DNA Replication and Repair – SUMMARY
By: Hina Laxmi Trivedi and Timothy Au
Background Information:
DNA contains the genetic instructions used in the development and functioning of living organisms. DNA replication occurs because cells and organisms need to reproduce. To give rise to new cells, the new cells will need to receive a copy of the genetic instructions as well to guide their development and function. As a result, DNA replication needs to take place, and this happens during the growth of cells, formation of new cells, and the repair of damaged tissues.
1. Separation of DNA Strands:
DNA Helicase: - The enzyme that unwinds double-helical DNA by disrupting hydrogen bonds.
Anneal: - The pairing of complementary strands of DNA through hydrogen bonding.
Single-Stranded Binding Proteins (SSBs): - The protein that keeps the separated strands apart.
DNA gyrase: - The bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication.
2. Replication:
Replication Fork: - The region where the enzyme replicating a DNA molecule are bound to untwist single stranded DNA.
Replication Bubble: - The region where two replication forks are in close proximity to each other producing a bubble in the replicating DNA.
3. Building Complementary Strands
Leading Strand: - The new strand of DNA that is synthesized continuously during DNA replication.
Lagging Strand: - The new strand of DNA that is synthesized in short fragments which are later joined together.
Qkazaki Fragments: - Short fragments of DNA formed as a result of the synthesis of lagging strands.
DNA Polymerase I: - Enzyme that removes RNA primer and replaces them with the appropriate Deoxyribonucleoside.
DNA Ligase: - The enzyme that joins DNA fragments together by catalyzing the formation of bond.
DNA polymerase III: - The enzyme responsible for synthesizing complementary DNA strands of DNA during replication.
Primase: - The enzyme that builds RNA primers.
Deoxyribonucleoside Triphosphates: - Molecules composed of deoxyribose bonded to three phosphate groups and a nitrogenous base.
RNA Primer: - Sequence of 10 to 60 RNA bases that is annealed to a region of singe-stranded DNA for the purpose of initiation of DNA replication.
4. DNA Repair
As the complementary sequence formation completes; DNA polymerase III and DNA polymerase I works as quality control checkers. These enzymes check incorrectly paired nucleotide on the template, excises it and add correct nucleotide sequence on the strand. These enzymes are known as exonuclease. These enzymes work immediately to avoid mistakes during replication.
Semi-Conservative Replication
During DNA Replication, each strand of the original DNA becomes the template for the new strand of DNA. Note, however, that each strand is not a duplicate of itself, but the compliment of itself. It will not look like the template it is copying from, but rather the antiparallel strand of the double helix. For example, this is how the original template and the newly strand will appear:
Original Strand: AATTCCG
Copied Strand: TTAAGGC
So the original strand and the copied strand will anneal forming a double helix of an old and new strand of DNA. Because each new strand contains one original strand and one copied strand, it is called semi-conservative replication.
Advance Preparation:
1. Review and ensure students understand the following about DNA structure before beginning to teach about DNA replication:
a. DNA is made up of polynucleotide chains spirally coiled on a central axis
b. The two polynucleotide chains are held together by Phosphodiester Bonds.
c. Each nucleotide is composed of a Phosphate Group, a Deoxyribose Sugar and a Nitrogenous Base.
d. The “steps of the ladder” in DNA are made up of Nitrogenous Bases held together by Hydrogen Bonds.
e. The two strands of polynucleotide are anti-parallel to each other.
f. One strand runs from 5’ to 3’ direction whereas the other strand runs from 3’ to 5’ direction.
g. The breaking of hydrogen bonds results in separation of the two strands of DNA.
2. DNA Replication Activity – Sample patterns of the following parts of the DNA molecule (the four bases—A, C, T, G; a sugar—S; and a phosphate—P) needs to be created for each group in the class. (See diagram on the right)
Special Materials:
· LCD projector and laptop computer to show video clips of DNA replication
· Computers with internet access (i.e., book computer lab at school) for student access to Gizmo activity on DNA Replication (www.explorelearning.com)
· DNA patterns (prepared ahead of time using construction paper or cardboard, pencil/pens, and scissors) for DNA Replication Activity
Annotated References:
Digiuseppe, Maurice et. al. (2003). Nelson Biology 12. Nelson Education Ltd.: Toronto, Canada.
