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CHEMISTRY & ENZYMOLOGY
OF REPLICATION
Dr. M. Sonia Angeline
KJC
INTRODUCTION
• A fundamental property of living organisms is their ability to reproduce.
• Organisms produce offspring that are similar to themselves.
• The process occurs by which a single parental cell divides to produce two identical daughter
cells.
• In this processes, the genetic material must be duplicated prior to cell division so that the
daughter cells receive a full complement of the genetic information.
• Replication means “Synthesis of daughter nucleic acid molecules identical to the parental
nucleic acids”.
• Thus accurate and complete replication of the DNA is essential to the ability of a cell
organism to reproduce.
• It is the basis for biological inheritance.
• DNA is made up of a double helix of two complementary strands. During replication, these
strands are separated.
• There are many enzymes they participate in the process of replication.
ENZYMES INVOLVED IN DNA REPLICATION
This is the list of Enzymes involved in DNA Replication.
– DNA Helicase
– DNA Polymerase
– DNA clamp
– Single-Strand Binding (SSB) Proteins
– Topoisomerase / DNA Gyrase
– DNA Ligase
– Primase
DNA HELICASE
• Helicases were discovered in E. coli in 1976
and are a class of enzymes vital to all living
organisms.
• Also known as helix destabilizing enzyme,
they separates the two strands of DNA at the
Replication Fork behind the topoisomerase.
• They are motor proteins that move
directionally along a nucleic acid
phosphodiester backbone, separating two
annealed nucleic acid strands (i.e., DNA,RNA,
or RNA-DNA hybrid) using energy derived
from ATP hydrolysis.
• They have molecular weight 300,000, which
contain SIX identical sub units.
DNA POLYMERASE
• DNA polymerases are enzymes that
synthesize DNA molecules from
deoxyribonucleotides, the building blocks of
DNA.
• These enzymes are essential to DNA
replication and usually work in pairs to create
two identical DNA strands from a single
original DNA molecule.
• During this process, DNA polymerase
“reads” the existing DNA strands to create
two new strands that match the existing ones.
• Also performs proof-reading and error
correction.
• A polymerase enzyme catalyzes the formation of a polymer, i.e. DNA polymerases are
involved in the formation of DNA – a polymer.
• DNA polymerase adds nucleotides (triphosphates) to the DNA chain (that contains
monophosphates).
• Phosphate of a nucleoside triphosphate molecule forms a 3', 5' phosphodiester bond
with a free 3'-OH in the growing polynucleotide chain, and a molecule or
pyrophosphate (P~P) is simultaneously released.
• Pyrophosphate contains a ‘‘high-energy’’ bond, meaning that when the released
pyrophosphate is hydrolyzed into two phosphate molecules, energy is liberated which
drives the polymerization process forward.
• The resultant polymerization will always proceed in a net 5´→3´ direction.
• There are three types of DNA polymerases in prokaryotes,
• DNA polymerase I and II are meant for DNA repair, and DNA polymerase III is meant
for actual DNA replication.
DNA Polymerase I: It is also called the Kornberg enzyme (after its discoverer – Arthur Kornberg).
• It is a DNA repair enzyme.
• It is mainly involved in removing RNA primers from Okazaki or precursor fragments and filling the
resultant gaps, and it can also remove thymine dimers produced due to UV-irradiation and fill the gap
(these are called the proofreading or editing functions of DNA polymerase I).
• It has five active sites, namely: (1) template site, (2) primer site, (3) 5´ → 3´ cleavage or exonuclease site,
(4) nucleoside triphosphate site, and (5) 5´ → 3´ cleavage site (or 5´ → 3´ exonuclease site).
DNA Polymerase II: It resembles DNA polymerase I and is also a repair enzyme.
DNA Polymerase III: DNA polymerase-III plays an essential role in DNA replication.
• It is a multimeric (having multiple subunits) enzyme or holoenzyme having ten subunits. The core
enzyme comprises three subunits: α, β, and θ.
• The remaining seven subunits increase processivity (processivity means rapidity and efficiency with
which a DNA polymerase extends growing chain)
DNA polymerases can be further subdivided into two different families.
Chemistry and Enzymology of  Replication
DNA CLAMP
• A DNA clamp, also known as a sliding
clamp, is a protein fold that serves as a
processivity- promoting factor in DNA
replication.
• As a critical component of the DNA
polymerase III holoenzyme, the clamp
protein binds DNA polymerase and
prevents this enzyme from dissociating
from the template DNA strand.
• The clamp-polymerase protein–protein
interactions are stronger and more
specific than the direct interactions
between the polymerase and the
template DNA strand.
SINGLE-STRAND BINDING (SSB) PROTEINS
• Single stranded binding proteins
prevent reannealing (binding of
complementary DNA sequences),
protect the single-stranded DNA
from being digested by nucleases,
and prevent secondary structure
formation, thereby allowing other
enzymes to function effectively
on the single strand.
• Molecular weight of the SSB
protein is 75,600.
• It contains FOUR identical
subunits, which binds single
stranded DNA.
