tag:blogger.com,1999:blog-37148773.post4325731749298822119..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Better Biochemistry: The Free Energy of ATP HydrolysisLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-37148773.post-24634760502305995532017-08-31T01:45:28.233-04:002017-08-31T01:45:28.233-04:00Thanks for your reply. My questions are simple and...Thanks for your reply. My questions are simple and understandable. If we can not measure the process X, then we can not say that our interpretation of this process is true (regardless of funding). If you are interested in details, you may run through the article: http://www.bioparadigma.spb.ru/files/Ling-1997-Debunking.the.Alleged.Resurrection.of.the.Sodium.Pump.Hypothesis.pdf It seems to me that this article does not solve the problem, but it raises important questions.Vladimir Matveevhttps://www.blogger.com/profile/03641053704116426070noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36802766181205499932017-08-30T08:53:37.720-04:002017-08-30T08:53:37.720-04:00"The" sodium pump
Can you precisely meas..."The" sodium pump<br />Can you precisely measure ATP made / ATP used with time resolution?<br />Where would one get the funding to answer your ill-defined questions?MitoSwitchhttps://www.blogger.com/profile/01205088922081484486noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84217634801486751532017-05-26T01:32:45.651-04:002017-05-26T01:32:45.651-04:00As usual, two important questions were left unansw...As usual, two important questions were left unanswered.<br />1. In the decay of a chemical compound, energy is released in the form of heat. How is the heat used to perform the work of the sodium pump and other mechanisms?<br />2. Why has no one compared the amount of synthesized ATP and the amount of utilized ATP in a cell per unit of time in the last 70 years?Vladimir Matveevhttps://www.blogger.com/profile/03641053704116426070noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-85832468627349034872011-11-23T06:21:42.703-05:002011-11-23T06:21:42.703-05:00roxton
If standard Gibbs free energy change for t...roxton<br />If standard Gibbs free energy change for the ATP → AMP + PPi reaction is close to -45 kJ /mol and the respective value for the PPi hydrolysis is -29 kJ/mol, what is than Gibbs free energy for ADP → AMP + Pi ( -42 kJ/mol? )?schellenoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-47469775139413892992011-11-02T06:59:21.422-04:002011-11-02T06:59:21.422-04:00One thing that has always puzzled me, however (fee...One thing that has always puzzled me, however (feel free to ignore, or refer me to your book!): what is the role of the nucleoside - the base-ribose group - in energy transfer? The same base-ribose-phospate group appears in FAD and NAD, which would suggest some deep connection with early metabolism. The fact that that same group is also an RNA subunit puts a completely unrelated constraint on it - whatever its role in the energetics of polymerisation, it also needs the stereochemistry to allow it to be stacked in the polymer, and base-paired.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-25638272991856710742011-11-02T06:27:48.519-04:002011-11-02T06:27:48.519-04:00Rat liver biochemistry used to be very popular.
...<i>Rat liver biochemistry used to be very popular. </i><br /><br />I remember my visits to the 'rat man'. He would select one of his charges, cradle it and stroke it so as not to stress it, then .... whump! The unfortunate animal would be unceremoniously whacked on the edge of a desk, and its liver neatly snipped out and plopped into our petri dish. I decided to do my PhD on plants.Allan Millernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-6659442317034833242011-11-01T21:52:45.917-04:002011-11-01T21:52:45.917-04:00Robert Alberty and his colleagues have calculated ...<i>Robert Alberty and his colleagues have calculated the transformed free energies of hydrolysis for many biochemical compounds ... and those are the values we should use in biochemistry courses.</i><br /><br />"Should"? Why? Alberty's calculations (I am looking at "Thermodynamics of Biochemical Reactions", 2003) are very much idealized and should be treated as nothing more than back of the envelop estimates. For teaching purposes, it should be perfectly sufficient to say "large negative" with real value in the cell further significantly larger and give some random close enough numbers. <br /><br />If anything, IMHO, it is essential to emphasize that we don't know what the actual numbers are. And that, in general, there is hardly any single biochemical parameter whose value in the real cell we know with any reasonable degree of precision. This is important because to this day there are many people who believe that a faithful computer model of a whole cell is forthcoming very soon because computers are getting exponentially more powerful.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90038749981668789052011-11-01T17:06:53.030-04:002011-11-01T17:06:53.030-04:00between this, and your post on modified nucleotide...between this, and your post on modified nucleotides, I'm sold. I have to get this textbook...Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63903646256934172622011-11-01T16:52:05.780-04:002011-11-01T16:52:05.780-04:00Thanks, Larry! I was JUST thinking about this toda...Thanks, Larry! I was JUST thinking about this today as I work on my syllabus for next semester's cell biology class.G Radicehttps://www.blogger.com/profile/11915129913766976834noreply@blogger.com