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03.09.2012 ATP Synthase
An amazing molecular machine, ATP synthase, can run use electrostatic potential energy stored in a proton gradient to generate ATP. Under different conditions, it can run in the opposite direction, using ATP to build a proton gradient. Created by Graham Johnson of fivth.com and Graham Johnson medical media www.grahamj.com, for Molecular Biology of the Cell, 4e by Alberts, Walter, et al, Gardland Publishers. ©2002  

Please visit www.grahamj.com for examples of other molecular machines.

Update:
Glad to hear my APT synthase movie has helped so many people learn an otherwise complicate subject.

I put a lot of time into making this with Peter Walter (UCSF) and Mike Morales (Garland Publisher) back in 2001. http://www.youtube.com/user/garlandscience/featured

A new software project I work on with Ludovic Autin in Art Olson's lab, can make it a lot easier to make a movie like this, and we distribute it for free.  Check out:  http://epmv.scripps.edu if you want to try it out.
-Graham

08.10.2012 mRNA Translation (Advanced)
The job of the mRNA is to carry the gene's message from the DNA out of the nucleus to a ribosome for production of the particular protein that this gene codes for.
Originally created for DNA Interactive ( http://www.dnai.org ).
TRANSCRIPT: The job of this mRNA is to carry the genes message from the DNA out of the nuceus to a ribosome for production of the particular protein that this gene codes for. There can be several million ribosomes in a typical eukaryotic cell these complex catalytic machines use the mrna copy of the genetic information to assemble amino acid building blokes into the three dimensional proteins that are essential for life. Lets see how it works. The ribosome is composed of one large and one small sub-unit that assemble around the messenger RNA, which then passes through the ribosome like a computer tape. The amino acid building blocks (that's the small glowing red molecules) are carried into the ribosome attached to specific transfer RNAs. That's the larger green molecules also referred to as tRNA. The small sub-unit of the ribosome positions the mRNA so that it can be read in groups of three letters known as a codon. Each codon on the mRNA matches a corresponding anti-codon on the base of a transfer RNA molecule.The larger sub-unit of the ribosome removes each amino acid and join it onto the growing protein chain. As the mRNA is ratcheted through the ribosome, the mRNA sequence is translated into an amino acid sequence. There are three locations inside the ribosome, designated the A-site, the P-site and the E-site. The addition of each amino acid is a three step cycle: First, the tRNA enters the ribosome at the A-site and is tested for a codon/anti-codon match with the mRNA. Next, provided there is a correct match, the tRNA is shifted to the P-site and the amino acid it carries is added to the end of the amino acid chain. The mRNA is also ratcheted on three nucleotides or one codon. Thirdly, the spent tRNA is moved to the E-site and then ejected from the ribosome to be recycled. As the protein synthesis proceeds, the finished chain emerges from the ribosome. It folds up into a precise shape, determined by the exact order of amino acids. Thus the Central Dogma explains how the four letter DNA code is - quite literally - turned into flesh and blood.