Bio 9D: Wednesday, 2.16.11 Title: Using DNA to Make Proteins (Day 1)

1. Bio 9D: Wednesday, 2.16.11Title: Using DNA to Make Proteins (Day 1) • Homework: • Read pages 302-306 in the textbook. Take notes on: • Important vocab words • How does the genetic code work? • What are the steps of translation? • Silent Do Now: (in NB w/ title and date) • How do DNA, RNA, and proteins all relate to each other? • How is the functionof RNA different from the functionof DNA? • Today’s Objectives: • Describe the major differences between DNA and RNA • Explain the purpose of the three types of RNA • Explain the steps of transcription

2. Gene Expression:Using DNA to make proteins PHA Biology 9 Moretti and Dickson

3. A Day in the Life of The Cell Released into blood stream and used as hormone or other bodily structure Golgi Apparatus (Modifies and shapes the protein) Ribosome Protein being formed at Ribosome Protein Nucleus Cytoplasm Protein could go to membrane to be released into blood stream RNA Vesicles (“bubbles” that transport proteins) E.R. (transports and packages proteins) Cell Membrane RNA ::Blood Stream:: DNA Ribosomes (Holds genetic information) (Copies genetic from DNA and carries it to the Ribosome to make proteins)

4. Overview: Using DNA to Make Proteins [Leave 4-5 lines of space above this, and write it big!] DNA RNA Protein Trait • Stays in the nucleus • Copies itself and gets passed on to new cells • Holds instructions for making proteins • Observable characteristic • “Who you are” • Made in the nucleus and goes to the cytoplasm • Uses DNA instructions to make proteins • Used as body structures (muscle, bone, skin, hair), enzymes, transporters, hormones, etc.

6. DNA RNA Protein Trait Overview: Using DNA to Make Proteins Transcription: The process of making RNA by copying DNA Translation: The process of using info in RNA to make proteins • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation

7. Differences between DNA and RNA DNA RNA • Deoxyribose sugar • Double strand (forms a helix) • Bases: A, T, G, C • Ribose sugar • Single strand (can form different shapes) • U instead of T (A, U, G, C) • Objectives for Class: • Describe the major structural differences between DNA and RNA • Differentiate between structure and function differences between the types of RNA

8. Base Pairing between DNA and RNA DNARNA A ------ U T ------ A C------ G G ------ C • Objectives for Class: • Describe the major structural differences between DNA and RNA • Differentiate between structure and function differences between the types of RNA

9. Transcription: Copying DNA into RNA DNA (the red & green strands) mRNA (the orange strand) • Objectives for Class: • Describe the major structural differences between DNA and RNA • Differentiate between structure and function differences between the types of RNA

10. Transcription • Overview: • A DNA gene is copied into RNA • Occurs in the nucleus • Steps: • RNA Polymerase separates (unzips) DNA strands • RNA Polymerase makes RNA by matching complementary nucleotides with the DNA strand • mRNA leaves nucleus and DNA winds back up! • Final Result: mRNA copy of a gene Video link: 17_13ProteinSynthesis.mpg • Objectives for Class: • Describe • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation mRNA

11. Are we now ready to make proteins? What do we need besides instructions? • Needed for making proteins: • Amino acids (protein building-blocks) • Ribosome (to connect the amino acids into a protein chain)

12. Bio 9D: Thursday, 2.17.11Title: The Genetic Code • Homework: Finish the Decoding Worksheet if you don’t finish in class. • Silent Do Now: (NOT in notebook – on handout) • Answer the questions on the half-page handout! • Today’s Objectives: • Use a DNA sequence and transcribe it into an RNA sequence • Use the Genetic Code to translate RNA into a protein

13. Trade papers & correct your partner’s Do Now • mRNA’s job = carry a copy of DNA’s instructions to the ribosome to make a protein • Transcription = copying DNA into RNA • RNA sequence: A U G C A U G C A • Amino acid = monomer of proteins. You put a lot of them in a chain to make a protein. • Codon = 3-letter word on mRNA. Each codon stands for one amino acid in the protein chain.

14. Today’s Agenda: • Do Now • Explanation of the Genetic Code • Follow along with the examples on the worksheet! • Decoding Worksheet

15. Reading The Genetic Code • The letters in the wheel are mRNA codons • Start in the middle! • This is the first letter in the codon • Move to the middle ring (2nd letter in the codon) • Then go to the outer ring of letters (3rd letter in the codon) • Outermost ring = amino acids!

16. Reading The Genetic Code: Examples • Follow along with the examples in your packet! • Example 1: CAG • 1st base = C • 2nd base = A • 3rd base = G • Therefore the • amino acid is… • Glutamine! • Example 2: GUU • Valine

17. Reading The Genetic Code: Longer Example • Example 3: GCCAGCUAG • Step 1: Break it into 3-letter sections (codons) • GCC AGC UAG • Step 2: Decode each codon • GCC = Alanine • AGC = Serine • UAG = STOP(end of protein sequence) 1 3 2

18. Today’s Agenda: • Do Now • Explanation of the Genetic Code • Decoding Worksheet: Work quietly with your partner at your table to finish the rest of the packet • Finish it for HW if you don’t finish in class.

