Welcome to My
Molecular Biology
Lecture
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
Part II,Maintenance of the Genome
Dedicated to the structure of
DNA and the processes that
propagate (传递 ),maintain (保持 )
and alter (改变 ) it from one cell
generation to the next
Maintenance of the Genome
Ch 6,The structures of DNA and RNA
Ch 7,Chromosomes,chromatins and
the nucleosome
Ch 8,The replication of DNA
Ch 9,The mutability and repair of DNA
Ch 10,Homologous recombination at
the molecular level
Ch 11,Site-specific recombination and
transposition of DNA
PROPAGATE & MAINTAIN
ALTER
CHAPTER 6
The Structures of
DNA and RNA
How do the structures of DNA
and RNA account for their
functions?
OUTLINE
1.DNA Structure
2.DNA Topology
3.RNA Structure
DNA STRUCTURE
1,The building blocks and base
pairing.
2,The structure,two
polynucleotide chains are
twisting around each other in
the form of a double helix.
DN
A
S
TR
UC
TU
RE
(
1)
DNA building blocks
Base (碱基 )
Nucleoside (核苷 )
Nucleotide (核苷酸 ) is the
fundamental building block of
DNA.
Purines
pyrimidines
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
N9
N1
Bases in DNA
Each bases has its preferred
tautomeric form (Related to Ch 9)
The strictness of the rules for,Waston-Crick” pairing
derives from the complementarity both of shape and
of hydrogen bonding properties between adenine and
thymine and between guanine and cytosine.
“Waston-Crick” pairing
Maximal hydrogen bonding
A:C incompatibility
glycosidic bond
phosphoester bond
NucleosideNucleosides &
Nucleotides
3’
5’
Asymmetric
A DNA molecule is composed
of two antiparallel
polynucleotide chains
DNA polarity,is defined by the asymmetry of
the nucleotides and the way they are joined.
Phosphodiester linkages,repeating,sugar-
phosphate backbone of the polynucleotide chain
The two strands are held together by base
pairing in an antiparallel orientation,a
stereochemical (立体化学的 ) consequence of the
way that A-T and G-C pair with each other,
(Related to replication and transcription)
DN
A
S
TR
UC
TU
RE
(
2)
DNA structure
two antiparallel polynucleotide
chains are twisting around
each other in the form of a
double helix.
1,The Two Chains of the Double
Helix Have Complementary Sequences
Example,If sequence 5’-ATGTC-3’ on
one chain,the opposite chain MUST
have the complementary sequence 3’-
TACAG-5’
Watson-Crick Base Pairing
(Related to replication and transcription)
2,Hydrogen Bonding determines the
Specificity of Base Pairing,while
stacking interaction determines the
stability a helix.
Hydrogen bonding also contribute to the
thermodynamic stability of the helix (?)
Stacking interactions (p-p) between
bases significantly contribute to the
stability of DNA double helix
H2O molecules lined up on the
bases are displaced by base-base
interactions,which creates
disorder/hydrophobicity.
3,Two different models illustrate
structure a DNA double helix.
Schematic model Space-filling model
4,DNA is usually a right-handed
double helix,
(See the Structural
Tutorial of this
chapter for details)
It is a simple
consequence of the
geometry of the
base pair.
5,The double helix has Minor and
Major grooves (What & Why)
The Major groove is rich in chemical
information
(What are the biological relevance?)
The edges of each base pair are exposed
in the major and minor grooves,creating a
pattern of hydrogen bond donors and
acceptors and of van der Waals surfaces
that identifies the base pair.
A,H-bond acceptors D,H-bond donors
H,non-polar hydrogens M,methyl groups
The B form (10 bp/turn),which is
observed at high humidity,most closely
corresponds to the average structure of
DNA under physiological conditions
A form (11 bp/turn),which is observed
under the condition of low humidity,
presents in certain DNA/protein
complexes,RNA double helix adopts a
similar conformation,
6,The double helix exists in multiple
conformations.
