Tag: DNA Replication

Tag: DNA Replication

  • DNA Replication: Steps, Diagram, and Mechanism

    DNA Replication: Steps, Diagram, and Mechanism

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  • DNA Replication, Replication Fork, DNA Polymerase, Replication...

    DNA Replication

    • DNA replication is semiconservative.

    • This means that when a new double strand is created, it contains one strand from the original DNA, and one newly synthesized strand.

    • It is similar for both Prokaryotes and Eukaryotes.

    • The process of DNA replication is governed by a group of proteins called a replisome.

    DNA Replication Diagram

    DNA Replication - research tweet 2

    • It is made up of a number of subcomponents that each provide a specific function during the process of replication.

    • Replication doesn’t begin at the end of chromosomes, but toward the middle at a site called the origin of replication.

    • A single eukaryotic chromosome contains multiple origins on each chromosome, while replication in prokaryotes usually takes place for a single origin on the circular chromosome.

    • From the origin, two replisomes proceed in opposite directions along the chromosome making replication a bidirectional process.

    • The point where a replisome is attached to the chromosome is called the replication fork.

    DNA Replication Fork

    Replication Fork Definition Structure Diagram and Function - research tweet

    • Each chromosome of eukaryotic DNA is replicated in many discrete segments called replication units or replicons.

    • A replicon is a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication.

    • For most prokaryotic chromosomes, the replicon is the entire chromosome.

    • For eukaryotic chromosomes, there are multiple replicons per chromosome.

    • The definition of replicons is somewhat confused with mitochondria, as they use unidirectional replication with two separate origins.

    "Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain"

    • DNA helicase uses the energy of ATP hydrolysis to actively unwind the two strands.

    • DNA polymerase, the enzyme that builds the new DNA, cannot initiate a strand from two nucleotides, but can only add nucleotides to an existing strand.

    • Therefore it requires an RNA primer to get started.

    •  It reads the parental strand in the 3’ → 5’ direction.

    • Since it can only add new subunits to the 3’ end of the chain, it must create the new complementary strand in the 5’ → 3’ direction

    • Besides being a polymerase, one of the subunits in DNA polymerase has 3’ → 5’ exonuclease (it removes nucleotides from the strand) capabilities.

    • Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain

    • There are 3 types of polymerase molecules This enzyme automatically proofreads each new strand, and makes repairs when it discovers any mismatched nucleotides.

    • Primase, an RNA polymerase, creates an RNA primer approximately 10 ribonucleotides long to initiate the strand.

    • Each nucleotide added to the new strand requires the removal of a pyrophosphate group (two phosphates binded together) from a DNTP (deoxynucleotide triphosphate).

    • Some of this energy derived from the hydrolysis of the pyrophosphate is used to drive replication.

    • SSB tetramer proteins (also called helix destabilizer proteins) prevent the two strands from reattaching after the helix is opened.

    • The interrupted strand is called the lagging strand; the continuous new strand is called the leading strand.

    • The lagging strand is made from a series of disconnected strands called Okazaki fragments.

    • Okazaki fragments are about 100-200 nucleotides long in eukaryotes and about 1000-2000 nucleotides long in prokaryotes.

    "SSB tetramer proteins (also called helix destabilizer proteins) prevent the two strands from reattaching after the helix is opened"

    • DNA Ligase moves along the lagging strand and ties the Okazaki fragments together to complete the polymer.

    • Since the formation of one strand is continuous and the other fragmented, the process of replication is said to be semidiscontinuous.

    • The ends of eukaryotic chromosomal DNA possess telomeres.

    • Telomeres are repeated 6 nucleotide units from 100-1000 units long that protect the chromosomes from being eroded through repeated rounds of replication.

    • Telomerase catalyze the lengthening of telomeres at the 3’ ends of DNA strands.

    • Eukaryotic chromosomes contain linear DNA molecules; Prokaryotic chromosomes are usually circular.

    • So telomeres aren’t required by Prokaryotes that have circular DNA.

    DNA Replication Citations

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  • DNA Replication: Definition, Stages, and Mechanism

    About DNA and DNA Replication

    We all know that DNA is a self-replicating structure. DNA replicates in a semi-conservative manner which are catalysed by the set of enzymes.

    In this process the DNA makes multiple copies of itself. It is considered as a process of biological polymerization where the process consists of initiation, elongation and the termination.

