This news item was created by students Rachel Bredfelt, Brian Wirth and Justin Kreuter as part of their Chemistry 212 Collaborative Group Activities in WS00 under the guidance of Prof. Rainer Glaser.

Glaser's "Chemistry is in the News"
To Accompany Wade Organic Chemistry 4/e.
Chapter 23. Carbohydrates and Nucleic Acids.


For each of the following questions, please refer to the following article:

WIDESPREAD GENETIC FINGERPRINTING UNDER DEBATE.
By Pierre Thomas et al. (CNN.com, March 1, 1999)

Editorial Comments

We are in the midst of a scientific revolution that will potentially affect every facet of society. Behind this revolution are three simple letters - DNA. The technology surrounding this amazing organic molecule has simultaneously been lauded as a scientific miracle promising to wipe out disease and hunger, and protested as the futures greatest threat to civil life and liberty. The sheer volume of controversy involving DNA serves as an indicator of the enormous impact it has had on society.

DNA is short for deoxyribonucleic acid. It is composed of small organic molecules called nucleotides. Each nucleotide consists of three units: a sugar molecule called deoxyribose, a phosphate group, and one of four different nitrogen-containing compounds called bases. A molecule of DNA consists of two chains of nucleotides linked together by dehydration synthesis to form phosphodiester bonds between the phosphate group of the 5' carbon of one nucleotide linked to the 3' hydroxyl group of the deoxyribose of the adjacent nucleotide. The four bases contained in DNA are comprised of two purines-adenine and guanine, and two pyrimidines-cytosine and thymine. These bases occur as specific sets of complimentary pairs--A will pair only with T, and G will pair only with C. The A-T base pairs are held together by two hydrogen bonds, and the G-C base pairs are held together by three hydrogen bonds. The sequence of these base pairs form unique codes that act as blueprints or instructions used to make proteins.

Everyone except identical twins has unique DNA sequences and from this arises the notion of DNA identification. Since we have about 3 billion base pairs of DNA in our chromosomes, only a small handful of sites are examined for variations during DNA fingerprinting. The DNA can be cut or "cleaved" by enzymes (restriction endonucleases) at specific sites corresponding to specific base pair sequences. This forms many DNA fragments of varying length that begin and end with those specific DNA sequences. These fragments can then be radioactively labeled and separated according to size using DNA electrophoresis. The result is a series of black bars sort of like a bar code that can be analyzed for similarities and differences. This is, in a nutshell, the theory of DNA "fingerprinting" or "typing."

Advances in DNA biotechnology have been occurring at a phenomenal pace. One of the most significant technological advances was the development of a method to amplify tiny samples of DNA through the Polymerase Chain Reaction (PCR). Interestingly, the enzyme that makes this possible was discovered from thermophillic bacteria in the hot springs of Yellowstone National Park. PCR allows a small portion of DNA to be exponentially copied making it possible to start with a sample of DNA from a single cell and get enough DNA to analyze it.

At first DNA typing was only done on blood samples to determine paternity. Quickly this technology began being used to analyze bloods stains found at crime scenes. The development of PCR revolutionized the use of DNA typing in forensics. Now, thanks to PCR, it is not only possible to analyze blood samples, but even the root of a hair or saliva from a licked envelope contains enough DNA to be analyzed!

The issue that sparks debate is whether people who have been arrested (but not necessarily convicted) should be required to give a sample of their DNA to be put into a database. There has even been a great deal of discussion about creating a national database of everyone's DNA type! The strategy is that DNA sample from crimes scenes could be analyzed and the criminal found by comparing the sample to the database. Many states in addition to the FBI have already formed DNA databases.

The accuracy of DNA analysis has been called into question. Criminal trials are likely to have the most use for such technology and conviction of the innocent is not acceptable. Dr. Tom Blake of Montana State University wrote "the accuracy of the technology is limited by the accuracy of the process, and by errors in interpretation." Furthermore, it is often up to the judge or a jury who lack the understanding of scientific methods and procedures to critically evaluate the validity of scientific evidence or the competence of a scientific witness.

Another major concern is the use of such databases for much less noble purposes. Insurance companies may use this information to deny coverage. Employers could use it to deny employment or prevent promotion. Scientists working with the Council for Responsible Genetics, a nonprofit advocacy group based in Cambridge, Massachusetts, have documented hundreds of cases in which this has happened to healthy people. Has anyone seen the movie GATTACA?

The ACLU has spearheaded the opposition of such national databases. Check out this link and read their article concerning the privacy issues of DNA databases.

The Yen & Yang nature of the possible consequences of this revolutionary technology are evident in the remarks of President Clinton as he declared during the 1996 presidential campaign that genetic testing "will enable every set of parents that has a little baby to get a map of the genetic structure of their child." The parents would then be able to "plan that child's life to organize the diet plan, the exercise plan, the medical treatment that would enable untold numbers of people to have far more full lives." Unfortunately, as Clinton also noted in the 1998 State of the Union address, the very same information can also be legally used by insurers to deny medical coverage or by companies to deny employment.

As an interesting side note, check out the progress of the Human Genome Project. Click here to learn about a possible timeline for when we may have a map of the human chromosomes.

Pertinent Text References
Chapter 16-9-11: Heterocyclic Aromatic Compounds
Chapter 23: Carbohydrates and Nucleic Acids
Chapter 23-20-23: Nucleic Acids


Questions

Question 1: Provide structures of adenine (a purine) and cytosine (a pyrimidine).

Question 2: The origin of replication in DNA is the sequence that is initially split apart to begin DNA replication. Why is it that origins of replication (such as TATA box) usually contain a high percentage of the bases A and T? (Hint: Think of the bonding of the bases.)

Question 3: Explain how two nucleotides are joined in a DNA chain.

Question 4: Gel electrophoresis is commonly used in paternity cases. Explain how this test can identify a parent.

Question 5: Give two instances in which DNA databases would be beneficial to society. Give two instances in which DNA databases would detrimental. Would you favor the establishment of a national DNA database?



Answers

Question 1: See text.

Question 2: A and T are connected by two hydrogen bonds and thus bonded less tightly that G and C which are connected by three hydrogen bonds.

Question 3: Two nucleotides are joined by the phosphate group of the 5' carbon of one nucleotide linked to the 3' hydroxyl group of the deoxyribose of the adjacent nucleotide. When this high-energy bond forms water is removed.

Question 4: DNA from the known parent, child, and possible parent are all "cut" with the same enzyme. The enzyme is very specific for where it will cut DNA. Once the DNA has been cut at places that are specific to the enzyme, the samples of DNA from all three individuals are placed in adjacent "dents" in the gel. Electricity is used to transport the DNA the length of the gel slab. After a certain amount of time the electricity is stopped and the gel is examined. Because the segments cut by the enzyme have various length and mass the smaller segments will travel farther in a given time. Thus in gel electrophoresis the relative distances traveled by the segments will show a specific pattern for a specific person. A child will have a mixture of his or her mother and father's DNA.

Question 5: Open.