Free Unit Notes

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I. Structure of Water and Hydrogen Bonding (Topic 1.1)
  A. Water polarity
    1. A covalent bond forms when atoms share electrons. In water, oxygen attracts shared electrons more strongly than hydrogen does.
    2. Oxygen has a partial negative charge, and the hydrogens have partial positive charges. Water’s bent shape makes the molecule polar, with an uneven distribution of charge.
    3. A hydrogen bond forms between the partially positive hydrogen of one water molecule and the partially negative oxygen of another.
    4. Hydrogen bonds between water molecules are weaker than the covalent bonds within each molecule.

  B. Cohesion, adhesion, and surface tension
    1. Cohesion occurs when water molecules attract one another through hydrogen bonding. It helps maintain continuous columns of water in plant xylem.
    2. Adhesion occurs when water attracts other polar or charged substances. It helps water cling to plant cell walls.
    3. Surface tension is resistance to breaking water’s surface. Cohesion produces this effect, allowing small organisms to rest on the surface.

  C. Temperature regulation
    1. Water has a high specific heat capacity, so it absorbs or releases considerable heat with relatively little temperature change. This helps stabilize body and environmental temperatures.
    2. Water has a high heat of vaporization, so considerable energy is needed for evaporation. Sweating and transpiration remove heat as water evaporates.

  D. Solvent properties and ice
    1. Water dissolves many ionic and polar substances by surrounding their ions or molecules. This supports transport and chemical reactions in cells.
    2. Hydrophilic substances interact favorably with water because they are polar or charged.
    3. Hydrophobic substances are nonpolar and interact poorly with water. They tend to cluster together in water.
    4. Hydrogen bonds hold water molecules farther apart in ice than in liquid water. Ice is less dense, so it floats and can insulate the water beneath it.

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II. Elements of Life (Topic 1.2)
  A. Elements in biological molecules
    1. Organisms obtain atoms and molecules from their environment to build biological molecules.
    2. Carbon, hydrogen, and oxygen occur in carbohydrates, lipids, proteins, and nucleic acids.
    3. Nitrogen occurs in amino acids and the nitrogenous bases of nucleic acids.
    4. Phosphorus occurs in nucleic acids, ATP, and phospholipids.
    5. Sulfur occurs in certain amino acids and can help stabilize protein structure.

  B. Carbon and functional groups
    1. Carbon can form four covalent bonds, allowing chains, branches, and rings. These structures form the backbones of organic molecules.
    2. Functional groups are groups of atoms that influence a molecule’s chemical properties.
      a. Hydroxyl and carboxyl groups contribute to polarity.
      b. Amino groups contain nitrogen.
      c. Phosphate groups usually carry negative charges under cellular conditions.
    3. A molecule’s properties depend on how its atoms and functional groups are arranged.

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III. Introduction to Macromolecules (Topic 1.3)
  A. Building blocks
    1. A monomer is a small molecular subunit. A polymer contains many covalently linked monomers.
    2. Polysaccharides contain sugar monomers, proteins contain amino acids, and nucleic acids contain nucleotides.
    3. Lipids are a major class of biological molecules, but they generally are not polymers of repeating monomers.

  B. Building and breaking molecules
    1. Dehydration synthesis joins smaller molecules through a covalent bond while releasing water.
      a. An H from one subunit and an OH from another form the released water molecule.
    2. Hydrolysis uses water to break a covalent bond, separating a larger molecule into smaller components.
      a. The components of water become attached to the separated parts.
    3. Enzymes control these reactions in cells. The reaction names alone do not indicate whether the overall reaction requires or releases energy.

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IV. Carbohydrates (Topic 1.4)
  A. Structure and functions
    1. Carbohydrates contain carbon, hydrogen, and oxygen. They provide energy, store energy, and support structures.
    2. A monosaccharide is a single sugar unit, such as glucose.
    3. A disaccharide contains two linked sugars. A polysaccharide contains many sugar units in a linear or branched chain.
    4. Glycosidic bonds are covalent bonds that connect sugar units.

  B. Important polysaccharides
    1. Starch stores glucose in plants.
    2. Glycogen is a highly branched glucose-storage polymer in animals, especially in liver and muscle cells.
    3. Cellulose forms strong fibers in plant cell walls.
    4. Chitin provides support in arthropod exoskeletons and fungal cell walls.

  C. Structure determines function
    1. Sugar identity, bond arrangement, and branching affect a carbohydrate’s shape and function.
    2. Starch and cellulose both contain glucose, but their different linkages produce different structures.
    3. Human digestive enzymes break starch’s linkages but cannot break cellulose’s linkages.

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V. Lipids (Topic 1.5)
  A. General properties and fats
    1. Lipids contain large nonpolar regions, making them mostly hydrophobic. Their functions include energy storage, insulation, membrane formation, and signaling.
    2. A triglyceride contains glycerol joined to three fatty acids by covalent ester linkages.
    3. Fats store chemical energy for long-term use. Stored fat also helps insulate mammals.