TOPOISOMERASE
• Every cell has enzymes that increase (or) decrease the extent of DNA unwinding are called “Topoisomerases.
• Topoisomerase is also known as “DNA Gyrase” and that act on the topology of DNA.
• “Topoisomerases bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA
strands, this intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes,
the DNA backbone is resealed again.
• Topoisomerases” is an enzyme that can change the “Linking number”(Lk).
• The linking number (Lk) is a topological property, it can be defined as “ the number of times the second strand
pierces the second strand surface”.
• There are two classes of topoisomerases. ―a) Type-I Topoisomerases ―b) Type-II Topoisomerases
• a) Type-I Topoisomerases: This act by transiently breaking one of the two DNA strands, rotating one of the ends
about the unbroken strand, and rejoining the broken ends; they change Lk in increments of 1.
• b) Type-II Topoisomerases: The enzyme breaks both DNA strands and change Lk in increments of 2.
DNA LIGASE
• DNA ligase is a specific type of enzyme, a ligase, that facilitates the joining of DNA strands together by
catalysing the formation of a phosphodiester bond.
• DNA ligase is used in both DNA repair and DNA replication.
• The mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one
nucleotide, ("acceptor") with the 5' phosphate end of another ("donor").
• ATP is required for the ligase reaction, which proceeds in three steps:
i. Adenylation (addition of AMP) of a lysine residue in the active center of the enzyme, pyrophosphate is released;
ii. Transfer of the AMP to the 5' phosphate of the so- called donor, formation of a pyrophosphate bond;
iii. Formation of a phosphodiester bond between the 5' phosphate of the donor and the 3' hydroxyl of the acceptor.
PRIMASE
• DNA primase is an enzyme involved in the
replication of DNA and is a type of RNA
polymerase.
• Primase catalyzes the synthesis of a short RNA
(or DNA in some organisms) segment called a
primer complementary to a ssDNA template.
• Primase is of key importance in DNA
replication because no known replicative DNA
polymerases can initiate the synthesis of a
DNA strand without an initial RNA or DNA
primer (for temporary DNA elongation).
• After this elongation the RNA piece is
removed by a 5' to 3' exonuclease and refilled
with DNA.
NUCLEASES
• Nuclease enzymes act to hydrolyze or break down a polynucleotide chain into its
component nucleotides.
• The nuclease enzymes may be of the following two kinds:
• (a) Exonucleases: Exonucleases are nuclease enzymes which begin their attack from a
free end of a polynucleotide.
• Depending on the specificity of the enzyme, an exonuclease will either begin at a free 3'-
OH end of a polynucleotide or a free 5'-P end.
• In both cases the enzyme travels along the chain in a stepwise manner, liberating single
nucleoside monophosphate molecules and eventually digesting the entire polymer.
• (b) Endonucleases: Endonuclease enzymes attack one of the two sides of phosphodiester
linkages, but they react only with those bonds that occur within the interior of a
polynucleotide chain.
Chemistry and Enzymology of  Replication

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Chemistry and Enzymology of Replication

  • 1. CHEMISTRY & ENZYMOLOGY OF REPLICATION Dr. M. Sonia Angeline KJC
  • 2. INTRODUCTION • A fundamental property of living organisms is their ability to reproduce. • Organisms produce offspring that are similar to themselves. • The process occurs by which a single parental cell divides to produce two identical daughter cells. • In this processes, the genetic material must be duplicated prior to cell division so that the daughter cells receive a full complement of the genetic information. • Replication means “Synthesis of daughter nucleic acid molecules identical to the parental nucleic acids”. • Thus accurate and complete replication of the DNA is essential to the ability of a cell organism to reproduce. • It is the basis for biological inheritance. • DNA is made up of a double helix of two complementary strands. During replication, these strands are separated. • There are many enzymes they participate in the process of replication.
  • 3. ENZYMES INVOLVED IN DNA REPLICATION This is the list of Enzymes involved in DNA Replication. – DNA Helicase – DNA Polymerase – DNA clamp – Single-Strand Binding (SSB) Proteins – Topoisomerase / DNA Gyrase – DNA Ligase – Primase
  • 4. DNA HELICASE • Helicases were discovered in E. coli in 1976 and are a class of enzymes vital to all living organisms. • Also known as helix destabilizing enzyme, they separates the two strands of DNA at the Replication Fork behind the topoisomerase. • They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands (i.e., DNA,RNA, or RNA-DNA hybrid) using energy derived from ATP hydrolysis. • They have molecular weight 300,000, which contain SIX identical sub units.
  • 5. DNA POLYMERASE • DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. • These enzymes are essential to DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. • During this process, DNA polymerase “reads” the existing DNA strands to create two new strands that match the existing ones. • Also performs proof-reading and error correction.
