Blog Archives
Arsenic-Based Life! (On Earth) Feel the hype.
Arsenic-based lifeform, from XKCD webcomic. Click to go there.
The world has been all a-twitter with NASA’s news of a new life-form discovery. Putting ‘NASA‘ and ‘life-form‘ together in one sentence seems to have got a lot of people worked up that they have discovered life on other planets and that the invaders are coming, but really it’s all a bit closer to home and rather tamer.
GFAJ-1 bacteria - from NASA (link)
Closer to home, maybe, but still really interesting. These bacteria from Mono Lake in California are able (with a lot of lab-based prodding*) to use arsenic in place of phosphates to build the backbone of their DNA molecules. An interesting link to DNA structure there, and news-worthy in that this species has been able to substitute one fundamental element of living organisms for another, usually more toxic, molecule.
As always, for the best possible write-up of this primary research in the news, head on over to NotExactlyRocketScience. You can also read the original release from NASA.
IB Biology curriculum links:
- 3.3 DNA Structure (and AHL 7.1 here)
- 3.1 Chemical Elements and Water
- 2.2 Prokaryotes
- 2.1 Cell Theory (calculate the magnification)
Helpfully, TED has put together a playlist of related talks to put the discovery, and the search for ET, in perspective. Here’s one from Penelope Boston:
“Life on Mars? Let’s look in the caves.”
Live long and prosper.
*this clause is an edit to clarify.
Wade Davis – “The Plants Talk To Us” (TOK)
[Note: I wrote this in 2010 after seeing Wade Davis speak, and was reminded of it as I wrote Curriculum as a Compass?. I still love these stories – the ayahuasca one blows my mind. Stephen.]
……….o0O0o……….
I saw Wade Davis speak at the 2008 IB Regional conference, and he was brilliant. He gave an extended version of this talk from TED, and the focus on disappearing languages and cultures was brilliant. He really ventured into TOK, especially with the different ways of knowing demonstrated by various cultures.
There is a great example in the talk below of an amazonian shaman who makes a powerful psychoactive preparation of Ayahuasca, from a vine. Tryptamines are the active component and are similar to tryptophan (our famous amino acid/ end product inhibition example – animation). They act as neurotransmitters and include serotonin, which regulates mood. It is broken down by enzymes bound to the plasma membrane of cells in the digestive tract called monoamine oxidase (MAO), so can’t be taken orally. The amazing thing is the shaman uses a preparation from another plant that inhibits this enzyme, so that the potion can be ingested and is effective. This is amazing knowledge, gleaned from a totally alternative scientific method to the one we are used to, and demonstrates an advanced naturalistic intelligence.
When he asked how they knew this and were able to combine these two extracts from the thousands available, they answered “The plants talk to us.”
……….o0O0o……….
Discussion and questions:
1. In what ways can this specific example link the elements of the IB Biology course together?
Think about cells, membranes, amino acids, neurotransmitters, innate vs learned behaviour, reward pathways, evolution, enzymes and inhibition, genetics and the universality of the genetic code, ecology and conservation.
2. Think about the statement “other people, with their differences, can also be right” (from the IBO’s mission statement). To what extent is the ancient knowledge of indigenous cultures an example of this? What further questions does this inspire?
3. To what extent are these ways of knowing demonstrated in the contrast between modern scientific understanding of the effects of the active ingredients and the ancient wisdom of the shaman: sense perception, reason and emotion.
4. Discuss the impacts of disappearing cultures on scientific knowledge and understanding. How could modern science & technology be used to help preserve cultures and wisdom?
If you liked this, find out more about becoming an ethnobotanist!
Enzymes, Core and AHL/Option C
One great enzymatic dollop, for the core content and AHL/ SL Option C. Make sure you use this theory in your write-ups, can relate the action of enzymes to their structure as proteins and look for examples of enzymes in action throughout the course.
Essential Biology 3.6 & 7.6/C2: Enzymes
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Check out this article on the potential use of an enzyme in second-generation biofuels.
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Enzyme Basics:
What is an enzyme? from Northland (the best one – including inhibitors, pathways and feedback inhibition)
How enzymes work from McGraw Hill
Enzyme basics from KScience.co.uk
A full collection of savable enzyme animations from Husam Medical
And John Giannini’s Enzyme collection is nice and clear.
