Proteins and Enzymes

ID #2376

Is there a difference between COOH and COO- ? Also In the book, it says that when an amino acid is ionized it has an NH3+ and a COO-. Do proteins in our body exist in an ionized form? Also are these positive and negative charges what make hydrogen bonding possible in a alpha helix?

To answer your first question, COOH can lose its hydrogen (become deprotonated) to form COO-. Whether or not this occurs depends on the pH that the molecule containing the carboxylic acid group is in and the pKa of that group. The pKa for the C-terminal carboxyl group of most amino acids is about 2, which means that it will lose its hydrogen atom at pH readings above 2. (This is somewhat beyond what you need to worry about for this class, but it is good to know that whether or not the amino and carboxyl groups of an amino acid are charged depends on pH). 
The pH of the human body is approximately 7.4 (give or take... the stomach is more acidic). At that pH, the N-terminal amino and C-terminal carboxyl groups of amino acids are in the ionized form. It is more complex than that, however, because when proteins fold some amino acids will wind up on the outside and some will wind up on the inside of the protein. Amino acids facing outwards will likely experience an environment with a pH of about neutral, but the pH inside a protein can vary. Also, remember that enzyme active sites can provide favorable localized pH using acidic or basic R groups. So, exactly how the amino, carboxyl, and R groups are charged is dependent on the environment. 
The negative and positive charges of the amino and carboxyl groups of peptide bonds is not what makes hydrogen bonding possible. Remember, hydrogen bonds form between partially positive hydrogens and partially negative atoms (like oxygen). A water molecule can hydrogen bond with another water molecule, so oxygen does not need to be charged for hydrogen bonds to form. 

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