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Genes Are DNA
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Ex Biochem c1-genes DNA
1.1 Introduction
Figure 1.2
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Ex Biochem c1-genes DNA
1.5 Polynucleotide Chains


Nitrogenous Bases 鹼基Linked to a Sugar–Phosphate
Backbone
A nucleoside consists of a purine or pyrimidine base
linked to position 1 of a pentose sugar.
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Ex Biochem c1-genes DNA
Transfection

DNA can enter
eukaryotic cells and
produce functional
proteins


Become part of the
genome
DNA can also be
introduced into eggs
by microinjection

Become part of the
genome
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Ex Biochem c1-genes DNA
Nucleic acid structure


Positions on the ribose ring are described with a prime (′) to
distinguish them.
The difference between DNA and RNA is in the group at the
2′ position of the sugar.

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A nucleotide consists of a nucleoside linked to a phosphate
group on either the 5′ or 3′ position of the (deoxy)ribose.
Successive (deoxy)ribose residues of a polynucleotide chain
are joined by a phosphate group


DNA has a deoxyribose sugar (2′–H)
RNA has a ribose sugar (2′–OH)
Between the 3′ position of one sugar and the 5′ position of the next
sugar
One end of the chain (left) has a free 5′ end

The other end has a free 3′ end
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Ex Biochem c1-genes DNA
Nucleosides

Nucleoside: a compound that consists of Dribose 核糖or 2-deoxy-D-ribose 去氧核糖
bonded to a nucleobase by a -N-glycosidic
bond
uracil
O
HN
-D-riboside
O
5'
H OCH2
4'
H
1
N
O
H
3'
H
2'
HO
OH
Uridine
a -N-glycosidic
bond
1'
H
anomeric
carbon
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Ex Biochem c1-genes DNA
Nucleotide

Nucleotide: a nucleoside in which a molecule
of phosphoric acid is esterified with an -OH
of the monosaccharide, most commonly
either the 3’-OH or the 5’-OH
N H2
N
O
-
5'
O
-
H
H
N
O
O-P- O-CH2
3'
H
1'
H
HO
OH
Adenos ine 5'-monophosphate
(5'-AMP)
N
N
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Ex Biochem c1-genes DNA
Nucleotides

Deoxythymidine 3’-monophosphate (3’dTMP)
O
CH3
HN
5'
HOCH2
O
O
H
H
H
3'
O
H
-
O P
O
-
O
N
1'
H
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Ex Biochem c1-genes DNA
DNA Structure
O
phosphorylated
5' end
CH3
HN
O
5'
O-P- O-CH2
O
H
H
O
O
O
O
H
1'
N
HN
H
2'
H
N
N
H 2N
5'
O= P
O
N
O
-
CH2
O
H 1'
H
H
free 3' end
3'
H
2'
OH
H
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Ex Biochem c1-genes DNA
Pyrimidine/Purine Bases
3
4
N
2
N
5
N
6
O
1
1
N
2
N
N
8
N
4
3
Purine
N9
H
N
N
O
H
Thymine (T)
(DNA and
some RNA)
H
Uracil (U)
(in RNA)
O
N
N
HN
N
N H2
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5
O
O
CH3
HN
H
Cytosine (C)
(DNA and
some RNA)
Pyrimidine
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O
N H2
N
H
Adenine (A)
(DNA and RNA)
N
HN
H 2N
N
N
H
Guanine (G)
(DNA and RNA)
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Ex Biochem c1-genes DNA
Other Bases

Several “unusual” bases occur, principally but
not exclusively, in transfer RNAs
H3 C
O
N
HN
N
N
H
Hypoxanthine
N
CH3
N H2
N
N
N
H
N 6 -Dimethyladenine
CH3
N
N
O
O
N
H
5-Methylcytosine
HN
O
N
H
5,6-Dihyrouracil
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Ex Biochem c1-genes DNA
Figure 1.07: A polynucleotide has a repeating structure.
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Ex Biochem c1-genes DNA
DNA Structure

