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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
DNA ligase
- 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
Topoisomerase
- 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
What structure of DNA replication is the focus of anti-cancer drug design?
topoisomerase *specifically for ovarian, cervical, and lung cancers
28
What are DNA polymerase alpha and delta used for?
- 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
What does the primosome consist of?
- helicase (unwinds DNA duplex ahead of replication fork) | - primase (synthesizes short RNA primers on lagging strand)
30
What is Camptothecin
an anti-topoisomerase drug
31
What is toptecan?
anti-topoisomerase drug *used for ovarian, cervical, and lung cancers
32
What three features does a double-stranded DNA molecule require to function as a chromosome?
- origins of replication - a single centromere - telomeres
33
Where is the origin of replication in mammalian DNA sequences?
- 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
What is the function of a centromere?
- 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
What are the a-satellite DNA regions on centromeres for?
they function as the assembly site for a protein complex called the kinetochore, which then attaches to microtubules during cell division
36
What are telomeres?
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
Why are telomeres formed?
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
What are telomeres composed of?
thousands of nucleotides of the repeating unit GGGTTA
39
What enzyme synthesizes the repeating, G-heavy units of telomeres?
telomerase, which contains an RNA template molecule that is used to code the telomere
40
What happens to the remainder of the telomere (the region that is unreplicated, single-stranded)?
it folds back on itself to form a special secondary structure that is bound by specific telomere binding proteins
41
In what functions are telomerase enzymes active?
- during gamete formation - in both embryonic and adult stem cells *not in normal somatic cells
42
Why do telomeres gradually shorten as cells undergo more rounds of replication?
due to failure to replicate chromosome ends
43
What happens when telomeres become too short?
cells stop dividing and become senescent *senescence: loss of a cell's power of division and growth
44
What happens to telomeres in many cancers?
- 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
What is dyskeratosis congenita?
- 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
What is a good example of telomerase-associated cancer?
melanoma - pre-melanoma skin lesions have inactive telomerase - malignant melanomas have active telomerase

Foundations Week 6 (12 decks)

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