DNA and RNA: Structure and Function. 阮雪芬 May 14, 2004

Transcription

1 DNA and RNA: Structure and Function 阮雪芬 May 14, 2004

2 Two Fundamental types of nucleic acids participate as genetic molecules DNA: deoxyribonucleic acid Found in the chromosome form in the cell s nucleus In mitochondria and chloroplast RNA: ribonucleic acid Ribosomal Messanger Transfer

3 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

4 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

5 Components of Nucleotides Nitrogenous bases A five-carbon carbohydrate One, two, or three phosphate group DNA RNA

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7 Major Bases Minor Bases

8 A five-carbon carbohydrate: Aldopentose RNA DNA

9 A Nucleoside Consists of a purine or pyrimidine base linked to a carbohydrate

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11 Synthetic Nucleosides Treat for AIDS

12 Synthetic Nucleosides Treat for AIDS

13 Purines and Pyrimidines with Caffeine: Physiological Activity (1) a trimethylated derivative of the fundamental purine ring Stimulates the cerebral cortex by inhibiting the enzyme phophodiesterase, which is involved in cell-signaling processes.

14 Purines and Pyrimidines with Physiological Activity (2) 6-mercaptopurine (6-MP) Block the synthesis of nucleic acids Effective for treatment of leukemia

15 Purines and Pyrimidines with Acyclovir Physiological Activity (3) Used in treatment of herpes viral infections Acts by inhibiting the DNA polymeraase of herpes viral infections

16 Purines and Pyrimidines with Physiological Activity (4) 5-fluorouracil (5-FU) A potent inhibitor of DNA synthesis and used in cancer treatment

17 Structures for Three Types of Nucleotides

18 Structures for Three Types of Nucleotides ATP is the principal carrier of chemical energy in the cell. ATP + H 2 O ADP + Pi + energy GTP, cyclic AMP, and cyclic GMP are transient intermediates that send messages via signal transduction through cell membranes Pi: HPO 4 2-

19 Phosphodiester bonds linking mononucleotides into nucleic acids

20 Comparison of DNA from Different Species

21 RNA Molecules in E. coli

22 Nucleic acids Have acidic and basic regions H bond is important in nucleic acids folding Hydrophobic Hydrophilic

23 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

24 History Landmarks

25 The DNA Double Helix

26 The DNA Double Helix Two right-handed, helical, polynucleotide chains are coiled around a common axis to form a double helix. Antiparallel Deoxyribose and phosphatein on the outside of the helix; hydrophobic purine and pyrimidine base on the inside of the helix Is stabilized by two types of forces Hydrogen bonds Van der Waals and hydrophobic interactions

27 Hydrogen Bonding

28 A-DNA, B-DNA and Z-DNA A-DNA: right-handed helix 11 bases per helix turn a greater diameter (26 Å) B-DNA right-handed helix 10.5 bases per helix turn a diameter (20 Å) Z-DNA left-handed helix 12 bases per helix turn a diameter (18 Å)

29 Physical and Biological Properties of Double Helix By Watson and Crick Now our model for deoxyribonucleic acid is, in effect, a pair of templates, each of which is complementary to the other. We imagine that prior to duplication the hydrogen bonds are broken and the two chains unwind and separate. Each chain then acts as a template for the formation onto itself of a new companion chain, so that eventually we shall have two pairs of chains, where we only had one before. Moreover, the sequence of the pairs of bases will have been duplicated exactly. Nature 171: , 1953.

30 Replication of the DNA Double Helix

31 DNA during Denaturation and Renaturation C for many DNA molecules melting annealing

32 Melting Curves for DNA Molecules

33 Tertiary Forms of DNA Topoisomerases Less stable

34 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

35 RNA Structural Elements Two fundamental differences in DNA and RNA RNA contains the carbohydrate ribose rather than 2-deoxyribose. This makes RNA more susceptible to hydrolysis than DNA. One of the major bases in RNA is uracil (U) instead of thymine (T) in DNA.

36 General Features of RNA Secondary and Tertiary Structure Hairpin turns Right-handed double helixes: similar to A-DNA Internal loops and bulges

37 trna Structure nucleotides in a single chain methylguanosine dihydrouridine dimethylguanosine psedouridine methylinosine

38 The Three-dimensional Structure of Yeast trna for Phenylalanine

39 Proposed Secondary Structure for E. coli 16S rrna

40 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

41 Nucleases Catalyze the hydrolysis of phosphodiester bonds. Deoxyribonucleases (DNases) and ribonucleases (RNases) Exonucleases: catalyze the hydrolytic removal of terminal nucleotides

42 Exonucleases and Endonucleases Exonucleases Endonucleases

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44 DNA Restriction Enzymes Restriction endonucleases Was discovered in DNA molecules. Recognize specific base sequences in double-strand DNA and catalyze hydrolytic cleavage of the two strands in or near that specific region.

45 DNA Restriction Enzymes The enzyme consists of a three-letter abbreviation. EcoRI: the first restriction enzyme to be isolated from E. coli (strain R) 5 G-A-A-T-T-C 3 3 C-T-T-A-A-G 5 OH 5 G + A-A-T-T-C 3 3 C-T-T-A-A G 5 A specific hexanucleotide sequence OH

46 DNA Restriction Enzymes It is unlikely that this set of fragments will be the same for any two different DNA molecules, so the fragmentation pattern is unique and can be considered a fingerprint of DNA substrate.

47 Outline RNA and DNA Chemical Structures DNA Structural Elements RNA Structural Elements Cleavage of DNA and RNA by Nucleases Nucleic Acid-Protein Complexes

48 Nucleic Acid-Protein Complexes Nucleoproteins Complexes of nucleic acids and proteins. Viruses Stable, infective particles composed of nucleic acid, either DNA or RNA, and protein subunits. Bacteriophage or phages Viruses are specific for bacteria The majority of phages are DNA viruses

49 Viruses ØX174: Infects E. coli DNA genome with relatively small, singlestranded, circular molecules (5386 b) Tobacco mosaic virus (TMV) Infects the leaves of the plant. RNA genome with single strand (6390 b)

50 Viruses Rous sarcoma: causes tumors. Human immunodeficiency virus (HIV) : causes AIDS Gp41 and gp121

51 Chromosomes Are packages composed of DNA and protein in eukaryotic cells. The nucleoprotein complex in eukaryotic cell nucleus is called chromatin. Histones: are a family of small proteins that containing relatively large numbers of basic amino acid residues Arg and Lys. Nucleosomes: are held together by ionic bonds between positively charged Arg nad Lys protein residues with the negatively charged phosphate groups in the DNA backbone.

52 snrnps Play a role in RNA processing. These active clusters composed of small nuclear ribonucleic acids (snrnas) and proteins are called small nuclear ribonucleoprotein particles (snrnps)

53 Fig RNA Processing

54 Ribosomes Supramolecules assemblies of RNA and protein that function as the intracellular sites for protein synthesis.

55 Fig 12.1 Ribosomes

56 Ribonucleases Onconase: The frog enzyme

57 Exercises