Flashcards in BIOCHEM LAB - Nucleic Acids Deck (169):
1
monomer unit of nucleic acids
nucleotides
2
NA carries a __ charge on the oxygen of the phosphate component
-
3
not nutrient biomolecules because ---
they can be biosynthesized
4
NA are branched or unbranched?
unbranched
5
a 5-carbon monosaccharide in ring form as heterocyclic hemiacetal derived from furan
PENTOSE
6
has a deoxyribose sigar with OH group on 3' position of sigar ring
DNA
7
has a ribose sugar with OH group at 2' and 3' positions of sugar ring
RNA
8
No NA, NO ___
Organism
9
blueprint of an organism is encoded in
NA
10
nitrogen base is attached to the 1' carbon of sugar through a what type of bond
glycosidic
11
fused bicyclic base
purine
12
monocyclic base, 6membered rin
pyrimidine
13
purines are attached to sugar by what beta-glycosidic bond
N9 - C1
14
pyrimidines are attached to sugar by what beta-glycosidic bond
N1-C1
15
More susceptible to H hydrolysis due to greater dipositivity of glycosyl bonds
glycosidic bonds to purine
16
IUPAC name of cytosine
2-oxo-4-aminopyrimidine
17
IUPAC name of thymine
5-methyl-2,4-dioxopyrimidine
18
IUPAC name of uracil
2,4-dioxopyrimidine
19
bases that are planar
pyrimidine
20
bases that are very nearly planar with a slight pucker
purine
21
IUPAC name of adenine
6-aminopurine
22
IUPAC name of guanine
2-amino-6-oxopurine
23
most polar base
Guanine
24
least polar base
thymine
25
gives NA their acidic and anionic character
phosphate
26
phosphate is attached to what carbon atom
5' c of the sugar component
27
type of bond between phosphate groups
phosphate anhydride or pyrophosphate bond
28
small proteins containing basic amino acids: lysine and arginine
histones
29
in circular DNA, the type of hydrogen bonding is intra or inter
INTRA
30
forms the solenoid supertstructure
DNA-histone complex
31
DNA-histone complex forms ____ structure when it undergoes coiling
solenoid supertstructure
32
Chromatinf iber is formed by
solenoid interaction with scaffold protein
undergoes compaction by folding and coiling
33
short-lived NA
synthesized as the need arises
RNA
34
mostly found in cytoplasm with non-histone proteins in ribosome
RNA
35
found in nucleolus of nucleus where ribsomes are synthesized
rna
36
WHERE THE DNA IS ALSO FOUND
in mitochondria and chloroplast
37
responsible for the 3d structure of DNA
James Watson and Francis Crick
38
xray diffraction data
Maurice Wilkins
Rosalind Franklin
39
double-helical forms by which DNA exists
A B C D E H Z L
40
natural DNA
most stable and dominant under physiological conditions
B-DNA
41
handedness of B-DNA
right handed (2 helix)
42
pitch of B-DNA
3.4 nm
43
rise of B-DNA
0.34 nm
44
helical diamtere of of B-DNA
2.0 nm
45
number of base pair per turn of of B-DNA
10
46
has minor and major grooves and is found in the cells
B-DNA
47
coiling od B-DNA is described as
plectonemic
48
this NA may contain local regions of short complementary base-pairing
RNA
49
NA that has a strong tendency to adopt a random coil conformation
RNA
50
NA found in RER
RNA
51
CHARGAFF'S RULES
Base composition of DNA ___ from one species to another
varies
52
CHARGAFF'S RULES
DNA of closely related species have ___ base composition
similar
53
CHARGAFF'S RULES
DNA of diff tissues of an organism have ___ base composition
same
54
CHARGAFF'S RULES
base composition of DNA (change or does not?) with age, nutritional, state etc
NOT CHANGE
55
CHARGAFF'S RULES
the ratios of adenine to T and G-C were nearly
1.0
56
CHARGAFF'S RULES
total number of purines in one strand is ____ to total number of pyrimides in complementary strand
same
57
structure which descirbes nucleotide base sequence
polarity of sugar backbone
primary
58
by convention, sequences are written in what direction
5' to 3'
59
stabilizing factos in primary structure
covalent bonds
tautomerism
resonance energy
60
it is a phosphodiester bond bet nucleotide monomers
the main stabilizing factor
covalent bonds
61
covalent PHOSPHODIESTER bonds are stable between what ph
pH 3 AND 12
62
at extremes in pH, phosphodiester bonds are ___
HYDROLYZED resulting in scission or shearing of DNA
63
stabilizing factor of primary struc that is pH dependent
tautomerism
64
a stabilizing factor formed when nitrogen bases are stabilized by electron delocalization
tautomers
65
what is formed when nitrogen bases are stabilized by electron delocalization
tautomers
66
type of tautomer that is predominant and more stable
