1. Chapter 12 DNA Technology Student Misconceptions and Concerns
DNA Technology
Student Misconceptions and Concerns
1. The roles of restriction enzymes and nucleic acid probes, as well as many other aspects of recombinant DNA techniques, rely upon a firm and comfortable understanding of basic molecular genetics. Consider addressing Chapter 12 after an exam that addresses the content in Chapters 10 and 11.
2. Students might bring some awareness and/or concerns about biotechnology to the classroom, for example, controversies regarding genetically modified (GM) foods. This experience can be used to generate class interest and to highlight the importance of good information when making judgments. Consider starting class with a headline addressing one of these issues.
Teaching Tips
1. Annual flu vaccinations are a common example of using vaccines to prevent diseases that cannot be easily cured. However, students might not understand why many people receive the vaccine every year. A new annual vaccine is necessary because the flu viruses keep evolving.
2. Genetically engineered organisms are controversial, creating various degrees and directions of social resistance. Yet, many debates around issues of science are confused by misinformation. This may be an opportunity for you to make an extra credit or regular assignment for students to take a position, one side or the other, on some aspect of this or related issues. The science would need to be accurate. Students might debate whether a food product made from GM/transgenic organisms should be labeled as such, or students can discuss the risks or advantages of producing GM organisms.
3. The origin of the name “restriction enzymes” may be of interest. In nature, these enzymes protect bacterial cells against foreign DNA. Thus, these enzymes “restrict” the invasion of foreign genetic material.
4. The ability to swap genes between prokaryotes and eukaryotes using the technologies described in this chapter reveal the fundamental genetic mechanisms shared by all forms of life. This very strong evidence of common descent is a lesson about evolution that may be missed by your students.
5. Students might think you are just making a bad joke by noting that laboratory-synthesized genes are “designer genes,” but this is a common term. Search the Internet using the keywords “designer genes,” and many scientific (and unscientific) sites will be found.
6. A genomic library of the sentence you are now reading would be all of the sentence fragments that make up the sentence. One could string together all of the words of this first sentence, without spaces between letters, and then conduct a word-processing edit placing a space between any place where an “e” is followed by the letter “n” The resulting fragments of this original sentence would look like this, and would be like a type of “genomic library.”
Age nomiclibraryofthese nte nceyouare nowreadingwouldbeallofthese nte ncefragme ntsthatmadeupthese nte nce.
7. Some Internet search programs rely upon a methodology similar in one way to the use of a nucleic acid probe. For example, if you want to find the lyrics to a particular song, but you do not know the song title or artist, you might search the Internet using a unique phrase from the song. (For example, search using “yellow submarine”.) The search engine will scan millions of web pages to identify those sites containing that particular phrase. However, unlike a nucleic acid probe, you would search for the song by using a few of the lyrics. A nucleic acid probe would search using a sequence complementary to the desired sequence.
8. Roundup Ready Corn, a product of Monsanto, is resistant to the herbicide Roundup. The general strategy for farmers is to spray fields of Roundup Ready corn with the herbicide Roundup, killing weeds but not the corn. A search of the Internet will quickly reveal the controversy associated with this and other genetically modified organisms (GMO), which can encourage interesting discussions and promote critical thinking skills.
9. As gene therapy technology expands, our ability to modify the genome in human embryos, created through in vitro fertilization, permits genetic modification at the earliest stages of life. Future generations of humans, like our crops today, may include those with and without a genetically modified ancestry. The benefits and challenges of these technologies raise issues many students have never considered. Our students, and the generations soon to follow, will face the potential of directed human evolution.

2. Recombinant DNA technology Application Techniques
DNA profiling and Forensic Science
Genomics and proteomics
Human genome project
Comparing genomes
Genome mapping techniques
Proteomics
Human Gene Therapy
We will learn
Recombinant DNA technology
Application
Techniques
DNA profiling (is used to determine whether two DNA samples come from the same individual) and Forensic Science
Genomics and proteomics
Human genome project
Comparing genomes
Genome mapping techniques
Proteomics
Human Gene Therapy

3. Recombinant DNA Technology
Modern laboratory techniques for studying and manipulating genetic material.
Scientists can modify specific genes and move them between organisms like bacteria, plants, and animals.
Biotechnology today means the use of DNA technology, methods for:
Studying and manipulating genetic material,
Modifying specific genes, Moving genes between organisms
Recombinant DNA Technology
When scientists combine pieces of DNA from two different sources (different species) to form a single DNA molecule.
Recombinant DNA technology is widely used in genetic engineering, the direct manipulation of genes for practical purposes

