Introduction to Biology: Key Terms and Concepts 4

Theme 1: Evolution is the core theme of biology

• Life is distinguished by unity and diversity; evolution explains both unity and diversity.
• Darwin + natural selection: organisms with traits better suited to their environment have higher survival and reproduction, passing traits to next generation.
• Process outcome: populations change over time as advantageous traits become more frequent.
• Example of natural selection dynamics: populations with varied inherited traits; elimination of less-fit traits increases the frequency of advantageous traits over generations when resources are limited.
• Unity and diversity are connected through evolution; all life shares a common ancestry yet has diversified into many forms.

Theme 2: Life depends on the flow of information

• DNA stores genetic information and programs cellular activities by encoding proteins via transcription and translation.
• Central Dogma (Big Idea): ext{DNA}
  ightarrow ext{RNA}
  ightarrow ext{Protein}
• Genes in DNA are used to make proteins; RNA serves as the intermediary (mRNA, tRNA, rRNA).
• RNA plays multiple roles in protein synthesis and gene expression; the ribosome translates RNA into a chain of amino acids.

Theme 3: Structure and function are related

• At all life levels, structure determines function.
• Example: protein structure affects function; hemoglobin’s quaternary structure enables efficient oxygen transport.
• Molecular structure and bonding patterns shape macromolecule function.

Theme 4: Life depends on the transfer and transformation of energy and matter

• Energy flow in ecosystems is unidirectional: sunlight → chemical energy via producers → consumers → heat loss.
• Matter cycles within ecosystems: atmosphere, soil, producers, consumers, decomposers, back to environment.
• Roles in ecosystems:
  • Producers (photosynthesizers) create chemical energy from light.
  • Consumers obtain energy by eating others.
  • Decomposers recycle nutrients back to the environment.
• Energetics: energy transfer is inefficient; some energy is lost as heat at each transfer.
• Matter cycling examples: carbon, nitrogen, phosphorus cycles.

The Scientific Method and Science as a Way of Knowing

• Science is a method of answering questions using observations and experiments; evidence-based inquiry.
• Steps: Observe → Question → Hypothesize → Test → Analyze → Conclude → Share.
• Hypotheses must be testable; non-testable explanations (supernatural) are outside science.
• Hypothesis testing uses controlled experiments:
  • Independent variable: the factor deliberately changed.
  • Dependent variable: the measured outcome.
  • Control group: used for comparison; isolates the effect of a single variable.
• Data types: quantitative vs. qualitative.
• A theory is a well-supported explanation backed by multiple lines of evidence.
• Feedback regulation in biology: negative feedback reduces the initial stimulus; positive feedback amplifies a product.

Chemistry for Biology: Atoms, Bonds, and Water

• Atoms: basic unit of matter; composed of protons, neutrons, electrons; atomic number = number of protons; atomic mass ≈ protons + neutrons.

• Ions and isotopes:

  • Ions: atoms with a net charge due to loss/gain of electrons (e.g., Na⁺, Cl⁻).
  • Isotopes: same proton/electron count, different neutron numbers; may be stable or radioactive.

• Valence electrons: electrons in the outermost shell; determine bonding behavior; octet rule drives bond formation.

• Types of bonds:

  • Ionic bonds: transfer of electrons, forming oppositely charged ions.
  • Covalent bonds: sharing of unpaired electrons; can be nonpolar (even sharing) or polar (uneven sharing).
  • Hydrogen bonds: weak attractions between partially charged regions of polar molecules (e.g., H–O–H interactions in water).

• Water properties:

  • Water is a polar molecule with two covalent bonds to H and a V-shaped geometry; polarity drives solvent power and hydrogen bonding.
  • Water exhibits cohesion (molecules stick together) and adhesion (water sticks to other surfaces).
  • High specific heat and high heat of vaporization: water stabilizes temperatures and buffers environmental fluctuations.
  • Water as solvent: dissolves many solutes; forms aqueous solutions.
  • Ice floats: water density decreases upon freezing due to hydrogen bonding arrangements, insulating liquid water below.

• pH, acids, and bases:

  • pH measures hydrogen ion concentration: ext{pH} = -\log [H^+].
  • Most biological fluids are around pH 6–8; buffers stabilize pH.
  • A buffer system typically contains a weak acid and its conjugate base.

• Organic chemistry basics:

  • Carbon’s tetravalence enables diverse organic frameworks; carbon skeletons form the backbone of most biomolecules.
  • Functional groups (e.g., hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl) confer specific properties and reactivity.
  • Isomerism: compounds with the same formula but different structures have different properties (e.g., glucose vs. fructose).
  • Alpha and beta glycosidic linkages in carbohydrates define polysaccharide structure (alpha-1,4 vs. beta-1,4 linkages).

Biomolecules: Macromolecules, Monomers, and Polymers

• Macromolecules (biomolecules) are large polymers built from monomers via dehydration synthesis; broken by hydrolysis.
• General formula for dehydration synthesis:
  • ext{Monomer}1 + ext{Monomer}2
    ightarrow ext{Polymer} + H_2O
• Hydrolysis reaction (breakdown):
  • ext{Polymer} + H2O ightarrow ext{Monomer}1 + ext{Monomer}_2
• The four major classes: carbohydrates, proteins, nucleic acids, lipids.
• Monomers and polymers: monomers link to form polymers; polymerization requires energy input for most anabolic reactions.
• Lipids are not polymers but are diverse hydrophobic molecules; major types include fats (triglycerides), phospholipids, and steroids.
• ATP as energy currency: hydrolysis yields energy for cellular processes (e.g., ext{ATP} + H2O ightarrow ext{ADP} + ext{P}i + ext{energy}).

