Enzymes (Core and AHL & C2)
Covering the core and AHL/ SL Option C content, here is a rundown of enzymes, from active sites to end-product inhibition. Again, there are lots of animation resources out there, many of which are used in the presentation – click on the shadowed images to go there.
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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:
Protein Synthesis: Transcription and Translation (2009)
This is a re-post for the class of 2009 to revise and the 2010 group to catch on the first time… As always, click on the shadowed images for a link to an animation, or visit the links posted below.
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Core (for everyone):
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Additional Higher Level:
Click4Biology page: Transcription – Translation
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Further resources:
There are many decent Flash animations and the like on the internet, but the majority cannot be embedded. Below this YouTube video, there are some direct links to resources, some of which can be easily saved.
Learn.Genetics @ Utah
Transcribe and Translate (good, basic, interactive)
How do fireflies glow? (puts it in context)
University of Nebraska:
Protein Synthesis overview (Good enough for SL)
Transcription Details (fits DP Bio HL very well)
Translation Details (fits DP Bio HL very well)
John Kyrk: (visit the parent site at www.johnkyrk.com – excellent)
Transcription (fits DP Bio HL very well)
Translation (fits DP Bio HL very well)
St. Olaf College
Transcription (clear and simple)
Translation (clear and simple)
EDIT: Two more animations (from mrhardy’s wikispace, original source unknown)
WH Freeman
RNA Splicing tutorial (HL only)
Bio3400
Translation with a genetic code dictionary (shows position in the ribosome)
Some more in-depth animations (newly added):
Translation from Wiley Interscience
Translation from LSU Medschool
Translation from The Chinese University in Hong Kong
Protein targeting from Rockefeller University
The Transport System (Core and HL-FHP)
The Transport System (Core)
Click4Biology page here.
And loads of useful links from North Harris College.
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Higher Level Students:
Download here: transport-system.ppt
And here’s the Click4Biology link
Medmovie.com has a large collection of animations which are great for this unit. We can’t link to them directly, but it’s worth having a look around.
The Cardiac Cycle:
Hyper Heart animation and graphs from the Chinese University of Hong Kong
Biointeractive from the Howard Hughes Medical Institute
Control of the Heart Beat:
A few good links to try from Washburn Rural High School
And don’t forget the Medmovie resource…
Atherosclerosis and Coronary Heart Disease:
Medmovie has good animations for atherosclerosis, heart attacks and heart bypass surgery. There aren’t many that are better…
Production of Tissue Fluid and Lymph:
Hydrostatic and osmotic pressure (fluid exchange) from McGraw Hill
Capillary exchange from coolschool.ca (they have other good resources, too)
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Bonus features:
For a good (tricky) prac, here’s a virtual EKG package from skillstat.com
And here’s a decent heart structure tutorial from Gateway Community College
And why not have a go at open heart surgery from abc.net.
DNA Replication (Core and AHL)
This topic is well-resourced on the internet – almost too well! Standard level students need to know the bare basics, which equates to the process of replication of the leading strand for the HL students. Here is the presentation, with some good links to follow:
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DNA Replication animations:
St. Olaf’s nice and clear animation.
Another clear one from Wiley.
Nicely illustrated one from Harvard.
John Kyrk’s complicated molecular animation.
The Meselsohn Stahl experiment from Sumanas.
More animations from North Harris College and from LearnersTV.
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Revision materials:
Click4Biology pages: Core & HL
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Here is the top-rated video on the subject on YouTube:
Nature’s YouTube Channel (and some others)
On the heels of the NewScientist YouTube channel we have the offering from Nature. Where NewScientist provides a news-style clip of current Science headlines, Nature’s YouTube channel takes the approach of a video background to articles published in their journal. So far they have ten videos, though they provide useful background to articles such as the Antikythera mechanism, whale evolution and this one on sequencing the platypus genome:
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It’s an encouraging trend to see these journals reach out into internet video publishing – cheap, easy and a great starting place for students getting involved in science. Let’s hope Nature can keep their channel going longer than ScientificAmerican, who started strongly but seem to have given up.
Of course, the bees knees of YouTube channels so far are NationalGeographic, with 847 videos to date. Here’s a gratuitous Great White clip:
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JoVE
Another great channel (though not on YouTube) is the Journal of Visualised Experiments – actually publishing scientific research papers as videos. A good idea, and some really effective videos – especially for letting us see what is going on in the experiment or operation. Unfortunately, their videos can’t be embedded, so get yourself on over there and have a look.
Now comes the question of citing online videos in your work – and here is the answer! (pdf)
Other ‘tube’ resources worth a look are DNAtube and TeacherTube.
Parthenogenesis – Virgin Births in Nature
Happy (belated) Christmas!
How do you really reproduce without sexual reproduction? Asexual reproduction, of course. Simple, really… but not for the females of some species.
There are loads of links in this post, so click on them to learn more.
Parthenogenesis
Some plants, insects, shark and lizard species are known to reproduce by parthenogenesis – embryo development is carried out without fertilisation by a male -so called ‘virgin creations.’
Parthenogenesis can take a range of pathways :
- The egg can be fertilised by a polar body (a ‘leftover’ of egg production), making the chromosome number diploid and triggering embryo development. Here is a simple explanatory animation from amateurmicrography.net.
- Chromosomes in the egg can self-replicate, making up the diploid number and the embryo develops from there.
Other methods include suppression of male genotypes (technically still sexual reproduction?), or eggs cells dividing by meiosis.
