THEME:
Most of the amino acid residues in a given protein are found in some form of secondary structure such as α helix, β strands, or turns.
The Ψ and Φ angles of every residue in the protein are plotted. Note that for the all-α protein (left) almost all the angles cluster around the region identified as α helix. Similarly, for the all-β proteins (right) the angles cluster in the upper left-hand corner of the plot where you expect to find residues in β strands. | Position | Assistant Professor (2) |
| Location | Department of Biochemistry, University of Toronto |
| Position Description | The Department of Biochemistry, University of Toronto invites applications for two tenure-track positions at the rank of Assistant Professor commencing on July 1, 2008. Closing date for applications is April 30, 2008, or until the positions are filled. |
| Eligibility | We seek candidates with a Ph.D. in biochemistry, biophysics, cell biology or a related discipline. Candidates must also have at least two years post-doctoral training and have an excellent publication record. |
| Contact | Interested candidates are encouraged to apply to: Chair, Department of Biochemistry Room 5205, Medical Sciences Building University of Toronto Toronto, Ontario, M5S 1A8, Canada. |
| Posted | March 13, 2008 |
THEME:
The peptide bond has some interesting properties that play an important role in determining the three-dimensional structure of proteins. Look at the traditional depiction of the peptide bond in part (a) (top) of the figure on the left. It shows the actual peptide bond as a single bond and the bond between the carbon atom and the oxygen atom as a double bond. Note that the nitrogen atom has a pair of unshared electrons represented by the two red dots.
The peptide bond has enough of a double bond characteristic to prevent rotation of the two newly joined amino acid residues. Thus, the O—C—N—H atoms around the peptide bond lie in a single plane shown in blue in the figure on the right. 
The angle of rotation around the N—Cα bond is called Φ (phi) and the angle around the Cα—C bond is called Ψ (psi). For each pair of amino acid residues, these two angles are all that's needed to specify the three-dimensional shape of the polypeptide backbone of the protein.
The days are getting warmer and the snow is melting away. Spring is the time when a young person's fancy turns to .... poster presentations.1. I'm not a fan of the program, especially the sub-specialty called "Health & Disease" that these students are taking. I don't think that's an appropriate area of concentration for an Honors B.Sc. degree from the University of Toronto. I'd prefer to have them concentrate on basic fundamental science.
The latest issue of Tangled Bank is #102. It's hosted at Further Thoughts [Tangled Bank #102].Welcome to the latest issue of The Tangled Bank, the blog carnival dedicated to the world of biology, medicine, natural history…and Sarah Silverman.
We’re all getting older. And as we get older, we lose the ability to hear some frequencies. Diane Kelly of Science Made Cool offers Is That…A Dog Whistle? – a tale of a test that lets you know just how much damage you did to your hearing back in your clubbing days…or will do when you finally finish grad school and are able to emerge onto the social scene ....
If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.
David K.Y. Chiu is Professor of Computing and Information Science and Professor of Biophysics Interdepartmental Group. He has a Ph.D. in Systems Design Engineering from the University of Waterloo (Canada). Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins", Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]Professor Chiu is a Fellow of the International Society for Complexity, Information, and Design. Other fellows include Michael Behe, Paul Nelson, Guillermo Gonzalez, William Dembski, Jonathan Wells and Scott Minnich.
Chiu, D.K.Y. and K. Zhang (2007) Biomolecular data analysis: a post-genomic reflection. Biomolecular Engineering, 24:319-320.
Chiu, D.K.Y. and Y. Wang (2006) Multipattern consensus regions in multiple aligned protein sequences and their segmentation. EURASIP Journal on Bioinformatics and Systems Biology, Vol.2006:1-8.
Ma, P.C.H., K.C.C. Chan, X. Yao and Chiu, D.K.Y. (2006) An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. on Evolutionary Computation 10:296-314.
Hwang, C., Chiu, D.K.Y. and Sohn, I. (2005) Analysis of exon structure using PCA and ICA of short-time Fourier transform. L. Wang, K. Chen, and Y.S. Ong (Eds.): ICNC LNCS 3611, pp.306-315, 2005, Springer-Verlag Berlin Heidelberg 2005.(also Second Intern. Conf. on Fuzzy Systems and Knowledge Discovery, joint ICNC'05-FSKD'05, 27-29 Aug. 2005, Changsha, China.)
