Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

biochem > (M) Gel Electrophoresis (LAB) > Flashcards

(M) Gel Electrophoresis (LAB) Flashcards

1
Q

This technique is used:
- to separate (sometimes purify) macromolecules especially proteins and nucleic acids
- to determine the presence of DNA and separate them from each other based on their size
- in DNA fingerprinting
- to analyze PCR results

A

Gel Electrophoresis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

T or F: Macromolecules don’t differ in size, only conformation

A

False (they differ in both)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

When charged molecules are within an electric field, they migrate towards an area of what charge?

A

Opposite

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

T or F: Proteins can have only have a negative charge because of their phosphate backbone

A

False (that description is for nucleic acids)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

This material in gel electrophoresis:
- has ions to carry a current
- maintains the pH at a relatively constant value

A

Buffer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

This is a polysaccharide extracted from seaweed, is non-toxic, and is to be used at concentrations of 0.5% to 2%

A

Agarose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

T or F: More agarose = stiffer gel

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

T or F: Agarose has a small range of separation but high resolving power

A

False (polyacrylamide; the opposite is for agarose)

Resolving power is the ability to differentiate two lines or points in an object

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the range of base pairs agarose can separate?

A

200 - 50,000

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

This is a cross-linked polymer of acrylamide, is to be used with concentrations from 3.5% to 20%, and is more annoying to prepare than the other kind of gel

A

Polyacrylamide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why are polyacrylamide gels more annoying to prepare than agarose?

A

O2 inhibits polymerization (they need to be poured between glass plates or cylinders)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

T or F: Polyacrylamide is a potent neurotoxin

A

False (acrylamide is the potent neurotoxin while polyacrylamide is harmless, although some acrylamide can be left out)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the range of base pairs that polyacrylamide can separate?

A

Less than 500 only (due to its low separation range)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

This is a GENERAL method of separating electrically charged substances in a mixture (DNA, RNA, proteins, etc.) where the sample is placed on a supporting medium to which an electrical field is applied

A

Electrophoresis (lang)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Which is the positive and negative terminal between anode and cathode?

A

Cathode - negative
Anode - positive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Which terminal will positively charged molecules migrate to?

A

Cathode (negative)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Which terminal will negatively charged molecules migrate to?

A

Anode (positive)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

T or F: The speed of migration depends on charge, size, and shape

A

True

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

The General Parts of Electrophoresis:
→ responsible for allowing the charged molecules to move

→ the voltage depends on the protocol

A

Voltage or power supply

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

The General Parts of Electrophoresis:
→ a fluid/aqueous solution around the supporting medium and is present within the chamber

A

Buffer system/solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

He is the Father of Electrophoresis who did pioneer work on moving boundary electrophoresis in 1930 and later developed a zone method for biomolecule purification

A

Arne Tiselius

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

T or F: Arne Tiselius, despite his contributions, did not win a Nobel prize

A

False (he did)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Arne Tiselius used this specimen for his research on electrophoresis

A

Serum

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

These three made tools for DNA gel electrophoresis in the 1970s and used agarose gel extracted from seaweed

A

Phil Sharp, Joe Sambrooke, and Bill Sugden

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

T or F: The gel material acts as a “molecular sieve” by retarding/completely obstructing the movement of micromolecules and allowing macromolecules to migrate freely

A

False (obstructs MACROmolecules while allowing MICROmolecules to move freely)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Which among the 2 gels separates large molecules?

A

Agarose (polyacrylamide is for small molecules)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Which among the gels are casted horizontally?

A

Agarose (polyacrylamide is casted vertically)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

T or F: Polyacrylamide is used for DNA or protein separations

A

True (due to its high resolving power)

*Agarose is commonly used for DNA separation only

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

When can staining be done when using polyacrylamide gel?

A

After pouring the gel

*Agarose staining can be done before or during the pouring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

At what temperature does agarose begin to solidify and become a gel?

A

40ºC

31
Q

This is a linear carbohydrate polymer composed of repeating units of agarobiose (alternating units of galactose and 3,6-anhydrogalactose)

A

Agarose

32
Q

T or F: The gelling/solidifying property of agarose is due to polymerization

A

False (that is for polyacrylamide; agarose gelling is due to both inter- and intramolecular H bonding which shifts from random coils in a solution to chains bundled into double helices)

33
Q

This piece of equipment contains black and red wires and is where the electrophoresis will occur

A

Electrophoresis chamber

34
Q

What color are the wires for the anode and cathode?

A

Cathode is black
Anode is red (this is where molecules will migrate towards)

35
Q

T or F: The buffer already comes in diluted form prior to the procedure

A

False (comes in concentrated forms; you will need to dilute)

36
Q

This adheres to DNA. gives off fluorescent light, and allows visual monitoring of how far the process has proceeded

A

Staining agent or tracking dye

37
Q

This chemical is added to the gel with a final concentration of 0.5 µg/ml to facilitate visualization after electrophoresis (this intercalates between DNA and RNA bases)

A

Ethidium Bromide

38
Q

The agarose solution is allowed to cool until what temperature before being poured into the casting tray?

