DNA Replication

Question 1

DNA Replication:

DNA replication is ______ and ______.

Answer 1

DNA replication is bidirectional and semiconservative.

Question 2

DNA Replication:

Bidirectional means that replication begins in the _____ of a DNA molecule, and proceeds in both directions.

Answer 2

interior

Question 3

DNA Replication:
Semiconservative means that each copy of the DNA molecule, after replication, contains one strand from the ______ template and one newly _____ strand. It conserves 1 strand and makes a new one.

Answer 3

Semiconservative means that each copy of the DNA molecule, after replication, contains one strand from the original template and one newly synthesized strand. It conserves 1 strand and makes a new one.

Question 4

DNA Replication:
Prokaryotes has ___ origin of replication and _____ DNA. There are replication forks at multiple sites.
Eukaryotes have ____ origins of replication, in order to replicate in a reasonable amount of time.

Answer 4

Prokaryotes has one origin of replication and circular DNA. There are replication forks at multiple sites.
Eukaryotes have multiple origins of replication, in order to replicate in a reasonable amount of time.

Question 5

Prokaryotic DNA Replication:

Separation of the two ______ DNA strands. Origin of replication needs to be melted. Origin of replication sequences are usually almost exclusively composed of ____ bases. It is accomplished by 20-50 monomers of DnaA protein.

Answer 5

Separation of the two complementary DNA strands. Origin of replication needs to be melted. Origin of replication sequences are usually almost exclusively composed of A-T bases. It is accomplished by 20-50 monomers of DnaA protein. (Note: DnaA is a protein that activates initiation of DNA replication in bacteria.)

Question 6

_____ is a protein that activates initiation of DNA replication in bacteria.

Answer 6

DnaA

Question 7

Formation of the Replication Fork (at the site of melting): ________ bind to single strands to prevent reannealing and protect DNA from nuclease degradation. They bind and stabilizes DNA and protects it from damage. Note: The ___________ keep the two strands of DNA separate.

Answer 7

Formation of the Replication Fork (at the site of melting): Single stranded binding proteins (SSBs) bind to single strands to prevent reannealing and protect DNA from nuclease degradation. They bind and stabilizes DNA and protects it from damage. Note: The single-stranded DNA-binding proteins (SSBs) keep the two strands of DNA separate.

Question 8

DNA _____ then moves toward the double stranded region (toward the replication fork) and force the strands apart. The SSBs bind the newly separated strands.

Answer 8

DNA helicase then moves toward the double stranded region (toward the replication fork) and force the strands apart. The SSBs bind the newly separated strands.

Question 9

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

Answer 9

supercoiling

Question 10

Topoisomerases alleviate supercoiling ahead of the replication fork. _______ creates a nick in one strand which allows the DNA to swivel around the intact strand, then seals the nicked strand.

Answer 10

Type 1 topoisomerase

Question 11

Topoisomerases alleviate supercoiling ahead of the replication fork. _______ cuts both strands to relieve the supercoil, then re-ligates the two strands. (Note: Type II cutes BOTH strands; there’s no swivel!)

Answer 11

Type II topoisomerase

Question 12

There is a special kind of Type II topoisomerase called ______. The DNA gyrase introduces negative (-) supercoils. The prokaryotic DNA replication is inhibited by quinolones. DNA gyrase is also important for the separation of circular chromosomes after replication.

Answer 12

DNA gyrase

Question 13

Type ___: Cleaves one strand of a DNA molecule to relieve supercoiling, then religates the strand.

Answer 13

Type 1 topoisomerase

Question 14

Type __: Cleaves BOTH strands of a DNA molecule to relieve supercoiling, then religates the strand.

Answer 14

Type 2 topoisomerase

Question 15

A special type of Type II topoisomerase that is found in bacteria. It is called DNA gyrase which introduces _____. It is important for replication, packaging of the chromosome, and separation of replicated circular chromosomes. DNA gyrase also targets _______which inhibits prokaryotic DNA replication.

Answer 15

supercoils

quinolones

Question 16

Direction of DNA Replication:

At each replication fork, one strand (_____) of the DNA fragment can be replicated continuously as the replication fork advances.

Answer 16

leading strand

Question 17

Direction of DNA Replication:

On the other hand, the _____ is synthesized discontinuously. As the replication fork advances, small fragments of DNA are synthesized 5’ to 3’ away from the replication fork.

Answer 17

lagging strand

Question 18

Direction of DNA Replication:

The discontinuously synthesized fragments are called ________ and are later joined to become a continuous segment of DNA.

