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BIOC 3622 - Biochemistry Lab > Genetically Modified Organisms and PCR > Flashcards

Genetically Modified Organisms and PCR Flashcards

1
Q

What is the name of today’s lab?

A

Genetically Modified Organisms and PCR

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2
Q

What is the acronym PCR?

A

Polymerase Chain Reaction

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3
Q

What is PCR?

A

DNA amplification

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4
Q

Traits possible through genetic modification include herbicidal resistance, ________, fungal resistance, and even increased _______ tolerance.

A

delayed ripening; drought

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5
Q

The ability to genetically modify crops relies on our ability as researchers to both identify and fully understand __________ with the potential to improve our target organism.

A

candidate gene

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6
Q

Using crop plants as an example, it is first important to identify and _____ (clone) for a protein that may bestow beneficial characteristic to the plant.

A

isolate

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7
Q

While the gene’s coding region may only consist of a few _____ base pairs, the inclusion of non-coding regions (introns) can extend the gene’s length well into the range of _______ or more base pairs.

A

hundred; ten thousand

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8
Q

The cloning of an entire gene can be extremely ______, and can take several ____ to complete.

A

laborious; years

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9
Q

Once a gene is successfully ____ for a ___ organism, it must be successfully _____ so that it expresses properly as part of its adopted organism’s _____.

A

cloned; host; engineered; genome

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10
Q

Given that the signals regulating expression of genes may differ greatly between the host and target organism, it is optional that the streamlined in such a way that it will properly manufacture its product regardless of its location. True or False?

A

False. It is imperative that the gene is streamlined.

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11
Q

Given that the signals regulating expression of genes may differ greatly between the host and target organism, it is imperative that the streamlined in such a way that it will properly manufacture its product regardless of its location. True or False?

A

True

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12
Q

This is achieved first by removing any _____ sections from the gene, known as ______, and replacing the gene’s native _________ and ______ sequence.

A

non-coding; introns; promoter; terminator

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13
Q

In modified genes, the promoter and terminator are specific sequences of the gene that serve as the regulatory mechanisms. True or False? If false, how would you make the statement true?

A

False. In *unmodified* genes…

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14
Q

In unmodified genes, the promoter and terminator are general sequences of the gene that serve as the regulatory mechanisms. True or False? If false, how would you make statement true?

A

False. The promoter and terminator are *specific* sequences of the gene.

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15
Q

In unmodified genes, the promoter and terminator are specific sequences of the gene that serve as the regulatory mechanisms. True or False? If false, how would you make the statement true?

A

True

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16
Q

The promoter region serves as a docking station for __________ and acts as a signal for where _________ should begin.

A

RNA polymerase; gene transcription

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17
Q

The terminator serves as a signal to _____ transcription.

A

stop

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18
Q

For genes involved in genetic modification, the natural promoters and terminators may behave unreliably within their new hosts. True or False? If false, how would you make the statement true?

A

True

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19
Q

To circumvent the problem of unreliability among the promoters and terminators, scientists can engineer the construct for a ___________ so that the foreign gene is continually transcribed, and the protein product is produced throughout the entire plant.

A

genetically modified organism (GMO)

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20
Q

For GM crops, the most common promoter is the 35S promoter from the __________ virus (CaMV 35S).

A

cauliflower mosaic

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21
Q

The most common terminator in GM crops is the _________ (___) terminator from Agrobacterium tumefaciens.

A

nopaline synthase; NOS

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22
Q

____ is the process in which a gene’s DNA sequence is copied (______) to make an RNA molecule.

A

Transcription; transcribed

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23
Q

______ is the main transcription enzyme.

A

RNA polymerase

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24
Q

Transcription begins when RNA polymerase binds to a ______ sequence near the beginning of a gene (directly or through helper proteins).

A

promoter

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25
Q

RNA polymerase uses one of the DNA strands (the _________) as a template to make a new, complementary RNA molecule.

A

template strand

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26
Q

Transcription ends in a process called _________.

A

termination

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27
Q

A second method is ______, in which an electric current creates pores within the cellular membranes to allow entry of the engineered DNA.

A

electroporation

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28
Q

A third method involves the use of a ________ that physically shoots gold particles coated with engineered DNA into the plant’s cells.

A

“gene gun”

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29
Q

Unfortunately methods 1-3 lack _____, and it is necessary to ____ and ____ cells that have been successfully transformed from those that have not.

A

efficiency; identify; isolate

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30
Q

To assist in this process, selectable markers are often inserted in addition to the engineered gene. These markers may include ______ resistance, or visual markers like the gene _______.

A

antibiotic; Green Fluorescent Protein

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31
Q

To properly identify whether or not a plant has been genetically modified, we will be using the ________________ (___).

A

polymerase chain reaction; PCR

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32
Q

The PCR reaction can identify ______ of ___ that have been inserted in the GM plant.

A

sequences; DNA

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33
Q

Because genetic engineers only use a small number of regulatory sequences (______ and _____) to control the expression of inserted genes, _____ can be used to identify a large portion of all GM crops relatively easy.

