Chapter 5: Large Biological Molecules

Monomers and Polymers

• Monomer: A small molecule that can join with other similar molecules to form a polymer. Example: Glucose is a monomer of starch.

• Polymer: A large molecule made up of repeating monomer units. Example: Cellulose is a polymer of glucose.

• Dehydration Reaction: A chemical reaction that joins two monomers by removing a water molecule.

• Hydrolysis: A reaction that breaks a polymer into monomers by adding water.

Carbohydrates

• Carbohydrates: Organic molecules composed of carbon, hydrogen, and oxygen (typically in a 1:2:1 ratio).

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose = glucose + fructose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

• Glycosidic Linkage: Covalent bond joining carbohydrate monomers.

• Starch: Storage polysaccharide in plants; Glycogen: storage polysaccharide in animals.

• Functions: Energy storage (starch, glycogen), structural support (cellulose in plants, chitin in fungi/arthropods).

Lipids

• Lipids: Hydrophobic molecules including fats, phospholipids, and steroids.

• Fats (Triglycerides): Composed of glycerol and three fatty acids joined by ester linkages.

• Phospholipids: Glycerol, two fatty acids, and a phosphate group; major component of cell membranes.

• Steroids: Lipids with four fused carbon rings (e.g., cholesterol).

• Saturated Fats: No double bonds in fatty acid tails; solid at room temperature.

• Unsaturated Fats: One or more double bonds; liquid at room temperature.

• Hydrogenated Fats: Unsaturated fats chemically converted to saturated fats; may produce trans fats.

• Ester Linkage: Bond between glycerol and fatty acid in fats.

Proteins

• Proteins: Polymers of amino acids; perform structural, enzymatic, transport, and regulatory functions.

• Amino Acids: Building blocks of proteins; contain amino group, carboxyl group, hydrogen, and R group.

• Peptide Bond: Covalent bond between amino acids formed by dehydration reaction.

• Functional Groups in Peptide Bonds: Amino group (-NH2) and carboxyl group (-COOH).

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helices and beta sheets (hydrogen bonding).

  • Tertiary: 3D folding due to side chain interactions.

  • Quaternary: Multiple polypeptide chains assembled together.

Nucleic Acids

• Nucleic Acids: DNA and RNA; store and transmit genetic information.

• Nucleotides: Monomers of nucleic acids; consist of a sugar, phosphate group, and nitrogenous base.

• Polynucleotides: Long chains of nucleotides.

• Phosphodiester Linkage: Covalent bond joining nucleotides in nucleic acids.

• DNA: Double-stranded, deoxyribose sugar, bases A, T, C, G.

• RNA: Single-stranded, ribose sugar, bases A, U, C, G.

• Monomers of Biological Polymers:

  • Carbohydrates: Monosaccharides

  • Proteins: Amino acids

  • Nucleic acids: Nucleotides

  • Lipids: Fatty acids and glycerol (not true polymers)

Chapter 6: Cells

Basic Features of All Cells

• All cells have:

  1. Plasma membrane

  2. Cytosol (semifluid substance)

  3. Chromosomes (carry genes)

  4. Ribosomes (make proteins)

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic Cells: No nucleus, DNA in nucleoid, lack membrane-bound organelles, generally smaller.

• Eukaryotic Cells: DNA in nucleus, membrane-bound organelles, generally larger.

• Commonalities: Both have plasma membrane, cytosol, DNA, and ribosomes.

Animal vs. Plant Cells

• Plant Cells: Have cell wall, chloroplasts, central vacuole.

• Animal Cells: Have lysosomes, centrioles, extracellular matrix; lack cell wall and chloroplasts.

Cell Size

• Cells are small to maximize surface area-to-volume ratio, facilitating efficient exchange of materials.

Organelles and Their Functions

• Nucleus: Contains DNA, nucleolus (makes ribosomes), nuclear envelope with pores for transport.

• Ribosomes: Synthesize proteins; free in cytosol or bound to rough ER.

• Endomembrane System: Includes nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, plasma membrane.

• Rough ER: Protein synthesis and modification.

• Smooth ER: Lipid synthesis, detoxification.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Contain hydrolytic enzymes for digestion.

• Vacuoles: Storage (central in plants), contractile (protists), food vacuoles (phagocytosis).

• Plasma Membrane: Selective barrier; regulates entry/exit of substances.

• Mitochondria: Site of cellular respiration; produce ATP.

• Chloroplasts: Site of photosynthesis in plants/algae.

• Unique Features of Mitochondria and Chloroplasts: Double membranes, own DNA and ribosomes, replicate independently (supporting endosymbiont theory).

• Endosymbiont Theory: Mitochondria and chloroplasts originated as free-living prokaryotes engulfed by ancestral eukaryotic cells.

• Phagocytosis: Process by which a cell engulfs large particles or cells.

Cytoskeleton

• Network of protein fibers for support, movement, and transport.

• Three main types:

  • Microtubules: Largest; hollow tubes; cell shape, chromosome movement, cilia/flagella.

  • Intermediate Filaments: Medium size; structural support.

  • Microfilaments (Actin Filaments): Smallest; cell shape, muscle contraction, cell division.

