IB Biology · Theme B Form and function · Molecules
B1.2 Proteins
Every amino acid shares one backbone; only the R-group differs, and that difference drives everything. Peptide bonds link amino acids in any order and any length, so possible proteins are endless. The sequence fixes the fold; heat or wrong pH undoes it and the protein stops working.
Compiled from the IB Biology guide (first assessment 2025, updated May 2026 for 2028) and our question bank ·
Specialist review in progress
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Assessed in Paper 1A (multiple choice), Paper 1B (data-based) and Paper 2 (short and extended response). IB Biology guide (first assessment 2025, updated May 2026 for 2028).
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B1.2.1 The parts of any amino acid
From 2028 this is supplied in the Biology data booklet — you need to recognise and interpret it, not reproduce it from memory.
The alpha carbon carries an amine group, a carboxyl group, hydrogen and an R-group.
The amine group (−NH₂) and carboxyl group (−COOH) are the same in every amino acid.
Only the R-group differs; it alone tells one amino acid from another.
The amine group can gain H⁺ (−NH₃⁺); the carboxyl can lose H⁺ (−COO⁻).
Students often think amino acids differ in their amine or carboxyl groups. In fact those are identical in all; only the R-group varies.
Students often think the amine group is NH₃, like ammonia. In fact it is −NH₂: nitrogen bonded to the alpha carbon and two hydrogens.
B1.2.2 Condensation makes dipeptides and longer chains
The carboxyl group of one amino acid reacts with the amine group of the next.
A peptide bond (−CO−NH−) forms and one molecule of water is released.
Each link forms one peptide bond and releases one water molecule.
Students often think the peptide bond forms between R-groups. In fact it joins a carboxyl carbon to an amine nitrogen; R-groups stick out from the backbone.
Students often count one bond and one water per amino acid. In fact both are counted per link: 150 amino acids means 149 of each.
B1.2.3 Which amino acids must come from food
An essential amino acid cannot be made in the body; it must come from food.
A non-essential amino acid can be made from other amino acids.
Non-essential does not mean unimportant; it refers only to the diet.
Vegan diets need a range of plant proteins; one plant protein may lack some essentials.
Students often think essential amino acids are the ones the body needs most. In fact "essential" means the body cannot synthesise it, nothing more.
Students often think only animal foods supply essential amino acids. In fact plant foods do too, provided a range of sources is eaten.
B1.2.4 Why the variety of peptide chains is endless
20 amino acids are coded for in the genetic code.
A chain can have any number of amino acids, from a few to thousands.
Any amino acid can appear at any position, any number of times.
For n positions there are 20ⁿ possible sequences, so variety is effectively infinite.
Insulin has 51 amino acids; lysozyme 129; collagen about 1000 per chain; titin over 30 000.
Students often multiply 20 by the chain length to count sequences. In fact each position holds any of 20 independently: three positions give 20³ = 8000.
Students often think only the amino acids present matter, not their order. In fact a different order is a different primary structure, shape and function.
B1.2.5 Heat and pH change a protein's shape
Denaturation is a change in a protein's three-dimensional shape, so it no longer works.
Heat makes the molecule vibrate, breaking the weak bonds that hold the fold.
A pH outside the normal range changes charges, disrupting the bonds that depend on them.
Peptide bonds are not broken, so the sequence is unchanged; the change is usually permanent.
Students often think denaturation breaks the protein into amino acids. In fact only the weak bonds holding the fold break; the sequence stays intact.
Students often think cold denatures a protein as heat does. In fact low temperature only slows reactions; activity returns on warming.
B1.2.6 R-groups give proteins their diversity (HL) HL
Hydrophobic R-groups are non-polar; they do not hydrogen-bond with water and sit away from it.
Hydrophilic R-groups attract water: they are polar or charged.
Charged R-groups are acidic (carboxyl loses H⁺, −COO⁻) or basic (amine gains H⁺, −NH₃⁺).
R-groups set a polypeptide's properties, so their pattern largely decides how it folds.
