2.4 Proteins

Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids.

Part of the universality of life is the observation that all living organisms construct proteins out of the same pool of 20 amino acids.  These 20 were identified in a rapid era of discovery after the development of partition chromatography in 1943.  However, this has now been expanded to include two additional amino acids – selenocysteine and pyrrolysine, giving a total of 22 amino acids.

Selenocysteine, as the name suggests, is similar to the amino acid cysteine but it has a Selenium atom as part of its side-chain (R-Group). It is a highly reactive and potentially dangerous substance – cells have to use some tricky metabolic pathways in order to prevent it from moving freely and building up in the cytoplasm.   It is used in certain redox reactions and has been found in all three domains of life, although it is not universal amongst them

Pyrrolysine is rarer, having only been found in some species of Archaeans and bacteria. It is structurally similar to lysine, but with the addition of a a pyrroline ring to the side-chain. It’s role and possible existence in other organisms is the focus of many ongoing studies.

Both of these amino acids are not encoded in the DNA – they are instead encoded by the stop codons UGA for selenocysteine and UAG for pyrrolysine and expressed via interactions with specific tRNA molecules, a process known as cotranslation. The biochemistry involved is fairly complex and difficult to summarise for IB biology purposes, but if you are interested the links below are a good place to start.

In summary, then:

  • all living organisms use the traditional 20 amino acids to construct proteins and code for these amino acids in their DNA
  • all three domains of life (thought not every species in them) also use a 21st amino acid selenocysteine in some proteins (humans included)
  • Archaeans and bacteria have developed a mechanism to use a 22nd amino acid, pyrrolysine.
  • both of these amino acids are not coded for in the DNA but are expressed through the use of a stop codon and tRNA
  • the presence of Selenocysteine in all three domains strongly suggests it was present in the last universal common ancestor, and is thus a very ancient biochemical pathway

 

Selenocysteine and pyrrolysine are powerful examples of the versatility inherent in the genetic code. (Rother and Krzycki).

Like so many aspects of biology, once a rule is determined, the incredible variety of life shows us an exception.

For an interesting TOK-linked discussion, consider this quote, also from the Rother/Krzycki article:

They further provide examples of how precedent, though valuable, is not always the best predictor in scientific investigation…

What do the authors mean by this?  Does this mean that inductive reasoning is not always a reliable form of reason? What other examples from science can you think of to illustrate this quote?

Sources:

Das, Gunajyoti & Mandal, Shilpi. (2013). Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides. Biochemistry research international. ResearchGate. Accessed on 2 October, 2018
https://www.researchgate.net/figure/Chemical-structures-of-selenocysteine-Sec-and-pyrrolysine-Pyl_fig1_258037372

Dinmann, J. (2012). Control of gene expression by translational recoding. Advances in Protein Chemistry and Structural Biology via ScienceDirect. Accessed on 2 October, 2018. https://www.sciencedirect.com/topics/neuroscience/pyrrolysine

Gutiérrez-Preciado, A., Romero, H. & Peimbert, M. (2010) An Evolutionary Perspective on Amino Acids. Nature Education. Accessed on 2 October, 2018.
https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445

Rother, Michael, and Joseph A. Krzycki. “Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea.” Archaea 2010 (2010): 453642. PMC. Web. 2 Oct. 2018.

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2.3 Carbohydrates and Lipids

Evaluating claims—health claims made about lipids in diets need to be assessed. (5.2) (IBO; 39)

This NOS links nicely to to syllabus knowledge statements:

  1. Unsaturated fatty acids can be cis or trans isomers. (IBO; 39)

  2. Application: Scientific evidence for health risks of trans fats and saturated fatty acids. (IBO; 39)

  3. Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids. (IBO; 39)

The concept of evaluating claims also lends itself to TOK.  Thus it is possible to teach necessary content, the NOS and provide TOK integration, all in the one lesson.  This is the best way, in my opinion, to incorporate the NOS (or TOK for that matter)- not as “additional content” but complementary to the learning that is already going on.

The first lesson involves covering the understandings: the molecular structure of fatty acids, the differences between saturated and unsaturated FAs and the difference between cis and trans unsaturated FAs.  This covers the content needed.  In our next lesson, the students are placed in groups and have one of the following four articles allocated to them:

We should ban Trans Fats – The Guardian

Dairy Products Don’t Cause Heart Disease– The Guardian

Are Fats Bad? – New York Times

Butter is Back – New York Times

As part of their reading, the students are asked to identify the First Order Knowledge Claims made in the article.  These are claims about knowledge within specific subject areas – for instance, Trans fats increase the risk of heart disease.

The students then share their knowledge claims on the board, using the Sustainability Compass (Compass Education). The board is divided into the four compass points (N, E, S, W), representing the four key dimensions of sustainability: NatureEconomySociety, and Well-being. This adds another layer to the discussion by having the students incorporate systems thinking – environmental effects of industrial animal farming, econmoic impacts of chronic health problems, the personal impacts of diet choices and lifestyles etc.

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The Sustainability Compass (Compass Education

The next part is, as a class, to select 3-5 of these First Order Knowledge Claims and identify the TOK concepts and vocabulary that match them best and to then develop them into Second Order Knowledge Claims.  These are the focus of TOK – claims about the nature of knowledge.  Students must be able to distinguish between first and second order claims as a central part of their TOK course. The final task is to develop the second order knowledge claims into appropriate knowledge questions (open-ended, general and about knowledge) – which are cornerstone of the TOK presentation and essay.

