1. Bio 9C: Thursday, 2.17.11 Title: RNA Structure and Function  Homework:  Read pages 302-306 in the textbook. Take active reading notes, paying attention to important vocabulary terms and to the following purpose questions: How does the genetic code work? What are the steps of translation?  Do Now: In your notebook:  If you had a DNA sequence of T A C A G C T, what would the matching RNA sequence be?  Hit the space bar to see the answer… A U G U C G A  Today’s Objectives:  Describe the major structural differences between DNA and RNA  Differentiate between structure and function differences between the types of RNA

2. RNA: STRUCTURES & FUNCTIONS PHA Biology 9 Moretti and Dickson

3. RNA Structure & Function of Different Types

4. RNA Structure: Base Pairing  4 Nitrogen Bases in RNA:  Adenine  Guanine  Uracil  Cytosine  RNA –> DNA Base Pairing:  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

5. RNA Structure: DNA vs. RNA 3 Major Structural Differences DNARNA Deoxyribose SugarRibose Sugar Double Strand Single Strand (generally) Uses Thymine (T)Uses Uracil (U) Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

6. Types of RNA: Overview Type of RNABasic Function Messenger RNA (mRNA) Copy genes on the DNA (transcription) Transfer RNA (tRNA) Translate mRNA into a protein Carry amino acid to the ribosome Ribosomal RNA (rRNA) (we will not focus on rRNA) Part of the ribosome Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

7.  Basic Structure:  Single Strand of RNA  Basic Function  Make a copy of DNA instructions to make a protein  Takes those instructions from DNA to Ribosome to make a protein  Every 3 bases is a Codon Remember: Small enough to leave the nucleus. DNA is too big! Types of RNA: Messenger RNA (mRNA) Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

8.  Basic Structure:  Coiled RNA strand  Amino Acid attached to the top  Anti-codon on the bottom  Basic Function:  Transfer amino acids to the ribosome to make a protein  Anti-codon on tRNA matches/ reads codon on mRNA Types of RNA: Transfer RNA (tRNA) Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

9. Types of RNA: Transfer RNA (tRNA) Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

10. Decoding the Genetic Code

11. The Genetic Code  The 64 Codons that code for Amino Acids Objectives for Class: Use the genetic code to translate a DNA or RNA sequence into an amino acid sequence to make a protein.

12. Reading The Genetic Code  mRNA codons are 3 bases long and specify a particular amino acid.  To use the wheel, the 1 st base (letter) of codon matches the biggest letter and you move out from the middle to read the rest of the codon.  Therefore, the 2 nd base in the codon is the second biggest letter (the one in the middle ring) and the 3 rd base In the codon is the smallest letter (the one in the outer ring).  The arrows show the direction you should read it.

13. The Genetic Code  Complete Part I of the “Decoding the Genetic Code!” Activity. (we will review the first 3 examples of question 1 after you have had a chance to complete them) Objectives for Class: Use the genetic code to translate a DNA or RNA sequence into an amino acid sequence to make a protein.

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

15. 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 2 3

16. Bio 9C: Friday, 2.18.11 Title: Transcription and Translation with RNA  Homework:  No Homework over the break!  Do Now: In your notebook:  Next slide…  Today’s Objectives:

17. MCAS Prep Question The mold Aspergillus flavus grows on grain. A. flavus produces a toxin that binds to DNA in the bodies of animals that eat the grain. The binding of the toxin to DNA blocks transcription, so it directly interferes with the ability of an animal cell to do which of the following? A. Produce ATP using energy released from glucose and other nutrient B. transport glucose across the cell membrane into the cytoplasm C. Transfer proteins from the endoplasmic reticulum to Golgi complexes D. Send protein-building instructions from the nucleus to the cytoplasm and ribosomes

18.  Overview:  What is the hidden message in Part II of the homework assignment?  “Give Neighbor High 5” Yesterday’s Class work Review Question Objectives for Class: Describe the purpose and major steps of transcription Describe the purpose and major steps of translation

19.  Overview:  A DNA gene is copied in the form of mRNA  Occurs in the nucleus  Steps: 1. RNA Polymerase separates DNA strands 2. RNA Polymerase moves along one of the DNA strands (template) 3. RNA Polymerase makes mRNA by attaching RNA nucleotides that match the DNA template mRNA Transcription Detail Objectives for Class: Describe the purpose and explain the major steps of transcription.

