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Apr
22
comment Electron Transport Chain in Mitochondria
Great Answer (and +1). But to be pedantic, the transfer of four electrons to $O_2$ produces one water molecule.
Apr
9
comment Why are amino acids in biology homochiral?
I like your final sentence
Apr
9
comment Why are amino acids in biology homochiral?
I think that 'why not D-amino acids' makes perfect sense. Dehydrogenases (dhs) also show a type of stereospecificity, where some dhs transfer the pro-4R hydrogen from NAD(P)H (A-type) and others transfer the pro-4R (B-type), which has also been conserved in evolution: no dh of the A-type has evolved from an ancestor of the B-type, and vice versa. Your argument about not fitting can be also be applied to A-dhs or B-dhs, but in my view this means very little and does not answer the question: why not a ribosome that can use D-amino acids?
Apr
9
comment Why are amino acids in biology homochiral?
Well, I think the great mystery is that all amino acids incorporated into proteins on the ribosome are left-handed, with the exception of glycine which is not chiral. This includes selenocysteine and pyrrolysine. However, not all biologically-active amino acids are L-isomers. D-alanine, which occurs in the bacterial cell wall, is an obvious example, but there are many others.
Apr
9
comment Why are amino acids in biology homochiral?
@yamad. The site you link to contains the line 'all living molecules are left-handed'. This, of course, is nonsense.
Apr
8
comment Can ELISA be used to detect a plant enzyme? Creating assay for a new enzyme
I think a very important distinction needs to be made here. An ELISA will allow you to detect the presence of a specific enzyme and to quantify the AMOUNT of that enzyme present. Your ELISA assay will be specific for a given protein, which happens to be an enzyme This is not the same as developing an assay for your enzyme based on the reaction it catalyzes. You might develop a spectrophotometeric assay based on the decrease or increase in absorbance of a product or substrate. Consider the difference where the enzyme is 'dead' because you have extracted at too low a pH.
Apr
5
comment Structure of proteins
See here for a great account by Perutz of his own reaction to the discovery of the alpha-helix by Pauling and Corey. Also a great introduction to secondary structure (alpha-helix and beta-sheet). (I wish I had make you angry earlier, by Max Perutz)
Apr
5
comment 'Obviously True' Statements that turned out to be false?
I think this is a great question. The example that immediately springs to mind is Newton's laws, which at one time were considered axiomatic and 'true' laws of nature. We now know that although Newton was not wrong, his laws are only a (very good) approximation and Einstein showed that there is a better way of looking at things (relativity). Other examples: proteins were at one time thought to be the carriers of genetic information. A 'high-energy' intermediate was accepted to be the key to understanding oxidative phosphorylation (and some had even claimed to have isolated it).....
Mar
16
comment What is ATP and why is it said to be a source of energy?
See The Demise of the Squiggle and Why Is ATP an Important Energy Currency in Biochemistry? and A Long Life in Times of Great Upheaval for very stimulating articles about the question posed.
Mar
16
comment What is ATP and why is it said to be a source of energy?
"Energy can't release energy because energy is ... energy". But Gibbs free energy (the type 'released' by ATP) is not energy in this sense, surely?
Mar
16
comment What is ATP and why is it said to be a source of energy?
(+1) And, of course the hydrolysis of $ADP$ to $P_i$ + $AMP$ proceeds with an almost identical free of hydrolysis to that of $ATP$ to $ADP$ + $P_i $. When dealing with ATP, 'energy changes' invariably refer to changes in Gibbs free energy of hydrolysis.
Mar
15
revised Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible
added a reference (Dalziel, Acta Chem Scand)
Mar
14
comment Artificial reduction of NADP into NADPH by means of an electrical current
(2) ... The 'experiment' to show NAD(P)H instability in acid is to add NAD(P)H to a cuvette containing any suitable buffer at pH 5.0 (or below) and monitor the change in A340 with time using a spectrophotometer. The absorbance will start at ~0.62 and decrease with time to (almost) zero over a minute or two, as the acid breakdown product does not absorb at 340nm. This, of course, 'plagues' the study of the behavior of dehydrogenases at low pH when assayed by A-340 changes and the initial rate method. But you probably know all that.
Mar
14
comment Artificial reduction of NADP into NADPH by means of an electrical current
(1) I know very little about your system, but it seems a great experiment. I was merely commenting on a possible pitfall, that is the instability of NAD(P)H in acid (see here or ?here). You would need to titrate acetate to pH 5, but any buffer with a pK in this range will do. As NAD(P)H has an extinction coefficient of 6220 M<sup>-1</sup> cm<sup>-1</sup>, 100uM will have an A340 of 0.62 (whereas a 1mM soln will have a (predicted) A340 of 6.22 and will be 'off-scale') ...
Mar
10
comment Does the Michaelis-Menten equation take in account the non-enzyme formation of products?
I don't know of any other name, but the equation you give is almost exactly that given by Dixon & Webb, p 461: $v$ = $w$ + ${V_{max}\ s}\over{{K_m + s}}$, where $w$ is the blank rate
Mar
10
comment Artificial reduction of NADP into NADPH by means of an electrical current
Well, I wouldn't use strong acid. NADP(H) is unstable in acid leading to a decrease in the absorbance at 340 nm. Try adding 100 micromolar NADH to 100mM acetate, pH 5 (or below) and monitor the A-340.
Mar
10
answered Does the Michaelis-Menten equation take in account the non-enzyme formation of products?
Mar
10
revised Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible
removed superfluous 'both'
Mar
10
revised Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible
Corrected a typo
Mar
10
revised Is it possible to derive the Michaelis-Menten equation under conditions where the product formation is reversible
Major edit to original answer, correcting quite a few errors