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Bacterial Physiology (BIOL 471) > Ch. 3 > Flashcards

Ch. 3 Flashcards

1
Q

What are the properties of prokaryotic DNA?

A
  • 2 complementary, antiparallel strands
  • Semiconservative replication
  • Helical conformation
  • Covalently closed circle
  • Supercoiled loops
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2
Q

What topological problems result from circular DNA and supercoiled loops?

A
  1. Pulling apart supercoiled DNA strands at the replication fork
    - Greater coiling ahead of fork
    - Bunched up and prevent unwinding
  2. Replicated strands will be intertwined and must be separated
  3. Newly replicated DNA must be partitioned into daughter cells
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3
Q

What is the solution to DNA getting bunched up behind the replication fork?

A

DNA gyrase (topoisomerase II)
- Continuously removes supercoils by breaking and resealing dsDNA

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4
Q

What are the three stages of DNA replication?

A
  1. Initiation
  2. Elongation
  3. Termination
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5
Q

What are the steps of initiation for DNA replication?

A
  1. Formation of open complex
  2. Formation of pre-priming complex
  3. Formation of replication fork (replisome)
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6
Q

Explain the formation of the open complex.

A
  • DnaA –> binds oriC
  • HU (histone-like protein) activates ATP-dependent reaction that unwinds the A-T-rich region at the 5’ end of the origin sequence
  • SSB (single strand binding proteins) coat ssDNA
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7
Q

Explain the creation of the pre-priming complex.

A
  • Opening is unwound by DnaB (helicase)
  • Bi-directional –> 2 replication forks form
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8
Q

Where in the cell does the formation of the replication fork take place?

A

In the cytoplasm in a “replisome”

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9
Q

What is the initiation site?

A

Origin = oriC locus

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10
Q

What proteins are involved in elongation (DNA replication)?

A
  • DNA polymerase
  • DnaG (aka primase)
  • Sliding clamps
  • Clamp loader
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11
Q

How many DNA polymerases does E. coli have?

A

5

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12
Q

What is the function of DNA polymerase I?

A

Attaches Okazaki fragments

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13
Q

What is the function of DNA polymerase II, IV, and V?

A

Repairs damaged DNA

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14
Q

What is the function of DNA polymerase III?

A

Replicates DNA at the fork

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15
Q

What is the function of DnaG?

A

Synthesizes the RNA primer for the Okazaki fragments (perhaps also the RNA primer for the leading strand)

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16
Q

What is the function of sliding clamps?

A

Tethers DNA pol to the DNA template

17
Q

What is the function of the clamp loader?

A

Load sliding clamps on
- Tethered to DNA pol –> interacts with clamps
- Stimulates the release of Okazaki fragments

18
Q

Where does DNA replication stop?

A

Stops at region of chromosome opposite oriC = Ter

19
Q

What makes Ter sites unusual?

A
  • Ter sites allow replication to proceed in only 1 direction
  • Several Ter sites in termination zone facing both directions
20
Q

What is the function of the Tus protein?

A

Tus protein binds to Ter site and imposes one-way travel by inhibiting DnaB (replicative helicase)
- Binds with sequence specificity –> gives Ter its directionality

21
Q

What are the two mechanisms of chromosome separation?

A
  1. None or equal recombination events occur –> chromosomes are linked non-covalently
    - Topoisomerase IV separates sister chromosomes via decatenation
  2. Unequal number of recombination events occur –> covalently linked sister chromosomes
    - Must be separated by recombination
    - Occurs at dif sites
22
Q

Explain chromosome partitioning.

A
  • Prokaryotes don’t have a spindle apparatus
  • Proteins compact the chromosomes and pull/guide origins to the poles
23
Q

When does septum formation begin?

A

Begins soon after completion of DNA replication

24
Q

What is the first morphological sign of cell division?

A

Septum formation

25
Q

Where on the cell does the septum form?

A

Forms at midpoint by inward growth of the plasma membrane and peptidoglycan layers

26
Q

_____ must be enzymatically split for cell separation to occur.

A

The double layer of peptidoglycan

27
Q

What proteins are involved in cell division?

A
  • FtsZ and FtsA (cytoplasmic)
  • FtsZ and ZipA form Z-ring (tubulin-like structure)
  • Other Fts proteins recruited sequentially
28
Q

What antibiotics inhibit DNA gyrase?

A
  • Novobiocin
  • Ciprofloxacin
  • Norofloxacin
29
Q

How do acridine dyes inhibit DNA replication?

A

By insertion between bases of the same strand of DNA –> distort double helix

30
Q

How does mitomycin C inhibit DNA replication?

A

By cross-linking bases

31
Q

How does methotrexate inhibit DNA replication?

A

By inhibiting synthesis of enzymes involved in nucleotide synthesis

Bacterial Physiology (BIOL 471) (15 decks)

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