11.2 DNA Replication
4 min read•june 18, 2024
is a crucial process that ensures genetic information is accurately copied and passed on to new cells. This complex mechanism involves various enzymes and steps, working together to create identical molecules from a parent template.
The semiconservative model and bidirectional nature of DNA are key concepts to understand. These processes, along with the formation of , allow for efficient and accurate copying of genetic material in both prokaryotic and eukaryotic cells.
DNA Replication Models and Processes
Semiconservative model of DNA replication
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- Two strands of parent DNA molecule separate during replication
- Each parent strand serves as template for synthesis of new ()
- Newly synthesized strands paired with respective parent strands
- Forms two daughter DNA molecules
- Each daughter DNA molecule consists of one parent strand and one newly synthesized strand
- Daughter molecules considered "semiconservative" as they contain half of original parent DNA (conserves one strand from parent)
Bidirectional nature of DNA replication
- DNA replication occurs simultaneously in both directions from
- speeds up process (allows for faster completion)
- synthesized continuously in 5' to 3' direction
- synthesizes without interruption as it moves along template strand (no stopping and starting)
- synthesized discontinuously in short fragments called
- synthesizes in 5' to 3' direction, but opposite direction of movement
- Discontinuous synthesis due to nature of DNA strands (strands run in opposite directions)
Okazaki fragments in DNA replication
- fragments are short segments of DNA synthesized on lagging strand
- About 100-200 nucleotides long in bacteria (1000-2000 in eukaryotes)
- Formation of Okazaki fragments necessary due to:
- Antiparallel nature of DNA (strands run in opposite directions)
- Unidirectional activity of DNA polymerase (only synthesizes in 5' to 3' direction)
- synthesizes short RNA primers that provide starting point for DNA polymerase to initiate Okazaki fragment synthesis
- removes RNA primers and fills gaps between Okazaki fragments
- DNA seals nicks between Okazaki fragments, creating continuous strand of DNA (joins fragments together)
Enzymes and Steps in DNA Replication
Key steps of bacterial DNA replication
- : unwinds double-stranded DNA at
- Single-stranded DNA binding proteins (SSB) stabilize single-stranded DNA (prevents reannealing)
- synthesis: synthesizes short RNA primers complementary to single-stranded DNA
- Primers provide starting point for DNA synthesis (DNA polymerase requires primer to begin)
- : (DNA pol III) extends primers, synthesizing new DNA strands
- Leading strand synthesis occurs continuously, lagging strand synthesis occurs discontinuously through Okazaki fragments
- Primer removal and gap filling: DNA polymerase I (DNA pol I) removes RNA primers and replaces with DNA
- DNA pol I also fills gaps between Okazaki fragments (creates continuous strand)
- Joining fragments: DNA ligase seals nicks between newly synthesized DNA fragments, creating continuous strand
Bacterial vs eukaryotic DNA replication
- Similarities:
- Both use (each parent strand serves as template for new strand synthesis)
- Both have bidirectional replication with leading and lagging strands
- Both require similar enzymes (, , DNA polymerases, ligase)
- Differences:
- Eukaryotes have multiple origins of replication, bacteria typically have single origin
- Eukaryotic DNA replication occurs during S phase of cell cycle, bacterial replication occurs throughout cell cycle
- Eukaryotes have multiple types of DNA polymerases (DNA pol α, δ, ε), bacteria primarily use DNA pol III
- Okazaki fragments shorter in eukaryotes (100-200 nucleotides) compared to bacteria (1000-2000 nucleotides)
Rolling circle replication mechanism
- Alternative mechanism of DNA replication found in some and
- Single-stranded DNA molecule replicated to form long, continuous strand with multiple copies of original sequence
- Process begins with nick in one strand of double-stranded DNA molecule
- Nicked strand displaced and serves as template for synthesis of new complementary strand
- Newly synthesized strand continuously extended, forming long, linear DNA molecule with multiple copies of original sequence
- Long, linear DNA molecule then cleaved into individual units, each representing copy of original DNA molecule
- Important for replication of certain genetic elements:
- Single-stranded DNA viruses ()
- Plasmids in bacteria (extrachromosomal DNA)
- Mitochondrial DNA in some eukaryotes (organelle DNA)
DNA Replication Fidelity and Chromosome Ends
- ensures accurate DNA replication
- Adenine pairs with thymine, guanine pairs with cytosine
- Replication fork is the Y-shaped region where DNA strands separate for replication
- DNA polymerases have ability to correct errors during replication
- Enhances accuracy of DNA replication
- are specialized structures at chromosome ends
- Protect chromosome ends from degradation and fusion
Key Terms to Review (79)
Antiparallel: Antiparallel refers to the orientation of the two strands of a DNA molecule, where the sugar-phosphate backbones run in opposite directions. This arrangement is crucial for the structure and function of DNA, as well as the process of DNA replication.
