Today is Monday, November 25 th , 2013

1. In This Lesson: Mutations, Introns, Exons (Lesson 3 of 3) Today is Monday,November 25th, 2013 Pre-Class: Where does transcription take place? Where does translation take place? What is the name for a group of three mRNA bases? What about three tRNA bases? You need your Universal Genetic Code tables.

2. Today’s Agenda • Mutations! • Normal Whippet • Whippet with single base genetic mutation http://media.canada.com/idl/vitc/20070625/2192-640.jpg http://static.gotpetsonline.com/pictures-gallery/dog-pictures-breeders-puppies-rescue/whippet-pictures-breeders-puppies-rescue/pictures/whippet-0027.jpg

3. Today’s Agenda • First, how does all this stuff start up? That’s our focus for today. • Then, we’re going to add one more little detail to transcription: exonsandintrons. • Where is this in my book? • P. 215-218, mainly.

4. Chromosome Mutations • Most of the mutations we’re going to talk about today have to do with specific bits of DNA. • (DNA mutations) • There are several really bad ones, though, that have to do with entire chromosomes or chromosome pieces “going wrong.” • (Chromosome mutations)

5. Chromosome Mutations • Deletion • A chunk of the chromosome is lost. • Duplication • A part of the chromosome is copied. • Inversion • A part of the chromosome is flipped. • Others on next slides… http://depts.washington.edu/chdd/outlook/images/LgChromosomalChanges.png

6. Nondisjunction • Nondisjunctionbasically means the chromosomes didn’t come apart properly in meiosis (either 1 or 2). • Nondisjunction is the cause of Down Syndrome and related aneuploid defects. • It occurs when, during metaphase and anaphase, the spindles attach to the wrong set of chromosomes, so the chromosomes are not divided evenly. • Animation: • http://www.biostudio.com/d_%20Meiotic%20Nondisjunction%20Meiosis%20I.htm

7. Nondisjunction (Meiosis I) End with sperm or egg cells that have the wrong number of chromosomes. Start meiosis with one diploid cell that has 46 chromosomes. 46 NONDISJUNCTION 24 22 24 24 22 22

8. Nondisjunction (Meiosis II) End with sperm or egg cells that have the wrong number of chromosomes. Start meiosis with one diploid cell that has 46 chromosomes. 46 23 23 NONDISJUNCTION 23 23 24 22

9. Side Note: Maternal Age • Interestingly, risk of Down Syndrome (and other trisomies) increases with maternal age. • Mom’s age | risk of Down | risk of trisomy: • Age 20 | 1 in 1667 | 1 in 526 • Age 25 | 1 in 1250 | 1 in 476 • Age 30 | 1 in 952 | 1 in 384 • Age 35 | 1 in 385 | 1 in 192 • Age 40 | 1 in 106 | 1 in 66 • Age 45 | 1 in 30 | 1 in 21 http://downsyndrome.about.com/od/diagnosingdownsyndrome/a/Matagechart.htm

10. Translocation • During crossing over, a part of a chromosome winds up on another, non-homologous chromosome. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html

11. Translocation Analogy • Imagine you’ve got two copies of the same book (let’s say, the dictionary). • If you tore out the last 50 pages of each and put them in the other book, you’d still have a complete dictionary. • That’s normal crossing-over. • However, if you took the dictionary and the autobiography of Mickey Mouse, you’d end up with two very jumbled endings. • That’s translocation.

12. Mutation Introduction • Video: Mutations

13. DNA and RNA Mutations • Today, for simplicity’s sake, we will be talking about RNA mutations. • RNA mutations lead to protein changes which lead to trait changes. • Of course, there are also DNA mutations. • DNA mutations lead to RNA mutations…which lead to protein changes and trait changes too. Protein DNA RNA Trait

14. Mutations • Kinds of mutations: • Point Mutations (occur at only one base): • Insertion/Deletion (InDel Mutations) • Substitution

15. Mutations • Results of mutations: • Frame-shift mutations • Missense mutations • Nonsense mutations • Neutral/silent mutations (no effect)

16. AUG UUU GAG UGA UCC • Methionine • Phenylalanine • Glutamate • [Stop] • [Serine]

17. AUG UUU GAG UGA UCC • Mutation 1: What if I add a C here? • This is an insertion mutation. • AUG UUU CGA GUG AUC C • What happens? • Methionine • Phenylalanine • Arginine • Valine • Isoleucine • No stop codon!

18. AUG UUU GAG UGA UCC • Mutation 1 is what is called a frame-shift mutation because all the following codons are “shifted over.” • In other words, frame-shift mutations are bad news because they throw off the whole resulting protein. • Mutation 1 is also a missense mutation because it changed an amino acid (or stop) codon to a different amino acid.

19. Frame-Shift Analogy • Imagine you are bubbling-in answers on a standardized test and decide you want to skip a question and return to it later. • However, on your answer sheet, you don’t skip a line. What happens? • All your following answers are thrown off by one, just like a frame-shift.

20. AUG UUU GAG UGA UCC • Mutation 2: What if I add the AAA codon here? • (not a point mutation or frame-shift) • AUG UUU AAA GAG UGA UCC • What happens? • Methionine • Phenylalanine • Lysine • Glutamate • [Stop] • There’s an extra amino acid, but not a frame-shift mutation. Bad, but not that bad.

21. AUG UUU GAG UGA UCC • Mutation 3: What if I add a GA here? • This is a frame-shift mutation. • AUG UGA UUG AGU GAU CC • What happens? • Methionine • [Stop] • The early stop codon prevents the full protein from forming.

