Thermodynamics in a nutshell

Firstly, what is thermodynamics? Well it’s all about heat energy changes and how energy is transferred through chemical systems. For example, in exothermic reactions the overall potential energy of the products in less than that of the reactants so more energy is released than is required to break the necessary bonds. And vice versa for endothermic reactions.

So, let’s look at the fundamental laws of thermodynamics. The first is one most of us will have heard at some point: energy cannot be created nor destroyed but merely transferred from one form to another. The second is that energy will always flow from being concentrated to being dispersed and that no process can have 100% efficiency for the conversion of heat energy into “work” which is essentially the energy transfer into our desired product. This is where it starts to get all confusing, when we consider entropy. We’ve all seen water evaporate from a pan and seen salt dissolve in water, both of these happen because particles have a tendency to spread out and disorder. This disordering or randomness, known as entropy can be calculated using the entropy change of both the surroundings and the system so that we can determine whether a reaction is feasible or not feasible. For this we use the equation: ΔG = ΔH –TΔS where ΔH is the enthalpy change, ΔS in the entropy change, T is the temperature of the reaction and ΔG is the Gibbs free energy. When ΔG is negative the reaction is said to be feasible and when positive, not feasible. This feasibility of a reaction is different at different temperatures. The third law states that as a system approaches 0K the entropy change also approaches 0JK^-1, theoretically though because reaching 0K is impossible.  This happens only in perfect crystals because in non-pure ones energy is required for the imperfect alignment of the bonds within the crystal. 

Author: Grace Ronnie

Resonance structures

Resonance is a way of defining delocalised structures, such as benzene, of which a single Lewis structure is not sufficient. Numerous resonance structures can be used to show the structure, but no single one is correct. What this means is that an approximate intermediate between the resonance structures is in fact the real structure, often referred to as the resonance hybrid. If we take benzene as the example, we know that the Kekulé structure, devised by Freidrich August Kekulé in 1972, is incorrect and benzene, with its delocalised ring is the correct structure. It does not have three double bonds but six bonds that are half way between single and double carbon-carbon bonds and a delocalised pi cloud above and below it, bearing in mind it is a planar molecule. The idea behind the Kekulé structures (see image below) was that it shifted between the two structures so fast that it is never one or the other in one moment. We now know that is doesn’t shift but is a midway state.

A common analogy to explain these structures is that a rhinoceros is a resonance hybrid between a unicorn and a dragon, neither is actually real but both share characteristics of a rhinoceros. A rhinoceros does not shift between a unicorn and a dragon; it is just simply a rhino.

You hopefully have expected that benzene is not the only compound that resonance structures are used for, there are others such as the nitrile group (-NO₂), sulphur dioxide (SO₂), the carbonate ion (CO₃^2-) and more.

Above shows the two resonance structures for the nitrile group

Above shows the two resonance structures for sulphur dioxide

Above shows the three resonance structures used to show the carbonate ion

Note that not one of these contain double bonds but all do contain a delocalised structure that is half way between the length of a single and double bond.

Author: Grace Ronnie.

Enantiomer (optical) isomerism

Enantiomers are mirror images of asymmetrical compounds with one or more chiral centre. Chiral is just a term used to show that the molecule is asymmetric and thus non-superimposable and is most commonly caused by a carbon atom. What this means is that though they are essentially exactly the same chemicals, and mainly work in the same way, they don’t have the exact same spacial arrangement and thus need to be recognised.

To visualise this, it may help to imagine both your hands as optical isomers of one another; with the backs of your hands facing you, try lining up your fingers and thumbs and you'll see your thumbs don't match up. Both hands have four fingers and one thumb and are used just the same but aren't exact copies which is the important difference when these compounds are used in living systems. Enzymes, as I'm sure we're all aware, require specifically shaped compounds. While one enantiomer may be specific, the other will not. Most of the time one enantiomer will be useful and the other simply won’t bind to the enzyme. Other times, like with for example Limonene, both will cause different affects such as one enantiomer having a scent characterised as orange and the other lemon. A more known example of this difference is seen in the drug Thalidomide which in the late 50s was prescribed to pregnant women to reduce morning sickness but unfortunately caused birth defects. One optical isomer causes these malformations whereas the other is the effective sedative. It’s important now that all drugs with a chiral centre have all the possible isomers tested separately for separate side effects and in the interest of saving money and resources, only the useful enantiomer is likely used.

