Nucleotide Structure, Function and Metabolism Flashcards
1
Q
Nucleosides are what
A
bases bonded to sugars only
2
Q
How are nucleosides named
A
by naming base with -sine or -dine added
3
Q
What is the structure of nucleotides
A
sugar, phosphate, and base
4
Q
how are nucleotides named
A
by adding -ylate
5
Q
Why does thyamine not have to have deoxy added to it
A
because it is not found in RNA
6
Q
What kind of linkages attach the base to the sugar backbone
A
Beta-glycosidic linkage
7
Q
The C-1’ of a sugar is attached by a beta-glycosidic linkage to a ____ of a purine
A
N-9
8
Q
The C-1’ of a sugar is attached by a beta-glycosidic linkage to a ____ of a purine
A
N-1
9
Q
What is the portion of DNA that codes for a protein
A
Gene
10
Q
The phosphodiester bridge has what kind of charge
A
negative
11
Q
What is the most common site of phosphate esterification
A
C-5’
12
Q
Addition of beta and gamma phosphates are added via
A
anhydride bonds to each other
13
Q
In DNA what carbon of the ribose is deoxygenated
A
The C-2
14
Q
What affect does the absence of oxygen at C-2’ have
A
it makes the DNA more resistant to hydrolytic attack, therefore increasing stability
15
Q
DNA is written and read in what direction
A
5’-3’
16
Q
How many hydrogen bonds are between A-T
A
2
17
Q
How many hydrogen bonds are between C-G
A
3
18
Q
The stacking of bases contributes to the stability of DNA in two ways what are they
A
Hydrophobic effect
- The hydrophobic bases cluster into the interior whereas the polar backbone faces the exterior
Van der Waals “stacking” forces
- The stacked base attract one antoher
- Although individually are weak when summed together they are strong
19
Q
DNA exists in 3 forms
A
A form
B form
Z form
20
Q
What is the A form of DNA
A
shorter and wider than B form
base pairs are tilted to the axis and in right handed spiral
only occurs in non-physiological conditions
21
Q
What is the B form of DNA
A
Is the most common form b/c it is hydrated like living cellular environments
is longer and narrower than A form
right handed spiral w/base pairs perpendicular to the axis
22
Q
What is the Z form of DNA
A
Occurs in segments of DNA that have been methylated
turn about the helical axis in a left handed spiral and the phosphate backbone zigzagged
23
Q
____ + ____= chromatin
A
Protien + Nuclear DNA
24
Q
how many nucleotides are in out genome
A
3 billion
25
an incredible amount of ____ is needed to package DNA
condensation
26
Mitotic chromosomes are condensed _____ times compared to interphase DNA
500 times
27
DNA binding proteins involved in forming chromosomes are
histones and non-histone chromosomal proteins
28
Polynucleotides are called
Nucleic acids
29
Nucleotids contain
a base, a sugar, and a phosphate
30
Nucleotides are _____ esters of nucleosides
phosphate esters
31
nucleosides consist of
a base and a sugar
32
Sugars are attached to a base via a ________
N-glycosidic linkage (in DNA it is a beta-glycosidic linkage because it is above the plane)
33
The C-1 of a sugar is attached by beta-linkage to what location of a purine
N-9
34
The C-1 of a sugar is attached by beta-linkage to what location of a pyrimidine
N-1
35
What is the purpose of the phosphodiester bridge having a negative charge
it repels nucleophilic species (like hydroxide ions) thus makes them less susceptible to hydrolytic attack than other esters
36
What is the most common site of phosphate esterification
C-5'
37
Phosphates are attached to a sugar via a
ester bond
38
phosphates are attached to each other via a
anhydride bond
39
DNA is deoxygenated at what carbon
C-2'
40
What is the purpose of the deoxygenation of DNA at C-2'
it makes DNA more resistant to hydrolytic attack and thus more stable
41
What direction is DNA written
5'-3'
42
how far apart are adjacent bases on DNA double helix
3.4 angstroms
43
