DNA Replication - The Definitive Guide | Biological dictionary (2023)

Definition

DNA replication is a process that takes place during cell division where two identical DNA molecules are made from one DNA molecule. In a semi-conservative process, a single molecule containing two DNA strands forming a double helix is ​​separated, with each strand serving as a template for new DNA molecules. Because the double helix is ​​antiparallel and DNA polymerase only synthesizes new DNA from 5'-3', reading the template strand 3'-5' results in a continuous, leading strand, while reading the template strand 5'-3' results in a discontinuous, lagging strand. Because it is a highly regulated process, multiple proteins are required during and after replication to quickly correct errors and damage.

Background

Deoxyribonucleic acid, simply known as DNA, is the blueprint for all living things. DNA contains genes that code for physical and metabolic information that is expressed in an individual while having the potential to pass on to future offspring. Almost all cells have DNA, which is usually stored in the nucleus. Notable cells that do not have DNA include nucleated cells (or nucleated cells, such as red blood cells). In addition, some cells may still have DNA despite not having a nucleus, such as bacterial cells.

DNA nucleotides

DNA is made up of four building blocks of monomers, also known asnucleotides. Nucleotides consist of three groups:

1. Deoxyribose sugar group
2. Phosphate group
3. Nitrogen base

All nucleotides have the same sugar group and phosphate group, but different nitrogenous bases.The nitrogen bases in DNA are adenine, guanine, cytosine and thymine.Adenine and guanine are classified aspudding, while cytosine and thymine are classified aspyrimidine. Purines have two rings in their basic structure while pyrimidines have one ring in their basic structure.

(Helpful tip: A simple pneumonia to remember adenine and guanine as purines is "PureASGster"!)

DNK structure

Nucleotides are arranged in chains that become single strands of DNA, which is half of an entire DNA molecule. Each chain has a sugar-phosphate backbone formed when the phosphate of one nucleotide is covalently attached to the sugar of the nextphosphodiesterbinding. More precisely, the phosphate is located on the 5' carbon atom of one nucleotide, while the ahydroxyl group (-OH) is located on the 3' carbon atom of the sugar group of the next nucleotide. The -OH from the 3' carbon is removed, with the phosphate group on the 5' carbon now also attached to the 3' carbon.

Nitrogen bases protrude from this spine. The second strand of DNA is base-wise aligned with this first strandfree basic coupling, where one purine joins one pyrimidine. Special,adenine pairs with thymine and guanine pairs with cytosine.Hydrogen bonds connect complementary base pairs, with the adenine-thymine pair having two hydrogen bonds and the guanine-cytosine pair having three hydrogen bonds. One DNA molecule resultsdouble helixform when two DNA strands line up and connect.

DNA has an orientation that can run 3'-5' or 5'-3' based on the carbon in the sugar group. The two strands of DNA in a double helix must run opposite each other in theantiparallelfashion. Therefore, if the first strand starts at the 3' end and ends at the 5' end, then the second strand should go in the opposite direction, starting at the 5' end and ending at the 3' end.

Example:

3′- AATCGTAA -5′

5'- TTAGCAT -3'

DNA replication is semi-conservative

DNA must be fully replicated before cells divide by mitosis to ensure that all daughter cells have identical DNA. It was discovered that DNA replicationsemi-conservative. In semiconservative replication, the double helix splits into two separate strands. During the replication process, a whole new strand of DNA is created by using the original template strand and matching the complementary bases.

The process of DNA replication

Proteins in DNA Replication

DNA replication is highly regulated and requires multiple proteins to function efficiently. Most of these proteins act as stabilizers and enzymes, and enzymes are proteins that act as catalysts to create and speed up biochemical reactions.

Some of the key proteins in DNA replication include the following:

helicopter: An enzyme that opens the double helix by breaking hydrogen bonds between complementary base pairs

Single-stranded DNA binding proteins (SSBPs): These proteins stabilize individual DNA strands to prevent them from recombining.

Topoisomerase: Because helicase unwinding of DNA causes tension further down the strand, this enzyme relieves tension by making cuts in the DNA and rejoining them before the replication fork arrives.

prime: An enzyme that adds a primer (a short segment of ribonucleic acid, known as RNA) where DNA polymerase III will bind

DNA-polymerase III: An enzyme that makes a new DNA strand by adding nucleotides that are complementary to the template strand

DNA-polymerase I: An enzyme that replaces the RNA primer with DNA

DNA ligaza: An enzyme that joins Okazaki fragments on the lagging strand by closing the sugar-phosphate backbone, creating a single strand of DNA

Sliding clamp: A protein that holds DNA polymerase III in place

Replication bubble

When DNA begins to replicate, a replication bubble forms that can be visually detected by electron microscopy. A specific sequence of bases - known asorigin of replication– determines where this replication bubble starts. Inside the bubble, two Y-shapedreplication forksa result where DNA actively replicates on both sides of the region. Replication forks are formed when DNA double strands are separated by helicase in both directions from the origin of replication. DNA replication proteins attach to the replication fork to perform their functions.

