This article reviews our current understanding of how the internal quark structure of a nucleon bound in nuclei differs from that of a free nucleon. The interpretation of measurements of the European Muon Collaboration (EMC) effect for valence quarks, a reduction in the deep inelastic scattering cross-section ratios for nuclei relative to deuterium, and its possible connection to nucleon-nucleon short-range correlations (SRCs) in nuclei are focused on. This review and new analysis (involving the amplitudes of non-nucleonic configurations in the nucleus) of the available experimental and theoretical evidence shows that there is a phenomenological relation between the EMC effect and the effects of SRCs that is not an accident. The influence of strongly correlated neutron-proton pairs involving highly virtual nucleons is responsible for both effects. These correlated pairs are temporary high-density fluctuations in the nucleus in which the internal structure of the nucleons is briefly modified. This conclusion needs to be solidified by the future experiments and improved theoretical analyses that are discussed herein.