Job 38:36

1. Job 38:36 36 Who hath put wisdom in the inward parts? or who hath given understanding to the heart?

2. The Eukaryotic Genome Timothy G. Standish, Ph. D.

3. Eukaryotes Have Large Complex Geneomes • The human genome is about 3 x 109 base pairs or ≈ 1 m of DNA • That’s a lot more than a typical bacterial genome • E. coli has 4.3 x 106 bases in its genome • Because humans are diploid, each nucleus contains 6 x 109 base pairs or ≈ 2 m of DNA • That is a lot to pack into a little nucleus!

4. Only a Subset of Genes is Expressed at any Given Time • It takes lots of energy to express genes • Thus it would be wasteful to express all genes all the time • By differential expression of genes, cells can respond to changes in the environment • Differential expression, allows cells to specialize in multicelled organisms. • Differential expression also allows organisms to develop over time.

5. Eukaryotic DNA Must be Packaged • Eukaryotic DNA exhibits many levels of packaging • The fundamental unit is the nucleosome, DNA wound around histone proteins • Nucleosomes arrange themselves together to form higher and higher levels of packaging.

6. T G A Histone octomer C GC TA Histone proteins GC CG TA AT AT CG 2 nm GC TA Packaging DNA B DNA Helix

7. Histone proteins 2 nm Packaging DNA T G A Histone octomer C GC TA GC CG TA AT AT CG B DNA Helix GC TA

8. 11 nm Histone proteins Nucleosome 2 nm Packaging DNA T G A Histone octomer C GC TA GC CG TA AT AT CG B DNA Helix GC TA

9. GC CG TA AT AT CG GC TA Packaging DNA

10. GC CG TA AT AT CG GC TA Packaging DNA

11. 11 nm GC CG TA AT 30 nm 200 nm AT CG GC TA Protein scaffold Packaging DNA “Beads on a string” Looped Domains Tight helical fiber

12. 11 nm Nucleosomes 30 nm 700 nm 200 nm T Looped Domains Tight helical fiber G C A 2 nm Protein scaffold B DNA Helix Packaging DNA Metaphase Chromosome

13. Highly Packaged DNA Cannot be Expressed • The most highly packaged form of DNA is “heterochromatin” • Heterochromatin cannot be transcribed, therefore expression of genes is prevented • Chromosome puffs on some insect chromosomes illustrate where active gene expression is going on

14. Cytoplasm Nuclear pores Degradation AAAAAA AAAAAA DNA Transcription Modification RNA RNA Processing G G Degradation etc. Ribosome mRNA G AAAAAA Export Translation Nucleus Control of Gene Expression Packaging Transportation

15. Increasing cost Logical Expression Control Points The logical place to control expression is before the gene is transcribed • DNA packaging • Transcription • RNA processing • mRNA Export • mRNA masking/unmasking and/or modification • mRNA degradation • Translation • Protein modification • Protein transport • Protein degradation

16. A “Simple” Eukaryotic Gene Transcription Start Site 3’ Untranslated Region 5’ Untranslated Region Introns 5’ 3’ Int. 1 Int. 2 Exon 1 Exon 2 Exon 3 Promoter/ Control Region Terminator Sequence Exons RNA Transcript

17. DNA 5’ 3’ Enhancer Promoter Transcribed Region 3’ 5’ TF 3’ 5’ TF TF RNA Pol. RNA Pol. RNA 5’ Enhancers Many bases TF TF TF

18. Eukaryotic mRNA 5’ Untranslated Region 3’ Untranslated Region 5’ 3’ G AAAAA Exon 1 Exon 2 Exon 3 Protein Coding Region 5’ Cap 3’ Poly A Tail • RNA processing achieves three things: • Removal of introns • Addition of a 5’ cap • Addition of a 3’ tail • This signals the mRNA is ready to move out of the nucleus and may control its life span in the cytoplasm

19. “Junk” DNA • It is common for only a small portion of a eukaryotic cell’s DNA to code for proteins • In humans, only about 3 % of DNA actually codes for the about 100,000 proteins; 50,000 in older estimates, 150,000 in more recent estimates • Non-coding DNA was once called “junk” DNA as it was thought to be the molecular debris left over from the process of evolution • We now know that much non-coding DNA plays important roles like regulating expression and maintaining the integrity of chromosomes

20. a b Fe b a The Globin Gene Family • Globin genes code for the protein portion of hemoglobin • In adults, hemoglobin is made up of an iron containing heme molecule surrounded by 4 globin proteins: 2 a globins and 2 b globins • During development, different globin genes are expressed which alter the oxygen affinity of embryonic and fetal hemoglobin

21. Ancestral Globin gene Duplication Mutation a b Transposition Chromosome 16 Chromosome 11 a b Duplication and Mutation z a e g b Duplication and Mutation a2 a1 yz ya2 yq ya1 z Gg yb Ag e d b Embryo Fetus and Adult Embryo Fetus Adult Model For Evolution Of The Globin Gene Family Pseudo genes (y) resemble genes, but may lack introns and, along with other differences, typically have stop codons coming soon after the start codons.

22. Antibody Diversity Results From Differential Splicing • Humans produce antibodies to many millions of different antigens • The human genome codes for less than 200,000 genes • Antibodies are proteins, so how are many millions of different antibodies produced by so few genes? • The answer lies in differential splicing of DNA

23. Antigen binding site Antigen binding site V V V V Constant Constant Constant Constant SS SS Light Chain Light Chain SS SS Antibody Structure Heavy Chains

24. Antigen 3 Variable Heavy Variable Light Antigen Binding Antigen 1 Antigen 2

25. V1 V2 V3 V4 J1 J2 J3 Random splicing of DNA as cell differentiates V1 V2 V3 J2 Intron Constant Transcription V3 J2 Intron Constant RNA Processing Translation produces a light chain with a variable region at one end V3 J2 Constant V3 J2 Constant An Antibody “Gene” • DNA coding for antibodies are made up of many exons referred to as genes • Different exons are spliced together to make the many different antibodies Intron Constant

26. IgM - A pentamer - First antibody to appear following exposure to an antigen. Because it declines rapidly in the blood, high IgM levels indicate a current infection. IgG - A monomer - Most abundant antibody in blood. IgG easily leaves the circulatory system to fight infection and crosses the placenta conferring passive immunity to a fetus. IgD - A monomer - Found on the surface of B cells probably allowing recognition of antigens thus triggering differentiation into plasma and memory B cells IgE - A monomer - The least common antibody. The tails attach to mast cells and basophils. When antigens bind, they signal release of histamine. IgA - A dimer - Produced by cells in the mucus membranes to prevent attachment of pathogens. IgA is also found in many body secretions including milk. Classes of Immunoglogulins

27. Cancer • Regulation of cell division is vital in multi-celled organisms • Cancer can be defined as uncontrolled division of cells • As regulation of cells is achieved through genes expressed in those cells mutation of those genes can result in the loss of regulation and consequently cancer

28. The End