AP Biology- Unit 1

Polar and Nonpolar

Polar- Electrons are shared unequally. Positive end and a negative end on molecule.

Nonpolar- Electrons are shared equally. There are no permanent charged ends.

Covalent and ionic bonds

Covalent bond- A chemical link where two atoms share valence electrons.

Ionic bond- A chemical link created by the electrostatic attraction between oppositely charged ions.

Electronegative

Electronegativity is an atom's tendency to attract shared electrons toward itself in a chemical bond.

Partially negative and partially positive

• The side where electrons spend more time becomes partially negative

• The side where electrons spend less time becomes partially positive

• Oxygen and Nitrogen will always be partially negative

• Hydrogen and Carbon will always be partially positive

Cohesion and Adhesion and Capillary Action

Cohesion- The attraction between molecules of the same substance.

Adhesion- The attraction between water and other substances.

Capillary Action- The tendency of water to move up narrow tubes.

Specific heat

Specific heat- The amount of energy required to raise the temperature of a substance.

Water has a high specific heat because added heat energy is often used first to break hydrogen bonds rather than immediately increasing molecular motion.

High heat of vaporization

A high heat of vaporization means a large amount of energy is required to transform a liquid into a gas at a constant temperature

Solvent and solute

The solvent does the dissolving, and the solute is what gets dissolved.

Water does not dissolve nonpolar substances well (like oils).

Biological elements

Most of living matter is built primarily from:

• Carbon (C)

• Hydrogen (H)

• Oxygen (O)

• Nitrogen (N)

You’ll often see the mnemonic CHNOPS to remember additional essential elements:

• Phosphorus (P)

• Sulfur (S)

These elements matter because they form the backbone of biological macromolecules:

• Proteins (C, H, O, N, often S)

• Nucleic acids like DNA/RNA (C, H, O, N, P)

• Carbohydrates (C, H, O)

• Lipids (mostly C and H, some O and P depending on type)

Subatomic particles and isotopes

Subatomic particles:

• Protons: positive charge, in the nucleus

• Neutrons: no charge, in the nucleus

• Electrons: negative charge, occupy regions around the nucleus

The identity of an element is determined by the number of protons (its atomic number). Atoms of the same element can differ in neutrons; these variants are isotopes.

• Isotopes are not different elements; they are the same element with different neutron numbers.

Van der Waals interaction

Very weak attractions due to temporary, fluctuating charges when electrons are unevenly distributed moment-to-moment.

Individually tiny, they become significant when many parts of molecules are close together (common in large macromolecules).

Macronutrients and trace elements

• Macronutrients: needed in relatively large quantities (C, H, O, N, P, S are major examples)

• Trace elements: required in very small amounts but still essential

Cation and anion

• A cation is positively charged (lost electrons).

• An anion is negatively charged (gained electrons).

Monomers and polymers

A monomer is a small molecular subunit that can be linked into a larger structure.

A polymer is a long molecule made of repeating monomer units.

Many biological macromolecules are polymers:

• carbohydrates (many sugars)

• proteins (many amino acids)

• nucleic acids (many nucleotides)

Lipids are an important exception: they are large biological molecules but are not true polymers with repeating monomer units in the same way.

Carbohydrates

Carbohydrates are organic compounds containing carbon, hydrogen, and oxygen, often in an approximate ratio of 1:2:1.

Carbohydrates are categorized as:

• Monosaccharides (one sugar; monomers)

• Disaccharides (two sugars)

• Polysaccharides (many sugars; polymers)

Monosaccharides often form rings in water, and ring structure influences how they link together.

Glycoproteins and Glycolipids

Carbohydrates can attach to proteins or lipids on the cell surface:

• Glycoproteins: proteins with carbohydrates attached

• Glycolipids: lipids with carbohydrates attache

Functional groups

Chemical motifs, or patterns of atoms, that display consistent “function” (properties and reactivity) regardless of the exact molecule they are found in.

Monosaccharides

Monosaccharides are an important energy source for cells and also serve as building blocks.

Examples: glucose, fructose, and galactose. Glucose and fructose, share the formula C6H12O6.

Glucose is a major fuel for cells, is an important part of many foods, and is produced by plants during photosynthesis.

Glucose and fructose can be depicted as either “straight” chains or rings, with OH and H groups attached.

Disaccharides and glycosidic linkages

When two monosaccharides are joined, the bond is a glycosidic linkage, formed by dehydration synthesis. The disaccharide formed from two glucose molecules is maltose.

