Lesson 4 of 7 / Biological molecules
From amino acids to a folded protein
How does a sequence produce a specific three-dimensional shape?
I can explain amino acids, peptide bonds and four levels of protein structure.
I can describe glucose isomers, glycerol, fatty acids and amino acids.Syllabus
Syllabus 9477, Core 1(g). Describe glucose isomers, glycerol, fatty acids and amino acids.
I can explain condensation and hydrolysis of glycosidic, ester and peptide bonds.Syllabus
Syllabus 9477, Core 1(h). Explain condensation and hydrolysis of glycosidic, ester and peptide bonds.
I can explain protein structural levels and stabilising interactions.Syllabus
Syllabus 9477, Core 1(m). Explain protein structural levels and stabilising interactions.
About 7 min
Make a guess. You are not marked.
Every protein has primary, secondary and tertiary structure. Does every protein also have quaternary structure?
Show the answer
Just proteins with two or more chains.
Quaternary structure is the arrangement of several subunits. A single-chain protein has none.
The key idea
Amino-acid sequence constrains folding; different interactions stabilise secondary, tertiary and quaternary structures.
Explore the idea
Move between levels of structure
Peptide bonds join amino acids in a particular order. Different colours represent different R groups.
Inspect an amino acid and its peptide link
Condensation between a carboxyl group and an amino group forms the backbone link -CO-NH- and releases water. The R groups remain side chains. This conventional uncharged structural formula identifies the groups; their ionisation depends on pH.
Hydrogen and ionic interactions and hydrophobic clustering help determine folded shape. A disulfide bridge is a covalent S-S link between suitable cysteine side chains; it is not a peptide bond.
Explanation
An amino acid has an amino group, a carboxyl group, hydrogen and a variable R group attached to a central carbon. R groups differ in properties such as charge and polarity. Condensation between amino and carboxyl groups forms a peptide bond; hydrolysis reverses the join. The amino-acid sequence is the primary structure.
Secondary structure is local folding of the backbone into arrangements such as alpha helices and beta-pleated sheets. Hydrogen bonds form between backbone carbonyl and amino groups. These are not new peptide bonds and do not require a second polypeptide.
Tertiary structure is the overall three-dimensional conformation of one polypeptide. Hydrogen bonds, ionic interactions, covalent disulfide bridges between suitable cysteine residues, and hydrophobic interactions involving non-polar R groups help stabilise it. Hydrophobic residues often cluster away from surrounding water.
Quaternary structure describes the association of two or more polypeptide subunits into a functional protein. Not every protein has this level. The positions of R groups create binding sites and surfaces with particular shapes and chemical properties; sequence changes can therefore alter function without changing the total length of a protein.
Step by step
- 1
Start with the sequence
Identify the covalent peptide backbone.
- 2
Separate local and overall folding
Do not confuse a helix with the whole protein shape.
- 3
Name appropriate interactions
Disulfide bridges are covalent; hydrogen and ionic interactions are different.
Worked example
Work through the evidence
A functional protein contains four folded polypeptide chains. What levels of structure are present?
One way to explain it
Each chain has primary, secondary and tertiary structure. Their association produces quaternary structure.
Why this answer works
- A polypeptide chain is not the same as an amino-acid monomer.
- Quaternary structure concerns subunits, not a fourth type of bond.
Watch out for this
A student says: "Every protein must have all four levels." What is wrong with this?
Show the answer
A protein with one polypeptide may have no quaternary structure.
Check your understanding
Which stabilises a typical alpha helix?
Show the answer
Hydrogen bonds between backbone groups
Regular backbone hydrogen bonding stabilises the helix.
Exam-style questions
Check your understanding
Which bond or interaction is NOT involved in maintaining the tertiary structure of a protein?
Show the answer
Glycosidic bonds
Glycosidic bonds join sugars. Tertiary structure is held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions.
Quick recall
How does a sequence produce a specific three-dimensional shape?