University Biology: Exhaustive Study Guide

Defining Life and Biological Organization

• Definition of Life: Life is a self-sustaining chemical system capable of Darwinian evolution.
• Properties of Life: Essential properties include organization, reproduction, response to stimuli, homeostasis, evolution, metabolism, growth, and reproduction.
• Structure and Function: A primary principle in biology where the structure of an entity is directly correlated to its specific biological function.
• Unity and Diversity: While life is divided into many domains, all organisms share the same universal genetic code (unity), which is explained by evolution.

The Chemical Basis of Life

• Elements: A pure substance consisting of one type of atom.
  • Four elements make up 96% of living matter: Carbon ($C$), Hydrogen ($H$), Nitrogen ($N$), and Oxygen ($O$).
  • There are approximately 20 other essential elements required for life.
• Basic Atomic Structure:
  • Protons: Mass of $1\,Da$ (dalton), positive charge, located in the nucleus. The number of protons defines the atomic number.
  • Neutrons: Mass of $1\,Da$, neutral charge, located in the nucleus. Mass Number = Protons + Neutrons.
  • Electrons: Very little mass, negative charge, located in orbitals. Elements differ by their valence (outer shell) electrons.
• Isotopes: Atoms of a single element with different numbers of neutrons (different mass numbers).
  • Example: Carbon-12 ($6p, 6n$) and Carbon-14 ($6p, 8n$).
  • Radioactive Isotopes: Unstable isotopes that undergo decay, releasing particles and energy. Applications include:
  • Carbon dating ($^{14}C$).
  • Cancer therapy ($^{60}Co$, $^{131}I$).
  • Tracers for labeling macromolecules in PET scans.
• Electron Arrangement:
  • Electrons exist in orbitals grouped into electron shells.
  • The first shell holds $2e^-$, the second holds $8e^-$.
  • Inert Atoms: Occur when the valence shell is full (non-reactive).
  • Reactive Atoms: Occur when the valence shell is not full.

Molecules, Compounds, and Chemical Bonds

• Molecules: Atoms held together in a stable association.
• Compound: A substance consisting of two or more elements combined in a fixed ratio.
• Electronegativity: The affinity an atom has for electrons. In human biology, Oxygen ($O$) has an EN of $3.5$, Nitrogen ($N$) is $3.0$, Carbon ($C$) is $2.5$, and Hydrogen ($H$) is $2.1$.
• Chemical Bonds:
  • Covalent Bonds: Formed when two nonmetal atoms share unpaired electrons (e.g., $H_2$).
  • Nonpolar Covalent: Electrons are shared equally (e.g., $H_2$, $O_2$, $CH_4$). Occurs with similar EN values.
  • Polar Covalent: Electrons are not shared equally, creating partial charges (e.g., $H_2O$, $NH_3$).
  • Ionic Bonds: The attraction between oppositely charged ions (metals and nonmetals). They result from the transfer of electrons.
  • Cation: Gains positive charge by losing an electron.
  • Anion: Gains negative charge by gaining an electron.
  • Examples: $NaCl$, $MgO$.
  • Weak Chemical Bonds: Help reinforce molecule shape and adhesion.
  • Electrostatic Forces: Attraction between opposite charges (e.g., $NH_3^+\dots^-OOC$).
  • Hydrogen Bonds: Non-covalent attraction between Hydrogen and highly electronegative elements like Oxygen or Nitrogen. These bonds are responsible for the boiling point of water ($100^\circ\text{C}$).
  • Van der Waals Forces: Fluctuations in electron clouds that oppositely polarize neighboring atoms.
  • Hydrophobic Forces: Interactions that exclude water molecules.

