Proteins (IB Topic B1.2)

Essential Idea(s): Proteins are the “workhorses” of life. They carry out a wide range of functions in living organisms.

Unit Length: 2 Lessons (+2 AHL)

Guiding Questions

◊ What is the relationship between amino acid sequence and the diversity in form and function of proteins?

◊ How are protein molecules affected by their chemical and physical environments?

Materials:

Self-Teaching Slides (SL) / Self-Teaching Slides (AHL)	Quizlet Vocab Set (SL + AHL)
Teaching Slides (AHL)	Notes Template (SL) / Notes Template (AHL)

IB Statement(s) and Objective(s)
B1.2.1: Generalized structure of an amino acid Draw the generalized structure of an amino acid B1.2.2: Condensation reactions forming dipeptides and longer chains of amino acids Describe polypeptide chain formation (inc. the formation of peptide bonds and condensation reactions) Draw peptide bond formation via a condensation reaction B1.2.3: Dietary requirements for amino acids Define “essential” and “non-essential” as related to dietary nutrients Outline the need for the vegan diet to ensure essential amino acids B1.2.4: Infinite variety of possible peptide chains State the number of amino acids used by living organisms to make polypeptides Explain the evolutionary implication from the assembly of all polypeptides from the same amino acids Define dipeptide, oligopeptide and polypeptide Explain the infinite variety of possible peptide chains B1.2.5: Effect of pH and temperature on protein structure Define denaturation Outline the effects of pH and temperature on protein structure
Additional Higher Level Topics B1.2.6: Chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function Given an image of an amino acid, classify the amino acid chemical properties based on R group properties Explain the relationship between the diversity in amino acid R-groups and the immense diversity in protein form and function B1.2.7: Impact of primary structure on the conformation of proteins Outline the levels of protein organization Describe the primary structure of a protein, including the type of bonding involved B1.2.8: Pleating and coiling of secondary structure of proteins Describe the secondary structure of a protein, including the type of bonding involved Identify the alpha-helix and beta-pleated sheet in images of protein structure B1.2.9: Dependence of tertiary structure on hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions B1.2.10: Effect of polar and non-polar amino acids on tertiary structure of proteins Describe the tertiary structure of a protein, including the types of R group interactions involved Explain the role of the amino acid cysteine in forming disulfide bonds Describe the role of disulfide bonds in maintaining the tertiary structure of a protein Define zwitterion Outline how R-groups in amino acids can function as both acids and bases Define ion and ionic bond Outline why hydrophobic amino acids are clustered in the core of globular proteins Explain how the polarity of integral proteins serves as an example of the “form and function” concept B1.2.11: Quaternary structure of non-conjugated and conjugated proteins Outline the quaternary structure of protein folding Describe the structure of a conjugated protein, including the prosthetic group Outline the structure and function of one conjugated and two non-conjugated proteins NOS Concept: Technology begets discovery B1.2.12: Relationship of form and function in globular and fibrous proteins Contrast the structure of globular proteins with the structure of fibrous proteins Using insulin and collagen as 2 examples, explain how the form/shape of a protein suits its function

IB Statement(s) and Objective(s)

B1.2.1: Generalized structure of an amino acid

Draw the generalized structure of an amino acid

B1.2.2: Condensation reactions forming dipeptides and longer chains of amino acids

Describe polypeptide chain formation (inc. the formation of peptide bonds and condensation reactions)
Draw peptide bond formation via a condensation reaction

B1.2.3: Dietary requirements for amino acids

Define “essential” and “non-essential” as related to dietary nutrients
Outline the need for the vegan diet to ensure essential amino acids

B1.2.4: Infinite variety of possible peptide chains

State the number of amino acids used by living organisms to make polypeptides
Explain the evolutionary implication from the assembly of all polypeptides from the same amino acids
Define dipeptide, oligopeptide and polypeptide
Explain the infinite variety of possible peptide chains

B1.2.5: Effect of pH and temperature on protein structure

Define denaturation
Outline the effects of pH and temperature on protein structure

Additional Higher Level Topics

B1.2.6: Chemical diversity in the R-groups of amino acids as a basis for the immense diversity in protein form and function

Given an image of an amino acid, classify the amino acid chemical properties based on R group properties
Explain the relationship between the diversity in amino acid R-groups and the immense diversity in protein form and function

B1.2.7: Impact of primary structure on the conformation of proteins

Outline the levels of protein organization
Describe the primary structure of a protein, including the type of bonding involved

B1.2.8: Pleating and coiling of secondary structure of proteins

Describe the secondary structure of a protein, including the type of bonding involved
Identify the alpha-helix and beta-pleated sheet in images of protein structure

B1.2.9: Dependence of tertiary structure on hydrogen bonds, ionic bonds, disulfide covalent bonds and hydrophobic interactions

B1.2.10: Effect of polar and non-polar amino acids on tertiary structure of proteins

Describe the tertiary structure of a protein, including the types of R group interactions involved
Explain the role of the amino acid cysteine in forming disulfide bonds
Describe the role of disulfide bonds in maintaining the tertiary structure of a protein
Define zwitterion
Outline how R-groups in amino acids can function as both acids and bases
Define ion and ionic bond
Outline why hydrophobic amino acids are clustered in the core of globular proteins
Explain how the polarity of integral proteins serves as an example of the “form and function” concept

B1.2.11: Quaternary structure of non-conjugated and conjugated proteins

Outline the quaternary structure of protein folding
Describe the structure of a conjugated protein, including the prosthetic group
Outline the structure and function of one conjugated and two non-conjugated proteins
NOS Concept: Technology begets discovery

