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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

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

Why was hydrolysis performed

To separate the components of nucleic acids isolates

169

absorbance of RNA if ti has contaminants such as phenol, polysaccharides, peptides

230nm

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