Students often think only charged R-groups are hydrophilic. In fact polar uncharged R-groups hydrogen-bond with water and are hydrophilic too.
Students often think an acidic R-group is positive because acids have H⁺. In fact it releases H⁺ and becomes negative.
B1.2.7 Sequence decides shape (HL) HL
Primary structure is the amino acid sequence, amine end to carboxyl end.
It decides where the chain coils, pleats and folds, and which R-groups come close.
So a protein's conformation is precise, predictable and repeatable: same sequence, same shape.
Students often think the cell moulds a protein into shape after synthesis. In fact the sequence itself determines the shape.
Students often think only active-site amino acids matter. In fact every position contributes, so a change anywhere can alter the shape.
B1.2.8 Coils and pleats in the backbone (HL) HL
Secondary structure is regular coiling or pleating, held by backbone hydrogen bonds at regular positions.
Bonds link one peptide bond's C=O to another's N–H; R-groups play no part.
An alpha helix is a coiled backbone; a beta-pleated sheet is side-by-side strands.
One polypeptide may contain both, joined by less regular regions.
Students often think secondary structure is held by R-group bonds. In fact the hydrogen bonds are between backbone C=O and N–H groups only.
B1.2.9 Four kinds of bond hold the fold (HL) HL
Tertiary structure is the whole polypeptide's 3D fold, held by interactions between R-groups.
Hydrogen bonds between polar R-groups; ionic bonds between oppositely charged R-groups.
Disulfide bonds: covalent links between two cysteines, far stronger than the rest.
Hydrophobic interactions: non-polar R-groups pack together, excluded by water.
R-group charges come from binding or losing H⁺, so a pH change can break ionic bonds.
Students often think a disulfide bridge is a strong hydrogen bond broken by heat. In fact it is covalent, between sulfur atoms, and survives moderate heating.
Students often think R-group charges are permanent. In fact they depend on hydrogen ions, so pH change removes them and the ionic bond goes.
B1.2.10 Where polar and non-polar amino acids sit (HL) HL
In a soluble globular protein, hydrophobic R-groups cluster in the core, away from water.
Hydrophilic R-groups sit on the surface, keeping the protein in solution.
An integral protein has hydrophobic regions that embed in the bilayer's centre.
Its hydrophilic regions project into the watery solutions on either side.
Students often think an integral protein must be hydrophobic all over. In fact it has both kinds of region; only the embedded parts are hydrophobic.
Students often think a soluble protein must be hydrophilic throughout. In fact its hydrophobic amino acids are simply hidden in the core.
B1.2.11 Proteins from several polypeptides (HL) HL
Quaternary structure is two or more polypeptides joined into one functional protein.
Insulin (two chains, disulfide-linked) and collagen (three chains wound together) are non-conjugated.
A conjugated protein also has a non-polypeptide prosthetic group: haemoglobin's four chains each carry haem.
Cryogenic electron microscopy images single protein molecules, showing structures no unaided sense could see.
Students often think "conjugated" means more than one polypeptide. In fact it means a non-polypeptide part is present, such as haem with its iron.
Students often think insulin is one short chain with no quaternary structure. In fact it is two polypeptides linked by disulfide bonds.
B1.2.12 Globular and fibrous: shape fits job (HL) HL
Globular proteins are compact and rounded, usually soluble, with hydrophilic surfaces.
Their precise shape lets them bind specific molecules: insulin binds receptors on target cells.
Fibrous proteins are long and narrow, usually insoluble, with structural roles.
Collagen is three chains in a rope-like triple helix; linked fibres give tendons tensile strength.
Students often think fibrous proteins are simply unfolded chains. In fact collagen's triple helix is a precise, repeatable structure.
Students often think a collagen fibre is one very long polypeptide. In fact it is many triple helices, each of three chains, linked side by side.
Diagnostic a bearings check, not a test
10 questions, one per part of the topic where we can. Answer them, then see which statements you own and which to read.
