Lecture 12a

Question 1

For the nucleotides used in DNA replication, how many phosphates do they start off with?

Answer 1

Start off with 3 phosphates.

Question 2

How do the nucleotides in DNA replication initially appear?

Answer 2

The nucleotides used in DNA replication start off with 3 phosphates. This is seen as dTTP (thymine), dATP (adenine), dGTP (guanine), and dCTP (cytosine).

Question 3

What happens to the bond between the 1st and 2nd phosphate?

Answer 3

The chemical energy of the bond between the 1st and 2nd phosphates is used to make the bond to the sugar.

Question 4

Once the bond between the 1st and 2nd phosphate breaks, what are we left with (besides the new bond to the sugar)?

Answer 4

We are left with a Pyrophosphate (PP) molecule.

Question 5

Besides DNA replication, what other instance can we use nucleotides as sources of chemical energy? What is the difference here?

Answer 5

Nucleotides used in TRANSCRIPTION (RNA SYNTHESIS) are also used as sources of chemical energy.

The difference is that UTP (Uracil) is present instead of TTP (thymine)

Question 6

For the nucleotides used in transcription, how many phosphates do we begin with?

Answer 6

The nucleotides used in transcription also start off with 3 phosphates.

Question 7

What is used as the energy to make the bond to the sugar in DNA replication and transcription?

Answer 7

The chemical energy of the bond between the 1st and 2nd phosphates is used to make the bond to the sugar.

Question 8

Besides using the nucleotides as energy for transcription, what else can we use them for?

Answer 8

The nucleotides used in transcription can also be used as sources of chemical energy to drive other reactions.

Question 9

What are 2 examples of the use of RNA nucleotides to drive chemical reactions?

Answer 9

1) DNA replication: helicase uses ATP to separate DNA strands.

2) Protein synthesis: aminoacyl-tRNA synthase uses ATP to attach amino acids to tRNAs (‘charging’ tRNAs).

Question 10

What are telomeres?

Answer 10

These are the ends up linear eukaryotic chromosomes.

Question 11

T/F: Telomeres have no repetitive sequences.

Answer 11

False! Telomeres were found to have a repetitive sequence.

Question 12

What is telomerase? What does it do?

Answer 12

An enzyme that synthesizes the ends of eukaryotic linear chromosomes.

Telomerase adds the repeats using an RNA template.

Question 13

How does telomerase add the repetitive telomere sequences during replication?

Answer 13

Telomerase adds the repeats using an RNA template.

It synthesizes a 6-nucleotide repeat, then moves 6 nucleotides to the right and begins to make another repeat.

Question 14

What makes the complementary telomere strand?

Answer 14

Primase, DNA polymerase, and ligase.

Question 15

How do we terminate bacterial transcripts?

Answer 15

We can terminate many bacterial transcripts by using the protein r (rho).

Question 16

T/F: Rho helicase does NOT require ATP.

Answer 16

False! Rho helicase requires ATP.

Question 17

Where does the r protein bind to in RNA? Then, what direction does it move?

Answer 17

The rut site. Then, it moves towards the 3’ end.

Question 18

Once RNA polymerase reaches the terminator, what causes it to pause?

Answer 18

A stem-loop causes RNA polymerase to pause once it reaches the terminator.

Question 19

Once the RNA polymerase stops due to its interaction with the stem-loop structure, what happens?

Answer 19

r proteins are able to catch up and separate the RNA-DNA hybrid.

Question 20

What do bacterial transcripts that are NOT terminated using rho need to utilize?

Answer 20

They need to utilize stem-loop structures also.

Question 21

Describe the termination of eukaryotic transcription.

Answer 21

1) RNA polymerase II transcribes a gene past the polyadenylation signal sequence.
2) The RNA is cleaved just past the polyadenylation signal sequence. RNA polymerase continues transcribing the DNA after the break.

Question 22

What is the Allosteric model?

Answer 22

After transcribing the polyadenylation signal sequence, RNA polymerase II is destabilized and dissociates from the DNA. This may be caused by the release of elongation factors or the binding of termination factors. Termination occurs.

Question 23

What is the Torpedo model?

Answer 23

An exonuclease binds to the 5’ end of the RNA that is still being transcribed and degrades it in a 5’ to 3’ direction. The exonuclease will eventually catch up to the RNA polymerase II and cause termination.

Question 24

Which model is there evidence for: Torpedo or Allosteric?

Answer 24

There is evidence that the termination of eukaryotic transcription involves both of these mechanisms.

Question 25

What is the endosymbiosis theory?

Answer 25

It states that mitochondria and chloroplasts arose from bacteria that took up residence within a primordial eukaryotic cell.

Question 26

According to the endosymbiosis theory, what did chloroplasts originate as?

Answer 26

Cyanobacteria (the only bacteria capable of photosynthesis)

Question 27

According to the endosymbiosis theory, what did mitochondria originate as?

Answer 27

Nonsulfur purple bacteria

Question 28

According to the endosymbiosis theory, what happened to the intracellular bacterial cells during evolution?

Answer 28

During evolution, the intracellular bacterial cells gradually became organelles that cannot live independently.

Question 29

What 2 observations support the endosymbiotic origin of organelles?

Answer 29

1) Organelles have circular chromosomes (like bacteria).
2) Organelle genes are more similar to bacterial genes than to those found within the nucleus.

Question 30

What benefit would a cyanobacterium going into a eukaryotic cell have?

Answer 30

The eukaryotic cell would now be able to undergo photosynthesis.

Question 31

What benefit would a purple bacterium going into a eukaryotic cell have?

Answer 31

The eukaryotic cell would now be able to synthesize greater amounts of ATP.

Additionally, the bacterial cell may have gained a more stable environment with more nutrients.

Question 32

T/F: Chloroplasts are inherited from both mother and father.

Answer 32

False! Chloroplasts are inherited only from the mother.

Question 33

What is maternal inheritance?

Answer 33

This is when chloroplasts and mitochrondria are only inherited from the mother.

Question 34

What is Mirabilis jalapa (the four o’clock plant)? What is this an example of?

Answer 34

Certain mutations in chloroplasts resulted in white leaves or variegated leaves (both green and white sections).

White or variegated leaves are only inherited from the mother, so it is an example of maternal inheritance.

Question 35

T/F: Mitochondria are only inherited from the father.

Answer 35

False! Mitochondria are also only inherited from the mother (maternal inheritance).

Question 36

How many human mitochondrial diseases have been identified?

Answer 36

Over 200 human mitochondrial diseases have been identified.

Question 37

What do human mitochondrial diseases generally look like?

Answer 37

They are typically chronic degenerative disorders affecting cells requiring high levels of ATP.

Question 38

What cells require the most ATP?

Answer 38

Nerve and muscle cells.

Question 39

What are two ways in which human mitochondrial diseases occur?

Answer 39

1) Because human mtDNA is transmitted from mother to offspring via the cytoplasm of the egg, the transmission of human mitochondrial disease follows a strict maternal inheritance pattern.

2) Mitochondrial mutations may occur in somatic cells

Question 40

Describe mitochondrial mutations in somatic cells.

Answer 40

They accumulate as a person ages.

Mitochondria are very susceptible to DNA damage.

Question 41

Why are mitochondria very susceptible to DNA damage?

Answer 41

High oxygen consumption leads to free radicals, which can damage the DNA. Mitochondrial DNA has very limited repair abilities.