Biology · AP Biology
Chemistry of life
the molecules that make it go
A living thing is built from a few kinds of atoms, arranged into a few kinds of large molecules, all of it bathed in water.
The figure is liquid water. Each molecule is one oxygen (red) and two hydrogens (white). The blue links are hydrogen bonds: weak attractions between one molecule’s hydrogen and the next one’s oxygen. They form and break constantly as the molecules tumble.
Those bonds explain why water sticks to itself and to surfaces, and why it resists changes in temperature.
This chapter starts with water, then the elements of life, then the reactions that join small molecules into large ones. It ends with the four classes of biological macromolecules: carbohydrates, lipids, nucleic acids and proteins. In each, the order and shape of the parts decide what the molecule does.
and hydrogen bonds hold it together
Oxygen pulls on shared electrons harder than hydrogen does. That uneven sharing makes water polar, and polarity makes hydrogen bonds.
Each O–H bond in water is a covalent bond: the atoms share a pair of electrons. Oxygen is more electronegative (3.44 on the Pauling scale, against 2.2 for hydrogen), so the shared electrons spend more time near the oxygen. The bond is a polar covalent bond.
The result is a partial negative charge (δ−) on the oxygen and a partial positive charge (δ+) on each hydrogen. The molecule is bent, at 104.5°, so the charges don’t cancel: water is a polar molecule.
A hydrogen bond is the attraction between a δ+ hydrogen and a δ− atom (oxygen or nitrogen) of another molecule, or of another part of the same large molecule. It is much weaker than a covalent bond. Each water molecule can hydrogen-bond to up to four neighbours; in the liquid the bonds last only fractions of a nanosecond, then re-form.
| H2O | NH3 | H2S | CH4 |
|---|
| molar mass (g/mol) | 18.02 | 17.03 | 34.08 | 16.04 |
|---|
| boiling point (°C) | 100.0 | −33.3 | −60.3 | −161.5 |
|---|
Molecules of similar size, very different boiling points. Water boils 261.5 °C above methane because boiling must break its hydrogen bonds. Hydrogen bonds also hold the two strands of DNA together and help fold proteins.
water pulls on water, and on surfaces
The hydrogen bonds between neighbouring water molecules give water cohesion, adhesion and surface tension.
Cohesion is water sticking to water: hydrogen bonds hold the molecules together. Adhesion is water sticking to another polar or charged surface, such as glass or a plant cell wall. Surface tension is cohesion at a surface: the top layer of molecules is pulled inward and sideways, so the surface acts like a stretched film. It holds up a water strider.
In the figure, three glass tubes stand in water. Adhesion pulls water up the glass, curving the surface (the meniscus); cohesion drags the rest of the column up behind it. The narrower the tube, the more wall there is for each gram of water, and the higher the water climbs:
| tube radius (mm) | 1 | 0.5 | 0.25 |
|---|
| height of rise (mm) | 14.9 | 29.7 | 59.5 |
|---|
Halve the radius and the height doubles. This climb is capillary action.
In a plant. Water evaporates from the leaves, and the column of water in the xylem is pulled up behind it. The column holds together by cohesion and clings to the xylem walls by adhesion, so a tree can lift water tens of metres without a pump.
high specific heat, high heat of vaporization
Heat has to break hydrogen bonds before it can speed water molecules up. So water warms slowly and evaporates only by carrying away a lot of heat.
Specific heat is the energy needed to warm 1 g of a substance by 1 °C. Water’s is 4.18 J/(g·°C), high for a liquid. In the figure, equal 50 W heaters run for 120 s under 100 g of water and 100 g of ethanol, each starting at 20 °C:
| specific heat (J/(g·°C)) | after 120 s (°C) |
|---|
| water | 4.18 | 34.4 |
| ethanol | 2.44 | 44.6 |
Worked example. Each liquid receives 50 W × 120 s = 6000 J. For water, ΔT = q/(mc) = 6000/(100 × 4.18) = 14.4 °C. The same heat warms the ethanol 24.6 °C.
A high specific heat lets an organism, a lake or a coastline hold a steady temperature while the air around it swings: part of maintaining homeostasis.
Heat of vaporization is the energy needed to evaporate 1 g of liquid. Water’s is 2.41 kJ/g at body temperature (ethanol’s, 0.84 kJ/g). The molecules that escape take that heat with them: evaporative cooling. If a 70 kg person evaporates 100 g of sweat, it carries off 100 × 2.41 = 241 kJ, enough to cool the body by about 1.0 °C.
atoms from the environment, built into new molecules
An organism builds its molecules from atoms it takes in. Carbon, hydrogen and oxygen make up most of every biological molecule; nitrogen, phosphorus and sulfur go into some classes and not others.
| carbohydrates | lipids | proteins | nucleic acids |
|---|
| C | ✓ | ✓ | ✓ | ✓ |
| H | ✓ | ✓ | ✓ | ✓ |
| O | ✓ | ✓ | ✓ | ✓ |
| N | | | ✓ | ✓ |
| P | | ✓* | | ✓ |
| S | | | ✓ | |
* Phosphorus is in phospholipids, the lipids of membranes (whose heads often carry nitrogen too); fats and steroids are only C, H and O.
