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When does DNA replicate actually?

When does DNA replicate actually?


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I read on Wikipedia that when the cell enters prophase during mitosis , the DNA has already been duplicated , that is the DNA is replicated in the chromatin form , but here I see the picture which shows the already condensed DNA ( now chromosome ) divide into sister chromatids. When does DNA divide actually ?

link to wikipedia -https://en.wikipedia.org/wiki/Prophase


According to This paper and most biology textbooks, S-phase or synthesis phase is literally defined by the beginning and ending of DNA replication. The first picture does not accurately represent the nature of DNA replication and is instead a model to help people track DNA copies during stages of cell division. DNA is replicated as chromatin and condenses to "double" chromosome form. You can see some micrographs of DNA condensation in this paper. You'll see that they don't condense as single chromatids, but they are already replicated.


DNA replication

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. [1] DNA replication occurs in all living organisms acting as the most essential part for biological inheritance. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. [2] The cell possesses the distinctive property of division, which makes replication of DNA essential.

DNA is made up of a double helix of two complementary strands. The double helix describes the appearance of a double-stranded DNA which is thus composed of two linear strands that run opposite to each other and twist together to form. [3] During replication, these strands are separated. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. [4] Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. [5] [6]

In a cell, DNA replication begins at specific locations, or origins of replication, in the genome [7] which contains the genetic material of an organism. [8] Unwinding of DNA at the origin and synthesis of new strands, accommodated by an enzyme known as helicase, results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the replication fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each (template) strand. DNA replication occurs during the S-stage of interphase.

DNA replication (DNA amplification) can also be performed in vitro (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to start DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples. In March 2021, researchers reported evidence suggesting that a preliminary form of transfer RNA, a necessary component of translation, the biological synthesis of new proteins in accordance with the genetic code, could have been a replicator molecule itself in the very early development of life, or abiogenesis. [9] [10]


Chargaff's Rules

Other important discoveries about DNA were made in the mid-1900s by Erwin Chargaff. He studied DNA from many different species. He was especially interested in the four different nitrogen bases of DNA: adenine (A), guanine (G), cytosine (C), and thymine (T) (see Figure below). Chargaff found that concentrations of the four bases differed from one species to another. However, within each species, the concentration of adenine was always about the same as the concentration of thymine. The same was true of the concentrations of guanine and cytosine. These observations came to be known as Chargaff&rsquos rules. The significance of the rules would not be revealed until the structure of DNA was discovered.

Nitrogen Bases in DNA. The DNA of all species has the same four nitrogen bases.

The Double Helix

After DNA was found to be the genetic material, scientists wanted to learn more about it. James Watson and Francis Crick are usually given credit for discovering that DNA has adouble helix shape, like a spiral staircase (see Figure below). The discovery was based on the prior work of Rosalind Franklin and other scientists, who had used X rays to learn more about DNA&rsquos structure. Franklin and these other scientists have not always been given credit for their contributions. You can learn more about Franklin&rsquos work by watching the video at this link: http://www.youtube.com/watch?v=s3whouvZYG8 (7:47).

The DNA molecule has a double helix shape. This is the same basic shape as a spiral staircase. Do you see the resemblance? Which parts of the DNA molecule are like the steps of the spiral staircase?

The double helix shape of DNA, together with Chargaff&rsquos rules, led to a better understanding of DNA. DNA, as a nucleic acid, is made from nucleotide monomers, and the DNA double helix consists of two polynucleotide chains. Each nucleotide consists of a sugar (deoxyribose), a phosphate group, and a nitrogen-containing base (A, C, G, or T).

Scientists concluded that bonds (hydrogen bonds) between complementary bases hold together the two polynucleotide chains of DNA. Adenine always bonds with its complementary base, thymine. Cytosine always bonds with its complementary base, guanine. If you look at the nitrogen bases in Figure above, you will see why. Adenine and guanine have a two-ring structure. Cytosine and thymine have just one ring. If adenine were to bind with guanine and cytosine with thymine, the distance between the two DNA chains would be variable. However, when a one-ring molecule binds with a two-ring molecule, the distance between the two chains is kept constant. This maintains the uniform shape of the DNA double helix. These base pairs (A-T or G-C) stick into the middle of the double helix, forming, in essence, the steps of the spiral staircase.

