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Molecular Biology > Ch. 8b Extrachromosomal Replicons (Exam 2) > Flashcards

Ch. 8b Extrachromosomal Replicons (Exam 2) Flashcards

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1
Q

What happens to the ends of linear DNA molecules after successive rounds of replication?

A

Shortening

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2
Q

Where is the natural position for the priming site of the lagging strand?

A

Near the replication fork

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3
Q

Why isn’t the extreme 3’ end of the lagging strand always copied?

A

Because primers are only placed at the replication fork, which does not exist until helicase starts unwinding the parent strands. Ergo, the 3’ tip of the lagging strand isn’t formed

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4
Q

What happens to the 3’ end of the lagging strand when a true 3’ end doesn’t form?

A

There is a missing Okazaki fragment, which causes the lagging strand to be shorter than it should be

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5
Q

What are telomeres?

A

DNA sequences made up of multiple copies of short repeats, or satellites

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6
Q

What is the function of telomerase?

A

They extend telomeric DNA at the 3’ overhang to reverse the loss of DNA from the lagging strand’s missing 3’ end Okazaki fragment

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7
Q

What is telomerase made of?

A

RNA and protein

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8
Q

What is unusual about telomerase (HINT: use of RNA and protein)?

A

Because the RNA is used as a template for 3’ extension, and the protein synthesizes DNA via reverse transcriptase

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9
Q

What happens after the protein component of telomerase synthesizes enough DNA?

A

Polymerase primes and synthesizes a new Okazaki fragment from the telomerase’s 3’ extension, forming a complete double strand

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10
Q

How does mitochondrial replication fit into the cell cycle (HINT: describe as flowchart in 4 steps)?

A

DNA replication > DNA segregation > mitochondrial duplication > mitochondrial/organelle segregation

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11
Q

What is meant when we say that mitochondrial replication appears to be stochastic?

A

Each copy is randomly redistributed

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12
Q

What is the overall result of such random distribution of mitochondria?

A

Some mitochondrial DNA molecules are replicated more times than others

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13
Q

What is the protein involved in the formation of the membranous vesicles in animal mitochondria?

A

Dynamin

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14
Q

In mitochondrial DNA (mtDNA) replication, the number of genomes increases in proportion to the…

A

Mitochondrial mass

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15
Q

Does each mitochondrial genome replicate the same number of times after each replication?

A

No

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16
Q

Since each genome replicates a variable number of times, it leads to changes in…

A

Allelic representation in the daughter mitochondria

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17
Q

What does the “D” in the term “D-loop” stand for?

A

Displacement

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18
Q

What is a D-loop?

A

Non-coding region that acts as a promoter of the heavy and light strands

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19
Q

What does the RNA primer do in the first step of D-loop replication?

A

It initiates replication at the origin of the H strand

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20
Q

What happens after the primer initiates replication at the H strand in the second step of D-loop replication?

A

DNA is synthesized from the primer to form a new L strand, and a D-loop is created, which displaces the original L strand

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21
Q

In the third step of D-loop replication, after the D-loop displaces the original L strand, what happens?

A

Replication of the new L strand continues 2/3 of the way around the H strand until it passes the origin of the old L strand

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22
Q

In D-loop replication, what is prompted after the new L strand passes over the old L strand’s origin?

A

Synthesis of the new H strand

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23
Q

Nearing the end of D-loop replication, the completion of the new L strand prompts this action.

A

The release of daughter genomes

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24
Q

At the end of D-loop replication, why does the daughter genome with the new L strand seal itself quicker than the daughter with the new H strand?

A

Synthesis of the new H strand began when the new L strand was already 2/3 of the way sealed, so the new L strand ended up completing first

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25
Q

What are the two independently replicating genetic units that bacteria can host?

A

Plasmids and bacteriophages

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26
Q

What is a plasmid?

A

Autonomous circular DNA that constitutes a separate replicon

27
Q

Some plasmids and all phages use this type of process to transfer information from a donor to a recipient.

A

Infective

28
Q

What is an episome?

A

A special type of plasmid with the ability to integrate itself into chromosomal DNA, whereas a typical plasmid cannot

29
Q

All episomes are plasmids, but…

A

Not all plasmids are episomes

30
Q

How are plasmids useful for bacterial survival?

A

They help bacteria adapt to and resist unfavorable conditions

31
Q

What 2 factors affect plasmid replication mechanisms?