Polarimeters are thus used to distinguish between the different optical isomers. Only chiral molecules will rotate the visible light (after passing plane-polarized light through a polarimeter) and are said to be optically active. Racemic solutions (50/50 opposite enantiomer isomer solutions) or solutions without any chiral molecules have no effect on plane polarized light. Different enantiomers will rotate the light left or right and are said to be +/-, R/S or D/L. 


Resources: http://en.wikipedia.org/wiki/Thalidomide , http://en.wikipedia.org/wiki/Enantiomer , http://www2.vuw.ac.nz/staff/paul_teesdale-spittle/organic/chiral_web/context.htm , http://www.chemistryexplained.com/Ce-Co/Chirality.html#b , http://en.wikipedia.org/wiki/Chirality_(chemistry)#The_identity_of_the_stereogenic_atom and http://www.chemguide.co.uk/basicorg/isomerism/optical.html
Author: Grace Ronnie

The ins and outs of centrifugation

What is centrifugation? Centrifugation is the separation of organelles in order for further analysis of specific parts of the cells, for example, the nucleus. An ultra-centrifuge containing the homogenised organelle is rotated at a high speed in order for the centrifugal force to separate the sections of the organelle with heaviest sections separating first. Each time the centrifugation terminate, a pellet is collected and analysed. Throughout the different medical sciences and chemical industries centrifugation is predominately the process of putting liquids into test tubes, placing them in the ultra-centrifuge, and spinning it to apply the centrifugal force. From this technique we can isolate parts of the organelle such as the mitochondria, the nucleus and ribosomes. Each of these providing benefits for the scientific community. By studying the nucleus we can study the DNA for any genetic estrangements and correlations within particular diseases, as with the ribosomes and mitochondria, we can study the production of proteins and respiration etc.
The product that is received is dependent on the rotation speed, rotor size as well as the solvent density. Each of which can result in different organelle sectors being centrifuged.
This use of a centrifuge is valuable to scientists because the centrifuge separates supernatant containing  homogenised organelles into layers based on their mass. Larger components of the liquid are pressed toward the outside of the centrifuge with more centrifugal force, so they settle to the bottom of the test tube. Smaller components settle in layers higher up or the supernatant, with the least massive at the top. When medical staff use a centrifuge on blood, for example, the blood cells collect at the bottom while the blood plasma moves to the top due to it being of low density.
By applying  centrifugal forces in a confined and controlled space, a centrifuge can be a useful tool not only for scientists and medical practitioners, but for other industries as well. Centrifuges are used in sewer management, in the oil industry, and also in the processing of sugar and milk. They also play a part in the nuclear power industry to separate isotopes and enrich uranium.

Sources: http://en.wikipedia.org/wiki/Differential_centrifugation
http://coursesite.uhcl.edu/NAS/StephensB/SH%20CENTRIFUGATION.pdf
www.wisegeek.com%2Fwhat-is-a-centrifuge.htm&h=DAQFB6ZjY
Author: Katie-Jo Mawson

Multiple sclerosis and research

Multiple sclerosis is an autoimmune disease in which T-cells of the immune system attack the myelin sheath (cells that surround the axon of neurons) of the sufferer’s central nervous system. In this case the body cannot recognise what is self and foreign so it destroys host cells. Legions appear in the brain and can be seen from an MRI scan. Sclerosis refers to scarring, usually in the white matter of the brain and the spinal cord, which interrupts the communication of these nerve cells and thus prevent or slow many instructions for movement, sight and memory (as well as many others listed in a link below). The cause for all this is however completely unknown, all that is known is that there is a slight genetic factor involved. By this I mean that those diagnosed with MS usually have a relative somewhere in their family who also has MS, for example my father was diagnosed in 2001 and found that his cousin's daughter also has MS, which means I have a slight higher risk of MS than those without the family link. But, and there’s always a but, there are many cases of MS that seem to have no genetic link and so by no stretch is there a causal link. This is all very confusing but what it points towards are alternative factors such as environment, age, geography etc. It is likely that genes define who is most susceptible to developing the disease, but environmental factors are what define who actually develops the disease.

 So, a virus or bacterial infection may be the trigger. Back to my father again, at the age of 10 he had glandular fever (Epstein Barr virus) many of his friends suffering from MS had the same at an early age, yet somewhat frustratingly not all MS patients have had this.

 It is also thought that a lack of vitamin D can increase risk, and research into that theory will be looked at during the course of this year.

