This extra calculation in the spreadsheet is only meant to keep the students from obtaining counting errors for the number of times a given amino acid appears in a given sequence. Finally, repeat the calculation for each amino acid desired. This cell will then return a value that corresponds to the number of times a given amino acid appears in the sequence. Next, in a second cell, type the following code, referencing the cell of your sequence: =(LEN(cell reference for sequence)-LEN(SUBSTITUTE(cell reference for sequence,amino acid letter to be counted,""))). First, copy a protein or peptide sequence in FASTA format into one cell in the spreadsheet. One can use the spreadsheet to count the number of each amino acid present in a particular sequence. Spreadsheets have the capability of counting letters in addition to counting numbers. I would also like to propose a powerful addition to the spreadsheet that Sims has developed. Students can then easily understand the importance of determining the p I of a protein.
Providing students with an opportunity to construct their own titration curves of amino acids, peptides, and proteins and learn the theory of why they receive a particular set of results enhances the students’ understanding. This spreadsheet was immediately incorporated into the curriculum for my undergraduate biochemistry class. The number 10 needs to be multiplied by itself 3 times to equal 1000. From my experience, students respond well to using computers in the classroom. This is achieved by representing all the numbers in question by the number of times a factor needs to be multiplied by itself to equal the original value. The kinetics of protons dissociating (and associating) from an acid, A, can be treated like any other reaction.I enjoyed Paul Sims’s recent article regarding the use of a spreadsheet to calculate net charges of peptides and proteins (1).
The reason a negative logarithm is used is that it converts a huge range of concentrations into an easy range of positive numbers (although it is technically possible to have a negative pH: a 10 molar solution of H⁺ would have a pH of -1, and a pH of -3.6 has been reported, although this is due to the activity of the protons and not just their concentration). A pH of 7 therefore corresponds to 10-7 molar H⁺ (100 nM). More specifically pH is the negative logarithm (in base 10) of the molar concentration of H⁺. So what does pH measure? pH is a measure of the concentration of H⁺ in a solution (technically it's a measure of the activity of H⁺, but that is roughly the same thing under normal circumstances). If we then add a chemical that is even better at donating protons to water, the first chemical will now accept protons from the second, thus acting as a base. If we add a chemical to water and it donates protons to water, then it is an acid. For our purposes, acids are chemicals that can donate a proton, while bases (or alkaline substances) are chemicals that accept a proton.Īn interesting result of this definition is that acidity is relative: whether a chemical is an acid or not depends on the other chemicals in the solution. The Lewis theory defines acids as chemicals that accept electrons, which is often, but not always, the same thing. Most people know that pH is a measure of acidity, but what is acidity? The Brønsted-Lowry theory tells us that an acid is a chemical that donates a proton (H⁺), while a base is a chemical that accepts a proton.