Roles of DNA polymerases and other replication enzymes. Leading and lagging strands and Okazaki fragments.
Key points:
DNA replication issemiconservative. Each strand in the double helix acts as a template for synthesis of a new, complementary strand.
New DNA is made by enzymes calledDNA polymerases, which require a template and aprimer(starter) and synthesize DNA in the 5' to 3' direction.
During DNA replication, one new strand (theleading strand) is made as a continuous piece. The other (thelagging strand) is made in small pieces.
DNA replication requires other enzymes in addition to DNA polymerase, includingDNA primase,DNA helicase,DNA ligase, andtopoisomerase.
Introduction
DNA replication, or the copying of a cell's DNA, is no simple task! There are about33 billionstart text, b, i, l, l, i, o, n, end textbase pairs of DNA in your genome, all of which must be accurately copied when any one of your trillions of cells divides1start superscript, 1, end superscript.
The basic mechanisms of DNA replication are similar across organisms. In this article, we'll focus on DNA replication as it takes place in the bacteriumE. coli, but the mechanisms of replication are similar in humans and other eukaryotes.
Let's take a look at the proteins and enzymes that carry out replication, seeing how they work together to ensure accurate and complete replication of DNA.
The basic idea
DNA replication issemiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.
This process takes us from one starting molecule to two "daughter" molecules, with each newly formed double helix containing one new and one old strand.
Schematic of Watson and Crick's basic model of DNA replication. DNA double helix. Hydrogen bonds break and helix opens. Each strand of DNA acts as a template for synthesis of a new, complementary strand. Replication produces two identical DNA double helices, each with one new and one old strand.
In a sense, that's all there is to DNA replication! But what's actually most interesting about this process is how it's carried out in a cell.
Cells need to copy their DNA very quickly, and with very few errors (or risk problems such as cancer). To do so, they use a variety of enzymes and proteins, which work together to make sure DNA replication is performed smoothly and accurately.
DNA polymerase
One of the key molecules in DNA replication is the enzymeDNA polymerase. DNA polymerases are responsible for synthesizing DNA: they add nucleotides one by one to the growing DNA chain, incorporating only those that are complementary to the template.
Here are some key features of DNA polymerases:
They always need a template
They can only add nucleotides to the 3' end of a DNA strand
They can't start making a DNA chain from scratch, but require a pre-existing chain or short stretch of nucleotides called aprimer
Theyproofread, or check their work, removing the vast majority of "wrong" nucleotides that are accidentally added to the chain
The addition of nucleotides requires energy. This energy comes from the nucleotides themselves, which have three phosphates attached to them (much like the energy-carrying molecule ATP). When the bond between phosphates is broken, the energy released is used to form a bond between the incoming nucleotide and the growing chain.
[See the polymerization reaction]
In prokaryotes such asE. coli, there are two main DNA polymerases involved in DNA replication: DNA pol III (the major DNA-maker), and DNA pol I, which plays a crucial supporting role we'll examine later.
Starting DNA replication
How do DNA polymerases and other replication factors know where to begin? Replication always starts at specific locations on the DNA, which are calledorigins of replicationand are recognized by their sequence.
E. coli, like most bacteria, has a single origin of replication on its chromosome. The origin is about245245base pairs long and has mostly A/T base pairs (which are held together by fewer hydrogen bonds than G/C base pairs), making the DNA strands easier to separate.
Specialized proteins recognize the origin, bind to this site, and open up the DNA. As the DNA opens, two Y-shaped structures calledreplication forksare formed, together making up what's called areplication bubble. The replication forks will move in opposite directions as replication proceeds.
Bacterial chromosome. The double-stranded DNA of the circular bacteria chromosome is opened at the origin of replication, forming a replication bubble. Each end of the bubble is a replication fork, a Y-shaped junction where double-stranded DNA is separated into two single strands. New DNA complementary to each single strand is synthesized at each replication fork. The two forks move in opposite directions around the circumference of the bacterial chromosome, creating a larger and larger replication bubble that grows at both ends.
Diagram based on similar illustration in Reece et al.2squared.
