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Foundations Week 6 > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

What are telomeres critical for?

A

critical regulators of cellular senescence and aging

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2
Q

What causes DNA to form a spiral?

A

natural properties of the bases and backbone

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3
Q

In which direction is the DNA strand oriented?

A

5’ to 3’
two strands run in opposite directions

*polymerization of DNA can only occur in this direction (new strand forms as 5’–>3’, but copies template starting at the template’s 3’ tail)

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4
Q

What composes DNA strands?

A
  • hydrogen-bonded nucleotide base pairs (A-T; G-C)

- sugar-phosphate backbone

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5
Q

What does it mean that DNA replication is semi-conservative?

A
  • one strand of DNA helix is retained (will stay entirely intact) as one half of the new double stranded DNA helix
  • this strand acts as the template while the other strand is completely new
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5
Q

DNA replication is ____-directional

A

bi

  • DNA replication would take too long if only started at one end of molecule
  • there are tens of thousands of independent regions of DNA where it is being replicated
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6
Q

What of the structure of DNA implies a mechanism for duplication of the genetic material?

A

the complementary base pair structure (where the sequence of one strand defines the sequence of the other strand)

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7
Q

What are the open sections of DNA strands where replication is taking place called?

A

replicons

*there are 10,000-30,000 replicons

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9
Q

During cell division, about how long does DNA replication take?

A

8 hours

  • rate of about 500-100 bases per second per fork
  • DNA replication is rapid and accurate; 1 error in a billion nucleotides
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10
Q

Is DNA replication symmetric or asymmetric?

A

asymmetric: one strand is synthesized continuously, while the other strand is not

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11
Q

Which strand is synthesized continuously?

A

Leading strand

3’ - 5’ strand (replication strand is 5’-3’)

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12
Q

Which strand is the lagging strand?

A

the one discontinuously synthesized (Okasaki fragments)

*requires RNA primers

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13
Q

Can DNA synthesis begin spontaneously?

A

No, it needs a DNA or RNA primer

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14
Q

What is the enzyme that makes the short RNA primers on the lagging strand?

A

DNA primase

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15
Q

DNA is polymerized using what?

A

short RNA primers

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16
Q

What composes the Okazaki fragments?

A
  • short RNA primer

- DNA polymerase adds to new RNA primer to start new Okazaki fragment

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17
Q

Each leading strand is also a lagging strand. Why?

A

replication is occurring in both directions, so each strand has a leading and lagging strand (leading is started where fork starts, but before that it is “lagging”)

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18
Q

What are the proteins required for DNA replication in eukaryotes?

A
  • DNA polymerase alpha and delta
  • sliding clamp (sliding ring) complex
  • DNA helicase and primase int he primosome
  • single strand DNA binding protein
  • Ribonuclease H (RNase H)
  • DNA ligase
  • topoisomerase
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19
Q

What is the sliding clamp/sliding ring complex?

A
  • this complex attaches DNA polymerase to the DNA
  • on lagging strand, it detaches from the DNA immediately when it encounters a double stranded structure (end of an Okazaki fragment)
20
Q

Does DNA polymerase have innate affinity for DNA?

A

no

it needs the ‘sliding clamp’ to attach it to DNA

21
Q

DNA helicase

A
  • unwinds the DNA duplex ahead of the replication fork
  • it rides along DNA with primase

*unwinding basically refers to separation of two strands

22
Q

What does primase do?

A

synthesizes the short RNA primers (6-12 bases long) onto lagging strand

23
Q

Single strand DNA binding protein

A
  • stops DNA from base-pairing to itself (in parts of the DNA single strand that has not yet been replicated)
  • otherwise this base pairing within the single strands could interfere with replication
  • these self-base paired regions are called “hairpins”
24
Q

Ribonuclease H (RNase H)

A
  • degrades the RNA primer region of the Okazaki fragment
  • DNA polymerase now fills in the short sections
  • this leaves multiple DNA fragments on the lagging strand, but no gaps
25
Q

DNA ligase

A
  • this enzyme joins a 3’OH group at one end of a DNA molecule to a 5’ monophosphate on another molecule
  • two bases must be adjacent, because ligase cannot bridge a gap
  • seals the nick (joins new Okazaki fragment to the growing DNA)
  • *this is for joining Okazaki fragments to make one continuous strand
26
Q

Topoisomerase

A
  • located ahead of the replication fork
  • it covalently binds to the DNA, and then cuts the phosphodiester bond backbone on one side of the helix (now you have one free backbone left to rotate freely
  • constantly allows DNA to rotate to prevent torsion
  • topoisomerase reseals the cut to restore the double helix
27
Q

What structure of DNA replication is the focus of anti-cancer drug design?

