, March 31, 2014: Jon Binkley
#236, April 7, 2014: no winner
#237, April 21, 2014: Dean Bruce
#238, April 28, 2014: Dean Bruce
#239, May 5, 2014: Piotr Gąsiorowski
#240, May 12, 2014: James Wagstaff
#241, May 19, 2014: no winner
#242, Oct. 7, 2024: Elie Huvier
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve
#245, Nov. 12, 2024: no winner
#246, Nov. 18, 2024: Chris Dicus

The figure is from the ACS website: Doxyxycline.

Thiotimoline

There's been a lot of talk recently about scieintific misinformaton on the internet. I started reminiscing about what things were like when I was growing up. I remember when I learned about DNA and when I first heard about black holes.

Then I remembered how excited I was when I first heard about the properties of thiotimoline from a well-known biochemist (Asimov, 1948). I can't say for sure that this tilted me toward choosing a career in biochemistry but it certainly played a role.

Some of you may not be familiar with thiotimoline. Here's the most important characteristic of this amazing molecule as reported in the original paper.

Thursday, November 14, 2024

The success of protein structure prediction software depended on the solved structures deposited in the Protein Data Bank (PDB)

The development of protein structure prediction programs began fifty years ago and culminated in the remarkable success of AlphaFold, developed by Google DeepMind. Demis Hassabis and John Jumper of Google DeepMind received the Nobel Prize in Chemistry (2024) for their work on AlphaFold.

AlphaFold and its predecessors were trained on a database of known protein structures called the Protein Data Bank (PDB). PDB began in 1971 as a collaboration between the Cambridge Crystallographic Centre in the UK and Brookhaven National Laboratory in the US. It utilized standardizing software for collecting and storing atomic coordinates and allowing researchers to search the database from remote locations. It soon became a requirement for researchers to deposit their data in PDB when they published.

Tuesday, November 12, 2024

Monday's Molecule #245

It's Tuesday so it must be time for Monday's Molecule! :-)

Today's molecule is the little green ladder-like thing in the figure. You have to name the class of molecule it refers to and give a brief description of its properties. You also have to indicate that you know something about the pink blob.

You can use whatever tricks you want to identify today's molecule. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #245. 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 coffee and donut at Tim Hortons if you are ever in Toronto or Mississauga (Ontario, Canada).

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.)

In order to win you must give your correct name. Anonymous and pseudoanonymous players can't win.

Comments are closed for at least 24 hours.

UPDATE: There was no winner this week.