1 Which feature is shared by all 20 of the amino acids that are coded for in the genetic code?
Answer and reasoning
An amine group, a carboxyl group, a hydrogen atom and an R-group are all bonded to one alpha carbon atom. — This is the generalized structure of an amino acid: a central alpha carbon carrying the amine group, the carboxyl group, a hydrogen atom and the R-group. Only the R-group differs between the 20 amino acids.
The R-group is identical in every amino acid, and the amine and carboxyl groups are what vary. — A student who takes the fully drawn groups to be the variable parts picks this. In fact it is the other way round: the amine group, carboxyl group and hydrogen are the same in every amino acid, and only the R-group differs.
The amine group is bonded directly to the carbon atom of the carboxyl group, with no carbon between. — A student who writes an amino acid as NH₂–COOH picks this. In fact both groups are attached to the alpha carbon, which sits between them and also carries a hydrogen and the R-group.
The amine group is an NH₃ group, with the same structure as a molecule of ammonia. — A student who carries ammonia's three hydrogens over to the amine group picks this. In fact one of the nitrogen's bonds is to the alpha carbon, so the amine group is –NH₂; it becomes –NH₃⁺ only when it binds a hydrogen ion.
2 Two amino acids react to form a dipeptide. Which statement describes this reaction?
Answer and reasoning
A molecule of water is taken in to provide the atoms needed to link the two amino acids together. — A student who confuses condensation with hydrolysis picks this. In fact water is a product: a hydroxyl group from the carboxyl group and a hydrogen from the amine group are removed and combine to form the water that is released.
The carboxyl group of one amino acid reacts with the amine group of the other, and water is released. — This is the condensation reaction: amino acid + amino acid → dipeptide + water. The peptide bond forms between the carbon of the carboxyl group and the nitrogen of the amine group, and one molecule of water is released.
The R-group of one amino acid bonds to the R-group of the other, forming the peptide bond between them. — A student who assumes the distinctive R-groups must do the chemistry picks this. In fact the R-groups take no part in the reaction; the peptide bond is in the backbone, between a carboxyl group and an amine group.
The amine group of one amino acid forms a hydrogen bond with the carboxyl group of the other, and no water is released. — A student who thinks the link between amino acids is a hydrogen bond picks this. In fact the peptide bond is a covalent C–N bond formed by a condensation reaction between the carboxyl group and the amine group, and one molecule of water is released as it forms.
One that the body needs in larger quantities than the non-essential amino acids. — A student who reads essential in its everyday sense of important picks this. In fact the term says nothing about quantity: an essential amino acid is one that cannot be synthesized in the body and so must be obtained from food.
One of the 20 amino acids, all of which must be supplied by the protein in the diet. — A student who thinks every amino acid has to come from food picks this. In fact only the essential amino acids must come from food; the non-essential ones can be made in the body from other amino acids.
One that is found in animal protein but is absent from all plant-based foods. — A student who believes plant proteins contain no essential amino acids picks this. In fact plant proteins contain essential amino acids, although a single plant protein may be low in one or more of them; the definition concerns the body's inability to make them.
One that cannot be synthesized in the body and must be obtained from food. — This is the definition: essential amino acids cannot be synthesized and must be obtained from food, whereas non-essential amino acids can be made from other amino acids.
4 Why is the number of different possible polypeptides described as effectively infinite?
Answer and reasoning
The 20 amino acids can be arranged in any order, but each amino acid can be used only once in a given chain. — A student who pictures a polypeptide as a rearrangement of the 20 amino acids picks this. In fact any amino acid can occur any number of times, which is how chains of thousands of amino acids are possible.
There are very many combinations of amino acids, and the order of the amino acids does not affect the protein. — A student who treats a polypeptide as a mixture of ingredients picks this. In fact the order matters: each different sequence is a different polypeptide with a different shape, which is a large part of why the variety is so great.