commone
67
N bases are aromatic, which means they are
thermodynamically stable
68
the higher resonance energy, __
more thermodynamically stable
69
which type of base is more thermodynamically stable
purines
70
degree or thermodynamic stability
A>G>C>U>T
71
structure which descirbes the helical conformation of NA
secondary
72
conformation that is more thermodynamicallys table
helical instead of random coil
73
conseuqence of RNA being SS with regard t degree of secondary structure
lesser in degree than DNA
74
stabilizing factors in secondary structure
complementary base-pairing via intermolecular HB in DNA or intra in RNA
base stacking via pi-pi complexation rxns
75
T or F
E delocalization becomes more extensive when complementary bases are HB to each other
T
76
Properties of DNA related to 2ndary structure
DNA is relatively stable but not inert. Why
strands separate during repli/transcrip
77
Properties of DNA related to 2ndary structure
DNA solutions are viscous because
1.rigidity of double helix
2. high length/diameter ratio
78
Properties of DNA related to 2ndary structure
DNA is most stable and soluble in salt solutions with ___ high or low conc
HIGH
79
salt solutions of less than ___ M would weaken HB
0.1 M
80
effect caused by exposure of nitrogen bases
hyperchromic effect
81
effect of hyperchromic effect to absorbance
increase in 260nm
82
denaturation is reversible or irreversible?
reversible
83
hyperchroic effect is caused by the
exposure of nitrogen bases caused by unstacking caused by Hbonds disruption caused by unwinding
84
conformation of SS DNA after hyperchromic effect
random coil
85
process by which denatured complementary strands of DNA can reform a duplex DNA structure
renaturation or annealing
86
as DNA anneals, its absorbance will ______
decrease - causing hypochromic effect
87
relationship of rate of renaturation to concentration of complementary strands
direct
88
when does dna become less viscous
high temp
treatment with alkali
89
temp at which dna dissociate or unwinds
80-90
90
temp related denaturation
melting
91
temp at which 50% of double helix is unwound
melting pt or transition temp
92
Tm is determined using a
thermal denaturation curve
temperature profile
melting curve
93
temp at which dna renatures
below Tm
94
the more GC pairs, the ___ melting point
higher
95
the more GC pairs, the ___ melting point
lower
96
structure which describes degree of supercoiling
tertiary
97
level of structure which describescovalent modification of RNA
tertiary
98
NA makes up how many percent of cell's dry weight
5-15
99
what type of organs are rich in NA
highly cellular
spleen liver thymus pancreas
100
what type of organs are poor in NA
brain muscle tissues
101
choice sample for DNA
tissues with cells with high nuc to cytoplasm volume ratio
102
very good source of dna
lymphoid tissue
103
best sourceof dna
thymus
104
good substitute for source of dna
spleen
105
types of interactions responsible for the rigid molecular configuration of NA
phosphodiester bonds
HB
VDW forces
106
interactions involved in complementary base-pairing via HB inDNA and RNA
phosphodiester bonds
HB
107
factors for choosing material for experiments
high content of DNA RNA
low DNase and RNase activity which are both hydrolases
NA from source are readily obtainable in essentially pure form
108
HB bonding bet complementary base strans is stable between what pH
4 and 10
109
N,C glycosidic bonds to purine bases are hydrolyzed at pH
3 OR LESS (APURINIC SITES)
110
phosphodiester bonds and N,C glycosidic bonds are stable up to what temp
100C
111
condition in which cell wall releases DNA when tissue is homogenized
lysis or disruption
112
enzyme that causes most serious damage or degradation of DNA
DNAses or deoxyribonucleases
113
enzymes that catalyze hydrolysis of 3',5' phosphodiester linkages
DNAses or deoxyribonucleases
114
enzyme present on fingertips
causes spurious degradation of NA during purification
nucleases
115
in the absence of required ___ and in the __, degradative enzyme becomes nonfunctional
ion and in the cold
116
used to avoid degradation of dna
glass
rubber
plastic tools and ocntainers
117
native dna is present in cell as what type of complex
DNA-protein complexes
118
During the extraction process, proteins must be ____from DNA
dissoaciated or separated from DNA
119
examples of mechanical stress that may cause cleavage shearing or scission of DNA chains
