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Biology Of The Cell > Week 8: Dna Replication And Cell Cycle In Bacteria > Flashcards

Week 8: Dna Replication And Cell Cycle In Bacteria Flashcards

1
Q

What is the formula for bacterial growth?

A

N = N0 2n

Where N is the number of cells at time n, and N0 is the number of cells at time 0.

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2
Q

What is the approximate doubling time for E. coli in LB medium?

A

20 minutes

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3
Q

What are the doubling times for the following bacteria?
- E. coli
- Helicobacter pylori
- Neisseria gonorrhoeae
- Mycobacterium tuberculosis
- Mycobacterium leprae

A
  • E. coli: 20 min
  • Helicobacter pylori: 50 min
  • Neisseria gonorrhoeae: 90 min
  • Mycobacterium tuberculosis: 18-24 h
  • Mycobacterium leprae: 14 days
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4
Q

What are the growth phases of E. coli?

A
  • Lag phase: bacteria are adjusting to new environment
  • Log phase: rapid growth and division
  • Stationary phase: growth rate slows down due to limited resources
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5
Q

What role does the FtsZ protein play in E. coli cellular division?

A

Forms a septum ring

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6
Q

What happens during the constriction of the septum ring in E. coli?

A

Divides the cell

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7
Q

Fill in the blank: The doubling time for Helicobacter pylori is _______.

A

50 min

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8
Q

True or False: Mycobacterium leprae has a doubling time of 14 days.

A

True

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9
Q

Fill in the blank: The log phase in E. coli is characterized by _______ and _______.

A

rapid growth and division

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10
Q

What is the lag phase in E. coli growth?

A

Bacteria are adjusting to new environment

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11
Q

What occurs during the stationary phase of E. coli growth?

A

Growth rate slows down due to limited resources

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12
Q

What is the first phase of the E. coli cell cycle?

A

Gap phase: cell grows and prepares for replication

This phase involves cellular growth and preparation for the next steps in the cycle.

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13
Q

What occurs during the replication phase of the E. coli cell cycle?

A

DNA replication occurs

This phase is crucial for the duplication of genetic material.

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14
Q

What happens during the division phase of the E. coli cell cycle?

A

Cell divides

This phase results in two daughter cells.

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15
Q

How is the E. coli chromosome replicated?

A

By two independent replication machineries (replisomes)

This allows for efficient and accurate duplication of the chromosome.

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16
Q

What are the two chromosomal halves called after E. coli chromosome duplication?

A

Replichores

These are the two sections of the chromosome that are being replicated.

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17
Q

At which end are DNA strands elongated during replication?

A

3’ end

This is a fundamental aspect of DNA replication.

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18
Q

How is the lagging strand synthesized during DNA replication?

A

In Okazaki fragments

This is necessary because the lagging strand is synthesized discontinuously.

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19
Q

What is the E. coli beta sliding clamp?

A

A ring-shaped protein that encircles DNA

The sliding clamp is essential for DNA replication.

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20
Q

How is the E. coli beta sliding clamp loaded onto DNA?

A

By the clamp loader

The clamp loader is a multi-protein complex that facilitates the loading process.

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21
Q

What is the function of the E. coli beta sliding clamp?

A

Helps to keep DNA polymerase from dissociating from the DNA strand

This function is crucial for the process of DNA replication.

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22
Q

What is the role of DNA polymerase I?

A

DNA polymerase I removes DNA primers

DNA primers are short strands of nucleotides that initiate DNA replication.

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23
Q

How are Okazaki fragments joined?

A

Okazaki fragments are joined by DNA ligase

Okazaki fragments are short sequences of DNA synthesized on the lagging strand during DNA replication.

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24
Q

What is the origin of replication?

A

The origin of replication is a specific sequence of DNA where replication begins

This location is critical for the initiation of DNA synthesis.