DNA strands can separate
and reassociate
DN
A
S
TR
UC
TU
RE
(
3)
Key terms to understand
1.Denaturation (变性 )
2.Hybridization (杂交 )
3.Annealing/renature (复性 )
4.Absorbance (吸收度 )
5.Hyperchromicity (增色性 )
6.Tm (melting point) (熔点 )
DNA TOPOLOGY
DN
A
T
OP
OL
OGY
(
1)
Structure (1),Linking number is an
invariant topological property of
covalently closed,circular DNA (cccDNA)
Linking number is the number of
times one strand have to be passed
through the other strand in order for
the two strands to be entirely
separated from each other.
Species of cccDNA
1,Plasmid and circular bacterial
chromosomes
2,Linear DNA molecules of eukaryotic
chromosomes due to their extreme
length,entrainment (缠卷 ) in
chromatin and interaction with other
cellular components (Ch 7)
Structure (2),Linking number is
composed of Twist and Writhe
The linking number is the sum of the
twist and the writhe.
Twist is the number of times one strand
completely wraps around the other
strand.
Writhe is the number of times that the
long axis of the double helical DNA
crosses over itself in 3-D space.
DN
A
T
OP
OL
OGY
(
2)
Local
disruption
of base
pairs
Function (1),DNA in cells is negatively
supercoiled; nucleosomes introduces
negative supercoiling in eukaryotes
Negative supercoils serve as a store of
free energy that aids in processes
requiring strand separation,such as DNA
replication and transcription,Strand
separation can be accomplished more easily in
negatively supercoiled DNA than in relaxed DNA.
DN
A
T
OP
OL
OGY
(
3)
Function (2),Topoisomerases
(P115-119)
1,The biological importance of
topoisomerase?
2,The functional difference of the two
types of topoisomerases?
3,The working mechanism of
topoisomerase (See the animation for
detail)
DN
A
T
OP
OL
OGY
(
4)
RNA STRUCTURE
Biological roles of RNA
1,RNA is the genetic material of some viruses
2,RNA functions as the intermediate (mRNA)
between the gene and the protein-synthesizing
machinery.
3,RNA functions as an adaptor (tRNA) between
the codons in the mRNA and amino acids.
4,Through sequence complementarity,RNA
serves as a regulatory molecule to bind to and
interfere with the translation of certain mRNAs;
or as a recognition molecule to guide many
post-transcriptional processing steps.
5,Through the tertiary structures,some RNAs
function as enzymes to catalyze essential
reactions in the cell (RNase P ribozyme,large
rRNA in ribosomes,self-splicing introns,etc).
Structures of RNA
1.Primary structure
2.Sequence complementarity,
base pairing as DNA
3.Secondary structure
4,Tertiary structure
RN
A
S
TR
UC
TU
RE
RNA contains ribose and uracil and is
usually single-stranded
1.Primary structure
RN
A
S
TR
UC
TU
RE
(
1)
Watson-Crick base pairing
U A-U
G-C
2.Sequence complementarity,
inter- and intra-molecular base
pairing
3.Secondary structures and
interactions
RNA chains fold back on themselves to
form local regions of double helix
similar to A-form DNA
RNA
S
TR
UC
TU
RE
(
2)
hairpin
bulge
loop
RNA helix are the base-
paired segments between
short stretches of
complementary sequences,
which adopt one of the
various stem-loop
structures
2nd structure elements
Some tetraloop sequence can enhance the
stability of the RNA helical structures
For example,UUCG loop is unexpectedly stable
due to the special base-stacking in the loop
1
2
3
4
Special
interactions
Pseudoknots are complex secondary
structure resulted from base pairing of
discontiguous RNA segments
Figure 6-32 Pseudoknot.
Structurally special base-pairing
Non-Watson-Crick G:U base pairs represent
additional regular base pairing in RNA,which
enriched the capacity for self-complementarity.
