BIO 111 FINAL EXAM REVIEW

Atoms and Elements

Atom vs. Element- Atom: Smallest unit of matter retaining element properties; made of protons, neutrons, electrons.
- Element: Pure substance of one atom type; cannot be chemically simplified.
Essential Elements- Definition: Elements needed in large amounts for survival, growth, reproduction (e.g., C, H, O, N, P, S, Ca, K, Na, Cl, Mg, Fe).
- Periodic‐Table Location: First four periods; Groups 1–3 (metals: Na, K, Ca, Mg) and Groups 14–17 (non-metals: C, N, O, P, S, Cl).
Elements Making Up Most Living Matter- Four primary atoms contribute
$\approx96 \%$
of mass in most organisms: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

Subatomic Particles

Proton (p⁺)
• Charge: $+1$
• Mass: $\approx1\,\text{amu}$ (atomic mass unit).
• Location: Atomic nucleus.
Neutron (n⁰)
• Charge: $0$
• Mass: $\approx1\,\text{amu}$ (slightly heavier than a proton).
• Location: Nucleus.
Electron (e⁻)
• Charge: $-1$
• Mass: $\approx\tfrac{1}{1840}\,\text{amu}$ (negligible).
• Location: Orbitals/electron cloud surrounding nucleus.
• Chemical-reaction role: Electrons—especially those in the valence shell—are directly involved in bond formation and breaking.

Atomic Number, Mass, & Particle Count

Atomic Number (Z): Number of protons. Defines the element.
Mass Number (A): Protons + neutrons. $A = p^+ + n^0$
Determining Particles
-Z $</li><li>Why Table Lists Whole Z but Decimal Mass: Z is integer; atomic mass is weighted average of isotopes.</li></ul><h5 id="8264e51b-bc7e-4f97-b92c-9e52f2145a14" data-toc-id="8264e51b-bc7e-4f97-b92c-9e52f2145a14" collapsed="false" seolevelmigrated="true">Isotopes vs. Ions</h5><ul><li>Isotopes: Same Z (element), different A (neutrons); neutral charge; altered mass; identical chemical behavior; some radioactive.</li><li>Ions: Atom/molecule with net charge (lost/gained$ e^- $). Cation: positive (lost$ e^- $). Anion: negative (gained$ e^-). Altered charge affects electrical, osmotic, chemical properties.

Electron Shells & Reactivity

Electron Shell (Energy Level): Region where electrons with similar energy are found.
Filling Order (first 3 shells) 1. 1st shell: Max 2 e^- $.<ol start="2"><li>2nd shell: Max 8$ e^- $.</li><li>3rd shell: Max 8$ e^- $(for main-group elements). Lower energy shells fill first.</li></ol></li><li>Valence Shell: Outermost occupied shell; valence electrons determine reactivity.</li><li>Inert vs. Reactive• Inert: Full valence shell (e.g., noble gases); no tendency to gain/lose/share$ e^- $. • Reactive: Incomplete valence shell; seeks stability via bond formation (Octet Rule:$ 8 $valence$ e^- $optimal,$ 2 for H & He).
Atoms ‘Seek’: Minimization of potential energy by achieving full/empty valence shells through bonding.

Electronegativity & Polarity

Electronegativity (EN): Atom’s tendency to attract shared electrons in a covalent bond.
Approximate Trend (Pauling scale): O (3.5) > N (3.0) > C (2.5)
\approx $ H (2.1).</li><li>Polarity: Unequal sharing of electrons (differing EN) → partial charges (δ⁺, δ⁻).</li></ul><h5 id="64a688a8-1f25-45b6-bec1-0664cab5b7d1" data-toc-id="64a688a8-1f25-45b6-bec1-0664cab5b7d1" collapsed="false" seolevelmigrated="true">Types of Chemical Bonds</h5><ul><li>Ionic Bonds• Complete$ e^- $transfer (metal to non-metal); electrostatic attraction; medium strength, weaker in water.</li><li>Covalent Bonds• Shared$ e^- pair(s). Non-polar: Equal sharing (ΔEN < 0.4) e.g., \text{C–H} $,$ \text{O}2 $. Polar: Unequal sharing (ΔEN 0.5–1.9) → partial charges e.g.,$ \text{H–O} $in$ H2O. Strongest biological bonds.
Hydrogen Bonds (H-bonds)
• Electrostatic attraction between δ⁺ H (bonded to O, N, F) and δ⁻ EN atom of another molecule. Individually weak but numerous → major stabilizing force (DNA, proteins, water).

Valence Electrons, Vacancies, & Bonding Capacity

Atom

Valence e^- $</th><th colspan="1" rowspan="1">Vacancies (to octet/duet)</th><th colspan="1" rowspan="1">Max Covalent Bonds</th></tr><tr><td colspan="1" rowspan="1">Carbon (C)</td><td colspan="1" rowspan="1">4</td><td colspan="1" rowspan="1">4</td><td colspan="1" rowspan="1">4</td></tr><tr><td colspan="1" rowspan="1">Oxygen (O)</td><td colspan="1" rowspan="1">6</td><td colspan="1" rowspan="1">2</td><td colspan="1" rowspan="1">2</td></tr><tr><td colspan="1" rowspan="1">Nitrogen (N)</td><td colspan="1" rowspan="1">5</td><td colspan="1" rowspan="1">3</td><td colspan="1" rowspan="1">3</td></tr><tr><td colspan="1" rowspan="1">Hydrogen (H)</td><td colspan="1" rowspan="1">1</td><td colspan="1" rowspan="1">1</td><td colspan="1" rowspan="1">1</td></tr></tbody></table><h5 id="07459ef0-7a85-4d7c-8e8a-11f68a864fdb" data-toc-id="07459ef0-7a85-4d7c-8e8a-11f68a864fdb" collapsed="false" seolevelmigrated="true">Formulas vs. Equations</h5><ul><li>Molecular/Chemical Formula: Symbolic representation of composition (e.g.,$ C6H{12}O_6 $).</li><li>Chemical Equation: Depicts reaction (reactants → products), often balanced (e.g.,$ 2H2 + O2 \rightarrow 2H_2O).

