Name: dna replication teams in the replisome
Uploaded: 2020-11-23T11:47:35.000Z
Duration: 3 min 1 s
Channel: JoVE

K12 Standards

Alabama Course of Study Science

9-12

Biology

from-molecules-to-organisms-structures-and-processes

From Molecules to Organisms: Structures and Processes

9-12.B.1.3

The Replisome

Replikacja DNA odbywa się przez wysoce skoordynowany zespół wielobiałkowy znany jako maszyneria replikacji DNA lub replikosom, co zwiększa wydajność replikacji DNA.
Podstawowymi składnikami maszynerii są helikaza, jednoniciowe białka wiążące DNA, prymaza DNA, przesuwne zaciski, ładowarka zaciskowa i wiele polimeraz DNA, które są ze sobą powiązane w pobliżu widełek replikacyjnych.
Reformatywne polimerazy DNA mają procesywność około 10 nukleotydów, czyli liczbę nukleotydów, które mogą dodać do nici potomnej przed dysocjacją od nici matrycowej. 
Jest to zbyt nieefektywne, aby skopiować całe genomy w rozsądnym czasie, a problem ten można rozwiązać za pomocą przesuwanych białek klamrowych.
Kiedy ATP połączy się z białkiem ładującym klamrę, zwiążą się i otworzą przesuwny zacisk, tak aby jego struktura przypominająca pierścień mogła otaczać kompleks DNA starter-matryca. Po związaniu ładowarka zaciskowa hydrolizuje ATP do ADP, powodując dysocjację ładowarki zaciskowej i zamknięcie zacisku wokół DNA.
Następnie polimeraza DNA wiąże się z białkami klamrowymi i razem przesuwają się wzdłuż matrycy DNA, wiążąc polimerazę DNA z nicią i zwiększając jej procesowość do 1000 nukleotydów. 
Ta zwiększona procesywność pozwala polimerazie DNA na przeprowadzanie ciągłej replikacji DNA na nici wiodącej.
Jednak na matrycy opóźnionej nici inna polimeraza DNA przeprowadza nieciągłą replikację DNA w sposób, który umożliwia cząsteczkom polimerazy DNA jednoczesną syntezę nici wiodących i opóźnionych. Proces ten jest czasami opisywany jako "model puzonu".
Opóźniona nić i jej nić matrycowa tworzą pętlę, gdy polimeraza DNA inicjuje syntezę fragmentów Okazaki ze startera RNA. 
Pętla DNA rośnie z obu kierunków, gdy helikaza rozwija DNA i syntetyzuje opóźnioną nić.
Kiedy polimeraza DNA napotyka następny starter RNA, odłącza się od nici matrycowej. W międzyczasie prymaza dodaje kolejny starter do opóźnionej nici i uwalniana jest rosnąca pętla DNA. 
Białka zaciskowe i ładujące klamrę umożliwiają polimerazie DNA szybkie ponowne powiązanie się z zapoczątkowaną matrycą DNA.
Powstawanie i zapadanie się podsekwencji pętli DNA powtarza się wraz z syntezą każdego nowego fragmentu Okazaki.

<ol>
	<li>O'Donnell, Michael, Lance Langston i Bruce Stillman. "Zasady i koncepcje replikacji DNA u bakterii, archeonów i eukarii". Cold Spring Harbor Perspectives in Biology 5, nr 7 (2013): a010108.</li>
	<li>Alberts, Bruce. "Replikacja i rekombinacja DNA". Nature 421, nr 6921 (2003): 431.</li>
	<li>Kelch, Brian A., Debora L. Makino, Mike O'Donnell i John Kuriyan. "ATPazy ładowarki zaciskowej i ewolucja maszynerii replikacji DNA." BMC Biology 10, nr 1 (2012): 34.</li>
	<li>Hedglin, Mark, Ravindra Kumar i Stephen J. Benkovic. "Zaciski replikacyjne i ładowarki zaciskowe". Perspektywy Cold Spring Harbor w Biologii 5, nr 4 (2013): a010165.</li>
	<li>Gardner, Andrew F. i Zvi Kelman. "Maszyneria replikacji DNA jako cele terapeutyczne". Granice w biologii molekularnej 6 (2019): 35.</li>
</ol>

