1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: How Eukaryotic Genomes Work and Evolve Two features of eukaryotic genomes are a major information-processing challenge: – First, the typical eukaryotic genome is much larger than that of a prokaryotic cell – Second, cell specialization limits the expression of many genes to specific cells The DNA-protein complex, called chromatin, is ordered into higher structural levels than the DNA- protein complex in prokaryotes

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 19.1: Chromatin structure is based on successive levels of DNA packing Eukaryotic DNA is precisely combined with a large amount of protein Eukaryotic chromosomes contain an enormous amount of DNA relative to their condensed length

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nucleosomes, or “Beads on a String” Proteins called histones are responsible for the first level of DNA packing in chromatin The association of DNA and histones seems to remain intact throughout the cell cycle In electron micrographs, unfolded chromatin has the appearance of beads on a string Each “bead” is a nucleosome, the basic unit of DNA packing Animation: DNA Packing Animation: DNA Packing

4. LE 19-2a DNA double helix Histone tails His- tones Linker DNA (“string”) Nucleosome (“bead”) 10 nm 2 nm Histone H1 Nucleosomes (10-nm fiber)

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Higher Levels of DNA Packing The next level of packing forms the 30-nm chromatin fiber

6. LE 19-2b 30 nm Nucleosome 30-nm fiber

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In turn, the 30-nm fiber forms looped domains, making up a 300-nm fiber

8. LE 19-2c 300 nm Loops Scaffold Protein scaffold Looped domains (300-nm fiber)

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In a mitotic chromosome, the looped domains coil and fold, forming the metaphase chromosome

10. LE 19-2d Metaphase chromosome 700 nm 1,400 nm

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Interphase chromatin is usually much less condensed than that of mitotic chromosomes Much of the interphase chromatin is present as a 10-nm fiber, and some is 30-nm fiber, which in some regions is folded into looped domains Interphase chromosomes have highly condensed areas, called heterochromatin, and less compacted areas, called euchromatin

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 19.2: Gene expression can be regulated at any stage, but the key step is transcription All organisms must regulate which genes are expressed at any given time A multicellular organism’s cells undergo cell differentiation, specialization in form and function

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Differential Gene Expression Differences between cell types result from differential gene expression, the expression of different genes by cells within the same genome In each type of differentiated cell, a unique subset of genes is expressed Many key stages of gene expression can be regulated in eukaryotic cells

14. LE 19-3 Signal NUCLEUS DNA RNA Chromatin Gene available for transcription Gene Exon Intro Transcription Primary transcript RNA processing Cap Tail mRNA in nucleus Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Translation Degradation of mRNA Polypeptide Cleavage Chemical modification Transport to cellular destination Degradation of protein Active protein Degraded protein

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings DNA Methylation DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species In some species, DNA methylation causes long- term inactivation of genes in cellular differentiation In genomic imprinting, methylation turns off either the maternal or paternal alleles of certain genes at the start of development

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Roles of Transcription Factors To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called transcription factors General transcription factors are essential for the transcription of all protein-coding genes In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Enhancers and Specific Transcription Factors Proximal control elements are located close to the promoter Distal control elements, groups of which are called enhancers, may be far away from a gene or even in an intron An activator is a protein that binds to an enhancer and stimulates transcription of a gene Animation: Initiation of Transcription Animation: Initiation of Transcription

20. LE 19-6 Distal control element Activators Enhancer DNA DNA-bending protein TATA box Promoter Gene General transcription factors Group of mediator proteins RNA polymerase II RNA polymerase II RNA synthesis Transcription Initiation complex

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Some transcription factors function as repressors, inhibiting expression of a particular gene Some activators and repressors act indirectly by influencing chromatin structure

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Coordinately Controlled Genes Unlike the genes of a prokaryotic operon, coordinately controlled eukaryotic genes each have a promoter and control elements The same regulatory sequences are common to all the genes of a group, enabling recognition by the same specific transcription factors

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Mechanisms of Post-Transcriptional Regulation Transcription alone does not account for gene expression More and more examples are being found of regulatory mechanisms that operate at various stages after transcription Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings RNA Processing In alternative RNA splicing, different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns Animation: RNA Processing Animation: RNA Processing

25. LE 19-8 Primary RNA transcript DNA or Exons RNA splicing mRNA

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings mRNA Degradation The life span of mRNA molecules in the cytoplasm is a key to determining the protein synthesis The mRNA life span is determined in part by sequences in the leader and trailer regions

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Initiation of Translation The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA Alternatively, translation of all mRNAs in a cell may be regulated simultaneously

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Protein Processing and Degradation After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control Proteasomes are giant protein complexes that bind protein molecules and degrade them Animation: Protein Processing Animation: Protein Processing Animation: Protein Degradation Animation: Protein Degradation

29. LE 19-10 Protein to be degraded Ubiquitinated protein Proteasome Protein entering a proteasome Protein fragments (peptides) Proteasome and ubiquitin to be recycled Ubiquitin

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 19.3: Cancer results from genetic changes that affect cell cycle control The gene regulation systems that go wrong during cancer are very same systems that play important roles in embryonic development Thus, research into the molecular basis of cancer has benefited from and informed many other fields of biology