A

promoters; terminators; PCR

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34
Q

Two of the most common regulatory sequences are the _________ of cauliflower mosaic virus and the _________ of the Agrobacterium tumefaciens.

A

35S promoter; nopaline synthase terminator

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35
Q

What is step 1 to genetically modify an organism?

A

isolate plant cells

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36
Q

What is step 6 to genetically modify an organism?

A

Grow transgenic plant

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37
Q

What is step 6 to genetically modify an organism?

A

Grow transgenic plant

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38
Q

What is step 5 to genetically modify an organism?

A

Redifferentiate callus

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39
Q

What is step 2 to genetically modify an organism?

A

Grow undifferentiated cells

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40
Q

What is step 4 to genetically modify an organism?

A

Select cells

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41
Q

What is step 3 to genetically modify an organism?

A

Transform callus

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42
Q

Which two methods are used to identify which foods and crops contain GM genomes?

A

ELISA and PCR

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43
Q

What is the acronym ELISA?

A

enzyme-linked immunosorbent assay

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44
Q

What is the acronym PCR?

A

polymerase chain reaction

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45
Q

Which method identifies proteins?

A

ELISA

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46
Q

Which test identifies sequences of DNA?

A

PCR

47
Q

ELISA can test both fresh and old produce. True or false? If false, make the statement true.

A

False. It can only test fresh produce due to protein degradation during food processing.

48
Q

ELISA can test only fresh produce. True or false? If false, make the statement true.

A

True

49
Q

ELISA can test only old produce. True or false? If false, make the statement true.

A

False. It can only test fresh produce.

50
Q

ELISA is accurate yet expensive and can be performed in the field with little expertise. True or false? If false, make statement true.

A

False. ELISA is inexpensive.

51
Q

ELISA is accurate yet inexpensive and can only be performed in the field with someone that has a lot of expertise. True or false? If false, make statement true.

A

False. It can be performed in the field with little expertise.

52
Q

ELISA is accurate yet inexpensive and can be performed in the field with little expertise. True or false? If false, make statement true.

A

True

53
Q

In contrast to proteins, DNA is a relatively ____ molecule, thus DNA fragments can be isolated from highly processed foods and are sufficiently _____ to be ____ by PCR.

A

stable; intact; amplified

54
Q

In contrast to an ELISA test that is specific to a single crop, a single ____ test can detect ____ of all GM crops.

A

PCR; 85%

55
Q

Why can a PCR test detect 85% of all GM crops?

A

Only a small # of regulatory sequences (promoter and terminator) control the expression of the inserted genes, so these sequences are common to the majority of GM crops.

56
Q

When detecting GM foods by PCR, ______ is extracted from test foods, and then two __________ are performed on each test food genomic DNA sample.

A

genomic DNA; PCR reactions

57
Q

One PCR reaction uses _____ specific to a common plant gene (____) to verify that viable DNA was successfully extracted from the food.

A

primers; plant primers

58
Q

No matter whether the food is GM or not, this PCR reaction should sometimes amplify the DNA. True or false? If false, make statement true.

A

False. PCR reaction should *always* amplify the DNA.

59
Q

No matter whether the food is GM or not, this PCR reaction should always amplify the DNA. True or false? If false, make statement true.

A

True

60
Q

This PCR reaction will only amplify DNA if the test food is _____.

A

GM

61
Q

If the test food is non-GM, then the GMO primers will not be ________ to any within the test food genomic DNA and will not _____, so no DNA will be ____.

A

complimentary; anneal; amplified

62
Q

To find out whether DNA has been amplified or not, the PCR products are ______ on a gel and stained to visualize _____ as bands.

A

electrophoresed; DNA

63
Q

A ________ ruler is ________ with the samples to allow the sizes of the DNA to be ____.

A

molecular weight; electrophoresed; determined

64
Q

When detecting GM foods by PCR, ________ is extracted from test foods, and then two ______ are performed on each test food genomic _______ sample.

A

genomic DNA; PCR reactions; DNA

65
Q

One PCR reaction uses ______ specific to a common plant gene (_______) to verify that viable DNA was successfully extracted from the food.

A

primers; plant primers

66
Q

No matter whether the food is GM or not, this PCR reaction should sometimes amplify DNA. True or false? If false, make statement true.

A

False. PCR reaction should *always* amplify DNA.

67
Q

No matter whether the food is GM or not, this PCR reaction should always reduce DNA. True or false? If false, make statement true.

A

False. PCR reaction should always *amplify* DNA.

68
Q

No matter whether the food is GM or not, this PCR reaction should always amplify RNA. True or false? If false, make statement true.

A

False. The PCR reaction should always amplify *DNA*.

69
Q

No matter whether the food is GM or not, this PCR reaction should always amplify DNA. True or false? If false, make statement true.

A

True

70
Q

The other PCR reaction uses _____ specific to sequences commonly found in GM crops (GM _____).

