The rules of disorder or why disorder rules

Hi everyone,

Apologies for not posting this sooner. The paper I have chosen for this week is called "The rules of disorder or why disorder rules". It focuses on a group of proteins found in eukaryotic cells that don't have a unique three-dimensional structure, but are still functional. These proteins adopt different folds when they interact with different partners - so in essence, their function defines the structure of the protein.

I'd never heard of these kind of proteins before, so was interested to learn something more. The paper itself doesn't focus on just one protein, but gives a few different examples.

See you all at the session!

(Also - at Tomas, who I'm assuming has done up the poll that has appeared - I can't possibly answer a question that asks two questions in one with only one poll option! Have two polls for two questions :P )

Photophysics and GFP

Hi all,

A reminder that this week we're reading about photophysics. If everyone was able to post their reading on the blog as soon as possible that would be much appreciated - that way when we get to the tutorial we can discuss things that we found interesting about other people's papers, or things that we didn't understand.

This week I've chosen a paper about GFP (green fluorescent protein), for which the Nobel Prize in Chemistry was awarded last year for its discovery and development. The paper is titled 'Excited state reactions in fluorescent proteins' from Chem Soc. Rev., 2009, vol 38 p 2922- 2934 (If you're not at uni, you will be able to find the paper through the library or Web of Science).Whilst the paper at first glance appears to be a bit long, I think that the most interesting sections to us are the Introduction (which gives a good background) and section 3 - Photophysics and proton transfer in wtGFP. It turns out that the wild type version of GFP described in section 3 fluoresces much better than the chromophore of GFP on its own (described in section 2). Section 4 describes how things change when GFP is mutated, and section 5 is on 'second generation fluorescent proteins'. If you're running seriously short of time, I would at least recommend reading sections 1 (Introduction) and 3.

For those who aren't familiar with the terminology, 'quantum yield' essentially refers to the ratio of photons in to photons out. This is either expressed in percentages, or a decimal. A high quantum yield means that your molecule is very fluorescent and a high amount of light that goes in is converted into fluorescence. A low quantum yield means that most of the light that goes in decays non-radiatively, and most of the light energy is not re-emitted.

For those that are stuck as for where to look, some good examples of photophysics are molecules that use FRET, or the use of FRET to get information about your molecules of interest, biological molecules that fluoresce or absorb light, articles about the use of GFP (the one I have posted is mostly about energy transfer in the molecule itself) or in photosynthesis (I only discussed purple bacteria in my talk). Once you start looking, you should find lots of examples.

This week's reading

Hi all,

Just a reminder to everyone that we're supposed to be posting our reading for the week on the blog so everyone else can have a look at it and so we have something to discuss at our meeting tomorrow. If someone else could post something before late tonight so that I have a chance to look at it before tomorrow that would be great.

Kristen

Neural Networks Introduction

I had a flick through the Biophysics textbook by Cotterill, which had a section on neural networks. Since we probably don't all have access to that particular book, I've done a summary of it and uploaded my summary here. It's pretty basic, but I thought it would be good background reading to get us started. Let me know if you have any problems with the file.

I tried to look for some of Steinbuch's original papers. Unfortunately, the UQ library doesn't seem to have access to a lot of them, and the ones that I did manage to view were all in German.

If I get the time, I'll try to post a relevant paper.

If there is anything confusing or that doesn't make sense in the summary, feel free to comment.

This week

Welcome back!
I trust you had a good week with a break from lectures (n.b., I did not say holiday).
Tomorrow we will discuss the last chapter of Nelson. It is a great one.

Biological question: How can a leaky cable (e.g., a neuron) carry a sharp electrical signal over long distances?

Physical idea: Nonlinearity in the cell membrane's conductance turns the membrane into an excitable mdedium, which can transmit waves by continuously regenerating them.

On more mundane matters on tuesday I want to
-give you a TEVAL to complete
-pin you down on paper presentation topics
-remind you of the assessment details

Also, I will be away for the following 3 weeks, but Seth will attend the tuesday tutorials and talks.