B1.2.12: Relationship of form and function in globular and fibrous proteins

Contrast the structure of globular proteins with the structure of fibrous proteins
Using insulin and collagen as 2 examples, explain how the form/shape of a protein suits its function


Activities: ⓟ = podcast / ⍰ = inquiry 5 / ⓦ = Write it / Ӕ = The academy / Ⓡ = Read it
ⓟ/ⓦ (recommended): The 2024 Nobel Prize in Chemistry Goes to… Protein-Predicting AI! (and the scientists who built it) (💁 [writeup] / 👭 [podcast – max 3]) Imagine solving one of biology’s most elusive mysteries — called “the protein-folding problem” — with the click of a button, or designing entirely new proteins to combat diseases, or new proteins to clean up the environment. This is the legacy of the Nobel-winning breakthroughs in AI in 2024. Demis Hassabis, John Jumper, and David Baker brought together biology and artificial intelligence to transform how we study proteins. Watch Baker’s 2019 Ted Talk here, and/or read through this summary article, do whatever further research you feel necessary then discuss: What makes proteins essential for life, and how does their structure influence their function? Why was predicting protein structure such a difficult problem, and how does AlphaFold solve it? How are AlphaFold and protein design changing real-world research and applications? What kind of work will scientists be doing (around the same time you are pursuing a career? 😉) What ethical, scientific, or societal questions arise from these technologies? (Side note: It’s super interesting to align this task to David Baker’s 2019 TED Talk below to see how far we’ve progressed in 5 years.) ⓟ/ⓦ: The Most Amazing Machines in the World (💁 [writeup] / 👭 [podcast – max 3]) From TED.com: “Proteins are remarkable molecular machines: they digest your food, fire your neurons, power your immune system and so much more. What if we could design new ones, with functions never before seen in nature?” Watch this 10-minute TED Talk about a potentially huge future realm of science: *custom proteins. Then, write/discuss some inquiry prompts related to the talk. Here are a few to get you started: What exactly is it that proteins DO in the world of biology? How are proteins manufactured in the body (hint: Outline what DNA transcription and translation are) What do you think about the idea of customizing proteins? Would this be a good thing, or a bad thing, and why? Lab ⓟ/ⓦ: Fry an Egg and Teach Denaturing Proteins* (💁/ 👭max 2) You need 3 simple things for this at-home lab: Egg whites Ethanol, or a hard liquor (such as vodka…with parental permission, of course) A stovetop + pan “Denaturing” is the fancy science word that refers to killing a protein (individual proteins are obviously not alive, so the word ‘killing’ doesn’t quite work). How can we denature a protein? Read through this lab and, complete the ethanol/heating parts, and then discuss your observations with some good analytical follow up questions/prompts. Here are a few to get started: Protein Denaturation lab Record what happens to egg whites with both heat and ethanol, and why Explain what happens when a protein denatures How and why pH and temperature can denature proteins (You can disregard the pH measurements if attempting this lab at home) ⓟ/ⓦ: Proteins: Our Ticket to a COVID-free World (💁 [writeup] / 👭 [podcast – max 3]) The COVID vaccine currently being rolled out is unique: it introduces mRNA into the body, which the body reads to make the spike proteins found on the outside of the virus (see the spike proteins in this image). Then, the body makes immunoglobulin proteins (antibodies) to attack these spike proteins. Should the real coronavirus ever show up…those antibodies will be ready for the fight, and will keep you from getting sick. Read the article and discuss: 1) How the coronavirus spike proteins are “coded for” from RNA; 2) How the variety of proteins in nature gives us everything from spike proteins to antibodies; and 3) How you could clearly ease the mind of someone nervous that the COVID vaccine might accidentally give them the disease (see me if you need any clarification…I’m happy to discuss!). ⓟ/ⓦ: “Inquiry 5″: Q&A on Proteins** (💁/ 👭max 2) Create a list of 5 inquiry questions related to protein structure and function. Remember that good inquiry questions are conceptual / open-ended…such as: “How can proteins be both structural and functional; NOT: “What is the secondary structure of protein structure?” If working solo, write out answers to your own questions; if working in pairs, record yourselves asking each other your 5 questions. Lab (simulation) ⓟ/ⓦ: Protein Simulation Lab (💁) Get familiar with this simulation, then use it to make a brief screencast, explaining how protein folding takes place. Make sure you cover all the key features of protein structure from amino acid –> quaternary protein structure. Also discuss how this simulation can function as a model, and how such a model can help us understand real-world applications. Ӕ: The Academy: Protein Structure (💁) Celebrate! You’re almost done with drawing molecular structures (at least at this stage in your biology career). Fine tune your skills with further drawing practice – this time, sketch an amino acid (see all groups from 2.1.S1), then use it to show how polypeptides form. Then, come up with your own creative/visual way to show the structural organization of proteins – make sure you cover primary, secondary, tertiary, and quaternary structures. ⓟ/ⓦ: Protein Misfolding and the Seeds of Dementia (💁) It’s hard to fathom, but something as seemingly unharmful as a misfolded protein might be responsible for several forms of dementia; including Alzheimer’s to Parksinson’s disease. Read this article and/or this article, and discuss: 1) What protein folding actually is (refer specifically to tertiary/quaternary structure); 2) How misfolding can lead to terrible consequences, such as disease; and 3) If there is any hope to overcome the diseases caused by misfolding proteins. Other: Teach It: Summarizing Proteins (💁) Choose a platform (screencast, slideshow, podcast, etc) and use this article to help you summarize all the key features we have learned about proteins thus far. Make sure you include details on the various structures and functions of proteins. Just for Practice: Old school worksheet on proteins. Great for taking notes!