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Biology Study Notes: Cells, Chemistry, and Biomolecules

Features of Life, Organisms, and the Scientific Method

  • Features of Life
    • Living things are made up of one or more cells.
    • Cells require energy for growth, reproduction, and maintaining stability (homeostasis).
    • Homeostasis involves keeping internal and external environments stable—especially chemically.
    • Example: Humans use energy from food to grow and repair tissues.
  • Types of Organisms
    • Producers (Autotrophs): Use energy from the sun to make food (e.g., plants).
    • Consumers: Eat other organisms to obtain energy (e.g., cows, humans).
    • Decomposers: Break down dead organisms (e.g., fungi, bacteria).
    • Consumers are further divided into:
    • Primary consumers (herbivores): Eat plants.
    • Secondary consumers (carnivores/omnivores): Eat herbivores.
    • Tertiary consumers (top predators): Eat other carnivores.
    • Example: Cows (primary consumer) eat grass; wolves (secondary consumer) eat other animals.
  • The Scientific Method
    • Ask a question based on observations.
    • Do background research and check reliable sources.
    • Formulate hypotheses and test them experimentally.
    • Analyze data, communicate results, and revise based on new evidence.
    • Example: Testing which fertilizer helps plants grow fastest.

Limitations of Science

  • Science cannot answer questions about the meaning of life or personal beliefs.
  • It relies on evidence, not opinions or biases.

Atoms, Elements, and Essential Concepts

  • Atomic structure basics
    • Atoms: Smallest units of matter retaining elemental properties.
    • Elements: Pure substances that cannot be broken down by chemical or physical means.
    • There are ~90 naturally occurring elements; additional synthesized elements exist.
    • Essential elements for life: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O); Trace elements are needed in small amounts.
  • Atomic structure and isotopes
    • Subatomic particles: Protons (+), Neutrons (neutral), Electrons (−).
    • Atomic number Z = number of protons (and usually electrons in a neutral atom).
    • Mass number A = protons + neutrons.
    • Ions: Atoms with a charge due to loss or gain of electrons.
    • Isotopes: Atoms of the same element with different numbers of neutrons (e.g., Carbon-12, Carbon-13, Carbon-14).
  • The Periodic Table and bonding basics
    • Elements arranged by increasing atomic number; groups share properties.
    • Chemical bonds form via electron interactions to achieve stable electron configurations.
    • Key relationships:
    • Protons = Atomic number
    • Neutrons = Mass number − Atomic number
    • Electrons = Protons (in neutral atoms)
    • Common bond types: Ionic, Covalent (nonpolar and polar), Hydrogen bonds (intermolecular, especially in water).
  • Water and properties
    • Water is a polar solvent that dissolves many substances; participates in condensation and hydrolysis reactions.
    • Water has high heat capacity and significant role in temperature regulation.
    • Hydrogen bonds contribute to water’s cohesion and unique properties.
    • Hydrophilic vs. Hydrophobic substances determine solubility behavior.
  • Acids, bases, and pH
    • pH measures hydrogen ion concentration; scale is 0 (acidic) to 14 (basic) with 7 neutral.
    • Blood pH is tightly regulated, around
      ext{pH} \, \approx \, 7.4
    • Acids donate H⁺; bases accept H⁺; strong acids dissociate fully; weak acids dissociate incompletely.
  • Oxidation and free radicals
    • Oxidation involves electron transfer.
    • Free radicals have unpaired electrons; can cause cellular damage but are also involved in signaling.
    • Antioxidants neutralize free radicals (e.g., Vitamin C).
  • Compounds, elements, and mixtures
    • Elements: Pure substances consisting of one type of atom.
    • Compounds: Substances formed from two or more elements in fixed proportions (e.g.,
      ext{H}_2 ext{O}, \ \text{NaCl}).
    • Mixtures: Physical combinations of two or more substances with variable composition (e.g.,
      ext{salt+water}).
    • Separation:
    • Compounds require chemical reactions to separate.
    • Mixtures can be separated physically.