Figure 6-33 G:U base pair
Chemically special base-pairing
The double helical structure of RNA resembles
the A-form structure of DNA.
The minor groove is wide and shallow,but
offers little sequence-specific information,
The major groove is so narrow and
deep that it is not very accessible to
amino acid side chains from interacting
proteins,Thus RNA structure is less well
suited for sequence-specific interactions
with proteins.
RNA
S
TR
UC
TU
RE
RNA has enormous rotational freedom
in the backbone of its non-base-paired
regions.
Why?
4,RNA can fold up into complex
tertiary structures
The structure of
the hammerhead
ribozyme
Interactions in the tertiary structure
Unconventional base pairing,such as base
triples,base-backbone interactions
Proteins can assist the formation of
tertiary structures by large RNA molecule
The crystal structure of a 23S ribosme
Some RNAs with tertiary structures can
catalyze
RNA
S
TR
UC
TU
RE
(
4)
Ribozymes are RNA molecules that
adopt complex tertiary structure and
serve as biological catalysts.
RNase P and self-splicing introns are
ribozymes
Structure & Function,The hammerhead
ribozyme cleaves RNA by formation of a
2’,3’ cyclic phosphate
RNA
S
TR
UC
TU
RE
(
5)
See animation for detail
C17
Key points for Chapter 6
1,DNA structure
Building blocks and base pairing
Double helical structure
Application of the property of strand separation
and association in DNA techniques
Critical thinking,how DNA structure influence the
processes of genome maintenance and
expression? [You are encouraged to take this question
and find out the answers when we discuss the related
contents]
2,DNA topology
The biological relevance of cccDNA
Linking number,twist and writhe,how these
topological features are changed during DNA
replication [answer the question after the related
lecture].
Topoisomerases
3,RNA structure
Composition,structure (2nd and tertiary) and
functions (differences from DNA)
Molecular Biology
Lecture
Molecular Biology of the Gene,
5/E --- Watson et al,(2004)
Part I,Chemistry and Genetics
Part II,Maintenance of the Genome
Part III,Expression of the Genome
Part IV,Regulation
Part V,Methods
Part II,Maintenance of the Genome
Dedicated to the structure of
DNA and the processes that
propagate (传递 ),maintain (保持 )
and alter (改变 ) it from one cell
generation to the next
Maintenance of the Genome
Ch 6,The structures of DNA and RNA
Ch 7,Chromosomes,chromatins and
the nucleosome
Ch 8,The replication of DNA
Ch 9,The mutability and repair of DNA
Ch 10,Homologous recombination at
the molecular level
Ch 11,Site-specific recombination and
transposition of DNA
PROPAGATE & MAINTAIN
ALTER
CHAPTER 6
The Structures of
DNA and RNA
How do the structures of DNA
and RNA account for their
functions?
OUTLINE
1.DNA Structure
2.DNA Topology
3.RNA Structure
DNA STRUCTURE
1,The building blocks and base
pairing.
2,The structure,two
polynucleotide chains are
twisting around each other in
the form of a double helix.
DN
A
S
TR
UC
TU
RE
(
1)
DNA building blocks
Base (碱基 )
Nucleoside (核苷 )
Nucleotide (核苷酸 ) is the
fundamental building block of
DNA.
Purines
pyrimidines
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
N9
N1
Bases in DNA
Each bases has its preferred
tautomeric form (Related to Ch 9)
The strictness of the rules for,Waston-Crick” pairing
derives from the complementarity both of shape and
of hydrogen bonding properties between adenine and
thymine and between guanine and cytosine.
“Waston-Crick” pairing
Maximal hydrogen bonding
A:C incompatibility
glycosidic bond
phosphoester bond
NucleosideNucleosides &
Nucleotides
3’
5’
Asymmetric
A DNA molecule is composed
of two antiparallel
polynucleotide chains
DNA polarity,is defined by the asymmetry of
the nucleotides and the way they are joined.
