A Great Team

One of the great things about my six months at Victoria University of Wellington has been being part of the marine natural products research laboratory.  The marine natural products group is lead by Associate Professor Peter Northcote.  A second natural products laboratory is headed by Dr. Rob Keyzers.  As well as marine natural products, Rob's group also investigates compounds that are important to the flavour of wine.  Researchers in both laboratories meet together once a week.  At these meetings members of the group update each other on their research and also on reading they have done about marine natural products research being carried out by other groups around the world.  Peter and Rob are busy academics who run courses, deliver lectures, oversee research and carry out a range of administrative duties.  Both, however, made time to take an interest in my research and to explain the relevant chemistry to me.

Below are profiles of the researchers I worked with in my laboratory.  As you will see, they come from a variety of backgrounds and few of them would have predicted that they would one day be carrying out high level chemical research.  (So keep an open mind and work hard because you too may one day end up doing something that right now you cannot even imagine.)  The researchers I worked with were really supportive of me and a lot of fun to be with.

Helen Woolner 

Helen is a Ph.D. student and has been my mentor – she has taught me all the techniques I have used in the

lab, explained the relevant chemistry and generally kept me on track. Helen attended Porirua College where

she was initially a diligent student but began to lose her way in Year 11 and ended up wagging school quite a bit. In Year 12 she became pregnant and started attending He Huarahi Tamariki School for Teenage Parents (HHT). Helen’s main interest was in art, but while at HHT she started picking up other subjects including biology which, thanks to a great teacher, she found she really enjoyed.

Helen decided she wanted to do science as a career and enrolled to do a B.Sc. at Victoria University. Initially she planned to major in biology but found that she was getting good grades in chemistry papers and ended up majoring in chemistry. At the end of her 2nd Year Helen did a summer internship in the marine natural products lab and a couple of years later did a summer internship in a natural products lab at IRL (Industrial Research Ltd – now called Callaghan Innovation). These experiences resulted in Helen deciding to do a M.Sc. in marine natural products. Once she successfully gained her M.Sc. Helen worked in a commercial laboratory for a while before taking up the opportunity to return to the marine natural products lab where she is now doing research towards her Ph.D.

Taitusi Taufa

Taitusi is another Ph.D. student in the marine natural products lab. He is from Tonga and, as a result of

enjoying science at school, completed a B.Sc. majoring in biology and chemistry at the University of the South Pacific in Fiji. After graduating Taitusi returned to Tonga where he became a school teacher and taught at the high school he had previously attended as a student. Taitusi wanted to do postgraduate studies and was awarded a NZ Aid scholarship to undertake his M.Sc. in the marine natural products lab here at Victoria University. On the successful completion of his masters degree, Taitusi returned to Tonga to teach for a further two years before coming back to Wellington to commence his Ph.D.

Taitusi will not be the first person in his family to complete a doctorate – his wife was awarded her Ph.D. earlier this year. She completed her doctorate in fisheries economics at Kagoshima University in Japan. Taitusi’s research is based around finding novel compounds in a number of different sponges.

Dr Jonathan Singh

Jono is a post-doctoral Research Fellow in the marine natural products lab. This means that he has already completed his Ph.D. and is now carrying out further research. In particular, he is working with the New Zealand company Magritek to design experiments suitable for undergraduate university students to carry out

using Magritek’s new benchtop NMR spectrometers. Jono attended Onslow College where physics was his strongest science and the one he intended to focus on at university. However, once he started his B.Sc. Jono found that chemistry was now the science that he was experiencing most success with and decided to major in chemistry. The further he went with chemistry, the more Jono enjoyed it. He decided to join the marine natural products lab to pursue his M.Sc., partly because he preferred organic chemistry to inorganic chemistry. During his M.Sc. research Jono got to work on an exciting project based around a compound called peloruiside A which has good potential as an anti-cancer drug and this encouraged him to continue on and do his Ph.D. As the senior researcher in the lab, Jono looks after the day-to-day running of the lab and provides advice to the other students working in the lab.

