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
The Structures of DNA and RNA CHAPTER 6 How do the structures of DNA and RNA account for their functions?
OUTLINE 1.DNA Structure 2.DNA Topology 3.RNA Structure
DNA STRUCTURE Structure: two polynucleotide chains are twisting around each other in the form of a double helix.
Schematic model Space-filling model
DNA STRUCTURE (1) DNA is composed of polynucleotide chains Nucleoside & Nucleotide, the fundamental building block of DNA
phosphoester bond glycosidic bond Nucleoside
Asymmetric 5’ 3’
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.
Bases in DNA Adenine (A) purines N9 Guanine (G) Cytosine (C) pyrimidines Thymine (T) N1
Each bases has its preferred tautomeric form (Related to Ch 9) DNA STRUCTURE (2)
The two strands of the double helix are held together by base pairing in an antiparallel orientation, Which is a stereochemical(立体化学的)consequence of the way that adenine and thymine, and guanine and cytosine, pair with each other. (Related to replication and transcription) DNA STRUCTURE (3)
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)
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.
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
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
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)
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.
A: H-bond acceptors D: H-bond donors H: non-polar hydrogens M: methyl groups
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.
DNA strands can separate (denature) and reassociate (anneal) DNA STRUCTURE (8) • 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)
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.
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)
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.
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
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)
RNA contains ribose and uracil and is usually single-stranded RNA STRUCTURE (1)
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).
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
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 3 4 1
Pseudoknots are complex structure resulted from base pairing of discontiguous RNA segments Figure 6-32 Pseudoknot.
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
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.
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
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
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
Structure & Function: The hammerhead ribozyme cleaves RNA by formation of a 2’,3’ cyclic phophate RNA STRUCTURE (5) See animation for detail
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
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.