A

60ºC

39
Q

These are available in many sizes, are composed of UV-transparent plastic, and is where the gel is poured

A

Gel casting trays

40
Q

T or F: The open ends of the casting trays can be enclosed with tape that can stay until the end of electrophoresis

A

False (needs to be removed before electrophoresis)

41
Q

These form wells in the gel

A

Sample combs

42
Q

What are the 2 common buffers in electrophoresis?

A
  • Tris-acetate-EDTA (TAE)
  • Tris-borate-EDTA (TBE)
43
Q

T or F: A loading buffer must contain something light

A

False (must be dense in order to sink the sample, like glycerol)

44
Q

T or F: Ethidium bromide is a mutagen

A

True

45
Q

This UV lightbox is used to visualize the ethidium bromide-stained DNA

A

Transilluminator

46
Q

There is evidence of a current if ______ are observed coming off of the electrodes

A

Bubbles

47
Q

Bromophenol blue migrates at the same rate as DNA fragments with how many base pairs?

A

300

48
Q

Xylene cyanol migrates at the same rate as DNA fragments with how many base pairs?

A

4000

49
Q

T or F: Ethidium bromide can only be incorporated after electrophoresis has took place

A

False (it can be incorporated during electrophoresis or afterwards by soaking it in dilute ethidium bromide solution)

50
Q

T or F: DNA will diffuse within the gel overtime so examination/photography should take place immediately after the process is done

A

True

51
Q
  • This is aka a molecular weight marker
  • Is placed on the first or middle well
  • Serves as a basis for the estimation of DNA size or the number of base pairs
  • Each line corresponds to DNA sizes
A

DNA ladder

52
Q
  • This is a mixture of glycerol and tracking dye to be mixed in with the sample
  • Glycerol adds density to the sample in order for it to sink into the well
A

Loading dye

53
Q

Viewing the Samples:
→ use of a UV transilluminator to view the fluorescent DNA in the gel

A

DNA detection

54
Q

Viewing the Samples:
→ dye and size must be the same to the DNA being measured

A

DNA quantification

55
Q

Viewing the Samples:
→ bands appear as compact, no double or faint bonds

A

Evaluation of the quality of DNA

56
Q

This is expressed in molecular weight equivalent to the number of base pairs

A

Molecular size

57
Q

T or F: Small fragments travel faster and farther while large fragments travel slower due to greater frictional drag

A

True

58
Q

T or F: Small fragments find other small holes in the gel to pass through

A

False (large)

59
Q

Factors that Determine Migration Rate:

A linear DNA fragment of a given size migrates at different rates with different concentrations of the gel

A

Agarose concentration

60
Q

T or F: Higher concentrations of agarose facilitates separation of larger DNA fragments

A

False (smaller)

*Lower concentrations = larger fragments
*Higher concentrations = smaller fragments

61
Q

Factors that Determine Migration Rate:

Supercoiled circular, relaxed circular, and linear DNA of the same molecular weights will migrate at different rates

A

DNA conformation

62
Q

What is the order in of DNA conformation that travels the fastest to slowest?

A

Supercoiled > Linear DS > Circular

Explanation:
- supercoiled DNA become smaller in size therefore they will have less frictional resistance and are more compact
- when supercoiled DNA is broken due to nicks or cuts, it goes back to its normal relaxed circular conformation (this is now larger and therefore has more frictional drag)
- if the circular DNA is cut, it becomes linear (this migrates at a normal speed and in accordance to size)

63
Q

Factors that Determine Migration Rate:

The rate of migration is directly proportional to this

A

Voltage

64
Q

T or F: Higher voltage = faster migration while lower voltage = slower migration

A

True

65
Q

T or F: If the voltage is too low, the gel may melt and result to sample smearing, DNA denaturation, and sample damage

A

False (high)

66
Q

T or F: Sharper resolution of larger DNA fragments for low voltages is a con

A

False (pro)

*The con is that slower migration may cause diffusion of DNA fragments

67
Q

Factors that Determine Migration Rate:

The composition and ionic strength of this affects DNA mobility

A

Electrophoresis buffer

68
Q

If _____ is used, electrical conductivity is minimal therefore DNA migrates slower

A

Water

69
Q

T or F: If a buffer with high ionic strength is used (10x) then electrical conductance is efficient

A

True (however this concentrated buffer generates more heat leading to gel melting and DNA denaturation)

70
Q

Factors that Determine Migration Rate:

→ dyes used to stain are usually intercalating agents

→ addition to the gel may retard the migration rate of DNA

A

Presence of DNA stains in the buffer

71
Q

Factors that Determine Migration Rate:

Has something to do with their melting temperature

A

Type of agarose

72
Q

This type of agarose:
→ gels at 35-38ºC and melts at 90-95ºC
→ detects DNA fragments ranging from 1,000 bps to 25,000 bps

A

High melting temperature (standard)

73
Q

This type of agarose:
→ gels at 35ºC and melts at 65ºC
→ is used for rapid recovery of DNA from the gel

A

Low melting temperature

biochem (31 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions