IB BIOLOGY · THEME B · FORM AND FUNCTION

Twenty amino acids, endless shapes

Every protein in you is a chain of the same twenty building blocks. The order they are joined in decides the shape the chain folds into, and the shape decides the job. Heat or the wrong pH and the shape, and the job, are gone.

IB Biology B1.2SL and HL2 hours SL, 4 HL12 chapters

Start learningTeach it

Fourteen beads, made one at a time, fold into a compact shape: a protein in miniature.

01Learn

Twelve chapters, the last seven for higher level. Read one, play its figure through or tap its parts, and make each prediction before you open the answer.

  1. 1Every amino acid is built on the same core
  2. 2Peptide bonds join amino acids, and water leaves
  3. 3Some amino acids you must eat
  4. 4Twenty amino acids, endless chains
  5. 5Heat and pH unfold a protein
  6. 6The R groups decide how a chain behaves HL
  7. 7The sequence sets the shape HL
  8. 8Coils and pleats held by hydrogen bonds HL
  9. 9Four kinds of bond hold the fold HL
  10. 10Oily inside, watery outside HL
  11. 11More than one chain: quaternary structure HL
  12. 12Balls and ropes: globular and fibrous proteins HL

B1.2.1 Generalised structure of an amino acid

Every amino acid is built on the same core

A protein is a polymer (B1.1), a long chain of the same kind of unit joined end to end. The units are amino acids, and every one of them starts from the same pattern.

At the middle sits one carbon atom, the alpha carbon. Carbon always makes four bonds, and here they go to four different things: an amine group (-NH2), a carboxyl group (-COOH), a single hydrogen atom and an R group. The name says it: “amino” from the amine group, “acid” from the carboxyl group, which can give up a hydrogen ion.

The R group is the only part that varies. The genetic code uses twenty different R groups, so there are twenty amino acids. The smallest R group is a single hydrogen atom, and others are chains or rings, some containing oxygen, nitrogen or sulfur. At standard level you do not need to name any of them.

  • Draw the alpha carbon in the middle, the amine group on one side and the carboxyl group on the other, hydrogen and R above and below.
  • Show every atom and every bond, in the un-ionised form (-NH2 and -COOH), as the markschemes do.
  • Count the bonds: four on carbon, three on nitrogen, two on oxygen, one on hydrogen.

Remember it The four groups on the alpha carbon

  • AAmine group-NH2, on one side
  • CatCarboxyl group-COOH, on the other side
  • HasHydrogenone H atom
  • RhythmR groupthe only part that varies
Watch out R is not an element. It stands for the side chain, whatever it is in that amino acid. And check every drawing by counting bonds: four on every carbon, three on nitrogen, two on oxygen, one on hydrogen.

A student draws an alpha carbon bonded to -NH2, -COOH, R and -OH. What is wrong with the drawing?

CCNHHCNHHCOOHCNHHCOOHHCNCOOHHHHRalpha carbonamine groupcarboxyl groupR group: the only part that variesCNCOOHHHHHCNCOOHHHHH3CCNCOOHHHHHSH2Csame in all twentythe only difference
  1. The alpha carbon makes four bonds.
  2. An amine group goes on the left bond: a nitrogen with two hydrogens.
  3. A carboxyl group goes on the right bond: a carbon with a double bond to one oxygen and a single bond to an OH.
  4. One hydrogen atom goes on the bottom bond.
  5. The last bond carries the R group. It stands for whatever side chain this amino acid has.
  6. Three different amino acids: the same core in each, and only the R group differs.

B1.2.2 Condensation reactions forming dipeptides and longer chains

Peptide bonds join amino acids, and water leaves

Amino acids join by the same move as every other monomer in B1.1, a condensation reaction. The OH from the carboxyl group of one amino acid and an H from the amine group of the next leave together as a molecule of water. The carbon of the carboxyl group is then left bonded to the nitrogen of the amine group, and that C-N bond is a peptide bond, a strong covalent bond. Two amino acids make a dipeptide.

The word equation is amino acid + amino acid → dipeptide + water.

The dipeptide still has a free amine group at one end and a free carboxyl group at the other, so more amino acids can join on in the same way. A long chain is a polypeptide (a short chain of a few amino acids is sometimes called an oligopeptide). A chain of n amino acids has n − 1 peptide bonds, and n − 1 molecules of water were released making it. Hydrolysis, adding water back, reverses it, which is what digestion does to the proteins in food. In cells, ribosomes make the peptide bonds, in the order a gene sets (D1.2).

