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

שכפול DNA מתבצע על ידי הרכבה רב-חלבונית מתואמת ביותר המכונה מנגנון שכפול DNA או replisome, אשר מגביר את היעילות של שכפול DNA.
מרכיבי הליבה של המכונות הם הליקז, חלבונים קושרי DNA חד-גדיליים, פרימז DNA, מלחציים מחליקים, מעמיס מהדק ופולימרזות DNA מרובות, שכולם קשורים זה לזה ליד מזלג השכפול.
לפולימראזות דנ"א משוכפלות יש תהליך של כ-10 נוקלאוטידים, שהוא מספר הנוקלאוטידים שהוא יכול להוסיף לגדיל הבת לפני שהוא מתנתק מגדיל התבנית. 
זה לא יעיל מדי להעתיק גנומים שלמים בזמן סביר ובעיה זו נפתרת בעזרת חלבוני מהדק מחליקים.
כאשר ATP מתחבר לחלבון המהדק, הם ייקשרו ויפתחו את מהדק ההזזה כך שהמבנה דמוי הטבעת שלו יוכל להקיף את קומפלקס הדנ"א של תבנית הפריימר. לאחר הקשירה, מעמיס המהדק מבצע הידרוליזה של ה-ATP ל-ADP, מה שגורם למעמיס המהדק להתנתק ולמהדק להיסגר סביב הדנ"א.
לאחר מכן, DNA פולימראז נקשר לחלבוני המהדק ויחד הם מחליקים לאורך הדנ"א התבנית, קושרים DNA פולימראז לגדיל ומגבירים את התהליכות שלו עד 1000 נוקלאוטידים. 
תהליך מוגבר זה מאפשר לדנ"א פולימראז לבצע שכפול דנ"א רציף על הגדיל המוביל.
עם זאת, בתבנית הגדיל המפגר, DNA פולימראז אחר מבצע שכפול DNA לא רציף באופן המאפשר למולקולות הדנ"א פולימראז לסנתז את הגדילים המובילים והמפגרים בו זמנית. תהליך זה מתואר לעיתים כ"מודל טרומבון".
הגדיל המפגר וגדיל התבנית שלו יוצרים לולאה כאשר DNA פולימראז יוזם סינתזת מקטע אוקזקי מפריימר RNA. 
לולאת הדנ"א גדלה משני הכיוונים כאשר הליקייס משחרר את הדנ"א והגדיל המפגר מסונתז.
כאשר הדנ"א פולימראז פוגש את פריימר הרנ"א הבא, הוא מתנתק מגדיל התבנית. בינתיים, פרימר מוסיף פריימר נוסף לגדיל המפגר, ולולאת הדנ"א הגדלה משתחררת. 
חלבוני המהדק והמהדק מאפשרים ל-DNA פולימראז להתחבר מחדש במהירות לתבנית ה-DNA הדרוכה.
קריסת ההיווצרות ותת-הרצף של לולאת הדנ"א חוזרת על עצמה עם הסינתזה של כל מקטע אוקזקי חדש.

<ol>
	<li>אודונל, מייקל, לאנס לנגסטון וברוס סטילמן. "עקרונות ומושגים של שכפול DNA בחיידקים, ארכאה ואיקריה." קולד ספרינג הארבור פרספקטיבות בביולוגיה 5, מס '7 (2013): a010108.</li>
	<li>אלברטס, ברוס. "שכפול דנ"א ורקומבינציה". טבע 421, מס' 6921 (2003): 431.</li>
	<li>קלץ', בריאן א., דבורה ל. מקינו, מייק אודונל וג'ון קוריאן. "מהדק מטעין ATPases ואת האבולוציה של מכונות שכפול DNA." BMC ביולוגיה 10, מס '1 (2012): 34.</li>
	<li>הדגלין, מארק, רבינדרה קומאר וסטיבן ג'יי בנקוביץ'. "מהדקי שכפול ומעמיסי מהדקים." קולד ספרינג הארבור פרספקטיבות בביולוגיה 5, מס '4 (2013): a010165.</li>
	<li>גרדנר, אנדרו פ. וצבי קלמן. "מנגנון שכפול הדנ"א כמטרות טיפוליות". גבולות במדעי הביולוגיה המולקולרית 6 (2019): 35.</li>
</ol>

הרפליזום

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שכפול ה-DNA מתבצע על ידי קומפלקס גדול של חלבונים הפועלים באופן מתואם כדי להשיג שכפול DNA עם איכות גבוהה. ביחד מורכב זה ידוע כמנגנון שכפול ה-DNA או הרפליזום.

