Due tuesday 23 september
chapter 9 people
Problem 9.1 and 9.2 in Nelson
and any two of 9.5, 9.6, 9.7, 9.8, 9.9, C9.12, C9.13 9 (see pages 594 ff.)
chapter 10 people
10.1, 10.4
and any two of 10.5, 10.6, 10.7, 10.8, C10.10 to C10.14
Showing posts with label assignment. Show all posts
Showing posts with label assignment. Show all posts
Monday, September 14, 2009
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.
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
Monday, August 10, 2009
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
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.
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