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The following are videos created from detailed computer simulations of real natural processes. They are not just “artists’ conceptions”; they are based on decades of quantitative molecular biology research.
This video shows the essential processes needed in the replication of cells. In part 1, the coiling of the DNA molecule, which is over three feet long if unfurled, into the tightly packed chromosomes which are separated in cell division. Because the DNA is very stiff, the effective pressure needed to pack it into a tiny cell is many times atmospheric pressure. This is accomplished by rolling it onto “beads” and then packing these beads together. Note the role of the molecular machines doing the packing. In part 2, the replication of DNA is shown. The double helix of DNA is “unzipped” into two separate strands which are then each replicated. The molecular machine which does the replicating (“polymerase”) works inward on one strand and outward on the other strand, since they have opposite handedness. The one working outward will run out of uncopied DNA unless a new loop of DNA is pulled out and the polymerase is reattached to a position further in. There is thus a complicated “weaving” process, a constant dance of the different loops of the DNA. Note that these replication processes must work before replication of the cell can occur, that is, before natural selection can be an active force, because natural selection relies on the existence of replication. Last, in part 3, the process of converting the information stored in DNA into a molecular machine is shown. The DNA information is first copied into RNA, and this RNA is translated into a sequence of amino acids which will make a protein (the basic element of a molecular machine), in this case, hemoglobin. This process also must be in place (or something equivalent to it) before natural selection can work, since the molecular machines are what actually do the work in a cell.
“The Inner Life of the Cell”
The source of the video is Harvard’s XVIVO project. Voice-over narration is by Jed Macosko of Wake Forest University.
Many cell processes are shown, including the hard-to-believe kinesin molecular machine which looks like a walking man dragging a large bundle. Kinesin is the main method of transporting things inside a cell; various things are put into bags (“vesicles”) and tagged for their final delivery location. The kinesin carries these bags along the microtubules which act as highways inside the cell. These microtubules are constantly being unbuilt and rebuilt to take cargo to new locations inside the cell.
This shows the complicated “weaving” process involving many molecular machines in the creation of a bacteria flagellum, which is what many bacteria use to move, essentially a “propeller”. The flagellum involves a “universal joint” which translates rotation around a right angle, so that the flagellum does not become tangled.
There are several versions of video of this molecular machine, known as ATP synthase, on the web. The video source for this version is creation.com; see also this video from the Medical Research Council Mitochondrial Biology Unit at Cambridge University in the UK.
Instead of music it seemed appropriate to set this to a machine sound. Note the gear-like action. This molecular machine is the central source of all energy supply in the cell. A gradient of proton concentration (hydrogen ions) can be used to produce ATP, or the machine can be run backwards to use ATP to produce a proton concentration gradient.
It shows the process by which information is transcripted from DNA inside the nucleus through messenger RNA to construction of proteins via the three-letter code. Some of the graphics in this video are a bit simplified, but this video shows very nicely the mapping of each three positions in DNA to one of the 20 amino acids that make up proteins. As one example of a simplification, messenger RNA does not travel like a train in a straight line through the nuclear pores, but instead is “shaken” out via thermal fluctuations. (For a better external picture of the ribosome see the “Body Code” video above.)
“Polymerase as an engineering project”
The source of this video is David Keller, professor of chemistry at the University of New Mexico.
In part 1, the video shows a detailed picture of the polymerase molecular machine in action, which copies DNA using elements from the environment inside the cell (see the “Body Code” video above for the whole replication assembly, of which this is a part). In part 2, the same operation is shown with realistic thermal fluctuations. In part 3, the polymerase is depicted as a set of functional parts. There are approximately 90 free parameters which play a role in the function, including the positions of 15 interaction points, the strength and direction of hinges, and the shapes and stiffnesses of the parts. For example, two atoms in the polymerase must line up exactly with the spacing between the rungs of the DNA ladder, although the DNA and the polymerase are generated by two entirely different processes in the cell.