Bonding in DNA and RNA.mp4


Our hereditary information is carried in large
molecules called deoxyribonucleic acid, or DNA. Just like all other molecules, DNA is
governed by the laws of chemistry. In the Foundations II tutorial, we explored bonding,
and we can apply these principles to better understand the structure of DNA. Take a look at DNA (show zoomed out image
of DNA). This image shows two DNA molecules, that have come together to form a double-stranded
structure. Each strand, which is a molecule of DNA, is a polymer of nucleotides (zoom
in to show stacked nucleotides). A polymer is a molecule made up of repeating units,
called monomers, that are covalently bonded together. The repeating units of DNA are nucleotides,
and they’re shown here. Each nucleotide is made up of a phosphate group, a deoxyribose
sugar, and a nitrogenous base, all covalently bonded together (point to each as they’re
mentioned). So in a sense, DNA is a series of stacked nucleotides. When the two DNA molecules
come together to form the double-stranded structure, the stacked nucleotides of each
strand look like this. Another way to think about DNA is as a backbone
(highlight backbone) made up of alternating phosphate and deoxyribose sugars, with nitrogenous
bases (highlight nitrogenous bases) sticking out from that backbone. In this tutorial,
we’ll start by reviewing the chemistry of the backbone, and then we’ll take a look
at the chemistry of the nitrogenous bases. Here’s a close-up of deoxyribose. Here,
all the bonds are drawn in, but remember from the last tutorial that a simplified drawing
of deoxyribose looks like this. Notice all of the carbon-oxygen bonds in deoxyribose.
Oxygen is more electronegative than carbon, so the bonds between carbon and oxygen are
polar covalent bonds. Deoxyribose has 5 carbon atoms, and we label them from 1’ to 5’
like this. Biologists often refer to this labeling when talking about DNA. Deoxyribose
is very similar to a different sugar called ribose, which we’ll come to later when we
talk about RNA. The only difference between ribose and deoxyribose is that deoxyribose
is missing an –OH group at the 2’ carbon. This is how deoxyribose gets its name – it’s
a deoxygenated version of ribose. Here’s a close-up of phosphate. The oxygen
atoms are covalently bonded to the phosphorus atom, but notice that the oxygen atoms are
negatively charged. This is because there was electron transfer between the oxygen atom
and two hydrogen atoms, but the hydrogen atoms dissociated into the watery environment of
the cell, leaving the negatively charged oxygen atoms of phosphate. The backbone of DNA is made up of alternating
deoxyribose and phosphate, covalently bonded together. Two oxygen atoms from each phosphate
are each linked to a deoxyribose sugar, and each deoxyribose sugar is linked to two phosphate
groups, one at the 3’ carbon and one at the 5’ carbon of deoxyribose. These bonds
that join deoxyribose and phosphate are polar covalent bonds, and they are called phosphodiester
bonds. We use the numbering of deoxyribose to label the two ends of a DNA strand. The
end with a 5’ carbon bound only to phosphate is the 5’ end, and the end with a 3’ carbon
bound to the OH of deoxyribose is the 3’ end. Now, let’s think about the nitrogenous bases
that project off of this backbone. The sequence of these nitrogenous bases is really important,
because this is what encodes your genes. In DNA, there are four different nitrogenous
bases: thymine, cytosine, adenine, and guanine, which are usually abbreviated T, C, A, and
G. These bases are divided into two categories: the pyrimidines and the purines. Pyrimidines
are made of one chemical ring, or atoms that are covalently bonded into the shape of a
ring. Thymine and cytosine are pyrimidines. Purines are made of two chemical rings, and
adenine and guanine are purines. All of the nitrogenous bases have some polar covalent
bonds, forming some partially negative and some partially positive atoms. Here, I’ve
drawn the partially negative atoms in blue, and the partially positive atoms in red. Remember
that these partial charges are formed because of electronegativity differences between the
atoms forming the polar covalent bond. Nitrogenous bases are covalently bonded to
the 1’ carbon of deoxyribose. Here’s a deoxyribose sugar, and here is the 1’ carbon.
Take away H’s on nitrogenous bases and reveal bonds to 1’ carbon of deoxyribose, attached
to phosphate on other side. The covalent bond between deoxyribose and a nitrogenous base
is formed through a condensation reaction. A condensation reaction is the joining of
two molecules and the loss of a small molecule, in this case water. These atoms leave as water,
and a covalent bond is formed between the 1’ carbon of deoxyribose and this nitrogen
of thymine. A similar reaction occurs to join the other nitrogenous bases with deoxyribose.