Reactants: Consumed substances. Products: Formed substances.

Solutions & Solubility

Solution: Homogeneous mixture (Solvent: greatest amount; Solute: dissolved components).
Hydrophilic vs. Hydrophobic
• Hydrophilic: Polar/charged; form H-bonds/ionic interactions with H_2O → soluble.
• Hydrophobic: Non-polar; cannot interact with water → aggregate, insoluble, drive membrane formation.
• Polarity dictates solubility/reactivity.

Water: Molecular & Intermolecular Bonds

Intramolecular: Two polar covalent \text{H–O} $bonds within each$ H_2O $molecule.</li><li>Intermolecular: Hydrogen bonds between δ⁺ H of one molecule and lone-pair O of another.</li></ul><h5 id="791fdbca-4ebc-4828-9d5f-6d5613e0ec44" data-toc-id="791fdbca-4ebc-4828-9d5f-6d5613e0ec44" collapsed="false" seolevelmigrated="true">Cohesion vs. Adhesion</h5><ul><li>Cohesion: Attraction between water molecules via H-bonds (surface tension, water columns).</li><li>Adhesion: Attraction between water and other polar surfaces (capillary rise).</li></ul><h5 id="7b36af54-2af2-482a-8e40-9fc542d42f2e" data-toc-id="7b36af54-2af2-482a-8e40-9fc542d42f2e" collapsed="false" seolevelmigrated="true">Water as ‘Universal Solvent’</h5><ul><li>Polarity + up to 4 H-bonds → surrounds ions/polar molecules (hydration shells) and dissociates ionic lattices.</li></ul><h5 id="3153cd1f-561c-4669-84d9-73632f9ff7ca" data-toc-id="3153cd1f-561c-4669-84d9-73632f9ff7ca" collapsed="false" seolevelmigrated="true">Thermal Concepts</h5><ul><li>Kinetic Energy (KE): Energy of motion; for molecules, proportional to$ \frac{1}{2}mv^2.
Temperature: Average KE of particles. Higher temp = faster motion.
Specific Heat of Water: High because many H-bonds must break. moderates climate/organismal temp.

Density Anomaly of Ice

Rigid lattice maximizes H-bond spacing → molecules fixed farther apart → lower density.
Biological Significance
• Ice floats, insulating water bodies → aquatic life survives; seasonal turnover oxygenates lakes.

pH and Hydrogen Ions

Definition of a Proton: A hydrogen ion (H+) is a proton, central to acid-base chemistry.
pH Values: Acids have pH < 7 (high H+). Bases have pH > 7 (low H+).
Relationships and Calculations: The balance between [H+] and [OH-] determines pH.
- pH Calculation: pH=−log[H+]pH=−log[H+]. A decrease in pH means increased [H+]; each whole number change is a tenfold change in [H+].
Buffers: Substances that stabilize pH (e.g., bicarbonate in blood) by absorbing or releasing H+, essential for homeostasis.
Biological Sensitivity: Most organisms thrive near neutral pH (around 7); deviations can cause cell damage or death, as enzymes are often pH-sensitive.

Organic vs Inorganic Molecules

Definitions:
- Organic Molecules: Compounds with carbon and hydrogen (e.g., carbohydrates, proteins).
- Inorganic Molecules: Lack carbon-hydrogen bonds (e.g., water, salts).
Hydrocarbons: Composed solely of carbon and hydrogen; low polarity, crucial for energy and structure.

Carbon and Functional Groups

Unique Qualities of Carbon: Carbon's four valence electrons, moderate electronegativity, short bond lengths, and small atomic size allow it to form diverse organic compounds, including chains and rings.
Functional Groups: Groups of atoms that confer specific chemical properties to a compound. Major functional groups include:
- Hydroxyl (-OH): Polar and can form hydrogen bonds; increases solubility in water.
- Carboxyl (-COOH): Acts as an acid by donating H+, important in amino acids and fatty acids.
- Amino (-NH2): Basic functional group that can accept H+, forming part of amino acids.
- Phosphate (-PO4): Contributes to the energy transfer in ATP and DNA structure.
- Methyl (-CH3): Nonpolar, hydrophobic; influences the shape and function of organic molecules.

Macromolecules

Dehydration Synthesis: A process where covalent bonds are formed by removing water molecules, linking monomers to create polymers. This is essential in the formation of carbohydrates, proteins, and nucleic acids.
Hydrolysis: The reverse process where polymers are broken down by the addition of water; this is a key process during enzymatic digestion and cellular metabolism.