  • 6. • A polymerase enzyme catalyzes the formation of a polymer, i.e. DNA polymerases are involved in the formation of DNA – a polymer. • DNA polymerase adds nucleotides (triphosphates) to the DNA chain (that contains monophosphates). • Phosphate of a nucleoside triphosphate molecule forms a 3', 5' phosphodiester bond with a free 3'-OH in the growing polynucleotide chain, and a molecule or pyrophosphate (P~P) is simultaneously released. • Pyrophosphate contains a ‘‘high-energy’’ bond, meaning that when the released pyrophosphate is hydrolyzed into two phosphate molecules, energy is liberated which drives the polymerization process forward. • The resultant polymerization will always proceed in a net 5´→3´ direction. • There are three types of DNA polymerases in prokaryotes, • DNA polymerase I and II are meant for DNA repair, and DNA polymerase III is meant for actual DNA replication.
  • 7. DNA Polymerase I: It is also called the Kornberg enzyme (after its discoverer – Arthur Kornberg). • It is a DNA repair enzyme. • It is mainly involved in removing RNA primers from Okazaki or precursor fragments and filling the resultant gaps, and it can also remove thymine dimers produced due to UV-irradiation and fill the gap (these are called the proofreading or editing functions of DNA polymerase I). • It has five active sites, namely: (1) template site, (2) primer site, (3) 5´ → 3´ cleavage or exonuclease site, (4) nucleoside triphosphate site, and (5) 5´ → 3´ cleavage site (or 5´ → 3´ exonuclease site). DNA Polymerase II: It resembles DNA polymerase I and is also a repair enzyme. DNA Polymerase III: DNA polymerase-III plays an essential role in DNA replication. • It is a multimeric (having multiple subunits) enzyme or holoenzyme having ten subunits. The core enzyme comprises three subunits: α, β, and θ. • The remaining seven subunits increase processivity (processivity means rapidity and efficiency with which a DNA polymerase extends growing chain) DNA polymerases can be further subdivided into two different families.
  • 9. DNA CLAMP • A DNA clamp, also known as a sliding clamp, is a protein fold that serves as a processivity- promoting factor in DNA replication. • As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. • The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand.
  • 10. SINGLE-STRAND BINDING (SSB) PROTEINS • Single stranded binding proteins prevent reannealing (binding of complementary DNA sequences), protect the single-stranded DNA from being digested by nucleases, and prevent secondary structure formation, thereby allowing other enzymes to function effectively on the single strand. • Molecular weight of the SSB protein is 75,600. • It contains FOUR identical subunits, which binds single stranded DNA.
  • 11. TOPOISOMERASE • Every cell has enzymes that increase (or) decrease the extent of DNA unwinding are called “Topoisomerases. • Topoisomerase is also known as “DNA Gyrase” and that act on the topology of DNA. • “Topoisomerases bind to double-stranded DNA and cut the phosphate backbone of either one or both the DNA strands, this intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA backbone is resealed again. • Topoisomerases” is an enzyme that can change the “Linking number”(Lk). • The linking number (Lk) is a topological property, it can be defined as “ the number of times the second strand pierces the second strand surface”. • There are two classes of topoisomerases. ―a) Type-I Topoisomerases ―b) Type-II Topoisomerases • a) Type-I Topoisomerases: This act by transiently breaking one of the two DNA strands, rotating one of the ends about the unbroken strand, and rejoining the broken ends; they change Lk in increments of 1. • b) Type-II Topoisomerases: The enzyme breaks both DNA strands and change Lk in increments of 2.
  • 12. DNA LIGASE • DNA ligase is a specific type of enzyme, a ligase, that facilitates the joining of DNA strands together by catalysing the formation of a phosphodiester bond. • DNA ligase is used in both DNA repair and DNA replication. • The mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide, ("acceptor") with the 5' phosphate end of another ("donor"). • ATP is required for the ligase reaction, which proceeds in three steps: i. Adenylation (addition of AMP) of a lysine residue in the active center of the enzyme, pyrophosphate is released; ii. Transfer of the AMP to the 5' phosphate of the so- called donor, formation of a pyrophosphate bond; iii. Formation of a phosphodiester bond between the 5' phosphate of the donor and the 3' hydroxyl of the acceptor.
  • 13. PRIMASE • DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. • Primase catalyzes the synthesis of a short RNA (or DNA in some organisms) segment called a primer complementary to a ssDNA template. • Primase is of key importance in DNA replication because no known replicative DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation). • After this elongation the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
  • 14. NUCLEASES • Nuclease enzymes act to hydrolyze or break down a polynucleotide chain into its component nucleotides. • The nuclease enzymes may be of the following two kinds: • (a) Exonucleases: Exonucleases are nuclease enzymes which begin their attack from a free end of a polynucleotide. • Depending on the specificity of the enzyme, an exonuclease will either begin at a free 3'- OH end of a polynucleotide or a free 5'-P end. • In both cases the enzyme travels along the chain in a stepwise manner, liberating single nucleoside monophosphate molecules and eventually digesting the entire polymer. • (b) Endonucleases: Endonuclease enzymes attack one of the two sides of phosphodiester linkages, but they react only with those bonds that occur within the interior of a polynucleotide chain.