Durston, K. and Chiu, D.K.Y. (2005) A functional entropy model for biological sequences. in supplementary volume of the journal, Dynamics of Continuous, Discrete and Impulsive Systems, Series B, 2005 (also Proc. 4th Intern. Conf. on Engineering Applications and Computational Algorithms), pp.722-725.
Kirk Durston is National Director of the New Scholars Society whose aim is to "be a resource to those faculty and scholars who have an interest in developing the spiritual area of their lives from a Christian perspective." Durston has a B.Sc. in Physics from the University of Manitoba (Canada), a B.Sc. in Mechanical Engineering from the University of Manitoba (Canada) and an M.A. in Philosophy from the University of Manitoba (Canada). He is currently a Ph.D. candidate in the Biophysics Interdepartmental Group at the University of Guelph [Kirk Durston]. 
Jack Trevors is a Professor in the Dept. of Environmental Biology [Jack Trevors] and he's also a member of the Biophysics Interdepartmental Group [Jack Trevors]. Abel, D.L. and J.T. Trevors. (2006) Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews 3:211-228. [doi:10.1186/1742-4682-2-29]Jack Trevors is not a creationist according to this profile at the University of Guelph. He's a "self-proclaimed atheist."
Trevors, J.T. and Abel, D.L. (2004) Chance and necessity do not explain the origin of life. Cell Biology International 28:729-739. [doi:10.1016/j.cellbi.2004.06.006]
Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins. Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]
Take that question about the origins of life. It's hardly a new line of inquiry for Trevors, who was about 10 when he began wondering about the existence of God. He's still wondering. Indeed, it's a question that has consumed a fair amount of his own life recently, albeit now voiced in the language of a professional scientist: Where and how did the genetic code and its instructions arise?The same profile article describes his association with David Abel ...
No small question. “The origin of genetic instructions in the DNA is the most pressing question in science,” he says. “Genetic instructions don't write themselves, any more than a software program writes itself.”
He adds that the issue goes far beyond deciphering the recipes for making proteins. Given that our genetic material constitutes the stuff of our own identity, “it's the search for ourselves, our origins,” he says.
Call it looking for God in our DNA — or at least that's how a person of faith might phrase it. Trevors, a self-proclaimed atheist, is more circumspect. “If you're a religious person, you say God. If you're an evolutionist, you say evolution.”
He notes, however, that not even evolution deigns to tell us where or how life itself first came about or how DNA's instructions came to be. Perhaps the birthplace of those instructions — like the very creation of the universe itself — is, in Trevors' words, both “unknowable and ‘undecidable' at this point in time.”
It's a million-dollar question, literally. That's the size of the prize in a contest being run by the Origin-of-Life Foundation based near NASA's Goddard Space Flight Centre in Maryland. All the winner needs to do to claim the reward — actually annual instalments of $50,000 for 20 years — is to explain how the initial genetic code arose — or, in the words of the contest rules, provide "a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life."I don't know about the rest of you but I don't often hear atheists say things like that. Maybe he's thinking of aliens who write genetic programs? I also don't know too many atheists who would publish papers with known creationists who use the data to support their religious agenda.
The Gene Emergence Project is a program of the foundation, a scientific and educational body of about 200 scientists in 40 countries.
"We want the international scientific community to help us prove that genetic instructions don't write themselves," says Trevors, who got involved by contacting David Abel, the project's program director, two years ago.
"Jack relentlessly looks for evolutionary explanations for everything we observe in biology," says Abel, adding that his Guelph colleague helps ensure that "life-origin theory" remains empirically responsible, or answerable to the test of repeated observation. "He likes to include the full gamut of microbiological phenomena to make sure our models are explaining all aspects of genetic control."