Dr Sa Weon Hong

Sa Weon is a post-doctoral Research Fellow. Sa Weon grew up in South Korea and enjoyed science subjects when he was at school. At one stage Sa Weon thought about doing a medical degree but decided .

that he would like a career in scientific research. Sa Weon studied for his B.Sc. and M.Sc. degrees atHanyang University and then did his Ph.D. at Yonsei University which is one of the oldest universities in South Korea. At Hanyang University Sa Weon majored in biochemistry but for his Ph.D. he majored in chemistry. After obtaining his Ph.D. Sa Weon moved to the United States to do post-doctoral research at the University of Illinois at Chicago. While there he worked on synthesising a drug to fight tuberculosis. After two years in Chicago Sa Weon returned to Korea to do further post-doctoral research and to be a chemistry lecturer. He is now settled in Wellington and researching several species of sponges with the aim of discovering a molecule that will one day be  used as a drug to combat a disease.

Ethan Woolly
Ethan attended Te Puke High School. At school he did okay but says that he didn’t excel in his studies. However Ethan did have an interest in chemistry, partly because he found it to be a practical subject. Ethan enrolled in a B.Sc. degree here at Victoria University and found that the more chemistry he did, the more

interesting the subject became for him. Ethan is now in the second year of a M.Sc. degree and has a real passion for chemistry. When he completes his M.Sc. degree Ethan hopes to go on and do a Ph.D. Ethan is currently hunting for new molecules in a sponge that is found in the waters off Northland (and has already found some). In his photo Ethan is holding a solution that he produced during his research. If you look carefully you will see that it has a faint pink tinge. When he came to show his solution to the rest of us the pink colour had mysteriously disappeared. We found that the colour was present under the lights in the lab, but not in the presence of natural light coming through the window. Strange! And so far, unexplained.

A Little TLC

Now that we have collected our different fractions, it is time to begin to consider what may be in the different fractions and, in particular, whether there is potentially a new and exciting molecule in one of them.

The first step towards doing this involves a process called thin layer chromatography (TLC).  Before carrying out TLC each fraction is redissolved in a small volume of 'Magic Brew' (a mixture of methanol and dichloromethane).

In TLC a capillary tube is used to add small amounts of each sample onto a TLC plate.  A TLC plate is a thin piece of plastic covered in silica.  The plate has a horizontal line near the bottom and you place a labelled pencil mark where you want each sample to go on the line.  The aim is to get a nice small circle of sample on each location.  To achieve this you 'spot' a small amount of sample, let it dry, and then add some more sample.  (If you put too much sample on at the start it spreads out too far and you will not get good results.)

Once we have spotted all our samples onto the plate, the plate gets lowered into a glass container with a small amount of solvent in the bottom.  The solvent used was 5% methanol in dichloromethane.  A lid is placed on the container so that fumes from the solvent are kept in the container.

The solvent begins to rise up the plate and as it does so it carries molecules with it. The surface of the TLC plate is quite polar. This results in polar molecules sticking to the plate while molecules of lower polarity continue to travel up the plate with the solvent. You end up with the most polar molecules at the bottom of the plate and the least polar molecules at the top.

The plate to the right shows my three P. microcladioides fractions. The 100% fraction contains a number of coloured compounds which have traveled varying distances up the plate.  There appear to be no compounds in the 30% and 75% fractions but this this only because none of them are coloured.  To see more compounds the plate is put under 2 different wavelengths of UV light.

The image to the left shows the plate when placed under a 350 nm UV light source while the image on the right is of the plate under a 254 nm UV light source. As you can see, new spots have shown up on the plate.  These are for molecules that contain chromophores. A chromophore is a part of a molecule that absorbs certain wavelengths of UV or visible light and reflects other wavelengths. (Chromophores often contain alternating single and double bonds.)

