Cell Biology Chapter 17

Question 1

Cells must be able to accurately do what? Without it what would result? Cells must also repair damage to what?

Answer 1

accurately reproduce, or replicate, their genetic material at each cell division; unaccurate replication, the genetic material of resulting cells would be damaged with errors; their genetic material

Question 2

New DNA molecules are derived from what and what is it called?

Answer 2

derived from when the parent molecule and the other strand is newly synthesized; semiconservative replication

Question 3

Replication is very similar in what? What are replication forks?

Answer 3

in Prokaryotes and eukaryotes; formed where replication begins and then proceeds in bidirectional fashion away from the origin

Question 4

At each origin of replication what happens? What is the origin of replication?

Answer 4

two replication forks synthesize DNA in opposite directions forming a “replication bubble”; the site where DNA replication initiates by several groups of initiator proteins. Consist of AT-rich regions

Question 5

The sequence varies among what? Replication origins of multicellular eukaryotes are generally what and more what?

Answer 5

bacterial species but contains recognizable similar sequences, called consensus sequences; generally larger and more variable in sequence but also contain regions that are AT-rich

Question 6

In E. Coli how many enzymes bind and to what and what does it initiate? Binding to part of the what sequence results in what?

Answer 6

3 enzymes bind to oriC (origen of replication) and initiate replication; part of the oriC sequence results in unwinding of DNA

Question 7

To stabilize the single strands of DNA what binds? DNA helicase unwinds what?

Answer 7

SSB (single stranded binding protein) binds to the unwound regions; unwinds the DNA strands as replication proceeds

Question 8

DNA polymerase is a what? Incoming nucleotides are added to what?

Answer 8

an enzyme that can copy DNA molecules; added to 3’ hydroxyl end of the growing DNA chain, so elongation occurs in the 5’ to 3’ direction

Question 9

DNA is synthesized in which direction, but the 2 strands of the double helix are oriented where? The lagging strand is synthesized in what?

Answer 9

5’ to 3’ direction, oriented in opposite directions; in discontinuous fragments called Okazaki fragments

Question 10

The leading strand is synthesized as what? DNA synthesis from the lagging strand is synthesized in what? These are then joined by what to form what?

Answer 10

as a continuous chain; synthesized in Okazaki fragments; joined by DNA ligase to form a continuous new 3’ to 5’ DNA strand

Question 11

About how many nucleotides incorporated during DNA replication is incorrect? How are the mistakes usually fixed? Almost all DNA polymerases have a what?

Answer 11

1 of every 100,000 nucleotides; fixed by proofreading mechanism; have a 3’ -> 5’ exonuclease activity

Question 12

Exonucleases degrade what? The exonuclease activity of DNA polymerase allows it to remove what?

Answer 12

degrade nucleic acids from the ends of the molecules; remove incorrectly base-paired nucleotides and incorporate the correct base

Question 13

DNA polymerase can add nucleotides only to what? Cells contain an enzyme called what that synthesizes what?

Answer 13

only to the 3’ end of an existing nucleotide chain; contain an enzyme called primase that synthesizes short chains of RNA using DNA as a template

Question 14

After the RNA primer is made, DNA polymerase adds what? For the leading strand what is needed? For the lagging strand a series of what are needed?

Answer 14

deoxynucleotides to the 3’ ends of the primer; just one primer is needed; a series of primers are needed to initiate each Okazaki fragment

Question 15

When DNA chain reaches the next Okazaki fragment the RNA is what? Then, adjacent fragments are joined together by what?

Answer 15

degraded and replaced with DNA; DNA ligase

Question 16

During DNA replication, the two strands of the double helix must unwind at each what? 3 classes of proteins facilitate the what?

Answer 16

each replication fork; the unwinding;

Question 17

DNA helicases: The DNA double helix is what? Helicases breaks the what between what of the what?

Answer 17

unwound ahead of the replication fork by helicase; the hydrogen bonds between nitrogeneous bases of the nucleotides of the DNA duplex as they go

Question 18

Single-stranded DNA binding proteins: Once strand separation has begun, molecules of SSB move how and attach to what? They keep the DNA how?

