Chapter 3-6 Lectures on Macromolecules, Cells, and Membrane Structure

Chapter 3 - Macromolecules

• Carbon

  • Carbon is the backbone of life.

  • It can form 4 covalent bonds.

  • Organic molecules contain carbon and hydrogen.

• Macromolecules

  • Definition: Large, complex organic molecules.

• Functional Groups:

  • Amino

  • Location: Amino acids (proteins).

  • Properties: Weakly basic, polar.

  • Connections: Forms peptide bonds.

  • Carboxyl

  • Location: Amino acids, fatty acids.

  • Properties: Acidic.

  • Connections: Forms peptide bonds.

  • Hydroxyl

  • Location: Steroids, alcohol, carbohydrates, amino acids.

  • Properties: Polar.

  • Connections: Forms hydrogen bonds with water.

  • Methyl

  • Location: DNA, proteins, carbohydrates.

  • Properties: Nonpolar.

  • Phosphate

  • Location: Nucleic acids, ATP, phospholipids.

  • Properties: Polar, weakly acidic.

  • Sulfhydryl

  • Location: Amino acid cysteine.

  • Properties: Polar.

  • Connections: Forms disulfide bridges.

• Isomers

  • Definition: Compounds with the same chemical formula but different structures.

• Monomers and Polymers

  • Monomer: A small molecule.

  • Polymer: A large molecule made of many repeating small molecules.

• Chemical Reactions

  • Dehydration Reaction: Forms bonds by removing a water molecule.

  • Hydrolysis Reaction: Breaks bonds by adding a water molecule.

  • These reactions are sped up via enzymes.

• Types of Macromolecules

  • The four macromolecules are carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrates

• Function: Energy storage and structure.

• Monosaccharides: The simplest carbohydrates.

  • Examples: Glucose, ribose, deoxyribose.

• Disaccharides: Formed from two monosaccharides joined by a glycosidic bond.

  • Examples: Sucrose, maltose, lactose.

• Polysaccharides: Long chains of monosaccharides.

  • Storage Polysaccharides:

  • Starch: Storage polysaccharide in plants (includes amylose and amylopectin).

  • Glycogen: Storage polysaccharide in animals, highly branched.

  • Structural Polysaccharide:

  • Cellulose: Found in plant cell walls; humans cannot digest cellulose.

Lipids

• Properties: Extremely nonpolar and insoluble in water.

• Lipids are not made up of monomers, thus are not polymers.

• Types of Lipids:

  • Fats: Store long-term energy.

  • Phospholipids: Make up cell membranes.

  • Steroids: Act as signaling molecules.

• Fatty Acids:

  • Saturated: No double bonds between carbon atoms, solid at room temperature.

  • Unsaturated: One or more double bonds, liquid at room temperature (double bonds create "kinks").

• Energy Storage:

  • Carbohydrates store about 2x more energy per gram than fats (false).

• Structure of Phospholipids:

  • Consists of 1 glycerol, 2 fatty acids, 1 phosphate group, and a nitrogenous chemical.

  • Phospholipids are amphipathic with hydrophilic heads and hydrophobic tails, forming plasma membranes.

Proteins

• Function: Diverse roles including gene expression/regulation, transport, defense, enzymatic activity, cell signaling, and structure.

• Amino Acids: Monomers of proteins.

  • The variable group in an amino acid is called the R-group.

• Peptide Bond Formation: A carboxyl group + amino group forms a peptide bond.

• Polypeptides: A linear chain of amino acids. Not all polypeptides are proteins; a protein can consist of 1 or more functional polypeptides.

• Protein Structures:

  • Primary Structure: Specific sequence of amino acids.

  • Secondary Structure: Formed by hydrogen bonds, creating ɑ-helices and β-pleated sheets.

  • Tertiary Structure: Overall 3-D shape formed by R-group interactions.

  • Quaternary Structure: Occurs when 2+ polypeptide chains combine to form 1 functional protein (example: hemoglobin).

• Denaturation: The process when a protein’s shape is undone; it loses functionality.

• Bonding Forces in Proteins:

  • Important forces are hydrogen bonds, ionic bonds, hydrophobic effects, and Van der Waals forces.

