DNA Replication

Question 1

DNA replication is ____ & ______.

Answer 1

Bidirectional and semiconservative

Question 2

Semiconservative: each copy of the DNA molecule, after replication, contains one strand from the __________ and one from the ________

Answer 2

Original template, newly synthesized

Question 3

Prokaryotes have ______ origin of replication and _____ DNA

Answer 3

1, circular

Question 4

Origins of replication sequences are almost exclusively ____ and _____ bases.

Answer 4

A-T bases

Question 5

These proteins bind to single strands to prevent reannealing and protect DNA from nuclease degradation.

Answer 5

SSBs: Single-Stranded binding proteins

Question 6

This enzyme unwinds the DNA helix.

Answer 6

DNA Helicase

Question 7

DNA is a helix, so when helicases separate the strands of DNA, _________ ahead of the replication fork will occur.

Answer 7

Supercoiling

Question 8

________ alleviate supercoiling ahead of the replication fork.

Answer 8

Topoisomerases

Question 9

____________ creates a nick in one strand which allows the DNA to swivel around the intact strand, then seals the nicked strand.

Answer 9

Type I topoisomerase

Question 10

__________ cut both strands to relieve the supercoiling then re-ligates the two strands

Answer 10

Type II topoisomerase

Question 11

A special Type II topoisomerase (found in bacteria), __________ - introduces (-) supercoils - inhibited by ________

**Also important for the separation of circular chromosomes after replication.

Answer 11

DNA Gyrase, quinolones

Question 12

All polymerases that synthesize nucleic acids only catalyze synthesis in the ____ to _____ direction.

Answer 12

5’ to 3’

Question 13

Since DNA is antiparallel, the template must be read in the ____ to _____ direction.

Answer 13

3’ to 5’

Question 14

Nucleic Acid Synthesis direction: _______

Template Reading Direction: _______

Answer 14

5’ to 3’

3’ to 5’

Question 15

During DNA replication, this strand is synthesized continuously.

Answer 15

Leading Strand

Question 16

During DNA replication, this strand is synthesized discontinuously away from the replication fork.

Answer 16

Lagging Strand

Question 17

In DNA replication, the discontinuously synthesized fragments are called _____ fragments and are later joined to become a continuous segment of DNA

Answer 17

Okazaki

Question 18

DNA polymerases require a free _________group to begin synthesis.

During DNA replication, this problem is solved by the action of ________.

Answer 18

3’ hydroxyl, Primase

Question 19

Primase is an ____________ and does not require a free 3’ OH group to begin synthesis. It copies the first ~10 nucleotides to prime synthesis.

DNA polymerases then begin synthesis from the free 3’OH group from the RNA primer.

Answer 19

RNA polymerase

Question 20

Each new DNA fragment on the lagging strand begins with the action of ________ laying down an _______

Answer 20

Primase, RNA primer

Question 21

________ recognizes the RNA primer and begins to synthesize the DNA

Answer 21

DNA polymerase III

Question 22

___________ catalyze a reaction between the 3’OH group of the strand being synthesized and the ______________ of an incoming nucleotide specified by the template being copied.

Answer 22

DNA polymerases, 5’ triphosphate

Question 23

Net reaction of DNA Polymerase = addition of a ______ to a growing DNA strand and the release of __________.

_________ is further cleaved to _____________ to make the reaction irreversible and drive the reaction in the forward direction.

Answer 23

Nucleotide, pyrophosphate, Pyrophosphate, 
inorganic phosphate (Pi)

Question 24

_______ - a common theme in many condensation reactions in biochemistry

Answer 24

A coupled irreversible reaction -

Question 25

_______ high energy bonds are cleaved for each added nucleotide in a growing DNA chain.

Answer 25

2

Question 26

________ is the enzyme in prokaryotes that elongates both the leading and lagging strands

Answer 26

DNA polymerase III | pol III

Question 27

DNA polymerase III (pol III) is the enzyme in _________ that elongates both the leading and lagging strands.

Answer 27

Prokaryotes

Question 28

DNA replication needs to be as accurate as possible - a single nucleotide mutation can have devastating consequences. Pol III, as well as many other DNA polymerases, have ______ _____

Answer 28

Proofreading Activity

Question 29

If DNA polymerase mispairs a nucleotide with the template, it uses its ________ to excise the mismatched nucleotide.

Answer 29

3' to 5' exonuclease activity

Question 30

________ checks each added nucleotide to make sure it is correctly base-paired with the template strand.

Answer 30

Pol III

Question 31

When pol III detects a mistake, it __________ one nucleotide and she's the misincorporated nucleotide. This is called ________

Answer 31

Shifts backward | 3' to 5' exonuclease activity

Question 32

This enzyme has 5' to 3' polymerase activity, and exonuclease activity in BOTH the 3' to 5' and 5' to 3' directions

Answer 32

DNA polymerase I (pol I)

Question 33

RNA primer is elongated by ______ until another stretch of RNA is encountered. RNA primer is excised by ______, one ribonucleotide at a time. Gap is filled by _____. Remaining nick is sealed by ______.

Answer 33

DNA polymerase III DNA polymerase I DNA polymerase I DNA-ligase

Question 34

_______ lays down an RNA primer to begin each new strand.

Answer 34

Primase

Question 35

______ extends the leading and lagging strands.

Answer 35

Pol III

Question 36

________ removes RNA primers and replaces them with DNA.

Answer 36

Pol I

Question 37

In Eukaryotic Cell Cycle, this phase is the most variable in terms of time, growth, and metabolism

Answer 37

G1 Phase (G stands for gap)

Question 38

This phase occurs when DNA is replicated.

Answer 38

S Phase (S stands for synthesis)

Question 39

This phase has a second "gap" phase where the cell prepares to divide.

Answer 39

G2 Phase

Question 40

This phase is the phase of Cell Division.

Answer 40

M phase (M for Mitosis)

Question 41

Eukaryotic DNA Polymerases: Pol (alpha) - contains ______ + ______ (begins strand synthesis) Pol (delta) - _______ + _______ (extends strands)

Answer 41

Primase + DNA polymerase DNA polymerase + proofreading (Know that alpha and delta cooperate)

Question 42

Eukaryotic chromosomes are _______. At the end of the DNA molecule, the _______ strand will have a gap once the ________ is removed. Eukaryotes solve this problem by the action of enzymes called _______.

Answer 42

Linear Lagging RNA Primer telomerases

Question 43

The ends of eukaryotic chromosomes contain repeated sequences called ______.

Answer 43

Telomeres.

Question 44

___________ extends the ends of linear chromosomes.

Answer 44

Telomerase

Question 45

Telomerase also contains a _________ - it copies its own template (RNA) into DNA extending the 3' overhang on the chromosome. This process is repeated many times.

Answer 45

Reverse transcriptase

Question 46

Cells that do not express _______ have their chromosomes shortened after every cellular division (cellular equivalent of aging)

Answer 46

Telomerase

Question 47

A defect in mismatch repair is responsible for ____________, one of the most common inherited cancers.

Answer 47

HNPCC | Hereditary nonpolyposis colorectal cancer

Question 48

UV light usually causes pyrimidine dimers - usually _____ dimers.

Answer 48

Thymine

Question 49

In humans, a rare genetic disorder called ____ _____ most often results from a deficiency in excision endonuclease.

Answer 49

Xeroderma pigmentosum

Question 50

In humans, a rare genetic disorder called xeroderma pigmentosum most often results from a deficiency in ______ ______.

Answer 50

Excision endonuclease.