Is It DNA Activity
One summer vacation, I visited the widow of a cousin of mine.  Jesse Marcel (1st cousin, 3x removed) had passed away in the 1980s, but his wife lived into the 90s.  During the visit, she showed me a box engraved with the numbers "1947." The box is empty except for an 8cm x 10 cm piece of an unknown substance. It is extremely thin, silver in color, and less dense than water. The substance is so durable that it does not bend or dent.

On one side of the "metal" you notice a coating that appears to be organic. Because of Jesse's history at Roswell, I become curious as to the nature of the substance. If it came from a living organism, it should contain DNA and protein. You decide to have the mysterious coating analyzed to determine if it contains DNA and if it's human DNA.


During this investigation you will complete a three sections.
     In the first part, you will learn about the methods involved in the replication of deoxyribonucleic acid (DNA) by using polymerase chain reaction (PCR). Then you will review the technique, cycle sequencing, used to determine the nucleotide sequences in a strand of DNA. 
     In Part 2, you will submit two nucleotide sequences to a database for analysis. Based on the results, you will make conclusions regarding the source of the DNA. 
     Finally, in Part 3, you will show the relationship between DNA, RNA and protein. The assignment will be to first determine the complementary sequence of a mRNA strand that corresponds to a portion of a DNA strand. Then, you will decode the mRNA into the primary structure of the protein (sequence of amino acids). 


Part 1: DNA PREPARATION AND SEQUENCE DETERMINATION
If there is DNA in your sample, it will be first be isolated from the other substances through an extraction procedure. This is the first step in the analysis process.

After DNA has been isolated from a tissue sample, the amount of DNA in the sample must be amplified before its nucleotide sequence can be determined. During the amplification process, the DNA is replicated by a technique called polymerase chain reaction (PCR).

When a substantial amount of DNA has been produced using the PCR technique, it is possible to determine nucleotide sequences in the DNA through the use of the cycle sequencing.



FOLLOW THE DIRECTIONS BELOW TO COMPLETE PART 1:
IS IT DNA? IS IT HUMAN? WORKSHEET
NAME______________________   PERIOD________    DATE_____________

Activity 1.a

PCR
1. Describe the purpose of the polymerase chain reaction (PCR) process: 
 
 
2. Each cycle consists of three main phases. List and describe each event: 
    -
    -
    -
3. Why is it necessary to heat the DNA? 
  
4. How many copies of DNA are present after 30 PCR cycles? 

Activity 1.b

SEQUENCING

1. The following steps are involved in the sequencing of DNA using the Sanger method. Place the following events in the correct sequence from first to last. 
     ____ TAZ polymerase binds 
     ____ Electrophoresis 
     ____ DNA denatures 
     ____ The simulated gel is read from bottom to top starting with the smallest fragments 
     ____ Primers anneal 
     ____ Deoxynucleotides and dideoxynucleotides are added 
     ____ Laser beam detects color emitted from each dideoxynucleotide as fragments migrate through the gel 
     ____ Sequencing reaction loaded onto lane of polyacrylamide gel 

2. What role do dideoxynucleotides play in this procedure?
 

- Read about the extraction process by visiting the links below. 
- Visit the animated polymerase chain reaction site above and complete the Activity 1.a Worksheet. 
- Read about DNA sequencing online (links below). Then visit the animated cycle sequencing site above and complete the Activity 1.b Worksheet. 
- Submit the worksheet for the above activities to your teacher and proceed on to Activity 2. 
 

Part 2
Part 3

GLOSSARY
Amino Acid: An organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of proteins. 
Complementary: The two strands of DNA are said to be complementary to each other; that is, the sequences of bases on one strand determines the sequences of bases on the other. For example adenine pairs with thymine and guanine pairs with cytosine. Likewise, mRNA is also complementary to DNA. However, uracil replaces thymine in DNA. The DNA sequence ATTCGA would be copied by mRNA UAAGCU. 
Deoxyribonucleic Acid (DNA): A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins.
Cycle Sequencing: A method used for determining the nucleotide sequence of DNA molecules. It involves synthesizing in vitro DNA strands complementary to one of the strands of DNA being sequenced. The method is based on the random incorporation of a modified nucleotide. A series of DNA fragments is synthesized that reflects all the positions of the modified nucleotides, and thus ultimately the sequence of the DNA.
Messenger RNA (mRNA): A type of RNA synthesized from DNA in the genetic material that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
Nucleotide: Structural unit of a nucleic acid (subunit of RNA or DNA) consisting of three parts: a sugar, a phospate group, and a base (DNA: ATCG or RNA: AUCG).
Polymerase Chain Reaction (PCR): A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules and nucleotides.
Primary Structure: The level of protein structure referring to the specific sequence of amino acids.
Protein: A three-dimensional biological polymer constructed from a set of 20 different monomers called amino acids.
Ribonucleic Acid (RNA): A single-stranded nucleic acid molecule involved in protein synthesis, the structure of which is specified by DNA.

LINKS:
     - 1947 Roswell UFO Incident 
     - Roswell 1947 Incident
     - Roswell: 1947
     - 1947 Roswell UFO Encounter
     - Project 1947 - The Roswell Page 
     - Protein Structure
     - Codon Chart
     - DNA Pictures
     - DNA Learning Center
     - Transcription Animation
     - Molecular Biology Quiz: DNA to Protein
     - The Biology Project, TheUniversity of Arizona
     - Protein Synthesis
     - PCR Animation
     - Cycle Sequencing Animation
     - Recombinant DNA
     - Recombinant DNA
     - Recombinant DNA [PDF]
     - Speaking the Language of Recombinant DNA
     - Recombinant DNA Technology
     - General Requirements and Procedures for Recombinant DNA Research at Texas A&M
     - Protocols for Recombinant DNA Isolation, Cloning, and Sequencing
     - Recombinant DNA technology [PDF] (large file)
     - Recombinant DNA Technology 
     - Recombinant DNA Technology Problem Set
     - National Human Genome Research Project
     - Human Genome Project Information
     - A New Gene Map of the Human Genome
     - DNALC: Biology Animation Library
     - Genomic DNA Library
     - Cloning Genes
     - Mapping: A Hypothetical Example
     - An Introduction to Genetics
          - Genetic Engineering
          - Genetic Engineering and Bioltechnology