Writing a DNA strand

an abbreviated notation
dA
dC
dG
OH
3'
P
5'
dT
P
3'
P
P
5'

even more abbreviated notations:
pdApdCpdGpdT, or pdACGT, or ACGT
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Ex Biochem c1-genes DNA
1.6 DNA Is a Double Helix

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The B-form of DNA is a double helix
consisting of two polynucleotide chains that
run antiparallel.
The nitrogenous bases of each chain are flat
purine or pyrimidine rings


They face inward
They pair with one another by hydrogen bonding
to form A-T or G-C pairs only
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Ex Biochem c1-genes DNA
Figure 1.08: The double helix has constant width.
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Ex Biochem c1-genes DNA
Figure 1.09: Flat base pairs connect the DNA strands.
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Ex Biochem c1-genes DNA

The diameter of the
double helix is 20 Å

There is a complete turn
every 34 Å

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Ten base pairs per turn
The double helix forms:


a major (wide) groove
a minor (narrow) groove
Figure 1.10
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Ex Biochem c1-genes DNA
DNA double helix
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1.7 DNA Replication Is
Semiconservative
Ex Biochem c1-genes DNA

The Meselson–Stahl experiment used density
labeling to prove that:

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The single polynucleotide strand is the unit of DNA
that is conserved during replication
Each strand of a DNA duplex acts as a template
模版 to synthesize a daughter strand.
Ex Biochem c1-genes DNA
DNA replication is semiconservative
Figure 1.11: Base pairing accounts for specificity of replication.
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Ex Biochem c1-genes DNA
Semiconservative Replication
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Ex Biochem c1-genes DNA
Enzymes

The enzymes that synthesize DNA are called DNA
polymerases (DNA聚合脢)

The enzymes that synthesize RNA are called RNA
polymerases

Nucleases are enzymes that degrade nucleic acids


They include DNAases and RNAases
They can be divided into endonucleases and
exonucleases.
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Ex Biochem c1-genes DNA
Figure 1.14: Endonucleases attack internal bonds.
Figure 1.15: Exonucleases nibble from the ends.
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Ex Biochem c1-genes DNA
1.9 Genetic Information Can Be
Provided by DNA or RNA

Cellular genes are DNA
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Figure 1.16
Viruses and viroids may have
genomes of RNA
DNA is converted into
RNA by transcription
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RNA may be converted into
DNA by reverse transcription
The translation of RNA into
protein is unidirectional.
Ex Biochem c1-genes DNA
Figure 1.18: Genomes vary greatly in size.
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Ex Biochem c1-genes DNA
1.10 Nucleic Acids
Hybridize by Base Pairing
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Heating causes the two strands of a DNA duplex to
separate.
The Tm is the midpoint of the temperature range for
denaturation.
Complementary single strands can renature when
the temperature is reduced.
Denaturation and renaturation/hybridization 雜交
can occur with the combinations:

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DNA–DNA
DNA–RNA
RNA–RNA
They can be intermolecular or intramolecular
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Ex Biochem c1-genes DNA
Figure 1.20: DNA can be denatured and renatured.
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1.11 Mutations Change the
Sequence of DNA
Ex Biochem c1-genes DNA

All mutations 突變
consist of changes in
the sequence of DNA.

Mutations may:


occur spontaneously
be induced by
mutagens
Figure 1.22
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Ex Biochem c1-genes DNA
1.12 Mutations May Affect Single
Base Pairs or Longer Sequences
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A point mutation changes a single base pair.
Point mutations can be caused by:
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the chemical conversion of one base into another
mistakes that occur during replication
Insertions are the most common type of
mutation

They result from the movement of transposable
elements
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Ex Biochem c1-genes DNA

Figure 1.23
A transition replaces a G-C base pair with an
A-T base pair or vice versa.
Figure 1.24
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Ex Biochem c1-genes DNA
1.13 The Effects of Mutations
Can Be Reversed

Forward mutations inactivate a gene


Back mutations (or revertants) reverse
their effects
Insertions can revert by deletion of
the inserted material
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Deletions cannot revert
Suppression occurs when a
mutation in a second gene bypasses
the effect of mutation in the first
gene.
Figure 1.25