Lesson Explainer: DNA Replication Biology

In this explainer, we will learn how to describe the process of semiconservative DNA replication, including the role of different enzymes, and recall how errors made during DNA replication can be corrected.

One of the key characteristics of any living organism is its ability to grow and reproduce. Both of these processes, at the cellular level, involve simple cell division, or the splitting of one cell into two. We know that every living cell carries genetic material in the form of DNA (deoxyribonucleic acid). The genetic material controls every characteristic of a living cell, from its size and appearance to the functions it performs.

When one cell divides into two, therefore, each new cell must contain a copy of the DNA in its nucleus for it to be able to function properly. For example, when a liver cell divides into two new liver cells, each new cell must receive a copy of the original cell’s DNA, so that it can perform its role to support the natural functions of the liver.

Key Term: Deoxyribonucleic acid (DNA)

DNA is the molecule that carries the genetic instructions for life. It is composed of two strands of deoxynucleotides that coil around each other to form a double helix.

DNA replication is the process by which a dividing cell generates a copy of its DNA. As we know, in eukaryotes, a molecule of DNA resides in the nucleus and is made of two individual strands that coil around one another to form a “twisted ladder” shape called the double helix as we can see in Figure 1. The process of DNA replication takes place in the nucleus of the cell and is controlled by a set of enzymes, each of which performs a specific function. In this explainer, we will learn how DNA replication takes place and understand the roles played by each of the enzymes involved.

Key Term: Double Helix

A double helix is a “twisted ladder” shape, specifically the shape of a molecule of DNA.

Key Term: DNA Replication

DNA replication is the process by which two identical DNA molecules are produced from a single original DNA molecule.

Before we begin learning about DNA replication, let’s quickly go over the basic structure of a DNA molecule.

As we mentioned earlier, a molecule of DNA contains two strands coiled around one another. These two strands are called polynucleotide chains, and they are made of repeating smaller units called nucleotides. As we can see in Figure 1, each nucleotide has three components: a pentose sugar, a phosphate group, and a nitrogenous base. Each nucleotide links to the next through covalent bonds called phosphodiester bonds.

Key Term: Nucleotide

A nucleotide is a monomer of a nucleic acid polymer. Nucleotides consist of a pentose sugar, a phosphate group, and a nitrogenous base.

The two polynucleotide chains connect to one another through the pairing of the nitrogenous bases facing each other on the inside of the ladder. In DNA, there are four different types of nitrogenous bases: adenine (A), guanine (G), thymine (T), and cytosine (C).

When the nitrogenous bases on one strand pair with the nitrogenous bases on the opposite strand, they follow certain base-pairing rules. In a molecule of DNA, adenine can only bind to thymine on the opposite strand, and guanine can only bind to cytosine. This rule is called “complementary base-pairing” and is one of the defining features of DNA. Adenine binds to thymine through two hydrogen bonds, while guanine binds to cytosine through three hydrogen bonds, as shown in Figure 2.

Key Term: Complementary Base-Pairing

DNA bases can pair according to specific rules, where adenine (A) binds to thymine (T), while guanine (G) binds to cytosine (C). In RNA, uracil (U) is substituted for thymine (T). These rules of complementary base-pairing are critical for DNA replication and transcription.

Another important feature of DNA is its antiparallel nature. Each DNA strand has two ends: one end is called the 5 end, and the other end is called the 3 end. These two ends are named for the last carbon atoms of the nucleotide at each end. The two strands are antiparallel as one strand runs in the 5 to 3 direction, while the other runs in the 3 to 5 direction, as shown in Figure 3.

The 3 carbon atom of every nucleotide is bonded to a hydroxyl group (OH). The 3 end of a strand of DNA, therefore, ends with a hydroxyl group, as you can see in Figure 3. The 5 carbon atom of every nucleotide is bonded to a phosphate group. The 5 end of a strand of DNA, therefore, ends with a phosphate group, represented by the yellow circles in Figure 3.