Biological Macromolecule Classification

Carbohydrates: Composed of carbon (C), hydrogen (H), and oxygen (O); serve as energy sources and structural components. Includes sugars (like glucose), starches, and fibers which are essential for energy metabolism.
Lipids: Composed predominantly of carbon and hydrogen with small amounts of oxygen; essential for energy storage, forming cell membranes (phospholipids), hormonal regulation (steroids), and insulation. Lipids also serve as signaling molecules.
Proteins: Formed from carbon, hydrogen, oxygen, and nitrogen; crucial for enzymatic activity, cellular structure, and signaling. The diversity arises from combinations of 20 different amino acids, which connect via peptide bonds. Each protein's function is intricately linked to its structure, which can vary in the four structural levels: Primary (sequence of amino acids), Secondary (alpha helices and beta sheets), Tertiary (three-dimensional folding), and Quaternary (assembly of multiple polypeptides).
Nucleic Acids: Composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus; vital for the storage and transfer of genetic information (DNA and RNA). They play critical roles in heredity and protein synthesis, with their polymeric structures defining the encoding of biological information.

Distinguishing Macromolecules

Carbohydrates: Function in energy production, storage, and cell structure. Types include monosaccharides (e.g., glucose), disaccharides (e.g., sucrose), and polysaccharides (e.g., cellulose, starch).
Proteins: Perform essential functions within cells and are built from amino acids, linked by peptide bonds. Each protein's shape is specific to its function; enzymes serve as biological catalysts.
Nucleic Acids: DNA stores genetic information in a double helical structure, while RNA is involved in gene expression and typically single-stranded. Nucleotides consist of a sugar, phosphate, and nitrogenous bases which form the structural backbone of nucleic acids.
Lipids: Lipids include various types based on fatty acid structure; fatty acids can be saturated (no double bonds) or unsaturated (one or more double bonds). Types include monoglycerides (1 tail), diglycerides (2 tails), and triglycerides (3 tails), with cholesterol serving significant structural and regulatory roles in membranes, including the maintenance of fluidity.

Key Molecule Recognition for Exam

Functional Groups: Identify structures of Hydroxyl, Carboxyl, Amino, Phosphate, and Methyl groups and their functionalities in biological molecules.
Carbohydrates: Familiarize with structures of glucose, cellulose, starch, and glycogen, including recognition of isomeric variations.
Proteins: Understand the common structure of amino acids, including polar, nonpolar, and charged side chains that influence protein folding.
Nucleic Acids: Recognize the components of DNA and RNA, including nucleotide structures and base pairing, focusing on adenine-thymine and guanine-cytosine pairings in DNA.
Lipids: Identify glycerol and structures of both saturated and unsaturated fatty acids, including configurations of cis and trans fats, along with cholesterol and its role in membrane integrity.

1) Cell Theory

Three parts of the cell theory:
- The cell is the fundamental unit of life.
- All organisms are made of one or more cells.
- All cells arise from pre-existing cells.

2) Prokaryotic Cell Structures and Functions

Chromosome: Circular DNA in the nucleoid, usually one, for genetic information.
Plasma Membrane: Phospholipid bilayer forming the cell boundary, regulating substance passage.
Cell Wall: Peptidoglycan (in bacteria) layer providing structural support and protection.
Ribosomes: Free-floating in cytoplasm, responsible for protein synthesis.
Capsule: Gelatinous layer outside cell wall, protects from desiccation and aids immune evasion.
Flagella: Whip-like appendages for motility (taxis).
Pili: Hair-like projections for adherence and genetic transfer (conjugation).

3) Size and Age Differences: Prokaryotic vs Eukaryotic Cells

Size: Prokaryotic cells (0.1−5μm0.1−5μm) are smaller than eukaryotic cells (10−100μm10−100μm).
Age: Prokaryotic cells are older (3.5 billion years ago) than eukaryotic cells (1.5 billion years ago).

4) Eukaryotic Cell Structures and Functions

Cell Wall: Provides structure and protection; composed of cellulose (plants) or chitin (fungi).
Central Vacuole: Large membrane-bound sac (in plants) for turgor pressure, nutrient storage, waste, and growth.
Centrosome and Centriole: Organizes microtubules, crucial for cell division.
Chloroplast: Double-membraned organelle containing chlorophyll; site of photosynthesis.
Cilia: Short, hair-like structures of microtubules for movement and sensory functions.

5) Additional Eukaryotic Cell Structures

Cytoskeleton: Protein filament network for cell shape, support, and organelle movement.
Cytoplasm and Cytosol: Cytoplasm holds organelles; cytosol is the liquid portion for metabolic processes.
Golgi Apparatus: Stacked membrane sacs that modify, sort, and package proteins/lipids for transport.
Lysosomes: Membrane-bound organelles with digestive enzymes for waste breakdown.
Mitochondria: Double-membraned organelle with its own DNA; generates ATP via cellular respiration.
Nuclear Pore: Protein complexes in the nuclear envelope, regulating passage between nucleus and cytoplasm.
Nucleolus: Dense region within the nucleus, produces rRNA and assembles ribosomes.
Nucleus: Membrane-bound organelle containing genetic material (chromosomes); regulates gene expression.
Peroxisomes: Membrane-bound organelles that breakdown fatty acids and detoxify substances.

6) Plasma Membrane Structure and Functions

Fluid Mosaic Model: Describes the flexible membrane with moving phospholipids and proteins.
Selectively Semi-Permeable: Allows specific substances to pass while excluding others.