replisom

Replikacja DNA jest przeprowadzana przez duży kompleks białek, który działa w skoordynowany sposób, aby osiągnąć replikację DNA o wysokiej dokładności. Razem ten kompleks jest znany jako mechanizm replikacji DNA lub replisom. Synteza nici wiodącej i opóźnionej jest procesem wysoce skoordynowanym. Aby to wyjaśnić, w 1980 roku Bruce Alberts zaproponował „model puzonu”. Tworzenie pętli DNA rozpoczyna się w momencie syntezy startera na macierzystej nici opóźnionej. Pętla rośnie wraz z syntezą fragmentu Okazaki i ostatecznie rozpuszcza się po zakończeniu syntezy fragmentu. Następnie polimeraza DNA przyłącza się do innego startera i cały cykl, od utworzenia pętli do zapadnięcia się, powtarza się. Replisom umożliwia koordynację wszystkich działań w ramach kompleksu maszyn replikacyjnych. Replisomy Helikazy rozwijają i oddzielają dwuniciowy DNA. Enzymy te występują w postaci pojedynczego pierścienia heksamerowego u prokariotów i jako podwójny pierścień heksamerowy u eukariontów. Funkcjonowanie helikaz eukariotycznych zależy od dodatkowych białek, Cdc45 i GINS. Białka wiążące jednoniciowy DNA (SSB) zapobiegają ponownemu łączeniu się nici DNA. U prokariotów SSB składają się z pojedynczej podjednostki, podczas gdy u eukariontów są heterotrimerycznym białkiem znanym jako białko replikacyjne A (RPA). Primaza dodaje starter RNA do miejsca, w którym rozpocznie się synteza DNA. U prokariotów prymaza występuje w postaci pojedynczej podjednostki enzymu zwanej DnaG, która syntetyzuje starter RNA składający się z około 12 nukleotydów. U eukariontów wielopodjednostkowy enzym, polimeraza DNA-α prymaza, syntetyzuje hybrydowy starter RNA-DNA o długości około 25 nukleotydów. Oprócz polimerazy-α, polimeraza replikacyjna przedłuży nowo zsyntetyzowany DNA. Podczas gdy u prokariotów występuje jeden typ polimerazy replikacyjnej, polimeraza DNA III, u eukariotów występują dwa różne typy polimeraz replikacyjnych, Pol ε i Pol δ, odpowiedzialne odpowiednio za syntezę nici wiodącej i opóźnionej. Białka Sliding Clamp utrzymują polimerazy przyłączone do matrycy DNA. β-clamp, białko homodimeryczne, działa jako zacisk u prokariotów. U eukariontów to samo zadanie spełnia antygen jądrowy proliferujących komórek (PCNA), białko homotrimeryczne. Centralny otwór zacisku przesuwnego jest naładowany dodatnio, co umożliwia mu oddziaływanie elektrostatyczne z ujemnie naładowanym szkieletem fosforanowym DNA. Zacisk jest mocowany do DNA za pomocą ładowarki zaciskowej. Te pentameryczne białka należą do klasy AAA+ ATPaz. Eukariotyczny moduł ładujący klamrę jest znany jako współczynnik replikacji C, podczas gdy prokariotyczny moduł ładujący klamrę E. coli jest znany jako kompleks γ; jednakże uważa się, że białka zaciskające i moduły ładujące są homologami ewolucyjnymi, w przeciwieństwie do wielu innych składników replisomu.

Replisom

Replikacja DNA jest przeprowadzana przez duży kompleks białek, które działają w skoordynowanej materii, aby osiągnąć replikację DNA o wysokiej wierności. Razem to ...

