The three mother letters correspond to the final part of the first verse where it is stated that the Holy One created his world with text (Sepher), with number (Sephar), and with communication (Sippur). We know this is so since the root letters of text, number, and communication (Samech-Peh-Resh) have a numerical sum of 340 which is the same as the Name (Shin-Mem). Since the letter Aleph is silent, we have not added its value to Shin-Mem. Instead, it serves as the unmanifest connecting link between the two opposites.
Mem stands for Mayim (water) and represents mercy, while the letter Shin, which is shaped like flames rising from a burning coal
represents fire and severity. The silent letter Aleph represents air which is invisible but which, nevertheless, connects the Shin and Mem since we cannot vocalize the word Shem (Name) without the invisible breath. Furthermore, since the Hebrew word Ruach means both "wind" and "spirit", we learn that it is the invisible spirit which connects all manifestation.
A very deep lesson regarding the Name can be drawn from the Zohar (vol I, 6b). Here a hint is given that the Egyptian that Moses killed is none other than Moses himself. This conclusion is arrived at through Exodus 2:19 which states, "An Egyptian delivered us from the hand of the shepherds."
""He smote an Egyptian": this signifies the light of Israel's great luminary, to wit, Moses, who is called an Egyptian, as it is written, "And they said, an Egyptian delivered us, etc." (Exod. II, 19), for there he was born, there he was brought up and there he was vouchsafed the higher light. -Zohar I, 6b"
The riddle of this reference can be solved by first noting that the Hebrew word for Egypt, Mitzrayim, also means "boundaries" or "a narrow place", and then observing that the Hebrew word for Egyptian, Mitzri, has a numerical value of 340 (Mem-Zaddi-Resh-Yud) which is the same as the numerical value of the Name (Shin-Mem). Also, observe that Moses spelled backwards is HaShem (The Name, Hey-Shin-Mem). Hence, we can now derive a teaching that Moses' killing of the Egyptian refers to the transformation of his restricted self into his divine self. Notice also that the letter Hey in Moses' name is one of the letters of God's most sacred Name and that it additionally represents the Shechinah. Hence, when God's presence enters into our physical selves, we are transformed from constricted beings into holy beings. We also see the addition of this holy letter Hey occurring elsewhere in the Bible in the transformation of "Abram" into "Abraham" and in the change of "Sarai" to "Sarah".