The bases on DNA double helix are located
nearly perpendicular to the helix axis
44
The helical structure of DNA repeats every
10 bases or 34 angstroms
45
each base of the DNA alpha helix contributes ____ degrees of turn, so ____ bases per turn
36 degrees, so 10 bases per turn
46
The sugar backbone is located on the _____ of the DNA double helix
outside
47
The bases are located on the _____ side of the DNA double helix
inside
48
The ratio of purines and pyrimidines is
1:1
49
The ratio of what varies considerably form species
A-G
50
DNA with high ___ content is more stable
GC
51
what does ribonucleotide reductase due to a nucleotide diphosphate (note that NADPH is required)
It makes 2'- deoxynucleotide diphosphate
52
ATP does what to ribonucleotide reductase
activates it
53
dATP does what to ribonucleotide reductase
it inhibits it
54
What converts long strand RNA to short RNA
Ribonucleases
55
What converts long DNA chain to DNA oligomer or short chain DNA
Deoxyribonucleases
56
What does cleaves the phosphodiester bond of DNA and RNA oligomers to form monophosphates
Phosphodiesterase
57
What cleaves the phosphate off a nucleotide to form a nucleoside
Nucleotidase
58
what cleaves the base of a nucleoside to form a base and separate ribose/deoxyribose
nucleosidase
59
Allopurinol inhibits what specific enzyme
Xanthine oxidase
60
allopurinaol inhibits xanthine oxidase and therefore does not allow ____ to be converted to ____ and ____ to be converted to _____
hypoxanthine to be converted to xanthine and xanthine to uric acid
61
What does urate oxidase do
it is an enzyme not present in humans that converts uric acid to a more water soluble form Allantoin
62
Plays an important role in adenosine homeostasis and modulates signaling by extracellular adenosine and so contributes indirectly to signaling
Adenosine Deaminase (ADA)
63
The overproduction of Adenosine Deaminase (ADA) in erythrocytes causes
hemolytic anemia. It is rare.
| increased degradation of adenosine depletes adenine nucleotide pool and triggers premature destruction of RBCs.
64
What is the final product of purine catabolism
Uric Acid
65
Underproduction of Adenosine Deaminase ADA is associated with
The second most common form of severe combined immunodeficiency (SCID)
66
What catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid
Xanthine Oxidase
67
The inhibition of what enzyme by allopurinol is a major target for the treatment of Gout
Xanthine oxidase
68
What is the structure of xanthine oxidase
2 Flavin adenine dinucleotides (FADs), 2 Mo atoms, and 8 Fe atoms per molecule of enzyme
69
Deficiency of ADA leads to
SCID, high amounts of adenosine which is then converted into dATP, high levels of which block the synthesis of all other dNDPs and dNTPs,
Impaired DNA synthesis and compromised immune system
70
What is the most commonly affected area for GOUT
Big toe (metatarsal pharangeal joint)
71
High uric acid levels in the blood, leading to sodium urate crystals precipitate in the synovial fluid joints
Gout
72
What is primary hyperuricemia
overproduction of uric acid
73
What is secondary hyperuricemia
under-excretion of uric acid
74
What is the level for hyperuricemia
uric acid concentrations exceed plasma solubility (about 7 mg/dL)
75
What kind of diet increases the risk of gout
Rich in Purines (beans, lentils, spinach) together with meat, seafood, and alcohol
76
What are some treatments for GOUT
colchicine- decrease movement of granulocytes to the affected area
Allopurinol- inhibits xanthine oxidase to form the more soluble hypoxanthine
urate oxidase- catalyzes uric acid to allantoin, which is more water soluble
77
What is the normal serum uric acid level in adult males
4-8.6 mg/dL
78
What is the normal serum uric acid level in adult females
3.0-5.9 mg/dL
79
Serum urate levels greater than
>9 mg/dL means an increased risk of gout
