IB Biology HLProteins & Their StructurePaper 1 & 2~11 min read
Amino Acid Diversity
Twenty amino acids share the same backbone, so everything that makes one different from another is hanging off the side. Get the R groups straight and the next three topics become much easier.
📚 What you need to know
Around 500 amino acids have been found in nature, but only 20 are commonly found in proteins.
11 can be made inside human cells; the other 9 are essential and must come from the diet.
Amino acid names are usually shortened to three letters, e.g. Gly for glycine. You do not need to memorise them.
The R group is the only part that differs, and it gives a lot of chemical diversity.
R groups may be acidic, basic, polar or non-polar.
Hydrophilic R groups are polar and may be acidic or basic; hydrophobic R groups are non-polar.
In a neutral environment the carboxyl group donates a hydrogen ion and the amine group accepts one, leaving a negative and a positive charge on the same molecule.
This diversity of R groups is the basis of diversity in protein form and function.
Twenty out of five hundred
Nature has produced something like 500 different amino acids, but living organisms only build their proteins from 20 of them. The same 20 make up most of the proteins found on Earth, which is one of the strongest pieces of evidence that all life shares a common ancestor.
Of those 20:
Eleven can be synthesised inside human cells from other amino acids — the non-essential ones.
Nine cannot, so they have to be in your diet — the essential ones.
Their names are usually written as three-letter abbreviations. The full set is Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr and Val, and the nine essential ones are His, Ile, Leu, Lys, Met, Phe, Thr, Trp and Val.
You do not have to learn these. The syllabus does not ask you to remember the names of the amino acids or to give examples of essential and non-essential ones. It helps to recognise a few, though, so that an unfamiliar name in a question does not throw you.
The R group is the whole story
Every amino acid has the same central carbon carrying an amine group, a carboxyl group and a hydrogen atom. The R group, or variable group, is what makes each one different.
R groups range from a single hydrogen atom (which gives glycine, the smallest amino acid) all the way up to complex aromatic ring structures (which gives phenylalanine). Because they vary so much, there is a lot of chemical diversity between the 20 amino acids.
Non-polar R groups avoid water. Polar, acidic and basic R groups get on with it. That one difference decides how a protein folds.
Watch out for one thing here. An R group that contains an –OH, like the one in serine, is polar but not basic. Basic R groups contain nitrogen that can accept a hydrogen ion, as in lysine. Some resources label serine “basic” — it is not, and an examiner will not thank you for it.
Hydrophilic and hydrophobic
The most useful way to sort the R groups is by how they behave around water, because a cell is mostly water.
Type of R group
Behaviour in water
Where you find it in a folded protein
Polar (hydrophilic), including acidic and basic
Attracted to water, dissolves happily
On the outside, facing the watery surroundings
Non-polar (hydrophobic)
Avoids water, clusters with other non-polar groups
Tucked into the centre, away from water
This is not a small detail. It is the reason a protein folds the way it does. As the chain twists about in the cytoplasm, the water-hating R groups get pushed inwards and the water-loving ones end up on the surface, and the molecule settles into the arrangement that suits its R groups best.
Proteins with a lot of polar amino acids on the surface are soluble. Enzymes are like this, so they can work in watery environments.
Membrane proteins have a band of non-polar amino acids around the middle, which lets them sit comfortably in the hydrophobic core of the bilayer.
Channel proteins can have polar R groups lining the pore, creating a hydrophilic channel that polar molecules and ions can pass through.
Why amino acids carry charges
All amino acids have the same carboxyl and amine group on the same central carbon, and in a neutral environment both of them ionise.
The carboxyl group donates a hydrogen ion, so it is left with a negative charge (–COO−).
The amine group accepts a hydrogen ion, so it gains a positive charge (–NH3+).
Because both charges are present, an amino acid can behave as an acid or as a base depending on its surroundings.
Acidic and basic R groups behave the same way, and that is where the link to protein structure comes in. A negatively charged R group and a positively charged one will attract each other, forming an ionic bond that pins two parts of the chain together.
It also explains why pH matters so much. Change the pH and you change those charges, the attractions disappear, and the protein loses its shape.
🧠
Remembering the four R group types
PAN-B: Polar, Acidic, Non-polar, Basic. Three of them (polar, acidic, basic) are hydrophilic and face the water. Only the non-polar one hides in the middle.
Worked examples
WE 1
Predicting where an R group sits
An amino acid has a non-polar R group. Predict where it is most likely to be found in a globular protein dissolved in the cytoplasm, and explain your answer. (3 marks)
Point 1: the prediction
It will be found in the centre of the protein.
Point 2: the reason
A non-polar R group is hydrophobic, so it is repelled by the water in the cytoplasm.
Point 3: the consequence
As the chain folds, hydrophobic R groups cluster together away from water while the polar hydrophilic ones face outwards, which is also what makes the protein soluble.
Non-polar R groups fold inwards, away from water“hydrophobic” and “away from water” are the two phrases the mark scheme looks for
WE 2
Explaining amino acid diversity
Explain how amino acids can be chemically very different from one another when they all share the same basic structure. (3 marks)
Point 1: what is the same
Every amino acid has a central carbon bonded to an amine group, a carboxyl group and a hydrogen atom.
Point 2: what is different
Only the R group varies, from a single hydrogen atom in glycine to a large ring structure in phenylalanine.
Point 3: why it matters
R groups may be acidic, basic, polar or non-polar, so the amino acids differ in charge and in whether they are attracted to water.
Same backbone, 20 different R groups, 20 different chemistriesgive at least one named example of an R group — it turns a vague answer into a scoring one
WE 3
Charges and ionic bonds
Explain how the ionisation of amino acids leads to ionic bonds forming inside a protein. (3 marks)
Point 1: the ionisation
In a neutral environment the carboxyl group donates a hydrogen ion and becomes negative, while the amine group accepts one and becomes positive.
Point 2: R groups do it too
Acidic R groups end up negatively charged and basic R groups positively charged.
Point 3: the attraction
Opposite charges on R groups in different parts of the folded chain attract each other, and that attraction is an ionic bond holding the tertiary structure in place.
Opposite charges on R groups attract, holding the fold togetherthis is also the reason a pH change denatures a protein — a useful link to make
💡 Exam tips
Learn the numbers: about 500 in nature, 20 in proteins, 11 non-essential, 9 essential.
Say R group or variable group, not “the side bit”.
Match the pairs: polar = hydrophilic = outside, non-polar = hydrophobic = inside.
Remember that acidic and basic R groups are also polar, so they are hydrophilic too.
Use glycine (R = H) and phenylalanine (a ring) to show the range of R group sizes.
If a question gives you an unfamiliar amino acid, look at the R group: –COOH means acidic, –NH2 means basic, a hydrocarbon chain means non-polar.
⚠ Common mistakes
Saying all 500 natural amino acids are found in proteins. Only about 20 are.
Thinking “essential” means “more important”. It means essential in the diet.
Calling an –OH R group basic. It is polar and uncharged, like the one in serine.
Saying hydrophobic R groups are on the outside. They hide in the centre, away from water.
Forgetting that the backbone ionises too. Both the carboxyl and the amine group carry a charge at neutral pH.
Mixing up the R group with the whole amino acid. The R group is only the variable side chain.
Up next: Levels of Protein Structure — now that you know what the R groups can do, you can follow a chain all the way from a sequence to a finished, working molecule.
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