AP Biology

Water is the most abundant molecule in living organisms, comprising 70-95% of most cells. Understanding water's unique properties begins with its molecular structure. A water molecule consists of one oxygen atom covalently bonded to two hydrogen atoms. The oxygen atom is more electronegative than hydrogen, meaning it attracts shared electrons more strongly. This unequal sharing creates a polar molecule with a partial negative charge near the oxygen and partial positive charges near the hydrogens.

The polarity of water molecules allows them to form hydrogen bonds with each other. A hydrogen bond occurs when the partially positive hydrogen of one water molecule is attracted to the partially negative oxygen of another water molecule. Each water molecule can form up to four hydrogen bonds with neighboring molecules. Although individual hydrogen bonds are weak compared to covalent bonds, collectively they give water remarkable properties essential for life.

Cohesion refers to water molecules sticking together through hydrogen bonding. This property creates surface tension, allowing some insects to walk on water and enabling water to form droplets. Adhesion is the attraction between water molecules and other polar surfaces. Together, cohesion and adhesion enable capillary action, which helps water move upward through plant xylem against gravity.

Water has a high specific heat capacity, meaning it can absorb or release large amounts of heat with relatively small temperature changes. This property helps organisms maintain stable internal temperatures and moderates Earth's climate. The high heat of vaporization means significant energy is required to convert liquid water to vapor. When water evaporates from skin or leaf surfaces, it carries away substantial heat, providing an effective cooling mechanism.

Ice floats because water expands as it freezes. Hydrogen bonds in ice form a crystalline lattice that spaces molecules farther apart than in liquid water. This property is critical for aquatic life because floating ice insulates underlying water, preventing lakes and oceans from freezing solid.

Water is an excellent solvent for polar and ionic substances. When ionic compounds like sodium chloride dissolve, water molecules surround individual ions, separating them from the crystal lattice. This dissolving ability makes water the medium for most biochemical reactions and enables transport of nutrients and wastes in organisms.

Hydrophilic substances interact favorably with water due to their polar or ionic nature. Hydrophobic substances, such as oils and fats, do not dissolve in water because they lack polar regions. In aqueous environments, hydrophobic molecules cluster together, minimizing their contact with water. This hydrophobic effect drives important biological processes including membrane formation and protein folding.

Living organisms contain four major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids. These large molecules perform diverse functions including energy storage, structural support, catalysis, information storage, and cell signaling.

Macromolecules are polymers built from smaller subunits called monomers. Dehydration synthesis (condensation) reactions link monomers together by removing a water molecule. One monomer contributes a hydroxyl group while another contributes a hydrogen atom, forming water as a byproduct while creating a covalent bond between the monomers. Hydrolysis reactions reverse this process by adding water to break covalent bonds, releasing individual monomers. Enzymes catalyze both types of reactions in living cells.

Carbohydrates include sugars, starches, and cellulose. Their primary functions are energy storage and structural support. Monosaccharides are simple sugars with the general formula (CH2O)n. Glucose, fructose, and galactose are common six-carbon monosaccharides. Disaccharides form when two monosaccharides join through a glycosidic linkage. Sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose) are important disaccharides. Polysaccharides are long chains of monosaccharides. Starch and glycogen store energy in plants and animals respectively. Cellulose and chitin provide structural support in plant cell walls and arthropod exoskeletons.

Lipids are hydrophobic molecules that include fats, phospholipids, and steroids. Unlike other macromolecules, lipids are not polymers. Fats consist of glycerol linked to three fatty acids through ester bonds, forming triglycerides. Saturated fatty acids have no double bonds between carbons and pack tightly, making them solid at room temperature. Unsaturated fatty acids contain one or more double bonds, creating kinks that prevent tight packing and keeping them liquid at room temperature. Phospholipids have two fatty acids and a phosphate group attached to glycerol. Their amphipathic nature, with hydrophilic heads and hydrophobic tails, makes them ideal for forming biological membranes. Steroids share a four-ring carbon skeleton. Cholesterol is a steroid that modulates membrane fluidity, and steroid hormones regulate many physiological processes.