Answer 18

move in quickly and attach to the exposed single strand; unwound and accessible to the replication machinery

Question 19

Topisomerases: The unwinding of the helix would create too much what?

Answer 19

supercoiling if not for topisomerases

Question 20

What proteins are involved in replication? What is a replisome?

Answer 20

DNA helicase, DNA topoisomerase, SSBs, primase, DNA polymerase, and DNA ligase; proteins that are closely associated in a large complex

Question 21

As the replisome moves along the DNA, it must accomadate what? A key element of the replisome is what?

Answer 21

for the fact that DNA is being produced on both leading and lagging strands; the folding of the lagging strand template into a loop

Question 22

What is the trombone model? What is a sliding clamp protein?

Answer 22

model for how the replisome works; attaches to a DNA polymerase catalytic subunit allows the polymerase to “process” along the DNA without falling off

Question 23

The leading and lagging strand differ regarding how?

Answer 23

how long the sliding clamp and associated polymerase remain attached

Question 24

It can remain associated with the what? On the lagging strand as each Okazaki fragment is completed, the polymerase what?

Answer 24

with the leading strand throughout replication; detaches and the sliding clamp must be reloaded

Question 25

Linear DNA molecules have a problem in completing what? Each round of replication would end with what?

Answer 25

in completing DNA replication on the lagging strand because primers are required; with the loss of some nucleotides from the ends of each linear molecules

Question 26

Eukaryotes solve this problems with what? A polymerase called what can do what?

Answer 26

telomeres, highly repeated sequences at the ends of chromosomes; telomeres can catalyze the addition of repeats to chromosome ends

Question 27

Telomerase is composed of what? This enzyme-bound RNA acts as a template for what?

Answer 27

of protein and RNA; for adding the DNA repeat sequence to the telomere ends

Question 28

Telomere capping proteins bind to what to protect what? In multicellular organisms, telomerase function is restricted to what?

Answer 28

the exposed 3’ end to protect from degradation; to germ cells and a few other types of actively proliferating cells

Question 29

Telomere length is a what? If a cell divides too many times what could be lost? Cells at risk of loss of what undergo what?

Answer 29

counting device for how many times a cell has divided; telomeres; loss of telomeres undergo apoptosis programmed cell death

Question 30

Telomerase has been detected in almost what?

Answer 30

all types of human cancers

Question 31

Several mechanisms are in place to ensure what? What are the 3 types of mechanisms?

Answer 31

minimal mistakes on DNA; Accuracy, Immediate proofreading, Post replication repair

Question 32

What is accuracy?

Answer 32

incorporation of correct nucleotide (complementary base pairing)

Question 33

What is immediate proofreading?

Answer 33

DNA polymerase proofreading mechanism

Question 34

What is post-replication repair?

Answer 34

Mismatch double strand breaks

Question 35

Trinucleotide repeats are susceptible to what? In this process DNA polymerase replicates what?

Answer 35

strand slippage; a short stretch of DNA twice due to repeats matching with each other

Question 36

Errors remaining after DNA replication are repaired by what?

Answer 36

excision repair in which abnormal nucleotides are removed and replaced

Question 37

How does excision repair happen?

Answer 37

a protein detects the mismatch, a repair endonuclease introduces a nick in the unmethylated strand, an exonuclease removes the incorrect nucleotides form the nicked strand and these are replaced with the correct sequence, DNA ligase seals the DNA backbone

Question 38

Double-strand breaks cleave DNA into what? It is difficult for the repair system to what?

Answer 38

2 fragments; identify and rejoin the correct broken ends without loss of nucleotides

Question 39

What two pathways are used for double-strand break repair?

Answer 39

non homologous end-joining, homologous recombination

Question 40

Non homologous end-joining uses a set of what?

Answer 40

proteins that bind to ends of broken DNA fragments and join them together

Question 41

Non homologous end-joining is error-prone because of what?

Answer 41

nucleotides can be lost from the broken ends, and there is no way to ensure the correct DNA fragments are joined

Question 42

Homologous recombination involves the process of what?

Answer 42

crossing over, genetic exchange between DNA molecules with extensive sequence similarity

Question 43

IF the DNA molecule from one chromosome is broken, the homologue is what?

Answer 43

available as a template to guide accurate repair