Welcome to My Molecular

Biology Lecture

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 GenomeCh 6: The structures of DNA and RNA Ch 7: Chromosomes, chromatins and the nucleosomeCh 8: The replication of DNACh 9: The mutability and repair of DNA

Ch 10: Homologous recombination at the molecular levelCh 11: Site-specific recombination and transposition of DNA

PROPAGATE & MAINTAIN

ALTER

CHAPTER 6

The Structures of DNA and RNA

The Structures of DNA and RNA

The structure of

the genetic

materials

sustaining the

beautiful living

creatures

1. Appreciate the simple and stable beauties of the DNA structure.

2. Appreciate the flexible beauty of RNA structure

3. Appreciate the beautiful link between the structures of DNA and RNA and their biological 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.

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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 and the same sugar-sugar distance

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)

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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

modelSpace-filling model

Considering the extraordinary length/width ratio of your genomic DNA, take some time to appreciate its amazingly ordered packing in your cells, to give thanks to the creator, and to think of the possible ways to ensure DNA function.

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

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Key terms to understand1. 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

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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 cccDNA1. 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 WritheThe 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

Biological (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.

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Function (2): Topoisomerases

1.Two different types of topoisomerases:

--Type I makes transient single-stranded breaks in DNA, changes the linking number of DNA in steps of one, do not require ATP

--Type II makes transient double-strand breaks in DNA, changes the linking number of DNA in steps of two, requires ATP

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Function (2): Topoisomerases

2. Biological functions:

--Relax supercoiled DNA.

--introduce supercoils into DNA

--unknot and disentangle DNA

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RNA STRUCTURE

Biological roles of RNA

1. RNA is the genetic material of some viruses2. 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 structure2.Sequence

complementarity: base pairing as DNA

3.Secondary structure4. Tertiary structure5. Ribozymes are catalytic

RNAs

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RNA contains ribose and uracil and is usually single-stranded

1.Primary structure

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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

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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

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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.

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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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

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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

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Key points for Chapter 61. DNA structure

• Building blocks and base pairing• Double helical structure • Application of the property of strand separation and

association in DNA techniquesAppreciate the beauty of four bases in supporting the

amazingly diverse creatures.

2. DNA topology• cccDNA, Linking number, twist and writhe• Topoisomerases3. RNA structure

Composition, structure (2nd and tertiary) and functions (differences from DNA)