Bacteriophages: Bacteriophages are viruses that infect and replicate within bacteria. They play a crucial role in bacterial genetics and microbial diversity.
Bidirectional Replication: Bidirectional replication is the process by which DNA is replicated in both the 5' to 3' direction simultaneously from a central origin. This allows for the efficient and rapid duplication of the entire genome during the cell division process.
Blackburn: Elizabeth Blackburn is a Nobel Prize-winning scientist known for her discovery of the enzyme telomerase, which plays a crucial role in maintaining chromosome integrity during DNA replication. Her work has significantly advanced our understanding of cellular aging and cancer.
Complementary Base Pairing: Complementary base pairing is a fundamental principle of DNA structure and replication, where the four DNA bases (adenine, thymine, guanine, and cytosine) form specific pairs that hold the two strands of the DNA double helix together. This pairing pattern is essential for the accurate storage and transmission of genetic information.
Complementary strand: A complementary strand is the sequence of DNA that is formed during replication, matching the original template strand according to base-pairing rules. Each base pairs with its specific partner: adenine (A) with thymine (T), and cytosine (C) with guanine (G).
Crick: Francis Crick was a British molecular biologist, biophysicist, and neuroscientist, best known for co-discovering the double-helix structure of DNA with James Watson. His work laid the foundation for understanding DNA replication and genetic mechanisms.
Density Gradient Centrifugation: Density gradient centrifugation is a powerful technique used to separate and purify different biomolecules, organelles, and cells based on their unique densities. It involves the creation of a density gradient, typically using solutions of varying densities, and the application of centrifugal force to separate the components within a sample.
DNA: DNA (Deoxyribonucleic Acid) is the hereditary material in almost all living organisms, carrying genetic information essential for growth, development, and reproduction. It consists of two strands forming a double helix structure.
DNA gyrase: DNA gyrase is an enzyme that introduces negative supercoils into DNA, which is essential for DNA replication and transcription in bacteria. It is a type of topoisomerase that helps to relax positive supercoils formed ahead of the replication fork.
DNA Helicase: DNA helicase is an enzyme that plays a crucial role in the process of DNA replication by unwinding the double-stranded DNA molecule, separating the two strands to allow the replication machinery to access and copy the genetic information.
DNA polymerase: DNA polymerase is an enzyme that synthesizes new strands of DNA using a template strand during DNA replication. It plays a critical role in copying the genetic material accurately and efficiently.
DNA Polymerase: DNA polymerase is a critical enzyme responsible for the replication and repair of DNA, ensuring the accurate transmission of genetic information during cell division. It plays a central role in the structure and function of DNA, as well as the overall function of genetic material within cellular genomes.
DNA polymerase I: DNA polymerase I is an enzyme responsible for the replication and repair of DNA in prokaryotic cells. It plays a crucial role in the process of DNA replication by catalyzing the addition of new nucleotides to the growing DNA strand, ensuring the accurate duplication of genetic information.
DNA polymerase III: DNA polymerase III is a key enzyme involved in the process of DNA replication, responsible for rapidly and accurately duplicating the genetic material within a cell. It is the primary enzyme responsible for the synthesis of new DNA strands during the process of DNA replication.
DNA Replication: DNA replication is the fundamental process of creating two identical copies of a DNA molecule from a single parent molecule. This process is essential for cell division, growth, and the maintenance of genetic information in all living organisms.
Double-stranded origin (dso) site: A double-stranded origin (dso) site is a specific DNA sequence where the initiation of double-stranded DNA replication begins. It is crucial for the proper duplication of plasmid or chromosomal DNA in cells.
