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Flashcards in 2.11 Replication Deck (102)
1

Bonds that join the 3'hydroxyl group of the deoxypentose of one nucleotide to the 5'hydroxyl group of the deoxypentose of an adjacent nucleotide through a phosphate group

Phosphodiester bonds

2

Single unique nucleotide sequence wherein prokaryotic DNA replication begins

Origin of Replication

3

Protein that binds to specific nucleotide sequences at the origin of replication, causing short, tandemly arranged AT regions in the origin to melt

DNA-A Protein

4

Enzyme that binds to ssDNA forces the strands apart, unwinding the double helix

DNA helicases

5

Proteins that bind to newly separated ssDNA in order to hold them apart.

Single stranded DNA binding proteins (SSBP)

6

Enzymes that cut one strand of the double helix to relieve supercoiling

DNA Topoisomerase Type 1

7

Enzymes that make transient breaks in both dsDNA strands

DNA Topoisomerase Type II

8

Monomeric units or building blocks of nucleic acids

Nucleotides

9

Functions of nucleotides

Precursors for informational molecules
Part of coenzyme
Donors of phosphoryl groups
Regulatory nucleotides
Synthetic analogues as drugs

10

Nitrogen-containing cyclic compounds whose rings contain both carbon and other elements

Nitrogenous bases

11

Purine

Guanine
Adenine

12

Pyrimidine

Cytosine
Uracil
Thymine

13

Has two rings

Purine

14

Has one ring

Pyrimidine

15

Has a planar characteristic that facilitates stacking of rings one on top of each other

Nitrogenous bases

16

Pair with two H-bonds

Adenine and Thymine/
Adenine and Uracil

17

Pair with three H-bonds

Guanine and Cytosine

18

Also known as methyl uracil
Comes from folate system

Thymine

19

Nitrogenous base + sugar

Nucleoside

20

Link between nitrogenous base and ribose sugar

beta-N-glycosidic bond

21

Anomeric carbon is attached to ___ for pyrimidine, and __ for purine

N1; N9

22

Nucleosides + phosphate
Phosphorylated nucleosides

Nucleotide

23

Esterified to a hydroxyl group of the sugar

Phosphoryl group

24

Phosphoryl group usually attached to __ of the pentose

C-5

25

5'-phosphoryl group forms a ___ with the 3'-OH of another nucleotide

Phosphodiester bond

26

Catalyze the hydrolysis of phosphodiester bonds

Phosphodiesterases

27

True or False
DNA is more table than RNA.

True
Presence of hydroxyl group in carbon 2 of RNA makes it suscpetible to base-catalyzed hydrolysis

28

5' end

Phosphoryl group

29

3' end

Hydroxyl group

30

Polymer composed of nucleotide building blocks
Chemical basis of heredity

DNA

31

DNA can be cleaved ___ by chemicals and hydrolyzed enzymatically by ___ or ___

Hyrolytically
Exonucleases
Endonucleases

32

DNA has ___, meaning the strands run in opposite directions

Antiparallel strands

33

True or false
DNA, regardless of the number of strands, follows Chargaff's rules

False
Chargaff's rule does not apply in single-stranded DNA (ssDNA)

34

Supercoiling of the DNA is being regulated by ___

Topoisomerases

35

Name the 3 processes in central dogma

Replication
Transcription
Translation

36

A process in which DNA makes identical copies of itself, which are transmitted to the daughter cells during cell division

Replication

37

Occurs during the S (synthesis) phase of the cell cycle

Replication

38

New complementary strand is synthesized from 2 old single strands
The base sequence of each old strand predicts base sequence of the new complementary strand

Semiconservative

39

Basis for the accuracy of DNA replication

Complementarity

40

Enzyme that catalyzes addition of DNA nucleotides to a gw

DNA polymerase

41

Entire DNA template used for replicaton

Conservative

42

Resulting DNA molecule interspersed with fragments of old and new DNA

Dispersive

43

Each strand serves as template for new DNA molecule

Semiconservative

44

Based from the Messelson-Stahl experiment, DNA replication does not follow the ____.