4. Cutting and Pasting DNA with Restriction Enzymes
Recombinant DNA is produced by combining two ingredients a bacterial plasmid and a gene of interest
To combine these ingredients, a piece of DNA must be spliced into a plasmid.
This splicing process can be accomplished using restriction enzymes which cut DNA at specific nucleotide sequences
these cuts produce pieces of DNA called restriction fragments with “sticky ends” important for joining DNA from different sources
DNA ligase connects the DNA pieces into continuous strands by forming bonds between adjacent nucleotides.
A restriction enzyme cuts the DNA into fragments between the bases G and A within a recognition sequence, producing a restriction fragment. The staggered cut yield 2-ds DNA fragments with ss ends called sticky ends
A piece of DNA strand from another source is added which has s-s ends identical in base sequence to the sticky ends of green DNA

5. Recombinant DNA Techniques
Bacteria represent the workhorses of modern biotechnology. To manipulate genes in the laboratory, bacterial plasmids
- small, circular DNA molecules that are separate from the much larger bacterial chromosome are used
- are ideal for gene cloning, the production of multiple identical copies of a gene-carrying piece of DNA
Plasmids:
Can easily incorporate foreign DNA
Are readily taken up by bacterial cells
Can act as vectors, a DNA carriers that move genes from one cell to another
Plasmids
Bacterial
chromosome
Remnant of
bacterium
Colorized TEM
To work with genes in the laboratory, biologists often use bacterial plasmids, small, circular DNA molecules that are separate from the much larger bacterial chromosome.

6. for a restriction enzyme
Cutting and pasting DNA
Recognition sequence
for a restriction enzyme
Restriction
enzyme
Sticky
end
DNA
ligase
Recombinant DNA molecule
A DNA fragment is added
from another source.
A restriction enzyme cuts
the DNA into fragments.
Fragments stick together by
base pairing.
DNA ligase joins the
fragments into strands.
A restriction enzyme cuts the DNA into fragments between the bases G and A within a recognition sequence, producing a restriction fragment. The staggered cut yield 2-ds DNA fragments with ss ends called sticky ends
A piece of DNA strand from another source is added which has s-s ends identical in base sequence to the sticky ends of green DNA

7. Using recombinant DNA technology to produce useful products
Plasmid
Bacterial cell
Isolate
plasmids.
Some uses
of genes
Gene for pest
resistance
Inserted
into plant
Gene for
toxic-cleanup
bacteria
Genes may be
inserted into
other organisms.
Find the clone with
the gene of interest.
The gene and protein
of interest are isolated
from the bacteria.
Clone the bacteria.
Recombinant bacteria
Bacterial clone
Gene of interest
Recombinant DNA plasmids
Bacteria take up recombinant plasmids.
Harvested
proteins may be
used directly.
of proteins
Protein for
“stone-washing”
jeans
DNA
Cell containing
the gene of interest
Protein for dissolving
clots in heart attack
therapy
DNA.
DNA fragments
from cell
Cut both DNAs
with same
enzyme.
Gene of
interest
Other
genes
Mix the DNAs and
join them together.
Figure 12.8 Using recombinant DNA technology to produce useful products (Step 8)
A rec-DNA is crated by combining a bacterial plasmid and the gene of interest, to understand how these DNA molecules are spliced together, one should know how enzymes cut and paste DNA
How can a researcher obtain DNA that encodes a particular gene of interest?

8. Applications of DNA Technology :
From Humulin to Foods to “Pharm” Animals
DNA technology is used to produce medically valuable molecules, including:
Humulin is human insulin produced by genetically modified bacteria
Human growth hormone (HGH)
The hormone EPO (Erythropoietin), which stimulates production of red blood cells
Vaccines,  harmless variant of a disease - causing microbe 
(bacteria or virus) that is used to prevent an infectious disease.

