Because it has different levels of structure providing functionality
Keith S. Taber
I have been working on a book about pedagogy, and was writing something about sequencing teaching. I was setting out how well-planned teaching has a structure that has several levels of complexity – and I thought a useful analogy here (as the book is primarily aimed at chemistry educators) might be protein structure.
Proteins are usually considered to have at least three, or often four, levels of structure. Protein structure is not just of intellectual interest, but has critical functional importance. It is the shape, conformation, of the protein molecule which allows it to have its function. Now, I should be careful here, as I am well aware (and have discussed on the site) how the language we often use when discussing organisms can seem teleological.
We analyse biological structures and processes, and when considering the component parts can see them as having some function in relation to that overall structure or process. That can give the impression of purpose – as though someone designed the shape of the protein with a particular function in mind. That can give the impression of teleological thinking – seeing nature as having a purpose. The scientific understanding is that proteins with their complex shapes that are just right for their observed functions have been subject to natural selection over a very long period – evolving along with the structures and processes they are part of.
The importance of protein shape
The shape of a protein can allow it to act as a catalyst that will allow, say, a polysaccharide to break down into simple sugars at body temperature and at a rate that can support an organism's metabolism (when the rate without the enzyme would only give negligible amounts of product ). The shape of a protein, as in haemoglobin, may allow a complex to exist which either binds with oxygen or releases it depending on the local conditions in different parts of the body. And so forth.
Now, chemically, proteins are of the form of polyamides – substances that can be understood to have a molecular structure of connected amide units (above left, source: Wikipedia) in a long chain that results from polymerising amino acid units (amino acid structure shown above right, source: Wikipedia). An amino acid molecule has two functional groups – an amide group (-NH2) which allows the compounds to react with carboxylic acids (including amino acids for example), and a carboxylic acid group (-COOH) that allows the compound to react with amides (including amino acids for example). So, amino acids can polymerise as each amino acid molecule has two sites that can be loci for the reaction.
Special examples of polyamides
So, proteins are polyamides. But this does not mean that polyamides are proteins. In the same way that chemistry Nobel prize winners are scientists – but not all scientists are Nobel laureates. So, being a polyamide is a necessary, but not a sufficient, condition for being a protein. For examples, nylons are also polyamides, but are not proteins. 1
Proteins tend to be very complex polyamides, which are built up from a number of different amino acids (of which 20 are found in proteins). Each amino acid has a different molecular structure – there is the common feature which allows the peptide linkages to form, but each amino acid also has a different side chain or 'residue' as part of its molecule. But just being a large, complex, polypeptide built from a selection of those 20 amino acids does not necessarily lead to a protein found in livings things. The key point about the protein is that its very specific shape allows it to have the function it does. Indeed there are many billions of polyamide structures of similar complexity to naturally found proteins which could exist (and perhaps do somewhere), but which have no role in living organisms (on this planet at least!)
A simple teaching analogy often used to explain enzyme specificity is that of a lock and key. Whilst somewhat simplistic, if we consider that the protein has to have just the right shape to 'fit' the 'substrate' molecule then it is clear that the precise shape is important. A key that opens a door lock has to be precisely shaped. (The situation with an enzyme is actually more demanding, as the molecule can change its shape according to whether a substrate is bound – so it needs to be the right shape to bind to the substrate molecular and then the right shape to release the product molecule.)
So a functioning protein molecule has a very specific shape, indeed sometimes a specific profile of shapes as it interacts with other molecules, and this can be understood to arise from several levels of structure.
Four levels of structure
The primary structure is the sequence of amino acid residues along the polypeptide skeleton.
The chain is not simply linear, or a zigzag shape (as we might commonly represent an organic molecules based on a chain of carbon atoms). Rather the interactions between the peptide units, causes the chain to form a more complex three-dimensional structure, such as a helix. This is the secondary structure.
Because the secondary structure allows the amino acid residues on different parts of the chain to be close, interactions, forms of bonding, form between different points on the chain. (As shown in the representation of the insulin structure above.) This depends on the amino acid sequence as the different residues have different sizes, shapes and functional groups – so interactions will occur between particular residue pairs. This adds another level of structure.