    This process is usually catalysed by the enzyme which mainly involves DNA polymerase which is the main element in the replication process.

    We know that the Genetic material consists of a nucleic acid which is almost DNA in all organism except those of viruses. Which is considered as the storage site of all information’s, where it is stored in the form of nucleotide sequences such as sequence of amino acids, which is also referred to as genetic code.

    The stored information is then copied as RNA molecules by transcription, and are translated by the process of translation. Where transcription and translation are not a direct process.

    Where as proteins does not serve as a template for synthesis of proteins, but in few cases RNA acts as a template for synthesizing DNA, it is known as the central Dogma by Francis crick.

    What is DNA Replication?

    Genetic information present in the double strands of DNA is transmitted from one cell to another during the process of mitosis, to the offspring from the parent by the replication of parental DNA molecules.

    DNA is a soiled double helical structure which exists in variety of types which serves as a risk during the replication process by imposing it to several restriction enzymes and uncoiled to form a single strand for the process of replication.

    Steps in DNA Replication

    This process was introduced when Watson and Crick replicated DNA as such in its Double helical structure. It is one of the complex process which involves many enzymes.

    DNA Replication - research tweet 2
    I. DNA Replication: Initiation

    It is the first step involved in the process of replication. Here the parental strands are uncoiled permanently into a single stranded structure before beginning the synthesis of DNA. By this the new daughter strand is introduced in the replication fork.

    DNA Replication - research tweet 1
    II. DNA Replication: Elongation

    Initiation is followed by elongation where the new complementary strands are added. The nucleotides which are added in the newly formed strands are dictated by the bases which are present as sequences on the template strand.

    Like this way new nucleotides are added by the enzyme DNA polymerase from one end of the strand to the other end.

    The nucleotides are namely Deoxyribonucleotide triphosphates DGTP, DATP, DTTP which are present in the cytoplasm of the cell.

    III. DNA Replication: Termination

    The end of the reaction is known as termination where the duplicated DNA molecules are separated as a single strand. Because the process of replicating DNA is to create two new strands which are similar to the parent molecules.

    DNA Replication: Semi-Conservative

    The DNA replication is semi-conservation and it was first proposed by Watson and Crick. Here it states that half of the DNA is conserved. Where half of the strand is original template which is retained form the parent and it serves as a template for the newly formed complimentary strand.

    The newly formed strand is made up of hydrogen bond which connects itself to the parental strand forming a double helical structure. Thus, each of the double helical structure is made up of one parental strand and the other newly formed strand.

    Enzymes Involved in DNA Replication

    There are several important enzymes which take part in the process of replication, which has the ability to copy DNA molecules that has millions of bases. They perform accurate functions with high speed though it is compact. It is also been bound with proteins.

    Maintaining the integrity of genetic information is the main role of replication process. Where as in Escherichia coli two enzymes play a role in the process of replication. They are namely DNA polymerase I and DNA polymerase II which involves in the repairing process of DNA. And the other enzymes such as DNA polymerase IV and DNA polymerase V are involved in adding the nucleotides, almost thousand of nucleotides are added per second.

    DNA Dependent DNA Polymerase

    These enzymes help in polymerization and catalyses the process of DNA replication with the help of other enzymes.

    Deoxyribonucleosides are energy providers along with the role of acting as substrates.

    DNA polymerase is classified as three types.

    I. DNA Polymerase I

    It is considered as one of the DNA repair enzymes which is involved in the following activities.

    5’-3’ polymerase activity

    5’-3’ exonuclease activity

    3’-5’ exonuclease activity

    II. DNA Polymerase II

    This enzyme is responsible for proof reading and for primary extension.

    III. DNA Polymerase III

    This enzyme is responsible for DNA replication in vivo.

    DNA Helicase

    This enzyme helps in unzipping the DNA strands. This process is carried out by breaking the hydrogen bonds present between them. Which results in formation of a replication fork.

    DNA Ligase

    Ligase helps in sticking the DNA strands which are discontinuous.

    DNA Primase

    This enzyme plays an important role in synthesising the RNA primer, which is complementary to the template strand of DNA.

    Endonuclease

    This enzyme helps in cleaving the single or double stranded DNA.

    Single Stranded Binding Proteins

    This enzyme helps in binding the single stranded DNA which protects it from forming other secondary structures.

