DNA 1 and 2 Flashcards
1
Q
RNA stands for
A
ribonucleic acid
2
Q
DNA stands for
A
Deoxyribonucleic acid
3
Q
what is responsible for storing and translating the information encoding each of the proteins and performing other chemistry
A
ribose-phosphate polymers
4
Q
RNA is responsible for
A
enzymatically synthesizing all proteins
5
Q
about how much of DNA is protein encoding
A
2%
6
Q
how many monomers are found in each DNA set in the human cell
A
3x10^9
3 billion
7
Q
total length of polymer of DNA in a cell
A
1 meter/cell
8
Q
what two things contribute to errors
A
translation and transcription
9
Q
in what organisms are mutation rates low
A
bacteria and humans
10
Q
low mutation rate
A
1 per 1-^8or9
11
Q
what organisms have a high mutation rate
A
viruses and cancers
12
Q
high mutation rate
A
1 per 1000
13
Q
why might a high mutation rate be a good thing?
A
it helps the virus evade the immune system.
makes cancer harder to treat
14
Q
two types of bases
A
purines and pyrimidines
15
Q
purines
A
adenine
guanine
16
Q
pyrimidines
A
uracil
cytosine
thymine
17
Q
how are bases linked to the ribose sugar
A
N-linked
via the nitrogen on the base
18
Q
another name for a ribose sugar
A
furanose
19
Q
what does ribose do in water
A
cyclizes and puckers
20
Q
nucleoside
A
a base linked to a pentose sugar
NO PHOSPHATE
21
Q
nucleotide
A
a base linked to a phosphate ester of a pentose
base, sugar and phosphate
22
Q
base, nucleoside, nucleotide nomenclature for A
A
adenine
adenosine
adenylate
23
Q
base, nucleoside, nucleotide nomenclature for G
A
guanine
guanosine
guanylate
24
Q
base, nucleoside, nucleotide nomenclature for U
A
uracil
uridine
uridylate
25
base, nucleoside, nucleotide nomenclature for C
cytosine
cytidine
cytidylate
26
base, nucleoside, nucleotide nomenclature for T
thymine
thymidine
thymidylate
27
DNA at base pair levels form what kinds of bonds
hydrogen bonds
28
A and T/U form how many base pairs
2
29
C and G form how many base pairs
3
30
the hydrogen bonds between the bases make the DNA
flexible
31
in purines, where does the first nitrogen come from
aspartate
32
in purines where does the second carbon come from
N10-Formyl-tetrahydrofolate (THF)
33
in purines, where does the third nitrogen come from
glutamine
34
in purines, where does the 4th carbon come from
glycine
35
in purines where does the 5th carbon come from
glycine
36
in purines where does the 6th carbon come from
CO2
37
in purines where does the 7th nitrogen come from
glycine
38
in purines, where does the 8th carbon come from
N10-Formyl-tetrahydrofolate (THF)
39
in purines where does the 9th nitrogen come from
glutamine
40
PRPP
5-phosphoribosyl-1-pyrophosphate
41
what is the activated donor of the sugar unit in biosynthesis of nucleosides using a phosphoribosyl transferase
PRPP
42
the purine rings are synthesizes on the
ribophosphate
43
what amino acid is needed to start the process of turning PRPP into a purine
glutamine
44
what is the initial purine made from the PRPP pathway
Inosinate (IMP)
hypoxanthine base
45
Inosinate (IMP) can be turned into
Adenylate (AMP)
Guanylate (GMP)
46
Free bases can be recycled and attatched directly in what is known as
a salvage reaction
47
how is a salvage reaction done
using a phosphoribosyl transferase reaction
48
the monophosphates are enzyme ... for their own synthesis
inhibitors
49
AMP production from IMP is inhibited by
AMP
50
GMP production from IMP is inhibited by
GMP
51
IMP production from PRPP is inhibited by
IMP, AMP, and GMP
52
in pyrimidines where is the 1st nitrogen from
aspartate
53
in pyrimidines where is the second carbon from
carbamoyl phosphate
54
in pyrimidines where is the 3rd nitrogen from
carbamoyl phosphate
55
in pyrimidines where is the 4th carbon from
aspartate
56
in pyrimidines where is the 5th carbon from
aspartate
57
in pyrimidines where is the 6th carbon from
aspartate
58
aspartate and carbamoyl phosphate come together to make
orotate
59
orotate is used to make the precursor pyrimidine called
uridylate (UMP)
60
How is RNA reduced to DNA
