Test 1

Here is a study guide for Chapters 2 through 5, combining high-yield test concepts, detailed mechanisms, and core definitions to ensure full preparation for exams.

Chapter 2: The Chemistry of Life1. Major Chemical Elements & Atomic Structure

• Six Major Elements of Life: Oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus make up $98.5\%$ of body mass.

  
  

• Valence Electrons: Electrons in the outermost shell that determine chemical bonding properties and reactivity.

  
  

• Free Radicals & Antioxidants:

  
  
  

  • Free Radicals: Particles with an unpaired electron, making them highly reactive and destructive to cellular structures (cause oxidative stress).

    
    

  • Antioxidants: Neutralize free radicals (e.g., Superoxide Dismutase [SOD], Vitamin C, Vitamin E).

    
    

2. Chemical Bonds & Reactions

• Types of Bonds:

  
  
  

  • Ionic Bond: Attraction between oppositely charged ions (cation $+$ and anion $-$); easily dissociate in water.

    
    

  • Covalent Bond: Sharing of electron pairs; nonpolar covalent (equal sharing, hydrophobic) vs. polar covalent (unequal sharing, hydrophilic).

    
    

  • Hydrogen Bond: Weak attraction between a partially positive hydrogen atom and a partially negative oxygen or nitrogen atom; responsible for water's properties and protein 3D structure.

    
    

  • Van der Waals Forces: Very weak, brief attractions between neutral atoms due to random electron fluctuations.

    
    

• Electrolytes: Ionized salts in solution capable of conducting electricity; critical for muscle contraction, nerve signaling, and osmotic balance.

  
  

• Reaction Types:

  
  
  

  • Decomposition (Catabolism): $\text{AB} \rightarrow \text{A} + \text{B}$ (exergonic, releases energy).

    
    

  • Synthesis (Anabolism): $\text{A} + \text{B} \rightarrow \text{AB}$ (endergonic, requires energy).

    
    

  • Exchange: $\text{AB} + \text{CD} \rightarrow \text{AD} + \text{CB}$.

    
    

  • Oxidation-Reduction (Redox): Oxidation is electron loss (exergonic); Reduction is electron gain (endergonic).

    
    

3. Solutions, pH, & Biological Macromolecules

• Liquid Mixtures:

  
  
  

  • Solution: Solute $< 1\text{ nm}$; clear; does not separate on standing; passes through membranes.

    
    

  • Colloid: Particles $1\text{--}100\text{ nm}$; cloudy; does not separate; cannot pass through membranes (e.g., albumin in blood).

    
    

  • Suspension: Particles $> 100\text{ nm}$; opaque; settles out on standing (e.g., blood cells in plasma).

    
    

• pH Scale: Negative logarithm of hydrogen ion concentration ($-\log[\text{H}^+]$). Neutral = 7; Acidic $< 7$; Basic $> 7$. Buffers resist pH changes.

  
  

• Macromolecules:

  
  
  

  • Carbohydrates: Monosaccharides (glucose, fructose), Disaccharides (sucrose, lactose), Polysaccharides (glycogen = animal energy storage; starch = plant storage; cellulose = indigestible fiber).

    
    

  • Lipids: Hydrophobic molecules.

    
    
    

    • Triglycerides: Glycerol $+$ 3 fatty acids (energy storage, thermal insulation).

      
      

    • Phospholipids: Amphipathic (hydrophilic phosphate head $+$ 2 hydrophobic fatty acid tails); basic unit of cell membranes.

      
      

    • Steroids: 4-ring carbon backbone derived from cholesterol (precursor to steroid hormones like estrogen, testosterone, cortisol).

      
      

  • Proteins: Polymers of 20 amino acids joined by peptide bonds.

    
    
    

    • Structures: Primary (amino acid sequence), Secondary ($\alpha$-helix, $\beta$-sheet via hydrogen bonds), Tertiary (3D folding via disulfide bonds/hydrophobic interactions), Quaternary (association of multiple polypeptide chains).

      
      

    • Denaturation: Irreversible destruction of protein structure caused by heat or extreme pH.

      
      

  • Enzymes: Biological catalysts; lower activation energy to accelerate reactions. Bind specific substrates at an active site.

    
    

  • Nucleotides: Composed of a sugar, phosphate, and nitrogenous base. ATP (Adenosine Triphosphate) stores energy in high-energy phosphate bonds.