A protein is one or more polypeptides folded into a working shape. Model this reaction with a kit first (see Teach), then try the bond builder below and draw a dipeptide.

Watch out The peptide bond is not between the two alpha carbons, not through an oxygen (C-O-N), and never involves an R group. And the water takes its OH from one amino acid and its H from the other, not both from the same one.
Example Insulin has two polypeptides. The shorter has 21 amino acids and so 20 peptide bonds, and the longer has 30 and so 29. (Insulin itself comes back at higher level.)

Two different amino acids, A and B, are joined by one peptide bond. How many different dipeptides could they make?

CNCOOHHHHR1CNCOOHHHHR2CNCOOHHHHR1CNCOOHHHHR2+amino acid 1amino acid 2CNCOHHHR1CNCOOHHHR2peptide bondHHOwaterpeptide bondamine group(free end)carboxyl group(free end)alpha carbonR group
  1. Two amino acids, R1 and R2, with the carboxyl group of the first facing the amine group of the second.
  2. The OH from the carboxyl group and one H from the amine group are lit: they will leave as water.
  3. The carbon bonds to the nitrogen and the water drifts away. The new C-N bond is a peptide bond.
  4. A dipeptide, drawn as an examiner wants it. It still has an amine group at one end and a carboxyl group at the other.
CNCOHHHR1CNCOOHHHR2+OHHOHHCNCOHHHR1CNCOOHHHR2dipeptideHHOamino acid + amino aciddipeptide + watercondensationhydrolysis
  1. Two amino acids.
  2. The OH of one's carboxyl group and an H of the other's amine group face each other.
  3. They leave as water, and a peptide bond joins the carbon to the nitrogen: condensation, making a dipeptide.
  4. Add water and the peptide bond splits again, the OH back to the carbon and the H to the nitrogen: hydrolysis.
Join the amino acids, both ways round, then add water to split them again. Count the peptide bonds and the water released.

B1.2.3 Dietary requirements for amino acids

Some amino acids you must eat

Your cells need all twenty amino acids to build their proteins. They can make some of them from other amino acids: these are non-essential amino acids. They cannot make the rest, which must come from food: essential amino acids. For an adult, nine of the twenty are essential. You do not need to name any of them.

“Essential” is about the diet, not importance: a protein needs every amino acid in its sequence, so the non-essential ones matter just as much. You just do not need to eat them.

The body keeps no store of spare amino acids, as it does for glycogen and fat, so essential ones are needed regularly. Food protein is digested (hydrolysed) to amino acids, which are absorbed and built into your own proteins. If one essential amino acid runs short, every protein that needs it cannot be finished: the gene sets the sequence, and no other amino acid can stand in.

Plants and animals differ here. A plant makes all twenty amino acids itself, from sugars and nitrate taken up from the soil, so it needs no amino acids from food. An animal cannot make all of them and must eat the essential ones. Some amino acids are conditional: the body can make them, but not fast enough at certain times such as infancy, pregnancy or illness. Vegan diets take all their protein from plants. Most plant foods contain every essential amino acid, but some have little of one: cereals are low in one, and beans and lentils in a different one. A variety over the day, such as rice with lentils or hummus with bread, supplies them all, and soya and quinoa have all of them in good amounts. A vegan diet needs attention, not luck. Meat, eggs and dairy carry all of them in proportions close to what we need.

Watch out Non-essential amino acids are not unimportant: they are in your proteins too, you just do not need them in food. And “vegans cannot get essential amino acids” is false: they need a variety of plant proteins.

You eat plenty of protein, but it lacks one essential amino acid. What happens to the proteins that need it?

non-essential: made in your cells from other amino acidsessential: must come from foodribosome12345678the chain grows in one set ordergrainone jar lowpulsea different jar low+=togetherevery jar fulla day of rice onlyOne jar low.
  1. Twenty jars feed the line, and the chain grows in one order, set by the gene.
  2. Eleven jars are filled by a pipe from the cells: non-essential amino acids, which your cells can make from other amino acids.
  3. Nine jars are filled only from the plate: essential amino acids, which must come from food.
  4. A varied plant plate: grain runs a little low in one jar and pulses in a different one, and together they fill every jar. A vegan diet covers all nine with variety.
  5. A day of rice only: one jar runs low.

