The nucleus is the control center of the cell and houses the genetic material (DNA) organized into chromosomes. It controls protein and enzyme synthesis by regulating gene expression through Transcription(DNA's genetic information (genes) is transcribed into messenger RNA (mRNA) within the nucleus), transportation(mRNA then moves from the nucleus to the cytoplasm) and translation (the mRNA attaches to ribosomes, which translate the code to assemble amino acids into proteins).

A. DNA: DNA contains the instructions for protein synthesis but it is a molecule, not an organelle, and it remains in the nucleus (mostly). It does not directly "control" the synthesis in the cytoplasm as a singular controlling unit in the way the entire nucleus does by initiating and regulating the process via mRNA.

C. Chromosome: Chromosomes are structures made of DNA and protein found within the nucleus. They carry the genes, but the nucleus is the overall organelle that manages the use of these chromosomes for synthesis.

D. Mitochondria: Mitochondria are primarily responsible for cellular respiration and energy production (ATP synthesis). They have their own small amount of DNA and ribosomes for synthesizing some of their own specific proteins, but they do not control the majority of general protein and enzyme synthesis in the cell's cytoplasm.