Topic 3

Biology 107, Fall 2025 Topic 3: Macromolecules Lecture Notes

Introduction to Macromolecules

  • Definition: Macromolecules are large, complex molecules essential for life.

  • Four classes of macromolecules:

    • Carbohydrates

    • Lipids

    • Nucleic acids

    • Proteins

  • Polymers are molecules consisting of many similar or identical building blocks linked together by covalent bonds.

Learning Objectives

  • At the end of this lecture topic, students should be able to:

    • List the four major classes of macromolecules.

    • Explain how monomers are used to build polymers.

    • Compare dehydration and hydrolysis reactions.

    • Identify the chemical structure of a carbohydrate (sugar or polysaccharide) and distinguish it from non-carbohydrates.

    • Distinguish between monosaccharides, disaccharides, and polysaccharides.

    • Identify a glycosidic bond and describe its formation.

    • Describe the structure and function of starches, glycogen, and cellulose.

    • Explain the distinction of lipids from other macromolecule classes.

    • Describe the properties, building blocks, and biological importance of fats, phospholipids, and steroids.

    • Identify the chemical structures of fats, phospholipids, and steroids and distinguish them from non-lipids.

    • Identify an ester linkage and name the reaction that forms it.

    • Explain phospholipid bilayer formation in water.

    • Distinguish between saturated and unsaturated fatty acids and list properties resulting from structural differences.

    • Distinguish between cis and trans unsaturated fatty acids and properties arising from structural differences.

    • Describe how chemical diversity is created in sterols.

    • Name and identify the components of a nucleotide, and outline differences between ribonucleotides and deoxyribonucleotides.

    • Identify a phosphodiester bond and describe its formation between nucleotides.

    • Explain the directional nature of nucleic acids and label the ends of a DNA molecule.

    • Describe structural features of a DNA double helix and base-pairing contributions to its formation.

    • Compare the structural features of DNA double helix and RNA strand.

    • Provide biological functions of proteins in the cell.

    • Identify a protein and distinguish it from other macromolecule classes.

    • Identify components making up an amino acid structure.

    • Identify a peptide bond and describe its formation.

    • Explain directional nature of proteins and label their ends.

    • Distinguish polypeptide from protein.

    • Describe the four hierarchical levels of protein structure and bonds important at each level.

    • Explain how changes in primary structure can affect protein function.

    • Describe differences between conservative and non-conservative changes.

    • Define denaturation and explain its effect on protein function.

    • Distinguish between denaturation and degradation of a protein.

Background Reading

  • Primary source for this material is the textbook: "Biology: Exploring the Diversity of Life."

  • Relevant sections:

    • Carbohydrates: 5th Ed. F-25 to F-29; 4th Ed. F-24 to F-27

    • Lipids: 5th Ed. F-39 to F-42; 4th Ed. F-39 to F-42

    • Nucleic Acids: 5th Ed. F-37 to F-39; 4th Ed. F-36 to F-38

    • Proteins: 5th Ed. F-29 to F-36; 4th Ed. F-28 to F-35

Topic 3.1: Introduction to Macromolecules

  • Macromolecules are categorized into four classes in the cell:

    • Carbohydrates

    • Lipids

    • Nucleic acids

    • Proteins

  • Polymers are formed from monomers linked together by covalent bonds.

  • Monomers are smaller molecules that serve as building blocks in a polymer formation.

Synthesis and Degradation of Polymers

  • Polymer synthesis:

    • Completed through dehydration reactions.

    • Definition: Covalent bonds form between monomers, removing a water molecule, requiring energy and enzymes.

  • Polymer degradation:

    • Occurs via hydrolysis reactions.

    • Definition: Covalent bonds are broken between two monomers by the addition of a water molecule, requiring energy and enzymes.

Topic 3.2: Carbohydrates

  • Definition: Sugars and sugar polymers.

  • Functions of carbohydrates include:

    • Serving as a primary energy source.

    • Providing carbon for the synthesis of other molecules.

    • Acting as structural components of cells.

  • Monomer: Monosaccharide

    • Description: A simple sugar comprising one carbonyl group and multiple hydroxyl groups (one per carbon).

    • Stability: Monosaccharides may form rings in solution.

Variations in Monosaccharides

  • Variations arise from:

    • Length of the carbon skeleton.

    • Position of the carbonyl group:

    • Aldose: Carbonyl at the end carbon (aldehyde).

    • Ketose: Carbonyl at a middle carbon (ketone).

    • Spatial arrangement of functional groups (Example: glucose and galactose are enantiomers).

Polysaccharides

  • Definition: More than two monosaccharides joined by glycosidic linkages.

  • Functions:

    1. Storage Polysaccharides:

    • Starch:

      • Found in plants.

      • Polymer of glucose monomers connected by extα−1,4−glycosidicbondsext{α-1,4-glycosidic bonds}.

      • Structure: Helical.

      • Example: Amylose, an unbranched glucose polymer.

    • Glycogen:

      • Found in animal liver and muscle cells and bacteria.

      • Known for branched structure with extα−1,4−glycosidicbondsext{α-1,4-glycosidic bonds}.

    1. Structural Polysaccharides:

    • Cellulose:

      • Found in plant cell walls.

      • Polymer of glucose with extβ−1,4−glycosidiclinkagesext{β-1,4-glycosidic linkages}, which leads to a linear structure.

      • Forms strong bundles in cell walls.

Application Questions

  • Enzymes in the digestive system assist in breaking down starches by facilitating the hydrolysis reaction, ultimately producing glucose.

  • Blood sugar levels are affected by differing rates of digestion: simple sugars increase blood sugar rapidly while starches provide a slower and more sustained increase after being broken down into sugars.

  • Humans cannot digest cellulose due to lack of enzymes for breaking extβ−1,4−glycosidicbonds,ext{β-1,4-glycosidic bonds}, emphasizing dietary fiber's importance for digestion.

Topic 3.3: Lipids

  • Types of lipids present in cells:

    1. Fats

    2. Phospholipids

    3. Sterols

  • Hydrophobic Characteristics:

    • At least partially hydrophobic due to high number of non-polar covalent bonds.

    • Low solubility in water.

  • Despite being categorized as macromolecules, lipids are not polymers.

Fats

  • Functions of fats: Energy storage, insulation, and cushioning in organisms.

  • Structure: Consists of glycerol linked to three fatty acids, forming triacylglycerol (fat).

    • Ester linkages connect glycerol and fatty acids, formed via dehydration reactions.

  • Components of fats:

    • Glycerol:

    • 3-carbon backbone with hydroxy groups.

    • Fatty acids:

    • Hydrocarbon chains with a carboxyl group on one end.

Phospholipids

  • Main component of biological membranes.

  • Amphipathic nature allows for spontaneous assembly into bilayers, forming boundaries within cells.

    • Structure: Similar to fat, but the third carbon of glycerol is attached to a phosphate group.

Sterols

  • Functions include acting as components of cell membranes and signaling molecules.

  • Characterized by a carbon skeleton consisting of four fused rings (example: cholesterol).

    • Cholesterol:

    • Integral component of cell membranes and precursor for other sterols.

    • Synthesized in the liver and also sourced from animal fats, excessive amounts can contribute to arteriosclerosis.

Topic 3.4: Structural Variation in Lipids

  • Variation in fatty acids results from:

    • Length of hydrocarbon chains.

    • Number, location, and type of double bonds.

  • Saturated fatty acids:

    • No double bonds; straight molecules; solid at room temperature due to compact packing (examples: red meat, butter).

  • Unsaturated fatty acids:

    • One or more double bonds; cause bends in the structure preventing straightforward packing; liquid at room temperature (examples: oils from fish and plants).

