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					CHAPTER 14: DNA: THE GENETIC MATERIAL
WHERE DOES IT ALL FIT IN?

Chapter 14 takes the general principles of inheritance and looks deeper at the molecular structure of
DNA. It also provides the basic foundations for understanding protein synthesis. This chapter is a
connector for Chapters 13 and 15. So, it is important that students have a fresh understanding of
Chapters 13 and 14 before moving into the molecular biology of genetics coverage. This information
is also critical for building a picture of the mechanisms driving natural selection.

SYNOPSIS

Scientific advances are a result of proper experimental design mixed with insight and a little luck.
The events leading to the discovery of DNA as the material of heredity are especially good examples
of how individual experiments build upon one another to answer a larger scientific question. Among
the first experiments were those that indicated that the hereditary material was stored within the
nucleus of every cell. Although this now seems intuitive, there are many structures within a cell that
segregate during meiosis other than the chromosomes. The role of the nucleus was further clarified
by observing embryonic development after physical manipulation of the nucleus. Several different
kinds of experiments were performed to prove that the hereditary material was nucleic acid rather
than protein. Among these were the Griffith and Avery experiments in which nonvirulent bacteria
were made virulent by a nonprotein-transforming principle. The Hershey Chase experiments
indicated that it was the DNA within viruses and not their protein exteriors that was the infecting
material that killed bacteria.

Chemical analysis of nucleic acids illustrated their structure but did not hint as to how these units
were assembled into a working blueprint. Chargaff determined that DNA was not a simple repeating
polymer and that the proportions of the adenine and thymine nitrogenous bases were always equal as
were the proportions of guanine and cytosine. X-ray diffraction of impure samples of DNA by
Rosalind Franklin gave Watson and Crick sufficient information to construct their three-dimensional
model of the DNA molecule. A key point of the model was the complementarity of the DNA strands,
a result of the bonding of their bases, adenine to thymine and guanine to cytosine. The Watson-Crick
DNA model consists of two complementary phosphodiester strands wound around each other
forming a double helix. The two phosphodiester strands are anti-parallel with the bases oriented
within the molecule. The two strands are held together by hydrogen bonds forming between the
complementary bases.

The Meselson Stahl experiments began to explain DNA replication by determining that it was a
semiconservative process; each strand served as a template for the production of a new one and each
old and new strand then intertwined to become a new helix. DNA replication is a complex process
involving many enzymes (DNA polymerases, primase, helicase, ligase, etc.). At the replication fork,
several of these enzymes form a complex assemblage known as the replisome. Furthermore, double-
stranded DNA replication is complicated since new nucleotides must be added to both the 5’ to 3’
strand and the 3’ to 5’ strand at the same time, but DNA polymerase can only add onto the 3’ end.
The 5’ to 3’ or leading strand is replicated simply by adding nucleotides as the old strands unzip. The
3’ to 5’ lagging strand is replicated in batches via discontinuous synthesis. Segments called Okazaki


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fragments are made in the usual way. These fragments are then connected by phosphodiester bonds
by DNA ligase. Since one strand is processed continuously and the other discontinuously, replication
as a whole is semidiscontinuous.

The relationship between DNA and proteins was determined by Beadle and Tatum using nutrient
deficient strains of mold. They found that each mutated gene was responsible for the production of a
single enzyme in a biochemical pathway and postulated the one gene-one enzyme hypothesis. Later
experiments showed that the proteins coded for by DNA were composed of amino acid units strung
together; somehow the sequence of DNA was related to the protein sequence of amino acids.

LEARNING OUTCOMES

   Describe the experiments that first supported the hypothesis that a cell’s hereditary material
    is located in the nucleus.
   Understand the theory and conclusions associated with the Griffith and Avery experiments using
    Pneumococcus and mice.
   Explain the evidence that supports the identity of DNA as hereditary material.
   Identify the three subunits of DNA and describe how they are put together to construct an intact
    molecule.
   Understand the importance of Chargaff’s rules and the complementary nature of nucleotide
    bases.
   Describe Watson and Crick’s three-dimensional model of DNA based upon Franklin’s X-ray
    crystallography.
   Know what is meant by semiconservative replication of DNA and how it was determined.
   Explain the process of semidiscontinuous replication in both strands of the DNA double helix.
   Understand the one gene-one polypeptide hypothesis and the experimental evidence behind it.