9. The modified organisms have acquired one or more genes artificially.
Applications of DNA Technology: Genetically Modified Foods
DNA technology is improving productivity of agriculture and quickly replacing traditional plant-breeding programs
The modified organisms have acquired one or more genes artificially. 
If the new gene is from another organism (another species) the recombinant organism is  called a transgenic organisms.
In the United States today, roughly
one-half of the corn crop and over
three-quarters of the soybean and
cotton crops are genetically modified

10. Applications of DNA Technology: GM Foods II
“Golden rice” has been genetically modified to contain beta-carotene.
Our bodies use beta-carotene to make vitamin A.

11. Applications of DNA Technology: “Pharm” Animals
While transgenic plants are used today as commercial products, transgenic whole animals are currently only in the testing phase.
These transgenic sheep carry a gene for a human blood protein.
This protein may help in the treatment of cystic fibrosis.
While transgenic animals are currently used to produce potentially useful proteins, none are yet found in our food supply.
It is possible that DNA technology will eventually replace traditional animal breeding.
Transgenic animals raised for the purposes of producting pharmaceuticals are called pharm animals

12. DNA Profiling and Forensic Science
Forensics the scientific analysis of evidence from crime scenes, has been revolutionized by DNA technology.
DNA profiling is used to determine whether two DNA samples come from the same individual.
To produce a DNA profile, scientists compare genetic markers, sequences in the genome that vary from person to person
Investigating Murder, Paternity, and Ancient DNA
DNA profiling (DNA fingerprinting) can be used to establish innocence or guilt of a criminal suspect, identity victims, determine paternity, identify illegally exported animals products, trace the evolutionary history of organisms and contribute to research.
Trace the evolutionary history of organisms: DNA extracted from 27,000 years old Siberian mammoth was 98.6% identical to modern African elephants
A 9,000 years-old cheddar man skeleton provided evidence he was a direct ancestor of a present-day school teacher who lived only half a mile from the cave

13. Overview of DNA profiling
Collect cells
Extract DNA
Cut the DNA in fragments using the same restriction enzyme
4. Separate the fragments using gel electrophoresis
Crime scene
Suspect 1 1
Suspect 2
DNA isolated 2
DNA amplified 3
DNA compared
Figure
Figure Overview of DNA profiling (step 3)

14. Profiling Techniques
The Polymerase Chain Reaction (PCR)-specific segment of DNA is targeted and copied. Scientists can obtain enough DNA in blood or tissues to allow profiling.
Short Tandem Repeat (STR) Analysis- used to compare genomes in two samples to prove they came from the same person. This is used by a series of short sequences (Repetitive DNA) that is repeated many times one after another.
Gel Electrophoresis - Comparing length of DNA fragments by sorting  macromolecules. 

15. Profiling Techniques: The Polymerase Chain Reaction (PCR)
Is a technique to copy quickly and precisely any segment of DNA and
Can generate enough DNA, from even minute amounts of blood or other tissue, to allow DNA profiling
a single DNA molecule can be replicated in a test tube to make 30 million identical copies in a few hours

16. Polymerase Chain Reaction: DNA Replication in a Test Tube
Exponential Increase in the Number of DNA Molecules each Cycle

17. Profiling Techniques: Short Tandem Repeat (STR) Analysis
How do you test if two samples of DNA come from the same person?
Repetitive DNA:
Compares dozen of short segment of repetitive sequences, present in multiple copies, that makes up much of the DNA that lies between genes in humans
Short tandem repeats (STRs) are short sequences of DNA that are repeated many times, tandemly (one after another), in the genome
Used as a method of DNA profiling by comparing the lengths of STR sequences at certain sites in the genome

18. Short tandem repeat (STR) sites
Crime scene DNA
Suspect’s DNA
Same number of
short tandem repeats
Different numbers of
STR site 1
STR site 2
AGAT
GATA
STR sites contain tandem repeats of 4-nucleotide sequences. The number of repetitions at each site vary from individual to individual. Here, both the samples have same number of repeats (7) at first site but different numbers in the second site
STR sites contain tandem repeats of 4-nucleotide sequences. The number of repetitions at each site vary from individual to individual. Here, both the samples have same number of repeats (7) at first site but different numbers in the second site

19. Gel Electrophoresis STR analysis compares the lengths of DNA fragments
Uses gel electrophoresis, a method for sorting macromolecules - usually proteins or nucleic acids—primarily by their electrical charge and Size
The DNA fragments are visualized as “bands” on the gel.
The differences in the locations of the bands reflect the different lengths of the DNA fragments.
Mixture of DNA
fragments of
different sizes
Power
source
Gel
Completed gel
Band of
longest
(slowest)
fragments
shortest
(fastest)