B1.2.4 Infinite variety of possible peptide chains

Twenty amino acids, endless chains

The genetic code (A1.2) codes for twenty amino acids. A polypeptide can have any number of them, from a few to thousands, in any order, and the same amino acid can appear again and again.

That makes the number of possible chains enormous. There are 20 × 20 = 400 different dipeptides, 20 × 20 × 20 = 8,000 tripeptides, and 20n chains of length n. Past about 62 amino acids there are more possible sequences than there are atoms in the observable universe, and real proteins are much longer than that.

Living things use only a tiny fraction of the possible sequences. Most protein-coding genes code for one polypeptide, and all the proteins an organism makes are its proteome. You should know some examples of polypeptides:

  • Glucagon, a hormone, has 29 amino acids.
  • Insulin, a hormone, has 51 in two chains of 21 and 30.
  • Lysozyme, an enzyme in egg white and tears, has 129.
  • Each haemoglobin chain has 141 or 146.
  • A collagen chain has about 1,000.
  • Titin, a springy protein inside muscle, has about 34,000, the largest known in humans.
Watch out Twenty amino acids do not mean twenty proteins. And a protein’s identity is its order: the same amino acids in a different order make a different polypeptide.
Linking question What is the relationship between the genome and the proteome? The genome is all of an organism’s genes, and most of them code for a polypeptide, so the genome sets which proteins the organism can make, its proteome. Different cells use different parts of it, so a liver cell’s proteins differ from a muscle cell’s (D1.2, and D2.2 at higher level).

How many different dipeptides can be made from the 20 amino acids?

choices at each position20…1 amino acid

Chain of 1 amino acid: 201 = 20. Twenty choices for a chain of one.

1

ribosomeR+SALIND−FR+AR+SALIND−FR+ANK+LINnon-polarpolarpolar, with a chargecysteine (C)8 weak bonds holdits shapeS-S0 strong bondsbetween two cysteinesEach letter isan amino acid15 amino acidsleave the ribosomeone at a time
  1. Type ROSALIND FRANKLIN: each letter is the code for one amino acid (the O is skipped: no amino acid has that letter). Its 15 amino acids are joined by 14 peptide bonds: one of 2015 (about 3 × 1019) possible chains this long. A ribosome makes the chain one amino acid at a time, and it starts to fold as it comes out.
  2. It folds into a shape of its own, held by weak bonds between its side chains.
Type your name: it is a polypeptide.

B1.2.5 Effect of pH and temperature on protein structure

Heat and pH unfold a protein

A protein works because of its precise three-dimensional shape: a pocket that fits one molecule, a surface that binds one partner. That shape is held in place by many weak bonds between parts of the folded chain, hydrogen bonds (met in A1.1) and attractions between charged groups.

At higher level you will meet the four kinds of bond in chapter 9.

Heat. The atoms vibrate more and more, and past a point the weak bonds break. The chain unfolds, its shape is lost and it can no longer do its job: it is denatured. The peptide bonds are covalent and much stronger, so the sequence of amino acids is unchanged.

pH. Hydrogen ions attach to groups in the R groups, or leave them, and so change their charges. The attractions between oppositely charged groups are lost and the shape changes. Each protein keeps its shape over a range of pH, and far outside it the protein denatures.

Denaturation is usually permanent. Heated chains tangle with each other and do not refold when cooled, which is why an egg white stays white and solid. Each protein’s limits suit where it works: proteins in the stomach keep their shape at about pH 2, and the proteins of microbes in hot springs stay folded at temperatures that would denature ours. Cooling slows a protein down but does not unfold it.

Watch out Denatured does not mean dead (a protein was never alive), melted or dissolved. Cold does not denature: a protein in the fridge is slow but whole. And cooling a heat-denatured protein does not usually bring its shape back.
Try it The enzyme in your spit, a home lab in C1.1, times salivary amylase breaking down starch at cold, room and warm temperatures. Amylase is a protein, and denaturation is the reason the hottest tube behaves as it does.
Linking question How do abiotic factors influence the form of molecules? Temperature and pH change a protein’s shape by breaking the bonds that hold it. The same idea runs through the course: heat breaks hydrogen bonds between water molecules (A1.1), warmth melts fats with more C=C bonds sooner (B1.1), and every enzyme has an optimum (C1.1).