Imagine taking a coiled cable somewhat like the helical secondary structure), such as used for some headphone, and folding this into a more complex shape. This is the tertiary structure, and gives the protein its unique shape, which it turn makes it suitable to act as an enzyme or hormone or whatever.
Proteins may be even more complex, as they may comprise complexes of several chains, closely bound together by weak chemical bonds. Haemoglobin, for example, has four such subunits arranged in a quaternary structure.
But what has this got to do with sequencing curriculum?
When planning teaching, such as when developing a course or writing a 'scheme of work', one has to consider how to sequence the introduction of course material as well as learning activities. This can be understood to have different levels in terms of the considerations we might take into account.
Primary structure and conceptual analysis
A fundamental question (once we have decided what falls within the scope of the course, and selected the subject matter) is how to order the introduction of topics and concepts. There is usually some flexibility here, but as some concepts are best understood in terms of other more fundamental ideas, there are more and less logical ways to go about this. 'Conceptual analysis' is the technique which is used to break down the conceptual structure of material to see what prerequisite learning is necessary before discussing new material.
For example, if we wish to teach for understanding then it probably does not make sense to introduce double bonds before the concept of covalent bonds, or neutralisation before teaching something about acids, or d-level splitting before introducing ideas about atomic orbitals, or the rate determining step of a reaction before teaching about reaction rate. In biology, it would not make sense to teach about mitochondria before the concept of cells had been introduced. In physics, one would not seek to teach about conservation of momentum, before having introduced the concept of momentum. The reader can probably think of many more examples. The sequence of quanta of subject matter in the curriculum sequence can be considered a first level of curriculum structure.
Secondary structure and the spiral curriculum
We also revise topics periodically at different levels of treatment. We introduce topics at an introductory level – and later offer more sophisticated accounts (atomic structure, acidity, oxidation…). We distinguish metals form non-metals and later introduce electronegativity. We distinguish ionic and covalent bonds and later introduce degrees of bond polarity. In recent years this has been reflected in the work on developing model 'learning progressions' that support students in more sophisticated scientific thinking over several grade levels.
This builds upon the well-established idea of a 'spiral curriculum' (Bruner, 1960) where the learner resists topics in increasing levels of sophistication over their student career. So, here is a level of structure beyond the linear progression of topics covered in different sessions, encompassing revisiting the same topic at different turns of the 'spiral' (perhaps like the alpha helices formed in may proteins).
This already suggests there will be linkages across the 'chain' of teachings units (whether seen as lectures/lesson or lesson episodes) as references are made back to earlier teaching in order to draw upon more fundamental ideas in building up more complex ideas, and building on simplified accounts to develop more nuanced and sophisticated accounts.
Tertiary structure – drip feeding to reinforce learning
The skilled teacher will also be making other links that are not strictly* essential but are useful unless the students have exemplary study skills usually ARE essential!]
To support students in consolidating learning (something that is usually essential if we want them to remember the material and be able to apply it months later) the teacher will 'drip feed' reinforcement of prior learning by looking for opportunities to revise key points form earlier teaching.
We have defined what we mean by 'compound' or 'oxidising agent' or 'polymer', so now we spot opportunities to reinforce this whenever it seems sensible to do so in teaching other material. We have taught students to calculate molecular mass, or assign oxidation states, or recognise a Lewis acid – so we look for opportunities to ask students to rehearse and apply this knowledge in contexts that arise in later teaching. At the end of a previous lesson everyone seemed to understand the difference between respiration and breathing – but it sensible to find opportunity for them to rehearse the distinction. 2
There is then a level of structure due to linkages back and forth between the components of the teaching sequence.