Answer 18

Okazaki fragments

Question 19

RNA Primer:

DNA polymerases require a free _________ to begin synthesis.

Answer 19

3’ OH group

primase

Question 20

RNA Primer:
DNA polymerases require a free 3’ OH group to begin synthesis. During DNA replication, this problem is solved by the action of ____ .

Answer 20

primase

Question 21

RNA Primer:
____ is an RNA polymerase. (RNA polymerase does not require a free 3’ OH group to begin synthesis.) It copies the first 10 nucleotides to “prime” synthesis.

Answer 21

Primase

Question 22

RNA Primer:
DNA polymerases then begin synthesis from the free 3’ OH group from the _____. Each new DNA fragment on the _____ strand begins with the action of primase laying down an RNA primer.

Answer 22

RNA primer

lagging

Question 23

RNA Primer:
DNA polymerases 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 23

5’ triphosphate

Question 24

RNA Primer:

Net reaction = addition of a ____ to a growing DNA strand and the release of _____.

Answer 24

nucleotide

pyrophosphate

Question 25

RNA Primer: Pyrophosphate is further cleaved to _____ to make the reaction ____, and drive the reaction in the forward direction. It is an important aspect of DNA and transcription.

Answer 25

``` inorganic phosphate (Pi) irreversible ```

Question 26

RNA Primer: A coupled irreversible reaction is a common theme in many condensation reactions in biochemistry. Two high energy bonds are cleaved for each added nucleotide in a growing DNA chain. ______is the enzyme in prokaryotes that elongate both the leading and lagging strands.

Answer 26

DNA polymerase III (pol III)

Question 27

RNA Primer: Proofreading: DNA replication needs to be as accurate as possible. A single nucleotide mutation can have devastating consequences. _____ (as well as many other DNA polymerases) have proofreading activity. ____ checks each added nucleotide to make sure it is correctly base-paired with the template strand. _____activity in the 3’ to 5’ activity is to excise mismatched nucleotides.

Answer 27

Pol III Pol III Exonuclease

Question 28

RNA Primer: When pol III detects a mistake, it shifts backward one nucleotide, and excises the misincorporated nucleotide. It is called__________.

Answer 28

3’ to 5’ exonuclease activity

Question 29

Excision of the RNA primers and their replacement by DNA: To complete replication of circular DNA and the joining of Okazaki fragments, the ______ must be removed and replaced with dNTPs.

Answer 29

RNA primer

Question 30

Excision of the RNA primers and their replacement by DNA: DNA polymerase (pol I): 5’ to 3’ polymerase activity ______ activity: 3’ to 5’ and 5’ to 3’ exonuclease activity.

Answer 30

exonuclease

Question 31

Excision of the RNA primers and their replacement by DNA: Pol I removes RNA primer (5’ to 3’ exonuclease) and it replaces the ____ with the correct dNTP (5’ to 3’ polymerase). It proofreads and corrects misincorporated nucleotides (3’ to 5’ exonuclease).

Answer 31

rNTPs

Question 32

Excision of the RNA primers and their replacement by DNA: Pol I’s 5’ to 3’ exonuclease activity can actually remove correctly base paired _____- (in this case, the RNA primer). The 5’ to 3’ exonuclease activity is important for another pol I function, DNA repair.

Answer 32

nucleotides

Question 33

DNA ____ ‘seals’ the nick that remains after the RNA primer is removed and replaced with dNTPs. The initial strand separation is _____ protein which has a high AT content. The SSB proteins prevent reannealing.

Answer 33

ligase | DnaA

Question 34

DNA Replication: | ______ unwinds DNA at the replication fork.

Answer 34

Helicase

Question 35

DNA Replication: _______ relieves supercoiling ahead of the replication fork. The leading strand synthesized continuously and the lagging strand synthesized discontinuously in pieces called Okazaki fragments.

Answer 35

Topoisomerase

Question 36

DNA Replication: ____ lays down an RNA primer to begin each new strand. Pol II extends the leading and lagging strands. Pol I removes RNA primers and replaces them with DNA.

Answer 36

Primase

Question 37

DNA Replication: | DNA ____ seals the nick in the fragments so it makes it continuous.

Answer 37

ligase

Question 38

Eukakryotic Cell Cycle: G1 phase is the most variable in terms of ____; _____ and _____ (“G” stands for “gap”).

Answer 38

time, growth and metabolism

Question 39

Eukakryotic Cell Cycle: | G0 phase is the _____ G1 phase, the appropriate signals can cause a reentry into the cell cycle.

Answer 39

semipermanent

Question 40

Eukakryotic Cell Cycle:S phase: Replication of DNA (“S” stands for synthesis). G2 phase: A second “gap” phase where the cell prepares to _____.

