Monday, August 31, 2009
Drag profiles of mammals
For some interesting information on the drag profiles of several mammals in the laminar and turbulent regimes, skim through pages 82-88 of Fish, FE (1994). Influence of Hydrodynamic-Design and Propulsive Mode on Mammalian Swimming Energetics.Australian Journal of Zoology42, 79–101..
Friday, August 28, 2009
Turning back the clock in these turbulent times
I am enjoying reading Nelson at 2am saturday morning in Toronto. (I am still jet-lagged). I found several nice videos about turbulent and laminar flow.
This video shows how as the velocity of flow increases above a critical value (determined by the magnitude of the Reynolds number) that there is a transition to turbulent flow.
This video shows dramatically what the static photos in Figure 5.1 show. That at low Reynolds number (i.e., for laminar flow) it looks like mixing does not happen.
Enjoy!
This video shows how as the velocity of flow increases above a critical value (determined by the magnitude of the Reynolds number) that there is a transition to turbulent flow.
This video shows dramatically what the static photos in Figure 5.1 show. That at low Reynolds number (i.e., for laminar flow) it looks like mixing does not happen.
Enjoy!
Wednesday, August 26, 2009
"Real" Biophysics, Levinthal's Paradox and Dawkin's Weasel
In the last session, we made some hash about the "what is biophysics?" question, and at some points the idea of "real" biophysics came up. I have thought some more about this, and have something to write on the issue.
I am always nervous about putting a pin on a "real" anything, because "real" is often defined as the complement of "not real", and I usually am loathe to throw anything out.
Instead, let's use "ideal"...
Seth's definition of Ideal Biophysics: Ideal Biophysics is what occurs when you can't understand the biology without physics, and you can't understand the physics without biology.
OK. It is apparent (to my biased view) that there are more examples of where physics makes sense out of biology than the other way around. But, I can think of an example. The example is Levinthal's "paradox". Like most paradoxes in physics, it isn't. It is a "straw man". It does make a point though. Here goes...
Consider an idealized protein. It is a polymer of N amino acids (AAs). Now, assume the bond between each AA can only take a few orientations M. Now the total number of protein conformations is N^M (^ is "to the power"). To put a more concrete face on it, let's say N=101 and M=3. Then there are 3^101 conformations of the protein. Now, let's assume that the protein can switch conformations at the rate of 10^13 per second (this is actually ~100-1000 times too fast to be realistic). Then we conclude the following: if the protein finds it's native state by a random, serial, sampling of the available states, then it should take ~10^27 years to fold, approximately. This is longer than the age of the universe.
However, protein's fold in, at most, minutes and usually in milliseconds or seconds (101 residues is not large, so the latter is more reasonable for our ideal case). How does this happen?
We'll answer it by posing another example, put forward by Dawkins (of "Selfish Gene" fame). Dawkins asked how long it would take a monkey to write Hamlet's quote "Methinks it is like a weasel." There are 28 characters, including 5 spaces. The alphabet has 27 characters for each location (26+space). If the monkey only had these letters on a keyboard, it would take ~10^40 keystrokes. However...
If the monkey cannot change those letters that are already correctly in place, then the monkey takes only a few thousand keystrokes!
OK. So what's the point? Is it time to put me in a straight jacket? I hope not. The point is that getting around the "paradox" requires the presupposition that certain arrangements are "correct". This is not spooky, really. What it means is that understanding the physics of protein folding requires understanding that evolution has taken place and is ongoing - a biological fact. Put another way, what it means is that when we start by saying "consider a protein" we are automatically excluding those sequences which can only fold by executing a serial search of the available conformational space.
More precisely, and to bring in more ideas from the last session, the statement should read more like "consider a functional, single-domain protein". What Levinthal was getting at (he wasn't confused - he set up the paradox to shoot it down) was that the ensemble of possibilities given "functional single-domain protein" automatically must exclude a very large number of possible amino acid sequences. The ability to fold in biologically relevant time is a constraint on the ensemble.
