S377: Book 3 - The Dynamic Cell (Vol 2)

Book 3 which is confusingly entitled The Dynamic Cell - Volume 2 carries on from the previous book.
There are just three chapters in this, although some of them are pretty big.

Cpater 12 Transport and Compartmentalization: It starts with a chapter on transport and compartmentalisation. This covers how the cell moves stuff around, how signal in the code are recognised as labels to send the packages to the correct destination. It also looks at hte transport network, which moves these vesicles around. It covers endocytosis (bringing stuff into the cell) and exocytosis - the opposite. 64 pages in this chapter!

Chapter 13 Signal Transduction: The next chapter is about signal transduction. How signal are recognised on the cell surface and how they trigger cascades. Also some words on the different receptors and ligands that are in common usage.

Chapter 14 Cell Death: The final chapter is on the subject of cell death. All cells have the ability to commit suicide, either on command or if they detect things are going wrong. So this chapter covers some of the mechanisms that trigger these events.

So 180 pages or so in this book.  Some of it is pretty heavy going, but interesting.

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S366: TMA-2

TMA 2

This is a bit of a weird one. Its one of 5 pieces of coursework for this course, but this only counts 5% towards the total of assessed work. You have to pick a sort of project thing to do that explores evolution a bit There are 4 projects on offer.

• Bird Predation Project -this is where you bake little bits of coloured pastry and look to see if there is selection of the bait favoured by the birds coming to feed on it in your garden.
  
• Conservation genetics project -Looking at two different species of tree or flower and making measurements.
  
• Hybridisation project -A computer based butterfly project, where you look at microsatellite information to see what populations of butterflies exhibit and how related they are.
  
• Snail shell project -collecting common garden snails and looking at the banding on them. This is an extension of the S170 work.

I chose the conservation genetics project, as I like computers and am fundamentally lazy!
Anyway - apparently this TMA is a forerunner for TMA-4 which counts for 30% of the marks, and requires you to write up two experiements for the project. So this TMA is for you to make mistakes in, and mess up calculations and graphs so it can be corrected.

I spent a long time on it though, far longer than the 5% justified. However I hope quite a lot of it will be reusable for the TMA4.

The TMA also has a proforma like thing where it tells you what data to put in, what calculations to make and what questions to answer, so it is fairly easy to tick all the boxes.

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S366: The book

As I've said, this course is a combination of two books. The text book that comes with it, and the companion text which tells you which bits to read. Sometimes this directs you to read a whole chapter, sometimes just bits and the companion text then has lots of text to read that replaces or supplements that in the text book. So what do we do in this course? Well here are the first few chapters. All labelled with letter of the alphabet.

Section A Evolutionary biology - this is an introduction to evolution. Where it stands, what its principles are, how secure it is etc. Sets the scene nicely.

Section B Adaptation - here we look at some examples of adaptation. It includes a DVD video on Adaptation in Svalbard reindeer. Some reindeer that are unique to a small island, which has influenced their evolution.

Section C The Tree of Life: classification and phylogeny. Lots of stuff on constructing cladograms, and phylogenetic analysis. Several exercises to do here, some stuff for TMA 1 too.

Section D Patterns of evolution - more on phylogeny, and a look at trends and adaptive radiation.

Section E Evolution in the fossil record - some examples including the origin of feathers and the ancestry of birds. A look at fossil trends, punctuated equilibrium, and this is where the brachipod stuff fits in.

Section F A history of life on Earth - From Earth’s earliest life, through evolution in the precambrian to evolution in the more recent eras.

Section G The geography of evolution - looking at geographical influences, barriers, climates, ecologies.

Section H The evolution of biodiversity - which looks at how to quantify taxonomic diversity, mass extinctions, and so on.

Section I The origin of genetic variation and Evolution of genes and genomes - here we look at genes and genomes, how mutations occur and the randomness of it. Also things like recombination, the origin of new genes and then some parts on the phylogenetic processes applied to genes.

Section J Variation - Distinguishing sources of phenotypic variation, some work on population genetics, molecular markers and qunatative traits. Some maths involved here.

So - thats about half the course.

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S377: Book 2 - The Dynamic Cell (Vol 1)

This is the 2nd book of the S377 course.

We start to get into a lot of the cellular stuff here. The chapter numbers follow on from the first book - so it starts with Chapter 7.