A molecule of DNA carries genetic information in the form of a genetic code, formed by the sequence of nitrogenous bases. A type of RNA called messenger RNA or mRNA is synthesized according to the sequence of DNA. This sequence encodes the information needed for the synthesis of proteins, which then go on to control the cell’s functions and characteristics.

Key Term: Genetic Code

The genetic code is formed by the sequence of nitrogenous bases in a strand of messenger RNA (mRNA) molecule that is synthesized from the DNA and codes for the information needed for a cell to synthesize specific proteins.

So how is this genetic code read? When we read English, we always read from left to right. Similarly, when a cell “reads” the sequence of nitrogenous bases to interpret the genetic code, it is read from the 5 end of the DNA strand to the 3 end.

In 1953, when James Watson and Francis Crick proposed the double helix model of DNA that we are familiar with today, they also made an interesting observation about DNA replication. Their model was based on the base pair specificity of the two strands in a DNA molecule. They realized that the two strands carry complementary versions of the same sequence. Because of this feature, both strands of DNA in a molecule could potentially be used as templates to synthesize complementary strands creating two new double helices with the same information! The sequence of nitrogenous bases on each strand is used as a guide for the sequence of new, complementary bases required to make up the new strand.

In eukaryotes, which are organisms with a well-organized nucleus, the DNA within the nucleus is present in the form of highly coiled, linear structures called chromosomes. Each chromosome contains one molecule of DNA, and within each molecule, replication begins at several different points.

In prokaryotes, on the other hand, the genetic material is present in the form of a single, circular molecule of DNA in the central area of the cell but is not surrounded by a nuclear membrane. In this case, replication begins at one point, called the origin of replication.

Now that we have had a quick recap of the structure of a molecule of DNA, let’s take a look at the mechanism of DNA replication. This process is controlled by three main enzymes. Let’s walk through the steps of this process and learn about each of the enzymes as we go along.

In order for the two strands of a DNA molecule to be used to make two new DNA molecules in the nucleus, the two strands must unwind and separate, making their nitrogenous bases accessible. We know that the strands are held together by hydrogen bonds between the nitrogenous bases of the two strands. In order for the strands to separate, these hydrogen bonds must be broken. This is accomplished by an enzyme called DNA helicase.

Key Term: DNA Helicase

DNA helicase is the enzyme responsible for separating or unwinding two complementary strands of DNA by breaking the hydrogen bonds between them, creating the replication fork in preparation for DNA replication.

Figure 4 shows how the strands of DNA separate through the action of DNA helicase. As the hydrogen bonds between the two strands are broken, a “replication fork” is formed, which is so named because the two unwinding strands of DNA have a forked appearance. The replication fork is the point at which the DNA molecule unwinds into two separate strands. You can picture the DNA helicase enzyme “unzipping” the molecule of DNA, beginning at the replication fork.

Key Term: Replication Fork

The replication fork is formed by the two separated or unwound strands of DNA in preparation for DNA replication.

Example 1: Understanding the Role of DNA Helicase

In the process of DNA replication, what is the primary role of DNA helicase?

  1. DNA helicase detects and repairs any errors that are made by incorrect base-pairing during DNA replication.
  2. DNA helicase breaks the hydrogen bonds between base pairs, separating the two strands of DNA.
  3. DNA helicase forms phosphodiester bonds between nucleotides to form a strand of DNA.
  4. DNA helicase adds nucleotides to a growing DNA chain, synthesizing a strand of DNA complementary to the template strand.
  5. DNA helicase joins the gaps in the backbone between newly formed DNA fragments.

Answer

When a cell undergoes division, its DNA replicates itself, so as to provide each new cell with a copy of DNA, which can control the cell’s characteristics and functions. We know that a single molecule of DNA is composed of two complementary polynucleotide strands. Each of these strands is made up of multiple individual units called nucleotides that form a sequence of nitrogenous bases. The order or sequence of nitrogenous bases along a strand of DNA encodes the “genetic information” that needs to be replicated when a cell divides.

When two strands of DNA bind together to form the familiar double helix shape, they do so by pairing their nitrogenous bases according to the rules of complementary base-pairing, in which adenine binds to thymine through two hydrogen bonds and guanine binds to cytosine through three hydrogen bonds.