When an egg sets in a hot pan, which bonds break?

in the panprotein molecules, magnified
  1. Raw egg white: clear and runny. Magnified, the proteins are folded, each on its own among the water molecules.
  2. Heat makes the molecules jiggle harder and breaks the bonds that hold the folds.
  3. The chains unfold: with the bonds gone, their shape is gone.
  4. Unfolded chains tangle together and the egg white sets, white and solid. The proteins are denatured.
Raise the temperature, then bring it back down: does the shape come back? Then try the pH at either end.

B1.2.6 Chemical diversity in the R groups

The R groups decide how a chain behaves

R groups differ in size, shape and chemistry, and those differences give a polypeptide its properties: which parts face water, what binds to what, and where the chain carries charge. You do not need to name any R group, but you do need to sort them.

There are two big classes. Hydrophobic R groups are non-polar, mostly carbon and hydrogen, and water does not attract them. Hydrophilic R groups are attracted to water, and they are either polar, with partial charges that let them form hydrogen bonds, or charged.

Charged R groups are acidic or basic. An acidic R group contains a carboxyl group, which loses a hydrogen ion and becomes negative (-COO−). A basic R group contains an amine group, which gains a hydrogen ion and becomes positive (-NH3+). At the pH inside a cell both are charged, and a change in pH changes that (chapters 5 and 9).

Remember it The four kinds of R group

  • HungryHydrophobicnon-polar, hides from water
  • PandasPolarpartial charges, hydrogen bonds
  • AteAcidicloses H+, negative
  • BambooBasicgains H+, positive
Watch out Hydrophilic does not mean charged: polar R groups are hydrophilic with no overall charge. Acidic R groups are negative, not positive. And a charge can come and go with pH.

An R group contains a carboxyl group. Inside a cell, at about pH 7, it is:

R groupHydrophilicSix R groups to sort-CH2-OH-(CH2)4-NH3+​-CH3​-CH(OH)-CH3​-CH2--CH2-COO−​HydrophobicPolarAcidic (−)Basic (+)

Pick an R group (tap it, or Tab to it and press Enter), then pick the bin it belongs in.

0 of 6 sorted

Six R groups, drawn as condensed formulas, and four bins. Which bin does each belong in, and what tells you?

B1.2.7 Impact of primary structure on conformation

The sequence sets the shape

The primary structure of a protein is the sequence of amino acids in its polypeptide, and a gene sets it. The sequence, and the exact position of each amino acid in it, decide the three-dimensional shape (its conformation): where the chain coils or pleats (secondary structure, chapter 8), how the whole chain folds (tertiary, chapters 9 and 10) and how chains fit together (quaternary, chapter 11).

So proteins have precise, predictable and repeatable structures, despite their complexity. Every insulin molecule your pancreas makes has the same shape, and fits insulin receptors anywhere in your body. Change one amino acid in a key position and the shape can change: in D1.3 you will meet a single changed amino acid in haemoglobin with large effects.

Watch out Primary structure is the sequence, not a shape, but it decides every level after it. Folding is not random.
How we know Christian Anfinsen unfolded the enzyme ribonuclease with chemicals and then removed them. The chains refolded by themselves into the working shape, so the information for the shape is in the sequence (Nobel Prize in Chemistry, 1972). Since 2020 a computer model trained on known structures, AlphaFold, has predicted the shape of many proteins from their sequence alone, often close to what experiments find, and its database holds predictions for over 200 million proteins. Models earn trust by being tested against evidence.

Two people make insulin from the same gene sequence. Do their insulin molecules have the same shape?

1primarythe sequence2secondarycoils and pleats3tertiarythe whole chain folded4quaternarytwo or more chainspeptide bonds join every neighbourcoilpleatsame sequence,same shape
  1. Primary structure: a sequence of amino acids, each joined to the next by a peptide bond.
  2. Secondary structure: one stretch coils and another pleats beside itself, held by dashed hydrogen bonds.
  3. Tertiary structure: the whole chain folded into a compact shape.
  4. Quaternary structure: two or more folded chains together. Not every protein has one.
  5. A second copy of the same sequence folds into the same shape: same sequence, same shape, every time.

B1.2.8 Pleating and coiling of secondary structure

Coils and pleats held by hydrogen bonds

The polypeptide backbone is the repeating N-C-C pattern (the amine nitrogen, the alpha carbon, the carboxyl carbon) with the R groups hanging off it. Every peptide bond sits between a C=O group, whose oxygen is slightly negative, and an N-H group, whose hydrogen is slightly positive. These backbone groups are polar (A1.1), so a C=O and an N-H further along the chain can form a hydrogen bond. Where the chain makes these bonds in regular positions, it settles into a regular shape, its secondary structure.