הסינתזה של הגדילים המובילים והאחרים היא תהליך מתואם מאוד. כדי להסביר זאת, "מודל הטרומבון" הוצע על ידי ברוס אלברטס בשנת 1980. היווצרות לולאת ה-DNA מתחילה כאשר פריימר מסונתז על חוט האב המפגר. הלולאה גדלה עם הסינתזה של שבר אוקאזאקי ולבסוף מתמוססת כאשר הסינתזה של השבר מסתיימת. לאחר מכן ה-DNA פולימראז נצמד לפריימר אחר וכל המחזור, מיצירת לולאה ועד לקריסה, חוזר על עצמו. הרפליזום מאפשר לתאם את כל הפעילויות כמתחם מכונות שכפול.

רכיבי רפליזום

Helicases מרגיעים ומפרידים את ה DNA הדו-גדילי. אנזימים אלו קיימים כטבעת הקסאמר בודדת בפרוקריוטים וכטבעת הקסאמר כפולה באוקריוטים. הליקות אוקריוטיות תלויות בחלבונים נוספים, Cdc45 ו-GINS, כדי לתפקד. חלבוני קושר DNA חד-גדילי (SSB) מונעים מגדילי ה-DNA להתאחות מחדש. בפרוקריוטים, SSBs מורכבים מתת-יחידה אחת, בעוד שבאוקריוטים הם חלבון הטרוטרימרי המכונה חלבון שכפול A (RPA).

פרימאז מוסיף פריימר של RNA למקום שבו תיווצר סינתזת DNA. בפרוקריוטים, פרימאז קיים כאנזים תת-יחידה אחת בשם DnaG, המסנתז פריימר RNA של כ-12 נוקלאוטידים. באוקריוטים, אנזים רב תת-יחידות, DNA polymerase-α primase, מסנתז פריימר היברידי של RNA-DNA של כ-25 נוקלאוטידים. בנוסף לפולימראז-α, פולימראז רפליקטיבי ירחיב את ה-DNA החדש שסונתז. בעוד שסוג יחיד של פולימראז משוכפל, DNA פולימראז III, קיים בפרוקריוטים, שני סוגים שונים של פולימראזות רפליקטיביות, Pol ε ו-Pol δ, קיימים באוקריוטים, עבור סינתזת גדילים מובילים וגדילים מפגרים, בהתאמה.

חלבוני Sliding Clamp שומרים על הפולימראזות מחוברות לתבנית ה-DNA. β-clamp, חלבון הומודימרי, פועל בתור מהדק בפרוקריוטים. באוקריוטים, אותה משימה מבוצעת על ידי אנטיגן גרעיני של תאים מתרבים (PCNA), חלבון הומטרימרי. הנקבובית המרכזית של מהדק ההזזה טעון חיובי, מה שמאפשר לו לקיים אינטראקציות אלקטרוסטטיות עם עמוד השדרה הפוספט הטעון שלילי של ה-DNA. המהדק מחובר ל-DNA על ידי מטעין מהדק. חלבונים פנטאמריים אלו שייכים למחלקת AAA+ של ATPases. מטעין המהדק האוקריוטי ידוע כגורם שכפול C, בעוד מטעין המהדק הפרוקריוטי של E. coli ידוע בתור קומפלקס γ; עם זאת, החלבונים המהדקים ומעמיסי המהדק נחשבים להומולוגים אבולוציוניים בשונה ממרכיבים רבים אחרים של הרפליזום.
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שכפול DNA מתבצע על ידי קומפלקס גדול של חלבונים הפועלים בחומר מתואם כדי להשיג שכפול DNA באיכות גבוהה. יחד זה ...

Education

JoVE Core

Molecular Biology

ביולוגיה מולקולרית

Unit 1

יחידה 1

DNA Replication

שכפול DNA

KEY TERMS AND CONCEPTS

מונחים ומושגים מרכזיים

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

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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

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell&#39;s genetic blueprint and have instructions for its ...

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group ...

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the ...

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the ...

The DNA Helix

Overview

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most ...

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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