20. Types of RNA: Messenger RNA (mRNA) mRNA (the orange strand) DNA (the red & green strands) Objectives for Class: Describe the major structural differences between DNA and RNA Differentiate between structure and function differences between the types of RNA

21. tRNAtRNA mRNA tRNAtRNA Ribosome Codons & AntiCodons  Codon  3 base sequence on mRNA that specifies a single amino acid to be added to the polypeptide (protein)  Anticodon  3 base sequence on tRNA that are match up with the mRNA codon Objectives for Class: Describe Polypeptide Anticodon Codon Amino Acid

22. Translation Detail  Overview:  mRNA copy provides instructions for assembling amino acids into a protein  Occurs at the ribosome  Steps: 1. mRNA enters the ribosome 2. tRNA molecules bring amino acids to the ribosome 3. tRNA anticodons match with mRNA codons to put amino acids in the right order According to the Genetic Code Objectives for Class: Describe the purpose and major steps of transcription Describe the purpose and major steps of translation

23. Translation Objectives for Class: Describe the purpose and major steps of transcription Describe the purpose and major steps of translation

24. Transcription & Translation TranscriptionTranslation Objectives for Class: Describe the purpose and major steps of transcription Describe the purpose and major steps of translation

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

26. Bio 9C: Monday, 2.28.11 Title: Transcribe and Translate a Gene Computer Lab  Homework:  Pass in the codons and amino acid decoding practice homework  Complete Part II of the Transcription & Translation Computer Lab  Do Now:  Sign into a computer and turn around with your back to the computers to wait for your next instructions.  Today’s Objective:  Use the steps of transcription and translation to turn a section of DNA into a protein.

27. Transcribe and Translate a Gene Computer Lab TranscriptionTranslation Objectives for Class: Use the steps of transcription and translation to turn a section of DNA into a protein. Procedure:  Log onto http://learn.genetics.utah.edu/http://learn.genetics.utah.edu/  Click on DNA TO PROTEIN. Then click the link entitled TRANSCRIBE AND TRANSLATE A GENE.  A DNA sequence should appear on the screen.  Record the original DNA sequence  Transcribe the DNA strand by typing in the corresponding RNA bases for the original strand. The new mRNA strand will now appear on the screen.  Locate the “start” codon and click on it with your mouse. The mRNA sequence will now move to the top of the field and a flashing box will appear around the “start” codon.  Using the “Universal Genetic Code” to the right, find the amino acid that corresponds with the three-base mRNA codon. Click on the appropriate amino acid and drag it to the corresponding mRNA codon (signaled by the flashing box). Repeat until the mRNA sequence has been Translated.  Record the amino acid sequence of your translated polypeptide (1 pt):  Look carefully at your polypeptide. Compare and contrast the 4 different amino acids in the polypeptide chain.  Describe the overall shape of your polypeptide (protein). (Consider how the R-groups (the side chains) of each amino acid are oriented in relation to each other.  How do you think the protein would change if you switched one amino acid for a different one?

28. Remember R-groups?

29. Bio 9C: Tuesday, 3.1.11 Title: Genetic Mutations Day 1 – Types of Mutations  Homework:  Complete Part II of the Genetic Mutations Activity For Thursday  Pass Computer-Based Lab to the left.  Do Now:  Complete Part I of the Genetic Mutations Dry-Lab (this should take a total of 5 min)  Today’s Objective:  Describe the major differences between substitution and frame-shift mutations

30. 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

32. Gene Mutations Activity Part II  Complete Part II of the Gene Mutations Activity by comparing substitution & frame-shift mutations  Part II Review:  Original DNA Sequence Objectives for Class: Describe the major differences between substitution and frame-shift mutations