Nucleic Acids

• Components of Nucleotides:

  • Each nucleotide is made of a phosphate group, a five-carbon sugar, and a nitrogenous base.

  • Sugars:

  • DNA sugar: deoxyribose.

  • RNA sugar: ribose.

• Linking Nucleotides: Nucleotides are linked into a polymer by a sugar-phosphate backbone joined by phosphodiester bonds.

• Nitrogenous Bases:

  • Purines: Adenine (A) and Guanine (G).

  • Pyrimidines: Cytosine (C), Thymine (T), Uracil (U).

• Base Pairing in DNA:

  • A pairs with T (3 hydrogen bonds).

  • G pairs with C (2 hydrogen bonds).

  • Thymine is used in DNA, while uracil is present in RNA.

• Strands: DNA is typically found as a double helix, while RNA is single-stranded.

Chapter 4 - General Features of Cells

• Prokaryotic vs Eukaryotic Cells:

  • Prokaryotic cells lack a true nucleus; eukaryotic cells enclose their genetic material within a nucleus.

  • Nucleoid Region: The area in prokaryotes where DNA is concentrated.

  • Eukaryotes contain membrane-bound organelles, compartmentalizing different functions (e.g., chloroplasts, mitochondria, Golgi apparatus).

• Characteristics:

  • Eukaryotes are larger and do not possess a cell wall (differences from prokaryotes).

• Origin of Organic Molecules:

  • Nucleotides and amino acids were produced prior to the existence of cells.

  • Polymers of nucleotides and amino acids formed DNA, RNA, and proteins.

  • Organic polymers became enclosed in membranes, leading to the capability of cellular properties.

• Microscopy Basics:

  • Magnification: Ability to enlarge an image.

  • Resolution: Ability to distinguish two objects as separate and distinct.

  • Contrast: Degree to which structures differ from one another.

• Types of Microscopes:

  • Light Microscope: Uses visible light to illuminate specimens.

  • Electron Microscope: Uses beams of electrons for higher resolution.

• Proteome: Complete set of proteins expressed by a cell, determines cell structure and function.

• Cytoskeleton: Composed of three major types of filaments:

  • Microtubules: Thickest filaments composed of tubulin.

  • Intermediate Filaments: Provide tensile strength and maintain cell shape.

  • Actin Filaments (Microfilaments): Important for cell movement and muscle contraction.

• Nucleus: Surrounded by a double-membrane called the nuclear envelope; contains the nucleolus where ribosomal RNA is produced.

• DNA and Proteins: Form a complex called chromatin in the nucleus.

  • Nuclear Pores: Regulate movement of molecules into and out of the nucleus.

• Cytosol: Fluid portion of the cell, where organelles are suspended, and many metabolic reactions occur.

  • Cytoplasm: Includes everything inside the plasma membrane except the nucleus.

• Cellular Appendages:

  • Flagella: Long, whip-like structures that propel cells (e.g., sperm cells).

  • Cilia: Short, hair-like structures that move fluid/materials along cell surfaces.

• Membrane-Bound Organelles:

  • Lysosomes: Contain enzymes for digesting waste materials and worn-out cell parts.

  • Peroxisomes: Contain enzymes that remove hydrogen from toxic molecules, producing hydrogen peroxide.

  • Vacuoles: Large sacs for storage, often found in plant cells (typically one large central vacuole).

• Chloroplasts: Organelles where photosynthesis takes place, converting light energy into chemical energy (sugars).

• Mitochondria: Known as the "powerhouses" of the cell, generating ATP through cellular respiration.

• Endoplasmic Reticulum:

  • Rough ER: Covered with ribosomes, responsible for protein synthesis and processing.

  • Smooth ER: Lacks ribosomes; functions in lipid synthesis, carbohydrate metabolism, and detoxification.

• Plasma Membrane: A selective barrier regulating substance passage into and out of the cell, primarily made of a phospholipid bilayer with proteins embedded.

  • Role in communication with the environment and cell signaling.

• Endosymbiotic Theory: Proposes mitochondria and chloroplasts originated from ancient prokaryotic cells that formed symbiotic relationships.

  • Both organelles have their own DNA and ribosomes.

• Protein Synthesis and Processing:

  • Ribosomes on Rough ER synthesize proteins, which are sent to the Golgi apparatus for sorting and modification.

  • Proteins are packaged into vesicles that fuse with the plasma membrane to release contents.

• Difference Between Cell Types:

  • Bacteria are prokaryotic, lacking a nucleus and membrane-bound organelles.

  • Plant cells have a central vacuole, cell wall, and chloroplasts (absent in animal cells).

  • Animal cells have lysosomes and peroxisomes (absent in plant cells).

• Extracellular Matrix (ECM): A network of materials secreted from cells, formed of collagen, providing tissue strength and flexibility.

Chapter 5 - Membrane Structure, Synthesis, and Transport

• Fluid-Mosaic Model: Describes plasma membrane structure as a mosaic of components including phospholipids, proteins, and carbohydrates.

• Membrane Proteins:

  • Transmembrane Proteins: Span the entire bilayer, often forming channels or transporters.

  • Lipid-Anchored Proteins: Covalently attached to a lipid in the bilayer.

  • Peripheral Proteins: Loosely bound to the membrane surface through non-covalent interactions.

• Membrane Fluidity:

  • Affected by fatty acid tail length in phospholipids; shorter tails increase fluidity.

  • Presence of double bonds also increases fluidity.

  • Cholesterol: Stabilizes membrane fluidity at low temperatures (prevents rigidity) and at high temperatures (prevents excessive fluidity).

• Glycosylation: The covalent bonding of carbohydrates to proteins or lipids helps modify membrane functionality.

• Transport Mechanisms:

  • Simple Diffusion: Movement of substances from high to low concentration without help.

  • Facilitated Diffusion: Diffusion through membrane proteins.

  • Both are forms of passive transport (do not require energy).

  • Active Transport: Movement against the concentration gradient (low to high), requiring energy (ATP).

• Osmosis: The diffusion of water across a selectively permeable membrane.

  • Effects on cells in different solutions:

  • Isotonic: No net movement of water.

  • Hypertonic: Cell loses water and shrinks (crenation).

  • Hypotonic: Cell gains water and may burst (lysis); plant cells become turgid.

• Net Water Movement: Water moves from low solute concentration to high solute concentration.

  • If the extracellular environment is hypertonic, net flow of water is out of the cell; if hypotonic, it is into the cell.

• Transport Proteins:

  • Channel Proteins: Allow specific molecules/ions to pass through (many are gated).

  • Aquaporins: Specific channels for water.

  • Transporter Proteins: Bind to substances and change shape to move them across the membrane.

  • Pumps: Use energy to move substances against their gradient (example: Na+/K+-ATPase pump).

• Exocytosis and Endocytosis:

  • Exocytosis: Release materials outside by fusing vesicles with the plasma membrane.

  • Endocytosis: Plasma membrane folds inward to bring materials into the cell; includes:

  • Pinocytosis: Known as "cell drinking," taking in extracellular fluid and solutes.

  • Phagocytosis: Known as "cell eating," engulfing large particles or cells.

Chapter 6 - Energy, Enzymes, and Metabolism

• Matter: Anything that takes up space and has mass.

• Energy: Capacity to do work or promote change.

  • Kinetic Energy: Associated with movement.

  • Potential Energy: Stored due to structure/position.

  • Chemical Energy: Type of potential energy stored in chemical bonds.

• Thermodynamics: The study of energy transformation.

  • First Law: Energy cannot be created or destroyed.

  • Second Law: Energy transformations increase entropy (disorder).

• Free Energy (G): Amount of energy available to do work; also referred to as Gibbs free energy.

• Key Variables in Thermodynamics:

  • H = enthalpy or total energy.

  • G = free energy available for work.

  • S = entropy or unusable energy.

  • T = absolute temperature in Kelvin.

• Chemical Reactions:

  • Spontaneous reactions have negative riangle G (free energy change).

  • Exergonic Reactions: Release energy and are spontaneous.

  • Endergonic Reactions: Require energy input and are not spontaneous.

• ATP (Adenosine Triphosphate): The primary energy carrier in cells.

  • The third phosphate bond in ATP is a high-energy bond.

  • Hydrolysis of ATP is an exergonic reaction, releasing -7.3 ext{ kcal/mole} of energy.

• Ongoing Study Note: Further expansions and clarifications to be added.