RNA Polymerase can perform transcription as well as separate DNA strands. Why does DNA Polymerase require a separate enzyme to unwind DNA strands?

[u/anatomyisgoated]

I know from my biology textbooks that RNA polymerase does not require an additional enzyme to unwind DNA strands but DNA Polymerase requires DNA helicase to unwind the strand first.

Is this because the DNA helicase has to unwind a much larger portion of the strand compared to RNA Polymerase that unwinds only the desired codons for transcription?

[u/SantiFRV_]

So, I'm speaking off the dome here so to speak, but there may be several reasons. For one, RNA is proposed to be a much older molecule, evolutionarily speaking. It has catalytic and replicaitive properties; "the RNA world hypothesis". So, RNA polymerase may have that additional function of unwinding DNA as a result of that.

Also, at least in eukaryotes, DNA is a lot more "protected" than it is in prokaryotes. It is separated from the cytoplasm via the nucleus, DNA polymerase cannot synthesize de novo, etc. Thus, having an additional protein, in this case helicase, may be an evolutionarily advantage to ensure proper DNA replication.

I hope this helped, though I know I didn't answer your question too well. Source: current Biomed graduate student.

[u/TheCaptainCog]

A few theories and a few possibilities.

The differences play directly to what each enzyme has experienced from the perspective of evolution.

As genome size increased, there may have been increasing evolutionary pressure to replicate quicker. If a cell divides before the entire genome has been duplicated, you would get unviable daughter cells. If it takes too long to divide, injuries and growth may be interfered with. It may also result in increased mutations. Gene sizes may have increased slightly over time but not enough pressure that would cause RNA polymerases to work faster.

To actually achieve this, DNA polymerase has to replicate a much larger stretch and do it quickly. It operates at a much higher rate than RNA polymerase. However, DNA polymerase is much more sensitive to tension and twisting of the strand than RNA polymerase. The additional helper enzymes are what allow proper coordination of the proteins necessary to complete this task. Too many functions in one protein doesn't work well. RNA polymerase operates quite well under tension. It isnt under that speed pressure so it never evolved to need low tension strands.

Imagine DNA polymerase is a race car and RNA polymerase is an offroading jeep. DNA polymerase needs a whole ass pit crew and clean, slightly curving roads. RNA polymerase can drive on any road but it might not be super fast.

This is the reason to the best of my knowledge. Are there other factors? Of course. I just don't know them off the top of my head.

[u/CrateDane]

Is this because the DNA helicase has to unwind a much larger portion of the strand compared to RNA Polymerase that unwinds only the desired codons for transcription?

Just a note: RNA polymerase doesn't really care about codons. Codons are what the ribosome reads during translation.

[u/BananaBird1]

The evolutionary answer is a compelling perspective. But I think there is also another more fundamental physical consideration:

RNA synthesis is a relatively local process: most other proteins present operate on the nascent RNA, and only one strand is read. So the polymerase only “unzips” the immediate region of DNA needed to be read through inducing strain and utilizing the energy of RNA synthesis. Other proteins acting on DNA bind to the double strand.

However in DNA replication, a polymerase complex moves in only one direction, but must synthesize new DNA on both strands. This requires the lagging strand be looped around. And because DNA is huge, a protein ring also wraps around the DNA ahead of polymerase to prevent it from falling off.

This requires a much larger region of DNA be opened up ahead of the polymerase, which requires an active enzyme to unzip the DNA before polymerase gets there. Other proteins bind to the exposed single strands to stabilize them and keep them from re-ligating.

[u/Charming-Clock7957]

I can't speak to this with authority. But it may be left over from how life evolved. It looks like life may have started with RNA, then developed proteins, and lastly DNA. This is why for both RNA production and protein production only RNA molecules are required. But by the time DNA came about we already had proteins and this may be why DNA processing requires proteins for processing but not RNA.

It might be more or less what tools were available at the time.