IB Biology HLProteins & Their StructurePaper 1 & 2~12 min read
How Proteins Form
Every protein in your body is a chain of small units joined end to end. Learn how two of those units join together, and you have learnt how every protein in every living thing is built.
📚 What you need to know
Proteins are polymers (and macromolecules) made from monomers called amino acids.
Every amino acid has the same central carbon bonded to an amine group, a carboxyl group, a hydrogen atom and an R group.
The R group is the only part that changes. There are 20 amino acids used in the proteins of all living organisms.
Amino acids join in a condensation reaction that makes a peptide bond and releases one molecule of water.
Two amino acids give a dipeptide; three or more give a polypeptide.
Hydrolysis is the reverse: adding water breaks peptide bonds and frees the amino acids again.
Humans can make 11 amino acids in their own cells (non-essential); the other 9 must come from food (essential).
The sequence, type and number of amino acids fix the shape of a protein, and the shape fixes the job.
Proteins are polymers
A polymer is a long molecule built by joining lots of small identical-ish units. Starch is a polymer of glucose. DNA is a polymer of nucleotides. A protein is a polymer of amino acids.
That one sentence explains a lot. Because proteins are built from a small set of repeating parts, cells only need one joining reaction and one breaking reaction to build or recycle any protein at all.
Proteins matter more than any other group of molecules in the cell, because almost everything a cell does is done by one:
Enzymes that speed up reactions
Carrier and channel proteins in cell membranes
Hormones such as insulin
Immunoproteins such as antibodies
Transport proteins such as haemoglobin
Structural proteins such as keratin and collagen
Contractile proteins such as myosin in muscle
Genes code for proteins. So every reaction that keeps you alive depends, one step back, on a protein working properly.
Inside one amino acid
All 20 amino acids share the same design. A central carbon atom (often called the alpha carbon) has four things bonded to it:
an amine group, –NH2
a carboxyl group, –COOH
a hydrogen atom, –H
an R group, the variable side chain
Cover the R group and every amino acid looks the same. Uncover it and you get 20 different personalities.
The R group can be tiny — in glycine it is just another hydrogen atom. It can also be large, such as the ring structure in phenylalanine. Everything interesting about an amino acid comes from its R group: whether it is acidic or basic, whether it likes water or avoids it.
Draw the general structure a few times from memory now. Examiners often show you an unfamiliar molecule and ask “is this an amino acid?” You answer that by looking for the two functional groups, the amine and the carboxyl, on the same carbon.
Joining two amino acids
Amino acids join because one end of one is a carboxyl group and one end of the other is an amine group. Those two groups react.
A hydroxyl group (–OH) is lost from the carboxyl group of the first amino acid.
A hydrogen atom is lost from the amine group of the second amino acid.
Those three atoms leave together as one molecule of water.
The carbon left behind (still holding its double-bonded oxygen) bonds to the nitrogen of the second amino acid.
That new C–N bond is the peptide bond. Because water is released as the bond forms, the reaction is a condensation reaction.
The reaction to know
amino acid + amino acid → dipeptide + water
The red atoms are the ones that leave. Notice the R groups are never involved — they hang off to the side while the backbone does the joining.
🧩 Drawing a peptide bond in an exam
Draw both amino acids facing the same way, amine group on the left, carboxyl group on the right. Line them up so the carboxyl of the first sits next to the amine of the second.
Circle the three atoms that leave: the –OH from the carboxyl group and one –H from the amine group. Label them “water”.
Join the leftover carbon to the nitrogen with a straight line and label it “peptide bond”.
Show the water as a separate product with a plus sign. Marks are often given just for this.
Leave the R groups alone. They stay exactly where they were.
Building a whole polypeptide
Nothing new happens after the first bond. The dipeptide still has a free amine group at one end and a free carboxyl group at the other, so another amino acid can join on, then another.
Dipeptide — two amino acids joined by one peptide bond.
Polypeptide — three or more amino acids joined in a chain.
A protein may be a single polypeptide chain, or several chains working together as one molecule.
Polypeptides are assembled at a ribosome, one amino acid at a time, in the order set by the mRNA. Each new amino acid is added to the growing chain by exactly the same condensation reaction.
A quick counting rule. Join n amino acids and you make n − 1 peptide bonds and n − 1 water molecules. Insulin, for example, has chains of 21 and 30 amino acids — that is 51 residues in total and 50 peptide bonds.
