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MTAP 2 BABY > MODX > Flashcards

MODX Flashcards

1
Q

Attachment of the 5’ phosphate and hydroxyl groups of an incoming nucleotide to the 3’ hydroxyl group of the last nucleotide on the growing chain

A

Nucleic acid chain

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2
Q

A macromolecule made of nucleotides bound together by the phosphate and hydroxyl groups on their sugars

A

Nucleic acid

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3
Q

DNA is oriented in a

A

5’ to 3’ directions

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4
Q

A macromolecule of carbon, nitrogen, oxygen, phosphorous, and hydrogen atoms

A

DNA

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5
Q

4 nitrogen bases that makes up the majority of DNA

A

Adenine, cytosine, guanine, thymine

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6
Q

Nitrogen bases are attached to a ____ sugar, which forms a polymer with the deoxyribose sugars of other nucleotides through a ______

A

Deoxyribose sugar, phosphodiester bond

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7
Q

Published a paper on NUCLEIN in 1871

A

Johann Friedrich Miescher

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8
Q

First one who describe the double helical stucture of DNA

A

James watson and Francis Crick

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9
Q

Each nucleotide consists of a five-carbon sugar, the first carbon of which is covalently joined to a ______ and the fifth carbon to a _____

A

Nitrogen base, phosphate moiety

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10
Q

The nitrogen base bound to an unphosphorylated sugar is

A

Nucleoside

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11
Q

Nucleoside is composed of

A

Adenosine, guanosine, cytidine, and thymidine

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12
Q

Nucleotides can be converted to nucleosides by

A

Hydrolysis

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13
Q

Important for forming the phosphodiester bond that is the backbone of the DNA strand

A

Hydroxyl group on the third carbon

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14
Q

Are planar carbon-nitrogen ring structures

A

Nitrogen bases

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15
Q

Four common nitrogen bases in DNA

A

Adenine, Guanine, Cytosine, and Thymine

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16
Q

Nitrogen bases with a SINGLE ring structure are called

A

Pyrimidines (Thymine, cytosine)

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17
Q

Bases with DOUBLE ring structures are called

A

Purines (Guanine, adenine)

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18
Q

The key to the specificity of all nucleic acid-based tests used in the molecular laboratory

A

Hydrogen bonds

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19
Q

How the information held in the linear order of the nucleotides is maintained

A

Specific Hydrogen bond formation

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20
Q

The formation of hydrogen bonds between two complementary strands of DNA is called

A

Hybridization

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21
Q

The double helix are identical not complementary

True or false

A

FALSE

The double helix are complementary not identical

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22
Q

DNA has an ____ orientation because of the way it is replicated

A

Antiparallel orientation

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23
Q

Products of transcription and translation of the nucleic acid

A

Proteins

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24
Q

Defined as the ordered sequence of nucleotides on a chromosome that encodes a specific functional product

A

Gene

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25
Q

Translation takes place on

A

Ribosomes

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26
Q

DNA transcribed and then translated into protein, this process is called

A

Gene expression

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27
Q

Copying of one strand of DNA into RNA by a process similar to that of DNA replication

A

Transcription

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28
Q

Transcription is catalyzed by

A

RNA polymerase

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29
Q

Transcription occurs in

A

Interphase

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30
Q

Prokaryotes ribosome is 70s
70S Ribosomes is composed of

A

30S small subunit and 50S large subunit

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31
Q

The 30S subunit is composed of? And what is it’s weight

A

1 million daltons

composed of: 16S ribosomal RNA and 21 ribosomal proteins

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32
Q

What is the weight of the 50S subunit and what is its composition

A

1.8 Million daltons

Composed of 23S Ribosomal RNA and 34 ribosomal proteins

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33
Q

Eukaryotic ribosome = 80S
80S is composed of

A

40S small subunit and 60S Subunit

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34
Q

The 40S small subunit from eukaryotes is composed of? What is its weight

A

1.3 million daltons

Composed of 18S Ribosomal RNA and 30 ribosomal proteins

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35
Q

The 60S subunit from eukaryotes is composed of? What is its weight

A

2.7 million daltons

Composition:
5S Ribosomal RNA, 5.8S Ribosomal RNA, 28S ribosomal RNA and about 40 ribosomal proteins

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36
Q

Protein synthesis in the ribosome almost always starts with

A

The amino acid methionine in eukaryotes and N-formylmethionine in bacteria and chloroplasts

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37
Q

First peptide bond is formed between the amino acids in the A and P sites by transfer of the _____ group of the first amino acid to the amino group of the second amino acid, generating a dipeptidyl-tRNA in the A site

A

N-formylmethionyl

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38
Q

This step is catalyzed by an enzymatic activity in the large subunit called

A

Peptidyl transferase

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39
Q

During translation, the growing polypeptide begins to fold into its mature conformation. This process is assisted by molecular ____

A

chaperones

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40
Q

These specialized proteins bind to the large ribosomal subunit, forming a hydrophobic pocket that holds the emerging polypeptide

A

Molecular chaperones

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41
Q

Protects the growing unfinished polypeptides until they can be safely folded into mature protein.

