Ch 19 Chromatin structure is based on successive levels of DNA packing DNA + protein packed together = chromatin

1. Ch 19 • Chromatin structure is based on successive levels of DNA packing • DNA + protein packed together = chromatin • Nucleosomes= DNA(-) & histones(+) folded together like beads on a string • Histones bind tightly b/c they are + and DNA is - • Nucleosomes- basic structural unit of DNA

2. 2 nm DNA double helix Histone tails His- tones 10 nm Histone H1 Linker DNA (“string”) Nucleosome (“bad”) (a) Nucleosomes (10-nm fiber) • In electron micrographs • Unfolded chromatin looks like beads on a string • Each “bead” is a nucleosome • The basic unit of DNA packing Figure 19.2 a

3. Euchromatin-stringy form/active txn • Heterochromatin-condensed (chromosomes/cell division)

4. Regulation of gene expression: • In both prok & euk’s gene expression is primarily regulated at the level of txn • DNA methylation inactivates genes/↓’s txn (inactive X chromosomes) • Histone acetylation-acetyl groups added to aa’s of histone proteins/so the chromatin is packed less tight & so ↑’s txn

5. During DNA replication. methylation of the DNA is maintained b/c methylation enzymes act at DNA sites where 1 strand is already methylated & thus correctly methylates daughter strands after replication. • Methylation, acetylation, & regulation of chromatin structure are all forms of epigenetic inheritance

6. Regulation @ txn initiation: • Have control elements: distal (also called enhancers) & proximal • Activators bind to the enhancers to activate txn

7. Gene regulation can occur after txn, during RNA processing, B4 tsln, & after tsln • Oncogenes-cancer causing genes • Proto-oncogenes-code for proteins that regulate normal cell growth • ** normally help regulate cell division. • They can be involved in producing proteins for cell adhesion • They are similar to oncogenes found in retroviruses • Protoonco become onco when there is a mutation causes an ↑ in the product of the protoonce gene

8. Tumor suppressor genes also can lead to cancer if a mutation occurs in the gene • Risk of cancer ↑’s w/age b/c the longer we live the more mutations we accumulate

9. Transposons- sections of DNA that move around w/in the genome • Retrotransposons-can move around BUT w/ an RNA intermediate

10. One of the unique characteristics of retrotransposons is that tsln of their RNA transcript produces an enzyme (reverse transcriptase) that converts the RNA back to DNA • **so reverse transcriptase can be found in cells NOT infected w/retrovirus

11. Duplications, rearrangements, & mutations of DNA contribute to evolution • Identical or similar genes that have evolved from gene duplication are called multigene families • Rearrangement of the genome also plays an important role in the immune system

12. Ch20 • Biotechnology • Bacteria are good candidates for us to manipulate/ they have a genome & plasmids • Plasmids are small circular pieces of DNA that are not a regular part of the bacteria DNA & can be used to produce gene products for us

13. Plasmids are important in biotechnology b/c they are a vehicle for the insertion of foreign genes into bacteria

14. Plasmids are isolated from bacteria cell & then has foreign DNA inserted into it to form a recombinant DNA molecule • Then the plasmid is returned to a bacteria cell making a recombinant bacteria which then reproduces to form clones • Cloned genes are useful to make many copies of a gene & to make a protein product

15. Process of cloning genes: • Extract plasmid DNA from bacterial cells. • Cut the plasmid DNA using restriction enzymes • Hydrogen-bond the plasmid DNA to nonplasmid DNA fragments • Use ligase to seal plasmid DNA to nonplasmid DNA. • Transform bacteria with recombinant DNA molecule

16. Probes can be used then to identify the colonies that contain the gene of interest • Probes are short, ss DNA or RNA segments used to identify DNA fragments w/ a particular seq

17. In order to identify a specific restriction fragment using a probe: • The fragments must be separated by electrophoresis • fragments must be treated w/ heat or chem’s to separate the DNA strands • The probe must be hybridized with the fragment

18. Bacteria also have restriction enzymes • Restriction enzymes are enzymes that cut/cleave nucleic acids (DNA/RNA) at specific sites • They protect the bacteria from DNA from other organisms (phages, etc..)