19. Bio 9D: Friday, 2.18.11Title: Using DNA to Make Proteins (continued) • Homework: Finish the Computer-Based Transcription & Translation Lab if you don’t finish in class. • Silent Do Now: (NOT in notebook – on handout) • Get a lab handout • Silently read the first two paragraphs • In the space next to the Key Words, write a quick definition of transcription and translation • Today’s Objectives: • Use the Genetic Code to make a protein • Analyze amino acid sequences to determine the shape of a protein • Analyze how changes in DNA (mutations) affect proteins

20. Computer Lab:Transcribe and Translate a Gene • Get a laptop • Follow the instructions to complete the lab • Then complete Part 2 on a separate sheet of paper • When most people are finished or during 2nd period, we will watch a video

21. Seats At Back TablesWork alone or with your partner but do not talk/wander across tables! Lorreno Miguel Marcelo Carlheb Kayla Owen Warren Samantha Nekeyla Christine Davnys TraeLoveng Jackson Joas Hannah Nicholas Dyani Courtney Rayoni Celeste

22. Bio 9D: Monday, 2.28.11Title: RNA and Translation • Homework: Two paragraphs on transcription and translation (in your notebook – see assignment sheet for details) • Silent Do Now: • Get an assignment sheet and a Do Now sheet • Get started on the Do Now, then use your notes to help answer all the questions • Today’s Objectives: • Explain the purpose of the three types of RNA • Explain the steps of transcription and translation

24. Transcription • Overview: • A DNA gene is copied into RNA • Occurs in the nucleus • Steps: • RNA Polymerase separates (unzips) DNA strands • RNA Polymerase makes RNA by matching complementary nucleotides with the DNA strand • mRNA leaves nucleus and DNA winds back up! • Final Result: mRNA copy of a gene • Objectives for Class: • Describe • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation mRNA

25. Three Types of RNA: • Messenger RNA (mRNA) - Carries a copy of protein-making instructions to the ribosome • Every 3 letters is a codon that stands for one amino acid to make the protein

26. Three Types of RNA: • Transfer RNA (tRNA) – Carries amino acids to the ribosome • Contains anticodonsthat match up with mRNA codons to put amino acids in the correct order

27. Three Types of RNA: • Ribosomal RNA (rRNA) – Part of the ribosome (helps bond amino acids together)

28. Making Proteins at the Ribosome Amino Acid Growing Protein t RNA t RNA Ribosome Anticodon Codon mRNA • Objectives for Class: • Describe • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation

29. Translation Ribosome Growing protein chain mRNA strand • Objectives for Class: • Describe • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation

30. Transcription and Translation: Video • Transcription and Translation Video: 17_13ProteinSynthesis.mpg • Objectives for Class: • Describe the purpose and major steps of transcription • Describe the purpose and major steps of translation

31. Translation Details • Overview: • The gene sequence in mRNA is translated into a chain of amino acids that forms a protein • Occurs at the ribosome • Steps: • mRNA enters the ribosome • tRNA molecules bring amino acids to the ribosome • tRNAanticodons match with mRNA codons to put amino acids in the right order • According to the Genetic Code • Ribosome connects the amino acids into a long chain • Final Result: A polypeptide (protein)

32. Transcription & Translation Transcription Translation • Objectives for Class: • Describe

33. Homework: • Two paragraphs on transcription and translation • See assignment sheet for details

34. Bio 9A/9D: Tuesday, 3.1.11Title: Genetic Mutations Day 1 – Types of Mutations • Homework: • Finish up through Example #4 in the Genetic Mutations packet • Do Now: (on the Genetic Mutations packet) • Answer Preview Questions #1-3 • Today’s Objective: • Describe the major differences between substitution and frame-shift mutations

35. Gene Mutations Activity: Part I Review • What is a Genetic Mutation? • A change in the base-pair sequence of DNA • The three types of point mutations: • substitution (switch one DNA nucleotide for another) • insertion (add an extra nucleotide into the DNA sequence) • deletion (leave out one nucleotide in the DNA sequence) • Objectives for Class: • Describe the major differences between substitution and frame-shift mutations

36. Genetic Mutations Activity • Complete Part II of the Genetic Mutations packet (Examples #1-4) • Finish for HW if you don’t finish in class • Analysis Questions are not due tomorrow but will be due later in the week – start them now if you have time! • Work quietly with ONE partner sitting near you (we will not have groups bigger than 2!) • Objectives for Class: • Describe the major differences between substitution and frame-shift mutations