E. coli: Escherichia coli (E. coli) is a gram-negative, rod-shaped bacterium commonly found in the lower intestine of warm-blooded organisms. While most strains are harmless, some can cause serious food poisoning and infections.
Elongation: Elongation is the process of extending or lengthening a molecule or structure. In the context of molecular biology, it refers to the continuous addition of subunits to a growing polymer, such as DNA, RNA, or a polypeptide chain, during the processes of replication, transcription, and translation, respectively.
Elongation in DNA replication: Elongation in DNA replication is the process where nucleotides are added to a new strand of DNA, extending it in the 5' to 3' direction. This step occurs after the initiation phase and involves enzymes like DNA polymerase.
Exonuclease: Exonuclease is an enzyme that removes nucleotides one at a time from the end of a DNA or RNA strand. It plays a crucial role in DNA repair, replication, and degradation.
Helicase: Helicase is an essential enzyme in DNA replication that unwinds the double-stranded DNA, creating two single strands. This action is critical for allowing other enzymes to synthesize new complementary DNA strands.
Helicase: Helicase is an enzyme that plays a crucial role in the process of DNA replication by unwinding the double-stranded DNA molecule, allowing the replication machinery to access and copy the genetic information.
Histone: Histones are proteins that package and order DNA into structural units called nucleosomes. They play a crucial role in gene regulation by controlling access to DNA.
Histones: Histones are proteins that package and order DNA into structural units called nucleosomes. They play a crucial role in gene regulation and DNA replication.
Human genome: The human genome is the complete set of DNA in a human, encompassing all genetic information needed for growth, development, and functioning. It includes both genes and non-coding sequences of DNA.
Initiation: Initiation is the critical first step in various biological processes, including DNA replication, RNA transcription, and protein synthesis. It marks the beginning of these fundamental mechanisms that are essential for cellular function and gene expression.
Initiation of replication: Initiation of replication is the process where DNA synthesis begins at specific sites called origins of replication. It involves the assembly of various proteins and enzymes to form a replication complex.
Lagging strand: The lagging strand is the DNA strand that is synthesized discontinuously during DNA replication. It forms short segments called Okazaki fragments which are later joined together.
Lagging Strand: The lagging strand is one of the two strands of DNA that is synthesized discontinuously during the DNA replication process. It is the strand that is replicated in the opposite direction to the movement of the replication fork, resulting in the formation of Okazaki fragments that are later joined together.
Leading strand: The leading strand is a continuous DNA strand synthesized in the 5' to 3' direction during DNA replication. It is built toward the replication fork by DNA polymerase.
Leading Strand: The leading strand is the continuously synthesized DNA strand during the process of DNA replication. It is the strand that is replicated in the same direction as the overall replication fork movement.
Ligase: Ligase is an enzyme that catalyzes the joining or ligation of two molecules, often DNA fragments, by forming a new chemical bond. It plays a crucial role in the process of DNA replication by sealing the gaps between Okazaki fragments during the synthesis of the lagging strand.
Meselson: Meselson, along with Franklin Stahl, conducted an experiment in 1958 that provided strong evidence for the semi-conservative model of DNA replication. Their work demonstrated that each new DNA molecule consists of one old and one new strand.
Nucleotide: A nucleotide is the fundamental building block of nucleic acids, such as DNA and RNA. It consists of a nitrogenous base, a pentose sugar, and a phosphate group. Nucleotides play a crucial role in various biological processes, including energy production, cellular signaling, and the storage and transmission of genetic information.
Okazaki: Okazaki fragments are short sequences of DNA nucleotides synthesized discontinuously on the lagging strand during DNA replication. They are later joined together by DNA ligase to form a continuous strand.
Okazaki fragments: Okazaki fragments are short sequences of DNA nucleotides synthesized discontinuously on the lagging strand during DNA replication. They are later joined by DNA ligase to form a continuous strand.
Okazaki Fragments: Okazaki fragments are short, discontinuous DNA sequences that are synthesized during the lagging strand replication of DNA. They are named after the Japanese scientist Reiji Okazaki, who first discovered this process of DNA replication.