Replicate the leader sequence

As mentioned earlier, DNA strands have an anti-parallel nature, with one strand running 3'-5' and the other running opposite 5'-3'.DNA polymerase can synthesize alonenewstill DNA in5'-3'direction.For DNA polymerase to do this, it needs to readtemplatestrands of 3'-5'. Therefore, replication of the template strand spanning 3'-5' results in synthesisimportant bundle. The leading strand is the new strand of DNA that is synthesized into a single, continuous strand that begins at the 5' end and ends at the 3' end.

Replication of leading strand DNA using the 3'-5' template strand is as follows:

1. The double helix of DNA is opened into single strands by helicase. Topoisomerase relieves tension further down the double helix.
2. SSBPs stabilize single strands of DNA to prevent them from joining back together.
3. The RNA primer is added to the leading strand by primase at complementary bases.
4. DNA polymerase III binds to the primer. The sliding clamp stabilizes DNA polymerase III.
5. DNA polymerase III moves down the leader strandtowards the replication fork, adding a base to the new strand from the 5' end to the 3' end.

Replicate a backlog

DNA polymerase can create alonenewDNA strands from 5'-3'. Therefore, when 5′-3′templatestrand is replicated - requiring the new strand to run in the opposite direction in the 3'-5' direction - the new strand cannot be synthesized in a continuous fashion as the leading strand was. To overcome this challenge, additional steps are required to replicate the 5'-3' template strand, where this newly synthesized strand is known aslagging strand.

In order to synthesize the lagging strand, the DNA must be broken down into smaller segments known asOkazaki fragments. Because of these multiple segments, the lagging strand is also calledinterrupted pram. Creating these multiple segments allows DNA polymerase III to synthesize a small portion of the new DNA strandaway from the replication forkin the correct 5′-3′ direction. As the replication fork continues along the double helix in the 3' direction of the template strand, a second Okazaki fragment closer to the fork can be generated. DNA polymerase III binds again to synthesize a different portion of the new DNA strand away from the fork until it reaches the previously synthesized portion. These fragments are then linked, resulting in a single strand of DNA. This process continues along the entire length of the DNA.

Replication of lagging strand DNA using the 5'-3' template strand is as follows:

1. The double helix of DNA is opened into single strands by helicase. Topoisomerase relieves tension further down the double helix.
2. SSBPs stabilize single strands of DNA.
3. Primase adds an RNA primer to the lagging strand.
4. DNA polymerase III binds to the primer and creates a short segment of newly synthesized DNA from 5'-3',synthesize in the opposite direction of the replication fork. This is the first Okazaki fragment.
5. As the helicase continues to unwind the double helix and the replication fork moves down the strand, another primer is added closer to the fork. DNA polymerase III binds to this primer to synthesize a second Okazaki fragment 5'-3' of the replication fork.
6. Once DNA polymerase III reaches the first Okazaki primer fragment, DNA polymerase I removes the primers and replaces them with the appropriate complementary bases.
7. DNA ligase joins DNA segments by closing the sugar-phosphate backbone. The two segments are now connected into a single wire.
8. This process is repeated as the replication fork continues down the length of the DNA.

Prokaryotes against eukaryotes

DNA replication is generally quite conserved throughout life. However, there are general differences in itenzymes and mechanisms used, as well as the time it takes between species. The greatest differences are between the domains of prokaryotes (bacteria and archaea) and eukaryotes (all other plant and animal cells).

Minor differences between these groups include faster replication times in prokaryotes and shorter Okazaki fragments in eukaryotes. Moreover, prokaryotes have only one origin of replication while eukaryotes have multiple origins of replication.The main difference between these groups is that prokaryotes have circular DNA while eukaryotes have linear DNA.Linear eukaryotic DNA poses an additional challenge to be regulated. This brings us to telomeres.