Proteins perform the widest variety of functions among macromolecules. They serve as enzymes, structural components, transport molecules, antibodies, hormones, and receptors. Amino acids are the monomers of proteins. Each amino acid has an amino group, a carboxyl group, a hydrogen atom, and a variable R group attached to a central carbon. The R group determines each amino acid's properties: nonpolar, polar, acidic, or basic. Twenty different amino acids are commonly found in proteins. Peptide bonds link amino acids together, forming polypeptide chains.

Nucleic acids store and transmit genetic information. DNA (deoxyribonucleic acid) stores hereditary information, while RNA (ribonucleic acid) plays multiple roles in gene expression. Nucleotides are the monomers of nucleic acids. Each nucleotide contains a five-carbon sugar, a phosphate group, and a nitrogenous base. DNA contains deoxyribose sugar and the bases adenine, guanine, cytosine, and thymine. RNA contains ribose sugar and uses uracil instead of thymine.

Carbohydrate structure directly relates to function. Monosaccharides exist primarily as ring structures in aqueous solutions. Glucose can form either alpha or beta configurations depending on the position of the hydroxyl group on carbon 1. This seemingly minor difference has major functional consequences. Alpha glucose forms starch and glycogen, which are easily digestible energy storage molecules. Beta glucose forms cellulose, which provides rigid structural support because most organisms cannot break beta glycosidic linkages.

Starch consists of amylose (unbranched chains of alpha glucose) and amylopectin (branched chains). The helical structure of amylose allows compact storage. Glycogen resembles amylopectin but is more highly branched, enabling rapid glucose mobilization when energy is needed. Cellulose consists of long, unbranched chains of beta glucose. Hydrogen bonds between parallel chains create microfibrils with tremendous tensile strength. Chitin is similar to cellulose but contains nitrogen-modified glucose units, providing even greater strength for arthropod exoskeletons and fungal cell walls.

Lipid structure varies considerably among different types. In triglycerides, the length and saturation of fatty acid chains affect physical properties. Longer chains and more saturation increase melting points. Trans fats, produced by partial hydrogenation, have straight chains despite containing double bonds, making them solid at room temperature and associated with health risks.

Phospholipid structure creates the bilayer arrangement of biological membranes. The hydrophilic phosphate heads face aqueous environments on both membrane surfaces while hydrophobic fatty acid tails cluster in the membrane interior. This arrangement creates a selectively permeable barrier. Membrane fluidity depends on fatty acid composition: more unsaturated fatty acids increase fluidity, while cholesterol buffers fluidity changes across temperature ranges.

Protein structure exists at four levels. Primary structure is the linear sequence of amino acids in a polypeptide chain, determined by genetic information. Secondary structure results from hydrogen bonding between backbone atoms. Alpha helices form when hydrogen bonds connect amino acids four residues apart, creating a spiral. Beta pleated sheets form when hydrogen bonds connect parallel or antiparallel polypeptide segments, creating a zigzag pattern.

Tertiary structure is the overall three-dimensional shape of a single polypeptide. It results from interactions between R groups including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges between cysteine residues. Quaternary structure exists when multiple polypeptide subunits assemble into a functional protein complex. Hemoglobin, with its four subunits, exemplifies quaternary structure.

Nucleic acid structure reflects function. DNA's double helix consists of two antiparallel strands wound around each other. The sugar-phosphate backbone runs along the outside while nitrogenous bases face inward. Complementary base pairing (adenine with thymine, guanine with cytosine) holds the strands together through hydrogen bonds. Adenine-thymine pairs form two hydrogen bonds; guanine-cytosine pairs form three. This complementarity enables accurate DNA replication and transcription.

RNA is typically single-stranded but can form complex secondary structures through intramolecular base pairing. Transfer RNA folds into a characteristic cloverleaf shape essential for its role in translation. Ribosomal RNA forms complex structures that contribute to ribosome function. Messenger RNA structure affects stability and translation efficiency.

The central theme of biology is that structure determines function. This principle applies at all levels from molecules to ecosystems, but is particularly evident in macromolecules.

Enzyme function depends on precise three-dimensional structure. The active site is a pocket or groove where substrates bind and reactions occur. Active site shape is complementary to substrate shape, explaining enzyme specificity. The induced fit model describes how enzyme and substrate shapes adjust upon binding to optimize catalysis. Any change in enzyme structure, whether from temperature, pH, or mutation, can alter active site geometry and reduce or eliminate function.

