Short on time? This page is the recap. For explanations, figures and worked examples, use the full study guide.
Recap
- Proteins are linear chains of amino acids joined by covalent peptide bonds.
- Every amino acid has a central carbon bonded to an H, an amine group (−NH₂), a carboxyl group (−COOH) and a variable R group. You do not need the structures of particular amino acids.
- R groups are nonpolar (hydrophobic), polar (hydrophilic) or ionic (charged). Their interactions decide the structure and function of each region of the protein.
- A peptide bond forms by dehydration synthesis between the carboxyl group of one amino acid and the amine group of the next. Hydrolysis breaks it.
Key relationships
| Level | What it is | What holds it together |
|---|---|---|
| Primary | sequence of amino acids | peptide bonds (covalent) |
| Secondary | α-helices and β-pleated sheets | hydrogen bonds between backbone atoms (C=O and N–H) |
| Tertiary | 3D shape of one chain | R-group interactions: hydrogen bonds, hydrophobic interactions, ionic interactions, disulfide bridges (covalent S–S) |
| Quaternary | two or more chains together | the same interactions, between chains |
| Rule | Use |
|---|---|
| peptide bonds = water released = n − 1 per chain | for several chains: total amino acids − number of chains |
| mass of protein = (amino acids × mean mass) − (bonds × 18 Da) | estimating protein mass |
Assumptions behind the numbers
- Mean amino acid masses are averages; real proteins differ.
- The mass lost when a disulfide bridge forms (about 2 Da) is ignored.
- A small experiment (few trials) supports a prediction about structure; it does not prove it.
Mistakes to avoid
- Saying amino acids join through their R groups.
- Calling a peptide bond a hydrogen bond.
- Saying secondary structure comes from R groups.
- Giving every protein a quaternary structure.
- Counting n peptide bonds instead of n − 1, or subtracting 1 only once for several chains.
- Saying denaturation breaks peptide bonds.
- Predicting an effect without the full chain: change in R group → interaction gained or lost → shape → function.
Quick self-check
- How many water molecules are released when a chain of 50 amino acids forms? (49)
- A protein has three chains of 40 amino acids each. How many peptide bonds? (3 × 39 = 117)
- A buried nonpolar R group is replaced by an ionic one. Predict the effect. (The charged group is trapped away from water and the hydrophobic core is disrupted, so the tertiary structure is likely to change and the protein may lose function.)
Next: practice questions.