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MABS Biochemistry > DNA Replication Preserving the Code > Flashcards

DNA Replication Preserving the Code Flashcards

1
Q

DNA synthesis occurs by the process of _____?

A

replication

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2
Q

during replication, each of the two parental strands of DNA serve as a _____? Why is this important?

A

template; important for the synthesis of a complementary strand

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3
Q

during the process of replication what strands do you have?

A

parental strand and one newly synthesized strand

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4
Q

briefly describe prokaryotic DNA?

A

circular and supercoiled

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5
Q

T/F, unidirectional and anti-conservative in prokaryotes?

A

bidirectional and semiconservative

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6
Q

where does replication begin in prokaryotes?

A

oriC

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7
Q

once replication is initiated at the site of origin in prokaryotes, are both strands copied simultaneously and if so, in what direction?

A

yes; both directions at the same time

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8
Q

why is replication in prokaryotes said to be semi-conservative?

A

because each daughter chromosome contains one parental DNA strand and one newly synthesized complementary strand.

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9
Q

T/F, Replication requires separation of parental DNA stands and unwinding of the helix ahead of the replication fork?

A

T

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10
Q

what are the major players for DNA synthesis in Prokaryotes?

A
  • helicases
  • single stranded binding proteins
  • topoisomerases
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11
Q

what is the helicase?

A

separate the DNA strands and unwind the parental duplex

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12
Q

what are single stranded binding proteins?

A

prevent the strands from reassociating and protect the strands from enzymatic cleavage

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13
Q

what is topoisomerase? example?

A

enzymes that can break phosphodiester bonds and rejoin them, relieve the supercoiling caused by unwinding.

DNA gyrase

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14
Q

what are the DNA proteins involved in the DNA synthesis of Prokaryotes?

A

DNA B
DNA C
DNA G
DNA A

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15
Q

what is DNA B?

A

helicase

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16
Q

what is DNA C?

A

helicase loader which helps helicase to bind to and properly accommodate ssDNA

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17
Q

what is DNA G?

A

primase

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18
Q

what is DNA A?

A

activates DNA replication in bacteria. It’s a replication factor that binds upstream of OriC which leads to strand separation at OriC for the AT rich repeats

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19
Q

what are the three polymerases involved in DNA synthesis?

A

Pol I,II,III

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20
Q

what is Pol I?

A
  • filling of gap after removal of RNA primer
  • DNA repair
  • removal of RNA primer with RNAse H

exonuclease activity
5’to3’ and 3’to5’

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21
Q

what is Pol II?

A

DNA repair

exonuclease activity
3’-5’

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22
Q

what is Pol III?

A

replication -synthesis of DNA

exonuclease activity
3’-5’

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23
Q

what are the enzymes that catalyze the synthesis of DNA known as?

A

DNA polymerase

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24
Q

DNA polymerase can initiate synthesis, T/F?

A

F, cannot; It always requires the presence of a free 3’-OH group to function

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25
Q

in what direction can DNA polymerase produce the complementary strand?

A

5’-3’ direction

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26
Q

what is the significance of RNA polymerase?

A

it adds an RNA oligonucleotide primer by copying the DNA template strand

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27
Q

how does RNA polymerase (primase) work?

A

Incoming nucleotide forms complementary base pair with nucleotide on template strand.

Ester bond is formed between a 5’-P of incoming nucleotide and 3’-OH at the end of the growing chain.

Pyrophosphate is released (β and γ –P) and subsequent cleavage by pyrophosphatase provides energy to drive polymerization.

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28
Q

because the parental strands run in opposite directions, how does synthesis occur?

A

in a 5’-to-3’ direction toward the fork on one template strand and in a 5’-to-3’ direction away from the fork on the other template strand.

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29
Q

what is the leading strand in the DNA synthesis in Prokaryotes?

A

continuous 5’-to-3’ synthesis toward the fork

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30
Q

what is the lagging strand in the DNA synthesis in Prokaryotes?

A

discontinuous 5’-to-3’ synthesis away from the fork. DNA synthesized in short fragments, called Okazaki fragments.

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31
Q

how are fragments joined in the DNA synthesis in prokaryotes?

