AP Biology Unit 1: Chemistry of Life

Polarity

• Unequal election sharing between oxygen and hydrogen, resulting in a partial negative charge the oxygen atom and partial positive charges near the hydrogen

• Water is polar molecule

Hydrogen Bonds

• Weak intermolecular bonds that form between oppositely charged sides of polar molecules

• Weaker than covalent or ionic bonds

Cohesion

• Property of water where hydrogen bonds between water molecules enable water to stick to itself

• This property contributes to water’s high heat of vaporization, high specific heat, and high surface tension

Adhesion

• Property of water where water molecules stick to other substances, such as cellulose in the conductive tubes that move water from the roots to the upper parts of plants called the xylem

• Supports processes like capillary action and transpiration in plants.

Surface Tension

• Property of water where hydrogen bonds between water molecules create a “molecular net” on the surface of a body of water, enabling objects like paper clips and organisms like water striders to rest on water without sinking.

Acidic Solutions

• Contain more hydrogen ions (H⁺) than hydroxide ions (OH⁻). pH is below 7.

Basic Solutions

• Contain more hydroxide ions (OH⁻) than hydrogen ions (H⁺). pH is above 7.

Carbon

• Because carbon has four valence electrons, it can form a wide variety of covalent bonds, including single, double, and triple bonds with itself and other elements.

• This enables carbon to form rings, chains, and branched molecules of any length and shape.

Hydrogen

• Plays a role in energy storage and exchange, creating acidic micro-enviroments, and creating proton gradients during the process of chemiosmosis

Nitrogen

• Nitrogenous bases are key to the structure of DNA and RNA

• Nitrogen-containing amino groups are key to the structure of proteins.

Oxygen

• Plays a key role in cellular respiration

Phosphorous

• Found in phosphate groups (e.g., ATP). Phosphate groups are key to the structure of phospholipids (which make up cell membranes) and in nucleic acids (DNA and RNA).

Sulfur

• Plays a key role in protein structure

Polymers

• Describes three groups of biological macromolecules (carbohydrates, proteins, and nucleic acids) built from smaller units called monomers

Monomer

• A small, basic molecular unit that acts as a building block for larger biological macromolecules, known as polymers

Dehydration Synthesis

• Process of joining monomers to form polymers by removing a water molecule (H₂O).

• Enzymes facilitate the reaction by removing a hydroxyl group from one monomer and a hydrogen from the other.

Hydrolysis

• Opposite of dehydration synthesis; breaks polymers into monomers by inserting a water molecule between the monomers.

• Example: Enzymes break apart lactose (a disaccharide) into two carbohydrate monomers: glucose and galactose by inserting a water molecule between the two monomers.

Functional Groups

• Phosphate group: Key in energy exchange ( ATP) and DNA structure.

• Methyl group: Enzymes use methyl groups to silence DNA (methylation).

• Hydroxyl and carbonyl groups make molecules hydrophilic (able to dissolve in water).

• Carboxyl group (carboxylic acid): Present in amino acids and other molecules, making them acidic

• Amino group: Found in amino acids. Makes molecules basic.

• Sulfhydryl group: Stabilizes protein structures.

• Acetyl group: Found in a molecule that’s important in cellular respiration (Acetyl-CoA). Adding acetyl groups to DNA-associated proteins (acetylation) is used to activates DNA for gene expression (the opposite of methylation).

Carbohydrates

• Organic macromolecules composed of carbon, hydrogen, and oxygen

Monosaccharides

• (Simple sugars like glucose) are the monomers (building blocks) of carbohydrates.

• Product of photosynthesis

Disaccharides

• Two linked monosaccharides (lactose and sucrose).

• Used for energy transfer (lactose transfers energy between a mother and its babies; sucrose transfers energy between leaves and other parts of plants).

Polysaccharides

• Three or more linked monosaccharides

• Functioned for energy storage (starch) in plants and (glycogen) in animals

• Cellulose (example of a polysaccharide) is primarily component of plant cell walls

Illustrative Example: Cellulose Digestion

• Humans and most other animals lack the digestive enzymes to hydrolyze cellulose into the glucose monomers that make it up.

• As a result, cellulose can’t serve us as an energy source (but serves as an important source of fiber in the diet).

• Cellulose can be hydrolyzed into glucose by a group of mammals called ruminants (such as cows, deer, goats, etc). which have symbiotic relationships with bacteria that can break bonds in cellulose and release the glucose monomers.

