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New DNA repair enzyme discovered

Published: 13 January 2011 (GMT+10)
alkD Repair Enzyme
Figure 1: Bacillus cereus alkylpurine DNA glycosylase alkD bound to DNA containing a G-T mismatch.

(www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=84991)

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Our information is stored on the famous DNA double helix molecule. This is so efficient that just five round pinheads full of DNA could hold all the information of the earth’s entire human population.1 Just one of these pinheads would have 2 million times the information content of a 2 TB hard drive. And each of our 100 trillion cells has 3 billion DNA ‘letters’ (called nucleobases) worth of information.2

But chemically, DNA is actually a very reactive molecule (and RNA is even more so), so it’s highly implausible that it could have arisen in a hypothetical primordial soup.3 Indeed, about a million DNA ‘letters’4 are damaged in a cell on a good day. One common form of DNA damage is called alkylation—this means a small hydrocarbon group is attached to one of the ‘letters’, and there are many places for the attachment. This changes the shape enough so it can no longer fit into the double helix. This can prevent DNA replication or reading the gene.

So living creatures must have elaborate DNA repair machinery. University of Chicago biologist James Shapiro points out that:

all cells from bacteria to man possess a truly astonishing array of repair systems which serve to remove accidental and stochastic sources of mutation. Multiple levels of proofreading mechanisms recognize and remove errors that inevitably occur during DNA replication. … cells protect themselves against precisely the kinds of accidental genetic change that, according to conventional theory, are the sources of evolutionary variability. By virtue of their proofreading and repair systems, living cells are not passive victims of the random forces of chemistry and physics. They devote large resources to suppressing random genetic variation and have the capacity to set the level of background localized mutability by adjusting the activity of their repair systems.5

For example, there is ‘base excision repair’: special enzymes called DNA glycosylases run down the DNA molecule, detect the damaged ‘letter’, grab it, put it in a specially shaped pocket, then chop it out. Then other enzymes repair the resulting gap.

Natural selection requires that the information selected for can be reproduced accurately. But without an already functioning repair mechanism, the information would be degraded quickly.

Scientists at North American universities have discovered another ingenious repair enzyme in bacteria, called AlkD.6 This has a very different structure. It works by flipping a positively charged damaged base—highly unstable—and the one it’s paired with, from the inside to the outside of the helix. Then they are both detached, and the gap filled. Understanding these enzymes could lead to more effective chemotherapy.

Evolution has a major problem in explaining repair machinery. Natural selection requires that the information selected for can be reproduced accurately. But without an already functioning repair mechanism, the information would be degraded quickly. Furthermore, the instructions to build this repair machinery is encoded on the very molecule it repairs, another vicious circle for evolution.7

There is seemingly no end to the machinery required even for the first “simple” cell to evolve. See the related articles as well as following clips from our YouTube channel, CreationClips:

The 20-nanometer motor (height), ATP synthase (one nanometer is one thousand-millionth of a metre). These rotary motors in the membranes of mitochondria (the cell’s power houses) turn in response to proton flow (a positive electric current). Rotation of the motor converts ADP molecules plus phosphate into the cell’s fuel, ATP.

Kinesin is the miniscule longshoreman (stevedore) of the cell, toting parcels of cargo on its shoulders as it steps along a scaffolding of microtubules. Each molecule of ATP fuel that kinesin encounters triggers precisely one 8-nanometer step of the ‘longshoreman’.
See www.umich.edu/news/MT/04/Fall04/story.html?molecular.



References

  1. Gitt, W., Dazzling Design in Miniature, Creation 20(1):6, 1997. Return to text.
  2. Sarfati, J., DNA: marvellous messages or mostly mess? Creation 25(2):26–31, 2003; creation.com/message. Return to text.
  3. According to Brooks, J., and Shaw, G., Origins and Development of Living Systems, Academic Press, London and New York, 1973: “If there ever was a primitive soup, then we would expect to find at least somewhere on this planet either massive sediments containing enormous amounts of the various nitrogenous organic compounds, acids, purines, pyrimidines, and the like; or in much metamorphosed sediments we should find vast amounts of nitrogenous cokes. In fact no such materials have been found anywhere on earth [emphasis added].” Return to text.
  4. Even formation of the DNA ‘letters’ has major problems—see Sarfati, J., Origin of life: instability of building blocks, J. Creation 13(2):124–127, 1999 P-I-P-E creation.com/blocks; Nucleic acid bases in Murchison meteorite? Have they proved that life came from outer space? J. Creation 22(3):5–7, 2008 P-I-P-E creation.com/murchison. Return to text.
  5. Shapiro, J.A., A Third Way, Boston Review, p. 2, February/March 1997. Return to text.
  6. Newly Discovered DNA Repair Mechanism, Science News, sciencedaily.com, 5 October 2010. Return to text.
  7. Cf. Sarfati, J., Self-replicating enzymes? A critique of some current evolutionary origin-of-life models, J. Creation 11(1):4–6, 1997; creation.com/replicating. Return to text.

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