A

DNA ligase

32
Q

RNA primers are removed from the Okazki fragments by the combined action of _____ and _____ in Prokaryotic DNA synthesis?

A

DNA polymerase I and RNase H

33
Q

what enzyme fills in the gaps produced by the removal of the primer in Prokaryotic synthesis?

A

DNA polymerase I

34
Q

what is the action of DNA ligase in Prokaryotic synthesis?

A

performs the ligation reaction to join the two chains together.

35
Q

in the DNA synthesis in Prokaryotes, how does the elimination of base pair errors occur?

A

DNA Polymerase III performs proofreading or editing function with 3’-to-5’ exonuclease activity in addition to its polymerase activity.

36
Q

what happens if an incorrect nucleotide is inserted?

A

Pol II removes the nucleotide before continuing to lengthen the chain via exonuclease activity and then adds the correct base via polymerase activity.

37
Q

what are the 4 phases in DNA synthesis for Eukaryotes?

A

G1, S, G2, M

G1, S, G2 is considered interphase for the cell

M is considered the process of cell division

38
Q

What is S phase in the DNA synthesis of Eukaryotes?

A

used for DNA replication

39
Q

why is S phase important?

A

Nucleosomes disassemble as replication forks advance

Synthesis of histones and other proteins associated with DNA are increased.

The amounts of DNA and histones both double (2n 4n) and chromosomes are duplicated.

40
Q

How many points of origin do eukaryotes have?

A

multiple points of origin

41
Q

what happens at these points of origin for the DNA synthesis of Eukaryotes?

A

“Bubbles” appear at these points on the chromosomes. Each bubble has 2 replication forks.

As the bubbles enlarge, they eventually merge, and replication is completed.

Because of the multiple points of origin, duplication of large chromosomes can occur within a few hours.

42
Q

how many polymerases are involved in the DNA synthesis of Eukaryotes?

A

many, diverse up to 15 different polymerases

43
Q

what are the important polymerases we named for the DNA synthesis of eukaryotes?

A

Pol δ and Pol ε
Pol α
Pol γ

44
Q

what is Pol δ and Pol ε?

A

major replicative enzymes

Pol ε - replication (processive DNA synthesis on the leading strand)

Pol δ - replication (processive DNA synthesis on the lagging strand)

45
Q

what is Pol α?

A

involved in replication, replication (in a complex with primase and aids in starting the primer)

46
Q

what is Pol γ?

A

mitochondria DNA replication, DNA replication in mitochondria

47
Q

describe the replicative process in DNA synthesis for Eukaryotes?

A

Primase w/ Pol α produces an RNA primer on a DNA template strand. Pol α adds ~ 20 nt to the RNA and dissociates (low processivity)

On leading strand, pol ε adds dNTP to the strand

On the lagging strand, Okazaki fragments are initiated by Pol α and primase. After pol α dissociates, pol δ adds dNTPs. Pol δ stops synthesizing one fragment when it reaches the start of a previous fragment

RNA primers are removed by flap endonuclease 1 (FEN1) and RNaseH.

Gap from primer is filled by Pol δ and DNA Ligase joins fragments together.

48
Q

what are the major proteins involved in replication in DNA synthesis for Eukaryotes?

A

DNA polymerase

Primase

Helicases

SSBP

Enzymes that remove primers

DNA ligase

Proliferating cell nuclear antigen

49
Q

what are the end of chromosomes called?

A

telomeres

50
Q

what is the purpose of telomeres?

A

If the chromosome became shorter with each successive replication…genes would be lost and telomeres prevent this

51
Q

so because telomeres have 3’ overhangs, what happens to these?

A

lengthened by telomerase

52
Q

what is telomerase?

A

Telomerase acts as an RNA-dependent DNA polymerase adding a repeating sequence of bases (TTAGGG in humans) to the 3’ overhang using its internal complementary RNA sequence

53
Q

despite proofreading and mismatch repair during replication, mismatching can also occur. what are other types of DNA damage?

A

mutagens and radiation

54
Q

what are mutagens? examples?

A

chemicals produced in cells, inhaled, or absorbed from the environment that cause mutations; cigarette smoke and sunlight

55
Q

what is the term used to describe mutagens that cause normal cells to become cancer cells?

