Amino acids and proteins

The building blocks

A protein is a long chain. Its links are amino acids. An amino acid is an organic compound with an amino group and an acidic carboxyl group on the same carbon, the alpha carbon. So these are alpha-amino acids.

Four groups sit around the alpha carbon:

• a hydrogen atom,
• an amino group, $\text{NH}_2$,
• a carboxyl group, $\text{COOH}$,
• a variable group, the R group.

The R group makes each amino acid different. In glycine the R group is a single hydrogen. In alanine it is $\text{CH}_3$. In serine it is $\text{CH}_2\text{OH}$.

There are 20 amino acids in proteins. By the R group they fall into classes.

• Acidic, such as glutamic acid, with a second carboxyl group.
• Basic, such as lysine, with a second amino group.
• Neutral, such as valine.
• Aromatic, such as tyrosine, phenylalanine and tryptophan.

Some are essential. The body cannot make them, so they must come in food. The others are non-essential, because the body makes them.

In water, an amino acid carries both a positive and a negative charge. The amino group takes a proton and becomes $\text{NH}_3^+$. The carboxyl group gives one up and becomes $\text{COO}^-$. Such an ion is a zwitterion. Its charges change with the pH of the solution.

Joining them into a chain

The carboxyl group of one amino acid joins the amino group of the next. A molecule of water leaves, and a peptide bond forms. Many amino acids joined this way make a polypeptide.

A chain of $n$ amino acids has $n - 1$ peptide bonds, and $n - 1$ molecules of water are released. One end of the chain keeps a free amino group, the N-terminal. The other keeps a free carboxyl group, the C-terminal.

A protein is a heteropolymer, because it is made of several kinds of unit. A homopolymer repeats one unit again and again.

You should find that a chain of $5$ amino acids has $4$ peptide bonds. Each added amino acid adds one bond and one released water.

Four levels of structure

A protein works only when it is folded in the right shape. The shape builds up in four levels.

• Primary: the sequence of amino acids in the chain, from the N-terminal to the C-terminal.
• Secondary: the chain coils into a right-handed helix, or folds into a sheet.
• Tertiary: the coil folds upon itself, like a hollow woolen ball. This shape is needed for most biological activity.
• Quaternary: several folded chains, the subunits, pack together. Adult human haemoglobin has four subunits: two alpha and two beta.

What proteins do

Collagen is the most abundant protein in the animal world. RuBisCO is the most abundant protein in the whole biosphere.

Try it in Python

The program builds a peptide from one-letter codes. It counts the bonds, adds up the mass and sorts the amino acids by class.

Practise with new numbers

Common mistakes

• Counting one bond for each amino acid. A chain has one bond fewer than it has amino acids.
• Thinking the R group is the same in every amino acid. The other three groups are the same; the R group varies.
• Giving a protein only one level of structure. Every protein has a primary structure; the higher levels build on it.
• Joining chains by peptide bonds in the quaternary structure. The subunits pack together; they are not one chain.

Remember these

• Alpha carbon: hydrogen, amino group, carboxyl group and R group.
• Twenty amino acids: acidic, basic, neutral and aromatic by the R group; some are essential.
• Peptide bond: carboxyl to amino, with a water released. A chain of $n$ has $n - 1$ bonds.
• Levels: primary (sequence), secondary (helix), tertiary (fold), quaternary (subunits, as in haemoglobin, two alpha and two beta).

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

1. Which four groups are attached to the alpha carbon?

2. How many peptide bonds join a chain of nine amino acids?

3. What is an amino acid called when it carries both $\text{NH}_3^+$ and $\text{COO}^-$ in water?

4. What is the quaternary structure of adult haemoglobin?

5. Name the most abundant protein in the animal world, and the most abundant in the biosphere.