    
    

Chapter 3: Cellular Form and Function1. Plasma Membrane & Structure

• Fluid Mosaic Model: Consists of phospholipids ($75\%$), cholesterol ($20\%$, regulates membrane fluidity), and glycolipids/glycoproteins ($5\%$, form the glycocalyx for cell recognition).

  
  

• Membrane Proteins:

  
  
  

  • Transmembrane Proteins: Pass completely through the membrane (e.g., channels, pumps, receptors).

    
    

  • Peripheral Proteins: Adhere to one surface of the membrane.

    
    

• Cell Extensions:

  
  
  

  • Microvilli: Non-motile; expand cell surface area for absorption (e.g., intestinal epithelium).

    
    

  • Cilia: Motile projections with a $9+2$ microtubule array (axoneme); move mucus/materials across surfaces.

    
    

  • Flagella: Long, single projection used for cell motility (sperm).

    
    

2. Transport Mechanisms (High Exam Weight)

• Passive Transport (No ATP required):

  
  
  

  • Filtration: Hydrostatic pressure forces fluid and small solutes through structural gaps.

    
    

  • Simple Diffusion: Net movement of particles from high to low concentration.

    
    

  • Osmosis: Net movement of water through a selectively permeable membrane toward higher solute concentration via aquaporins.

    
    

• Tonicity:

  
  
  

  • Hypotonic Solution: Lower solute concentration than cytoplasm $\rightarrow$ water enters cell $\rightarrow$ cell swells and undergoes lysis.

    
    

  • Hypertonic Solution: Higher solute concentration than cytoplasm $\rightarrow$ water leaves cell $\rightarrow$ cell shrivels (crenation).

    
    

  • Isotonic Solution: Equal solute concentration $\rightarrow$ no net water movement.

    
    

• Carrier-Mediated Transport:

  
  
  

  • Facilitated Diffusion: Passive transport using a protein carrier down a concentration gradient.

    
    

  • Primary Active Transport: Carrier uses ATP directly to move solutes against their gradient (e.g., $\text{Na}^+\text{--K}^+$ Pump moves $3\text{ Na}^+$ OUT for every $2\text{ K}^+$ IN).

    
    

  • Secondary Active Transport: Carrier moves a solute against its gradient by pairing it with another solute moving down its gradient (e.g., SGLT glucose transporter).

    
    

  • Carrier Types: Uniport (1 solute), Symport (2 solutes, same direction), Antiport (2 solutes, opposite directions).

    
    

• Vesicular Transport (Uses ATP):

  
  
  

  • Endocytosis: Phagocytosis ("cell eating"), Pinocytosis ("cell drinking"), Receptor-Mediated Endocytosis (selective uptake using clathrin-coated pits).

    
    

  • Exocytosis: Secretion of intracellular contents out of the cell.

    
    

3. Organelles & Cytoskeleton

• Nucleus: Double-membrane nuclear envelope with nuclear pores; contains nucleoli where ribosomes are assembled.

  
  

• Endoplasmic Reticulum (ER):

  
  
  

  • Rough ER: Parallel cisternae covered in ribosomes; synthesizes membrane and secreted proteins.

    
    

  • Smooth ER: Tubular cisternae without ribosomes; synthesizes lipids, detoxifies drugs, and stores calcium ($\text{Ca}^{2+}$).

    
    

• Ribosomes: Protein synthesis engines; unattached in cytosol or bound to Rough ER.

  
  

• Golgi Complex: Receives newly synthesized proteins from Rough ER; modifies, packages, and routes them into vesicles.

  
  

• Lysosomes: Vesicles containing digestive enzymes for autophagy (recycling damaged organelles) and autolysis (programmed cell destruction).

  
  

• Peroxisomes: Oxidize fatty acids and toxic chemicals; produce hydrogen peroxide ($\text{H}_2\text{O}_2$) as a byproduct and neutralize it via catalase.

  
  

• Mitochondria: Double-membrane organelle with internal folds (cristae); main site of ATP production via aerobic respiration.

  
  

• Cytoskeleton: Microfilaments (actin), Intermediate Filaments (keratin), Microtubules (tubulin).

  
  

Chapter 4: Genes and Cellular Function1. Molecular Genetics: DNA & RNA Structure

• DNA Structure: Polymer of nucleotides (Deoxyribose sugar $+$ Phosphate group $+$ Nitrogenous base).

  
  
  

  • Base Pairing Rules: Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds; Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.

    
    

  • Chromatin: DNA wrapped around histone proteins; repeating units are called nucleosomes.

