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I
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The sequence is always read and written in the 5’ to 3’ direction and in terms of genetic
information, this corresponds to the “N terminal to C terminal” in proteins
3’ to 5’ phosphodiester
bridges link nucleotides
together in order to form
these polynucleotide
chains

5’ end
Nitrogenous
Base

Nucleoside

Nucleotide

Adding deoxyribose
nucleoside 5’triphosphate to the
growing strand

Sugar

3’ end
••

A
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DNA contains 2’-deoxyribose

The presence of the OH at the 2’ position makes RNA susceptible to alkaline hydrolysis

A nucleophile such as OH- can abstract the H of the 2'–OH, producing 2'–O– which
attacks the δ+ Phosphate of the phosphodiester bridge:

Garrett, R
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M
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Biochemistry
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Belmont, CA: Brooks/Cole Cengage Learning, p
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2
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This is because cytosine has the
ability to spontaneously deaminate to form uracil

DNA is composed of two strands where the cytosine of the one strand pairs with the
guanine of the second strand
...

If cytosine were to spontaneously deaminate and form uracil, it could cause a heritable
change from a C:G pair to a U:A pair, resulting in a mutation
...
and Grisham, C
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(2010)
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4th
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307
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These repair
enzymes need to be able to distinguish naturally occurring uracil from mutant uracil
...
There are different classes of nucleic acids
DNA – there is one type with one purpose
RNA – there are 3 types (that will be spoken about, there are additional ones) and 3
purposes
- Ribosomal RNA (rRNA) – basis of structure and function of ribosomes
- Messenger RNA (mRNA) – transports the message
- Transfer RNA (tRNA) – carries the amino acids

B
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Ribosomal RNA (rRNA)
Ribosomes synthesise proteins -they are ~ 2/3 RNA and 1/3 protein
All ribosomes are composed of a large and a small subunit
a
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Structural and catalytic functions
rRNA provides a scaffold for ribosomal proteins
-

23s rRNA in E
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Secondary Structure
There is high intrastrand sequence complementarity (intra – within the strand as
opposed to between two strands) which leads to extensive base pairing
Secondary structural features tend to be conserved, however the sequence does not
appear to be
Therefore, there must be common designs and functions that are conserved
2
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General
Several bases are generally methylated
Each amino acid has at least one unique tRNA that will carry the amino acid to the
ribosome
The 3’-terminal sequence is always CCA – linked to an amino acid residue
Aminoacyl tRNA molecules constitute the substrates of protein synthesis

b
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Three of which are capped by loops and the fourth by a stem
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Messenger RNA (mRNA)
mRNA is the transcription products of DNA
a
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Eukaryotes – a single mRNA will code for only one protein
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Complementarity of base pairing
Base composition of DNA – purines will bind with pyrimidines (A:T and G:C)
Chargaff’s rule: the total number of purines in DNA will be equal to the total number of
pyrimidines
1
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These have nearly identical
dimensions overall
Two hydrogen bonds occur between A and T
Three hydrogen bonds occur between G and C
-

DNA regions that are rich in G:C are more stable

2
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The double helical structure of DNA is a stable structure
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Hydrogen bonds occur between the complimentary bases and between the sugarphosphate backbone and H2O

ii
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These negative phosphate groups also interact with Mg2+

iii
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The helix is anti-parallel – one strand runs 5’-3’ and the other strand runs 3’-5’
5’

5’

3’

3’

c
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Major and Minor grooves
As we draw the bases – the tops line the “floor” of the major groove
...

The

∗ above corresponds to the major groove, therefore the underside is the minor

groove
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D
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B DNA: common conformation
This is a right handed helical structure that is longer and thinner
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4nm

2
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There are 11 bp per turn with a pitch of 2
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Z DNA: G-C rich sequence
This is a left handed helix that is elongated and slim
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56nm

a
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G will be in the syn
conformation whereas C remains in the anti conformation
i
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This is because guanine is in the
syn conformation (G has flipped)
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ii
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iii
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The effects of intercalating agents on DNA structure
Flat hydrophobic molecules composed of fused heterocyclic rings called aromatic
macrocycles are able to slip between the stacked base pairs of DNA
This forces the bases apart in order to accommodate these intercalating agents resulting
in the unwinding of the helix to form a more ladder like structure
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Intercalating agents include
i
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Acridine orange

iii
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Secondary Structure of DNA – denaturation and renaturation
The UV absorbance of DNA can be increased by 30 – 40% by heating to greater than
80°
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Keeping in mind the pKa values – note that NDA can also be denatured using an alkali
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Melting curves of DNA
In the native state, the stacked base pairs of DNA absorb less light
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Reducing the
temperature results in a decrease in absorbance
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The melting temperature (Tm) of DNA is equal to the half maximum temperature
and is when half the DNA is denatured
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Therefore, an organism
(indicated by the coloured lines above) with a lower content of G:C base pairs will
have a lower melting temperature as half the DNA will be denatured at a lower
temperature
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Tertiary structure
i
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The bacterial
chromosome is circular

d
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Therefore, DNA is compressed over 100 000 times
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Nucleosome structure
Chromatin is the nucleoprotein complex which consists of both histone and
nonhistone proteins

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