25
How is the origin of replication regulated?
The origin of replication is regulated by methylation ## Footnote Methylation can influence the activity of the DNA and its replication.
26
What is the methylation status of newly replicated DNA?
Newly replicated DNA is hemimethylated ## Footnote Hemimethylation means that only one strand of the DNA is methylated after replication.
27
What do SeqA proteins do?
SeqA proteins bind to hemimethylated DNA and prevent methylation ## Footnote This action helps regulate the timing of DNA replication.
28
For what duration does SeqA ensure the origin of replication remains unmethylated?
SeqA ensures that the origin of replication remains unmethylated for 1/3 of the cell cycle ## Footnote This timing is crucial for proper cell division and replication.
29
What terminates replication in bacterial DNA?
Replication terminates when the two forks meet in an area opposite of oriC.
30
What protein binds to ter sites to assist in replication termination?
Ter protein binds to ter sites.
31
What is the role of Tus protein in replication?
Tus protein binds to ter sites, forming a replication fork trap.
32
What is a replication fork trap?
A structure that forks can enter but not leave.
33
What type of collisions are problematic during DNA replication?
Head-on collisions between replication forks and transcription complexes.
34
In many bacteria, how are replication and transcription oriented?
Replication and transcription are co-directional.
35
How do many replicative polymerases resemble a physical object?
They resemble a right hand with fingers, a thumb, and a palm.
36
Where is the nucleotide to be incorporated located in the polymerase structure?
At the bottom of the fingers.
37
What is the selection of the correct nucleotide in DNA replication primarily considered?
A geometric problem.
38
Which domain of polymerase relies on the catalytic mechanism?
The palm domain.
39
Can wrong base pairs be formed during replication?
Yes, but they do not fit into the active center very well.
40
What is the error rate of chemical polymerisation without a polymerase?
Approximately 1 wrong base in 100 incorporation steps (1 × 10^-2) ## Footnote This indicates a significant potential for errors during DNA synthesis without the involvement of polymerases.
41
How many errors are estimated in an E. coli chromosome due to chemical polymerisation without a polymerase?
46,000 errors ## Footnote This highlights the potential inaccuracies that can arise in genetic material during replication processes lacking proper enzymatic mechanisms.
42
What is the error rate of chemical polymerisation during DNA synthesis?
1 wrong base in 100 incorporation steps (1 × 10^-2) ## Footnote This represents the baseline error rate before any accuracy-enhancing mechanisms are applied.
43
How much does E.coli Polymerase III increase the accuracy of DNA synthesis?
1000-fold (1 × 10^-5) ## Footnote This enzyme significantly reduces the error rate during DNA replication.
44
What is the accuracy improvement provided by proofreading in DNA synthesis?
100-fold (1 × 10^-7) ## Footnote Proofreading is a mechanism where incorrect bases are identified and corrected during DNA synthesis.
45
What is the function of mismatch repair in DNA synthesis?
Recognises and corrects mismatched bases ## Footnote This repair mechanism ensures that any errors in base pairing are corrected to maintain genetic fidelity.
46
What binds to a hemimethylated GATC sequence in the methyl-directed mismatch repair mechanism?
MutH ## Footnote MutH is an enzyme that plays a critical role in identifying the strand that needs to be repaired.
47
Which proteins form a complex that recognizes mismatches in the DNA during repair?
MutL and MutS ## Footnote This complex is essential for the initial detection of mismatched bases in the DNA sequence.
48
What does the MutL and MutS complex activate in the mismatch repair process?
MutH to cleave the unmethylated strand ## Footnote This activation is a key step in initiating the repair of mismatched bases.
49
What role does UvrD helicase play in the mismatch repair mechanism?
Unwinds the DNA ## Footnote Unwinding the DNA is necessary for the repair enzymes to access and correct the mismatched bases.
50
What is the function of exonucleases in the mismatch repair process?
Degrade the unmethylated strand ## Footnote This degradation is part of the process of removing the erroneous segment of DNA to allow for correct synthesis.
51
What mechanism does methyl-directed mismatch repair use to identify the original strand of DNA?
Methylation ## Footnote Methylation marks the original DNA strand, allowing the repair system to distinguish it from the newly synthesized strand.
52
What are the three main steps in the process of methyl-directed mismatch repair?
* Binding * Repair synthesis * Ligation ## Footnote These steps outline how the repair system interacts with mismatches in DNA.
53
What occurs during the 'Repair synthesis' step of methyl-directed mismatch repair?
The damaged strand is excised and repaired ## Footnote This step involves removing the incorrect DNA segment and synthesizing the correct one.
54
What is the outcome of mismatch repair deficiency in cells?
Mutator phenotype ## Footnote Cells with mismatch repair deficiency are more likely to accumulate mutations.
55
What is the error rate of chemical polymerization during DNA synthesis?
1 in 100 base pairs ## Footnote This indicates the inherent error rate during the initial process of DNA replication.
56
How much does proofreading increase the accuracy of DNA synthesis?
By 100-fold ## Footnote Proofreading is a mechanism by which DNA polymerases check and correct errors during replication.
57
How much does mismatch repair increase the accuracy of DNA synthesis?
By 100-fold ## Footnote Mismatch repair further enhances the fidelity of DNA replication beyond proofreading.
58
What can mismatch repair defects in humans lead to?
Tumours in various tissues ## Footnote These tissues include colon, skin, ovaries, and stomach.
59
List the tissues where tumours can develop due to mismatch repair defects.
* Colon * Skin * Ovaries * Stomach

Biology Of The Cell (23 decks)

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