A

topoisomerase

*specifically for ovarian, cervical, and lung cancers

28
Q

What are DNA polymerase alpha and delta used for?

A
  • the major DNA polymerase enzymes present at the replication fork
  • responsible for most of DNA synthesis
  • very large >200 kDa
    (adds nucleotide for each base pair)

*no innate affinity for DNA, needs sliding clamp/ring

29
Q

What does the primosome consist of?

A
  • helicase (unwinds DNA duplex ahead of replication fork)

- primase (synthesizes short RNA primers on lagging strand)

30
Q

What is Camptothecin

A

an anti-topoisomerase drug

31
Q

What is toptecan?

A

anti-topoisomerase drug

*used for ovarian, cervical, and lung cancers

32
Q

What three features does a double-stranded DNA molecule require to function as a chromosome?

A
  • origins of replication
  • a single centromere
  • telomeres
33
Q

Where is the origin of replication in mammalian DNA sequences?

A
  • extended and poorly defined regions of DNA
  • one known origin is beta-globin region
  • these origins of replication serve as the sites for assembly of a large protein complex (origin recognition complex) that commences the process of DNA replication
  • each human chromosome contains thousands of independent origins of replication
34
Q

What is the function of a centromere?

A
  • site that allows duplicated DNA molecules to be pulled apart into daughter cells during cell division
  • assembly site for spindle microtubules that separate the chromosomes
  • in human chromosomes, centromeric DNA is very large and contains many repeats of simple DNA sequences (a-satellite DNA)
  • these sequences function as the assembly site for a protein complex called the kinetochore, which then attaches to microtubules during cell division
35
Q

What are the a-satellite DNA regions on centromeres for?

A

they function as the assembly site for a protein complex called the kinetochore, which then attaches to microtubules during cell division

36
Q

What are telomeres?

A

the special repeating DNA structures at the end of linear chromosomes

*in the human chromosomes, there are about 10,000 nucleotides of the repeating unit, GGGTTA; these repeats are synthesized by telomerase

37
Q

Why are telomeres formed?

A

the ends of chromosomes cannot be replicated using normal DNA replication mechanisms
- ultimately, there is no place for primase to synthesize the RNA primer for an Okazaki fragment

38
Q

What are telomeres composed of?

A

thousands of nucleotides of the repeating unit GGGTTA

39
Q

What enzyme synthesizes the repeating, G-heavy units of telomeres?

A

telomerase, which contains an RNA template molecule that is used to code the telomere

40
Q

What happens to the remainder of the telomere (the region that is unreplicated, single-stranded)?

A

it folds back on itself to form a special secondary structure that is bound by specific telomere binding proteins

41
Q

In what functions are telomerase enzymes active?

A
  • during gamete formation
  • in both embryonic and adult stem cells

*not in normal somatic cells

42
Q

Why do telomeres gradually shorten as cells undergo more rounds of replication?

A

due to failure to replicate chromosome ends

43
Q

What happens when telomeres become too short?

A

cells stop dividing and become senescent

*senescence: loss of a cell’s power of division and growth

44
Q

What happens to telomeres in many cancers?

A
  • telomerase is re-activated, allowing cells to undergo more divisions (unlimited number) and to evade senescence
  • drugs are currently being developed to block telomerase in tumor cells as a possible treatment of cancer
45
Q

What is dyskeratosis congenita?

A
  • human disease associated with abnormal telomere extension in the embryo
  • patients born with unusually short telomere sequences
  • disease particularly effects tissues that require frequent cell division, including skin, nails, and bone marrow cells
  • consequences are very widespread
  • patients generally give the appearance of premature aging
  • in children, symptoms include dry skin, pigmentation, and spots
  • affected individuals usually die before the age of 20
46
Q

What is a good example of telomerase-associated cancer?

A

melanoma

  • pre-melanoma skin lesions have inactive telomerase
  • malignant melanomas have active telomerase

Foundations Week 6 (12 decks)

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