Water and Its Properties

• Composition: The human body is approximately 55% water; the highest concentration is in the lungs for gas exchange.
• The Solvent of Life: Water is an efficient solvent because its polar nature allows it to form a sphere of hydration around polar molecules and ions.
  • Hydrophilic: Substances that readily react/dissolve in water.
  • Hydrophobic: Uncharged, nonpolar substances that do not dissolve (e.g., octane $C_8H_{18}$, vegetable oil).
• Adhesion and Cohesion:
  • Adhesion: Water binding to solid surfaces (causes the meniscus).
  • Cohesion: Water binding to itself (causes high surface tension).
• Density: Maximum density of $H_2O$ is at $4^\circ\text{C}$. Unlike most substances, water expands as it freezes due to the formation of a crystal lattice held by hydrogen bonds, making ice less dense than liquid water.
• Heat Capacity:
  • Specific Heat: The energy needed to raise the temperature of $1\,g$ of a substance by $1^\circ\text{C}$. Water has the highest specific Equation for stability in oceans.
  • Heat of Vaporization: The energy required to change $1\,g$ of substance from liquid to gas. Used for cooling in mammals (sweating).
• Dissociation of Water: Water can dissociate at chemical equilibrium: $2H_2O \rightleftharpoons H_3O^+ + OH^-$.

Acids, Bases, and Buffers

• Acids: Give up $H^+$ in reactions, raising $H_3O^+$ concentration (e.g., $HCl \rightarrow H^+ + Cl^-$).
• Bases: Acquire $H^+$ in reactions, lowering $H_3O^+$ concentration (e.g., $NH_3 + H^+ \rightarrow NH_4^+$).
• pH Scale: Expresses $H^+$ concentration: $\text{pH} = -\log_{10}[H^+]$.
  • Range: 0–14. Neutral is 7 ($10^{-7}\,mol/L$). Acidic is $< 7$, Basic is $> 7$.
  • A 1-unit change in pH represents a 10x change in $H^+$ concentration.
  • Biological enzymes work at specific pH levels (Stomach = 3 pH; Intestine = 8.5 pH). Changes in pH can denature proteins.
• Buffers: Compounds minimizing pH changes, containing weak acids and conjugate bases.
  • Blood Buffer System: $CO_2 + H_2O \rightleftharpoons H_2CO_3 \rightleftharpoons H^+ + HCO_3^-$.
  • Bicarbonate Ion ($HCO_3^-$): Conjugate base.
  • Carbonic Acid ($H_2CO_3$): Weak acid.

Organic Molecules and Functional Groups

• Carbon Versatility: Carbon has 4 valence electrons, allowing it to form various shapes (chains, rings).
• Functional Groups:
  • Amino ($-NH_2$): Attracts protons, acts as a base.
  • Carboxyl ($-COOH$): Drops protons, acts as an acid.
  • Carbonyl ($C=O$): Links molecules. Aldehydes are at the end of a molecule ($R-COH$); Ketones are in the middle ($R-CO-R$).
  • Hydroxyl ($-OH$): Found in alcohols, highly polar, makes compounds soluble.
  • Phosphate ($PO_4$): Hydrophilic (e.g., ATP, phospholipids).
  • Sulfhydryl ($-SH$): Forms disulfide bonds.
• Isomers: Molecules with the same formula but different structures (e.g., glucose and fructose $C_6H_{12}O_6$ differ in carbonyl location).

Protein Structure and Function

• Building Blocks: Made of 20 amino acids. In water, these ionize to $NH_3^+$ and $COO^-$.
• Amino Acids: Differ only by their R-group (Side chain).
  • Three types: Charged (acidic/basic), Uncharged polar, and Uncharged nonpolar.
• Polypeptide Formation: Amino acids polymerize through condensation (monomer in, water out) forming a peptide bond ($C-N$ bond).
• Structure Levels:
  • Primary: Sequence of amino acids.
  • Secondary: Hydrogen bonds between carbonyl and amino groups (Alpha-helices and Beta-pleated sheets).
  • Tertiary: Folds caused by R-group interactions (H-bonds, hydrophobic interactions, disulfide bonds, ionic bonds, Van der Waals).
  • Quaternary: Multiple polypeptides interacting (e.g., Hemoglobin is a tetramer).
• Function and Folding: Specific shapes are required for function. Unfolded proteins are "denatured."
  • Sickle-Cell: Valine substituted for the 6th amino acid causes misfolding, lowering oxygen capacity.
  • Alzheimer’s: Linked to amyloid plaques from protein misfolding.
• Enzymes: Catalytic proteins that speed up reactions by bringing substrates together at the active site ("lock and key" model).
• SARS-CoV-2 and Vaccines:
  • Coronavirus spike proteins bind to ACE2 receptors in lungs.
  • Novavax Vaccine: Inserts SARS-CoV-2 spike gene into moth cells, harvests spike proteins, adds saponin (plant immune booster), and injects them to trigger antibodies.