Trevors has written on the topic, including a paper last year with Abel called: "Chance and Necessity Do Not Explain the Origin of Life." There and in a more recent piece, they frame the genesis-of-life discussion in terms that might resonate with a computer programmer, including referring to genes as linear strings of digital instructions and describing DNA's four nucleotide building blocks as four-way switches. If genes are merely algorithms, albeit highly sophisticated ones, another obvious question occurs, says Trevors. “Computer programs don't write themselves. Why would scientists or anyone else think genetic programs write themselves? The question has to be asked and examined from a scientific perspective.”
Here's the opening paragraphs from a news item on the National Geographic website ["First Sex" Found in Australian Fossils?].Sex is part of the "oldest profession" and often called the subject of the "world's oldest joke." Now scientists think they've found evidence of the oldest known creatures to engage in sexual reproduction.This is an example of bad science writing. Sexual reproduction is a phenomenon seen in many bacteria and in all eukaryotes (with minor exceptions). Animals are not the only eukaryotes that have sex. Plants, do it; fungi do it; and so do all single-cell eukaryotes.
A new study suggests that nature's first sexual encounter took place among tubular invertebrates called Funisia dorothea, which lived about 565 million years ago.
The branching patterns and rarity of branching of Funisia is consistent with metazoan asexual budding. The consistency of tube widths on individual bedding surfaces (Fig. 1, A, I, and J), the densely packed nature of the attachment structures, and the clustering pattern of developmental stages of attachment structures on individual bedding planes suggests that the juveniles settled as aggregates in a series of limited cohorts.There's nothing in the paper about these organisms being the first to reproduce sexually—that wouldn't have survived the reviews. The only remaining question is why did the author (Droser) allow herself to be quoted in a press release when she must have known that it was misrepresenting the paper?
These solitary organisms thus exhibit growth by addition of serial units to tubes and by the division of tubes, and dispersed propagation by the production of spats. Among living organisms, spat production is almost ubiquitously the result of sexual reproduction but is known to occur rarely in association with asexual reproduction (8). Hence, despite its morphological simplicity the Neoproterozoic F. dorothea provides evidence of a variety of growth modes and a complex arrangement for the propagation of new individuals. In living organisms, synchronous aggregate growth may result from a variety of factors—including response to competition, sediment disturbance, and heterogeneity of the substrate—and has the advantage of reducing competition for space between clones and can also decrease gamete wastage (9, 10).
Droser, M.L. and Gehling, J.G. (2008) Synchronous Aggregate Growth in an Abundant New Ediacaran Tubular Organism. Science 319:1660-1662. DOI: 10.1126/science.1152595
Fritz Haber (1868 - 1934) was awarded the 1918 Nobel Prize in Chemistry for working out a method to synthesize ammonia (NH3) from nitrogen (N2) and hydrogen (H2). This process, now known as the Haber-Bosch process, is an essential step in the production of artificial fertilizer. At the time, it was not known how long the natural sources of nitrogen such as Chile saltpetre (sodium nitrate) would last. Harber worked at the Kaiser-Wilhelm-Institut (now Fritz-Haber-Institut) für physikalische Chemie und Electrochemie in Berlin-Dahlem, GermanyThe Royal Swedish Academy of Sciences has decided to confer the Nobel Prize in Chemistry for 1918 upon the Director of the Kaiser Wilhelm Institute at Dahlem near Berlin, Geheimrat Professor Dr. Fritz Haber, for his method of synthesizing ammonia from its elements, nitrogen and hydrogen.
In accordance with Nature's plan of economy, soil fertility under normal circumstances is maintained at an even level if the waste products from the crop are returned to the soil; if, however, substantially increased productivity is required from the soil, then additional fertilizer must be used. Since meanwhile a large proportion of the annual harvest is consumed by the yearly increasing population of towns, and since the towns' waste products are returned to land under cultivation only to a very incomplete extent, the inevitable consequence is that the soil becomes exhausted and the harvest yield diminishes. This has, in turn, led to the manufacture of artificial fertilizers which has also increased year by year in importance to such an extent that, at least in Europe, hardly a country exists which can do entirely without them.Among these substances nitrogenous compounds occupy an important position, since usually the soil does not possess a large store of these to be released to suit the plants' needs by weathering as in the case of phosphoric acid and potash; added to which there is the fact that part of the effective nitrogen turns into inactive atmospheric nitrogen during the cyclic process. Admittedly a part of this loss is compensated by rainfall and through the activity of bacteria, but so far experience has shown that intensive cultivation cannot be maintained without artificial nitrogenous fertilizers. This applies, above all, to one of today's most important crops, sugar-beet.