DNA Replication

Knowledge of DNA&rsquos structure helped scientists understand how DNA replicates. DNA replication is the process in which DNA is copied. It occurs during the synthesis (S) phase of the eukaryotic cell cycle. DNA replication begins when an enzyme, DNA helicase, breaks the bonds between complementary bases in DNA (see Figure below). This exposes the bases inside the molecule so they can be &ldquoread&rdquo by another enzyme, DNA polymerase, and used to build two new DNA strands with complementary bases, also by DNA polymerase. The two daughter molecules that result each contain one strand from the parent molecule and one new strand that is complementary to it. As a result, the two daughter molecules are both identical to the parent molecule. DNA replication is a semi-conservative process because half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.

The process of DNA replication is actually much more complex than this simple summary. You can see a detailed animation of the process at this link: http://www.youtube.com/watch?v=-mtLXpgjHL0 (2:05).

DNA Replication. DNA replication is a semi-conservative process. Half of the parent DNA molecule is conserved in each of the two daughter DNA molecules.


Biology 171

By the end of this section, you will be able to do the following:

  • Explain how the structure of DNA reveals the replication process
  • Describe the Meselson and Stahl experiments

The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. In their 1953 paper, Watson and Crick penned an incredible understatement: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” With specific base pairs, the sequence of one DNA strand can be predicted from its complement. The double-helix model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested ((Figure)): conservative, semi-conservative, and dispersive.


In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands acts as a template for new DNA to be synthesized after replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed.

Meselson and Stahl were interested in understanding how DNA replicates. They grew E. coli for several generations in a medium containing a “heavy” isotope of nitrogen ( 15 N), which gets incorporated into nitrogenous bases, and eventually into the DNA ((Figure)).


The E. coli culture was then placed into medium containing 14 N and allowed to grow for several generations. After each of the first few generations, the cells were harvested and the DNA was isolated, then centrifuged at high speeds in an ultracentrifuge. During the centrifugation, the DNA was loaded into a gradient (typically a solution of salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its buoyant density: the density within the gradient at which it floats. DNA grown in 15 N will form a band at a higher density position (i.e., farther down the centrifuge tube) than that grown in 14 N. Meselson and Stahl noted that after one generation of growth in 14 N after they had been shifted from 15 N, the single band observed was intermediate in position in between DNA of cells grown exclusively in 15 N and 14 N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in 14 N formed two bands: one DNA band was at the intermediate position between 15 N and 14 N, and the other corresponded to the band of 14 N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. And for this reason, therefore, the other two models were ruled out.

During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strands will be complementary to the parental or “old” strands. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells.

Click through DNA Replication (Flash animation).

Section Summary

During cell division, each daughter cell receives a copy of each molecule of DNA by a process known as DNA replication. The single chromosome of a prokaryote or each chromosome of a eukaryote consists of a single continuous double helix. The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In the conservative model of replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative model suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized after replication, each double-stranded DNA retains the parental or “old” strand and one “new” strand. The dispersive model suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA. The Meselson and Stahl experiment supported the semi-conservative model of replication, in which an entire replicated chromosome consists of one parental strand and one newly synthesized strand of DNA.

Free Response

How did the scientific community learn that DNA replication takes place in a semi-conservative fashion?

Meselson’s experiments with E. coli grown in 15 N deduced this finding.

Imagine the Meselson and Stahl experiments had supported conservative replication instead of semi-conservative replication. What results would you predict to observe after two rounds of replication? Be specific regarding percent distributions of DNA incorporating 15 N and 14 N in the gradient.

Following two rounds of conservative replication, two bands would be detected after ultracentrifugation. A lower (heavier) band would be at the 15 N density, and would comprise 25% of the total DNA. A second, higher (lighter) band would be at the 14 N density, and would contain 75% of the total DNA.


