Download (a) DNA and

Reference:
DNA Structure
DNA and Its Structure
• From 1953
Discovering the structure of DNA
• Structure was discovered in 1953 by James
Watson and Francis Crick
Discovering the structure of DNA
Rosalind Franklin’s DNA image
“Chargoff’s rule”
A=T & C=G
•DNA and RNA are nucleic acids
•An important macromolecule in
organisms that stores and carries genetic
information
What is the Double Helix?
•Shape of DNA
•Looks like a twisted
ladder
•2 coils are twisted
around each other
•Double means 2
•Helix means coil
The Structure of DNA
• Made out of nucleotides
•Includes a phosphate group,
nitrogenous base and 5-carbon
pentose sugar
Nucleotide
Structure
1
“link”
in a
DNA
chain
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Bases
Phosphate group
Sugars
Purines
(double ring)
NH2
5′
HOCH2
H
O
H
H
P
H
5
7
H
6
N
9
4
O
CH3
1N
8
H
HO
O
N
2′
3′
O
OH
1′
4′
O–
Pyrimidines
(single ring)
5
2
6
3
H
N
O–
1′
4′
H
H
3′
HO
N
OH
O
H
H
2′
OH
D-Ribose (in RNA)
6
5
7
H
8
N
9
2
6
O
4
NH 2
H
1N
H
5
2
3
N
H
6
NH2
H
4
1
3N
2
N
H
Guanine (G)
H
4
1
N
3N
2
O
H
Thymine (T) (in DNA)
O
HOCH2
5
H
Adenine (A)
5′
1
H
3N
N
H
D-Deoxyribose (in DNA)
4
O
Cytosine (C)
O
Uracil (U) (in RNA)

These atoms are found within individual nucleotides

However, they are removed when nucleotides join together to make
strands of DNA or RNA
A, G, C or T
A, G, C or U
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
O P
O
Base
O
O–
Phosphate
CH2
5′
4′
H
O
O
1′
H
3′
H
H
2′
OH
H
Deoxyribose
(a) Repeating unit of
deoxyribonucleic
acid (DNA)
P
Base
O
O–
Phosphate
CH2
5′
4′
H
O
H
3′
H
1′
H
2′
OH
OH
Ribose
(b) Repeating unit of
ribonucleic acid (RNA)
The structure of nucleotides found in (a) DNA and (b) RNA
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Adenosine triphosphate
Adenosine diphosphate
Adenosine monophosphate
Adenosine
Adenine
Phosphoester bond
NH2
N
N
H
O
–O
P
O–
O
O
P
O
O
O–
P
N
O
O–
CH2
5′
4′
Phosphate groups
O
H
H
H
3
1′
H
Base always
attached here
2′
HO
Phosphates are
attached here
N
OH
Ribose
12
A Polynucleotide
• MANY
nucleotides
(“links”)
bonded
together
DNA has a
overall
negative
charge b/c
of the PO4-3
(phosphate
group)
The Structure of DNA
Backbone = alternating P’s and sugar
•Held together by COVALENT bonds
(strong)
•Inside of DNA molecule = nitrogen
base pairs
•Held together by HYDROGEN
bonds (weaker)
Backbone
• Phosphodiester
Bond
–The covalent that
holds together the
backbone
–Found between P
& deoxyribose
sugar
–STRONG!!!
Minor
Groove
Major
Groove
DNA is antiparallel
• Antiparallel means that the 1st
strand runs in a 5’ 3’
direction and the 2nd 3’ 5’
direction
– THEY RUN IN
OPPOSITE or
ANTIPARALLEL
DIRECTIONS
• P end is 5’ end (think: “fa” sound)
• -OH on deoxyribose sugar is 3’
end
– 5’ and 3’ refers to the carbon # on
the pentose sugar that P or OH is
attached to
DNA Double Helix
10.4 nucleutides/turn; 3.4 nm between nucleutides
2 nm
Key Features
5 P 3
S P
P
A S
• Two strands of DNA form a
right-handed double helix.
• The bases in opposite strands
hydrogen bond according to the
AT/GC rule.
• The 2 strands are antiparallel with
regard to their 5′ to 3′ directionality.
