IB Biology SLTopic 2 — Proteins & Their StructurePaper 1 & 2Core idea~10 min read
How Proteins Form
Every amino acid has exactly the same middle. Same central carbon, same amino group, same carboxyl group, same lone hydrogen. Only one corner is different — the R group. Twenty versions of that one corner are enough to build enzymes, antibodies, hair, muscle and haemoglobin. This page is about how those units lock together.
📘 What you need to know
Proteins are polymers made from monomers called amino acids. They are also macromolecules.
Every amino acid has a central (alpha) carbon bonded to four things: an amino group (—NH2), a carboxyl group (—COOH), a hydrogen atom and an R group.
The R group is the only part that differs. There are 20 amino acids common to all living organisms.
Two amino acids join by condensation: an —OH leaves the carboxyl group and an —H leaves the amino group, and they go as water.
The bond formed is a peptide bond, joining the carbon of one amino acid to the nitrogen of the next.
Two amino acids give a dipeptide; three or more give a polypeptide. Hydrolysis reverses it.
The sequence, type and number of amino acids decides the protein’s shape, and the shape decides the job.
Why proteins matter so much
Genes code for proteins, and proteins do the work. Almost every reaction that keeps you alive depends on one. Here is the range:
Enzymes — speed up reactions.
Membrane proteins — carriers and channels that decide what crosses.
Hormones — chemical messengers such as insulin.
Immunoproteins — antibodies (immunoglobulins).
Transport proteins — haemoglobin carrying oxygen.
Structural proteins — keratin in hair, collagen in skin and tendons.
Contractile proteins — myosin in muscle.
The shape of one amino acid
Learn this once and it never changes. A central carbon with four things attached, and only one of them varies.
If a molecule in an exam has both an amino group and a carboxyl group on the same carbon, it is an amino acid. That is the identification test.
Notice that the amino acid carries an acidic group and a basic group at the same time. That is why R groups matter later: some are acidic, some basic, some polar, some not — and those differences are what fold the finished chain into a shape.
Making the peptide bond
Line two amino acids up so the carboxyl group of the first faces the amino group of the second. Then three atoms leave: an —OH from the carboxyl group and an —H from the amino group. Together they are H2O.
What is left behind is a carbon (still carrying its double-bonded oxygen) bonded straight to a nitrogen. That C—N link is the peptide bond, and it is covalent, so it is strong.
The reaction to learn
amino acid + amino acid → dipeptide + H2O
This is the same condensation reaction you met with sugars and fats. Different groups react, different bond name, identical idea.
🧩 How to draw a peptide bond in three steps
Draw the two amino acids side by side. Line them up the same way round, so amino acid 1’s carboxyl group faces amino acid 2’s amino group.
Circle the atoms that will leave. The —OH from the carboxyl group and one —H from the amino group. Two hydrogens and one oxygen, which is exactly H2O.
Join the C to the N and write the water molecule as a separate product. Keep the double-bonded oxygen on that carbon — it does not go anywhere.
Dipeptides, polypeptides and going backwards
Two amino acids condensed together give a dipeptide.
Three or more give a polypeptide. Chains can run to thousands of amino acids.
A protein may be a single polypeptide chain, or several chains interacting with each other.
Hydrolysis reverses the whole thing: water is added, peptide bonds break, and you get individual amino acids back. That is protein digestion.
Essential and non-essential amino acids
Of the 20 amino acids, your cells can build 11 from other amino acids — these are the non-essential ones. The remaining 9 cannot be made in the body, so they have to come from food. Those are the essential amino acids.
What the syllabus actually asks. You are not expected to name them. You need to know that 9 of the 20 must come from the diet, that meat contains all nine, and that a plant-based diet needs a range of different foods to supply all nine.
“Essential” here does not mean more important. All 20 are needed. It simply means essential in the diet, because your body cannot make them.
Worked examples
WORKED EXAMPLE
Eight amino acids join to form a single polypeptide chain. State the number of peptide bonds formed and the number of water molecules released. [2]
Step 1: count the gaps, not the units8 − 1 = 7 peptide bondsStep 2: one water per bond
Every peptide bond is made by one condensation reaction.
7 peptide bonds and 7 water moleculesSame rule as every other polymer: n monomers, n − 1 bonds.
WORKED EXAMPLE
Three amino acids with relative molecular masses of 75, 89 and 117 join to form a tripeptide. Calculate its relative molecular mass. [2]
Step 1: add the amino acids75 + 89 + 117 = 281Step 2: subtract the water lost
3 amino acids means 2 peptide bonds, so 2 waters leave.
281 − (2 × 18) = 281 − 36 = 245Relative molecular mass = 245Two bonds, not three. Count the gaps between the three units.
WORKED EXAMPLE
Describe how a peptide bond is formed between two amino acids. [3]
Point 1
A hydroxyl group is removed from the carboxyl group of one amino acid.
Point 2
A hydrogen atom is removed from the amino group of the other amino acid; these leave as water.
Point 3
The carbon of the first amino acid bonds covalently to the nitrogen of the second, in a condensation reaction.
C bonds to N, water releasedNaming the two groups involved is worth more than saying “they join together”.
💡 Exam tip
To identify an unfamiliar molecule as an amino acid, look for an amino group and a carboxyl group on the same carbon.
To find a peptide bond on a diagram, look for N bonded to a C that carries a double-bonded O.
The R group is never involved in forming a peptide bond. Examiners like to test this.
Say condensation and mention the water. “They bond together” on its own scores nothing.
Use precise names: amino group, carboxyl group, peptide bond, polypeptide.
Sequence, type and number of amino acids → shape → function. That chain answers a lot of questions.
⚠ Common mix-up
Drawing the R group into the peptide bond. It sits to the side and takes no part.
Saying the whole carboxyl group leaves. Only the —OH leaves. The C=O stays and becomes part of the bond.
Confusing amino and amine spellings with “ammonia”. The group is —NH2, written amino or amine.
Thinking “essential” means most important. It means it must come from your diet.
Counting amino acids instead of bonds. 8 amino acids give 7 bonds and 7 waters.
Mixing up peptide and glycosidic bonds. Peptide joins amino acids; glycosidic joins sugars.
Up next: The Variety of Proteins — how just 20 building blocks give a number of possible proteins so big it may as well be infinite, and what some of the famous ones actually do.
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