RNA polymerases

Synthesizing Polymerase	Type of RNA Produced	Function
RNA polymerase I	18S, 5.8S & 28S ribosomal RNA	Forms essential ribosomal components
RNA polymerase II	mRNA	Translated by ribosomes to form specific proteins
	Small nuclear RNA	Involved in mRNA splicing & transcription regulation
	MicroRNA	Causes gene silencing via translation arrest or mRNA degradation
RNA polymerase III	Transfer RNA	Adaptor molecule linking codons with specific amino acids
	5S ribosomal RNA	Essential component of 60S ribosomal subunit

Mnemonic

I, II, and III are numbered in the same order that their products are used in protein synthesis: rRNA, mRNA, then tRNA.

A fundamental concept in molecular biology is that synthesis of new DNA and RNA strands always occurs in the 5’ → 3’ direction. This means nucleotides are added to the 3’-hydroxyl (-OH) group of the growing strand. However, the enzymes read the template strand in the opposite direction.

5’ → 3’ Processes/Enzymes

This is the direction of synthesis for all new nucleic acid chains.

• DNA Polymerase (Replication)

  • 5’ → 3’ Polymerase Activity: Synthesizes the new DNA strand by adding dNTPs to the 3’ end. This is true for both the leading and lagging strands (Okazaki fragments).
  • 5’ → 3’ Exonuclease Activity: Found in DNA Polymerase I (prokaryotes). This activity is crucial for removing the RNA primers from the lagging strand and replacing them with DNA.

• RNA Polymerase (Transcription)

  • 5’ → 3’ Polymerase Activity: Synthesizes the new mRNA strand using the DNA template. It adds ribonucleotides to the 3’ end of the growing RNA molecule.

• Ribosome (Translation)

  • The ribosome reads the mRNA transcript in the 5’ → 3’ direction to synthesize protein from the N-terminus to the C-terminus.

3’ → 5’ Processes/Enzymes

This directionality is associated with reading the template strand and proofreading.

• Template Strand Reading

  • DNA Polymerase (Replication): Moves along the template strand in the 3’ → 5’ direction to synthesize the new 5’ → 3’ strand.
  • RNA Polymerase (Transcription): Reads the DNA template (antisense) strand in the 3’ → 5’ direction to create the complementary 5’ → 3’ mRNA transcript.

• Exonuclease (Proofreading) Activity

  • 3’ → 5’ Exonuclease Activity: This is the proofreading function found in high-fidelity DNA polymerases (like DNA Pol I, II, and III in prokaryotes). If an incorrect nucleotide is added, the polymerase can back up and excise the mismatched base from the 3’ end of the new strand before continuing synthesis. This significantly increases replication fidelity.

Process/Enzyme	Activity	Direction	Function
DNA & RNA Polymerase	Synthesis (Polymerase)	5’ → 3’	Elongating the new nucleic acid strand
DNA Polymerase	Reading Template Strand	3’ → 5’	Guiding the synthesis of the new strand
RNA Polymerase	Reading Template Strand	3’ → 5’	Guiding the synthesis of mRNA
DNA Polymerase I	Exonuclease	5’ → 3’	Removing RNA primers
DNA Polymerase (most)	Exonuclease (Proofreading)	3’ → 5’	Excising mismatched nucleotides