Colours of blood

Did you know that some organisms have violet blood? It’s all in the d-orbitals, I understand. Read about blood chemistry and see a larger diagram: iron makes red or green or violet, while copper makes blue,



What is squalene, anyway?

The short answer is given here, in the organic molecule directory, alkenes page:

Squalene is found in shark liver oil, and is also a major component of the lipids on the surface of human skin. Although it is not obvious from the way the structure above is drawn, squalene is a precursor for the biosynthesis of cholesterol. Through a complex series of enzymatically controlled reactions, squalene is converted into an intermediate called lanosterol, which undergoes a number of subsequent reactions to become cholesterol.

Here is what the molecule looks like. Every angle or terminus has a carbon atom, with enough hydrogen atoms to fill the unused bonds up to carbon’s complement of four per atom. A double line indicates a double bond.


In memoriam: Frederick Sanger

250px-Frederick_Sanger2Frederick Sanger, the only Briton to have won two Nobel prizes, has died. He worked in biochemistry, studying DNA and proteins. His first Nobel prize was awarded for being the first to sequence a protein, insulin. At the time, it required years of work to do so.  He found that it was made up of two peptide chains: all proteins are one or more peptide chains. He spent nearly ten years removing one amino acid at a time from the end of the protein and identifying it, then going on to the next.

Winning the prize enabled him to afford better facilities and gather bright students around him. His second prize was for an ingenious and efficient way of discovering the sequence of nucleotide bases in a molecule of DNA or RNA. The linking of base pairs gives the molecule its ladder structure. The Sanger method cuts the molecules at different places, sorts them by weight (and therefore length) and identifies the base on the end using fluorescent dyes of different colours. According to Wikipedia, he used the method sequence human mitochondrial DNA (16,569 base pairs) and bacteriophage λ (48,502 base pairs). His method was used to sequence the human genome and many others.

His work allowed us to understand the genetic basis of mutations and diseases and was important for the development of better vaccines. Frederick Sanger was also honoured with the Order of Merit for distinguished service in science as well as several other awards.

The Telegraph has quite a nice obituary: Frederick Sanger.

Giant viruses join as another ancestral superkingdom

Mimivirus in amoeba. Credit: Professor Didier Raoult, Rickettsia Laboratory, La Timone, Marseille, France

A study of the proteins of giant viruses adds them to the list of primitive life forms that have existed since the dawn of life.  They seem to constitute a fourth superkingdom. Professor Gustavo Caetano-Anollés led the analysis.

Scientists found ancient structural patterns in the folds of the virus proteins, which are virtually molecular fossils. Folds that are common to all organisms studied are the oldest. Less common folds are, literally, new wrinkles.

The researchers looked at archaea, bacteria, eukaryotes, and both kinds of viruses. The giant viruses have  biochemistry for making proteins, which small viruses have lost.

Modern viruses have lost much of their biochemical machinery and become obligate parasites of an extreme kind.

Giant Viruses Coexisted With the Cellular Ancestors and Represent a Distinct Supergroup Along With Superkingdoms Archaea, Bacteria and Eukarya

Aphids can make carotenoids to capture solar energy



Aphids can make their own carotenoids and may be able to capture chemical energy directly from the sun. Green or orange individuals contain more carotenoids and more ATP than white ones. The secret of plant growth is that they capture photons and use them to create high-energy atomic bonds that can be used elsewhere to run chemical reactions that build plant material.

Unlike other organisms, they are not ingesting or otherwise harbouring photosynthetic symbionts such as bacteria or algae. They are making their own photosynthetic chemicals. They may not be able to do full photosynthesis as plants do, but among animals they are unique.

It will be interesting to find out how they evolved this unique (for animals) biochemical machinery.

Transitional forms: muscle proteins

How old is evolution? How conservative? Try this: the proteins that an amoeba (ameba) uses to move are essentially the same as those that make up the muscle fibres in a vertebrate such as ourselves.

Though it appears to have nothing in common with muscular movement, ameboid movement probably depends on contractile components and mechanisms surprisingly similar to those in the muscle cells of animals. …[T]he cytoplasm of an ameba is found to contain thick and thin microfilaments similar in appearance and dimensions to thick (myosin) and thin (actin) microfilaments of striated muscle. Extracts of muscle myosin appear to cross-react with the thin filaments from amebas. And cytoplasm from amebas uses the nucleotide adenosine triposphate (ATP) as an energy source for movement, as muscle does.

From Living Invertebrates, page 27 (chapter on “Protozoans”), by Vicki Pearse, John Pearse, Mildred Buschbaum, & Ralph Buschbaum.

Evolution of complexity in molecular “machines”

V-ATPase proton pump and evolutionary pathway

A proton pump is a ring of proteins embedded in a cell wall, which moves molecules, atoms, or ions through the wall in a preferred direction. Research into the V-ATPase proton pump in eukaryotes has a ring of  six linked protein molecules in the membrane wall and a ring of eight inside the cell. As its name implies, it moves hydrogen ions (protons), through the cell wall. Research into its history shows that greater complexity can evolve without a change in function. The “V” indicates a plant vacuolar pump. They are found not in the external cell wall but in the walls of vacuoles, or liquid-filled spaces, within the cell.

…the complexity of an essential molecular machine—the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump—increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

“Evolution of increased complexity in a molecular machine,” Gregory C. Finnigan, Victor Hanson-Smith, Tom H. Stevens & Joseph W. Thornton. Nature (2012). doi:10.1038/nature10724.

I won’t be able to give a detailed explanation until the description comes out from behind a paywall. There’s an explanation at Nature blog and one at  Kurzweil.

Look here for a diagram of V-ATPase. This diagram shows the ancestral molecule, in green, and its more specialized descendents, which need their increased complexity to properly assemble and function. The ancestor is on the left.

Evolution of V-ATPase protein chains

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