2.11 Replication Flashcards
1
Q
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
A
Phosphodiester bonds
2
Q
Single unique nucleotide sequence wherein prokaryotic DNA replication begins
A
Origin of Replication
3
Q
Protein that binds to specific nucleotide sequences at the origin of replication, causing short, tandemly arranged AT regions in the origin to melt
A
DNA-A Protein
4
Q
Enzyme that binds to ssDNA forces the strands apart, unwinding the double helix
A
DNA helicases
5
Q
Proteins that bind to newly separated ssDNA in order to hold them apart.
A
Single stranded DNA binding proteins (SSBP)
6
Q
Enzymes that cut one strand of the double helix to relieve supercoiling
A
DNA Topoisomerase Type 1
7
Q
Enzymes that make transient breaks in both dsDNA strands
A
DNA Topoisomerase Type II
8
Q
Monomeric units or building blocks of nucleic acids
A
Nucleotides
9
Q
Functions of nucleotides
A
Precursors for informational molecules Part of coenzyme Donors of phosphoryl groups Regulatory nucleotides Synthetic analogues as drugs
10
Q
Nitrogen-containing cyclic compounds whose rings contain both carbon and other elements
A
Nitrogenous bases
11
Q
Purine
A
Guanine
Adenine
12
Q
Pyrimidine
A
Cytosine
Uracil
Thymine
13
Q
Has two rings
A
Purine
14
Q
Has one ring
A
Pyrimidine
15
Q
Has a planar characteristic that facilitates stacking of rings one on top of each other
A
Nitrogenous bases
16
Q
Pair with two H-bonds
A
Adenine and Thymine/
Adenine and Uracil
17
Q
Pair with three H-bonds
A
Guanine and Cytosine
18
Q
Also known as methyl uracil
Comes from folate system
A
Thymine
19
Q
Nitrogenous base + sugar
A
Nucleoside
20
Q
Link between nitrogenous base and ribose sugar
A
beta-N-glycosidic bond
21
Q
Anomeric carbon is attached to ___ for pyrimidine, and __ for purine
A
N1; N9
22
Q
Nucleosides + phosphate
Phosphorylated nucleosides
A
Nucleotide
23
Q
Esterified to a hydroxyl group of the sugar
A
Phosphoryl group
24
Q
Phosphoryl group usually attached to __ of the pentose
A
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
