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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2.5 Enzymes

Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. (3.2)
This links to Practical 3 – Experimental investigation of a factor affecting enzyme activity.

Working with enzymes is something that all biology students get very familiar with over their studies!  This is particular true in the new syllabus as Practical 3 requires an enzyme experiment and they are popular as topics for the IA.

IMG_2768
Testing the effect of substrate concentration on potato catalase.

Although there are several other practical-themed NOS statements, this one makes particular reference to the idea of reliability and replicates.  In terms of assessment this is most likely to appear in the Section A of Paper 3, when students are provided with experimental scenarios and have to apply their knowledge. However, it is also important for the IA.  The chosen investigation must design a methodology that will collect sufficient data, the data must be processed with appropriate awareness of uncertainties, and the reliability of the results reviewed and evaluated in the conclusion and evaluation.

This is thus an important lesson to not just experience the practical side of biology, but to understand the importance of replicates and how this impacts the IA.  So what could this look like? Here are a few ideas:

  • If an enzyme-based experiment, aim for five variations of the independent variable (five different pHs; five different temperatures etc). As enzyme experiments are invariably time-based, this will allow you to plot a graph with more confidence (five data points rather than, say, three).
  • Try to repeat each variation five times.  This will provide enough data to calculate the average and standard deviation. Of course there are more processing options than this (think rate of reaction) but these two are the basics.
  • The conclusion/evaluation needs to then assess how the range of the independent variable, the sample size and the processed data contribute to the reliability of the experiment. The more replicates you have, the more robust this section will be.
  • There are always time constraints on how many replicates you can collect – so factor this into your methods.  If your experiment is only collecting data for three minutes for each run, then you should be able to get more replicates (and you will be expected to collect more data).  If, in contrast, you are collecting data for more than an hour per experiment, then you will need to be aware of this.
  • Finally, remember that design, processing and evaluation are all relative to the specific experiment you carried out – so always think in terms of the context for your investigation and the resources available to you.

 

5.1 Evidence for Evolution

Looking for patterns, trends and discrepancies—there are common features in the bone structure of vertebrate limbs despite their varied use.

This Nature of Science statement fits neatly into the syllabus content for this topic.  One of the applications for 5.1 is – “Comparison of the pentadactyl limb of mammals, birds, amphibians and reptiles with different methods of locomotion.” (IBO, p67). Thus understanding the importance of the pentadactyl limb as an example of a homologous structure should allow you to understand it as an example of seeking patterns, trends and discrepancies.

All amphibians, birds, reptiles and mammals descended from a common ancestor that had a tetrapod (4-legged) body plan and lived some 360 million years ago. However, as the different vertebrate groups then radiated outwards, this basic structure became adapted for different functions, some more radically than others.  Snakes have lost their legs, birds developed their forelegs into wings and whales and icthyosaurs returned to the water, with fore limbs adapted for paddling. However, despite these differences in function, an analysis of anatomy shows the same underlying structure.

The pattern is the repeated form of bone and limb structure (1 long bone-2 shorter bones-smaller bones-5 digits); the trend is that this developed among all four tetrapod classes and the discrepancies are the evolution of different functions and forms (wings-flying; flippers-swimming; arms-grasping etc. )

Vertebrate limb
Homologous Tetrapod Limbs (University of California Museum of Palaeontology)

 

As Stephen Jay Gould wrote, “Why should a rat run, a bat fly, a porpoise swim and I type this essay with structures built of the same bones unless we all inherited them from a common ancestor? (Gould, 258).

 

Gould, Stephen Jay. Hen’s Teeth and Horses Toes. New York, Penguin. 1990. Print.

“Homologous Tetrapod Limbs (4 Of 6)”. Evolution.berkeley.edu. University of California, Museum of Paleontology, 2016. Web. 24 May 2016.

IBO. Biology guide: First assessment 2016. Cardiff, IBO. 2014. Print.

3.4 Inheritance

Making quantitative measurements with replicates to ensure reliability. Mendel’s genetic crosses with pea plants generated numerical data.

Gregor Mendel, the “Father of Genetics”, made his discoveries on inheritance by using the garden pea, Pisum sativum. Mendel’s experiments and data collection over eight years formed the foundation of theoretical genetics and were able to be used in diagnosing and explaining genetic diseases at the turn of he 20th-century.  Just as important as his discoveries, though, was his meticulous following of the scientific methods, illustrating perfectly that replicates in quantitative experiments allow for greater reliability in the conclusions.

peas
The seven traits Mendel studied (Griffiths et al.)

Mendel worked with the seven traits outlined above and bred them for two years to establish pure, or homozygous, breeding strains. He then pollinated the parental flowers that showed variation in the trait – for example, crossing purple flowers with white flowers.  This produced in the F1 generation 100% purple flowers.  When these flowers were self-pollinated, Mendel noticed a curious relationship in the F2 offspring: a ratio of almost exactly 3:1 in the phenotype.

Screen Shot 2016-05-02 at 3.24.45 PM
The data of the F2 ratio from Mendel’s experiments, a total of over   18, 000 breeding experiments. (Griffiths et al.)