A

Chaperones

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42
Q

E. coli can synthesize a ___ - ___ amino acid protein in 10-20 seconds

A

300-400 amino acid protein

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43
Q

In nucleated cells, the majority of translation occurs in

A

the Cytoplasm

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44
Q

Purpose of nucleic acid extraction

A

To release the nucleic acid from the cell for use in subsequence procedures

Should be free of contamination with protein, carbs, lipids, or other nucleic acid

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45
Q

The initial release of the cellular material is achieved by breaking the cell and nuclear membranes also known as

A

Cell lysis

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46
Q

Following lysis, the target material is ___, and then the concentration and purity of the sample can be determined

A

Purify

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47
Q

A highly branched sucrose polymer that does not penetrate biological membranes

A

Ficoll

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48
Q

Least damaging among tested fixatives

A

Buffered formalin

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49
Q

Less toxic xylene substitutes

A

Histosolve, Anatech Pro-Par, or ParaClear

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50
Q

More rapid and comparably effective DNA extraction can be performed using solid matrices to bind and wash the DNA

A

Solid-Phase Isolation

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51
Q

The carrier in solid-phase separation requires the nucleic acid of more than ____ nucleotides in length

A

200

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52
Q

Promega DNA IQ holds a specific amount of DNA. What is the amount?

A

100ng

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53
Q

Will digest proteins in the sample, lysing the cells and inactivating other enzymes

A

Proteinase K

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54
Q

A cation-chelating resin that can be used for simple extraction of DNA

A

Chelex (Chelating resin)

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55
Q

Most commonly used in forensic applications but may also be useful for purification of DNA from clinical samples and fixed, paraffin-embedded specimens

A

Extraction with Chelating Resin

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56
Q

Provides sufficiently clean DNA that can be used for amplification

A

DNA extraction/storage card

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57
Q

RNA is labile due to the ubiquitous presence of

A

RNAses

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58
Q

Small proteins that can renature, even after autoclaving, and regaining activity

A

RNAses

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59
Q

T/F
RNAses must be eliminated or inactivated before isolation of RNA

A

True

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60
Q

Glassware must be baked for 4 to 6 hours at ____C to inactivate the RNAses

A

400C

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61
Q

Most abundant RNA in all cells

A

Ribosomal RNA

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62
Q

2nd most abundant RNA

A

Messenger RNA

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63
Q

Reticulocytes in blood and bone marrow samples are lysed by ____ or separated from WBCs by ___

A

Lysed by osmosis, separated from wbcs by centrifugation

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64
Q

Organic method of extraction

A

Phenol - Chloroform

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65
Q

Inorganic method of extraction

A

Salt precipitation to remove proteins

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66
Q

Solid phase method of extraction

A

Column Filter, magnetic beads

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67
Q

Purification of DNA

A

DNA precipitated by alcohol

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68
Q

RNAses

A

Ubiquitous

Very high concentration on hands

Act at wide range of temperatures: -20 to >100C

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69
Q

Special considerations for RNA isolation

A

Storage: Liquid nitrogen or at -80C
Gloves should always be worn because hands have high concentration of RNAse
Use equipment dedicated to RNA testing
Reserve areas in the laboratory for storage and RNA work
Use disposable items direct from manufacturer
Avoid reusable glassware or bake 4-6 hours at >270C to inactivate RNAse
Uses RNAse inhibitors during cell lysis e.g guanidine thiocyanate

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70
Q

Hydrophobic portion of organicmethod

A

Lipids and debris on the bottom

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71
Q

Hydrophilic portion of organic method

A

aqueous phase contains the DNA/RNA on top of isopropyl alcohol

72
Q

low pH and high salt precipitate proteins leaving DNA in solution (Supernatant)

A

Inorganic method

73
Q

1 million eukaryotic cells or 10 to 50mg of tissue will yield how many amounts of RNA?