Chains can be of any length, and the 20 amino acids can occur in any order and be used any number of times. — Twenty amino acids are coded for in the genetic code, peptide chains can have any number of amino acids from a few to thousands, and the amino acids can be in any order. The number of possible sequences, 20ⁿ for a chain of n amino acids, is therefore effectively infinite.
Each extra amino acid added to a chain adds 20 to the number of different polypeptides that are possible. — A student who adds rather than multiplies picks this. In fact each extra position multiplies the number of possible sequences by 20, so the total is 20ⁿ, which grows far faster than 20 × n.
5 When egg white is heated, its soluble proteins turn into a white solid. What has happened to the protein molecules?
Answer and reasoning
Heat has broken the peptide bonds, so the polypeptides have been split into amino acids. — A student who thinks denaturation breaks the protein down picks this. In fact the covalent peptide bonds are unaffected by cooking temperatures; it is the weak bonds holding the folded shape that break, so the sequence is intact but the shape is lost.
Heat has killed the proteins, so they are no longer able to carry out their functions. — A student who uses everyday language about heat killing things picks this. In fact proteins are molecules and cannot be killed; they have been denatured, meaning their conformation has changed so that they no longer function or dissolve.
Heat has changed their shape temporarily, and they will refold as soon as the egg white cools. — A student who expects denaturation to reverse picks this. In fact denaturation is in most cases permanent: a cooked egg white does not become clear and liquid again when it cools, because the unfolded chains do not refold correctly.
Heat has broken the bonds holding their folded shape, so they have unfolded. — This is denaturation. Heat makes the molecules vibrate more, breaking the bonds that maintain the three-dimensional shape; the unfolded chains tangle with one another, which is why the egg white becomes an insoluble solid.
6 Thousands of copies of the same enzyme are synthesized in a cell, and every copy has the same three-dimensional shape. Why? HL
Answer and reasoning
The ribosome and Golgi apparatus mould each polypeptide into the shape the cell needs after it has been synthesized. — A student who thinks a cell structure imposes the shape picks this. In fact the chain folds according to its own sequence; the ribosome joins the amino acids and the Golgi apparatus modifies proteins, but neither determines the conformation.
Every copy contains the same set of amino acids, and the order in which they occur has no effect at all on the final shape. — A student who treats a polypeptide as a mixture of ingredients picks this. In fact the shape depends on the sequence, not just the composition; the same amino acids in a different order would fold into a different shape.
The sequence of amino acids, each in its precise position, determines the conformation, so folding is repeatable. — The primary structure determines the three-dimensional shape: the R-groups in their exact positions can form only one set of bonds, so every polypeptide with that sequence folds the same way. Proteins therefore have precise, predictable and repeatable structures.
Only the few amino acids that form the active site affect the shape, and these are the same in every copy. — A student who sees the rest of the enzyme as filler picks this. In fact the precise position of every amino acid in the sequence contributes to the conformation, and the copies match because their whole sequences are identical.
7 What stabilizes the alpha helices and beta-pleated sheets of a protein's secondary structure? HL
Answer and reasoning
Hydrogen bonds between the R-groups of amino acids brought close together by folding. — A student who attaches every bond in a protein to R-groups picks this. In fact the R-groups project outwards from helices and sheets and take no part; the hydrogen bonds of secondary structure are between backbone groups.
Disulfide bonds between cysteines spaced at regular intervals along the polypeptide. — A student who applies tertiary-structure bonding to secondary structure picks this. In fact disulfide bonds are between cysteine R-groups and belong to tertiary structure; helices and sheets depend on backbone hydrogen bonds.
Hydrogen bonds forming the peptide links between the amine and carboxyl groups of neighbours. — A student who thinks peptide bonds are hydrogen bonds picks this. In fact peptide bonds are covalent and form the primary structure; the hydrogen bonds of secondary structure are additional, between the C=O and N–H groups of different peptide bonds.
Hydrogen bonds at regular positions between C=O and N–H groups of the backbone. — Alpha helices and beta-pleated sheets are stabilized by hydrogen bonding in regular positions between the C=O group of one peptide bond and the N–H group of another in the polypeptide backbone.
