IB Biology HLProteins & Their StructurePaper 1 & 2~13 min read
Levels of Protein Structure
A protein is described at four levels, and each one is built on the one below it. Once you can say what holds each level together, most protein questions answer themselves.
📚 What you need to know
Primary structure is the sequence of amino acids, joined by peptide bonds and determined by the DNA of the cell.
Secondary structure is the pleating and coiling of the chain into alpha helices and beta pleated sheets, held by hydrogen bonds between carbonyl (C=O) and amine (N–H) groups.
Tertiary structure is the whole chain folded into a 3D shape, held by interactions between R groups.
Tertiary interactions are hydrogen bonds, hydrophobic interactions, ionic bonds and disulfide bridges (covalent, between two cysteines).
Quaternary structure exists when a protein has two or more polypeptide chains, each called a subunit.
A quaternary protein is conjugated if it contains a non-protein prosthetic group, and non-conjugated if it does not.
Haemoglobin: four subunits, conjugated, each with a haem group containing an iron ion (Fe2+). Insulin: two subunits, non-conjugated. Collagen: three subunits, non-conjugated.
Cryo-electron microscopy now allows single protein molecules to be imaged without crystallising them.
The four levels at a glance
Not every protein reaches level four. A protein with a single polypeptide chain has no quaternary structure at all.
Primary structure
The primary structure is simply the sequence of amino acids in the polypeptide, held together by peptide bonds.
The DNA of the cell determines it, by instructing the ribosome to add amino acids in a specific, ordered sequence.
The precise position of each amino acid decides the eventual three-dimensional shape of the protein.
The same sequence always gives rise to the same 3D shape, so proteins have precise, predictable and repeatable structures.
That last point is worth sitting with. A protein does not need instructions on how to fold. Put the amino acids in the right order and the folding happens by itself, because the R groups interact in only one arrangement that is comfortable.
Say sequence or order of amino acids when you describe primary structure. Writing “a chain of amino acids” will not be enough — it is the exact position of each amino acid that determines every level above.
Secondary structure
Secondary structure forms when parts of the chain pleat or coil into regular repeating patterns. It is held together by weak hydrogen bonds.
Those hydrogen bonds form between the carbonyl (C=O) group of one amino acid and the amine (N–H) group of another on a parallel strand. Notice what that means: secondary structure hydrogen bonds are along the backbone, not between R groups.
Shape
What it looks like
Example
Alpha (α) helix
The chain coils into a spiral, like a spring, with hydrogen bonds running up the inside
Keratin in hair, and the coiled parts of most globular proteins
Beta (β) pleated sheet
The chain folds back on itself in a zigzag, and neighbouring strands hydrogen bond side by side
Silk fibres, and the flat regions of many enzymes
Most proteins contain both, in different regions of the same chain, joined by loops that have no regular pattern at all.
Tertiary structure
Tertiary structure is the complex three-dimensional shape into which the secondary structure folds. It gives proteins the very specific shapes they need for function — the active site of an enzyme or a receptor site on a membrane are both tertiary structure.
Folding happens because of interactions between the R groups of the amino acids, and between R groups and the surrounding environment.
Four interactions, one shape. Break the weak three and the protein denatures; the disulfide bridges are much harder to shift.
Hydrogen bonds between polar R groups. Note this is a different place from the hydrogen bonds of secondary structure.
Hydrophobic interactions between non-polar R groups and the water around them, which pushes those amino acids into the inside of the protein.
Covalent disulfide bridges between the R groups of two cysteine amino acids. These are strong.
Ionic bonds between positively and negatively charged R groups, formed when amine and carboxyl groups within R groups gain or lose hydrogen ions.
Quaternary structure
Some proteins are made of more than one polypeptide chain working together as a single protein. Each chain is called a subunit, and the way they fit together is the quaternary structure.
A protein with only one polypeptide chain has no quaternary structure.
A conjugated protein contains a non-protein part called a prosthetic group.
A non-conjugated protein does not.
Protein
Subunits
Conjugated?
