IB Biology HLProteins & Their StructurePaper 1 & 2~12 min read
The Variety of Proteins
Only 20 amino acids exist in living organisms, yet no two species make quite the same set of proteins. A little bit of maths shows why that is not surprising at all.
📚 What you need to know
There are 20 amino acids that make up the polypeptides of living organisms.
Polypeptides vary in length (from a few amino acids to thousands) and in sequence.
At every position in the chain, any one of the 20 amino acids can be used, so the number of possible polypeptides is almost infinite.
A short protein of 50 amino acids already has 2050, or about 1.13 × 1065, possible sequences.
The DNA base sequence decides the number and order of amino acids; the mRNA codon decides which amino acid is added at each step.
This variety makes proteins versatile: catalysis, transport, defence, movement, structure, signalling and more.
You should be able to give named examples: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk.
Why there are so many different proteins
Polypeptides are put together at a ribosome, one amino acid at a time. Each time the ribosome adds one, there is a free choice of 20, and the mRNA codon makes that choice.
So think about a chain that is only three amino acids long. There are 20 options for the first position, 20 for the second and 20 for the third:
Counting the possibilities
20 × 20 × 20 = 8000 different tripeptides
Three amino acids and there are already 8000 answers. Now scale that up.
There are only about 1080 atoms in the observable universe. A 50-amino-acid chain already has 1065 possible versions.
Four things together create this variety:
20 amino acids to choose from at every position.
Chain length varies — from a handful of amino acids to several thousand.
The sequence varies — the same amino acids in a different order make a completely different protein.
DNA varies — the base sequence of a gene codes for the number and the order of the amino acids, and there is a huge number of possible base sequences.
Do not just write “there are 20 amino acids” and stop. The mark is usually for the reasoning: 20 choices at each position, chains of different lengths, so the number of possible sequences is enormous.
What all those proteins do
Because there are so many possible shapes, proteins can be shaped to fit almost any job. This is what makes them the most versatile molecules in the cell.
Six jobs, six shapes, one type of molecule. Learning one example for each role is usually enough for the exam.
Role
What the protein does
Catalysis
Enzymes speed up cellular reactions
Blood clotting
Blood proteins form a gel-like scab across a wound
Strengthening
Fibres in skin, hair, tendons and blood vessels, e.g. collagen and keratin
Transport
Carrying vital substances, e.g. oxygen carried by haemoglobin
Cytoskeleton
A network of tubules that moves chromosomes during the cell cycle
Cell adhesion
Holding cells of the same tissue together
Hormones
Chemical messengers made in one place that act somewhere else
Packing DNA
Histone proteins compact DNA in chromosomes for storage
Immunity
Antibodies, the most diverse group of proteins of all
Membrane transport
Channel and carrier proteins decide what crosses a membrane
Receptors
Binding sites for hormones, tastes, light and sound
Named examples worth learning
Rubisco
Its full name is ribulose bisphosphate carboxylase, which is where “Rubisco” comes from.
It is the enzyme that fixes carbon dioxide from the atmosphere during photosynthesis.
It is a globular protein made of 16 polypeptide chains.
It is the most abundant enzyme on Earth, because it is in every leaf.
It is a famously slow catalyst, but it is the best thing evolution has produced for the job — and essentially all the organic carbon in you passed through it first.
Insulin
A hormone made and secreted by the beta cells of the pancreas.
It binds reversibly to insulin receptors on liver, fat and muscle cells, causing them to absorb glucose from the blood.
It is a short, globular protein of 2 polypeptide chains.
Immunoglobulins
Also called antibodies, and they are globular.
They have a general Y shape, with a specific binding site at each tip of the Y.
Those binding sites are highly variable, so antibodies can be made against millions of different antigens. That makes them the most diverse group of proteins.
Rhodopsin
A membrane protein found in the rod cells of the retina.
It contains a light-sensitive part called retinal, made from vitamin A.
When a photon hits it, rhodopsin changes shape, and that shape change starts a nerve impulse along the optic nerve to the brain.
