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Lecture 3

by OC2

Biological Sciences
Course Code
Clare Hasenkampf

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BGYA01H Lecture 3 September 17, 2007
Please note- there was a slight mistake on the lecture schedule and relevant textbook readings. For
lectures 11 and 12, the relevant textbook chapter is Chapter 10.
Now I would like to begin our study of the last category of macromolecules, the nucleic acids.
There two types of nucleic acids are DNA and RNA.
Both DNA and RNA are examples of polymers. Therefore they are both made by adding monomer units
together via condensation reactions.
Nucleic acid polymers are very different in their characteristics from the polypeptides and complex
carbohydrates because they have different monomer units.
For both nucleic acids, the monomer starting units, are molecules called nucleotides.
Each nucleotide, is itself, made of three different chemical groups. Each nucleotide has
1) A 5-carbon, ring sugar (each carbon of the sugar molecule is numbered). Figure 3.14, page 50
Middle section)
2) a phosphate group, Figure 3.23, page 58.
3) and a nitrogen-containing molecule known as a nitrogenous base.
(Figure 3.23 is very diagrammatic and does not show what the phosphate groups and sugars really look
like. The purpose of this figure is to show how the components are connected.)
The nitrogenous base is attached to the first carbon of the sugar, and the phosphate is attached to the fifth
carbon of the sugar.
Please be aware that all of the bonds connecting the elements within the nucleotide are covalent
(strong) bonds.
The monomers for RNA and DNA are slightly different from each other, but they share many structural
features. (These similarities and differences are summarized in Table 3.3, page 459.
The monomer units for RNA are called ribonucleotides. Ribonucleotides each have the sugar ribose.
Each ribonucleotide has one of the 4 bases either adenine, uracil, guanine or cytosine. The last
component of the ribonucleotide is the phosphate group.
The monomer units for DNA are called deoxyribonucleotides. Deoxyribonucleotides consist of the
sugar deoxyribose. Each Deoxyribonucleotide has one of the 4 bases : adenine, thymine, guanine or
cytosine. The last component of the deoxyribonucleotide is the phosphate group.
In their active form deoxyribonucleotides and ribonucleotides occur as nucleotide triphosphates. There is
a lot of energy stored in the pyrophosphate bond. Figure 6.5, page 124

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We will mainly be looking at nucleotide triphosphates as the monomer units for making larger nucleic
acids. But guanine nucleotide triphosphates (GTP) and adenine nucleotide triphosphates are important
energy molecules in the cell. Often if enzymes need energy to make or break a covalent bond, it gets the
energy from ATP.
As I have already mentioned, RNA and DNA are both examples of polymers; so we can expect that the
monomer units of each will be put together by condensation reactions to make the polymers.
Let’s look at a small polymer of RNA Overhead of Figure 3.24, page 58, left side, page 47. Here we
can see what the sugar ribose looks like and can also see what the phosphate group’s structure is. The
individual ribonucleotides (the monomer units) of RNA are held together to form a polymer by covalent
bonds known as phosphodiester linkages.
All of the bonds holding the ribonucleotides together are strong, covalent bonds.
We call one polymer of RNA a strand of RNA.
If we look at a strand of RNA we can see it has a polarity(here polarity means the two ends of the
molecule are different). One end has a free phosphate group; this end is called the 5’ end (because the
phosphate comes off the 5th carbon). The other end is called the 3’ end; it has a free OH group (that
comes off the third carbon). This polarity is important.
Now let’s think about DNA.
DNA is the hereditary material for the cell.
p233-237 (left side) Figures 11.2, 11.3, 11.4 and 11.5 The experiments described under the general
heading “What is the evidence that the gene is DNA.”
The hereditary material must contain an organism’s plan for where and when it will synthesize its needed
proteins, carbohydrates and lipids, and in doing it is determining the structures within cells, the pattern of
growth of the organism and how the organism will cope with its environment; the plan will even need to
have details on when to make a copy of itself.
So The hereditary material must be able to be copied faithfully so that every time a cell divides into two
cells each cell gets a complete copy of the DNA. Also, as the hereditary material DNA must be able to
direct cellular activity (implement the plan).
So as we look at the structure of DNA be on the look out for how DNA’s structure can allow it to function
as the hereditary material.
Now let’s look at the structure of DNA. Overhead of Figure 3.24 right side, page 58. but a better figure
can be seen in Figure 11.9, page 240.
Two neighboring deoxyribonucleotides (the monomers) of a larger DNA molecule are held together by
phosphodiester bonds. Therefore all of the bonds holding together the polydeoxyribonucleotide (of a
single polymer) are strong bonds.
An individual polymer of DNA is also called a strand of DNA.

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If we look at a strand of DNA we can see it has a polarity. One end has a free phosphate group; this end
is called the 5’ end (because the phosphate comes off the 5th carbon). The other end is called the 3’ end;
it has a free OH group (that comes off the third carbon).
If we just look at a single strand of RNA and a single strand of DNA they are not very different.
But in cells there is a BIG difference, because in cells RNA occurs as single strands and DNA occurs as
double strands.
In nature, DNA is usually found as two polymers (also called two strands) held together to form a
structure we call the DNA double helix seen in Figure 11.9, page 240.
Having seen the polymers of DNA and RNA we can see the function of the phosphate groups, and of the
sugar group.
The phosphate groups of each nucleotide serve to link adjacent nucleotides together (via phosphodiester
The sugar molecules serve to connect the phosphate groups to the nitrogenous bases.
What is the function of the nitrogenous bases?
We will see that the nitrogenous bases are essential to DNA’s function as the hereditary material.
Why does DNA occur in cells in the double stranded state? What brings the two strands together?
Two polymers (strands) of DNA come together, as the nitrogenous bases of each strand form hydrogen
bonds, across the helix (the red dots represent hydrogen bonds).
We call the pairing up of nitrogenous bases via hydrogen bonds Base pairing.
Thus the function of the nitrogenous bases is to form hydrogen bonds with the nitrogenous bases of
another strand of DNA, and in doing so it promotes formation a double stranded structure.
In order for the hydrogen bonds to from across the helix, the two strands of the DNA must be oriented
antiparallel. This means that the free phosphate group is at the top of one strand, and at the bottom of the
other strand. Similarly the free OH group is at the bottom of one strand and is at the top of the other
strand. (Inspect figure 11.9 page 240 carefully).
Clicker question?
Why does DNA form a double stranded structure and RNA does not?
a) Only DNA nucleotides are capable of forming hydrogen bonds with another nucleotide
b) RNA molecules are not long enough to form enough hydrogen bonds to be stable
c) In cells proteins block RNA from forming hydrogen bonds
d) RNA molecules don’t regularly have a perfect partner.
The answer is d.
RNA’s ribonucleotides are very similar to DNA’s deoxyribonucleotides, such that RNA’s bases can form
fine base pairs. Often an RNA molecule can base pair with itself, to form a 3D shape Figure 3.25, page
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