Winners

#145, Oct. 17, 2011: Bill Chaney, Roger Fan
#146, Oct. 24, 2011: DK
#147, Oct. 31, 2011: Joseph C. Somody
#148, Nov. 7, 2011: Jason Oakley
#149, Nov. 15, 2011: Thomas Ferraro, Vipulan Vigneswaran
#150, Nov. 21, 2011: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
#151, Nov. 28, 2011: Philip Rodger
#152, Dec. 5, 2011: 凌嘉誠 (Alex Ling)
#153, Dec. 12, 2011: Bill Chaney
#154, Dec. 19, 2011: Joseph C. Somody
#155, Jan. 9, 2012: Dima Klenchin
#156, Jan. 23, 2012: David Schuller
#157, Jan. 30, 2012: Peter Monaghan
#158, Feb. 7, 2012: Thomas Ferraro, Charles Motraghi
#159, Feb. 13, 2012: Joseph C. Somody
#160, March 5, 2012: Albi Celaj
#161, March 12, 2012: Bill Chaney, Raul A. Félix de Sousa
#162, March 19, 2012: no winner
#163, March 26, 2012: John Runnels, Raul A. Félix de Sousa
#164, April 2, 2012: Sean Ridout
#165, April 9, 2012: no winner
#166, April 16, 2012: Raul A. Félix de Sousa
#167, April 23, 2012: Dima Klenchin, Deena Allan
#168, April 30, 2012: Sean Ridout
#169, May 7, 2012: Matt McFarlane
#170, May 14, 2012: no winner
#171, May 21, 2012: no winner
#172, May 29, 2012: Mike Hamilton, Dmitri Tchigvintsev
#173, June 4, 2012: Bill Chaney, Matt McFarlane
#174, June 18, 2012: Raul A. Félix de Sousa
#175, June 25, 2012: Raul A. Félix de Sousa
#176, July 2, 2012: Raul A. Félix de Sousa
#177, July 16, 2012: Sean Ridout, William Grecia
#178, July 23, 2012: Raul A. Félix de Sousa
#179, July 30, 2012: Bill Chaney and Raul A. Félix de Sousa
#180, Aug. 7, 2012: Raul A. Félix de Sousa
#181, Aug. 13, 2012: Matt McFarlane
#182, Aug. 20, 2012: Stephen Spiro
#183, Aug. 27, 2012: Raul A. Félix de Sousa
#184, Sept. 3, 2012: Matt McFarlane
#185, Sept. 10, 2012: Matt Talarico
#186, Sept. 17, 2012: no winner
#187, Sept. 24, 2012: Mikkel Rasmussen
#188, Oct. 1, 2012: John Runnels
#189, Oct. 8, 2012: Raúl Mancera
#190, Oct. 15, 2012: Raul A. Félix de Sousa
#191, Oct. 22, 2012: Mikkel Rasmussen
#192, Nov. 12, 2012: Seth Kasowitz, Bill Gunn
#193, Nov. 19, 2012: Michael Rasmussen
#194, Dec. 4, 2012: Paul Clapham, Jacob Toth
#195, Dec. 10, 2012: Jacob Toth
#196, Dec. 17, 2012: Bill Chaney, Dima Klenchin, Bill Gunn
#197, Jan. 14, 2013: Evey Salara
#198, Jan. 21, 2013: Piotr Gasiorowski
#199, March 11, 2013: Bill Gunn, River Jiang
#200, March 18, 2013: Bill Gunn
#201, April 8, 2013: Michael Florea
#202, April 15, 2013: no winner
#203, April 29, 2013: Anders Ernberg
#204, May 6, 2013: Alex Ling, Michael Florea
#205, May 13, 2013: Bill Chaney
#206, June 24, 2013: Michael Florea
#207, July 2, 2013: Matt McFarlane
#208, July 8, 2013: no winner
#209, July 15, 2013: Rosie Redfield, Thuc Quyen Huynh
#210, July 22, 2013: Jacob Toth
#211, July 29, 2013: Alex Ling, Matt McFarlane
#212, August 5, 2013: Brian Shewchuk
#213, Sept. 2, 2013: no winner
#214, Sept. 9, 2013: Bill Chaney
#215, Sept. 16, 2013: Zhimeng Yu
#216, Sept. 23, 2013: Mark Sturtevant, Jacob Toth
#217, Sept. 30, 2013: Susan Heaphy
#218, Oct. 7, 2013: Piotr Gasiorowski, Jacob Troth
#219, Oct. 14, 2013: Jean-Marc Neuhaus
#220, Oct. 21, 2013: Jean-Marc Neuhaus
#221, Oct. 28, 2013: Zhimeng Yu
#222, Nov. 10, 2013: Caroline Josefsson, Andrew Wallace
#223, Nov. 18, 2013: Dean Bruce, Ariel Gershon
#224, Nov. 25, 2013: Jon Nuelle, Ariel Gershon
#225, Dec. 2, 2013: Jean-Marc Neuhaus
#226, Dec. 9, 2013: Bill Gunn
#227, Dec. 16, 2013: Piotr Gasiorowski
#228, Jan. 13, 2014: Tom Mueller
#229, Jan. 20, 2014: Tommy Stuleanu
#230, Jan. 27, 2014: Bill Gunn, Ariel Gershon
#231; March 3, 2014: Keith Conover, Nevraj Kejiou
#232, March 10, 2014: Philip Johnson
#233, March 17, 2014: Jean-Marc Neuhaus
#234, March 24, 2014: Frank Schmidt, Raul Félix de Sousa
#235, March 31, 2014: Jon Binkley
#236, April 7, 2014: no winner
#237, April 21, 2014: Dean Bruce
#238, April 28, 2014: Dean Bruce
#239, May 5, 2014: Piotr Gąsiorowski
#240, May 12, 2014: James Wagstaff
#241, May 19, 2014: no winner
#242, Oct. 7, 2024: Elie Huvier
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve
#245, Nov. 12, 2024: no winner

The figure is modified from Hung and Slotkin (2021) The initiation of RNA interference (RNAi) in plants. Current Opinion in Plant Biology 61:102014 [doi: 10.1016/j.pbi.2021.102014] -

Wednesday, October 23, 2024

Nobel Laureate: Vincent du Vigneaud


The Nobel Prize in Chemistry 1955
"for his work on biochemically important sulphur compounds, especially for the first synthesis of a polypeptide hormone"

Vincent du Vigneaud (1901-1978) was an American biochemist who was awarded the Nobel Prize in Chemistry in 1955 for his work on biological molecules containing sulfur, especially methionine cystine, and biotin. The prize was for solving the structure of the peptide hormone oxytocin and synthesizing an active molecule. (See Monday's Molecule #244.) From 1938 to 1967 Vigneaud's lab was at Cornell Medical College in New York City.