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Enzyme activity and kinetics
Nice virtual lab from KScience.co.uk
Enzyme kinetics from Wiley Interscience
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Denaturation:
Protein denaturation from McGraw Hill
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Inhibition
Complete tutorial from Wiley Interscience
What is an enzyme? from Northland
Feedback (end product) inhibition from McGraw Hill
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And here’s a quick run down on YouTube:
Proteins (AHL & C1)
Although we are learning this in the Chemistry of Life unit, it is actually part of the SL Option C and HL additional material, so look for the book chapters in the right place!
Essential Biology 7.5 & C1: Proteins
Proteins:
Life Cycle of a Protein from Sumanas
Making polypeptides from John Kyrk
Check that you know the different levels of protein structure, including the roles of hydrogen bonds and disulfide bridges. Think about how the properties of the R-groups on amino acids cause the protein to fold up in a set configuration.
FoldIt!
Make sure you can give examples of fibrous and globular proteins and that you can name some examples of uses of proteins that are not structural or related to the plasma membrane.
And don’t forget to play FoldIt – the brilliant protein puzzle that helps medicine!
DNA Structure (Core and AHL)
This is a short one – class presentation is here (click shadowed images for animations and movies):
Here’s a decent video from BBC AS Guru with David Suzuki:
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And here’s a very stylized video of DNA structure from Hybrid Medical Animation. See if you can narrate it:
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The story of the discovery of the double-helix structure is a good example international collaboration and competition, and led to the Nobel prize for Crick, Watson and Wilson (who we never hear about). You’ve got to feel for Rosalind Franklin – her work was key in their discovery and she wasn’t cited for it until after her death.
Here’s a great video, though the presenter sound like he has a mouth full of marbles:
Carbohydrates, Lipids and Proteins
Here’s the class presentation – click the shadowed images for animations.
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For more information on condensation and hydrolysis reactions:
Simple explanation by Terry Brown
Collection of examples from North Harris College
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Carbohydrates:
Explanation and animation from National Louis University
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Proteins:
Life Cycle of a Protein from Sumanas
Making polypeptides from John Kyrk
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Lipids:
Structures of Fats from HHMI
Lipids (and condensation animation) from National Louis University
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Proteins (AHL & C.1)
After the Carbohydrates, Lipids and Proteins last week, we’re taking a closer look at Proteins and their structures.
Here is the class presentation – click the shadowed images for links to animations:
Check that you know the different levels of protein structure, including the roles of hydrogen bonds and disulfide bridges. Think about how the properties of the R-groups on amino acids cause the protein to fold up in a set configuration.
Make sure you can give examples of fibrous and globular proteins and that you can name some examples of uses of proteins that are not structural or related to the plasma membrane.
The revision notes from Click4Biology are here.
Bio-Alive: a huge resource of animations and videos
Bio-Alive Biology and Life Sciences has a massive set of links to online tutorials, videos, animations, interactives, lectures and games. Huge. Loads.
One of the highlights has to be the video archive of surgical operations!
Follow these links for IB topic help:
Cells: animations – tutorials – virtual labs – lectures
Chemistry of Life: animations – tutorials – lectures
Genetics: animations – tutorials – virtual labs – lectures
Evolution: animations – tutorials – virtual labs – lectures
Or just visit their page for masses of links.
Foldit – help science by playing a game
Foldit is ridiculously addictive.
It is a protein-folding game/simulation, designed and produced collaboratively between the University of Washington’s Computer Science and Engineering and Biochemistry departments. There is a great introduction to the roles of proteins in metabolism and disease, as well as protein folding, on their about page.
Apart from the great software and in-game tutorials in protein structures, players at the highest level may be contributing to medicine! The University and associated labs are setting problems of protein folding for players to solve – each one an important molecule in its own right and some even the key to curing some diseases.
There is a great article about the game on RichardDawkins.net: ‘Computer game’s high score could earn the Nobel prize in medicine.’ There’s even a classic quote from co-developer Prof. David Baker:
“I imagine that there’s a 12-year-old in Indonesia who can see all this in their head.”
Too right. Let’s represent for Indonesia!
Here’s a quick clip of the game in action at a high level:
Download the game here and get playing!
Chemical Elements and Water
Here is the class presentation:
You can click on the shadowed images in the presentation to be taken to the animations and videos.
i-Biology 
