1. Understanding DNA Biology 12 Ms. Bowie

2. Understanding DNA DNA stands for deoxyribonucleic acid DNA is the genetic material. –transfer from parent cell to daughter cell and –from parent organism to offspring.

3. The 3 main components of DNA are: Understanding DNA A Phosphate Group A deoxyribose Sugar A nitrogenous base

4. A Nucleotide of DNA

5. There are four nitrogenous bases in DNA. –Adenine (A), –Guanine (G) –Thymine (T) –Cytosine (C) –Uracil (U) The Nitrogenous Bases which are double ringed purines (Hint: “pure” = Always Good) which are single ringed pyrimidines (Hint : “pyro” = Take Care) found in RNA instead of thymine

7. DNA is made of polymers of many nucleotides held together by phosphodiester bonds between the phosphate group and the adjacent sugars. Nitrogenous bases are held together by hydrogen bonds. Two between A & T and Three between C & G Bonds in DNA

8. Erwin Chargaff determined that: –Adenine always pairs with Thymine –Cytosine always pairs with Guanine Chargaff’s Rule

9. Numbering Carbons in the Ring Carbons are numbered clockwise, starting with the carbon atom to the immediate right of the oxygen atom. The first one would be called 1’, the next would be 2' (2 prime)... The nitrogenous base attaches to the sugar at the 1' location (via a glycosyl bond). The phosphate group attaches to the sugar at the 5' location (via an ester bond).

10. The Race for DNA Linus Pauling –building ball and stick models using his expertise in chemistry. He proposed 1 model – it did not show how copying of the DNA could occur. His son, Peter Pauling, went to work with another group in Cambridge, England.

11. The Race for DNA Rosalind Franklin and Maurice Wilkins –King's College in London –studies using the diffractions with X-ray crystallography. –Work was based on serious scientific evidence, –They have great difficulty working TOGETHER. –Franklin uncovered the shape of DNA when she found an x-ray diffraction in a cross pattern. –Wilkins shared this data with Watson who used it to further his own work.

12. The Race for DNA James Watson and Francis Crick –considered lazy slackers – neglected experimentation and evidence –focused on the structure of DNA using 3D modelling –when Wilkins showed the x-pattern of Franklin's x-ray diffraction, he immediately knew what the structure might look like. –They came up with the modern structure of DNA that accurately answered the question as to how DNA can create perfect copies of itself.

13. The Race for DNA Watson, Crick and Wilkins won Noble Prizes for their Discovery of the structure of DNA. However, Franklin did not receive one as she died before the awards were given.

14. DNA Double Helix Structure DNA is made of 2 antiparallel strands of nucleotides. It is important to be able to identify the 3' and 5' ends of each strand.

15. DNA Double Helix Structure Thanks to Chargaff's Rule, we only state the 5' to 3' strand, since the complementary strand can be easily deduced. 5' - GCAATCTA - 3' 3' - CGTTAGAT - 5'

16. Replicating DNA DNA must be copied in order for single cells to be replaced as they age or are damaged. It also happens so organisms can grow.This process is known as mitosis.

17. Replicating DNA Semiconservative: each DNA molecule is made of one parent strand and one newly synthesized strand. Conservative: each DNA molecule reforms so that both new strands stay together and both parent strands stay together. Dispersive: where bits and pieces of the parent and new strands are interspersed in both strands following the replication.

18. Replicating DNA

19. The Process of Replicating DNA The two DNA strands separate Each strand serves as a template DNA replication begins at the origin of replication.

20. The Process of Replicating DNA DNA replication begins at the origin of replication.

21. The Process of Replicating DNA Replication proceeds (following the AT/CG rule) outward from the origin in opposite directions. This is a process called bidirectional replication. In simple bacteria, which have a small circular chromosome, there is a single origin of replication.

22. The Process of Replicating DNA The origin of replication forms a bubble that creates two DNA replication forks. Replication begins near the opening of each fork.

23. The Process of Replicating DNA The building of the new DNA always begins with a primer. New DNA is always built in the 5' to 3' direction.

24. The Process of Replicating DNA One strand will be the leading strand. The other will be the lagging strand. The leading strand moves in the same direction as the fork is moving. The leading strand is replicated as one long continuous molecule.

25. The Process of Replicating DNA The lagging strand is made in a series of small fragments which will eventually form a continuous strand. Synthesis of this strand goes in the direction away from the fork. These fragments are known as Okazaki fragments.

26. DNA Replication Proteins »DNA helicase is an enzyme binds to one of the strands at the origin and travels in the 5' to 3' direction. »It uses energy from ATP to keep the fork moving forward (away from the origin). »The movement of the helicase causes additional coiling just ahead of the replication fork. To reduce this, another enzyme is needed. »DNA topoisomerase (also called DNA gyrase) alleviates the additional coiling above the replication fork. »Once the strands have been separated, they must be held apart to prevent them from rebinding annealing until the complimentary daughter strands can be formed. This is done with the help of single-strand binding protein. Step 1: Formation and Movement of the Replication Fork

27. DNA Replication Proteins Step 1: Formation and Movement of the Replication Fork

28. DNA Replication Proteins »In prokaryotes, 3- 5 enzymes that serve to replicate and repair the DNA strand. These are DNA polymerase I, II, III, IV & V. »In eukaryotes, there are 12+ DNA polymerases involved. Step 2: Synthesis of the Leading and Lagging Strands

29. DNA Replication Proteins »As DNA polymerase III slides along the DNA, free nucleotides with 3 phosphate groups, called deoxynucleoside triphosphates, hydrogen bond to the exposed bases in the template strand according to the AT/GC rule. DNA polymerase III breaks the bond between the 1 and 2nd phosphate groups releasing a pyrophosphate (2 phosphate groups, which are recycled. » Step 2: Synthesis of the Leading and Lagging Strands

30. DNA Replication Proteins »DNA polymerase III can't polymerize a DNA strand unless a DNA or RNA strand is already attached to the template. »An enzyme called DNA primase is needed if the template is bare. DNA primase makes a complimentary primer that is actually a short segment of RNA, usually about 10-12 nucleotides long. At a later stage in replication, the RNA primer is removed and replaced with DNA by DNA Polymerase I. Step 2: Synthesis of the Leading and Lagging Strands

31. DNA Replication Proteins »DNA polymerase can only synthesize new DNA in the 5' to 3' direction (of the new strand). »The Okazaki fragments must be linked together (bonded) on the lagging strand. »This bond is reformed by an enzyme known as DNA ligase. Step 2: Synthesis of the Leading and Lagging Strands

32. DNA Replication Proteins There are many other proofreading enzymes known as exonucleases that correct and repair mistakes in the newly forming DNA strands. If they detect a mismatched pair, they will backtrack, cut it out and replace it with the correct pair. If the repairs are done immediately to avoid being copied in the next replication. Mistakes that make it through can result in mutations. Step 3: Proofreading and Repair of newly formed DNA strands

33. DNA Replication Proteins Step 3: Proofreading and Repair of newly formed DNA strands

35. http://www.wiley.com/college/pratt/0471393878/in structor/animations/dna_replication/index.htmlhttp://www.wiley.com/college/pratt/0471393878/in structor/animations/dna_replication/index.html http://highered.mcgraw- hill.com/sites/0072943696/student_view0/chapter 3/animation__dna_replication__quiz_1_.htmlhttp://highered.mcgraw- hill.com/sites/0072943696/student_view0/chapter 3/animation__dna_replication__quiz_1_.html http://www.johnkyrk.com/DNAreplication.html