For many years only two artificial nitrogenous compounds existed, namely potassium nitrate and ammonium chloride. The older methods by which these were made, however, ceased to play a part, at least in Europe and America, when Chile saltpetre (sodium nitrate) came into the picture and use was made of the by-products from dry distillation of mineral coal for this purpose.The consumption of Chile saltpetre, calculated in terms of nitrogen, amounts to about 500,000 or more tons per annum. Under normal circumstances the vast majority of this saltpetre is used for fertilizer purposes. The burning question, therefore, has long been: how long will the saltpetre deposits in Chile last? The Chilean authorities give very widely varying estimates, and experts in Europe are of the opinion that at current production rates the deposits will be exhausted within the foreseeable future.
Be that as it may. The protracted World War has sufficiently demonstrated to every country the need of organizing, wherever possible, production of essential commodities within its own borders in sufficient quantities to meet its own needs.
Now, since saltpetre is among the most important of these substances, particularly in those countries which possess neither large mineral coal deposits nor cheap hydro-electric power, the artificial production of ammonia and nitric acid has reached an unprecedented degree of importance.
A substance on the borderline between natural and artificial products is the ammonia obtained by dry distillation of bituminous and brown coal. This ammonia comes from the nitrogen content of these minerals, amounting to approximately 1.3 % by weight, of which however the largest portion (around 85%) remains behind in the coke or is liberated as nitrogen during distillation.
During the first ten years of this century several methods were published, based on binding the nitrogen from the air, but few of these survived the trial stage. The first of these was Frank-Caro's cyanamide method. Indeed it appears that calcium cyanamide did not come fully up to expectations as a fertilizer, but since its nitrogen content can be converted to ammonia relatively easily, this has not so far proved to be an obstacle to the application of the method to an ever-increasing extent.
Using the main principles of thermodynamics every quantitative condition with regard to the combustion of atmospheric nitrogen to produce nitric oxide can be calculated. Birkeland and Eyde were, of course, the first to apply this technically with successful results.
Until 1904 nobody had been able to bring about a direct combination of nitrogen and hydrogen to form ammonia without the help of dark electrical discharge, although the experiments of Berthelot and Thomson proved that the combination occurred exothermically. With the experience we now have we can easily see that this negative result was due to the slowness of the reaction at low temperatures, and unfavourable equilibrium conditions at high temperatures. Admittedly, in 1884 Ramsay and Young had conducted some experiments on this, using iron fillings as a catalyst, but these yielded only uncertain results.
In 1904 Haber and van Oordt began a methodical study of this relevant field, based on modern physico-chemical methods, after a single previous experiment had given Haber a hope of finding a technical solution to the problem. They worked at a temperature of about 1,000° C and normal pressure, using iron as a catalyst. From these experiments it emerged that from red heat onwards, and also at higher pressures, only traces of ammonia could be formed.
During this work it was also shown experimentally for the first time that a real state of equilibrium existed in the system
N2+ 3H2 → NH3, which is in fact the real basis for the synthesis of ammonia.
In the "Zeitschrift für Elektrochemie" of 1913 can be found the treatment of this question, by Haber and Le Rossignol which has the most important practical meaning: "Über die technische Darstellung von Ammoniak aus Elementen" (On the technical production of ammonia from the elements). This treatise provided the groundwork for the development of the method on a factory scale at the "Badische Anilin- und Sodafabrik" in Ludwigshafen, the main development occurring under the guidance of Dr. C. Bosch.
Earlier experiments had shown the pointlessness of exceeding dark red heat, i.e. about 600° C. On the other hand, the reaction formula showed that combination occurs with a contraction of from 4 to 2 volumes.
