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New Section Nucleic Acids - final group of macromolecules Nucleotides - monomers

transcription. translation. New Section Nucleic Acids - final group of macromolecules Nucleotides - monomers. Central Dogma. RNA. Protein. DNA. replication. Higher levels of cellular organization . Central dogma cannot explain how a cell works.

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New Section Nucleic Acids - final group of macromolecules Nucleotides - monomers

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  1. transcription translation New SectionNucleic Acids - final group of macromolecules Nucleotides - monomers Central Dogma RNA Protein DNA replication

  2. Higher levels of cellular organization Central dogma cannot explain how a cell works Higher levels of organization - e. g. making a chloroplast - require complex interactions of hundreds (thousands) of genes and the context of an existing cell

  3. Lecture Outline Nucleic acid structure *Nucleotide Monomer Linear DNA strand Double-stranded DNA Packaging of DNA into a chromosome DNA replication

  4. Nucleotide has three parts Bases: purines or pyrimidines One to three phosphates DNA - deoxyribose RNA - ribose Panel 2-6

  5. Carbons numbered 1’ - 5’ 5’ Bonds through 5’ and 3’ C form polymer (DNA or RNA) 4’ 1’ 2’ 3’ 2’OH - Ribose 2’H (no OH) deoxyribose Pentose (Monosaccharide) Panel 2-6

  6. Only in RNA Only in DNA Pyrimidines (one N-containing ring) Purines (two N-containing rings) Bases Uracil (U) Adenine (A) cytosine (C) Guanine (G) Thymine (T) Panel 2-6

  7. RNA AMP, GMP, CMP, UMP ADP, GDP, CDP, UDP ATP, GTP, CTP, UTP Monophosphates Diphosphates Triphosphates Energy metabolism DNA dAMP, dGMP, dCMP, dTMP dADP, dGDP, dCDP, dTDP dATP, dGTP, dCTP, dTTP Monophosphates Diphosphates Triphosphates Nucleotide nomenclature Sugar + base = nucleoside Sugar + base + phosphate = nucleotide

  8. Nucleotide to Nucleic Acid ... Bases Linear strand has polarity: 5’ to 3’ ECB 2-25

  9. 5’ C is bonded to Pi base sugar Bonding of nucleotides into strand: Ester bonds through 5’C and 3’C... phosphate

  10. 5’ 3’ 5’ Pi -Pi Chain held together by phosphodiester bonds 3’ 5’ Pi -Pi 3’ Pi -Pi Phosphodiester bond Panel 2-6

  11. Nucleic Acids Nucleic acid structure Nucleotide Monomer Linear DNA strand *Double-stranded DNA Packaging of DNA into chromosome DNA replication Where in the cell do we find DNA?

  12. DNA strands are antiparallel and H bonded Double helix held together by H bonds between bases ECB 5-2

  13. Strands held together by base pairs A + T 2 H-bonds Purine-pyrimidine pairs G + C 3 H-bonds ECB 5-6

  14. 5’ end 3’ end Sugar-phosphate backbone 5’ end 3’ end DNA double helix Bases In center Strands are complementary - if know 1 predict other ECB 5-7

  15. Space filling model Minor groove 10 base pairs per turn Major groove 1 double helix can be millions of base pairs long ECB 5-8 2 nm

  16. DNA is the genetic material Debate raged in 1920s to 1940s; protein or nucleic acid or.. Mid 1940s; Avery MacLeod and McCarthy

  17. DNA sequencing The linear sequence of nucleotides can be determined by DNA sequencing technologies - facility on campus  globin ECB 5-11 Genome Projects Complete sequence of all nuclear DNA from an organism (prokaryotes, yeast, plant, man etc) Human genome (3,000,000,000 nucleotides) Arabidopsis genome: 5,000,000 nucleotides Last lecture in this section - Biotechnology

  18. Introduction to nucleic acids DNA structure Nucleotide Monomer Linear DNA strand Double-stranded DNA *Packaging of DNA into chromosomes DNA Replication

  19. Prokaryotes- Circle of ds DNA Few million base pairs DNA packaging not a big issue Eukaryotes- Multiple chromosomes Few billion base pairs total DNA packaging a big issue Prokaryotes versus eukaryotes ECB 5-12

  20. Levels of DNA packaging in a eukaryotic cell Typical human cell contains about 2 meters of DNA in nucleus Yet the nucleus is only ~10 m in diameter ECB 5-24

  21. DNA condenses in preparation for mitosis and cell division Cell cycle Chromosome Extended Condensed ECB 5-17

  22. Transmission EM view of a chromosome Mitotic Chromosome (H shape) Interphase ECB 5-20

  23. Telomeres Centromere - region where two chromatids are held together CHROMOSOME STRUCTURE Condensed chromosome has two copies of each double helix held together Duplicated chromosome drawn as an ‘H’ Each line is double-stranded DNA 1 strand is a chromatid

  24. Extent of chromatin condensation varies at different locations on chromosome Heterochromatin Condensed chromatin Stays condensed throughout cell cycle Common around centromeres and telomeres Does not code for protein Euchromatin “true chromatin” Condenses prior to division Transcription occurs from euchromatin that is not highly condensed Most chromatin in humans does not code for RNA or protein

  25. X-chromosome Inactivation (heterochromatin) Female mammals - 2 X chromosomes Early embryos, random selection of X chromosome for inactivation (condensed into inactive heterochromatin) Calico Cat. Black coat color gene is on one X chromosome, yellow coat color is on the other X chromosome. Random inactivation (condensation) during early embryogenesis results in patches of different coat colors.

  26. Introduction to nucleic acids DNA structure Nucleotide Monomer Linear DNA strand Double-stranded DNA Packaging of DNA into chromosomes *DNA Replication

  27. Outline Replication is semi-conservative and bidirectional Biochemistry of replication transcription translation Problem of replicating chromosome ends (telomeres) Central Dogma DNA RNA Protein replication Begin with DNA replication (Nucleus of eukaryote, cytoplasm of prokaryote)

  28. ECB 6-3 Semiconservative- both new DNA helices contain 1 old and 1 new strand Replication is semi-conservative ECB 6-2 Parental DNA strand = template

  29. 1. Selection of sites for initiation of DNA synthesis 2. Separate DNA strands (form open complex) 3. Directionality of DNA synthesis 4. Assemble molecules for DNA synthesis

  30. Double-stranded DNA 5’ 5’ 3’ 3’ 3’ 3’ 5’ 5’ Single-stranded DNA ready for DNA synthesis Double helix opened with aid of initiator proteins 2 Replication forks Parental DNA = template specific sequence Origin of replication

  31. Eukaryotes- Multiple origins on each chromosome Human-~10,000 origins total Prokaryotes versus eukaryotes ori Prokaryotes- 1 origin of replication ~100 base pairs

  32. Origins of replication Bidirectional fork movement Replication forks Replication bubble Replication is bidirectional ECB 6-9 Prok or Euk?

  33. 1. Selection of sites for initiation of DNA synthesis 3. Directionality of DNA synthesis 2. Separate DNA strands (form open complex) 4. Assemble molecules for DNA synthesis

  34. template 3’ end ECB 6-10 5’ end DNA polymerase -adds nuclotides at 3’ end 3’ OH Incoming nucleotide (triphosphate) adds at 3’OH of growing chain (condensation rx driven by cleavage of PiPi) Synthesis occurs in 5’ - 3’ direction Specificity of which base adds depends on base pairing with template strand

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