A

primers; primers

71
Q

This PCR reaction will only amplify DNA if the test food is ___.

A

GM

72
Q

If the test food is non-GM, then the GMO primers will not be ____ to any sequence within the test food genomic DNA and will not ____, so no DNA will be ____.

A

complementary; anneal; amplified

73
Q

To find out whether DNA has been ____ or not, the PCR products are _____ on a gel and ____ to visualize DNA as bands.

A

amplified; electrophoresed; stained

74
Q

A ________ is electrophoresed with the samples to allow the sizes of the ____ bands to be determined.

A

molecular weight ruler; DNA

75
Q

In today’s lab, we see many of the times GM crop and DNA GM… What is the acronym “GM” stand for?

A

Genetically modified

76
Q

In today’s lab, it discusses something called a “callus”. What does that mean?

A

A clump of undifferentiated cells.

77
Q

How do callus cells develop roots, shoot and eventually grow into entire plants?

A

Growth hormones can be added to the media which trigger the callus to grow.

78
Q

What is 9?

A

Quantify GM content by real-time

79
Q

What is 8?

A

Food contains no GMO.

80
Q

What is 3?

A

Extract DNA

81
Q

What is 1?

A

Detect GMOs by PCR

82
Q

What is 5?

A

not viable

83
Q

What is 7?

A

Food contains GMO

84
Q

What is 4?

A

viable

85
Q

What is 6?

A

No conclusions can be made. Repeat test.

86
Q

What is 2?

A

Detect GMOs by ELISA

87
Q

What are 1 & 2 respectively?

A

Non-GM food; GM food

88
Q

What are 9 & 10 respectively?

A

455 bp; No GMO

89
Q

What are 11 & 12 respectively?

A

455 bp; 200 bp

90
Q

What are 3 & 4 respectively?

A

Extract genomic DNA; extract genomic DNA

91
Q

What are 7 & 8 respectively?

A

Plant primers; GMO primers

92
Q

What are 5 & 6 respectively?

A

Plant primers; GMO primers

93
Q

In this section of the lab, you will ___ DNA from a control ____ food and a grocery store food item, and you will test for the presence of _____.

A

extract; non-GMO; GMOs

94
Q

What are the two most commonly modified food items?

A

corn and soy based

95
Q

Which control will you process first?

A

non-GMO

96
Q

During the extraction of the food samples, you will first weigh your food sample, then ____ it with water to make a ____.

A

grind; slurry

97
Q

You will then add a tiny amount of the slurry to a _____ tube containing _______ matrix and heat it for ___ minutes.

A

screwcap; InstaGene; 5

98
Q

What are the name of the enzymes that you are releasing from the ground-up sample?

A

DNases

99
Q

What can the enzyme DNases do to DNA?

A

degrade the DNA attempting to be extracted

100
Q

The InstaGene matrix is made of ___ charged microscopic beads that _____ or grab metal ions out of solution.

A

negatively; “chelate”

101
Q

What metal ions are among being chelated?

A

Mg2+

102
Q

Why is Mg2+ required?

A

It is a cofactor in enzymatic reactions

103
Q

When DNA is released from your sample without the presence of the InstaGene matrix, the charged beads grab the Mg2+ and make it unavailable to the enzymes that would degrade the DNA you are trying to extract. True or false? If false, make statement true.

A

False. This only happens if the DNA is released from your sample *in* the presence of the InstaGene matrix.

104
Q

When DNA is released from your sample in the presence of the InstaGene matrix, the charged beads grab the Mg2+ and make it available to the enzymes that would degrade the DNA you are trying to extract. True or false? If false, make statement true.

A

False. The charged beads grab the Mg2+ and make it *unavailable* to the enzyme…

105
Q

When DNA is released from your sample in the presence of the InstaGene matrix, the charged beads avoid the Mg2+ and make it unavailable to the enzymes that would degrade the DNA you are trying to extract. True or false? If false, make statement true.

A

False. The charged beads *grab* the the Mg2+.

106
Q

What allows you to extract DNA without degradation?

A

When DNA is released in the presence of the InstaGene matrix.

107
Q

Boiling the samples _______ these enzymes.

A

destroys

108
Q

After you _____ the samples to remove the INstaGene matrix and debris, the _____ will contain the intact extracted ____.

A

centrifuge; supernatant; DNA

109
Q

What will be used as your target DNA?

A

the extracted DNA

110
Q

When DNA is released from your sample in the presence of the InstaGene matrix, the charged beads grab the Mg2+ and make it unavailable to the enzymes that would degrade the DNA you are trying to extract. True or false? If false, make statement true.

A

True

111
Q

ALWAYS process the ______ control before the test sample to reduce the risk of _____.

A

non-GMP; contamination

112
Q

PCR has 3 steps. Write them in the correct order.

A

Denature DNA.

Anneal them.

Extend them.

113
Q

The most commonly used thermostable DNA polymerase is the TAQ DNA polymerase. True or false? If false, make statement true.

A

True

BIOC 3622 - Biochemistry Lab (8 decks)

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