How does replication actually get going at the forks?Helicaseis the first replication enzyme to load on at the origin of replication3cubed. Helicase's job is to move the replication forks forward by "unwinding" the DNA (breaking the hydrogen bonds between the nitrogenous base pairs).
Proteins calledsingle-strand binding proteinscoat the separated strands of DNA near the replication fork, keeping them from coming back together into a double helix.
Primers and primase
DNA polymerases can only add nucleotides to the 3' end of an existing DNA strand. (They use the free -OH group found at the 3' end as a "hook," adding a nucleotide to this group in the polymerization reaction.) How, then, does DNA polymerase add the first nucleotide at a new replication fork?
Alone, it can't! The problem is solved with the help of an enzyme calledprimase. Primase makes an RNAprimer, or short stretch of nucleic acid complementary to the template, that provides a 3' end for DNA polymerase to work on. A typical primer is about five to ten nucleotides long. The primerprimesDNA synthesis, i.e., gets it started.
Once the RNA primer is in place, DNA polymerase "extends" it, adding nucleotides one by one to make a new DNA strand that's complementary to the template strand.
Leading and lagging strands
InE. coli, the DNA polymerase that handles most of the synthesis is DNA polymerase III. There are two molecules of DNA polymerase III at a replication fork, each of them hard at work on one of the two new DNA strands.
DNA polymerases can only make DNA in the 5' to 3' direction, and this poses a problem during replication. A DNA double helix is always anti-parallel; in other words, one strand runs in the 5' to 3' direction, while the other runs in the 3' to 5' direction. This makes it necessary for the two new strands, which are also antiparallel to their templates, to be made in slightly different ways.
One new strand, which runs 5' to 3' towards the replication fork, is the easy one. This strand is made continuously, because the DNA polymerase is moving in the same direction as the replication fork. This continuously synthesized strand is called theleading strand.
The other new strand, which runs 5' to 3' away from the fork, is trickier. This strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA. This tricky strand, which is made in fragments, is called thelagging strand.
The small fragments are calledOkazaki fragments, named for the Japanese scientist who discovered them. The leading strand can be extended from one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments.
The maintenance and cleanup crew
Some other proteins and enzymes, in addition the main ones above, are needed to keep DNA replication running smoothly. One is a protein called thesliding clamp, which holds DNA polymerase III molecules in place as they synthesize DNA. The sliding clamp is a ring-shaped protein and keeps the DNA polymerase of the lagging strand from floating off when it re-starts at a new Okazaki fragment4start superscript, 4, end superscript.
Topoisomerasealso plays an important maintenance role during DNA replication. This enzyme prevents the DNA double helix ahead of the replication fork from getting too tightly wound as the DNA is opened up. It acts by making temporary nicks in the helix to release the tension, then sealing the nicks to avoid permanent damage.
Finally, there is a little cleanup work to do if we want DNA that doesn't contain any RNA or gaps. The RNA primers are removed and replaced by DNA through the activity ofDNA polymerase I, the other polymerase involved in replication. The nicks that remain after the primers are replaced get sealed by the enzymeDNA ligase.
Summary of DNA replication inE. coli
Let's zoom out and see how the enzymes and proteins involved in replication work together to synthesize new DNA.
Illustration shows the replication fork. Helicase unwinds the helix, and single-strand binding proteins prevent the helix from re-forming. Topoisomerase prevents the DNA from getting too tightly coiled ahead of the replication fork. DNA primase forms an RNA primer, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. On the lagging strand, DNA synthesis restarts many times as the helix unwinds, resulting in many short fragments called “Okazaki fragments.” DNA ligase joins the Okazaki fragments together into a single DNA molecule.
Helicaseopens up the DNA at the replication fork.
Single-strand binding proteinscoat the DNA around the replication fork to prevent rewinding of the DNA.
Topoisomeraseworks at the region ahead of the replication fork to prevent supercoiling.
primasesynthesizes RNA primers complementary to the DNA strand.
DNA polymerase IIIextends the primers, adding on to the 3' end, to make the bulk of the new DNA.
RNA primers are removed and replaced with DNA byDNA polymerase I.