COMMON STUDENT MISCONCEPTIONS

There is ample evidence in the educational literature that student misconceptions of information
will inhibit the learning of concepts related to the misinformation. The following concepts
covered in Chapter 14 are commonly the subject of student misconceptions. This information on
“bioliteracy” was collected from faculty and the science education literature.

       Students have trouble distinguishing chromatin from chromosomes
       Students do not fully understand the role of genetics and environment on determining
        observable variation in organisms
       Students are unfamiliar with the roles of the two different DNA strands
       Students are unaware of the chemical differences between nucleic acids and proteins
       Students are unaware of the role in viral DNA in the host cell
       Students commonly confuse the complementary base pairs
       Students do not associate base pair sequence with DNA function
       Students believe prokaryotic and eukaryotic DNA structure and function are identical
       Students do not understand that DNA replication produces a discontinuous strand



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      Students believe that X-ray crystallography produces a visible double-helix image of
       DNA

INSTRUCTIONAL STRATEGY PRESENTATION ASSISTANCE

This chapter illustrates the additive effects of scientific discovery and the need for scientists to
openly communicate with one another (i.e., publish) very well. Mendel, Darwin, and Einstein are
rare exceptions in the scientific world. Even Watson and Crick used someone else’s data to
derive their model of DNA.

There are a lot of names presented in this chapter. Most of them are important within the
historical construct of biology. Plus it is much easier to describe an experiment as “The Griffith
Experiment” than to talk about the experiment that used virulent bacteria and so forth. After all,
if psychology students learn about Skinner, and English students about Emily Dickinson, why
can’t biology students be familiar with a few of the biggies in their field?

Students frequently get confused with directionality in the DNA helix even though it seems
simple that one strand runs 5’ to 3’ and the other 3’ to 5’. They also expect one strand to always
be the sense strand. Sense strand recognition is explained in the next chapter.

Students also become confused with the many enzymes involved. A clear demonstration of the
function of each enzyme may be necessary for the average student to completely understand the
process. This may be done simply by writing a series of bases on the board, indicating where
phosphodiester bonds link adjacent nucleotides. Next, write the complementary strand, starting
with “RNA” bases. Demonstrate how DNA pol I “removes” the primer and “fills the gap” with
DNA bases. Finally, demonstrate how DNA ligase seals the strand by connecting adjacent
nucleotides.

Many students confuse nucleotide base names with amino acid names (i.e., thymine and
thymidine). Some hints just in case students can’t seem to keep the mechanisms of base pairing
straight: (1) A and T are both angular letters and with the addition of U, they have an upright
orientation. C and G are curved letters and both open toward the right.
(2) A and G are in the same class and both have horizontal lines in their middles.
(3) Structurally, the class of base with the shorter name (purine) is larger (having a double ring)
while the longer name (pyrimidine) is the smaller molecule.



HIGHER LEVEL ASSESSMENT

Higher level assessment measures a student’s ability to use terms and concepts learned from the
lecture and the textbook. A complete understanding of biology content provides students with the
tools to synthesize new hypotheses and knowledge using the facts they have learned. The
following table provides examples of assessing a student’s ability to apply, analyze, synthesize,
and evaluate information from Chapter 14.




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Application            Have students predict the type of DNA replication carried out by
                        chloroplasts and mitochondria.
                       Have students design an experiment showing the presence of
                        semiconservative replication.
                       Ask students to design a synthetic DNA molecule that can be used to
                        block replication of a DNA strand containing the sequence:
                        ATTCGCCCATTATCCCCGCAATCCCATTATC.
Analysis               Have students explain the differences and similarities between
                        prokaryotic and eukaryotic DNA replication.