You may notice that the spots for the 30% fraction are all fairly low.  This makes sense as you will recall that the molecules in the 30% fraction are the most polar ones and it is these polar molecules that stick to the relatively polar surface of the plate and therefore don't travel very far.

Drying Down

Once we have obtained a number of solutions containing groups of molecules extracted from our red algae, it is time to dry down those solutions.  This involves evaporating off the solvent so that solid compounds remain.  To do this we use a rotary evaporator.

A rotary evaporator works by spinning the solution in a round-bottomed flask. The solution is spread around the inside surface of the flask and this increases the surface area from which the solvent can evaporate.

The rotary evaporator is attached to a pump which removes some of the air from inside the evaporator and therefore creates a partial vacuum. As the gas pressure above the surface of the solution is decreased, the solvent will evaporate off more quickly than it would under normal pressure.

The rotary evaporator to the left has a cold finger. This is the cone shaped object you can see inside the top part of the evaporator.  This is made very cold by filling it with dry ice (by removing the yellow lid at the top).  Solvent gas that has evaporated from the solution condenses into liquid when it comes into contact with the cold finger.  The liquid then drips into the flask at the bottom of the condenser.

As the solvent evaporates from the flask, the flask begins to get very cold and ice may even begin to form on the outside of it.  This is because when liquids evaporate they take heat from their surroundings.  If the flask gets too cold it will slow down the rate at which the solvent evaporates.  To get around this, the flask can be lowered into a water bath which prevents the flask from getting too cold.

On of the tricky things about drying down solutions is that they sometimes become unstable (particularly if they contain a mixture of water and acetone).  This can result in them bumping and spurting material up towards the condenser.  This would be a problem as we would be losing precious material and also contaminating the rotary evaporator.  For this reason, there is a glass trap above the round-bottomed flask. (It is between the red and green clips in the picture.)  Material that spurts gets caught in the trap and can be retrieved from there.


Once the solution has been dried down, you are left with a mixture of solid compounds attached to the the inside of the flask.  As the flask would be bulky to store (and we want to free it up so we can use it again), the next step is to transfer the compounds into a small glass vial. Before doing this we use a balance to find the mass of the vial so that we can later calculate the mass of material in the vial.


To transfer the material we need to redissolve it.  In the lab we use a solvent referred to as Magic Brew.  It is called this as it will dissolve most molecular compounds.  Magic Brew is a mixture of methanol and dichloromethane.  A small amount of Magic Brew is added to the flask in order to redissolve the solid compounds.  A glass pipette is then used to transfer the solution into the glass vial. The solution then needs to be dried down again on the rotary evaporator.  

The final step is to remove any traces of water that may not have evaporated on the rotary evaporator (as water has a higher enthalpy of vaporisation than most of the organic solvents we are using).  Any water needs to first be frozen and this is done by rolling the flask in liquid nitrogen.  The flask is then attached to a freeze dryer. As with the rotary evaporator, a freeze dryer creates a partial vacuum. This causes the frozen water to sublime (turn straight into  gas).  The water vapour is continually removed from the system by the freezer component of the freeze dryer.

Finally, the vial is reweighed and then stored in the fridge until we next want to work on the sample.

Pram Students @ Vic

One of the great things about being at Victoria University is catching up with past students of Paraparaumu College who are now doing Chemistry courses.  I have managed to track down seven of them.

Briana Hunt
Briana was a Year 13 Paraparaumu College student in 2013. She is currently in her first year of study towards a Biomedical Science degree, majoring in molecular pathology. Once she has finished her degree Briana intends to carry on further studies in the medical industry, pursue a career in sport medicine or complete her post-graduate degree. Briana is currently doing the First Year chemistry paper CHEM 113 Concepts of Chemistry. Students doing Biomedical Science need to take the First Year chemistry paper CHEM 114 Principles of Chemistry. CHEM 113, is a extra paper Briana wished to complete to gain further knowledge and skills to prepare her for CHEM 114. Briana is really enjoying Chemistry at Victoria, especially the practical experiments within the laboratories.

