Strands and Sheets

Sandwalk: Strands and Sheets
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SANDWALK
STROLLING WITH A SKEPTICAL BIOCHEMIST
LAURENCE A. MORAN
MONDAY, MARCH 10, 2008
Strands and Sheets

The &alpha helix is one form of secondary structure in proteins. When a polypeptide chain contains the right sequence of amino acids it can adopt a helical conformatio n. There are other conformations commonly found in proteins. One of them is the structure, which is characterized by long extended polpeptide chains in contrast to the compact helix of the helix. Single strands are rarely found in proteins because the structure is not that much more stable than a random coil. However, when two adjacent strands line up they can from bridges of hydrogen bonds. This creates a very stable structure known as a sheet. In the example shown (left) three parallel strands line up edge to edge to form a highly stable sheet with multiple hydrogen bond (shown in yellow). sheets can also be formed when antiparallel strands align edge to edge. As a matter of fact, the antiparallel conformation is more stable, and more common, than the parallel conformation. strands are usually drawn
Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.
SANDWALK
The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper lefthand corner of this image.
RECENT COMMENTS
http://sandwalk.blogspot.com/2008/03/strands-and-sheets.html
27/9/2011
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steve oberski wrote...

@DennyIt's all in your tummy.Belief in God Boils Down to a Gut FeelingBy STEPHANIE PAPPAS - LIVESCIENCE.COM http://www.livescience.com/16151 -god-belief-intuition.html

@Denny Besides, I cant figure out how atheists/naturalists/evolutionists would be better at traversing these disciplines, if they insist that one of the most common traits of humans doesnt exist... Continue >>
as wide arrows with the tip of the arrow head representing the C-terminal end of the polypeptide chain. As shown in the cartoon on the right, the strands are often twisted and the amino acid side chains project above and below the plane of the strand. The amino acid composition of strands tends to favor hydrophobic (water fearing) amino acid residues. The side chains of these residues tend to be less soluble in water than those of more hydrophilic (water loving) residues. As you might imagine, structures tend to be found inside the core structure of proteins where the hydrogen bonds between strands are protected from competition with water molecules. One of the common motifs in proteins is the sandwich, formed when two sheets are stacked on top of one another. The example shown below is the coat protein of grass pollen grains [PDB 1BMW]. For those people who are allergic to grass pollen, this protein is the main culprit. This example is the simplest form of a sandwich since each sheet consists of only two strands.

Ian H Spedding By presuming its right to life you are keeping open the unborn's options until it has reached the stage when it can choose for itself.By completely denying the rights of the mother... Continue >>
Denny wrote...
Allan, re. your comments about Common Descent - we are looking at the tips of a vast branching tree. A lot of us no longer see a conventional metaphorical tree of life that shows simple life at... Continue >>
Allan Miller wrote...

@Denny,I agree that traversing these disciplines with equal clarity and ease is a challenge. Thats a focus of RTB to bring together all the aspects of human life (natural, supernatural, personal... Continue >>
Denny wrote...
Larry Moran said... It's crap. Her last articlethe only one I readcontains factually incorrect statements and misrepresentations of the scientific literature. That's typical behavior for... Continue >>
Denny wrote...
Allan. Your word picture is helpful, but I never saw an illustration with evolutionary theorists at the central core. When I think of the ultimate meaning of life (not the narrow focus of...
PRINCIPLES OF BIOCHEMISTRY 5TH EDITION
In order to appreciate why this is such a stable (and common) motif we need to add in the amino acid side chains. (They are usually ignored in the kinds of structures shown above so we can trace the polypeptide
27/9/2011
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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.
backbone.) In the figure on the right I've drawn the hydrophobic side chains in blue so you can see how they cluster together to form the interior "filling" of the sandwhich. You can think of these hydrophobic regions as being like the oil in a mixture of oil and water. The oil droplets tend to come together to exclude the water molecules. Similarly, the hydrophobic residues tend to come together in the middle of the protein and exclude water molecules. This is called hydrophobic interaction and it's one of the dominent weak forces n biochemistry. Most proteins are made up of combinations of helices and strands. The third kind of secondary structure is turns.
[Figures are from Horton et al. (2006) Laurence A. Moran, Pearson/Prentice Hall] Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)
POS TED BY LA RRY MORA N A T 3:5 6 P M LA BELS :BI OCHEMI S TRY RECENT POSTS
2 COMMENTS:
The Protein Engineer
Sep 26, 2011 Two former undergraduate students of mine have started a blog called The Protein Engineer.A blog started by two graduate students, 11000 kilometres apart, on a quest to discover, or otherwise... Continue >>
mwcsaid... That's a good introduction to this structural element. I especially liked the discussion of amphipathicity in strands. Showing an integral membrane protein like porin might reinforce the point, while also displaying part of the great diversity of structures possible with strands. MONDAY , M ARCH 10 , 2008 7 :25: 00 PM Tegumai Bopsulai, FCD said... Web site aims to help mail-order brides "TORONTO (Reuters) - Canada can be a bewildering, even frightening place for immigrant women who arrive as mail-order or Internet brides, but now they have a new Web site to help smooth the transition..." THURSDAY, M ARCH 13, 20 08 9: 32:0 0 AM
Countries That Execute Their Own Citizens

Sep 22, 2011 Most civilized, democratic countries have abolished capital punishment. This is especially true of those countries with a Christian tradition.The last execution in Canada took place in 1962 and... Continue >>
When Will They Ever Learn?

Sep 17, 2011 In my class on Scientific Misconceptions and Controversies we discuss the ways in which scientific reasoning is used and
27/9/2011
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The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.
Charles Darwin (c1880)
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Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.
Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...
Peter Atkins
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Macroevolution Random Genetic Drift Michael Denton and Molecular Clocks The Modern Synthesis of Genetics and Evolution Evolution Is a Fact and a Theory What Is Evolution? Have Humans Stopped Evolving? Mammalian Gene Families: Humans and Chimps Differ by 6% Michael Behe's Criticism of Biochemistry Textbooks O157:H7 Outbreak in Taco Bell Restaurants Calico Cats The HSP70 Sequence Database
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The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982) I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot
27/9/2011
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discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339 The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977) Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so storiesand the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980) Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335 The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
27/9/2011
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Stephen Jay Gould (1999) p.84
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My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.
Jerry Coyne Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.
Sydney Brenner TIBS Dec. 2000

It is nave to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any preexisting variations
Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.
Francis Crick
27/9/2011
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There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.
Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist
Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.
Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.
Richard Lewontin
PRINCIPLES OF BIOCHEMISTRY 4TH EDITION
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Principles of Biochemistry
PRINCIPLES OF BIOCHEMISTRY: INTERNATIONAL EDITION
Principles of Biocemistry: International Edition
BIOCHEMISTRY 2ND ED. (1994)
Moran, L.A., Scrimgeour, K.G. et al.
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Strands and Sheets

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Sandwalk: Strands and Sheets

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MONDAY, MARCH 10, 2008