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Educerie · IB Diploma · Biology
Theme B Form and function · B1.2 Proteins
What you must be able to do
| You must be able to | Level | What it looks like in the exam |
|---|---|---|
| Draw a generalised amino acid, labelling the alpha carbon, amine group, carboxyl group, R-group and hydrogen | SL, HL | "Draw the structure of a generalised amino acid" (2 marks) |
| Write the word equation for dipeptide formation and draw a generalised dipeptide | SL, HL | "Draw a dipeptide, showing the peptide bond" (3 marks) |
| Distinguish essential from non-essential amino acids and apply it to vegan diets | SL, HL | "Explain why a vegan diet needs planning" (2 marks) |
| Explain why the variety of possible polypeptides is effectively infinite, and calculate numbers of sequences | SL, HL | Paper 1A: "How many different tripeptides are possible?" |
| Explain the effect of pH and temperature on protein structure, using "denaturation" | SL, HL | Data question on a protein heated or placed in acid (3–5 marks) |
| Explain how the chemistry of R-groups creates diversity in proteins | HL only | "Outline the properties of R-groups" (3 marks) |
| Explain why the primary structure decides the conformation | HL only | Part of an extended response (3–4 marks) |
| Describe α-helices and β-pleated sheets and the bonds that hold them | HL only | "Distinguish between secondary and tertiary structure" (3 marks) |
| Explain the four kinds of bond in tertiary structure, including disulfide bonds between cysteines | HL only | "Explain how the tertiary structure of a protein is stabilised" (4 marks) |
| Explain where polar and non-polar amino acids sit in soluble and in membrane proteins | HL only | "Explain how an integral protein is held in a membrane" (3 marks) |
| Distinguish non-conjugated and conjugated quaternary structure using insulin, collagen and haemoglobin | HL only | Multiple choice, or "Outline the quaternary structure of haemoglobin" (2 marks) |
| Relate form to function in globular and fibrous proteins, using insulin and collagen | HL only | "Compare the structure and function of insulin and collagen" (4–5 marks) |
Before you start
You need condensation and hydrolysis from B1.1, because a polypeptide is built and digested by exactly those two reactions. You need hydrogen bonds and the difference between polar and non-polar from A1.1, because every level of protein folding depends on them. HL students will meet the phospholipid bilayer again in section 9; B1.1 section 12 is enough.
1The idea in one paragraph
A protein is one or more chains of amino acids folded into a precise shape. There are twenty amino acids, all sharing the same skeleton and differing only in a side group called the R-group. They are joined by condensation into a polypeptide, and because a chain can be any length with the amino acids in any order, the number of possible polypeptides has no practical limit. The order of R-groups decides how the chain folds, the fold decides the shape, and the shape decides what the protein can do: carry oxygen, speed up a reaction, signal to a cell, or hold a tendon together. Heat and extremes of pH break the weak bonds that hold the shape, which is called denaturation, and a protein that has lost its shape has lost its function, even though its chain is still intact.
2The generalised amino acid
An amino acid is a molecule with a central carbon atom, the alpha (α) carbon, bonded to four different things:
- an amine group, –NH₂;
- a carboxyl group, –COOH;
- a hydrogen atom;
- an R-group, the variable side chain.
Figure 1 is the drawing the guide expects you to reproduce.
Every amino acid in your body has this same skeleton. What makes glycine different from cysteine or lysine is the R-group alone, which can be as small as a single hydrogen atom or as large as a double ring. So when you draw "a generalised amino acid", you draw the skeleton and write R for the side chain; you are not asked to draw any particular one.
3Condensation: from amino acids to polypeptides
Two amino acids join by a condensation reaction. The –OH of the carboxyl group of one amino acid and an –H from the amine group of the next are removed together as a water molecule, and a covalent bond forms between the carbon of the carboxyl group and the nitrogen of the amine group. That C–N bond is the peptide bond. Figure 2 shows the reaction.
The word equation, which you must be able to write:
amino acid + amino acid → dipeptide + water
The product of two amino acids is a dipeptide. Keep adding amino acids, one condensation at a time, and you have a polypeptide. Notice two things about the dipeptide in Figure 2.
- It still has a free amine group at one end and a free carboxyl group at the other. So another amino acid can be added at the carboxyl end, and the chain can grow indefinitely. In cells, it is ribosomes that add them, one at a time, in the order the mRNA specifies (D1.2).
- The backbone runs N–C–C–N–C–C, repeating. The R-groups stick out from it, one on every alpha carbon.
The guide asks you to model this reaction with molecular models, physical or digital, before drawing it. If you do it with a kit, you will find that the only way to join two amino acids is to pull off an –OH and an –H, which is the best way to remember that condensation releases water.
Counting rule, the same as for polysaccharides: a chain of n amino acids has n − 1 peptide bonds and released n − 1 water molecules when it formed. Hydrolysis reverses it, using one water per bond broken. Protease enzymes do this in your stomach and small intestine.
4Dietary requirements: essential and non-essential amino acids
Your cells need all twenty amino acids to build their proteins, but they cannot make all twenty.
- Essential amino acids cannot be synthesised by the body, so they must be obtained from food. For adult humans there are nine.
- Non-essential amino acids can be made in the body from other amino acids, so they do not have to be eaten as such.
The guide does not ask you to name any of them. What it asks is that you understand the consequence: protein in the diet is not just "protein". A diet can contain plenty of protein and still be short of one essential amino acid, and then every protein that needs that amino acid is made more slowly.
Vegan diets. Animal foods such as meat, eggs and milk generally contain all the essential amino acids in useful proportions. Many single plant foods are low in one or more of them. Cereals and pulses (beans, lentils) happen to be short of different ones, so eating both across the day covers the gap. Some plant foods, such as soya, are good sources of all of them. A vegan diet can supply every essential amino acid; it needs attention to variety to do so.
5An infinite variety of possible polypeptides
Three facts together give proteins their range.
- Twenty different amino acids are coded for by the genetic code.
- A chain can have any number of amino acids, from a few to thousands.
- The amino acids can be in any order.
So the number of possible sequences multiplies with each position. For a chain n amino acids long, each position has 20 options, so there are 20ⁿ possible sequences.
Real polypeptides span that range. Some examples, which the guide asks you to be familiar with:
| Polypeptide | Length (amino acids) | What it does |
|---|---|---|
| Oxytocin | 9 | hormone of childbirth and bonding |
| Insulin | 51, in two chains of 21 and 30 | hormone that lowers blood glucose |
| Each chain of haemoglobin | about 140–150 | carries oxygen in red blood cells |
| Each chain of collagen | about 1,000 | structural fibre in skin, tendon and bone |
| Titin | more than 30,000 | a giant elastic protein in muscle |
Living things use only a tiny fraction of the possible sequences, but that fraction is still enough to give every organism thousands of different proteins, each with its own shape.
6Denaturation: the effect of temperature and pH
A protein's function depends on its precise three-dimensional shape, its conformation. That shape is held by many weak bonds and interactions between parts of the chain (section 9 names them). Denaturation is a change to the conformation of a protein caused by breaking those bonds, so that it loses its shape and, with it, its function. Figure 3 shows what is lost and what is kept.
The peptide bonds are not broken. A denatured protein has the same amino acids in the same sequence. What has gone is the fold. In most cases the change is permanent, because the chain cannot find its way back to the right shape.
High temperature. Heat makes the atoms of the protein vibrate more strongly. Past a certain temperature the vibrations break the hydrogen bonds and other weak interactions holding the shape, and the chain unfolds. Cooking an egg is the familiar case: the clear, runny proteins of egg white unfold, tangle together, and become white and solid, and cooling the egg does not reverse it.
pH. Some R-groups carry an electrical charge, and whether they do depends on the concentration of hydrogen ions around them. A pH far from a protein's normal range adds or removes H⁺ ions from those R-groups, changing their charges. Bonds between oppositely charged R-groups break, new repulsions appear, and the shape collapses. Each protein has a pH range where it keeps its shape: most proteins in your blood work near pH 7.4, but the digestive enzyme pepsin works in stomach acid at about pH 2 and is denatured in the neutral conditions of the small intestine.
Reading a denaturation graph. Figure 4 is the kind of data Paper 1B gives you. The data are invented, but the pattern is real.
