Honors Biology Unit 2 Review: Biochemistry - The Chemistry of Life

Water is polar. Oxygen pulls shared electrons harder than hydrogen does, so the oxygen end carries a partial negative charge ($\delta^-$) and each hydrogen carries a partial positive charge ($\delta^+$). Water's bent shape keeps those charges on opposite sides of the molecule.

Polarity lets neighboring water molecules form hydrogen bonds. A hydrogen bond is a weak attraction between a hydrogen on one molecule and the oxygen on another. One hydrogen bond is weak, but water forms huge numbers of them.

Cohesion (water sticking to water) creates surface tension strong enough to hold up a water strider. Adhesion (water sticking to other surfaces) works with cohesion to move water up narrow xylem tubes in plants. Water dissolves ions and polar molecules, so most cell reactions happen in it. Ice floats because hydrogen bonds lock frozen molecules into an open lattice that is less dense than liquid water. As a result, lakes freeze from the top and fish survive underneath.

Worked example. How much energy does it take to warm 200 g of water from 20°C to 25°C? Use $q = mc\Delta T$ with water's specific heat of 4.18 J/g°C. Then $q = (200)(4.18)(5) = 4180$ J. Warming 200 g of iron (0.45 J/g°C) the same amount takes only about 450 J. That gap explains why oceans and your body resist fast temperature swings.

An atom has protons and neutrons in its nucleus and electrons outside it. The number of protons is the atomic number, and it sets the element's identity. Every carbon atom has 6 protons.

Neutron counts can vary, and these variants are called isotopes. Carbon-14 has a mass number of 14, so it has $14 - 6 = 8$ neutrons. Carbon-12 has 6 neutrons. Carbon-14 is radioactive, which is why scientists use it to date old organic material.

Bonding depends on valence electrons, the electrons in the outermost shell. Carbon has 4 valence electrons, so it forms 4 covalent bonds. This lets carbon build the chains and rings found in biological molecules.

In a covalent bond, atoms share electrons. If the atoms pull equally, as in $O_2$, the bond is nonpolar. C-H bonds in fats are also usually treated as nonpolar because the difference in electron attraction is small. If one atom is more electronegative, the sharing is unequal and the bond is polar. The oxygen in water is an example. An ionic bond is an attraction between oppositely charged ions. Sodium can transfer an electron to chlorine, forming $Na^+$ and $Cl^-$, which attract each other in table salt.

Hydrogen bonds work differently. They are attractions between molecules, or between distant parts of one large molecule. They do not hold the hydrogen and oxygen atoms together within a water molecule. Because hydrogen bonds are much weaker than covalent bonds, DNA's two strands can unzip while each strand stays intact.

Cells build polymers by linking monomers. Dehydration synthesis joins two monomers by removing a water molecule. Hydrolysis reverses this by adding water to split the bond, which is what happens during digestion.

There are four macromolecule groups.

• Carbohydrates are made of C, H, and O in about a 1:2:1 ratio. They supply quick energy (glucose) and structure (cellulose in plant cell walls).
• Lipids aren't true polymers. Fats are hydrophobic and store about 9 kcal/g, compared with about 4 kcal/g for carbohydrates and proteins. Phospholipids have hydrophilic heads and hydrophobic tails and form cell membranes.
• Proteins are chains built from 20 kinds of amino acids joined by peptide bonds. Their folded shapes let them work as enzymes, channels, antibodies, and fibers.
• Nucleic acids (DNA and RNA) are chains of nucleotides that store and pass on genetic information.

Saturated fatty acid tails have only single C-C bonds and can pack tightly. Cis double bonds in unsaturated tails create kinks that make tight packing harder. Fats rich in saturated fatty acids, like butter, are often solid at room temperature, while oils rich in cis unsaturated fatty acids, like olive oil, are often liquid.

Worked example. Two glucose molecules ($C_6H_{12}O_6$ each) join to make maltose. What is maltose's formula? Adding the atoms gives $C_{12}H_{24}O_{12}$. Dehydration synthesis removes one $H_2O$, which leaves $C_{12}H_{22}O_{11}$. The same logic scales up. A linear protein of 100 amino acids has 99 peptide bonds. In the dehydration synthesis model, forming those bonds would release 99 water molecules. Protein synthesis in a cell uses activated amino acids and does not directly release one water molecule per peptide bond.

Enzymes are biological catalysts, almost always proteins, that speed up reactions without being used up. They lower activation energy, the energy hill reactants must climb before a reaction can start. They do not change the overall free-energy difference or the equilibrium of the reaction they catalyze.

Each enzyme has an active site whose shape and charges match a specific substrate. In the induced fit model, the active site shifts slightly as the substrate binds. Together they form an enzyme-substrate complex that holds the substrate in position so the reaction happens. The products then leave, and the enzyme binds another substrate. Amylase in your saliva, for example, breaks starch into maltose over and over.

An enzyme's activity depends on its shape and on conditions such as temperature, pH, and substrate concentration. Many human enzymes function well near body temperature, about 37°C. Pepsin in the stomach works best near pH 2, while many other enzymes prefer pH 7 to 8. Too much heat or an extreme pH can disrupt interactions that maintain a protein's fold and denature the enzyme. As substrate concentration increases, the reaction rate approaches a maximum as active sites become saturated.

A competitive inhibitor binds at the active site, and extra substrate can reduce its effect by competing for that site. A noncompetitive inhibitor binds elsewhere and reduces enzyme activity. Adding more substrate does not restore the original maximum rate.