Georgina Bird
Georgina is another Biomedical Science student who is currently doing CHEM 113 in preparation for taking CHEM 114 in the second trimester. She was in Year 13 in 2005 and has since traveled and worked overseas. Georgina hopes that her qualification will eventually lead into a career in genetic counselling. She is enjoying being at Vic and getting back into study.


Lizzie Tafili, Rose McLellan & Bryony Ixer
Lizzie, Rose and Bryony are all currently taking CHEM 114 Principles of Chemistry and are in the same laboratory session (hence the combined photo).

Lizzie was in Year 13 last year and is now studying for a Bachelor of Biomedical Science majoring in medicinal chemistry and molecular pharmacology. As well as CHEM 114 she is taking a number of maths and biology papers, and next trimester intends taking CHEM 115 Structure and Spectroscopy. Lizzie is thoroughly enjoying CHEM 114. She likes the fact the paper contains some concepts learnt in physics and calculus as well as building on knowledge from NCEA Level Three chemistry. She describes it as a "really cool paper". Lizzie would like to one day do medical or chemistry related research so that she can "contribute and give back to the world".

Rose is another member of the class of 2013. She is now studying for a Bachelor of Science majoring in chemistry and biotechnology. Like Lizzie, Rose is currently taking CHEM 114 and I will take CHEM 115 next trimester.  She particularly enjoys the lab component of the course "because you get some fun practical experience that helps you understand all the new concepts you learn".  After graduating with her B.Sc. Rose would be interested in going into some form of research. She believes that her area of research will be determined by the components of chemistry that she is most compelled by in the later years of her degree. Teaching is also an option for Rose in the future because she "would love to have that interaction with people and share what I have learnt with them".  "Studying Chemistry at Victoria is really exciting and I know that it will only get better. The workload is hefty as with any university course but so far it has only inspired me to continue forward in Chemistry."

Bryony was in Year 13 at Paraparaumu College in 2012.  Last year she had a gap year and is now at Victoria University studying for a Bachelor of Science majoring in chemistry and economics.  At this stage Bryony is keeping her options open as to whether she eventually pursues a career in chemistry or economics (or maybe even manages to combine the two).  Bryony is currently doing the First Year Chemistry paper CHEM 114 Principles of Chemistry.  She is finding it challenging returning to study after having a gap year but is enjoying her time at Vic.

Lindsay Morris

Lindsay was in Year 13 in 2011 and is now in his final year of a Bachelor of Science majoring in chemistry and statistics. This year he is taking CHEM 301 - Organic Chemistry, CHEM 302 - Inorganic and Materials Chemistry, CHEM 303 - Physical and Process Chemistry and CHEM 305 - Organic Synthesis Laboratory. Next year Lindsay intends moving onto studying at the honors level with a particular focus on Organic Synthesis and Natural Products. If all goes well, his ultimate goal would be to either work on synthesizing molecules of particular biological interest, or discovering new compounds from marine sponges and alga.  "Studying Chemistry at Vic has been extremely challenging, however, it has been even more rewarding. I can't imagine what life would be like without having done Chemistry. I encourage students to take the challenge, and head to Vic to make the most of the best Science department and facilities New Zealand has to offer!"

Charlotte Page

Like Lindsay, Charlotte studied Chemistry at Paraparaumu College up until 2011. With an interest in Science, she has pursued a Bachelor of Biomedical Science specializing in molecular pathology and medicinal chemistry. She is currently in the third and last year of her degree, Charlotte has taken a variety of Chemistry courses, this year focusing on CHEM 301 - Organic Chemistry and CHEM 305 - Organic Synthesis Laboratory. She is considering options in postgraduate study, hopefully working towards a career in clinical pharmacology. "I have thoroughly enjoyed studying at Vic. I feel they offer a wide range of courses in Science, including Chemistry. Although challenging at times, there has always been assistance in a great community of scientists."

