KE0026 Biochemistry Labs

DNA modelling tutorial

Litterature: Stryer chapters 5 and 27; Horton et al. chapters 19 and 20 - 23
Materials: Push-fit molecular models from Nicholson, Labquip, England

Introduction
In today’s practical you will use the same standardized system as you used for the model building of peptides/proteins. The scale is still 1 cm = 1 Å (0.1 nm) and the interatomic distances are automatically set by the depth of the socket in each unit.

Model building
You are going to build a DNA model where you can study the configuration of the ribose ring and base pairing in detail. Each person gets a bag with units for one base pair.The ready-built base pairs will subsequently be connected to a DNA helix. To be able to do this it is important that you follow the instructions below EXACTLY.

The colour coding is as follows:

Atoms:
Carbon		white tetrahedrons (in the ribose-ring)
Carbon		grey tetrahedrons (as methyl groups)
Oxygen		red sphere - Note! different connection sizes
Phosphorus		red (yellow strip marked) tetrahedrons
Nitrogen		light blue
Bases:
Adenine		light green
Thymine		dark green
Uracil		dark green
Cytosine		purple
Guanine		light grey
Metal pins: are to be used as hydrogen bonds within a base pair

Start by building the deoxyribose rings after the scheme on the next page. You are supposed to make two identical deoxyribose units. (The structure of deoxyribose is shown in fig. 5.2 Stryer p 118; Horton page 600 fig. 19.1 shows the structure of a deoxyribonucleotide).

Build the bases independently and connect to each ribose.

Connect the bases with hydrogen-bonds, i.e. the metal-pins. (Stryer p. 122 fig. 5.12, p. 748 fig. 27.7; Horton p. 603 fig. 19.6, p. 608 fig. 19.12).

Time to connect all nucleotides from the group to a beautiful DNA helix. Think about the configuration of the ribose, the twist, the direction of the chains etc.

Read the bases of your DNA in triplets and translate to their corresponding amino acids. To make sure that you get directions correctly (3' or 5') you may look in Stryer p. 131 fig 5.26 (Horton p. 625 fig. 22.5) for information about the orientation of a gene and at Table 5.4 p.134 (Horton p. 657) for the genetic code.
Write the answer under question 7 below.

Building of the ribose-phosphate unit
material: 5 white tetrahedrons (one is cut), one oxygen with a narrow connection and one phosphate.

Start by connecting the oxygen at the 3' carbon (behind the plane of the paper) and continue to complete the ribose ring as shown in the figure.

It is important that the 5' carbon is connected to the bond above the plane of the paper as well as later also the base (see figure).

Questions to answer

Which type of bonds hold the following parts of the DNA molecule together:

the sugar-phosphate chain?
the base-pairs?

Study the differences between ribonucleotides and deoxyribonucleotides. Why is the DNA double helix built from the latter?

Which are the largest differences between A-, B- and Z-DNA (Stryer p. 746-750; Horton p 612-614)?

You have built the "most common" form of DNA, which?

Now some dimensions of this DNA:
How many base-pairs on one helix-turn?
How long is a helix-turn in Ångstrm (1Å = 10^-10m)?
What is the diameter of this form of DNA?

Where are the major and minor groves located?

What is a propeller-twist?

Write down the amino acid sequence that "your" DNA is coding for!

What is the difference between relaxed and supercoiled DNA and why is supercoiling important?

What functions do the histones have in eucaryotic cells?