- Nitrogen is in proteins (every amino acid has an amine group) and in nucleic acids (every base).
- Phosphorus is in nucleic acids (the phosphate of every nucleotide) and phospholipids. Proteins and carbohydrates have none.
- Sulfur is in proteins (in the R groups of two amino acids) but not in nucleic acids.
That difference is a tool. A tracer of radioactive sulfur labels a cell’s proteins and not its DNA; radioactive phosphorus labels its DNA and RNA and not its proteins.
The atoms come from the environment: a plant takes carbon from CO2, hydrogen and oxygen from water, and nitrogen, phosphorus and sulfur from ions in the soil. An animal takes them in as food. By mass, a human is 65% O, 18.5% C, 9.5% H, 3.3% N.
dehydration synthesis and hydrolysis
Large biological molecules are polymers: chains of small subunits, monomers, joined by covalent bonds. Each bond is made by removing a water molecule and broken by adding one back.
Dehydration synthesis. A hydroxyl group (–OH) is removed from one monomer and a hydrogen from the other. The two monomers bond covalently, and the OH and H leave together as one H2O. Joining many monomers this way is polymerization.
Hydrolysis (“water splitting”) is the reverse. Water is added across the bond between two monomers: the H goes to one monomer, the OH to the other, and the covalent bond is broken. Digestion is hydrolysis.
The figure runs the same film forward (water out) and backward (water in). A chain of n monomers has n − 1 bonds, so it released n − 1 water molecules as it formed, and takes up n − 1 to come apart.
Worked example. Glucose has a molar mass of 180.16 g/mol; water, 18.02. Two glucose joined: 2 × 180.16 − 18.02 = 342.30 g/mol. The chain of 6 in the figure: 6 × 180.16 − 5 × 18.02 = 990.86 g/mol.
Cells use enzymes to speed both reactions. Building polymers takes energy; hydrolysis releases it.
sugars, and chains of sugars
Monosaccharides, simple sugars such as glucose and fructose, are the monomers of carbohydrates. Covalent bonds join them into polysaccharides, complex carbohydrates that may be linear or branched.
Two monosaccharides make a disaccharide (sucrose, lactose, maltose); hundreds to thousands make a polysaccharide. Carbohydrates are made only of C, H and O.
Shape follows function:
| polysaccharide | shape | job |
|---|
| cellulose | linear | plant cell walls: chains lie side by side, hydrogen-bonded into strong fibres |
| starch | linear and branched | energy store in plants |
| glycogen | highly branched | energy store in animals (liver, muscle) |
| chitin | linear | fungal cell walls, insect exoskeletons |
In the figure both chains add one sugar per growing end per step. The linear chain has one end. The branched chain has an end on every branch, so in the same time it gains far more sugars, and an enzyme can take them off as fast. That is why glycogen, heavily branched, is the store an animal draws on in a hurry.
Even a small change in how the monomers are linked changes the molecule: humans digest starch, but no human enzyme hydrolyses cellulose.
how a kink in a tail melts a fat
Lipids are mostly nonpolar, hydrophobic molecules: they don’t mix with water. What a lipid does depends on how its parts are put together.
Many lipids are built from fatty acids: long hydrocarbon chains with a carboxyl group at one end. A fat (a triglyceride) is three fatty acids joined to glycerol by dehydration synthesis.
A saturated fatty acid has only single bonds between its carbons: it holds as many hydrogens as it can, and its chain is straight. An unsaturated fatty acid has at least one carbon–carbon double bond, which puts a kink in the chain. The more double bonds, the more unsaturated it is.
Straight chains pack tightly and attract each other along their whole length, so saturated fats are solid at room temperature (butter, lard). Kinked chains can’t pack, so unsaturated fats are liquid (olive oil). Four 18-carbon fatty acids:
| fatty acid | C=C bonds | melting point (°C) |
|---|
| stearic acid | 0 | 69.3 |
| oleic acid | 1 | 13.4 |
| linoleic acid | 2 | −5.0 |
| α-linolenic acid | 3 | −11.0 |
The more unsaturated a lipid is, the more liquid it is at a given temperature. Membranes rich in unsaturated tails stay fluid in the cold.
store energy, signal, and build membranes
Fats, steroids and phospholipids are all lipids, and each does a different job.
Fats store energy and support cell function; under the skin of mammals they also insulate. A gram of fat yields about 37 kJ, more than twice the 17 kJ of a gram of carbohydrate. To store 1000 kJ takes 27 g of fat but 59 g of carbohydrate.
Steroids are lipids built of four fused carbon rings. Many are hormones (testosterone, estrogen, cortisol) that regulate growth and development, energy metabolism and homeostasis.
Cholesterol is a steroid that sits among the tails of animal cell membranes (blue in the figure) and gives them structural stability.