A lot of disagreement has came about from Dr Paolo Zamboni’s claims that up to 90% of MS is caused by narrowed veins and blockages that obstruct the flow of blood from the brain back to the heart, as the theory has been undermined by a few other scientists claiming that the blood flow is normal in MS patients.

There are many theories such as Zamboni’s that remain very much unclear and one could potentially hold the answers we’re looking for. 

If you’re interested in other research into the cause of MS please visit this website: http://www.mssociety.org.uk/ms-news-and-research/ms-research/research-projects/cause#CD86

And if you’re wanting to looking into symptoms: http://www.mssociety.org.uk/what-is-ms/signs-and-symptoms?gclid=CKSa7LnP-K4CFdISfAoddRy61A

Other resorces:

http://www.bbc.co.uk/news/health-16086004

http://www.chg.duke.edu/diseases/ms.html

http://www.multiplesclerosisinformation.co.uk/#/about-ms/4534155497

http://www.klearview.co.uk/MS.html

http://www.mult-sclerosis.org/blog/

http://www.knowswhy.com/why-is-multiple-sclerosis-an-autoimmune-disease/

http://articles.latimes.com/2010/aug/02/science/la-sci-ms-treatment-20100803
Author: Grace Ronnie

Gill lamellae.

Today in Biology we were all let loose with some scalpels and a pair of scissors with the attempt of finding the gill lamellae in fish heads. The experience taught us more about the satisfaction you can get from mauling the eye out of dead fish, than what the actual purpose of the gill lamellae is.

Above: The delightful Grace holding the product of 40 minutes dissection.

The gill lamellae is an important respiratory structure in the gills of a fish, it uses the idea of a countercurrent flow, which is where a constant low diffusion gradient is necessary to transport oxygen around the respiring tissues. This system is efficient due to the use of at least 75 per cent of oxygen from the water. These structures are founded upon gill filaments which are stacked upon one another. The lamellae are important as they increase the surface area of the gills which in turn increases the rate of diffusion withing the fish itself.
The countercurrent flow system previously mentioned is a more effective method of diffusion of oxygen than the system us mammals possess; parallel flow. This is because the blood and water which flow over the lamellae do so in opposite directions. This means that blood that is well loaded with oxygen meets water, which also is well loaded with oxygen. Therefore little, but sufficient, oxygen will diffuse over the small diffusion gradient into the blood. The system also ensures that when the water contains little oxygen, diffusion will still occur. This is because there will always be a diffusion gradient favouring the diffusion of oxygen from water into the blood all the way across the gill lamellae hence then 75 per cent oxygen use.
Contrasted with the countercurrent flow, the diffusion system we posses only uses up a maximum of 50 per cent of oxygen available for diffusion due to the gradient being cancelled out. This is because of the flow of water and blood being 'parallel' to each other, creating a high diffusion gradient between the water's high saturation of oxygen, and the blood's low saturation of oxygen.
Fish contain these structures as they have a small surface area to volume ratio meaning they would simply not be able to survive without developing a specialised internal gas exchange surface.


Sources: AQA AS Biology textbook and Mrs Palmer, biology teacher.
Author: Katie-Jo Mawson

Brief on intragenic regions and research

Introns are sections of DNA that don't code for any instructions or proteins: non-coding sections. They can be found in pre-messanger RNA as well as the parts that code for proteins (exons). Pre-mRNA goes through a modification process (splicing) to produce the mRNA of only exons. The question now posed to scientists is: why do introns exist and what is their purpose? The questions are yet to be definitely answered, so it leaves plenty room for research for those of you who may be interested. The most popular belief is that they’re caused by evolution. Introns in modern genetic material could have been a gene in ancestral genetic material that proved not to be strong enough to last and was weaned out by natural selection. Or, the introns exist to leave room for new genes to be created. However, there have been recent breakthroughs in understanding them more; in a study conducted at Indiana University Bloomington and University of New Hampshire, there showed considerable proof to point toward the theory of “hot spots”, these are loci on the complete genetic material where introns seem to be likely. This contradicts prior belief as it would point towards introns being actually quite common instead of a rarity. 

References: 
http://www.sciencedaily.com/releases/2009/12/091210111148.htm

http://www.rae.org/introns.html

https://www.utoledo.edu/med/depts/bioinfo/pdf/facpdfs/fedorova10.pdf

Author: Grace Ronnie