Week 5- DNA Replication Flashcards

1
Q

What direction do DNA polymerases synthesize DNA?

A

5’ to 3’

DNA polymerases can only add nucleotides to the free 3’ end of a growing strand.

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2
Q

What are the two types of activity that DNA polymerase possesses?

A

3’ to 5’ exonuclease activity

This activity allows for proofreading during DNA replication.

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3
Q

What is the size of DNA molecules typically measured in?

A

Base pairs (bp)

1 bp corresponds to approximately 0.34 nm of length along the strand.

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4
Q

What is the range of DNA sizes mentioned?

A

5 kb to over 250,000 kb

kb = kilo base pairs, Mb = mega base pairs, Gb = giga base pairs.

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5
Q

What temperature can E. coli undertake DNA replication down to?

A

70°C

Some extremophiles, like P. halocryophilus, can replicate DNA at -150°C.

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6
Q

Who won the Nobel Prize in 1959 for the discovery of the mechanisms of DNA synthesis?

A

Arthur Kornberg

He shared the prize with Ochoa.

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7
Q

What is the primary role of DNA polymerase I?

A

DNA repair

It is involved in removing RNA primers during DNA replication.

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8
Q

Which DNA polymerase is the major replicative enzyme in E. coli?

A

DNA polymerase III

Temperature-sensitive mutants of Pol III cannot replicate DNA at restrictive temperatures.

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9
Q

What are the nucleotides used in DNA synthesis called?

A

Nucleoside triphosphates (dNTPs)

Examples include dATP, dTTP, dGTP, and dCTP.

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10
Q

What is the rate of elongation for DNA replication in bacteria?

A

500 nucleotides per second

In human cells, the rate is approximately 50 nucleotides per second.

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11
Q

What initiates the synthesis of RNA primers during DNA replication?

A

RNA primase

DNA polymerase III cannot initiate synthesis de novo.

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12
Q

What are Okazaki fragments?

A

Short segments synthesized on the lagging strand

They are later joined together by DNA ligase.

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13
Q

How many origins of replication do prokaryotes have?

A

One origin of replication

This leads to a single replication bubble.

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14
Q

What is the typical replication time for prokaryotes?

A

<1 hour

Eukaryotes, with multiple chromosomes, take approximately 2-3 hours.

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15
Q

What is the role of helicase in DNA replication?

A

Unwinds the double helix

ATP is required for this process.

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16
Q

What is the purpose of single-strand binding proteins during DNA replication?

A

Prevent the re-annealing of unwound DNA strands

They stabilize the unwound template strands.

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17
Q

What is the mechanism of proofreading during DNA replication?

A

3’ → 5’ exonuclease activity

This activity clips back unpaired or misinserted nucleotides.

18
Q

What must occur before DNA polymerases can add nucleotides?

A

A primer must be synthesized

The initial nucleotide chain produced is actually a short stretch of RNA.

19
Q

Fill in the blank: The lagging strand is synthesized as a series of _______.

A

Okazaki fragments

20
Q

True or False: DNA polymerases can initiate the synthesis of a polynucleotide.

A

False

They can only add nucleotides to an existing chain.

21
Q

What are the four main proteins involved in the initiation of DNA replication?

A
  • Topoisomerase
  • Helicase
  • Primase
  • Single-strand binding proteins
22
Q

What is the role of DNA ligase during DNA replication?

A

Joins Okazaki fragments

It seals the gaps between newly synthesized DNA segments.

23
Q

What is the outcome of the proofreading mechanism in DNA replication?

A

Reduces error rate to ~1 in 10^9

This results in approximately 0.04 potential mutations per genome replication.

24
Q

What is the primary function of DNA ligase?

A

Joins two Okazaki fragments

DNA ligase is essential in DNA replication to connect segments of DNA.

25
Q

What is the role of DNA polymerase I?

A

Removes RNA primer from 5’ end of 2nd fragment and replaces with DNA

DNA polymerase I is crucial for DNA replication, particularly in the removal of RNA primers.

26
Q

How does eukaryotic DNA replication differ from that in E. coli?

A

Has significant similarities and differences

Key differences include initiation mechanisms and genome size.

27
Q

What are the key characteristics of bi-directional DNA replication?

A

Leading and lagging strands, primers, and proofreading

This is a fundamental process in DNA replication ensuring accuracy and efficiency.

28
Q

List the major differences in eukaryotic DNA replication compared to prokaryotic.

A
  • Different DNA replication initiation
  • Larger genomes
  • Multiple replication sites
  • Linear chromosomes
  • Lower rates of DNA synthesis
  • More complex enzymology

These differences reflect the complexity of eukaryotic organisms.

29
Q

What is the significance of the Origin Replication Complex in humans?

A

Loads onto DNA first for fork initiation

The Origin Replication Complex is crucial for starting DNA replication in eukaryotic cells.

30
Q

What is the primary function of DNA polymerase α?

A

Chromosomal replication 5’ to 3’ but lacks exonuclease activity

DNA polymerase α is always associated with a primase for initiation.

31
Q

What is the role of DNA polymerase δ?

A

5’ to 3’ polymerase activity and a 3’ → 5’ exonuclease activity

DNA polymerase δ is involved in the elongation phase of DNA replication.

32
Q

What is the mitochondrial genome structure?

A

Circular, 16,569 base pairs encoding 37 genes

Mitochondrial DNA is inherited maternally in most species.

33
Q

Which DNA polymerase is specialized for mitochondrial DNA replication?

A

Pol γ/PolG

This polymerase is essential for the replication of mitochondrial DNA.

34
Q

What is the composition of telomerase?

A

Catalytic subunit (hTERT) and template RNA (hTR)

Telomerase plays a critical role in maintaining telomere length during cell division.

35
Q

Fill in the blank: Telomeres in humans consist of repeated sequences of _______.

A

(TTAGGG)n

These repeated sequences help protect chromosome ends.

36
Q

True or False: Telomerase is active in most somatic cells.

A

False

Telomerase is repressed in most somatic cells, leading to telomere shortening.

37
Q

What happens when D loop integrity is compromised in telomeres?

A

Triggers irreversible exit from the cell cycle producing replicative senescence

This process is crucial for cellular aging and the prevention of uncontrolled cell division.

38
Q

What is the primary challenge posed by linear chromosomes during replication?

A

Okazaki fragment placement cannot be replicated by conventional machinery

This challenge leads to the need for specialized mechanisms like telomerase.

39
Q

List the methods that can be used to assay DNA replication.

A
  • 32P incorporation
  • Fluorescence

These methods allow researchers to track and analyze DNA replication processes.

40
Q

What is a characteristic of the chloroplast genome?

A

Circular and typically 12-17 Kbp, encodes ~100 genes

Chloroplasts, like mitochondria, are derived from ancient prokaryotic organisms.