    Importance of DNA Replication

    DNA replication is one of the important biological processes which helps in producing two identical replicas of DNA from the one parental molecule.

    It also acts as a most important part of biological inheritance which is helpful during the growth and repair phases of cell division.

    It also checks that whether all new cells receive an appropriate copy of DNA. As the cell makes the distinctive property of cell division the replication process is very much important.

    DNA replication helps in distributing the same copies of DNA within the gene through all cells of the body. Which helps the body to have same genetic material throughout the body.

    Where as in lower organisms replication is used to have the same genes in their progeny during the reproduction.

    DNA Replication

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  • DNA Replication: Steps, Process, and Mechanism I...

    What is DNA Replication?

    In atomic science, DNA replication is the organic cycle of delivering two indistinguishable replicas of DNA from one unique DNA particle.

    DNA replication happens in all living beings going about as the most fundamental part for natural legacy.

    It is perused in the 3 ‘to 5’ direction by the DNA polymerase, which implies that the subsequent strand is combined in the 5 ‘to 3’ direction.

    Replication includes the creation of indistinguishable DNA helices from a double stranded DNA molecule.

    Catalysts are basic to DNA replication as they promote vital strides in this cycle.

    The whole DNA replication measure is critical for both cell development and growth in organisms. It’s likewise significant in cell fix.

    Beginning of DNA Replication

    Replication consistently starts at a particular point on the DNA, which is known as the origin of replication and is perceived by its sequence.

    DNA Replication Steps DNA Replication - research tweet 2

    Steps of DNA Replication

    A) Initiation: Preparatory step

    • Step 1: Replication fork formation.

    B) Elongation: DNA Synthesis Begins

    • Step 2: Primer binding

    • Step 3: Synthesis of leading and lagging strands

    • Step 4: Remove primer and gap fill

    • Step 5: Proofreading

    C) Termination:

    • Step 6: End of the replication

    Step 1: Replication Fork Formation

    Before DNA can be duplicated, the double stranded molecule should be “unzipped” into two solo strands.

    DNA has four bases called adenine (A), thymine (T), cytosine (C), and guanine (G) that form pair between the two strands. Adenine just combines with thymine and cytosine just ties to guanine.

    To loosen up DNA, these base-pair interactions should be broken. This is finished by a protein known as DNA helicase.

    Notwithstanding, there is a unique initiator protein that is needed to sets off DNA replication, to be specific DnaA.

    It ties areas at the oriC site all through the cell cycle.

    To start the replication, notwithstanding, the DnaA protein should tie to a couple of explicit oriC groupings that have five repeats of the 9 bp arrangement also known as the R site.

    At the point when DnaA ties to the oriC site, it enlists a helicase catalyst (DnaB helicase). Presently the DNA helicase breaks the hydrogen bond that holds reciprocal DNA bases together.

    The detachment of the two single strands of DNA makes a two Y-formed design called a replication fork.

    Together they structure a bubble-like design called a replication bubble. These two separate strands fill in as a layout for the creation of the new DNA strands.

    Helicase is the main replication compound to be stacked at the beginning of replication. Helicase’s responsibility is to just move the replication forks forward by “unwinding” the DNA.

    As we probably are aware, DNA is entirely unstable as a single strand. Along these lines, cells can keep them from returning together in a double helix.

    To do this, a particular protein called single-stranded DNA binding proteins (SSBs) covers and keeps the isolated strands of DNA close to the replication fork.

    When the helicase rapidly unwinds the double helix. It raises the tension on the remaining DNA particle.

    Topoisomerase plays a significant support part during DNA replication. This protein forestalls the DNA double helix in front of the replication fork from turning out to be too tight when the DNA is opened.

    It does this by making impermanent nicks in the helix to release tension and afterward fixing the nicks to forestall perpetual harm.

    Elongation of DNA Replication: DNA Synthesis Begins

    Step 2: Primer binding

    Another enzyme was presented in this progression, which assumes the main part in the fabrication of DNA, called as DNA polymerase.

    It can just add nucleotides at the 3 ‘end of a current DNA strand. Primase forms the RNA primer, or short nucleic acid strand, that finishes the format, providing a 3 ‘end for working on DNA polymerase.

    A commonplace primer has around five to ten nucleotides. The primer starts the synthesis of DNA. When the RNA primer is set up, DNA polymerase “extends” it and consecutively adds nucleotides to make another strand of DNA that is complementary to the template strand.