7) Components of the Plasma Membrane

Cholesterol: Hydrophobic steroid within the bilayer, stabilizing fluidity and reducing permeability.
Phospholipids: Form the bilayer barrier with hydrophilic heads and hydrophobic tails, enabling selective permeability.
Membrane Proteins: Integral or peripheral proteins with roles in transport, reception, enzymatic activity, and attachment.

8) Motor Proteins

Facilitate intracellular movement and transport along the cytoskeleton, using ATP for energy.

9) Endomembrane System

Components: Nuclear Envelope, ER, Golgi, Lysosomes, Vacuoles, Cell Membrane. Moves molecules throughout the cell.

10) Evidence for the Endosymbiotic Theory

Suggests mitochondria and chloroplasts were once free-living bacteria engulfed by host cells, explaining their semiautonomous nature.

11) Evidence for the Invagination Theory

Proposes that organelles like the nucleus and Golgi apparatus originated from infoldings of the plasma membrane.

Energy

Energy is the ability to do work, existing as kinetic (motion, e.g., thermal, light) or potential (stored, e.g., chemical) energy.
Thermodynamics: Study of energy transformations.
- 1st Law: Energy is conserved.
- 2nd Law: Energy is lost as heat; entropy increases.
Chemical Reactions: Include metabolism (sum of reactions), anabolism (building), catabolism (breaking down), endergonic (requires energy), exergonic (releases energy), oxidation (electron loss), and reduction (electron gain).
Biological Reactions: Such as photosynthesis (light to chemical), cellular respiration (chemical to ATP), hydrolysis (breaks bonds with water), and dehydration synthesis (forms bonds by removing water).

ATP

ATP (Adenine, ribose, three phosphates) stores energy via covalent bonds created by phosphorylating ADP, enabling enzyme function through mechanical changes.

Enzymes

Enzymes are catalysts that speed up reactions by lowering activation energy without being consumed.
- Key Terms: Active site (where substrate binds), substrate (reactant), product (result), cofactors/coenzymes (required for activity), inhibitors (decrease activity), activators (increase activity).
- Function within specific pH and temperature ranges; denature (lose shape/function) outside these.
- Metabolic Pathway: Series of enzyme-catalyzed reactions.
- Feedback Mechanisms: Negative (product slows pathway) and positive (product speeds pathway).

Membrane Function

Transport proteins move molecules across membranes.
- Passive Transport: No ATP; moves down concentration gradient (high to low).
  - Simple Diffusion: Direct movement.
  - Facilitated Diffusion: Requires protein.
- Active Transport: Requires ATP; moves against concentration gradient (low to high).
Diffusion: Net movement from high to low concentration.
Osmosis: Diffusion of water.
Tonicity: Cell response to solute concentration.
- Hypertonic: Shrinks (water out).
- Hypotonic: Swells (water in).
- Isotonic: No net movement.
Central Vacuole: Maintains turgor pressure in plants.
Pumps: Active transport against gradient (e.g., Proton Pump).
Bulk Transport: Moves large amounts.
- Endocytosis: Into cell.
- Exocytosis: Out of cell.