In an alpha helix the chain coils, and each C=O bonds with the N-H four amino acids further along. The bonds fall in regular positions along the coil, and the R groups point outwards. In a beta-pleated sheet, stretches of the chain lie side by side, running the same way or opposite ways, and C=O groups in one stretch bond to N-H groups in the next. The chain zigzags, which makes the pleats, and the R groups point alternately above and below the sheet.

Each bond is weak, but hundreds in regular positions make the structure stable. One protein usually has stretches of both, joined by less regular loops.

Watch out Secondary structure bonds are between backbone groups, not R groups. An alpha helix is one coiled polypeptide, nothing to do with the double helix of DNA. And collagen’s helix is not an alpha helix (chapter 11).

Which groups form the hydrogen bonds that hold an alpha helix?

C=ON-Hhydrogenbondzoom on one bondalpha helixR groups point outhydrogen bondsbeta-pleated sheetthree strands side by side, running opposite waysR groups alternateabove and belowalpha helixbeta-pleated sheetloopsOne chain usually has stretches of both, joined by less regular loops.

Tap a dashed line to see what it joins.

B1.2.9 Dependence of tertiary structure on four kinds of bond

Four kinds of bond hold the fold

Tertiary structure is the three-dimensional shape of the whole polypeptide. It is held by bonds between R groups, often far apart in the sequence.

  • Hydrogen bonds between polar R groups.
  • Ionic bonds between a positively charged (basic) and a negatively charged (acidic) R group. The amine and carboxyl groups in R groups become charged by gaining or losing a hydrogen ion, and only then can they form ionic bonds.
  • Disulfide bonds, covalent bonds between the sulfur atoms of two cysteines, the only amino acid you need to name. This is the strongest of the four.
  • Hydrophobic interactions: non-polar R groups cluster together, away from water.

This links back to chapter 5. Heat breaks hydrogen bonds, ionic bonds and hydrophobic interactions, and a change of pH alters charges and so breaks ionic bonds. The disulfide bonds are covalent, so they survive much more.

Remember it The bonds that hold a tertiary structure

  • HappyHydrogen bondsbetween polar R groups
  • HipposHydrophobic interactionsnon-polar R groups huddle away from water
  • IgnoreIonic bondsbetween + and − R groups
  • DentistsDisulfide bondstwo cysteines; the only covalent one
Watch out A disulfide bond is covalent and forms only between two cysteines: it is not a kind of hydrogen bond. Ionic bonds need charged R groups, not just polar ones. And hydrophobic interactions are not attractions between the R groups and water.

An ionic bond holds two parts of a protein together. The pH falls to 2. Why might the bond break?

non-polarpolar−acidic+basicScysteineS-SS+S−S+S-O-HO=C-two polar R groups-COO−+H3N-acidic meets basic-CH2-SS-CH2-two cysteines-COO−H-COOHthe carboxyl gains H+

Hydrogen bonds join polar R groups: an O-H or N-H on one, an O on the other. Each is weak.

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

Oily inside, watery outside

In proteins that dissolve in water, such as the globular proteins of chapter 12, the hydrophobic R groups cluster in the core, away from the water. The hydrophilic R groups, polar and charged, sit on the surface, where they interact with water. That watery surface is why the protein dissolves.

Why? Water molecules form hydrogen bonds with each other and with polar groups, but not with non-polar ones, so the non-polar R groups end up pushed together. This drives much of the folding. Water does not push them away as a magnet would: it simply bonds to itself and to polar groups instead.

Integral proteins work the other way round. They have regions of hydrophobic amino acids where they cross the membrane, lying among the hydrophobic tails of the phospholipids (B1.1), and hydrophilic regions where the protein meets water on each side (B2.1). A stretch of about 20 hydrophobic amino acids, coiled as a helix, is enough to cross the bilayer once. In a channel protein the chain crosses several times, and the hydrophilic amino acids face inwards to line the pore that ions or water pass through, while the hydrophobic ones face the lipids outside.

Watch out Hydrophobic amino acids are not “bad”: without them there would be no core and no membrane protein. And a chain does not fold because someone puts it there: it folds by itself as it jostles in water.