The gaps between DNA fragments are sealed byDNA ligase.
DNA replication in eukaryotes
The basics of DNA replication are similar between bacteria and eukaryotes such as humans, but there are also some differences:
Eukaryotes usually have multiple linear chromosomes, each with multiple origins of replication. Humans can have up to100,100, comma000000origins of replication5start superscript, 5, end superscript!
Most of theE. colienzymes have counterparts in eukaryotic DNA replication, but a single enzyme inE. colimay be represented by multiple enzymes in eukaryotes. For instance, there are five human DNA polymerases with important roles in replication5start superscript, 5, end superscript.
Most eukaryotic chromosomes are linear. Because of the way the lagging strand is made, some DNA is lost from the ends of linear chromosomes (thetelomeres) in each round of replication.
Explore outside of Khan Academy
Do you want to learn more about DNA replication? Check out thisscrollable interactivefrom LabXchange.
LabXchange is a free online science education platform created at Harvard’s Faculty of Arts and Sciences and supported by the Amgen Foundation.
[References]
FAQs
Molecular mechanism of DNA replication (article) | Khan Academy? ›
DNA replication is semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand. This process takes us from one starting molecule to two "daughter" molecules, with each newly formed double helix containing one new and one old strand.
What is the molecular mechanism of DNA replication? ›DNA replication is semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand. This process takes us from one starting molecule to two "daughter" molecules, with each newly formed double helix containing one new and one old strand.
What is the point of DNA replication worksheet answers? ›The sole purpose of DNA replication is to generate identical DNA molecules, as they are the blueprint that makes life possible.
How do you memorize DNA replication? ›Breaking the word O-ka-za-ki in to fragments allows for the remembering of what the fragments are called. DNA polmerase I then replaces the RNA primers with DNA.
What is the mechanism of DNA replication as suggested by Watson and Crick? ›According to Watson and Crick, in preparation for DNA replication, the two strands of DNA first unwound and separated. Next, each DNA strand functioned as a template for a new DNA strand, with the bases on each parent strand dictating new bases on the new daughter strands.
What are the 3 possible mechanisms for DNA replication? ›There were three models for how organisms might replicate their DNA: semi-conservative, conservative, and dispersive.
What are the molecular mechanisms of DNA replication in eukaryotes? ›Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ.
What is DNA replication short answer questions? ›DNA replication is the process of copying the parent DNA helix into two identical daughter helices. The process is semi-conservative, which means that one parent strand is passed down to each daughter strand.
What is the basic summary of DNA replication? ›DNA replication is the process by which the genome's DNA is copied in cells. Before a cell divides, it must first copy (or replicate) its entire genome so that each resulting daughter cell ends up with its own complete genome.
How many DNA molecules do you start with in replication? ›The result of DNA replication is two DNA molecules consisting of one new and one old chain of nucleotides. This is why DNA replication is described as semi-conservative, half of the chain is part of the original DNA molecule, half is brand new.
What is DNA in brief with Watson and Crick model? ›
In “A Structure of Deoxyribose Nucleic Acid,” Watson and Crick described DNA as a double helix that contained two long, helical strands wound together. In their model, each DNA strand contained individual units called bases, and the bases along one DNA strand matched the bases along the other DNA strand.
What and how did Crick and Watson discover DNA and make their model? ›At King's College London, Rosalind Franklin obtained images of DNA using X-ray crystallography, an idea first broached by Maurice Wilkins. Franklin's images allowed James Watson and Francis Crick to create their famous two-strand, or double-helix, model.
How did Watson and Crick describe the structure of DNA quizlet? ›The Watson and Crick's model of DNA is a double helix structure of the deoxyribonucleic acid (DNA). It consists of two sugar phosphate backbones that make up the sides and nitrogen bases, which are held by hydrogen bonds, that make up the steps.
What are the 3 most important enzymes in DNA replication? ›DNA Polymerase: It helps in the replication of double-stranded DNA into two identical DNA molecules. Helicase: It helps in the separation of double-stranded DNA into single strands allowing each strand to be copied. Ligase: It acts as glue by joining 2 DNA fragments to form a new DNA strand.
