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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
Q

How is the origin of replication regulated?

A

The origin of replication is regulated by methylation

Methylation can influence the activity of the DNA and its replication.

26
Q

What is the methylation status of newly replicated DNA?

A

Newly replicated DNA is hemimethylated

Hemimethylation means that only one strand of the DNA is methylated after replication.

27
Q

What do SeqA proteins do?

A

SeqA proteins bind to hemimethylated DNA and prevent methylation

This action helps regulate the timing of DNA replication.

28
Q

For what duration does SeqA ensure the origin of replication remains unmethylated?

A

SeqA ensures that the origin of replication remains unmethylated for 1/3 of the cell cycle

This timing is crucial for proper cell division and replication.

29
Q

What terminates replication in bacterial DNA?

A

Replication terminates when the two forks meet in an area opposite of oriC.

30
Q

What protein binds to ter sites to assist in replication termination?

A

Ter protein binds to ter sites.

31
Q

What is the role of Tus protein in replication?

A

Tus protein binds to ter sites, forming a replication fork trap.

32
Q

What is a replication fork trap?

A

A structure that forks can enter but not leave.

33
Q

What type of collisions are problematic during DNA replication?

A

Head-on collisions between replication forks and transcription complexes.

34
Q

In many bacteria, how are replication and transcription oriented?

A

Replication and transcription are co-directional.

35
Q

How do many replicative polymerases resemble a physical object?

A

They resemble a right hand with fingers, a thumb, and a palm.

36
Q

Where is the nucleotide to be incorporated located in the polymerase structure?

A

At the bottom of the fingers.

37
Q

What is the selection of the correct nucleotide in DNA replication primarily considered?

A

A geometric problem.

38
Q

Which domain of polymerase relies on the catalytic mechanism?

A

The palm domain.

39
Q

Can wrong base pairs be formed during replication?

A

Yes, but they do not fit into the active center very well.

40
Q

What is the error rate of chemical polymerisation without a polymerase?

A

Approximately 1 wrong base in 100 incorporation steps (1 × 10^-2)

This indicates a significant potential for errors during DNA synthesis without the involvement of polymerases.

41
Q

How many errors are estimated in an E. coli chromosome due to chemical polymerisation without a polymerase?

A

46,000 errors

This highlights the potential inaccuracies that can arise in genetic material during replication processes lacking proper enzymatic mechanisms.

42
Q

What is the error rate of chemical polymerisation during DNA synthesis?

A

1 wrong base in 100 incorporation steps (1 × 10^-2)

This represents the baseline error rate before any accuracy-enhancing mechanisms are applied.

43
Q

How much does E.coli Polymerase III increase the accuracy of DNA synthesis?

A

1000-fold (1 × 10^-5)

This enzyme significantly reduces the error rate during DNA replication.

44
Q

What is the accuracy improvement provided by proofreading in DNA synthesis?

A

100-fold (1 × 10^-7)

Proofreading is a mechanism where incorrect bases are identified and corrected during DNA synthesis.

45
Q

What is the function of mismatch repair in DNA synthesis?

A

Recognises and corrects mismatched bases

This repair mechanism ensures that any errors in base pairing are corrected to maintain genetic fidelity.

46
Q

What binds to a hemimethylated GATC sequence in the methyl-directed mismatch repair mechanism?

A

MutH

MutH is an enzyme that plays a critical role in identifying the strand that needs to be repaired.

47
Q

Which proteins form a complex that recognizes mismatches in the DNA during repair?

A

MutL and MutS

This complex is essential for the initial detection of mismatched bases in the DNA sequence.

48
Q

What does the MutL and MutS complex activate in the mismatch repair process?

A

MutH to cleave the unmethylated strand

This activation is a key step in initiating the repair of mismatched bases.

49
Q

What role does UvrD helicase play in the mismatch repair mechanism?

A

Unwinds the DNA

Unwinding the DNA is necessary for the repair enzymes to access and correct the mismatched bases.

50
Q

What is the function of exonucleases in the mismatch repair process?

A

Degrade the unmethylated strand

This degradation is part of the process of removing the erroneous segment of DNA to allow for correct synthesis.

51
Q

What mechanism does methyl-directed mismatch repair use to identify the original strand of DNA?

A

Methylation

Methylation marks the original DNA strand, allowing the repair system to distinguish it from the newly synthesized strand.

52
Q

What are the three main steps in the process of methyl-directed mismatch repair?

A
  • Binding
  • Repair synthesis
  • Ligation

These steps outline how the repair system interacts with mismatches in DNA.

53
Q

What occurs during the ‘Repair synthesis’ step of methyl-directed mismatch repair?

A

The damaged strand is excised and repaired

This step involves removing the incorrect DNA segment and synthesizing the correct one.

54
Q

What is the outcome of mismatch repair deficiency in cells?

A

Mutator phenotype

Cells with mismatch repair deficiency are more likely to accumulate mutations.

55
Q

What is the error rate of chemical polymerization during DNA synthesis?

A

1 in 100 base pairs

This indicates the inherent error rate during the initial process of DNA replication.

56
Q

How much does proofreading increase the accuracy of DNA synthesis?

A

By 100-fold

Proofreading is a mechanism by which DNA polymerases check and correct errors during replication.

57
Q

How much does mismatch repair increase the accuracy of DNA synthesis?

A

By 100-fold

Mismatch repair further enhances the fidelity of DNA replication beyond proofreading.

58
Q

What can mismatch repair defects in humans lead to?

A

Tumours in various tissues

These tissues include colon, skin, ovaries, and stomach.

59
Q

List the tissues where tumours can develop due to mismatch repair defects.

A
  • Colon
  • Skin
  • Ovaries
  • Stomach

Biology Of The Cell (23 decks)

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