A protein dissolves in blood plasma. Where are most of its hydrophobic R groups?

+−+−+−waterwaterlipid tails(hydrophobic)phospholipid headson both sidesnon-polarpolar−acidic+basic

A chain just made, lying loose in water. Its non-polar, polar and charged beads are in the order its gene set.

ribosomeR+SALIND−FR+AR+SALIND−FR+ANK+LINhydrophobic (non-polar)polaracidic, −basic, +cysteine (C)6 hydrophobicinteractions1 hydrogen bond1 ionic bondS-S0 disulfide bondsEach letter isan amino acid15 amino acidsleave the ribosomeone at a time
  1. Type ROSALIND FRANKLIN: each letter is the code for one amino acid (the O is skipped: no amino acid has that letter). A ribosome makes the chain one amino acid at a time, and it starts to fold as it comes out.
  2. In water it folds: the non-polar ones gather inside, away from the water (6 of 7), and the polar ones face outwards. Hydrophobic interactions, hydrogen bonds and ionic bonds hold it.
Type your name or pick a gene, press Fold and watch which bonds form and where the non-polar amino acids end up. Fold the made-up membrane protein across a membrane. Then change one base: try the sickle cell change and make a second copy, then a frameshift.

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

More than one chain: quaternary structure

Some proteins are a single polypeptide. Others are two or more polypeptides held together, and their arrangement is the quaternary structure, held by the same kinds of bond as the tertiary.

A non-conjugated protein is made of polypeptide only. Insulin has two polypeptides, of 21 and 30 amino acids, linked by two disulfide bonds, with a third disulfide bond within the shorter chain. Collagen has three polypeptides, each about 1,000 amino acids long, wound round each other into a triple helix like a rope. Every third amino acid is the smallest one, which lets the chains pack tightly, and hydrogen bonds between the chains hold the rope together.

A conjugated protein includes a part that is not polypeptide, a prosthetic group. Haemoglobin has four polypeptides, two of one kind and two of another, each holding a haem group with an iron ion at its centre. Each haem binds one oxygen molecule, so one haemoglobin carries up to four.

Remember it The three named proteins, in order of chains

  • IInsulin2 chains; globular; non-conjugated
  • SeeCollagen3 chains; fibrous; non-conjugated
  • HimHaemoglobin4 chains plus haem; globular; conjugated
Watch out Quaternary means more than one chain, not four (haemoglobin just happens to have four). Conjugated means joined to a non-protein group, not to another protein. And collagen’s triple helix is not three alpha helices: each chain is a narrower helix of its own.
How we know Technology lets us see what our senses cannot. A haemoglobin molecule is about 5 to 6 nm across, and a light microscope cannot resolve anything smaller than about 200 nm. Cryogenic electron microscopy (cryo-EM) freezes proteins so fast that the water around them turns to glass-like ice, not crystals, then images single molecules with electrons. A computer combines thousands of images of molecules lying at different angles into a 3D structure, so it shows single proteins and the molecules they bind without growing crystals, as X-ray crystallography needs (Nobel Prize in Chemistry, 2017).

A haemoglobin molecule is about 5 to 6 nm across. Could you see one with the best light microscope?

S-SS-SS-SA chain: 21 amino acidsB chain: 30 amino acidstwo chainsone folded proteinChains: 2 · Non-polypeptide part: nonethree chains wound into a ropeevery third amino acid is the smallest onedashed: hydrogen bonds between the chainsChains: 3 · Non-polypeptide part: noneO2haemiron ionfour chains:two of one kind,two of anotherChains: 4 · Non-polypeptide part: haem (one in each chain)

Insulin has two polypeptides, joined by two disulfide bonds, with a third within the shorter chain. It is non-conjugated: polypeptide only.

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

Balls and ropes: globular and fibrous proteins

Globular proteins are folded into compact, rounded shapes. Their hydrophilic surfaces make most of them soluble, and their precise shapes let them bind specific molecules: enzymes, hormones, transport proteins and antibodies.

Insulin shows how form suits function. It is small and compact. It is soluble, so it is carried dissolved in the blood plasma from the pancreas to every tissue. Its precise shape binds the insulin receptor on target cells (liver, muscle and fat cells), and its disulfide bonds keep that shape stable.