What is the mechanism and type of replication? ›Mechanism of Replication: separation of strands, specific coupling of free nucleic acids. DNA replication is the process by which DNA is copied, usually before a cell divides, and this process requires the action of many different proteins to ensure replication occurs accurately and quickly.
What are three mechanisms used by cells to prevent replication errors? ›Proofreading, which corrects errors during DNA replication. Mismatch repair, which fixes mispaired bases right after DNA replication. DNA damage repair pathways, which detect and correct damage throughout the cell cycle.
What are the molecular mechanisms of DNA replication in prokaryotes? ›DNA Replication Process in Prokaryotes
The two strands of DNA unwind at the origin of replication. Helicase opens the DNA and replication forks are formed. The DNA is coated by the single-strand binding proteins around the replication fork to prevent rewinding of DNA. Topoisomerase prevents the supercoiling of DNA.
Eukaryotic DNA replication requires multiple replication forks, while prokaryotic replication uses a single origin to rapidly replicate the entire genome. DNA replication always occurs in the nucleus. Eukaryotic DNA replication involves more polymerases than prokaryotic replication.
What is the difference between prokaryotic and eukaryotic DNA replication mechanism? ›The prokaryotic replication occurs in the cytoplasm whereas the eukaryotic replication occurs in the nucleus. 2. The replication can take place in prokaryotes at any time, and is followed by the cell division. In eukaryotes, the replication takes place particularly, during the S phase of the cell cycle.
Which process best explains how DNA is replicated? ›DNA replication is done by a semi-conservative process in which the two strands separate and serve as templates for the complementary strands such that each daughter molecule has one parent strand and one new strand as shown in figure.
What is 1 step of DNA replication? ›
The very first step in DNA replication is unzipping the double helix of the DNA molecule, the unwinding of DNA occurs by enzyme helicase and gyrase. After unwinding the DNA forms a replication fork and both the strands act as a template for the formation of new strands.
What are the enzymes of DNA replication in prokaryotes and eukaryotes? ›DNA replication occurs in both prokaryotes and eukaryotes in similar steps where DNA unwinding is done with the help of an enzyme DNA helicase and the manufacturing of new DNA strands is accomplished by enzymes known as polymerases.
What is the importance of DNA replication? ›The process of DNA replication helps in the inheritance process by transfer of the genetic material from one generation to another. Therefore it is required for the growth, repair, and regeneration of tissues in living organisms.
Why is DNA replication important simple? ›Cells must replicate their DNA before they can divide. This ensures that each daughter cell gets a copy of the genome, and therefore, successful inheritance of genetic traits. DNA replication is an essential process and the basic mechanism is conserved in all organisms.
What is the importance of DNA reproduction? ›It ensures that each daughter cell produced at the end of cell division receives an identical amount of DNA. It causes evolution by generating variety during sexual reproduction. It aids the transmission of information or traits from parents to children.
What are the major key players in DNA replication? ›There are four main enzymes that facilitate DNA replication: helicase, primase, DNA polymerase, and ligase.
Where does DNA replication occur? ›DNA replication occurs in the nucleus in eukaryotes, whereas in cytoplasm in prokaryotes.
What is the structure of DNA and its replication? ›Watson and Crick discovered that DNA has a double helix shape, consisting of two polynucleotide chains held together by bonds between complementary bases. DNA replication is semi-conservative: half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.
What 2 enzymes are used during DNA replication? ›Helicase (separate double-stranded DNA into single strands allowing each strand to be copied) DNA gyrase (reduces supercoiling which builds up during DNA unwinding)
How is RNA different from DNA? ›Whereas DNA always occurs in cells as a double-stranded helix, RNA is single-stranded. RNA chains therefore fold up into a variety of shapes, just as a polypeptide chain folds up to form the final shape of a protein (Figure 6-6).
What is DNA replication called? ›
Semiconservative replication is the mechanism by which DNA replication occurs in all known cells. DNA replication is the process of dividing a double-stranded DNA molecule into two identical DNA molecules.
