( ( ( neutron and ) protons ) ( , ( themselves ( ( consist ( of ( ( smaller particles ) ( called quarks ) ) ) ) . ) ) ) )
(ROOT (S (NP (NP (NN neutron)) (CC and) (NP (NNS protons))) (, ,) (NP (PRP themselves)) (VP (VBP consist) (PP (IN of) (NP (NP (JJR smaller) (NNS particles)) (VP (VBN called) (NP (NNS quarks)))))) (. .)))
neutron and protons, themselves consist of smaller particles called quarks.
(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))))))))))) (. .)))