( ( ( Protons and ) neutrons ) ( ( ( make up ) ( ( the ( ( nucleus or ) center ) ) ( of ( the atom ) ) ) ) . ) )
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP make) (PRT (RP up)) (NP (NP (DT the) (NN nucleus) (CC or) (NN center)) (PP (IN of) (NP (DT the) (NN atom))))) (. .)))
Protons and neutrons make up the nucleus or center of the atom.
(ROOT (S (NP (NP (DT The) (NN atom)) (PP (IN in) (NP (DT a) (NN neutron)))) (VP (VBZ is) (VP (VBN found) (PP (IN in) (NP (DT the) (DT the) (NN nucleus))))) (. .)))