Welcome to My Molecular Biology Lecture Li Xiaoling Office: M1623 QQ: 313320773 E-MAIL: 313320773 @qq.com 2017/4/25

Chapter 2 The Structures of DNA and RNA Content Chapter 1 Introduction Chapter 2 The Structures of DNA and RNA Chapter 3 DNA Replication Chapter 4 DNA Mutation and Repair Chapter 5 RNA Transcription Chapter 6 RNA Splicing Chapter 7 Translation Chapter 8 The Genetic code Chapter 9 Regulation in prokaryotes Chapter 10 Regulation in Eukaryotes 2017/4/25

How to learn this course well？ To learn effectively To preview and review Problem-base learning Making use of class time effectively Active participation Bi-directional question in class Group discussion Concept map Tutorship To call for reading, thingking and discussing of investigative learning 2017/4/25

Evaluation (grading) system Question in-class and attendance : 10 points Group study and attendance: 20 points Final exam: 70 points Bonus 2017/4/25

The Structures of DNA and RNA CHAPTER 2 The Structures of DNA and RNA How do the structures of DNA and RNA account for their functions? 2017/4/25

OUTLINE 1.DNA Structure 2.DNA Topology 3.RNA Structure 2017/4/25

DNA STRUCTURE The building blocks and base pairing. The structure: two polynucleotide chains are twisting around each other in the form of a double helix. 2017/4/25

DNA building blocks Base Nucleoside DNA STRUCTURE (1) Base Nucleoside Nucleotide is the fundamental building block of DNA. 2017/4/25

Bases in DNA Purines pyrimidines Adenine (A) Guanine (G) Cytosine (C) Thymine (T) N1 2017/4/25

Each bases has its preferred tautomeric form (Related to Ch 9) 2017/4/25

“Waston-Crick” pairing 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. Maximal hydrogen bonding 2017/4/25

A:C incompatibility 2017/4/25

Nucleosides & Nucleotides glycosidic bond phosphoester bond 2017/4/25

Asymmetric 5’ 3’ 2017/4/25

A DNA molecule is composed of two antiparallel polynucleotide chains 2017/4/25

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. 2017/4/25

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) 2017/4/25

DNA structure DNA STRUCTURE (2) two antiparallel polynucleotide chains are twisting around each other in the form of a double helix. 2017/4/25

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1. The Two Chains of the Double Helix Have Complementary Sequences 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) 2017/4/25

2. Hydrogen Bonding determines the Specificity of Base Pairing, while stacking interaction determines the stability a helix. 2017/4/25

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. 2017/4/25

3. Two different models illustrate structure a DNA double helix. Schematic model Space-filling model 2017/4/25

4. DNA is usually a right-handed double helix. 2017/4/25

5. The double helix has Minor and Major grooves (What & Why) It is a simple consequence of the geometry of the base pair. (See the Structural Tutorial of this chapter for details) 2017/4/25

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. 2017/4/25

H: non-polar hydrogens M: methyl groups A: H-bond acceptors D: H-bond donors H: non-polar hydrogens M: methyl groups 2017/4/25

6. The double helix exists in multiple conformations. 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. 2017/4/25

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DNA strands can separate and reassociate DNA STRUCTURE (3) Key terms to understand Denaturation (变性) Hybridization (杂交) Annealing/renature (复性) Absorbance (吸收度) Hyperchromicity (增色性) Tm (melting point) (熔点) 2017/4/25

DNA TOPOLOGY 2017/4/25

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. 2017/4/25

Plasmid and circular bacterial chromosomes Species of cccDNA Plasmid and circular bacterial chromosomes Linear DNA molecules of eukaryotic chromosomes due to their extreme length, entrainment (缠卷) in chromatin and interaction with other cellular components (Ch 7) 2017/4/25

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. 2017/4/25

Local disruption of base pairs 2017/4/25

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. 2017/4/25

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) 2017/4/25

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RNA STRUCTURE 2017/4/25

Biological roles of RNA 2017/4/25

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. 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. 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). 2017/4/25

Structures of RNA Primary structure 2.Sequence complementarity: base pairing as DNA 3.Secondary structure 4. Tertiary structure 2017/4/25

Primary structure RNA STRUCTURE RNA contains ribose and uracil and is usually single-stranded 2017/4/25

2.Sequence complementarity: inter- and intra-molecular base pairing RNA STRUCTURE (1) Watson-Crick base pairing U G-C A-U 2017/4/25

3.Secondary structures and interactions 2017/4/25

RNA chains fold back on themselves to form local regions of double helix similar to A-form DNA RNA STRUCTURE (2) 2nd structure elements 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 2017/4/25

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 2 Special interactions 3 4 1 2017/4/25

Pseudoknots are complex secondary structure resulted from base pairing of discontiguous RNA segments Figure 6-32 Pseudoknot. Structurally special base-pairing 2017/4/25

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 2017/4/25

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. 2017/4/25

4. RNA can fold up into complex tertiary structures RNA STRUCTURE Why? RNA has enormous rotational freedom in the backbone of its non-base-paired regions. 2017/4/25

The structure of the hammerhead ribozyme 2017/4/25

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 2017/4/25

The crystal structure of a 23S ribosme 2017/4/25

Some RNAs with tertiary structures can catalyze 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 2017/4/25

Structure & Function: The hammerhead ribozyme cleaves RNA by formation of a 2’,3’ cyclic phosphate RNA STRUCTURE (5) C17 See animation for detail 2017/4/25

Key points for Chapter 6 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] 2017/4/25

2. DNA topology 3. RNA structure 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) 2017/4/25