On the basis of this data, Mendel was able to draw key conclusions about the nature of inheritance.  These were:

  1. The existence of what we now know as genes.
  2. That these genes come in pairs
  3. Gene pairs segregate during the production of gametes
  4. Each gamete thus only contains one gene of a pair.
  5. Fertilisation is random

These statements were able to be tested by a new round of experiments, because they were based on quantitative data, had significant repetition and suggested certain patterns in inheritance.  His subsequent experiments provided confirmation of his analysis.  Not bad, considering the structure of DNA wouldn’t be determined for another century!

Mendel also did some interesting work on dihybrids, but that’s for a later topic!

Sources:

Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. Mendel’s experiments. Web. May 2, 2016.

Miko, I. Gregor Mendel and the principles of inheritance. Nature Education 1(1):134. 2008. Web. May 2, 2016.

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.

A.4 Innate and learned behaviour

Looking for patterns, trends and discrepancies—laboratory experiments and field investigations helped in the understanding of different types of behaviour and learning.

Both laboratory experiments and field investigations have been essential in understanding animal behaviour and learning.  Both forms of investigation are necessary: lab experiments allow for the precise control and manipulation of variables, but provide an artificial setting; field investigations provide the natural setting required but can face challenges in controlling the boundaries of the experiment.

A classic 1950s lab study investigated mimicry in butterflies in the lab by providing caged birds with different species and recording their feeding behaviour (van Zandt Brower, 1958). This was based on the observed toxicity of monarch butterflies (Danaus plexippus) and its presumed mimic, the viceroy butterfly (Limenitis archippus). The butterflies were prevented from flying by folding the wings together and then presented to the birds. Control butterflies that did not mimic the coloration of the monarchs  were eaten in every trial by all birds. The monarch was not eaten in any of the trials and the butterfly that mimicked the coloration of the monarch (the Viceroy) was similarly avoided.  The study helped expand our understanding of mimicry and bird foraging behaviour in a very controlled setting.

In contrast, field studies have a range of challenges in ensuring that the behaviour observed is free of bias or manipulation by the presence of the observers. One recent interesting study investigates foraging behaviour of harbour seals in Alaska (Womble et al.). Dive duration and depth were inversely correlated with prey density, which depended on the habitat of the seals (glacial or terrestrial). As part of the investigation, seals had to be captured, sedated, weighed and fitted with data logging devices to record temperature, time and depth. They were then released and the data provided by the devices used to determine their foraging strategy. Obviously, there is some invasiveness in this method, but it does enable the researchers to then collect data on the natural feeding behaviour of the seals.  Field studies regularly involve such trade-offs. Similarly to lab experiments, they must also acknowledge the potential ethical concerns of these studies.

Screen Shot 2016-03-15 at 10.05.26 AM
Data from Womble et al. (2014; p1368)

Extension: Using the graph above, consider the following possible DBQ-style questions:

  1. State the average dive depth for both locations at hour 12. (1)
  2. Compare and contrast the data for terrestrial and glacial seals over the 24 hour period. (2)
  3. Using the data, evaluate the hypothesis that glacial seals spend more time foraging than terrestrial seals. (3).

Sources

Jane van Zandt Brower. “Experimental Studies of Mimicry in Some North American Butterflies: Part I. The Monarch, Danaus Plexippus, and Viceroy, Limenitis Archippus Archippus”. Evolution 12.1 (1958): 32–47. Web. Mar 15, 2016.

Womble, J.N. et al. “Linking marine predator diving behavior to local prey fields in contrasting habitats in a subarctic glacial fjord.” Marine Biology 161. (2014): 1361–1374. Web. Mar 15, 2016. Full-text available for download at: https://www.researchgate.net/publication/261870558_Linking_marine_predator_diving_behavior_to_local_prey_fields_in_contrasting_habitats_in_a_subarctic_glacial_fjord 

1.4 Membrane Transport

Experimental design—accurate quantitative measurement in osmosis experiments are essential. (3.1)

This is one of the NOS that is relatively easy to incorporate into your learning.  Prescribed practical 2 is Estimation of osmolarity in tissues by bathing samples in hypotonic and hypertonic solutions; when you do this lab, you get a first-hand experience in why these measurements are important.

In my class we use potatoes and sucrose solutions of 0.1-0.5M, plus distilled water. We cut them into approximately equal-sized “chips” and place them in test tubes containing each of the six solutions.  Next class (or within 24h) we then remove them, measure again and investigate the changes.

While the potatoes are bathing in the solutions, we discuss the NOS as a class.  Here are some of our talking points:

  • The movement of water, which will influence the change in size of the potatoes, is likely to be small. Thus accurate measurements are needed to demonstrate that there has indeed been change, rather than just random variation.
  • Following on from this, the more measurements that can contribute to the data, the more accurate picture we might have – thus we need to accurately measure length, height, width and mass.
  • Accurate replicates will enable us to process the data to investigate any changes with confidence.
  • Measuring grams/mm requires careful attention to the uncertainties attached to those measurements.
  • While qualitative data is still important, it is less objective than accurate quantitative measurements.
  • These measurements need to be coupled with carefully controlled variables to allow the most accurate conclusion to be drawn.