Chapter 7 - Introducing the Dynamic Cell is quite brief, and is an introduction to the cell and its contents. Nothing particularly new here, but it sets the scene.

Chapter 8 - The Cell Cycle is much more in depth. We cover the mechanisms of mitosis, the cell cycle meiosis and cell division. However this is in quite gory detail. I'm sure many people have seen videos of chromosomes lining up and then separating to opposite ends of the cell. All very nice, I've even seen it under the microscope, although of cells caught in the act rather than dynamic. However you have to ask here, how do the chromosomes move around, how do they pair up, how do they line up? What causes them to separate and how does the cell arrange for it to happen without error.

Chapter 9 - DNA Replication and Repair - again something I've covered many times before. However not in this detail. The typical animated image shows DNA unzipping and getting copied just like that. However its a lot more complicated than that. For instance as the strands separate under the influence of a enzyme, the twisted nature of DNA means that further up the molecule it starts to get all twisted and under tension . Its like unwinding the strands of string, as you pull them apart if starts to ravel up further down. DNA is also often packed up into compact structures, which have to be unpacked before you can even start the replication. Then there is the problem of replicating the lagging strand, the fact that to replicate something like human DNA in any reasonable time you have to have lots of replication at the same time doing different bits, that then all have to get joined together. Yes - its complicated. Then there is repair...

Chapter 10 - Gene Expression - this chapter is all about how genes are switched on and off. Lots of stuff on operon, enhancers, silencers and so on. The infamous Trp operon is considered.

Chapter 11 - Translation and Protein Turnover - the last chapter of this book. Considers how the ribosomes work, how they match the tRNA to the mRNA, and how the tRNA gets the right amino acid attached to itself - again something normally skated over. There is also alternate splicing, mRNA regulation, post transcription modification, nuclear export - lots of details here.

Some fascinating stuff here - and some stuff that is not too well understood.

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S377: TMA-1

The first TMA of the course - and its a long time until the submission date. Given I started the reading before Christmas, the April submission date is a long way in, and I've read past most of the relevant material, so some rereading is required.

So there are 5 questions to answer.

Question 1 is about enzyme structure. It looks at a kinase and you have to make some general comments on structure, domains and function.

In Question 2 we have to look at a 3-d molecular model and identify and measure parts of it. There are also tasks to perform. Also required is to include an image of the enzyme active site.

Question 3 simply gives you some concentration data and asks you to work out the equilibrium dissociation coefficient of a ligand and its receptor. The question is a little sparse as it doesn't really give much guidance on what is wanted in the answer except the value.

Question 4 is about SDS-PAGE and requires you to run gels on the computer simulation with a number of kinases and antibodies to work out what the results tell you.

Question 5 is all about reading scientific literature. You are given a piece of writing and then have to make sense of it and answer a number of questions about what its conclusions are.

Not a bad TMA in some ways - but a little disappointed with the mark I get.

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S366: TMA-1

So - time for the first TMA. Its quite a long way into the course, so you have a lot of time to devote to it if you want - or alternatively to ignore it!
So whats in this TMA?

Well - first thing to say is its big! Its 12 pages long, and for 3 questions thats quite a lot.

The first question is all about phylogenies.
First you have to identify a range of features in a sample, preparatory to doing an analysis on it.
Next you have to look the cladogram of these species and pick out some features in it.
Then you have to indicate the most parsimonious transitions on the diagram, which means finding the transition points for the 10 different features being considered.
Then there is more commentary required on the shape of the cladogram, and what this says for the inter-relatedness of the species.
The next step is to input the characteristics into a program, and perform your own cladogramatic analysis.

The next question is about statistical analysis - and it brings in the home kit.
A while lot of work is required to analyse some given data, and relate it to the data you have worked out from the home kit. There is a log of statistical manipulation required here. None of it is hard, but one figure feeds into the next, and its easy to make a mistake - subtract rather than add, or pick the wrong figure to divide by.
A couple of graphs have to be drawn or amended, and then commentary has to be made on the results and what they show of the species and now they are related. Whether their growth patterns are similar. You also have to make some predictions on what this might mean if you found new samples.

Finally question 3, which is 10% of this, is a SWOT analysis of each of the potential projects that need to be undertaken for the next TMA. It also includes a risk analysis section, which I struggle to take seriously, but complete through gritted teeth!

The course team reckoned 5 hours to complete the TMA, I wouldn't like to think how long I spent on it though.

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