22. AUG UUU GAG UGA UCC • Mutation 3 is also called a nonsense mutation because it took a normal protein and terminated it early. • The protein “makes no sense,” thus, a nonsense mutation.

23. AUG UUU GAG UGA UCC • Mutation 4: What if I delete this A? • This is a deletion mutation. • AUG UUU GAG UGU CC • What happens? • Methionine • Phenylalanine • Glutamate • Cysteine • No stop codon expressed - protein keeps going!

24. AUG UUU GAG UGA UCC • Mutation 5: What if I change this A to a G? • This is a substitution mutation. • AUG UUU GAG UGGUCC • Methionine • Phenylalanine • Glutamate • Tryptophan • Serine • No stop codon expressed - protein keeps going!

25. AUG UUU GAG UGA UCC • Mutation 6: What if I change this U to a C? • This is a substitution mutation. • ACG UUU GAG UGA UCC • No start codon expressed - protein never formed!

26. AUG UUU GAG UGA UCC • Mutation 7: What if I change this A to a U? • This is a substitution mutation. • AUG UUU GUG UGA UCC • Methionine • Phenylalanine • Valine • [Stop] • [Serine] • Glutamate is changed to Valine. • Not a frame-shift mutation (isa missense). • Unfortunately, this is all it takes to get sickle-cell anemia.

27. Sickle-Cell Anemia • Protein in red-blood cells is deformed to the point that they’re not happy round red-blood cells. • Limited oxygen-carrying capacity and painful blood flow. • (draw a picture) http://adultstemcellawareness.files.wordpress.com/2007/10/sickle-cell.jpg

28. Sickle-Cell Anemia • Video

29. AUG UUU GAG UGA UCC • Mutation 8: What if I change this U to a C? • This is a substitution mutation. • AUG UUCGAG UGA UCC • Methionine • Phenylalanine • Glutamate • [Stop] • [Serine] • No change - this is a neutral mutation!

30. Neutral Mutations • Mutation 8 shows that not all mutations can cause problems. • This is what scientists think is part of the reason for there being many more codons than there are amino acids. • Neutral mutations are often called silent mutations.

31. Challenge • AUG UUU CAU UGA UCC • What happens if I change this G to an A?

32. Transcriptlate Lab • Now it’s time to try #5 on the lab. • Example DNA strand (line 1) is: • AACTGGACT • Suppose we delete the fourth base – what happens? • There is a frame-shift mutation. • Threonine is changed to Proline – a missense mutation. • Our stop codon has been deleted. That last one’s a stop codon.

33. So after all of this… • How is it a person can naturally have two different color eyes? • Mutations! • Now for my question to you: • Is it a mutation in the mRNA or the DNA? Why?

34. DNA vs. RNA • To answer this question, use an analogy: • Imagine I’m baking a cake, but I accidentally put in 4 sticks of butter instead of 2. • My cake will taste like poo. • If I bake it again, however, I probably won’t make the same mistake twice. • My cake is awesometastic.

35. DNA vs. RNA • However, what if it’s not really my mistake? What if the recipe has a typo in it? • I will continue making the same mistake each time I follow the recipe. • All my cakes will taste like poo.

36. DNA vs. RNA • In the case of the cell, if a mistake is made in the RNA, it’s probably not a big problem. • One bad protein in one cell won’t kill you. • But what if it’s a mistake in the DNA? • All proteins will be malformed. • This is especially bad if the DNA experiences a mutation early in pregnancy.

37. Therefore… • People that have two different eye colors, or some other kind of lasting mutation, likely have a mutation in their DNA, not their RNA.

38. Now for an activity… • Lightly stick your piece of masking tape to the desk horizontally. • Write exactly the following on it, making sure to leave some space between all the letters: APproPRIAteLYJOinED

39. APproPRIAteLYJOinED • Now, carefully tear your letters apart so you have separate sequences of lower case and capital letters. • In other words, whenever the case changes, tear between those two letters. • Junk the capitals…what did you spell?

40. Uh…huh. • Okay, so what’s the point? • It turns out, not all of an mRNA molecule is made into proteins. • Only some sections are; the rest are “junk.” • So why make the junk in the first place? • Well, suppose some damage to the mRNA occurs. • If all of the mRNA is important, our protein will be deformed. • BUT! If some of the mRNA is junk and damage occurs, the damage may not affect the important parts of the mRNA.

41. Exons and Introns http://upload.wikimedia.org/wikipedia/commons/1/12/DNA_exons_introns.gif

42. Exons and Introns • Exons(lower-case letters) are the parts of mRNA that are expressed (not cut out). • Introns(capital letters) are the parts of mRNA that interrupt (are cut out). • This happens in the nucleus. • Cut by structures called spliceosomes.

43. The Big Summary ofTranscription & Translation • We start with _______ in the _______. • DNA is _________ into _______. • _______ are removed, while _______ are kept. • mRNA leaves the nucleus and goes to the _______ in the cytoplasm. • mRNA is translated into a chain of __________, which makes up a _________. • Ta-da! DNA nucleus transcribed mRNA Introns exons ribosome amino acids polypeptide

44. Don’t Forget the Enzymes! • Which enzyme unwinds the DNA helix and breaks the hydrogen bonds holding together the two sugar-phosphate backbones during replication? • DNA Helicase • Which enzyme places new RNA nucleotides on the growing mRNA strand during transcription? • RNA Polymerase (also unwinds DNA helix) • Which enzyme places new DNA nucleotides on the growing DNA strand during replication? • DNA Polymerase

45. Closure • Transcriptlate Lab • Finish it! • Remember, if there’s a frame-shift, be sure to check “downstream” of the mutation. • Frame-shift errors often lead to problems with the stop codon. • Whether it gets deleted or shows up early.