If you missed the life upgrade that is in the Clock Tower (in the room where you are getting Spike Beasts thrown at you), you can still get the upgrade later in the game by using the Scorpion Sword. After you get the sword and leave the library, you will break through a wall which leads into the Clock Tower. Instead of heading down towards the central chamber, head up and you will eventually reach the room where the Brute was throwing Spike Beasts at you. It doesn't throw them anymore but you can now break the wall on the left by using the Scorpion Sword.