A phospholipid has two fatty-acid tails and a head that carries a phosphate group. The head is polar, hydrophilic; the tails are nonpolar, hydrophobic. A molecule with both kinds of end is amphipathic.
In water, phospholipids gather into a lipid bilayer: two sheets, heads facing the water on either side, tails hidden in between. Every cell’s plasma membrane, and the membranes of its organelles, is a bilayer like this. Small nonpolar molecules can slip through its interior; ions and large polar molecules can’t.
a strand of nucleotides, with two different ends
DNA and RNA store biological information as a sequence of monomers called nucleotides.
Every nucleotide has three parts:
- a five-carbon sugar: deoxyribose in DNA, ribose in RNA;
- a phosphate group;
- a nitrogenous base: adenine (A), guanine (G), cytosine (C), and thymine (T) in DNA or uracil (U) in RNA.
Covalent bonds link the phosphate of one nucleotide to the sugar of the next, making a sugar–phosphate backbone with the bases sticking out. The order of the bases along it is the information.
The strand has direction. Its sugars’ carbons are numbered, and the two ends differ: the 5′ end (“five prime”) has a free phosphate on the sugar’s 5′ carbon; the 3′ end has a free hydroxyl on the sugar’s 3′ carbon.
When a nucleic acid is made, each new nucleotide is joined to the 3′ end of the growing strand, as in the figure. So strands always grow 5′ → 3′, and a sequence is written in that direction: 5′-ATGCCGTA-3′.
antiparallel strands, paired bases
DNA is two strands wound into a double helix, running in opposite directions and held together by hydrogen bonds between their bases.
The strands are antiparallel: one runs 5′ → 3′ up the helix, the other 5′ → 3′ down. The sugar–phosphate backbones are on the outside; the bases pair in the middle.
Pairing is specific. Adenine pairs with thymine (A–T), by two hydrogen bonds; guanine pairs with cytosine (G–C), by three. So each strand fixes the sequence of the other: they are complementary. In RNA, adenine pairs with uracil (A–U).
Because A always pairs with T and G with C, double-stranded DNA has as much A as T and as much G as C. Chargaff measured human DNA:
| base | A | T | G | C |
|---|
| mole % | 30.9 | 29.4 | 19.9 | 19.8 |
|---|
Worked example. If a DNA sample is 30% A, it is also 30% T; the other 40% is G and C in equal shares, 20% each.
The 12 pairs in the figure, ATGCGCATTAGC, are 50.0% G–C, held by 30 hydrogen bonds. More G–C pairs means more hydrogen bonds, and a higher temperature needed to separate the strands.
| DNA | RNA |
|---|
| sugar | deoxyribose | ribose |
| bases | A, T, G, C | A, U, G, C |
| strands | usually two | usually one |
peptide bonds and R groups
A protein is one or more linear chains of amino acids, joined by covalent peptide bonds. A chain is a polypeptide.
Every amino acid has a central carbon bonded to four things: a hydrogen, an amine group (–NH2), a carboxyl group (–COOH), and a variable R group (side chain). The twenty amino acids differ only in their R groups.
A peptide bond forms by dehydration synthesis between the carboxyl of one amino acid and the amine of the next, releasing one H2O. The chain has an N-terminus (a free amine) and a C-terminus (a free carboxyl), and grows at the C-terminus, as in the figure.
R groups fall into three kinds by chemical property:
| R group | behaviour in water |
|---|
| nonpolar (grey) | hydrophobic: clusters away from water |
| polar (blue) | hydrophilic: hydrogen-bonds with water |
| charged, ionic (red) | hydrophilic: attracts opposite charges |
How the R groups interact decides the shape, and so the function, of each region of the protein.
Worked example. A polypeptide of 300 amino acids has 299 peptide bonds; with residues of about 110 daltons on average, it has a mass of about 300 × 110 = 33 kDa.
primary, secondary, tertiary, quaternary
The sequence of amino acids decides how a chain folds, and the folded shape decides what the protein does.
Primary structure is the sequence of amino acids, held by peptide bonds. It determines all the levels above it.
Secondary structure is local folding, held by hydrogen bonds between atoms of the backbone (not the R groups): coils called α-helices and folded β-pleated sheets.
Tertiary structure is the whole chain’s three-dimensional shape, held by interactions among R groups: hydrogen bonds, hydrophobic interactions (nonpolar R groups clustering inside, away from water), ionic bonds between charged R groups, and covalent disulfide bridges between two cysteines (red in the figure).
Quaternary structure is the arrangement of two or more polypeptides in one protein. Hemoglobin has four: two α chains of 141 amino acids and two β chains of 146.
All four levels together give the protein its function. Heat, extreme pH or some chemicals break the weak bonds of the higher levels, and the protein unfolds and stops working: it is denatured. The peptide bonds of the primary structure survive.
Change one amino acid and the folding can change. In sickle-cell hemoglobin, a single charged R group is replaced by a nonpolar one, and the protein sticks to its neighbours.
Cell structure and function →