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Mol Bio Lab > (M) L2.1 : Gel Electrophoresis > Flashcards

(M) L2.1 : Gel Electrophoresis Flashcards

1
Q

commonly used to separate DNA fragments from each other

A

electrophoresis

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2
Q

we use electrophoresis to see the presence and sizes of ______

A

DNA fragments

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3
Q

can be used to analyze restriction-digestion of products

A

electrophoresis

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4
Q

Electrophoresis is a method of separating __________ _________ substances in a mixture

A

electrically charged substances

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5
Q

enumerate the three electrically charged substances mentioned

A

DNA, RNA, and proteins

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6
Q

where is the sample of the mixture is placed on?

A

supporting medium

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7
Q

use this card to familiarize examples of supporting medium (or enumerate if you’re a masochist)

A

paper
starch gel
cellulose acetate
agarose gel
polyacrylamide gel

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8
Q

Selecting the type of supporting medium depends on the _____

A

experiment

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9
Q

a technique used for separation of charged molecules such as DNA, RNA, or protein molecules through liquid or gel medium according to their size and charge using an electrical current

A

electrophoresis

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10
Q

negative or positive electrode?

net positive charge migrates toward the cathode?

A

negative electrode

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11
Q

negative or positive electrode?

net negative charge move toward the anode

A

positive electrode

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12
Q

this allows the biomolecules to migrate towards the electrode of opposite charge

A

electrostatic attraction

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13
Q

the ________ in electrical field depends on its net charge, size, shape, strength of electrical field, properties of supporting medium and temperature

A

rate of migration of an ion

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14
Q

factors that affect the rate of migration of an ion

A

net charge
size
shape
strength of electrical field

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15
Q

these molecules have positive or negative charges

A

biological molecules

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16
Q

what is the charge of biological molecules in acidic conditions?

A

positively charged

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17
Q

what is the charge of biological molecules in alkaline conditions?

A

negatively charged

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18
Q

who pioneered the work on moving boundary electrophoresis in 1930?

A

Arne Tiselius

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19
Q

What did Arne Tiselius developed after moving boundary electrophoresis?

A

zone method for the purification of biomolecules

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20
Q

when was tools for DNA gel electrophoresis was developed?

A

1970

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21
Q

who developed the tools for DNA gel electrophoresis in 1970

(3 people)

A

Phil Sharp
Joe Sambook
Bill Sudgen

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22
Q

what did the inventors of the tool for DNA gel electrophoresis use?

A

agarose gel from seaweed

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23
Q

Why did Arne Tiselius develop electrophoresis?

A

to study serum proteins

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24
Q

what are the 3 parts of electrophoresis?

A

voltage
supporting medium
buffer system

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25
Q

this component of gel electrophoresis contains ions to conduct electricity

A

running buffer

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26
Q

type of electrophoresis in which supporting medium is a gel

A

gel electroforesis

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27
Q

the gel material acts as a __________ by retarding or completely obstructing the movement of macromolecules while allowing the smaller molecules to migrate freely

A

molecular sieve

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28
Q

T or F

gel electrophoresis is widely used to combine proteins and nucleic acids

A

F (used to separate)

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29
Q

what are the 2 set-ups of gel electrophoresis

A

vertical and horizontal gel electrophoresis

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30
Q

type of gel used for nucleic acids

A

agarose

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31
Q

type of gel used for smaller nucleic acid

A

polyacrylamide

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32
Q

gel structure held together by covalent cross-linking of acrylamide and N,N’-methylene bisacrylamide

A

polyacrylamide gel (PAG)

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33
Q

T or F

PAG can be used to separate DNA smaller than 1000 bp

A

F (less than 100 bp only)

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34
Q

component of discontinuous gel electrophoresis that contains a low percentage of acrylamide concentration and low pH

A

stocking gel

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35
Q

component of discontinuous gel electrophoresis that has a varying concentration of acrylamide and a higher pH

A

running / separating gel

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36
Q

T or F

in PAG electrophoresis DNA mobility observed in the gel (rate of migration) are dependent on the electrical field of strength used for the electrophoresis

A

F (it’s INDEPENDENT on the electrical field strength)

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37
Q

PAG electrophoresis depends on what?

3

A

size of analyte
pore size
concentration of acrylamide gel

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38
Q

T or F

concentration of gel is inversely proportional to the pore size

A

T

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39
Q

what should be the concentration and pore size needed for analysis of high molecular weight

A

low gel concentration, large pore

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40
Q

what should be the gel concentration and pore size for low molecular weight samples

A

high gel concentration, small pore

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41
Q

does PAG have high or low resolving power?

42
Q

measures the ability of an electrophoretic system to separate DNA molecules of similar sizes’ effectiveness of separation

43
Q

PAG or Agarose?

can accommodate larger quantities of DNA

44
Q

T or F

Extremely turbid DNA may be recovered from PAG

45
Q

T or F’

PAG are stable over the wide range of pH and temperature

46
Q

T or F

PAG can withstand high voltage ingredients

47
Q

PAG or Agarose

most effective in separating DNA fragments of varying sizes from 100 bp to 25 kb

A

Agarose (less than 100 bp lang for PAG)

48
Q

Agarose gels are formed by suspending dry agarose in _______

A

aqueous buffer

49
Q

at what temp is agarose heated?

