5. Diagrammatically explain how Okazaki fragments are formed and how they ligate to become full strands during the DNA replication process.
5. Diagrammatically explain how Okazaki fragments are formed and how they ligate to become full strands during the DNA replication process.
Okazaki fragments:
- These are short DNA nucleotide sequences are discontinuously synthesized and further associated by ligase enzyme which gives rise to the lagging strand at the time of DNA replication.
- They are formed in the lagging strand by the initiation of the creation of a new RNA primer by primo some.
Okazaki Fragments Definition
Okazaki fragments are the short lengths of DNA that are produced by the discontinuous replication of the lagging strand.
The range of length of these fragments in the bacterial cells is about 1000-2000 nucleotides, while that in eukaryotic cells is approximately 100-200 nucleotides in length. The Okazaki fragments on the lagging strand are associated to generate a continuous new molecule of DNA.
Whenever there is cell division, the genetic information, the cell comprises in the long strands of DNA, is copied by the enzymes referred to as the DNA polymerases. Each of the DNA strands renders a template which is used by the DNA polymerases to synthesise a complementary strand. One strand at the replication fork is continuously synthesised in the 5′ to 3′ direction (leading strand) while the (lagging strand) second strand is discontinuously synthesised in the 3′ to 5′ direction in short fragments which are referred to as the Okazaki fragments.
Reiji Okazaki and Tuneko Okazaki, the Japanese molecular biologists, are said to be the ones who discovered these fragments in the 1960s, along with the contribution of some of their colleagues.
how Okazaki fragments are formed :
Formation of Okazaki fragments:
- These fragments are formed on the lagging strand for the synthesis of DNA.
- The direction is 5' to 3' toward the replication fork.
- These fragments make the replication of only one of the two strands possible hence increasing the efficiency of replication.
Formation of Okazaki fragments:
- These fragments are formed on the lagging strand for the synthesis of DNA.
- The direction is 5' to 3' toward the replication fork.
- These fragments make the replication of only one of the two strands possible hence increasing the efficiency of replication.
Okazaki Fragments Formation
As the DNA polymerase synthesises a part and then should wait for the helicase to open up more of the DNA helix upstream, the Okazaki fragments are formed on the lagging strand. Upon the opening up of the DNA by helicase, the primase gets in and puts down a new complementary RNA primer, which permits the DNA polymerase to associate the DNA and create the new Okazaki fragment.
As the DNA polymerase synthesises a part and then should wait for the helicase to open up more of the DNA helix upstream, the Okazaki fragments are formed on the lagging strand. Upon the opening up of the DNA by helicase, the primase gets in and puts down a new complementary RNA primer, which permits the DNA polymerase to associate the DNA and create the new Okazaki fragment.
Why are Okazaki Fragments Formed?
In most of the entities, the DNA acts as the genetic material. The DNA is double-stranded, comprising two DNA strands running antiparallel, which are linked by the hydrogen bonds. At the time of cell division, the entire DNA in the genome must be replicated, which doubles the DNA found in the original cell. In a semi-conservative mode, DNA replication takes place wherein one of the strands in the freshly created DNA (double-stranded) is the parent or the original strand. As a result, both the strands must act as templates in the replication of DNA. DNA polymerases are enzymes involved in the replication of DNA. They only synthesise DNA in the direction 5’ to 3’. But, due to the antiparallel nature of the double-stranded DNA, the synthesis of DNA must take place in either direction. Hence, the fragments take form at the time of synthesis of the lagging template strand.
Typically, the DNA polymerase adds the nucleotides in the direction 5’ to 3’. The enzymes are capable of continuously adding nucleotides to the growing strand on the leading strand. But, as the strand is running in the direction 5’ to 3’, the growth of the chain of the newly synthesised strand of DNA is put on hold when it arrives at the 5’ terminal of the strand. The synthesis of yet another DNA then starts at the replication fork.
This fork is the location on the DNA double-stranded wherein the unwinding starts, which is vital in synthesising the new strands of DNA on the parent strands. After the replication fork approaches the double-strand, the DNA polymerase can join nucleotides found on the lagging strand. But the synthesis gets halted when it arrives at the 5’ terminal of the RNA primer of the stretch of DNA that is already synthesised. Consequently, the synthesis of DNA at the lagging strand is not continuous, while the resultant stretches of DNA are the Okazaki fragments.
In most of the entities, the DNA acts as the genetic material. The DNA is double-stranded, comprising two DNA strands running antiparallel, which are linked by the hydrogen bonds. At the time of cell division, the entire DNA in the genome must be replicated, which doubles the DNA found in the original cell. In a semi-conservative mode, DNA replication takes place wherein one of the strands in the freshly created DNA (double-stranded) is the parent or the original strand. As a result, both the strands must act as templates in the replication of DNA. DNA polymerases are enzymes involved in the replication of DNA. They only synthesise DNA in the direction 5’ to 3’. But, due to the antiparallel nature of the double-stranded DNA, the synthesis of DNA must take place in either direction. Hence, the fragments take form at the time of synthesis of the lagging template strand.
Typically, the DNA polymerase adds the nucleotides in the direction 5’ to 3’. The enzymes are capable of continuously adding nucleotides to the growing strand on the leading strand. But, as the strand is running in the direction 5’ to 3’, the growth of the chain of the newly synthesised strand of DNA is put on hold when it arrives at the 5’ terminal of the strand. The synthesis of yet another DNA then starts at the replication fork.
This fork is the location on the DNA double-stranded wherein the unwinding starts, which is vital in synthesising the new strands of DNA on the parent strands. After the replication fork approaches the double-strand, the DNA polymerase can join nucleotides found on the lagging strand. But the synthesis gets halted when it arrives at the 5’ terminal of the RNA primer of the stretch of DNA that is already synthesised. Consequently, the synthesis of DNA at the lagging strand is not continuous, while the resultant stretches of DNA are the Okazaki fragments.
how they ligate to become full strands during the DNA replication process :
Extension of the new Okazaki fragment is accomplished by DNA polymerase III (a DNA-dependent DNA polymerase). The polymerization of deoxynucleotides continues until it reaches the 3′ hydroxyl of the primer on the prior Okazaki fragment. The primer on the prior Okazaki fragment is removed one base at a time by DNA polymerase I, which has 5′ to 3′ exonuclease activity. Each ribonucleotide is replaced with the corresponding deoxyribonucleotide, and any errors associated with the RNA primer are corrected. The last deoxyribonucleotide is joined by a different enzyme, DNA ligase, which uses one ATP to join the Okazaki fragment into the growing lagging strand.
conclusion :
Okazaki fragments are primarily involved in enabling the DNA polymerase in synthesising the lagging strand, even though it is oriented in the opposite direction. A type of DNA polymerase, DNA polymerase I, arrives and removes the RNA primers, replacing them with DNA. The Okazaki fragments should be attached into one continuous strand once replication occurs. This is achieved by the DNA ligase that seals the sugar-phosphate backbone of the Okazaki fragments. This enables the replication of two continuous, identical daughter DNA strands.
Before cell division occurs, it is vital to replicate DNA wherein one parent cell splits to produce two daughter cells, which makes sure that both the daughter cells obtain the same genetic material. Cell division in unicellular entities could be a mode of asexual reproduction, while cell division in multicellular entities is vital for the repair and growth of the entity and to give rise to cells required for sexual reproduction.
Extension of the new Okazaki fragment is accomplished by DNA polymerase III (a DNA-dependent DNA polymerase). The polymerization of deoxynucleotides continues until it reaches the 3′ hydroxyl of the primer on the prior Okazaki fragment. The primer on the prior Okazaki fragment is removed one base at a time by DNA polymerase I, which has 5′ to 3′ exonuclease activity. Each ribonucleotide is replaced with the corresponding deoxyribonucleotide, and any errors associated with the RNA primer are corrected. The last deoxyribonucleotide is joined by a different enzyme, DNA ligase, which uses one ATP to join the Okazaki fragment into the growing lagging strand.
conclusion :
Okazaki fragments are primarily involved in enabling the DNA polymerase in synthesising the lagging strand, even though it is oriented in the opposite direction. A type of DNA polymerase, DNA polymerase I, arrives and removes the RNA primers, replacing them with DNA. The Okazaki fragments should be attached into one continuous strand once replication occurs. This is achieved by the DNA ligase that seals the sugar-phosphate backbone of the Okazaki fragments. This enables the replication of two continuous, identical daughter DNA strands.
Before cell division occurs, it is vital to replicate DNA wherein one parent cell splits to produce two daughter cells, which makes sure that both the daughter cells obtain the same genetic material. Cell division in unicellular entities could be a mode of asexual reproduction, while cell division in multicellular entities is vital for the repair and growth of the entity and to give rise to cells required for sexual reproduction.
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