    DNA Replication Steps DNA Replication - research tweet 1
    Step 3: Synthesis of Leading and Lagging Strands

    One of the strands is arranged in the 3′ to 5′ bearing (towards the replication fork), this is the leading strand.

    The other strand is situated in the 5′ to 3’direction (away from the replication fork), this is the trailing strand. Due to their diverse direction.

    Leading Strand Synthesis

    A short piece of RNA called a primer (made by enzyme known as primase) comes by and attach to the terminal of the leading strand.

    The primer fills in as the beginning stage for DNA synthesis.

    The DNA polymerase ties to the leading strand and afterward strolls alongside it, adding new complementary nucleotide bases (A, C, G, and T) in the 5′ to 3′ direction to the DNA strand.

    This sort of replication is known as continuous.

    Lagging Strand Synthesis

    The DNA polymerase consistently runs in the 5 ‘to 3’ direction. At the point when the two strands have been incorporated consistently while the replication fork is moving.

    One strand would consequently must be exposed to a 3 to 5 synthesis. Okazaki tracked down that one of the new strands of DNA was integrated in short pieces known as Okazaki fragments.

    This work eventually prompted to concluded that one strand is synthesized persistently and others irregularly.

    DNA polymerase III uses one bunch of its core subunits (the core polymerase) to continuously synthesize the leading strand. While the other two sets of the core subunit lie starting with one Okazaki fragment then onto the next on the looped duct.

    In vitro, there are just two arrangements of core subunits containing DNA polymerase III holoenzymes that can combine both the leading and lagging strand.

    Nonetheless, the third arrangement of core subunits expands the productivity of delayed strand synthesis just as the processivity of the in general replisome.

    At the point when DnaB helicase ties before DNA polymerase III. It starts by unwinding the DNA on the replication fork as it moves alongside the trailing strand template in the 5 ‘to 3’ direction.

    Primase every so often connects with DnaB helicase and synthesize a short RNA primer.

    Another slide clamp is currently situated on the primer through the clamp loading complex of DNA polymerase III. At the point when the union of the Okazaki fragment is complete.

    Replication stops and the core subunits of DNA polymerase III separate from their slide clamps and associate with the new clamp.

    This starts the synthesis of another Okazaki fragment. Two sets of core subunits can be engaged with the union of two unique Okazaki fragments simultaneously.

    When an Okazaki piece is complete, its RNA primers are taken out by DNA polymerase I or RNase H1. What’s more, that space is supplanted by DNA by the polymerase. The leftover nick has now been fixed by the DNA ligase.

    Step 4: Remove Primer and Gap Fill

    When both the continuous and discontinuous strands are framed, an enzyme called an exonuclease (DNA polymerase I or RNase H1) eliminates all RNA primers from the first strands.

    These primers were supplanted by appropriate DNA bases. The excess nick was fixed by the DNA ligase.

    DNA ligase catalyzes the development of a phosphodiester bond between a 3′-hydroxyl group on the end of one strand of DNA and a 5′-phosphate on the end of another strand.

    Step 5: Proofreading

    The DNA replication happens with high constancy. It contains some unacceptable nucleotide once for each 104–105 polymerized nucleotides.

    The exactness of replication relies upon the capacity of replicative DNA polymerases to choose the right nucleotide for the polymerization reaction.

    This high devotion isn’t accomplished in a single step yet rather is produced through the activity of a few progressive error avoidance and processing steps.

    These steps incorporate the selection of the right DNA base by the DNA polymerase, the editing of polymerase miss addition mistakes by exonucleolytic proofreading, lastly, the post-replicative DNA crisscross repair, which recognizes DNA mismatch and corrects recently replicated DNA.

    Termination of DNA Replication

    DNA replication stops when two forks of replication meet on a similar stretch of DNA, and the accompanying occasions happen, however not really in a specific order: forks converge until the entirety of the mediating DNA is loosened up; remaining gaps are filled and tied; Catenans are removed, and replication proteins are discharged.

    Step 6: End of DNA Replication

    At last, the parent strand and its complementary DNA strand coils into the recognizable double helix shape. The outcome is two DNA atoms comprising of one new and one old chain of nucleotides.

    Every one of these two little daughter helices is an almost precise of the parental helix.

    DNA Replication Citations

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