It is the same spell so it would be treated as a single spell.
Share Spells
At the master’s option, he may have any spell (but not any spell-like ability) he casts on himself also affect his familiar. The familiar must be within 5 feet at the time of casting to receive the benefit.
If the spell or effect has a duration other than instantaneous, it stops affecting the familiar if it moves farther than 5 feet away and will not affect the familiar again even if it returns to the master before the duration expires. Additionally, the master may cast a spell with a target of "You" on his familiar (as a touch range spell) instead of on himself.
A master and his familiar can share spells even if the spells normally do not affect creatures of the familiar’s type (magical beast).
Protection from Energy
Abjuration
Level: Clr 3, Drd 3, Luck 3, Protection 3, Rgr 2, Sor/Wiz 3
Components: V, S, DF
Casting Time: 1 standard action
Range: Touch
Target: Creature touched
Duration: 10 min./level or until discharged
Saving Throw: Fortitude negates (harmless)
Spell Resistance: Yes (harmless)
Protection from energy grants temporary immunity to the type of energy you specify when you cast it (acid, cold, electricity, fire, or sonic). When the spell absorbs 12 points per caster level of energy damage (to a maximum of 120 points at 10th level), it is discharged.
Note: Protection from energy overlaps (and does not stack with) resist energy. If a character is warded by protection from energy and resist energy, the protection spell absorbs damage until its power is exhausted.