Biomolecules

Main notes

Every cell in your body is built from just four classes of chemical building blocks: carbohydrates, lipids, proteins, and nucleic acids. These biomolecules store and release energy, build cellular structure, and carry the instructions for making everything else. This chapter is the foundation for the rest of the course, because the enzymes introduced here run the metabolic pathways of Topics 06 and 07, and the nucleic acids described here are copied during DNA replication in Topic 12.

Carbohydrates

Carbohydrates are molecules of carbon, hydrogen, and oxygen, usually in a ratio of one carbon to two hydrogens to one oxygen. The name means hydrated carbon, because the hydrogen and oxygen appear in the same two-to-one ratio as in water. Carbohydrates are the primary fuel for most cells and supply about 4 kcal per gram of energy. They also form structural materials, such as the walls around plant cells.

The smallest carbohydrates are monosaccharides, single sugar units such as glucose, fructose, and galactose. Glucose is a six-carbon sugar with the formula C6H12O6 and is the central fuel molecule of the cell. Glucose, fructose, and galactose all share that formula but arrange their atoms differently, so they are isomers.

Two monosaccharides join through a glycosidic bond to form a disaccharide, releasing one molecule of water. Glucose plus fructose forms sucrose, the sugar on your table. Glucose plus glucose forms maltose, a product of starch breakdown. Glucose plus galactose forms lactose, the sugar in milk. Joining monomers while losing water is a condensation reaction, and splitting them by adding water is hydrolysis.

Long chains of sugars are polysaccharides. Starch stores glucose in plants, and glycogen stores glucose in animals, packed into liver and muscle cells for quick release. Cellulose is also a glucose polymer, but its units are linked in a different geometry, making straight, rigid fibers that form plant cell walls. Humans cannot digest cellulose, so it passes through the gut as dietary fiber. Chitin, a nitrogen-containing polysaccharide, strengthens the shells of insects and crustaceans.

Common Mistake: Starch and cellulose are both polymers of glucose, but they are not the same molecule. Their glucose units are joined by different kinds of glycosidic bonds, so starch coils and digests easily while cellulose stays straight and rigid. Humans can digest starch but not cellulose.

ELI-10

Think of sugar molecules as identical toy bricks. Cells snap bricks together into chains to build bigger molecules, and they snap chains apart when they need fuel. A long chain of sugar bricks is a carbohydrate. The body breaks these chains down to release energy for work.

Lipids

Lipids are a large and varied group of molecules that share one trait: they are hydrophobic, meaning they do not mix with water. Because their molecules are rich in carbon-hydrogen bonds, lipids pack more energy per gram than any other biomolecule, about 9 kcal per gram. Lipids also form the barrier of every cell membrane and act as signaling molecules.

The best-known lipids are fats and oils, which are triglycerides: three fatty acids attached to a small three-carbon molecule called glycerol. Each fatty acid is a long hydrocarbon chain with a carboxyl group at one end. When every carbon in the chain holds its full share of hydrogen atoms, the fatty acid is saturated. When two carbons share a double bond instead, the chain holds fewer hydrogens and is unsaturated. Saturated chains are straight, so they pack tightly and are solid at room temperature, as in butter. Unsaturated chains bend at each double bond, pack loosely, and stay liquid at room temperature, as in olive oil.

Phospholipids are the key building blocks of membranes. Each one has a water-loving phosphate head and two hydrophobic fatty acid tails, making the molecule amphipathic. In water, phospholipids line up into a bilayer: heads face the water on both sides, and tails tuck together in the middle. That bilayer is the base of every cell membrane.

Steroids are lipids with a skeleton of four fused rings. Cholesterol is a steroid that stiffens animal membranes and serves as the raw material for steroid hormones such as testosterone and estrogen. Waxes are long-chain lipids that coat leaves, fur, and feathers to slow water loss.

Common Mistake: Cholesterol is not a fat. It is a steroid built from ring-shaped carbons, not from fatty acids, and it is not used for energy storage. Most of the cholesterol in your body is made by your liver, not taken in from food.

ELI-10

Pour oil and water into a jar and they separate on their own. Fat molecules behave the same way inside the body because they avoid water. Cells use this trick to build their outer walls and to store fuel in neat, packed drops.

Protein Structure Levels 1-4

Proteins are polymers of amino acids and do most of the work in a cell: they speed up reactions, carry oxygen, fight infection, and build structure. Exactly 20 standard amino acids exist, and each one has an amino group, a carboxyl group, a central carbon, and a unique R group (side chain) that gives it its personality. Amino acids link end to end through peptide bonds, formed by condensation reactions between the carboxyl group of one amino acid and the amino group of the next. A chain of amino acids is a polypeptide, and a folded, working polypeptide is a protein.

A protein's final shape is described at four levels. Primary structure is the linear sequence of amino acids, written like beads on a string. Secondary structure is local folding into repeating patterns, the alpha helix and the beta pleated sheet, held together by hydrogen bonds between backbone atoms. Tertiary structure is the full three-dimensional fold of one polypeptide chain, shaped by interactions among R groups: hydrogen bonds, ionic bonds, hydrophobic contacts, and covalent disulfide bridges. Quaternary structure is the assembly of two or more folded chains into one working machine; hemoglobin, the oxygen carrier in red blood cells, is a quaternary protein built from four subunits.

Shape decides function, and shape is decided by the primary sequence. A single wrong amino acid can change the fold and cause disease; sickle cell anemia, for example, comes from one amino acid change in hemoglobin. When a protein is heated or exposed to extreme pH, it may denature: the weak bonds of the folded shape break, the chain unfolds, and the protein stops working, much like an egg white turning solid when cooked.

