That answer was pretty helpful but after reading this answer as well, I had another question. So if the variable groups don't react during the condensation reaction, how do they make react to make bonds between them during the secondary structure? I don't know how clear that was, sorry!
Yeah - so remember the secondary structure does not include covalent bonds between amines or carboxyls. They're formed purely by hydrogen bonding. Yes, the amines and carboxylic acids are involved in that hydrogen bonding, but the energy required to form a hydrogen bond is MUCH less than the energy required for a reaction to occur. And again, it's not that those R groups are inert and can't react. They absolutely can (in fact, I have some colleagues who react the amino acid side-chains so that they can attach things to proteins). The fact is that there's not enough energy for them to react, and so they require either the body to heat up a lot (like, get to 100 degrees. Not going to happen, the person would die), or for a catalyst to become involved. There are enzymes around, but the enzymes are designed such as to not react with the R groups when making proteins. Hence, secondary structure is all hydrogen bonds - things that the R groups can form with a limited supply of energy - and not covalent bonds - which the R groups can't form with their limited supply of energy.
Hopefully that makes sense