A

10ug of RNA

74
Q

Fluorescent dyes that binds specifically to DNA are used to visualize the sample preparation

A

Ethidium bromide or SybrGreen I

75
Q

SybrGreen II are used to detect

A

Single stranded DNA or RNA

76
Q

Used to detect small amounts of DNA by visual insepction

A

Silver stain

77
Q

Nucleic acids absorb light at

A

260nm

78
Q

Phenol absorbs ultraviolet light at

A

270nm to 275nm

79
Q

May be used to estimate the purity of nucleic acid

A

Spectrophotometric measurement

80
Q

Common contaminants and their wavelengths of peak absorbance

A

Organic compounds = 230nm
Phenol = 270nm
Protein = 280nm
Particular matter = >330nm

81
Q

Absorbs light at 280nm through the aromatic tryptophan and tyrosine residues

A

Proteins

82
Q

The absorbance of nucleic acid at 260 nm should be

A

1.6 to 2.00 times more than the absorbance at 280nm

83
Q

Early methods use this. A dye that combines with alpha methylene aldehydes/Ribosomes to yield a fluorescent product

A

3,5-Diaminobenzoic acid 2HCl DABA

84
Q

This dye combines with adenine-thymine base pairs in the minor groove of the DNA double helix and is thus speicific for intact double-stranded DNA

A

Hoechst 33258

85
Q

Other DNA-specific dyes that can be used for fluorometric quantification

A

PicoGreen and OliGreen

86
Q

More sensitive than Hoechst dye due to brighter fluorescence upon binding to double-stranded DNA

A

PicoGreen

87
Q

Designed to bind to short pieces of Single-stranded DNA

A

OliGreen

88
Q

A microfluidics-based instrument used for lab on a chip technology that has been applied to nucleic acid quantification and analysis

A

Agilent 2100 Bio-analyzer

89
Q

Useful for analysis of studies on small RNAs, such as mucroRNAs in eukaryotes and gene expression in bacteria

A

Microfluidics

90
Q

Used in Horizontal orientation electrophoresis

Polysaccharide extracted from seaweed

Easy and cost-effective

Larger fragments (20bp - 10Mb)

A

Agarose Gel

91
Q

Used in vertical orientation electrophoresis

Synthetic material

Higher resolution, finer matrix, higher resolution capability

Dangerous neurotoxin

Smaller sequences/fragments

A

Polyacrylamide gel

92
Q

Choice of agarose concentration for DNA cells

A

0.3 = 5000 - 60,000 bp
0.6 = 1000 - 20,000 bp
0.8 = 800 - 10,000 bp
1.0 = 400 - 8,000 bp
1.2 = 300 - 7,000 bp
1.5 = 200 - 4,000 bp
2.0 = 100 - 3,000 bp

93
Q

Choice of polyacrylamide concentration for DNA cells

A

3.5 = 100 - 1,000 bp
5.0 = 80 - 500 bp
8.0 = 60 - 400 bp
12.0 = 40 - 200 bp
20.0 = 10 - 100 bp

94
Q

Monitors the progress of the electrophoresis run as the dye approaches the end of the gel

Runs ahead of the smallest fragment of DNA; not associated with the sample DNA

Example is Bromophenol blue, Xylene cyanol

A

Tracking Dye

95
Q

Increases the density of the sample as compared with the electrophoresis buffer

Density gradient examples are: Ficoll, Sucrose, Glycerol

A

Loading Dye

96
Q

Compare the nucleic acid fragments with a ladder

Molecular weight size marker

Set of standards that are used to identify the approximate size of a molecule on a gel during electrophoresis

Mixture of fragments with known size to compare the PCR products (Amplicons)

A

Ladder

97
Q

Agarose gel is comprised of

A

Agaropectin and agarose

98
Q

Used for very large pieces of DNA (50,000 - 250,000 bp)

A

Pulse field Gel electrophoresis

99
Q

Works by alternating the positive and negative electrodes during electrophoresis

Requires temperature control and a switching mechanism

A

Field Inversion Gel Electrophoresis

100
Q

Very small DNA fragments and single-stranded DNA are best resolved on?

A

Polyacrylamide gels in polyacrylamide gel electrophoresis

101
Q

Acrylamide in combination with the cross-linker methylene bisacrylamide

Originally applied mostly for protein separation

Used for sequencing nucleic acids, mutation analyses, nuclease protect assays

A

Polyacrylamide gels

102
Q

Catalyst of polyacrylamide gel to polymerize it

A

Ammonium persulfate + Tetrametyhlethylenediamine

or

Light activation

103
Q

Widest application of this is the separation of such organic chemicals such as pharmaceuticals and carbohydrates

Applied to the separation of inorganic anions and metal ions

Faster analytical runs and lower cost per run than HPLC

Used for the separation and analysis of nucleic acid

A

Capillary electrophoresis

104
Q

Analyte is resolved in a thin glass capillary (Fused silica)

