The shape of the lesson
By the end of the lesson, learners can
- From amino acid to polypeptide: Start on the amino acid in the simulator, then step through primary, secondary, tertiary and quaternary structure, and finally collagen.
- Four levels of structure: Each level builds on the one below.
- Haemoglobin and collagen: Compare the quaternary view (haemoglobin) with the collagen view in the simulator: one is a compact ball, the other a rope.
- Primary: sequence, peptide bonds.
- Secondary: α-helix and β-sheet, backbone hydrogen bonds.
- Tertiary: R-group bonds: hydrophobic, hydrogen, ionic, disulfide.
- Globular soluble and physiological; fibrous insoluble and structural.
One picture every idea returns to
Every amino acid has a central carbon carrying an amine group (NH2), a carboxyl group (COOH), a hydrogen atom and a variable R group. Amino acids join by condensation to form peptide bonds. The primary structure is the sequence of amino acids; secondary structure is the α-helix or β-pleated sheet held by hydrogen bonds in the backbone; tertiary structure is the overall 3D folding held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bonds between R groups; quaternary structure is two or more polypeptides together. Globular proteins such as haemoglobin are soluble with physiological roles; fibrous proteins such as collagen are insoluble with structural roles.
Forty-five minutes, phase by phase
| Time | Phase | What happens in the room | Grouping |
|---|---|---|---|
| 0 to 5 min | Hook: predict | Open with the question in the title, A chain that folds into a job.. Twenty amino acids, one type of bond between them, and yet proteins carry oxygen, catalyse reactions and hold your skeleton together. Put the figure on the board: it is the one picture every idea in the lesson returns to. | Whole class, then pairs |
| 5 to 13 min | Teach and check: From amino acid to polypeptide | Start on the amino acid in the simulator, then step through primary, secondary, tertiary and quaternary structure, and finally collagen. Project tab 5 of the lab (Biological molecules lab, proteins) and let a student drive it while the class predicts. | Whole class, then pairs |
| 13 to 21 min | Teach and check: Four levels of structure | Each level builds on the one below. | Pairs |
| 21 to 30 min | Teach and check: Haemoglobin and collagen | Compare the quaternary view (haemoglobin) with the collagen view in the simulator: one is a compact ball, the other a rope. | Connect-Extend-Challenge |
| 30 to 36 min | Check | The four Stage 1 questions from the student lesson, answered on mini whiteboards or by show of fingers. Re-teach the one most get wrong. | Individual, then whole class |
| 36 to 43 min | Plenary | The exam-style questions from Stage 2, one at a time: thirty seconds alone, then a random call. The feedback lines in the key give the examiner's wording. | Individual, random call |
| 43 to 45 min | Exit and homework | Set the worksheet below (6 questions, 20 marks). Learners self-assess against the objectives before they leave. | Individual |
Protect the parts that carry the learning
The sequence carries about fifty minutes of material, so the lab is driven by one student while the class predicts rather than explored freely. Times are a guide.
Protected: the check at 30 minutes. It is the only individual read on whether the key idea landed, and it is not cut.
Cut first if the build overruns: the last check in Haemoglobin and collagen, never the check or the plenary.
In a 60 minute block: run worksheet questions 1 to 3 in class as a Rally Coach set and model both the hardest worked example and its check live.
Connect-Extend-Challenge
After the new idea, each student writes three lines: how it connects to what they knew, how it extends their thinking, and what still challenges them. Pairs compare, then the challenges become the plenary.
The full structure, with its variations and the other twelve, is on the cooperative-learning page.
What to head off, and how
| Trap learners fall into | Teaching move that pre-empts it |
|---|---|
| The hydrogen bonds of secondary structure are between atoms of the polypeptide backbone (C=O and N-H), not between R groups. | The hydrogen bonds that help hold tertiary structure are between R groups. |
Proteins: worksheet
6 questions, 20 marks. Written in the style of the papers; no past paper question is reproduced.
Describe the general structure of an amino acid.
Describe how a peptide bond is formed and how it is broken.
Explain the meaning of the terms secondary structure and tertiary structure, naming the bonds involved in each.