Carbohydrates

• Molecular Formula: $(CH_2O)_n$. Includes monosaccharides, oligosaccharides, and polysaccharides.
• Monosaccharides: Distinguished by carbon number (Triose = 3, Pentose = 5, Hexose = 6), carbonyl location (Aldose vs. Ketose), and spatial arrangement.
  • Glucose: Used in cellular respiration to harness ATP. Forms Alpha and Beta ring isomers in solution.
  • Fructose: Energy for sperm motility; linked to fatty liver and diabetes when used in HFCS.
• Polysaccharides:
  • Starch: Energy storage in plants ($\alpha$-glucose, amylose/amylopectin).
  • Glycogen: Energy storage in animals ($\alpha$-glucose, highly branched). Stored in liver and muscle.
  • Cellulose: Structural material in plant cell walls ($\beta$-glucose, linear).
  • Peptidoglycan: Bacterial cell walls ($\beta$-1,4-linkages with amino acid cross-links).
  • Chitin: Fungi cell walls and insect exoskeletons (monomer: N-acetylglucosamine/NAG).
• Cell Identity: Glycoproteins and glycolipids on surfaces serve as Pathogen-associated molecular patterns (PAMPs) for immune recognition.

Nucleic Acids

• Types: DNA (Deoxyribonucleic acid) and RNA (Ribonucleic acid).
• Nucleotide Structure: Phosphate group + 5C Sugar + Nitrogenous Base.
  • Sugar: Ribose (RNA) vs. Deoxyribose (DNA).
  • Bases: Purines (A, G - two rings) and Pyrimidines (C, U, T - one ring).
• Linkage: Phosphodiester bonds between $5'$ phosphate and $3'$ hydroxyl.
• DNA Structure: Double helix, $2.0\,nm$ wide. Antiparallel strands ($5' \rightarrow 3'$ vs. $3' \rightarrow 5'$) held by H-bonds ($G \equiv C$ and $A = T$).
• DNA Origami: Folds a scaffold (long ssDNA) with staples (short strands) to create nanoscale shapes (e.g., logic-gated nanorobots).
• RNA Types:
  • mRNA: DNA copy that leaves the nucleus.
  • tRNA: Brings proteins to the ribosome via anticodons.
  • rRNA: Makes up ribosomes.
• Vaccine Technology:
  • mRNA Vaccines: Cell receives mRNA to produce spike proteins for immune response.
  • Viral Vector DNA Vaccines: Uses a defective virus to deliver DNA encoding spike proteins.

Lipids and Membranes

• Fats/Fatty Acids: Hydrocarbon chains linked to $-COOH$.
  • Saturated: Single bonds only; solid at room temperature.
  • Unsaturated: Double bonds cause bends; liquid at room temperature.
  • Omega-3/6: Number corresponds to the first double bond from the methyl end.
• Steroids: Bulky four-ring structure (e.g., Estrogen, Testosterone, Cholesterol). Estrogen loss at age 50 contributes to osteoporosis.
• Phospholipids: Glycerol + Phosphate + 2 Fatty Acids. Amphipathic (hydrophilic head, hydrophobic tail). Form bilayers or micelles.
• Membrane Fluidity: The Fluid-Mosaic Model describes the membrane as a mosaic of proteins, cholesterol, and carbohydrates.
• Selective Permeability:
  • Easy: Small nonpolar molecules ($O_2, CO_2$).
  • Intermediate: Water, Glycerol.
  • Hard: Ions, large polar molecules.

