Chemistry 501 Handout 24 Genes and Chromosomes Chapter 24

1. Chemistry 501 Handout 24Genes and ChromosomesChapter 24 Dep. of Chemistry & Biochemistry Prof. Indig Lehninger. Principles of Biochemistry. by Nelson and Cox, 5th Edition; W.H. Freeman and Company

2. Colinearity of the coding nucleotide sequences of DNA and mRNA and the amino acid sequence of a polypeptide chain. codon

3. DNA molecules are much longer than the cellular or viral packages that contain them

4. DNA from a lysed E.coli cell

6. Eukaryotic Chromosomes Sister chromatids

7. A dividing mitochondrion The mtDNA is replicated each time the mitochondrion divides

8. Introns in two eukaryotic genes

9. Types of sequences in the human genome Short interspersed elements 100 to 300 bp Long interspersed elements 6 to 8 kbp (encode enzymes for transposition) 1.5 to 11 kbp Simple sequence repeats Large segmental duplications

10. Important structural elements of a yeast chromosome centromere

11. Supercoiling of DNA Supercoiling induced by separating the strands of a helical structure

12. Relaxed and supercoiled plasmid DNAs

13. Most cellular DNA is underwound DNA underwinding is defined by topological linking number 84 bp

14. Superhelical density s = DLk/Lk0 = -2/200 = -0.01 1% of the helical turns present in the DNA (in its B form) has been removed Linking number applied to closed-circular DNA molecules Negative and positive supercoils underwinding overwinding topoisomers 2,100 bp

15. Linking number can be broken down into two structural components Twist (Tw) and Writhe (Wr) Measure of the coiling of the helix axis Local twisting or spatial relationship of neighboring base pair Lk = Tw + Wr

17. In addition of causing supercoiling and making strand separation somewhat easier, the underwinding of DNA facilitates structural changes in the molecule facilitates the partial strand separation needed to promote cruciform formation at appropriate sequences

18. Topoisomerases catalyze changes in the linking number of DNA Type 1: single strand breaks; changes Lk in increments of 1 Type 2: double strand breaks; changes Lk in increments of 2 Type 1 (Dt)

19. Bacterial type 1 topoisomerase alter linking number Generally relax DNA by removing negative supercoils (increasing Lk)

22. Proposed mechanism for the alteration of linking number by eukaryotic type IIA topoisomerase Two ATPs are bound and hydrolyzed during this cycle

23. Without topoisomerases, cells cannot replicate or package their DNA, or express their genes, and they die. They are important drug targets for bacterial infections and cancer Topoisomerase inhibitors are important pharmaceutical agents antibiotics Chemotherapeutic agents

24. DNA compaction requires a special form of supercoiling The supercoils are right-handed in a negatively supercoiled DNA molecule, and they tend to be extended and narrow rather than compacted, often with multiple branches. Plectonemic supercoiling

25. DNA compaction requires a special form of supercoiling Solenoidal supercoiling provides a much greater degree of compaction (tight left-handed turns) Same DNA molecule, drawn in scale

27. Chromatin assembly

28. Histone cores do not bind randomly to DNA; rather, they tend to position themselves at certain locations In some cases seems to depend on a local abundance of A=T base pairs in the DNA helix where it is in contact with the histone

29. The structure of chromosomes The chromosomal material, chromatin, consists of DNA and proteins. Nucleosomes are the fundamental organizational unit of chromatin Beginning with nucleosomes, eukaryotic chromosomal DNA is packed in a sucession of higher-order structures that ultimately yield the compact chromosome beads-in-a-string Nucleosomes

30. DNA wrapped around the nucleosome core Eight histone proteins Two of each: H2A, H2B, H3, and H4 Top view Side view Histone complex Nucleosome with 146 bp of bound DNA The DNA binds in a left-handed solenoidal supercoil that circumnavigates the histone complex 1.8 times

31. The 30 nm fiber, a higher-order organization of nucleosomes.

32. Compaction of DNA in a eukaryotic chromosome. Loops of chromosomal DNA attached to a nuclear scaffold. Next level of organization (after 30 nm fiber) DNA compaction in eukaryotes is likely to involve coils upon coils upon coils….

33. Structure of SMC proteins. (Structural Maintenance of Chromosomes) also bound to additional regulatory proteins (not shown)

34. Model for the roles of cohesins and condensins during the eukaryotic cell cycle.

35. Bacterial DNA is also highly organized. Looped domains of the E. coli chromosome. E. coli nucleoids.

36. Changes in chromosome structure during the eukaryotic cell cycle

37. A partially unraveled human chromosome, revealing numerous loops of DNA attached to a scaffoldlike structure.

38. Several variants of histones H3, H2A, and H2B are known Information that is passed from one generation to another but is not encoded in DNA is referred to as epigenetic information. Much of it is in the form of covalent modification of histones and/or placement of histone variants in chromosome Histone-fold domain (common to all core histones) Sites of Lys/Arg residue methylation and Ser phosphorylation are indicated

39. ChIP-chip experiment designed to reveal the genomic DNA sequences to which a particular histone variant binds.

40. The pattern of hybridization on the microarray reveals the DNA sequences bound by the nucleosomes with the histone variant.