It looks like there are two questions here, so let me try rewording and answering them:
“What makes up a logic gate that is not itself a logic gate?”
Short answer, transistors. In digital circuitry, a transistor has three wires; an input, and output, and a gate. If the gate is off then the transistor will not allow current to flow from input to output, and if the gate is on then current can flow. With a mix of transistors and resistors, all of the basic logic gates can be produced
“How do we manufacture the large number of logic gates in a computer chip?”
We can make a transistor basically by laser printing. You coat the silicon with a chemical that turns into a transistor when exposed to light. You then use a series of lenses to shine a very small image of all the transistors that you want on that chip, and it becomes the desired arrangement.
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