grinding, shaking, stirring, squiritng sol'n through narrown orifices
120
does not cause damage to secondary structure of dna but reduces length of molecules
mechanical stress
121
purified dna is best kept in solution or dry
in solution
122
if precipitated DNA is kept dry, it tends to undergo
denaturation
123
how to maintain dna in its secondary structure
keep it in 0.1 M acetate buffer
124
what to do to inhibit growth of microorganism after purifying dna
add 0.001M sodium azide
storage temp must be 4C
125
RNA of low MW is best kept dry or slurry
dry
126
RNA of high MW is best kept dry or slurry
slurry under 75% aqueous alcohol
with 2% sodium azide at 4C
127
scientific name of onion
Allium cepa
128
steps in dna isolation
homogenization
dissociation and denaturation
purification of NA
129
steps in dna isolation
disruption of cell membrane and membrane of subcellular particles to release nucleoprotein
homogenization
130
steps in dna isolation
separates protein (deproteinization) and releases NA
NA is then precipitated out
dissociation and denaturation
131
steps in dna isolation
based on principles of MW, size, structure, base composition etc
purification of NA
132
homogenization involves what process to inactivate nucleses
denaturation
133
onion sample is treated at what temp with a homogenizing solution
60C
134
homogenizing solution
dilute saline solution
to precipitate nucleoproteins and separate it from other proteins
0.15M
135
homogenizing solution
breaks ionic interaction between protein and NA and binds to the protein by hydrophobic interaction
makes it negatively charged
5% SDS
136
homogenizing solution
binds Ca and Mg ions needed to activate nucleases and RNAse and which can form salts with anionic phosphate groups of NA
0.15M sodium citrate
137
homogenizing solution
to dissolve proteins and bind Ca and Mg ions
0.001M EDTA
138
WHY heat the onion sample at 60C
to dissolve NA separated from the protein without affecting HB in both NA and potein
139
why cool in an ice bath
slow down activity of nucleases
140
why treat with papain or meat tenderizer (dna)
denature all protein in aqueous medium
141
what does denaturation do with the hydrophobic portion of proteins
expose them to be precipitated out
142
why add ice cold 95% ethanol
to precipitate DNA and RNA
143
after isolation describe dna
white fibrous or threadlike ppt which can be collected by spooling onto a glass rod
144
scientific name of yeast
saccharomyces cerevisiae
145
how much RNA does yeast contain
4% by weight
146
in rna isolation, why heat with dilute alkali
separate from protein
extract rna and water soluble proteins
inactivate nucleases
147
in rna isolation, why mix ethanol with conc HCl
to make alcohol more polar, thus precipitating the less polar NA, RNA
148
buffer or solution used
tris-EDTA buffer of SSC solution
149
meaning of TE and SSC
standard saline citrate
tris-EDTA
150
why does dna and rna have sufficient absorptionin uv range
presence of aromatic nitrogen bases which contain conjugated double bonds
151
major absorption band for purified dna and rna peaks at about
260nm
152
primary contaminant in dna and rna
protein material with trp phe and tyr
153
peak absorbance of protein material with trp phe and tyr
280 nm
154
TYPICAL absorbance ratio for good quality NA
1.8-2
155
absorbance ratio for isolated dna
1.8
156
what does a small ratio indicate
increased contamination by protein
157
what does a bigger ratio indicate
increased contamination by rna or denatured dna
158
amt of NA and protein in sol'n can be determined using
monograph
159
RNA has higher or lower absorption at 260 nm than DNA
higher
160
why does RNA have higher absorption at 260 nm than DNA
because it is SS, nitrogen bases are exposed
161
A ratio of highly purified RNA
1.85-2
162
absorbance of RNA if ti has contaminants such as phenol, polysaccharides, peptides
230nm
162
The symmetry of the sugar-phosphate backbone imparts a ---- to the nucleic acid
Polarity
163
The single-stranded nucleic acids may contain ----- regions of ----
local regions of short complementary base pairing
164
Since NA is single stranded, it has a strong tendency to adopt what conformation?
Random coil
165
Location of RNA
Cytoplasm, rER, nucleolus
166
Thermodynamically stable means lower or higher free energy?
Lower
167
Intermolecular forces present in pi-pi complexation rxn
Van der Waals
Intermolecular interaction
168