The basics - continued

More about proteins

There are 20 basic amino acids that only differ in the composition and structure of the side chain (generally called the R-group). Each amino acid has its own specific properties like size, hydrophobicity, charge, and the possibility to form hydrogen or covalent bonds.

The structures, three-letter, and one-letter codes for the 20 amino acids will be the subject of many of our exercises. We recommend that you familiarise yourself with them.

The properties of the amino acids are very important for the folding of the protein chain. For instance, two oppositely charged side chains can form so-called salt bridges through ionic interactions. These interactions can also involve other molecules. Cysteine amino acids contain a very interesting sulfur atom: two cysteines can become linked by sulfur bridges which are very important for the structure of peptide chains.

Exercise 6:

Mark the following items in the figure above: polypeptide backbone, ionic interaction (salt bridge), disulfide bond, Hydrophobic interaction, and hydrogen bond. Answer

You may think that twenty different amino acids are not that much considering the enormous variation in proteins. Let's just see...

Exercise 7:

How many different dipeptides can you make with the twenty amino acids? And how many different proteins consisting of 100 amino acids? Answer

The consensus in the scientific community is that amino acid sequences are always read from the N-terminus to the C-terminus, in other words, from the amino end to the carboxyl end.
The amino acid sequence cannot be inverted: Alanine - Glycine - Valine and Valine - Glycine - Alanine are two completely different tripeptides. Try to draw them if you don't believe it. Another rule is that scientists use the one-letter code for amino acids.

Exercise 8:

Use the amino acid structures to draw the dipeptides Leu - Asp and Asp - Leu. Note the differences. Answer

The shape or 3D structure of a protein is very important for its function. It is dependent on:

1. The primary structure or the sequence: the order in which the amino acids are linked together
2. The secondary structure: this describes the basic structural elements that can be found in polypeptide chains,  α-helices or β-sheets. These structure elements are primarily held together by hydrogen bonds between the N-H and the C=O groups in the backbone.
3. The tertiary structure: the way helices and sheets are oriented with respect to one another. This is called the fold of the protein.
4. The quaternary structure: this describes the way several peptide chains are packed together in a complex.

Exercise 9:

Add the following labels to the figure below: primary structure, secondary structure, tertiary structure, quaternary structure, α-helix and β-sheet, N-terminus, C-terminus. Answer

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