Chapter 5: Biological Macromolecules

Monomer vs Polymer

Biological macromolecules are large molecules composed of smaller subunits called monomers. When monomers join together, they form polymers through specific chemical reactions.

• Monomer: A small molecule that can join with others to form a polymer (e.g., glucose, amino acid).

• Polymer: A large molecule made up of repeating monomer units (e.g., starch, protein).

Synthesis and Breakdown of Polymers

• Dehydration: Chemical reaction that joins monomers by removing a water molecule.

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

• Example Equation:

Carbohydrates

Carbohydrates are organic molecules consisting of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. They serve as energy sources and structural components.

• Structure and Function: Monosaccharides (simple sugars), disaccharides, oligosaccharides, and polysaccharides.

• Linkage: Glycosidic bonds connect monosaccharide units.

• Monosaccharide vs Disaccharide vs Oligosaccharide vs Polysaccharide:

  • Monosaccharide: Single sugar unit (e.g., glucose, fructose).

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

  • Oligosaccharide: 3-10 monosaccharide units.

  • Polysaccharide: Many monosaccharide units (e.g., starch, glycogen, cellulose).

• Storage Polysaccharides: Starch (plants), glycogen (animals).

• Structural Polysaccharides: Cellulose (plants), chitin (arthropods, fungi).

Lipids

Lipids are hydrophobic molecules, including fats, phospholipids, and steroids, important for energy storage, membrane structure, and signaling.

• Fats (Triglycerides):

  • Structure: Glycerol + 3 fatty acids.

  • Function: Long-term energy storage, insulation.

  • Linkage: Ester bonds.

  • Saturated vs Unsaturated Fatty Acids: Saturated have no double bonds (solid at room temp); unsaturated have one or more double bonds (liquid at room temp).

• Phospholipids:

  • Structure: Glycerol, 2 fatty acids, phosphate group.

  • Function: Main component of cell membranes; form bilayers.

  • Behavior in Bilayer: Hydrophilic heads face water, hydrophobic tails face inward.

• Steroids:

  • Structure: Four fused carbon rings.

  • Examples: Cholesterol, steroid hormones (e.g., estrogen, testosterone).

Proteins

Proteins are polymers of amino acids that perform a wide range of functions, including catalysis, structure, transport, and signaling.

• Structure and Function: Determined by amino acid sequence and folding.

• Linkage: Peptide bonds between amino acids.

• Monomer vs Polymer: Amino acid (monomer), polypeptide/protein (polymer).

• Structure of Amino Acid: Central carbon, amino group, carboxyl group, hydrogen, R group (side chain).

• 20 Amino Acids:

  • Categories: Non-polar, polar, acidic, basic, aromatic.

  • Naming: 3-letter and 1-letter abbreviations.

  • Classification: Know which amino acids fall into each category.

Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information.

• Structure and Function: Polymers of nucleotides.

• Linkage: Phosphodiester bonds.

• DNA vs RNA:

  • Nucleotide vs Nucleoside: Nucleotide = base + sugar + phosphate; nucleoside = base + sugar.

  • Bases: Purines (A, G) vs Pyrimidines (C, T, U).

  • Sugars: Deoxyribose (DNA) vs Ribose (RNA).

  • Double vs Single Stranded: DNA is usually double-stranded; RNA is usually single-stranded.

  • Complementary Base Pairing: A-T (or A-U in RNA), G-C.

• Gene Expression: DNA → RNA → Protein (Central Dogma).

Chapter 6: Cell Structure

Eukaryotic vs Prokaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on internal structure.

• Eukaryotic: Nucleus, membrane-bound organelles (e.g., plants, animals, fungi, protists).

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

The Nucleus

• Structure: Nuclear envelope, nucleolus, chromatin.

• Function: Stores genetic material, site of RNA synthesis.

Ribosomes

• Structure: Composed of rRNA and proteins.

• Function: Protein synthesis.

