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
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.,
).Mixtures: Physical combinations of two or more substances with variable composition (e.g.,
).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):
Citric acid (Krebs) cycle (in mitochondria):
Pyruvate is broken down; products include $NADH,$FADH2$.
Electron transport chain (ETC) (in mitochondria):
Uses electrons from NADH and FADH₂ to produce about 32\ ATP\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}\text{Per turn: } 2\ \text{ATP},\; \text{CO}2,\; \text{NADH},\; \text{FADH}2\text{ATP}_{ETC} \approx 32\ \text{ATP}\text{ATP}_{\text{total}} \approx 36\ \text{ATP per glucose}\text{Blood pH} \approx 7.4\mathrm{H_2O}\text{NaCl}\text{HCl} \rightarrow \text{H}^+ + \text{Cl}^-\mathrm{CH_3COOH}\text{Osmosis: water moves across a semi-permeable membrane from low solute to high solute}36\ \text{ATP per glucose}222\sim 32\text{--}342 + 2 + 32\text{--}34 = 36\text{--}3836\text{--}38$$ ATP, acknowledging that the exact number can vary depending on cellular conditions and shuttle mechanisms.