Learn Russian: Куда ты сейчас бежишь?

бежишь is a form of бежать, the unidirectional verb for running. The word сейчас (now) and the question word куда (where to) show that the person is currently running in one specific direction toward a destination. If you were asking about running as a general habit or running around a park in multiple directions, you would use the multidirectional verb бегаешь (from бегать).

Why use куда for "where" instead of где?

куда specifically means "where to" and must be used when there is motion directed toward a destination. Because the person is running toward a place, we use куда. где means "where at" and is used to ask about a static location where something is situated or happening.

Is бежишь an exception to the usual present tense endings?

Yes, бежать is an irregular verb that mixes first and second conjugation endings, and it features a consonant shift. The present tense forms are: я бегу, ты бежишь, он/она бежит, мы бежим, вы бежите, они бегут. Notice how it uses second conjugation "и" endings for most forms, but the "я" and "они" forms use "у" and feature a "г" instead of a "ж"!