Unit 10

DNA can rotate around these 6 bonds

Glycosidic bond

Th bond between the 4’ and 5’ carbons on the sugar

4 bonds in the phosphodiester bridge

The helix can be in what different conformations

Bent into an arc

Supercoiled

Wrapped around proteins

Kinked/bent at discrete sites

What does DNA’s ability to change conformations allow for

Allows for the DNA to fit in the cell as well as for proteins to target specific DNA sequences which can up regulate or down regulate receptor response elements

How the major and minor grooves arise

The glycosidic bond of the base pairs are not diametrically opposite of each other

Why is the major groove important

Because it is larger and more distinct, it is made available for forming bonds with proteins that recognize specific DNA sequences

Origin / ori

The point at which replication begins

Enzymes that degrade DNA

Nucleases or DNases

Exonucleases

Degrade nucleic acids from one end of the molecule

They are essential for DNA replication

Endonucleases

Degrades DNA at specific sites within the strand

DNA polymerase enzymes

Synthesize DNA

Template driven enzyme

Requires a primer

4 types

Primer

20 RNA bases (oglionucleotide) that is complimentary to DNA

Low fidelity

Transient and ultimately removed

Primer terminus

The free 3’ OH

Discrimination between correct and incorrect nucleotides depends upon these things

Complimentary pairing

Geometry of the standard AT GC pairing

The active site of DNA polymerase I only accommodates nucleotides in what conformation

In their proper geometry

If incorrect, it will not fit in the active site

All DNA polymerase contain this proof reading enzyme

Exonuclease running 3’ to 5’

(Hydrolysis)

How often proof reading enxonuclease removes a correct nucleotide

1 in 10

(Measure of vigilance)

Primary functions of DNA polymerase I exonuclease function

Remove the RNA primer

Correct errors/damage that are different from those corrected by the 3’-5’ exonuclease