1. The Chromosomes of Organelles Outside the Nucleus Exhibit Non- Mendelian Patterns of Inheritance

2. Outline of Chapter 15 The structure and function of mitochondrial and chloroplast genomes, including a description of their size, shape replication, and expression The structure and function of mitochondrial and chloroplast genomes, including a description of their size, shape replication, and expression How genetic transmission revealed and explained non-Mendelian patterns of inheritance How genetic transmission revealed and explained non-Mendelian patterns of inheritance A comprehensive example of mutations in mitochondrial DNA that affect human health A comprehensive example of mutations in mitochondrial DNA that affect human health

3. Mitochondrial and chloroplasts are organelles of energy conversion that carry their own DNA Chloroplasts – capture solar energy and store it in carbohydrates Chloroplasts – capture solar energy and store it in carbohydrates Mitochondria – release energy from nutrients and convert it to ATP Mitochondria – release energy from nutrients and convert it to ATP

4. Mitochondria are sites of the Krebs cycle and an electron transport chain that carries out the oxidative phophorylation of ADP to ATP Fig 15.2

5. Two stages by which mitochondria convert food to energy Krebs cycle Krebs cycle Metabolize pyruvate and fatty acids Metabolize pyruvate and fatty acids Produce high-energy electron carriers NADH and FADH 2 Produce high-energy electron carriers NADH and FADH 2 Oxydative phosphorylation Oxydative phosphorylation Reactions that create ATP Reactions that create ATP Molecular complexes I, II, III, IV form a chain that transports electrons from NADH and FADH 2 to the final electron acceptor, oxygen Molecular complexes I, II, III, IV form a chain that transports electrons from NADH and FADH 2 to the final electron acceptor, oxygen Complex V uses the energy released by the electron transport chain to form ATP Complex V uses the energy released by the electron transport chain to form ATP

6. Chloroplasts are sites of photosynthesis Capture, conversion, and storage of solar energy in bonds of carbohydrates Capture, conversion, and storage of solar energy in bonds of carbohydrates Fig. 15.3

7. Photosynthesis takes place in two parts Light trapping phase Light trapping phase Solar energy is trapped and boosts electrons in chlorophyll Solar energy is trapped and boosts electrons in chlorophyll Electrons are conveyed to electron transport systeme to convert water to oxygen and H + Electrons are conveyed to electron transport systeme to convert water to oxygen and H + Electron transport forms NADPH and drives synthsis of ATP Electron transport forms NADPH and drives synthsis of ATP Sugar-building phase Sugar-building phase Calvin cycle enzymes use ATP and NADPH to fix atmospheric carbon dioxide into carbohydrates Calvin cycle enzymes use ATP and NADPH to fix atmospheric carbon dioxide into carbohydrates Energy is stored in carbohydrate bonds Energy is stored in carbohydrate bonds

8. The genomes of mitochondria Location Location mtDNA lies within matrix of the organelle in structures called nucleoids mtDNA lies within matrix of the organelle in structures called nucleoids mtDNA of most cells does not reside in single location mtDNA of most cells does not reside in single location

9. The size and gene content of mtDNA vary from organism to organism

10. Unusually organized mtDNAs of Trypanosoma, Leishmania, Crithidia Protozoan parasites with single mitochondrial called kinetoplast Protozoan parasites with single mitochondrial called kinetoplast mtDNA exists in one place within kinetoplast mtDNA exists in one place within kinetoplast Large network of 10-25,000 minicircles 0.5 – 2.5 kb in length interlocked with 50-100 maxicircles 21-31 kb long Large network of 10-25,000 minicircles 0.5 – 2.5 kb in length interlocked with 50-100 maxicircles 21-31 kb long Maxicircles contain most genes Maxicircles contain most genes Minicircles involved in RNA editing Minicircles involved in RNA editing

11. Human mtDNA carries closely packed genes 16.5 kb in length, or 0.3% of total genome length 16.5 kb in length, or 0.3% of total genome length Carries 37 genes Carries 37 genes 13 encode polypeptide subunits that make up oxydative phosphorylation apparatus 13 encode polypeptide subunits that make up oxydative phosphorylation apparatus 22 tRNA genes 22 tRNA genes 2 genes for large and small rRNAs 2 genes for large and small rRNAs Compact gene arrangement Compact gene arrangement No introns No introns Genes abut or slightly overlap Genes abut or slightly overlap Fig. 15.5 a

12. The larger yeast mtDNA contains spacers and introns Four times longer than human and other animal mtDNA Four times longer than human and other animal mtDNA Long intergenic sequences called spacers separate genes accounting for more than half of DNA Long intergenic sequences called spacers separate genes accounting for more than half of DNA Introns form about 25% of yeast genome Introns form about 25% of yeast genome Figure 15.5 b