8 In one region of a polypeptide there are two cysteines, an amino acid whose R-group contains a carboxyl group and an amino acid whose R-group contains an amine group. Which statement about the bonds these could form in the tertiary structure is correct? HL
Answer and reasoning
The cysteines can form a covalent disulfide bond; the carboxyl and amine R-groups can form an ionic bond once the first has lost and the second has bound a hydrogen ion. — Pairs of cysteines form disulfide covalent bonds. The carboxyl group in an R-group becomes negatively charged by dissociation of a hydrogen ion and the amine group in an R-group becomes positively charged by binding one, and the two charged R-groups can then form an ionic bond.
The cysteines can form a disulfide bridge, which is a strong hydrogen bond and so is broken by heating as easily as the other hydrogen bonds. — A student who lumps the disulfide bond with the weak interactions picks this. In fact it is a covalent bond between two sulfur atoms, far stronger than a hydrogen bond, and it survives heating and pH changes that break the other interactions.
The carboxyl R-group becomes positively charged and the amine R-group becomes negatively charged, so the two attract and form an ionic bond. — A student who links acid with positive charge picks this. In fact the charges are the other way round: the carboxyl group loses a hydrogen ion and becomes negative, and the amine group binds one and becomes positive.
The carboxyl and amine R-groups carry fixed charges, so an ionic bond between them is unaffected by any change in the pH of the solution. — A student who thinks of protein charges like the fixed charges in sodium chloride picks this. In fact the charges depend on binding or dissociation of hydrogen ions, so a change in pH can remove them and break the ionic bond.
9 A globular enzyme is dissolved in the cytoplasm, and an integral protein spans the plasma membrane. Where are the amino acids with hydrophobic R-groups located in each protein, and why? HL
Answer and reasoning
Absent from the soluble enzyme, because a protein containing hydrophobic amino acids could not dissolve in water. — A student who judges solubility by adding up the amino acids picks this. In fact soluble globular proteins do contain hydrophobic amino acids; they are clustered in the core, away from water, while the surface is hydrophilic.
Throughout the whole of the integral protein, which must be hydrophobic on all of its surfaces to stay in the membrane. — A student who thinks anything in a membrane must be hydrophobic all over picks this. In fact only the region within the bilayer has hydrophobic R-groups; the parts projecting into the aqueous solutions on either side are hydrophilic.
In the enzyme's core and the integral protein's membrane region, because water molecules bond to each other and exclude non-polar R-groups. — In proteins that are soluble in water, hydrophobic amino acids are clustered in the core of the globular protein, and integral proteins have regions with hydrophobic amino acids that sit in the hydrophobic centre of the bilayer. They end up there because water molecules hydrogen-bond to one another and not to non-polar R-groups, which are therefore excluded from the water.
In the enzyme's core and the integral protein's membrane region, because their non-polar R-groups repel the water molecules and push them away. — A student who pictures hydrophobic groups pushing water away picks this. The locations are right but the mechanism is not: there is no repulsion; water molecules bond to each other and exclude non-polar groups, so hydrophobic R-groups end up away from water.
10 Which statement correctly compares insulin, collagen and haemoglobin? HL
Answer and reasoning
All three are conjugated proteins, because each of them is built from more than one polypeptide chain. — A student who thinks conjugated means multi-chain picks this. In fact all three have quaternary structure, but only haemoglobin is conjugated, because it contains non-polypeptide haem groups; insulin and collagen consist of polypeptides only.
The haem groups of haemoglobin are short polypeptides, so all three of these proteins are non-conjugated. — A student who assumes everything in a protein is made of amino acids picks this. In fact a haem group is not a polypeptide: it is a ring structure containing an iron ion, and its presence is what makes haemoglobin a conjugated protein.
Insulin is a single polypeptide, so unlike collagen and haemoglobin it does not have quaternary structure. — A student who assumes a small hormone must be a single chain picks this. In fact insulin consists of two polypeptides linked by disulfide bonds, so it has quaternary structure and is the guide's example of a non-conjugated protein.
