Welcome to My Molecular Biology Lecture

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Welcome to My Molecular Biology Lecture
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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
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Part II Maintenance of the Genome
Dedicated to the structure of DNA and the
processes that propagate (??), maintain (??) and
alter (??) it from one cell generation to the next
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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
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CHAPTER 6

• The Structures of DNA and RNA

How do the structures of DNA and RNA account for
their functions?
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OUTLINE
1.DNA Structure
2.DNA Topology
3.RNA Structure
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DNA STRUCTURE
Structure two polynucleotide chains are twisting
around each other in the form of a double helix.
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Schematic model
Space-filling model
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DNA is composed of polynucleotide chains

• DNA STRUCTURE (1)

Nucleoside Nucleotide, the fundamental building
block of DNA
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Nucleoside
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Asymmetric
5
3
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Phosphodiester linkages repeating,
sugar-phosphate backbone of the polynucleotide
chain
DNA polarity is defined by the asymmetry of the
nucleotides and the way they are joined.
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Bases in DNA
Adenine (A)
purines
N9
Guanine (G)
Cytosine (C)
pyrimidines
Thymine (T)
N1
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Each bases has its preferred tautomeric form
(Related to Ch 9)
DNA STRUCTURE (2)
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The two strands of the double helix are held
together by base pairing in an antiparallel
orientation, Which is a stereochemical (?????)
consequence of the way that adenine and thymine,
and guanine and cytosine, pair with each other.
(Related to replication and transcription)
DNA STRUCTURE (3)
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The Two Chains of the Double Helix Have
Complementary Sequences
DNA STRUCTURE (4)
Watson-Crick Base Pairing
Example If sequence 5-ATGTC-3 on one chain,
the opposite chain MUST have the complementary
sequence 3-TACAG-5
(Related to replication and transcription)
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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.
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AC incompatibility
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Hydrogen Bonding Is Important for the Specificity
of Base Pairing
DNA STRUCTURE (5)

• The hydrogen bonds between complementary bases
  determines the specificity of base pairing

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• 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
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The double helix has Minor and Major grooves
(What Why)
DNA STRUCTURE (5)
It is a simple consequence of the geometry of the
base pair.
(See the Structural Tutorial of this chapter for
details)
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The Major groove is rich in chemical information
(What are the biological relevance?)
DNA STRUCTURE (6)
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.
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A H-bond acceptors
D H-bond donors
H non-polar hydrogens
M methyl groups
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The double helix exists in multiple
conformations.
DNA STRUCTURE (7)

• 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.

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DNA strands can separate (denature) and
reassociate (anneal)
DNA STRUCTURE (8)

• Key terms to understand
• Denaturation (??)
• Hybridization (??)
• Annealing/renature (??)
• Absorbance (???)
• Hyperchromicity (???)
• Tm (melting point) (??)

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DNA TOPOLOGY
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Structure (1) Linking number is an invariant
topological property of covalently closed,
circular DNA (cccDNA)
DNA TOPOLOGY (1)
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.
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• Species of cccDNA
• Plasmid and circular bacterial chromosomes
• Linear DNA molecules of eukaryotic chromosomes
  due to their extreme length, entrainment in
  chromatin and interaction with other cellular
  components (Ch 7)

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Structure (2) Linking number is composed of
Twist and Writhe
DNA TOPOLOGY (2)
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.
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Local disruption of base pairs
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Function (1) DNA in cells is negatively
supercoiled nucleosomes introduces negative
supercoiling in eukaryotes
DNA TOPOLOGY (3)
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
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Function (2) Topoisomerases (P115-119)
DNA TOPOLOGY (4)

• The biological importance of topoisomerase?
• The functional difference of the two types of
  topoisomerases?
• The working mechanism of topoisomerase (See the
  animation for detail)

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RNA STRUCTURE
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RNA contains ribose and uracil and is usually
single-stranded
RNA STRUCTURE (1)
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Biological roles of RNA

• RNA is the genetic material of some viruses
• RNA functions as the intermediate (mRNA) between
  the gene and the protein-synthesizing machinery.
• RNA functions as an adaptor (tRNA) between the
  codons in the mRNA and amino acids.
• RNA serves as a regulatory molecule, which
  through sequence complementarity binds to, and
  interferes with the translation of certain mRNAs.
• Some RNAs are enzymes that catalyze essential
  reactions in the cell (RNase P ribozyme, large
  rRNA, self-splicing introns, etc).

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Structure (1) RNA chains fold back on themselves
to form local regions of double helix similar to
A-form DNA
RNA STRUCTURE (2)
hairpin
RNA helix are the base-paired segments between
short stretches of complementary sequences, which
adopt one of the various stem-loop structures
bulge
loop
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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
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3
4
1
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Pseudoknots are complex structure resulted from
base pairing of discontiguous RNA segments
Figure 6-32 Pseudoknot.
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Non-Watson-Crick GU base pairs represent
additional regular base pairing in RNA, which
enriched the capacity for self-complementarity
Figure 6-33 GU base pair
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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.
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Structure (2) RNA can fold up into complex
tertiary structures
RNA STRUCTURE (3)
Why?
RNA has enormous rotational freedom in the
backbone of its non-base-paired regions
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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

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The crystal structure of a 23S ribosme
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Function Some RNAs are enzymes
RNA STRUCTURE (4)
Ribozymes are RNA molecules that adopt complex
tertiary structure and serve as biological
catalysts. RNase P and self-splicing introns are
ribozymes
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Structure Function The hammerhead ribozyme
cleaves RNA by formation of a 2,3 cyclic
phophate
RNA STRUCTURE (5)
See animation for detail
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Homework (on the CD)

• See the animations for DNA topology,
  Topoisomerase, as well as Ribozyme Structure and
  Activity. Answering the questions in applying
  your knowledge is required.
• Play the structural tutorial Introduction to the
  DNA structure to better understand DNA structure
• Finish all the critical thinking exercise

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Key points for Chapter 6

• Definitions topoisomerase, ribozyme, double
  helix, DNA denaturation, Tm, linking number,
  pseudoknot.
• What are the structural differences between DNA
  and RNA? How the structural properties of DNA and
  RNA determine their distinct biological
  functions.