The sequence of nitrogenous bases on each strand of DNA in the double helix acts as a template for the formation of a new strand of DNA. In order for this to happen, the two strands of DNA must unwind and separate, so that their nitrogenous bases are accessible. This function is carried out by the enzyme DNA helicase. DNA helicase breaks the hydrogen bonds between the nitrogenous bases on each strand, “unzipping” the DNA and separating the two strands.

Now that we have this information, let’s take a look through the options in the question. The one that best fits what we have learned is “DNA helicase breaks the hydrogen bonds between base pairs, separating the two strands of DNA,” and therefore, this is the correct option.

Once the strands have unwound, new strands of DNA that are complementary to each of the original strands can be synthesized. This is where an enzyme called DNA polymerase comes into play. The word “polymerase” is used to describe an enzyme that binds individual small units (nucleotides, in the case of DNA) together to form a long, repeating chain or polymer (a DNA strand). As we have learned, a molecule of DNA is a polymer made of multiple individual units called nucleotides.

Key Term: DNA Polymerase

DNA polymerase is an enzyme that adds nucleotides complementary to the template strand to synthesize a new strand. This enzyme plays an essential role in DNA replication.

DNA polymerase generates a new strand of DNA along each original strand by adding nucleotides to the new strand, ensuring that the rules of complementary base-pairing, which we learned about earlier, are followed. To build the new strand of DNA, the DNA polymerase uses a pool of free-floating nucleotides that remain available in the cell. Figure 5 represents a simple diagram of the action of DNA polymerase.

The DNA polymerase enzyme is a highly efficient one; it synthesizes complementary strands very rapidly and with a high level of accuracy. Another important feature of this enzyme is that it can only synthesize a new strand of DNA in the 5 to 3 direction. This feature poses a problem in a dividing cell. You might be wondering how! Well, let’s take a look at a replication fork in a strand of DNA. As we know, the two strands of DNA run antiparallel to one another. As you can see in Figure 6, the strand at the top of the image has a 3 open end at the fork, while the strand at the bottom has a 5 open end.

As new strands of DNA are synthesized, they must also run antiparallel to their complementary original strand. Although the two new strands are synthesized simultaneously, let’s first consider the formation of a new strand along the strand at the top of the figure, bearing in mind the fact that DNA polymerase can only synthesize a new strand in the 5 to 3 direction. In this case, a new strand is able to form continuously, without any interruptions or breaks.

Let’s now consider the strand at the bottom. As the DNA molecule unwinds, DNA polymerase encounters the 5 end of this strand. This would require a new complementary strand to be synthesized in the 3 to 5 direction, which DNA polymerase cannot do!

The DNA polymerase works around this problem by moving further along the strand, as shown in the figure, and synthesizing a short fragment of new DNA in the 5 to 3 direction, toward the open end of the replication fork. It then moves further along, behind this fragment, and does the same, synthesizing another short fragment. As the enzyme progresses along the strand, a discontinuous complementary strand begins to take shape. In Figure 8, you can see how this happens.

These fragments are called Okazaki fragments. If you now take a look at the molecule of DNA, you can see that along one template strand, a new strand is formed continuously, in the same direction as the opening fork, with no breaks. This template strand is therefore called the “leading strand.” The opposite template strand is called the “lagging strand,” since the new strand of DNA is synthesized discontinuously in fragments.

Key Term: Leading Strand

In DNA replication, the leading strand is the strand of DNA along which the new strand is synthesized continuously, in the same direction as the fork.

Key Term: Lagging Strand

In DNA replication, the lagging strand is the strand of DNA along which the new strand is synthesized discontinuously, in fragments.

Key Term: Okazaki Fragments

Okazaki fragments are the short fragments of DNA that are synthesized discontinuously along the lagging strand during DNA replication.

Another enzyme, DNA ligase, is responsible for joining these fragments together along the lagging strand. As you can see in Figure 9, DNA ligase moves along the fragmented strand, joining or “ligating” the fragments together by forming new phosphodiester bonds between one fragment and the next.