Modelling complex systems

I'm yet to finish my Chapter 9 reading, but I thought I would post an idea from Chapter 9 which is probably more widely applicable.

At the beginning of Chapter 9 of Nelson, it is argued that when studying a system which has a large number of constituents which are allowed to interact - such as a biological system - the analysis of the system can be greatly simplified, using just a few degrees of freedom to effectively describe a system's behaviour.

So when you have a large interacting system - our analysis can be made more simple if we first stop to think about what are the parameters that we can use that will more widely describe the bulk behaviour of the system. I think that at times this might seem like an oversimplification, but I think when analysing a large complicated system, we need to think about what questions we're really trying to answer, and what parameters are the most important that will allow us to answer that question. If you tried to take everything into account, then at times it's going to take far too long and will be far too complex to model, when some of the minor details may not matter when trying to answer a particular question about your system.

This week's Reading

Just a reminder about the reading for this week:

We decided at the Tuesday tutorial that we wanted to be able to have time to cover topics outside of Nelson, and we knew that Alex wanted to cover some of the Enzyme material on a week when he'd definitely be able to make it. To that end, this week we're reading Chapters 9 and 10 of Nelson. Since two chapters is a lot of reading, Ack and myself will be reading Chapter 9 and Tomas, Michael and Alex will read Chapter 10, and we'll get together and teach each other any material we've missed out on at the Tuesday session.

Ross and Seth - I'm guessing you guys could just pick whichever one you found more interesting.

Kristen

Comments on Chapter 6 so far...

I have found the beginning of Chapter 6 to be very dry. To me it seems like it presents a lot of formulae all at once, and had I not seen some of that material before, I don't think I'd be able to take it in all at once. To that end, to anyone who is more interested in learning more about statistical thermodynamics I would recommend having a flick through the relevant chapters from Physical Chemistry by Atkins (any edition) or An Introduction to Thermal Physics by Schroeder. Having said that, we've probably already got a lot to digest!

It strikes me as odd in that in the entire Chapter 6 of Nelson, there is no mention of the equipartition theorem (where you have 1/2 kT of internal energy per degree of freedom in your system), but it is implied when Nelson presents a lot of results about ideal gases. I would have thought that it would be important to explain how you get, for example, the internal energy of an ideal gas, rather than just presenting the results and using them to derive other results. Perhaps it's more of a physicist thing to be concerned about the equipartition theorem - do 'biophysicists' not care about it as much?

Upcoming Reading

So for next week, we're doing the reading for Chapter 4 of Nelson, but the week after (if we follow the book), we'd be set to read Chapter 5, entitled "Life in the Slow Lane: The Low Reynolds-Number World". While the contents of the chapter are definitely important to some aspects of biophysics, the year I did PHYS2170, the second year biophysics course, we covered a lot of that material in quite a bit of depth. To that end, I'd like to propose that we skip Chapter 5 in our reading.

If I'm outvoted and everyone else would like to study Chapter 5, then that's fine, but I just thought I'd put the suggestion out there. Thoughts?

Tutorial Tues 18 August

For those of you that weren't at the tutorial on Tuesday, here is a summary of what we discussed.

We discussed Chapter 3 of Nelson. The first part of the chapter gave some details of statistical analysis, and went on to talk about Activation energy, and how it was related to a distribution of molecules. Not all molecules in the system will have the same energy and the high energy molecules are the ones that are able to get over the barrier first.

There also seemed to be two sections of Chapter 3, which seemed to be unrelated at first glance. We spent a little bit of time discussing the link between the two sections, and concluded that the second part of the chapter was trying to emphasis that there was a stable entity that could encode genetic information, and the stability arose from the high activation energy due to chemical bonds.

We talked about how the distribution of energy of molecules in a system had a Gaussian shape, and that this held regardless of the details of the system (the type of molecules, for example), as long as we could treat the system as an ideal gas.

