Chapter 13

Question 1

What is replication?

Answer 1

replication is the process of making copies more DNA

Question 2

template strand

Answer 2

a strand of DNA that is used to synthesize a complementary strand of DNA or RNA

Question 3

parental strand

Answer 3

DNA strand that is used as a template in replicaiton

Question 4

What were the 3 models proposed for DNA replication?

Answer 4

Conservative model, semiconservative model, and dispersive model

Question 5

Conservative model

Answer 5

An incorrect model that proposed that both strands of parental DNA remain together following DNA replication

Question 6

Semiconservative model

Answer 6

The correct model for DNA replication that proposes that the newly made double-stranded DNA contains one parental strand and one daughter strand

Question 7

Dispersive model

Answer 7

An incorrect model for DNA replication that proposed that segments of parental DNA and newly made DNA are interspersed in both strands following the replication process

Question 8

Who proved the semiconservative model?

Answer 8

Matthew Meselson and Franklin Stahl

Question 9

What is the origin of replication?

Answer 9

a nucleotide sequence that functions as an initiation site for the assembly of several proteins required for DNA replication

Question 10

What is a replication bubble?

Answer 10

structure that forms during the process of DNA replication. It appears when the double-stranded DNA molecule unwinds and separates into two single strands, creating an open region where replication can occur

Question 11

What is a replication fork?

Answer 11

region where the parental DNA strands have separated, and new daughter strands are being made

Question 12

how is replication different with circular DNA compared to linear dna?

Answer 12

Replication of circular DNA (found in prokaryotes) involves a single origin of replication, proceeds bidirectionally, and has no end replication problem because the DNA is continuous. The process is simpler and faster, ending when the replication forks meet.

Replication of linear DNA (found in eukaryotes) has multiple origins to speed up the process, involves more complex regulation, and faces an end replication problem due to the chromosome’s ends. This problem is managed by telomeres and the enzyme telomerase to maintain chromosome stability. Linear DNA replication is slower and more intricate due to the larger genome and chromatin structure.

Question 13

oriC

Answer 13

Origin of chromosomal replication studied in E. Coli

Question 14

DnaA protein

Answer 14

binds to the DnaA box at the oriC and initiates DNA replication in bacteria

Question 15

DnaA box

Answer 15

a recognition site for the binding of the DNaA protein, which is involved in the initiation of bacterial DNA replication

Question 16

AT-rich region

Answer 16

A region at a bacterial origin of replication that has a high percentage of A-T base pairs and easily separates so that replication forks can form

Question 17

bidirectional replication

Answer 17

The phenomenon in which two DNA replication forks move in opposite directions from an origin of replication

Question 18

GATC methylation sites

Answer 18

DNA sequence in bacteria that is methylated; it plays a role in preventing DNA replication from happening too early

Question 19

Primase

Answer 19

synthesizes short RNA primers

Question 20

primer

Answer 20

a short strand of RNA that is used to elongate a strand of DNA during DNA replication

Question 21

How many primers are needed?

Answer 21

Leading strand: a single primer
Lagging strand: multiple primers

Question 22

Leading strand

Answer 22

strand that is synthesized during DNA replication continuously in the same direction as the replication fork is moving

Question 23

Lagging strand

Answer 23

strand that is synthesized during DNA replication as short Okazaki fragments in the direction away from the replication fork

Question 24

What is the difference between continous replication and discontinuous replication?

Answer 24

Directionality: Continuous replication aligns with the movement of the replication fork, while discontinuous replication occurs in the opposite direction.
Process: Continuous replication synthesizes one uninterrupted strand, while discontinuous replication forms short, separate fragments that are later connected.
Number of Primers: The leading strand requires only one primer at the start, while the lagging strand requires multiple primers for each Okazaki fragment.

Question 25

What is an okazaki fragment?

Answer 25

Okazaki fragments enable the synthesis of the lagging strand in a direction that opposes the overall direction of the replication fork movement, ensuring that the entire DNA molecule is accurately replicated.

Question 26

DNA polymerase

Answer 26

enzyme that catalyzes the covalent attachment of nucleotides to form a strand of DNA

Question 27

Which DNA polymerase are involved in normal replication and which for repair in bacteria?

