In response to Charlotte and Emma or Emily, or possibly both, a little clarification of meiosis.

I think  it is probably the language that becomes confusing here, since there are chromosomes, chromatids and bivalents all floating around in the mix.

Unlike mitosis, there is no cell cycle. This is because after mitosis each daughter continues in a cycle like the parent cell of growth, DNA and organelle replication etc. Gametes end up with  a haploid chromosome number, so they do not divide again. However, it is worth considering the cell cycle in terms of the cell just prior to the gamete (primary spermatocytes and primary oocytes) since it is during interphase that the DNA is replicated. Remember that you can’t actually see that the DNA strand (and therefore each chromosome) has replicated until the supercoiling during prophase. Nevertheless, the replication occurs during the cell cycle so that each chromosome strand now consists of two sister chromatids.

Refer to it as a chromosome when single strand, a chromosome comprising two sister chromatids after DNA replication.

The first stage of meiosis is similar to mitosis (PMAT) but are numbered, e.g. prophase 1, metaphase 1. During P1 the chromosomes condense and become visible. This is when they take on the characteristic ‘X’ shape with the centromere holding the two sister chromatids together. Each of the homologous chromosomes (e.g. pair number 22, or pair number 9) pair up near the other (remember each of the pair of chromosomes is made up of two sister chromatids, so there are now 4 strands of DNA involved). When the homologous pairs are adjacent they are referred to as bivalents.

The bivalents then undergo crossing over, or chiasmata (singular chiasma) where portions of genetic material are swapped between non-sister chromatids within a bivalent. The 23rd pair of chromosomes only show a small amount of crossover. 

in M1, the bivalents line up opposite each other at the cell equator, and are pulled apart by spindle fibres in A1. This is the key step to remembering the difference between mitosis and meiosis stages: in meiosis the bivalents are opposite each other, in mitosis the chromosomes all line up across the equator. Remember that in each bivalent, there is a chromosome (made of two sister chromatids that have undergone chiasmata) from the mother and one from the father. It is random as to which side of the equator the maternal and paternal chromosomes line up, another source of variation.

After T1, the second phase of meiosis occurs (P2, M2, A2, T2), to produce the 4 haploid gamete cells. The second part od meiosis proceeds in pretty much the same way as mitosis, but with only half the number of chromosomes present.


It’s all about the lymph…

In response to Sophie’s question…


Tissue fluid (or interstitial fluid) is the fluid that surrounds our cells. It is basically water with dissolved solutes like sugars, salts, amino acids and waste products from the cells. Blood vessels have pores in them that allow the movement of molecules between the tissue fluid and the blood plasma (which is pretty much the same composition as the tissue fluid. You can think of the cells as balloons full of water sitting in a bath also full of water. Molecules are moving between tissue fluid and the cells (osmosis, diffusion for example) constantly; the presence of the cell membranes allow some molecules to build up in concentration and to separate the cell from its surroundings.

Lymph is tissue fluid that has entered the lymph channels (the system of vessels that lymph fluid moves through).  Lymph transports excess tissue fluid and proteins back to the blood. Lymph nodes are ‘blobs’ along the lymph channels filled with white blood cells that destroy pathogens. The lymph is moved along the channels by the incidental movement of skeletal muscle and some peristalsis.  Unfortunately, lymph channels also sometimes act as a quick route around the body for cancerous cells that have broken off from a tumour, which are carried around the body and may start growing in other tissues (metastasis).

What is the point of wasps?

Since summer is coming to a close, and I was in my back garden this morning, I thought I’d write a little bit on this common question from the classroom. It comes in several varieties, but mostly it has stemmed from some unpleasant encounter with the little striped beasties that resulted in stings and tears, or at the least a flurry of ineffective arm waving. It’s an interesting question because we can look at it from a number of perspectives.

1) Biological – When we talk about wasps, we are usually referring to the common wasp Vespula vulgaris (notice the latin here – Vespa is Italian for wasp, vulgar refers to common or popular, not bad taste! You will find many common organisms have the species name vulgaris in the binomial naming system). There are however hundreds of different wasp species, any of which are important parasites of other insect pests. The common wasp is omnivorous, preying on insects early in the yearly cycle (late spring to autumn) as food for larvae, and feeding on sugary nectar early in spring and summer. Larvae produce a sugary secretion the adults feed on, but later in summer this is insufficient for adults that start to feed on high sugar sources (like your drinks and food). So the ‘point’ of a wasp is the that it is a part of an ecosystem and food chain. Removing the wasps would affect other organisms in the ecosystem. From this perspective, the question of what is the point of any particular organism becomes redundant. Which brings us to…

2) Philosophy of the question – Asking what is the ‘point’ of something comes with a lot of assumptions. For example, it is an assumption that there is a point, at least in the a way that would make sense to us. If we asked what was the point of bees, worms and giraffes, you might answer something along the lines of pollination, soil aeration and…well, what is the point of a giraffe? The first two answers of course look at what is the point of the animal in relation to us – we get something out of pollination and healthy soils. This is the root of the problem; the original question could be rephrased with the missing assumption ‘What do wasps do for me?‘. Not a lot, but why do you think they should? is a reasonable answer.