Membrane Transport mechanisms

• Diffusion: Spontaneous net movement from high to low concentration.
• Osmosis: Diffusion of water across a membrane.
  • Isotonic: No net movement.
  • Hypotonic: Water flows into cell (swelling).
  • Hypertonic: Water flows out (shrinking).
• Facilitated Diffusion: Passive transport requiring a protein channel or carrier (e.g., GLUT-1 for glucose).
• Active Transport: Moves substances against a gradient using ATP (e.g., Sodium-Potassium Pump).
• Secondary Active Transport: Potential energy from an electrochemical gradient drives another molecule against its gradient.
• Vesicular Transport:
  • Endocytosis: Ingestion via vesicles (Phagocytosis, Pinocytosis, Receptor-mediated).
  • Exocytosis: Vesicle fusion to deposit proteins outside the cell.

Microscopy and Cell Structure

• Microscopes:
  • Compound Light: Uses visible light. Total Mag = Ocular x Objective. Resolution $D = \frac{0.61\lambda}{\text{N.A.}}$.
  • Fluorescent: Uses high-intensity light and fluorophores (e.g., Mitotracker).
  • Stereo: Provides 3D visualization and pancratic magnification ($1\times$ to $20\times$).
  • Electron (SEM/TEM): Uses electron beams. High resolution but kills the sample.
• Domains of Life: Bacteria, Archaea, Eukaryotes.
• Prokaryotes: No nucleus, circular DNA, plasmids, FtsZ ring for division, pili/fimbriae. Peptidoglycan cell walls (Penicillin targets this).
• Eukaryotic Organelles:
  • Nucleus: Store information; Nuclear Localization Signal (NLS) targets proteins for entry.
  • Ribosomes: Protein synthesis ($80S$ in eukaryotes: $60S + 40S$).
  • Endoplasmic Reticulum: Smooth (lipid synthesis, $Ca^{2+}$ reservoir) and Rough (protein synthesis).
  • Golgi Apparatus: Cis-to-trans processing and shipping of proteins.
  • Lysosomes: Digestion (autophagy).
  • Peroxisomes: Detoxification; contains catalase to break down $H_2O_2$.
  • Mitochondria/Chloroplasts: Endosymbiosis theory. Mitochondria perform oxidative phosphorylation via ATP synthase.
  • Cytoskeleton: Microtubules (centrosomes, cilia $9+2$), Microfilaments (actin/myosin), Intermediate filaments (keratin).

Animal Tissues and Physiology

• Basic Principles: Form follows function; Homeostasis (negative/positive feedback).
• Tissue Types:
  • Epithelial: Simple/Stratified (Squamous, Cuboidal, Columnar). Found in skins/linings. Polarized (Apical/Basal).
  • Muscular: Skeletal (voluntary/striated), Cardiac (involuntary/striated/intercalated disks), Smooth (involuntary).
  • Nervous: Neurons and Neuroglia (Astrocytes, Oligodendrocytes, Schwann cells).
  • Connective: Loose, Dense (tendons/ligaments), Cartilage (chondrocytes), Bone (osteocytes), Adipose, Blood.

Cell Cycle and Genetics

• Binary Fission: Prokaryotic clonal reproduction ($FtsZ$ ring).
• The Eukaryotic Cell Cycle:
  • Interphase: $G_1$ (growth), $S$ (DNA replication), $G_2$ (mitosis prep).
  • Mitosis: Prophase, Prometaphase (nuclear membrane disappears), Metaphase (checkpoints), Anaphase (sister chromatids separate), Telophase.
  • Cytokinesis: Cleavage furrow (animals) and cell plate (plants).
• Chromosome Structure: Chromatin (40% DNA, 60% Protein). DNA wraps around positively charged Histone proteins to form Nucleosomes.
• Genetics:
  • Homologous Chromosomes: Same genes, possibly different alleles.
  • Mendel's Laws: Segregation of alleles (Meiosis I); Independent Assortment.
  • Punnett Squares: Predictive genotypes (Homozygous, Heterozygous, Hemizygous for XY).
  • Dominance Types: Complete, Incomplete (intermediate phenotype), Codominance (both expressed).
• Cell Cycle Control: Regulated by Cyclins and Cyclin-dependent Kinases (Cdks).
  • MPF (Maturation-Promoting Factor): Cyclin + Cdk complex.
  • Tumor Suppressors: $p53$ (checks DNA), $Rb$ (binds $E2F$).
  • Oncogenes: Mutated proto-oncogenes causing uncontrolled growth.

