Category Archives: Chemistry of Life (Core & AHL)

Hybrid Hearts: Stem Cell Transplants 2.0

“Can we use stem cells to make a new heart/eye/lung/liver etc?”

This is the predictable and perennial question that comes up from at least one student when we are looking at stem cells, genetic engineering, cell differentiation and transplanting. Until now, the answer has (perhaps in an oversimplified way) been ‘no’.

We can use stem cell transplants to treat lymphoma. Recently a young woman had a trachea transplant based on stem cell technology. Skin grafts from a patient’s own cultured cells are also possible, as are stem cell-based bladders. However, these are all rather simple technologies.

To treat lymphoma, bone marrow cells are replaced, and are all the same. The trachea transplant was a pre-existing trachea simply coated in the patient’s stem cells to prevent immune rejection. Skin transplants are basically sheets of epidermis that cover a wound, yet do not have the intricate functions of original skin: temperature regulation, secretion, senses. The bladder is a bag.

The challenge with using stem cells to transplant a more complex organ, such as a heart, is that it is not a simple sheet made of one type of cell. It is complex 3D structure, with a range of cells performing specific tasks within the organ. These cells have differentiated to perform their functions: cardiomyocytes (beating cells), vascular endothelial cells (smooth internal surfaces) and smooth muscle cells (blood vessel walls).

How can we get the stem cells to become the right type of cell, in the right position?

The answer to this question could be the key to opening up new doors in the search for viable transplantable organs in medicine, and bears much in common with the trachea case. It also marks a return to form for the NewScientist YouTube channel, who have this short clip of the new hearts in action:

A full article to accompany the footage is here.

In a nutshell:

Decellularised pig heart: the scaffold (NewScientist)

Decellularised pig heart: the scaffold (NewScientist)

1. Find a suitable transplant organ, such as a pig’s heart.

2. Strip of all cells and DNA, using a detergent. Only the collagen ‘scaffold’ remains, as in the image of the decellularised heart to the right.

3. Coat the scaffold with the recipient’s stem cells.

4. Ensure that the blood supply is adequate and will provide the right signals for differentiation.

What is amazing in this case is how the cells ‘knew’ what specialised cells to become. The leader of the research group, Dr. Doris Taylor, puts it down to the mechanical stimulus of the pressure of the blood in the vessels and chambers and chemical signals from growth factors and peptides that remained on the stripped heart structure.

They even went as far as replacing a healthy rat’s heart with one of these new hybrid hearts. The rat survived for the trial, but she says they need to focus on producing more muscular hearts in order to ensure long-term survival of transplant recipients.

Food for thought:

Read the whole article and some of the links within it. Discuss these questions:

1. What are the potential uses for this kind of transplant technology?

2. What are the current limitations of this method and how might they be overcome?

3. What are the ethical issues related to using hybrid (pig-human) organs in medical transplants? How would you feel if you were the patient?

4. Who are the various stakeholders in this technology and what are their viewpoints?

Useful Sources:

Dr Doris Taylor’s research page from the University of Minnesota

NewScientist Article: Hybrid hearts could solve transplant problem

BioAlive stem cells links and resources

Can stem cells repair a damaged heart? from the NIH

Research reveals how stem cells build a heart, from Harvard news.

Periodic Table for Biologists

Shortlink to this page:

Periodic Table for Biologists, AO printable version (.png, 3MB). Last updated Jan 2013.

Click on this link to go to the periodic table page and download the A0 poster:

MOLO: The Molecular Logic Project

The Molecular Logic Project aims “to improve the ability of all students to understand fundamental biological phenomena in terms of the interactions of atoms and molecules”. They achieve this with an extensive database of online java-based simluations and models for students to use. The animations are simple, and there are a lot of activities to choose from. To make it work, you’ll need to install their software.

Some highlights for IB Bio:

How do mutations affect protein folding?

How does gene mutation affect protein folding?

How does gene mutation affect protein folding?

Sickle cell anemia

Cell growth and regulation


Properties of Water

And loads more here: Biology, Molecular Biology (Chem of life), Physics/Chemistry.

Genetics – Megapost

Get the Essential Biology 04 – Genetics Revision guides here:  Standard LevelHigher Level

Top websites:

Learn.Genetics@Utah awesome resources

Click4Biology Genetics pages: CoreHigher Level

BioEthics Education Project: The Human GenomeGenetic Technology

And as always, click on the shadowed images in the presentations to be taken to source videos and animations.


Here are all the presentations for the Genetics topics.


More presentations after the jump…

Read the rest of this entry

Attenborough on Darwin: The Tree of Life

This is on my shopping list for sure – and one of those rare occasions I miss British TV. Attenborough kicks the Year of Darwin off with his new documentary, The Tree of Life. Sadly the BBC iPlayer thingy is only available in the UK, though I’m sure some will know how to fool it – if you hurry there are a few days left to download it!

Here’s the man himself (Attenborough, not Darwin – that would be cool) in an interview with Nature magazine:

And if you’re up for an interesting quick read, here are the Top Ten Myths of Darwin from The Rough Guide to Evolution blog.

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.

Check out this article on the potential use of an enzyme in second-generation biofuels.

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

A full collection of savable enzyme animations from Husam Medical

And John Giannini’s Enzyme collection is nice and clear.

Enzyme activity and kinetics

Nice virtual lab from

Enzyme kinetics from Wiley Interscience


Protein denaturation from McGraw Hill


Complete tutorial from Wiley Interscience

What is an enzyme? from Northland

Feedback (end product) inhibition from McGraw Hill

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.


Core (for everyone):

Click4Biology page


Additional Higher Level:

Click4Biology page: TranscriptionTranslation


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 – 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)


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

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:

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.

Revision materials:

Click4Biology pages: Core & HL

Wikipedia page

Here is the top-rated video on the subject on YouTube:

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.



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 :

  • 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

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.

Parthenogenesis in sharks

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.

So can it work in us?

Let’s let House MD explain:

In short, no. Not naturally.

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.

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?

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?


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.

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:

And here’s a very stylized video of DNA structure from Hybrid Medical Animation. See if you can narrate it:

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:

%d bloggers like this: