Chapter 5: Biomolecules

Monomers and Polymers

Biological macromolecules are large molecules composed of smaller units called monomers. These monomers join together to form polymers through specific chemical bonds.

• Monomer: A small molecule that can join with others to form a polymer.

• Polymer: A large molecule made up of repeating monomer units.

• Examples:

  • Starch: Polymer of alpha-glucose monomers.

  • Proteins: Polymers of amino acids.

  • Nucleic acids: Polymers of nucleotides.

  • Lipids: Not true polymers, but often formed from fatty acids and glycerol.

Types of Sugars

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose). Most have 3-7 carbons (e.g., glucose has 6 carbons).

• Disaccharides: Two monosaccharides joined together (e.g., sucrose = glucose + fructose).

Bonds Between Monomers

• Glycosidic bond: Joins monosaccharides in carbohydrates.

• Peptide bond: Joins amino acids in proteins.

• Phosphodiester bond: Joins nucleotides in nucleic acids.

• Ester bond: Joins fatty acids to glycerol in lipids.

Polymer Synthesis and Breakdown

• Dehydration synthesis (condensation): Reaction that joins monomers by removing water.

• Hydrolysis: Reaction that breaks polymers into monomers by adding water.

• Note: These reactions are used for all major biological polymers.

Macromolecules and Their Monomers

• Carbohydrates: Monomer = monosaccharide (e.g., glucose).

• Proteins: Monomer = amino acid.

• Lipids: Not true polymers, but built from fatty acids and glycerol.

• Nucleic acids: Monomer = nucleotide.

Structures of Lipids

• Triglyceride: One glycerol + three fatty acids.

• Phospholipid: One glycerol + two fatty acids + phosphate group.

• Cholesterol: Four fused hydrocarbon rings (steroid structure).

Structures of Nucleic Acids

• Nucleoside: Nitrogenous base + sugar.

• Nucleotide: Nitrogenous base + sugar + phosphate group.

• Pyrimidines: Single-ring bases (cytosine, thymine, uracil).

• Purines: Double-ring bases (adenine, guanine).

• Base pairing in DNA: Adenine (A) pairs with Thymine (T); Guanine (G) pairs with Cytosine (C).

• Base pairing in RNA: Adenine (A) pairs with Uracil (U).

• DNA backbone: Sugar-phosphate.

• Sugar in DNA: Deoxyribose.

• Sugar in RNA: Ribose.

Saturated vs. Unsaturated Fatty Acids

• Saturated fatty acids: No double bonds; straight chains; solid at room temperature.

• Unsaturated fatty acids: One or more double bonds; kinked chains; liquid at room temperature.

Protein Structure

• Primary structure: Sequence of amino acids.

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

• Tertiary structure: 3D folding due to R-group interactions (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

• Quaternary structure: Multiple polypeptide chains assembled together.

• Importance of sequence: Determines protein shape and function.

• R-groups: Particularly important in tertiary structure.

• Methionine and cysteine: Both contain sulfur (unique among amino acids).

Chapter 6: Cell Structure and Function

Cell Types

• Prokaryotic cells: No nucleus, no membrane-bound organelles (e.g., bacteria).

• Eukaryotic cells: Have nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

Organelles and Their Functions

• Nucleus: Contains DNA; controls cell activities.

• Ribosomes: Protein synthesis.

• Endoplasmic reticulum (ER): Rough ER (protein synthesis), Smooth ER (lipid synthesis, detoxification).

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

• Lysosomes: Digestion of macromolecules.

• Peroxisomes: Breakdown of fatty acids and detoxification.

• Mitochondria: ATP production (cellular respiration).

• Chloroplasts: Photosynthesis (plants and algae).

• Vacuoles: Storage and structure (large in plant cells).

Endomembrane System

• Includes nuclear envelope, ER, Golgi apparatus, lysosomes, vesicles, and plasma membrane.

• Responsible for synthesis, modification, and transport of proteins and lipids.

Flow of Information

• DNA → RNA → Protein (central dogma).

• Proteins are synthesized in the cytoplasm or on the rough ER, then transported to their destinations.

Cytoskeleton

• Microtubules: Hollow tubes; cell shape, chromosome movement, organelle movement.

• Microfilaments (actin filaments): Thin rods; cell shape, muscle contraction, cell movement.

• Intermediate filaments: Structural support.

• Motor proteins: Move along cytoskeletal tracks (e.g., kinesin, dynein, myosin).

Cilia and Flagella

• Cilia: Short, numerous; move fluid over cell surface.

• Flagella: Long, few; propel cells (e.g., sperm).

• Both have a "9+2" arrangement of microtubules.

Cell Junctions

• Tight junctions: Seal cells together.

• Desmosomes: Anchor cells together.

• Gap junctions: Allow communication between cells.

Chapter 7: The Plasma Membrane

Structure and Composition

• Phospholipid bilayer: Hydrophilic heads face outward, hydrophobic tails inward.

• Proteins: Integral (span membrane) and peripheral (surface-associated).

• Cholesterol: Modulates membrane fluidity.

Membrane Transport

• Passive transport: No energy required (diffusion, osmosis, facilitated diffusion).

• Active transport: Requires energy (e.g., sodium-potassium pump).

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

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

• Tonicity: Relative concentration of solutes (hypotonic, hypertonic, isotonic).

• Example: Animal cell in hypotonic solution swells; plant cell becomes turgid.

Membrane Fluidity

• Fatty acid tails: Unsaturated tails increase fluidity; saturated tails decrease fluidity.

• Cholesterol: Reduces fluidity at high temperatures, prevents solidification at low temperatures.

Membrane Proteins

• Integral proteins: Span the membrane; involved in transport and signaling.

• Peripheral proteins: Attached to membrane surface; involved in signaling and cell recognition.

Selective Permeability

• Membrane allows some substances to pass more easily than others.

• Small, nonpolar molecules cross easily; large or polar molecules require transport proteins.

• Endocytosis: Cell takes in materials (phagocytosis, pinocytosis, receptor-mediated).

• Exocytosis: Cell expels materials.

Membrane Potential and Electrogenic Pumps

• Membrane potential: Voltage across the membrane due to ion distribution.

• Electrogenic pump: Generates membrane potential (e.g., sodium-potassium pump in animals, proton pump in plants).

Chapter 11: Cell Signaling

Overview of Cell Signaling

Cells communicate using chemical signals that are detected by receptors, leading to a cellular response.

• Local signaling: Paracrine (nearby cells), synaptic (neurons).

• Long-distance signaling: Hormonal (endocrine system).

Cell Surface Receptors

• G protein-coupled receptors (GPCRs): Activate G proteins to relay signals.

• Ligand-gated ion channels: Open or close in response to ligand binding, allowing ions to pass.

• Receptor tyrosine kinases: Activate signaling pathways via phosphorylation.

Intracellular Receptors

• Located inside the cell; bind small or hydrophobic molecules (e.g., steroid hormones).

• Steroid hormone-receptor complex can act as a transcription factor to initiate gene expression.

Signal Transduction Pathways

• Kinases: Enzymes that add phosphate groups (phosphorylation).

• Phosphatases: Enzymes that remove phosphate groups (dephosphorylation).

• Phosphorylation acts as a molecular switch to turn pathways on or off.

Second Messengers

• cAMP (cyclic AMP): Amplifies signal inside the cell.

• Ca2+ (calcium ions): Another common second messenger.

Summary Table: Types of Cell Signaling

Additional info:

• Phosphorylation cascades are common in signal transduction, allowing for amplification and regulation of cellular responses.

• Specificity of cell signaling ensures that only target cells respond to particular signals.