What is Semi-Log Graph paper…. And WHY do I need to know?

What is Semi-Log Graph paper…. And WHY do I need

to know?

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DNA can be cut, using RESTRICTION ENZYMES… into

segments of differing lengths.

After DNA is separated on an agarose gel by electrophoresis,

the migration of fragments of known size can be compared to

that of fragments of unknown size.

• Suppose we have digested DNA from two viruses ~ both with Hind III,

• And electrophoresed the DNA from both on an agarose gel

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• Electrophoresing the DNA on an agarose gel ~~ causes the migration of the fragments.

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• After running the gel ~ you measure the distance the DNA migrated.

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Table 1. Restriction enzyme analysis of λ and UPCFV DNA

λ Virus U.P. Cabin Fever Virus (UPCFV)

DNA Hind III digest DNA Hind III digest

Size (kb) Distance (mm) Size Distance (mm)migrated migrated

23.1 3 ? 5 9.42 14 ? 12 6.56 18.5 ? 15 4.36 23.5 ? 27 2.32 32. 2.03 34 0.56 50

In order to determine the sizes of the U.P. Cabin Fever Virus DNA, you will make a standard

curve for the known Lamda DNA

• YUK! This does not show a linear relationship between the fragment size and distance migrated… down towards the right side of the graph, it would be difficult to determine size…

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Size of fragment

Leng

th m

igra

ted

• A logarithmic graph, basically takes an EXPONENTIAL graph and changes it to a LINEAR one … but using funky graph paper & by using the log function. (log function is the inverse of an exponential function)

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Size of fragment

Leng

th m

igra

ted

• When a curve is not straight.. It can be made straight with logarithms.

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migration

Log

of f

ragm

ent

leng

th

Scientists use logarithmic graph paper to manage

large amounts of data easily

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• And when you are talking kilo base pairs…. And DNA….

You are discussing a

LARGE amount of data

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See the funky graph paper?The axis with

the logarithmic info runs in

cycles…

The cycles differ by a factor of 10

btw, this is an example of 6 cycle graph paper

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See the funky graph paper?

One of the virtues of

semi-logarithmi

c plots is their

ability to show a

very wide range of

values.