Final answer:
Cdk7 of TFIIH phosphorylates primarily Serine 5 and Serine 7 residues in the carboxy-terminal domain (CTD) of RNA polymerase II, which is necessary for the start of mRNA synthesis during gene transcription.
Step-by-step explanation:
Cdk7, part of the transcription factor TFIIH, phosphorylates the carboxy-terminal domain (CTD) of RNA polymerase II as a critical step in the initiation of gene transcription. The specific amino acid residues that are phosphorylated by Cdk7 within the CTD are the serine residues, primarily Serine 5 and Serine 7. This phosphorylation event is crucial for the transition from transcription initiation to elongation, which includes the release of some transcription factors and the progression of RNA polymerase II along the DNA template to start synthesizing mRNA.