VGEC: Student Notes
DNA Structure Tutorial
Intended learning outcomes

To be able to recognise the structural elements of DNA at the molecular level: base pairs, sugarphosphate backbone and double helix.

To understand the base-pairing rules, and be able to recognise the purine and pyrimidine bases.

To be able to identify the nucleotide sequence of a given DNA section (say, 10 or 20 nucleotides) and
replicate the sequence using a mini-model.
A Examining the large DNA model
Work in pairs or groups of 3.

Carbon = black

Oxygen = red

Nitrogen = blue

Hydrogen = white

Phosphorus = purple
Look at the display DNA molecular model and think about its scale. A section of double-stranded DNA of
about 10 base pairs (bp) is approximately 3.4 nm long in its helical form. The DNA model you are looking at
is either 10 base pairs or 20 base pairs in length.
The Guinness World Record DNA display model (using the same modelling system) is 300 base pairs long
and measures approximately 13.5 m!
1
What is the scale of the Molymod DNA model?
2
The haploid human genome contains approximately 3000 million base pairs. Approximately how
long would all DNA from one cell be? How many Molymod DNA models would that represent per
human cell? (Remember that a diploid human cell contains two copies of the haploid genome.)
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
1
Now look closely at the DNA model and identify areas that are similar and areas that are different. DNA is
often described as a ‘twisted rope-ladder’. The inner core of the double helix has atomic structures that are
flat, and these represent the bases (the steps of the ladder). The twisted outer backbones (the ropes of the
ladder) are formed by sugar-phosphate groups.
Familiarise yourself with the helixes of the DNA model and make sure you are aware that DNA is indeed a
double helix!
3
How many bases are there per helical turn?
Note the presence of a ‘major groove’ and a ‘minor groove’ (easier to see in a longer model).
4
Which groove do you think is used most often for DNA–protein binding?
Figure 1 shows the chemical structures of the four DNA building blocks: guanine (G), adenine (A), thymine
(T) and cytosine (C). Remember, guanine pairs with cytosine (G–C) and adenine pairs with thymine (A–T).

The pyrimidines, thymine and cytosine, have one identical 6-ring structure with different side chains.

The larger purines, guanine and adenine, have two-ring structures, an interlinked 5-ring and 6-ring.
Figure 1
Each pyrimidine pairs up with a purine, forming hydrogen bonds (depicted by the dotted lines in the
chemical structure).
5
Which base pair is formed using three hydrogen bonds? Which base pair is formed using two
hydrogen bonds? Identify the four bases in Figure 1.
You have been given four colour pictures (Figure 2). Use the colour coding for the Molymod DNA models to
determine which base is shown in each picture. Mark where the hydrogen bonds will be formed during base
pairing.
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
2
Figure 2
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
3
Figure 2
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
4
Each group has been given a model of a ‘nucleotide’, which is made up of three components: a base, a
deoxyribose and a phosphate group.
6
Which base have you been given?
Look at the sugar component and note that it is a 5-ring, a 5-carbon sugar. Carbon C1 is connected to the
base and C5 has a phosphate group connected to it. The oxygen has been removed from the C2 carbon (a
hydrogen instead of an OH-group as expected in sugars), hence ‘de-oxy’.
(Note: DNA = Deoxyribo Nucleic Acid.)
Figure 3
Which carbon is covalently linked to the phosphate group of its neighbouring nucleotide? The neighbouring
nucleotide is either ‘one level down’ or ‘one level up’, depending on which DNA strand you are looking at
(look at the Molymod model).
Every single stranded DNA molecule is directional, having a 5’ end with a free phosphate group and a 3’end
with a free OH-group. By convention a given DNA sequence written as a single line of letters is 5’ to 3’. The
two strands of a DNA double helix are anti-parallel, one strand ascending and one strand descending (as
you should have just noticed).
Find the 5’ and 3’ ends of both strands in the Molymod model. Now write down the DNA sequence of 10
base pairs, including the 5’ to 3’direction (you will be told which 10 base pairs).
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
5
B
Building a mini-DNA model
Each group has been given a mini-DNA model, which has the following components:

the four DNA bases (blue, green, orange and yellow)

sugar groups (red)

phosphate groups (purple)

spacers (clear)

a stand.
The pegs that connect the bases indicate the hydrogen bonds (green to yellow – three pegs / blue to orange
– two pegs). Use this information and the information concerning the size of purines and pyrimidines to
determine which colour represents which base.
Look at the sugar group and the diagram below. Build nucleotides by connecting a phosphate group to the
C5-peg and then insert the C1-connector of the sugar–phosphate to each base.
Compare this to the nucleotide model you have been given.
Now rebuild a replica of the 10 or 20 base pairs of the molecular model you have examined, in an identical
orientation and sequence, using the miniDNA model.
Get your model checked by a tutor.
Virtual Genetics Education Centre: http://www.le.ac.uk/ge/genie/vgec/
6