Tutorial: DNA Replication
Index
DNA Polymer | Replication Enzymes | Free Nucleotides | Replication Overview | Replication Animation | Replication Explanation | Discontinuous Replication | Bubble | Quiz


Copyright © Steve Kuensting, 2004, All Rights Reserved.
This web tutorial may not be distributed by any means
without the expressed permission of the author!



Introduction

If cells are capable of producing new cells, then they must have a way of producing new copies of their DNA to pass on to the new cells. The Watson and Crick model of DNA explains easily how the double-stranded molecule of DNA duplicates, or replicates itself.

Replication introduction



DNA Polymer

Basically, the double stranded DNA molecule unzips and unwinds in order to allow each single strand to serve as a mold or template for the construction of new complementary strands.

DNA polymer



Replication Enzymes

Several basic enzymes are needed by a cell nucleus in order to complete DNA replication. One is called helicase - it is responsible for separating the complementary strands of DNA. Another is topoisomerase - it is responsible for untwisting the DNA molecule. The last and most important is DNA polymerase - it is responsible for putting together new complementary strands that match the separated strands. Note the symbols used to represent two of the enzymes.

Replication enzymes



Free Nucleotides

In order for replication to take place, a cell has new nucleotides floating around in the nucleus. These are free nucleotides (not bound to DNA). They are obtained from foods and diffuse into the nucleus of a cell.

Free nucleotides



Replication Overview

Before we begin to demonstrate the entire process, remember, replication takes place in the NUCLEUS - that is where the DNA, free nucleotides, and enzymes are, for replication to take place.

Locations




Replication Animation

Replication animation
The animations are Copyright © 1989, Steve Kuensting, All Rights Reserved.
Speed = | Delay = milliseconds | Frame # =
Loop

Leading and Lagging Strands

You should have noticed that the direction of replication was opposite on the two strands of DNA after helicase unzipped the double-stranded DNA. Furthermore, the upper strand replicated in sections while the lower strand replicated smoothly. The replication on the upper strand is referred to as "lagging" and the replication on the lower strand is referred to as "leading". The lower strand only required DNA polymerase (paintbrush) while the upper strand required DNA polymerase and ligase (green icon), which bonds the disjointed small sections of lagging-strand DNA.

Leading vs Lagging



Explanation

If you had checked the original DNA nucleotide sequences you could now see that the copy process is usually exact. Both new double stranded pieces of DNA are identical to each other.

DNA Strands are Identical



Replication Explanation

Below are the original strand of DNA and the 2 copies. Check to see that they are identical.

Replication explanation



DNA Directionality

You can see then that cells have a simple and relatively error-free method for copying their genetic code. Copy mistakes could be costly - they could easily result in the death of the cell. Also, note that DNA is actually a spiral helix, something like a "twisted" ladder, but this would have been too difficult to show on a simulation. The DNA polymerase enzymes can only work in specific directions on a DNA molecule. To explain this direction, biologists name the ends of each strand as 3' (sugar end) or 5' (phosphate end). Note that the two strands of a DNA molecule are antiparallel to each other. The DNA polymerase enzymes only move in the 3' to 5' direction on an existing DNA strand.
DNA directionality



Nucleotide Directionality

Each DNA nucleotide consists of a nitrogen base and a phosphate attached to a deoxyribose sugar. The carbons of the sugar are numbered from 1 to 5 and are referred to as 1' (1-prime), 2' (2-prime), 3' (3-prime), 4' (4-prime) and 5' (5-prime). The important carbons are: 1' for attaching the nitrogen base, 5' for attaching the phosphate, and 3' for attaching to the next nucleotide. The 2' carbon differs between DNA and RNA nucleotides: RNA has an -OH group attached there while DNA has only a -H group. Below are DNA nucleotides. RNA directionality

Okazaki Fragments and DNA Replication

In 1966, replication was shown to be both continuous and discontinuous. Two Japanese scientists, Kiwako Sakabe and Reiji Okazaki were working with Escherichia coli and discovered small DNA fragments being produced during DNA replication. They developed a theory that explained this finding. The small fragments are still referred to as "Okazaki fragments". The reason for their findings is in the enzyme DNA polymerase. DNA polymerase can only work in the 3' to 5' direction during replication. On one strand it works continuously, following helicase as it opens the DNA strands. That side is called the "leading side". On the other side, DNA polymerase works discontinuously, traveling away from helicase and producing the Okazaki fragments that Reiji Okazaki discovered. That side is called the "lagging side". Another enzyme - ligase - is needed to join the Okazaki fragments together on the discontinuous side.

DNA replication
DNA replication

By LadyofHats Mariana Ruiz [Public domain], via Wikimedia Commons


Replication Symbols

Below is an animation of the process. Ligase is represented by:Ligase. DNA polymerase is represented by eitherContinuous side (continuous side) orDiscontinuous side (discontinuous side).

Discontinuous DNA Replication - Top Strand
Continuous DNA Replication - Bottom Strand


The animations are Copyright © 2013, Steve Kuensting, All Rights Reserved.
Speed = | Delay = milliseconds | Frame # =
Loop



Replication Bubbles

Linear chromosomes are replicated at many regions simultaneously, forming "bubbles" that merge over time. Special enzymes bind to a chromosome and open up a bubble, which allows helicase and many polymerases to work simultaneously. Each bubble has two replication forks. Each fork has one region of continuous replication and one region of discontinuous replication. Okazaki fragments are found on the discontinuous/lagging side (in red). DNA polymerase ALWAYS slides on the existing strand in the 3' to 5' direction, putting together nucleotides in the opposite orientation (5' to 3'). The diagram below shows continuous/leading side replication in blue.
Replication bubble



Whole Chromosomes Replication - Merging Bubbles

Each chromosome in a human cell has multiple replication origins. Each origin produces its own replication bubble with forks moving in opposite directions. As one fork merges with an opposing fork from a different bubble, the two bubbles fuse. Eventually as all bubbles fuse on a chromosome, replication is complete.
Merging DNA bubbles
Merging DNA bubbles

By Boumphreyfr (Own work) [CC-BY-SA-3.0 or GFDL], via Wikimedia Commons



Quiz


       Quiz        Quiz
  1. What is the name of the enzyme labelled 'A'?

  2. What is the name of the enzyme labelled 'B'?

  3. Which number represents the bonds which must be broken for replication to occur?

  4. What molecule is represented by the part labelled by number 1?

  5. What molecules are represented by the part labelled by number 3?


Answers