Video Transcript
In this video, we’ll cover DNA
replication. We’ll first go over the basic
structure of DNA including the complementary base pairings. Then, we’ll describe the process of
semiconservative DNA replication and the role of the enzymes DNA helicase, DNA
polymerase, and DNA ligase. Finally, we’ll describe how errors
introduced in DNA replication can be corrected.
We all started out as a single cell
that divided into two cells, which then each divided to form four cells, which then
divided again to form eight cells. And this went on and on until
eventually we became us, made up of trillions of cells. Trillion is a really big
number. There’s 80,000 seconds in one day,
three million seconds in one year, and three trillion seconds is about 100,000
years. It’s pretty amazing that our cells
can divide in this way to produce such a massive number. And with each cell division, the
DNA inside the nucleus of these cells must be faithfully copied every time.
So before we get into how DNA can
be copied or replicated, let’s first go over the basic structure of DNA. DNA is made of two individual
strands that coil around each other to form a double-helix shape as we can see
here. The colored boxes within DNA are
known as nucleotides or base pairs. Let’s zoom in on this section of
DNA so we can get a closer look at the chemical structure. In black is the sugar–phosphate
backbone of DNA and is made up of a phosphate group and a deoxyribose sugar. The colored box are the different
nitrogenous bases. These three components make up a
nucleotide. And each strand of DNA is made up
of a polymer of these nucleotides.
So on this strand here, there’s
one, two, three nucleotides. Each nucleotide is joined by a
phosphodiester bond, which includes the carbon atoms on both sides of the phosphate
group. And the two strands are connected
by their nitrogenous bases to form base pairs. In DNA, there’s four kinds of
nitrogenous bases: guanine or G for short, cytosine, adenine, and thymine. These bases can pair with their
complementary base by forming hydrogen bonds with each other. These hydrogen bonds are what keeps
the two strands stuck together. Guanine always base-pairs with
cytosine with three hydrogen bonds, while adenine always base-pairs with thymine
with two hydrogen bonds.
Another important feature of DNA is
its directionality. One strand goes in this direction,
while the other strand goes in this direction. This is sometimes called
antiparallel. The direction of each strand is
defined by the position of the carbon atoms in the deoxyribose sugar. The carbon atoms are numbered one
prime to five prime as indicated here.
One strand is labeled the five
prime to three prime strand, which we can also see over here, while the opposing
strand goes in the opposite direction. We call this the three prime to
five prime strand but draw our arrow in the five prime to three prime direction
because that’s actually the direction that DNA is synthesized in as we’ll see. And if you look on the left, you
can see this labeled on the diagram here as well.
Now that we’ve looked at the
structure of DNA in some detail, let’s start talking about how DNA can be
replicated. So here’s a section of DNA that
needs to be replicated with the direction of these strands indicated. First, the DNA molecule needs to
unwind so the two strands can be separated so the different nitrogenous bases can be
accessed. To do this, a special enzyme called
DNA helicase unwinds or unzips the helix by breaking the hydrogen bonds between the
bases.
Now that the two strands are
separated, a structure called the replication fork is formed. We can also see the individual
bases here and here. We’re showing the letters for these
bases, so you can see how DNA synthesis will take place. Two new strands of DNA will be
synthesized using each of these original strands as a template.
Let’s first look at what happens on
the top strand that goes in the five prime to three prime direction. An enzyme called DNA polymerase
attaches and is the enzyme involved in DNA synthesis. The word polymerase refers to how
this enzyme can form polymers of nucleotides that will form the new strand of
DNA. Inside the nucleus of eukaryotic
cells, where DNA replication takes place, there are many free-floating nucleotides
that DNA polymerase can use to make a new strand of DNA. Each of these nucleotides are
indicated here with their sugar–phosphate backbone indicated in red to differentiate
it as the newly synthesized strand of DNA.
These nucleotides base-pair with a
complementary base, and DNA polymerase can link them together by catalyzing the
formation of phosphodiester bonds between them. DNA polymerase moves along the
strand while these nucleotides are added. If we look at the orientation of
the new strand, we can see that it’s three prime to five prime. However, if we picture it from the
perspective of DNA polymerase, we see that this enzyme is moving in the five prime
to three prime direction. This is an important point because
DNA polymerase can only add nucleotides to a newly synthesized DNA strand in the
five prime to three prime direction.
So now when we consider the
opposing strand in the three prime to five prime direction, DNA polymerase can’t
synthesize DNA like the top strand because from the perspective of DNA polymerase,
it would be moving in the three prime to five prime direction, which it cannot
do. So what it does is it still moves
in the five prime to three prime direction as we can see here, but the enzyme now
has to detach and bind to another section further along the strand. Here, another fragment can be
synthesized in the five prime to three prime direction just like that.
