Organization of the Genome Flashcards
1
Q
What are spacer sequences?
A
separate genes
2
Q
What are Introns?
A
non-coding sequences within a gene
3
Q
What type of RNAs do not have a protein counterpart?
A
rRNA, miRNA, snoRNA, snRNA
4
Q
What are repetitious DNA sequences?
A
most abundant class of non-coding DNA sequences
5
Q
What is satellite DNA also referred to?
A
simple-sequence DNA
6
Q
What is satellite DNA?
A
comprises identical repeats of relatively short sequences
7
Q
How long are satellite DNA?
A
14 - 500 base pairs
8
Q
How long are satellite DNA long tandem arrays?
A
20 - 100 thousand base pairs
9
Q
Where is most satellite DNA confined?
A
centromere or telomere
10
Q
What is the most abundant class of repetitious DNA?
A
interspersed repeats
11
Q
Where are interspersed repeats primarily located?
A
transposons and retrotranspsosns
12
Q
What are exons?
A
sequences that are translated into proteins
13
Q
What are longer, introns or exons?
A
introns
14
Q
What are gene families?
A
redundancies in genes
15
Q
What do gene families arise from?
A
gene duplication events
16
Q
What are pseudogenes?
A
when the duplicate genes develop mutations and become inactivated
17
Q
What does it mean to be clustered?
A
when a gene family is located on one chromosomal locus
18
Q
What is the function of H5?
A
to seal the nucleosome
19
Q
List four types of non-coding DNA
A
spacer sequences, introns, non-protein coding RNA, repetitious DNA
20
Q
What is satellite DNA composed of? Generally, how long is satellite DNA? Where is most satellite DNA confined?
A
nearly identical repeats of short sequences
20 - 100 base pairs
centromere or telomere
21
Q
What is the most abundant class of repetitious DNA?
A
interspersed repeats
22
Q
How much of the total human DNA is accounted for by interspersed repeats?
A
approximately 45%
23
Q
What two classes of DNA do interspersed repeats contribute to?
A
transposons and retrotransposons
24
Q
Are the genes in eukaryotes continuous or discontinuous?
A
discontinuous
25
What are longer, exons or introns?
introns
26
Where do gene families arise from?
gene duplication events
27
What is a pseudogene?
a duplicated gene that has mutated and become inactive
28
What are the fractions of chromatin composition?
1/3 DNA and 2/3 protein
29
How many base pairs of DNA are wrapped around a histone protein?
146 bp
30
What is a nucleosome?
DNA wrapped around histone protein
31
What cell cycle phases are part of the division phase?
G2 and M
32
What is the name of the place where chromatids adhere to each other at?
centromeres
33
What is the role of cohesin?
to secure centromeres together
34
What are chromatids?
two identical copies of chromosomes
35
What are homologous chromosomes?
maternal and paternal copies of the same chromosome
36
What type of fiber is DNA condensed into for replication?
700 nm
37
How are prokaryotic RNA's translated?
as they are synthesized
38
What is the function of the nucleolus?
to produce rRNA
39
Where does the assembly of ribosomal subunits take place?
periphery of nucleolus
40
What two nuclear constituents are attached to the nuclear envelope?
centromeres and telomeres
41
What is the nuclear lamina?
meshwork of filaments on the inner surface of the nucleus
42
Where is the perinuclear space?
enclosed by double nuclear membrane
43
What is the perinuclear space contiguous with?
endoplasmic reticulum
44
What is the function of the nuclear pore?
to regulate traffic between the nucleus and the cytoplasm
45
Is protein import into the nucleus energy dependent?
yes
46
Are mRNA, proteins and RNA-protein complex exported from the nucleus in an energy dependent process?
Yes
47
Where is the nuclear basket located?
inside of nuclear pore
48
Where is the protein ring of the nuclear pore?
anchored in the double membrane
49
Where are the filaments of the nuclear pore located?
outside
50
The central transporter is unspecific for size up to what size?
50 kDa
51
What are the three molecules that must be selectively transported into/out of the nuclear pore?
mRNA, proteins, ribosomal subunits
52
Where are ribosomal subunits synthesized?
cytoplasm
53
Where are ribosomal subunits transported to?
cytoplasm --> nucleus --> nucleolus
54
Import of a protein into the nucleus requires its' association with what protein?
Importin
55
What does importin associate with inside the nucleus? What does this cause?
