生命的化学

Ice floats, so lakes freeze from the top and fish survive the winter underneath. A single wrong amino acid among hundreds in haemoglobin causes sickle cell disease. Both start at the scale of atoms and bonds, which is where this unit begins.

Water is polar 极性: its oxygen pulls electrons more strongly than its hydrogens, giving a slightly negative O and slightly positive H. This lets water molecules form hydrogen bonds 氢键 with each other, which explains water's life-supporting properties:

• Cohesion 内聚力 and adhesion 附着力 (surface tension, capillary action, water rising in plants),
• high specific heat 比热容 (resists temperature change, stabilizing organisms),
• high heat of vaporization (evaporative cooling),
• ice floating (less dense solid), and being a great solvent for polar and ionic substances.

Living matter is built mostly from a few elements – carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. Carbon 碳 is central because it forms four stable covalent bonds, building long chains, branches, and rings – the skeletons of organic biological molecules.

Many large biological molecules – macromolecules 大分子 – are polymers 聚合物 built from repeating monomers 单体. Lipids are also studied among the major biological molecule classes, but are not generally repeating-unit polymers. Cells join monomers by dehydration synthesis 脱水缩合 (removing water to form a bond) and break polymers by hydrolysis 水解 (adding water). Four classes: carbohydrates, lipids, nucleic acids, and proteins.

Carbohydrates 碳水化合物 are made of sugar monomers (monosaccharides 单糖 like glucose). They store energy (starch, glycogen) and provide structure (cellulose 纤维素 in plant walls). Many small sugars are polar and dissolve readily in water. Large carbohydrate polymers differ: cellulose, for example, does not dissolve readily in water.

Lipids 脂质 contain large nonpolar, water-repelling (hydrophobic 疏水) regions. Some also have polar regions, so they are not uniformly nonpolar. They include fats (long-term energy storage), phospholipids 磷脂 (which build membranes), and steroids. A phospholipid has a polar "head" and nonpolar "tails," the key to the cell membrane.

Nucleic acids 核酸 (DNA and RNA) store and carry genetic information. Their monomers are nucleotides 核苷酸, each a sugar, a phosphate, and a nitrogen base. The base sequence encodes instructions; cellular DNA is usually double-stranded, while RNA is usually single-stranded and can fold into paired regions.

Proteins 蛋白质 are polymers of amino acids 氨基酸 joined by peptide bonds 肽键. Their amino-acid sequence contributes to their 3-D shape (primary, secondary and tertiary structure; quaternary structure applies when multiple polypeptide chains assemble), and shape determines function – as enzymes, transporters, receptors, and structural parts. Changing the environment (heat, pH) can denature 变性 a protein, unfolding it and stopping its function.

Worked example. Building a polymer from 10 monomers by dehydration synthesis forms 9 bonds and releases 9 water molecules — one per bond, so $N$ monomers release $N-1$ waters. Hydrolysis reverses this exactly: adding those 9 waters breaks the polymer back into 10 monomers. This is why biosynthesis (dehydration) and digestion (hydrolysis) are chemical opposites.

Worked example (Chargaff's rule). In double-stranded DNA, A pairs with T and C pairs with G, so the amount of A equals the amount of T, and C equals G. A sample is $30\%$ adenine. Then thymine is also $30\%$, which leaves $40\%$ for C and G together: $20\%$ each. The rule fails for single-stranded RNA, which has no partner strand.

Worked example (tracing elements). Which molecules would take up a radioactive label?

• Sulfur ($^{35}\text{S}$) is found in some amino acids, so it labels proteins, not DNA.
• Phosphorus ($^{32}\text{P}$) is in every nucleotide's phosphate group, so it labels nucleic acids, and also phospholipids, but not most proteins.
• Nitrogen is in amino acids and in nucleotide bases, so it labels both proteins and nucleic acids, but not carbohydrates or fats.

This logic is how Hershey and Chase showed that DNA, not protein, enters a cell to carry the genes.

Worked example (predicting a change in shape). A protein's interior is packed with nonpolar R groups, away from water. A mutation replaces one interior nonpolar amino acid with a charged one. Predict the effect: the charged group is attracted to water and disrupts the hydrophobic core, so the tertiary structure is likely to change. Because shape determines function, the protein may work less well, or not at all.

Common mistakes.

• Calling the O–H bond inside a water molecule a hydrogen bond. That bond is covalent; hydrogen bonds are the weaker attractions between neighbouring water molecules.
• Saying dehydration synthesis adds water. Dehydration synthesis removes a water molecule for each bond; hydrolysis adds one to break it.
• Calling lipids polymers. Fats and phospholipids are not chains of repeating monomers, though they are major biological molecules.
• Saying DNA's two strands run the same way. They are antiparallel 反向平行: one runs 5′→3′, the other 3′→5′.
• Saying a protein's shape comes from its peptide bonds alone. The R groups and their interactions (hydrogen bonds, ionic bonds, hydrophobic clustering, disulfide bridges) fold the chain into its tertiary shape.
• Labelling DNA with $^{35}\text{S}$. DNA contains no sulfur; sulfur labels proteins and phosphorus labels nucleic acids.

Answer each before reading the answers below.

1. Explain, using hydrogen bonds, why sweating cools the body.
2. A DNA sample contains $18\%$ guanine. Find the percentages of the other three bases.
3. How many water molecules are released when 25 amino acids join into one polypeptide?
4. A cell is grown with radioactive $^{32}\text{P}$. Which two kinds of molecule become radioactive?
5. A student says: "Boiling an egg breaks the peptide bonds in its proteins." Correct the student.

1. Evaporating water must break many hydrogen bonds, which takes a large amount of energy (a high heat of vaporization). That energy is taken from the skin as the sweat evaporates, cooling it.
2. C $=18\%$, so G and C together are $36\%$, leaving $64\%$ for A and T: A $=32\%$ and T $=32\%$.
3. $25-1=24$ water molecules, one per peptide bond.
4. Nucleic acids (DNA and RNA) and phospholipids, the two kinds containing phosphate groups.
5. Heat denatures the protein: it breaks the weak bonds (such as hydrogen bonds) that hold the folded shape. The peptide bonds, and so the primary structure, stay intact.

• Trace every property of water back to its polarity and hydrogen bonding (cohesion, high specific heat, solvent power).
• Know the four macromolecule classes and their monomers; polymers are built by dehydration synthesis and broken by hydrolysis.
• For proteins, structure (shape) determines function — heat or a pH change denatures them and stops them working.
• In DNA the bases pair A–T and C–G on antiparallel strands; RNA is single-stranded and uses U.
• Link each molecule to its role (carbohydrates: energy/structure; lipids: membranes/storage; nucleic acids: information).