So, what exactly do I do?

Jul 29th, 2007

One of the problems with working in science is explaining what you do. For some people a quick, “I’m a Scientist,” is enough. Science either scares them slightly, or at least confuses them, or perhaps they are just not interested, either way they don’t push the matter any further. However sometimes I find someone whose interested, at which point its good to establish how much background they have in science. Obviously an explanation to another molecular biologist is fairly different to that given to a lawyer, chartered accountant (who incidentally need to explain to me what they do) or a history teacher. But on occasions, differences in background and experience means that even a Biochemist, or a Mouse Geneticist can get lost quickly.

This post forms the first of a series, in which I will explain what I actually do. Firstly I will start by outlining the field, later posts will discuss the scientific method, actual techniques, and possible applications. Its a long story, even just this first bit, and is clearly not something thats easy to reel off in a pub.

Proteins, is there anything the don’t do?

Although most people without a biological background will have heard of proteins, not all of them will be aware of exactly what they do. The answer is, a fair amount.
Proteins are large biological molecules which are vital to almost all life processes. They are found both within cells and outside of cells, in every domain of life, from humans, to animals, to plants to bacteria. Even viruses rely on proteins to help package up their genetic and move from one host to the other.
The role proteins play is too large to list in its entirety. Some proteins, called enzymes, conduct reactions, such as breaking down food, destroying old damaged proteins, and even making new proteins. Virtually every (desired) chemical reaction that occurs within the cell has an enzyme to govern it. Without these enzymes these reactions would be too slow and uncontrollable and it would be nigh on impossible for an organism to achieve any degree of organisation.
But proteins are not just limited to enzymes. Other proteins govern the movement of molecules in and out of the cell and separate sub-cellular compartments, known as organelles. (Organelles are a diverse group of small structures within cells which have specialised functions.
Its just like the seperate organs in your body, only at a much smaller level and in every cell of your body.) This regulation can be through little channels, made of proteins, or by regulating the movement of the plasma membrane, the ‘bag’ which surrounds the cell.
Proteins are also able to associate with each other before sliding against each other. This movement is regulated by nerve impulses (The signals of which rely on gates within the nerve fibre,which are, you guessed it, proteins) and use energy in the processes, but is responsible for causing the muscular contractions that allow you to move.
Another series of proteins are known as morphogens. As an organism grows these are produced, and form concentration gradients. That is, there is more of it at one point than another. The cells in the developing embryo can use the level of each morphogen (along with other factors) to determine where they are, and therefore what the should become. Sonic hedgehog (Yes, it is called Sonic Hedgehog) is an example of such a morphogen, and helps determine which finger is which. If this system goes wrong you can end up with extra fingers and toes.
This should give you an impression of what a diverse role proteins play in life. Indeed they are behind virtually all of life’s processes. So clearly they are vitally important. Yet the role of proteins depends on them being controllable. Not only does a heart cell need to produce a different set of proteins to a brain cell, but it must also respond to occasionally rapidly changing conditions, including those which may not only put the cell in danger, but the whole organism.

Controlling all this

Yet we cannot hope to throw a bunch of proteins in a bag and expect them to do something, so this whole shebang must be regulated. One way in which this is achieved is through controlling when (and where) proteins are made, another is by regulating them once they are made, and finally the cell can also control when they are destroyed. My work largely looks at the latter two of these processes, especially destruction, although ultimately all three are important.

Ubiquitin is itself a small protein which belongs to a family of similar proteins known as ubiquitin like proteins. Previous posts have already mentioned Nedd8 and, despite Suicyte‘s interest in this topic my work has drifted slightly from this focus. These proteins are molecular tags, which are added to other proteins to modify their function. One of the key roles of ubiquitin for example is to target proteins for destruction by a system known as the proteasome (which may be thought of as a shredder), although the tag is also involved in many other regulatory steps.

The lab I work in focuses on ubiquitin and ubiquitin like proteins, the proteasome, and the various other proteins associated with this whole system. In particular I’m looking at Cdc48, a protein which interacts with ubiquitinated proteins and mediates some of the downstream processes.

[tags]science, ubiquitin, nedd8, yeast, molecular biology, genetics, Schizosaccharomyces pombe, Biology[/tags]

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