Cells, Organisms, and Cell Theory

  • The Cell Theory
    • All living organisms are made up of one or more cells (unicellular or multicellular).
    • The cell is the basic unit of life.
    • All cells arise from pre-existing cells.
    • Cells carry out all essential life functions (energy use, growth, reproduction).
  • General characteristics of cells
    • Use energy (metabolism).
    • Contain genetic material (DNA).
    • Have a cell (plasma) membrane.
    • Contain cytoplasm.
    • Can communicate and interact with other cells.
    • Example: Humans are multicellular; bacteria are unicellular.
  • Types of cells
    • Prokaryotic cells (e.g., bacteria, archaea):
    • No nucleus; DNA in the cytoplasm.
    • No membrane-bound organelles.
    • Usually smaller and simpler.
    • Eukaryotic cells (e.g., human, plant cells):
    • Have a nucleus with DNA inside.
    • Contain membrane-bound organelles (mitochondria, Golgi, etc.).
    • Larger and more complex.
  • Human body cell facts
    • Only about 20 ext{%} of cells in the body are human; the rest are mostly bacteria (microbiota).
    • The type and number of bacteria vary between people and body sites (e.g., gut bacteria help digestion and immunity).
  • Common cell structures
    • Plasma (cell) membrane: Semi-permeable barrier; controls movement of substances in and out of the cell.
    • Cytoplasm: Gel-like fluid inside the cell where organelles are suspended.
    • DNA: Genetic material; inside the nucleus in eukaryotes or in the cytoplasm in prokaryotes.
    • Example: All cells have a plasma membrane, cytoplasm, and DNA.
  • Plasma membrane details
    • Phospholipid bilayer with hydrophilic (polar) heads and hydrophobic (nonpolar) tails.
    • Contains proteins (integral, peripheral), glycoproteins, and glycolipids for communication and transport.
    • Selectively permeable: small nonpolar molecules diffuse easily; others require transport proteins.
    • Examples: Oxygen (O₂) and carbon dioxide (CO₂) diffuse directly; glucose and ions need transporters.
  • Transport across membranes
    • Passive transport: No energy; moves down a concentration gradient.
    • Diffusion
    • Osmosis (water movement)
    • Facilitated diffusion (via transport proteins)
    • Active transport: Requires energy (ATP) to move substances against their gradient;
    • Example: Sodium-potassium pump (Na⁺/K⁺-ATPase) as an active transporter.

Cell Organelles, Structure, and Function

  • Major organelles and functions
    • Nucleus: Contains DNA; control center of the cell.
    • Ribosomes: Sites of protein synthesis; in cytoplasm or on rough endoplasmic reticulum (RER).
    • Endoplasmic reticulum (ER):
    • Rough ER: Ribosomes present; makes and processes proteins.
    • Smooth ER: Synthesizes lipids and steroids.
    • Golgi apparatus: Packages and ships proteins and lipids.
    • Lysosomes: Digest and recycle cellular waste and foreign material.
    • Mitochondria: Powerhouse of the cell; site of cellular respiration and ATP production.
    • Cytoskeleton: Network of protein filaments for structure, support, and movement.
    • Cytoskeleton components:
    • Microfilaments (Actin): Cell movement and shape.
    • Intermediate Filaments: Mechanical strength (e.g., keratin).
    • Microtubules (Tubulin): Move chromosomes during cell division; tracks for organelle movement; cilia and flagella are made of microtubules.
  • Energy and metabolism in cells
    • Cells use ATP (adenosine triphosphate) for energy.
    • Major metabolic pathways:
    • Anabolism: Building up molecules (e.g., protein synthesis).
    • Catabolism: Breaking down molecules (e.g., glucose breakdown for energy).
  • Cellular respiration steps (mitochondria)
    • Glycolysis (in cytoplasm):
    • ext{Glucose}
      ightarrow 2\ pyruvate + 2\ ATP
    • Citric acid (Krebs) cycle (in mitochondria):
    • Pyruvate is broken down; products include 2\ ATP, CO2, $NADH, and $FADH2$.
    • Electron transport chain (ETC) (in mitochondria):
    • Uses electrons from NADH and FADH₂ to produce about 32\ ATP; oxygen is the final electron acceptor, producing water.
    • Overall ATP yield from glucose (aerobic):
    • \text{ATP yield (aerobic)} \approx 36\ \text{ATP per glucose}
  • Examples
    • After running, muscles may produce lactic acid when oxygen is limited (fermentation).
    • Fats and proteins can also be broken down for energy.
  • Other important terms
    • Osmosis: Movement of water from low solute concentration to high solute concentration across a semi-permeable membrane.
    • Tonicity:
    • Isotonic: Equal solute inside and outside; cell size unchanged.
    • Hypotonic: Lower solute outside; water enters; cell swells.
    • Hypertonic: Higher solute outside; water leaves; cell shrinks.
    • Endocytosis: Bulk import of material into the cell.
    • Exocytosis: Bulk export of material out of the cell.