How DNA Works

­DNA carries the information for making all of the cell's proteins. These pro­teins implement all of the functions of a living organism and determine the organism'­s characteristics. When the cell reproduces, it has to pass all of this information on to the daughter cells.

Before a cell can reproduce, it must first replicate, or make a copy of, its DNA. Where DNA replication occurs depends upon whether the cells is a prokaryotic or a eukaryote (see the RNA sidebar on the previous page for more about the types of cells). DNA replication occurs in the cytoplasm of prokaryotes and in the nucleus of eukaryotes. Regardless of where DNA replication occurs, the basic process is the same.

The structure of DNA lends itself easily to DNA replication. Each side of the double helix runs in opposite (anti-parallel) directions. The beauty of this structure is that it can unzip down the middle and each side can serve as a pattern or template for the other side (called semi-conservative replication). However, DNA does not unzip entirely. It unzips in a small area called a replication fork, which then moves down the entire length of the molecule.

  1. An enzyme called DNA gyrase makes a nick in the double helix and each side separates
  2. An enzyme called helicase unwinds the double-stranded DNA
  3. Several small proteins called single strand binding proteins (SSB) temporarily bind to each side and keep them separated
  4. An enzyme complex called DNA polymerase "walks" down the DNA strands and adds new nucleotides to each strand. The nucleotides pair with the complementary nucleotides on the existing stand (A with T, G with C).
  5. A subunit of the DNA polymerase proofreads the new DNA
  6. An enzyme called DNA ligase seals up the fragments into one long continuous strand
  7. The new copies automatically wind up again

Different types of cells replicated their DNA at different rates. Some cells constantly divide, like those in your hair and fingernails and bone marrow cells. Other cells go through several rounds of cell division and stop (including specialized cells, like those in your brain, muscle and heart). Finally, some cells stop dividing, but can be induced to divide to repair injury (such as skin cells and liver cells). In cells that do not constantly divide, the cues for DNA replication/cell division come in the form of chemicals. These chemicals can come from other parts of the body (hormones) or from the environment.

The DNA of all living organisms has the same structure and code, although some viruses use RNA as the information carrier instead of DNA. Most animals have two copies of each chromosome. In contrast, plants may have more than two copies of several chromosomes, which usually arise from errors in the distribution of the chromosomes during cell reproduction. In animals, this type of error usually causes genetic diseases that are usually fatal. For some unknown reasons, this type of error is not as devastating to plants.


During Which Stage of the Cell Cycle Does DNA Replication Occur?

During the cell cycle, DNA replication occurs during the S-phase portion of the interphase. Interphase occurs between cell divisions and is a necessary precursor step for cell division.

Interphase is divided into three successive stages: the G1 phase, S phase and G2 phase. The flanking G phases involve cell growth and preparation for division of the cell to occur the "G" in G phase stands for growth. In between these growth periods, the cell undergoes the synthesis, or S, phase. During the S phase, the chromosomes within the cell are copied so that the divided cells have matching copies of DNA. The cell then undergoes the more visibly active stages of cell division: prophase, anaphase, telophase and cytokinesis.

Typical human cells take around 24 hours to complete a full cycle of cell replication and division. The longest portion of this process is interphase, which takes around 23 hours. The replication of chromosomes during the S phase takes about 8 hours. Other types of cells complete cell division more rapidly for example, during early embryonic development, the complete cell cycle can occur in about 30 minutes. In these rapid cell divisions, the growth phases are often skipped or drastically reduced and replication takes place more quickly. Even when the G1 and G2 phases don't occur, the cell must complete the S phase of interphase in order to replicate its DNA before division.


Initiation

The process of making the RNA sequences is performed by RNA Polymerase, along with the help of a transcription factor. The transcription factor helps the RNA Polymerase to recognize and bind to a sequence called the promoter sequence. The polymerase unwinds around 14 base pairs of DNA and forms an RNA polymerase-promoter open complex. This single-stranded form of DNA is known as the &lsquotranscription bubble&rsquo.

Now for the Polymerase to continue its job and add nucleotides to make the mRNA, it needs to detach from the promoter. This happens through a process known as Abortive initiation. During this process, the Polymerase creates short mRNA transcripts that are released before the polymerase detaches itself from the promoter.

