Part of the answer is that the proteins have the ability to specifically recognize their targets by virtue of the structure of complementary structures of the proteins and targets. For example, DNA replication in E. coli begins by recognition of the origin of replication (oriC) DNA sequence by the protein DnaA. DNA polymerase recognizes the 3'-OH of the primer and the adjacent single-stranded DNA. DNA ligase specifically recognizes the structure of a nick in the DNA backbone, which consists of a missing bond in the phoshophodiester backbone between a 5'-phosphate group and a 3'-OH group.

Another part of the answer is diffusion. Because the volume of the space in which they are confined is so small, it is possible for protein molecules to sample the space pretty quickly by random diffusion.

In addition, proteins can form complexes with each other that bring multiple parts of the machinery together, such as the primosome in E. coli DNA replication that consists of about 10 proteins with various functions that serve different roles in DNA replication. These complexes result from specific protein-protein interactions.

Maybe add the concept of turnover of proteins and the concept of time. When proteins are made, it is taken in vesicles to RE and very occasionally, to other sides of the cell. This happens as it is made. There are proteins which guide the machinery with more proteins to the position indicated by a stimulus. This means the proteins stable the region and start to replicate. This stimulus ( and the replication means mitosis and not a temporal protein) signalling ( and normally CA+2) means this region of the DNa opens and starts the replication. These signals come from the membrane (kinases). The nucleus membrane have holes. The replication of the DNA means nucleus disappears. This promoter have enhancers of replication. There are guides to the zone and part of the answer is epigenome.

Another form of guidance is the peptide signal. Not all mRNA is the coding protein. This means some of the protein does not translate. Maybe this could be exons or Exon shuffling. Why do different exons give different genes. It is not a question in the genome,but the combination of genes which turn to coding areas or ORF (Open reading frame). This means we could cover from virus or jumping DNA. tRNA converts the section of DNA to amino acids but animals need these amino acids whilst plants make them. From the ribosomes the proteins are taken to the RE normally. A very specific protein must be for not to be taken to RER ( and then into vesicles). The glycosylation starts and then turns into a specific protein. It may be random but it must be specific to this place. There are diseases of autophagy. The peptide signals takes it to the ribosomes. The proteins can be taken by the cytoskeleton in chains by miosin and actin. (Some of the proteins although we can say most of them). The u uracyl is specific to the ribosomes. They match together at the same time (or almost at the same time). tRNA match the amino acids with the triplet of the genetic code.