He was interested in various areas of research and when he decided to work on something, he made significant contributions. Three recurring themes were enzymology, pancreatic development, and virology. He graduated from Harvard and originally planned to attend medical school at the University of Utah, but after taking classes in medical school, he became interested in enzymes and decided to focus on basic research. He received his master's degree from Utah in 1950 and then his PhD in 1952 from the University of Illinois, studying metabolic enzymes and their role in disease.
Rutter received his PhD in enzyme chemistry with Henry Lardy at the University of Wisconsin, Madison (1952–1954). His interest in enzyme mechanism led him to Sweden, where he spent another year of postdoctoral work with Hugo Theorell at the Nobel Institute (1954–1955). When asked about how his research began, he said that understanding how nutrition could lead to muscle stiffness in young chickens drew him to enzymology and sparked his interest in biological problems. In his own laboratory in the chemistry department at the University of Illinois at Urbana (1955–1965), he studied malic enzymes and aldolase and explored how multiple forms of the same enzyme activity could exist and how their different activities could be influenced by their quaternary structure. The discovery of differential expression of enzymes in different tissues initiated his research into the regulation of RNA transcription. A sabbatical at Stanford in 1962 with Clifford Grobstein on the embryonic development of the pancreas was a turning point for him, when he began to use his understanding of chemistry to study biological processes. During this time, he became interested in the tissue-specific expression of enzymes in various tissues and studied the development of the pancreas and epithelial differentiation in the presence of mesenchyme. In 1965, he accepted a teaching position in the Department of Biochemistry and Genetics at the University of Washington (1965–1969). Together with graduate student Robert Roeder, he discovered three distinct RNA polymerase systems operating in eukaryotes, a fundamental cornerstone of our understanding of gene expression in higher organisms. While continuing his work on the development of the pancreas, he also began to focus on the mechanisms of eukaryotic DNA transcription in yeast.
