Names of reactants

Names of reactants and products for each regulated enzyme and each enzyme making or using ATP equivalents... 

In writing chemical equations and biochemical equations it is important to be careful with names of reactants. Chemical reactions are written in terms of species. In chemical reaction equations, atoms of all elements and electric charges must balance. Biochemical reaction equations are written in terms of reactants, that is in terms of sums of species, H+ is not included as a reactant and electric charges are not shown or balanced. In biochemical reaction equations, atoms of all elements other than hydrogen must balance. The names of the reactants that must be used in making calculations with this data base are given later. 

Gibbs energy of reaction in kJ molA-l at specified pHs and ionic strengths for a biochemical reaction typed in the form atp+h2o+de adp+pi. The names of reactants call the appropriate functions of pH and ionic strength. pHlist and is list can be lists. ) energy = Solve [eq, de] energy[[l, 1, 2J /. pH - pHlist /. is - islist]... 

This table can be helpful in estimating the pATs of other weak acids from their structures. In using this table it is important to remember that -log [H ] is used in the expression for the acid dissociation constant in terms of pH. To obtain pKs based on -log y (H ) [H ], add 0,0.08, 0.11,0.12, and 0.14 at ionic strengths of 0, 0.05, 0.10,0.15, and 0.25 M, respectively, at 298.15 K as indicated by Table 1.3. PaddedForm rounds the output to two figures to the right of the decimal point. There is a list of full names of reactants in the Appendix of this book. The reactants bpg, nmn, pep, and prpp are bisphosphoglycerate, nicotinamidemononucleotide, phosphoenolpyruvate, and 5-phosphoribosyl-alpha-pyrophosphate, respectively. 

Notice that the first and sixth columns are redundant and so one has to be eliminated. Delete the sixth and label the first as glucosebphos, which represents the pseudoisomer group G6P " and HG6P". Notice that the third and fifth columns are also redundant, and so we will delete the fifth. Label the third as pi. Now the columns are for glucosebphos, h2o, pi, and glucose. Notice that we have gone back to the names of reactants (sums of species). 

These functions are given the following Mathematica names of reactants, which have to be cleared first. 

In Mathematica reactants need to named with words starting with lower case letters because words starting with capital letters refer to operations. Also the names of reactants need to be as short as convenient and cannot involve spaces, subscripts, superscripts, hyphens, dots or other symbols that are Mathematica operations. Therefore, ATP is referred to as atp both in the text and in computer programs. Most of these abbreviated names will be recognized immediately, but a glossary of names is provided in the Appendix. 

The Appendix contains a copy of the Mathematica notebook BasicBiochemDataS.nb, Tables of Transformed Thermodynamic Properties, the Glossary of Names of Reactants, the Glossary of Symbols for Thermodynamic Properties, a List of Mathematica programs, and Sources of Biochemical Thermodynamic Information on the Web. The Mathematica package BasicBiochemData3.m, which is also available at... 

It is not necessary to be a programmer in order to use the programs and procedures illustrated in this book. Names of reactants, temperatures, pHs, and ionic strengths are readily changed in using the various programs. 

Five tasks must be performed in this problem (1) Represent the reaction by a chemical equation in which the names of reactants and products are replaced with formulas. (2) Balance the formula equation by inspection. (3) Determine the limiting reactant. (4) Calculate the theoretical yield of sodium nitrite based on the quantity of limiting reactant. (5) Use... 

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