Question

Outline and describe the differences between prokaryotic and eukaryotic repair mechanisms.

Please CITE. Thank you.

Answer 1

Generally, we see two types of cells prokaryotic and eukaryotic cells where in terms of advanced eukaryotic is better . There are plenty of advantages in the case of eukaryotic cells compared to prokaryotic cells.

There are some differences between prokaryotic and eukaryotic replication :

Replication is a very process that is related to both prokaryote and eukaryote , it linked with cell division of all organisms. The cell cycle is a part of cell division which is 20 minutes for prokaryotes and 18 to 24 hours for eukaryotes. The cell cycle consists of 4 phases: G1, S, G2, and M.

Details :

• G1 = growth and preparation of the chromosomes for replication
• S = synthesis of DNA (and centrosomes)
• G2 = preparation for M
• M = mitosis

G1, S, and G2 are called interphase. When cells are not able to divide further, such as terminally differentiated cells, they are stays in the G0 phase. When the cell passes through a phase of cell cycle, there are certain checks that must be carried out. In some critical stages, the level of special cytoplasmic proteins which also called cyclins rises then subside once the cell has passed through the phase. There is a lot of enzymes, which known as cycline-dependent kinases (cdks), this is phosphorylated protein targets , which is involved in cell cycle control. The most interesting thing is that although the cdks are present at fairly steady concentrations in the cell, regardless of the cell cycle phase, they are only activated when they bind the appropriate cycline.

There are some key indicator which is used at each checkpoint. Just like the presence of Okazaki fragments , that is nothing but a check for the completion of the S phase (replication). If the replication is completed, then there is no Okazaki fragments that should be present. At the time of DNA checking G1 before the cell enters, S. Spindles are checked before the cell that they are actually divided or not  (M phase).

Although we know plenty of reasons why eukaryotic is better than prokaryotic but there are some unique problems faced by eukaryotes that are not faced by prokaryotes:

1. Linear chromosomes with ends
2. More genetic material
3. The typical animal cell has 50 times more DNA than the average bacterium (E). coli has 4.6 million base pairs, humans have 3 000 million base pairs or 650 times as much!!)
4. Much more packaging
5. The nucleosomes (DNA wound around histone protein)
6. the DNA polymerase enzyme of eukaryotes works much slower.

Protein synthesis is a key part of replication :

a)Prokaryote (enzymes with direction mentioned)

1. DNA Polymerase I - 5' to 3' polymerase, 3' to 5' exonuclease, 5' to 3' exonuclease
2. DNA Polymerase III - 5' to 3' polymerase, 3' to 5' exonuclease
3. DNA gyrase - Type II topoisomerase

b)Eukaryotes (enzymes with direction mentioned):

1. DNA Polymerase α - 5' to 3' polymerase, complexes with the primase enzyme then start DNA synthesis from the RNA primers, low processivity (~100 nt), no exonuclease activity
2. DNA Polymerase 5' to 3' polymerase, 3' to 5' exonuclease, high processivity when complexed with PCNA
3. DNA Polymerase 5' to 3' polymerase, high processivity, the probable regulatory role
4. DNA PolymeraseMitochondrial DNA polymerase (5' to 3')
5. Telomerase - Reverse transcriptase activity (5' to 3 ) using an endogenous RNA template  

Now we will talk about the most important thing that is a DNA repair mechanism in which a cell itself identifies and corrects to the DNA molecules and then after that encode its genome

DNA repair mechanisms divided into 2 categories
- Repair of damaged bases
- Repair of incorrectly base-paired bases during replication

There are four repair pathways exist to repair single-stranded DNA damage:

i) Nucleotide excision repair (NER)
ii) Base excision repair (BER)
iii) DNA mismatch repair (MMR)
iv) Repair through alkyltransferase-like proteins (ATLs)

Nucleotide excision repair (NER) : This is an important DNA repair mechanism. NER system recognizes that is there any damaged strand or not if yes then identifies the damaged DNA strand, cleave it on both sides of the lesion, finally remove and re-synthesize those fragments. UvrB is a central component of the bacterial NER system which is involved in damage recognition, strand excision, and repair synthesis. UvrB contains two domains related to the structure of the helicase enzyme and two other additional domains unique to the repair of proteins. The structure contains all elements of an intact helicase and shows that UvrB uses ATP hydrolysis to move along the DNA to check for damage. The location of the conserved residues and structural comparisons allows us to predict the path of the DNA and suggest that the tight pre-incision complex of UvrB and the damaged DNA is formed by the insertion of a flexible Ž²-hairpin between the two DNA strands.

Base excision repair (BER) is a type of cellular mechanism which repairs the damaged DNA throughout the cell cycle. It is primarily responsible for removing small, non-helix-distorting base lesions from the genome. Then the associated nucleotide excision starts their work by repairing pathway and after that repairs bulky helix-distorting lesions. BER is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to DNA breaks during replication. BER is initiated by DNA glycosylases that recognize and remove specific damaged or inappropriate bases forming AP sites. Finally, the resulting single-strand break can then be processed by either short-patch (where a single nucleotide is replaced) or long-patch BER (where 2-10 new nucleotides are synthesized)

Mismatch Repair (MMR) : This repair is also an important pathway in this process our cells repair base-base mismatches and insertion/deletion mispairs generated at the time of  DNA replication and recombination. Mismatch repair systems maintain the integrity of our genomes by suppressing non-homologous recombination and have recently been shown to play a role in the signaling of DNA damage in eukaryotic cells. The most important feature of this MMR is to unlimited cell division related disease identify , This  MMR defects increase the spontaneous mutation rate and are associated with both hereditary and sporadic cancers. Proteins unique to MMR were first identified in prokaryotes, which resulted in increased mutations and a mutated phenotype due to the loss of such proteins. These proteins are known as the Å“Mut proteins. Of all the Å“Mut proteins, MutS, MutL, MutH are essential in detecting the mismatch and directing repair machinery to it.

Alkylated DNA is directly involved in repairing enzymes, which is known as alkyltransferase (AGTs). Alkyltransferase-like proteins (ATLs) enzymes, can also protect against the alkylation damage, but lack of some alkyltransferase activity.