Haemoglobin is a conjugated protein with haem groups; insulin and collagen are non-conjugated. — Haemoglobin is conjugated because each of its four polypeptides carries a haem group, a prosthetic group not made of amino acids. Insulin (two polypeptides) and collagen (three polypeptides) have quaternary structure but no prosthetic group, so they are non-conjugated.
Read the ones marked not yet in Learn, then Verify.
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8 more questions. Every wrong answer here is a real misconception, and you see why it is wrong straight away.
1 A polypeptide of 150 amino acids is assembled by condensation reactions. How does the number of water molecules change as the whole chain is formed?
Answer and reasoning
150 released — A student who counts one water molecule per amino acid picks this. In fact one water molecule is released per peptide bond, and 150 amino acids are joined by 149 peptide bonds, because the two ends of the chain are unreacted.
300 released — A student who counts both the amine and the carboxyl group of every amino acid as releasing water picks this. In fact one peptide bond uses one carboxyl group and one amine group together and releases a single water molecule, so the total is 149.
149 released — Each condensation reaction links two amino acids with one peptide bond and releases one molecule of water. Joining 150 amino acids into one chain needs 149 peptide bonds, so 149 water molecules are released.
149 consumed — A student who thinks water is a reactant in condensation picks this. In fact water is a product: it is formed from the –OH of a carboxyl group and the –H of an amine group and released, so 149 molecules are produced, not used up.
2 A dietitian advises someone following a vegan diet to eat a range of plant protein sources rather than rely on one. Which statement best explains the advice?
Answer and reasoning
Individual plant proteins may be low in one or more essential amino acids, which cannot be synthesized in the body, so a range makes sure all are consumed. — Vegan diets require attention to ensure essential amino acids are consumed. Because these cannot be made in the body, and a single plant protein may be low in one or more of them, eating a variety of plant protein sources ensures that all of them are obtained.
Plant foods contain only non-essential amino acids, so eating several kinds is needed to raise the total amount of protein consumed. — A student who thinks essential amino acids occur only in animal foods picks this. In fact plant proteins contain essential amino acids; the issue is that an individual plant protein may be low in one or more of them, which variety corrects.
None of the 20 amino acids can be synthesized in the body, so all of them must be taken in, which needs more than one food source. — A student who thinks all amino acids must come from food picks this. In fact non-essential amino acids can be made from other amino acids; the advice concerns only the essential ones, which the body cannot synthesize.
Essential amino acids are the ones the body needs in the largest amounts, so several sources are needed to supply enough of them. — A student who takes essential to mean needed most picks this. In fact essential refers to the body's inability to synthesize the amino acid, not to the quantity required, and the advice is about making sure none is missing.
3 A chemist makes tripeptides using only four different amino acids. Each of the three positions in a chain can hold any of the four amino acids. How many different tripeptides are possible?
Answer and reasoning
24 — A student who assumes an amino acid cannot be used twice in a chain calculates 4 × 3 × 2 = 24. In fact amino acids can be repeated, so each position is an independent choice of four, giving 4 × 4 × 4 = 64.
64 — Each of the three positions can independently hold any of the four amino acids, and amino acids can be repeated, so the number of sequences is 4 × 4 × 4 = 4³ = 64. With 20 amino acids and long chains the same reasoning gives an effectively infinite variety.
12 — A student who multiplies the number of amino acids by the chain length picks 4 × 3 = 12. In fact the choices at the three positions multiply together, so the number is 4³ = 64, not 4 × 3.
81 — A student who puts the numbers the wrong way round calculates 3⁴ = 81. In fact the base is the number of amino acids available at each position and the power is the number of positions, so the answer is 4³ = 64.
4 An enzyme's activity at its optimum pH of 7 was 100 units. One sample was placed at pH 2 for 10 minutes, then returned to pH 7: its activity was 4 units after 1 hour and 4 units after 24 hours, and its polypeptide chains were found to be intact. A second sample was cooled to 5 °C for 10 minutes, then returned to 37 °C: its activity was 100 units. What do these results show?
