Cell Structure & Function: Study Notes

• These are study notes on cell structure, microscopy, biochemistry, thermodynamics, and protein structure and function.

Functional Anatomy of Cellular Organelles

• The nucleus stores DNA and controls gene expression
• Mitochondria perform cellular respiration for ATP production
• Ribosomes synthesize proteins, either free-floating or attached to the rough ER
• The rough ER synthesizes and processes proteins due to ribosomes
• The smooth ER synthesizes lipids and detoxifies substances, lacking ribosomes
• The Golgi apparatus modifies, sorts, and packages proteins
• Lysosomes contain digestive enzymes to break down waste and cellular debris
• Peroxisomes break down fatty acids and neutralize toxins
• The cytoskeleton provides structure and facilitates movement by way of microtubules, actin filaments, and intermediate filaments

Different Types of Microscopy

• Light microscopy uses light and is fit for live cells, but has limited resolution
• Electron microscopy (EM) uses electron beams for higher resolution
• Scanning EM (SEM) provides 3D surface images
• Transmission EM (TEM) provides detailed internal structures
• Fluorescence microscopy utilizes fluorescent dyes to highlight structures in cells

Cell Theory & Endosymbiosis

• The cell theory states that all living things consist of cells, cells are the basic unit of life, and all cells arise from preexisting cells
• Endosymbiosis is the theory that mitochondria and chloroplasts originated from ancient bacteria engulfed by a larger cell, forming a symbiotic relationship
• Mitochondria and chloroplasts have their own DNA
• They reproduce independently within cells
• Their ribosomes are similar to bacterial ribosomes

Importance of Model Organisms

• Model organisms like E. coli, yeast, fruit flies, and mice share similar genes to humans
• Model organisms are easy to grow and study in a lab
• Model organisms help reveal important evolutionary relationships

Chemical Bonding in Biological Molecules

• Covalent bonds are strong bonds where atoms share electrons (e.g., C-H, O-H)
• Ionic bonds form between charged atoms (e.g., NaCl)
• Hydrogen bonds are weak attractions between hydrogen and electronegative atoms, important in water and DNA
• Van der Waals forces are weak interactions between nonpolar molecules

Importance of Noncovalent Interactions in Macromolecules

• Noncovalent interactions help proteins fold into 3D shapes
• Noncovalent interactions stabilize the DNA double helix through hydrogen bonds
• Noncovalent interactions allow enzymes to bind to substrates with specificity

Monomers That Form Macromolecules

• Carbohydrates consist of monosaccharides (glucose) and are used for energy and structure
• Proteins consist of amino acids and form enzymes and structural proteins
• Lipids consist of fatty acids and glycerol, form cell membranes, and store energy
• Nucleic acids consist of nucleotides (A, T, G, C, U) and store genetic information

Importance of Water

• Water's polarity makes it a great solvent
• Hydrogen bonding helps maintain biological structures
• Cohesion and adhesion are important for capillary action in plants
• Heat capacity helps regulate temperature in organisms

Basic Thermodynamic Principles

• The 1st Law of Thermodynamics states energy can only be transformed
• The 2nd Law of Thermodynamics states entropy (disorder) in the universe always increases
• AG (Gibbs Free Energy) determines if a reaction may occur spontaneously
• Negative AG is spontaneous
• Positive AG is non-spontaneous

Oxidation vs. Reduction

• Oxidation is the loss of electrons
• Reduction is the gain of electrons
• During cellular respiration, glucose is oxidized to CO2, and oxygen is reduced to water

Activation Energy & Enzymes

• Activation energy is the energy needed to start a reaction
• Enzymes lower activation energy and speed up reactions without being consumed

Coupled Reactions

• An exergonic reaction (releases energy) can drive an endergonic reaction (requires energy)
• ATP hydrolysis (exergonic) powers muscle contraction (endergonic)

High-Energy Bonds & Activated Carriers

• ATP stores energy in its phosphate bonds
• NADH & NADPH act as electron carriers in metabolic reactions
• NADH is used in cellular respiration; NADPH in photosynthesis

Michaelis-Menten & Lineweaver-Burk Plots

• These plots describe enzyme kinetics
• The Michaelis-Menten curve shows how reaction rate depends on substrate concentration
• The Lineweaver-Burk plot is a double-reciprocal plot used to determine enzyme efficiency

Condensation vs. Hydrolysis

• Condensation joins two molecules, releasing water (e.g., peptide bond formation)
• Hydrolysis breaks a bond with water (e.g., digestion of starch into glucose)

Protein Structures

• Primary (1°) structure is the sequence of amino acids
• Secondary (2°) structure consists of a-helices and B-sheets, held by hydrogen bonds
• Tertiary (3°) structure is a 3D shape due to side chain interactions
• Quaternary (4°) structure is when multiple polypeptide chains interact (e.g., hemoglobin)

Importance of Chaperone Proteins

• Chaperone proteins help proteins fold correctly
• Chaperone proteins prevent misfolding that can cause diseases like prions (mad cow disease)

α-Helix vs. β-Pleated Sheet Proteins

• An a-helix is a coiled structure, for example, keratin in hair
• A B-pleated sheet is a folded structure, for example, silk, collagen, and elastin in connective tissue
• Parallel vs. antiparallel B-sheets determine folding stability

Membrane Protein Folding

• Some proteins fold into structures that fit within the hydrophobic membrane like ion channels

Enzyme Action & Regulation

• Cofactors & coenzymes help enzymes function
• The active site is where the substrate binds
• Allosteric regulation occurs when molecules bind at a site other than the active site to change enzyme activity
• Feedback inhibition is when the end product of a pathway inhibits an earlier enzyme to prevent overproduction

Comprehensive study notes covering cell structure, microscopy types, basic biochemistry, thermodynamics, and protein structure and function. Key topics include the anatomy of cellular organelles and their functions, microscopy techniques, and energy principles governing biological systems.