The stone paladins that protect Hogwarts when summoned are like the cell wall they do their duty to protect the cell.

Like the cell membrane the magical boundary/gate decides what gets to come in and out of Hogwarts school.

Professor Dumbledore is the Headmaster of Hogwarts. Just like the nucleus Dumbledore is in charge of all his cell/school's activities.

The moving staircases take students to different parts of Hogwarts. The staircases are like the endoplasmic reticulum, an organelle that carries proteins and other materials to one part of a cell to another.

Platform 9 3/4 is where students board the train at the beginning of the school year with their luggage to be sent off to Hogwarts. This is similar to the job of Golgi bodies, they package proteins and send them through the endoplasmic reticulum.

The greenhouse on the inside and outside of Hogwarts are used for botany and potions classes. The greenhouses are like chloroplast they let in sunlight allowing them to create food for the cell and plant.

The vacuole stores food and water. The food platters always have food on them almost as if they store food inside of them. The Black can also be like a vacuole it takes a significant area to the south of Hogwarts.

Mitochondria are the "powerhouses" of the cell, they're cell's power supply. Magic is what runs Hogwarts just like how the mitochondria run a cell

The students of Hogwarts school of Wizardry and Witchcraft create magic like how ribosomes create proteins. Magic and proteins are needed to sustain Hogwarts and a cell.