The answer is the DNA in the nucleus.
A protein is formed by the DNA going through the processes of transcription and translation. All the information needed to produce a specific protein is stored in the DNA region which corresponds to that specific protein. When there is a need for a specific protein, the DNA is transcribed into an RNA strand, and the RNA strand is then translated into a chain of amino acids that form the structure of the protein.
A lysosome is an organelle which contains degradative enzymes and has a role in degrading proteins that have been used, or proteins that are not needed at a specific time. The polysaccharides are a structural part of the cytoplasm and they don't have a big role in the formation of proteins, and phospholipids in the plasma membrane are a structural part that keeps the shape of the membrane and they have a role in the transport of proteins.
So to answer your question, if a scientist were to prevent the production of a specific protein, they would most likely modify the DNA segment in the nucleus of the cell that corresponds to that protein, so that when the cells start to transcribe that part of the DNA, they fail.