2.6 Making Models – DNA

Topic 2.6:  Using models as representation of the real world—Crick and Watson used model making to discover the structure of DNA. (IBO, 2014)

This year, while trying to locate our ball-and-stick DNA models, we found an old cardboard-puzzle DNA kit.

Piecing together the puzzle
Piecing together the puzzle

It proved a great (and unplanned) way to introduce the structure of DNA and have the students examine the chemical features to deduce their own answers to the structural significance of DNA.  The advantage of this kit was that it had the chemical structure painted onto the puzzle pieces and the students, much like Watson and Crick in the early 1950s, were able to experiment with no guidance from me and determine which pieces needed to fit where.   There were many “Aha” moments as different students determined out where the different chemical pieces fit best.

The finished product!
The finished product!

We were thus able to figure out the significance of anti-parallel strands, purine + pyramidine pairing, 3′ →5′ linkages and the sugar-phosphate backbone.  Models in action!

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7.3 Translation

Developments in scientific research follow improvements in computing—the use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.

Bioinformatics is the application of computer science to molecular biology, allowing the creation of massive databases of molecular information (proteins, genes, DNA sequences etc.) You might remember from our Crash Course video on replication that one cell contains genetic information equivalent to a stack of single A4 pages nearly 100m high! It is only the advent of powerful (and affordable) computers over the last 25 years that has enabled the collection and synthesis of genetic information on a large scale.

To explore this topic, we will be performing a BLAST search using resources from the European Molecular Biology Lab (EMBL).  We will be searching for information about the Protein PAX6 through a series of databases on the web.  The activity we are doing can be found through the EMBL’s education section, the European Learning Laboratory for Life Sciences.

7.1 DNA Structure and Replication

7.1 Making careful observations—Rosalind Franklin’s X-ray diffraction provided crucial evidence that DNA is a double helix. (AHL)

Photo 51 is Rosalind Franklin’s famous image of the DNA double helix. When he saw this image, James Watson is reported to have said, ” The instant I saw the picture my jaw fell open and my pulse began to race.”  To the trained eye, this cryptic, black-and-white image immediately reveals the helical structure of DNA, as well as the relative positions of the sugar-phosphate backbone and the nitrogen bases. It was the scientific evidence needed to understand the structure of DNA.

Watson and Crick, although they knew that this meant a helix, were not fluent in the chemical knowledge that would allow them to calculate ratios and distances.  This information was provided by Maurice Wilkins, their co-recipient of the Nobel Prize and Rosalind Franklin’s co-worker. Additionally, it was Franklin’s work as part of a chemical report in 1952 that finally convinced them to put the bases on the inside, rather than the outside. While Wilkins shared in the Nobel Prize, Rosalind Franklin did not. Her research was not published until after Crick and Watson’s article and so she was not cited in their list of references (though she was thanked in the acknowledgements section). Speculation remains that she was taken advantage of to one degree or another and  did not receive the accolades she deserved.  The controversy was only heightened as she died at age 37 in 1958 and so was ineligible for the Nobel Prize.

Sources:

“Secret of Photo 51.” PBS. PBS, 2003. Web. 17 Oct. 2014.  <http://www.pbs.org/wgbh/nova/photo51/&gt;.

All original research papers from 1953 on the discovery of the structure can be downloaded as PDFs from the journal Nature.

2.7 DNA Replication

Obtaining evidence for scientific theories—Meselson and Stahl obtained evidence for the semi-conservative replication of DNA.

Evidence is central to the scientific process; without it, there is no way to support or refute theories. In many cases, the process by which evidence is obtained can be just as interesting as the final results.

As we discussed in class, there were three possible ways that the DNA molecule could replicate itself. Meselson and Stahl provided an elegantly designed experiment that provided proof of the semi-conservative replication predicted by Watson and Crick.

Dna ftb
DNA FTB

Follow this animation on their experiment here and read their biographies here. Their original paper, published by the Proceedings of the National Academy of Sciences (USA), is also available online, though can be technical at times.

You can follow this up with a look at the McGraw-Hill animation below:

McGraw-Hill Animations
McGraw-Hill Animations

Dnaftb.org,. ‘DNA Replication :: DNA From The Beginning’. N. p., 2015. Web. 11 Nov. 2015.

Highered.mheducation.com,. ‘Meselson And Stahl Experiment’. N. p., 2015. Web. 11 Nov. 2015.

2.6 Watson and Crick – Making Models

Using models as representation of the real world—Crick and Watson used model making to discover the structure of DNA.


In 1953, Francis Crick and James Watson published their article proposing the Double-Helix structure of DNA. This represented the culmination of nearly 50 years of research into the function and structure of nucleic acids.  One of the important steps they undertook in determining this was the building of a relatively simple model. 


Models are important tools for scientists as they enable the observation of processes that may not be observable.  Like theories, models may be improved upon and replaced with more accurate ones.  Much important science has advanced through of models in molecular and cell biology and genetics.  However, there may be limitations to this and it raises an important knowledge question:

Is there any distinction to be drawn between knowledge claims dependent upon observations made by sense perception and knowledge claims dependent upon observations assisted by technology?


You can download the original published paper of their discovery from the journal Nature.

Watson and Crick (together with Maurice Wilkins) were awarded the Nobel Prize for Physiology or Medicine in 1962.  More information is at the Nobel Prize website.

Sources:

Biology Guide. Publication. Cardiff: IBO, 2014. Print. Diploma Programme

Hewitt, Alison. Watson and Crick with the double-helix model. Digital image. Watson and Cancer. UCLA, 7 Mar. 2011. Web. 9 Oct. 2014. <http://newsroom.ucla.edu/stories/watson-and-cancer-193383&gt;.

The Discovery of the Molecular Structure of DNA. Nobel Media, n.d. Web. 08 Oct. 2014. <http://www.nobelprize.org/educational/medicine/dna_double_helix/readmore.html&gt;.