37. Bio 9A/9D: Wednesday, 3.2.11Title: Genetic Mutations • Homework: • Study for tomorrow’s QUIZ by answering the study guide questions (see back of assignment sheet) • Silent Do Now: (in notebook w/ title & date) • What is a genetic mutation? • Based on the packet from yesterday, what is the difference between a substitution mutation and a frame shift mutation? • What are two things that result in a frame shift? • Today’s Objective: • Describe the major differences between substitution and frame-shift mutations

38. Today’s Agenda • (As a class) Review Examples #1-4 from the Mutations packet • (On your own) Answer the Analysis Questions at the end of the Mutations packet • (On your own) Begin studying for tomorrow’s quiz by answering the study guide questions on the back of the assignment sheet – finish this for HW!

39. Genetic Mutations Activity – Substitution Mutations • Original DNA Sequence • Substitution Changes the Amino Acid • Substitution/ Silent Mutation Does not Change the Amino Acid • Objectives for Class: • Describe the major differences between substitution and frame-shift mutations

40. Genetic Mutations Activity –Frame-Shift Mutations • Frame-Shift Mutations • Original DNA Sequence • Frame-Shift: Deletion of nucleotide Changes all Amino Acid after mutation • Frame-Shift: Insertion/ Addition of nucleotide Changes all Amino Acid after mutation • Objectives for Class: • Describe the major differences between substitution and frame-shift mutations

41. Today’s Agenda • (As a class) Review Examples #1-4 from the Mutations packet • (On your own) Answer the Analysis Questions at the end of the Mutations packet • (On your own) Begin studying for tomorrow’s quiz by answering the study guide questions on the back of the assignment sheet – finish this for HW!

42. Bio 9A/9D: Thursday, 3.3.11Title: Quiz – Transcription, Translation, and Mutations • Homework: • None • Do Now: • Clear your desks and get ready to take the quiz… • Start as soon as you get the quiz • Stay silent and focus on your work. • If you finish early:Do the extra credit reading • Today’s Objective: • Demonstrate your understanding of how the processes of transcription and translation create proteins from the genetic code on DNA

43. Bio 9A/9D: Friday, 3.4.11Title: Sickle Cell Anemia Lab • Homework: • Write at least the first 3 sections of your Sickle Cell Lab Report • Silent Do Now: (in notebook w/ title & date) • Do a brainstorm about sickle cell anemia: • Have you heard of this disease? If so, what do you know about it? What do you think you know? • What questions do you have about sickle cell anemia? • What else comes to mind? • Today’s Objectives: • Identify important pieces of background information about sickle cell anemia • Determine a procedure for analyzing DNA sequences to determine the cause of sickle cell anemia

44. Lab: Sickle Cell and Genetic Mutations A Case Study of Sickle Cell Disorder • Read through the Introduction to the lab. • Watch 5 minute video on sickle cell disorder • PBS Evolution Library: A Mutation Story • http://www.pbs.org/wgbh/evolution/library/01/2/l_012_02.html • In small groups brainstorm the Background Information needed for this lab • You should have 2 parts: • General genetics background info • Info related to sickle cell anemia • Come back together as a class to brainstorm final list • Objectives for Class: • Brainstorm and organize the background information necessary to successfully explain what sickle cell anemia is and how it is caused.

45. Lab: Sickle Cell and Genetic Mutations

46. Bio 9A/9D: Monday, 3.7.11Title: Sickle Cell Anemia Lab (Day 2) • Homework: • Complete your Sickle Cell Anemia Lab Report • Silent Do Now: (in notebook w/ title & date) • Today’s Objectives: • Identify important pieces of background information about sickle cell anemia • Determine a procedure for analyzing DNA sequences to determine the cause of sickle cell anemia

47. Valine: • Glutamic acid:

48. Second Half of Double Block Lab: Sickle Cell and Genetic Mutations Individual Work Time… • Two Options: • Type Analysis and Conclusion sections of lab report and revise your other sections • Guided peer review of Background Information section • Objectives for Class: • Analyze the DNA sequence for the sickle cell gene and the normal gene to determine how DNA is mutated to result in sickle cell anemia • Complete the Sickle Cell Mutation Lab Report

49. Bio 9A: Tuesday, 3.8.11Title: Sickle Cell Lab Report – Peer Editing • Homework: • Revise your lab report and have the final draft printed and ready to turn in. • Do Now: • Take out your lab report. • On the top of the page, answer these questions: • What part of your lab report do you think is the best? • What part needs the most improvement, or what part do you have questions about? • Today’s Objective: • Peer edit lab reports in order to make revisions and produce excellent final drafts!

50. Peer Editing 20 minutes: • Silently read and comment on your partner’s lab report • Fill out the rubric and the form on the back 15 minutes: • Meet w/ your partner • Discuss comments and top 3 priorities for revision