Education

JoVE Core

Molecular Biology

Biologia molekularna

Unit 1

Jednostka 1

DNA Replication

Replikacja DNA

KEY TERMS AND CONCEPTS

Kluczowe terminy i pojęcia

dna replication teams in the replisome

DNA replication depends on the replisome, a coordinated complex of proteins that copies DNA with high accuracy. This DNA replication machinery brings many parts together so the leading and lagging strands can be made at the same time.

A key idea in this process is the trombone model, proposed by Bruce Alberts in 1980. In this model, a loop forms on the lagging strand when a primer is made. The loop grows as an Okazaki fragment is synthesized, then falls apart when that fragment is finished. DNA polymerase then moves to a new primer, and the cycle repeats.

Helicases start the process by unwinding and separating double-stranded DNA. In prokaryotes, helicase is a single hexamer ring, while in eukaryotes it forms a double hexamer ring. Eukaryotic helicases also need the extra proteins Cdc45 and GINS to work. Single-stranded DNA binding proteins keep the separated strands from reannealing. In prokaryotes, these are SSB proteins with one subunit. In eukaryotes, the equivalent protein is replication protein A, or RPA, which is a heterotrimer.

Primase adds the RNA primer that gives DNA synthesis a starting point. In prokaryotes, primase is the single-subunit enzyme DnaG, and it makes an RNA primer of about 12 nucleotides. In eukaryotes, DNA polymerase-alpha primase makes an RNA-DNA hybrid primer of about 25 nucleotides. After that, the replicative polymerase extends the new DNA strand. Prokaryotes use DNA polymerase III, while eukaryotes use Pol epsilon for the leading strand and Pol delta for the lagging strand.

Sliding clamp proteins hold the polymerases on the DNA template so copying can continue efficiently. The prokaryotic beta-clamp is a homodimer, and the eukaryotic clamp is proliferating cell nuclear antigen, or PCNA, which is a homotrimer. The clamp has a positively charged central pore that interacts with the negatively charged DNA backbone. A clamp loader places the clamp onto DNA. These pentameric AAA+ ATPases include the eukaryotic replication factor C and the E. coli gamma complex. The clamp proteins and clamp loaders are thought to be evolutionary homologs, unlike many other replisome components.

DNA Replication Teams in the Replisome

replication in prokaryotes

Prokaryotic DNA Replication Steps

Prokaryotic DNA replication copies the chromosome before a cell divides. In bacteria, this process starts at a specific DNA site called the origin of replication. From there, the cell builds new DNA strands using enzymes that match each base with its partner. The DNA double helix first opens so replication can begin. As the strands separate, each original strand serves as a template. New nucleotides are added in a set order, which helps the cell make an accurate copy of its genetic material. <br...

replication in eukaryotes

Eukaryotic DNA Replication Steps

Eukaryotic DNA replication copies the genome before a cell divides. In eukaryotes, this process happens in a controlled sequence so each new cell can receive genetic information. Replication begins at specific sites on the DNA called origins. The DNA is opened, and each original strand serves as a template, meaning it guides the building of a new complementary strand. This sets up two DNA molecules from one original molecule. The process then continues as enzymes add matching nucleotides to...

dna base pairing

DNA Base Pair Rules

DNA base pairing follows specific rules that help DNA carry genetic information. In DNA, the bases pair in a regular way, with adenine matching thymine and cytosine matching guanine. These pairs fit together because of their chemical shapes and bonding patterns. These base pairs also support accurate DNA replication. When DNA copies itself, each strand can guide the formation of a new partner strand using the pairing rules. Understanding base pairing helps explain how DNA stays organized and...

the dna replication fork

DNA Replication Stress and Fork Stalling

DNA replication stress and fork stalling can disrupt the copying of a cell’s genome. The replication fork is the Y-shaped site where DNA strands separate and new complementary strands are made at the same time. This linked unwinding and synthesis helps cells duplicate DNA efficiently and with fewer errors. In organisms with small circular DNA, such as E. coli, replication often begins at a single origin. That setup creates two replication forks that move in opposite directions from the opening...

