Double Helical Structure of DNA It is a ladder like structure which is made up of poly nucleotide chains spirally coiled on a central axis. The two strands are made up of polynucleotide held together by Phosphodiester Bonds. Each nucleotide is composed of a Phosphate Group, a Deoxyribose Sugar and a Nitrogenous Base. The steps of the ladder looking DNA are made up of Nitrogenous Bases which are united by Hydrogen Bonds. The two strands of polynucleotide are anti- parallel to each other. One strand runs from 5 to 3 direction whereas the other strand runs from 3 to 5 direction. The breaking of hydrogen bonds results in separation of two strands. Why does DNA replicate??? The fundamental properties of cells and organisms is their ability to reproduce. To give rise to new cells by undergoing DNA replication and cell division. Any organism grows from embryonic development until death as a result of DNA replication. The DNA replication results in growth of the cells, formation of new cells and repair of the damaged tissues. 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 D2.1 use appropriate terminology related to molecular genetics, including, but not limited to: polymerase I, II, and III, DNA ligase, helicase, Okazaki fragment, mRNA, rRNA, tRNA, codon, anticodon, translation, transcription, and ribosome subunits [C]. D2.2 analyze a simulated strand of DNA to determine the genetic code and base pairing of DNA (e.g., determine base sequences of DNA for a protein; analyze base sequences in DNA to recognize an anomaly) [AI] D3.1 explain the current model of DNA replication, and describe the different repair mechanisms that can correct mistakes in DNA sequencing. Important Terminologies: 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. Important Terminologies: 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. Important Terminologies: 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 add complementary nucleotide in 5 to 3 using RNA primers as starting points. Okazaki Fragments Newly synthesized DNA strand Old Strand 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. Important Terminologies: 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. Gyrase Helicase SSB Protein Leading Strand Lagging Strand Exonuclease 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. Inquiry based gizmo activity on DNA Building and Replication. Students would think critically and follow the process of DNA replication. Students would be asked to complete the lab attached along with the gizmo and would be marked on it. Link to the gizmo:esource.dspDetail&ResourceID=439esource.dspDetail&ResourceID=439 Here is a link to the video demonstration of the entire process of DNA Replication:lege/pratt/ /s tudent/animations/dna_re plication/index.html After the entire lesson for DNA Replication, the class would be divided into groups of 4- 5 students. Each student in each group would be assigned one enzyme involved in the DNA Replication process. 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. Every group would present the information to the class. Objective Students will model the semi-conservative replication of DNA. Materials For each group 1. DNA patterns (see preparation) 2. Paper 3. Pencil 4. 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 1. Ask students to use the DNA patterns to trace and cut out 16 each of sugar and phosphate, and 8 of each base. 2. 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. 3. 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. 4. Have students create new double-stranded DNA by matching complementary nucleotides to the bases on each single strand. Discussion Questions 1. Compare the two new strands of DNA. Are they the same or different? (The same.) Why? (Because each strand contains complementary pairs, so that each daughter molecule consists of one-half of the original DNA chain, and one-half new material.) 2. How does the structure of a DNA molecule help account for the great variety of life that exists on earth? (The seguence of the base pairs determines how the organism will form. The variety in the sequence of the base pairs accounts for the variety of life forms.) Misconception 1: Students always have a confusion about the direction of the formation of the new DNA strands. Resolution: The new strands of DNA are always built from the 5 direction to the 3 direction. Misconception 2: When does DNA replication occurs in a cell? Resolution: DNA replication always occurs at the beginning of the process of cell division. 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. This process can be used in genetic engineering such as in creating clones. This process is also used to create genetically modified foods and organisms using the Recombinant DNA technology. The students would have a chance of working on a culminating project on the topic DNA Replication and they can present in any way possible such as a PPT presentation, Bristol board, Oral / verbal presentation, through role plays or skits, communicating through songs or videos or using a case study etc. The students understanding would also be assessed through a unit test which would be an Assessment of learning. The choice of the way of the presentations by the students would act as a mode of assessment for learning.