Organisms: Plants, algae, cyanobacteria (autotrophs).
Autotrophs produce their own food; Heterotrophs consume others.
Definition: Plants use light energy to produce glucose (C6H{12}O6 $) and oxygen ($ O2 $).</li><li>Balanced Chemical Equation:$ 6CO2 + 6H2O + \text{light energy} \rightarrow C6H{12}O6 + 6O2 $<ul><li>Reactants:$ CO2 $(stomata),$ H2O $(roots).</li><li>Fates: Carbon from$ CO2 $to Glucose;$ H2O $is oxidized to$ O2 $;$ CO2 $is reduced to Glucose.</li></ul></li><li>Nature: Endergonic (requires energy), Anabolic (builds molecules).</li><li>Pigments: Chlorophyll a (primary), absorbs violet-blue and red light. Leaves are green due to reflection of green light.</li><li>Chloroplast Anatomy: Double membrane; Thylakoids (sacs, contain chlorophyll, stacks are grana); Stroma (fluid-filled space).</li><li>Light Reactions:<ul><li>Location: Thylakoid membrane.</li><li>Requirements: Light.</li><li>Process:$ H2O $split ($ O2 $released), light energy excites electrons.</li><li>Intermediate: NADP+ becomes NADPH (electron carrier).</li><li>Energy Source: Light.</li></ul></li><li>Carbon Reactions (Calvin Cycle):<ul><li>Location: Stroma.</li><li>Requirements: ATP and NADPH (from light reactions).</li><li>Process:$ CO_2 $converted to glucose.</li><li>Carbon Source:$ CO2 $; Hydrogen Source:$ H2O $.</li><li>Energy Source: ATP and NADPH.</li></ul></li><li>Oxygen Gas Source: Oceans (algae) and photosynthesis.</li></ul><h5 id="d53bb692-ab4f-4f04-9392-08441faf93d9" data-toc-id="d53bb692-ab4f-4f04-9392-08441faf93d9" collapsed="false" seolevelmigrated="true">Intro to Cellular Respiration (Section 6.1)</h5><ul><li>ATP Synthesis:<ul><li>Components of ATP: Adenine, ribose, three phosphate groups.</li><li>Energy is stored in ATP's phosphate bonds via phosphorylation (ADP to ATP).</li><li>Importance: Drives most embryonic reactions.</li></ul></li><li>Aerobic Cellular Respiration:<ul><li>Definition: Mitochondria process using oxygen to break down glucose, producing$ CO2 $,$ H2O $, and ATP.</li><li>Balanced Chemical Equation:$ C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + \text{ATP} $</li><li>Reactant Entry: Glucose (food), Oxygen (inhalation).</li><li>Atom Fate: Carbon from glucose to$ CO2 $; Hydrogen from glucose and oxygen to$ H2O $.</li><li>Product Exit:$ CO2 $(exhaling),$ H2O $(sweat).</li><li>Oxidation: Glucose becomes$ CO2 $. Reduction: Oxygen becomes$ H2O $.</li></ul></li><li>Nature: Catabolic (breaks down), Exergonic (releases energy).</li><li>Reverse Reaction: Photosynthesis.</li><li>ATP Phosphorylation Equation:$ ADP + P_i \rightarrow ATP $<ul><li>Nature: Endergonic (requires energy), Anabolic (builds ATP).</li></ul></li></ul><h5 id="5a4f7b0e-cb8b-4d4a-b37d-92dba4f55a0c" data-toc-id="5a4f7b0e-cb8b-4d4a-b37d-92dba4f55a0c" collapsed="false" seolevelmigrated="true">Anatomy of Mitochondria (Section 6.3)</h5><ul><li>Function: Energy production.</li><li>Cytosol: Surrounds mitochondria.</li><li>Structures:<ul><li>Outer Membrane: Smooth.</li><li>Inner Membrane: Folded (cristae) to increase surface area.</li><li>Intermembrane Compartment: Space between membranes.</li><li>Matrix: Innermost liquid portion.</li></ul></li></ul><h5 id="d3b8a094-3d47-40f5-b562-00daa36b8d22" data-toc-id="d3b8a094-3d47-40f5-b562-00daa36b8d22" collapsed="false" seolevelmigrated="true">Anaerobic Respiration</h5><ul><li>Utilizes the complete cellular respiration pathway (glycolysis, pyruvate oxidation, Krebs cycle, electron transport chain, and chemiosmotic phosphorylation).</li><li>Differs from aerobic respiration by using a final electron acceptor other than oxygen.</li><li>Employs a substance with high electronegativity to extract electrons at the end of the electron transport chain, producing water or other molecules.</li><li>Example:<ul><li>Normal aerobic respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O</li><li>Anaerobic respiration with elemental sulfur:$ C6H{12}O6 + S \rightarrow H2S + CO_2 $</li></ul></li><li>Still produces a substantial amount of ATP, although possibly less than aerobic respiration.</li><li>Performed by obligate anaerobes (bacteria, fungi) that are poisoned by oxygen and can only conduct anaerobic respiration.</li><li>Obligate vs. Facultative:<ul><li>Obligate: Required or restricted to a specific condition (e.g., anaerobic).</li><li>Facultative: Flexible and able to adapt to different conditions.</li></ul></li></ul><h5 id="6db9845b-779d-4fc3-9b9b-88dae9e5a2eb" data-toc-id="6db9845b-779d-4fc3-9b9b-88dae9e5a2eb" collapsed="false" seolevelmigrated="true">Fermentation</h5><ul><li>An anaerobic process that doesn't use all steps of cellular respiration; relies primarily on glycolysis.</li><li>Recycles NADH back to$ NAD^+ $to sustain glycolysis.</li><li>Process:<ul><li>Glucose +$ NAD^+ \rightarrow NADH $+ Pyruvate (Glycolysis).</li><li>In the absence of oxygen and if the organism is a facultative anaerobe, fermentation occurs.</li><li>NADH + Pyruvate$ \rightarrow NAD^+ $+ Lactic Acid (or Ethanol +$ CO_2 $).</li></ul></li><li>Two sub-types:<ul><li>Lactic acid fermentation.</li><li>Alcohol fermentation.</li></ul></li></ul>Lactic Acid Fermentation<ul><li>NADH donates electrons to pyruvate, forming lactic acid (lactate) and regenerating$ NAD^+ $.</li><li>Lactic acid build-up causes muscle cramping.</li><li>Muscle cells can perform this.</li><li>Lactate is a three-carbon molecule.</li><li>Lactose is a completely different molecule, not related at all</li></ul>Alcohol Fermentation<ul><li>Yeast converts pyruvate into ethanol (alcohol) and$ CO_2 $.</li><li>Used in making wine, beer, bread, etc.</li><li>Yeast + Sugar (berries, grapes, barley, corn, potatoes. rice)\rightarrow just alcohol after that</li><li>The$ CO_2 $by-product causes bread to rise and creates bubbles in beer and champagne.</li><li>Ethanol is a two-carbon molecule, and carbon dioxide is a one-carbon molecule.</li><li>The alcohol percentage reaches 12 - 14% with naturally fermented sugars and grain otherwise it kills all the yeast.</li><li>This is bypassed by Distillation separates the alcohol and concentrate, evaporates much quicker. Collects the alcohol.</li></ul>Summary Table:<table style="min-width: 100px"><colgroup><col style="min-width: 25px"><col style="min-width: 25px"><col style="min-width: 25px"><col style="min-width: 25px"></colgroup><tbody><tr><th colspan="1" rowspan="1">Feature</th><th colspan="1" rowspan="1">Aerobic Respiration</th><th colspan="1" rowspan="1">Anaerobic Respiration</th><th colspan="1" rowspan="1">Fermentation</th></tr><tr><td colspan="1" rowspan="1">Oxygen</td><td colspan="1" rowspan="1">Yes</td><td colspan="1" rowspan="1">No</td><td colspan="1" rowspan="1">No</td></tr><tr><td colspan="1" rowspan="1">Steps Used</td><td colspan="1" rowspan="1">All 5</td><td colspan="1" rowspan="1">All 5</td><td colspan="1" rowspan="1">Glycolysis Only</td></tr><tr><td colspan="1" rowspan="1">Final Product</td><td colspan="1" rowspan="1">$ H2O $,$ CO2 $</td><td colspan="1" rowspan="1">Various</td><td colspan="1" rowspan="1">Lactic Acid or Ethanol +$ CO_2 $</td></tr><tr><td colspan="1" rowspan="1">Relative ATP Production</td><td colspan="1" rowspan="1">High</td><td colspan="1" rowspan="1">Moderate</td><td colspan="1" rowspan="1">Low (ATP produced only during glycolysis, not fermentation itself)</td></tr><tr><td colspan="1" rowspan="1">Terminal Electron Acceptor</td><td colspan="1" rowspan="1">Oxygen</td><td colspan="1" rowspan="1">Something Else</td><td colspan="1" rowspan="1">N/A</td></tr><tr><td colspan="1" rowspan="1">Organisms</td><td colspan="1" rowspan="1">Obligate Aerobes</td><td colspan="1" rowspan="1">Obligate Anaerobes</td><td colspan="1" rowspan="1">Facultative Anaerobes (can switch between aerobic and fermentation)</td></tr><tr><td colspan="1" rowspan="1">Role of Carbonation</td><td colspan="1" rowspan="1">N/A</td><td colspan="1" rowspan="1">N/A</td><td colspan="1" rowspan="1">Is used to recycle NADH back to$ NAD^+

