200ms to charge 470uf from the Arduino 5v output? That sounds like you’re powering the Arduino from the same 9v battery you’re using with the step up converter.
Charging a capacitor requires charge or more importantly, current. The more current and the lower the total resistance, the faster it will charge. A battery has internal resistance. In general, the smaller the battery, the higher the resistance. Those little rectangular 9v batteries cannot deliver any appreciable current and they will severely limit the time required to charge your capacitor.
In a perfect world, without resistance, charging 470uf to 25 volts in .005 seconds (200 Hz) requires 2.35 amps. But, there is resistance everywhere. In the battery, in the capacitor, in the wires. So, it will take more current, more voltage or more time. Take your pick.