Here's part of the Presentation Speech.

THEME:
Nobel Laureates

Underneath the brain, there is a small, well-protected gland, the pituitary gland. In man it is about as big as a bean. There are secreted several hormones, that is, substances which regulate important physiological functions. spite of its small size, the pituitary gland is made up of several distinct parts with different functions. We are interested here in the posterior lobe, which contains two substances called oxytocin and vasopressin. The former stimulates the contractions of the uterus and also the lactation, the latter raises the blood pressure and regulates the function of the kidneys. As early as in 1933, when rather impure preparations from the posterior lobe were used in experiments, du Vigneaud found a high percentage of sulphur, which seemed to be correlated to the physiological activity.

Using the experimental methods, which the development of science has put at his disposal and making the best of his own intimate knowledge of the organic chemistry of sulphur, du Vigneaud has step by step forced his way. Both hormones were isolated in a state of purity, and it was found that they are built up from amino acids in the same way as proteins, but with a far lower molecular weight. Such compounds are, as distinguished from real proteins, called polypeptides. The nature of the amino acids and their positions in the molecule could be determined. The sulphur is present in cystine. The two hormones have a very similar structure; both contain eight amino acids, connected to a chain, which at one point is closed to a ring. The molecule has some resemblance to a figure six or nine, where the loop contains five amino acids and the “tail” three. Two sulphur atoms, linked to each other, form a part of the ring.

The design of the molecule was thus known. It remained to build it up by synthesis and check the correctness of the design. That was perhaps the most difficult part of the work. The interest was first concentrated on the synthesis of oxytocin. Step by step the amino-acid chain was built up with the two sulphur atoms in the proper positions, one at the end of the chain and the other near the middle. At last the ring was closed by formation of a bond between the sulphur atoms. Now followed the most thrilling moment, the testing of the chemical properties and the physiological activity; perhaps there had been some mistake after all. It turned out, however, that the synthetic polypeptide was identical with the natural product.



The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Monday, October 21, 2024

Monday's Molecule #244

You can use whatever tricks you want to identify today's molecule but I'll be really impressed with anyone who recognizes it right away. Regular readers will know that it's related to at least one Nobel Prize Laureate who will be revealed on Wednesday. I don't think that's going to help you very much.

Email your answer to me at: Monday's Molecule #244. 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 coffee and donut at Tim Hortons if you are ever in Toronto or Mississauga (Ontario, Canada).

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.)

In order to win you must give your correct name. Anonymous and pseudoanonymous players can't win.

Comments are closed for at least 24 hours.

UPDATE: The winner is Santi Garcia-Vallve who correctly guessed that the molecule is the peptide hormone oxytocin. Santi lives in Spain so he won't be able to collect his coffee and donut anytime soon.

