DNA Replication (HS Tutorial)

Click the following link for a DNA Structure and Replication Student Learning Guide (coming soon)

1. Introduction

In the last tutorial, we looked at the structure of DNA.

DNA’s structure lends itself to replication. That’s essential for a molecule that gets passed from one generation to the next during reproduction, and from one cell to the next as an organism grows and develops.

DNA’s structure explains how cells can do this. Here’s how I explain this in the first two verses of my  DNA Replication music video.

DNA’s structure with its bases complementary
Makes replication easy, but not quite elementary
Since A only bonds with T and C with G
The Double Helix seems to copy naturally,

Or as Crick and Watson said:

“It has not escaped our notice that the specific pairing
We have postulated immediately suggests
A possible copying mechanism
For the genetic material”

The last verse is a quote from a paper written in 1953 that first correctly described the structure of DNA. The paper was written by James Watson and Francis Crick, who were the co-discoverers of the structure of DNA. Their work relied heavily on the work of two other scientists:, Rosalind Franklin and Maurice Wilkins.

In what follows, we’ll explain how replication works.

3. During DNA Replication, each strand serves as a template for the synthesis of a complementary strand

Here’s a big picture view of what happens during DNA Replication.

1. An enzyme separates the single strands that make up the DNA double helix. The enzyme that does this is called helicase. That’s easy to remember because it’s the enzyme that opens the helix. Helicase does this by breaking the hydrogen bonds that connect the base pairs.

   

2. With the nitrogenous bases (A, T, C, or G) on each strand exposed, each single strand now serves as a template for synthesis of a new strand. A template is  “a molecule … that serves as a pattern for the generation of another molecule” (source: Merriam-Webster on-line dictionary). For example, consider the single strand on the left side below. The base “T” is in the first position. Because of the base pairing rules, the only nucleotide that could bond with “T” is “A.” Similarly, the only nucleotide that could bond with the second nucleotide, “G,” is “C.” The key idea is that the information in one strand gives the cell the information needed to build the complementary strand.

   

3. Following the base pairing rules, complementary nucleotides form hydrogen bonds with the nucleotides on the template strands. Where do these new nucleotides come from? It depends. Plant cells can synthesize the nucleotides from scratch. Animals synthesize them from other molecules that they’ve eaten,

   

4. Another enzyme called DNA polymerase creates covalent bonds between the sugars and the phosphates of adjacent nucleotides on the newly synthesized strand. Once these sugar phosphate bonds have been created, DNA replication is complete. Where there was one DNA molecule, now there are two.

   

This model of replication is called semi-conservative: in each new daughter molecule, one strand is old (from the parent), and one strand is new. You can see this in the color coding of the diagram below. The original DNA is colored red. The newly synthesized strands are colored orange.

Here’s the same explanation in verse:

You first unzip the DNA in one or more places,
Breaking hydrogen bonds to separate the bases.
Each resulting single strand serves as a template,
Allowing enzymes to replicate 

New strands with complementary bases that match
And through hydrogen bonds these bases attach
Each nucleotide now bonds to the next
Through a sugar-phosphate bond they connect 

Meselsohn and Stahl proved in ‘58 ^{(read about their experiment)}
That this is how the double helix replicates
One strand new, the parent strand preserved,
In other words the whole thing is semi-conserved

4. Checking Understanding: DNA Replication (the big picture)

 

5. How DNA replication occurs in cells

Imagine that you were given the task of taking a paper cutout model of DNA (like the one at left) and replicating it. You’d  probably find this to be pretty easy. After all, you can see the bases, think of the base pairing rules, and manipulate the model (pulling it apart, adding new nucleotides, etc.) to create two new daughter strands from the parent strand.

How can cells, which can’t see or think, perform this task?

Cells do this all by enzymes, which have to do everything by touch and feel. You learned about two of these enzymes above. What follows expands and deepens that discussion.

DNA helicase (represented by “B” in the diagram below) starts the process. Helicase finds a sequence of bases called the origin of replication (A). The origin of replication acts as a signal that says “start replicating here.” Once it finds the origin of replication, DNA helicase breaks open the double helix by breaking the hydrogen bonds between complementary bases.

The structure that results from the opening of the helix is called a replication fork.

Replication forks are always created in pairs, creating a replication bubble (the entire structure below). In the diagram below, the original is at shown in dark blue at C. Helicases are shown at B. Newly synthesized DNA is shown in light blue at “D.” The two replication forks are at “E,” and the origin of replication is at “A.” 

Check out this amazing electron micrograph. It’s showing DNA replication in the nucleus of a eukaryotic cell. Each of the white arrows is pointing to a replication bubble.

 

With the nitrogenous bases of the template  strand exposed, the cell can now create a complementary DNA strand. As we learned above, the enzyme that does this is DNA polymerase (“G” below). DNA polymerase rides along the template strand. As new nucleotides form hydrogen bonds with their complements on the template strand, DNA polymerase catalyzes a sugar-phosphate bond between the new nucleotide and the previous one. 

6. Here’s What it Really Looks Like…

The process I described above is simplified model of some of the key events of DNA replication. But it’s actually much more complex. Watch this computer animation from the Howard Hughes Medical Institute. Unbelievably, the model below is also a simplified version of the process.

7. Prokaryotic v. Eukaryotic DNA Replication

Because of the different sizes and organization of the genomes of prokaryotic and eukaryotic organisms, there are differences in how DNA replication proceeds in these two groups of organisms.

We’ll start with DNA replication in bacteria. In the diagram below, “A” represents the parent cell, and 4 represents its DNA. The other parts shown are the cytoplasm at “3,” the membrane at “4,” and an outer capsule (found in many bacteria, at “1”).

Bacteria have a single, circular (or looped) chromosome (as shown in “1” below). Replication begins at an origin of replication, shown at “A” in diagram 1.  Helicases (at “D”) open up the helix, creating two replication forks (at “C”). DNA polymerases (at “B”) synthesize new strands of DNA.  “E” represents the ever-widening replication bubble.

When replication is complete we have two daughter strand, each a perfect copy of the parent strand at “1.”

In terms of DNA replication, eukaryotic DNA differs from prokaryotic way in two notable ways. First, eukaryotic DNA is organized into linear chromosomes. That means that rather than a circular loop of DNA, the chromosomes have a beginning and an end. The diagram below shows a chromosome in a fruit fly. Fruit flies are among the most studied organisms on Earth. This diagram shows some of the genes on this chromosome, and the distance between these genes.

 

Because eukaryotic chromosomes are linear (and much longer than bacterial chromosomes), replication involves multiple replication bubbles (shown at E below). In each replication bubble, there  will be helicases  (D) and polymerases (B) working away.

8. Quiz: DNA Replication (with some DNA structure review)

That’s all you need to know about DNA replication. Take the quiz below to consolidate your learning.

 

 

Links

This ends this high school level module on DNA structure and Replication. In most courses, you’ll move on to RNA, Transcription, and Translation (HS version), but check with your instructor first. You might also want to check out my DNA Replication Rap (a salsa-themed music video, with AP and College Level content).