    
    

• RNA Structure: Single-stranded; Ribose sugar; Uracil (U) replaces Thymine (T).

  
  

2. Protein Synthesis (Transcription & Translation)

• Genetic Code: Codons are 3-base sequences on mRNA. Start Codon: AUG (Methionine). Stop Codons: UAG, UGA, UAA.

  
  

• Transcription (Nucleus): RNA Polymerase reads DNA template strand to build pre-mRNA.

  
  
  

  • Splicing: Introns (non-coding sequences) are removed; Exons (coding sequences) are spliced together.

    
    

  • Alternative Splicing: Allows a single gene to encode multiple distinct protein variants.

    
    

• Translation (Cytoplasm): Ribosome reads mRNA codons. Transfer RNA (tRNA) carries matching amino acids via its anticodon.

  
  

• Protein Folding & Processing: Chaperone proteins assist in folding. Rough ER modifies proteins $\rightarrow$ Transport vesicles $\rightarrow$ Golgi complex $\rightarrow$ Secretory vesicles/lysosomes.

  
  

3. DNA Replication & The Cell Cycle

• Semiconservative Replication: Each original DNA strand serves as a template for a new strand.

  
  
  

  • DNA Helicase: Unzips the double helix.

    
    

  • DNA Polymerase: Synthesizes new complementary DNA strands.

    
    

• Cell Cycle Phases:

  
  
  

  • Interphase:

    
    
    

    • $G_1$ (First Gap): Cell growth, protein synthesis, normal metabolic functions.

      
      

    • $S$ (Synthesis): Replication of genomic DNA.

      
      

    • $G_2$ (Second Gap): Final preparation for cell division, centriole replication.

      
      

    • $G_0$ Phase: Non-dividing resting state.

      
      

  • Mitosis (Nuclear Division):

    
    
    

    • Prophase: Chromosomes condense; nuclear envelope breaks down; mitotic spindle forms.

      
      

    • Metaphase: Chromosomes line up along the equatorial plate.

      
      

    • Anaphase: Sister chromatids separate and move to opposite poles.

      
      

    • Telophase: Chromatids uncoil; new nuclear envelopes reform.

      
      

  • Cytokinesis: Cytoplasmic division via an actin cleavage furrow.

    
    

4. Inheritance & Cancer Concepts

• Chromosomes: Somatic cells are diploid ($2n = 46$ chromosomes); Gametes are haploid ($n = 23$chromosomes).

  
  

• Inheritance Patterns:

  
  
  

  • Alleles: Dominant (masks recessive allele) vs. Recessive.

    
    

  • Codominance: Both alleles fully expressed (e.g., ABO blood group $I^A I^B$).

    
    

  • Incomplete Dominance: Intermediate phenotype expressed.

    
    

  • Polygenic Inheritance: Multiple genes dictate one trait (e.g., skin color, height).

    
    

  • Pleiotropy: Single gene affects multiple un-related traits (e.g., Sickle-cell anemia).

    
    

• Cancer Genetics:

  
  
  

  • Proto-oncogenes: Normal genes coding for cell growth signals; mutated form becomes an oncogene (causes uncontrolled growth).

    
    

  • Tumor-Suppressor Genes: Genes that inhibit cell division or repair DNA damage (e.g., $p53$); inactivation leads to cancer.

    
    

Chapter 5: The Human Tissues1. Primary Germ Layers & Classification

• Four Primary Tissue Classes: Epithelial, Connective, Nervous, Muscular.

  
  

• Embryonic Germ Layers:

  
  
  

  • Ectoderm: Gives rise to nervous system and epidermis.

    
    

  • Mesoderm: Forms mesenchyme $\rightarrow$ muscle, bone, blood, cartilage.

    
    

  • Endoderm: Gives rise to inner mucous membrane lining of digestive and respiratory tracts.

    
    

2. Epithelial Tissue (Avascular, High Cellularity)

• Simple Epithelia (Single layer):

  
  
  

  • Simple Squamous: Rapid diffusion/filtration (alveoli, glomeruli, endothelium).

    
    

  • Simple Cuboidal: Secretion and absorption (kidney tubules, liver).

    
    

  • Simple Columnar: Absorption; features goblet cells (mucus) and microvilli (GI tract).

    
    

  • Pseudostratified Columnar: Looks layered but all cells touch basement membrane; ciliated with goblet cells (respiratory tract).

    
    

• Stratified Epithelia (Multiple layers):

  
  
  

  • Keratinized Stratified Squamous: Dead surface layer containing keratin; resists abrasion and water loss (epidermis).

