1Amino acids and their R groups

All amino acids share the same core, a central carbon with four things attached:

• a hydrogen atom;
• a carboxyl group, –COOH;
• an amine group, –NH₂;
• an R group (side chain), which is different in each kind of amino acid.

There are 20 kinds of amino acid in proteins, but the CED does not examine their individual structures. What you need is the three categories of R group, because they decide how each part of the chain behaves:

2Peptide bonds and the polypeptide chain

Two amino acids join by dehydration synthesis. The –OH is removed from the carboxyl group of one amino acid and an –H from the amine group of the next; they leave as water, and a covalent peptide bond forms between the carbon of the carboxyl group and the nitrogen of the amine group. Each new amino acid joins the same way, so the chain grows one peptide bond at a time.

A finished chain still has a free amine group at one end and a free carboxyl group at the other, so it has direction, just as a DNA strand does. The R groups stick out from the repeating backbone (nitrogen, central carbon, carboxyl carbon, over and over), and they are what makes one protein different from another.

Counting works as in topic 1.3: a chain of n amino acids has n − 1 peptide bonds and released n − 1 water molecules when it was built.

3Four levels of structure

Figure 1 shows the four levels, from a string of amino acids to a finished protein of several chains. Each coloured bead in the top row is one amino acid; the colours stand for different kinds of R group.

Primary structure is the sequence of amino acids, held by peptide bonds. It is set by the gene that codes for the protein (Unit 6). Everything else follows from it, because the sequence decides which R groups sit where and so how the chain can fold.

Secondary structure is local folding into regular shapes, held by hydrogen bonds between atoms of the backbone (not the R groups). The δ+ hydrogen of one amine group's N–H is attracted to a δ− oxygen of a carboxyl-derived C=O a few amino acids along. The two common shapes are the α-helix, a coil, and the β-pleated sheet, where stretches of chain lie side by side.

Tertiary structure is the overall three-dimensional shape of one polypeptide, made by interactions between R groups:

• hydrogen bonds between polar R groups;
• hydrophobic interactions: nonpolar R groups cluster together in the middle of the protein, away from water;
• ionic interactions (ionic bonds) between R groups of opposite charge;
• disulfide bridges: strong covalent bonds between the sulfur atoms of two sulfur-containing R groups.

Quaternary structure is two or more polypeptides held together as one functional protein by the same kinds of interaction. Haemoglobin, the oxygen carrier in red blood cells, is four polypeptide chains. Not every protein has a quaternary level; a protein of one chain stops at tertiary.

The amino acid sequence decides how a chain folds, the fold decides the shape, and the shape decides the function.

4Shape is function

A protein works by its shape. An enzyme's active site is a pocket of exactly the right shape and chemistry for its substrate (Unit 3). A channel protein's pore is lined with R groups that let some ions through and not others (Unit 2). An antibody's tips fit one particular antigen. Change the shape and you change or destroy the function.

Two ways a shape changes:

• A change in sequence. If a mutation swaps one amino acid for another with a different kind of R group, the folding can change. Sickle cell disease is the textbook case: in one of haemoglobin's chains, a charged R group at one position is replaced by a nonpolar one. That hydrophobic patch on the surface makes haemoglobin molecules stick together into long fibres when oxygen is low, distorting the red blood cells.
• A change in conditions. High temperature or an extreme pH breaks the hydrogen bonds and ionic interactions that hold secondary, tertiary and quaternary structure. The protein unfolds and stops working; this is denaturation, which you meet properly in Unit 3. The peptide bonds, and so the primary structure, are not broken.

5Predicting from data: a worked example

An invented experiment. A research team made three altered versions of an enzyme, each with one amino acid replaced, and measured activity as a percentage of the normal enzyme (mean of five trials).

Claim: a change matters most when it alters the kind of R group in a place that holds the fold together. Evidence: swapping one polar R group for another on the surface left 97% of activity; putting a charged R group into the hydrophobic core cut activity to 4%; losing a disulfide bridge cut it to 31%. Reasoning: a charged R group cannot sit in the nonpolar core, so the chain folds differently and the active site loses its shape; removing the sulfur breaks one covalent link in the tertiary structure, loosening but not destroying the fold; a like-for-like swap on the surface changes no interaction that holds the shape.

Counting for a protein with quaternary structure. Human haemoglobin has two chains of 141 amino acids and two of 146. How many peptide bonds does it contain?

The chains are held to each other by interactions between R groups, not by peptide bonds, so you subtract one for each chain.