AP Biology Unit 1 - 1.1-1.4

Topic 1.1 Notes - Structure of Water & Hydrogen Bonding

Structure of Water

• Polar molecule, with O2 being highly electronegative, pulling electrons toward itself leading to partial charges

  • O2 = Partial Negative

  • H2 = Partial Positive

• Allows water to form hydrogen bonds

• Interacts well with other polar molecules “like dissolves like”

Key Properties of Water That Support Life

Cohesion

• Attraction of water molecules to itself via hydrogen bonding

• Helps in water transport in plants (ex: water moves upward during transpiration)

Adhesion

• Attraction between water molecules and other polar or charged surfaces.

• Works with cohesion for capillary action (upward movement of water from roots=>leaves) in plant vessels

Surface Tension

• Energy needed to break the surface of a liquid that is high in water due to cohesion

• Allows light insects to “walk” on water

High Specific Heat

• Water absorbs a lot of energy before changing temperature because energy goes to breaking hydrogen bonds

• Helps organisms/ecosystems maintain stable internal temps

High Heat of Vaporization/Evaporative Cooling

• Water absorbs a lot of heat to go from liquid=>gas

• Sweat cools our bodies as it evaporates, carrying heat away

Ice Floats

• Solid water is less dense than liquid water because stable hydrogen bonds hold molecules farther apart.

• Ice insulates water below, protecting aquatic life in cold climates.

Universal Solvent

• Water dissolves ionic & polar molecules promoting chemical reactions & transport of materials in cells

Hydrophilic vs. Hydrophobic Interactions

Hydrophilic

• Water loving substance that is polar/charged and dissolves in water

• Multiple Hydroxyl groups (-OH) present that overcome the amount of Nonpolar groups present

• Faces out in protein folding

• Example: Sugars, salts

Hydrophobic

• Water fearing substance that is no polar and doesn’t mix well with water

• Nonpolar structure (no lone pairs on central atom)

• Clusters inward in protein folding

• Example: lipids, oils => forms cell membranes

pH, Acids, & Bases: How Water Can Shift

Neutral Water

• Behaves like an acid or base that determines how organisms manage pH

• H2O =><= H+ + OH-

Acid

Increases H+ concentration (ex: HCl)

Base

Increases OH- or decreases H+ (ex: NaOH)

pH Scale

• Ranges from 0-14

• Acidic: <7

• Neutral: 7

• Basic: >7

• Most biological fluids are around 6-8

Buffer

Systems that maintain pH stability by absorbing or releasing H⁺ when levels drop

Water’s Role in Biological Molecules

Water doesn't just exist in the background — it directly influences the structure and function of biomolecules.

Water’s Role in Proteins

• Hydrogen bonds help stabilize secondary, tertiary, and quaternary structures

• Hydrophilic/hydrophobic interactions shape folding.

Water’s Role in DNA

• Hydrogen bonds between base pairs hold strands together (A-T and G-C).

Water’s Role in Cell Membranes

• Hydrophobic tails of phospholipids avoid water, forming the bilayer structure.

1.2 Notes - Elements of Life

Big Idea: Life Runs on Atoms

Matter

• Anything with mass & volume needed for organisms to survive via a steady exchange of matter from their environment to fuel growth, repair, and energy production

Atom

• Smallest unit of an element that retains its properties made of protons, neutrons, and electrons

Elements

Pure substance (can’t be broken down further)

Elements essential for Life

• CHNOPS

• 6 key elements in biomolecules

Carbon: MVP of Life

Carbon

• Element that makes up all living organisms

• Found in all major biological macromolecules that bond with CHNOPS

• Four bond versatility makes it the backbone of organic molecules

Atoms => Molecules => Life

Life builds big molecules from small building blocks. Know what atoms go into what kinds of macromolecules.

Carbohydrates

• Biological molecules made of carbon, hydrogen, and oxygen; used for quick energy and structural support.

Lipids

• Made of C, H (some O; P in phospholipids)

• Used for long term energy, membranes, insulation

Proteins

• Made of C, H, O, N

• Used for enzymes, movement, communication, & transport

Nucleic Acid

• Made of: C, H, O, N, P

• Used for storing & transmitting genetic information (DNA & RNA)

Critical Elements: C, N, P

Three elements you’ll absolutely be asked about.