Three things to say, in this order, when asked to analyse a graph like this.
- Describe the trend. Both proteins stay fully folded at low temperatures, then the percentage still folded falls steeply over a narrow range of about 20 °C.
- Quote the data. Half of protein X is denatured at about 55 °C, between the readings of 78% at 50 °C and 22% at 60 °C. Half of protein Y is denatured at about 85 °C.
- Explain and connect. Protein Y comes from a bacterium that lives in hot springs, so natural selection has favoured a sequence whose shape is held by more, or stronger, bonds. Its structure survives temperatures that denature a human protein. The DNA polymerase used in the polymerase chain reaction comes from exactly such a bacterium, for exactly this reason.
7HLR-groups: where the diversity comes from
SL students can skip to section 12.
Section 5 counted the sequences. This section explains why different sequences give genuinely different proteins, not just different labels. The answer is that the R-groups differ chemically, and the R-groups determine the properties of the assembled polypeptide. Figure 5 sorts them.
- Hydrophobic R-groups are non-polar, made mostly of carbon and hydrogen. They are not attracted to water and tend to cluster together, away from it.
- Hydrophilic R-groups are attracted to water. They come in two kinds. - Polar but uncharged, such as those carrying an –OH group. They form hydrogen bonds. - Charged. These are either acidic, with a carboxyl group that can lose H⁺ and become negative (–COO⁻), or basic, with an amine group that can gain H⁺ and become positive (–NH₃⁺).
You do not need to name examples. What you need is the idea that a polypeptide is a string of these different behaviours in a fixed order, and that the order is what decides the shape.
8HLPrimary structure decides the shape; secondary structure is the first fold
Protein structure is described at four levels, drawn in Figure 6.
Primary structure is the sequence of amino acids in the polypeptide, held by peptide bonds. The guide's central point is that the sequence, and the precise position of each amino acid in it, determines the three-dimensional shape of the protein. Each R-group interacts with water and with other R-groups in its own way, so a given sequence folds into one particular shape. That is why proteins, despite their complexity, have precise, predictable and repeatable structures: every molecule of haemoglobin in your blood has the same shape, because every one has the same sequence.
It also means one change can matter. In sickle cell anaemia a single amino acid in each β chain of haemoglobin is replaced by another (D1.3). That one substitution, out of 146, changes how the molecules behave at low oxygen, and the red blood cells deform.
Secondary structure is the regular folding of parts of the chain into two repeating shapes.
- The α-helix: the chain coils into a spiral. Every C=O group in the backbone forms a hydrogen bond with the N–H group of the amino acid four places further along the chain.
- The β-pleated sheet: two or more stretches of chain lie side by side, and hydrogen bonds form between the C=O groups of one stretch and the N–H groups of the stretch beside it. The sheet is pleated, like a folded fan.
In both, the hydrogen bonds are between groups in the backbone, not between R-groups, and they form at regular positions along it. That regularity is what makes the shapes repeat. Each single hydrogen bond is weak; hundreds of them in step make a stable structure. A protein may contain several helices and sheets, joined by stretches of chain with no regular pattern.
9HLTertiary structure: the bonds between R-groups
Tertiary structure is the folding of the whole polypeptide, helices, sheets and all, into its final three-dimensional shape. It is held by interactions between R-groups, and the guide names four, shown in Figure 7.
- Hydrogen bonds between polar R-groups, for example between an –OH on one R-group and an O on another.
- Ionic bonds between R-groups carrying opposite charges. An amine group in an R-group becomes positive by gaining a hydrogen ion (–NH₃⁺); a carboxyl group becomes negative by losing one (–COO⁻). Once charged, they attract. This is also why pH matters so much (section 6): change the H⁺ concentration and you change the charges.
- Disulfide bonds between two cysteines. Cysteine's R-group contains sulfur, and the sulfur atoms of two cysteines, which may be far apart in the sequence, can form a covalent S–S bond. It is the only covalent bond in the list, so it is much stronger than the others. Cysteine is the one amino acid the guide expects you to name.
- Hydrophobic interactions between non-polar R-groups. They are pushed together because water is excluded from between them, in the same way that oil droplets merge.
Where polar and non-polar amino acids end up. The last of those four is the one that decides the overall plan of the protein, and Figure 8 shows it in two settings.
- In a protein that is soluble in water, the chain folds so that hydrophobic R-groups cluster in the core, away from water, and hydrophilic R-groups are on the surface, in contact with it. The polar surface is what makes the protein soluble.
- An integral membrane protein sits across the phospholipid bilayer. The part inside the bilayer has a band of hydrophobic R-groups on its outer surface, in contact with the hydrophobic fatty acid tails, and that is what holds the protein in the membrane. The parts outside the bilayer, in contact with water on either side, are hydrophilic.
The rule is the same in both: non-polar R-groups end up where there is no water.
10HLQuaternary structure: non-conjugated and conjugated proteins
Many proteins are a single polypeptide, and for them tertiary structure is the final level. Others are made of two or more polypeptides joined together, and the way they fit is the quaternary structure. Figure 9 shows the guide's three examples.
A non-conjugated protein is made of polypeptides only.
- Insulin: two polypeptide chains, of 21 and 30 amino acids, held together by two disulfide bonds. (It is made as one chain and then cut, but the finished hormone is two chains.)
- Collagen: three long polypeptide chains wound around one another into a triple helix, like the strands of a rope.
A conjugated protein includes a non-polypeptide component, called a prosthetic group, as a permanent part of its structure.
- Haemoglobin: four polypeptide chains (two α and two β), each holding a haem group. The haem group contains an iron ion, and that is where oxygen binds. Without the haem, the protein cannot carry oxygen at all.
How do we know these shapes? (nature of science). Protein molecules are far too small to see with a light microscope, and for most of the twentieth century their shapes were worked out indirectly, from the patterns X-rays make when they pass through protein crystals. Cryogenic electron microscopy (cryo-EM) now images single protein molecules, frozen so fast in a thin film of ice that they keep their natural shape, and combines many thousands of images into a three-dimensional model. It can show proteins that will not crystallise and proteins caught in the act of binding to other molecules. Its developers shared the 2017 Nobel Prize in Chemistry. The general point the guide makes is that technology extends what we can observe far beyond the unaided senses, and new observations follow new instruments.
11HLGlobular and fibrous proteins: insulin and collagen
Proteins fall into two broad shapes, and each shape suits a kind of job.
| Globular proteins | Fibrous proteins | |
|---|---|---|
| Shape | rounded, compact, folded | long, narrow strands or sheets |
| Solubility in water | usually soluble (polar surface) | insoluble |
| Sequence | varied, irregular | often repetitive |
| Typical function | enzymes, hormones, transport, receptors: jobs needing a precise binding site | structural: strength, support, elasticity |
| Guide's example | insulin | collagen |
Insulin: a globular hormone. Insulin is secreted by cells in the pancreas when blood glucose is high, and it travels in the blood to target cells in the liver, muscles and fat tissue.
- It is small and compact, with a hydrophilic surface, so it dissolves in blood plasma and is carried round the body.
- It has a precise, stable shape, held by its disulfide bonds, that fits a specific receptor in the plasma membrane of its target cells. Only cells with that receptor respond. The binding triggers the cell to take in glucose.
Collagen: a fibrous structural protein. Collagen is the most abundant protein in mammals, in skin, tendons, ligaments, cartilage, bone and the walls of blood vessels.
- Its three chains are long and wound into a triple helix. Every third amino acid is glycine, the one with the smallest R-group (a single hydrogen atom), which lets the three chains pack tightly together.
- Neighbouring triple helices are cross-linked into fibrils and fibres, so collagen has very high tensile strength: a tendon made of it transmits the pull of a muscle to a bone without stretching or tearing.
- It is insoluble, so it stays where it is built, which is what a structural material must do.
Put the two side by side and the lesson of the whole subtopic is in one sentence: a compact, soluble shape with a precise binding site makes a messenger; a long, cross-linked, insoluble shape makes a rope.
12Where marks are lost
Saying denaturation breaks peptide bonds. It does not. It breaks the bonds holding the shape (hydrogen bonds, ionic bonds, hydrophobic interactions). The primary structure is unchanged.
"The protein dies" or "the protein is killed". Proteins are molecules; they are not alive. Write "denatured", "loses its shape", "loses its function".
Drawing the peptide bond between the wrong atoms. It joins the carbon of one carboxyl group to the nitrogen of the next amine group. A C–C or N–N link scores nothing.
Forgetting the water. A condensation drawn or written without "+ water" is incomplete, and the word equation mark needs it.
Confusing "essential" with "important". All twenty amino acids are needed. "Essential" means only that the body cannot make it, so it must be eaten.
Calculating 20 × n instead of 20ⁿ. Each position multiplies the possibilities by 20. A tripeptide gives 20 × 20 × 20 = 8,000, not 60.
(HL) Putting secondary-structure hydrogen bonds between R-groups. In helices and sheets they form between C=O and N–H groups of the backbone. Hydrogen bonds between R-groups belong to tertiary structure.
(HL) Calling insulin conjugated because it has disulfide bonds. Conjugated means it contains a non-polypeptide part. Insulin is only polypeptide; haemoglobin, with its haem groups, is conjugated.
13Draw it right
- Amino acid: the alpha carbon in the centre, bonded to H₂N– on the left, –COOH on the right, R above and H below. Four bonds on the alpha carbon, no more.
- Show the carboxyl group in full if you can: C, with a double bond to O and a single bond to OH.
- Dipeptide: two alpha carbons, each with its own R-group (label them R₁ and R₂), joined through –CO–NH–. Circle or label the peptide bond: the C–N bond.
- Write + H₂O on the product side of the equation, and "condensation" beside the arrow.
- Keep the free amine group at one end and the carboxyl group at the other end of the dipeptide.
- (HL) For an α-helix, show a coil with hydrogen bonds between turns; for a β-pleated sheet, show parallel or antiparallel strands with hydrogen bonds between them. Label the bonds as hydrogen bonds.
- (HL) For a disulfide bond, write S–S between two cysteine R-groups, and say "covalent".
14Try it
Marks in brackets. Answers and marker's notes are at the end.
Q1. How many different polypeptides of exactly five amino acids could be made from the 20 amino acids in the genetic code? 1 mark
A. 100
B. 25
C. 3.2 × 10⁶
D. 9.5 × 10¹³
Q2. Draw a dipeptide formed from two generalised amino acids, labelling the peptide bond, and state the other product of the reaction. 3 marks
Q3. A student investigated two proteins by keeping samples at different pH values for 30 minutes and then measuring the percentage of molecules that still had their normal shape. Protein P comes from the stomach; protein Q from blood plasma. The data are invented. 5 marks
| pH | 1 | 3 | 5 | 7 | 9 | 11 |
|---|---|---|---|---|---|---|
| Protein P, % normal shape | 96 | 98 | 90 | 35 | 5 | 0 |
| Protein Q, % normal shape | 0 | 10 | 82 | 97 | 85 | 20 |
(a) State the pH range over which protein Q kept at least 80% of its molecules in their normal shape. 1 mark
(b) Compare the effect of pH on proteins P and Q. 2 marks
(c) Explain why protein Q loses its shape at pH 1. 2 marks
Q4. Explain why a person following a vegan diet needs to eat a variety of protein sources. 3 marks
Q5 (HL). Explain how the tertiary structure of a protein is stabilised. 4 marks
Q6 (HL). Compare and contrast the structure and function of insulin and collagen. 5 marks
15In one breath
An amino acid is an alpha carbon carrying an amine group, a carboxyl group, a hydrogen and an R-group, and only the R-group differs among the twenty. Condensation joins the carboxyl of one to the amine of the next by a peptide bond and releases water; amino acid plus amino acid gives dipeptide plus water, and the chain can keep growing. Essential amino acids cannot be made by the body and must be eaten, so a vegan diet needs variety. Twenty amino acids, any length, any order: 20ⁿ sequences, effectively infinite. Heat and pH break the weak bonds holding a protein's shape, not its peptide bonds; that is denaturation, and the function goes with the shape. HL: R-groups are hydrophobic or hydrophilic, and hydrophilic ones are polar or charged, acidic or basic, so the sequence of R-groups decides the fold, which is why structures are precise and repeatable. Secondary structure is α-helices and β-pleated sheets held by regular hydrogen bonds in the backbone; tertiary structure is held by hydrogen bonds, ionic bonds, cysteine disulfide bonds and hydrophobic interactions between R-groups, with non-polar R-groups buried away from water or facing the membrane core. Quaternary structure joins chains: insulin and collagen are non-conjugated, haemoglobin with its haem groups is conjugated. Globular insulin is soluble with a precise shape to bind its receptor; fibrous collagen is a long, insoluble, cross-linked triple helix with great tensile strength.
