Mastering Biology: Chapter 20 Biotechnology

The sticky end of the DNA restriction fragment shown here will pair with a DNA restriction fragment with the sticky end _____.

-ACGT

Part complete During which step in the PCR cycle do primers form bonds with a single-stranded template?

Annealing.

This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 2?

C

This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 1?

B

Part complete In recombinant DNA experiments, what is used to cut pieces of DNA and what joins the resulting fragments to form recombinant DNA?

a restriction enzyme ... DNA ligase

Which of the following is an example of "recombinant DNA technology?"

introducing a human gene into a bacterial plasmid

The allele that causes cystic fibrosis is recessive. An individual who is heterozygous for cystic fibrosis

is a carrier

Gel electrophoresis separates DNA fragments on the basis of what characteristic?

length

According to the producers of the genetically modified salmon, the meat _____.

looks and tastes the same as unmodified salmon

cDNA is synthesized from what molecule using an enzyme known as what?

mRNA ... reverse transcriptase

In gel electrophoresis DNA molecules migrate from _____ to _____ ends of the gel.

negative ... positive

Which of the following is LEAST likely to be a health problem for someone with cystic fibrosis?

obesity

If someone is a carrier of a recessive genetic disorder, it means he or she has __________ of the allele, and __________ exhibit symptoms of the disorder.

one copy; does not

What is the most commonly used vector for introducing transgenes into plants?

the Ti plasmid

Part E

the profile from suspect 2 matches the crime scene

Which of the four treatments was the control for the experiment?

the wild-type mouse

As you read the post, think about what the writer's agenda might be with regard to GMOs. What seems to be the main purpose of the blog post?

to convince the public that genetic engineering is not the solution to citrus greening

The questions below will help determine which restriction enzyme should be used to make a plasmid that contains both an intact vgp gene and a functional ampR gene. Answer questions 1-4 by selecting from the answer choices on the left. Drag the correct answer to the right of each question.

1. BamHI, HaeIII, and HindIII 2. BamHI, EcoRI, and HaeIII 3. BamHI, EcoRI, and HindIII 4. BamHI only

In this example the marker DNA includes fragments that have 23,130, 9,416, 6,557, 4,361, 2,322, 2,027, and 564 base pairs. Approximately how many base pairs are in the DNA fragment indicated by the letter A?

6,557

The fish in the video have been genetically engineered to _____.

grow faster

Which enzyme(s) will produce a DNA fragment that contains the entire vgp gene (shown in red) and has "sticky ends"? Select all that apply.

- BamHI - HindIII

Part D

A

DNA fragment B consists of _____ base pairs.

1,405

Which of the following conclusions do the data support? Select all that apply.

- A different set of genes is transcribed in cells from patients in Group I compared to cells from patients in Group II. - For some genes, there is variation in the amount of mRNA present, even among patients in the same group. - If you were given microarray data from the cells of a new patient belonging to either Group I or Group II, you would probably be able to tell which group the patient belongs to.

Which of the following is a concern expressed by opponents of the use of genetically modified (GM) food crops?

- The protein products of transgenes in GM food crops might lead to allergic reactions in human consumers. - GM food crops might pass their new genes to close relatives in nearby wild areas.

If Sophie conceives a child, and the father neither has cystic fibrosis nor is a carrier, what are the chances that the child would have cystic fibrosis?

0%, because the child must receive the bad gene from both parents

Drag the labels onto the table to indicate whether each patient is likely to have AML, ALL, or neither.

17. ALL 18. neither 19. ALL 20. AML

Assign a numerical score for each category. Then add up the total score. (The highest possible score is 6; the lowest is 0.) In what range does this source fall?

2 to 4

If Sophie has a brother or sister from the same parents, what are the chances that sibling would have cystic fibrosis?

25%

How many DNA molecules would there be after four rounds of PCR if the initial reaction mixture contained two molecules?

32

On a scale of 0 to 6, where 6 is the most trustworthy, how would you rate this site? (Note that all responses will be marked as "correct" at this point.)

5-6 (very trustworthy)

What is the polymerase chain reaction (PCR)?