We’ll see many more examples of condensation reactions when we study metabolism. The bond
between deoxyribose and a nitrogenous base is called a glycosidic bond, and it was formed
through a condensation reaction. Let’s connect this to the structure of the
backbone that we just looked at. Here’s what we drew for the backbone: We know that nitrogenous bases are bonded
to the 1’ carbon of deoxyribose. I’ve chosen arbitrary bases, and here’s what
a segment of a DNA strand could look like: So far, we’ve looked at the structure of
one strand of DNA, which is one molecule of DNA. But a property of DNA is that it is double-stranded.
The interaction of two DNA strands all comes down to the nitrogenous bases. Here’s part
of the backbone of a second strand of DNA. The nitrogenous bases on this strand determine
whether or not it can interact with the strand we’ve already drawn. There are two major
factors that determine how the strands interact: size compatibility and hydrogen bonding. Let’s talk about size compatibility, going
back to see the structures of the nitrogenous bases drawn above. We talked about how purines
are made of two rings and pyrimidines are made of one, and you can see from the structures
of the nitrogenous bases that this makes purines and pyrimidines very different in size. In
order for these two strands to fit together without bulges or spaces, a large nitrogenous
base must interact with a small one. So a purine must pair with a pyrimidine. But these interactions are very specific.
Guanine doesn’t pair with thymine, it only pairs with cytosine; and in DNA thymine specifically
interacts with adenine. The reason for this specificity is hydrogen bonding. Drawing in these complementary base pairs,
we see that the second strand of DNA looks like this. Here’s how these bases interact
to bring the two strands together. Hydrogen bonds are formed between adenine and thymine,
and hydrogen bonds are formed between guanine and cytosine. Maximum hydrogen bonding only
occurs between thymine and adenine, and between guanine and cytosine, and this explains the
base pairing specificity. Notice that three hydrogen bonds are formed
between G and C, while only two hydrogen bonds are formed between A and T. There’s more
attraction holding G and C together, so that base pairing is slightly stronger between
G and C than between A and T. When two DNA strands come together to form
double stranded DNA, the strands are antiparallel. In other words, they run in opposite directions.
This DNA strand is from 5’ to 3’ in this direction, and the complementary DNA strand
is from 5’ to 3’ in the other direction. Remember that hydrogen bonds are much weaker
than covalent bonds. While each hydrogen bond is weak, along the entire length of two DNA
strands, these weak hydrogen bonds add up to a lot, and they’re very effective at
holding the strands together. This cumulative effect has huge implications for DNA replication
and transcription. A strand of DNA pairs only with its complementary strand, because of
base pair specificity that comes from size and hydrogen bonding. And the cumulative strength
of all the hydrogen bonds together keeps the two strands in the same part of the cell.
But when the strand needs to be replicated, it isn’t difficult to break any individual
hydrogen bond to open up the strands at the replication fork, because each individual
hydrogen bond is weak. The overall structure of DNA is a double helix.
It’s double, because two strands of DNA come together via base pairing. It’s also
helical, which means that the two strands twist around each other. This allows the base
pairs to interact maximally. RNA: RNA behaves very similarly to DNA. RNA is
also a polymer of nucleotides, and it also has backbone with nitrogenous bases projecting
off of it. There are three major differences between DNA and RNA. The first is that RNA
has ribose as a sugar instead of deoxyribose. We saw at the beginning of the tutorial that
the difference between ribose and deoxyribose is the –OH group bonded to the 2’ carbon.
In RNA, this OH prevents really tight formation of the double helix. Which brings us to the
second difference between DNA and RNA. Because of this OH group that prevents tight formation
of the double helix, RNA is generally single-stranded. The third difference is that RNA uses uracil
as a nitrogenous base instead of thymine. Here are the nitrogenous bases of DNA. In
RNA, adenine, guanine, and cytosine are exactly the same. But instead of thymine, RNA uses
uracil. Here’s what uracil looks like. The only difference between uracil and thymine
is a CH3 that’s bonded to thymine is not there in uracil. Take a look again – here’s
thymine, with that CH3 group; and here’s uracil, without it. Here’s a summary of the three major differences
between DNA and RNA. DNA has deoxyribose, while RNA has ribose; DNA is double stranded,
while RNA is often single-stranded; and DNA has thymine, while RNA has uracil.

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