Answers
Q1. C. Each of the five positions can hold any of 20 amino acids, so 20⁵ = 3,200,000 = 3.2 × 10⁶. A is 20 × 5; D is 5²⁰, the calculation the wrong way round. C only.
Q2. Drawing as in Figure 2: an amine group (H₂N–) at one end; alpha carbon with R₁ and H; carbon with a double-bonded O; the peptide bond from that carbon to an N carrying an H; the second alpha carbon with R₂ and H; a carboxyl group (–COOH) at the other end. Other product: water. 1 for a correct backbone with both alpha carbons, each carrying an R-group and an H, and terminal amine and carboxyl groups; 1 for the peptide bond correctly placed between C and N and labelled; 1 for water. A dipeptide with the peptide bond drawn as C–C scores 0 for the second mark.
Q3. (a) pH 5 to pH 9. (b) Protein P keeps its shape at low (acidic) pH, 90% or more between pH 1 and 5, whereas protein Q keeps its shape best near neutral pH, 82–97% between pH 5 and 9; P is almost fully denatured at pH 9 and above, whereas Q is almost fully denatured at pH 3 and below. (c) At pH 1 the high concentration of hydrogen ions changes the charges on R-groups, for example by adding H⁺ to –COO⁻ groups. Ionic bonds (and hydrogen bonds) holding the tertiary structure break, so the protein unfolds and is denatured. (a) 1 for 5–9. (b) 1 for P stable at acidic pH and Q near neutral, 1 for a comparison using data from both proteins; two separate descriptions without a comparison score 1 at most. (c) 1 for H⁺ ions altering the charges on R-groups, 1 for the bonds holding the shape breaking, so the conformation changes. "The protein dies" scores 0.
Q4. Essential amino acids cannot be synthesised by the body, so they must be obtained from food. Many individual plant foods contain too little of one or more essential amino acids. Different plant foods, such as cereals and pulses, are short of different ones, so eating a variety supplies all the essential amino acids. 1 for the meaning of essential, 1 for single plant sources being low in some essential amino acids, 1 for combining sources to cover all of them. "Plants have no protein" scores 0.
Q5 (HL). Tertiary structure is the folding of the whole polypeptide into its three-dimensional shape, held by interactions between R-groups. Hydrogen bonds form between polar R-groups. Ionic bonds form between positively charged amine R-groups (–NH₃⁺) and negatively charged carboxyl R-groups (–COO⁻). Covalent disulfide bonds form between the sulfur atoms of two cysteine R-groups. Hydrophobic interactions hold non-polar R-groups together in the core, away from water. 1 for each of the four named with a correct detail, up to 4. Naming all four with no detail scores 2. Hydrogen bonds between C=O and N–H of the backbone describe secondary structure and do not score here.
Q6 (HL). Similarities: both are proteins made of more than one polypeptide chain, so both have quaternary structure; both are non-conjugated. Differences: insulin is globular, whereas collagen is fibrous; insulin has two short chains (21 and 30 amino acids) held by disulfide bonds, whereas collagen has three long chains wound into a triple helix; insulin is soluble in water, so it is carried in blood plasma, whereas collagen is insoluble; insulin has a precise shape that binds a specific receptor on target cells, so it works as a hormone signalling to take up glucose, whereas collagen's cross-linked fibres give high tensile strength, so it has a structural role in tendons, skin and bone. 1 per valid point to 5, with at least one similarity and at least one difference for full marks, and each difference written as a comparison. At least one point must link a feature of form to a function.
Educerie · written from the published IB Diploma Programme Biology guide, first assessment 2025, section B1.2 Proteins. Original text, examples and questions. Diagrams drawn by Educerie. Last reviewed 25 September 2026.
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