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Blue hair, yellow sweater, big smile

Biological joviality

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Edited by Vicky Fraser, Wednesday, 13 July 2011, 14:00

I've the afternoon off work to complete the Tutor Marked Assessment for Book 5: Life. And I haven't blogged in a while. I am also Sick with an unknown malaise of the throat. So, I give you: Biology Jokes!*

Biology is the only science in which multiplication is the same thing as division!


Did you hear about the famous microbiologist who traveled in thirty different countries and learned to speak six languages? He was a man of many cultures.


Confucius once said, "When you breathe, you inspire, and when you do not breathe, you expire."


The bad news is that the American Society for the Prevention of Cruelty to Amoebas is shrinking. The good news is that none of the amoebas has lost any of their members.


At NIH (National Institute of Health), there is a sign on the door of a microbiology lab that reads "STAPH ONLY!"


Q: What is the fastest way to determine the sex of a chromosome? A: Pull down its genes.


The teacher asks, "Jessica, what part of the human body increases ten times when excited?" Jessica blushes and says, "That's disgusting, I won't even answer that question."

The teacher calls on Johnny: "What part of the human body increases ten times when excited?" "That's easy," says Johnny. "It's the pupil of the eye."

"Very good, Johnny," responds the teacher. "That's correct."

She then turns to Jessica and says, "First, you didn't do your homework. Second, you have a dirty mind. And third, you're in for a BIG disappointment."


A man goes into a bar and asks: "Can I have a pint of energy please?" The barman pulls the pint and says: "That'll be 80p please!"


Enzymes are things invented by biologists that explain things which otherwise require harder thinking.


Did you hear about the biologist who had twins? She baptized one and kept the other as a control.


One day the zoo-keeper noticed that the orang-utang was reading two books - the Bible and Darwin's Origin of Species. In surprise he asked the ape, "Why are you reading both those books?"

"Well," said the orang-utang, "I just wanted to know if I was my brother's keeper or my keeper's brother."


It has recently been discovered that research causes cancer in rats.


I do apologise. I'll get me coat! *Shamelessly stolen from the Internet.

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Blue hair, yellow sweater, big smile

Plants are busy little things, aren't they?

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Edited by Vicky Fraser, Thursday, 16 June 2011, 10:54

Today's topic is the light-dependent reactions of photosynthesis. Now, you may think that it's all fairly straightforward, thinking back to your GCSE biology classes (or O-Level for you oldies).

A bit of light for the leaves provides energy to turn water and carbon dioxide into sugar and oxygen. Simples, I hear you say. That is what I thought too. Just a short chapter, I imagined. How complicated can it be?

Well. Let me tell you that it's very bloody complicated. I've drawn two diagrams, and I'm still not entirely sure I've understood it. And I've only done the light-dependent reactions! The dark reactions are yet to come. I'm expecting them to involve Voldemort in some way.

Here is a short account of the principle reactions involved in this stage of photosynthesis, which I wrote as part of an activity to help us to understand the processes. I would include my diagram, but I'm not drawing it on a crappy laptop. It's not an Etch-a-sketch, you know. So I've pinched this one from my OU course book.

light-reactions2.png
The light-dependent reactions of photosynthesis

The thylakoids are part of the chloroplast in plants. I apologise for the word "thylakoid". All its consonants are in the wrong place, making it a bit of an assault course for the tongue. It reminds me of trying to learn German at school - I never was very good at German, partly because I had trouble getting my tongue around their words. I do, however, love the phrase: "Schnell, schnell, kartoppelkopf!"

They have an outer membrane, and a really convoluted internal membrane which is stacked into grana - and each little disc (or sac) in an individual granum is a thylakoid. The space inside the thylakoid membrane is called the thylakoid lumen, while the space outside the membrane is called the stroma. As illustrated above.

My summary is as follows. It's supposed to simplify the description of what's going on, and complement the diagram above. I'm not sure I've achieved that; any and all feedback is welcome!

When light strikes a chlorophyll molecule, a photochemical reaction takes place in which the hydrogen atoms of water molecules are split into their constituent protons (H+ ions) and electrons. (Oxygen is released as a by-product.) As shown above, the electrons move from the thylakoid lumen through the membrane to the stroma, by means of protein carriers within an electron transport chain (ETC). The protons are left behind, increasing the concentration of protons in the lumen. With me?

In the stroma, coenzyme NADP collects a couple of electrons and combines them with a couple of protons, reducing to NADP.2H (see above). This lowers the concentration of protons in the stroma. This will be important later.

One of the electron carrier proteins in the ETC is a little shuttle that collects protons from the stroma, bimbles across the membrane, and deposits them in the lumen, further increasing the concentration of protons in the lumen.