Origin of replication: The origin of replication is a specific sequence in the genome where DNA replication begins. It is essential for the initiation and proper regulation of DNA replication.
Origin of Replication: The origin of replication is a specific DNA sequence where DNA replication is initiated and proceeds bidirectionally along the DNA molecule. It is a critical component of the DNA replication process, ensuring the accurate and complete duplication of genetic material during cell division.
Phosphodiester Bond: A phosphodiester bond is a covalent chemical bond that links the phosphate group of one nucleotide to the sugar (deoxyribose or ribose) of the next nucleotide, forming the backbone of DNA and RNA molecules. This bond is essential for the structural integrity and information storage capabilities of genetic material.
Plasmids: Plasmids are small, circular, double-stranded DNA molecules that exist independently of the chromosomal DNA in bacteria. They often carry genes beneficial for survival, such as antibiotic resistance.
Primase: Primase is an enzyme involved in the synthesis of RNA primers during DNA replication. It provides a starting point for DNA polymerase to begin synthesizing the new DNA strand.
Primase: Primase is an enzyme involved in the process of DNA replication. It is responsible for synthesizing short RNA primers that serve as starting points for DNA synthesis by DNA polymerase.
Primer: A primer is a short strand of RNA or DNA that serves as a starting point for DNA synthesis. Primers are necessary because DNA polymerases can only add new nucleotides to an existing strand of DNA.
Proofreading: Proofreading is the process of carefully reviewing and correcting errors in written text before it is finalized or published. It involves checking for mistakes in spelling, grammar, punctuation, formatting, and overall consistency to ensure the accuracy and quality of the final document.
Quinolones: Quinolones are a class of broad-spectrum antibiotics that inhibit bacterial DNA gyrase and topoisomerase IV, enzymes crucial for DNA replication. They are used to treat various infections by preventing bacterial cell division.
Replication: Replication is the process by which a cell makes an exact copy of its DNA. It is a critical mechanism that ensures genetic information is accurately transmitted to daughter cells during cell division.
Replication bubble: A replication bubble is a region of DNA where the double helix has unwound and opened to allow for replication. It forms at the origin of replication and includes two replication forks moving in opposite directions.
Replication Fork: The replication fork is a Y-shaped structure that forms during the process of DNA replication, where the double-stranded DNA molecule is unwound and replicated to produce two identical copies. It is the site where the DNA is actively being copied, with the two new strands growing outward from the point of separation.
Replication forks: Replication forks are Y-shaped structures formed during DNA replication, where the double-stranded DNA is split into two single strands. They are pivotal in allowing the synthesis of new DNA strands.
RNA polymerase: RNA polymerase is an enzyme that synthesizes RNA from a DNA template during transcription. It plays a crucial role in gene expression by creating mRNA, tRNA, and rRNA molecules.
RNA primase: RNA primase is an enzyme that synthesizes a short RNA primer during DNA replication. This primer is essential for DNA polymerase to begin synthesis of the new DNA strand.
RNA Primase: RNA primase is an enzyme responsible for synthesizing short RNA primer sequences that initiate DNA replication. It plays a crucial role in the process of DNA replication by providing a starting point for the DNA polymerase enzyme to begin the process of duplicating the genetic material.
RNase H: RNase H is an enzyme that specifically degrades the RNA strand of RNA-DNA hybrids. It plays a crucial role in DNA replication and repair by removing RNA primers used during these processes.
Rolling circle replication: Rolling circle replication is a process of DNA replication in circular DNA molecules where a nick in one strand allows the 3' end to serve as a primer for synthesis. It produces multiple linear copies of the circular DNA, which can be used for various cellular processes.
Rolling Circle Replication: Rolling circle replication is a mechanism of DNA replication where a single-stranded DNA molecule is used as a template to produce multiple copies of a circular DNA molecule. It is a highly efficient process that allows for rapid and continuous DNA synthesis.
Semiconservative replication: Semiconservative replication is the process by which DNA is replicated in cells, producing two copies that each contain one original strand and one newly synthesized strand. This ensures genetic continuity from one generation to the next.
Semiconservative Replication: Semiconservative replication is the process by which DNA makes copies of itself during cell division, where the original double-stranded DNA molecule is used as a template to produce two new, identical DNA molecules. This process ensures the accurate transmission of genetic information from one generation of cells to the next.