Carbon (C)

• Backbone of all biological molecules

• Universal across all 4 macromolecules

Nitrogen (N)

• Found in amino acids (proteins) & nitrogenous bases (nucleic acids)

• Also in enzymes & hormones

Phosphorous (P)

• Found in nucleotides (DNA/RNA), phospholipids (cell membranes), & ATP

• Also in enzymes & hormones

Functional Groups = Function Changes

• Specific groupings of atoms within molecules that given them different chemical properties (like polarity, acidity, reactivity)

Key Functional Groups to Know

Hydroxyl

• (-OH) polar, helps sugar dissolve in water

Carbonyl

• (>C=O) polar, found in sugars

  • Aldehyde (end of molecule)

  • Ketone (middle)

Carboxyl

• (-COOH) acidic (releases H+), found in amino acids/fatty acids

Phosphate

• (-PO4) acidic, important in energy (ATP) and nucleic acids

Sulfhydryl

• (-SH) forms disulfide bridges in proteins

Isotopes & Electron Shells

• Isotopes: atoms of same element w/ diff # of neutrons

  • Ex: carbon-14 used in carbon dating

• Electrons fill energy levels/shells => outer shell determines chemical behavior

  • Electrons prefer full outer shells (octet rule)

NOTE: Skip memorizing isotopes/electrons for now unless your teacher emphasized it

Why This All Ties Together

• Biology from DNA replication to metabolism depend on how matter comes into the organism & is used to build molecules

  • Living things:

    • Constantly interact w/ the environment

    • Take in atoms (C, N, P) to grow & function

  • The structure of macromolecules = determines their function

    • Example: Different lipid structures let them form membranes vs store fat

• AP FRQ Pro Tip: If asked to explain how organisms build molecules, connect the element => what it’s used for => why the cell needs it => what it does (function/result)

1.3 Introduction to Biological Macromolecules

Macromolecules

• Large, carbon based molecules that support life

• Most are polymers, chains of repeating units (monomers) linked by covalent bonds

Four key types of macromolecules with a unique monomer & bond type

• Carbohydrates => monosaccharides

• Proteins => amino acids

• Nucleic acids => nucleotides

• Lipids => not true polymers, but built from fatty acids & glycerol

Monomers and the Bonds that Build Polymers

All biological polymers form when monomers join via covalent bonds—each type has its own version

Carbohydrates

• Macromolecules made of sugar units that can provide energy or structural support.

• Monomer: monosaccharides (glucose, fructose)

• Bond: glycosidic linkage:

  • (C—O—C)

• Structure of polysaccharides affects digestibility (e.g., cellulose vs starch)

Proteins

• Monomer: amino acids

• Bond: peptide bond between carboxyl and amino groups

• Order of amino acids (primary structure) → protein shape → function

• Even one substitution can change function (e.g., sickle cell anemia)

Nucleic Acids

• Monomer: nucleotides (has sugar, phosphate, nitrogen base)

• Bonds:

  • Phosphodiester bonds (super phosphate backbone)

  • Hydrogen bonds (between bases in DNA)

• Sequence of bases = genetic code

• Double-stranded structure held together by hydrogen bonds

Lipids

• Made of fatty acids & glycerol that is Nonpolar and hydrophobic

• Bond: ester linkage (between hydroxyl and carboxyl)

• Key functions:

  • Long term energy storage

  • Membrane structure (phospholipids)

  • Signaling (steroids like hormones)

Chemical Bonds and Interactions Recap

Understanding atom-level bonding helps explain how macromolecules form and behave.

Covalent Bonds

• Atoms share electrons w/ strong bonds used to form macromolecules

• Two types: Nonpolar (equal sharing) and polar (unequal sharing)

Hydrogen Bonds

• Weak attractions between polar molecules

• Key in DNA base pairing and protein folding

Bond Rules to Know

• Covalent = within molecules (intramolecular)

• Hydrogen bonds = between molecules (intermolecular)

Dehydration Synthesis vs Hydrolysis

These two reactions are essential for building up or breaking down all macromolecules.