13. The 186 kb mtDNA of the liverwort carries many more genes than animals and fungi 12 electron transport genes 12 electron transport genes 16 ribosomal protein genes 16 ribosomal protein genes 29 genes with unknown function 29 genes with unknown function Fig. 15.5 c

14. Mitochondrial transcripts undergo RNA editing, a rare variation on the basic theme of gene expression Discovered in trypanosomes Discovered in trypanosomes Sequence of maxicircle DNA reveals only short, recognizable gene fragments instead of whole genes Sequence of maxicircle DNA reveals only short, recognizable gene fragments instead of whole genes RNAs in kinetoplast are same short fragments and full length RNAs RNAs in kinetoplast are same short fragments and full length RNAs kDNA encodes a precursor for each mRNA kDNA encodes a precursor for each mRNA RNA editing – conversion of pre-mRNA to mature mRNA RNA editing – conversion of pre-mRNA to mature mRNA Also found in mitochondria of some plants and fungi Also found in mitochondria of some plants and fungi

15. RNA editing in trypanosomes Fig. 15.6

16. Translation in mitochondria shows that the genetic code is not universal

17. The genomes of chloroplasts: the liverwort, M. polymorpha

18. Mitochondrial and chloroplast genomes require cooperation between organelle and nuclear genomes Fig. 15.8

19. Origin and evolution of organelle genomes: molecular evidence Endosymbiont theory Endosymbiont theory 1970s, Lynn Margulis 1970s, Lynn Margulis Mitochondria and chloroplasts orginated more than a billion years ago Mitochondria and chloroplasts orginated more than a billion years ago Ancient precursors of eukaryotic cells engulfed bacteria and established symbiotic relationship Ancient precursors of eukaryotic cells engulfed bacteria and established symbiotic relationship Molecular evidence Molecular evidence Both chloroplasts and mitochondria have own DNA Both chloroplasts and mitochondria have own DNA mtDNA and cpDNA are not organized into nucleosomes by histones, similar to bacteria mtDNA and cpDNA are not organized into nucleosomes by histones, similar to bacteria Mitochondrial genomes use N-formyl methionine and tRNA fmet in translation Mitochondrial genomes use N-formyl methionine and tRNA fmet in translation Inhibitors of bacterial translation have same effect on mitochondrial translation, but not eukaryotic cytoplasmic protein synthesis Inhibitors of bacterial translation have same effect on mitochondrial translation, but not eukaryotic cytoplasmic protein synthesis

20. Gene transfer occurs through an RNA intermediate or movement of pieces of DNA Genes transfer between organelles and the nucleus Genes transfer between organelles and the nucleus COXII gene COXII gene mtDNA genome in some plants mtDNA genome in some plants Nuclear genome in other plants Nuclear genome in other plants Nuclear copy lacks intron – suggests transferred by RNA intermediate Nuclear copy lacks intron – suggests transferred by RNA intermediate Movement among organelles Movement among organelles Plant mtDNAs carry fragments of cpDNA Plant mtDNAs carry fragments of cpDNA Nonfunctional copies of organelle DNA are found around the nuclear genomes of eukaryotes Nonfunctional copies of organelle DNA are found around the nuclear genomes of eukaryotes

21. mtDNA has high rate of mutation 10 times higher than nuclear DNA 10 times higher than nuclear DNA Provides a tool for studying evolutionary relationships among closely related organisms Provides a tool for studying evolutionary relationships among closely related organisms maternal lineage of humans trace back to a few women who lived about 200,000 years ago maternal lineage of humans trace back to a few women who lived about 200,000 years ago

22. Maternal inheritance only in most species Maternal inheritance of Xenopus mtDNA Maternal inheritance of Xenopus mtDNA Purified mtDNA from two species Purified mtDNA from two species Hybridization only to probes from same species Hybridization only to probes from same species F1 hybrids retain only mtDNA from mother F1 hybrids retain only mtDNA from mother Fig. 15.9

23. Maternal inheritance of specific genes in cpDNA Interspecific crosses tracing biochemically detectable species specific differences in chloroplast proteins Interspecific crosses tracing biochemically detectable species specific differences in chloroplast proteins Isolated Rubisco proteins in tobacco plants in which interspecific differences could be seen Isolated Rubisco proteins in tobacco plants in which interspecific differences could be seen Progeny of controlled crosses contained version of Rubisco protein from maternal parent only Progeny of controlled crosses contained version of Rubisco protein from maternal parent only

24. A mutation in human mtDNA generates a maternally inherited neurodegenerative disease Leber’s hereditary optic neurophathy (LHON) leads to optic nerve degeneration and blindness Leber’s hereditary optic neurophathy (LHON) leads to optic nerve degeneration and blindness Substitution in mtDNA at nucleotide 11,778 Substitution in mtDNA at nucleotide 11,778 Fig. 15.10

