( Quarks ( ( ( ( make up ) ( the nucleus ) ) ( by ( composing ( ( neutrons and ) protons ) ) ) ) . ) )
(ROOT (S (NP (NNS Quarks)) (VP (VBP make) (PRT (RP up)) (NP (DT the) (NN nucleus)) (PP (IN by) (S (VP (VBG composing) (NP (NNS neutrons) (CC and) (NNS protons)))))) (. .)))
Quarks make up the nucleus by composing neutrons and protons.
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (VP (VBN made) (PP (IN of) (NP (NP (NNS quarks)) (, ,) (SBAR (WHNP (WDT which)) (S (VP (VBP are) (NP (NP (JJ fundamental) (NNS particles)) (PP (IN of) (NP (NN matter))))))))))) (. .)))