Promoter Escape. (Photo Credit: Luis E Ramirez-Tapia / Wikimedia Commons)


Virus Replication

Jennifer Louten , in Essential Human Virology , 2016

4.4.1 Class I: dsDNA Viruses

All living organisms have double-stranded DNA genomes. Viruses with dsDNA genomes therefore have the most similar nucleic acid to living organisms and often use the enzymes and proteins that the cell normally uses for DNA replication and transcription, including its DNA polymerases and RNA polymerases. These are located in the nucleus of a eukaryotic cell, and so all dsDNA viruses that infect humans (with the exception of poxviruses) enter the nucleus of the cell, using the various mechanisms of entry and uncoating mentioned above. Many recognizable human viruses have dsDNA genomes, including herpesviruses, poxviruses, adenoviruses, and polyomaviruses.

Transcription of viral mRNA (vmRNA) must occur before genome replication if viral proteins are involved in replicating the virus genome. In addition, certain translated viral proteins act as transcription factors to direct the transcription of other genes. As discussed in Chapter 3, “Features of Host Cells: Cellular and Molecular Biology Review , transcription factors bind to specific sequences within the promoters of cellular genes immediately upstream of the transcription start site to initiate transcription of those genes. Enhancers, regulatory sequences also involved in transcription, are located farther away from the transcription start site and can be upstream or downstream. dsDNA viruses also have promoter and enhancer regions within their genomes that are recognized not only by viral transcription factors but by host transcription factors, as well. These proteins initiate transcription of the viral genes by the host RNA polymerase II.

Processing of viral precursor mRNA (also known as posttranscriptional modification) occurs through the same mechanisms as for cellular mRNA. Viral transcripts receive a 5′-cap and 3′-poly(A) tail, and some viruses’ transcripts are spliced to form different vmRNAs. For example, the genes of herpesviruses are each encoded by their own promoter and are generally not spliced, but the human adenovirus E genome has 17 genes that encode 38 different proteins, derived by alternative splicing of vmRNA during RNA processing.

The dsDNA viruses transcribe their viral gene products in waves, and the immediate early and/or early genes are the first viral genes to be transcribed and translated into viral proteins. These gene products have a variety of functions, many of which help to direct the efficient replication of the genome and further transcription of the late genes that encode the major virion structural proteins and other proteins involved in assembly, maturation, and release from the cell. The replication of the viral genome requires many cellular proteins having the late genes transcribed and translated after the virus genome has been replicated ensures that the host enzymes needed for replication are not negatively affected by the translation of massive amount of virion structural proteins.

To create new virions, viral proteins must be translated and the genome must also be copied. With the exception of poxviruses, the genome replication of all dsDNA viruses takes place within the nucleus of the infected cell. Eukaryotic DNA replication , also reviewed in more detail in Chapter 3, “Features of Host Cells: Cellular and Molecular Biology Review,” is also carried out by DNA polymerases and other proteins within the nucleus. DNA polymerases, whether they are cell derived or virus derived, cannot carry out de novo synthesis, however. They must bind to a short primer of nucleic acid that has bound to the single-stranded piece of DNA, forming a short double-stranded portion that is then extended by DNA polymerase ( Fig. 4.8A ). Primase is the enzyme that creates primers during cellular DNA replication, and some viruses, such as polyomaviruses and some herpesviruses, take advantage of the cellular primase enzyme to create primers on their dsDNA genomes during replication. Other herpesviruses, such as HSV-1, provide their own primase molecule, although this process occurs less commonly. Still other viruses, such as the adenoviruses, encode a viral protein primer that primes its own viral DNA polymerase ( Fig. 4.8B ). Cellular DNA polymerases are used by polyomaviruses and papillomaviruses, while all other dsDNA viruses encode their own DNA polymerases to replicate the viral genome. Many other cellular enzymes and proteins are required for DNA synthesis, and viruses are dependent on these to varying degrees, depending upon the specific virus. The poxviruses are a notable exception to this: they encode all the proteins necessary for DNA replication. In fact, they also encode the proteins needed for transcription of RNA, and so, unlike all other dsDNA viruses, they do not need to gain entry into the nucleus of a host cell for either genome replication or transcription and processing of viral genes, allowing their replication to take place entirely in the cytoplasm.