25. Cells can contain one type or a mixture of organelle genomes Heterplasmic – cells contain a mixture of organelle genomes Heterplasmic – cells contain a mixture of organelle genomes Mitotic products may contain one type, a mixture of types, or the second type Mitotic products may contain one type, a mixture of types, or the second type Homoplastic – cells contain one type of organelle DNA Homoplastic – cells contain one type of organelle DNA Mitotic products contain same type, except for rare mutation Mitotic products contain same type, except for rare mutation

26. Mitotic segregation produces an uneven distribution of organelle genes in heteroplasmic cells Women with heteroplasmic LHON mutation Women with heteroplasmic LHON mutation Some ova may carry few mitochondria with LHON mutation and large number of wild-type Some ova may carry few mitochondria with LHON mutation and large number of wild-type Other ova may carry mainly mitochondrial with LHON mutation and few wild-type Other ova may carry mainly mitochondrial with LHON mutation and few wild-type Consequence of heteroplasmy after fertilization Consequence of heteroplasmy after fertilization Some cells produce tissues with normal ATP production and others with low production Some cells produce tissues with normal ATP production and others with low production If low production cells are in optic nerve, LHON results If low production cells are in optic nerve, LHON results

27. Experiments with mutants of cpDNA in Chlamydomonas reinhardtii reveal uniparental inheritance of chloroplasts Fig. 15.11 b

28. A cross of C. reinhardtii gametes illustrates lack of segregation of cpDNA at meiosis Fig. 15.11 c

29. Mechanisms of unipartental inheritance Differences in gamete size Differences in gamete size Degredation of organelles in male gametes of some organisms Degredation of organelles in male gametes of some organisms In some plants paternal organelle genomes are distributed to cells that are destined to not become part of the embryo during early development In some plants paternal organelle genomes are distributed to cells that are destined to not become part of the embryo during early development In some organisms, the zygote destroys paternal organelle after fertilization In some organisms, the zygote destroys paternal organelle after fertilization Other organisms, paternal organelles excluded from female gamete Other organisms, paternal organelles excluded from female gamete

30. In yeast, mtDNA-encoded traits show a biparental mode of inheritance and mitotic segregation Fig. 15.13

31. Recombinant DNA techniques to study genetics of organelles Gene gun – biolistic transformation Gene gun – biolistic transformation Small (1mm) metal beads with DNA are shot at cells Small (1mm) metal beads with DNA are shot at cells Rarely, DNA passes through cell wall and enters nucleus Rarely, DNA passes through cell wall and enters nucleus Used to transform cells Used to transform cells E.g., GFP constructs can be used as selectable markers to identify transformants E.g., GFP constructs can be used as selectable markers to identify transformants Fig. 15.14

32. How mutations in mtDNA affect human health Individuals with certain rare diseases of the nervous system are heteroplasmic Individuals with certain rare diseases of the nervous system are heteroplasmic MERRF, myoclonic epilepsy and ragged red fiber disease MERRF, myoclonic epilepsy and ragged red fiber disease Uncontrolled jerking, muscle weakness, deafness, heart problems, kidney problems, progressive dementia Uncontrolled jerking, muscle weakness, deafness, heart problems, kidney problems, progressive dementia Fig. 15.15 a

33. Maternal inheritance of MRRF Fig. 15.15 b

34. Proportion of mutant mtDNA and tissue in which they reside influence phenotype Fig. 15.16

35. Mitochondrial inheritance in identical twins Mitochondrial genomes not same in twins but nuclear genomes are identical Mitochondrial genomes not same in twins but nuclear genomes are identical Symptoms of neurodegenerative diseases or other mutations may manifest in one twin, but not other Symptoms of neurodegenerative diseases or other mutations may manifest in one twin, but not other In heteroplasmic mother, chance of phenotype depends on both partitioning of mutant mtDNA after fertilization, and tissue that receive mutation during development In heteroplasmic mother, chance of phenotype depends on both partitioning of mutant mtDNA after fertilization, and tissue that receive mutation during development

36. mtDNA mutations and aging Hypothesis: Accumulation of mutations in mtDNA over lifetime and biased replication of deleted mtDNA result in age-related decline in oxidative phosphorylation Hypothesis: Accumulation of mutations in mtDNA over lifetime and biased replication of deleted mtDNA result in age-related decline in oxidative phosphorylation Evidence: Evidence: Deleterious mtDNA mutations early in life diminish ATP production Deleterious mtDNA mutations early in life diminish ATP production Decreases in cytochrome c oxidase in hearts from autopsies (gene encoded in mtDNA) Decreases in cytochrome c oxidase in hearts from autopsies (gene encoded in mtDNA) Rate of deletions increases with age Rate of deletions increases with age Alzheimer’s individuals have abnormally low energy metabolism Alzheimer’s individuals have abnormally low energy metabolism