Quick Reference and Study Tips

  • Quick Reference: Prokaryote vs Eukaryote; Organelles; ATP yield from glucose.
  • Tips for studying
    • Draw and label cell diagrams with key organelles.
    • Make flashcards for organelle functions and transport types.
    • Practice explaining cell respiration steps aloud.
    • Connect examples to each concept (e.g., muscle fatigue = lactic acid production).
    • Relate atoms, elements, and bonds to real-world examples.

Levels of Biological Organization and Organ Systems (Human Biology Focus)

  • Major levels (simplest to most complex):
    • Atoms, Molecules, Organelles, Cells, Tissues, Organs, Organ systems, Organisms, Populations, Communities, Ecosystems, Biosphere
  • Cells and Tissues
    • Four main tissue types:
    • Epithelial tissue: Covers surfaces and lines cavities (e.g., skin, gut lining).
    • Connective tissue: Provides support and structure (e.g., bone, blood, tendons).
    • Muscle tissue: Movement (e.g., skeletal muscle, heart).
    • Nervous tissue: Communication (e.g., brain, spinal cord, nerves).
  • Organ Systems
    • Circulatory and respiratory systems interact to supply oxygen to tissues.
    • Pathway of a nerve impulse: Sensory receptor → sensory neuron → brain → motor neuron → effector (muscle/gland).
    • Digestion: Trace the journey of a food molecule from ingestion to absorption (mouth, esophagus, stomach, small intestine; absorption in small intestine).
  • Genetics and Development
    • DNA role: Heredity; genetic information passed from parent to offspring via egg and sperm.
    • Mutations and DNA repair: Mutations can impact health; repair mechanisms fix errors during replication.
    • Embryonic development: Major stages and their significance (brief overview).

Health, Ethics, and Society in Medicine

  • Health disparities
    • Systematic differences in health or health risks experienced by disadvantaged groups (racial/ethnic minorities, sexual/gender minorities, rural populations, socioeconomically disadvantaged).
  • Ethical issues in medical research
    • Informed consent: Participation must be voluntary and informed.
    • Beneficence: Research should benefit society, not exploit participants.
    • Historical examples: HeLa cells used without consent; Dr. J. Marion Sims surgeries without anesthesia or consent; Tuskegee Syphilis Study.
    • Regulations: Institutional guidelines and ethical codes (e.g., Nuremberg Code).
  • Animal research ethics
    • Minimize pain and use the smallest number of animals necessary; follow guidelines.
  • Review prompts and examples
    • Protein structure example: Hemoglobin quaternary structure (four chains).
    • Energy example: ATP production from glucose in muscle during exercise.
    • Transport example: Kidney sodium transport via active transport.
    • Signaling example: Insulin signaling for glucose uptake.
    • Ethical example: HeLa cells in cancer research and informed consent.

Cell Communication and Environmental Response

  • Overview of cell communication
    • Cells communicate internally and externally to respond to their environment.
    • Communication can be extracellular (signals from outside) or intracellular (signals inside after response starts).
    • Cell-to-cell communication forms: autocrine, paracrine, endocrine.
  • Ligands, receptors, and signaling steps
    • Ligand: signaling molecule (protein, lipid, or other biomolecule).
    • Receptor: protein on the cell surface that receives signals.
    • Three major steps: signal perception, signal transduction, cellular response.
  • Major sensing mechanisms
    • Diffusion: movement from high to low concentration.
    • Osmosis: water movement across a membrane.
    • Channels and carriers: passive transport via channels; pumps require energy (ATP).
    • Endocytosis & Exocytosis: bulk import/export via vesicles.
    • Cytoskeleton sensing: mechanical changes detected by cytoskeletal elements.
  • Types of cell signaling (examples)
    • Endocrine: hormones travel through blood to distant targets (e.g., adrenaline during fight/flight).
    • Paracrine: signals affect nearby cells (e.g., neurotransmitters between neurons).
    • Autocrine: signals affect the signaling cell itself (e.g., immune cells activating themselves).
  • Transport mechanisms and regulatory factors
    • Passive transport: diffusion, osmosis; no energy required.
    • Active transport: requires energy (ATP); pumps like Na⁺/K⁺-ATPase.
    • Co-transporters (symport): two substances move in the same direction (e.g., Na⁺ and glucose in intestinal cells).
    • Antiport: one substance moves in while another moves out (e.g., Na⁺/K⁺ exchanger).
  • Membrane permeability and cell responses
    • Size, charge, and concentration gradient influence permeability.
    • Cellular responses include changes in membrane permeability, protein expression, enzyme activity, and metabolic pathways (glycolysis, glycogen breakdown).
    • Possible outcomes: cell division or programmed cell death.

