( ( For example ) ( , ( ( ( ( ( ( ( ( ( ( ( an atom ) ( with ( ( six protons ) ( in ( its nucleus ) ) ) ) ) ( is ( a ( carbon atom ) ) ) ) ; ) ( ( seven protons ) ( makes ( it nitrogen ) ) ) ) ; ) ( ( eight protons ) ( makes ( it oxygen ) ) ) ) , ) and ) ( so on ) ) . ) ) )
(ROOT (S (PP (IN For) (NP (NN example))) (, ,) (S (NP (NP (DT an) (NN atom)) (PP (IN with) (NP (NP (CD six) (NNS protons)) (PP (IN in) (NP (PRP$ its) (NN nucleus)))))) (VP (VBZ is) (NP (DT a) (NN carbon) (NN atom)))) (: ;) (S (NP (CD seven) (NNS protons)) (VP (VBZ makes) (S (NP (PRP it)) (ADJP (JJ nitrogen))))) (: ;) (S (NP (CD eight) (NNS protons)) (VP (VBZ makes) (S (NP (PRP it)) (NP (NN oxygen))))) (, ,) (CC and) (ADVP (RB so) (RB on)) (. .)))
For example, an atom with six protons in its nucleus is a carbon atom; seven protons makes it nitrogen; eight protons makes it oxygen, and so on.
(ROOT (S (NP (DT All) (NN carbon) (NNS atoms)) (VP (VBP have) (NP (CD six) (NNS protons))) (. .)))