by a ribonucleotide reductase known as ribonucleoside diphosphate reductase
61
DNA bases are aromatic and therefore
stack well
62
what provides specific pairing and form specific structed in salt water in reguards to DNA
hydrogen bonds
63
what do the major and minor groove in DNA do
hold water, ions, and provide many recognition sites for other molecules including proteins
64
duplex (ds) DNA is often characterized as
a nearly rigid charged rod
65
duplex DNA has a persistance length (P) of
500 A
66
single stranded DNA (or RNA) had a persistance length (P) of
less than 10 A
66
two ways to measure persistance length (P)
FRET and FCS
67
what packs the DNA in phages
ATP consuming motor
68
many of the common cofactors are also
nucleotides
69
three common cofactors
coenzyme A
NAD+
FAD
70
how many phosphates can be added onto a nucleoside
1, 2, or 3
71
synthesis and degradation of the bases are very
material and energy intensive reactions
72
de novo synthesis molecule for pyrimidines
UMP
73
end products for pyrimidine degredation
B-alanine and B-aminoisobutyric acid
74
B-aminoisobutyric acid smells like
old tennis shoes
75
de novo synthesis molecule of purines
IMP
76
end/waste product of purine degredation
uric acid
77
the synthesis cycles are dependent on
energy molecules
78
AMP synthesis depends on
GTP
79
GMP synthesis depends on
ATP
80
essentially any -OH on the furanose ring could be substituted with
phosphates
81
3' and 5' OH substitutions on the furanose ring are for
the backbone
82
2' and 3' OH substitutions on the same furanose ring make
a Cyclic NMP molecule used in secondary messenger pathways
83
given the number of rotatable bonds, the number of conformations per base is
large meaning there is lots of flexibility
84
the glycosidic linkage at the base is called the
X dihedral
flagpole
85
syn
the base is turned toward the furanose ring
86
anti-
the base is turned away from the furanose ring
87
examples of less common bases
5-methylcytidine
N6-methyladenosine
N2-methylguanosine
5-hydroxymethylcytidine
inosine
pseudouridine
7-methylguanosine
4-thiouridine
88
the bases pair up specifically with H-bonds and yeild similar
C-1' to C-1' distances
89
differences between RNA and DNA
the OH in the backbone and the change of T for U
90
A problem with RNA stability
can be easily hydrolized on the 2'OH by water or OH
91
each base has a unique UV absorption spectrum due to
the electronic differences in the rings and substitutions
92
the bases have several titratable groups and as a result
several resonance tautomers exist
so pH plays a role
93
guanine tautomers
keto and enol
94
adenine tautomers
amine and imine
95
tautomers for pyrimidines
lactam, lactim and double lactim
96
tautomers cause what
mutations during replication and repair
97
different resonance states are allowed due to
the number of hetero atoms in conjuction in the rings
98
the absorption spectrum of the nucleic acids depends on
pH
99
nucleotide availability via synthesis is crucial to
dividing cells where a new copy of the chromosome is needed
100
nucleotide synthesis is a good candidate for
chemo therapeutics
101
an example of nucleotide synthesis for a target
dihydro-foliate reductase
folic acid
p-aminobenzoic acid
102
attractive forces in DNA
base pair hydrogen bonds
base pi stacking
103
repulsive forces in DNA
excluded volume
phosphate-phosphate repulsions
104
two charges q1 and q2 interact with each other by
coulomb's law
105
The interaction between two charges can be changes by the presence of
excess salt (debye and Huckel)
106
dipoles align to oppose the
external field in dielectric screening
107
all biochemistry requires
salt water or buffers
108
liquid state order: solvation shells
when the molecules are tumbling in solution and there is salt, the system is not crystalline the distribution has structure but is not periodic like a lattice.
109
The electric fild around DNA changes the probability of finding
salt and other DNA
110
counter ions pile up near
a helix or between two helices
111
counter ions increase
the ionic strength and screening locally