What binds Okazaki fragments? ›Ligase is an enzyme that joins together the Okazaki fragments of the discontinuous DNA strands.
What are the 3 functions of DNA? ›DNA now has three distinct functions—genetics, immunological, and structural—that are widely disparate and variously dependent on the sugar phosphate backbone and the bases.
What are four kinds of bases found in DNA? ›These chemical bonds act like rungs in a ladder and help hold the two strands of DNA together. There are four nucleotides, or bases, in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T).
Which of these is not required for DNA replication? ›Which of the following proteins is not necessary during DNA replication? Explanation: RNA polymerase is an enzyme that transcribes RNA from DNA; it is not essential for DNA replication.
What were the three main teams in the race to uncover the structure of DNA? ›Crick, Watson, and Franklin: The Race to Discover the Structure of DNA. In 1953, three English biochemists helped unlock the mystery of life by determining the double helix structure of the DNA molecule.
What method was used to find the structure of DNA? ›The discovery of the structure of DNA in 1953 was made possible by Dr Rosalind Franklin's X-ray diffraction work at King's. Her creation of the famous Photo 51 demonstrated the double-helix structure of deoxyribonucleic acid: the molecule containing the genetic instructions for the development of all living organisms.
What features of DNA were proposed by Watson and Crick? ›In Watson and Crick's model, the two strands of the DNA double helix are held together by hydrogen bonds between nitrogenous bases on opposite strands. Each pair of bases lies flat, forming a "rung" on the ladder of the DNA molecule.
How did Watson and Crick describe three dimensional structure of DNA? ›DNA's three-dimensional structure, first suggested in \[1953\] by James D. Watson and Francis H. C. Crick, consists of two long helical strands that are coiled to form a double helix around a central axis. Two polymer strands coiled around each other are used in each DNA molecule.
How does the structure of DNA identified by Watson and Crick differ? ›While Pauling's model was a triple helix with the bases sticking out, the Watson-Crick model was a double helix with the bases pointing in and forming pairs of adenine (A) with thymine (T), and cytosine (C) with guanine (G).
What is the molecular mechanism of DNA replication in prokaryotes? ›
DNA Replication Process in Prokaryotes
The two strands of DNA unwind at the origin of replication. Helicase opens the DNA and replication forks are formed. The DNA is coated by the single-strand binding proteins around the replication fork to prevent rewinding of DNA. Topoisomerase prevents the supercoiling of DNA.
The Molecular Mechanisms of Biological Processes profile covers the individual action of chemicals and proteins in living systems and will explore their role in orchestrating cellular processes.
What is the mechanism of replication of DNA viruses? ›DNA viruses replicate their genomes using DNA polymerase enzymes and transcribe their mRNA using DNA-dependent RNA polymerase enzymes. Both (+) and (−) ssRNA viruses replicate and transcribe their genomes using RdRp enzymes (Fig. 3.1).
What is the molecular mechanism of prokaryotes? ›The mechanism of transcription in prokaryotes typically occurs in three stages: initiation elongation and termination. Through the help of both DNA and mRNA, a pre mRNA molecule, which is then transformed into a mature mRNA molecule, is formed.
What are examples of molecular mechanisms? ›Epigenetic changes, including DNA methylation, histone acetylation and methylation, and miRNA expression, serve as molecular mechanisms that modulate the severity and pathogenesis of a number of human diseases.
What are the different molecular mechanisms? ›We selected three molecular mechanisms to explore knowledge integration in undergraduate MCB: DNA replication, transcription, and translation.
What is DNA mechanism? ›The process of DNA replication begins when the two strands of DNA separate. An enzyme called helicase unwinds and separates the bonds between the two DNA strands, and both these separated strands act as templates from which new DNA is made. DNA replication - 3D. DNA polymerases are a group of enzymes which make new DNA ...
How do viruses convert RNA into DNA? ›RNA viruses, such as retroviruses, use the enzyme to reverse-transcribe their RNA genomes into DNA, which is then integrated into the host genome and replicated along with it.
What are the 5 stages of viral replication? ›The viral life cycle can be divided into several major stages: attachment, entry, uncoating, replication, maturation, and release.