33. Bio 9C: Wednesday, 3.2.11 Title: No Class – Play for Ninth Grade  Homework:  Do Now:  Today’s Objective:

34. Bio 9C: Thursday, 3.3.11 Title: Genetic Mutations Day 2 – Sickle Cell Case Study  Homework:  Do Now:  Which of the different mutations has the biggest effect on the amino acid sequence? What effect does this have on the protein? What would happen to an enzyme that experienced this type of mutation?  Today’s Objective:  Describe the major differences between substitution and frame-shift mutations

35. Gene Mutations Activity Part II  Complete Part II of the Gene Mutations Activity by comparing substitution & frame-shift mutations  Part II Review:  Original DNA Sequence Objectives for Class: Describe the major differences between substitution and frame-shift mutations

36. Gene Mutations Activity Part II  Substitution Mutations  Original DNA Sequence  Substitution  Substitution/ Silent Mutation Changes the Amino Acid Does not Change the Amino Acid Objectives for Class: Describe the major differences between substitution and frame-shift mutations

37. Gene Mutations Activity Part II  Frame-Shift Mutations  Original DNA Sequence  Frame-Shift: Deletion of nucleotide  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

38. 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: 1. General genetics background info 2. 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.

39. Bio 9C: Wednesday, 3.10.10 Title: Quiz – Transcription, Translation, and Mutations  Homework:  Type the Background Information and Procedure sections of your lab report for Thursday. (NOTE: completed lab reports are due Friday at the start of class. You will have time to work on it during Thursday’s class, but if you need more time/ don’t have access to a computer at home, please make arrangements now to complete the lab Thursday after school). Begin typing Analysis and Conclusion sections.  Do Now:  Clear your desks and get ready to take the quiz…  Today’s Objective:  Demonstrate your understanding of how the processes of transcription and translation create proteins from the genetic code on DNA  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

40. Lab: Sickle Cell and Genetic Mutations Background Information Brainstorm Genetics Topics: three different types of mutations, (explain them – similarities & differences) General description of mutation What a gene is? where its found? How genes makes proteins One sentence about transcription & translation (the overview) DNA & RNA, structure & function Effects of mutation on protein structure How amino acids make up proteins Codons Ribosomes Sickle Cell Topics: how sickle cell is passed on (genetic disorder) What sickle cell is How it can be a good or bad mutation Changes shape of hemoglobin protein, what does it effect?

41. A Case Study of Sickle Cell Disorder… http://www.pbs.org/wgbh/evolution/library/01/2/l_012_02.html http://www.pbs.org/wgbh/evolution/library/01/2/l_012_02.html  Write the purpose of the lab  Develop your hypothesis based on the purpose  Analyze the DNA sequence for the sickle cell gene and the normal gene by transcribing and translating them.  Compare the sickle cell gene to the normal gene  Complete the analysis and conclusion sections of the lab report. Lab: Sickle Cell and Genetic Mutations 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

42. Bio 9C: Thursday, 3.11.10 Title: Genetic Mutations Day 3 – Sickle Cell Case Study  Homework:  Complete the Procedure, Analysis and Conclusion sections of your lab report. Completed lab report with all sections is due tomorrow, Friday, at the start of class!!!!  Do Now:  Decide if you want/ need support with the Background Information section or time to type the report. We will quickly divide the room.  Today’s Objective:  Complete the Sickle Cell Mutation Lab Report

43. Individual Work Time…  Two Options: 1. Type Analysis and Conclusion sections of lab report and revise your other sections 2. Guided peer review of Background Information section Lab: Sickle Cell and Genetic Mutations Objectives for Class: Complete the Sickle Cell Mutation Lab Report

44. Bio 9C: Friday, 3.12.10 Title: Sickle Cell Case Study – Lab Report Peer Review  Homework:  Complete the Sickle Cell lab report revision for Monday.  Complete the Bio-Blog homework for Thursday (Meiosis Vocab): http://phascience.wordpress.com/biology-9-moretti-dickson-powerpoint-notes-etc/ http://phascience.wordpress.com/biology-9-moretti-dickson-powerpoint-notes-etc/  Do Now:  Divide class into peer editing teams.  Today’s Objective:  Peer review and complete the Sickle Cell Mutation Lab Report