Biomolecules and the Chemistry of Life Questions

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Bring on the tough stuff

1. Compare and contrast ionic, covalent, and hydrogen bonds. How do these bonds work? Do they form between atoms, molecules, or ions? What is the role of electrical charge? How strong are the bonds, and how do they relate to the dissolving properties of water?
    
2. What kind of food would you want to eat for breakfast before running a mile in gym class? Why? If you were a rodent preparing for hibernation, or a bird preparing for an autumn migration, what type of biomolecule would you want to use for energy storage? Why?
     
3. During the winter, many species of amphibians and reptiles go into a hibernation-like state called overwintering. They eat little or no food, slow their metabolism and breathing rate dramatically, and most of their bodily functions shut down. Interestingly, many of these species choose to spend the winter underwater. Why might it be advantageous to overwinter at the bottom of a pond rather than on land?
     
4. Why are fats and waxes solid at room temperature, whereas oils are liquids? With your answer to that question in mind, how do you think the phospholipids of coldwater fish compare to warmwater fish? Would you expect to see differences in the amounts of saturated and unsaturated fatty acids?
     
5. In humans, blood pH is maintained fairly precisely around 7.4, and this is largely accomplished with the help of bicarbonate ion (HCO₃^-) and carbonic acid (H₂CO₃), both of which are floating around in the blood. If blood suddenly becomes acidic for some reason, bicarbonate turns into H₂CO₃. If blood suddenly becomes too basic, some H₂CO₃ turns into HCO₃^-. What’s going on here? Using your knowledge of acids, bases, and buffers, explain how pH is maintained at a constant level in this system.
     
6. Compare and contrast proteins and nucleic acids. What do these biomolecules have in common? In what ways are they different? Be sure to consider both their structures and their functions.

Biomolecules and the Chemistry of Life Answers

1. Answer: The three kinds of bonds (ionic, covalent, and hydrogen) can be ranked in terms of strength: covalent bonds are the strongest, followed by ionic bonds, and finally, hydrogen bonds as the weakest. Ionic bonds occur between two differently charged ions, or atoms that have gained or lost electrons. What holds them together is the fact that opposites attract: electrons are stolen rather than shared in the ionic bond. In contrast, in covalent bonding, the electrons are shared between the two atoms. In hydrogen bonds, the weakest kind of bond, the partial charge of the hydrogen atom is what attracts it to the slightly negative charge of another atom. The hydrogen bond is important in biologically significant macromolecules such as DNA, RNA, and proteins. In this case, no electrons are exchanged or shared. The best explanation of hydrogen bonding is in the case of the water molecule. Because hydrogen is such a poor electrophile, when it is covalently bound to oxygen, instead of evenly sharing this single electron, the electron spends more time around the oxygen atom. Therefore, the hydrogen becomes slightly positively charged while the oxygen becomes slightly negatively charged. These opposite charges on separate but adjacent molecules can then work to create hydrogen bonds between the molecules. Because of this special property of water, ionically bound molecules can easily dissolve in aqueous solution, as their negative and positively charged atoms can associate with the slightly negative and slightly positive charges on the water molecule.
    
2. Answer: Before running a mile in gym class, you would want to eat a simple carbohydrate. This would be a good idea because a mile is not a very long distance, and what you would need is quick energy. If you were preparing for hibernation, however, or a long distance migration, you would want to use fat for storage because fat stores, per gram, twice as much energy as carbs or protein, and can therefore last the distance.
    
3. Answer: It might be advantageous to overwinter in water because of water's heat of fusion. This fact means that you would be less likely to freeze to death during your overwintering.
    
4. Answer: Fats and waxes are solid at room temperature because they are made of saturated fatty acids. In contrast, oils are mostly unsaturated fatty acids. Saturated fatty acids are called as such because they do not have many double or triple bonds in their structure; each carbon is bound to four other atoms, and this fact makes it quite easy to stack the fatty acid molecules together closely. Therefore, saturated fats are solid at room temperature. In contrast, unsaturated fatty acids have several kinks in their structure and therefore, are liquid at room temperature. We would expect the phospholipids of cold water fish to be more heavily unsaturated compared to the phospholipids of warm water fish, due to their adaptation to temperature.
    
5. Answer: pH refers to the concentration of hydrogen in a solution. A buffer is a molecule that can help to control the pH of a solution by taking up a hydrogen or releasing one into solution, depending on the surrounding pH. If blood becomes too acidic, that fact means that there is an excess of hydrogen ions in the blood.  The bicarbonate ion can then take up the excess hydrogen ion and become H₂CO₃.  If, in contrast, the blood becomes too basic, that fact means that there is a lack of hydrogen ions, and bicarbonate can then release its extra hydrogen into solution, becoming HCO₃^-.
    
6. Answer: Proteins and nucleic acids are both important biological macromolecules. They both have carbon, nitrogen, and hydrogen, but are made of different molecular components. Proteins are made of amino acids, and nucleic acids are made of nucleotides. They are similar in that, during the synthesis of the macromolecules, these molecular components are covalently bound to each other, making a string of nucleotides or a string of amino acids. Proteins and nucleic acids are also similar in that both have tertiary structure to them. In proteins, the kinds of folds are alpha helices and pleated sheets, and in nucleotides, helices are formed by the DNA molecule, and a similar kind of structure is formed by the single-stranded RNA molecule. They are different in their functions. Proteins are synthesized from DNA, with an RNA intermediate.