Common Mistake: Denaturation does not break peptide bonds. It only unfolds the protein by breaking weaker hydrogen bonds and other interactions that held the shape together. The primary structure survives, so a denatured protein keeps its amino acid sequence even though it no longer functions.

ELI-10

Imagine a long beaded necklace that can fold up. First, the beads are strung in a line, and that order is the primary structure. The string then coils and folds into a squished ball with a very specific shape. That exact shape lets the protein grab the right partners and do its special job.

Nucleic Acids

Nucleic acids are polymers of nucleotides that store and transmit genetic information. The two kinds are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Each nucleotide has three parts: a phosphate group, a five-carbon sugar, and a nitrogenous base. DNA uses the sugar deoxyribose and the bases adenine (A), thymine (T), guanine (G), and cytosine (C). RNA uses the sugar ribose and swaps thymine for uracil (U).

Nucleotides link through phosphodiester bonds between the phosphate of one nucleotide and the sugar of the next, forming a sugar-phosphate backbone with bases sticking out to the side. In DNA, two strands wind around each other into the double helix, held together by hydrogen bonds between paired bases. Pairing is strict: A pairs with T, and G pairs with C. Because the two strands pair this way, the sequence of one strand determines the sequence of the other, which is the basis for copying DNA, the subject of Topic 12.

RNA is usually a single strand and works with the cell's protein factories, the ribosomes, to turn genes into proteins. The sequence of bases in a gene encodes the sequence of amino acids in a protein, so the order of letters spells the order of beads.

Common Mistake: Base pairing is not random. Adenine pairs only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Writing A-C pairs is wrong, because those bases cannot form matching hydrogen bonds.

ELI-10

Think of nucleotides as alphabet letters and DNA as a giant instruction book. The letters pair up in a fixed way, like puzzle pieces that only fit their matching partner. A cell reads the book to know what to build, and RNA carries the message to the building site.

Enzyme Structure and Kinetics

Enzymes are biological catalysts, mostly proteins, that speed up chemical reactions without being consumed. A few enzymes are made of RNA and are called ribozymes. Every enzyme has an active site, a pocket whose shape and chemistry fit its substrate, the molecule acted on. The classic lock and key model compared the fit to a key sliding into a lock, but we now know the enzyme flexes as the substrate binds, a refinement called induced fit. The bound enzyme holds the substrate in the right orientation, strains its bonds, and lowers the activation energy of the reaction, so the reaction proceeds far faster than it would alone. Enzyme speedups are dramatic: some enzymes process millions of substrate molecules per second.

Enzyme kinetics describes how fast enzymes work. At low substrate concentration, the rate climbs steeply as added substrate fills empty active sites. As concentration keeps rising, the rate gains less and less, flattening out at a ceiling called Vmax, the point where every active site is busy and the enzyme is saturated. The concentration of substrate that gives half of Vmax is Km; a low Km means the enzyme binds its substrate tightly and works well even in dilute solutions.

Regulation keeps enzymes in tune. Competitive inhibitors resemble the substrate and occupy the active site, and their effect shrinks when substrate concentration rises. Noncompetitive inhibitors bind away from the active site, distort the enzyme's shape, and cannot be outrun by extra substrate. Temperature and pH also matter: each enzyme has an optimum, and activity falls off sharply on either side.

The catalytic cycle of a single enzyme molecule looks like this:

1. Substrate binds to the active site.
2. Induced fit strains the substrate and lowers activation energy.
3. Bonds break and form, converting substrate into product.
4. Product releases, and the enzyme returns to its starting shape.

Common Mistake: Enzymes are not used up by the reactions they speed. One enzyme molecule can process thousands of substrate molecules a second and remain ready for more. The substrate is consumed, never the enzyme.

ELI-10

An enzyme is like a worker on an assembly line with one favorite spot on the bench. Only the piece that fits that spot gets worked on, and the worker speeds up the job. When the job is done, the worker is unchanged and ready for the next piece. Other molecules can block the spot so the worker slows down.

ELI-10

Picture a single cashier at a store. At first, the more customers arrive, the more the cashier serves. Once the line is longer than the cashier can handle, service tops out at a maximum speed. Extra customers past that point do not speed things up at all.

High-Yield:

• Carbohydrates and proteins supply about 4 kcal per gram; lipids supply about 9 kcal per gram.
• Protein function depends on folding: the primary sequence dictates shape, and denaturation unfolds proteins without breaking peptide bonds.
• Base pairing is specific: A pairs with T, and G pairs with C, with U replacing T in RNA.
• Enzymes lower activation energy, are never consumed, and obey saturation kinetics with Vmax and Km.

Quick Review

• The four biomolecule classes are carbohydrates, lipids, proteins, and nucleic acids.
• Monosaccharides join by glycosidic bonds to form disaccharides and polysaccharides, built by condensation and split by hydrolysis.
• Lipids are hydrophobic, supply about 9 kcal per gram, and form membranes as phospholipid bilayers.
• Saturated fats are solid at room temperature; unsaturated fats stay liquid because double bonds bend their chains.
• Proteins fold through four levels of structure, and the amino acid sequence dictates the final shape.
• The 20 standard amino acids link by peptide bonds into polypeptides.
• DNA is a double helix with A-T and G-C base pairs; RNA is usually single-stranded and uses uracil.
• Enzymes work at an active site, follow Vmax and Km kinetics, and are not consumed by catalysis.

Key terms

Key terms are emphasized and defined within the main notes.

Important formulas or processes

See the formulas, procedures, and process blocks in the main notes where applicable.

Common mistakes

See the labeled common-mistake callouts in the main notes where present.