                       Ask students to determine the how nondisjunction diseases would affect
                        DNA replication.

                       Ask to explain the effects of a disease that disrupts the DNA repair
                        system.
Synthesis              Ask students to determine if prokaryotes would be capable of producing
                        eukaryotic enzymes after inserting a gene for that enzyme.
                       Have students explain what factors need to be considered when putting
                        eukaryotic DNA into a prokaryote.
                       Ask students come up with a commercial use for replisomes.
Evaluation             Ask students to evaluate the use of a chemical that stops the discontinuous
                        part of DNA replication.
                       Ask students to determine the safety of antibacterial drug that causes a
                        cell to replace adenine with cytosine.
                       Ask to evaluate the effectiveness of a drug claimed to reducing DNA by
                        speeding up the activity of the DNA repair system.

VISUAL RESOURCES

One could construct all sorts of interesting visual aids associated with DNA replication using
zippers and/or Velcro®. The latter would be especially useful to show semiconservative
replication using different color strips as it sticks together quickly and pulls apart almost faster.
(We all know how zippers get stuck at the most inopportune moments.) Velcro® sewn into a
circle would also illustrate bacterial DNA replication readily. One circle should be simply basted
so it can be “nicked” easily.

Sigma sells an interesting, humorous, albeit slightly juvenile book called BIOKIT: A Journey
Into Life that may give you some ideas regarding presentation of this material to very
inexperienced students.


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Variously colored pop-it beads are handy for showing nucleotide and amino acid sequence.

IN-CLASS CONCEPTUAL DEMONSTRATIONS

A. Replicating Students

       Introduction

       This fun and fast demonstration engages students in demonstrating the process of
semidiscontinuous replication in eukaryotes. It uses student input to design the sequence the
events of DNA replication.

Materials

      2 Student volunteers
      Large black marker
      48 sheets of 8 1/2 “ by 11” white paper representing nucleotides
           o 10 sheets labeled with a large black “A”
           o 10 sheets labeled with a large black “C”
           o 10 sheets labeled with a large black “G”
           o 10 sheets labeled with a large black “T”
           o 4 sheets labeled with a large black “3 prime end”
           o 4 sheets labeled with a large black “5 prime end”
      20 sheets of 8 1/2 “ by 11” pink paper representing nucleotides
           o 10 sheets labeled with a large black “A”
           o 10 sheets labeled with a large black “C”
           o 10 sheets labeled with a large black “G”
           o 10 sheets labeled with a large black “T”
      Roll of tape

       Procedure & Inquiry

   1. Call two students to the front of the room.
   2. Tell the students to build the following DNA sense strand by taping the white nucleotide
      papers on the board keeping in the mind the 3’ and 5’ ends: AACGTACCGCTATCT
   3. Then have the class tell the students to build the complementary strand of DNA using the
      pink paper.
   4. Now have the class instruct the students to replicate the strand. Tell them that they must
      take into account the 3’ and 5’ ends of the nucleotides.
   5. Have the class evaluate if the replicated strands are correct and represented
      semidiscontinuous and semiconservative replication.

B. Virtual DNA Replication Concept Map

       Introduction


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        This fun and fast way to build a concept map engages students in developing a scheme
for reviewing all the facts and concepts associated with DNA replication. It helps student select
relevant information needed to understand DNA replication. In addition, it helps them
incorporate concepts learned in other sections of the book that contribute to an understanding of
DNA replication. The simple click and drag animated concept mapping tool should be practiced
before using in class.

