Do Now

1. Do Now • What happens to an egg when you fry it in a pan? Why do you think this is? Explain using your previous knowledge and experience. • P. 31 of INB 2-3 sentences

2. Think About it • How do you build a paragraph?

3. Build a protein • On your desk, you have pipe cleaners and ribbons • You may twist, bend, curl your pipe cleaners and ribbons • You may make knots with the ribbon or make small paper balls and push it through the pipe cleaner • You may not cut the ribbon or pipe cleaners.

4. Protein Structure Today we will understand protein structure and discuss how they are made!

5. Build a Protein • Why do proteins look like this? • How do you think the shapes are formed? • Can you try to undo your protein the way you made it earlier?

6. Do Now • Reflect on your test score: whatcould you have done differently to better increase it? What still confuses you? What do you needmost help on (study habits, note-taking, etc.) • P. 35

7. Notes • Rule of thumb for note taking • Take note of anything bolded, underlined, italicized it might be important later! • Look at the HEADLINES of the slide so you know what we’re currently discussing!

8. Protein Structures • Know that there are 4 general levels of protein structure • Primary • Secondary • Tertiary • Quaternary • The first 3 levels are always present in proteins

9. Primary Structure • Is the direct product we get after translation begins • A polypeptide is a chain of amino acids • This is the simplest level of protein structure • These are linked together by peptide bonds. • Made and broken by water • Hydrolysis= water breaking • Dehydration= water losing

10. Quick Build • With your materials in front of you predict what the primary structure of a protein might look like • Build using your pipe cleaners or ribbons or both!

11. Primary Structure

12. No one is Always Right • It is OK to be incorrect about predictions • Scientists usually are a majority of the time before they make a discovery • Don’t be afraid to fail! It’s part of being a scientist.

13. White-board quick check • Write on your whiteboards answering these questions: answer in either a drawing, a definition, or a brief explanation • How many levels of structure are there? • What is the first level of structure called? What does it kind of look like? • How do you build the primary structure? (think of the chemistry behind it).

14. Predict with a model • What do you think the secondary structure of a protein looks like? • Work independently first then share with your shoulder partner • Use your materials and manipulate them in what you think is right! • Use the knowledge we just presented!

15. Secondary Structure • This is the second level of protein formation • It involves hydrogen bonds interacting with each other • The end outcome of hydrogen bond interactions is a beta-pleated sheet or alpha helix • Loops, coils and sheets form from such interactions.

17. White board Quick-Check • Write a quick summary or draw an image on primary and secondary structure • Think about: • Chemistry behind how these are made • The best way to describe these structures

18. Whiteboard review • How are proteins formed? Describe the process in a concise paragraph using academic vocabulary • I will come check your responses.

19. Tertiary Structure • Predict what you think the tertiary structure might look like • Think about what you already know from primary structure. What else is there left to do?

20. Tertiary Structure • Is a 3-D shape that involves the R-groups of the amino acids in the protein chain • These side-chains interact with each other and conform to form a 3D structure. • Usually involves disulfide bridges, hydrogen bonds, and hydrophobic interactions

21. Quaternary Structure • Not always present in ALL proteins • Usually involves 2 or more protein complexes that come together due to bonds between adjacent polypeptides • This part of protein structure is “optional” and not always a necessitywhen building proteins.

22. White-board Quick Check • Draw, give a definition, or explain what the tertiary structure looks like and how it is formed. • Summarize the key difference between a quaternary structure and primary, secondary, and tertiary structure.

23. Chaperone Proteins • Chaperone proteins are involved in making sure the protein folds in the correct way • “hand holding” of polypeptide structure to make sure it folds properly • They stabilize partiallyfolded regions in their correct form • Help chemical bonds form as the shape comes to be • If something goes wrong, folding stops and more chaperone proteins are transcribed to help with proper folding.

24. #Tweet! • On the poster in the front of the class • Write a tweet (140 characters or less) on what you think you learned about protein structures • Use #’s and @ and get creative!

25. Article Read • Place the article on p.36 of your NB’s • Answer the following questions on p. 35 below your Do Now: complete sentences. • How are genetic disorders like PKU and amyloid neuropathy caused? • What would a pharmacological (chemical) chaperone do in this case? • What did the researchers do in order to test their chaperone protein (summarize methods in your own words) • What can be a potential drawback to starting human trials? What is the potential consequence? • How would scientists use proteins that are neither agonists or antagonists? (mimic drugs vs blocks release of drugs in body)

26. Exit Ticket • Please put away your notes • Take time to do this exit ticket for 10 minutes • Then We will switch and grade. Place graded exit tickets on p.38 • You will write a reflection on your score!

27. Do Now • What did you do over the weekend? How do you like to spend time with your friends and family? • P.37

28. Today we will… • Explain what happens to proteins when things go wrong in the folding process • How genes control which proteins are expressed • How cell specialization is determined

29. Protein Misfolding • Misfolded Protein are sent out to the ER into the cytoplasm, to be “tagged” • Tagged by ubiquitin: a protein that is used on misfolded proteins • 1 ubiquitin allows for the protein to straighten out and reform itself • More than 1 ubiquitin tag: protein is sent out to a proteasome mutli-protein structure used to break down a misfolded protein!

30. Protein Misfolding • Proteasomes also destroy proteins that are in excess and are no longer needed. • Allows for recycling of amino acids so they can be used again for other proteins • Also help to dismantle proteins from viruses • Ex. Sickle-cell anemia is caused by improper forming of hemoglobin protein • Can also cause “clogged proteasomes” when there is a disorder that prevents proteasomes from breaking down proteins.

32. Whiteboard Quick Check • Draw, describe in a paragraph, or write a definition for what a proteasome is • What occurs to a protein when it is misfolded?

33. Prions • Prions cause diseases in the brain. These are glycoproteins that are alternately folded • One conformation is considered infectious, thus causing another protein to change shape • The diseases that prions cause are called transimissible spongiform encephalopathies (TSE’s). • Cause the brain to be full of holes • Symptoms include tremors, dementia, and extreme weight loss

34. Mad Cow Disease • Things like “mad cow disease” also formerly known as BSE (bovine spongiform encephalopathy) are caused by feeding infected organisms to cattle, which then ingest these contagious prions • Cruetzfeldt-Jakob Disease is a genetic disorder that causes similar symptoms you would see in “mad cow”. • Sometimes these disorders occur spontaneously with no family history.

35. Summarize • Read section 10.4 in your genetics text book and be sure to answer the following questions after you have written a summary on p. 37 of your notebook. • 1. Build an acronym/short phrase to help you remember the levels of protein structure • 2. Draw a diagram that shows protein structure from primary to quaternary: color and label diagram • 3. Write a question you would ask on a quiz based on your knowledge of protein structure: • Make it highly rigorous if you feel extremely confident (analyze, evaluate, predict, paraphrase, etc.) come see me for key words for higher level questions.