A NE555 is used for generating a high-frequency PWM signal, feeding one 74HC's "Output Enable" port. This is because otherwise the LEDs are too bright, and playing with the serial signal to reduce brightness is not fast enough (it produces a perceptible blinking). Also, using the Arduino's internal PWM causes the serial transmission to behave erratically (because of timers interfering with transmission, and because frequency is too low). And of course, as 74HC uses logical gates, it needs a binary (PWM) signal, not analog.
D5 is used for the buzzer because its PWM frequency is greater than other pins.
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