Single-Strand Binding Proteins: Single-strand binding proteins (SSB) are essential regulatory proteins that bind to and stabilize single-stranded DNA (ssDNA) during crucial cellular processes like DNA replication, repair, and recombination. These proteins play a vital role in maintaining the integrity and proper functioning of the genetic material within cells.
Single-stranded binding proteins: Single-stranded binding proteins (SSBs) are essential during DNA replication, stabilizing the unwound DNA strands. They prevent the single strands from re-annealing or forming secondary structures.
Single-stranded origin (sso) site: A single-stranded origin (sso) site is a specific sequence in plasmid DNA where the conversion from single-stranded to double-stranded DNA begins. It is crucial for the replication of certain plasmids, particularly those that replicate via a rolling circle mechanism.
Sliding clamp: A sliding clamp is a protein complex that encircles DNA and anchors DNA polymerase during replication, ensuring high processivity. It allows the polymerase to synthesize long stretches of DNA without dissociating.
Sliding Clamp: The sliding clamp is a ring-shaped protein complex that acts as a processivity factor, encircling the DNA and sliding along it to keep DNA polymerase attached during replication. It helps increase the efficiency and speed of DNA replication by preventing the polymerase from dissociating from the DNA template.
Stahl: Stahl is a scientist known for his contribution to the understanding of DNA replication, particularly through the Meselson-Stahl experiment which confirmed the semi-conservative model of DNA replication.
Sugar-Phosphate Backbone: The sugar-phosphate backbone is the structural framework that forms the backbone of DNA and RNA molecules. It is composed of alternating sugar (deoxyribose or ribose) and phosphate groups, which provide the structural support and directionality for the nucleic acid strands.
Supercoiled: Supercoiled DNA is a form of DNA structure where the double helix is twisted upon itself. This conformation helps in compacting the DNA to fit within the confines of a cell.
Telomerase: Telomerase is an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes, called telomeres. This helps protect genetic information during DNA replication.
Telomere: Telomeres are repetitive nucleotide sequences at the ends of linear chromosomes that protect them from degradation and prevent fusion with neighboring chromosomes. They play a critical role in maintaining genomic stability during DNA replication.
Telomeres: Telomeres are the protective caps at the ends of chromosomes that play a crucial role in DNA replication and cellular aging. They are made up of repetitive DNA sequences that protect the genetic information from degradation and ensure the stability of chromosomes during cell division.
Template Strand: The template strand, also known as the coding strand or sense strand, is the DNA strand that serves as the template for the synthesis of RNA during the process of transcription. It provides the genetic information necessary for the cell to produce the corresponding RNA molecule.
Termination: Termination is the process by which a biological process or reaction is brought to an end. In the context of DNA replication, RNA transcription, and protein synthesis, termination refers to the specific mechanisms that signal the conclusion of these fundamental cellular processes.
Termination of DNA replication: Termination of DNA replication is the process by which DNA synthesis is concluded, ensuring that the entire genome is replicated accurately. It involves specific sequences and proteins that halt the replication machinery.
Topoisomerase: Topoisomerase is an enzyme that helps manage the topology of DNA during replication and transcription. It alleviates supercoiling and torsional strain by creating temporary breaks in the DNA strands.
Topoisomerase: Topoisomerases are enzymes that catalyze the breaking and rejoining of DNA strands to resolve topological problems that arise during essential cellular processes like DNA replication, transcription, and chromosome segregation.
Topoisomerase II: Topoisomerase II is an enzyme that alters the topological states of DNA during replication and transcription by creating transient double-strand breaks. It helps manage DNA supercoiling and untangles knots and tangles that arise during these processes.
Topoisomerase IV: Topoisomerase IV is an enzyme in bacteria that helps to separate replicated DNA strands during cell division. It plays a crucial role in the final stages of DNA replication by resolving intertwined DNA molecules.
Viruses: Viruses are infectious agents that require a host cell to replicate and propagate their genetic material. They can infect all forms of life, including bacteria, plants, animals, and humans.
Watson: Watson is one of the scientists who co-discovered the double-helix structure of DNA. His work laid the foundation for understanding DNA replication mechanisms.