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Important components of replication machinery

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This document summarizes several important components of DNA replication machinery, including DNA helicases, single-stranded DNA binding proteins, DNA topoisomerase, DNA primase, DNA polymerase, DNA ligase, DNA glycolyses, and telomeres. It describes what each component is, its role in DNA replication, and key properties. For example, it notes that DNA helicases use ATP to break hydrogen bonds between nucleotide base pairs, single-stranded DNA binding proteins prevent reformation of the DNA double helix, and DNA ligase reseals nicked DNA strands using ATP.

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Important components of Replication Machinery Dr. Asif Mir (Chairperson DBI&BT)
DNA helicases (require ATP) They are motor proteins that move directionally along a nucleic acid phosphodiester backbone. The process of breaking the hydrogen bonds between the nucleotide base pairs in double-stranded DNA requires energy. To break the bonds, helicases use the energy stored in a molecule called ATP, which serves as the energy currency of cells. Approximately 1% of eukaryotic genes code for helicases. The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of nucleic acid strands that necessitates the use of helicases.
Single stranded DNA binding proteins (SSBs) Single-stranded DNA-binding proteins (SSB) have high affinity to single-stranded (ss) DNA and participate in DNA replication, recombination, and repair as accessory protein . SSB plays a role in separating DNA strand during replication and prevent ssDNA from re-form a double helix. There are two kinds of complexes of SSB-ssDNA in different site sizes in the (SSB)35- and (SSB)65- binding modes. Single-stranded DNA can interact with two SSB subunits in the (SSB)35 complex, which has "smooth-contoured" structure as well as with all four SSB subunits in the (SSB)65 complex, which has "beaded" structure.
DNA topoisomerase DNA topoisomerases are ubiquitous enzymes found in all cell types from viruses to man. These enzymes act to regulate DNA supercoiling by catalysing the winding and unwinding of DNA strands. They do this by making an incision that breaks the DNA backbone, so they can then pass the DNA strands through one another, swivelling and relaxing/coiling the DNA before resealing the breaks.
DNA topoisomerase I & II
DNA primase DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit.
DNA polymerase The structure of DNA polymerase is highly conserved, meaning their catalytic subunits vary very little from one species to another, irrespective of how their domains are structured. This highly conserved structure usually indicates that the cellular functions they perform are crucial and irreplaceable and therefore require rigid maintenance to ensure their evolutionary advantage The DNA polymerases are enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from one original DNA molecule. During this process, DNA polymerase reads the existing DNA strands to create two new strands that match the existing ones.
DNA ligase (require ATP) DNA ligases close nicks in the phosphodiester backbone of DNA. Biologically, DNA ligases are essential for the joining of Okazaki fragments during replication, and for completing short-patch DNA synthesis occurring in DNA repair process. The reaction occurs in three stages in all DNA ligases: 1. Formation of a covalent enzyme-AMP intermediate linked to a lysine side-chain in the enzyme. 2. Transfer of the AMP nucleotide to the 5 phosphate of the nicked DNA strand. 3. Attack on the AMP-DNA bond by the 3-OH of the nicked DNA sealing the phosphate backbone and resealing AMP.
DNA glycolyases DNA glycosylases remove lesions generated by deamination of bases, alkylating agents, oxidative stress, ionizing radiation, or replication errors. All these lesions cause little perturbation of DNA structure. Most DNA glycosylases excise a wide variety of modified bases, while few of them have, so far, a very narrow substrate specificity.
Telomere The ends of the linear chromosomes are known as telomeres. Repetitive sequences that code for no particular gene. These telomeres protect the important genes from being deleted as cells divide and as DNA strands shorten during replication.
Important components of replication machinery

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Important components of replication machinery

  • 1. Important components of Replication Machinery Dr. Asif Mir (Chairperson DBI&BT)
  • 2. DNA helicases (require ATP) They are motor proteins that move directionally along a nucleic acid phosphodiester backbone. The process of breaking the hydrogen bonds between the nucleotide base pairs in double-stranded DNA requires energy. To break the bonds, helicases use the energy stored in a molecule called ATP, which serves as the energy currency of cells. Approximately 1% of eukaryotic genes code for helicases. The human genome codes for 95 non-redundant helicases: 64 RNA helicases and 31 DNA helicases. Many cellular processes, such as DNA replication, transcription, translation, recombination, DNA repair, and ribosome biogenesis involve the separation of nucleic acid strands that necessitates the use of helicases.
  • 3. Single stranded DNA binding proteins (SSBs) Single-stranded DNA-binding proteins (SSB) have high affinity to single-stranded (ss) DNA and participate in DNA replication, recombination, and repair as accessory protein . SSB plays a role in separating DNA strand during replication and prevent ssDNA from re-form a double helix. There are two kinds of complexes of SSB-ssDNA in different site sizes in the (SSB)35- and (SSB)65- binding modes. Single-stranded DNA can interact with two SSB subunits in the (SSB)35 complex, which has "smooth-contoured" structure as well as with all four SSB subunits in the (SSB)65 complex, which has "beaded" structure.
  • 4. DNA topoisomerase DNA topoisomerases are ubiquitous enzymes found in all cell types from viruses to man. These enzymes act to regulate DNA supercoiling by catalysing the winding and unwinding of DNA strands. They do this by making an incision that breaks the DNA backbone, so they can then pass the DNA strands through one another, swivelling and relaxing/coiling the DNA before resealing the breaks.
  • 6. DNA primase DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit.
  • 7. DNA polymerase The structure of DNA polymerase is highly conserved, meaning their catalytic subunits vary very little from one species to another, irrespective of how their domains are structured. This highly conserved structure usually indicates that the cellular functions they perform are crucial and irreplaceable and therefore require rigid maintenance to ensure their evolutionary advantage The DNA polymerases are enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from one original DNA molecule. During this process, DNA polymerase reads the existing DNA strands to create two new strands that match the existing ones.
  • 8. DNA ligase (require ATP) DNA ligases close nicks in the phosphodiester backbone of DNA. Biologically, DNA ligases are essential for the joining of Okazaki fragments during replication, and for completing short-patch DNA synthesis occurring in DNA repair process. The reaction occurs in three stages in all DNA ligases: 1. Formation of a covalent enzyme-AMP intermediate linked to a lysine side-chain in the enzyme. 2. Transfer of the AMP nucleotide to the 5 phosphate of the nicked DNA strand. 3. Attack on the AMP-DNA bond by the 3-OH of the nicked DNA sealing the phosphate backbone and resealing AMP.
  • 9. DNA glycolyases DNA glycosylases remove lesions generated by deamination of bases, alkylating agents, oxidative stress, ionizing radiation, or replication errors. All these lesions cause little perturbation of DNA structure. Most DNA glycosylases excise a wide variety of modified bases, while few of them have, so far, a very narrow substrate specificity.
  • 10. Telomere The ends of the linear chromosomes are known as telomeres. Repetitive sequences that code for no particular gene. These telomeres protect the important genes from being deleted as cells divide and as DNA strands shorten during replication.