19. They protect their own DNA by methylation of cytosines & adenines • Restriction enzymes cut the S-P backbone at specific DNA seq’s & the overlapping nt’s are called “sticky ends”

20. There can be problems putting euk genes into a prok plasmid • Bacteria can’t remove introns • Doesn’t have the tools for RNA processing

21. PCR polymerase chain rxn • Allows researchers to make many copies of a specified seq of DNA

22. Gel electrophoresis is used to separate nucleic acids or proteins based on size, charge, polarity, or other physical properties

23. Diff’s b/w a genomic library & cDNA library • A genomic library can be made using a restriction enzyme & DNA ligase only, a cDNA library needs both of these as well as reverse transcriptase & DNA pol • A genomic library has both noncoding seq’s & coding seq’s, a cDNA library has only coding seq’s • A genomic library is identical regardless of the cell type used to make it, the content of a cDNA library depends on the cell type used in its construction.

24. Ch 21 • Embryonic development involves cell division, cell differentiation, & morphogenesis • Cell division- zygote gives rise to a large # of cells • Cell differentiation- Cells become specialized in structure & funct • Morphogenesis-Processes that give shape to the organism & its various parts

25. Plants & animals have a few diff’s in their development • In animals, BUT not plants movements of cells & tissues are necessary to transform the early embryo into the 3D form of the organism • 1 striking diff b/w development in plants & development in animals is the importance of cell movement in animal embryos.

26. In plants, BUT not animals, morphogenesis & growth in overall size occurs throughout the life of the organism (apical meristems) • pattern formation is continuous in plants & limited to early development in animals. • Apical meristem- perpetually embryonic regions of plants responsible for continual growth & formation of new organs

27. Cloning can be done quite easily w/plants & you may have taken cuttings yourself & participated in cloning • Sometimes differentiation doesn’t cause irreversible changes in the DNA • Carrots were cloned using cells from the root

28. Cloning in animals is a little more tricky • They often show many defects that is likely b/c the epigenetic features of the chromatin in differentiated donor nuclei are not completely erased in the cloning process.

29. Stem cells is an unspecialized cell that can reproduce itself indefinitely & under special cond’s differentiate into 1 or more cell types • Pluripotent-can give rise to many but not all cell types • Totipotent-A cell that remains entirely flexible in its developmental possibilities • In animals, embryonic stem cells differ from adult stem cells in that embryonic stem cells are totipotent, & adult stem cells are pluripotent.

30. Homeotic genes-Master regulatory genes that control the overall body plan of animals & plants • Mutations in these genes lead to transformations in the identity of entire body parts

31. Apoptosis-cell suicide is triggered by signals that say “ITS TIME TO DIE”

32. The unit of genetic organization in all living organisms is the chromosome. Chromatin structure is based on successive levels of DNA packing. • Describe the structure & function of chromatin as it is packaged into chromosomes. You may wish to include a diagram as part of your description • Describe 2 ways that chromatin structure can be modified to regulate gene expression • Explain how duplications, mutations, & rearrangements of DNA contribute to evolution. • How does the structure & function of the chromosome differ in prokaryotes

33. Biotechnology has allowed us to use many diff techniques in order to study the genomes of living organisms • a.) Describe how a plasmid can be genetically modified to include a piece of foreign DNA that alters the phenotype of bacterial cells transformed with the modified plasmid. • b.) Describe a procedure to determine which bacterial cells have been successfully transformed.

34. The human genome illustrates both continuity & change. • Describe the essential features of 2 of the procedures/techniques below. For each of the procedures you describe, explain how its application contributes to your understanding of genetics. • -The use of a bacterial plasmid to clone & sequence a human gene • -Polymerase chain reaction (PCR) • -Restriction fragment length polymorphism (RFLP) analysis • b.) All humans are nearly identical in coding sequences & have many proteins that are identical in structure and function. Nevertheless, each human has a unique DNA fingerprint. Explain this apparent contradiction.

35. Describe the 3 stages of embryonic development Describe the process of cloning a multicellular animal. You may use a diagram to help you explain it.