• Among insects, termites can do the same (which is why they can digest wood)

Illustrative Example: Lactose Tolerance and Intolerance

• Lactose is a disaccharide; the enzyme lactase breaks it into two monosaccharides, glucose and galactose.

• Most mammals produce lactase only during infancy.

• Mutations in some human populations allowed lactase persistence into adulthood, leading to lactose tolerance in specific regions (e.g., parts of Africa, Europe, and the Indian subcontinent). This opened a new food source to these populations. But worldwide, most adults are lactose intolerant.

• Lactose-intolerant individuals can use lactase supplements or lactose-free products.

Lipids

• Hydrophobic biomolecules that are nonpolar and not composed of repeating monomers

Triglycerides (Fats & Oils)

• Used for energy storage, insulation (as blubber in whales and other marine mammals), and buoyancy (also in marine mammals)

• Structure consists of a glycerol bound to 3 fatty acids

• Fats are generally solid at room temperature, and are found more frequently in animals.

  • Fatty acids are saturated fats (without double bonds in the fatty acid chain.

Waxes

• Used for waterproofing (as in the upper surfaces of leaves)

Phospholipids

• Structural molecule in cell membranes composed of a hydrophilic (polar) head and two hydrophobic (nonpolar) tails

  • Connecting the head and tail is a glycerol molecule

• In water, they form bilayers, with heads facing outward toward water and tails inward creating the structural framework of cell membranes.

Steroids

• Signaling molecules (ex: hormones like estrogen and testosterone)

Proteins

• Macromolecules composed of amino acid chains (polypeptides) that fold into specific three-dimensional shapes, determining their function

• “Molecule of action”

Amino Acids

• Monomers of proteins composed of a carbon atom, basic amine group, acidic carboxyl group, hydrogen atom, and variable r group/side chain

• All life uses the same 20 amino acids

Primary Structure

• Linear sequence of amino acids linked by peptide bonds.

• Sequence is genetically determined.

• Built by ribosomes, not enzymes

• Forms the polypeptide backbone (alternating carbon and nitrogen atoms)

Secondary Structure

• Stabilized by hydrogen bonds between amine and carbonyl groups in the polypeptide backbone

• Shapes are:

  • Alpha helix: Corkscrew shape stabilized by hydrogen bonds.

  • Beta-pleated sheet: Parallel or antiparallel strands stabilized by hydrogen bonds.

Tertiary Structure

• Interactions between R groups:

  • Hydrogen bonds.

  • Ionic bonds.

  • Covalent bonds (e.g., disulfide bonds between sulfhydryl groups).

  • Hydrophobic clustering: Non-polar side chains cluster to avoid water

Quaternary Structure

• Involves interactions between multiple folded polypeptide chains

Illustrative Example: Hemoglobin and Sickle Cell Disease

• Hemoglobin Structure:

  • Quaternary protein composed of four polypeptide chains.

• Cause:

  • Mutation substituting valine (non-polar) for glutamic acid (acidic) in hemoglobin.

  • Results in hydrophobic interactions between hemoglobin molecules in deoxygenated blood.

• Effects:

  • Formation of fibers within red blood cells, causing a spiked shape.

  • Mutant cells clump in small arteries, leading to pain crises, tissue damage, and other symptoms.

Nucleic Acids

• Molecules of genetic information that come in two types:

  • DNA: Molecule of heredity, passed from generation to generation, and replicated during cell division.

  • RNA: Functions in information transfer (ex: mRNA) and can act as an enzyme (ex: ribozymes).

    • Serves as the molecule of heredity in certain viruses.

Nucleotides

• Monomers of nucleic acids composed of a five carbon sugar (deoxyribose in DNA, ribose in RNA), phosphate group, and nitrogenous base (AT/U CG)

Double Helix

• The structure of DNA consisting of two strands of nucleotides connected by hydrogen bonds between complementary bases:

  • A pairs with T

  • C pairs with G

• Strands are antiparallel meaning they are oriented in opposite directions to allow hydrogen bonding

• One strand runs 5’ to 3’ and another 3’ to 5’

Sugar-Phosphate Backbone

• Nucleotides in each strand are linked by sugar-phosphate bonds

5’ to 3’ Directionality

• Refers to the positions of carbons in the sugar-phosphate backbone

• DNA and RNA strands are built in the 5′ to 3′ orientation

• That’s because the key enzyme in DNA replication, DNA polymerase, can only add nucleotides to the 3′ end of a growing strand

RNA

• Single strand that can fold into various shapes and used for information transfer (mRNA), catalysis (RNA makes ribozymes in ribosomes), and regulation