Fused silica is covered with a polyimide coating for protection

A

Capillary electrophoresis

105
Q

Used for nucleic acid analysis

The platinum electrode close to the end of the capillary undergoes a transient high-positive charge to draw the sample into the end of the capillary

A

Electrokinetic injection

106
Q

Other application of capillary electrophoresis

A

Clonality testing, microsatellite instability detection, bone marrow engraftment analysis

107
Q

Advantage of capillary system over traditional slab gel electrophoresis

A

Increased sensitivity and immediate detection

108
Q

Purpose of this is to carry the current and protect the samples during electrophoresis

A

Buffer system

109
Q

Most common buffer for electrophoresis

A

Tris borate EDTA (TBE)
Tris Phosphate EDTA (TPE)
Tris acetate EDTA (TAE)

110
Q

T/F
TBE has a greater buffering capacity than TAE

A

True

111
Q

DNA will migrate twice as fast in ___ than in TBE in constant current

A

TAE

112
Q

Not recommended for some post electrophoretic isolation procedures

A

TBE

113
Q

Modifies sample molecules in ways that affect their migration

A

Buffer additives

114
Q

Example of buffer additinves

A

Formamide, urea, and various detergents

115
Q

Breaks hydrogen bonds between complementary strands or within the same strand of DNA or RNA

A

Denaturing agent

116
Q

___ and heat added to DNA and RNA breaks and blocks the hydrogen bonding sites, hindering complementary sequences from reannealing

A

Formamide and heat

117
Q

Denaturant used for RNA that reacts with amino groups on the RNA to prevent base pairing between homologous nucleotides and with aldehydes, which also disrupt base pairing

A

Methylmercuric Hydroxide (MMH)

118
Q

Examples of RNA buffers

A

Sodium phosphate,
MOPS buffer propanesulfonic acid
Sodium acetate

119
Q

Decrease of pH at the Cathode and increase of the pH at the anode is called

A

pH Drift

120
Q

What affects the current in electrophoresis

A

Thickness of the gel and the volume of the buffer

121
Q

Horizontal gels are also called

A

submarine gels

122
Q

Inserted into the top of the gel to create holes or wells

A

Comb

123
Q

Slowing migration in the outer lanes compared with lanes in the center of the gel due to the outer gel being cooler than the middle gel is called

A

Gel smiling

124
Q

What is the size of the spacers of the vertical gel

A

0.05mm to 4mm

125
Q

that are placed upside down, teeth up, not in contact with the gel to form a trough on the gel during polymerization is called

Wells can be loaded while this comb is in place

Advantage of this comb is the lanes are placed immediately adjacent to one another

A

Shark tooth’s comb

126
Q

SyBr Gold is used for

A

Both DNA and RNA staining

127
Q

Difference between Sybr green 1 and EtBr

A

Sybr green 1 differs from EtBr in that it does not intercalate between bases

128
Q

In agarose gel, SyBr staining is ____ times more sensitive than EtBr

A

25-100

129
Q

Originally developed for protein visualization

Sample is fixed with methanol and acetic acid

A

Silver stain

130
Q

Silver stain:
Best for thick gels -
More stable -

A

Silver stain:
Best for thick gels - Silver diamine
More stable - Silver nitrate

131
Q

Involves making copies of a target sequence to such a level that they can be detected in vitro

A

Target amplification

132
Q

Visualized the idea of amplifying DNA in vitro in 1983

A

Kary Mullis

133
Q

Real advantage of PCR

A

Ability to amplify specific targets

134
Q

Accomplished by heating the sample at 94C to 96C for several seconds to minutes.

Turns double stranded DNA into two single strands

A

Denaturation

135
Q

2nd and most critical step for the specificity of the PCR

Temperature range at 50C to 70C

A

Annealing

136
Q

Third and last step of the PCR cycle

The polymerase synthesizes a copy of the template DNA by adding nucleotides to the hybridized primers

Optimal temp for this step is 68C to 72C

A

Primer Extension step

137
Q

The critical component of the PCR because they determine the specificity of the PCR

A

Primers

138
Q

The building blocks of DNA

A

Nucleotide triphosphates

139
Q

Automation of the PCR procedure was greatly facilitated by the discovery of the thermostable enzyme called

A

TAQ polymerase

140
Q

From thermus thermophilus

A

Tth Polymerase

141
Q

Fragment that lacks the N-terminal 289 amino acids of Taq polymerase and its inherent 3’ to 5’ exonuclease activity

