chapter6structureofDNAandRNA

1、Welcome to My Molecular Biology Lecture1Molecular 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 GenomePart IV: RegulationPart V: Methods2Part II: Maintenance of the GenomeDedicated to the structure of DNA

2、and the processes that propagate (傳遞), maintain (保持) and alter (改變) it from one cell generation to the next3Maintenance 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 DNACh 10: Homologous

3、 recombination at the molecular levelCh 11: Site-specific recombination and transposition of DNAPROPAGATE & MAINTAINALTER4CHAPTER 6The Structures of DNA and RNA How do the structures of DNA and RNA account for their functions?5OUTLINE1.DNA Structure2.DNA Topology3.RNA Structure6DNA STRUCTUREStructur

4、e: two polynucleotide chains are twisting around each other in the form of a double helix.7Schematic modelSpace-filling model8DNA STRUCTURE (1) DNA is composed of polynucleotide chains Nucleoside & Nucleotide, the fundamental building block of DNA9glycosidic bondphosphoester bondNucleoside1035Asymme

5、tric11DNA polarity: is defined by the asymmetry of the nucleotides and the way they are joined.Phosphodiester linkages: repeating, sugar-phosphate backbone of the polynucleotide chain12Bases in DNApurinespyrimidinesAdenine (A)Guanine (G)Cytosine (C)Thymine (T)N9N113DNA STRUCTURE (2)Each bases has it

6、s preferred tautomeric form (Related to Ch 9)14The two strands of the double helix are held together by base pairing in an antiparallel orientation, Which is a stereochemical (立體化學的) consequence of the way that adenine and thymine, and guanine and cytosine, pair with each other. (Related to replicat

7、ion and transcription)DNA STRUCTURE (3)15The Two Chains of the Double Helix Have Complementary SequencesExample: If sequence 5-ATGTC-3 on one chain, the opposite chain MUST have the complementary sequence 3-TACAG-5DNA STRUCTURE (4)Watson-Crick Base Pairing(Related to replication and transcription)16

8、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.17A:C incompatibility18Hydrogen Bonding Is Important for the Specificity of Base PairingDNA STRUCTURE (

9、5)The hydrogen bonds between complementary bases determines the specificity of base pairing19Hydrogen bonding also contribute to the thermodynamic stability of the helix (?) Stacking interactions (p-p) between bases significantly contribute to the stability of DNA double helixH2O molecules lined up

10、on the bases are displaced by base-base interactions, which creates disorder/hydrophobicity20The double helix has Minor and Major grooves (What & Why)DNA STRUCTURE (5)(See the Structural Tutorial of this chapter for details)It is a simple consequence of the geometry of the base pair.21The Major groo

11、ve 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.22A: H-bond acceptorsD:

12、 H-bond donorsH: non-polar hydrogensM: methyl groups23The 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 conditionsA form (11 bp/turn), which is

13、observed under the condition of low humidity, presents in certain DNA/protein complexes. RNA double helix adopts a similar conformation. 242526DNA strands can separate (denature) and reassociate (anneal)DNA STRUCTURE (8)Key terms to understandDenaturation (變性)Hybridization (雜交)Annealing/renature (復性

14、)Absorbance (吸收度)Hyperchromicity (增色性)Tm (melting point) (熔點)27DNA TOPOLOGY28DNA TOPOLOGY (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 or

15、der for the two strands to be entirely separated from each other.29Species of cccDNAPlasmid 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)30Structure (2): Li

16、nking 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.DNA TOPOL

17、OGY (2)31Local disruption of base pairs32Function (1): DNA in cells is negatively supercoiled; nucleosomes introduces negative supercoiling in eukaryotesNegative supercoils serve as a store of free energy that aids in processes requiring strand separation, such as DNA replication and transcription.

18、Strand separation can be accomplished more easily in negatively supercoiled DNA than in relaxed DNADNA TOPOLOGY (3)33Function (2): Topoisomerases (P115-119)The biological importance of topoisomerase?The functional difference of the two types of topoisomerases? The working mechanism of topoisomeraseD

19、NA TOPOLOGY (4)3435RNA STRUCTURE36RNA STRUCTURE (1)RNA contains ribose and uracil and is usually single-stranded37Biological roles of RNARNA is the genetic material of some virusesRNA functions as the intermediate (mRNA) between the gene and the protein-synthesizing machinery.RNA functions as an ada

20、ptor (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, sel

21、f-splicing introns, etc).38Structure (1): RNA chains fold back on themselves to form local regions of double helix similar to A-form DNARNA STRUCTURE (2)hairpinbulgeloopRNA helix are the base-paired segments between short stretches of complementary sequences, which adopt one of the various stem-loop

22、 structures39Some 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 loop123440Pseudoknots are complex structure resulted from base pairing of discontiguous RNA segmentsFigure 6-32 Pseudokno

23、t.41Non-Watson-Crick G:U base pairs represent additional regular base pairing in RNA, which enriched the capacity for self-complementarityFigure 6-33 G:U base pair42The double helical structure of RNA resembles the A-form structure of DNA.The minor groove is wide and shallow, but offers little seque

24、nce-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.43Structure (2): RNA can fold up into complex tertiary structuresRNA STRUCTURE (3)RNA has enormous rotational freedom in the backbone of its non-base-paired regionsWhy?44Interactions in the tertiary structureUnconventional base pairing, such as base triples, base-backbone interac