Briana, Georgina, Lizzie, Rose, Bryony, Lindsay and Charlotte are all having a great time studying Chemistry at Vic and would love to see more Paraparaumu College students join them in the future. If you would like to find out more information from any of them, send an email to me at mkb@pcol.school.nz and I will pass your message on to the relevant person.

In the Dark

When working on solutions and separating molecules into fractions (groups of molecules) we want to try and ensure that none of the molecules break down and become something else.  For example, some molecules are light sensitive and can break down in the presence of too much light.  For this reason we try and keep solutions, and columns with molecules loaded onto them, in the dark when we are not working on them.

Solutions in small conical flasks, or dried down fractions in vials, are kept in a fridge.  Not only is it dark in the fridge (yes the light does go off when you shut the door), but it is also cold.  As you know, reactions happen at a much slower rate at low temperatures, so any potential reactions that could occur will hopefully be slowed right down.

Larger conical flasks containing solutions are kept in a dark cupboard.

Sometimes when large volumes of solution are being passed through a column, the column is left to run for quite a long period of time.  To keep light out the whole apparatus is wrapped in tinfoil.

Back-Loading

We now have three solutions containing dissolved molecules - the 30% fraction containing fairly polar molecules, the 75% fraction containing slightly polar molecules and the 100% fraction containing molecules of very low polarity.  The next step is to remove the water from these solutions so that we can obtain the dissolved compounds.  This will be done using a rotary evaporator.  This process will involve removing some of the air above the solution to create a partial vacuum. With the 30% and 75% fractions this is going to cause a problem as mixtures of water and acetone are unstable under those conditions and will tend to jump and spurt as we try to dry them down.  To get around this we need to first use a process called back-loading.

Back-loading a fraction involves reloading it onto a HP20 column. To encourage molecules back onto the non-polar column, the volume of the solution is doubled by adding water, thus making the solvent more polar. For example, my 75% fraction of P. microcladioides had a volume of 240 mL so I added 240 mL of water to it before passing it through the HP20 column.  This caused many of the molecules of low polarity to attach to the column.

In the photo to the right my 75% fraction of P. angustum is being back-loaded onto the left-hand column while my 75% fraction of  P. microcladioides  is being back-loaded onto the right-hand column.

Once the solution has passed through the column, the solvent is made still more polar by again doubling its volume by adding water.  So I added a further 480 mL of water to my 75% fraction of P. microcladioides.  It is then passed through the column again and the moderately polar molecules will now attach to the column.

As the volumes become larger, passing the solution through the column can become very time consuming.  You also have to watch out for compounds beginning to crash out of solution. This can happen when you are adding water and the solution becomes too polar for some of the compounds to remain dissolved. These compounds then begin to precipitate out of solution.  As soon as you see this begin to happen you need to stop adding water and start passing the solution through the column.

The picture to the left shows my 75% fraction of P. angustum part way through the back-loading process.  You can see that some orange coloured compounds have made their way to the bottom of the column while some green coloured compounds have attached further up.  While the coloured compounds are the interesting ones to look at, many of the compounds will actually be colourless.

Once the molecules have been back-loaded onto the column they are then removed by passing acetone through the column. The eluate collected contains the molecules and the solution can now be dried down on the rotary evaporator as the solvent is acetone rather than a mixture of acetone and water.

Elution

After cyclic loading molecules onto a HP20 column, the next step is to get them off again in groups of molecules with similar polarity.  We do this by passing solvents of different polarity through the column. Molecules on the column with similar polarity to that of the solvent will dissolve into the solvent and be carried out of the column and into a conical flask.  This process is called elution.   The solvent that passes through the column is the eluent. Once it emerges from the column containing dissolved molecules it is referred to as the eluate.