From the law of equilibrium it follows that the higher the pressure is the more the equilibrium must shift to the ammonia side. This provided the basic principles. A temperature of about 500° C had to be used at the highest possible pressure, which in practice meant at about 150-200 atmospheres. It could also be assumed that this high pressure speeded up the reaction. But work with a flow of gas in a circulation system at such high pressure and at a temperature approaching red heat posed very severe difficulties and up to then had never been tried. It was, however, completely successful. The treatise in question contains detailed drawings of the equipment used with which, using iron as a catalyst, about 250 grams of ammonia were produced per hour and per litre of contact volume; with uranium or osmium as a catalyst considerably more was produced.
The heating is done electrically. Since however the heat escaping from the equipment is largely regenerated in the entrant gases the required temperature can largely be maintained by the regenerated heat and by the heat liberated during the formation of ammonia. A very important point in Haber's observations is that the gases can be given a greater flow rate during the reaction which of course substantially increases the amount of ammonia produced per unit of time.
Haber found the best catalyst to be osmium, followed by uranium or uranium carbide. According to tests conducted mostly at the factories of the "Badische", the activity of the catalyst may be increased by oxides or certain salts of alkalis and alkaline earth metals, just as it may be decreased by catalytic poisons. Gradually more active catalysts have been discovered, and by this means it has been found possible to reduce substantially the pressure in the chamber.
In 1910 construction work was begun on the first large factory near Oppau in the neighbourhood of Frankfurt am Main, with an estimated annual output of 30,000 tons of ammonia.
The basic materials, nitrogen and hydrogen, are produced by standard methods.
Power consumption in the ammonia process is very low, amounting to no more than 0.5 kilowatt-hours per kilogram of ammonia. Per kilowattyear, therefore, no less than 10,000 kilograms of nitrogen are bound.
Since the position of the equilibrium of the reaction depends, among other things, upon the heat of formation of ammonia and its specific heat, Haber in a series of seven articles in the "Zeitschrift für Elektrochemie" of 1914-1915, has extensively described experiments carried out to confirm these figures with the greatest possible accuracy.
As, according to Ostwald's modified method, ammonia can be converted into nitric acid and the latter into calcium nitrate, the ratio between the overall costs of producing calcium nitrate is, according to the available calculations, approximately as follows:
Norwegian Hydro: 100
Haber: 103
Frank-Caro: 117
in other words, they are the same for the first two methods but approximately 15% higher for the last.
Since, however, of the three existing nitrogen methods, Haber's is the only one capable of operating independently of any available source of cheap hydroelectric power it can in future be applied in all countries; since furthermore it can be utilized on any convenient scale and because it can produce ammonia very much more cheaply and nitrate equally as cheaply as any other method, as explained above, it is of universal significance for the improvement of human nutrition and so of the greatest benefit to mankind.
German Haber factories, especially the recently built Leuna Works near Merseburg, are also in full production, providing the vast majority of all nitrogenous fertilizers obtainable in Germany. Moreover, the method has already been extensively applied in the United States of America.
[Hat Tip: Pretty shaved ape at Canadian Cynic
From Horton et al. (2006).The nitrogen needed for amino acids (and for the heterocyclic bases of nucleotides) comes from two major sources: nitrogen gas in the atmosphere and nitrate (NO3⊖) in soil and water. Atmospheric N2 which constitutes about 80% of the atmosphere, is the ultimate source of biological nitrogen. This molecule can be metabolized, or fixed, by only a few species of bacteria. N2 and NO3⊖ must be reduced to ammonia in order to be used in metabolism. The ammonia produced is incorporated into amino acids via glutamate, glutamine, and carbamoyl phosphate.
N2 is chemically unreactive because of the great strength of the triple bond (N≡N). Some bacteria have a very specific, sophisticated enzyme—nitrogenase1—that can catalyze the reduction of N2 to ammonia in a process called nitrogen fixation. In addition to biological nitrogen fixation there are two additional nitrogen-converting processes. During lightning storms, high-voltage discharges cause the oxidation of N2 to nitrate and nitrite (NO2⊖). Industrially, nitrogen is converted to ammonia for use in plant fertilizers by an energetically expensive process that requires high temperature and pressure as well as special catalysts to drive the reduction of N2 by H2. The availability of biologically useful nitrogen is often a limiting factor for plant growth, and the application of nitrogenous fertilizers is important for obtaining high crop yields. Although only a small percentage of the nitrogen undergoing metabolism comes directly from nitrogen fixation, this process is the only way that organisms can use the huge pool of atmospheric N2.