Detail to quote
Haemoglobin
4
Yes
Each subunit carries a haem prosthetic group containing an iron ion, Fe2+
Insulin
2
No
The two chains are joined by disulfide bridges
Collagen
3
No
A fibrous protein whose three chains are wound into a helix
Why the haem group matters. Oxygen does not bind to the protein part of haemoglobin at all — it binds to the iron ion in the haem group. The four polypeptide subunits are there to hold the haem groups in place and to pass the message along when one of them picks up oxygen.
Which bonds belong to which level
Bond
Primary
Secondary
Tertiary
Peptide
✓
✓
✓
Hydrogen
—
✓ between amine and carbonyl groups
✓ between R groups
Disulfide
—
—
✓
Ionic
—
—
✓
Hydrophobic interactions
—
—
✓
Peptide bonds appear at every level because the chain never stops being a chain. Everything else is added on top.
🧠
The hydrogen bond trap
Secondary hydrogen bonds are between the backbone groups (C=O and N–H). Tertiary hydrogen bonds are between the R groups. Same bond, different location — and examiners test it every year.
Seeing proteins: cryo-EM
Technology lets us image structures that no eye could ever see. Cryogenic electron microscopy (cryo-EM) is the technique that changed protein science.
A protein solution is rapidly frozen and then exposed to a beam of electrons to produce an image.
The images are used to recreate the 3D shape of the protein, and to see how it interacts with other molecules in a cellular environment.
It can be aimed at a particular protein or molecule, so observations can be extremely purposeful and exact.
Before cryo-EM, proteins had to be crystallised and studied by X-ray crystallography. That caused problems:
Crystallisation is slow and only works on a single purified protein.
Some proteins simply will not crystallise.
The structure has to be seen outside the cellular environment, which removes context such as interactions with other molecules.
Worked examples
WE 1
Comparing secondary and tertiary hydrogen bonds
Distinguish between the hydrogen bonds found in the secondary structure of a protein and those found in the tertiary structure. (2 marks)
Point 1: secondary
In secondary structure the hydrogen bonds form between the carbonyl (C=O) and amine (N–H) groups of the backbone on parallel strands, producing alpha helices and beta pleated sheets.
Point 2: tertiary
In tertiary structure they form between polar R groups in different parts of the folded chain.
Secondary = backbone groups. Tertiary = R groups.a “distinguish” question needs both sides written out, not just one
WE 2
Haemoglobin and quaternary structure
Explain why haemoglobin is described as having a quaternary structure and as being a conjugated protein. (3 marks)
Point 1: quaternary
It consists of four polypeptide subunits that function together as one protein, and a protein needs more than one chain to have a quaternary structure.
Point 2: conjugated
Each subunit contains a non-protein prosthetic group, called haem.
Point 3: the detail
Each haem group contains an iron ion (Fe2+), which is what oxygen actually binds to.
Four subunits = quaternary; haem prosthetic group = conjugatedcontrast it with insulin and collagen, which have quaternary structure but are non-conjugated
WE 3
The effect of one changed amino acid
A mutation changes one amino acid in the primary structure of an enzyme. Explain how this could stop the enzyme working. (4 marks)
Point 1: a different R group
The new amino acid has a different R group, so it can make different interactions from the one it replaced.
Point 2: the fold changes
Hydrogen bonds, ionic bonds, disulfide bridges or hydrophobic interactions may be lost or added, so the chain folds differently.
Point 3: the shape changes
The tertiary structure changes, and that can change the shape of the active site.
Point 4: the consequence
The substrate no longer fits, so no enzyme-substrate complexes form and the enzyme has no activity.
One R group changed → different bonding → different shape → no functiona change far away from the active site can still matter, because the whole fold shifts
💡 Exam tips
Use the word sequence for primary structure, every time.
Name the bond for each level: peptide, hydrogen, R group interactions, then subunit interactions.
State where hydrogen bonds are: backbone in secondary, R groups in tertiary.
Only disulfide bridges are covalent among the tertiary interactions, and they only form between cysteine R groups.
