Why Biochemistry Is So Slow

[PatrickPowers]

I happened to see a fancy computer simulation of a biological process. The main thing I thought was "this is SO slow." Actually there on my computer screen it looked like a pretty reasonable speed. But the real process was a million times smaller. If everything is a million times closer together then it should go a million times faster. But it doesn't.

Transcribing a protein takes about a minute. Multiply that times a million and you get an equivalent two years. That means about four days per building block in microbiology time. Why so slow? [A protein might be a chain of about 150 amino acids, which are the standard building blocks of proteins. 2 year/150 = 4 days.]

The answer is that biological process depend very heavily on luck, on random motion. Once some molecule is made it is simply dumped into the cytoplasm, where it jiggles around at random until it just happens to bump into something that needs it. Looking at it that way, four days per block seems not bad.

Why such an inefficient method? While very inefficient in time, there's a big advantage -- zero cost. Not near zero, not almost zero, but honest to God zero. It cost absolutely nothing to get that molecule from the place it was made to the place it was needed. While many other millions of unwanted molecules happened to bump into that place before the exact right thing showed up, that doesn't matter. That doesn't cost anything either.

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This explains many things. Like why the DNA in your body has so many copies of everything. Things are so slow that a great many copies are needed. Otherwise nothing much would get done.

It explains why your muscles fail after twenty or so pushups. There aren't that many of the molecule that carries energy around -- one to two hundred grams in your whole body. Your arm muscles have just a few grams of that, and it takes a few minutes to charge them up again.

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So why are things done this way? Consider those billions of years of evolution. Shortages of food happened many times. The process that uses zero energy survives while anything that uses more dies off. So what if it's slow?

[PatrickPowers]

Next I found out that water molecules in my body move around at about eight hundred miles per hour. A protein always feels like it's being hit by a bevy of supersonic baseballs, coming from all directions. It's amazing the thing doesn't fall apart. That may explain why we suffer fevers. I suppose that body temperature is right at the limit of what a simple protein can stand without getting knocked to pieces. Raise the speed of those water molecules even half a percent (three degrees Fahrenheit) and there are casualties. The smaller simpler proteins of bacteria and viruses are more vulnerable so this is an effective weapon against them.

Evolution again : given equal energy efficiency then the faster things move around the better. The faster process will beat out the slower, with the winner right on the edge. Being able to go over that edge and hurt your enemies more than they can hurt you is another advantage.