1. AP Biology Discussion Notes Wednesday 01/14/2015

2. Goals for Today Be able to describe how bacteria increase their genetic variation Be able to describe the “life” cycle of a virus Be able to describe the difference between a virus and a retrovirus Be able to describe a restriction enzyme, where it comes from, and what its potential uses are

3. Things to DO: 1.Look over material before the next class –Write down thoughts, connections or questions 2.Read the chapter –even when not “assigned” 3.Watch Videos about topics –even when not assigned 4.Start reviewing topics from last semester –Tie them to topics this semester and write down connections or questions 5.ASK QUESTIONS

4. When DNA replicates, each strand of the original DNA molecule is used as a template for the synthesis of a second, complementary strand. Which of the following figures most accurately illustrates enzyme-mediated synthesis of new DNA at a replication fork? Go to our website and enter your best answer to this question, then complete the question of the day

5. Question of the Day 1/14 Draw a replication bubble label the Following: –leading strands –lagging strands –5’ and 3’ ends on the new and template DNA –Origin of replication –Replication fork

6. Figure 16.15a Leading strand Lagging strand Overview Origin of replication Lagging strand Leading strand Primer Overall directions of replication

7. When DNA replicates, each strand of the original DNA molecule is used as a template for the synthesis of a second, complementary strand. Which of the following figures most accurately illustrates enzyme-mediated synthesis of new DNA at a replication fork? Go to our website and enter your best answer to this question, then complete the question of the day

9. Are there any choice we could eliminate right away? (Sometimes its best to play the……which of these is not like the other game……look at the differences and similarities in each picture.)

10. Two KEY pieces of information: 1.DNA strands are ANTIparallel, and therefore should be built in opposite directions. 2.There is a lagging and a leading strand because of the directionality of DNA Polymerase (that it can only build new strands in the 5’ to 3’ direction

11. Are there any choice we could eliminate right away? There would be 2 ways to eliminate 2 choices! 1.Both A & B show the leading strand () and lagging strand ( ) built in the same direction, but they are built in opposite directions, so you can eliminate both A & B.

12. Are there any choice we could eliminate right away? 2.A & C both show 2 strands being built continuously. However, during DNA replication there is a leading & lagging strand produced. The lagging strand is built discontinuously in pieces, and is later connected by the enzyme Ligase. This information allows us to eliminate both A & C.

13. Are there any choices we could eliminate right away? Eliminating choices where strands are built in the same direction and choices that contain only leading strands (no lagging strand) leaves us with only 1 choice, D.

14. D is built in two different directions, and has 1 lagging and 1 leading strand. The other key piece of information contained in this question is that DNA polymerase can only build in the 5’ to 3’ direction. Meaning the strand that it will build runs 5’ to 3’ and the strand that it is copying will run 3’ to 5’. Only the directionality of the template strand is shown, leaving you to infer that the other strand is opposite (anti-parallel). Directionality of Template strand 5’ 3’ Directionality of New strands

15. Bacteria Prokaryotic Circular DNA (couple million B.P.) Teeny “satellite” pieces of DNA called PLASMIDS (thousands of BP) Not much for organelles Cell wall that can be trashed by antibiotics –Penicillin, amoxicillin, ampicillin

17. How Do Bacteria Get Their DNA Changed NATURALLY? 1. Conjugation Sort of like Bacterial sex Sex Pilus (plural=pili) --plasmid transfer

18. How Do Bacteria Get Their DNA Changed? What scientist showed that traits from One bacteria could be transferred to another? What other scientist and his team showed the material responsible for that transformation was DNA?

19. 2. Transformation—bacteria takes in some DNA from its environment

20. 3. Transduction—a virus carries some DNA from one bacterium to another

21. Characteristics of Viruses Only two parts to them: --a protein outer coat --either some DNA or some RNA RNA viruses are also known as “retroviruses” (more on this later)

23. How Viruses Make Their Living 1.Attach to a “host” cell (animal, plant, or bacterium—virus = bacteriophage) 2.Injects its nucleic acid into the host 3.If it’s an RNA virus, then it also injects “Reverse Transcriptase” along with the RNA. 4.Viral N.A. integrates itself into the host’s DNA 5.Host is now “re-programmed” to make viruses 6.Host cell blows up because it can’t hold all of the baby viruses—this is called LYSIS 7.This is the LYTIC CYCLE of a virusLYTIC CYCLE

24. The Lytic Cycle of a (bacterio)Phage

26. We all go Retro, eventually !

27. Bacterial Enemies A bacterium’s nastiest natural enemy is a bacteriophage (a virus) In the 1970’s, it was discovered that bacteria had defense systems against viruses These defense molecules are called Restriction Enzymes

28. Restriction Enzymes (also called Restriction Endonucleases) Special enzymes produced by bacteria (NOT BY HUMANS!!!) They snip/cut DNA at specific base sequences Cut up DNA = harmless DNA The bacteria wins (maybe)

33. How important are restriction enzymes?

34. The Nobel Prize in Physiology or Medicine 1978 Werner Arber Daniel Nathans Hamilton O. Smith

35. Recombinant DNA “Splicing” the DNA from one organism into the DNA of another organism. The “new” DNA now has the ability to code for “new” proteins. Some examples: Human Insulin Human Growth Hormone Roundup-Ready Crops

37. Double Helix Discussion

38. Linus Pauling

39. Double Helix Discussion

40. Impressions of Watson

41. Reminder DNA Assignment DUE FRIDAY