Module 7

Question 1

DNA replication relies on the ____ of DNA strands, which can come apart and serve as the template for daughter strands

Answer 1

complementarity

Question 2

Products of DNA Replication

Answer 2

Two semiconserved daughter strands

Question 3

Conservative DNA Replication Model

Answer 3

Both parental strands stay together after replication

Question 4

Semiconservative DNA Replication Model

Answer 4

Double-stranded DNA contains 1 parental and 1 daughter strand following replication

Question 5

Dispersive DNA Replication Modele

Answer 5

Parental/daughter DNA segments are dispersed

Question 6

Meselson and Stahl Experimental Results

Answer 6

Used heavy N isotopes to initially grow bacterial colony, after 1 generation they observed that the DNA was “half heavy”, confirming the semiconservative theory

Question 7

Replication in bacterial chromosomes begins at the single ____

Answer 7

origin of replication (oriC in E. coli)

Question 8

oriC contains 3 types of functionally important sequences:

Answer 8

1. Dna boxes (sites for Dna protein to bind, causing strand to bend)
2. AT-rich regions (sites where strands separate)
3. GATC methylation sites (DNA adenine methyltransferase, prevents premature replication)

Question 9

At bacterial replication fork, ____ separates DNA strands while ____ alleviates supercoils forming upstream

Answer 9

DNA helicase, DNA gyrase (aka topoisomerase II)

Question 10

Single-strand Binding Proteins

Answer 10

Bind to separated DNA strands to keep them apart, serve as placeholders for new strand

Question 11

RNA Primers

Answer 11

“Prime” DNA synthesis, synthesized by primase enzyme. Leading strand has one continuous while lagging has fragments

Question 12

DNA Polymerase III

Answer 12

Responsible for most DNA replication, composed of 10 different subunits (forming DNA Polymerase III holoenzyme)

Question 13

Unusual enzymatic requirements of DNA polymerase include:

Answer 13

• Replicating only in the 5’-3’ direction (while moving in the 3’-5’ direction)
• Require RNA primers on nucleotides in order to synthesize a new strand

Question 14

Leading Strand Synthesis

Answer 14

One RNA primer made at the origin, DNA polymerase III attaches nucleotides in 5’-3’ direction as it slides toward replication fork

Question 15

Lagging Strand Synthesis

Answer 15

Synthesizes new strand in 5’-3’ direction, moves away from replication fork. Many RNA primers required, DNA polymerase III synthesizes small fragments using RNA primers (Okazaki fragments). Okazaki fragments have primers removes via DNA polymerase I, which fills the gap with DNA before ligase seals the strand

Question 16

Primosome

Answer 16

DNA helicase and primase bind to each other to form complex, better coordinates actions of the two enzymes

Question 17

Replisome

Answer 17

Primosome associates with 2 DNA polymerase holoenzymes (one for each strand) to form larger complex around replication fork

Question 18

Nucleotides are connected via DNA polymerase catalyzeing the formation of an ____ bond between innermost phosphate of the incoming deoxyribonucleoside triphosphate and the 3’ -OH of the sugar of the previous deoxynucleotide

Answer 18

ester (leads to release of other to P’s)

Question 19

Processivity

Answer 19

DNA polymerase remains attached to template strand as it synthesizes new daughter strand, due to the several holoenzyme subunits. B subunit forms dimer ring around strand “clamp protein” which freely slides along ds DNA

Question 20

3 reasons for the fidelity of DNA:

Answer 20

1. A-T, G-C stability
2. Structure of DNA polymerase on active site
3. Proofreading function of DNA polymerase (exonuclease activity)

Question 21

Origin of Replication in Eukaryotes

Answer 21

Begins with assembly of prereplication complex (preRC), including the origin recognition complex (ORC), a 6 subunit complex acting as the first initiator to replication (MCM helicase completes DNA replication licensing to create fork, begin synthesis)

Question 22

Primers are removed in eukaryotic cells using ____, which runs into primer of adjacent Okazaki fragment and “pushes” it into a short flap, which is removed by ____

Answer 22

DNA polymerase delta, flap endonuclease

Question 23

DNA Polymerase alpha

Answer 23

Associates with RNA primase to form RNA/DNA hybrid primer

Question 24

DNA Polymerase epsilon and delta

Answer 24

Exchanges primer on strands for DNA (epsilon on leading strand), (delta on lagging strand) in a process termed polymerase switching

Question 25

DNA Polymerase gamma

Answer 25

Replicates mitochondrial DNA

Question 26

Telomerase

Answer 26

Adds DNA to ends of telomeres in 3 step process (binding, polymerization (+6 nucleotides), and translocation), allowing for RNA primer to be added and polymerase to resume work

Question 27

____, DNA can be replicated to produce two double helices with the identical base sequences?

Answer 27

Due to the ATGC rule

Question 28

What are the expected results for the Meselson and Stahl experiment after 3 generations (i.e, 3 rounds of DNA replication in the presence of light nitrogen)? Note: during generation zero, the DNA is all heavy, and subsequent generations only make light DNA.

Answer 28

1/4 heavy, 3/4 light (1st gen is 100% heavy)