The exam - and one I have not been looking forward to.
There are just so many things that they can test you on here, it seems impossible to revise everything. Some things seems to come up regularly. Cancer, and cell structural proteins - but they are both quite big subjects.
Others seem to come up at random.
The format is to do eight questions out of 12 in the first part - all of these worth 10 points. Then answer questions on a research paper that you have been given beforehand for the remaining 20 points.
Q1 is about the microfilament network. I'm better on the microtubule network, but I gave this a go.
Q2 looked horrendous, asking you to draw a sketch graph of the activation energy of an enzyme catalysed reaction. After reflecting on it for a bit though - I decided this was really just the same as a normal chemical reaction graph that I'd done in S205. I'm hoping so anyway - so tried that too. Also covered SDM and catalytic sites.
Q3 was about membrane proteins and included secondary and tertiary structure questions. I tried this one too.
Q4 was about eukaryotic nucleosomes and apoptosis. I tried this, but really couldn't remember half the proteins involved (well half is probably an overstatement - I don't think I got any of them - until I was walking down the street after the exam!).
Q5 was about mRNA splicing and the removal of introns. It also covered RNAi methods - I tried this, but again couldn't remember the relevant proteins.
Q6 was about ribosomes, and I tried this working from first principles. I knew how they worked, but hadn't revised any of the details, so I sort of shot in the dark for the explanations they required.
Q7 was about RTK signalling receptors. I had revised this - but not quite in the form the question was asking. I scratched around - trawled my memory, and guessed at some of it.
Q8 was about apoptosis and necrosis, and a bit about tumour development. I tried this too.
Q9 was about tumour development - but I couldn't remember the techniques they asked about. I think I skipped this one
Q10 was about small G proteins, RAS and VEGF. I tried this one too.
Q11 was about ageing and mitochondria. I might have attempted this - I can't remember. I wouldn't have got far if so.
Q12 was about stem cells, intestinal cells and the WNT pathway. I couldn't remember enough detail to attempt this one.
The paper is a bit of a shock to most of us. Not so many of the common topics seem to come up, and quite a few oddities come out of the woodwork in the first part. Stuff that hasn't been on previous years papers and I think many of us were scratching around for things we could answer. In the end I did manage to find 8 questions to answer, but some of them rather badly. It was good in that the first question I could answer, but then as I scanned down the paper, circling those I might try, I'd got to the last question and only ringed about 3, and some of those rather hesitantly. At the end I attempted a couple more questions as I had lots of time spare, to see if I fared any better.
In contrast the research paper seemed a lot nicer - there were a couple of questions that had to be answered with knowledge from the course, rather than digging out figures and things.
So all in all - a bit of a shock and although it was never going to be an easy paper - it was harder than most of us were expecting I think.
Tuesday, 19 October 2010
Tuesday, 12 October 2010
S366: The exam
The exam - oh my!
So the exam comes around, as always a bit of a tense time. The exam consists of several sections.
The first section is 10 questions which comes in pairs. You have to answer 1 from each pair, plus two others. So 7 questions in total from 10, but narrowed down so you have to be able to focus on the topics within each pair.
Q1 concerns 5 statements, and you have to explain why each of them is false. From mutations to molecular clocks to the allometry of horses teeth.
Q2 picks pairs of definitions and you have to explain why they are related.
I did both of these in the end, despite not quite knowing what one of the terms was.
Q3 Is about area cladograms and vicariance. Two subjects that didn't stick with me, so I missed this out.
Q4 Is about mass extinctions and what can cause them. I attempted this one
Q5 Is about the neutral theory of evolution, and molecular clocks
Q6 Concerns the different type of selection, directional, stabilising and disruptive.
Both of these tried
Q7 is about birds and sexual selection, and life balance trade offs. I tried this one.
Q8 is about allopatric selection. I wished I could remember exactly what that was - on the day I wasn't certain enough to attempt it.