As a result of these processes, a transmembrane (yes, it's a word!) protein gradient is formed across the thylakoid membrane - this works much like a hydroelectric plant (think of the reservoir at the top, and all that potential energy waiting to be turned into electricity). Now there's an imbalance of proton concentration, enabling the protons to flow down the concentration gradient back into the stroma through channel proteins called ATP synthase (shown on the right of the diagram above).

The flow of electrons through these proteins enables the manufacture of ATP from ADP (adenosine diphosphate) and Pi and their transfer provides the energy required.

The products of these light reactions, ATP and NADP.2H, are used in the dark reactions of photosynthesis by the Dark Lord to reduce carbon dioxide to glucose.

I do apologise for the extreme biology - but this is the third time I've written the process in my own words, and I do believe it's finally beginning to sink in. In a manner that ensures I understand and remember it.

Stay tuned for the Dark Reactions - I suspect they may be sexier.

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Blue hair, yellow sweater, big smile

Farewell, sweet chemistry, for now

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Edited by Vicky Fraser, Thursday, 2 June 2011, 08:30

Well, I have reached the halfway point in my study of science with the Open University - farewell, Book 4. I have enjoyed you very much, and I do believe that we have surprised each other.

You surprised me by re-introducing me to The Mole, and making me love it. I surprised myself by not only enjoying chemistry, but understanding it too.

However, I must put in a complaint. Not about the chemistry, you understand; nor about the way in which it was taught (although really, some of the writers need to embrace the idea of "less is more"). No, my beef is with those who set the questions for the TMAs (tutor-marked assignments).

In this case, the person who required us to needlessly rearrange an equation, then arrange it back again, when we could find the answer quite easily using the original equation and the information in the graph - thereby confusing everyone on the course - should be punished by being locked in a room with Silvio Berlusconi and Celine Dion being played on a loop.

Failosaurus.

But apart from that little blip, the TMA is done and dusted, and is going through a checking process. I should have dispatched it by the end of the day today.

I feel I've achieved quite a lot from this module: I understand, do not fear, and in fact have grown to love Avogadro's mole; I am able to write balanced chemical equations; I understand acids, bases and equilibrium; I can find the hydrogen ion concentration of a substance from its pH; and I am beginning to understand how drugs work (and therefore, how enzymes and hormones work). It's really fascinating stuff.

Fuel, and evidence, is being added to my mini-crusade against quackery. Well, my own personal local crusade, partially inspired by Ben Goldacre (I had my doubts before I started studying science, and before I discovered his Bad Science writings).

I should clarify: the placebo effect is real, and documented, and I'm absolutely happy with that. What really grates my carrot is when people peddle something like homeopathy as "science". Some homeopathic remedies are sold at a dilution of 200C. That means that one drop of the "remedy" has been diluted in 200 drops of water - 100 times over. It has been diluted more than the number of atoms in the entire universe. (Thanks to Bad Science for this nugget!)

And that is only one of the ways in which homeopathy is quackery.

But as I said - the placebo effect is fine. I have no problem with people parting with their hard-earned cash for nonsense, or for a placebo. What I DO have a problem with is quacks encouraging seriously ill people to stop their medication, and start taking sugar pills. That is dangerous, arrogant and pretty close to evil. I saw a forum discussion, via a tweet from Le Carnard Noir, in which homeopaths were talking about how to encourage HIV and AIDS patients to stop taking their retrovirals in favour of taking sugar pills.

And then one of them demanded that everyone else stop making a link between HIV and AIDS. That's not just deluded, it's dangerous. And vulnerable people, who are desperate, will listen to them.

I've also learned that when people say that, "Natural is better; chemicals are bad, m'kay" they have not really thought about what it is that they're saying.

salicylic-acid.jpg?w=179
Salicylic acid - the active ingredient in willow bark

Take the example the OU gave us: aspirin was developed from willow bark, which has the active ingredient salicylic acid. In days of yore, willow bark was used to treat aches and pains, and was quite effective - except for the side effect of stomach irritation. Chemistry has enabled scientists to adapt the natural drug - salicylic acid - to acetylsalicylic acid, which does the same thing, but without the side-effects.

Acetylsalicylic acid - the active ingredient in modern aspirin

Another example is Ventolin (or to give it its proper name, salbutamol). It mimics adrenaline, a chemical released by our bodies in times of stress. As it happens, adrenaline is very effective at opening the airways, thus relieving asthma - but the last thing an asthmatic wants is increased heart rate, changed blood flow, and the jitters. Salbutamol was developed from adrenaline, but tweaked slightly so it only affects the lungs, without affecting the other organs.

The natural remedy was a great start; but most people forget (or likely don't think about it at all) that the plant evolved the chemicals for its own good; not for ours. Why would a natural remedy, "designed" to benefit the plant it came from, be ideal for use on humans with no tweaking?

Instead of bemoaning the work of modern chemistry, people should be celebrating it. It's an incredibly creative area of science, and has saved and improved countless lives.

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