Student Difficulties:
· Vocabulary and terminology (e.g., names of all the enzymes, parts of the DNA, etc.) can be difficult to learn, especially for English Language Learners – SOLUTION: Word Wall or Flash Cards
· Understanding and visualisation of all the steps involved with DNA replication, as there are many steps that can get complicated (e.g., leading strand versus lagging strand, etc.) – SOLUTION: Use a lot of diagrams, show a lot of video clips (visual learners), conduct an activity where students actually go through the process of replicating a DNA using a model (kinaesthetic learners)
· The following misconceptions:
o Misconception 1: Students always have a confusion about the direction of the formation of the new DNA strands—Resolution: New strands are always built from the 5’ to the 3’ direction.
o Misconception 2: When does DNA replication occurs in a cell?—Resolution: DNA replication always occurs at the beginning of the process of cell division.
o Misconception 3: Why are the RNA Primers made first on the replicated DNA strands when the process itself is DNA Replication—Resolution: The RNA Primers that are built, are used for the initiation of the formation of the new DNA strand on the template.
Teaching Ideas:
1. Use lots of diagrams (see pages 1-2 of this summary for sample diagrams) and video clips (http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html) to appeal to our visual learners
2. Use computer technology (an inquiry-based Gizmo Activity on DNA building and replication http://www.explorelearning.com/index.cfm?method=cResource.dspDetail&ResourceID=439) and an actual hands-on DNA replication activity in class to appeal to our kinaesthetic learners
Summary of Hands-on DNA Replication Activity
Objective: Students will model the semi-conservative replication of DNA.
Materials: DNA patterns (see preparation below), paper, pencil, scissors
Preparation: Create and duplicate sample patterns of the following parts of the DNA molecule: the four bases (A, C, T, G), a sugar (S), and a phosphate (P).
Instructions:
I. Ask students to use the DNA patterns to trace and cut out 16 each of sugar and phosphate, and 8 of each base.
II. Have students build a model of a segment of a DNA molecule. The segment should contain 4 base "rungs." Any bases can be used for the sequence, as long as the appropriate complementary bases are used for the pairs.
III. Once students have made their models, ask them to separate the models down the middle so that there are now two single strands of DNA.
IV. Have students create new double-stranded DNA by matching complementary nucleotides to the bases on each single strand.
Discussion Questions:
I. Compare the two new strands of DNA. Are they the same or different? Why?
II. How does the structure of a DNA molecule help account for the great variety of life that exists on earth?
3. Use JIGSAW Activity to foster cooperative learning
i. After the entire lesson for DNA Replication, the class would be divided into groups of 4-5 students.
ii. Each student in each group would be assigned one enzyme involved in the DNA Replication process.
iii. Each group would be provided with two strands of DNA and then the groups would organize their information into step by step manner and put all the pieces of the process together to complete the jigsaw.
iv. Every group would present the information to the class.
Evaluation Procedures:
Differentiated Assessment will be used for the culminating project so students can choose the method that they want to demonstrate their understanding of the concept of DNA Replication and Repair. Their task is to create explain to their classmates how DNA replication and repair works. They may choose to explain this using any of the following methods:
A. PowerPoint presentation
B. Display Board (with diagrams and explanations)
C. Dramatise the entire process through role play or skit
D. Write an essay explaining the process
E. Create a video/media presentation
F. Any other method they see fit (but they must get teacher approval first)**
All students will also be writing a unit test on the topic as well at the end of the unit.
Applications and Societal Issues/Implications:
· This process can be used in genetic engineering such as in creating clones for curing health problems and diseases.
· This process is also used to create genetically modified foods and organisms using the Recombinant DNA technology.
Lesson Sequence:
Lesson 1: The Replication Factory
Overview of the DNA replication.
Lesson 2: DNA replication Proteins
Terminology of all the proteins involved in the DNA replication
Lesson 3: Strand Separation
Action of enzymes
Lesson 4: New Strand synthesis
Leading and lagging strand
Lesson 5: Replication in action
The entire process of DNA replication
Lesson 6: DNA repair
Annotated Internet Addresses:
Gizmo Activity on DNA Building and Replication
http://www.explorelearning.com/index.cfm?method=cResource.dspDetail&ResourceID=439
DNA Replication Video – Charlotte Pratt, Wiley Publishers
http://www.wiley.com/college/pratt/0471393878/student/animations/dna_replication/index.html
Activity 2: DNA Replication – Access Excellence @ National Health Museum, Atlanta Georgie
http://www.accessexcellence.org/RC/AB/WYW/wkbooks/SFTS/activity2.php