A

100 degrees celsius

50
Q

T or F

dissolved agarose gel produces a turbid mixture

A

F (clear, clearer than your future ganern)

51
Q

At what temp does agarose solidify and form a gel

A

40-45 degrees celsius

52
Q

T or F

linear carbohydrate polymer is composed of alternating units of agarobiose, consisting of repeating units of galactose and 3,6 anhydrogalactose

A

F (repeating agarobiose, alternating galactose and anhydrogalactose)

53
Q

what is the charge of DNA and RNA molecules?

54
Q

Where does DNA pieces migrate to? anode or cathode?

A

anode (since their charge is negative, they’ll move to the positive pole)

55
Q

A procedure that separates molecules based on their rate of movement through agarose gel under the influence of an electrical field

A

agarose gel elctrophoresis

56
Q

familiarize the materials needed for agarose gel electrophoresis

A

electrophoresis chamber
agarose gel
gel casting tray
buffer
staining agent (dye)
comb
DNA ladder
sample
power supply

57
Q

wire color that represents positive electrode (anode)

58
Q

wire color that represents negative electrode (cathode)

59
Q

material for agarose gel electrophoresis

available in variety of sizes and composed of UV transparent plastic (size depends on the samples used)

A

gel casting trays

60
Q

material for agarose gel electrophoresis

placed in liquid agarose after it has been poured

61
Q

T or F

The comb can only be placed before pouring the liquid agarose

A

F (before or after)

62
Q

what does the comb produce in the hardened agarose gel?

A

series of wells

63
Q

what are the wells in the agarose for?

A

used to load / dispense the DNA

64
Q

Material needed for agarose gel electrophoresis

solution that contains the right ions to conduct electricity

A

running buffer

65
Q

What happens to DNA movement if water is used instead of running buffer

66
Q

Why is DNA movement slow if water is used instead of running buffer?

A

inefficient conduction of electricity because it has no ions

67
Q

purpose of buffer

A

resist pH changes

68
Q

most common buffer used in agarose gel electrophoresis

A

Tris buffer

69
Q

this should be your 69th card if you’re a concrete sequential learner <33

A

wala lang skl

70
Q

what does TAE stand for?

A

Tris acetate EDTA

71
Q

what does TBE stand for?

A

Tris borate EDTA

72
Q

what does EDTA inactivate?

A

DNA nucleases

73
Q

what does DNA nucleases degrade?

A

nucleic acids

74
Q

buffer mostly used for the analysis of larger samples (1500 bp and higher ; generates less current)

75
Q

buffer mostly used for smaller nucleic acid fragments

76
Q

in what for does buffers exist in?

A

neutral or cationic form

77
Q

what is the pH of TAE

78
Q

what is the pH of TBE?

79
Q

what is the pH of Tris Phosphate EDTA buffer?

80
Q

what is the pH of Tris-citrate (TCE) buffer

81
Q

what is the other name for DNA ladder

A

Molecular weight marker

82
Q

consists of known DNA sizes used to determine the size of an unknown DNA sample

A

DNA ladder

83
Q

T or F

DNA ladder contains regularly spaced sized samples which when run on an agarose gel, it resembles a ladder

84
Q

T or F

Each space on a DNA ladder represents a base pair

A

F (Each line)

85
Q

T or F

the DNA ladder depends on the manufacturer

86
Q

a set of standards used to identify the approximate size of molecule run on a gel during electrophoresis

A

DNA ladder

87
Q

These are usually generated by restriction enzyme digestion of plasmid or bacteriophage DNA

A

DNA fragments

88
Q

This runs alongside the DNA sample, usually on the first lane

A

DNA ladder

89
Q

What should be added in the sample before being loaded on the gel?

A

loading dye

90
Q

loading dye is composed of?

(2)

A

tracking dye and density agents

91
Q

use this to familiarize density agents

A

glycerol
ficoll
sucrose

92
Q

What is added to the sample to make it heavier in order for it to sink in the well

A

loading dye (because it contains a density agent)

93
Q

This component of loading dye provides a visual gauge of the progress of electrophoresis

A

tracking dye

94
Q

Does loading dye affect the separation of the sample?

95
Q

what is the other term for loading dyes?

*blue text sa trans

A

Gel loading buffers

96
Q

what are the two examples of tracking dye?

A

bromphenol blue
xylene cyanol

97
Q

A compound that can adhere to DNA and gives off fluorescent light when excited by UV light

98
Q

What is the standard concentration of DNA stain used in gels

A

0.5 - 1 ug / ml

99
Q

This inserts itself between the base pairs in the double helix

100
Q

most commonly used DNA stain

A

ethidium bromide

101
Q

safer and non-mutagenic examples of DNA stain

A

GelRed
SYBR green

102
Q

T or F

The color of the result is dependent on the type of sample, not the stain used

A

F (depends on the stain)

Mol Bio Lab (12 decks)

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