A method to amplify a fragment of DNA.

What is genetic cloning?

A method to produce many copies of a gene

Which of the following is true of stem cells?

All of the above

What enzyme forms covalent bonds between restriction fragments?

DNA ligase

To accomplish the screening, researchers synthesize a single-stranded DNA probe using vgp mRNA as a template. What will be the sequence of nucleotides in the probe? Drag the labels to their appropriate locations in the probe. Labels can be used once, more than once, or not at all.

DNA probe 5' - TCACACTG...GAATTCAT - 3'

Which of the following do you think contributed the most to the success of Rhys' gene therapy?

Doctors were replacing only one gene, and they only had to insert that gene into bone marrow cells.

Which of these DNA molecules is the shortest?

E

During which step in the PCR cycle are nucleotides used?

Extension.

True or false? The Taq enzyme is a type of DNA polymerase that allows researchers to separate the DNA strands during the annealing step of the PCR cycle without destroying the polymerase.

False

True or false? The use of growth hormone isolated from cadavers was banned mainly because there were not enough cadavers to supply the hormone.

False

Which of the following statements best describes the function of reverse transcriptase?

It makes complementary DNA (cDNA) from mRNA.

What defect causes pituitary dwarfism?

Lack of growth hormone

Which of the following steps would be performed last when screening a cDNA library?

Match the region of radioactivity on the filter with the corresponding plate.

Look more closely around the web page. Click the "serious risks" link in the fourth paragraph; then click the "scientific review" link in the sixth paragraph. What do you find when you click these two links?

One links to another page on the CFS web site, and one links to a paper in a peer-reviewed journal.

What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?

Only about 35% of the control amount of Hoxd13 mRNA was produced.

What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?

Only about 60% of the control amount of Hoxd13 mRNA was produced.

Now, search for information on GMOs on at least two other web sites, including the United States Department of Agriculture (USDA.gov) and the World Health Organization (WHO.int). Is the information provided by these sites consistent with what you found on the CFS web site?

Other sites discuss both the risks and benefits associated with GMOs.

Part B

PCR

As a first step in testing these two hypotheses, the researchers planned to compare data from pairs of patients. The table below identifies the patient pairs under study. Drag the labels onto the table to identify which hypothesis is being tested in each comparison and what result you would predict.

Patient 1 vs. Patient 10 Group 1: Patients with high topoisomerase II expression will respond to etoposide Group 2: Patient 1 Patient 6 vs. Patient 16 Group 1: Patients with low HOXA9 expression will survive better Group 2: Patient 6 Patient 3 vs. Patient 10 Group 1: Patients with low HOXA9 expression will survive better Group 2: Patient 10

Part A

Phosphate

How can large quantities of protein be produced from a bacterial colony containing the gene of interest?

Put a cDNA encoding the protein into a plasmid with a bacterial promoter sequence.

Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?

Quantitative data about Hoxd13 mRNA levels would have been missed.

A researcher is preparing to insert a human gene of interest into a bacterial plasmid in order to clone the human gene. She has genetically engineered the plasmid to carry a gene amp R , which confers resistance to the antibiotic ampicillin. She will include ampicillin in the plating medium when she grows the recombinant bacteria. Why has she engineered the plasmid to include an antibiotic resistance gene? Choose the best answer.

Recombinant bacteria that have taken up the plasmid can be recognized because they are able to survive in the presence of ampicillin.

Now scan the post to find the name and credentials of the person who wrote it. What is the affiliation of the writer?

She is on staff at the Center for Food Safety (CFS).

What are the first 11 nucleotides in the flow-gram shown, starting from the left? Enter your answer without spaces. (Ignore the very short lines.)

TCAGCGTAAGG

The vertebrate Pax-6 gene product (the PAX-6 protein) triggers a complex program of gene expression resulting in formation of the vertebrate eye, which has a single lens. The fly Pax-6 gene leads to formation of the compound fly eye. When scientists cloned a mouse Pax-6 gene and introduced it into a fly embryo, it led to formation of the compound eye of a fly. What did scientists induce from this?