    
    

  • Nonkeratinized Stratified Squamous: Moist surface layer; resists abrasion (esophagus, vagina).

    
    

  • Stratified Cuboidal: Secretion (sweat gland ducts).

    
    

  • Urothelium (Transitional): Stretches to accommodate fluid volume (urinary bladder, ureters).

    
    

3. Connective Tissue (Cells + Extracellular Matrix)

• Fibrous CT Components:

  
  
  

  • Cells: Fibroblasts (produce matrix/fibers), Macrophages (phagocytosis), Leukocytes, Plasma cells (antibodies), Mast cells (histamine/heparin), Adipocytes.

    
    

  • Fibers: Collagenous (tough, flexible, white), Reticular (thin, branching framework), Elastic (stretch and recoil).

    
    

• Types of Connective Tissue:

  
  
  

  • Loose CT: Areolar (underlies almost all epithelia), Reticular (structural mesh of spleen and lymph nodes).

    
    

  • Dense CT: Dense Regular (parallel collagen fibers; tendons and ligaments), Dense Irregular(randomly arranged fibers; dermis and organ capsules).

    
    

  • Adipose Tissue: White fat (energy storage, thermal insulation, cushioning) vs. Brown fat (heat generation via uncoupled respiration in infants).

    
    

  • Cartilage: Avascular; matrix rich in chondroitin sulfate; cells called chondrocytes inside spaces called lacunae.

    
    
    

    • Hyaline Cartilage: Smooth, glossy; clear matrix (articular joints, trachea).

      
      

    • Elastic Cartilage: Rich in elastic fibers (external ear, epiglottis).

      
      

    • Fibrocartilage: Coarse collagen bundles; absorbs shock (intervertebral discs, pubic symphysis).

      
      

  • Bone (Osseous Tissue): Calcified matrix containing osteocytes in lacunae; organized into osteonsin compact bone.

    
    

  • Blood: Liquid matrix (plasma) with formed elements (erythrocytes, leukocytes, platelets).

    
    

4. Nervous & Muscular Tissues (Excitable Tissues)

• Nervous Tissue: Specialized for fast electrical signaling.

  
  
  

  • Neurons: Consist of a soma (cell body), dendrites (input signals), and axon (output signal).

    
    

  • Neuroglia: Supporting glial cells that protect and assist neurons.

    
    

• Muscular Tissue: Specialized for contraction and movement.

  
  
  

  • Skeletal Muscle: Long cylindrical fibers, striated, multinucleated, voluntary.

    
    

  • Cardiac Muscle: Short branched cells (cardiomyocytes), striated, single nucleus, involuntary, joined by intercalated discs (gap junctions $+$ desmosomes).

    
    

  • Smooth Muscle: Fusiform cells, non-striated, single nucleus, involuntary (walls of digestive tract, blood vessels).

    
    

5. Junctions, Glands, & Tissue Alterations

• Intercellular Junctions:

  
  
  

  • Tight Junctions: Continuous outer seal blocking substances from passing between cells (epithelia).

    
    

  • Desmosomes: Patch-like structural rivets that prevent cells from pulling apart under mechanical stress. Hemidesmosomes anchor cells to basement membrane.

    
    

  • Gap Junctions: Ring of transmembrane proteins (connexons) surrounding a central pore; allows direct passage of ions and small solutes between cells.

    
    

• Glands:

  
  
  

  • Exocrine (maintain a duct to a surface) vs. Endocrine (ductless; secrete hormones directly into bloodstream).

    
    

  • Secretion Types: Merocrine/Eccrine (exocytosis, e.g., sweat glands), Apocrine (fatty droplet buds off, e.g., mammary glands), Holocrine (entire cell disintegrates, e.g., sebaceous glands).

    
    

• Tissue Growth, Modification, & Death:

  
  
  

  • Hyperplasia: Tissue growth via cell multiplication.

    
    

  • Hypertrophy: Tissue growth via enlargement of existing cells.

    
    

  • Metaplasia: Transformation of one mature tissue type into another (e.g., pseudostratified respiratory epithelium changing to stratified squamous in smokers).

    
    

  • Regeneration (replaces damaged tissue with same functional cell type) vs. Fibrosis (replaces damaged tissue with scar tissue/collagen).

    
    

  • Necrosis (pathological cell death due to injury/toxins) vs. Apoptosis (programmed, orderly cell suicide).