Hemispheres of Physiology: Homeostasis and Adaptation

  • Homeostasis and adaptation
    • Cells strive to maintain internal stability in response to stress.
    • Adaptation outcomes: cell survival with adjustment vs. cell death and replacement.
  • Organelles’ environmental regulation
    • Organelles maintain their own pH and environmental conditions (e.g., mitochondria slightly alkaline; lysosomes acidic).
    • Nucleus and nucleolus: gene expression and ribosome production.

Exam-Style Content and Diagrams

  • End-of-chapter prompts include:
    • Match each term with its definition (Prokaryote, Eukaryote, Organelle, Plasma membrane, Cytoplasm, Nucleus, Mitochondria, Ribosome).
    • Multiple-choice questions about cell structure and function (nucleus presence, plasma membrane function, Golgi role, diffusion vs active transport, osmosis).
    • True/False statements about active transport, osmosis, signaling, diffusion.
    • Short answer prompts on structural differences, mitochondria as powerhouses, ribosome roles, compartmentalization, diffusion vs facilitated diffusion, hypertonic effects, and signaling.
  • Diagram tasks may include labeling simple diffusion, facilitated diffusion, and active transport.

Examples and Connections to Foundational Principles

  • Example connections:
    • Hemoglobin’s protein structure relates to quaternary structure and function.
    • ATP production in mitochondria links to energy transformations in metabolism.
    • Kidney sodium transport demonstrates active transport in maintaining electrolytic balance.
    • Insulin signaling demonstrates endocrine communication and glucose uptake.
  • Foundational links:
    • Cell theory underpins all biology; structure and function of organelles enable life processes.
    • The chemistry of life (bonds, water, pH) underlies biomolecule behavior and cellular reactions.
    • Homeostasis ties together organ systems, signaling, and metabolism in health and disease.

Key Equations and Formulas (LaTeX)

  • Glycolysis (glucose to pyruvate and ATP):
    \text{Glucose} \rightarrow 2\ \text{pyruvate} + 2\ \text{ATP}
  • Krebs (Citric Acid) Cycle outputs per acetyl-CoA turn:
    \text{Per turn: } 2\ \text{ATP},\; \text{CO}2,\; \text{NADH},\; \text{FADH}2
  • Electron Transport Chain (ETC) ATP yield (mitochondria):
    \text{ATP}_{ETC} \approx 32\ \text{ATP}
  • Total ATP yield from glucose (aerobic):
    \text{ATP}_{\text{total}} \approx 36\ \text{ATP per glucose}
  • Blood pH reference:
    \text{Blood pH} \approx 7.4
  • Water: chemical formula
    \mathrm{H_2O}
  • Ionic compound example
    \text{NaCl}
  • Acids and bases (examples)
    • Strong acid dissociation: \text{HCl} \rightarrow \text{H}^+ + \text{Cl}^-
    • Weak acid example: \mathrm{CH_3COOH}
  • Osmosis definition (water movement):
    \text{Osmosis: water moves across a semi-permeable membrane from low solute to high solute}

Quick Reference Tables (conceptual, included in notes)

  • Prokaryote: no nucleus, small, bacteria/archaea, no membrane-bound organelles.
  • Eukaryote: nucleus, larger, plants/animals/fungi/protists.
  • Organelles: specialized structures (e.g., mitochondria, lysosomes).
  • ATP yield from glucose (aerobic): 36\ \text{ATP per glucose}$$

Quick Concepts for Review

  • Major cellular processes: diffusion, osmosis, facilitated diffusion, active transport, endocytosis, exocytosis.
  • Major macromolecules: proteins, carbohydrates, lipids, nucleic acids.
  • The four tissue types and their functions with examples.
  • Basic signaling modalities: autocrine, paracrine, endocrine.
  • Key ethical examples in health care: HeLa cells, Tuskegee, informed consent.
  • Laboratory concepts: dialysis tubing as a membrane model; tonicity (isotonic, hypertonic, hypotonic).