DNA Structure revisited......       

The DNA molecule is a double-stranded helix.

The diameter of the DNA molecule is uniform.

The twist in DNA is right-handed (the twist is in the same direction as the thread on most screws).

 

    

The DNA molecule is a double-stranded helix.

The diameter of the DNA molecule is uniform, and easily interpreted by proteins that "patrol" the DNA to maintain it's integrity.

The twist in DNA is right-handed (-the same direction as the threads on most screws)...right handed double-helix, although the "threading" is not always the same.....B-form Helix

The two strands run in different directions (they are antiparallel).

Hydrogen bonds -a type of attractive intermolecular force that exists between two partial electric charges of opposite polarity- between complementary bases hold the two strands together.

 

                   

Consequently, each base pair has one purine and one pyrimidine, so the diameter of the double helix remains constant.

As the genetic material of the cell, DNA must perform four important functions: 

It must be able to store all of an organism's genetic information.

It must be susceptible to mutation.

It must be precisely replicated in the cell division cycle.

It must be expressible -giving rise to the phenotype.

In prokaryotes the replication complex makes new DNA at a rate in approximating 500 - 1,000 base pairs per second, with an error rate of fewer than one base in a billion.

In eukaryotes, the rate approximates 10 -fold less, but retains a similar replication error rate.

In both eukaryotes and prokaryotes, DNA is replicated by a huge enzyme complex, called DNA polymerase or DNA Replicase, as it catalyzes the reactions of DNA replication. 

In eukaryotes, large chromosomes can have hundreds of origins of replication. Consequently, in eukaryotes, DNA replication occurs at many different sites simultaneously.

In both eukaryotes and prokaryotes, DNA is replicated by a large enzyme complex, called DNA polymerase or DNA Replicase, as it catalyzes the reactions of DNA replication. 

Theoretically, DNA could serve as its own template in one of three different ways:

Semiconservative replication would use each parent strand as a template for a new strand. Each new DNA double helix would then have one parent strand and one new strand.

Conservative replication would build an entirely new double helix based on the template of the old double helix. The new strand would contain none of the original DNA.

Dispersive replication would use fragments of the original DNA molecule as templates for assembling two molecules. All the resulting strands would be mixtures of old and new material.

DNA polymerases are incredibly faithful in their replication porcess, with 1 error in 1x 10⁹ bases replicated...., As a result, the process of DNA replication HAS to begin from an existing 3'OH group.... Consequently Replication of chromosomes by the Major replicase (DNA Polymerase) ALWAYS needs a "primer", which is a short strand of RNA complementary to the DNA template strand.

    

        An enzyme called a primase makes the RNA primer strand.
     The RNA primer is later degraded and replaced with DNA, so the final DNA molecule has no RNA.

DNA replication involves the activities of several "key" proteins,each with different roles:

       

DNA helicase & topoisomerase: which denature and untangle the double helix.
Single-strand binding proteins: keeps the two strands separate.
RNA primase: makes a primer strand that serves as a starting point for replication.
DNA polymerase: itself adds complementary nucleotides to the growing strand, proofreads the DNA, and repairs it.
DNA ligase: seals up breaks in the sugar–phosphate backbone.

      So both strands cannot be synthesized in exactly the same way.

Because of its relatively opposite orientation, the lagging strand of DNA must grow in relatively small, discontinuous pieces, called Okazaki fragments. after their discoverer, the Japanese biochemist Reiji Okazaki.

      Each Okazaki fragment requires an RNA primer to initiate strand synthesis, which is formed by an enzyme called RNA primase, which begins it synthesis of RNA some distance away from the previous Okazaki fragment.

      Ultimately, the gaps in the lagging strand DNA are filled in by a repair DNA polymerase, which is also able to remove the RNA primers that are left on this strand. 

      Finally, DNA ligase catalyzes formation of the final phosphodiester linkage that joins the two Okazaki fragments.

      Okazaki fragments range from around 100 to 200 nucleotides (bases) long in eukaryotes, and 1,000 to 2,000 nucleotides long in prokaryotes.

       In E. coli, the replication complex makes new DNA at a rate in approximating 500 -1,000 base pairs per second, with an error rate of fewer than one base in a billion.

In Eukaryotes, the rate approximates 10 -fold less, but retains a similar replication error rate.

In both eukaryotes and prokaryotes, DNA is replicated by a huge enzyme complex, called DNA polymerase or DNA Replicase, as it catalyzes the reactions of DNA replication. 

 

    

 

     HOWEVER, as stated previously, it is the RNA primase that always makes the primer strand, and as we have discussed, the resulting RNA primer is later degraded and replaced with DNA, so the final DNA molecule has no RNA.

As the genetic material, DNA must perform four important functions:

There are many steps between genotype and phenotype; as genes cannot (by themselves) directly produce a phenotype.

At the molecular level

- gene: "a sequence of DNA that gives rise to a functional gene product..." this product can (ultimately) be an RNA or a protein.

This is a little different from our first definition of a gene, way back in lecture 4, when we defined it as

- gene: A unit of heritable information -usually associated (at the molecular level) with a specific region located on the chromosome.

Given the central dogma, however, there are two steps which are commonly used to express a gene:

Transcription, which makes a single-stranded RNA copy of a segment of the DNA. 

Followed by the process of Translation, which uses information encoded in a portion of the RNA to make a polypeptide.

In eukaryotes, these two steps are physically distinct... in prokaryotes -not so much.

How does RNA differ from DNA