Twenty amino acids, one type of bond between them, and yet proteins carry oxygen, catalyse reactions and hold your skeleton together. It all depends on the sequence and on how the chain folds.
Every amino acid has a central carbon carrying an amine group (NH2), a carboxyl group (COOH), a hydrogen atom and a variable R group. Amino acids join by condensation to form peptide bonds. The primary structure is the sequence of amino acids; secondary structure is the α-helix or β-pleated sheet held by hydrogen bonds in the backbone; tertiary structure is the overall 3D folding held by hydrophobic interactions, hydrogen bonds, ionic bonds and disulfide bonds between R groups; quaternary structure is two or more polypeptides together. Globular proteins such as haemoglobin are soluble with physiological roles; fibrous proteins such as collagen are insoluble with structural roles.
Fig. 1: the general structure of an amino acid, and the peptide bond formed when two amino acids condense
Section 01
From amino acid to polypeptide.
Start on the amino acid in the simulator, then step through primary, secondary, tertiary and quaternary structure, and finally collagen. Read the legend for each level to see which bonds hold it.
Amino acid: central carbon with NH2, COOH, H and an R group. The 20 amino acids in proteins differ only in their R groups, which may be non-polar, polar, charged or, in cysteine, contain sulfur.
Peptide bond: the COOH of one amino acid and the NH2 of the next condense, releasing H2O and forming a C-N bond (Fig. 1). Two amino acids give a dipeptide; many give a polypeptide.
Hydrolysis: adding water breaks the peptide bond, as protease enzymes do in digestion.
Section 02
Four levels of structure.
Each level builds on the one below. Change the primary structure and every level above it can change too.
Level
What it is
Held by
primary
the sequence of amino acids in a polypeptide
peptide bonds
secondary
regular coiling (α-helix) or folding (β-pleated sheet) of the backbone
hydrogen bonds between C=O of one peptide bond and N-H of another
tertiary
further folding of the whole polypeptide into a precise 3D shape
bonds between R groups: hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bonds
quaternary
two or more polypeptides associated as one molecule
the same four types of interaction between the chains
Hydrophobic interactions: non-polar R groups cluster together inside the molecule, away from water.
Ionic bonds: between oppositely charged R groups (NH3+ and COO−); easily broken by changes in pH.
Disulfide bonds: covalent S-S bonds between the R groups of two cysteines; the strongest of the four, not broken by moderate heating.
Examiner trap
The hydrogen bonds of secondary structure are between atoms of the polypeptide backbone (C=O and N-H), not between R groups. The hydrogen bonds that help hold tertiary structure are between R groups.
Stage 1 · Learn
Check what the sim just showed you
Four quick checks. Each correct answer earns XP and records this skill on your profile.
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According to the simulator, how do the twenty amino acids differ from each other?
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Which bonds hold the α-helix and β-pleated sheet together?
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In the tertiary structure view, which of the labelled bonds is covalent?
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What is the primary structure of a protein?
Section 03
Haemoglobin and collagen.
Compare the quaternary view (haemoglobin) with the collagen view in the simulator: one is a compact ball, the other a rope.
Haemoglobin (globular)
Collagen (fibrous)
polypeptides
four: two α-globin and two β-globin chains
three, each a helix, wound into a triple helix
key feature
a haem group in each chain, containing Fe2+
every third amino acid is glycine
solubility
soluble: hydrophilic R groups on the outside, hydrophobic inside
insoluble
role
transports oxygen in red blood cells
tensile strength in skin, tendons, bone and artery walls
Iron: each Fe2+ binds one O2 reversibly, so one haemoglobin molecule carries up to four O2. Without enough iron, less haemoglobin is made and less oxygen is carried.
Collagen fibres: glycine, the smallest amino acid, lets the three chains pack tightly, held by hydrogen bonds. Many molecules lie side by side, joined by covalent cross-links, with their ends staggered so there is no line of weakness. These form fibrils, which bundle into fibres that are very strong and do not stretch.
Stage 2 · Exam
Exam-style questions
Unlocks once the four checks above are done. Worth more XP, written to AS Paper 1 and Paper 2 standard.
Finish the four checks above to unlock the exam questions
Exam style+20 XP
A small change in pH alters the shape of an enzyme. Which bonds are most likely to have been broken?
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Why is haemoglobin soluble in water?
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Why is glycine found at every third position in each collagen polypeptide?
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A polypeptide contains 150 amino acids. How many water molecules are needed to hydrolyse it completely into amino acids?
Skill unlocked
Proteins, mastered.
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