Understanding the energy transfer mechanisms of amino acids in real time can provide insight into the strain induced during modification of proteins. Protein phosphorylation, one of the most prevalent signal transduction mechanisms within biological cells, involves structure conformation and energy transfer using a phosphate group. In eukaryotic cells, specifically, there are three phosphorylatable amino acids: L-serine, L-threonine and L-tyrosine. These amino acids are particularly important because they are responsible for biochemical reactions and cellular functions such as metabolic regulation, muscular growth, cell differentiation and metastatic behavior. In an effort to study these energy transfer mechanisms in real time, this work focuses on noninvasive measurements, such as confocal Raman spectroscopy, using custom-designed microreactors and the flow of in-solution L-serine, L-threonine and L-tyrosine biomolecules during a wide range of measurement parameters. This study accounts for optical scattering, absorption, and reflection mechanisms of phosphorylatable amino acids in an effort to better understand the optical absorbance properties so that molecular fingerprinting before and after the chemical reaction can be precisely measured. The L-serine and L-threonine particles were elongated in shape while the L-tyrosine was a fine white powder. The confocal Raman spectroscopy tool produced a one-micron diameter laser spot, and spectra for each amino acid was collected and analyzed to account for optical energy scattered. Spectral data reveals relative resilience among the amino acid crystals. The absorbance characteristics at 532 nm Raman wavelength also reveal dependencies on optical power density and an attenuation spread approaching 12% among the amino acid group under study.