The first solvent used is water.  As water is quite polar and there should be few if any significantly polar molecules on the column, very little material should be removed by the water.  Its role is really just to rinse the column of any salts or very polar molecules that may have become attached.

The next solvent used is 30% acetone (30% acteone / 70% water by volume). This solvent is less polar than water and will remove moderately polar molecules from the column.  The eluate is collected in a conical flask.

Then it is the turn of 75% acetone (75% acetone / 25% water by volume). This removes a group of less polar molecules.

Finally 100% acetone gets passed through the column and removes molecules of very low polarity (and non-polar molecules).

We refer to the solutions gained as the 30% fraction, 75% fraction and 100% fraction.  Each fraction will contain a range of molecules that still need to undergo further sorting.

Communicating Controversial Science

One of the great things about being based at Victoria University is that there are always lots of events such as lunchtime seminars that you can go along and attend. One I went to recently was called Communicating Controversial Science.  It was presented by Dr Rebecca Priestley and Dr Rhian Salmon who are both lecturers in the School of Chemical and Physical Sciences.

The seminar focused on how scientists can go about communicating 'controversial science' to the public. Just about any area of science can become controversial, but some of the examples we were looking at were fluoridation of water supplies, vaccinations, climate change, nuclear energy, cloning, genetically modified food and nanotechnology.

In the seminar we divided into three groups - chemists, nanotechnologists and nuclear scientists.  Firstly each group took the perspective of members of the public concerned about one of the other two areas.  We listed concerns that people might have.  For example, people worried about nuclear power might have concerns about radioactive materials getting into the environment or a nuclear accident such as happened at Chernobyl. The 'specialist' groups then considered those concerns and discussed ways to communicate the relevant science to the public in order to reassure them.

Until about 2000 the main model used by scientists when communicating with the public was what is now referred to as the deficit model. This model assumed that people knew very little about the relevant science and the scientist's role was to educate them. It was thought that once people had been informed of the scientific facts, they would change their views and support the new technology or scientific theory.  However, this approach has been shown to be largely ineffective.  This is partly because it does not take into account people's existing knowledge (which may or may not be scientifically accurate), or their beliefs and personal experience.  Critically, it does not provide for people to have their say and enter into any dialogue with the scientist.

After 2000 a dialogue model of science communication became more commonly accepted.  Under this model the scientist and non-scientist engage in discussion where the non-scientist is able to voice their perspective, understandings and beliefs.  However, the scientist still views their role as one of bringing the other person around to accepting the science viewpoint.

This model has now evolved further to an engagement model.  This model recognizes that effective science communication requires a genuine respect for people's current knowledge, values, perspectives and goals. The objective is not to convince people to adopt your viewpoint, but rather to provide expert knowledge and to then accept that people will use a combination of that scientific knowledge and their own understandings and values when deciding what position they will adopt. Decisions around the application of scientific knowledge in communities are the responsibility of all members of the community.  It is the role of scientists to bring scientific evidence to the debate, but all citizens have the right to participate in the debate, to have their own viewpoint respected and to apply their own values in their decision-making.

An interesting paper about the changing nature of science communication can be found at: http://tinyurl.com/qbp4wxq

Cyclic Loading

Right, back to the business of hunting for undiscovered molecules in our red algae (seaweed).  You may remember that we have got as far as extracting a whole range of molecules which are now sitting in solution in a conical flask.  The next step is to start separating the molecules into groups.  To do this we are going to use the varying polarities of different molecules.

In class we have looked at covalent bonds having different degrees of polarity depending on the difference in electronegativity of the two atoms involved in the bond.  Some bonds are not polar at all (non-polar) while others may be only slightly polar or very polar.  We have tended to classify molecules as either non-polar or polar and left it at that. However molecules also have varying degrees of polarity.  For example, water is more polar than methanol which is more polar than acetone.  We are going to use the relative polarities of these three solvents to help us to separate our mixture of molecules.