A

carcinogens

56
Q

what are the three common steps of DNA repair?

A

excision

repair

ligation

57
Q

what are the major mechanisms of DNA repair?

A

nucleotide excision repair

base excision repair

mismatch repair

58
Q

what is nucleotide excision repair?

A

Local distortions of the DNA helix (i.e., mismatched bases or bulky adducts)

Specific repair endonucleases cleave the abnormal chain and remove distorted region

Gap filled by a DNA polymerase and DNA ligase finalizes repair

59
Q

what is base excision repair?

A

Small distortions in DNA involving lesions caused by damage to a single base

DNA glycosylases recognize damage and cleaves the N-glycosidic bond that joins the damaged base to deoxyribose.

The sugar-phosphate backbone of DNA now lacks a base at this site (known as an apurinic or apyrimidinic site, or an AP site)

AP endonuclease cleaves the sugar-phosphate strand and repair continues

60
Q

what is mismatch repair?

A

The mismatch repair enzyme complex acts during replication when an incorrect but normal base is incorporated into the growing chain.

Because there is no damage, the enzymes must be able to determine which base of the mismatch pair is incorrect.

61
Q

how can DNA be synthesized form RNA?

A

reverse transcriptase

62
Q

what is reverse transcriptase?

A

a RNA-dependent DNA polymerase that uses single stranded RNA template to make a DNA copy.

The RNA template can be transcribed from DNA by RNA polymerase OR obtained from another source such as and RNA virus.

63
Q

what is the DNA copy of the RNA referred to as?

A

cDNA

64
Q

the RNA of the DNA-RNA hybrid is degraded by?

A

RNase activity

65
Q

what is the single stranded cDNA used as a template for?

A

to make dsDNA

66
Q

what are the four hereditary DNA repair disorders?

A

all genetic

Hereditary nonpolyposis colon cancer

Cockayne syndrome

Xeroderma pigmentosum

Hereditary breast cancer

67
Q

Patient X responded to treatment for diabetes mellitus but subsequently developed a low-grade fever, an increase in urinary urgency and frequency, and burning at the urethral opening with urination (dysuria). A urinalysis showed a large number of white blood cells and many gram-negative bacilli. A urine culture indicated many colonies of Escherichia coli, which is sensitive to several antibiotics, including the quinolone ciprofloxacin

treatment?

A

Ciprofloxacin

68
Q

ciprofloxacin MOI/result?

A

Inhibits bacterial DNA gyrase (a topoisomerase) that unwinds the closed circular bacterial DNA helix ahead of the replication fork.

Inhibition of bacterial DNA synthesis. [Because eukaryotic cells have linear DNA and do not contain DNA gyrase, they are not affected by quinolones.

69
Q

what is responsible for cell aging and death?

A

An inability to replicate telomeres has been linked to cell aging and death.

70
Q

The burning of tobacco (or any organic material) produces many different carinogens, such as?

A

benzo[a]pyrene

71
Q

what is bento[a]pyrene?

A

Benzo[a]pyrene binds to the p53 gene segment of DNA, causing a mutation in the p53 gene that leads to lung cancer.

72
Q

what develops from UV radiation?

A

Melanomas develop from exposure of the skin to the UV rays to the sun. The UV radiation causes pyrimidine dimers to form in DNA. Mutations may result from non-repair of the dimers that produce melanomas, appearing as dark brown growths on the skin.

73
Q

this is an autosomal recessivegenetic disorderofDNA repairin which the ability to repair damage caused byultraviolet(UV) light is deficient and due to nucleotide excision?

A

xeroderma pigmentosum

74
Q

this is an autosomal dominant genetic disorder that carries a high risk of colorectal cancer.
The increased risk of cancer is due to inherited mutations in genes for proteins involved in DNA mismatch repair. What is this?

A

Hereditary nonpolyposis colorectal cancer (HNPCC or Lynch syndrome)

75
Q

how can the HIV genome mutate rapidly necessitating the use of multiple drugs in treatment?

A

reverse transcriptase lacks error checking capabilities like in internet HIV type 1 virus

MABS Biochemistry (54 decks)

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