Cell Walls and Extracellular Matrix (ECM)

• Cell Walls: Found in plants, fungi, some protists; provide structure and protection.

• ECM: Found in animal cells; network of proteins and carbohydrates outside the cell membrane; supports and anchors cells.

Intercellular Junctions

• Plasmodesmata: Channels between plant cells for transport and communication.

• Tight Junctions: Seal cells together in animal tissues; prevent leakage.

• Gap Junctions: Channels for communication between animal cells.

Chapter 7: Cell Membranes

Structure and Function

• Selective Permeability: Membrane allows some substances to cross more easily than others.

• Phospholipid Bilayer: Double layer of phospholipids; hydrophilic heads face outward, hydrophobic tails inward.

• Fluid Mosaic Model: Membrane is flexible (fluid) and composed of various proteins and lipids (mosaic).

• Membrane Proteins: Integral (span membrane) and peripheral (surface); six main functions: transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to cytoskeleton/ECM.

• Cell Recognition: Glycoproteins and glycolipids serve as cell markers.

Transport Across Membranes

• Diffusion: Movement of molecules from high to low concentration.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Tonicity: Relative concentration of solutes:

  • Hypotonic: Lower solute concentration outside; cell gains water.

  • Isotonic: Equal solute concentration; no net water movement.

  • Hypertonic: Higher solute concentration outside; cell loses water.

• Hydrophilic vs. Hydrophobic: Hydrophilic (water-loving) molecules do not pass easily; hydrophobic (water-fearing) molecules pass more easily.

• Passive Transport: No energy required; includes diffusion, osmosis, facilitated diffusion (via channel/carrier proteins).

• Active Transport: Requires energy (ATP); moves substances against concentration gradient (e.g., sodium-potassium pump).

• Facilitated Diffusion: Passive transport aided by proteins.

• Channel Proteins: Provide corridors for specific molecules/ions.

• Carrier Proteins: Change shape to move molecules across membrane.

• Sodium-Potassium Pump: Active transport protein; moves 3 Na+ out, 2 K+ in per ATP hydrolyzed.

• Membrane Potential: Voltage difference across membrane due to ion distribution.

• Bulk Transport: Movement of large molecules via vesicles (endocytosis, exocytosis).

Chapter 8: Metabolism

Metabolic Pathways

• Metabolism: All chemical reactions in an organism.

• Catabolic Pathways: Break down molecules, release energy (e.g., cellular respiration).

• Anabolic Pathways: Build molecules, consume energy (e.g., protein synthesis).

Energy and Thermodynamics

• Energy: Capacity to do work; exists as kinetic or potential energy.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed.

• Second Law of Thermodynamics: Every energy transfer increases entropy (disorder) of the universe.

• Exergonic Reaction: Releases energy; spontaneous.

• Endergonic Reaction: Requires energy input; non-spontaneous.

ATP and the ATP Cycle

• ATP (Adenosine Triphosphate): Main energy currency of the cell.

• ATP Synthesis: Produced by cellular respiration and photosynthesis.

• ATP Cycle: ATP hydrolyzed to ADP + Pi, releasing energy; ADP phosphorylated to regenerate ATP.

• Phosphorylation: Transfer of phosphate group to another molecule, often activating it.

Enzymes

• Enzymes: Biological catalysts that speed up reactions by lowering activation energy (EA).

• Activation Energy Barrier (EA): Energy required to start a reaction.

• How Enzymes Lower EA:

  1. Orienting substrates correctly

  2. Straining substrate bonds

  3. Providing a favorable microenvironment

  4. Covalently bonding to the substrate

• Factors Affecting Enzyme Activity: Temperature, pH, cofactors (inorganic/organic helpers), inhibitors (competitive/noncompetitive), regulation mechanisms (e.g., feedback inhibition).

• Feedback Inhibition: End product of a pathway inhibits an earlier enzyme, preventing overproduction.

Chapter 9: Cellular Respiration

Redox Reactions

• Redox Reaction: Transfer of electrons between molecules; oxidation = loss of electrons, reduction = gain of electrons.

Cellular Respiration Overview

• Definition: Process by which cells extract energy from glucose to produce ATP.

• Equation:

• Who Performs Cellular Respiration? Both plants and animals (all eukaryotes).

Steps of Cellular Respiration (up to Citric Acid Cycle)

• 1. Glycolysis: Occurs in cytosol; glucose split into two pyruvate; produces ATP and NADH.

• 2. Pyruvate Oxidation: Pyruvate transported into mitochondria; converted to acetyl-CoA; produces NADH and CO2.

• 3. Citric Acid Cycle (Krebs Cycle): Occurs in mitochondrial matrix; acetyl-CoA oxidized; produces ATP, NADH, FADH2, CO2.

• 4. Oxidative Phosphorylation: (Not required in detail for this exam) Electron transport chain and chemiosmosis; produces most ATP.

Table: Comparison of Fats and Phospholipids

Lab Topics to Review

• Lab #5: Microscopes and Cell Structure

• Lab #6: Membranes and Molecular Movement – Diffusion & Osmosis

• Lab #7: Membranes II - Graphing & Citations

• Lab #8: Enzyme Activity

Additional Info

• Review previous exam material as the exam is cumulative.

• Practice explaining concepts in your own words and answering application questions.