Gene Expression: The process from DNA to functional product.
- Transcription: DNA to RNA (in nucleus for eukaryotes, cytoplasm for prokaryotes) via RNA polymerase. Involves Initiation, Elongation, Termination, and Post-transcriptional modifications (e.g., G-cap, poly-A tail, splicing of introns/exons).
- Translation: mRNA to Protein (in cytoplasm on ribosomes). mRNA codons are read by tRNA to assemble amino acids. Starts at AUG (Methionine) and stops at specific stop codons.
Mutations: Changes in DNA sequence.
- Point Mutations: Single nucleotide changes.
  - Substitution: One base replaced. Can be Silent (no amino acid change), Missense (different amino acid), or Nonsense (premature stop codon).
- Frameshift Mutations: Insertion or deletion of nucleotides, altering the reading frame.
Gene Regulation: Controls when and how genes are expressed.
- Epigenetics: Heritable changes in gene expression without DNA sequence alteration (e.g., chromatin packing: Heterochromatin-tight/silenced, Euchromatin-loose/active; Methylation-silences genes).
- Prokaryotic Operons: Promoter + Operator + genes transcribed as one mRNA (e.g., lac operon).
Monomers/Polymers: DNA/RNA are nucleotide polymers; Proteins are amino acid polymers.
Key Definitions: Gene: Specific DNA sequence encoding a product. Chromosome: Highly condensed DNA molecule carrying many genes. Genome: Complete set of genetic material in an organism.

