Short answer:

• 108 beads are for the 108 virtues (gunas) of the Panch Parmeshthi: Arihant 12, Siddha 8, Acharya 36, Upadhyaya 25, Sadhu 27 = 108.
• The extra 3 beads are a customary addition to remind the sadhak of the Three Jewels (Ratnatraya): Samyak Darshan, Samyak Jnan, Samyak Charitra.
• Many malas also have one “Sumeru/Guru” bead. It marks the start/end and is not counted or crossed during japa.

Notes on practice:

• Both Shvetambar and Digambar traditions honor 108 for its scriptural meaning. The 3 additional beads (and the guru bead) are traditional aids, not a strict scriptural requirement. Hence you may see 108 only, 108+1 (guru), or 108+3 (+1 guru) depending on lineage or family practice.