And, as I mentioned, when you see a "funnel" representing a protein landscape, the usual X-axis is literally "the number of native contacts" in the same way that you could consider the "number of correct letters" as a suitable reaction coordinate for the Hamlet-writing monkey.
-Seth
I am always nervous about putting a pin on a "real" anything, because "real" is often defined as the complement of "not real", and I usually am loathe to throw anything out.
Instead, let's use "ideal"...
Seth's definition of Ideal Biophysics: Ideal Biophysics is what occurs when you can't understand the biology without physics, and you can't understand the physics without biology.
OK. It is apparent (to my biased view) that there are more examples of where physics makes sense out of biology than the other way around. But, I can think of an example. The example is Levinthal's "paradox". Like most paradoxes in physics, it isn't. It is a "straw man". It does make a point though. Here goes...
Consider an idealized protein. It is a polymer of N amino acids (AAs). Now, assume the bond between each AA can only take a few orientations M. Now the total number of protein conformations is N^M (^ is "to the power"). To put a more concrete face on it, let's say N=101 and M=3. Then there are 3^101 conformations of the protein. Now, let's assume that the protein can switch conformations at the rate of 10^13 per second (this is actually ~100-1000 times too fast to be realistic). Then we conclude the following: if the protein finds it's native state by a random, serial, sampling of the available states, then it should take ~10^27 years to fold, approximately. This is longer than the age of the universe.
However, protein's fold in, at most, minutes and usually in milliseconds or seconds (101 residues is not large, so the latter is more reasonable for our ideal case). How does this happen?
We'll answer it by posing another example, put forward by Dawkins (of "Selfish Gene" fame). Dawkins asked how long it would take a monkey to write Hamlet's quote "Methinks it is like a weasel." There are 28 characters, including 5 spaces. The alphabet has 27 characters for each location (26+space). If the monkey only had these letters on a keyboard, it would take ~10^40 keystrokes. However...
If the monkey cannot change those letters that are already correctly in place, then the monkey takes only a few thousand keystrokes!
OK. So what's the point? Is it time to put me in a straight jacket? I hope not. The point is that getting around the "paradox" requires the presupposition that certain arrangements are "correct". This is not spooky, really. What it means is that understanding the physics of protein folding requires understanding that evolution has taken place and is ongoing - a biological fact. Put another way, what it means is that when we start by saying "consider a protein" we are automatically excluding those sequences which can only fold by executing a serial search of the available conformational space.
More precisely, and to bring in more ideas from the last session, the statement should read more like "consider a functional, single-domain protein". What Levinthal was getting at (he wasn't confused - he set up the paradox to shoot it down) was that the ensemble of possibilities given "functional single-domain protein" automatically must exclude a very large number of possible amino acid sequences. The ability to fold in biologically relevant time is a constraint on the ensemble.
And, as I mentioned, when you see a "funnel" representing a protein landscape, the usual X-axis is literally "the number of native contacts" in the same way that you could consider the "number of correct letters" as a suitable reaction coordinate for the Hamlet-writing monkey.
-Seth
Just so we have it in writing: everyone seemed happy with the suggestion that the final due time for the assignments would be our old meeting time of 12:00 (midday) Thursday at the room we currently meet in. Tomas if you want to hand yours in at 11 because of you lab meeting at 12 I will be at the room from 10:50 to 11.05 for you but have a class I need to be at so cant be there any longer than that. Hope this works for everyone just comment here if there are any problems.
Michael.
Michael.
Monday, August 24, 2009
Recap & Chapter 4 Problem Set
The minutes of this weeks meeting (as I remember them):
1.We will read and discuss Chap 5 of Nelson.
2. Chap 3 problem sets are to go to Michael. I will furnish Michael with the answers as soon as I receive them. Michael will decide how to deal with late submissions (the only contraint being that the policy is dealt consistently in all cases, even his own).