80
Thymine derivatives final product (s) of catabolism
MethylmalonylCoA and Succinyl CoA
| Both are glucogenic
81
Cytosine and Uracil derivatives after catabolism
Malonyl CoA, which is ketogenic
82
Malonyl CoA, Methylmalonyl CoA, and succinyl CoA are all ____ soluble
water soluble
83
What is the source of rings atoms for Purine bases
CO2, Gln, Gly, Asp, N^10-formyl THF
84
What is the source of the rings atoms for prymidine bases
HCO3-, Gln, Asp, N^5, N^10- methylene THF
85
What is the committed step in the purine synthesis
formation of the phosphoribosyl amine (PRA)
86
How many phases are there to De Novo synthesis
4
87
Where does the alpha-D- ribose 5-phosphate from phase I of De novo purine synthesis come from
Pentose phosphate pathway
88
What is phase I of the De Novo synthesis of purines
Ribose-5P activation
89
What is the activated form of Ribose-5P
5-phospho-alpha-D-ribosyl-1- pyrophosphate (PRPP)
| note that it has 3 phosphates attached, 1 at C5' and 2 at C1'
90
What is phase II of De Novo Purine synthesis
conversion of PRPP to PRA (phosphoribosylamine) (note that this is the converted step)
91
Methotrexate blocks what phase of de novo purine synthesis
Phase III: construct IMP ring
92
How many steps is phase III of de novo purine synthesis
9 steps
93
What is phase IV of de novo purine synthesis
Convert IMP to adenosine and guanosine (deoxy) nucleotides
94
Ribonuclease reductase is an enzyme that catalyzes
a ribose to a deoxyribose
95
GMP and AMP inhibit what phases of de novo purine synthesis
Phase I,II, IV
96
IMP inhibits what phases of de novo purine synthesis
Phase I and II
97
Phosphates promote what phase of de novo purine synthesis
Phase I
98
PRPP promotes what phase of de novo purine synthesis
Phase II
99
Hypoxanthine ribose phosphate is the same thing as
Inosine monophosphate (IMP)
100
What is the product of phase III of de novo purine synthesis
Inosine monophosphate (IMP)
101
what are the two salvage enzymes of purine biosynthesis
Hypoxanthine guanine phosphoribosyl transferase
| Adenine phosphoribosyl transferase
102
what is the specific target of methotrexate
dihydrofolate reductase that converts in the liver
103
methotrexate binds dihydrofolate ___ times more tighlty than the forming IMP
100
104
AMP synthesis is stimulated by
GTP
105
GMP synthesis is stimulated by
ATP
106
how many phases is the de novo synthesis of pyrimidine nucleotides
3
107
What is phase I of pyrimidine synthesis
fabrication of orotate ring
108
What is phase II of De Novo synthesis of Pyrimidines
Attach PRPP to form UMP
109
What is phase III of de novo synthesis of pyrimidines
Convert UMP to uridine, cytosine and thymine (deoxy) nucleotides
110
The pyrimidine ring is sythesized from carbamoyl phosphate and aspartate by
aspartate-transcarbamoylase
111
What is the function of carbamoyl phosphate synthetase II in pyrymidine synthesis
it catalyzes the formation of carbamoyl phosphate from Gln, bicarbonate, and 2ATP
112
Why is uridine phosphorylase said to be versatile
It is able to convert Uridine/deoxyuridine and Deoxythymidine to uracil and thymine respectively
113
In purine de novo synthesis Methotrexate inhibits what
it inhibits dihydrofolate reductase that converts in the liver that converts dihydrofolate to tetrahydrofolate, which is then used to form the ring and thus IMP
114
What does 5-fluorouracil inhibit
it inhibits thymidylate synthase, which with Tetrahydrofolate converts dUMP to dTMP
115
Orotic aciduria is a deficiency in what enzyme
UMP synthase
116
What is orotic aciduria treated with
oral uridine
117
The deoxyribonucleotides are formed from the ribonucleotides by the reduction of the
ribonucleoside diphosphates
118
What is the immediate hydrogen donor for the reduction of ribonucleoside diphosphate is reduced
thioredoxin or glutaredoxin