Answer and reasoning
The low pH denatured the enzyme, changing its conformation in a way that was not reversed at pH 7, whereas the low temperature did not denature it. — The pH 2 sample lost almost all activity and did not recover even after 24 hours at the optimum pH, while its chains stayed intact: its shape had changed permanently, which is denaturation. The cooled sample regained full activity, so its conformation was unchanged.
Both treatments denatured the enzyme, but the denaturation caused by cooling was reversed when the sample was warmed again. — A student who thinks both sides of the temperature graph are explained by denaturation picks this. In fact low temperature does not change a protein's shape; it only slows molecular movement, so full recovery on warming shows the enzyme was not denatured.
The acid-treated enzyme was only temporarily denatured and would have regained full activity if left for longer at pH 7. — A student who expects a protein to refold once conditions are restored picks this. In fact the activity was the same after 1 hour and after 24 hours, showing no recovery; denaturation is in most cases permanent.
The acid hydrolysed the peptide bonds of the enzyme, so its polypeptide chains were broken into separate amino acids. — A student who thinks denaturation breaks peptide bonds picks this. In fact the chains were found to be intact, so the loss of activity was due to a change of shape, not to breakdown of the primary structure.
5 Which statement about the R-groups of amino acids is correct? HL
Answer and reasoning
Every hydrophilic R-group must carry a charge; a polar R-group that is uncharged is classed as hydrophobic. — A student who equates hydrophilic with charged picks this. In fact polar R-groups form hydrogen bonds with water and are hydrophilic even though they carry no overall charge; hydrophilic R-groups are polar or charged.
Hydrophilic R-groups are either polar but uncharged, or charged, and charged R-groups are acidic or basic. — R-groups are hydrophobic or hydrophilic. Hydrophilic R-groups are polar or charged; a charged R-group is acidic if its carboxyl group has dissociated to become negative, or basic if its amine group has bound a hydrogen ion to become positive.
An acidic R-group carries a positive charge, because an acid is a substance that contains hydrogen ions. — A student who links acid with H⁺ and so with positive charge picks this. In fact an acidic R-group releases its hydrogen ion and is left negatively charged; it is the basic R-group that binds a hydrogen ion and becomes positive.
R-groups have little effect on a polypeptide, whose properties come from its amine and carboxyl groups. — A student who sees the fully drawn amine and carboxyl groups as the important chemistry picks this. In fact those groups are used up in peptide bonds to make a backbone common to all polypeptides; it is the R-groups that determine the properties of the assembled polypeptide.
6 A soluble globular enzyme was tested. A reducing agent that breaks disulfide bonds cut its activity to 10%. Moving it from pH 7 to pH 4 cut its activity to 30%, and full activity returned when it was moved back to pH 7. Its polypeptide chain stayed intact in both experiments. What do these results show? HL
Answer and reasoning
The loss of activity at pH 4 cannot involve ionic bonds, because the charges on R-groups do not change at all when the pH changes. — A student who believes R-group charges are fixed picks this. In fact a fall in pH adds hydrogen ions to negatively charged carboxyl R-groups, removing their charge and breaking ionic bonds; restoring the pH restores the charges, which fits the recovery seen.
The tertiary structure depends on disulfide bonds and on ionic bonds between R-groups whose charges change reversibly with pH. — Breaking the disulfide bonds destroyed most of the activity, so they hold the tertiary structure. The pH change altered the charges on R-groups, which depend on binding or dissociation of hydrogen ions, disrupting ionic bonds; returning the pH restored the charges and the bonds.
The reducing agent broke hydrogen bonds, since a disulfide bridge is the strongest type of hydrogen bond found in a protein. — A student who thinks a disulfide bridge is a kind of hydrogen bond picks this. In fact it is a covalent bond between the sulfur atoms of two cysteines, which is exactly why a reducing agent, not gentle heating, is needed to break it.