To begin with the second extract is passed through a column filled with 'HP20'.  HP20 is comprised of small white beads of polystyrene divinylbenene.  These beads provide a very non-polar surface that molecules can attach themselves to. Molecules will do this if their polarity is closer to that of the HP20 than it is to the polarity of the solvent they are in. So molecules in the mixture that have a low polarity will come out of the moderately polar methanol solvent and attach themselves to the HP20.

Solution that passes through the column is collected in a conical flask at the bottom.  The flow rate is about one drop per second so it can be quite a slow process.  Once the second extract has passed through the column, it is the turn of the first extract which is loaded into the top of the column. Eventually both extracts have passed through the column and the solution containing all the molecules that have not attached to the column is in the conical flask at the bottom.

We now want to encourage some of the slightly more polar molecules onto the column.  To do this we need to make the solvent more polar.  This is achieved by doubling the volume of the solution by adding distilled water.  Remember that water is more polar than methanol so the solvent (now a mixture of water and methanol) is more polar than it was before. The solution is put through the column again and this time some of the slightly more polar molecules attach to the column.  This process is repeated one more time to make the solvent even more polar and to cause more molecules to attach to the column.

Molecules of high polarity will not, of course, attach to the column as they will prefer to remain in the polar solvent.  This is not a problem for us as the molecules that we are hunting for do not tend to be of high polarity.  However, just in case something important is still in the solution, we will keep it in the meantime.

A Professor Visits

Recently I was lucky enough to attend a Tertiary Chemistry Teaching Symposium held here at Victoria University.  It was a gathering of chemistry lecturers from different universities around New Zealand and had a particular emphasis on teaching and learning in First Year chemistry courses.  The lecturers shared ideas and discussed common challenges that they were facing.  One of those challenges is that different schools cover different NCEA Level 3 chemistry achievement standards and therefore students in a First Year chemistry course can have a range of backgrounds in chemistry.  This, of course, makes it challenging to design First Year chemistry courses.  The lecturers were particularly concerned that not all students were doing the three external NCEA Level 3 chemistry standards.

Guest speaker at the symposium was Professor Roy Tasker from the University of Western Sydney where he is Professor of Chemical Education. Professor Tasker's presentation was on Visualisation of the Molecular World for a Deep Understanding of Chemistry. His key message was that to understand the chemistry that we observe (for example, a precipitate forming) we need to be able visualise what is happening at a molecular level, rather than jumping straight to writing a chemical equation.

 Professor Tasker's team are responsible for producing the VisChem videos that we sometimes watch in class.  These videos, showing animations of chemical reactions at the molecular level are now available to anybody through Scootle - tinyurl.com/VisChemOnScootle

A YouTube video on VisChem Learning Design, which demonstrates best practice in using molecular animations in the classroom can be found at: tinyurl.com/k2x34sr This approach involves students observing a chemical reaction, recording their observations and then producing a storyboard to show what they think is happening at the molecular level. They then discuss their storyboard with a peer before being shown the VisChem animation.  After viewing the animation students then reflect on any similarities and discrepancies between their representations and the animation. Finally what is happening at a molecular level is linked to how that can be represented by a chemical equation. This approach is a constructivist one which takes into account a student's current model of what is happening. It involves cognitive conflict as a student's previously held perceptions may be challenged by what is in the animation.   

If you are interested in seeing some amazing animations of molecules at work in living things, you might like to have a look at a video of a presentation by Drew Berry called Animations of Unseeable Biology - tinyurl.com/7tkh9zw

Extracting Molecules

After sitting in methanol for 24 hours, it was time to separate the algae from the solution.  To do this I used a Buchner flask and funnel. The flask is attached to a simple pump that lowers the pressure inside the flask and helps to pull solution through the filter paper in the funnel.  I tipped the solution into the funnel and then added the algae so as to retrieve as much solution as possible.  The solution (with the extracted molecules) ended up in the flask while the algae was trapped in the funnel.  The solution is called the first extract.