Breaking proteins apart: hydrolysis
The reaction runs both ways. In hydrolysis, a water molecule is added back across the peptide bond and the bond breaks, so the polypeptide is broken down into its amino acids.
This is exactly what happens to the protein in your food. Enzymes in the stomach and small intestine hydrolyse it into single amino acids small enough to be absorbed. Your cells then use those amino acids to build the proteins you need.
“Condensation” and “hydrolysis” turn up in every macromolecule topic — starch, lipids, nucleic acids, proteins. Learn the pair once: condensation joins and gives out water, hydrolysis splits and uses up water. Same idea, different monomer.
Where amino acids come from
There are 20 amino acids in the proteins of living organisms, but you cannot make all of them yourself.
Group
How many
What it means
Non-essential
11
Your cells can build them from other amino acids, so they do not have to be eaten
Essential
9
Your cells cannot make them at all, so they must come from your diet
A healthy, varied, balanced diet contains all nine essential amino acids.
Diets that cut out whole food groups may need more planning, or supplements.
Meat contains all nine, so a vegetarian or vegan diet needs to be varied — beans, grains, seeds, nuts and soy between them supply the full set.
Good news. You are not expected to remember the names of the essential and non-essential amino acids. You only need to know that the split exists, and why it matters for diet.
Worked examples
WE 1
Describe how a dipeptide forms
Describe the reaction that joins two amino acids together. (3 marks)
Point 1: what is lost
A hydroxyl group (–OH) is removed from the carboxyl group of one amino acid and a hydrogen atom is removed from the amine group of the other.
Point 2: what forms
The carbon of the first amino acid bonds to the nitrogen of the second, forming a peptide bond.
Point 3: name the reaction
Because water is released, this is a condensation reaction.
amino acid + amino acid → dipeptide + waterthe word “water” is nearly always worth a mark on its own — never leave it out
WE 2
Counting bonds and water molecules
A polypeptide is made from 148 amino acids. State the number of peptide bonds in the chain and the number of water molecules released as it was made. (2 marks)
Step 1: spot the pattern
Every bond joins two amino acids, so the number of bonds is always one less than the number of amino acids.
Step 2: do the arithmetic
148 − 1 = 147 peptide bonds. Each bond released one water, so 147 water molecules.
147 peptide bonds and 147 water moleculespicture 148 beads on a string — there are 147 gaps between them
WE 3
Identifying a peptide bond
A student is shown the structure of an unfamiliar molecule. Outline how they could tell that it is a polypeptide and identify the peptide bonds. (3 marks)
Point 1: look for the functional groups
Check for a free amine group at one end and a free carboxyl group at the other — every polypeptide has both.
Point 2: look for the repeat
A polypeptide is a repeating backbone with different side chains (R groups) branching off it.
Point 3: find the bond
A peptide bond is where a nitrogen is bonded to a carbon that also has a double bond to an oxygen.
Nitrogen joined to a C=O carbon means a peptide bondR groups are never part of a peptide bond — do not point at a side chain
💡 Exam tips
Use the words monomer and polymer: amino acids are the monomers, the polypeptide is the polymer.
Say condensation, not “joining”, and always mention the water released.
Name the exact groups: amine (–NH2) and carboxyl (–COOH). “The ends” will not score.
For an unfamiliar structure, look for a nitrogen bonded to a carbon carrying a double-bonded oxygen.
Remember n − 1 for peptide bonds and water molecules.
You do not need to name individual amino acids, but glycine (R = H) and phenylalanine (a ring) are useful examples of how different R groups can be.
⚠ Common mistakes
Saying the R groups form the peptide bond. The bond always forms between the backbone groups; R groups take no part.
Forgetting the water. A condensation reaction that does not release water is not a condensation reaction.
Mixing up condensation and hydrolysis. Condensation gives water out; hydrolysis takes water in.
Counting bonds wrong. Ten amino acids make nine peptide bonds, not ten.
Calling a dipeptide a protein. A protein is a much longer chain, usually folded into a working shape.
Saying essential amino acids are the most important. “Essential” just means essential in the diet — your cells cannot make them.
Up next: The Variety of Proteins — if all proteins are built the same way from the same 20 parts, why is every one of them different?
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