The Pax-6 genes of flies and mice arose from an ancestral gene in a common ancestor.

Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?

The blue stain is generally lighter than in the control, but all four digit zones are still visible

Why is Suspect 1 considered more likely to have committed the crime than Suspect 2?

The crime scene sample contains DNA fragments from both the victim and Suspect 1

How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?

The digit zones are not visibly stained as they are in the control and the paw lacking B and C.

How does the company raising these fish claim to prevent the genetically modified fish from breeding with wild fish?

The genetically modified fish are sterile.

You are a member of the jury for a murder case. The prosecution has presented DNA evidence linking the defendant to the crime scene. The defense claims that DNA evidence using STR analysis with 13 markers is not sufficient to reliably distinguish between people. What do you think?

The prosecution is right. STR analysis with 13 markers gives a 1 in 10 billion or greater chance that two people will have the same pattern. This person was at the crime scene.

Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?

The spatial patterns of Hoxd13 gene expression in the paws would have been missed.

If the template strand has two or more identical nucleotides in a row, their complementary nucleotides will be added one after the other in the same flow step. The labels on the vertical axis of the flow-gram indicate how many of the same nucleotide in a row are detected; for example, where a peak for C extends into the 3 region, it indicates 3 Cs in a row, or CCC. How are two or more of the same nucleotide (in a row) detected in the flow-gram?

They show up as a higher peak in the flow-gram.

Cold case detectives are investigating a homicide that took place 30 years ago. In reexamining the evidence, they find a tiny spot of blood on the victim's clothing that was likely left by the murderer. The DNA in the blood has partially degraded over time. What technique(s) would the blood lab technicians use in their examination of this tiny, degraded blood sample?

They would use PCR to amplify the DNA.

True or false? Comparison of the sequences of the same gene across species can give some insight into the existence of a common ancestor with that gene.

True

True or false? The term "sticky ends" refers to the overhanging ends on DNA that are generated by restriction enzymes, which can base pair with any DNA molecules that contain complementary sticky ends.

True

Archaeologists unearthed a human skull with a small dried fragment of the scalp still attached. They extracted a tiny amount of DNA from the scalp tissue. How could they obtain sufficient DNA for an analysis of the ancient human's genes?

Use the polymerase chain reaction.

What information can not be obtained from the sequence of a gene?

Whether the gene is methylated.

To help sort out those bacteria that have the vgp gene, scientists first attempt to grow the bacteria both in a medium with ampicillin and in a medium without ampicillin. Demonstrate your understanding of this step by sorting the four bacterial classes based on where they will grow. Drag the icon for each bacterial class to the appropriate bin.

Will grow only in medium without ampicillin; - No plasmid Will grow in both media; - Recombinant plasmid but no vgp gene. - Recombinant plasmid with vgp gene. - Nonrecombinant plasmid

The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?

Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.

The modified salmon were created by _____.

adding genetic material from a Pacific salmon and an eel-like fish

What concerns do some consumer groups have about genetically modified fish?

all of the above

In order to insert a human gene into a plasmid, both must _____

be cut by the same restriction enzyme

In this example the marker DNA includes fragments that have 23,130, 9,416, 6,557, 4,361, 2,322, 2,027, and 564 base pairs. Approximately how many base pairs are in the DNA fragment indicated by the letter B?

between 6,557 and 4,361 base pairs

Theoretically, which of the following diseases should be the easiest to treat through gene therapy, considering the targeted organs and tissues where the corrected gene must be delivered?

diabetes, since the target cells are found only in the pancreas

For the first time, the U.S. Food and Drug Administration is considering whether to allow the sale of _____.

food from a genetically altered animal

Which "ingredients" for PCR and for the dideoxy chain-termination method of DNA sequencing are the same?

free nucleotides, DNA polymerase, DNA primers

If cells from a carrot are removed and placed in a culture medium, they can develop into a normal adult plant. This demonstrates that carrot cells _____.

retain all the genes that were in the zygote that developed into the original plant

The unpaired nucleotides produced by the action of restriction enzymes are referred to as _____.

sticky ends

Part C

the DNA will move up the gel