DNA and Chromosomes

1. DNA and Chromosomes

2. Genes are carried by Chromosomes Two plant cells visualized by light microscope, DNA stained with DAPI Chromosome in Cells DNA (deoxyribonucleic acid) AGTC Human 46 chromosomes 22 homologs, x, or x/y

3. Experimental procedures demonstrating that DNA is the genetic material 1940s

4. The Structure and Function of DNA • Genetic information is carried in the linear sequence of nucleotides in DNA • Genetic information contains instructions to synthesize proteins • DNA forms double helix with two complimentary strands holding together by hydrogen bonds between A-T (2 bonds) and G-C (3 bonds) • DNA duplication occurs using one strand of parental DNA as template to form complimentary pairs with a new DNA strand. • DNA is in nucleus in eucaryotes

5. 1953 Watson and Crick determined the structure of DNA DNA and its Building Nucleotides: Guanine (G), Adenine (A), Cytosine (C), Thymine (T). Polarized strand, 5’->3’ Base inside, sugar outside

6. DNA and its Building Antiparallel strands

7. DNA Pairs A always pairs with T, and G with C, A-T two hydrogen bonds, G-C three hydrogen bonds

8. DNA Double Helix 10.4 nucleutides/turn; 3.4 nm between nucleutides

9. DNA to Protein Genome: the complete set of information in an organism’s DNA Total length of DNA about 2 meters long in a human cell, encoding about 30000 proteins

10. To carry the genomic information to daughter cells DNA Duplication Using itself as template

11. Cell Nucleus, compartmentalized DNA activity Nuclear pores allow communication Nuclear lamina and cytoskeleton mechanically support the nucleus

12. Chromosomal DNA and its Packaging • A gene is a nucleotide sequene in a DNA molecule that act as a functional unit for protein production, RNA synthesis. • Introns and Exons • Chromosome: single long DNA contains a linear array of many genes. • Human genome contains 2.3x109 DNA nucleotide pairs, with 22 different autosomes and 2 sex chromosomes. • Chromosomal DNA: replication origins, telomeres, centromeres • Histones form the protein core for DNA wrapping • Nucleosome: repeating array of DNA-protein particles • Modification of Chromatin and nucleosomes: histone H1, ATP-driven chromatin remodeling complexes, and enzymatically catalyzed covalent modification of the N-terminal tails of Histones

13. Human Chromosome Complex of DNA and protein is called chromatin 44 homologous chromosomes and 2 sex chromosomes Complementary DNA with different Dyes The arrangement of the full chromosome set is called karyotype

14. Banding Pattern of human chromosomes Giemsa Staining Green line regions: centromeres Encoding ribosome

15. The organization of genes of a human chromosome

17. Conservation between human and mouse genomes Usually important genes are encoded by conserved regions Note: Human chromosome 1 and mouse chromosome 4 mouse human centromere

18. Cell Cycle DNA molecule not only carries genetic information, but also undergoes conformational change Chromosomes exist through the cycle Mitotic and interphase chromosome Single chromosome can only be visible during mitosis

19. Chromosomes at interphase and M phase

20. Three important DNA sequences Telomere, replication origin, centromere

21. DNA Molecules are highly condensed in chromosomes Nucleosomes of interphase under electron microscope Nucleosome: basic level of chromosome/chromatin organization Chromatin: protein-DNA complex Histone: DNA binding protein A: diameter 30 nm; B: further unfolding, beads on a string conformation

22. Nucleosome Structures Histone octamer 2 H2A 2 H2B 2 H3 2 H4

23. X-ray diffraction analyses of crystals Structure of a nucleosome core particle

24. Structural Organization of the Core Histones

25. The Assembly of the Core Histones

26. Notice the long tails of the octamer

27. The bending of DNA in a nucleosome 1. Flexibility of DNAs: A-T riched minor groove inside and G-C riched groove outside 2. DNA bound protein can also help

28. Zigzag model of the 30-nm chromatin fiber

29. Irregularities in the 30-nm fiber Flexible linker, DNA binding proteins Structural modulators: H1 histone, ATP-driven Chromatin remodeling machine, covalent modification of histone tails

30. The function of Histone H1

31. The function of Histone tails

32. Chromatin Remodeling

33. Cyclic Diagram for nucleosome formation and disruption

34. Covalent Modification of core histone tails Acetylation of lysines Mythylation of lysines Phosphorylation of serines Histone acetyl transferase (HAT) Histone deacetylase (HDAC)

36. Summary • DNA, Chromosome • Centromere, telomere, replication origin • Nucleosome, Chromatin, • Histone: H1, H2A, H2B, H3, H4 • Histone octamer, DNA packaging • DNA binding proteins, Histone modifications

37. The Global Structure of Chromosomes • Some rare cases of interphase chromosomes, certain features maybe universal • Representative forms forming typical interphase chromosome • Chromosome at mitosis

38. Lampbrush chromosomes (amphibian oocyte, immature eggs)

39. A model for the structure of a lampbrush chromosome Chromomeres: highly condensed and in general not expressed until unfolding

40. A polytene chromosome from Drosophila salivary gland Dark bands and interbands

41. Electron Microscope image of Drosophila polytene chromosome

42. Chromosome puffs Folding and refolding at a time course of 22 hours

43. RNA synthesis in Chromosome puffs Red: newly synthesized BrUTP; Blue: old ones diffused

44. RNA synthesis in Chromosome puffs

45. RNA synthesis in Chromosome puffs

46. Model of RNA synthesis in Chromosome puffs

47. A model for the structure of an interphase chromosome

48. Position Effects on Gene Expression Heterochromatin: condensed Euchromatin: loose

49. Speculative Model for the heterochromatin at the ends of yeast chromosomes Sir: Silent information regulator binding to unacetylated histone tails

50. Speculative Model for the heterochromatin at the ends of yeast chromosomes DNA-binding proteins recognize DNA sequence close to telomere, recruit Sir proteins and cause histone tail modification, forming heterochromatin