Materials

      Computer with live access to Internet
      LCD projector attached to computer
      Web browser with bookmark to Michigan State University C-Tool:
       http://ctools.msu.edu/ctools/index.html

       Procedure & Inquiry

   1. Tell students that you would like to do a quick review of the concepts associated with
      DNA replication.
   2. Then go to the Michigan State University C-Tool and add the concept map term “DNA
      Replication”. Use the “Add” and “Concept Word” feature to place a term on the map
      background.
   3. Solicit a few more terms or concepts and then ask the class how the concepts are
      connected to each other. Use the “Add” and “Linking Line” feature to build a connecting
      line.
   4. Then ask the students to justify the concept linking lines. Use the “Add” and “Linking
      Word” feature to place student comments on the map.
   5. Continue the activity until you feel the students made a comprehensive map.

USEFUL INTERNET RESOURCES

   1. Animations are a valuable classroom resource for reinforcing a lecture on DNA structure
      and replication. The Cell Biology Animation website provides a well-done animation
      sequence showing the three-dimensional structure of DNA and DNA replication. This
      website can be found at http://www.johnkyrk.com/DNAanatomy.html
   2. A good way to begin lecture on DNA structure is to present a brief history of the
      discovery of DNA. A website hosted by the National Health Museum provides a table
      highlighting the major events leading to the foundations of molecular genetics. The table
      can be projected to the class as a way showing the events that led to the work of Watson
      and Crick.. The website can be found at
      http://www.accessexcellence.org/AE/AEPC/WWC/1994/geneticstln.html.
   3. Faculty and students will be surprised to learn about The President’s DNA Iniative. This
      program investigates the accuracy and fairness of DNA technology in the criminal justice
      system. This website provides interesting information to stimulate discussions and further
      studies about the use of DNA in criminal investigations. This website can be found at
      http://www.dna.gov/.



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   4. Case studies are a highly effective way to reinforce the learning of complex topics in
      genetics. A case study called “ Right to Her Genes” has students investigating the value
      and ethical issues of DNA technology related to identifying disease genes. The website
      can be found at http://www.sciencecases.org/genes/genes.asp.

LABORATORY IDEAS

       This activity teaches students to use the initial investigations of Watson and Crick in
building structurally correct model of DNA. They designed a theoretical model of DNA by using
cardboard to build different DNA structures. It is a good critical thinking activity that promotes
an understanding of the use of models in answering scientific questions.

   a. Tell students that you would like them to design a model of DNA that demonstrates the
      chemistry of a double DNA strand. It is important to stress that they must take into
      account bonding and the shapes of the nucleic acids.
   b. The following materials should be provided to a small group of students:
          a. Scissors
          b. Markers
          c. A roll of cellophane tape
          d. A roll of Velcro-type adhesive tape
          e. Construction paper
          f. Small polystyrene balls
          g. Toothpicks
          h. Images of nucleic acids
   c. Have the students explain their models
   d. Then have the class briefly evaluate the various group models for accuracy

LEARNING THROUGH SERVICE

Service learning is a strategy of teaching, learning and reflective assessment that merges the
academic curriculum with meaningful community service. As a teaching methodology, it falls
under the category of experiential education. It is a way students can carry out volunteer projects
in the community for public agencies, nonprofit agencies, civic groups, charitable organizations,
and governmental organizations. It encourages critical thinking and reinforces many of the
concepts learned in a course.
    1. Have students do a presentation on the history of genetics to a civic group.
    2. Have students design an educational PowerPoint presentation on DNA structure and
        replication for middle school teachers.
    3. Have students tutor middle school or high school biology students studying genetics.
    4. Have students design and build an accurate DNA model for a local school or library.




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This project is funded by a grant awarded under the President’s Community Based Job Training Grant as implemented by the U.S.
Department of Labor’s Employment and Training Administration (CB-15-162-06-60). NCC is an equal opportunity employer and
does not discriminate on the following basis:
         against any individual in the United States, on the basis of race, color, religion, sex, national origin, age disability, political
          affiliation or belief; and
         against any beneficiary of programs financially assisted under Title I of the Workforce Investment Act of 1998 (WIA), on
          the basis of the beneficiary’s citizenship/status as a lawfully admitted immigrant authorized to work in the United States, or
          his or her participation in any WIA Title I-financially assisted program or activity.


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