6/29
Today we studied the crtstals that we had made withthe three different techniques. We found that all three methods gave us crystals which was very exciting. We took photos of the crystals using a digital camera.

We also sat in a seminar were a grad student talked about his research project. In his project he was taking a piece of DNA which generates the c-complex( part of the ATPsynthase molecule) and implanted in an ecoli bacteria with the idea of generating the C-complex protein. He was having problems detecting the C-complex. This may have been to the problems with dtection methods or because the bacteria was not generate the required protein.

I also found that all my wiki entries have disappeared

6/28

6/28

Today we created two more ways to crysrallize lysozome protein.
Free interface diffusion. Capillaries of protein solution are place in vials of salt solution of various concentrations. By adding solute we will create crystals
Vapor diffusion. We put drops of protein solution over a strong concentration resevoir. The drop will slowly evaporate leaving crystals

We also looked at yesterday’s experiment and we have crystals.

We also looked at an old plate(1 year) which was crystallizing an HIV protein,the source was a tobacco plant. Prof Fromme excited because there were good crystals where previously there were none.

Xenon and kryton gasses are used to create a reference point in the crystal structure. Also mercury is used.
To be a good scientist you need
Knowledge in chemistry, biology, physics, patience, sense of adventure, good team work, sense of humor.

Wed 27th June

Today we created crystallisation capillaries tubes of lysozome at different salt concentrations.

What did we learn
Measurements must be done very carefully. It took us 3 attempts to get the correct mixtures( 20 in all).
To get protein crystallographers passionate mention
- Rosalind Franklin(The female scientist who was the first to crystallize and use x-rays to study the structure of DNA)
- Stochiometry and dimensional analysis
- 9/11 and how this means that crystals can no longer be taken on airplanes because the compulsory x-ray machines degrade the crystals.

Copy of diary

MSTF Diary
Barry Siegwart
7/25
Prof Rebecca Watcher, Prof Petra Fromme
Lab installation
Green bubbler. Produces large amounts of cells (16 gm). Many liters. Gives cells correct heat (54C) and light and air to reproduce. Requires 2.3 days to run completely. Symbiotic cells needed for growth.
Cell walk breaker. Uses compressed nitrogen gas. Better that physical breakers (French press). Does less damage. Does not need protease inhibitors.
Centrifuge. Like spin dryers. Large high revs.
Small scale separator Uses a column of beads to attract ionized parts of the proteins. Then different concentrations of salt solution are passed through the column. Different proteins release from column at different salt concentrations. Equipment also has a frequency monitor (Not sure point/use of this equipment)
Large scale separator. Same principal as small scale. Used in green room because green light does not activate the photosynthesis proteins. The outputs at different salt concentrations are collected in a set of test tubes.

Prof Fromme first to find the structure of P1 and P2 which are the parts of the photosynthesis

Looking to find the structure of complete ATP protein which is used to create ATP (energy source) in both plants and animals. Use plants because the switch off at night, animal do not. Two Nobel prizes have been given for work in ATP.



7/26
We worked in the lab to create a protein crystals.(Lysozyme). Creation of correct molar solutions.
P2 has 150,000 atoms/molecule. Requires 3.4A.
Crystallization is an art/magic
Needs clean material
Needs the correct concentration of solution
Zero gravity. Use space shuttle. (4mm crystals)
Special detergent removes the P2 without destroying it.

Group is now trying to crystallize ATPsynthase. X-rays are high energy, need syncotron to generate. Brookhaven labs. X-rays generate an electron density map. This is used to generate a 3-D model.
Use cynobacteria instead of plant material. Plant material is not very stable.
Cynobacteria came into existence 2.5 billion years ago. Created oxygen. Cynobacteria is prokyatic not eukroactic.

There is a high degree of cooperation between researchers.

Humans have 23 pairs of chromosomes containing about 20,000 genes. DNA is the molecule that carries

Science observes and measures the natural world. From those data it infers laws that govern physical and biological processes. Explanations of large classes of phenomena must make testable predictions and be falsifiable. That is, there must be a way to make an observation that could disprove the explanation. The requirement of falsifiabilty rules out supernatural explanation. You cannot disprove, for instance , the claim that God scattered fossils throughout rock strata to make it look as if species had evolved over millions of years. God may have done that, but we may never know and there is no way to disprove it. I that way, faith is fundamentally different from science.
Good science distinguishes correlation from causation. If kids who play violent video games commit more violence, before you blame the game you’d better be sure that violence-prone kids are not more drawn to violent games than other kids. If so, then violent behavior causes the playing of violent videogames, and not the other way around.

6/26

We were impressed by how open Prof Petra Fromme was to us.