This approach of seeing things through your own perspective is a subtle trap for scientists, and one that you should try to avoid. In science we go to great lengths to take the personal out of the subject; we often write using the passive voice for example, and try to avoid personal bias in research and experiments. This is similar to anthropomorphism that we have mentioned in the class – giving human attributes to animals and inanimate objects (…the sugar molecules want to move through the membrane…) and although it is difficult to avoid doing it we should make efforts to be more scientific with our language. Ascribing meaning to events only in terms of cost or benefit to ourselves is sloppy thinking.

And eventually…alcohol dehydrogenase

I said I’d do this sometime back in response to a question from, um…someone. Now we are into the glorious long summer and I have more time, some words on alcohol dehydrogenase.

Its role on humans is to convert ethanol to less harmful substances. It does this by oxidising ethanol CH3CH2OH to the toxic chemical acetaldeyde CH3CHO (notice what has happened in the oxidation reaction, look at the enzyme name as well). This is then oxidised further into harmless acetic acid (bonus points for working out the name of that enzyme).

However, the place we first encountered alcohol dehydrogenase was in the anaerobic respiration pathway of yeast, where pyruvate was decarboxylated to ethanal, which was then reduced further to ethanol with hydrogen from reduced NAD. Remember that the advantage of this step is to re-oxidise NAD so that more H can be accepted during glycolysis. This presents a few questions.

1) what is the difference between acetaldehyde and ethanal?

Nothing, it is the same chemical. Ethanal is an internationally accepted name, whereas acetaldehyde is a name in common usage by some people. I’m afraid it’s an example of scientists from different areas using different names for the same thing. I’d suggest sticking with ethanal (if in doubt, go with the syllabus).

2) If enzymes are specific, how come it is doing two different things in two different places?

This is really the same reaction in reverse (although there are actually quite a lot of different versions of alcohol dehydrogenase, we’ll leave that aside). Enzymes speed up the rate of a reaction, but they do not alter the equlibrium. In simple terms, in the case of yeast and human liver we have different substrate concentrations, leading the equilibrium in one direction more than the other.

Ethanol production in yeast gives the fungus an advantage because it is toxic to other organisms. What is the advantage of alcohol dehydrogenase in humans? Ethanol occurs naturally when fruit begins to ferment. Our ancestors diets included fruits, so anyone with this enzyme would have had a natural advantage in removing the toxin.

You asked part 2

Jack raised the point about theories in the lesson this week. In science, a theory has a different meaning to how we use the word in everyday language. Theory can be used to mean a conjecture, idea, speculation or simply a guess about why something happens. This use is fine as long as you realise that words can have multiple meanings, and the context the word is used in is important.

In science, a theory denotes something else. It used to describe statements or principles that not only describe what is happening, they also provide an explanation. It has predictive power, in other words a theory can be used to predict an event or observation that has not yet happened. Theories are well tested and have evidence to support the statements. If you wanted to show that a theory is incorrect, you could show that the predictions it makes do not happen under experimental conditions.

To give an example, let’s take the good old theory of evolution. Broadly speaking, it would predict that organisms closely related would share more genetic similarities than more distantly related organisms. If you found a monkey more closely related to a fish than a gorilla, you could start questioning the theory. Older fossils should be found in older rocks – if you found a human remains mixed in with a T rex’s bones then you may have a problem. So far these things have not occurred, but if they did and were shown to be valid (e.g. not faked) then the theory would be changed. Theories are changed in reponse to new evidence, that’s how science works.

In the example Jack brought up (ATP synthase mechanism) the theory is incomplete because it doesn’t provide an explanation for all observations. Although there is no hierachy of theories, some have been tested more than others so we often consider them to be more robust. Many accepted theories are used simply because they work well enough for the time being, in other words they hold up to testing so far.

Scientific theories are often described as falsifiable. This means that you could potentially cause a theory to be changed or abandoned by evidence that shows its predictions do not hold up in experiment or observation. Knocking down established theories is a good way to get a Nobel prize. But there’s a reason why the big theories are rarely abandoned…

You asked part 1

Since Charlotte asked about the proton pumps, I thought I’d go into a bit more detail.

The pumps are referred to as complexes, given Roman numerals I, II, III and IV. Complex I is really an enzyme, called NADH dehydrogenase (why is it called a complex? There are 45 separate polypetide chains). 2 electrons are passed onto a substance called ubiquinone (or just Q), which is reduced to ubiquinol (QH2). This is lipid soluble, and moves easily through the membrane. 4 protons are pumped through the membrane.

Complex II (aka succinate dehydrogenase)  gives additional electrons to Q, which is then passed to Complex III (aka cytochrome bc complex). Here the electrons are passed on to another molecule, cytochrome C. 6 protons in total are translocated (moved across the membrane) at this point. Finally cytochrome C (whgich is a water soluble, integral protein membrane) electrons on to Complex IV, where the electrons are removed and used in reducing oxygen to water. Cytochrome C is inhibited by cyanide – a poison which will stop aerobic respiration.

Here’s a nice summary from wikipedia:

In eukaryotes, NADH is the most important electron donor. The associated electron transport chain is

NADHComplex IQComplex IIIcytochrome cComplex IVO2 where Complexes I, III and IV are proton pumps, while Q and cytochrome c are mobile electron carriers. The electron acceptor is molecular oxygen.

Remember, you will be tested on what is in the specification, but reading further in your subject will always help.