  B. Saturated and unsaturated fatty acids
    1. Saturated fatty acids have no carbon–carbon double bonds in their hydrocarbon chains. Their relatively straight chains pack tightly.
    2. Unsaturated fatty acids have one or more carbon–carbon double bonds. Cis double bonds create bends that reduce tight packing.
    3. At the same temperature, lipids with more cis-unsaturated chains generally remain more fluid than similar lipids with saturated chains.

  C. Phospholipids
    1. A phospholipid has a hydrophilic phosphate-containing head and hydrophobic fatty-acid tails.
    2. Phospholipids are amphipathic, meaning they have both hydrophilic and hydrophobic regions.
    3. In water, phospholipids form bilayers with their heads facing water and their tails facing inward. This arrangement forms the basic barrier of cell membranes.
    4. More cis-unsaturated tails generally increase membrane fluidity because their bends prevent tight packing.

  D. Steroids and cholesterol
    1. Steroids have four fused carbon rings. Some act as hormones that regulate growth, metabolism, reproduction, and other functions.
    2. Cholesterol helps stabilize animal cell membranes and is used to make steroid hormones.

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VI. Nucleic Acids (Topic 1.6)
  A. Nucleotides and information
    1. DNA stores hereditary information. RNA helps express and regulate that information.
    2. Their monomers are nucleotides, each containing a five-carbon sugar, a phosphate group, and a nitrogenous base.
    3. Covalent phosphodiester bonds link nucleotides into a sugar–phosphate backbone.
    4. The sequence of bases carries biological information.

  B. DNA and RNA differences
    1. DNA contains deoxyribose and the bases adenine (A), thymine (T), cytosine (C), and guanine (G). It is typically double-stranded.
    2. RNA contains ribose and the bases A, uracil (U), C, and G. It is typically single-stranded.

  C. Direction and complementary pairing
    1. A strand has a 5′ end and a 3′ end, named for carbon positions in its sugar. The 3′ end has a free hydroxyl group.
    2. New nucleotides attach to the 3′ end, so a strand grows in the 5′ to 3′ direction.
    3. DNA forms an antiparallel double helix: its two strands run in opposite directions.
    4. Complementary base pairing occurs through hydrogen bonds between specific bases.
      a. In DNA, A pairs with T, and C pairs with G.
      b. In complementary RNA pairing, A pairs with U, and C pairs with G.
    5. Hydrogen bonds connect complementary bases between DNA strands; covalent bonds hold each strand’s backbone together.
    6. A DNA sequence of 5′–ATGC–3′ pairs with 3′–TACG–5′. Written in the 5′ to 3′ direction, its complement is 5′–GCAT–3′.

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VII. Proteins (Topic 1.7)
  A. Amino acids and polypeptides
    1. Proteins function in catalysis, transport, signaling, movement, defense, and structural support.
    2. An amino acid has a central carbon attached to an amino group, a carboxyl group, a hydrogen, and a variable R group.
    3. A peptide bond connects the carboxyl group of one amino acid to the amino group of another. A chain of amino acids is a polypeptide.
    4. Each polypeptide has an amino end and a carboxyl end, giving the chain a direction.

  B. R-group properties
    1. R groups may be nonpolar, polar, or charged. Their properties affect protein folding and interactions.
    2. In water, nonpolar R groups often cluster inside a protein, away from water. Polar and charged R groups often interact with water or other groups.
    3. Hydrogen bonds, ionic attractions, hydrophobic interactions, and covalent disulfide bridges can stabilize protein shape.

  C. Levels of protein structure
    1. Primary structure is the amino-acid sequence, held together by peptide bonds. The sequence influences how the protein folds.
    2. Secondary structure consists of local folds, including alpha-helices and beta-pleated sheets. Hydrogen bonds between backbone groups stabilize these shapes.
    3. Tertiary structure is the overall three-dimensional shape of one polypeptide, stabilized largely by interactions involving R groups.
    4. Quaternary structure is the arrangement of multiple polypeptide subunits in a functional protein. Proteins with only one polypeptide lack this level.

  D. Changes in structure and function
    1. A protein’s shape determines how it interacts with other molecules. Changes in folding can alter binding and function.
    2. An amino-acid substitution may change folding if it changes an important R-group interaction. Its effect depends on the replacement’s properties and position.
      a. Replacing a charged R group with a nonpolar one may remove an ionic attraction and change a binding site.
    3. Denaturation is the loss of a protein’s normal three-dimensional structure, often reducing its function. Temperature, pH, or salt changes can disrupt stabilizing interactions.
    4. Denaturation generally leaves the primary sequence intact because peptide bonds remain unbroken. Some proteins can refold when suitable conditions return.

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