3.The course syllabus is up to the students. Paper discussion is on the agenda. We (Ross and myself) will suggest papers, but so can all of you.
4. The steady state is important for model problems in Biophysics, even if it is not the same as equilibrium. In many cases, it sets boundary conditions on the diffusion equation which lead to interesting and relevant solutions.
4. We all want to understand Maxwell's Demon.
5. Biophysics is difficult to define, but nonetheless interesting.
If I missed anything, please chime in.
The problem set for Chap. 4 is: 4.2 (a-c only), 4.3, 4.7. Enjoy!
1.We will read and discuss Chap 5 of Nelson.
2. Chap 3 problem sets are to go to Michael. I will furnish Michael with the answers as soon as I receive them. Michael will decide how to deal with late submissions (the only contraint being that the policy is dealt consistently in all cases, even his own).
3.The course syllabus is up to the students. Paper discussion is on the agenda. We (Ross and myself) will suggest papers, but so can all of you.
4. The steady state is important for model problems in Biophysics, even if it is not the same as equilibrium. In many cases, it sets boundary conditions on the diffusion equation which lead to interesting and relevant solutions.
4. We all want to understand Maxwell's Demon.
5. Biophysics is difficult to define, but nonetheless interesting.
If I missed anything, please chime in.
The problem set for Chap. 4 is: 4.2 (a-c only), 4.3, 4.7. Enjoy!
Tutorial Questions
Hey if anyone wants to discuss the tutorial questions for this week I will be in the physics tea room the same as last time from 9 to 10 just before our session.
Saturday, August 22, 2009
Myoglobin structure
The protein that I've chosen to look at is myoglobin, which incidentally was the first protein structure to be found. Here is a picture of the structure:
Myoglobin binds carries oxygen in muscles, and binds oxygen at the heme group. The heme group is a porphyrin, which contains an iron atom at the centre. Porphyrins are aromatic molecules which are highly conjugated, usually deeply coloured and like to form complexes with other atoms. In this case, it is iron. The heme group is the red group of atoms at around the middle of the structure. Oxygen molecules bind directly to the iron atom.
The heme group is stabilised by hydrophobic interaction between the pyrrole rings in the porphyrin and hydrophobic amino acids in the interior of the protein. Additionally, a nitrogen atom from a histidine residue above the plane of the heme ring is coordinated with the iron atom, which also stabilises the interaction. I was able to find this particular histidine atom, and while it is still hard to see, it is one of the light green residues with the pentagon-like shape at the end of it in this picture, situated above the plane of the heme ring:
In order to better see the heme group and the binding site, I also made a ribbon structure. The iron atom in the centre of the heme group can easily be seen.
Myoglobin binds carries oxygen in muscles, and binds oxygen at the heme group. The heme group is a porphyrin, which contains an iron atom at the centre. Porphyrins are aromatic molecules which are highly conjugated, usually deeply coloured and like to form complexes with other atoms. In this case, it is iron. The heme group is the red group of atoms at around the middle of the structure. Oxygen molecules bind directly to the iron atom.
The heme group is stabilised by hydrophobic interaction between the pyrrole rings in the porphyrin and hydrophobic amino acids in the interior of the protein. Additionally, a nitrogen atom from a histidine residue above the plane of the heme ring is coordinated with the iron atom, which also stabilises the interaction. I was able to find this particular histidine atom, and while it is still hard to see, it is one of the light green residues with the pentagon-like shape at the end of it in this picture, situated above the plane of the heme ring:
In order to better see the heme group and the binding site, I also made a ribbon structure. The iron atom in the centre of the heme group can easily be seen.
Thursday, August 20, 2009
Hey Sorry this is a bit late. I managed to get myself nice and sick and had close to 12 hours sleep the last few days.