We also discussed how crossing over is a process which creates diversity, and that it would probably be a rare occurance. The genetics section was trying to emphasise the point that if we take simple physical arguments, and apply statistical reasoning, we can infer things that we can't see - in this case, the encoding of information. It is also important to be able to find a good model system. For most genetics work, this model system is Drosophila Melanogaster, the fruit fly, which enabled study of genes more easily as it has large polytene chromosomes present in its saliva.

Chapter 3

Where are all your posts guys?
How are you going with the problems from chapter 2?

Here is my take on chapter 3.

Tomorrow morning I will select some problems for you to do and hand in by next tuesday.

See you 10am tuesday.

Biophysics vs. Biological Physics

I’ve wondered before if there’s any substantial difference between the terms “biological physics” and “biophysics”, because it seems that they’re sometimes used interchangeably. Then reading back over Ross’s condensed concepts post on July 22, I noted he had made a distinction between the two terms so I thought a bit of clarification early on would be a good idea. The best I’ve come up with is this:
Biophysics = existing physics applied to biological problems. We know the physics and we know the biological entities involved. Eg. action potentials in neuron firing.
Biological physics = developing new physical models relevant to biology. We might use existing physics concepts / approaches, but come up with descriptions that are “new” at least insofar as they are different qualitatively from existing models. Eg. ion channels?
Does this sound reasonable to you? Is there an example of biological physics that is more clearly different from biophysics? Does it matter?

This second definition sounds a little like the description Nelson gave in 1.3 of how physicists and biologists can best work together: as well as using powerful existing experimental and theoretical tools from physics to explore biology (eg. X-ray diffraction and…the maths used to describe co-operative helix-coil transitions in DNA), physicists can apply their knack for simplifying things to deduce new nontrivial, testable and relevant (!) hypotheses from simple accurate models of biological situations.
As a physics student with little background in biology, it’s been interesting to read chapter 2 this week while keeping in mind that a number of great “solutions” to problems in biological physics have, in the end, looked a lot like straight biology. That is, solutions have ended in suggesting the existence of new biological entities (some of which were among the different supramolecular complexes considered in ch. 2!!) such as ion pumps.

Reading chapter 2

I posted a few brief comments on condensed concepts

Free Energy

Chapter 1 of Nelson's book to me felt a bit like revision. It went over a few important concepts for us to know, focusing on thermodynamics, which is very important for a biological system. I think that there was a lot of focus on making sure we realise how physics, and physical methods can apply to biological systems.

I think a lot of the main concepts in the chapter have already been discussed by Ross, but an important concept for me was the concept of minimisation of free energy, which can spontaneously drive processes in a system. Whilst the book doesn't give many direct biological examples, I still think that this is important. Free energy minimisation can be an important tool in structure prediction of proteins, where it is used to try and determine how a protein will fold, based on its amino acid sequence. A likely structure is found when there is a free energy minimum, found using computational methods and taking into account forces between the atoms. Unfortunately, though, this free energy minimum may be only a local minimum, so several likely protein structures can be found. I am yet to find a good reference on the internet that explains this further - so if anyone has one, feel free to comment.

Molecular motors were described as "free energy transducers" by Nelson. This is a youtube video of the molecular motor kinesin. This molecule transports other molecules, and sometimes organelles such as mitochondria around the cell by converting ATP into energy, and using that energy to "walk" along.

For me, this chapter didn't bring much that was new to the table, but I think laid the foundation for future chapters. It will be interesting to see how Nelson further develops the main ideas in Chapter 1 as the book progresses.

- Kristen

Questions on chapter 1 of Nelson

I hope you are enjoying chapter 1 which I emailed around last week.
I have posted two items on my condensedconcepts blog about it. Now, that I can post
on this one I will start posting here.

What questions do you have?

What do you think the main points were?

Maybe someone could find a good youtube? video of
-reverse osmosis
-a molecular motor