Page 2 Chemical and Physical Foundations of Biological Systems Study Guide for the MCAT

Chemistry Concepts

In biological systems, chemistry is important to understand the nomenclature and characteristics of biological molecules. The chemical characteristics of biomolecules affect their interactions with each other.

Acid/Base Equilibria

An acid can react with a base to form the corresponding conjugate acid and the conjugate base. This reaction is reversible and in dynamic equilibrium. Acids and bases can be characterized as strong or weak based on their dissociation constant. For example, hydrogen ions completely dissociate in a strong acid solution. pH is used to describe the acidity (pH <7) or basic (pH > 7) nature of a solution.

Ions in Solutions

An ion is an atom or molecule that has a charge because the number of protons is different from the number of electrons. An anion has a negative charge and a cation has a positive charge. Important biological ions include phosphate and ammonium.


A solute is dissolved in a solvent to make a solution. Solubility is dependent on the physical and chemical properties of the solute and solvent. For, example sugar (solute) can be dissolved in water (a solvent) to make a simple syrup (solution). In contrast, oil is insoluble in water and will not dissolve. Typically, solutions are described in molarity.


Titration is a lab technique used to determine the concentration of an analyte. Titrations include a titrant, an analyte, and an indicator. Classic titration reactions include neutralization and redox reactions.

Covalent Bonding

A covalent bond is a chemical bond that occurs when electrons in the outer electron shell are shared, and usually these bonds allow electrons to stabilize the outer electron shells of the molecules involved. Covalent bonds occur between molecules with similar electronegativity. If electrons are shared between three or more atoms, the electrons are delocalized.

Liquids and Intermolecular Forces

A liquid is one of the four fundamental states of matter. Liquids have a fixed volume, but not shape. Important molecular interactions that occur in liquids include hydrogen bonds, Van der Waal’s interactions, and dipole interactions.

Separations and Purifications

Molecules can be separated and purified using a variety of techniques, including extraction, distillation, chromatography, and electrophoresis. Many methods of chromatography can be used to separate molecules based on their size or charge.

Nucleotides and Nucleic Acids

The two important biological nucleic acids are DNA and RNA. A nucleotide is a monomer of both DNA and RNA and consists of a covalently bonded sugar, a phosphate, and a nucleobase. The sugar is ribose and deoxyribose for RNA and DNA, respectively. DNA contains the nucleobases cytosine (C), guanine (G), adenine (A), and thymine (T). C, G, A, and uracil (U) are the nucleobases used to make RNA. DNA forms a double helix when two antiparallel strands of polynucleotides associate through H bonds of the nucleobases. A forms two hydrogen bonds with T and G forms three hydrogen bonds with C. RNA can be linear or form complex structures when A associates with U or G associates with C using hydrogen bonds. C, T, and U are pyrimidines. G and A are purines.

Amino Acids

All amino acids have an amine group and a carboxylic acid group. The R group or side chain is unique to each amino acid and is used to categorize amino acids as hydrophobic, polar uncharged, positively charged, or negatively charged. Cysteine, glycine, and proline have unusual side chains that allow for their unique properties. For example, disulfide bonds can form between two cysteines.


Peptides are short chains of amino acids (normally < 50) linked together through a peptide bond. The peptide bond forms when the amine group from one amino acid reacts with the carboxyl group of another amino acid.


Proteins are chains of covalently bonded amino acids and are longer than peptides. The primary structure of a protein is its amino acid sequence. The secondary structure includes alpha helices and beta sheets; hydrogen bonds are important for formation of the secondary structure. The arrangement of secondary structures makes the tertiary protein structure. The tertiary structure is determined by the hydrophobic interactions, hydrogen bonds, salt bridges, and disulfide bonds. Typically hydrophobic residues are buried inside a globular protein to shield them from the aqueous environment. The 3D structure of proteins is often important for its function (e.g., enzymatic function or binding to substrate). The quaternary structure of a protein occurs when two or more proteins interact.


Lipids are hydrophobic or amphiphilic small molecules. Important, biological lipids are cholesterol, fatty acids, sterols, fat-soluble vitamins, and phospholipids. Lipids are important components of the cell membrane. Lipids are also important for energy storage and signaling.


Carbohydrates are made of carbon, hydrogen, and oxygen. Disaccharides and polysaccharides can be hydrolyzed into monosaccharides. The number of carbons, the chirality, and the placement of the carboxyl group (e.g., ketose and aldose) are used to classify carbohydrates. Carbohydrates are important for metabolism (e.g., glucose), energy storage (e.g., glycogen), and components of nucleic acid (e.g., ribose).

Aldehydes and Ketones

Both aldehydes and ketones contain a carbonyl group. The carbonyl group is found at the terminal carbon of aldehydes and bonded to a carbon within the carbon backbone of ketones. Aldehydes and ketones with alpha hydrogens have an enol and keto form (enol-keto tautomers). The carbonyl group is very reactive and reacts with nucleophiles.


Alcohols contain a hydroxyl group bonded to a saturated carbon. The solubility of alcohols depends on the length of the carbon backbone and they are protic solvents. Alcohols are both a weak acid and base. Important reactions involving alcohols include deprotonation, nucleophilic substitution, esterification, and oxidation.

Carboxylic Acids

Carboxylic acids have a carboxyl group (e.g., amino acids). Carboxylic acids are generally polar and the most common type of organic acids. Carboxylic acids can be converted into esters, amides, and alcohols.

Acid Derivatives

Acid derivatives include esters, amides, acid chlorides, and anhydrides. Important reactions include nucleophilic substitutions of the carbonyl group, transesterifications, saponifications, hydrolysis, and Hofmann degradations. Generally, the reactivity is acid chloride > anhydride > esters > amides.


Phenols have a hydroxyl group bonded to an unsaturated aromatic hydrocarbon ring. Phenol is soluble in water and a weak acid. Oxidation of phenols is important for vitamin K and coenzyme Q.

Polycyclic and Heterocyclic Aromatic Compounds

Polycyclic and heterocyclic aromatic compounds contain one or more chemical rings that are made of a mixture of carbon, nitrogen, sulfur, and oxygen. These molecules are planar and their chemical properties are dependent on the types of atoms and bonds present in the rings. An example of a biologically relevant heterocyclic aromatic compound is a purine.


Enzymes are a class of proteins that catalyze biochemical reactions. Enzymes recognize a specific substrate (active site or induced fit models), so the 3D shape is important. If enzymes are denatured or unfolded, their specificity and function is typically lost. Some enzymes require cofactors or covalent modifications (e.g., phosphorylation) to function. The Michaelis–Menten equation is important for determining various properties of an enzymatic reaction.


Bioenergetics is the subsection of biochemistry that investigates the energy involved in making and breaking chemical bonds in biological molecules. Important bioenergetic reactions include ATP hydrolysis and the oxidation-reduction reactions that occur in the mitochondria.

Chemical Reactions and Energy Changes

Thermodynamics studies the relationships among temperature, energy, and work. The zeroth, first, and second laws describe these interactions. Chemical reactions can be endothermic or exothermic; reactions are spontaneous if delta G is negative.

Kinetics and Equilibrium

The physical state (e.g., gas, liquid), concentration, temperature, and pressure of the reactants contribute to the rate of a chemical reaction (kinetics). A catalyst lowers the activation energy needed for a chemical reaction. At equilibrium, the concentrations of the reactants and products do not change.

Important Terms for this Section

buffer, common ion effect, Le Chatelier’s principle, Lewis structures, Lewis acid, Lewis base, dipole moment, sigma bond, pi bond, isomers, stereoisomers, enantiomers, molecular orbital theory, ion exchange chromatography, size exclusion chromatography, affinity chromatography, high performance liquid chromatography, mass spectroscopy, thin layer chromatography, ionic bond, epimers, anomers, enantiomers, glycosidic bond, rate-determining step, Arrhenius Equation, equilibrium constant, deltaG, calorimetry, phase diagram, fusion, fission, entropy, enthalpy, Gibbs free energy, enzyme inhibitors (competitive, reversible, irreversible, allosteric), free energy