Key Term: DNA Ligase

DNA ligase is an enzyme that can join the gaps between the sugar–phosphate backbone of DNA by forming a phosphodiester bond.

Example 2: Understanding the Role of DNA Ligase

In semiconservative DNA replication, what is the primary role of DNA ligase?

  1. DNA ligase adds nucleotides to a growing DNA chain to synthesize a strand of DNA complementary to the template strand.
  2. DNA ligase joins the backbones of fragments formed on a complementary strand during replication.
  3. DNA ligase catalyzes the breaking of phosphodiester bonds in the sugar–phosphate backbone, so the DNA can be split into fragments that are ready for replication.
  4. DNA ligase breaks the hydrogen bonds between base pairs, separating the two strands of DNA that are ready for replication.
  5. DNA ligase joins RNA primers to the 5 end of a single strand of DNA to indicate where replication should begin.

Answer

When a molecule of DNA replicates, it unwinds so as to separate the two individual strands. Along each of these strands, a new strand of DNA is synthesized by the enzyme DNA polymerase, following the rules of complementary base-pairing.

We know that each strand of DNA has a 5 end and a 3 end and that the two strands of DNA in a DNA molecule must always run antiparallel, or in opposite directions, to one another. When synthesizing a new strand of DNA, DNA polymerase is only capable of adding nucleotides in the 5 to 3 direction.

Because of this feature of DNA polymerase, the two DNA strands in the molecule are replicated using two different methods. Along the “leading strand,” whose 3 end is at the opening of the replication fork, DNA polymerase can synthesize a continuous, unbroken complementary DNA strand. Along the “lagging strand,” whose 5 end is at the opening of the replication fork, DNA polymerase must instead synthesize short fragments of DNA in the 5 to 3 direction, as shown in the figure.

The fragments formed along the lagging strand are called Okazaki fragments. In order for the fragments to be functional, they must be joined together to form one long, continuous strand of newly synthesized DNA. This function is accomplished by DNA ligase that joins the sugar–phosphate backbones of adjacent fragments through phosphodiester bonds.

Let’s now take a look at the options provided in the question. The sentence that best fits the information we now have about DNA ligase is “DNA ligase joins the backbones of fragments formed on a complementary strand during replication.” This is therefore the right answer.

We have now been over the roles of the three important enzymes involved in DNA replication and have understood the mechanism of this process. Figure 10 shows a simple overview of how the whole process takes place and what the result of this process will be.

Let’s take a close look at each of the new DNA molecules on the right side of Figure 10. You may notice that each new DNA molecule contains one original strand and one newly synthesized strand. Because of this feature, the process of DNA replication is called “semiconservative replication”: the older strands of DNA are conserved as the molecule of DNA replicates.

Key Term: Semiconservative Replication

Semiconservative replication describes the mechanism of DNA replication in all living cells, in which each new DNA molecule is composed of one original strand of DNA and one newly synthesized strand of DNA.

Earlier on in this explainer, we talked about the genetic code formed by the sequence of nitrogenous bases along a strand of mRNA, which is synthesized from DNA. When a cell “reads” the sequence, it can interpret this information to produce specific proteins, which then go on to control the characteristics of the organism. Sections of DNA that contain a sequence of bases that code for a specific protein are called genes, which is a word you might have heard before.

Although the process of DNA replication is accurate and highly efficient, it is not completely error free. What would happen if, during DNA replication, the DNA polymerase were to make an error in adding a new nucleotide to the new strand? At one point, instead of adding a complementary nucleotide according to rules of base-pairing, what if a different nitrogenous base were accidentally added? Can you think about what this would mean?

On the newly synthesized DNA strand, this specific point in the strand would change the genetic code. You can think of this as something similar to a spelling mistake in a sentence. These errors, which are called mutations, can sometimes have serious consequences. Let’s consider a quick example. You might remember learning about hemoglobin, the molecule that carries oxygen in our blood. If the gene that codes for hemoglobin is mutated, the hemoglobin protein will be produced incorrectly. This can cause a condition called sickle cell anemia, which distorts the shape of the red blood cells in the body.

