1. Aim: How is DNA organized in a eukaryotic cell?

2. Why is the control of gene expression more complex in eukaryotes than prokaryotes ? Eukaryotes have: 1)more functional genes to regulate. ( estimated 35,000 genes in the human genome) (4300 genes in E.coli bacteria) 2) introns that must be excised before functional mRNA is made. 3) DNA wrapped in histone protein complexes called nucleosomes.

3. Why is the control of gene expression more complex in eukaryotes than prokaryotes ? (2) 4) cells that require cell specialization or differentiation (if multicellular) a) genes expressed in nerve cells may be different from genes expressed in muscle cells (only 3% - 5% of genes expressed at any one time) b) genes may be amplified (many copies) c) genes are affected by the way DNA is packaged in the nucleus Densely packed areas are inactivated. Loosely packed areas are being actively transcribed

4. How is DNA packaged in a eukaryotic genome ? Eukaryotic DNA combines with histone proteins to form chromatin fibers. - Histone proteins are small and contain a high proportion of positively charged amino acids (arginine & lysine) which bind tightly to negatively charged DNA. - Histones are universal in eukaryotes.

5. How is DNA packaged in a eukaryotic genome ? (2) - Heterochromatin remains highly condensed throughout the cell cycle and is not transcribed. It is found in Barr bodies. - Euchromatin is less condensed during interphase and is actively transcribed. It becomes highly condensed during mitosis.

6. Levels of DNA packing (smallest to largest) 1) Exposed DNA (2nm) 2) Nucleosomes (11nm) (beads) - basic unit of DNA packing. (DNA + 4 pairs of histone proteins) A fifth histone attaches to the “bead” further condensing the nucleosome.

7. Levels of DNA packing (smallest to largest) Nucleosomes may control gene expression by controlling access of transcription proteins to DNA.

8. Levels of DNA packing (smallest to largest) 3) Chromatin fiber (30 nm) 4) Looped domains – chromatin fibers that fold into loops. A nonhistone protein ‘scaffold’ maintains the loop and keeps it attached to the nuclear membrane.

9. Levels of DNA packing (smallest to largest) 5) Metaphase chromosome (1400 nm).

10. How do noncoding sequences and gene duplications account for much of the eukaryotic genome ? DNA in eukaryotes is organized differently from prokaryotes. Prokaryotes – most DNA codes for protein (mRNA), tRNA, or rRNA. Small amounts of noncoding DNA consist mainly of control sequences like promoters and operators. Eukaryotes – most DNA does NOT encode protein or RNA. Coding sequences may be interrupted by long stretches of noncoding DNA (introns or tandemly repetitive DNA) Interphase chromosomes have areas that remain highly condensed, heterochromatin, and less compacted areas, euchromatin.

11. What are some levels of tandemly repetitive DNA ? I: Highly repetitive DNA (10 – 25 % of the genome) A) also called satellite DNA B) never transcribed into protein C) multiple copies (thousands) II: Moderately repetitive DNA (20% of genome) III: Single gene DNA (70% of genome)

12. Types of highly repetitive DNA 1) centromeres (chromosome centers) 2) telomeres (chromosome ends). - may facilitate cell division - maintains chromosomes stability on lagging strand - in humans, composed of 250 – 1500 repetitions of the base sequence TTAGGG

13. Types of highly repetitive DNA 3) pseudogenes – nonfunctional gene that has DNA sequence similar to a functional gene; but because of a mutation, lacks sites necessary for gene expression. 4) Transposons – generally nonfunctional but may be disease-causing if they interrupt an essential gene.

14. Types of highly repetitive DNA 5) Genes coding for very small rRNA units (5SrRNA) (25000 copies) - adjacent to pseudogenes - needed in developing eggs so that ribosomes can be manufactured quickly - gene sequence reads: 5SrRNA--- pseudogene---spacer---5SrRNA------ pseudogene---spacer---5SrRNA---etc.

15. Moderately Repetitive DNA 1) repeats hundreds of times 2) codes for 3 other rRNA sequence reads: 18SrRNA---6SrRNA--- 28SrRNA---SPACER---18SrRNA---6SrRNA-- -28rRNA---spacer 3) moderately repetitive DNA makes many copies of itself while not affecting the rest of the chromosome. These multiple copies are called polytene regions and exist in what are called lampbrush chromosomes.

17. Single gene DNA o1) only 1% of the eukaryotic chromosome ever codes for mRNA that is actually translated. 2)The other 99% may be composed of intron genes, pseudogenes or transposons that are rarely transcribed into functional mRNA.

18. What are multigene families ? Multigene families – a collection of genes that are similar or identical in sequence a) possibly from same ancestor probably arose by transposition. b) may be clustered or dispersed in the genome

19. What are multigene families ? Example: globin gene family (alpha and beta polypeptide subunits of hemoglobin. embryonic and fetal hemoglobins have a higher affinity for oxygen than the adult forms, allowing efficient oxygen exchange between mother and developing fetus