Conservative model

45

Precursors in DNA synthesis

Deoxyribonucleoside triphosphate

46

Double-helix first unwinds into single-stranded DNA, which will serve as ____

Template

47

Enzyme that catalyzes addition of DNA nucleotides to a growing chain of DNA

DNA polymerase

48

DNA polymerase reads in a ___ direction

3'-> 5'

49

The new strand is being synthesized in ___ direction

5'->3'

50

DNA synthesis begins at ___, a short sequence composes almost exclusively of __ base pairs

Origin of replication
AT

51

DNA strands separate locally and form two ___

Replication forks

52

Replication of double stranded DNA is ___, begins at a single origin and proceeds in both direction

Bidirectional

53

Maintains the separation of of the parental strands by stabilizing them

Single-stranded DNA-binding proteins

54

Remove supercoils that interfere with the further unwinding of the double helix

DNA Topoisomerases

55

Two types of DNA Topoisomerases

Type I: Swivelase
Type II: Gyrase

56

Cleaves one strand

Type I: swivelase

57

Cleaves both strands
Target of fluoroquinolones

Type II: Gyrase

58

Synthesizes short stretches of RNA

Primase

59

Needed by DNA polymerase to begin DNA chain elongation

Primers

60

Catalyzes chain elongation in a 5'->3' direction

DNA polymerase II

61

DNA polymerase II uses ___ as substrates

5'-deoxyribonucleoside triphosphates

62

DNA can proofread the newly synthesized DNA using ___

3'->5' exonuclease activity

63

The ____ is synthesized continuously, but the ___ is synthesized in short fragmetns.

Leading strand
Lagging strand

64

Lagging strand in short fragments called ___

Okazaki fragment

65

Removes RNA primers using 5'->3' exonuclease activity

DNA Polymerase I

66

Seals the gaps between the Okazaki fragments by catalyzing the final phospholipid ester/phosphodiester linkage

Ligase

67

Group of proteins that recognize the origin of replication

DNA A protein

68

Unwind the double helix ahead of advancing replication fork

Helicase

69

Short strands of RNA needed to begin DNA chain

Primers

70

Enzyme that cleaves phosphodiester bonds in a nucleic acid

Nuclease

71

Two types of nucleases

Endonucleases
Exonucleases

72

Cleave internal phosphodiester bonds

Endonucleases

73

Cleave bonds at the 5' or 3' end

Exonuclease

74

Bacteria utilizes ___ for proofreading

3'-exonuclease activity

75

Only mismatched bases are removed

3' exonuclease activity

76

Base-paired nucleotides are removed from the 5' end
To erase the RNA primer and remove damaged portions of DNA during DNA repair

5' exonuclease activity

77

DNA Polymerase types
Gap filling and sythesis of lagging strand

Prokaryote: I
Mammalian: alpha

78

DNA Polymerase types
DNA proofreading and repair

Prokaryote: II
Mammalian: epsilon

79

DNA Polymerase types
DNA repair

Prokaryote: II
Mammalian: beta

80

DNA Polymerase types
Mitochondria DNA synthesis

Prokaryote: II
Mammalian: gamma

81

DNA Polymerase types
Processive, leading strand synthesis

Prokaryote: III
Mammalian: delta

82

Eukaryotic DNA is (circular/linear)

Linear

83

Bubble-like structures within the DNA strand, which indicate a site of replication in eukaryotic cells

Replication bubbles

84

Structure responsible for the chromosome stability during mitosis

Telomere

85

Acts as "cap" that protects DNA from being mistaken by the cell as broken DNA that needs repair

Telomere

86

Enzymes that replace telomeres in cells that do not age

Telomerase

87

Lengthens the template strand by adding DNA sequences

Telomerase

88

Use RNA as template for DNA replication

Reverse transcription

89

RNA-dependent DNA polymerase
Makes a DNA copy from the RNA genetic material

Reverse transcriptase

90

A retrovirus that employs reverse transcription in order for it to proliferate within the body

HIV

91

Host cell of HIV is the __

T-cell

92

Part of the HIV that attaches to the T-cell receptor

gp120 protein

93

The newly-produced DNA is integrated within the host cell's genome via the __

Integrase

94

The viral proteinase ___ becomes active resulting the generation of the mature form of HIV.

p160

95

Sulfonamides
Structural analogs and competitively inhibits the utilization of PABA of Folic Acid

para-Aminobenzoic acid analogs

96

Specific to bacteria
Humans do not synthesize folate but acquire it through diet

para-Aminobenzoic acid analogs

97

Inhibits the reduction of dihydrofolate to tetrahydrofolate, catalyzed by dihydrofolate reductase

Methotrexate

98

Inhibits purine synthesis
DNA replication is slowed down in mammalian cells

Methotrexate

99

Metabolically converted to 5-FdUMP which becomes permanently bound to the inactivated thymidylate synthase

5-fluorouracil

100

This results in deoxynucleotide pool imbalances and increased levels of deoxyuridine triphosphate, which cause DNA damage

5-fluorouracil

101

Inhibit bacterial type II topoisomerases

Ciprofloxacin, Nalidixic

102

Inhibit human type II topoisomerases, have some selectivity for cancer cells

Etoposide, doxorubicin