Fibrous proteins are long and narrow, often with a repeating sequence, usually insoluble and strong, and have structural jobs. Collagen is three chains wound into a rope. The ropes lie side by side, staggered, and are cross-linked into fibrils, which are bundled into fibres. It is insoluble and has great tensile strength, which means it resists pulling. It is in skin, tendons, ligaments, bone, cartilage and blood vessel walls, and it is the most abundant protein in the human body.

The rule of thumb is that globular proteins do something and fibrous ones are something. It has exceptions: actin and tubulin are globular units that link into structural filaments.

Watch out The functional and structural rule is only a rule of thumb (actin and tubulin). And a fibrous protein is fibrous in shape as a single molecule: it is not “made of fibres”.

A protein is long and thin, has a repeating sequence and does not dissolve in water. What is its most likely job?

insulincollagenone insulin moleculea small knot, a few nm acrossflow of bloodinsulin, dissolved in the plasmacarried from the pancreas to every tissueinsulin fits its receptoron a liver, muscle or fat cellreceptorabout 300 nm long,1.5 nm wideone collagen moleculea long, thin roperopes lie side by side,staggered and cross-linked: a fibrilfibrils bundled into a fibrepullmuscletendonbonetendon: ropes of collagen,taut and strong under pullNot to scale: the rope is about 100 times as long as the knot is wide.
  1. One insulin molecule is a small rounded knot among water molecules. One collagen molecule is a long, thin rope, about 100 times longer than the knot is wide.
  2. Insulin is soluble: dissolved in the plasma, it is carried round the body in the blood.
  3. Insulin has a precise shape that fits the receptor on its target cells, liver, muscle and fat cells, like a key in a lock.
  4. Collagen ropes lie side by side, staggered and cross-linked, into fibrils, and fibrils are bundled into fibres.
  5. In a tendon, collagen fibres are insoluble and strong: they stay taut when muscle pulls on bone.

02Check

A fresh paper from the exam bank on this guide's topics each time: past-paper style questions, marked as you go, and saved to your Exam practice progress when you are signed in. It opens on biologybybradford.com, so it needs the internet.

Exam practice

Exam questions on B1.2, marked

Start 15 marks of exam questionsYour exam practice

03Downloads

This file is the guide, saved to run without the internet.

Saved from biologybybradford.com/guides/ib-biology-b1-2-proteins, where the guide is kept up to date with the notes, the revision guide and, for the teacher, the lesson plans and slides.

04Teacher resources

The guide as two one-hour lessons, and two more at higher level. Each has a plan to print (the timings, what to project and where to stop, the activities with what they need, what students get wrong) and slides to teach it from, in the same order, with the teacher's moves in the notes.

LessonCoversFocusChaptersLesson planSlides
1Amino acids and peptide bonds B1.2.1, B1.2.2 and B1.2.460 min Drawing a generalised amino acid, joining two by condensation, and why chains of twenty kinds are endless 1, 2 Lesson planPDF 737 KB SlidesPPTX 556 KB
2Diet, variety and denaturation B1.2.3 to B1.2.560 min Essential amino acids in the diet, and how heat and pH denature a protein 3, 4, 5 Lesson planPDF 729 KB SlidesPPTX 4.6 MB
3R groups and the levels of structure HL B1.2.6 to B1.2.960 min Sorting R groups, then the primary, secondary and tertiary structure and the bonds that hold each 6, 7, 8, 9 Lesson planPDF 693 KB SlidesPPTX 1.4 MB
4Folding, quaternary structure, globular and fibrous proteins HL B1.2.10 to B1.2.1260 min Non-polar inside and polar outside, quaternary structure, and globular against fibrous proteins 10, 11, 12 Lesson planPDF 752 KB SlidesPPTX 1.3 MB
PDFEvery lesson planAll four plans in one PDF, with this overview at the front. 1.3 MB KEYNote template, filled inThe class’s note template with every gap filled. 1.6 MB

The note template, the revision guide and the offline copy are in Downloads, for you and the class.

PRACTISE AND REVISE

Make it for your class, or set it

Build for your class

Already on the site for B1.2

Card sets on splycr

Open a set to host it as a class game, or make a copy to edit.

How this was made. The course structure, the activities and the teaching choices come from my own classroom, my presentations and my years of teaching IB and AP Biology. I use Claude, an AI, to help write and build the interactive guides, lesson plans, slides and practice questions, and to draw the diagrams and code the interactives. I direct the work and review it against the IB and AP specifications before it goes live.