Answer 40

divide

Question 41

Eukakryotic Cell Cycle: | The M phase is the stage of cell ____ (“M” stands for mitosis).

Answer 41

division

Question 42

Telomeres and Telomerase: Eukaryotic chromosomes are linear; they are at the end of the DNA molecule, the lagging strand will have a gap once the _____ is removed. It has relevance to cancer.

Answer 42

RNA primer

Question 43

Eukaryotes solve this problem by the action of enzymes called ______. The ends of eukaryotic chromosomes contain repeated sequences called _____ which have 6-nucleotides that repeats (>1000 6-nucleotide repeats).

Answer 43

telomerases telomeres

Question 44

______extends the ends of linear chromosomes. It contains a segment of RNA that is complementary to the telomere repeat and extends beyond the repeat – the extension acts as a template.

Answer 44

Telomerase

Question 45

Telomeres and Telomerase: 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. It protects DNA from being degraded and it stops nucleases from chopping into DNA.

Answer 45

reverse transcriptase

Question 46

Telomeres and Telomerase: | After telomerase extends the repeat many times, the overhang is filled in by the action of ____ and _____.

Answer 46

primase and DNA polymerases

Question 47

Telomeres and Telomerase: However, there will always be a section of DNA left that is ______. This 3’ overhang assumes a special structure with the dsDNA and certain proteins to protect the end of the DNA.

Answer 47

single stranded

Question 48

Telomerase is not expressed in all cells and it is expressed in cells that continually divide and are not terminally differentiated. Cells that do not express telomerase have their chromosomes shortened at each cell division. They have a finite number of cell divisions called the ______________. Some cells can activate telomerase which is a molecular reason behind cancer.

Answer 48

cellular equivalent of aging

Question 49

Reverse Transcriptase: Normally genetic information flows from DNA to RNA to protein. Certain polymerases can copy RNA into DNA: 1. 2. 3. It’s the common strategy in many viruses like HIV. It lacks proofreading activity which brings on a high mutation rate in viruses.

Answer 49

1. Reverse transcriptase 2. RNA dependent DNA polymerase 3. Telomerase.

Question 50

DNA Repair: Strand-directed mismatch repair corrects errors made during replication. Some types of damage repair (similar process). Certain proteins (with 1._______ activity) recognize misincorporated bases (or damaged bases) and nick the damaged strand. Some of these proteins also remove the damaged region (alternatively, DNA Pol I can remove the damaged region). 2._____ is in the forward direction and 3.________is in the reverse direction and replaces what was removed.

Answer 50

1. endonuclease 2. endonuclease 3. exonuclease

Question 51

DNA Repair: | _______ mismatch repair corrects errors made during replication. Same types of damage repair (similar process).

Answer 51

Strand-directed

Question 52

DNA Repair: Certain proteins (with ______activity) recognize misincorporated bases (or damaged bases) and nick the damaged strand. Some of these proteins also remove the damaged region (alternatively, DNA Pol I can remove the damaged region).

Answer 52

endonuclease

Question 53

DNA Repair: ________is in the forward direction and ______is in the reverse direction and replaces what was removed.

Answer 53

Endonuclease is in the forward direction and exonuclease is in the reverse direction and replaces what was removed.

Question 54

DNA Repair: Pol I then fills in the previously damaged region, and DNA ligase seals the final nick. A defect in mismatch repair is responsible for ____________, one of the most common inherited cancers.

Answer 54

hereditary nonpolyposis colorectal cancer (HNPCC),

Question 55

DNA Repair: Mutations can be caused by other mechanisms besides replication errors. Spontaneous mutations, exposure to _______ or ______ (i.e. cigarette smoke).

Answer 55

chemical or radiation

Question 56

DNA Repair: Another type of mutation can be caused by UV light which causes pyrimidine dimers (usually ______ dimers).

Answer 56

thymine

Question 57

DNA Repair: Repair is through UV specific endonuclease (________, _________). It cuts DNA on both sides of damage and removes it. The gap is filled in by repair DNA polymerase (which is Pol I in prokaryotes).

Answer 57

excision endonuclease, exonuclease

Question 58

DNA Repair: | In humans, a rare genetic disorder called ____ most often results from a deficiency in excision endonuclease.

Answer 58

xeroderma pigmentosum