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Types of Genes Associated with Cancer Genes that normally regulate cell growth and division during the cell cycle include: – Genes for growth factors – Their receptors – Intracellular molecules of signaling pathways Mutations altering any of these genes in somatic cells can lead to cancer

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Oncogenes and Proto-Oncogenes Oncogenes are cancer-causing genes Proto-oncogenes are normal cellular genes that code for proteins that stimulate normal cell growth and division A DNA change that makes a proto-oncogene excessively active converts it to an oncogene, which may promote excessive cell division and cancer

33. LE 19-11 Proto-oncogene DNA Translocation or transposition: gene moved to new locus, under new controls New promoter Gene amplification: multiple copies of the gene Point mutation within a control element Oncogene Point mutation within the gene Normal growth-stimulating protein in excess Normal growth-stimulating protein in excess Normal growth-stimulating protein in excess Hyperactive or degradation- resistant protein

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Tumor-Suppressor Genes Tumor-suppressor genes encode proteins that inhibit abnormal cell division Any decrease in the normal activity of a tumor- suppressor protein may contribute to cancer

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Multistep Model of Cancer Development More than one somatic mutation is generally needed to produce a full-fledged cancer cell About a half dozen DNA changes must occur for a cell to become fully cancerous These changes usually include at least one active oncogene and mutation or loss of several tumor- suppressor genes Colorectal cancer, with 135,000 new cases and 60,000 deaths in the United States each year, illustrates a multistep cancer path

36. LE 19-13 Colon Colon wall Loss of tumor- suppressor gene APC (or other) Normal colon epithelial cells Small benign growth (polyp) Larger benign growth (adenoma) Activation of ras oncogene Loss of tumor- suppressor gene DCC Loss of tumor- suppressor gene p53 Additional mutations Malignant tumor (carcinoma)

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Certain viruses promote cancer by integration of viral DNA into a cell’s genome By this process, a retrovirus may donate an oncogene to the cell Viruses seem to play a role in about 15% of human cancer cases worldwide

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Inherited Predisposition to Cancer The fact that multiple genetic changes are required to produce a cancer cell helps explain the predispositions to cancer that run in some families Individuals who inherit a mutant oncogene or tumor-suppressor allele have an increased risk of developing certain types of cancer

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 19.4: Eukaryotic genomes can have many noncoding DNA sequences in addition to genes The bulk of most eukaryotic genomes consists of noncoding DNA sequences, often described in the past as “junk DNA” However, much evidence is accumulating that noncoding DNA plays important roles in the cell

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Relationship Between Genomic Composition and Organismal Complexity Compared with prokaryotic genomes, the genomes of eukaryotes: – Generally are larger – Have longer genes – Contain much more noncoding DNA

41. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The sequencing of the human genome reveals what makes up most of the 98.5% of the genome that does not code for proteins, rRNAs, or tRNAs Most intergenic DNA is repetitive DNA, present in multiple copies in the genome About three-fourths of repetitive DNA is made up of transposable elements and sequences related to them

42. LE 19-14 Exons (regions of genes coding for protein, rRNA, or tRNA) (1.5%) Alu elements (10%) Simple sequence DNA (3%) Large-segment duplications (5–6%) Unique noncoding DNA (15%) Introns and regulatory sequences (24%) Repetitive DNA that includes transposable elements and related sequences (44%) Repetitive DNA unrelated to transposable elements (about 15%)

43. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Transposable Elements and Related Sequences The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn McClintock identified changes in the color of corn kernels that made sense only by postulating that some genetic elements move from other genome locations into the genes for kernel color

44. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

45. Movement of Transposons and Retrotransposons Eukaryotic transposable elements are of two types: – Transposons, which move within a genome by means of a DNA intermediate – Retrotransposons, which move by means of an RNA intermediate

46. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Genes and Multigene Families Most eukaryotic genes are present in one copy per haploid set of chromosomes The rest of the genome occurs in multigene families, collections of identical or very similar genes

47. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The classic examples of multigene families of nonidentical genes are two related families of genes that encode globins Globin gene family clusters also include pseudogenes, nonfunctional nucleotide sequences that are similar to the functional genes

48. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 19.5: Duplications, rearrangements, and mutations of DNA contribute to genome evolution The basis of change at the genomic level is mutation, underlying much of genome evolution The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification

49. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Duplication of Chromosome Sets Accidents in meiosis can lead to one or more extra sets of chromosomes, a condition known as polyploidy The genes in one or more of the extra sets can diverge by accumulating mutations; these variations may persist if the organism carrying them survives and reproduces

50. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Duplication and Divergence of DNA Segments Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region

51. LE 19-18 Nonsister chromatids Transposable element Gene Crossover Incorrect pairing of two homologues during meiosis and

52. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolution of Genes with Related Functions: The Human Globin Genes The genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged After the duplication events, differences between the genes in the globin family arose from mutations that accumulated in the gene copies over many generations

53. LE 19-19 Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations Ancestral globin gene    11 11 22     AA  -Globin gene family on chromosome 16   -Globin gene family on chromosome 11          Evolutionary time

54. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Subsequent duplications of these genes and random mutations gave rise to the present globin genes, which code for oxygen-binding proteins

55. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation

56. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Evolution of Genes with Novel Functions The copies of some duplicated genes have diverged so much in evolution that the functions of their encoded proteins are now very different