This is what I ended up with for question 2.4 - I choose ATP as the small molecule to investigate and interestingly GrowEL came up as one of the molecules which binds to it. I covered this protein in one lecture and found it quite cool which is why it caught my attention. It is a chaperone protein so it helps other proteins fold by encasing them in the central pore shown in the picture included.
Both ends of the protein are capped by growes in this process and ATP is used when the growes is removed. Sadly I could not find the ATP binding sites as the protein is rather large but u can see in the central pore several little legs which stick out and interact with the protein being folded either hydrophobicly or electrostaticly if the protein has charged residues within it. These residues vary depending on the protein to be folded and help overcome energy barriers ect to prevent incorrect conformations being attained (which I think is really clever design to help the protein reach the desired conformation).
This is what I ended up with for question 2.4 - I choose ATP as the small molecule to investigate and interestingly GrowEL came up as one of the molecules which binds to it. I covered this protein in one lecture and found it quite cool which is why it caught my attention. It is a chaperone protein so it helps other proteins fold by encasing them in the central pore shown in the picture included.
Both ends of the protein are capped by growes in this process and ATP is used when the growes is removed. Sadly I could not find the ATP binding sites as the protein is rather large but u can see in the central pore several little legs which stick out and interact with the protein being folded either hydrophobicly or electrostaticly if the protein has charged residues within it. These residues vary depending on the protein to be folded and help overcome energy barriers ect to prevent incorrect conformations being attained (which I think is really clever design to help the protein reach the desired conformation).
Wednesday, August 19, 2009
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?
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.
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.
Monday, August 17, 2009
next assignment
Due tuesday August 25
Complete at least one of 2.2, 2.3, 2.4, or 2.5 and post the results on the blog.
Comment on the relationship between structure, property, and function for the molecule of choice.
Questions 3.1, 3.2, 3.3, 3.4 Nelson
Complete at least one of 2.2, 2.3, 2.4, or 2.5 and post the results on the blog.
Comment on the relationship between structure, property, and function for the molecule of choice.
Questions 3.1, 3.2, 3.3, 3.4 Nelson
Proton Pump
To add to our discussion last week's chapter (Ch 2), I thought I'd put up something on proton pumps. Below is a video with voice-over giving a simple explanation, and p56-57;59 from Ch 2 has some generic information on ion pumps.
And here is the full 3D structure of 3B8C, a P-type proton pump, determined from X-ray crystallography experiments.
Right-click on the Jmol applet above to interact with the structure (highlight domains, calculate hydrogen bonds, show surface et cetera). If you want to visualise how this might fit into the cell membrane, try colouring residues by charge (e.g Select→Protein→Basic Residues (+), Color→Surfaces→Blue||Color→Structures→Cartoon→Blue ).
(Edit: If the above widget fails, or you want to look examine this in more detail, you can view the structure here.)
And here is the full 3D structure of 3B8C, a P-type proton pump, determined from X-ray crystallography experiments.
Right-click on the Jmol applet above to interact with the structure (highlight domains, calculate hydrogen bonds, show surface et cetera). If you want to visualise how this might fit into the cell membrane, try colouring residues by charge (e.g Select→Protein→Basic Residues (+), Color→Surfaces→Blue||Color→Structures→Cartoon→Blue ).
(Edit: If the above widget fails, or you want to look examine this in more detail, you can view the structure here.)
Tuesday, August 11, 2009
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.
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.
Tutorial Question Session
Just wondering if anyone would like to got together Thursday morning to compare answers to the chapter 1 tutorial questions possible 9 or 10? I have an answer to each of them but a couple of them seem wrong so I would like to bounce ideas off someone or even work the questions through with anyone who hasn't had time to look at them yet.
Have a nice holiday tomorrow (for anyone who isn't currently bogged down in assignments amazingly early in the semester),
Michael.
Have a nice holiday tomorrow (for anyone who isn't currently bogged down in assignments amazingly early in the semester),
Michael.