Ran-GTP
dissociation of importin from its partner
56
Export of a protein from the nucleus requires the association of Ran-GTP with what?
exportin
57
How are the majority of RNAs exported from the cytoplasm?
in a Ran-independent fashion
58
What is the function of Dbp5?
may be involved in RNA export from the cytoplasm
59
What end of DNA do polymerases add to?
3' OH
60
What are the primers for DNA polymerase made of? What protein makes the primers?
RNA
Primase
61
What protein degrades the primers?
exonuclease
62
What is the significance of pyrophosphate?
its hydrolysis drives the reaction
63
What type of base is incorporated into the nascent strand? (phosphate)
triphosphate
64
What marks the origins of replication?
ORC (origin recognition complex)
65
What cell cycle phase begins synthesis of DNA?
S phase
66
What is the function of DNA pol alpha?
to synthesize RNA primers
67
DNA pol alpha activity is also referred to as what?
primase activity
68
What is the sequence of telomeres?
TTA-GGG
69
Telomerase contains what type of complimentary molecule?
complimentary RNA
70
What position of the ribose are bases attached?
1'
71
What type of RNA carries the most modifications?
tRNA
72
What is the only modification seen in DNA?
methylation of cytidine
73
What type of base stabilizes Z-form of DNA?
5-methylcytidine
74
How does doxorubicin work?
fits into the major groove of DNA
75
What type of DNA mutation do intercalating agents cause?
insertions and deletions
76
Name three intercalating agents
doxorubicin, ethidium, acridine dyes
77
triple helical structures are formed by long runs of what base?
pyrimidines
78
How many base pairs per turn?
10.4
79
Negative supercoiling happens when?
twisted in the direction that unwinds the helix
80
The majority of nuclear DNA is positively supercoiled or negatively supercoiled?
negative
81
When does positive supercoiling of DNA occur?
replication and txn
82
What is the MOA of type I topoisomerases?
cut-one strand
83
What is the function of topoisomerases?
to supercoil DNA
84
What is the MOA of type II topoisomerases?
cut two strands at once
85
What is the MOA of doxorubicin?
inhibit human topo. type II
86
What is the MOA of Nalidixic acid and ciprofloxacin?
act on bacterial topo. II
87
How many bp are wrapped around a histone protein?
146 bp
88
What is a nucleosome?
histone with DNA wrapped around it
89
What are the stages of the division process?
G2 and M
90
What are chromatids?
two identical DNA strands that make up a chromosome
91
Where do chromatids adhere to each other?
centromere
92
What is the function of cohesin?
to secure the chromatids together
93
What are telomeres?
the ends of the chromatids
94
Where does the assmebly of ribosomal subunits take place?
periphery of nucleolus
95
What is the function of the nuclear envelope?
to stabilize the nuclear envelope
96
What is the perinuclear space? What is the perinuclear space cotiguous with?
space between nuclear pore membranes
endoplasmic reticulum
97
What are the three main types of large molecules that must be transported between the nucleus and the cytoplasm?
mRNA, proteins, ribosomal subunits
98
What causes release of cargo from importin?
Importin association with Ran-GTP
99
How does importin leave the nucleus?
via its association with Ran-GTP
100
What causes dissocition of importin from Ran-GTP?
Ran-GTP hydrolysis to Ran-GDP
101
The majority of mRNA molecules are exported from the nucleus via what mechanism?
Ran-independent
102
What are the primers for DNA synthesis made of?
RNA
103
What do helicases use for energy?
ATP
104
Which DNA polymerase generates the primers?
DNA polymerase alpha
105
Does ligase require ATP?
yes
106
The telomere is on the end of the lagging strand or leading strand?
lagging strand
107
How does telomerase base pair to the telomere?
telomerase contains complimentary RNA to the telomere
108
Where are bases attached in DNA?
1' position
109
What is the only modification of a base in DNA?
methylation of cytidine to 5-methylcytidine
110
What do intercalating agents most often cause regarding DNA damage?
insertions and deletions
111
What base is involved in triple-helical structure?
pyrimidines
112
What defines negative supercoiling?
when DNA is twisted in the direction it is unwound
113
What causes positive supercoiling?
unwinding of the DNA helix
114
Nucleosomes associate to form how thick of fiber?
30 nm
115
What phase is the ORC activated?
S phase
116
Where does topoisomerase I function?
at the replication fork
117
The leading strand is synthesized by what polymerase?
DNA polymerase epsilon
118
The lagging strand is synthesized by what DNA polymerase?
DNA polymerase delta
