Perhaps your confusion would be helped if you consider that a gene codes for the production of a protein. It’s proteins that do the actual biological ‘work’. Proteins can be structural – you are protein (mostly collagen, in fact). Proteins can be enzymes that drive biochemical reactions. They can be chaperones that transport molecules in and out of our cells. They can be cell surface receptors that sense a huge range of stimuli in the environment. They can be signalling molecules that the cells of our body use to communicate with other cells. They can be transducers of mechanical work (muscle).
Now, a stereotypical depiction of a biochemical pathway might be:
Precursor --> intermediate 1 --> intermediate 2 --> intermediate 3 --> end product
This could be digestion of an ingested nutrient down to a basic constituent, breakdown of stored molecules for energy, build up of molecules for energy storage, production of a hormone or any number of things. Each of these steps is catalysed by a different enzyme without which the reaction would proceed too slowly. Production of the enzymes is coded for by their respective genes. So it can be said that genes (that code for enzymes) exert their influence on particular steps of biochemical pathways. Of course, real biochemical pathways are rarely simple linear reactions; they are complex interactions with inputs into, and inputs from, multiple other pathways.