proofreading

Proofreading in DNA Replication

Proofreading in DNA replication helps keep DNA copying accurate. It is a built-in check that reduces mistakes as new DNA is made. DNA polymerase is the enzyme that carries out this checking during replication. When it adds a wrong nucleotide, it can remove the error and replace it with the correct one. This correction step helps maintain the correct DNA sequence. Proofreading is an important part of DNA replication because it supports genetic accuracy. By catching mistakes as they happen, the...

dna helicases

Helicase Motor Proteins in DNA Unwinding

Helicase motor proteins help unwind DNA during key cell processes. They use energy from ATP hydrolysis, which is the breakdown of ATP to release usable energy. This movement lets helicases separate DNA strands when the cell needs access to the genetic code. These enzymes are involved in DNA replication, repair, recombination, and transcription. Helicases are found in all living organisms, but their structure, function, and movement can differ. In prokaryotes, the DnaB helicase moves along the...

the replisome

DNA replication depends on the replisome, a coordinated complex of proteins that copies DNA with high accuracy. This DNA replication machinery brings many parts together so the leading and lagging strands can be made at the same time. A key idea in this process is the trombone model, proposed by Bruce Alberts in 1980. In this model, a loop forms on the lagging strand when a primer is made. The loop grows as an Okazaki fragment is synthesized, then falls apart when that fragment is finished.

lagging strand synthesis

Okazaki Fragments in DNA Replication

DNA replication uses a leading strand and a lagging strand, and they are made at different rates. The leading strand starts first. The lagging strand starts later, moves more slowly, and is made in pieces. The two strands also differ in direction and starting steps. Leading strand synthesis follows the opening replication fork. Lagging strand synthesis goes in the opposite direction. The leading strand needs one RNA primer, while the lagging strand needs multiple RNA primers. After priming,...

mismatch repair

Fixing DNA Copying Errors

Mismatch repair helps fix DNA copying errors after replication. When DNA is copied, small mistakes can slip through. This repair system finds those mismatches and corrects them before they become permanent changes. The process depends on a group of mutator proteins. These proteins work together to detect the error, remove the incorrect section, and help replace it with the proper DNA sequence. In this way, mismatch repair supports the accuracy of genetic information. If the repair system does...

dna topoisomerases

How Topoisomerases Untwist DNA

DNA topoisomerases are enzymes that untwist DNA when it becomes overcoiled during cell processes such as DNA replication and transcription. They help regulate positive and negative DNA supercoiling without changing the nucleotide sequence. Clockwise overwinding creates positively supercoiled DNA, while counterclockwise underwinding produces negatively supercoiled DNA. Topoisomerases are grouped into two main types. Type I topoisomerases act on one strand of double-stranded DNA, and they...

telomeres and telomerase

How Telomerase Protects Chromosome Ends

Telomerase helps protect chromosome ends during eukaryotic DNA replication. When the final primer is removed, a single-stranded DNA fragment can remain at the end of the chromosome. That piece cannot be copied in the same way as the rest of the strand because there is no 3' end for new DNA to attach to. If this end piece is not replaced, chromosomal DNA is gradually lost each time a cell divides. The exposed single-stranded DNA can also trigger a DNA damage response from enzymes that detect it.

non-nuclear inheritance

Cytoplasmic Inheritance in Cells

Cytoplasmic inheritance explains how some traits are passed through cell structures outside the nucleus. These traits come from organelles such as mitochondria and chloroplasts. They do not follow the usual nuclear pattern of inheritance. Mitochondria and chloroplasts each contain their own DNA. Because of this, they can carry genetic information that affects cell function and certain visible traits. In high school biology, this topic helps explain why not all inherited traits come from...