Answer 27

Replication: 1 and 3 Repair: 2, 4, and 5

Question 28

DNA helicase

Answer 28

separates double stranded DNA

Question 29

Gyrase

Answer 29

a type of topoisomerase II, removes positive supercoiling ahead of the replication fork

Question 30

DNA polymerase I

Answer 30

removes RNA primers, fills in gaps with DNA

Question 31

DNA polymerase III

Answer 31

synthesizes DNA in the leading and lagging strands

Question 32

DNA ligase

Answer 32

covalently attaches adjacent okazaki fragments

Question 33

single stranded binding proteins

Answer 33

binds to single-stranded DNA and prevents it from re-forming a double-stranded structure

Question 34

What are the steps involved in DNA replication?

Answer 34

Initiation: DNA unwinding, stabilization of single strands, and relief of supercoiling. Primer Synthesis: Primase synthesizes RNA primers. Elongation: Continuous synthesis on the leading strand and discontinuous synthesis on the lagging strand. Termination: Completion of synthesis and joining of Okazaki fragments. Proofreading and Repair: Ensures high fidelity of DNA replication.

Question 35

Does DNA polymerase proofread as the nucleotides are added?

Answer 35

Yes, DNA polymerase does proofread the nucleotides as they are added during DNA replication. This proofreading function is an essential part of ensuring the accuracy of DNA synthesis.

Question 36

which DNA polymerase proofreads?

Answer 36

3

Question 37

What are some reasons that DNA replication is so accurate?

Answer 37

1. hydrogen bonding between g and C or between A and T are more stable than between mismatched pairs 2. helix distortions caused by mispairing usually prevent an incorrect nucleotide from properly occupying the site of DNA polymerase 3. DNA polymerase III can detect a mismatched nucleotide and remove it from the daughter strand-- called proofreading

Question 38

what are some key differences in eukaryotic and prokaryotic DNA replication?

Answer 38

Origins of Replication: Prokaryotes have one origin on circular DNA, while eukaryotes have multiple origins on linear chromosomes. Replication Rate: Faster in prokaryotes; slower in eukaryotes due to complex chromatin. DNA Polymerases: Prokaryotes mainly use DNA polymerase III and I. Eukaryotes use multiple polymerases (e.g., δ, ε, α). Priming: Primase alone in prokaryotes; a complex with DNA polymerase α and primase in eukaryotes. Chromosome Structure: Circular in prokaryotes, linear in eukaryotes with telomeres. Telomeres: Only eukaryotes face the end replication problem, solved by telomerase. Initiation Proteins: Prokaryotes use simpler systems; eukaryotes have complex protein interactions. Replication Forks: Simpler in prokaryotes; eukaryotes have more associated proteins like PCNA. Histones: Present only in eukaryotes, adding complexity to DNA replication

Question 39

Flap endonuclease

Answer 39

found in eukaryotes that removes flaps that are generated during DNA replication

Question 40

Telomerase

Answer 40

protein/RNA complex that recognizes telomeric sequences at the ends of eukaryotic chromosomes and synthesizes additional repeats of those sequences

Question 41

How does telomerase work?

Answer 41

1. binds to the 3' overhanging region of telomere 2. the rna sequence beyond the binding site functions as a template allowing for the synthesis of a six-nucleotide sequence at the end of the DNA strand (polymerization) 3. telomerase then moves to the new end of the dna strand (translocation)

Question 42

In what types of cells would you find active telomerase?

Answer 42

Germ Cells: These are reproductive cells (e.g., sperm and egg cells) that require active telomerase to maintain the length of their telomeres for future generations. Stem Cells: Telomerase is active in adult and embryonic stem cells to ensure their ability to divide repeatedly without telomere shortening, which is crucial for tissue renewal and repair. Certain Somatic Cells: Some cells with high regenerative capacity, such as those in the bone marrow and certain immune cells, can express telomerase to a limited extent. Cancer Cells: One of the hallmarks of many cancer cells is the reactivation of telomerase, which allows them to bypass normal cellular aging and continue dividing indefinitely, contributing to uncontrolled growth.

Question 43

how is telomerase related to aging?

Answer 43

As telomeres shorten in most somatic cells, this contributes to the gradual deterioration of tissue function, a hallmark of aging. Cells that cannot replicate effectively due to short telomeres accumulate in tissues, leading to signs of aging and age-related diseases.