Antibody function illustrates structure-function relationships in immune proteins. The variable regions of antibody arms form antigen-binding sites with shapes complementary to specific antigens. This complementarity enables antibodies to recognize and bind foreign molecules with high specificity. Different antibody classes have different constant regions that determine their location and function in immune responses.

Hemoglobin demonstrates how quaternary structure enables cooperative function. When one subunit binds oxygen, it changes shape in ways that increase oxygen affinity of the remaining subunits. This cooperativity produces a sigmoidal oxygen-binding curve rather than a hyperbolic curve, allowing efficient oxygen loading in lungs and unloading in tissues.

Collagen's triple helix structure provides tensile strength to connective tissues. Three polypeptide chains wind around each other, stabilized by hydrogen bonds. Glycine, the smallest amino acid, occurs at every third position, allowing tight packing of the helix. Hydroxyproline and hydroxylysine contribute additional hydrogen bonds. Mutations affecting collagen structure cause connective tissue disorders.

Membrane protein function depends on orientation within the lipid bilayer. Integral membrane proteins span the membrane with hydrophobic regions embedded in the lipid core and hydrophilic regions exposed to aqueous environments. This orientation enables functions like transport, signaling, and cell recognition. Peripheral membrane proteins associate with membrane surfaces through electrostatic interactions and perform functions including enzyme catalysis and cytoskeletal attachment.

Carbohydrate structure affects digestibility and function. Humans can digest starch because we produce amylase enzymes that hydrolyze alpha glycosidic linkages. We cannot digest cellulose because we lack enzymes to break beta linkages. Ruminant animals digest cellulose through symbiotic microorganisms that produce appropriate enzymes. The branching pattern of glycogen enables rapid glucose release because multiple chain ends are available for enzyme action simultaneously.

Nucleic acids serve as the molecular basis of heredity and gene expression. DNA stores genetic information in the sequence of nitrogenous bases along its length. The four-letter alphabet of A, T, G, and C can encode unlimited information in the same way binary code underlies all computer functions. Each gene contains hundreds to thousands of nucleotides encoding the information for one or more proteins or RNA molecules.

DNA's double helix structure enables faithful replication. When DNA replicates, the two strands separate and each serves as a template for synthesizing a new complementary strand. Base pairing rules ensure that the new strands are identical to the originals. This semiconservative replication produces two identical DNA molecules from one original.

RNA plays multiple roles in gene expression. Messenger RNA carries genetic information from DNA to ribosomes. Transfer RNA brings amino acids to ribosomes and contains anticodons that base-pair with mRNA codons. Ribosomal RNA is a structural and catalytic component of ribosomes. Other RNA types regulate gene expression, modify other RNAs, and catalyze various reactions.

The genetic code relates nucleotide sequence to amino acid sequence. Codons are three-nucleotide sequences that specify amino acids or stop signals. With 64 possible codons and 20 amino acids, the code is redundant: most amino acids are specified by multiple codons. This redundancy provides some protection against mutations. The code is nearly universal across all life forms, evidence of common ancestry.

Carbon is central to biological molecules because of its bonding properties. With four valence electrons, carbon can form four covalent bonds, enabling complex molecular structures. Carbon-carbon bonds can be single, double, or triple, and carbon chains can be linear, branched, or cyclic. This versatility allows carbon to form the backbone of all major biological molecules.

Carbon skeletons vary in length, branching, ring structure, and positions of double bonds. These variations create the enormous diversity of organic molecules. Functional groups attached to carbon skeletons determine chemical properties. Hydroxyl groups make molecules polar and water-soluble. Carboxyl groups donate hydrogen ions, making molecules acidic. Amino groups accept hydrogen ions, making molecules basic. Phosphate groups carry negative charges and participate in energy transfer.

The ability of carbon to form stable bonds with itself and other elements makes life as we know it possible. Silicon, the element most similar to carbon, cannot form comparably stable bonds at temperatures compatible with liquid water. Carbon chemistry in aqueous solution provides the foundation for the complexity and diversity of living systems.