20. Visualizing STR fragment patterns
Difference in the locations of the band reflect the different length of DNA fragments
Provide evidence that crime scene DNA did not come from the suspect
Amplified
crime scene
DNA
suspect’s
Longer
fragments
Shorter
Figure Visualizing STR fragment patterns

21. Genomics and Proteomics
Genomics  the study of complete sets of genes. Bacteria were the first targets of genomics. As of 2009, the genomes of nearly 1000 species have been published, including Baker’s yeast, Mice, Fruit flies, Rice and Sorghum
Genome - Mapping Techniques
The whole- genome shotgun method involves sequencing DNA fragments from an entire genome and then assembling the sequences.
Proteomics
The systematic study of the full set of proteins found in organisms.

22. The Human Genome Project
In 1990 an international consortium of government-funded the Human Genome Project. The goal was to sequence the human genome so scientists could have roadmap for finding genes
Completed in 2004:
Over 99% of the genome had been determined to % accuracy
3.2 billion nucleotide pairs were identified, about 21,000 genes were found and about 98% of the human DNA was identified as noncoding
The Human Genome Project can help map the genes for specific diseases such as:
Alzheimer’s disease
Parkinson’s disease

23. Genome-Mapping Techniques
Genomes are most often sequenced using whole-genome shotgun method in which:
The entire genome is chopped into fragments using restriction enzymes
The fragments are cloned and sequenced
Computers running specialized mapping software reassemble the millions of overlapping short sequences into a single continuous sequence for every chromosome—an entire genome
Begun in 2006, the Human Variome Project:
Seeks to collect information on all of the genetic variations that affect human health
Chromosome
Chop up with
restriction enzyme
Sequence
fragments
DNA fragments
Align
Reassemble
full sequence

24. Human Gene Therapy What is it?
Human Gene Therapy a recombinant DNA procedure intended to treat disease by altering an afflicted person's genes.
How?
Some cases, a mutant version of a gene is replaced or supplemented with the normal allele. Or replaced
long enough to fix the medical problem.

25. Human gene therapy: HUMAN GENE THERAPY Is a recombinant DNA procedure
Seeks to treat disease by altering the genes of the afflicted person
Often replaces or supplements the mutant version of a gene with a properly functioning one
Normal human
gene isolated
and cloned
gene inserted
into virus
Virus injected
into patient with
abnormal gene
Healthy person
Harmless
virus (vector)
Virus containing
normal human gene
Bone
marrow
Bone of person
with disease

26. Ethics of DNA Technology
Controversy over Genetically Modified Food
The debate about genetically modified crops centers on whether they might harm humans or damage the environment by transferring genes through cross-pollination with other species.
Ethical Questions raised by DNA Technology
Some ethical questions are how far should we take technology?
Some controversies are whether or not it is morally right to know your DNA when you are born and have a DNA profile, and how private that would be.
Also whether or not parents should be able to give their child who has dwarfism a growth hormone to make them grow.
Scientist are still weighing out the positive and negative effects of DNA technology.

27. The diagram here summarizes _____.
A) how a gene is cloned
B) how a human could be cloned
C) human gene therapy
D) how a vaccine is made
E) how viruses can cause disease
Answer: C
Skill: Knowledge/Comprehension

28. Please read the following scenario then answer the following question(s).
Molecular biologists have perfected DNA fingerprinting so that it is possible to use the technique to provide evidence to solve crimes and even identify a child's parents. Recently, a U.S. immigrant asked the U.S. Citizenship and Immigration Services for permission to have her young daughter who was living with grandparents in their homeland join her. Her request was denied because there was an apparent mix-up with the child's birth certificate and it could not be used as proof of maternity. Proof is required in cases such as this. The mother requested DNA fingerprinting to make her case. Samples of DNA were taken from the mother (Mom) and daughter (D1) as well as from another daughter (D2) and a son (S) living in the United States with her. Tandem repeat analysis was run on the four samples, and the results are shown here.

29. 1) The results indicate that ______.
A) she is not the mother of the son
B) she is the mother of daughter D1
C) she is not the mother of daughter D1
D) daughter D1 and daughter D2 are identical twins
E) the mother could not be the mother of both daughter D1 and daughter D2