Posted on 11/16/2005 3:40:35 AM PST by snarks_when_bored
* 14:02 15 November 2005
* NewScientist.com news service
* Gaia Vince
A new microscope sensitive enough to track the real-time motion of a single protein, right down to the scale of its individual atoms, has revealed how genes are copied from DNA – a process essential to life.
The novel device allows users to achieve the highest-resolution measurements ever, equivalent to the diameter of a single hydrogen atom, says Steven Block, who designed it with colleagues at Stanford University in California.
Block was able to use the microscope to track a molecule of DNA from an E.coli bacterium, settling a long-standing scientific debate about the precise method in which genetic material is copied for use.
The molecular double-helix of DNA resembles a twisted ladder consisting of two strands connected by “rungs” called bases. The bases, which are known by the abbreviations A, T, G and C, encode genetic information, and the sequence in which they appear “spell out” different genes.
Every time a new protein is made, the genetic information for that protein must first be transcribed from its DNA blueprint. The transcriber, an enzyme called RNA polymerase (RNAP), latches on to the DNA ladder and pulls a small section apart lengthwise. As it works its way down the section of DNA, RNAP copies the sequence of bases and builds a complementary strand of RNA – the first step in a new protein.
“For years, people have known that RNA is made up one base at a time,” Block says. “But that has left open the question of whether the RNAP enzyme actually climbs up the DNA ladder one rung at a time, or does it move instead in chunks – for example, does it add three bases, then jump along and add another three bases.
Light and helium
In order to settle the question, the researchers designed equipment that was able to very accurately monitor the movements of a single DNA molecule.
Block chemically bonded one end of the DNA length to a glass bead. The bead was just 1 micrometre across, a thousand times the length of the DNA molecule and, crucially, a billion times its volume. He then bonded the RNAP enzyme to another bead. Both beads were placed in a watery substrate on a microscope slide.
Using mirrors, he then focused two infrared laser beams down onto each bead. Because the glass bead was in water, there was a refractive (optical density) difference between the glass and water, which caused the laser to bend and focus the light so that Block knew exactly where each bead was.
But in dealing with such small objects, he could not afford any of the normal wobbles in the light that occur when the photons have to pass through different densities of air at differing temperatures. So, he encased the whole microscope in a box containing helium. Helium has a very low refractive index so, even if temperature fluctuations occurred, the effect would be too small to matter.
One by one
The group then manipulated one of the glass beads until the RNAP latched on to a rung on the DNA molecule. As the enzyme moved along the bases, it tugged the glass bead it was bonded too, moving the two beads toward each together. The RNAP jerked along the DNA, pausing between jerks to churn out RNA transcribed bases. It was by precisely measuring the lengths of the jerks that Block determined how many bases it transcribed each time.
“The RNAP climbs the DNA ladder one base pair at a time – that is probably the right answer,” he says.
“It’s a very neat system – amazing to be able see molecular details and work out how DNA is transcribed for the first time,” said Justin Molloy, who has pioneered similar work at the National Institute for Medical Research, London. “It’s pretty incredible. You would never have believed it could be possible 10 years ago.”
Journal reference: Nature (DOI: 10.1038/nature04268)
Sometimes, yes. It remains a fact, however, that both are ascertainable by scientific method. In fact, I don't know what other method would be able to detect intelligent design, do you? Or does prayer do the trick?
Yes, your flatulence: The Law of Gravity is currently in effect upon planet earth.
Two things are required for science to take place. Can you name them? Also, once you do, please elaborate upon how they can exist apart from either intelligence or design.
Thank you.
There's actually more than one way errors are checked for. During mRNA synthesis mistakes are checked during mRNA synthesis and in E. coli afterwards too. Then errors are checked during the process of translation into proteins if the wrong amino acid is substituted. These keep natural mutation rate down.
I'm not sure that one can draw such a clear distinction between "natural" and "supernatural" as you're trying to do, however. It seems that the distinction only works one way, and that it's largely a matter of perception.
Suppose we created artificial life in a computer. Our position would be in some sense "supernatural" with respect to the universe of that electronic life form, in much the same way that God is "supernatural" to us.
We, however, would see the "computer life" as merely a subset of the larger nature of which we're a part, and God would presumably see us in the same light.
It may be a mistake to assume that the true universe (whatever that is) consists only of those things which we can observe. There are many serious scientists whose work at least raises questions on that score.
You mistake agreement. That was like a breath and restart from another direction.
Fire is born, it has its begining from the point before which it did not exist.
Fire sure does consume and that is eating and it does leave waste behind.
If confronted with a log and a pile of cardboard and a body of water, logically it would consume its easiest target first being the cardboard and then it would consume the log, providing it had grown strong enough to do so. It would steer clear of the water unless of course it was strong enough to overpower it turning it into steam.
Willed by god eh? Seems like that is an awfully convenient statement to make and really it seems trite to me.
I offer that to claim it is the His will you must qualify that will exists. I just do not see that shown in any other way than JUST BELIEVE.