P
S
G
G
S
S
P
C
C
O P O
C
O P
P
S
P
A
T
P
S
G
C
S
P
3
-
NH2
CH2
C
H
H N
N
O
H
-
O
P
H
H
O
O
H
T
H
N
H2N
N
H
S
5
H H
N
A
N
H H
H
-
O
O
H
H
H
CH2 O P O
O
N
H
S
O P
-
O
O
H
G
O
H
H
N
H
H
H2N
N
CH2
N H
N
NH2
O
C
H
H
N
OH
H
H H
H
H
O
-
O
CH2 O P
O
3 end
P
O
H
One nucleotide
0.34 nm
S
-
CH2 O P
CH3
O
P S
O
O
O
P
P
H H
H
H
H
CH2
O
N
G
H2N
N
O P
H H
N
O
G S
C
G
-
CH2 O P
N
N
O
O
S
A
S
H
O
H
C P
P S
PS
P
S C
O
O
H
H
O
H
G
C
T
G
O
H
H H
H
O
H
S
S
S
N
N
HO
N
H
O
S
P S
P
H
A
O
P
P
One complete
turn 3.4 nm
N
O
H
T
A
P
G
S
P
S
-
CH2
T
NH2
H
H
G
P
O
N
H
H
P S
P
S P
S
A
T S
S
3 end
H
CH3
O
S
P
5 end
P
C
P S
S
• There are ~10.0 nucleotides in each
strand per complete 360° turn of
the helix.
S
P
5 end
-
O
C
Nucleotides
A
TC
G
C
AA
TC
G
C
AA
TC
G
A A T
C
Single strand
C
G
C A
T GT
T A
A
G T
A C
GA
T
C A
T GT
T A
A
G
Double helix
Three-dimensional structure
20
Why Does a Purine Always
Bind with A Pyrimidine?
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Backbone
Bases
5′
O
H
H
N
Uracil (U)
O–
O
P
O–
O
5′
4′
CH2
H
H
O
N
O
1′
H
2′
OH
H
H
3′
NH2
N
Phosphodiester
linkage
N
Adenine (A)
H
N
O
O
P
O–
O
5′
4′
CH2
H
1′
H
2′
OH
H
H
NH2
H
N
H
O
P
O
N
O
3′
O
H
O
–
5′
4′
CH2
O
N
O
H
H
Cytosine (C)
H
1′
H
Guanine
(G)
2′
OH
3′
O
H
N
N
H
N
O
RNA
nucleotide
O
P
O
5′
4′
–
O
Phosphate
CH2
H
O
H
3′
OH
Sugar (ribose)
3′
H
1′
H
2′
OH
N
NH2
A typical mitotic chromosome at
metaphase
SEM of a region near one
end of a typical mitotic
chromosome
Three important DNA sequences
Telomere, replication origin, centromere
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Radial loops
(300 nm in diameter)
Metaphase
chromosome
30 nm fiber
Nucleosomes
(11 nm in diameter)
DNA
(2 nm in diameter)
Histone
protein
Each chromatid
(700 nm in diameter)
DNA wound
around histone
proteins
Banding Pattern of
human chromosomes
Giemsa Staining
Green line regions:
centromeres
Encoding ribosome
DNA Molecules are highly condensed in chromosomes
Nucleosomes of interphase under electron microscope
Nucleosome: basic level of chromosome/chromatin organization
Chromatin: protein-DNA complex
Histone: DNA binding protein
A: diameter 30 nm; B: further unfolding, beads on a string conformation
Nucleosome Structures
Histone octamer
2 H2A
2 H2B
2 H3
2 H4
X-ray diffraction analyses of crystals
Structure of a nucleosome core particle
Chromatin Packing
Condensin plays important roles
The function of Histone H1
The function of
Histone tails
Histone Modification
Covalent Modification
of core histone tails
Acetylation of lysines
Mythylation of lysines
Phosphorylation of
serines
Histone acetyl
transferase (HAT)
Histone deacetylase
(HDAC)
Histone Modification
Speculative Model for the heterochromatin at the ends of yeast
chromosomes
Sir: Silent information regulator binding to unacetylated histone tails
DNA Replication
• DNA Replication =
DNA  DNA
– Parent DNA makes
2 exact copies of
DNA
– Why??
• Occurs in Cell
Cycle before
MITOSIS so
each new cell
can have its
own FULL copy
of DNA
Models of DNA Replication
DNA Replication
•
How does it occur?
