Why an extra helix becomes a third wheel in cell biology

dna3Every high school biology student knows the structure of DNA is a double helix, but after DNA is converted into RNA, parts of RNA also commonly fold into the same spiral staircase shape.

In a literal scientific twist, researchers are finding examples of a third strand that wraps itself around RNA like a snake, a structure rarely found in nature. Researchers recently have discovered evidence of a triple helix forming at the end of MALAT1, a strand of RNA that does not code for proteins. Yale postdoctoral fellow Jessica Brown and her colleagues working in the labs of Joan A. Steitz and Thomas A. Steitz describe the bonds that maintain the structure of a rare triple helix.

This extra strand of RNA, which is seen in the accompanying movie, prevents degradation of MALAT1. The formation of a triple helix explains how MALAT1 accumulates to very high levels in cancer cells, allowing MALAT1 to promote metastasis of lung cancer and likely other cancers.

The work is published in the journal Nature Structural and Molecular Biology.

news.yale.edu

RNA, DNA… TNA

Before DNA, before RNA: Life in the hodge-podge world


Take note, DNA and RNA: it’s not all about you. Life on Earth may have began with a splash of TNA – a different kind of genetic material altogether.

Because RNA can do many things at once, those studying the origins of life have long thought that it was the first genetic material. But the discovery that a chemical relative called TNA can perform one of RNA’s defining functions calls this into question. Instead, the very first forms of life may have used a mix of genetic materials.

RNA, DNA… TNA

Today, most life bar some viruses uses DNA to store information, and RNA to execute the instructions encoded by that DNA. However, many biologists think that the earliest forms of life used RNA for everything, with little or no help from DNA.

A key piece of evidence for this “RNA world” hypothesis is that RNA is a jack of all trades. It can both store genetic information and act as an enzyme, seemingly making it the ideal molecule to start life from scratch.

Now it seems TNA might have been just as capable, although it is not found in nature today.

It differs from RNA and DNA in its sugar backbone: TNA uses threose where RNA uses ribose and DNA deoxyribose. That gives TNA a key advantage, says John Chaput of Arizona State University in Tempe: it is a smaller molecule than ribose or deoxyribose, possibly making TNA easier to form.

Chaput and his colleagues have now created a TNA molecule that folds into a three-dimensional shape and clamps onto a specific protein. These are key steps towards creating a TNA enzyme that can control a chemical reaction, just like RNA.

The team took a library of TNAs and evolved them in the presence of a protein. After three generations, a TNA turned up that had a complex folded shape like an enzyme and could bind to the protein……….

Read more: www.newscientist.com

Life in the Universe by Stephen Hawking

In this talk, I would like to speculate a little, on the development of life in the universe, and in particular, the development of intelligent life. I shall take this to include the human race, even though much of its behaviour through out history, has been pretty stupid, and not calculated to aid the survival of the species. Two questions I shall discuss are, ‘What is the probability of life existing else where in the universe?’ and, ‘How may life develop in the future?’

It is a matter of common experience, that things get more disordered and chaotic with time. This observation can be elevated to the status of a law, the so-called Second Law of Thermodynamics. This says that the total amount of disorder, or entropy, in the universe, always increases with time. However, the Law refers only to the total amount of disorder. The order in one body can increase, provided that the amount of disorder in its surroundings increases by a greater amount. This is what happens in a living being. One can define Life to be an ordered system that can sustain itself against the tendency to disorder, and can reproduce itself. That is, it can make similar, but independent, ordered systems. To do these things, the system must convert energy in some ordered form, like food, sunlight, or electric power, into disordered energy, in the form of heat. A laptopIn this way, the system can satisfy the requirement that the total amount of disorder increases, while, at the same time, increasing the order in itself and its offspring. A living being usually has two elements: a set of instructions that tell the system how to sustain and reproduce itself, and a mechanism to carry out the instructions. In biology, these two parts are called genes and metabolism. But it is worth emphasising that there need be nothing biological about them. For example, a computer virus is a program that will make copies of itself in the memory of a computer, and will transfer itself to other computers. Thus it fits the definition of a living system, that I have given. Like a biological virus, it is a rather degenerate form, because it contains only instructions or genes, and doesn’t have any metabolism of its own. Instead, it reprograms the metabolism of the host computer, or cell. Some people have questioned whether viruses should count as life, because they are parasites, and can not exist independently of their hosts. But then most forms of life, ourselves included, are parasites, in that they feed off and depend for their survival on other forms of life. I think computer viruses should count as life. Maybe it says something about human nature, that the only form of life we have created so far is purely destructive. Talk about creating life in our own image. I shall return to electronic forms of life later on…… Continue reading Life in the Universe by Stephen Hawking

First life: The search for the first replicator

Life must have begun with a simple molecule that could reproduce itself – and now we think we know how to make one

Dawn of the living

4 BILLION years before present: the surface of a newly formed planet around a medium-sized star is beginning to cool down. It’s a violent place, bombarded by meteorites and riven by volcanic eruptions, with an atmosphere full of toxic gases. But almost as soon as water begins to form pools and oceans on its surface, something extraordinary happens. A molecule, or perhaps a set of molecules, capable of replicating itself arises.

This was the dawn of evolution. Once the first self-replicating entities appeared, natural selection kicked in, favouring any offspring with variations that made them better at replicating themselves. Soon the first simple cells appeared. The rest is prehistory.

Billions of years later, some of the descendants of those first cells evolved into organisms intelligent enough to wonder what their very earliest ancestor was like. What molecule started it all?

As far back as the 1960s, a few of those intelligent organisms began to suspect that the first self-replicating molecules were made of RNA, a close cousin of DNA. This idea has always had a huge problem, though – there was no known way by which RNA molecules could have formed on the primordial Earth. And if RNA molecules couldn’t form spontaneously, how could self-replicating RNA molecules arise? Did some other replicator come first? If so, what was it? The answer is finally beginning to emerge.

When biologists first started to ponder how life arose, the question seemed baffling. In all organisms alive today, the hard work is done by proteins. Proteins can twist and fold into a wild diversity of shapes, so they can do just about anything, including acting as enzymes, substances that catalyse a huge range of chemical reactions. However, the information needed to make proteins is stored in DNA molecules. You can’t make new proteins without DNA, and you can’t make new DNA without proteins. So which came first, proteins or DNA?….. Continue reading First life: The search for the first replicator