These are more difficult.
I don't think there is any more error based on neighbor bases. This is a guess.
I don't think certain sequences are more error prone. This is a better guess.
As far as amino acids are concerned, the answer is probably more "yes" than "no". Since organisms have preferred codon usages and rare codond are translated more slowly there could be a difference there. In addition not all tRNAs will probably bind their codons with the same binding energy and so that could also cause a mistake in amino acid insertion. But since making a mistake with putting in the wrong amino acid does not affect the gene, the defective protein will be recycled. Protein turnover rates can be quite rapid, but some are slow, but they all get turned over.
You ask interesting questions 8-)
As I've said in the past and in so many words, this is a bald-faced contrivance, much as is the word "supernatural." What does "supernatural" mean but "out of the ordinary?" Are you telling me that science is only allowed to address matters that fall within the realm of "ordinary" observation? If you want that to be science, be my guest. You and your cohorts can bottle yourselves up and drown in your self-sufficient definitions and conclusions. Don't expect the rest of the world to follow suit, and please don't sue us for rejecting your small-minded approach to education in general and science in particular.
Which is why I replied as I did. The statement makes a huge leap of logic, considering that nobody even has an idea how the incrementation is accomplished.
Yup. Blame on rush hour traffic addling my tired old noggin.
Simple proteins automatically fold into the appropriate structure. These can be modeled.
Yes, I was talking about the modeling...one hopes to predict the energetically favorable conformation of the known sequence of amino acids. Since a full quantum treatment is "beyond the state of the art" one uses parameterized functions for the various interactions.
If one starts the modeling with all of the amino acids already in the proper sequence, and then allows the structure to relax in search of an energetic / entropic minimum, you will end up with such-and-such a final answer for the most favorable conformations.
I was speculating / suggesting that if one starts with a single amino acid, then adds the second amino acid and allows that to relax (not much except rotational changes about a single bond, not very exciting...); then adds the third amino acid and allows that structure to relax; etc. how different would the final predicted structure be, from the one arrived at using the first method?
The second method "add one at a time and then relax" would appear to be a closer analogy to the actual physics of what is going on inside the cell...
For more complex proteins, other proteins may be involved in preventing them from taking the wrong configuration until translation is complete. Finished proteins can be a single protein, multiples of one protein or mixtures of more than two protein subunits. So he answer is not simple without a specific example.
That is exactly the info I was looking for, thanks.
Full disclosure: do you happen to know how hemoglobin in particular is built up?
Cheers!
It must be painfully apparent to you by now that I operate with a wider definition of science than most people. For darwin's sake, look it up in the dictionary.
Science is "the observation, identification, description, experimental investigation, and theoretical explanation of phenomena."
When physical matter demonstrates patterns of organization and can be categorized into a table of elements that is rarely appended or modified it stands to reason that perhaps, just maybe, elements of intelligence and design are involved. To attribute massive amounts of organized matter to a single, almighty intelligence is far from unreasonable or unscientific.
It certainly stands on the side of absurdity for kool-aid drinking ideologues to dismiss intelligent design as an unscientific notion while insisting that those who hold intelligent design as operative get on their knees and beg for "scientific" acceptance.
Choking and vomit of lying bastards aside, God created the heavens and the earth scientifically, and He scientifically sustains them.
That's the smartest thing you've done so far.
So then by that everything that happens has to be HIS WILL then right?
So Katrina Was His will?
Everything for all time has been and willbe His will? My will is actually his will? When I create fire is that my will or His will? you are saying that my will is because of His will. I understand your point I just do not agree with it.
You cannot belive something ANYThing is random. You state clearly it all has to be His will. His will that you are allowed to type. His will that an earthquake can happen because His will made the planet.
Everything cannot be exmplained by His will. That would be saying that everything is absolute. I do not subscribe to that idea. I do not belive anything is absolute
If I light a fire am I not its source and its creator?
Oh wait His will did that, no I did that, no, His will made me so actually His will lit the fire.....sorry man that is the silliest thing I have ever heard. That is a circular argument and I prefer to move forward, something that one does not do when they just go around and around in the same place.
It seems to me you hold onto the idea that ONE being controlled and controls everything. You can do so if you like, but I ain't buying it.
Aye, that's what got me thinking. Look at "rational drug design" where one selects various candidate substrates for high scores on binding to the active site of an enzyme...
By definition you have any number of candidates which bind more or less tightly to the site, some better than others.
In a biologically active system, one may attempting to tie up the active site of an enzyme with the drug molecule in order to prevent the enzyme from acting upon its 'naturally occuring' target; and of course there are other effects such as the drug interfering in other places, etc...
The analogy to protein construction (and even to building DNA) is that while the "proper" match is energetically favorable (the high score in the docking), there is nothing to forbid a different base pair, or amino acid from arriving first.
[Many deeper thoughts and pretentious drivel deleted...but available upon request.]
Cheers!
Sheez. Don't drive youself crazy. It'll all come out in the wash.
Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.