Online Book Reader

Home Category

Reinventing Discovery_ The New Era of Networked Science - Michael Nielsen [74]

By Root 380 0
it’s a crucial step along the way, because proteins carry out many of the most important processes in our bodies. Aside from its intrinsic scientific interest, Foldit is also interesting as a demonstration of the great complexity of work that can be done by volunteers. In Galaxy Zoo, participants mostly carry out simple tasks, such as classifying a galaxy as spiral or elliptical. In Foldit, players are asked to tackle tasks that would challenge a biochemistry PhD. And, as we’ll see, the top Foldit players are doing those tasks extraordinarily well.

Before we discuss Foldit in detail, let’s talk a bit about proteins in general. Biologists are obsessed by proteins, and with good reason: they’re molecules that do everything from digesting our food to contracting our muscles. A good example of a protein is the hemoglobin molecule. Hemoglobin is one of the main components in our blood: it’s the molecule our bodies use to move oxygen from our lungs to the rest of our body. Another important class of proteins are the antibodies in our immune system. Each antibody has its own special shape that lets it lock on to viruses and other intruders in our body, tagging them for attack by our immune system.

At present we only partially understand how DNA gives rise to proteins such as hemoglobin. What we do know is that certain sections of our DNA are protein coding, meaning that they describe a specific protein. So, for example, there’s a protein-coding section for hemoglobin somewhere in your DNA. That region is a long string of DNA bases, which starts: CACTCTTCTGGT. . . . It turns out to be helpful to divide that string of bases into triplets, which are called codons: CAC TCT TCT GGT. . . . The way proteins are formed is that each codon in the protein-coding section of your DNA is transcribed into a corresponding molecule in the protein called an amino acid. So, for example, the first codon for hemoglobin, CAC, gets transcribed into an amino acid known as histidine. I won’t explain exactly what histidine is, or what it does—for us it doesn’t much matter. What matters is that everywhere the CAC codon appears in the DNA sequence for hemoglobin (or any other protein), it gets transcribed to histidine. In a similar way, the second codon, TCT, gets transcribed into the amino acid serine. And so on. The resulting protein is a chain containing all those amino acids—so hemoglobin is a chain containing histidine, serine, and so on.

Okay, so far, so good: DNA can be used as a recipe for generating proteins. Proteins, however, differ from DNA in that they each have their own special shape, unlike the completely regular structure of DNA. That shape is tremendously important. For example, as I mentioned before, the antibodies in our immune system are proteins, and the shape of an antibody determines which viruses it can lock onto. What’s going on is that as the information in the DNA is transcribed to form the amino acids in the protein, the protein “folds” into its shape. How this folding occurs is still only partially understood, but there are some basic rules of thumb that should give you the flavor of what’s going on. Some amino acids like to be near water—they’re called hydrophilic, from the Greek roots “hydro” and “philia,” for water and love, respectively. Since proteins inside a cell are surrounded by water, the protein will tend to fold so the hydrophilic amino acids sit on the outside, near the water. Histidine and serine are both examples of hydrophilic amino acids. By contrast, hydrophobic amino acids—amino acids that don’t like water—end up bundled up tight inside the protein. Sometimes these tendencies conflict: neighboring amino acids in the protein may be alternately hydrophobic and hydrophilic, with the result that the protein can end up folding into a very complex shape.

There’s an incredibly clever trick here that nature is using. The DNA is a completely regular arrangement of information, which makes it both easy to copy and relatively straightforward to transcribe into amino acids. But then competition between hydrophilia,

Return Main Page Previous Page Next Page

®Online Book Reader