Winners

#145, Oct. 17, 2011: Bill Chaney, Roger Fan
#146, Oct. 24, 2011: DK
#147, Oct. 31, 2011: Joseph C. Somody
#148, Nov. 7, 2011: Jason Oakley
#149, Nov. 15, 2011: Thomas Ferraro, Vipulan Vigneswaran
#150, Nov. 21, 2011: Vipulan Vigneswaran (honorary mention to Raul A. Félix de Sousa)
#151, Nov. 28, 2011: Philip Rodger
#152, Dec. 5, 2011: 凌嘉誠 (Alex Ling)
#153, Dec. 12, 2011: Bill Chaney
#154, Dec. 19, 2011: Joseph C. Somody
#155, Jan. 9, 2012: Dima Klenchin
#156, Jan. 23, 2012: David Schuller
#157, Jan. 30, 2012: Peter Monaghan
#158, Feb. 7, 2012: Thomas Ferraro, Charles Motraghi
#159, Feb. 13, 2012: Joseph C. Somody
#160, March 5, 2012: Albi Celaj
#161, March 12, 2012: Bill Chaney, Raul A. Félix de Sousa
#162, March 19, 2012: no winner
#163, March 26, 2012: John Runnels, Raul A. Félix de Sousa
#164, April 2, 2012: Sean Ridout
#165, April 9, 2012: no winner
#166, April 16, 2012: Raul A. Félix de Sousa
#167, April 23, 2012: Dima Klenchin, Deena Allan
#168, April 30, 2012: Sean Ridout
#169, May 7, 2012: Matt McFarlane
#170, May 14, 2012: no winner
#171, May 21, 2012: no winner
#172, May 29, 2012: Mike Hamilton, Dmitri Tchigvintsev
#173, June 4, 2012: Bill Chaney, Matt McFarlane
#174, June 18, 2012: Raul A. Félix de Sousa
#175, June 25, 2012: Raul A. Félix de Sousa
#176, July 2, 2012: Raul A. Félix de Sousa
#177, July 16, 2012: Sean Ridout, William Grecia
#178, July 23, 2012: Raul A. Félix de Sousa
#179, July 30, 2012: Bill Chaney and Raul A. Félix de Sousa
#180, Aug. 7, 2012: Raul A. Félix de Sousa
#181, Aug. 13, 2012: Matt McFarlane
#182, Aug. 20, 2012: Stephen Spiro
#183, Aug. 27, 2012: Raul A. Félix de Sousa
#184, Sept. 3, 2012: Matt McFarlane
#185, Sept. 10, 2012: Matt Talarico
#186, Sept. 17, 2012: no winner
#187, Sept. 24, 2012: Mikkel Rasmussen
#188, Oct. 1, 2012: John Runnels
#189, Oct. 8, 2012: Raúl Mancera
#190, Oct. 15, 2012: Raul A. Félix de Sousa
#191, Oct. 22, 2012: Mikkel Rasmussen
#192, Nov. 12, 2012: Seth Kasowitz, Bill Gunn
#193, Nov. 19, 2012: Michael Rasmussen
#194, Dec. 4, 2012: Paul Clapham, Jacob Toth
#195, Dec. 10, 2012: Jacob Toth
#196, Dec. 17, 2012: Bill Chaney, Dima Klenchin, Bill Gunn
#197, Jan. 14, 2013: Evey Salara
#198, Jan. 21, 2013: Piotr Gasiorowski
#199, March 11, 2013: Bill Gunn, River Jiang
#200, March 18, 2013: Bill Gunn
#201, April 8, 2013: Michael Florea
#202, April 15, 2013: no winner
#203, April 29, 2013: Anders Ernberg
#204, May 6, 2013: Alex Ling, Michael Florea
#205, May 13, 2013: Bill Chaney
#206, June 24, 2013: Michael Florea
#207, July 2, 2013: Matt McFarlane
#208, July 8, 2013: no winner
#209, July 15, 2013: Rosie Redfield, Thuc Quyen Huynh
#210, July 22, 2013: Jacob Toth
#211, July 29, 2013: Alex Ling, Matt McFarlane
#212, August 5, 2013: Brian Shewchuk
#213, Sept. 2, 2013: no winner
#214, Sept. 9, 2013: Bill Chaney
#215, Sept. 16, 2013: Zhimeng Yu
#216, Sept. 23, 2013: Mark Sturtevant, Jacob Toth
#217, Sept. 30, 2013: Susan Heaphy
#218, Oct. 7, 2013: Piotr Gasiorowski, Jacob Troth
#219, Oct. 14, 2013: Jean-Marc Neuhaus
#220, Oct. 21, 2013: Jean-Marc Neuhaus
#221, Oct. 28, 2013: Zhimeng Yu
#222, Nov. 10, 2013: Caroline Josefsson, Andrew Wallace
#223, Nov. 18, 2013: Dean Bruce, Ariel Gershon
#224, Nov. 25, 2013: Jon Nuelle, Ariel Gershon
#225, Dec. 2, 2013: Jean-Marc Neuhaus
#226, Dec. 9, 2013: Bill Gunn
#227, Dec. 16, 2013: Piotr Gasiorowski
#228, Jan. 13, 2014: Tom Mueller
#229, Jan. 20, 2014: Tommy Stuleanu
#230, Jan. 27, 2014: Bill Gunn, Ariel Gershon
#231; March 3, 2014: Keith Conover, Nevraj Kejiou
#232, March 10, 2014: Philip Johnson
#233, March 17, 2014: Jean-Marc Neuhaus
#234, March 24, 2014: Frank Schmidt, Raul Félix de Sousa
#235, March 31, 2014: Jon Binkley
#236, April 7, 2014: no winner
#237, April 21, 2014: Dean Bruce
#238, April 28, 2014: Dean Bruce
#239, May 5, 2014: Piotr Gąsiorowski
#240, May 12, 2014: James Wagstaff
#241, May 19, 2014: no winner
#242, Oct. 7, 2024: Elie Huvier
#243, Oct. 14, 2024: Mikkel Rasmussen
#244, Oct. 21, 2024: Santi Garcia-Vallve