The Endomembrane System

• Nuclear Envelope: Double membrane surrounding nucleus.

• Endoplasmic Reticulum (ER): Rough (with ribosomes, protein synthesis) and smooth (lipid synthesis, detoxification).

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

• Lysosomes: Digestive organelles containing hydrolytic enzymes.

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

Mitochondria, Chloroplasts, Peroxisomes

• Mitochondria: Site of cellular respiration, ATP production.

• Chloroplasts: Site of photosynthesis (plants, algae).

• Peroxisomes: Break down fatty acids, detoxify harmful substances.

The Cytoskeleton

The cytoskeleton provides structural support, cell shape, and movement.

• Components: Microtubules, microfilaments (actin), intermediate filaments.

• Microtubules: Hollow tubes, form centrosomes, centrioles, cilia, flagella.

• Microfilaments: Thin filaments, interact with myosin for muscle contraction.

• Intermediate Filaments: Provide mechanical strength.

Extracellular Components

• Cell Wall: Found in plants, provides structure and protection.

• Extracellular Matrix (ECM): Network of proteins and carbohydrates outside animal cells.

• Cell Junctions: Plasmodesmata (plants), tight junctions, desmosomes, gap junctions (animals).

Chapter 7: Membranes and Transport

Passive vs Active vs Bulk Transport

• Passive Transport: Movement of substances down concentration gradient (no energy required).

• Active Transport: Movement against gradient, requires energy (ATP).

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

Plasma Membrane Structure

• Phospholipid Amphipathic Structure: Hydrophilic heads, hydrophobic tails.

• Fluid Mosaic Model: Membrane is a fluid structure with proteins embedded in or attached to a bilayer of phospholipids.

• Fluidity of Membranes: Affected by temperature, fatty acid composition, cholesterol.

Selective Permeability

• Solute vs Solvent: Solute is dissolved substance; solvent is the dissolving medium.

• Permeability: Some substances cross easily (small, nonpolar), others do not (large, charged).

Membrane Proteins

• Peripheral vs Integral Proteins: Peripheral are on membrane surface; integral span the membrane.

• Types: Transport, transmembrane (carrier, channel), receptor, enzymatic.

Transport Processes

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

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

• Facilitated Diffusion: Passive transport via proteins.

• Tonicity: Effect of solution on cell volume (hypotonic, hypertonic, isotonic).

Active Transport Mechanisms

• Requires Energy: ATP or other energy sources.

• Examples: Sodium-potassium pump, proton pump.

• Cotransport: Coupled transport of two substances (e.g., sucrose-proton cotransport).

Bulk Transport

• Exocytosis: Vesicles fuse with membrane to release contents outside cell.

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

Chapter 8: Metabolism and Enzymes

Metabolic Pathways

• Catabolic Pathways: Break down molecules, release energy.

• Anabolic Pathways: Build complex molecules, consume energy.

Forms of Energy

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy.

• Chemical Energy: Potential energy in chemical bonds.

Laws of Thermodynamics

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

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

ATP and Cellular Work

• ATP: Adenosine triphosphate, main energy currency of the cell.

• Energy Coupling: Use of exergonic processes to drive endergonic ones.

• ATP Regeneration:

Enzymes

• Function: Biological catalysts that speed up chemical reactions by lowering activation energy.

• Activation Energy: Minimum energy required to start a reaction.

• Substrate Specificity: Enzymes bind specific substrates at the active site (induced fit model).

• Enzyme Kinetics: Rate of reaction affected by substrate concentration, temperature, pH.

• Cofactors: Non-protein helpers (metal ions, vitamins).

• Regulation:

  • Allosteric Regulation: Enzyme activity regulated by binding of molecules at sites other than the active site (activation or inhibition).

  • Feedback Inhibition: End product inhibits an earlier step in the pathway.

• Compartmentalization: Enzymes localized in specific cell regions for efficiency.