Proteins that duplicate the DNA in interphase

[icakeov]

For some reason, I can't seem to be able to find this answer easily on the internet. Or it is there and I somehow I can't see the wood for the trees.

I know that in transcription (when DNA is read for protein production), "RNA polymerase" is the protein that creates the mRNA by creating the new strand.

What is the protein (or proteins) in charge when DNA is being duplicated during interphase, before mitosis happens?
(I just found out that there is helicase, DNA polymerase, primase and ligase! So I am guessing DNA polymerase would be the answer, which leaves me with the question below)

Furthermore, when would this protein be produced? Is the protein produced when the time comes to double the DNA so it can get to work of duplication, or is the protein floating around and goes into a conformational change to start the DNA duplication process?

And a new addendum to this question, I am pretty sure the answer is yes to this, but just want to make sure: does RNA polymerase create the mRNA that then creates the DNA polymerase hormone? And also does RNA polymerase also create itself?

I appreciate any feedback!

 

[Ygggdrasil]

There are many different types of RNA polymerases inside the cell. Specifically, RNA polymerase II is responsible for producing mRNAs that will eventually be translated into protein. The other two RNA polymerases (pol I and pol III) are involved in producing non-coding RNAs like tRNA and ribosomal RNA.

Similarly, there are many different kinds of DNA polymerases inside eukaryotic cells. The bulk of DNA in eukaryotic genomes is synthesized by pol δ and pol ε. Pol α is also required during S phase (see https://en.wikipedia.org/wiki/Eukaryotic_DNA_replication#Replicative_DNA_Polymerases for a description of their roles). Other DNA polymerases are invovled in DNA repair and are only occasionally involved in DNA replication (usually to bypass DNA damage). DNA replication, however, does not just involve the DNA polymerases—as you mention, there are a number of other enzymes, including helicases, primases, and ligases, that are required for DNA synthesis to occur. The large multi-protein complex that carries out DNA replication is often referred to as the replisome.

Like all proteins, the genes for DNA polymerases are transcribed by RNA pol II. AFAIK, the replicative DNA polymerases are present constitutively throughout the cell cycle. However, as I mentioned above, DNA polymerases must first be assembled together with many other components to form replisomes before they can perform DNA synthesis. This assembly step, the loading and activation of the pre-replication complexes onto DNA, is the step that controls when DNA replication occurs. See https://www.ncbi.nlm.nih.gov/books/NBK26856/#_A3215_ for an overview of how cells regulate entry into S-phase and the initiation of DNA synthesis.

 

[icakeov]

Thanks so much @Ygggdrasil! Super clear and helpful!

 

[icakeov]

Was just mulling over this whole thing a bit more.
The gene that codes for RNA polymerase has to use RNA polymerase (amongst all the other proteins) to make RNA polymerase. This sound a lot like a chicken and egg / catch 22 situation?

Also, is there a common name for the multi-protein complex that is in charge of making proteins? (tRNA, mRNA, ribosomes..)

 

[Fervent Freyja]

The multiple protein sub-units must assemble before it becomes an active enzyme; then, it can be called RNA polymerase. Most certainly not a chicken and egg situation. DNA primase itself is considered an RNA polymerase. Polymerases are usually active in Eukaryotes when within the nucleus, the protein sub-units may be in the cytoplasm when not being assembled. I think they are assembled a few minutes to a few hours beforehand.

I think it would be of help for you to review replication, it should be thought of as a different process than translation or transcription. This seems to be what you are trying to ask about, but your questions keep going to other processes...

 

[icakeov]

Thanks for your input Fervent Freyja! That's right, I am focusing on replication, what I am wanting to figure out is the actual "loop" in that "replicative machinery".

It goes from DNA that makes RNA polymerase (and a whole bunch of helper proteins), then RNA polymerase (with the bunch of helper proteins) makes DNA polymerase(and a whole bunch of helper proteins), and then DNA polymerase (with the bunch of helper proteins) codes for that DNA again.

Does that sound right?

I just noticed that I was wondering where RNA polymerase "came from", because it takes RNA polymerase to make RNA polymerase...

 

[Ygggdrasil]

Was just mulling over this whole thing a bit more.
The gene that codes for RNA polymerase has to use RNA polymerase (amongst all the other proteins) to make RNA polymerase. This sound a lot like a chicken and egg / catch 22 situation?

Yes, it is a chicken and egg problem. Life is a self-propagating system. In addition to the genetic material, cells contain the set of proteins necessary to replicate and read the genetic material. This set of proteins gets passed on to daughter cells during cell division, and get replenished through transcription and translation, so they will always be present. If these proteins stop functioning, the cell dies.

In practice, living systems always spring from other living systems. There was a point in the very far past where the first living system arose from non-living components (abiogenesis), but we do not yet understand how this works. Scientists have not yet been successful at creating living systems from scratch (though scientists can certainly create many parts of living systems, including entire genomes).

Also, is there a common name for the multi-protein complex that is in charge of making proteins? (tRNA, mRNA, ribosomes..)

The ribosome itself is a large complex between many proteins and three different RNA molecules. I'm not sure if there is a name for the fully assembled ribosome-mRNA-tRNA complex, though people use the term "polysome" to describe an mRNA that is being translated by a number of ribosomes simultaneously.

 

[BillTre]

In practice, living systems always spring from other living systems. There was a point in the very far past where the first living system arose from non-living components (abiogenesis), but we do not yet understand how this works. Scientists have not yet been successful at creating living systems from scratch (though scientists can certainly create many parts of living systems, including entire genomes).

How this happened is of course one of the great mysteries of biology.

One way to consider this relationship is to consider of the cell and its molecular machinery as providing a permissive environment for the genetically stored information to be expressed in an adaptive manner.
The cellular environment is maintained by the ongoing expression of a variety of genes, but how that environment that supports genetic expression came to be requires a different explanation.
Many think this may have started out a simpler system (RNA without DNA) in an RNA world which was later elaborated upon to make its functioning more efficient and dependable. RNA's without DNA can store information and depending on sequence, have enzymatic properties.

Viruses (whether considered living or non-living, or maybe sometimes living) do similar things, but rely on their host cells for the environment that supports the proper expression of their genetic information. They are parasites taking advantage of the special environment in a cell to fulfill their life cycle.

Small changes in these cellular environments could completely wreck the functioning of the system. Consider what would happen if one tRNA were changed (in a manner that encoded a different amino acid). All the proteins using its codon would be made as if they all had point mutations at the location of the codon. If this happened to too many proteins, it would be lethal.
tRNA's in simple organisms have been successfully changed in labs, but the sequence of the many genes using that codon were also changed at the same time. This required lots of changes throughout the genome and is unlikely to happen in a natural situation. The cellular environment was changed to suit the genetically encoded information by changing the genetic information that encodes components of the cellular environment.

 

[icakeov]

Fantastic! Thank you so much! That really clarified it.