The overall scheme for the interconversion of the major nitrogen-containing compounds is shown in Figure 17.1. The flow of nitrogen from N2 to nitrogen oxides, ammonia, and nitrogenous biomolecules and then back to N2 is called the nitrogen cycle. Most of the nitrogen shuttles between ammonia and nitrate. Ammonia from decayed organisms is oxidized by soil bacteria to nitrate. This formation of nitrate is called nitrification. Some anaerobic bacteria can reduce nitrate or nitrite to N2 (denitrification). Most green plants and some microorganisms contain nitrate reductase and nitrite reductase, enzymes that together catalyze the reduction of nitrogen oxides to ammonia.
This ammonia is used by plants, which supply amino acids to animals. Reduced ferredoxin (formed in the light reactions of photosynthesis) is the source of the reducing power in plants and photosynthetic bacteria.
Let’s examine the enzymatic reduction of N2. Most nitrogen fixation in the biosphere is carried out by bacteria that synthesize the enzyme nitrogenase. This multisubunit protein catalyzes the conversion of each molecule of N2 to two molecules of NH3 (ammonia). Nitrogenase is present in various species of Rhizobium and Bradyrhizobium that live symbiotically in root nodules of many leguminous plants, including soybeans, peas, alfalfa, and clover (Figure 17.2). N2 is also fixed by freeliving soil bacteria such as Agrobacteria, Azotobacter, Klebsiella, and Clostridium and by cyanobacteria (mostly Trichodesmium spp.) found in the ocean. Most plants require a supply of fixed nitrogen from sources such as decayed animal and plant tissue, nitrogen compounds excreted by bacteria, and fertilizers. Vertebrates obtain fixed nitrogen by ingesting plant and animal matter.
Nitrogenase is a protein complex that consists of two different polypeptide subunits with a relatively complicated electron-transport system. One polypeptide (called iron protein) contains a [4 Fe–4 S] cluster, and the other (called iron–molybdenum protein) has two oxidation–reduction centers, one containing iron in an [8 Fe–7 S] cluster, and the other containing both iron and molybdenum. Nitrogenases must be protected from oxygen because the metalloproteins are highly susceptible to inactivation by O2. For example, strict anaerobes carry out nitrogen fixation only in the absence of O2. Within the root nodules of leguminous plants, the protein leghemoglobin (a homolog of vertebrate myoglobin) binds and thereby keeps its concentration sufficiently low in the immediate environment of the nitrogen-fixing enzymes of rhizobia. Nitrogen fixation in cyanobacteria is carried out in specialized cells (heterocysts) whose thick membranes inhibit entry of O2.
A strong reducing agent—either reduced ferredoxin or reduced flavodoxin (a flavoprotein electron carrier in microorganisms)—is required for the enzymatic reduction of N2 to NH3. An obligatory reduction of 2 H⊕ to H2 accompanies the reduction of N2. For each electron transferred by nitrogenase, at least two ATP molecules must be converted to ADP and Pi (inorganic phosphate) so the six-electron reduction of a single molecule of N2 (plus the two-electron reduction of 2 H⊕) consumes a minimum of 16 ATP.
In order to obtain the reducing power and ATP required for this process, symbiotic nitrogen-fixing microorganisms rely on nutrients obtained through photosynthesis carried out by the plants with which they are associated.
Centre for Inquiry's CELEBRATION OF SCIENCE AND FREETHOUGHT
Is there a limit to how far back I can send email?Think carefully before using this new feature. Each person only gets ten messages.
Yes. You'll only be able to send email back until April 1, 2004, the day we launched Gmail. If we were to let you send an email from Gmail before Gmail existed, well, that would be like hanging out with your parents before you were born -- crazy talk.