Telomeres

Because eukaryotic DNA is linear, they have ends that pose a challenge. For the leading strand, DNA polymerase III can continue along the entire length of the DNA. However, in the lagging strand, a primer must be added before the Okazaki fragment being synthesized before DNA polymerase III can attach and synthesize a new DNA strand opposite the replication fork. After the last Okazaki fragment is synthesized, a small piece of DNA remains at the top of the strand.This segment cannot be left unattended. If this DNA is not replicated, the genetic material is lost with each replication. After several repetition cycles, this can result in lost information that can be critical to an individual's survival.

To solve this problem,telomeresare present in eukaryotes. Telomeres are short, repetitive segments of DNA found at the end of each chromosome that contain no coding sequences. It synthesizes those telomerestelomeraza, an enzyme containing a short RNA template used to extend the length of the lagging strand. Primers are placed on telomeres where DNA polymerase III can attach to synthesize the last piece of DNA residue on the lagging strand.

Telomere replication on the lagging strand is as follows:

1. Telomerase binds to the very end of the lagging strand and runs across the unreplicated portion of DNA.
2. Using its own RNA template, telomerase synthesizes an extended telomere, adding additional bases to the 3' end of the lagging strand.
3. Primase adds an example on the telomere.
4. DNA polymerase III binds to the primer and moves in the opposite direction to telomerase to complete lagging strand synthesis.

Telomeres affect cell age

Telomerase is most active in rapidly dividing cell types, such as embryonic cells, stem cells, sperm and immune cells. In most other cell types, telomerase activity is turned off and telomeres shorten with each DNA replication. This means that cells can divide a limited number of times through mitosis before sending signals to prevent further divisions and DNA damage. As a result, cells age.

Research has shown that increasing telomere length can also extend the lifespan of cells. Unfortunately, while this offers a possible cure for growth-restricting cellular diseases, it also aids in the onset and survival of cancer. About 90% of cancer cells are mutated to turn on telomerase activity in cell types where it should be turned off. This triggers another mechanism by which cancer cells can continue to divide uncontrollably and become immortal.Researchis ongoing to determine if/how inactivating telomerase activity can slow or stop cancer progression.

DNA repair and damage

Incorrect replication

DNA replication must be fast, but also extremely accurate. DNA replication occurs billions of times in one human being. Even if there were just one flaw in every replica, that would add up to trillions of flaws that could be detrimental to an individual's life. So how are errors regulated?

The first way to achieve this is to proofread your own work with DNA polymerase. Each complementary pair of nucleotides has a special shape. Therefore, when the wrong base is put in, the shape is different enough for DNA polymerase to recognize its own mistake. DNA polymerase can then remove this mismatch and replace it with the correct base.

Although DNA polymerase is capable of proofreading its own work, errors still sometimes fail. Once the DNA polymerase continues down the length of the strand,proteins for mismatch repairI can edit any additional errors. By using markers on the old DNA strand, mismatch repair proteins can distinguish sequence errors on the new strand. They then remove the mismatched nucleotide and replace it accordingly. With DNA polymerase proofreading and mismatch repair proteins correcting additional errors, there is approximately only one error for every 1 billion nucleotides synthesized.

Environmental damage

Environmental factors - such as UV radiation, X-rays and chemical exposure - can damage DNA. For example, UV radiation found in sunlight and tanning beds can create a thymine dimer where two thymine bases form a covalent bond with each other. This creates a bulge in the DNA strand that prevents DNA polymerase from synthesizing past this point. These conditions can become harmful andsystemit must be put in place to repair such damage.

In the case of UV radiation, eukaryotic cells have adapted to anucleotide excision repair systemwhich is able to detect distortions in the shape of the DNA helix. At least 18 different proteins work together to remove this distortion, using the undamaged strand as a template to repair the damaged strand. Prokaryotic cells have a simpler but similar nucleotide excision repair system that requires only three proteins. However, specifically for UV radiation, prokaryotes use an enzyme known asfotolyaselocate this damage and make repairs.

Conclusion

DNA replication is a highly regulated molecular process in which one DNA molecule is duplicated to produce two identical DNA molecules. As a semi-conservative process, the double helix is ​​broken apart into two strands, each strand serving as a template for the newly synthesized strand by matching complementary bases. Since DNA polymerase III can only synthesize new strands from 5'-3', this results in a leading strand being continuously synthesized and a lagging strand requiring the use of Okazaki fragments. Meanwhile, since eukaryotes have linear DNA, telomeres are necessary to ensure that genetic information is not lost during replication. Because DNA is essential to life, research continues to better understand and treat diseases caused by mutations and damage in an individual's DNA.

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