DNA polymerases cannot carry out de novo synthesis and so need a primer in order to replicate DNA. Some viruses take advantage of the cellular primase in order to create primers (A), while other viruses, such as adenoviruses, encode a protein primer that primes its own DNA polymerase (B). In the process of self-priming, the ssDNA genomes of parvoviruses fold back upon themselves to form hairpin ends that act as a primer for host DNA polymerase (C).


ALEVEL BIO dna replication

When does DNA polymerase only work from the 5' to 3' direction? its something I've just accepted but I'm really curious as to why that is the case.
please can someone explain this to me in really simple terms?
thank you for your help!

Not what you're looking for? Try&hellip

I think it something to do with DNA polymerase active site only being complementary to the 3' end
SO since each strand of DNA double helix are opposite meaning one end is 3'---5' and the other 5'---3'
The DNA polymerase will only add nucleotides to 3' end because its complementary to that end only
and the nucleotide it would bring and 'work' on will have to be 5'

(Original post by moriyanu)
I think it something to do with DNA polymerase active site only being complementary to the 3' end
SO since each strand of DNA double helix are opposite meaning one end is 3'---5' and the other 5'---3'
The DNA polymerase will only add nucleotides to 3' end because its complementary to that end only
and the nucleotide it would bring and 'work' on will have to be 5'

(Original post by lane_in_pain)
When does DNA polymerase only work from the 5' to 3' direction? its something I've just accepted but I'm really curious as to why that is the case.
please can someone explain this to me in really simple terms?
thank you for your help!

I am in year 13 and have spent a LOT of time going into unnecessary details like learning the chemistry in biology, and learning uni level chemistry topics like resonance stabilisation , which is well beyond the course's level. It is not worth doing this, but rather is much better to make sure you MASTER every wording, phrase etc, on your specifications mark schemes.

Stuff like 5' to 3' is what you learn in a biochemistry degree. I can say with a 98% certainty that it wont ever be tested, and if it is, it will probably manifest itself as an "AP mark" in a 9 marker, i.e where there are many potential answers.


S Phase and DNA Replication

Initiation

E. coli chromosomal DNA replication initiates within a 245-bp region, termed oriC. This region contains four 9-bp binding sites for the E. coli initiator protein, DnaA. Nearby are three repeats of a 13-bp A/T-rich sequence. oriC also contains specific binding sites for two small histone-like proteins called HU and IHF. Replication is initiated with the cooperative binding of 10 to 20 DnaA monomers to their specific binding sites ( Fig. 42.13 ). To be active, these monomers must each have bound ATP. Binding of DnaA permits unwinding of the DNA at the 13-bp repeats, in a reaction that requires the histone-like proteins. Next, DnaC binds to DnaB and escorts it to the unwound DNA. DnaB is the key helicase that will drive DNA replication by unwinding the double helix, but it binds DNA poorly on its own in the absence of its DnaC escort. Once DnaB has docked onto the DNA, DnaC is released, and the helicase can then start to unwind the DNA, provided that ATP, SSB, and DNA gyrase are present. SSB is a single-stranded DNA binding protein that stabilizes the unwound DNA, and DNA gyrase is a topoisomerase (see Chapter 8 ) that removes the twist that is generated when the two strands of the double helix are separated.

FIGURE 42.13 . FACTORS INVOLVED IN THE INITIATION OF DNA REPLICATION IN ESCHERICHIA COLI.

A, DNA sequences at OriC. B, Unwinding of the origin. C, Binding of helicase. D, The template, now ready for binding of DNA polymerase. ADP, adenosine diphosphate ATP, adenosine triphosphate SSB, single-stranded DNA binding protein.

(Modified from Baker TA, Wickner SH. Genetics and enzymology of DNA replication in Escherichia coli. Annu Rev Genet. 199226:447–477.)


Watch the video: Transcription and Translation: From DNA to Protein (January 2023).