Phosphodiester linkages,repeating,sugar-
phosphate backbone of the polynucleotide chain
The two strands are held together by base
pairing in an antiparallel orientation,a
stereochemical (立体化学的 ) consequence of the
way that A-T and G-C pair with each other,
(Related to replication and transcription)
DN
A
S
TR
UC
TU
RE
(
2)
DNA structure
two antiparallel polynucleotide
chains are twisting around
each other in the form of a
double helix.
1,The Two Chains of the Double
Helix Have Complementary Sequences
Example,If sequence 5’-ATGTC-3’ on
one chain,the opposite chain MUST
have the complementary sequence 3’-
TACAG-5’
Watson-Crick Base Pairing
(Related to replication and transcription)
2,Hydrogen Bonding determines the
Specificity of Base Pairing,while
stacking interaction determines the
stability a helix.
Hydrogen bonding also contribute to the
thermodynamic stability of the helix (?)
Stacking interactions (p-p) between
bases significantly contribute to the
stability of DNA double helix
H2O molecules lined up on the
bases are displaced by base-base
interactions,which creates
disorder/hydrophobicity.
3,Two different models illustrate
structure a DNA double helix.
Schematic model Space-filling model
4,DNA is usually a right-handed
double helix,
(See the Structural
Tutorial of this
chapter for details)
It is a simple
consequence of the
geometry of the
base pair.
5,The double helix has Minor and
Major grooves (What & Why)
The Major groove is rich in chemical
information
(What are the biological relevance?)
The edges of each base pair are exposed
in the major and minor grooves,creating a
pattern of hydrogen bond donors and
acceptors and of van der Waals surfaces
that identifies the base pair.
A,H-bond acceptors D,H-bond donors
H,non-polar hydrogens M,methyl groups
The B form (10 bp/turn),which is
observed at high humidity,most closely
corresponds to the average structure of
DNA under physiological conditions
A form (11 bp/turn),which is observed
under the condition of low humidity,
presents in certain DNA/protein
complexes,RNA double helix adopts a
similar conformation,
6,The double helix exists in multiple
conformations.
DNA strands can separate
and reassociate
DN
A
S
TR
UC
TU
RE
(
3)
Key terms to understand
1.Denaturation (变性 )
2.Hybridization (杂交 )
3.Annealing/renature (复性 )
4.Absorbance (吸收度 )
5.Hyperchromicity (增色性 )
6.Tm (melting point) (熔点 )
DNA TOPOLOGY
DN
A
T
OP
OL
OGY
(
1)
Structure (1),Linking number is an
invariant topological property of
covalently closed,circular DNA (cccDNA)
Linking number is the number of
times one strand have to be passed
through the other strand in order for
the two strands to be entirely
separated from each other.
Species of cccDNA
1,Plasmid and circular bacterial
chromosomes
2,Linear DNA molecules of eukaryotic
chromosomes due to their extreme
length,entrainment (缠卷 ) in
chromatin and interaction with other
cellular components (Ch 7)
Structure (2),Linking number is
composed of Twist and Writhe
The linking number is the sum of the
twist and the writhe.
Twist is the number of times one strand
completely wraps around the other
strand.
Writhe is the number of times that the
long axis of the double helical DNA
crosses over itself in 3-D space.
DN
A
T
OP
OL
OGY
(
2)
Local
disruption
of base
pairs
Function (1),DNA in cells is negatively
supercoiled; nucleosomes introduces
negative supercoiling in eukaryotes
Negative supercoils serve as a store of
free energy that aids in processes
requiring strand separation,such as DNA
replication and transcription,Strand
separation can be accomplished more easily in
negatively supercoiled DNA than in relaxed DNA.
DN
A
T
OP
OL
OGY
(
3)
Function (2),Topoisomerases
(P115-119)
1,The biological importance of
topoisomerase?
2,The functional difference of the two
types of topoisomerases?