The algae was then returned to its original flask and more methanol was added to it (300 mL for the P. angustum, 500 mL for the P. microcladioides).  It was then left for another 24 hours so that more molecules could be extracted from the algae.

After 24 hours the algae was separated from the solution in the same way as above. The solution obtained this time is called the second extract.

We have now probably finished with the algae, but rather than throwing it out, the algae is placed in a bag and stored in a freezer.  This is so that it is still available in case we need to use it again later.

Meet the Algae

My molecule hunting exploits are going to be based on two species of red algae - Plocamium angustum (to the right) and Plocamium microcladioides (to the left).  These are both types of seaweed found in New Zealand waters.  They contain chloroplasts as they produce food by photosynthesis.  The red colour is due to  pigments in the algae.

My first task is to extract a mixture of molecules from the algae.  This done by chopping a sample of the algae into small pieces, putting the pieces into a conical flask and then covering them with methanol.  The methanol acts as a solvent which molecules from the algae dissolve into.

I used 48.1 g of P. angustum and needed 300 mL of methanol to cover it.  The P. microcladioides was a larger sample.  It had a mass of 97.8 g and required 500 mL of methanol to cover it.

The conical flasks were then covered in aluminium foil and put into a dark cupboard.  Why? Some of the molecules being extracted could be light-sensitive - they might break down into something else if exposed to too much light.  The flasks were left overnight.

Almost immediately the methanol started turning green (not red!).  The green colour is probably due to chlorophyll from the chloroplasts in the algae.

You may notice that the flask has a code written on it. 'BPM1' refers to my 1st lab book - my initials are BPM. (If you look carefully you will see that I accidentally left the '1' off). '01A' means that it contains sample A (my P. angustum) and information about it can be found on page 01 of my lab book. Our lab books have pre-numbered pages and also produce a carbon copy of each page.  The lab books stay in the lab so anybody can check what is in a flask by going to the relevant lab book.  They also provide a permanent record of all practical work undertaken in the lab.

Out of the Classroom

I can usually be found at Paraparaumu College where I get to teach lots of great students about science and chemistry. However, for the first half of this year I wont be at Paraparaumu College, but instead I am based in the School of Chemical and Physical Sciences at Victoria University of Wellington. I am here on an Endeavour Fellowship which is administered by the Royal Society of New Zealand.  Along with about 20 other primary and secondary school teachers from around the country I have been given the opportunity to step outside the classroom, roll up my sleeves and experience working with scientists on real science challenges.  It is a great opportunity for me to learn more about how scientists create new scientific knowledge and to expand my own chemical knowledge, skills and experiences.

I am working in a marine natural products lab under the supervision of Dr Rob Keyzers and Associate Professor Peter Northcote.  With me in the lab are several PhD and post-doctoral (have already got their PhD) students who are hunting for undiscovered molecules in things that live in the sea such as sponges and seaweed.  Why are they doing this?  Some of the molecules that are discovered may prove to have uses that are beneficial to people.  For example, a molecular compound may be effective at killing certain types of bacteria and could therefore potentially be used as an antibiotic.  Even for molecules that don't prove to have any immediate use, by discovering them and working out their structure, the chemists in the lab are adding to the global chemistry community's collective knowledge.  Other chemists in other parts of the world can make use of that knowledge as they undertake their own projects.

If you follow this blog you will hopefully get to learn a bit about what chemists do.  If you take Year 13 Chemistry, my project is going to involve quite a bit of spectroscopy so will help you to gain an understanding of the spectroscopic techniques that you need to be familiar with for Achievement Standard 3.2.  I will also, from time to time, be talking about other things I am getting to do as part of my fellowship.

You are welcome to ask questions about what I am doing, or about what I have covered in a post, by submitting a comment.