In the overtone series there is a fundamental bass note that all of the other pitches are based on. When a pitch sounds, several other pitches sound in addition to that fundamental pitch. The pitches that sound closest to the fundamental pitch are perfect intervals--those further from the fundamental are major and those even further away are minor pitches. In this system, the first interval is an octave, followed by a perfect fifth and a perfect fourth. The series continues upward with a major third then a minor third. The series is complex but it explains why we have major and minor notes in a scale.
A major scale consists of half steps and whole steps. The half steps are called minor seconds and the whole steps are called major seconds. Two half steps make one whole step. The system of half and whole steps consists of whole, whole, half, whole, whole, whole and a half step between each of the seven scale degrees. Technically, there are no minor notes in a major scale since the entire scale consists of major notes that fit in the overtone series, but there are minor intervals. For instance, the distance between the 1st scale degree and the 7th scale degree is a minor seventh.
There are three forms of a minor scale and this is where all of our minor notes come from. The harmonic minor scale is a major scale with the 3rd and 6th lowered. This means that in a harmonic minor scale the 3rd and 7th notes are minor notes. Minor notes are minor notes because they are not closely related to the overtone series. They occur further in the overtone series, which is why minor keys were seldom used in the Classical period.
There are four types of chords in classical music. The major chord conforms to the notes found in the first octave and a half of the overtone series. The minor chord uses notes from the first two octaves. The root note of a minor chord and the 5th of the chord are considered to be perfect (major) intervals. The third is a minor interval, so the third of any minor chord is a minor note. In a diminished chord, the 3rd and 5th are considered minor notes. The augmented chord does not have any minor notes.