Q9 Is about chromosome counts and how breeding possibilities between near relatives such as horse and donkey. I tried this one
Q10 Is about morphological constraints and how they affect things - I think I skipped this one
The next section part 2 and mandatory, is usually a question on cladograms. You have to be able to draw one usually, and usually amend it. In this exam we had to draw the given one with state changes marked on it. Then redraw it in a different format, and see which version was more parsimonious. It concerned various birds and their ancestors. I found the cladograms easier to draw than I had on mocks for this one, although I messed up the definition of sister taxon, drawing a line parallel to its sister, rather than a branch. It became obvious when the two tree lengths were the same. After looking at it for a time, and checking all the transformation states twice, I spotted the branch and everything became better.
Part 3 is also mandatory and is to do with graphs and data associated with the breeding date of birds. You are then asked to relate these things to natural selection and say whats going on. Based on the results you found you then had to infer a few things about their histories.
Finally part 4 is about a paper that you are given before hand and have to read. Then the question asks various things about the paper, and the evolutionary concepts it relates to. The paper is one from Scientific American about the loss of hair in humans, the probable time it happened and the reasons behind it. I think this went ok - but its all a bit hazy now.
All in all, it wasn't a bad exam. I'm not sure I'll have done staggering well, but enough to pass I think. It was a fair test of the stuff learnt on the course, and seemed eminently achievable. I could have done better, I could have been better prepared for some of the questions - but that is always the case. In contrast to my other exam - this seemed like a breeze!
So the exam comes around, as always a bit of a tense time. The exam consists of several sections.
The first section is 10 questions which comes in pairs. You have to answer 1 from each pair, plus two others. So 7 questions in total from 10, but narrowed down so you have to be able to focus on the topics within each pair.
Q1 concerns 5 statements, and you have to explain why each of them is false. From mutations to molecular clocks to the allometry of horses teeth.
Q2 picks pairs of definitions and you have to explain why they are related.
I did both of these in the end, despite not quite knowing what one of the terms was.
Q3 Is about area cladograms and vicariance. Two subjects that didn't stick with me, so I missed this out.
Q4 Is about mass extinctions and what can cause them. I attempted this one
Q5 Is about the neutral theory of evolution, and molecular clocks
Q6 Concerns the different type of selection, directional, stabilising and disruptive.
Both of these tried
Q7 is about birds and sexual selection, and life balance trade offs. I tried this one.
Q8 is about allopatric selection. I wished I could remember exactly what that was - on the day I wasn't certain enough to attempt it.
Q9 Is about chromosome counts and how breeding possibilities between near relatives such as horse and donkey. I tried this one
Q10 Is about morphological constraints and how they affect things - I think I skipped this one
The next section part 2 and mandatory, is usually a question on cladograms. You have to be able to draw one usually, and usually amend it. In this exam we had to draw the given one with state changes marked on it. Then redraw it in a different format, and see which version was more parsimonious. It concerned various birds and their ancestors. I found the cladograms easier to draw than I had on mocks for this one, although I messed up the definition of sister taxon, drawing a line parallel to its sister, rather than a branch. It became obvious when the two tree lengths were the same. After looking at it for a time, and checking all the transformation states twice, I spotted the branch and everything became better.
Part 3 is also mandatory and is to do with graphs and data associated with the breeding date of birds. You are then asked to relate these things to natural selection and say whats going on. Based on the results you found you then had to infer a few things about their histories.
Finally part 4 is about a paper that you are given before hand and have to read. Then the question asks various things about the paper, and the evolutionary concepts it relates to. The paper is one from Scientific American about the loss of hair in humans, the probable time it happened and the reasons behind it. I think this went ok - but its all a bit hazy now.
All in all, it wasn't a bad exam. I'm not sure I'll have done staggering well, but enough to pass I think. It was a fair test of the stuff learnt on the course, and seemed eminently achievable. I could have done better, I could have been better prepared for some of the questions - but that is always the case. In contrast to my other exam - this seemed like a breeze!
Wednesday, 15 September 2010
S366: TMA-5
TMA 5 - the final one! Three questions - but as usual, big questions with lots of sub parts.