The resulting offspring are going to be all the same gender. In some species, the XY system determines gender and parthenogenesis produces all females. In other, the ZW system dictates that they will all be male.
Parthenogenesis is a reproductive strategy that sacrifices the genetic variation (a driving force of evolution) of sexual reproduction for the simple ability to reproduce. Small invertebrates, such as aphids, can use it to produce large numbers of females very quickly.
Komodo Dragons
Larger organisms, such as Komodo dragons (Indonesia link!), have been known to use parthenogenesis in the absence of males, producing an all-male clutch of eggs. It is thought that this might allow them to set up new populations on isolated islands, using just a single female. Here’s a quick video of a Komodo dragon parthenogen hatching:
Some interesting Komodo readers here from Richard Dawkins and Not Exactly Rocket Science.
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Parthenogenesis in sharks
Parthenogenesis has also been observed in captive sharks – the female had no access to males, yet gave birth to live young (though only one, where the normal litter would be larger). Genetic tests confirmed parthenogenesis, rather than the alternative hypothesis of superfecundation (storing sperm for a long period of time). Read the full paper here, and another on hammerheads here. BBC audio explanation here.
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So can it work in us?
Let’s let House MD explain:
In short, no. Not naturally.
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Generally, we use mitosis to replace and repair damaged cells and tissues and for growth and development – filling in the gaps with copied cells. Along the way, our cells differentiate to their function and we end up with a body full of specialised cells – each cell’s structure and biochemistry reflect its function.
We don’t use mitosis for reproduction, as it narrows genetic variation – one of the driving forces of evolution. Instead, when sperm and eggs are produced, meiosis is used – producing daughter cells with half a set of chromosomes. During meiosis, crossing over occurs, giving some recombinants – or ‘mixed up’ chromosomes – leading to some varation. The greatest variation comes from the process of sexual reproduction itself – the gametes – sperm and egg – meet in fertilisation, combining their chromosomes to make a new blastocyst, which becomes an embryo, then a fetus and out pops a baby.
All the offspring of organisms that reproduce sexually carry two copies of each chromosome – one from each parent – and each chromosome carries different alleles – ‘versions’ of each gene. This leads to a great deal of variation and this genetic diversity keeps the the population going.
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What about uses in technology?
Funny you should ask that…
Induced parthenogenesis is being pursued as a method for obtaining embryonic stem cells. Read this New Scientist article to learn more.
The disgraced Korean scientist Hwang Woo-Suk, who shot to infamy after faking stem cell results, was actually and inadvertently pivotal in the use of parthenogenesis as a method to produce human embryonic stem cell lines:
Normally these parthenogenic embryos die after a few days, yet researchers are able to harvest them for stem cells for research. Ethically, these are considered engineered eggs, rather than human embryos. How do you feel about that?
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Questions to think about:
1. How does parthenogenesis differ from binary fission in bacteria, or vegetative reproduction in some plants?
2. How do the XY and ZW gender systems work?
3. How does sexual reproduction lead to genetic variation?
4. What are the costs of parthenogenesis in terms of evolution or resistance to disease?
5. How would the genetic fingerprint of a parthenogen differ from its parent?
6. How would researchers use genetic fingerprinting to determine whether the offspring were parthenogens or were the product of sexual reproduction?
7. What are the ethical considerations of using parthenogenic human ambryonic stem cells?
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References:
Chapman et al. Parthenogenesis in a large-bodied requiem shark, the blacktip <i>Carcharhinus limbatus</i>. Journal of Fish Biology, 2008; 73 (6): 1473 DOI: 10.1111/j.1095-8649.2008.02018.x
Chapman et al. Virgin birth in a hammerhead sharkBiol Lett. 2007 August 22; 3(4): 425–427. Published online 2007 May 22. doi: 10.1098/rsbl.2007.0189.
2000 year-old Greek “computer” recreated
A British curator has recreated an ancient proto-computer, the Antikythera device, based on 2000 year-old salvaged parts, X-ray tomography and huge patience – and got it to work!
As you can see in the NewScientist video, it was an example of a mechanical computer – designed to pr
edict the relative positions of the planets, chart astrology and count down to the Olympics.It shows us just how advanced Greek science was, and makes us wonder – what would have happened if this technology had not been lost? Would the Greeks have been playing Spore in 200AD?
Some questions to think about:
– What makes this a computer?
– What sets it apart from an old alarm clock?
– Where do you think we would be now if this knowledge hadn’t been lost?
Digestion: Core and Higher Level
Here is the presentation for the Core section:
Class Notes to fill in here (pdf download – A3 size)
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Some good links:
Enzyme activity animations from McGraw Hill, Northland College and KScience.co.uk
A great animation/tuturial on digestion of different types of foods from kitses.com
And an introduction to absorption(and villi):
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Higher Level Content for the Further Human Physiology topic:
Class Notes to fill in are here (pdf file)
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Some links:
Click4Biology Digestion FHP page
North Harris College animations collection
Gastric secretion animation from McGraw Hill
Digestion of lipids from ZeroBio
Heliobacter pylori and gastric pathology from Johns Hopkins
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Absorption of Digested Foods:
Class Notes to fill in here (pdf download)
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Villi structure from the University of Lanacaster and 3d4 Medical.com
Colorado State has animations for active transport.
Nutrition from JBPub.com has animations for passive transport, fat uptake, facilitated diffusion, endocytosis.
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And, of course, here are JD and Turk to tell us about the diagnostic miracle of egestion:
i-Biology 