A

Stoffel Fragment

142
Q

Provides the optimal conditions for enzyme activity

A

PCR buffer

143
Q

Binds inhibitors and stabilizes the enzyme

A

Bovine serum albumin

144
Q

Provides reducing conditions that may enhance enzyme activity

A

Dithiothreitol

145
Q

Lower the denaturing temperature of DNA with high secondary structure, thereby increasing the availability for primer binding

A

Formamide

146
Q

Designed to rapidly and automatically ramp to the required incubation temperature. holding at each one for designated periods

A

Thermal cyclers or thermocyclers

147
Q

Work with small sample volumes in chambers that can be heated and cooled quickly by changing the air temperature surrounding the samples

A

Rapid PCR

148
Q

Equipped with fluorescent detectors to measure PCR product as the reaction proceeds

A

Real-time PCR

149
Q

Isolated from the bacterium Thermus aquaticus

A

TAQ DNA polymerase

150
Q

Complementary DNA is first produced from RNA targets by reverse transcription, and then the cDNA is amplified by PCR

Requires primers such as oligo dT primers or random hexamers to prime the synthesis of the initial DNA strand

A

Reverse-transcriptase PCR

151
Q

Developed to increase both the sensitivity and specificity of PCR

Uses two pairs of amplification primers and two rounds of PCR

One primer pair is used in the first round of the amplification of PCR of 15-30 cycles. The products of the first round of amplification are then subjected to a second round of amplification using the second set of primers

The second set of primers anneal to a sequence internal to the sequence amplified by the first primer set

A

Nested polymerase Chain Reaction

152
Q

Two or more primer sets designed for amplification of different targets are included in the same PCR reaction

Using this technique, more than one target sequence in a clinical specimen can be amplified in a single tube

A

Multiplex polymerase chain reaction

153
Q

Can be accomplished by capturing or isolating each individual nucleic acid molecule present in a sample within many chambers, zones, or regions that are able to localize and concentrate the amplification product to detectable levels

Detection and quantification of low levels of pathogen sequences, expression of rare genetic sequences in single cells, and clonal amplification of nucleic acid for sequencing mixed nucleic acid samples

A

Digital polymerase chain reaction

154
Q

Detects the accumulation of amplicon after each thermal cycle in real time

A

qPCR/Real-time pcr

155
Q

Inhibits enzymes used in molecular analysis such as reverse transcriptases and DNA polymerases in vitro

A

Heparin and occasionally ACD

156
Q

Fresh specimen

A

Fluorescent in situ hybridization (FISH) and karyotyping

157
Q

A specially designed labels are available for long-term nucleic acid storage at ultra-low temparature

A

Cryotubes

158
Q

Refrigeration of blood will cause neutrophils to

A

degranulate, releasing enzymes that affect free virus particles

159
Q

Storage for viral RNA in whole blood

A

22-25 C (Room temp)

160
Q

Isolated DNA of sufficient purity can be stored at room temp for

A

Several months at rt or at least 1 year in the refrigerator

161
Q

Purified DNA can be stored at

A

Freezer temp -20C to -70C in tightly sealed tubes for up to 10 years or longer

162
Q

Serves as internal controls in FISH analyses

A

Centromere-specific probes

163
Q

Monitored daily

A

Refrigerator and freezers

164
Q

Thermometers used in monitoring thermal cyclers

With flexible probes

A

Type K thermocouples

165
Q

Monitored at least annually using tachometer

A

Centrifuges and microcentrifuges

166
Q

Tested annually to ensure delivery of accurate voltage and current

A

Power supplies

167
Q

Background measurements are required on such instruments as

A

Fluorometric detectors, luminometeres, and denitometers

168
Q

Maintenance includes scanning through the range of wavelengths used (200 to 800nm)

Must be check annually

A

Spectrophotometers

169
Q

Monitored annually for proper air flow

A

Fume hoods and laminar flow hoods

170
Q

Checked for accuracy before use and at 6-month interval

A

Pipettors

171
Q

Most conveniently supplied in lyophilized (freeze-dried) from the DNA synthesis facilities

A

Primers

172
Q

Probes, primers, antibodies, and other test components that detect a specific target

A

Analyte-specific reagents

173
Q

MOST asr’s used in the molec lab are class _

A

Class I

174
Q

Class II and III ASRs include those used by

A

Blood banks to screen for infectious diseases and those used in diagnosis of certain contagious diseases

175
Q

Use in the diagnosis of a specific disease or other condition

A

In vitro diagnostic

176
Q

Refers to the analysis of external specimens supplied to independent laboratories from a reference source

Performed atleast twice a year

A

Proficiency testing

177
Q
A

MTAP 2 BABY (5 decks)

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