The first question covers quite a few basic definitions of evolution, and what causes genetic variation. You are presented with various scenarios and asked to hypothesis what is going on to give the resulting diversity. It also contains a part where a mutual relationship between plants and ants is considered, and the hybridisation of two species. Finally it finishes up with a bit on Bats and the genes that have probably changed to give them their ability with questions about these concepts.
Question 2 gives you a list of scenarios a) - k) and then a list of possible answers and asked to match them up. There is not necessarily a one to one relationship between questions and answers, and also there is the additional option of "none of the above" and you can insert your own answer into the question. Its reasonably tricky, as in some cases you could easily use more than one explanation for a given event. I got most of them right, with one or two exceptions, and some of my explanatory notes were a little off the mark.
Question 3 you are given a paper to read, in this case one about the origination of dogs in the new world. Did dogs come with the settlers that had already been domesticated before, and then came across the bearing straits, or did they come over and domesticate wolves in the Americas? So lots of questions on the paper. Interpreting their cladograms, looking at the stats, trying to find out the conclusions and the supporting data.
The first question covers quite a few basic definitions of evolution, and what causes genetic variation. You are presented with various scenarios and asked to hypothesis what is going on to give the resulting diversity. It also contains a part where a mutual relationship between plants and ants is considered, and the hybridisation of two species. Finally it finishes up with a bit on Bats and the genes that have probably changed to give them their ability with questions about these concepts.
Question 2 gives you a list of scenarios a) - k) and then a list of possible answers and asked to match them up. There is not necessarily a one to one relationship between questions and answers, and also there is the additional option of "none of the above" and you can insert your own answer into the question. Its reasonably tricky, as in some cases you could easily use more than one explanation for a given event. I got most of them right, with one or two exceptions, and some of my explanatory notes were a little off the mark.
Question 3 you are given a paper to read, in this case one about the origination of dogs in the new world. Did dogs come with the settlers that had already been domesticated before, and then came across the bearing straits, or did they come over and domesticate wolves in the Americas? So lots of questions on the paper. Interpreting their cladograms, looking at the stats, trying to find out the conclusions and the supporting data.
Sunday, 12 September 2010
S377: TMA-4
TMA-4 - the last one.
Question 1 - and we're back to ICAMs. This time interaction with other molecules and cells such as T-lymphocytes. It also goes into signalling with chemokines and things like that.
Question 2 - we;re into differentiation starting with embryos. This includes going through the different mechanisms and drawing a picture for asymmetric division. Then some discussion of how possible antibodies could distort the division and what its effect might be.
Question 3 looks at the enzyme G3PDH, two versions of it. One human the other lobster. First it has to be displayed with its active site visible and showing the interactions.
Then there is a list of comparisons to be done, to compare the amino acids between the two different forms, and show how much conservation there is in the structure. You also have to predict what effect changing some of the AA might do to the activity of the protein.
Question 4 and you have to write a report based on some virtual experiments. Its not quite the normal scientific paper I've come to know that they are asking for, but something similar. There are quite tight constraints on it though. Only 4 pages, a max of 800 word, max 1 table and 1-2 figures. So emphasis on conciseness.
Slightly better marks for this one - but overall lower than I'd hoped across the whole course.
Question 1 - and we're back to ICAMs. This time interaction with other molecules and cells such as T-lymphocytes. It also goes into signalling with chemokines and things like that.
Question 2 - we;re into differentiation starting with embryos. This includes going through the different mechanisms and drawing a picture for asymmetric division. Then some discussion of how possible antibodies could distort the division and what its effect might be.
Question 3 looks at the enzyme G3PDH, two versions of it. One human the other lobster. First it has to be displayed with its active site visible and showing the interactions.
Question 4 and you have to write a report based on some virtual experiments. Its not quite the normal scientific paper I've come to know that they are asking for, but something similar. There are quite tight constraints on it though. Only 4 pages, a max of 800 word, max 1 table and 1-2 figures. So emphasis on conciseness.
