Organelle genomes

Question 1

1. How is mitochondrial DNA inherited?

Answer 1

• non mendelian segregation patterns
• one parent usually contributes more - the extreme being uniparental inheritance
• most commonly maternal
• differs from maternal effect where nuclear genome of mother determines phenotype
• mitochondrial (the organelles) segregation is also stochastic
• Mitochondria from human sperm could diluted or killed (must have mitochondria, it can swim!). They have molecular tags that targets them for destruction after fertilization

Question 2

Is there a one to one correspondence bewteen the number of copies of nuclear and mitochondrial genomic DNA?

Answer 2

No, several genomic DNA copies per mitochindria, and several mitochindria per cell

Question 3

3. Are all the mitochondrial proteins encoded by mitochondrial DNA? Explain.

Answer 3

Only a few of the mitochondrial proteins are encoded by mitochondrial DNA. The great majority of proteins are transcriped from the nuclear genome and imported into the mitochondria. Over time most of the mitochondrial genes have been transferred to the nuclear genome – no longer capable of independent life.

Question 4

4. What are the origins of the mitochondria?

Answer 4

Mitochondria developed from bacteria engulfed by primitive cells – endosymbiosis. The bacteria (common ancestor to a-proteobacteria) provided the cell with the function of cellular respiration and in time developed into mitochondira. Genes transferred to the nucleus during evolution.

Question 5

5. Which present day organism is considered to be the closest relative of the mitochondria?

Answer 5

Rickettsia prowazekii. Obligate intracellular parasite – causes typhus.

Question 6

6. What are the origins of the chloroplasts?

Answer 6

• Chloroplasts shares an origin with cyanobacteria
• all chloroplasts can probably be traced back to a single endosymbiotic event (the cyanobacterium being engulfed by the eukaryote). Despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events.

Question 7

7. What is secondary endosymbiosis?

Answer 7

Secondary endosymbiosis is when the host cell with an endosymbiont from a primary endosymbiotic event is taken up by another host cell and becomes the endosymbiont. A cell inside a cell inside a cell  Secondary endosymbiosis consisted of a eukaryotic alga being engulfed by another eukaryote, forming a chloroplast with three or four membranes. his is often interpreted as meaning the outer chloroplast membrane is the product of the host’s cell membrane infolding to form a vesicle to surround the ancestral cyanobacterium—which is not true—both chloroplast membranes are homologous to the cyanobacterium’s original double membrane

Question 8

8. Which present day organism is considered to be the closest relative of chloroplasts?

Answer 8

Cyanobacteria

Question 9

9. Which genes are found in most mitochondrial genomes?

Answer 9

Cox1 and cob. PROTEOME: 400-600 proteins

Question 10

10. Which mitochondrial genes are found in the mitochondrial genome in some but not all organisms?

Answer 10

?

Question 11

11. Which genes are found in most chloroplast genomes?

Answer 11

rRNA, tRNA and genes involved in chloroplast functions – photosynthesis and electron transport. RNA polymerase
(transcription, translation and photosynthesis and electron transport)

Question 12

12. What evidence indicates that there has been a transfer of organelle genes to the nuclear genomes?

Answer 12

… Fragments of cpDNA found in maize genome

Question 13

14. Why have mitochondria not lost all genes? (Why have organelles retained their genomes?)

Answer 13

Not the universal genetic code – less tRNAs, less wobbling
Need autonomy in when proteins involved in it’s core functions should be expressed
tRNA genes not transferred, functional substation by genes from nuclear DNA

very hydrophobic proteins

Some prdoucts toxic?

Question 14

15. In which mitochondrial processes are genes encoded by mitochondrial DNA (mtDNA) involved?

Answer 14

Micochondria specific processes – electron transport chain and it’s own replication

Question 15

16. Describe some unusual gene organizations occurring in the in mitochondrial proteome.

Answer 15

• Gene fusion. Two genes, one open reading frame
• Chimeric genes – recognizable fractions of known genes in otherwise unassigned ORF
• Genes in pieces – broken into as many as eight modules, scrambled, on both strands in the mtDNA
• Genes in pieces – one on the mtDNA and one in the ncDNA
• Gene simplification – truncated tRNA

Question 16

17. Describe the mitochondrial genomes in yeast and humans (make a drawing).

Answer 16

Humans: 16.6 kB compact. 13 protein coding genes, 22 tRNA genes and 2 rRNA genes.
Yeast: 84kB. Likely less than 25 genes.CO1 and cytochrome B very intron rich. Almost stretches out over 16.6 kB.

Question 17

18. Compare the evolution of mitochondrial genomes from yeast to animals. Make a table that summarize mitochondrial genome sizes, gene numbers and genome organization. What conclusions can be drawn?

Answer 17

• Few protein coding genes – number does not correlate with mtGenome size.
• Introns found in most mtGenomes, but not in the small, compact mammalian ones.
• Two major rNRAs are always encoded by themtGenome
• tRNA varies from none to the full complements of 25-26
• Protein coding genes: components of the respiratory complex I-IV and a variable number of ribosomal proteins (involved in the electron transport chain)
• ALWAYS cytochrome b (cob) and cytochrome c oxidase I (cox1)

Species	Size (kb)	Protein -coding genes	RNA-coding genes
Fungi	19-100	8-14	10-28
Protists	6-100	3-62	2-29
Plants	186-366	27-34	21-30
Animals	16-17	13	4-24

Question 18

19. What is the D-­‐loop?

Answer 18

A region involved with initiation of DNA replication in the genome of mammalian mitochondria. Almost the only intergenic DNA.