So where the 'primary structure' is necessary to build up knowledge in a logical way in order that the teaching scheme functions to provide a coherent learning experience (teaching makes sense at the time), and the secondary structure allows progression toward more sophisticated accounts and models as students develop, the 'tertiary structure' offers reinforcement of learning to ensure the course functions as an effective long term learning experience (that what was taught is not just understood at the time, but is retained, and readily brought to mind in relevant contexts, and can be applied, over the longer term).
Quaternary structure – locating the course in the wider curriculum experience
What about quaternary structure? Well, commonly a student is not just attending one class or lecture course. Their curriculum consists of several different strands of teaching experiences. At upper secondary school level, for example, the learner may attend chemistry classes interspersed with physics classes, biology classes and mathematics classes. Their experience of the curriculum encompasses these different strands. Likely, there are both salient and other less obvious potential linkages between these different courses. Conservation of energy from physics applies in chemistry and biology. Enzymes are catalysts, so the characteristics of catalysts apply to them. The nature of hydrogen bonds may be taught in chemistry – and applied in biology. In that case, it would be useful for the learners if the topic was taught that concept in the chemistry class before it was needed in biology.
And just as there may be aspects of logical sequencing of ideas across the strands to be considered, there may be other potential links where the teacher in one subject can draw upon, exemplify, or provide opportunities to review, what has been taught in the other.
| Level of structure | Feature of sequencing |
| primary structure | logical sequencing of concepts to identify and later build on prerequisites |
| secondary structure | spiral curriculum to build up sophistication of understanding |
| tertiary structure | cross-linking between lessons along strand to reinforce learning by finding opportunities to revisit, review, and apply prior learning |
| quaternary structure | cross links between courses to build up integrated (inter-*)disciplinary knowledge |
(* in a degree course this may be coordinating different lecture courses within a discipline; in a school context this may be relating different curriculum subjects)
Afterword
How seriously do I intend this comparison? Of course this is just an analogy. It is easy to see that it does not hold up to detailed analysis – there are more ways that curricular structure is quite unlike protein structure, and the kinds of units and links being discussed in the two cases are of very different nature.
Is there any value in such a comparison if the analogy is somewhat shallow? Well, devices such as analogies operate as thinking tools. Most commonly we use teaching analogies to help 'make the unfamiliar familiar' by showing how something unfamiliar is somewhat like something familiar. This can be a useful first stage in helping someone understand some new phenomena or concept.
In teaching science we commonly make analogies with everyday phenomena to help introduce abstract science concepts. Here I am using a scientific concept (protein structure) as the analogue for the target idea about sequencing teaching.
Read about scientific analogies
My motivation here was to prompt teachers (and others who might read the book when it is finished) who are already familiar with general ideas about curriculum and schemes of work to think about a parallel (albeit, perhaps a somewhat forced one?) with something rather different but likely already very familiar – protein structure. Chemists and science teachers are likely to already appreciate the different levels of structure in proteins, and how the different aspects of the nature of polypeptide chains and the links formed between amino acid residues inform the overall shape, and therefore the functionality, of the structure.
Perhaps this thinking tool will entice readers to think about how conceptual links within and between courses of study can support the functionality of teaching? Perhaps they will dismiss the comparison, pointing out various ways in which the level of structure in a well-planned curriculum are quite different from the levels of structure in a protein. Of course, if they can do that insightfully, I might suspect that this 'teaching analogy' will have done its job.
Work cited:
- Bruner, J. S. (1960). The Process of Education. New York: Vintage Books.
- Taber, K. S. (2021). Squaring the circle: Circumnavigating an ontological tension between practical learning progression models and the complex, multi-facetted, and meandering nature of conceptual learning. In M. N. Bowman (Ed.), Topics in Science Education (pp. 1-100). New York: Nova Science Publishers Inc.
Note:
1 Sometimes the term polyamide is reserved for synthetic compounds and contrasted with polypeptides as natural products.
2 This can be useful even when students 'seem' to have grasped key ideas. When they remember that 'everything is made of atoms' we may not appreciate they think that implies chemical bonds contain atoms. When they seem to have understood that cellular metabolism depends upon respiration, we may not appreciate they think that this does not apply to plants when the sun is shining.