1. Nucleic Acids and DNA Replication

2. 1. What is the role of nucleic acid? 2. What is the monomer of a nucleic acid? 3. The monomer of a nucleic acid is made up of 3 things: a phosphate, base, and a _________________. 4. What is the difference between DNA and RNA? 5. A always pairs with T, and G always pairs with ____.

3. Nucleotides Include DNA and RNA

4. Components of a Nucleotide Phosphate Group (5’ end) Pentose Sugar (3’ end) Ribose in RNA Deoxyribose in DNA Nitrogenous bases Purine (2 rings) Adenine, A Guanine, G Pyrimidines (1 ring) Cytosine, C Thymine, T (only in DNA) Uracil, U (only in RNA)

5. Formation of Polynucleotides Dehydration reactions link nucleotides together Phosphodiester linkages are the bonds between the sugar of one nucleotide and the phosphate of the next New nucleotides can only be added to the 3’ end where there is an exposed hydroxyl group (from the sugar) This is why we say that DNA is built in a 5’ to 3’ direction Directionality in the structure of the DNA molecule influences how it functions

6. Formation of Polynucleotides

7. The DNA Double Helix

8. The two strands of the double helix are arranged in an antiparallel fashion, one of them going 5’-3’ and the other one going in the opposite direction

9. The “Backbone” Made up of alternating sugars and phosphates Connected by covalent bonds called phosphodiester linkages by dehydration reactions

10. The “rungs” of the Ladder Made up of nitrogenous bases Hydrogen bonded to each other The bases are hydrophobic and in their position inside the molecule they are shielded from the aqueous environment of the nucleus

11. Complimentary Base Pairing Each purine is bound to a pyrimidine A always to T (with 2 hydrogen bonds) C always to G (with 3 hydrogen bonds) Chargraff’s Rule: for any given species the % of Ts will by equivalent of the % of As while the % of Cs will be equivalent to the % of Gs

12. The DNA Double Helix

13. DNA vs. RNA DNARNA Number of Strands Pentose Sugar Nitrogenous Bases

14. Functions of DNA provides directions for its own replication directs RNA synthesis through RNA, controls protein synthesis (blueprints of the cell)

15. Function of Ribosomal RNA rRNA Together with proteins makes up the structure of the ribosomes, the site of protein synthesis

16. Function of Transfer RNA tRNA Recognizes the 3 base sequence on the messenger RNA and brings the appropriate amino acid to the ribosome fro protein synthesis

17. Function of Messenger RNA mRNA Carries the “code” from the DNA in the nucleus to the ribosome in the cytoplasm to instruct protein synthesis

18. Models of DNA Replication

19. Conservative model- the two parent strands rejoin after acting as a template for new strands

20. Models of DNA Replication Semiconservative model- the new strands of DNA are made of one parental template strand, and one newly synthesized strand; this is the accepted model of DNA synthesis

21. Models of DNA Replication Dispersive Model- the DNA completely breaks down and the new DNA is made of a mixture of pieces of the parental and new DNA

22. DNA Replication What does the curriculum say? DNA polymerase Ligase RNA polymerase Helicase topoisomerase

23. The Origin of Replication Site where DNA synthesis begins In prokaryotes there is only one because the DNA is circular In eukaryotes there are several replication bubbles that eventually fuse

24. Enzymes involved in early DNA replication: Helicase- unzips and unwinds the DNA double helix Topoisomerase- relieves the tension further down the strand that is caused by the unwinding at the origin Single Strand Binding Protein- helps stabilize the single stranded DNA

25. The Energy Requirements of DNA Synthesis Nucleoside Triphosphate The triphosphate portion contains a lot of potential energy Two phosphates are removed and the energy that was held in the bonds is used for the polymerization of the new DNA

26. Synthesis of the Leading Strand 1.The leading strand is synthesized continuously in the 5’ to 3’ direction; in the direction of the replication fork 2.Primase- an enzyme that lays down an RNA primer on which the new DNA can be synthesized 3.DNA Polymerase III adds new nucleotides to the 3’ end 4.DNA Polymerase I removes the RNA primer and replaces it with DNA nucleotides 5.DNA Ligase connects the DNA added by DNA Polymerase I with the remainder of the leading strand

27. Synthesis of the Leading Strand

28. Synthesis of the Lagging Strand DNA can only be synthesized in the 3’ to 5’ direction The lagging strand must be synthesized away from the replication fork; as the DNA unwinds, the lagging strand is synthesized in a series of small segments called Okazaki fragments

29. Synthesis of the Lagging Strand 1.Primase lays down multiple RNA primers 2.DNA Polymerase III adds new nucleotides until it reaches the next RNA primer 3.DNA Polymerase I removes the RNA primers and adds DNA nucleotides in their place 4.DNA Ligase connects the Okasaki fragments to make one continuous strand of DNA

30. Synthesis of the Lagging Strand

31. The DNA Replication Machine The various proteins that participate in DNA replication form one large complex The DNA replication machine is stationary and the DNA is fed through the machine like a thread through a needle In eukaryotic cells, multiple copies of the DNA machine are likely anchored in the nuclear matrix and copy multiple chromosomes at a time

32. Crash course

33. Proofreading Occurs simultaneously with replication DNA polymerase proofreads each nucleotide against the template and when mistakes are found, it fixes them

34. Nucleotide Excision Repair Nuclease- enzyme that cuts out problems in the DNA DNA polymerase replaces the excised nucleotides with good ones DNA ligase joins the nucleotides to the existing strand

35. Erosion of Gene Coding DNA and Aging The problem with the lagging strand in eukaryotic DNA DNA polymerase can only add nucleotides to the 3’ end After the primer at the end of the lagging strand is removed, DNA polymerase cannot add new nucleotides THE PROBLEM: eventually this would erode some of the genes coded for in the DNA

36. Erosion of Gene Coding DNA and Aging

37. The Solution: Telomers Short repeating segments of DNA that do not contain genes, but multiple repetitions of one short nucleotide sequence The protect the organisms genes from being eroded by successive rounds of DNA replication Telomers do not prevent DNA shortening, but do postpone the erosion of genes

38. Telomerase Enzyme that catalyzes the lengthening of telomers in eukaryotic germ cells (what are germ cells???) Telomerase is not active in most cells but is active in the germ cells of zygotes