Each α-globin chain of human haemoglobin has 141 amino acids and each β-globin chain has 146. Calculate the total number of peptide bonds in one haemoglobin molecule.
Relate the structure of haemoglobin to its function in transporting oxygen.
Explain how the structure of collagen molecules and collagen fibres relates to their function.
Answer key and marking notes
- A central carbon atom bonded to an amine group (NH2) and a carboxyl group (COOH).
- Also bonded to a hydrogen atom.
- And to a variable R group, which differs between the 20 amino acids.
- Formed by condensation between the carboxyl group of one amino acid and the amine group of another.
- A molecule of water is released and a C-N (peptide) bond forms.
- Broken by hydrolysis: water is added (catalysed by protease enzymes).
- Secondary: coiling into an α-helix or folding into a β-pleated sheet.
- Held by hydrogen bonds between the C=O and N-H groups of the polypeptide backbone.
- Tertiary: further folding of the whole polypeptide into a specific 3D shape.
- Held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bonds between R groups.
- Peptide bonds per chain = amino acids − 1: 140 per α chain and 145 per β chain.
- Total = 2 × 140 + 2 × 145 = 570.
- Quaternary structure of four polypeptides: two α-globin and two β-globin chains.
- Each chain has a haem group containing Fe2+, which binds one O2 reversibly, so one molecule carries four O2.
- Globular, with hydrophilic R groups outside, so it is soluble in the cytoplasm of red blood cells.
- Iron is essential: without it haem cannot bind oxygen.
- Three polypeptide chains wound into a triple helix, held by hydrogen bonds; glycine at every third position allows tight packing.
- Neighbouring molecules are joined by covalent cross-links.
- Molecules are staggered so their ends do not line up, avoiding weak points; they form fibrils and then fibres.
- This gives very high tensile strength and little stretch, suited to tendons, skin and artery walls; collagen is insoluble.
8 multiple-choice questions on this lesson
From the topic question bank. Assign them in the app for a marked score in your gradebook, or run the topic as a class game.
A globular protein is denatured by heating to 70 °C. Which level of its structure is not changed?
- Aprimary structure
- Bsecondary structure
- Ctertiary structure
- Dquaternary structure
Which two atoms are directly joined by a peptide bond?
- Athe carbon of one amino acid's carboxyl group and the nitrogen of the next amino acid's amine group
- Bthe central carbon atoms of two neighbouring amino acids
- Cthe oxygen of one carboxyl group and the nitrogen of the next amino acid's amine group
- Dthe nitrogen atoms of the amine groups of two neighbouring amino acids
Which statement about globular and fibrous proteins is generally true?
- Aglobular proteins are soluble and have physiological roles, such as transport or catalysis
- Bfibrous proteins are soluble and act mainly as enzymes and hormones
- Cglobular proteins are insoluble and provide tensile strength in tissues
- Dfibrous proteins all contain haem groups and have quaternary structure
Valine has a non-polar R group, -CH(CH3)2. In a soluble globular protein in the cytoplasm, where are valine R groups most likely to be found?
- Ainside the molecule, clustered together by hydrophobic interactions
- Bon the surface, forming hydrogen bonds with water molecules
- Con the surface, forming ionic bonds with dissolved ions
- Danywhere, forming disulfide bonds with cysteine R groups
A red blood cell contains about 2.7 × 108 haemoglobin molecules. What is the maximum number of oxygen molecules the cell can carry?
- A1.1 × 109
- B2.7 × 108
- C5.4 × 108
- D2.2 × 109
Hair is mostly the protein keratin. In a hair "perm", a reducing agent breaks one type of bond between R groups, the hair is set in a new shape, and an oxidising agent then re-forms bonds of the same type in new positions, so the new shape survives washing in water. Which interaction in the diagram is broken and re-formed?
- AA
- BB
- CC
- DD
A polypeptide is made of 120 amino acids. The mean Mr of the free amino acids used is 128. What is the Mr of the polypeptide? (Mr of water = 18)
- A13218
- B15360
- C13200
- D15342
In sickle cell anaemia, one glutamic acid (charged, polar R group) on the surface of each β-globin chain is replaced by valine (non-polar R group). At low oxygen concentration the haemoglobin molecules stick together in long fibres. Which explanation is best?
