Chapter 13

Question 1

What is semiconservative replication?

Answer 1

Describes DNA repl: half of the parent structure is retained in each of the daughter duplexes.

Question 2

What is conservative replication?

Answer 2

distinct and separation and segregation of parental and daughter stands

Question 3

What is dispersive replication?

Answer 3

daughter duplexes would contain strands that were composites of old and new DNA

Question 4

How does replication occur in bacteria?

Answer 4

1) Starts at the origin site, where a number of proteins bind to initiate replication
2) Proceeds bidirectionally

Question 5

What has been used to study replication in bacteria?

Answer 5

1) Temperature sensitive mutant used to identify the genes of replication
2) in vivo systems reconstituted from purified cellular components

Question 6

What relieves the tension in DNA once the unwinding process begins

Answer 6

DNA gyrase (topoisomerase II) relieves the tension by changing the DNA into negatively supercoiled DNA; uses ATP hydrolysis

Question 7

What are the properties of DNA polymerases?

Answer 7

1) responsible for synthesizing new DNA strands from a DNA template
2) requires a primer which provides the 3’ hydroxyl terminus on which to add new nucleotides
3) Occurs in the 5’-3’ direction
4) Cant initiate DNA chains

Question 8

What is used to initiate the synthesis of each Okazaki fragment and what assembles them?

Answer 8

short RNA fragments used as removable primers; Primase

Question 9

What removes the primers used in synthesis initiation of Okazaki fragments? and how what are the strands sealed by?

Answer 9

Exonuclease activity, DNA polymerase I (fills gaps); ligase

Question 10

What unwind the parental duplex and separate the two strands of DNA?

Answer 10

Helicase and single-stranded DNA binding proteins

Question 11

What moves protectively along the lagging strand template?

Answer 11

“primosome”-primase and helicase

Question 12

What allows for DNA polymerase to move from one nucleotide to the next?

Answer 12

1) beta “sliding clamp”

2) Assembly requires clamp loader, which is part of the DNA polymerase III holoenzyme

Question 13

What does the replisome consist of?

Answer 13

holoenzyme, helicase, SSBs, and primase

Question 14

What is DNA polymerase I involved in?

Answer 14

DNA repair and also removes RNA primers and replaces them with DNA

Question 15

How do exonucleases degrade nucleic acids?

Answer 15

by removing 5’ to 3’ terminal nucleotides

Question 16

What is the 5’-3’ exonuclease function?

Answer 16

removes approx. 10 nucleotides from the 5’ end of a single strand nick. The activity plays a key role in removing the RNA primer

Question 17

What is the 3’-5’ exonuclease function?

Answer 17

removes mispaired nucleotides from the 3’ end of the growing DNA. Key in maintaining the accuracy of DNA synthesis

Question 18

Replication in eukaryotic chromosomes begins at (blank) sites along the DNA

Answer 18

many

Question 19

How do eukaryotes replicate their genome?

Answer 19

in small portions (replicons)

Question 20

What is the characteristics of the origins of replication in yeast?

Answer 20

1) Called autonomous replicating sequences (ARS)
2) about 400 of them
3) 11 bp A-T rich region

Question 21

What are the steps in replication in the yeast replicon?

Answer 21

1) Origin bound by an ORC
2) MCM complex bind requiring Cdc6 and Cdt1 (licensing factors)
3) Protein kinases, Cdk and DDk, phosphorylate and activate pre-RC complex (activation factors)
4) Replication starts

Question 22

What is CAF-1?

Answer 22

histone chaperone that interacts with PCNA

Question 23

What cell molecule is most susceptible to environmental damage?

Answer 23

DNA

Question 24

The fidelity of DNA replication can be traced to three distinct activities:

Answer 24

1) Accurate selection of nucleotides
2) immediate proofreading
3) post-replicative mismatch repair

Question 25

What is nucleotide excision repair?

Answer 25

removes bulky lesions, such as pyrimidine dimers and chemically altered nucleotides

Question 26

What are the two pathways of nucleotide excision repair?

Answer 26

1) Transcription-coupled pathway which is the preferential pathway and selectively repairs genes of greatest importance to the cell 2) A global genomic pathway which is less efficient and corrects DNA strands in the remainder of the genome

Question 27

What the steps of nucleotide excision repair (global pathway)?

Answer 27

1) DNA strand separation (by XPB and XPD proteins, two helices subunits of TFIIH). TFIIH links transcription and DNA repair 2) Incision by endonucleases (XPG on 3' side and XPF-ERRCC1 complex on 5' side) 3) Excision (removal by helicase) 4) DNA repair fill-in (DNA polymerase δ/ε) 5) Ligation by DNA ligase I

Question 28

What is base excision repair?

Answer 28

removes altered nucleotides that produce distortions of the double helix

Question 29

What are steps of base excision repair?

Answer 29

1) DNA glycosylases recognize the alterations and cleave the base from the sugar; they are specific for a particular type of altered base 2) Endonuclease cleaves the DNA backbone and a polymerase fills the gap by inserting a nucleotide complementary to the undamaged strand 3) DNA ligase seals the strand

Question 30

What can cause double-strand DNA breaks?

Answer 30

ionizing radiation (x-rays, gamma rays)

Question 31

How can double-strand breaks be repaired and what are the steps?

Answer 31

1) Nonhomologous end joining 2) Ku proteins bind to the free, broken ends (not nicked) and catalyze reaction to rejoin the broken ends 3) Mediated through DNA-dependent protein kinase catalytic subunit

Question 32

What is translesion synthesis?

Answer 32

TLS polymerases accomodate altered nucleotides that would not fit within a classic polymerase and have no proofreading activity