Read The Infernal Devices.
Brother Zachariah only became a Silent Brother because of a Demon-inflicted addiction to Yin Fen. If he hadn't become a Silent Brother he would have died. In City of Heavenly Fire, Brother Zachariah tries to heal Jace. However, when he touches him, the Heavenly Fire is absorbed. This burns away the Yin Fen, thus meaning that he doesn't need to be a Silent Brother anymore.
It is also stated that Zachariah is more human than most of the Silent Brothers, as he wasn't able to take all of the runes. That is why he looks different.
Silent Brothers are also more angelic than regular Shadowhunters. This is because they have sacrificed some of their humanity for more Angelic power.