These fragments are called Okazaki
fragments. And in this example, the Okazaki
fragments are very small. In real life, they can be much
larger. In prokaryotes, they’re around
12,000 nucleotides long, while in eukaryotes, they’re about 200 nucleotides
long. So now we have these two Okazaki
fragments, and there’s a gap in between. This gap can be joined together
using another enzyme called DNA ligase. This enzyme can form a
phosphodiester bond between two fragments of DNA as we can see here. So that’s how DNA replication
happens. Because one strand is made
continuously without making these Okazaki fragments and then joining them, this
strand is called the leading strand, while the other strand is called the lagging
strand since it’s assembled in parts.
DNA replication moves along at a
continuous pace with DNA helicase unwinding the DNA ahead of it, while the DNA
polymerases behind it synthesize DNA. DNA replication happens very
quickly and adds about 50 nucleotides per second. Human cells contain billions of
nucleotides of DNA, so this would take an incredibly long time. The fact is that DNA replication
can happen all over a chromosome and form what are called replication bubbles. These replication bubbles can
expand from their origin until the DNA molecule is completely replicated.
And now we have two molecules of
DNA, both of which contain one strand from the original molecule shown in black and
a newly synthesized strand shown in red. Because of this, DNA replication is
said to be semiconservative. If DNA replication was
conservative, then we would see the original DNA molecule along with another
molecule containing both new strands of DNA. But this isn’t what happens because
DNA replication is semiconservative.
There’s a lot of nucleotides to be
added to make a new strand of DNA, so what happens if DNA polymerase makes a
mistake? These errors in replication can
introduce mutations in DNA. So if we have a molecule of DNA
being replicated, as shown here, and instead of adding guanine, which would be
correct, DNA polymerase incorrectly uses an adenine, then this newly synthesized DNA
strand will contain an error or a mutation in its DNA sequence. Sometimes, these mutations can be
in important regions of genes.
In the gene for hemoglobin, the
protein that carries oxygen in red blood cells, a single mutation of this gene can
result in sickle cell anemia. This causes the red blood cell to
change their shape to a sickle shape. People who have this mutation have
a version of hemoglobin in their red blood cells that doesn’t carry oxygen as
effectively, so they’re more likely to be anemic.
DNA polymerase makes one error
every 100,000 nucleotides, which would potentially introduce over 120,000 mutations
every time a cell divides. In order to prevent these mistakes
from happening, DNA polymerase has a special proofreading function. So as it’s synthesizing DNA, it can
detect if there is a mismatch and will remove the incorrect nucleotide. And now the correct nucleotide can
pair. This way, DNA replication errors
can be kept to a minimum.
Now let’s take a moment to try out
a practice question.
In the process of DNA
replication, what is the primary role of DNA helicase? (A) DNA helicase detects and
repairs any errors that are made by incorrect base pairings during DNA
replication. (B) DNA helicase breaks the
hydrogen bonds between base pairs, separating the two strands of DNA. (C) DNA helicase forms
phosphodiester bonds between nucleotides to form a strand of DNA. (D) DNA helicase adds
nucleotides to a growing DNA chain, synthesizing a strand of DNA complementary
to the template strand. Or (E) DNA helicase joins the
gaps in the backbone between newly formed DNA fragments.
This question is asking us what
the primary role of the enzyme DNA helicase is during DNA replication. To answer this, let’s first
clear the answer choices so we have more room to work with. In order for a cell to divide
and make a new cell, its DNA must first be copied or replicated to form a new
molecule of DNA. You’ll recall that DNA is a
double-stranded helix. These colored boxes that you
see are the different nucleotides that make up the DNA molecule.
Let’s zoom in here so we can
take a closer look. Here, we can see the two
strands of DNA. DNA is made up of repeating
subunits called nucleotides. Each nucleotide contains a
phosphate group, a deoxyribose sugar, and a nitrogenous base. In DNA, there’s four types of
nitrogenous bases: guanine, cytosine, adenine, and thymine. The sequence of these
nitrogenous bases along these strands of DNA can code for different genes. These bases form base pairs
because complementary bases can hydrogen-bond with each other. Guanine always pairs with
cytosine and forms three hydrogen bonds, while adenine always pairs with thymine
and forms two hydrogen bonds. These hydrogen bonds between
these bases are what hold these two strands of DNA together.
In order for DNA replication to
occur, these two strands need to be separated so the DNA can be copied. The enzyme that breaks these
hydrogen bonds and separates the two strands is called DNA helicase. Therefore, in the process of
DNA replication, the primary role of DNA helicase is to break the hydrogen bonds
between base pairs separating the two strands of DNA.
Now let’s go over the key points
that we covered in this video. DNA replication is the process of
making new copies of DNA from an original molecule of DNA. This process is made possible by
different enzymes, including DNA helicase to separate the two strands, DNA
polymerase to synthesize a new strand of DNA, and DNA ligase to join DNA fragments
together. DNA replication is
semiconservative, meaning that a new copy of DNA is made of one strand of the
original DNA and one strand of newly synthesized DNA. Errors in DNA replication can be
corrected by the proofreading function of DNA polymerase.