Collagen
A fibrous protein made of three polypeptide chains wound together.
It is the most abundant protein in the human body, roughly a quarter of all your protein.
Its fibres form networks in skin, blood vessel walls and connective tissue that resist tearing forces.
It is also found in teeth and bones, where it reduces brittleness.
Spider silk
The silk spiders use for draglines and web spokes is as strong as steel wire but far lighter.
It contains rope-like fibrous parts and also coiled parts that stretch under tension, so the thread can extend instead of snapping.
It does not denature easily at extreme temperatures.
Its strength and low weight make it attractive for engineering and textile design, and because spiders cannot be farmed at scale, the protein has been genetically engineered into goats’ milk.
Other silks the spider makes, such as the one used to wrap prey, are tougher but have lower tensile strength.
Tough or strong? They are not the same thing. Strength is the force a fibre can take before it breaks. Toughness is how much energy it absorbs before it breaks — a tough fibre stretches and soaks up the impact. Spider silk is remarkable because it manages both.
Worked examples
WE 1
Explaining the variety of polypeptides
Explain why an almost infinite number of different polypeptides can be made from only 20 amino acids. (3 marks)
Point 1: choice at every position
Polypeptides are assembled one amino acid at a time, and at each position there is a choice of 20.
Point 2: length varies
Chains can be anything from a few amino acids to several thousand, so the number of positions varies too.
Point 3: do the maths
A chain of only 50 amino acids already has 2050, about 1.13 × 1065, possible sequences.
20 choices per position × variable length = effectively infinite proteinsquoting one number, even roughly, shows the examiner you understand the scale
WE 2
Working out the number of sequences
Calculate how many different polypeptides of four amino acids could be made from the 20 amino acids found in living organisms. (2 marks)
Step 1: set it up
There are four positions, and any of the 20 amino acids can go in any position, so it is 20 × 20 × 20 × 20.
Step 2: calculate
204 = 160 000.
160 000 possible tetrapeptidesthe rule is 20n, where n is the number of amino acids in the chain
WE 3
Linking variety to function
Using named examples, outline how the variety of proteins allows them to perform very different roles. (4 marks)
Point 1: the link
A different amino acid sequence gives a different 3D shape, and the shape decides the function.
Point 2: catalysis
Rubisco has a shape with an active site that fits carbon dioxide, so it can fix carbon in photosynthesis.
Point 3: signalling
Insulin is a small globular hormone shaped to fit insulin receptors, causing cells to take up glucose.
Point 4: structure
Collagen is a long fibrous protein of three wound chains, shaped to resist tearing in skin and tendons.
Different sequence → different shape → different jobpick examples from different categories — three enzymes will not score four marks
💡 Exam tips
Learn the chain of reasoning: DNA base sequence → amino acid sequence → shape → function.
Quote 2050 = 1.13 × 1065 for a 50-amino-acid protein if you are asked to show scale.
Know one named example per role. Rubisco (enzyme), insulin (hormone), immunoglobulins (defence), rhodopsin (receptor pigment), collagen (structure), spider silk (structure).
Say globular for Rubisco, insulin and immunoglobulins; fibrous for collagen and silk.
Remember the chain counts: Rubisco 16, insulin 2, collagen 3.
“Versatile” is a useful exam word — it means the same type of molecule can do many jobs.
⚠ Common mistakes
Saying there are 20 possible proteins. There are 20 amino acids; the number of proteins is astronomically larger.
Ignoring order. The same amino acids in a different sequence give a different protein.
Writing 20 × 50 instead of 2050. Each position multiplies the possibilities; it is a power, not a product.
Calling rhodopsin an enzyme. It is a light-sensitive membrane protein, not a catalyst.
Saying spider silk is the same as collagen. Both are fibrous, but silk is made by spiders and is famous for stretching under tension.
Forgetting that DNA is behind all of it. The variety of proteins ultimately comes from the variety of base sequences.
Up next: Protein Structure: pH & Temperature — all this variety depends on proteins holding their shape, so what happens when the surroundings change?
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