Dehydration Synthesis

• Joins monomers => forms polymers

• Removes water (H+ from one monomer, OH- from the other)

• Requires enzymes

• Endergonic (req energy)

• Ex: peptide bond forming between amino acids

Hydrolysis

• Breaks polymers => releases monomers

• Adds water (breakup into H+ and OH-)

• Also needs enzymes

• Exergonic (releases energy)

• Example: Digesting starch into glucose

Structure Determines Function

This idea is core in AP Bio: shape and bonding dictate what a molecule can do.

1.4 Notes - Properties of Biological Macromolecules

Biological macromolecules

• Lrg molecules made by joining smaller subunits (monomers)

• Structure determines function: unique shape & chemical makeup of each macromolecule decide what it can do inside an organism

Main 4 types of macromolecules

• Carbohydrates (sugars)

• Proteins (polypeptides)

• Nucleic acids (DNA & RNA)

• Lipids (fats, oils, phospholipids, steroids)

Each type has a specific type of monomer that builds it, specific bonds that hold it together, and a structure that enables specific functions in the cell

Nucleic Acids: Info Storage & Transmission

Nucleic acids (DNA: double standard, stores info and RNA: helps made proteins) structure is a sequence of nucleotide monomers that determine gene expression & heredity

Monomer: Nucleotide

• Each nucleotide contains:

  • A 5-carbon sugar: deoxyribose in DNA, ribose in RNA

  • A phosphate group

  • A nitrogenous base: DNA: ATCG, RNA: AUCG

• The bond is a phosphodiester bond: links phosphate group to sugar

Proteins: Structure = Function

• Proteins include enzymes, muscle fibers, antibodies

• They do so many jobs due to their amino acids order and fold

Monomer: Amino Acids

• Each amino acid consists of an amino group, carboxyl group, and R group side chain with hydrophobic (inside), hydrophilic (outside) that are charged (ionic)

Bond: Peptide Bond

• Dehydration reaction forms peptide bonds between amino acids

Protein structure levels:

• Primary: Sequence of amino acids

• Secondary: local folding

• Tertiary: overall 3D shape from R group interactions

• Quaternary: multiple polypeptides joining

Carbohydrates: From Quick Energy to Structure

Carbs aren’t just sugar, they do a lot depending on how the sugars are arranged. Bonds and branching matter

Monomer: Monosaccharides

• Simple sugars like glucose or fructose

• Types:

  • monosaccharides: single sugars

  • disaccharides: two sugars

  • polysaccharides: many sugars

Important Polysaccharides & their Functions

• Bond: Glycosidic Linkage

• Starch: energy storage in plants, digestible by humans

• Glucogen: energy storage in animals

• Cellulose: structure in plant cell walls (not digestible)

• Chitin: structure in fungi

The same monomer (glucose) can be different depending how its bonded and arranged

Lipids: Durable and Diversely Useful

Lipids aren't made of repeating monomers like other macromolecules, but they’re still super important, especially in energy storage and membranes.

Key types of lipids

• Triglycerides (fats and oils)

  • Glycerol + 3 (fatty acids)

  • Energy storage, insulation, cushioning

Saturated lIpids

• Saturated fatty acids: Fatty acids with no double bonds in the carbon chain, making them straight

  • Solid at room temp:

• Unsaturated fatty acids: Fatty acids with one or more double bonds that create kinks in the chain.

  • Liquid at room temp

• Phospholipids: 2 fatty acids + glycerol + phosphate group

  • Amphipathic: Describes a molecule with both hydrophilic and hydrophobic regions.

    • Head = hydrophillic

    • Tails = hydrophobic

• Steroids: 4-ring carbon structure (cholesterol); important for hormones & membrane fluidity

• Bond: Ester linkage

Structure = Function: The Big Theme

• The shape & chemical properties of a molecule dictate what it can do

• Key examples:

  • DNA Double Helix: Supports stable info storage & accurate replication

  • Protein folding: R group interactions shave active sites for enzymes

  • Phospholipid bilayers: let membranes be selective barriers

  • Glycogen’s branching: enables fast release of glucose for energy