Cis and Trans Fatty Acids

  • Cis: Hydrogens on the same side of double bond.

  • Trans: Hydrogens on opposite sides, contributing to a straighter structure.

  • Hydrogenated oils: Created to convert unsaturated fats to saturated fats, often leading to health issues due to trans fats.

Topic 3.5: Building a Nucleic Acid

  • Types of nucleic acids:

    • DNA (deoxyribonucleic acid)

    • RNA (ribonucleic acid)

  • Functions:

    • DNA:

    • Contains genetic information and instructions for cellular activities, RNA synthesis.

    • RNA:

    • Carrier of information within cells and crucial for protein synthesis.

  • Monomer: Nucleotide

    • Comprised of a nitrogenous base, a pentose sugar, and a phosphate group.

Polymer Structure of Nucleic Acids

  • Nucleic acids are linear chains of nucleotides connected by phosphodiester bonds (formed between the 3'-OH of one nucleotide and the 5'-phosphate of another).

  • The directionality is critical, leading to 5'-ends and 3'-ends.

Topic 3.6: DNA and RNA Structure

  • DNA Structure:

    • Composed of two intertwined strands that form a double helix.

    • Fixed width due to specific base pairing.

    • Backbones consist of the sugar-phosphate structure, held together by phosphodiester bonds.

    • Nitrogenous bases project into the interior of the helix.

    • Base pairs consist of:

    • A-T pairs (Adenine and Thymine) with 2 hydrogen bonds.

    • G-C pairs (Guanine and Cytosine) with 3 hydrogen bonds (stronger).

  • RNA Structure:

    • Typically a single strand which may form complex shapes via internal base pairing.

Application Questions

  • Upon heating, DNA denaturation occurs; hydrogen bonds break, leading to separating strands while phosphodiester bonds remain intact.

Topic 3.7: Building a Polypeptide

  • Types of Polypeptides in Cells: Hemoglobin, collagen, insulin, etc.

  • Functions include:

    • Enzymatic activity

    • Transport mechanisms

    • Hormonal signaling

    • Receptor interaction

    • Structural support

    • Motor functions

  • Monomer: Amino acid

    • Comprised of an amino group, a carboxyl group, a central alpha carbon, and an R group that varies in structure among different amino acids.

Polymerization of Amino Acids

  • Amino acids form polypeptides through peptide bonds which occur between the carboxyl group of one amino acid and the amino group of another, a process catalyzed by dehydration reactions.

Directionality of Polypeptides

  • Polypeptides are directional due to the presence of an amino terminus (N-terminus) and a carboxyl terminus (C-terminus).

Topic 3.8: Protein Folding

  • Definition: A protein is a polypeptide (or multiple polypeptides) folded into a functional three-dimensional shape.

  • *Four Levels of Protein Structure:

    1. Primary Structure:

    • Unique sequence of amino acids.

    • Bond type: peptide bonds.

    • Determined by genetic information.

    1. Secondary Structure:

    • Formed by repetitive patterns like alpha helices and beta sheets through hydrogen bonds.

    1. Tertiary Structure:

    • The overall 3D shape of the polypeptide, dependent on interactions between side chains, including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

    1. Quaternary Structure:

    • Multiple polypeptides assembled together, stabilized by similar bonds as tertiary structure, allowing for functional complexes.

Topic 3.9: Protein Function

  • Functional Types of Proteins:

    • Enzymes

    • Transport proteins

    • Hormones

    • Receptors

    • Motor proteins

    • Structural proteins

    • Defensive proteins (e.g., antibodies)

  • Direct Correlation of Shape to Function: The shape of a protein is essential and can change by varying amino acid sequences, which ultimately dictate the protein's functionality.

  • Alterations in the primary structure can lead to changes in protein function, distinguishing between "conservative" changes that have minimal functional impact and
    "non-conservative" changes that dramatically affect protein characteristics and efficiencies, exemplified in diseases like sickle-cell anemia.