- Aa hydrophobic patch now lies on the surface, so molecules are less soluble and stick together by hydrophobic interactions
- Bthe peptide bonds on either side of valine are weaker, so the β-globin chains break into fragments
- Cvaline cannot form hydrogen bonds in the backbone, so all secondary structure in the molecule is lost
- Dthe haem group can no longer hold Fe2+ because valine has no sulfur to bind the iron
Quiz key
Heating makes the molecule vibrate until hydrogen bonds, ionic bonds and hydrophobic interactions break, but the covalent peptide bonds stay intact, so the sequence of amino acids (primary structure) is unchanged. Secondary structure is held by hydrogen bonds in the backbone, which break on heating, so helices and sheets unravel. Tertiary structure depends on the bonds between R groups, most of which are broken. Quaternary structure is held by the same kinds of interaction between chains, so the subunits may separate.
The COOH of one amino acid loses OH and the NH2 of the next loses H, forming water; the carbon of the C=O then bonds to the nitrogen, giving the C-N peptide bond. The central (α) carbons are not bonded to each other; there are two atoms between them. The oxygen of the OH leaves in the water molecule, so it cannot be in the bond. Two amine nitrogens cannot react together in a condensation; one carboxyl and one amine group are needed.
Globular proteins, such as haemoglobin and enzymes, fold with hydrophilic R groups outside, so they are generally soluble and carry out physiological roles. Fibrous proteins, such as collagen, are generally insoluble and structural, so the second and third options swap the two groups. Haem groups belong to haemoglobin, a globular protein; collagen has no haem.
Non-polar R groups are hydrophobic, so the chain folds to bury them in the centre of the molecule, where they cluster by hydrophobic interactions; this also leaves polar and charged groups on the surface, making the protein soluble. A non-polar group cannot form hydrogen bonds with water. Ionic bonds need charged R groups, and valine has none. Disulfide bonds form only between two cysteine R groups, which contain sulfur; valine does not.
Each of the four polypeptide chains has a haem group with one Fe2+, and each Fe2+ binds one O2, so each molecule carries up to four: 4 × 2.7 × 108 = 1.1 × 109. 2.7 × 108 assumes one O2 per molecule. 5.4 × 108 counts only two chains (as if only the α or only the β chains had haem). 2.2 × 109 assumes each haem binds two O2, perhaps counting the two atoms of each oxygen molecule.
A is a disulfide bond, a covalent S-S bond between two cysteine R groups. Reducing agents split it into two SH groups and oxidising agents re-form it, and because it is covalent it is not broken by water, so the shape is permanent. B is an ionic bond between COO− and NH3+; it is sensitive to pH, not to reducing agents. C is a hydrogen bond, which is broken by wetting and so changes when hair is washed; it is not a redox reaction. D is a hydrophobic interaction between non-polar groups, which involves no bond to reduce or oxidise.
Total for the free amino acids = 120 × 128 = 15360. A chain of 120 amino acids has 119 peptide bonds, each releasing one water: 15360 − 119 × 18 = 15360 − 2142 = 13218. 15360 forgets the water lost. 13200 subtracts 120 waters, one per amino acid rather than one per bond. 15342 subtracts only one water.
Replacing a charged, hydrophilic R group on the surface with a non-polar one reduces the solubility of the molecule, and the exposed hydrophobic valine can interact with a hydrophobic region on a neighbouring haemoglobin, so molecules bind together into fibres. Peptide bonds are the same whichever amino acids they join. Backbone hydrogen bonds in secondary structure involve C=O and N-H groups, which valine still has; R groups are not involved. Iron in haem is held by the haem ring and a histidine, not by sulfur, and the change is on the surface, away from the haem.
What to project
The student lesson embeds these tabs. Open them full screen on the projector; every slider has a drag handle on the stage.
Slides for this lesson
A projectable deck for every pack is on the way. Until then, present the student lesson full screen: its sections, figure and lab tabs follow the same order as the plan above.