|
Nate
03-20-2008
11:21 PM ET (US)
|
Batman Returns (36)... those plots are accurate with the new model, though it is always possible that the code used to make the plots themselves could have a typo... though it's not extremely likely. You may, however, try for equation 10.4 r6 = p11/(p11+p12)... that sounds more accurate to me but whichever you use in your analysis, you won't be penalized. Edited 03-21-2008 03:32 AM
|
|
Nate
03-20-2008
11:10 PM ET (US)
|
by changing the kf only, but keeping the Keq the same, the kr also will decrease... I don't believe that it's common for the Keq to change since it is a thermodyamic quantity that is based on the envioronmental conditions in the cell itself. Changes in enzyme properties can't change the thermodynamics... it can only change the kinetics of the system.
On Thu, Mar 20, 2008 at 7:06 PM, <*****@ucsd.edu> wrote:
It's me again. There's a bit of literature that says a mutation in pgk
changes both the forward and the backward reaction rates. Wouldn't this
change the Keq as well?
|
|
Batman Returns
03-20-2008
03:51 PM ET (US)
|
I have a question about the final project. Firstly, to ensure that my simulations are correct, I tried to repeat the plots on chapter 10 (pg 186 and pg 187 figs 10.7 and 10.8). Also I tried to match values such as concentrations and fluxes. However, I seem to be getting a problem with my pools and charges. I've been able to reproduce glycolytic energy charge, glycolytic redox charge, NADH redox charge, and AEC.
However, I'm not able to reproduce the values for "fraction of phosphates on the adenylates" nor am I able to reproduce "phosphate recycle ratio." Also, the behavior for "recylcled phosphate ratio" seems to increase with an increase in ATP load rather than decrease with an increase in ATP load. For these ratios I used the equations 10.4 and the one above it.
My pooling matrix and S matrix are as written on the text, and I even seem to match the product PS. Must there be a typo in the equations or in the pooling matrix ????
|
|
hi-larious
03-19-2008
07:57 PM ET (US)
|
i just have to say, that the "not so extreme pathway" someone drew on the test was freaking awesome. made my day. i woulda just died if they circled something on the diagram saying "TYPO"; maybe typo around an arrow leaving the cycle saying "Relax."
Props to that person! reveal thyself.
|
|
disease expression
03-19-2008
05:28 PM ET (US)
|
nvr mind at 33 :)
|
|
disease expression
03-19-2008
01:22 AM ET (US)
|
For my particular enzyme I'm not finding any disease based on an enzyme deficiency. I am, however, finding a couple diseases linked to over-expression of that enzyme. Is it ok to talk about those instead? (Because severe under-expression just leads to embryotic death, which isn't as interesting.)
|
|
hi
03-18-2008
06:33 PM ET (US)
|
What constitutes a treatment? Can we add a series of new reactions to compensate for the mutation? Also, when are office hours for the project?? Thanks!
|
|
FINAL
03-18-2008
01:33 AM ET (US)
|
Regarding the Final: Are we only being tested on the topics on the review sheet?
|
|
Nate
03-17-2008
02:03 PM ET (US)
|
Fluxes at steady state (23)... no
Just to clarify (24)... yes... i never was good at the whole alligator mouth thing in elementary school... and it's carried over to my graduate work 20+ years later
me (27)... only the k values. the k values represent kinetics, which catalysts such as enzymes can change. Keq, however, is derived from thermodynamics, which enzymes cannot change.
Rhymenoceros (28)... look at chapter 10. Each of those at their steady state values (and the adenylate energy charge) provide physiological information about where energy is stored in the system and what sorts of energy loads a person can handle. matt (29) is on the right track.
|
|
matt
03-16-2008
06:34 PM ET (US)
|
probably means look at the steady state values then perturb the system then explain the new values and how they got there.
|
|
Rhymenoceros
03-16-2008
04:43 PM ET (US)
|
You will want to assess several properties of the network, e.g. the glycolytic energy charge, the glycolytic
redox charge, the NAD redox charge, and the trafficking of phosphate bonds in the network.
what does this mean
|
|
me
03-16-2008
04:58 AM ET (US)
|
When we change our k values, should we also change the relevant K value, or assume that stays the same?
|
|
matt
03-15-2008
08:44 PM ET (US)
|
i figured it out and it was right. i had an error somewhere else, so hint hint to everyone else.
|
|
matt
03-15-2008
08:05 PM ET (US)
|
Does this look right for function dxdt? v_HK= k_HK * (x(1) .* x(17) - x(2) .* x(16) / K_HK) ? and dx_dt(1,1)= - v_HK + v_GLU_in? i am getting output but glucose seems to skyrocket Edited 03-15-2008 08:15 PM
|
|
Just to Clarify
03-15-2008
12:13 PM ET (US)
|
On the assignment, where it says >5%, do you actually mean <5% ?
|
|
Fluxes at steady state
03-15-2008
01:35 AM ET (US)
|
Did anybody else got a constant negative flux for the aldolase reaction at steady state? Also, the flux for the APK reaction experiencing a drastic decrease and then fluctuating around 0?
|
New Topic
My Topics
Views:
613
(Unique:
206
) / Subscribers:
0 | What's this?