Screen Shot 2017-09-27 at 4.31.36 PMScreen Shot 2017-09-27 at 4.32.01 PM

Ideally, we do this in one 85-minute lesson, though if you set the reading for homework it would be possible to complete this in a shorter period.

Thanks to Camille Garewal (@CDolmont) for pictures and inspiration for this post.

Sources:

IBO. Biology Guide: First Assessment 2016. IBO, 2014.

“Compass and Accelerator Tools.” Compass Education, AtKisson, 10 Aug. 2017, http://www.compasseducation.org/resources/compass-and-accelerator/.

IBO. Theory of Knowledge Guide: First Assessment 2015. IBO, 2013.

“Sustainability Compass.” Accelerator Pro, AtKisson, 2017, atkisson.com/tools/.

1.3 Membrane Structure

Falsification of theories with one theory being superseded by another—evidence falsified the Davson-Danielli model.

As we saw with Watson and Crick, models play an important role in developing knowledge in biology.  This is particularly important when studying microscopic structures. Davson (a physiologist) and Danielli (a chemist) proposed a model in 1935 that was based on twin layers of protein surrounding the membrane – a protein bilayer.

This was based on studies dating back to the 1890s. In particular, the work of Gorter and Grendel was instrumental in establishing that the membrane consisted of a lipid bilayer. The Davson-Danielli model appeared to be confirmed by subsequent electron micrographs taken in the 1950s that showed a darker band, thought to be protein, surrounding a lighter  core of phospholipids. One of the key tenets of this model was that the protein layer was embedded within the bilayer, thus preventing the phospholipids from moving around.

This model was adapted by Robertson in 1959 to have the protein layer on top of, but not embedded within, the membrane.  In his model, the internal layer was proposed to be composed of either polysaccharides or polypeptides.

Capture
Robertson Model – 1959 (Nuffield Foundation)

Developments in microscopy techniques, however, soon led to the revision of this theory and its replacement with the Singer-Nicholson model, which is the basis of our understanding today. They based their model on Freeze-Fracture techniques, which involved rapidly freezing cells and then fracturing them. This fracture plane is between the phospholipid bilayer.  Visible in these micrographs were a series of bumps or protrusions – which turned out to be the integral proteins embedded within the membrane.  The structure of the proteins themselves were also able to be studied in more detail and it was revealed that they were globular, rather than fibrous,  and thus unlikely to be find in a structural role. From this developed our modern understanding of a fluid, phospholipid bilayer containing a range of peripheral and integral proteins within it.

Freeze-Fracture Image (Childs)

We can summarise the development of membrane understanding over time like so, in the format of Scientist(s) – model – evidence – year:

  1. Gorter and Grendel – the phospholipid bilayer – extraction and measurement of cell membrane lipids – 1924
  2. Davson and Danielli – the lipid-protein sandwich – electron microscopy – 1935, revised 1954
  3. Robertson – modified lipid-protein sandwich model – electron microscopy – 1959
  4. Singer and Nicholson – fluid mosaic model – freeze/fracture microscopy – 1972

 

The current TOK Guide tells us that:

The methods of the natural sciences based on observation of the world as a means of testing hypotheses about it are designed to reduce the effects of human desires, expectations and preferences, in other words they are considered objective. (p36).

In what ways does this example demonstrate this? Why is it important to understand theories that are no longer used? If our understanding of science is dependent on technology, and technology is continually advancing, will we ever arrive at a single, final understanding of the natural world?

Sources:

Historical Development of Membrane Structure:

Childs, G. “Membrane Structure and Function.” Membrane Structure and Function. N.p., 19 July 2001. Web. 27 Jan. 2015.  http://163.178.103.176/Fisiologia/general/activ_bas_3/Membrane%20Structure%20and%20Function.htm

Eichman, P. “From the Lipid Bilayer to the Fluid Mosaic: A Brief History of Membrane Models.” SHiPS Resource Center || History of Biological Membranes. SHiPS Resource Centre, n.d. Web. 26 Jan. 2015. <http://www1.umn.edu/ships/9-2/membrane.htm&gt;.

“Lesson B: Cell Membranes.” Teaching about Science. The Nuffield Foundation. Web. 26 March, 2019. http://www.nuffieldfoundation.org/teaching-about-science/lesson-b-cell-membranes

Original Published Articles

Danielli, J. F., and H. Davson. “A Contribution to the Theory of Permeability of Thin Films.” Journal of Cellular and Comparative Physiology 5.4 (1935): 495-508. Wiley Online. Web. <http://onlinelibrary.wiley.com/doi/10.1002/jcp.1030050409/abstract&gt;.

Singer, S. J., and G. L. Nicolson. “The Fluid Mosaic Model of the Structure of Cell Membranes.” Science 175.4023 (1972): 720-31. Web. 27 Jan. 2015. <http://life.umd.edu/cbmg/Faculty/song/688D/Paperdiscussion/Singer%20and%20Nicolson%201972.pdf&gt;.

Other:

Allott, Andrew, and David Mindorff. Biology: Course Companion. Oxford: Oxford UP, 2014. Print.

Diploma Programme Theory of Knowledge Guide. Publication. Cardiff: IB, 2013. Print.