8.3 Photosynthesis

Developments in scientific research follow improvements in apparatus—sources of 14C and autoradiography enabled Calvin to elucidate the pathways of carbon fixation.

At the beginning of the 20th-century, the scientific understanding of photosynthesis was centred on the combination of Carbon Dioxide with chlorophyll to produce formaldehyde as an intermediate before being converted to a carbohydrate (Benson). This view predominated up to the discovery of radioactive Carbon-14 by Kamen and Benson in 1940 (Benson).

In 1945, C14 became readily available to researchers in the US. A young researcher in California, Melvin Calvin, was told by a senior scientist at the University of California-Berkley that he should start to do something interesting with it. So began a research focus that led to the Nobel Prize in Chemistry in 1961 “for his research on the carbon dioxide assimilation in plants” (“Melvin Calvin-Facts”).

The shape of the apparatus Calvin used led to it being called the “lollipop” experiment. The central “lollipop” contained a suspension of algae, to which was introduced the radioactive carbon.  Periodically, a sample of the algae was released into the tube below (the stick of the lollipop) where it was immediately killed by a solution of alcohol.  The compounds could then be analysed through chromatography.  By using the radioactively labelling isotope of carbon, it was possible to trace the path the isotope took and by analysing the intermediate compounds the researchers were able to determine what happened to the carbon – where was it absorbed and what was it used for? The series of experiments helped identify the sequence of carbon compounds produced in the Calvin Cycle and also disproved the idea that chlorophyl fixes carbon.

Lollipop PS
The “Lollipop” apparatus (The Bancroft Library)

These experiments were carried out be many individuals over a period of nearly 15 years and in some ways it seems unfair that Calvin tends to receive all the credit (as well as a solo Nobel Prize). A personal report by Andrew Benson (available here) gives a good idea of the collaborative nature of this process.

Sources:

Benson, A. Following the path of carbon in photosynthesis: a personal story. Photosynthesis Research. 73: 29–49, 2002. Web. April 20, 2016.

Calvin, Melvin. “The Path of Carbon in Photosynthesis.” Nobel Lectures, 1964, pp. 618–644., http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1961/calvin-lecture.pdf. Web. 30, Jan. 2018

“Calvin’s Lollipop Experiment.” The Bancroft Library, The University of Berkeley, California, bancroft.berkeley.edu/Exhibits/Biotech/Images/3-9lg.jpg. Web. Jan 30, 2018.

“Melvin Calvin – Facts”. Nobelprize.org. Nobel Media AB 2014. Web. 19 Apr 2016.

 

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8.2 Cell Respiration

Paradigm shift—the chemiosmotic theory led to a paradigm shift in the field of bioenergetics.

Paradigm shifts are something we see from time to time in biology but we also discuss them in TOK – they represent a way of looking at a problem from a completely new angle (van de Lagemaat).  In doing so, paradigm shifts can often be controversial and may take several years, or even decades, before they are accepted by the scientific community.

In 1961 Peter Mitchell proposed the chemiosmotic coupling theory to account for the production of ATP in oxidative phosphorylation. This theory went against the prevailing view that there were “energy-rich” chemical intermediates that explained the resulting ATP formation. As he writes in his landmark publication, from 1966,

“the study of the question of the coupling mechanism has continued to be ruled by the well-trodden and familiar tenets of the chemical coupling conception, no matter how fantastic the resulting tissue of hypothesis.” (Mitchell,1507)

Terms like “well-trodden” and “familiar” refer to the accepted theory that, despite results to the contrary, remains the only accepted explanation.  A paradigm shift must counter such ingrained views, which is why it can take time for the new explanation to become accepted.  Mitchell was awarded the Nobel Prize in Chemistry in 1978.  Part of his acceptance speech illustrates the challenges for the scientist trying to overturn entrenched theory:

 “…the originator of a theory may have a very lonely time, especially if his colleagues find his views of nature unfamiliar, and difficult to appreciate.” (“Peter Mitchell – Banquet Speech”)

There are many examples of paradigm shifts in biology – they make useful reference points for TOK discussion and analysis. Key terms to consider include bias, justification, subjective, objective and verification.

Sources

Mitchell, Peter. “Chemiosmotic coupling in oxidative and photosynthetic phosphorylation”.  Biochimica et Biophysica Acta (BBA) – Bioenergetics, Volume 1807, Issue 12, December 2011, Pages 1507-1538. Web. 19 April, 2016.

“Peter Mitchell – Banquet Speech”. Nobelprize.org. Nobel Media AB 2014. Web. 19 Apr 2016.

van de Lagemaat, R. Theory of Knowledge for the IB Diploma. Cambridge, Cambridge University Press. 2011. Print.

8.1 Metabolism

Developments in scientific research follow improvements in computing—developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways.

Bioninformatics is the “Synthesis of molecular biology and computer science that develops databases and computational tools to store, retrieve, and analyze nucleic acid and protein sequence data.” (Pierce, B) and we have encountered it already in 7.3 Translation.

In addition to genes, though, bioinformatics can screen metabolic pathways and protein structures in order to assess potential targets for new drugs. For example, the Malaria Drug Target database allows researchers to search for potential inhibitors and targets in the malarial parasite, based on protein structure and function cross-referenced with genetic sequences. Many of these potential targets are key enzymes within metabolic pathways.  Hasan et al. (2015) used a protein database to investigate the possibility of using the enzyme transketolase as a drug target.  The enzyme is important in the pentose phosphate pathway, which is part of  energy generation and nucleic acid synthesis (Hasan et al.).  Analysis using various databases and computer software allowed the researchers to identify the enzyme, determine its structure and compare it to the human version of the enzyme. The result is a promising avenue for testing drugs to control the spread of Plasmodium falciparum, the malaria parasite.

Hasan , A. et al. Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source Code for Biology and Medicine 2015. 10:7. Web .Accessed April 19, 2016.

Pierce, B. Genetics: A conceptual approach. 2nd Edition. 2005. Web. Accessed April 19, 2016.