•
Matthew Meselson & Frank Stahl
–
Discovered replication is semiconservative
–
PROCEDURE  varying densities of radioactive nitrogen (Nitrogen is in DNA)
DNA
DNA Replication: a closer look
Breaks the hydrogen
bonds between the
two strands
Keep the parental
strands apart
Alleviates
supercoiling
Synthesizes an
RNA primer
DNA polymerases cannot
initiate DNA synthesis
Problem is overcome by
the RNA primers
synthesized by primase
Problem is overcome by
synthesizing the 3’ to 5’
strands in small fragments
DNA polymerases can
attach nucleotides only in
the 5’ to 3’ direction
Unusual features of DNA polymerase function
Breaks the hydrogen
bonds between the
two strands
Keep the parental
strands apart
Synthesizes daughter
DNA strands
III
Alleviates
supercoiling
Covalently links DNA
fragments together
Synthesizes an
RNA primer
DNA Replication Complexes
Protein Synthesis
• Protein synthesis occurs in two primary steps
1
2
Protein Synthesis
• Transcription
Initiation
1) INITIATION
 RNA polymerase binds to a
region on DNA known as the
promoter, which signals the
start of a gene
 Promoters are specific to genes
 RNA polymerase does not need
a primer
 Transcription factors assemble
at the promoter forming a
transcription initiation complex
– activator proteins help stabilize
the complex
 Gene expression can be regulated (turned
on/off or up/down) by controlling the amount
of each transcription factor
(eukaryotes)
Protein Synthesis
• Transcription
Elongation
1) INITIATION
 RNA polymerase unwinds
the DNA and breaks the
H-bonds between the bases
of the two strands, separating
them from one another
 Base pairing occurs between
incoming RNA nucleotides
and the DNA nucleotides of
the gene (template)
• recall RNA uses uracil
instead of thymine
AGTCAT
UCAGUA
Protein Synthesis
• Transcription
Elongation
5’
 RNA polymerase unwinds
the DNA and breaks the
H-bonds between the bases
of the two strands, separating
them from one another.
 Base pairing occurs between
incoming RNA nucleotides
and the DNA nucleotides of
the gene (template)
• recall RNA uses uracil
instead of thymine
3’
+ ATP
5’
 RNA polymerase catalyzes bond to
form between ribose of 3’ nucleotide
of mRNA and phosphate of incoming
RNA nucleotide
3’
+ ADP
Protein Synthesis
• Transcription
Elongation
The gene occurs on only one of the DNA
strands; each strand possesses a separate
set of genes
The 7-Methyl Guanosine
(7-MG) Cap
Polyadenylation
Polyadenylation sequence
5
AAUAAA
G/U
3
Endonuclease cleavage occurs
about 20 nucleotides downstream
from the AAUAAA sequence.
5
AAUAAA
PolyA-polymerase adds
adenine nucleotides
to the 3 end.
5
AAUAAA
AAAAAAAAAAAA.... 3
PolyA tail
Protein Synthesis
• Alternative Splicing (eukaryotes only)
 Exons are
“coding” regions
 Introns are removed
 different combinations
of exons form
different mRNA
resulting in multiple
proteins from the
same gene
 Humans have 30,000
genes but are capable
of producing 100,000
proteins
Protein Synthesis
Transcription
tRNA
synthesis
1
2
mRNA
mRNAmRNA copy of a gene
is synthesized
Cytoplasm of prokaryotes
Nucleus of eukaryotes
mRNA is used by ribosome to
build protein
(Ribosomes attach to the
mRNA and use its sequence of
nucleotides to determine the order
of amino acids in the protein)
Cytoplasm of prokaryotes
and eukaryotes
Some proteins feed directly into
rough ER in eukaryotes
Translation
Protein Synthesis
Transcription
• Translation
tRNA
synthesis
 Every three mRNA nucleotides (codon) specify an amino acid
mRNA
Translation
Protein Synthesis
• Translation
 tRNA have an anticodon region that specifically binds to its codon
Protein Synthesis
Transcription
• Translation
tRNA
synthesis
 Each tRNA carries a
specific amino acid
mRNA
Translation
Protein Synthesis
Transcription
tRNA
synthesis
mRNA
Translation
Aminoacyl tRNA synthetases attach
amino acids to their specific tRNA
Protein Synthesis
Transcription
tRNA
synthesis
• Translation
Initiation
mRNA
 Start codon signals where the gene
begins (at 5’ end of mRNA)
5’
3’
Translation
AUGGACAUUGAACCG…
start codon
Protein Synthesis
Small ribosomal subunit
• Translation
Initiation
 Start codon signals where the gene
begins (at 5’ end of mRNA)
 Ribosome binding site (Shine
Dalgarno sequence) upstream from
the start codon binds to small
ribosomal subunit
– then this complex recruits the
large ribosomal subunit
Small ribosomal subunit
Large ribosomal subunit
Ribosome
Protein Synthesis
• Translation
Scanning
 The ribosome moves in 5’ to 3’ direction “reading” the mRNA and
assembling amino acids into the correct protein
large ribosome subunit
small
ribosome
subunit
Protein Synthesis
• Translation
Scanning
 The ribosome moves in 5’ to 3’ direction “reading” the mRNA and
assembling amino acids into the correct protein
Protein Synthesis
• Translation
Termination
 Ribosome disengages from the mRNA
when it encounters a stop codon
Protein Synthesis
• Multiple RNA polymerases can engage a
gene at one time
• Multiple ribosomes can engage a single
mRNA at one time
Transcription
DNA
mRNAs
Translation
Protein Synthesis
• Eukaryotes: transcription
occurs in the nucleus and
translation occurs in the
cytoplasm
• Prokaryotes: Transcription
and translation occur
simultaneously in the
cytoplasm