Key Term: Mutation

A mutation is an error or an alteration in a sequence of nucleotides.

In order to prevent such errors from arising during DNA replication, the enzyme DNA polymerase performs another crucial function. As it adds nucleotides to the growing new strand, it also “proofreads” or checks its own work. In this way, if the wrong nucleotide has accidentally been added, DNA polymerase will identify the error and swap the wrong nucleotide for the right one! It does this through exonuclease activity, which means it removes incorrect nucleotides and replaces them with correct ones. You can see an example of this in Figure 11.

As we learned earlier, DNA ligase is an enzyme that joins fragments of DNA together by forming new phosphodiester bonds, linking the fragments. When DNA is physically damaged, causing breaks in the strands, DNA ligase can function as a DNA repair enzyme. It uses the complementary strand of the DNA double helix as a template to form new phosphodiester bonds.

DNA repair, therefore, depends on the presence of two strands carrying the genetic information. When one strand is damaged, the intact information on the complementary strand can be used by DNA repair enzymes to replace the damaged sections. This is why it is so important for DNA replication to be an accurate, error-free process!

Example 3: Understanding how Proofreading Eliminates Errors During DNA Replication

When errors in DNA replication occur, the newly formed strand can be proofread and be recognized as not being complementary to the original strand. Which enzyme is responsible for correcting these errors during replication?

  1. DNA ligase
  2. DNA polymerase
  3. DNA helicase
  4. DNase

Answer

When a cell undergoes division, its DNA replicates itself, so as to provide each new cell with a copy of DNA which can control the cell’s characteristics and functions. We know that a single molecule of DNA is composed of two complementary polynucleotide strands. Each of these strands is made up of multiple individual units called nucleotides, which form a sequence of nitrogenous bases. The order or sequence of nitrogenous bases along a strand of DNA encodes the “genetic information” that needs to be replicated when a cell divides.

The enzyme DNA polymerase synthesizes new strands of DNA that are complementary to each of the original strands, by following the rules of complementary base-pairing: adenine binds to thymine through two hydrogen bonds, and guanine binds to cytosine through three hydrogen bonds.

The genetic information carried in these strands is crucially important to the normal functioning of a cell, as it forms a genetic code that provides the cell with instructions for the production of proteins. The process of DNA replication, though accurate, is not foolproof, which means that sometimes errors can arise in the new sequence, when a noncomplementary nitrogenous base is accidentally added.

Every word in the English language has a specific meaning. If a word is written down with a spelling mistake in it, the meaning of this word would be lost! This is similar to what happens when errors arise in a DNA sequence, which are also called mutations. Mutations in DNA can lead to several different diseases and disorders.

In order to prevent mutations during DNA replication, the enzyme DNA polymerase “proofreads” its own work, checking that each new nucleotide is complementary to the original strand as it goes along. If it detects an error, or a noncomplementary nucleotide, it quickly replaces this with the correct one!

The answer to this question is, therefore, DNA polymerase.

Let’s summarize the key points we have learned from this explainer.

Key Points

  • When a living cell divides, its DNA must replicate so that each new cell receives a copy of DNA.
  • DNA replication is a semiconservative process.
  • In order for a molecule of DNA to replicate, the two strands must first unwind. DNA helicase is responsible for this and “unzips” the DNA molecule by breaking the hydrogen bonds between the nitrogenous bases.
  • DNA polymerase synthesizes new strands of DNA along each template strand by adding complementary nucleotides to the chain.
  • DNA polymerase can only synthesize DNA in the 5 to 3 direction.
  • A new strand of DNA is synthesized continuously along the “leading” template strand.
  • A new strand of DNA is synthesized in fragments along the “lagging” template strand.
  • DNA ligase is responsible for joining the fragments of new DNA together to form a continuous complementary strand.
  • DNA polymerase is also responsible for “proofreading” the new strands of DNA to eliminate mutations.
  • If DNA is physically damaged or broken, DNA ligase can function as a DNA repair enzyme, linking the fragments back together through phosphodiester bonds.

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