[The Lone Ranger]

Originally Posted by cappuccino

Youtube has a movie about replication and transcription, it's one of my favorite science movies. Like many other molecular biology movies, it shows as though molecules themselves were magically seeking out each other even that's not actually the case. But then shortcuts have to be taken to show the really important features.

I left out a lot of details regarding DNA Synthesis and Protein Synthesis for that reason too. I figured that, for example, an explanation of how mRNA is processed before it's released and allowed to leave the nucleus would be pointlessly complicated and wouldn't be helpful in understanding the basic processes involved.

Does the movie get all of the process details correct?

From what I can tell, it's pretty good, aside from some forgivable oversimplification.

I had trouble with it on my computer; it doesn't play very well. It appears, though, not to have any narration. That may be because it's intended to be played while someone explains what's going on. Otherwise, some of what you see won't make any sense. For example, DNA polymerase can only copy DNA in the 5' → 3' direction. This means the leading strand and the lagging strand of a DNA molecule are copied differently during DNA replication. They actually show that in the animation, but if you didn't know it beforehand and therefore what to look for, you'd never be able to make sense of it.

I have a couple of questions, I've noticed in my molecular biology reading that sometimes it seems like they're talking about different kinds of DNA replication machinery all doing the same thing, I was wondering are they comparing various different replication enzymes from different species or are multiple redundant replication machinery at work in human cells?

I'm not entirely certain I can answer. As far as I know, DNA polymerase works more or less the same in all eukaryotes. As mentioned though, the leading strand and the lagging strand are copied differently. You have to keep this in mind when thinking about DNA replication; that might be a source of confusion.

Also, DNA replication works a bit differently in prokaryotes than it does in eukaryotes. (Also, transcription and especially translation work a little differently in prokaryotes and eukaryotes. This is largely because prokaryotes don't process their mRNA after it's synthesized. Eukaryotes, by contrast, heavily process their mRNA after it's synthesized, but before it leaves the nucleus.)

In any event, DNA polymerase and RNA polymerase are far from the only enzymes that take part in DNA synthesis/protein synthesis, so that might be a source of confusion. If a textbook or an instructor makes a random reference to helicase, for example, without explaining its role in DNA replication, that could easily lead to confusion.

It's also worth keeping in mind how big a molecule DNA is. Several different DNA polymerase molecules will be simultaneously operating during the replication of a DNA molecule -- otherwise, copying the molecule would take much more time. So you'll have lots of (more or less) identical molecules performing the same tasks during DNA replication; if this isn't understood, random reference to "the other" DNA polymerase molecules will be terribly confusing to the listener.

The other question, are the mRNA strands driven by random Brownian motion to move by themselves out of the nucleus into the cytoplasma to be united with a ribosome? Or are there helper molecules which ferry the mRNA from the transcription grounds to the ribosomes?

Random Brownian motion plays a big role, but it's a bit more complicated than that. "Mature" mRNA (that is, mRNA that has been processed and has had its introns spliced out, etc.) can bind to nuclear export proteins (is there anything proteins can't do?). Unprocessed mRNA typically won't bind to nuclear export proteins.

The mRNA apparently can't pass through the nuclear pores and thus into the cytoplasm unless bound by nuclear export proteins ("exportins"). Unbound mRNA is far too large a molecule to have much of a chance of passing through a nuclear pore on its own. I don't know off the top of my head how exportins work, but I'd guess they cause the mRNA to fold into a more compact shape that can more easily pass through a nuclear pore. The mRNA/exportin complex diffuses out into the cytoplasm (as far as I know, no active transport is involved), and the proteins are eventually released. The mRNA, should it encounter a ribosome, can then be used for protein synthesis. If it doesn't encounter a ribosome, it will sooner or later be degraded by RNases and broken down into its component nucleotides.

Your talk about ERVs made me think of a certain company's research aimed at eradicating HIV. They've developed a drug designed to accelerate the rate of mutation in HIV by tricking the reverse transcriptase into incorporating nucleotide analogues in the DNA chain. Fascinatingly, the drug causes random multiple point mutations in order to drive the virus into extinction by causing multiple knockout mutations over successive generations.

If the clinical trials bore out, then HIV could become another ERV in the humans infected by it. Who knows maybe it'll end up driving another evolutionary phase in humanity in the distant future.

I've read of this. It's a brilliant idea, in my estimation, and may prove the best way to deal with HIV.

Cheers,

Michael