A

1) Host specificity
2) Plasmid copy number

32
Q

How is copy number an effect of plasmid replication mechanisms?

A

Replication mechanisms may be set in place to control copy number

33
Q

The rolling circle replication mechanism is specific to what 2 things?

A

1) Bacteriophage family m13
2) Fertility F factor

34
Q

What is the purpose of the fertility F factor?

A

To encode for sex pili formation during recombination via conjugation

35
Q

How is rolling circle replication helpful in terms of speed of transfer?

A

It allows faster transfer of single-stranded replication product to the recipient via conjugation

36
Q

Does rolling circle occur in covalently closed pieces of double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA)?

A

dsDNA

37
Q

How does initiation occur in rolling circle replication?

A

Nickases break a phosphodiester bond (i.e. forming a nick), creating a 5’ P end and 3’ OH end

38
Q

In rolling circle replication, what happens after the nick occurs?

A

The 3’ OH is used by DNA polymerase to synthesize new DNA

39
Q

What is happening as the 3’ end is synthesizing new DNA (i.e. during elongation) in rolling circle replication?

A

The 5’ P end is getting displaced

40
Q

At the end of rolling circle replication, what happens to the displaced 5’ P end?

A

After reaching its unit length, elongation continues for a bit, and the displaced 5’ P end is nicked and then synthesizes a complementary strand

41
Q

What happens to an F plasmid’s replication system when the F plasmid integrates itself into a bacterial chromosome?

A

The F plasmid’s replication system is suppressed

42
Q

Define conjugation.

A

Process in which plasmid genome or host genome with an integrated episome is transferred from one bacterium to another i.e. bacterial sexy time

43
Q

Is an F plasmid a regular plasmid or an episome?

A

Episome because it integrates itself into the bacteria’s chromosome

44
Q

Does an F plasmid in its free form have its own replication origin and control over its replication?

A

Yes

45
Q

How is F DNA replicated when the F plasmid is integrated into the bacterial chromosome?

A

F DNA is replicated as part of the chromosome

46
Q

Are F-positive bacteria able to conjugate with other F-positive bacteria or F-negative bacteria?

A

F-negative only

47
Q

What does it mean when we say that the transfer of the F plasmid is one-way only?

A

The donor always give to the recipient, but the recipient can’t give back to the donor since it is now F-positive

48
Q

The { } region of the F plasmid is a large region that is required for conjugation.

A

Transfer

49
Q

F-positive bacteria have this surface appendage to allow for conjugation.

A

Pilus (plural pili)

50
Q

The { } region of the F plasmid contains genes needed for bacterial conjugation.

A

Tra

51
Q

Why can’t donor cells call out to other cells with the F plasmid (HINT: 2 genes are responsible for this)?

A

TraS & traT genes encode “surface exclusion” proteins that make calling out difficult

52
Q

What replication mechanism does conjugation rely on to transfer ssDNA?

A

Rolling circle

53
Q

To clarify, although rolling circle replication relies on covalently bonded dsDNA to initiate, it transfers…

A

ssDNA

54
Q

What is the purpose of single-copy control plasmid systems in the bacterial chromosome?

A

To allow only one replication per cell division and maintain that quantity throughout

55
Q

What is the purpose of multicopy control plasmid systems in the bacterial chromosome?

A

To allow multiple initiation events per cell cycle

56
Q

What is the result of multicopy control systems allowing multiple initiation events per cell cycle?

A

Several copies of the plasmid per bacterium

57
Q

How is each plasmid maintained in the bacterial host in terms of copy number?

A

Each is kept at a certain copy number via different replication mechanisms

58
Q

Phages using rolling circle replication consist ssDNA. What is the name of this single strand?

A

Plus strand

59
Q

What is the name of the strand complementary to the plus strand?

A

Minus strand

60
Q

What disease results from bacterial ti plasmid infecting plants?

A

Crown gall disease

61
Q

Describe the parasitic relationship between Agrobacterium tumefaciens (ti plasmid bacteria) and plants.

A

The bacterium changes the host’s genetic info to suit its needs, and the plant grows a tumor that feeds the bacterium

62
Q

What is an opine?

A

Derivative of arginine found in plant tumors

63
Q

How does the Ti plasmid integrate itself into the plant genome?

A

Part of it is transferred into the plant nucleus

64
Q

What is the name for the transferred portion of the Ti genome?

A

T-DNA

Molecular Biology (21 decks)

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