3,The working mechanism of
topoisomerase (See the animation for
detail)
DN
A
T
OP
OL
OGY
(
4)
RNA STRUCTURE
Biological roles of RNA
1,RNA is the genetic material of some viruses
2,RNA functions as the intermediate (mRNA)
between the gene and the protein-synthesizing
machinery.
3,RNA functions as an adaptor (tRNA) between
the codons in the mRNA and amino acids.
4,Through sequence complementarity,RNA
serves as a regulatory molecule to bind to and
interfere with the translation of certain mRNAs;
or as a recognition molecule to guide many
post-transcriptional processing steps.
5,Through the tertiary structures,some RNAs
function as enzymes to catalyze essential
reactions in the cell (RNase P ribozyme,large
rRNA in ribosomes,self-splicing introns,etc).
Structures of RNA
1.Primary structure
2.Sequence complementarity,
base pairing as DNA
3.Secondary structure
4,Tertiary structure
RN
A
S
TR
UC
TU
RE
RNA contains ribose and uracil and is
usually single-stranded
1.Primary structure
RN
A
S
TR
UC
TU
RE
(
1)
Watson-Crick base pairing
U A-U
G-C
2.Sequence complementarity,
inter- and intra-molecular base
pairing
3.Secondary structures and
interactions
RNA chains fold back on themselves to
form local regions of double helix
similar to A-form DNA
RNA
S
TR
UC
TU
RE
(
2)
hairpin
bulge
loop
RNA helix are the base-
paired segments between
short stretches of
complementary sequences,
which adopt one of the
various stem-loop
structures
2nd structure elements
Some tetraloop sequence can enhance the
stability of the RNA helical structures
For example,UUCG loop is unexpectedly stable
due to the special base-stacking in the loop
1
2
3
4
Special
interactions
Pseudoknots are complex secondary
structure resulted from base pairing of
discontiguous RNA segments
Figure 6-32 Pseudoknot.
Structurally special base-pairing
Non-Watson-Crick G:U base pairs represent
additional regular base pairing in RNA,which
enriched the capacity for self-complementarity.
Figure 6-33 G:U base pair
Chemically special base-pairing
The double helical structure of RNA resembles
the A-form structure of DNA.
The minor groove is wide and shallow,but
offers little sequence-specific information,
The major groove is so narrow and
deep that it is not very accessible to
amino acid side chains from interacting
proteins,Thus RNA structure is less well
suited for sequence-specific interactions
with proteins.
RNA
S
TR
UC
TU
RE
RNA has enormous rotational freedom
in the backbone of its non-base-paired
regions.
Why?
4,RNA can fold up into complex
tertiary structures
The structure of
the hammerhead
ribozyme
Interactions in the tertiary structure
Unconventional base pairing,such as base
triples,base-backbone interactions
Proteins can assist the formation of
tertiary structures by large RNA molecule
The crystal structure of a 23S ribosme
Some RNAs with tertiary structures can
catalyze
RNA
S
TR
UC
TU
RE
(
4)
Ribozymes are RNA molecules that
adopt complex tertiary structure and
serve as biological catalysts.
RNase P and self-splicing introns are
ribozymes
Structure & Function,The hammerhead
ribozyme cleaves RNA by formation of a
2’,3’ cyclic phosphate
RNA
S
TR
UC
TU
RE
(
5)
See animation for detail
C17
Key points for Chapter 6
1,DNA structure
Building blocks and base pairing
Double helical structure
Application of the property of strand separation
and association in DNA techniques
Critical thinking,how DNA structure influence the
processes of genome maintenance and
expression? [You are encouraged to take this question
and find out the answers when we discuss the related
contents]
2,DNA topology
The biological relevance of cccDNA
Linking number,twist and writhe,how these
topological features are changed during DNA
replication [answer the question after the related
lecture].
Topoisomerases
3,RNA structure
Composition,structure (2nd and tertiary) and
functions (differences from DNA)