Maintenance of Life: Systems

• Thermoregulation: Balancing heat exchange (Conduction, Convection, Radiation, Evaporation).
  • Ectotherms: External heat sources.
  • Endotherms: Metabolic heat (Birds, mammals).
  • Fever: Shift in the hypothalamus set point by pyrogens.
• Osmoregulation: Controlling water and solute balance.
  • Marine Fish: Hypoosmotic to environment; lose water, drink seawater.
  • Freshwater Fish: Hyperosmotic; gain water, excrete dilute urine.
• Excretion: Removal of nitrogenous waste (Ammonia in fish, Urea in mammals, Uric Acid in birds).
  • Kidney: Nephron processes: Filtration (glomerulus), Reabsorption (Loop of Henle), Secretion.
• Digestion:
  • Stomach: Secretes Pepsinogen (inactive) converting to Pepsin via $HCl$.
  • Small Intestine: Digestion of carbs, proteins, nucleic acids, and fats (Bile/Lipase).
• Hormones:
  • Antagonistic Hormones: Insulin (lowers glucose) vs. Glucagon (raises glucose); Calcitonin (lowers $Ca^{2+}$) vs. PTH (raises $Ca^{2+}$).
  • ADH: Controls water reabsorption in response to blood osmolarity.
• Neural Control: Action Potential ($-70\,mV \rightarrow +40\,mV$). Threshold is $-55\,mV$. Saltatory conduction occurs in myelinated axons.
• Circulation:
  • Heart: 4 chambers in birds/mammals. SA node (pacemaker) $\rightarrow$ AV node $\rightarrow$ Bundle branches.
  • Blood Pressure: Recorded as Systolic/Diastolic (Normal: $120/80\,mm\,Hg$).

Evolution and Diversity

• Darwin's Theory: Natural selection as the mechanism for "descent with modification." Evidence includes fossils, homology, and biogeography.
• Hardy-Weinberg Equation: $p^2 + 2pq + q^2 = 1$. Describes non-evolving populations.
• Speciation: Allopatric (geographic isolation) vs. Sympatric (overlapping populations).
• Biological Species Concept: Group of organisms capable of interbreeding and producing fertile offspring.
• Phylogeny: Reconstruction of evolutionary history using cladistics (clades, monophyletic groups).
• Domains: Bacteria, Archaea, Eukarya.
  • Archaea: Extremophiles (Methanogens, Thermophiles).
  • Animal Phyla: Porifera (sponges), Cnidaria, Platyhelminthes, Nematoda, Annelida, Mollusca, Arthropoda (most diverse), Echinodermata, Chordata.

Ecology and Behavior

• Biomes: Classified by temperature and precipitation (Tundra, Taiga, Desert, Rainforest).
• Behavior: Innate (FAPs triggered by sign stimuli) vs. Learned (Habituation, Imprinting, Conditioning).
• Population Ecology: Growth models: Exponential (J-curve) vs. Logistic (S-curve, carrying capacity $K$).
• Community Ecology: Interspecific interactions (Competition, Predation, Mutualism, Parasitism).
• Keystone Species: Large impact regardless of abundance (e.g., Sea Stars).
• Ecosystem Ecology: Energy flow (10% efficiency between trophic levels) and Nutrient Cycling (Carbon, Nitrogen, Phosphorus cycles).
• Biomagnification: Toxins concentrating at higher trophic levels.