animal mitochondrial genetics

Animal Mitochondrial DNA and Inheritance

Animal mitochondrial DNA has its own genome, separate from nuclear DNA. It is a double-stranded, closed circular molecule with about 20,000 base pairs. One strand is the heavy, or H-strand, because it is rich in guanine. The other is the light, or L-strand, because it is rich in cytosine. Compared with nuclear DNA, mitochondrial DNA has very little non-coding sequence. It also has no introns. Its genes are packed closely together, and some even overlap. The D-loop is the main non-coding...

comparing mitochondrial, chloroplast, and prokaryotic genomes

comparing-mitochondrial-chloroplast-and-prokaryotic-genomes

How Organelle Genomes Resemble Bacteria

Mitochondrial and chloroplast genomes still keep several traits from their bacterial ancestors. They also show changes that happened after these organelles evolved inside eukaryotic cells. Eukaryotic cells are cells with a nucleus, while prokaryotes are cells without one. Like prokaryotic genomes, mitochondrial and chloroplast genomes do not bind with histone-like proteins. They also do not show the complex chromosome-like packaging seen in eukaryotes. Mitochondria and chloroplasts divide by...

export of mitochondrial and chloroplast genes

export-of-mitochondrial-and-chloroplast-genes

How Organelles Pass Genes to the Nucleus

Eukaryotic cells can carry three genetic systems: nuclear, mitochondrial, and chloroplast. Over time, many genes from mitochondria and chloroplasts have moved into the nucleus. In some plant species, this gene transfer is still happening. This movement has affected large parts of the genome in some organisms. About 18% of the Arabidopsis thaliana nuclear genome is thought to come from the chloroplast's cyanobacterial ancestor. In yeast, around 75% of the genome is derived from the...

single-strand dna binding proteins

How SSB Proteins Protect DNA Strands

Single-strand DNA-binding proteins, or SSB proteins, help protect DNA during replication. When double-stranded DNA is unwound, the two strands separate. SSB proteins bind to the exposed single strands and keep them stable. These proteins bind in a sequence-independent manner. That means the order of the nitrogenous bases does not have to follow a specific pattern for SSB proteins to attach. Their binding straightens single-stranded DNA and makes it more rigid. This support may help DNA...

key terms and concepts

Explore how the replisome coordinates DNA replication, from helicase and primase to polymerases, sliding clamps, and the trombone model.

DNA Replication Teams in the Replisome | JoVE K12

molecular biology

JoVE Core Molecular Biology showcases the molecular processes of the cell through clear and concise animated video lessons. Additionally, in scientist-in-action videos, these concepts' application is demonstrated through real experiments in modern laboratories.

What are Cells?

Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium or trillions of them, ...

Cell Size

Cell sizes vary widely among and within organisms. Bacterial cells range between 1-10 micrometers (&#x3BC;m)and are considerably smaller than most ...

Eukaryotic Compartmentalization

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that carry ...

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains&#x2014;Archaea and Bacteria. Bacteria include many common organisms, such as ...

Cytoplasm

The cytoplasm consists of organelles and a framework of protein scaffolds called the cytoskeleton suspended in an aqueous solution, the cytosol. The ...

The Nucleus

The nucleus is a membrane-bound organelle that acts as a control center in a eukaryotic cell. It contains chromosomal DNA, which controls gene expression ...

Endoplasmic Reticulum

Endoplasmic ReticulumThe endoplasmic reticulum (ER) is an extensive network of membranous sacs and tubules in eukaryotic cells, continuous with the outer ...

Ribosomes

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that ...

Golgi Apparatus

As they leave the Endoplasmic Reticulum (ER), properly folded and assembled proteins are selectively packaged into vesicles. These vesicles are ...

Lysosomes

Lysosomes are membrane-enclosed spherical sacs derived from the Golgi apparatus. The most important function of the lysosome is degrading macromolecules ...

