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Nucleic Acids: Cell Overview and Core Topics

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  1. Nucleic Acids: Cell Overview and Core Topics

  2. Outline • Cellular Overview • Anatomy of the Nucleic Acids • Building blocks • Structure (DNA, RNA) • Looking at the Central Dogma • DNA Replication • RNA Transcription • Protein Synthesis

  3. DNA and RNA in the Cell Cellular Overview

  4. Classes of Nucleic Acids: DNA • DNA is usually found in the nucleus • Small amounts are also found in: • mitochondria of eukaryotes • chloroplasts of plants • Packing of DNA: • 2-3 meters long • histones • genome = complete collection of hereditary information of an organism

  5. Classes of Nucleic Acids: RNA FOUR TYPES OF RNA • mRNA - Messenger RNA• tRNA - Transfer RNA• rRNA - Ribosomal RNA• snRNA - Small nuclear RNA

  6. THE BUILDING BLOCKS Anatomy of Nucleic Acids

  7. Nucleic acids are linear polymers. Each monomer consists of: 1. a sugar 2. a phosphate 3. a nitrogenous base

  8. Nitrogenous Bases

  9. Nitrogenous Bases DNA (deoxyribonucleic acid): adenine (A) guanine (G) cytosine (C) thymine (T) Why ? RNA (ribonucleic acid): adenine (A) guanine (G) cytosine (C) uracil (U)

  10. Properties of purines and pyrimidines: • keto – enoltautomerism • strong UV absorbance

  11. Pentoses of Nucleic Acids This difference in structure affects secondary structure and stability. Which is more stable?

  12. Nucleosides linkage of a base and a sugar.

  13. Nucleotides - nucleoside + phosphate - monomers of nucleic acids - NA are formed by 3’-to-5’ phosphodiester linkages

  14. Shorthand notation: • sequence is read from 5’ to 3’ • corresponds to the N to C terminal of proteins

  15. DNA Nucleic Acids: Structure

  16. Primary Structure • nucleotide sequences

  17. Secondary Structure DNA Double Helix • Maurice Wilkins and Rosalind Franklin • James Watson and Francis Crick • Features: • two helical polynucleotides coiled around an axis • chains run in opposite directions • sugar-phosphate backbone on the outside, bases on the inside • bases nearly perpendicular to the axis • repeats every 34 Å • 10 bases per turn of the helix • diameter of the helix is 20 Å

  18. Double helix stabilized by hydrogen bonds. Which is more stable?

  19. Axial view of DNA

  20. A and B forms are both right-handed double helix. A-DNA has different characteristics from the more common B-DNA.

  21. Z-DNA • left-handed • backbone phosphates zigzag

  22. Comparison Between A, B, and Z DNA: • A-DNA: right-handed, short and broad, 11 bp per turn • B-DNA: right-handed, longer, thinner, 10 bp per turn • Z-DNA: left-handed, longest, thinnest, 12 bp per turn

  23. Major and minor grooves are lined with sequence-specific H-bonding.

  24. Consequences of double helical structure: • 1. Facilitates accurate hereditary information transmission • Reversible melting • melting: dissociation of the double helix • melting temperature (Tm) • hypochromism • annealing

  25. Tertiary Structure Supercoiling supercoiledDNA relaxed DNA

  26. Topoisomerase I – relaxation of supercoiled structures

  27. Topoisomerase II – add negative supercoils to DNA

  28. Structure of Single-stranded DNA Stem Loop

  29. RNA Nucleic Acids: Structure

  30. Secondary Structure transfer RNA (tRNA) : Brings amino acids to ribosomes during translation

  31. Transfer RNA • Extensive H-bonding creates four double helical domains, three capped by loops, one by a stem • Only one tRNA structure (alone) is known • Many non-canonical base pairs found in tRNA

  32. ribosomal RNA (rRNA) : Makes up the ribosomes, together with ribosomal proteins. • Ribosomes synthesize proteins • All ribosomes contain large and small subunits • rRNA molecules make up about 2/3 of ribosome • Secondary structure features seem to be conserved, whereas sequence is not • There must be common designs and functions that must be conserved

  33. messenger RNA (mRNA) : Encodes amino acid sequence of a polypeptide

  34. small nuclear RNA (snRNA) :With proteins, forms complexes that are used in RNA processing in eukaryotes. (Not found in prokaryotes.)

  35. DNA Replication, Transcription, and Translation Central Dogma

  36. Central Dogma

  37. Central Dogma DNA Replication

  38. DNA Replication – process of producing identical copies of original DNA • strand separation followed by copying of each strand • fixed by base-pairing rules

  39. DNA replication is semi-conservative.

  40. DNA replication is bidirectional. • involves two replication forks that move in opposite direction

  41. DNA Replication • Begins at specific start sites • in E. coli, origin of replication, oriC locus • binding site for dnaA, initiation protein • rich in A-T