Chapter 5: Biomolecules

Monomer vs Polymer

Biological macromolecules are formed by linking smaller units called monomers into larger structures known as polymers. This process is fundamental to the structure and function of cells.

• Monomer: A small molecule that can join with other similar molecules to form a polymer (e.g., glucose, amino acids, nucleotides).

• Polymer: A large molecule composed of repeating monomer units (e.g., starch, proteins, DNA).

Synthesis and Breakdown of Polymers

Polymers are synthesized and broken down by specific chemical reactions.

• Dehydration: Removal of water to form a covalent bond between monomers.

• Hydrolysis: Addition of water to break a covalent bond in a polymer.

• Example Equation:

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

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

• Linkage: Glycosidic bonds connect sugar monomers.

• Composition and Ratio: General formula:

• 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: Short chains of monosaccharides.

  • Polysaccharide: Long chains (e.g., starch, glycogen, cellulose).

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

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

• Starch vs Cellulose: Both are polymers of glucose but differ in glycosidic linkage and function.

Lipids

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

• Fats (Triglycerides):

  • Structure: Glycerol + 3 fatty acids.

  • Function: Energy storage, insulation.

  • Linkage: Ester bonds.

  • Saturated vs Unsaturated Fatty Acids:

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

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

• Phospholipids:

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

  • Function: Major component of cell membranes.

  • Behavior in Bilayer: Amphipathic nature forms bilayers in water.

• Steroids:

  • Structure: Four fused carbon rings.

  • Function: Hormones (e.g., cholesterol, steroid hormones).

Proteins

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

• Structure and Function: Primary, secondary, tertiary, and quaternary structures.

• Linkage: Peptide bonds between amino acids.

• Monomer vs Polymer: Amino acids (monomers) form polypeptides (polymers).

• Structure of the Amino Acid: Central carbon, amino group, carboxyl group, R group.

• 20 Amino Acids:

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

  • Name, 3-letter abbreviation, 1-letter abbreviation.

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

Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information. They are polymers of nucleotides.

• Structure and Function: DNA (double-stranded), RNA (single-stranded).

• Linkage: Phosphodiester bonds between nucleotides.

• 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 double-stranded; RNA is usually single-stranded.

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

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

• Denaturation: Loss of structure due to heat or chemicals.

Chapter 6: Cell Structure

Eukaryotic vs Prokaryotic Cells

Cells are classified as eukaryotic or prokaryotic based on the presence or absence of a nucleus and membrane-bound organelles.

• Eukaryotic: Nucleus, organelles, larger size (e.g., plants, animals, fungi).

• Prokaryotic: No nucleus, no organelles, smaller size (e.g., bacteria, archaea).

The Nucleus

The nucleus is the control center of eukaryotic cells, containing genetic material.

• Nuclear Envelope: Double membrane with pores.

Ribosomes

Ribosomes are the site of protein synthesis.

• Structure: Composed of rRNA and proteins.

• Location: Free in cytoplasm or bound to endoplasmic reticulum.

The Endomembrane System

This system includes organelles involved in synthesis, transport, and processing of biomolecules.

• Components: Nuclear envelope, endoplasmic reticulum (rough and smooth), Golgi apparatus, lysosomes, vacuoles.

Mitochondria, Chloroplasts, Peroxisomes

These organelles are involved in energy conversion and metabolism.

• Mitochondria: Site of cellular respiration.

• Chloroplasts: Site of photosynthesis (plants).

• Peroxisomes: Breakdown of fatty acids and detoxification.

The Cytoskeleton

The cytoskeleton provides structural support and facilitates movement within cells.

• Components: Microtubules, microfilaments, intermediate filaments.

• Microtubules: Hollow tubes, involved in cell shape, movement, and division.

• Microfilaments: Actin filaments, involved in muscle contraction and cell movement.

• Intermediate Filaments: Provide mechanical support.

Extracellular Components

Structures outside the cell membrane provide support and facilitate communication.

• Cell Wall: Found in plants, provides rigidity.

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

• Cell Junctions: Connections between cells (e.g., plasmodesmata in plants).

Chapter 7: Membranes and Transport

Passive vs Active vs Bulk Transport

Cells transport substances across membranes using passive, active, and bulk transport mechanisms.

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

• Active Transport: Requires energy (ATP), moves substances against concentration gradient.

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

Plasma Membrane Structure

The plasma membrane is a selectively permeable barrier composed of a phospholipid bilayer with embedded proteins.

• Phospholipid Amphipathic Structure: Hydrophilic heads, hydrophobic tails.

• Fluid Mosaic Model: Membrane is flexible, proteins and lipids move laterally.

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

Selective Permeability

The membrane allows selective passage of substances.

• Solute vs Solvent: Solute is dissolved, solvent does the dissolving.

• Components that cross easily: Small, nonpolar molecules.

Membrane Proteins

Proteins in the membrane serve various functions.

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

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

Cell Recognition

Cells recognize each other via membrane proteins and carbohydrates.

Transport Mechanisms

• Diffusion: Movement from high to low concentration.

• Osmosis: Diffusion of water across a membrane.

• Facilitated Diffusion: Passive transport via proteins.

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

Active Transport

• Needs Energy: ATP is required.

• Examples: Sodium-potassium pump, proton pump.

• Cotransport: Coupled transport of two substances (e.g., sodium/glucose transporter).

Bulk Transport

• Exocytosis: Export of materials via vesicles.

• Endocytosis: Import of materials (phagocytosis, pinocytosis, receptor-mediated endocytosis).

Chapter 8: Metabolism and Enzymes

Metabolic Pathways

Metabolism consists of all chemical reactions in a cell, organized into pathways.

• Catabolic: Breaks down molecules, releases energy.

• Anabolic: Builds molecules, requires energy.

Forms of Energy

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy.

• Open vs Closed System: Open exchanges energy/matter; closed does not.

Laws of Thermodynamics

• First Law: Energy cannot be created or destroyed.

• Second Law: Entropy (disorder) increases in spontaneous processes.

Exergonic vs Endergonic Reactions

• Exergonic: Releases energy, spontaneous ().

• Endergonic: Requires energy, non-spontaneous ().

ATP Powers Cellular Work

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

• ATP Regeneration:

Enzymes

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Energy of Activation: Minimum energy required for a reaction ().

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

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

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

• Regulation:

  • Allosteric Regulation: Activation or inhibition by molecules binding at sites other than the active site.

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

• Compartmentalization: Enzymes are localized within specific cell compartments.

Example: The sodium-potassium pump is an example of active transport, using ATP to move Na+ out of and K+ into the cell against their concentration gradients.

Additional info: Some details, such as the classification of amino acids and the specifics of enzyme regulation, were expanded for completeness and clarity.