2.2 DNA replication (in vivo)

Question 1

Key Properties of DNA Polymerase:

Answer 1

• DNA Pol “reads” the sequence on a template and links nucleotides together
• reads the template 3’ to 5’ and synthesizes new DNA in the direction 5’ to 3’
• DNA polymerase cannot “start on its own”.
• must always start from an existing 3’OH end of an existing template…
• the primer is RNA

Question 2

Polymerization of DNA
(adding nucleotides/nucleic acid monomers)

Answer 2

1. incoming nucleotides are accepted if they correctly base pair with the template
2. the 3’ OH of the growing strand attacks the high-energy phosphate bond of the incoming nucleotide, providing energy to drive the reaction

• The 5’ carbon of a new monomer is added to the 3’ carbon of the existing strand (or 1st monomer).
• catalyzed by DNA POLYMERASE

Question 3

requirements for the polymerization of DNA/RNA

Answer 3

1. Requires an enzyme (DNA or RNA Polymerase)
2. Requires a form of energy.

This energy form is a monomer with 2 or more phosphates Most common forms = triphosphates
Can be ATP, CTP, GTP, TTP

Question 4

why do DNA monomers begin as TRIphosphates

Answer 4

-binding of three phosphates creates an unfavorable state
(3 negative ions in close proximity).
-removing the outermost phosphates release energy.
-the energy can be used to link the monomer to the polymer.

Question 5

how the cell deaals with the issue of:
Can’t separate an entire genome – very messy!

Answer 5

Separate the DNA strands only a little at a time.

Question 6

how the cell deals with the issue that you can’t make a DNA primer without a DNA primer

Answer 6

Cell makes a RNA primer - can start without a 3’OH.

Question 7

how the cell deals with the challenge that DNA strands are anti-parallel yet DNA polymerization has to occur in the 5’ – 3’ direction.!

Answer 7

. Allow synthesis to happen simultaneously from the two template strands

leading and lagging strands

Question 8

what makes RNA primers

Answer 8

• RNA polymerase – or RNA Primase (an enzyme!!) makes RNA primers.
• DNA Polymerase can add dNTPs to the 3’OH end of this short RNA sequence.
• Synthesizes a short piece of RNA complementary to the DNA template

Question 9

continuous synthesis

Answer 9

leading strands

Question 10

discontinuous synthesis

Answer 10

lagging strands

Question 11

DNA polymerase I

Answer 11

(a different polymerase than DNA Pol III) removes the RNA primer (red) and replaces it with DNA.

Question 12

DNA ligase

Answer 12

• joins all Okazaki fragments
• joins leading and lagging strands at the origin of replication

Question 13

Topoisomerase

Answer 13

relieves stress on the winding helix.
protein

Question 14

Single-stranded binding proteins –

Answer 14

keep the single stranded DNA apart

Question 15

DNA polymerase I

Answer 15

(a different polymerase)
removes the RNA primer and replaces it with DNA.

Question 16

DNA ligase

Answer 16

catalyzes phosphodiester bond formation
joins the fragments together.

Question 17

helicase

Answer 17

• breaks hydrogen bonds
• unwinds DNA double helix

Question 18

primase

Answer 18

synthesizes RNA pirimers on leading and lagging strands

Question 19

SSBPs

Answer 19

coats single-stranded DNA
prevents form immediately reforming H-bonds

Question 20

DNA pol III

Answer 20

synthesizes DNA 5’ to 3’ on leading and lagging strands

Question 21

PROOFREADING

Answer 21

• a process where DNA polymerases can correct their own errors