dna structure/composition
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DNA Structure/Composition
TaryonoTaryonoFaculty of AgricultureFaculty of Agriculture
Gadjah Mada UniversityGadjah Mada University
Flow of Genetic Information
DNAReplication
RNATranscription
ProteinTranslation
DNADNA Discovery of the Discovery of the DNA double helixDNA double helix
A.A. 1950’s1950’s
B.B. Rosalind FranklinRosalind Franklin - X-ray photo of DNA.- X-ray photo of DNA.
C.C. Watson and CrickWatson and Crick - described the - described the DNA molecule from Franklin’s X-ray.DNA molecule from Franklin’s X-ray.
DNA is the Genetic Material DNA encodes all the information in the cellDNA encodes all the information in the cell The composition of the DNA is the same in all The composition of the DNA is the same in all
cells within an organismcells within an organism Variation among different cells is achieved Variation among different cells is achieved
by reading the DNA differentlyby reading the DNA differently DNA contains four bases that encode all the DNA contains four bases that encode all the
information to make a bacteria or a humaninformation to make a bacteria or a human In some viruses the genetic material is RNAIn some viruses the genetic material is RNA
How is Information Encoded in DNA?
DNA Consists of four kinds of DNA Consists of four kinds of bases (A,C,G,T) joined to a bases (A,C,G,T) joined to a sugar phosphate backbonesugar phosphate backbone
Bases carry the genetic Bases carry the genetic information while the information while the phosphate backbone is phosphate backbone is structuralstructural
Two complementary strands Two complementary strands of bases (C-G) and (A-T)of bases (C-G) and (A-T)
DNA is a Polymer of Deoxyribonucleotide Units
DEOXYRIBONUCLEOTIDE
DEOXY RIBO NUCLEOTIDE
Deoxyribonucleic Acid (DNA)Deoxyribonucleic Acid (DNA)
NucleotideNucleotide::1.1. Phosphate groupPhosphate group2.2. 5-carbon sugar5-carbon sugar3.3. Nitrogenous baseNitrogenous base
~2 nm wide~2 nm wide
DNA NucleotideDNA Nucleotide
OO=P-O O
PhosphatePhosphate GroupGroup
NNitrogenous baseNitrogenous base (A, G, C, or T)(A, G, C, or T)
CH2
O
C1C4
C3 C2
5
SugarSugar(deoxyribose)(deoxyribose)
DNA Double HelixDNA Double Helix
NitrogenousNitrogenousBase (A,T,G or C)Base (A,T,G or C)
““Rungs of ladder”Rungs of ladder”
““Legs of ladder”Legs of ladder”
Phosphate &Phosphate &Sugar BackboneSugar Backbone
DNA Double HelixDNA Double Helix
P
P
P
O
O
O
1
23
4
5
5
3
3
5
P
P
PO
O
O
1
2 3
4
5
5
3
5
3
G C
T A
Nitrogenous BasesNitrogenous Bases PURINESPURINES
1.1. Adenine (A)Adenine (A)
2.2. Guanine (G)Guanine (G)
PYRIMIDINESPYRIMIDINES3.3. Thymine (T)Thymine (T)
4.4. Cytosine (C)Cytosine (C)T or C
A or G
BASE-PAIRINGSBASE-PAIRINGSBaseBase # of # of
PurinesPurines PyrimidinesPyrimidines PairsPairs H-BondsH-BondsAdenine (A)Adenine (A) Thymine (T)Thymine (T) A = TA = T 2 2
Guanine (G)Guanine (G) Cytosine (C)Cytosine (C) C GC G 3 3
CG
3 H-bonds
BASE-PAIRINGSBASE-PAIRINGS
CG
H-bonds
T A
Chargaff’s RuleChargaff’s Rule AdenineAdenine must pair with must pair with ThymineThymine
GuanineGuanine must pair with must pair with CytosineCytosine
Their amounts in a given DNA molecule will be Their amounts in a given DNA molecule will be about the sameabout the same..