Glycosidic linkage geometry: alpha vs. beta

Small changes in linkage orientation can drastically change properties. In glucose polymers:

• alpha linkages often create helical structures and are commonly digestible by humans.

• beta linkages create straighter chains that can hydrogen bond to neighboring chains, producing strong fibers.

Polysaccharides

• Starch: plant energy storage; alpha-linked glucose.

• Glycogen: animal energy storage; alpha-linked glucose and typically more highly branched than starch, supporting rapid glucose addition/removal.

• Cellulose: plant structural support in cell walls; beta-linked glucose. Straight chains align and form many hydrogen bonds, creating strong fibers.

• Chitin: structural polysaccharide in arthropod exoskeletons and fungal cell walls; built from beta-linked modified glucose subunits (a nitrogen-containing derivative), which helps explain its strength.

Lipids

Lipids are organic molecules defined by a shared property: they are largely hydrophobic (nonpolar), meaning they do not dissolve in water.

1. Fats (Triacylglycerols)

• Structure: Composed of one glycerol backbone attached to three fatty acids (long hydrocarbon chains).

• Function: Used for concentrated, long-term energy storage in adipose (fat) tissue.

• Saturation:

  • Saturated fats: Have no carbon-carbon double bonds, pack tightly, and are usually solid at room temperature.

  • Unsaturated fats: Have one or more double bonds that create kinks, preventing tight packing, and are usually liquid at room temperature.

2. Phospholipids

• Structure: Consist of a hydrophilic (polar) head containing a phosphate group and two hydrophobic (nonpolar) tails. Because they have both regions, they are amphipathic.

• Function: Form the foundation of cell membranes. In water, they spontaneously assemble into a bilayer (heads facing out, tails facing in) stabilized by the hydrophobic effect and van der Waals forces, requiring no structural "glue."

3. Steroids

• Structure: Characterized by a four-ring carbon skeleton.

• Cholesterol: A crucial steroid in cell membranes that regulates membrane fluidity and serves as a precursor for vitamin D and hormones.

• Hormones: Many steroids function as chemical signaling molecules.

4. Waxes

• Structure & Function: Highly hydrophobic, long-chain lipids used primarily for waterproofing on plant leaves and animal coatings.

Proteins

Proteins are highly diverse macromolecules whose precise 3D shape controls their function (enzymes, transporters, structure, signaling).

Amino Acid Structure

Amino acids are the monomers of proteins. There are 20 types, each containing Carbon, Hydrogen, Oxygen, and Nitrogen. Every amino acid has a central carbon bonded to:

• An amino group (–NH₂)

• A carboxyl group (–COOH)

• A hydrogen

• An R group (side chain) — This is the only part that differs, and its chemistry drives protein folding.

Side-Chain Categories

R-group polarity determines how the protein folds based on environmental interactions:

• Hydrophobic: Nonpolar and uncharged.

• Hydrophilic: Polar and uncharged.

• Ionic: Polar and charged.

  • Negative: Glutamic acid, aspartic acid (donate protons).

  • Positive: Lysine, arginine (accept protons).

  • Sulfur-containing: Methionine, cysteine.

Bonding & Structure

• Peptide Bond: A covalent bond formed between the carboxyl group of one amino acid and the amino group of another via dehydration synthesis.

• Polypeptide: A chain of amino acids. It becomes a functional protein only after it twists and folds into its 3D shape.

Denaturation is the loss of a protein’s native shape due to changes in temperature, pH, or salt concentration.

Nucleic Acids

Nucleic acids contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. They are made of monomers called nucleotides

In DNA, two strands align with bases pairing via hydrogen bonds:

• A pairs with T

• C pairs with G

The strands run in opposite directions (antiparallel). Base pairing depends on hydrogen bonding and shape complementarity.

In action: predicting a complementary DNA sequence

If one strand contains:

• A G T C C A

The complementary strand is:

• T C A G G T

ATP (adenosine triphosphate) is a nucleotide-related molecule used for energy transfer in cells.

A key Unit 1 idea is that ATP’s structure—especially the phosphate groups and their charge interactions—makes ATP useful for coupling energy-requiring processes to energy-releasing reactions.

The Four Macromolecules and Their Elements

• Carbohydrates: Made of Carbon, Hydrogen, Oxygen (CHO).

• Lipids: Made of Carbon, Hydrogen, Oxygen (CHO), and phospholipids also include Phosphorus (P).

• Proteins: Made of Carbon, Hydrogen, Oxygen, Nitrogen, and Sulfur (CHONS).

• Nucleic Acids: Made of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus (CHONP)