Mitochondrial genome

Question 1

How large is the mitochondrial genome?

Answer 1

Tiny compared to the nuclear genome. 16 000 bp vs 3.2 billion bp

Question 2

What are 4 physical features of the mitochondrial genome?

Answer 2

1. Small, circular dsDNA
2. GC content of about 44%, similar to the nuclear genome
3. Heavy and light strands, distinct density difference between them
4. Small triple stranded region with the D-loop

Question 3

How are the heavy and light strands different from each other?

Answer 3

Base composition. The H strand has more G and the L strand has more C. They can be separated by density

Question 4

What physical features does the small triple stranded region have?

Answer 4

2 copies of the heavy strand and one of the light strand. Only one H strand is base pairing to the L strand. The other is displaced into the D-loop

Question 5

What sequences are found in the triple stranded region?

Answer 5

The sequence on the heavy and light strands base pairing to each other is 7S rDNA. The D-loop contains control sequences like origins and promoters

Question 6

What does the D-loop do?

Answer 6

We don’t know. It might help with replication or anchor mtDNA to the inner mitochondrial membrane

Question 7

What’s weird about the replication of mitochondrial DNA?

Answer 7

It’s unidirectional, instead of bidirectional like normal. Each strand has its own ori

Question 8

What are the steps in mitochondrial DNA replication?

Answer 8

1. The ori for the heavy strand, found in the D-loop, goes off
2. The H strand gets replicated counterclockwise until its about 2/3 of the way around
3. DNA around the ori of the light strand gets separated and it goes off
4. The L strand is replicated clockwise

Question 9

How many genes are in the mitochondrial genome? Are they evenly distributed on both strands?

Answer 9

37 total. 28 of them are on the H strand and 9 are on the L strand

Question 10

How many of the 37 genes in the mitochondrial genome are protein coding? What do they code for?

Answer 10

13. All of them encode some part of the electron transport chain

Question 11

Does the mitochondrial genome encode every component of the electron transport chain?

Answer 11

Nope. It encodes some, but the rest are encoded in the nuclear genome

Question 12

What’s encoded by the genes in the mitochondrial genome that do not encode proteins?

Answer 12

RNA. 22 of those 24 encode tRNA, and the other two are rRNA

Question 13

What is strange about mitochondrial DNA promoters?

Answer 13

There’s only 2 in the whole genome, one on each strand. The mRNA generated is polycistronic like it is in prokaryotes

Question 14

What 4 traits does the mitochondrial genome share with bacteria?

Answer 14

1. Circular
2. Polycistronic mRNAs
3. No introns
4. High gene density with little intergenic space

Question 15

What is the mutation rate of the mitochondrial genome compared to the nuclear genome?

Answer 15

10X higher than the nuclear genome

Question 16

Why does the mitochondrial genome have a high mutation rate?

Answer 16

1. High concentration of ROS
2. No histones, so easier access to DNA by mutagens
3. mitochondrial DNA polymerase sucks at proofreading
4. Concentrations of dNTPs in the mitochondria

Question 17

What is the result of this high mutation rate?

Answer 17

Heteroplasmy. Get a mixture of mtDNA molecules within the same mitochondria and within the same cell

Question 18

How can mitochondrial diseases be shown in certain cell lineages and not others?

Answer 18

Random segregation and a selective advantage of disease carrying mtDNA molecules. If the mutants end up in one cell but not another, then that lineage will keep propagating the diseased mitochondria

Question 19

Why are some tissues more affected in mitochondrial diseases than others?

Answer 19

They’ll show a worse phenotype if they have a higher demand for ATP and functioning mitochondria

Question 20

How did the in vitro replication experiment show that the imbalance in dNTP concentrations may be partially responsible for the high mutation rate?

Answer 20

The authors used mtDNA polymerase, both WT and a mutant with defective proofreading. They used the LacZ gene as a reporter, and 1 uM of each dNTP as a baseline. The mutation rate went up even with the WT enzyme when the dNTP concentrations were imbalanced

Question 21

What are 3 reasons why we typically consider mitochondrial diseases to be maternally transmitted?

Answer 21

1. Sperm mitochondria get diluted out by the sheer number of egg mitochondria
2. Egg destroys sperm mitochondria
3. The sperm mitochondria don’t get into the egg in the first place