Chemical Science Lesson Plan

Title: DNA and Genetic Testing

Grade Level: High School

Prepared by: Pat Shapley
Science standards

Science background

Introduction

Activity procedure

Materials

Summary and discussion


Objectives: This is a classroom activity that will help students understand
  • hydrogen bonding between DNA base pairs
  • how pieces of single strand DNA (cut by restriction enzymes) can be used to sequence DNA
  • that certain genetic diseases can be diagnosed through DNA sequencing


Science standards

12.A.5b Analyze the transmission of genetic traits, diseases and defects.

13.A.4c Describe how scientific knowledge, explanations and technological designs may change with new information over time (e.g., the understanding of DNA, the design of computers).

Science background

Nucleic Acids

Nucleic acids are biopolymers formed of nucleotides, molecules containing a sugar, a base and a phosphorous group.

The sugars used in forming the nucleotide background are the five-carbon sugars ribose and deoxyribose. As the names suggest, the difference between the two structures is the presence or absence of an oxygen.




Within the nucleotide, there is a glycosidic bond attaching the sugar to the base and an ester bond attaching the phosphorous to the sugar.

A nucleotide monomer is shown here.

The two nucleic acids important to living systems are DNA, which stores the genetic information of our cells, and RNA, which helps to transform the genetic information from storage in DNA to proteins that can be used for life, and also serves as the genetic storage medium for viruses.

DNA stands for deoxyribonucleic acid, and, as the name suggests, the principle sugar in its backbone is deoxyribose.

RNA, containing ribose rather than deoxyribose, is short for ribonucleic acid.

The bases attached to the sugars by glycosidic bonds are guanine, thymine (found only in DNA), cytosine, alanine, and uracil (found in RNA only). The structures are shown below.



RNA is only a single long strand of nucleotides, but in nature DNA is stored as two complementary strands, held together by hydrogen-bonding between the bases. Thymine bonds to adenine and guanine bonds to cytosine, and the two hydrogen-bonded strands take on the famous 'double helix' formation.

DNA extraction

To isolate DNA, the first step is to free it from the cell membranes and walls that hold everything inside the cell. A blender works well for this. Because cell walls are harder to break than cell membranes, it is easier to obtain DNA from animal cells than plant cells.

Adding a buffer and a detergent is the next step. The detergent breaks up the lipid membranes from the cell, making the extraction easier, and destroys enzymes that break down DNA. The buffer solution, at a pH of about 8, stabilizes the DNA.

After filtration, the DNA can be precipitated from the solution using cold ethanol, in which it is insoluble.

DNA sequencing

DNA can be identified and sequenced by several methods. In one of these, the DNA is clipped into pieces using enzymes. Each of the pieces is amplified, that is many copies of made of each piece. Then the pieces are "fitted" together. The sequence determined because enough of the pieces overlap that there is a single way of fitting them together.

Of course the sequencing is typically performed by instruments. In our activity, we'll use paper DNA fragments and fit them together by hand.

Ribozymes and Deoxyribozymes

A ribozyme is a strand of RNA that can act as a catalyst in a chemical reaction. Before the discovery of ribozymes (also called catalytic RNA, RNA enzymes, or simply RNAzymes) by Thomas Cech and Sydney Altman in the 1980s, the only known biological catalysts were enzymes, and it was commonly thought that biological reactions could not be catalyzed without proteins. The two scientists independently found that some RNA was able to alter its structure by cutting out or putting in sequences, and there didn't seem to be any protein component involved. A number of RNAzymes capable of cleaving other pieces of RNA have since been discovered in the cell or produced artificially in the laboratory, and Cech and Altman won the 1989 Nobel Prize in chemistry for their discovery.

Once RNA had been found capable of catalytic activity, the next obvious step was to look for DNAzymes. In the cell DNA is used for information storage, rather than in any sort of production capacity, and no natural deoxyribozyme has been discovered. In the laboratory, however, DNAzymes capable of catalyzing various biological reactions have been created, and current research in using DNAzymes as biosensors is underway.

Introduction

Spontaneous changes in sequence of the nucleotides in DNA are common. That is how organisms change over time. These changes continue in the next generation when the organism reproduces. Most of the time these changes cause no problems but some changes cause serious damage.

There are many human diseases that are associated with a disorder in a single gene. Certain types of kidney disease, Marfan syndrome, sickle cell anemia, and Huntington's disease are examples of this.

In this activity, you will work in teams to sequence a section of double-stranded DNA from single strand fragments. You will compare the sequence of the full reference strand with the one you have. If you find more than 1 sequence error relative to the reference strand in this portion of DNA, the subject would have a high likihood of having a genetic disease.

Your research question: Does the subject have a genetic disease?

Materials

Part 1: nucleotides. Download 1 copy for each group. Cut these out carefully around the hydrogen bond donors and acceptors.

Part 2: Strands Groups 1-3. Cut out the fragments for each group and scramble them.

tape

Comparison genome

    G-C-A-A-C-T-T-C-T-G-A-C-A-T-C-G-A-C-A-A
    C-G-T-T-G-A-A-G-A-C-T-G-T-A-G-C-T-G-T-T-


Activity procedure

Work in groups of 3. Take a packet of nucleotides. Fit them together and make base pairs using tape. Draw lines to show the hydrogen bonding interactions.

Take the fragments for your segment of DNA and put them together to make double stranded DNA.

With your strand and the strands from other groups, decide how many errors there are in this individual's DNA code.

Summary and discussion

  1. Hydrogen bonds are significantly weaker than covalent or ionic bonds. How do these interactions able to hold DNA strands together?

  2. DNA analysis is a very rapid process on television shows (CSI, NCIS, etc.). Is this realistic? What are some possible problems in DNA analysis?

  3. Genetic testing is becoming more and more common. In your opinion, should we test routinely for genetic diseases when there is no currently available cure?
EnLIST Chemistry Workshop, University of Illinois, 2010