Exercises: Proteins

What are amino acids and how many different types make up the proteins of living organisms? State which chemical groups all amino acids share and which endows each one with its particular properties.

Name four different functions of proteins in living organisms and give a specific example of a protein for each function.

What is a peptide bond? State between which chemical groups of the amino acids it forms and what molecule is released in the reaction.

Look at the diagram of the levels of protein organization, numbered from 1 to 4. Name each level, briefly describe its main feature, and give an example of a protein that exhibits level 4.

Haemoglobin loses its three-dimensional shape if the temperature or pH strays too far from normal values. What is this process called, which bonds are broken, and what consequence does it have on the protein's function?

What is an enzyme? Explain how it accelerates a chemical reaction with reference to activation energy and the enzyme-substrate complex.

Functional adult hemoglobin ($\text{HbA}$) is a soluble heterotetramer. In sickle cell anemia, a point mutation in the $\beta$-globin gene replaces a glutamic acid with valine at position 6 of the polypeptide chain ($\text{HbS}$), causing deoxyhemoglobin to polymerize into long insoluble fibers that deform erythrocytes.

1. a) Based on the chemical properties of the side chains of both amino acids, justify why this change in primary structure alters the conformation and solubility of the protein, and indicate what type of weak molecular interactions stabilize these fibers.
2. b) In a genetic screening, two alternative mutations are detected at that same codon 6 of $\beta$-globin:

• Variant A: glutamic acid is replaced by aspartic acid ($\text{Glu6Asp}$).

• Variant B: glutamic acid is replaced by leucine ($\text{Glu6Leu}$).

Predict with reasoning which of these two variants will maintain a biological function virtually identical to healthy $\text{HbA}$ and which will cause pathological aggregation similar to sickle cell anemia.

A patient with severe malnutrition is admitted to the emergency department with muscle weakness, disorientation, and severe lactic acidosis (symptoms compatible with beriberi). Biochemical tests show elevated plasma concentrations of pyruvate and lactate, along with a sharp drop in cellular ATP despite normal glucose levels. Urgent administration of thiamine (vitamin B1) reverses the symptoms.

1. a) Knowing that thiamine is the precursor of the coenzyme thiamine pyrophosphate (essential for the pyruvate dehydrogenase complex), explain what a coenzyme is and biochemically justify why its absence blocks cellular respiration and triggers lactate synthesis.
2. b) If concentrated glucose saline had been infused into the patient to "give him energy" before administering the vitamin, his acidosis would have rapidly worsened. Justify this statement based on carbohydrate metabolic pathways.
3. c) Since coenzymes are not consumed stoichiometrically in the reactions they catalyze (they are regenerated), reason why humans require a continuous dietary intake of water-soluble vitamins rather than a single lifetime dose.

In a biochemistry laboratory, the thermal stability of an intracellular human enzyme is investigated. Aliquots of the enzyme are incubated for 20 minutes at four different temperatures ($15\ \text{°C}$, $37\ \text{°C}$, $45\ \text{°C}$, and $70\ \text{°C}$). Each sample is then divided into two fractions:

• Fraction 1: its catalytic rate is measured immediately at the same temperature at which it was incubated.

• Fraction 2: the sample is returned to $37\ \text{°C}$, kept for 15 minutes, and its catalytic rate is then measured at $37\ \text{°C}$.

The results show that Fraction 1 has optimal activity at $37\ \text{°C}$, very low activity at $15\ \text{°C}$, and zero activity at $70\ \text{°C}$. In Fraction 2, the sample pretreated at $15\ \text{°C}$ recovers $100\ \%$ of its maximum activity, whereas the one pretreated at $70\ \text{°C}$ maintains an activity of $0\ \%$.

1. a) Interpret molecularly the results of Fraction 2 for the $15\ \text{°C}$ and $70\ \text{°C}$ samples, distinguishing between the kinetic energy of the system and protein denaturation.
2. b) Predict how the curve for Fraction 1 would change if an equivalent enzyme purified from the thermophilic bacterium Thermus aquaticus ($T_{\text{optimum}} \approx 75\ \text{°C}$) were used, and justify what adaptations in the bonds of its tertiary structure allow it to be functional at that temperature.