Monday, August 10, 2009
Getting Blog Updates By Email
Hey all just a quick tidbit of info i found:
If your anything like me its really hard to remember to regularly check the blog in the busyness of everyday life which is why I was excited to find that the blog can be set to send you an email when a post is made. Now I don't yet know if it will let you know if a comment is left on a past post but I know it emails you when a new post is made cause I just received an email telling me Ross posted.
To set it up just go "Customize" (top right corner), "Settings", click the tab "Email & Mobile" and type in you email, then click save settings down the bottom of the page.
Hope this helps and makes sense considering how heavy my eyelids currently feel.
Michael.
If your anything like me its really hard to remember to regularly check the blog in the busyness of everyday life which is why I was excited to find that the blog can be set to send you an email when a post is made. Now I don't yet know if it will let you know if a comment is left on a past post but I know it emails you when a new post is made cause I just received an email telling me Ross posted.
To set it up just go "Customize" (top right corner), "Settings", click the tab "Email & Mobile" and type in you email, then click save settings down the bottom of the page.
Hope this helps and makes sense considering how heavy my eyelids currently feel.
Michael.
How is your reading?
Post something!
Someone should post a summary of the discussion of the last tute.
If you come by my office between 9am and noon on tuesday I should be able
to give you a copy of the textbook.
Please post comments on your reading on chapter 2.
The next assignment (due 2 weeks from this thursday) will be most of the questions at the end of chapter 2. You can post most of the answers on the blog since it involves looking at cool pictures of biomolecules....
Someone should post a summary of the discussion of the last tute.
If you come by my office between 9am and noon on tuesday I should be able
to give you a copy of the textbook.
Please post comments on your reading on chapter 2.
The next assignment (due 2 weeks from this thursday) will be most of the questions at the end of chapter 2. You can post most of the answers on the blog since it involves looking at cool pictures of biomolecules....
Wednesday, August 5, 2009
Why Entropy?
Thomas asked a question at the end of the class today. If memory serves, it was something like: if you had access to all of the information, wouldn't you just keep track of the energy itself?
I am not going to answer this question now, although maybe later the answer can be revealed. However I will pose a question in return...
What - in practical terms - would it mean to "have access to all of the information" in such a way that this could be done?
I am not going to answer this question now, although maybe later the answer can be revealed. However I will pose a question in return...
What - in practical terms - would it mean to "have access to all of the information" in such a way that this could be done?
The second law of thermodynamics
For an adiabatically isolated system the entropy of the system can
never decrease.
But, a more practically useful form of the second law is:
for a system in equilibrium with an environment at a given temperature and pressure the Gibbs free energy, G = U + PV-T S, can never increase.
Consequently, in the equilibrium state of any system (whether a folded protein or a superconductor) the Gibbs free energy must be a minimum.
Never forget this! This is the most important idea in all of thermodynamics!
never decrease.
But, a more practically useful form of the second law is:
for a system in equilibrium with an environment at a given temperature and pressure the Gibbs free energy, G = U + PV-T S, can never increase.
Consequently, in the equilibrium state of any system (whether a folded protein or a superconductor) the Gibbs free energy must be a minimum.
Never forget this! This is the most important idea in all of thermodynamics!
Thursdays tutorial
Today I have done a three more posts on chapter 1 over on condensed concepts.
Tomorrow we will meet in the interaction room at noon (physics annex 424) since I hope it will be more congenial to round table discussion.
For the first assignment (due next thursday August 13 at noon) I propose problems 1.5, 1.6, and 1.7 in Nelson. We can discuss this.
Tomorrow we will meet in the interaction room at noon (physics annex 424) since I hope it will be more congenial to round table discussion.
For the first assignment (due next thursday August 13 at noon) I propose problems 1.5, 1.6, and 1.7 in Nelson. We can discuss this.
Monday, August 3, 2009
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
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
Sunday, August 2, 2009
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
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
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