Peroxisomes

Peroxisomes and mitochondria are two important oxygen-utilizing organelles in eukaryotic cells. Mitochondria carry out cellular respiration&#x2014;the ...

Introduction to the Cytoskeleton

Overview of the Cytoskeleton
The cytoskeleton is a network of protein filaments present within the cell, having three distinct filaments ...

Introduction to Actin

Actin is a highly conserved cytoskeletal protein found abundantly in eukaryotic cells. It constitutes 10% weight of the total cellular protein in muscle ...

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Overview of Myosin Structure and Function

Myosins are a family of molecular motor proteins, first identified in the skeletal muscles, where they are responsible for muscle contraction. Along with ...

Microtubules

Microtubules are the thickest cytoskeletal filaments with a diameter of 25 nm. In prokaryotic organisms, microtubules are commonly found in locomotory ...

The Structure of Intermediate Filaments

The intermediate filaments are one of three widely studied cytoskeletal filaments. They are so named as their diameter (10 nm) is in between that of ...

Types of Intermediate Filaments

The intermediate filaments are an essential component of the cytoskeleton. Presently six types of intermediate filament have been identified. Type I and ...

Gap Junctions

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The Extracellular Matrix

In order to maintain tissue organization, many animal cells are surrounded by structural molecules that make up the extracellular matrix (ECM). Together, ...

Tissues

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Plant Cell Wall

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Plasmodesmata

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pH Regulation in Cells

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ATP Energy Storage and Release

ATP and Macromolecule Synthesis

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1. Engage in evidence-based argument to relate a cell's function to the structure, function, and diversity of its components. Examples: Muscle cells have a large number of mitochondria, which create energy for contraction in the form of ATP. Some plant cells have a large vacuole which is used for storage and transport of excess nutrients in changing environments.

9-12.B.1.1

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised&#160; of nucleotides and proteins are ...

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form ...

Types of RNA

Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse ...

Transcription

Transcription is the synthesis of RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. ...

Bacterial RNA Polymerase

Eukaryotic RNA Polymerases

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of ...

RNA Polymerase II Accessory Proteins

Transcription Elongation Factors

pre-mrna-processing-modification-of-pre-mrna-ends

Pre-mRNA Processing: Modification of pre-mRNA Ends

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or ...

Pre-mRNA Processing: RNA Splicing

Chromatin Structure and RNA Splicing

Alternative RNA Splicing

Nuclear Export of mRNA

Transfer RNA Synthesis

Ribosomal RNA Synthesis

The Nucleolus

Additional Subnuclear Structures

Translation

Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes ...

tRNA Activation

Initiation of Translation

Termination of Translation

Improving Translational Accuracy

prokaryotic-transcriptional-activators-and-repressors

Prokaryotic Transcriptional Activators and Repressors

Nonsense-mediated mRNA Decay

The Eukaryotic Promoter Region

Molecular Chaperones and Protein Folding

Co-activators and Co-repressors

The Proteasome

Master Transcription Regulators

Regulated Protein Degradation

Regulated mRNA Transport

Proteins: From Genes to Degradation

mRNA Stability and Gene Expression

Cell Specific Gene Expression

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between ...

regulation-of-expression-occurs-at-multiple-steps

Regulation of Expression Occurs at Multiple Steps

Small interfering RNAs (siRNA)

Cis-regulatory Sequences

lncRNA - Long Non-coding RNAs

cooperative-binding-of-transcription-regulators

Cooperative Binding of Transcription Regulators

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. ...

2. Obtain and evaluate information to explain the role of DNA and RNA in transcription and translation leading to protein synthesis and cellular function.

9-12.B.1.2

Nucleic Acids and Nucleotides

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Nucleic Acid Structure

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Genomic DNA in Prokaryotes

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Genomic DNA in Eukaryotes

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a. Use a model to describe the structure and sequence of DNA, including nucleotide structure, base pairing, and the structure of the helix.

9-12.B.1.2.a

DNA Replication Teams in the Replisome

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