G CT A
Backbone Sugar MoleculesDeoxyribose (DNA) Ribose (RNA)
O
OH
HOH
H
H
H
HOCH2
HO
OH
OH
H
H
H
HOCH2
HO H
1´
2´3´
4´
5´1´
2´3´
4´
5´
Ribose= Five Carbon Sugar Molecule
Deoxy ribo nucleotide
The DNA Backbone is a Deoxyribose Polymer
Deoxyribose sugars are linked by Phosphodiester Bonds
OP OO
O-
H2C
O-
O-
OH
OH
H
H
HH
H2C
H2C
HH
H
H
OHH
O
OP OO
OOP
O HH
H
H
OHH
O
HO
5´
3´
5´
5´
3´
3´
2´
2´
2´
1´
1´
1´
5´-p 3´-OH
5´ 3´
5´
3´
5´
3´ 5´
3´OP OO
O-
H2C
O-
O-
OH
OH
H
H
HH
H2C
H2C
HH
H
H
OHH
O
OP OO
OOP
O HH
H
H
OHH
O
HO
5´
3´
5´
5´
3´
3´
2´
2´
2´
1´
1´
1´
OP OO
O-
H2C
O-
O-
OH
OH
H
H
HH
H2C
H2C
HH
H
H
OHH
O
OP OO
OOP
O HH
H
H
OHH
O
HO
5´
3´
5´
5´
3´
3´
2´
2´
2´
1´
1´
1´
Base
Base
Base
OP OO
O-
H2C
O-
O-
OH
OH
H
H
HH
H2C
H2C
HH
H
H
OHH
O
OP OO
OOP
O HH
H
H
OHH
O
HO
5´
3´
5´
5´
3´
3´
2´
2´
2´
1´
1´
1´
NCH
N
NHCN
NH2
O
H
HH
HO
HH
OCH2POO
POO
PO- O-O-
O-O
(dATP)
Deoxyadenosine 5´-triphosphateO
H
HH
HO
HH
NCH
N
NHCN
NH2
HOCH2
DeoxyRibonucleotide
DeoxyRibonucleoside Deoxyadenosine
DNA is Composed of Four Different Ribonucleotides
HN
CHNC
CNC
NCNH2
HHN
CHNC
CNC
NCO
H2N
H
NCC
CHN
C
OCH3
HO
HN
CC
CNC
HO
H
HNH2
Adenine Guanine
Thymine Cytosine
TwoPurines
TwoPyrimidines
9 9
1 1
5´
3´ 5´
3´
NCC
CNC
HO
HNH2
NCC
CHN
C
OCH3
HO
NCC
CHN
C
OCH3
HO
HO
OH
H
H
HHO
P OO
OOP
O
OH
H
H
HH
H2C
H2C
HH
H
H
HO
O-
O-
H2C
O-
OOP
O
T
C
T
A
G
A
Base Pairing Follows:Chargaff’s Rule:Chargaff’s Rule: DNA has equal numbers of thiamines DNA has equal numbers of thiamines
and adenines (A=T) and equal numbers and adenines (A=T) and equal numbers of guanines and cytosines (G=C)of guanines and cytosines (G=C)
Note that in each pair there is one purine and one pyrimidine
A-T G-C
Base Pairing Occurs Through Hydrogen Bonds
A-TG-C
=
G C
A T
Advantages of Double-Stranded Nature of DNA
Forms a stable structureForms a stable structure Hydrophobic bases stack on top of one Hydrophobic bases stack on top of one
another away from solventanother away from solvent Charged phosphate backbone is on the Charged phosphate backbone is on the
outside accessible to solventoutside accessible to solvent Each strand can serve as the template Each strand can serve as the template
For a new strand of DNA (replication)For a new strand of DNA (replication) For an RNA molecule (transcription)For an RNA molecule (transcription)
Double-stranded DNA Forms a Double Helix
Native DNA Forms a B-DNA Helix
Two strands wind about each Two strands wind about each other in a right-handed mannerother in a right-handed manner
Diameter: ~20ÅDiameter: ~20Å Bases per turn: 10 (~34Å)Bases per turn: 10 (~34Å) A major and a minor grooveA major and a minor groove
20Å
Major
Minor
DNA is Highly Packaged within the Cell If the DNA from a single human cell were stretched If the DNA from a single human cell were stretched
out end to end, it would be ~2 meters in lengthout end to end, it would be ~2 meters in length
Cell Nucleus5 x 10-8 M
DNA2 M
(magnified lots of times)
Mechanisms of Packaging Has to be Organized so that DNA can be Untangled for Replication and Has to be Organized so that DNA can be Untangled for Replication and
TranscriptionTranscription SupercoilingSupercoiling Wrapping around Proteins to Create ChromatinWrapping around Proteins to Create Chromatin
Enzymes that Modulate the Packaging of DNA are called TopoisomerasesEnzymes that Modulate the Packaging of DNA are called Topoisomerases
Supercoiling Most native DNA exists in a Most native DNA exists in a negativelynegatively
supercoiled statesupercoiled state This means that it is slightly unwound and it is a bit This means that it is slightly unwound and it is a bit
easier to pull the two strands aparteasier to pull the two strands apart
More supercoiling
Topoisomerases Modulate Supercoiling Topoisomerases act as Molecular ScissorsTopoisomerases act as Molecular Scissors
They can make a cut in the DNA and pass second They can make a cut in the DNA and pass second strand through that break to untangle the DNAstrand through that break to untangle the DNA
DNA is Coiled Around Histone Proteins DNA is wrapped DNA is wrapped
around abundant around abundant nuclear proteins nuclear proteins called called HistonesHistones
This forms a This forms a complex called a complex called a NucleosomeNucleosome
Histones are H1, Histones are H1, H2A, H2B, H3, H4H2A, H2B, H3, H4
DNA is Further Packaged
Take Home Message
DNA is a double helix composed of a sugar-DNA is a double helix composed of a sugar-phosphate backbone and base pairs (a polymer of phosphate backbone and base pairs (a polymer of deoxyribonucleotides)deoxyribonucleotides)
Composition/StructureComposition/Structure DNA is compacted to fit into the cell through:DNA is compacted to fit into the cell through:
SupercoilingSupercoiling Extensive interactions with proteinsExtensive interactions with proteins
These factors all contribute to how the DNA is ReadThese factors all contribute to how the DNA is Read
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