The basics - answers

Exercise 1:

There are many possible answers. A few examples: red blood cell, skin cell, nerve cell, liver cell, bacterial cell, and yeast cell.

Exercise 2:

Again, there are many possible answers. Examples: water, sugar (glucose), oxygen, CO₂, calcium, sodium, starch, fats, iron ions.

Exercise 3:

• Structural: keratin is the main component of hair and nails, microtubules in the cytoskeleton of the cell are made of protein, muscles are made of protein too.
• Signaling: hormones are the signal molecules in the body, a number of them are small proteins. The senses are all based on proteins that detect certain stimuli (e.g. the binding of small molecules in taste and smell) and send a signal to the brain. The sense of sight also works because a certain protein detects a signal, in this case light. You can learn more about that in the Retinitis pigmentosa practicum.
• Defence: our body defends itself against diseases using antibodies, bacteria defend themselves against antibiotics with certain enzymes, and snakes use protein toxins to defend themselves against attackers.
• Enzymes: The best known examples are probably the digestive enzymes (like pepsin, trypsin en amylase). All proteins with some kind of catalytic activity are in fact enzymes, so there are many other possible answers.

Exercise 4:

The groups are marked in the figure below.

Exercise 5:

The peptide bond is marked in the figure below.

Exercise 6:

• Polypeptide backbone: green/yellow strand
• Ionic interaction: NH₃⁺ - O^-
• Disulfide bond: S-S
• Hydrophobic interaction: two times CH₃-CH₃
• Hydrogen bond: H-O

Exercise 7:

You can make 20² = 400 dipeptides and 20¹⁰⁰ proteins of 100 amino acids.
Most proteins have more than one hundred amino acids, so there are many more unique proteins possible.

Exercise 8:

The molecule Leu-Asp has a Leu at the N-terminus and an Asp at the C-terminus. The reverse is true for Asp-Leu. when the backbone  of the dipeptides have the same orientation, the side chains (in the coloured frames) of the two molecules cannot be superimposed. They are therefore different.

Exercise 9:

Exercise 10:

The side chains are marked. Lysine is positively charged, glutamate negatively.

Exercise 11:

1. Iron is the co-enzyme in haemoglobin. It is bound to a so-called haem group.
2. Carbon monoxide is a haemoglobin inhibitor.

Exercise 12:

1. 37°C
2. pH 1 - pH 2

Exercise 13:

No, because they would only work in water with temperatures close to 37°C. The enzymes must be adapted to work at a much wider temperature range. The pH of the water is another problem: pepsin, the protease in your stomach, works best at low pH (between pH 1 and pH 2). That would damage your garments. Another problem is that proteases can also break down (digest) each other. The proteases must therefore be adapted to make them stable enough.

Exercise 14:

Exercise 15:

Because of base paring 33% G also means 33% C. 100% - 2 x 33% = 34% remains, which should be divided equally between T and A. We therefore have 17% T and 17% A.

Exercise 16:

transfer-RNA (tRNA) and ribosomal-RNA (rRNA)

Exercise 17:

First we transcribe the DNA to mRNA. This gives us:

AUGGUAGGCAAGUACUAG

We then translate it to the peptide: Met-Val-Cys-Lys-Tyr-stop.

Note that we disregard the directionality of transcription and translation.