Both treatments broke peptide bonds, and only the peptide bonds broken by the pH change were re-formed at pH 7. — A student who thinks loss of activity means the chain has been broken picks this. In fact the polypeptide chain stayed intact in both experiments; the activity was lost because bonds holding the tertiary structure, not peptide bonds, were disrupted.
7 Cryogenic electron microscopy has produced images of single protein molecules and of their interactions with other molecules. What does this illustrate about the role of technology in science? HL
Answer and reasoning
Technology allows the imaging of structures that would be impossible to observe with the unaided senses, so new knowledge of proteins can be gained. — This is the nature of science point in the guide: instruments extend observation far beyond what the senses can detect. Cryogenic electron microscopy has made the structures of single protein molecules and their interactions observable, producing knowledge that was previously unobtainable.
A light microscope with sufficient magnification could image single protein molecules, so the new technique is simply more convenient. — A student who explains what a microscope can show by magnification alone picks this. In fact the wavelength of light limits resolution, so no amount of magnification lets a light microscope separate structures the size of a protein molecule.
Molecules are far too small for any instrument to image, so protein structures can only be inferred, not observed directly. — A student who believes molecules can never be seen picks this. In fact cryogenic electron microscopy does image single protein molecules; it is an example of technology making observable what the unaided senses cannot detect.
Pictures of protein structure are artists' impressions based only on the amino acid sequence, so the images add nothing to knowledge. — A student who takes ribbon diagrams for drawings picks this. In fact such diagrams display structures that have been measured; cryogenic electron microscopy provides the observations from which the positions of atoms are determined.
8 Protein X is compact and roughly spherical, dissolves in blood plasma and binds to a specific receptor on target cells. Protein Y forms long insoluble fibres with high tensile strength in tendons. Which statement correctly relates the form of each protein to its function? HL
Answer and reasoning
Y is a polypeptide that has not folded up, and its lack of a defined structure is what allows it to form insoluble fibres. — A student who takes fibrous to mean unfolded picks this. In fact fibrous proteins such as collagen have a precise elongated structure, a triple helix of three polypeptides, and it is this organized structure that gives them strength.
X is globular like insulin, its precise shape fitting its receptor; Y is fibrous like collagen, its elongated shape suiting a structural role. — X has the properties of a globular protein: compact, soluble and able to bind specifically, as insulin binds its receptor. Y has the properties of a fibrous protein: elongated, insoluble and strong, as collagen is in tendons. In each case the shape makes the protein suitable for its function.
Y is a single very long polypeptide chain, and its tensile strength comes from the great length of that one chain alone. — A student who pictures a fibre as one thread picks this. In fact collagen consists of three polypeptides wound together into a triple helix, and many of these are linked into fibres; the winding and cross-linking, not chain length alone, give the strength.
X dissolves because it is built entirely from hydrophilic amino acids, and Y is insoluble because it is built entirely from hydrophobic amino acids. — A student who adds up the amino acids to judge solubility picks this. In fact a globular protein dissolves because its hydrophilic R-groups are on the surface while hydrophobic ones are in the core; solubility depends on the folded shape, not on the amino acids alone.
That was your twenty minutes. Real practice on B1.2 is past-paper questions marked against the mark scheme.
What the exam asks of B1.2
Paper 1A shows a generalised amino acid or dipeptide and asks what is attached where, or counts peptide bonds and water molecules for a chain. Paper 1B may give activity against temperature or pH and ask you to explain the fall in terms of denaturation. Paper 2 uses *draw* for the amino acid and dipeptide, *outline* for condensation and dietary requirements, and at HL *explain* and *distinguish* for the levels of structure: name the bond, say where it forms, and link it to the level. Use insulin, collagen and haemoglobin as your examples whenever a question asks for one.
Compiled from the IB Biology guide (first assessment 2025, updated May 2026 for 2028) and our question bank · Specialist review in progress. How these pages are made ·
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