Chapter 8: Cell Cycle & Mitosis
- Eukaryotic Cell Cycle: Ordered sequence of phases: G1 $\rightarrow$ S $\rightarrow$ G2 $\rightarrow$ M (Mitosis + Cytokinesis).
  - Interphase (G1, S, G2): G1 (growth), S (DNA replication, centrosome duplication), G2 (growth, error repair).
  - M Phase: Mitosis (nuclear division), Cytokinesis (cytoplasmic division) producing two genetically identical daughter cells.
- DNA Replication (S Phase): Semi-conservative process.
  - Key Enzymes/Components: Helicase (unzips), Primase (synthesizes RNA primers), DNA Polymerase (adds bases), Leading strand (continuous), Lagging strand (Okazaki fragments), Ligase (seals fragments).
- Mitosis Phases (IPPMAT): Asexual process leading to two diploid (2n \rightarrow 2n), identical cells.
  - Prophase: Chromatin condenses, spindle forms.
  - Prometaphase: Nuclear envelope fragments, spindle fibers attach to kinetochores.
  - Metaphase: Sister chromatids align at the equator (metaphase plate).
  - Anaphase: Sister chromatids separate and move to opposite poles.
  - Telophase: Chromosomes decondense, nuclear envelopes re-form.
- Cell Cycle Checkpoints: Crucial for proper division.
  - G1 Checkpoint: Assesses growth factors, nutrients, DNA integrity.
  - S Checkpoint: Verifies DNA replication accuracy.
  - G2 Checkpoint: Inspects for replicated DNA errors.
  - M (Metaphase) Checkpoint: Ensures proper spindle attachment; releases Separase to cleave cohesin.
- Regulation: Chemical (Growth Factors, Cyclins, CDKs, Nutrients) and Physical (Density-dependent inhibition, Anchorage dependence).
- Cancer Terminology:
  - Proto-oncogenes: Normal genes promoting growth. Oncogenes: Mutated proto-oncogenes causing excessive growth signals.
  - Tumor Suppressor Genes: Genes encoding STOP signals. Mutations remove cell division brakes.
  - Proofreader Genes: Repair replication errors.
  - Angiogenesis Inhibition: Blocking new blood vessel formation to starve tumors.
  - Telomeres: Protective ends of chromosomes that shorten (limits cell division); cancer cells often reactivate telomerase.
  - Apoptosis: Programmed cell death. Cancer cells often disable this.
  - Immune System Relation: Cancer cells evade recognition and suppression by the immune system.
Chapter 9: Meiosis & Genetic Diversity
- Meiosis Overview: Sexual reproduction process reducing chromosome number (2n \rightarrow n $) and creating genetic diversity, resulting in$ 4 $genetically unique haploid gametes.</li><li>Meiosis I (Homologs Separate):<ul><li>Prophase I: Chromosomes condense, Synapsis (homologous pairing), Crossing Over (DNA exchange between non-sister chromatids) occurs.</li><li>Metaphase I: Homologous pairs (tetrads) align at metaphase plate.</li><li>Anaphase I: Homologous chromosomes separate; sister chromatids remain joined. Each pole receives a haploid set ($ n $) of duplicated chromosomes.</li><li>Telophase I/Cytokinesis I: Two haploid daughter nuclei (with duplicated chromosomes) are formed.</li></ul></li><li>Meiosis II (Sister Chromatids Separate): Resembles mitosis but with haploid cells.<ul><li>Anaphase II: Sister chromatids separate (now individual chromosomes) to opposite poles. Resulting chromatids are non-identical.</li><li>Telophase II/Cytokinesis II: Yields a total of$ 4 $haploid ($ n $) daughter cells.</li></ul></li><li>Cytokinesis Differences: Mitosis usually equal. Meiosis has unequal cytokinesis in Oogenesis (1 large ovum + 2-3 polar bodies) but equal in Spermatogenesis (4 functional sperm).</li><li>Chromosomal Errors:<ul><li>Nondisjunction: Failure of homologous chromosomes (Meiosis I) or sister chromatids (Meiosis II/mitosis) to separate properly.</li><li>Aneuploidy: Missing or extra individual chromosomes (e.g.,$ 2n+1 $or$ 2n-1 $).</li><li>Polyploidy: Whole extra sets of chromosomes (e.g.,$ 3n $).</li><li>Trisomy 21 (Down Syndrome): Caused by nondisjunction, resulting in an extra chromosome$ 21 $(total$ 47 $chromosomes).</li></ul></li><li>Human Chromosome Counts:$ 2n+1 \rightarrow 47 $;$ 2n-1 \rightarrow 45 $;$ 3n \rightarrow 69 $;$ 1n \rightarrow 23.
- Cell Types & Genetics: Diploid (2n $): Somatic (body) cells (46 chromosomes). Haploid ($ n $): Gametes (sex cells: sperm/egg) (23 chromosomes). Zygote: Fertilized egg ($ 2n $), divides by mitosis to form embryo.</li><li>Karyotype: Chromosome arrangement for analysis. Autosomes: Pairs$ 1-22 $. Sex Chromosomes: Pair$ 23 $(XX-Female, XY-Male). Homologous Chromosomes: Matched pairs carrying same genes but potentially different alleles.</li></ul></li></ul><ul><li>Mendel's Experiments: Used garden peas due to short generation time, true-breeding varieties, and controlled pollination.</li><li>Particulate Inheritance: Disproved blending; traits are inherited as discrete, non-blending units (alleles).</li><li>Essential Terminology: True breeding (produces identical offspring when self-crossed), Carrier (heterozygote for recessive allele), Genotype (allele combination, e.g.,$ Aa $), Phenotype (observable trait), Dominant allele (masks recessive), Recessive allele (expressed only when homozygous).</li><li>Generational Labels: P (parental), F1 (first filial), F2 (second filial).</li><li>Allele Notation: Dominant as capital (e.g.,$ A $), recessive as lowercase (e.g.,$ a $).</li><li>Zygosity: Homozygous Dominant ($ AA $), Heterozygous ($ Aa $), Homozygous Recessive ($ aa).
- Test Cross: Crosses an unknown dominant phenotype with homozygous recessive to determine genotype (2:2 ratio for heterozygous unknown, 4:0 for homozygous dominant unknown).
- Punnett Squares & Ratios:
 - Monohybrid Cross: F2 genotype 1 ext{ }AA : 2 ext{ }Aa : 1 ext{ }aa $; F2 phenotype$ 3 $dominant$ : 1 $recessive.</li><li>Dihybrid Cross: F2 phenotype$ 9:3:3:1 $for independently assorting genes.</li></ul></li><li>Mendel’s Laws:<ul><li>Law of Segregation: Allele pairs separate during gamete formation, each gamete gets one allele.</li><li>Law of Independent Assortment: Alleles of genes on different chromosomes assort independently.</li></ul></li></ul><h4 id="45d8a069-a9b2-45e2-96b1-09d75c167754" data-toc-id="45d8a069-a9b2-45e2-96b1-09d75c167754" collapsed="false" seolevelmigrated="true">Probability Tools</h4><ul><li>Product Rule:$ P(A\;and\;B) = P(A) \times P(B) $for independent events.</li><li>66% Carrier Logic: A dominant-phenotype child from heterozygous parents has a$ 2/3 $probability of being a carrier ($ Aa $) if homozygous recessive ($ aa $) is ruled out.</li></ul><h4 id="469f3b7e-3aac-47c7-8a6e-6d29a0620d69" data-toc-id="469f3b7e-3aac-47c7-8a6e-6d29a0620d69" collapsed="false" seolevelmigrated="true">Beyond Mendel: Modified Patterns</h4><ul><li>Incomplete Dominance: Heterozygote shows intermediate/blended phenotype (e.g., pink snapdragons).</li><li>Codominance: Both alleles fully expressed (e.g.,$ AB blood type).
 - Linked Traits: Genes physically close on the same chromosome; inherited together unless separated by crossing-over.
 - Sex-Linked Traits: Genes on sex chromosomes (usually X), e.g., color blindness.
 - Multiple Alleles: More than two allele forms at a single locus (e.g., ABO blood system), resulting in several discrete phenotypes.
 - Polygenic Inheritance: Multiple genes contribute to a single trait, creating a continuous range of phenotypes (e.g., height).
 - Environmental Effects: Non-genetic factors influencing phenotype (e.g., hydrangea color by soil pH).
 - X-Inactivation: In female mammals, one X chromosome is inactivated (Barr body), leading to dosage compensation (e.g., calico cats).
 - Pleiotropy: Single gene affects multiple traits (e.g., sickle-cell).
 - Epistasis: One gene masks or modifies another's expression (e.g., Labrador coat color).
 Pedigree Interpretation
 - Symbols: Male (square), Female (circle), Affected (shaded), Carrier (half-shaded/dot).
 Foundational & Real-World Connections
 - Mendel’s work established modern genetics, impacting agriculture and medicine. Understanding these patterns is crucial for genetic counseling and gene-editing technologies.
 Genetic Engineering, Biotechnology & Foundational Vocabulary
 - Genetic Engineering (GE): Direct DNA manipulation, often via recombinant-DNA (rDNA).
 - Biotechnology: Broader field using organisms/bioprocesses; GE is a sub-discipline.
 - Recombinant DNA (rDNA): DNA from 2+ $sources, joined by restriction enzymes and DNA ligase.</li><li>Transgenic Organism (GMO): Carries foreign rDNA.</li><li>cDNA: Double-stranded DNA from mRNA, lacks introns.</li><li>Central Enzymes: RNA polymerase (DNA$ \to $RNA); Reverse transcriptase (RNA$ \to DNA).
 Vectors & Plasmids
 - Plasmid: Small, circular bacterial DNA, used as cloning vectors to carry foreign DNA.
 Restriction Enzymes & DNA Ligation
 - Restriction Enzyme: Cuts DNA at specific restriction sites, creating sticky or blunt ends.
 - DNA Ligase: Connects DNA fragments permanently.
 Recombinant Human Insulin Example
 - Human insulin gene cloned into bacterial plasmid, allowing bacterial production.
 Sanger (Chain-Termination) Gene Sequencing
 - Uses primer, normal dNTPs, and fluorescently labeled terminator ddNTPs with DNA Polymerase to sequence DNA fragments.
 Coding vs. Non-Coding DNA
 - Coding DNA (Exons): Translated into protein (1 ext{–}2\%$$ of human genome).
 - Non-Coding DNA: Regulatory or no known function (e.g., introns, promoters).
 Polymerase Chain Reaction (PCR)
 - Definition: In-vitro technique to exponentially amplify specific DNA regions (2^n copies).
 - Enzyme: Taq polymerase (thermostable).
 DNA Profiling (DNA Fingerprinting)
 - STRs (Short Tandem Repeats): Highly polymorphic units in non-coding regions, used as individual markers.
 Gel Electrophoresis
 - Purpose: Separates DNA by size; smaller fragments move farther/faster towards the positive electrode.
 Stem Cells
 - General Definition: Undifferentiated cells capable of self-renewal and differentiation.
 - Types: Totipotent (all embryonic + extra-embryonic), Pluripotent (all body cells), Adult (Multipotent) (restricted lineages).
 Somatic Cell Nuclear Transfer (SCNT) & Dolly
 - Process: Nuclear transfer from somatic cell into denucleated egg, creating a clone with nuclear DNA from donor and mitochondrial DNA from egg donor.
 Tissue Cloning (Therapeutic Cloning)
 - Creates genetically matched tissues/organs to avoid immune rejection.
 DNA Probes
 - Labeled single-stranded DNA/RNA fragments that hybridize to complementary targets.
 Genetic Testing Time-Points
 - Stages: Preconception, Preimplantation, Post-Implantation (Prenatal), Post-Delivery (Newborn).
 - Context terms: In vivo (within organism), In vitro (outside organism), In utero (within uterus).
 Gene Therapy & Genome Editing
 - Goal: Treat/cure disease by modifying genes.
 - Gene Silencing: Reduces/eliminates gene expression (e.g., siRNA, CRISPRi).
 - Gene Editing: Physically alters DNA sequence (insert, delete, substitute).
 - CRISPR/Cas9: Uses guide RNA to target Cas9 nuclease for DNA double-strand breaks.
 - Prime Editor: Introduces precise edits without double-strand breaks.
 Vaccines—Traditional vs. mRNA
 - Traditional: Delivers whole/weakened virus or antigen for immune stimulation.
 - mRNA Vaccines: mRNA encoding viral protein (e.g., spike) is delivered, host cells translate it to trigger an immune response.
 - mRNA Advantages: Rapid design, no live pathogen, strong immunity. Disadvantages: Ultra-cold storage, less stable.