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This nomenclature is due to the fact that amino acids are carboxylic acids. Near the carboxylic acid moiety, the carbon chain is unbranched and simple, so the positions are named like an unbranched, simple aliphatic carboxylic acid. The carboxylic acid ($\ce{-CO2H}$) is not indicated with a position. But the carbon immediately next to it is $\alpha$. The ...
Question 1: Why is that one(in space) considered alpha and not the carbon atom next to it? All human proteins consist of $\alpha$-amino acid residues. An $\alpha$-amino acid means the carboxylic acid group ($\ce{COOH}$) and amino group ($\ce{NH2}$) are separated by one $\ce{C}$ carbom atom, which is called $\alpha$-carbon ($\ce{C}_\alpha$; See the insert at ...