Wednesday, 1 September 2010
S366: The book - part 2
The rest of the book contains the following chapters:
Section K - Genetic drift: Evolution at random
This is one of the few random bits of evolution, where mutations and other characteristics which aren;t strongly selected for settle out at random. Like blue eyes/brown eyes. Eventually they would settle out just by chance.
Section L - Natural selection and adaptation
Section M - The genetical theory of natural selection
Onto the genetics and the cellular level of natural selection.
Section N - Evolution under domestication and its relevance to the origins of natural phenotypic traits.
This is about artificial selection and what changes and traits can be preserved.
Section O - Conflict and cooperation
Symbiotic relationships, predator prey and paracitism.
Section P - Species
The rise of species.
Section Q - Speciation
Different models of how species can come about - through isolation mostly, but also through other ways such as behavioural isolation
Section R - How to be fit: reproductive success
Looking into the metric that is fitness, and how to measure it.
Section S - Coevolution: evolving interactions among species
How one species can affect another in its evolution.
Section T - Evolution and development
The whole evo/devo debate. I regret not being able to quote ontology recapitulates phylogeny in my TMA's and exam.
Section U - Macroevolution: evolution above the species level
How big changes happen - mostly small changes and lots of time.
Section V- Contemporary evolution
All about recent changes to humans, domestication and so o.n.
Section K - Genetic drift: Evolution at random
This is one of the few random bits of evolution, where mutations and other characteristics which aren;t strongly selected for settle out at random. Like blue eyes/brown eyes. Eventually they would settle out just by chance.
Section L - Natural selection and adaptation
Section M - The genetical theory of natural selection
Onto the genetics and the cellular level of natural selection.
Section N - Evolution under domestication and its relevance to the origins of natural phenotypic traits.
This is about artificial selection and what changes and traits can be preserved.
Section O - Conflict and cooperation
Symbiotic relationships, predator prey and paracitism.
Section P - Species
The rise of species.
Section Q - Speciation
Different models of how species can come about - through isolation mostly, but also through other ways such as behavioural isolation
Section R - How to be fit: reproductive success
Looking into the metric that is fitness, and how to measure it.
Section S - Coevolution: evolving interactions among species
How one species can affect another in its evolution.
Section T - Evolution and development
The whole evo/devo debate. I regret not being able to quote ontology recapitulates phylogeny in my TMA's and exam.
Section U - Macroevolution: evolution above the species level
How big changes happen - mostly small changes and lots of time.
Section V- Contemporary evolution
All about recent changes to humans, domestication and so o.n.
Wednesday, 25 August 2010
S366: TMA-4
TMA-4 - the project.
In this TMA you have to write up two reports, in the style of a scientific paper. Its a little weird as there is a limit of 2500 words split how you like between the two papers. This is not too bad, as there is a lot of basic stuff to write about in the first paper, that you can then reference in the second. Calculations and meaning of variables etc.
I did mine on the computer project, which was the analysis of a virtual populations of the Adonis blue butterfly. It was a lot of analysis of data. Analysing virtual gels of DNA of the microsatellite markers. Then there were lots of calculations to see how related populations are, and what this might mean. This meant quite a lot of quality time with excel. The calculations aren't hard, but there are a lot of them, and its easy to get so of the steps the wrong way around.
Then there are references to find, and conclusions to write. I got a little confused about some of the statistical texts, not sure how to see if they were significant or not, but in the end I did something that seemed to sort of read ok, and got not too bad a mark.
After many reads, I got a friend to also ready it, and based on comments I had, I went back and explained a lot more what the variables were and what they meant, which in turn made me understand them a lot better. So that was useful, but I did miss out a few key things in the report.
So - one TMA left.
In this TMA you have to write up two reports, in the style of a scientific paper. Its a little weird as there is a limit of 2500 words split how you like between the two papers. This is not too bad, as there is a lot of basic stuff to write about in the first paper, that you can then reference in the second. Calculations and meaning of variables etc.
After many reads, I got a friend to also ready it, and based on comments I had, I went back and explained a lot more what the variables were and what they meant, which in turn made me understand them a lot better. So that was useful, but I did miss out a few key things in the report.
So - one TMA left.
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