Carbohydrates

• Monosaccharides: simple sugars (general formula ext{C}n ext{H}{2n} ext{O}_n); key examples include glucose and fructose.
• Disaccharides: two monosaccharides linked by a glycosidic bond (e.g., maltose from two glucose units).
• Polysaccharides: many sugar units; starch and glycogen store energy; cellulose is structural in plants; chitin forms arthropod exoskeletons.
• Glycosidic linkages:
  • Alpha (α) linkages: typically for energy storage polysaccharides (e.g., starch, glycogen).
  • Beta (β) linkages: provide structural rigidity (e.g., cellulose).
• Functions: energy storage (starch, glycogen) vs. structural support (cellulose, chitin).

Lipids

• Fats (triglycerides): glycerol backbone with three fatty acids; energy-dense storage (
  E ext{ per gram} o ext{fat} ext{ ~ } 9 ext{ kcal/g}).
• Phospholipids: glycerol, two fatty acids, and a phosphate group; form lipid bilayers; amphipathic (hydrophilic heads, hydrophobic tails).
• Steroids: four fused rings (e.g., cholesterol, sex hormones).
• Membranes: phospholipid bilayer with embedded proteins; cholesterol modulates fluidity; carbohydrate groups on lipids/proteins contribute to cell identity.

Proteins

• Functions: enzymes, transport, defense (antibodies), signaling, regulation, receptors, contraction, structure, storage.
• Amino acids: building blocks with amino group, carboxyl group, hydrogen, and a distinct R group; 20 standard amino acids; classification by side chain properties (nonpolar, polar, charged).
• Peptide bonds connect amino acids via dehydration synthesis; polypeptide chains form proteins.
• Four levels of protein structure:
  • Primary: sequence of amino acids; stabilized by peptide bonds.
  • Secondary: hydrogen bonds along the backbone form alpha helices or beta-pleated sheets.
  • Tertiary: three-dimensional shape arising from interactions among R groups (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).
  • Quaternary: interaction of multiple polypeptide subunits to form a functional protein.
• Denaturation: disruption of protein structure by heat, pH, or salts, altering function.
• Examples of protein roles: enzymes (catalysis), antibodies (defense), collagen (structure), hemoglobin (oxygen transport).

Nucleic Acids

• DNA and RNA store and transmit hereditary information; polymers of nucleotides.
• Nucleotides consist of a sugar (deoxyribose in DNA; ribose in RNA), a phosphate group, and a nitrogenous base.
• DNA structure:
  • Double helix; antiparallel strands; base pairing: A pairs with T, C pairs with G; hydrogen bonds stabilize pairs.
  • Directionality: 5' to 3' direction; phosphodiester backbone.
  • DNA length per turn: ~3.4 ext{ nm} with ~10 base pairs per turn.
• RNA structure: typically single-stranded; base pairing within a strand can form stems and loops; important for various roles in protein synthesis (mRNA, tRNA, rRNA).
• Central dogma (reiterated): DNA → RNA → Protein; transcription in nucleus; translation at ribosome in cytoplasm.
• Nucleic acid architecture: nucleotides linked by phosphodiester bonds; sugar-phosphate backbone, bases project inward; complementary base pairing enables replication and transcription.

Evolutionary and Genetic Contexts

• Lactase persistence: lactose tolerance in some human populations due to mutations in LCT gene and regulatory regions (MCM6) that keep lactase expression active into adulthood.
• Gene regulation: LCT gene expression is influenced by regulatory mutations; lactose tolerance illustrates evolutionary adaptation in humans.
• Endosymbiotic theory: mitochondria and chloroplasts originated from free-living prokaryotes that were taken up by ancestral eukaryotes; evidence includes:
  • Mitochondria and chloroplasts have their own circular DNA and ribosomes similar to bacteria.
  • They have double membranes and reproduce by binary fission-like processes.
  • Machineries resemble bacterial components more than nuclear eukaryotic components.

Origin of Life and Early Earth

• Early Earth conditions: formation ~4.6 billion years ago; hot, volatile environments; UV radiation, lightning, volcanic activity.
• Abiotic synthesis of organic molecules under reducing atmosphere with energy input (lightning, UV) suggested by Oparin-Haldane and later tested by Miller-Urey experiments.
• Four-stage origin model:
  1) Abiotic synthesis of small organic molecules (amino acids, nitrogenous bases).
  2) Polymerization of small molecules into proteins and nucleic acids.
  3) Formation of protocells (lipid membranes surrounding polymers).
  4) Emergence of self-replicating molecules enabling inheritance.
• RNA world hypothesis: RNA may have served as both genetic material and catalyst before DNA-based systems; ribozymes show RNA’s catalytic potential; DNA later supplanted RNA as genetic material due to stability.

Origin and Evolution of Cells

• Cell theory: cells are the basic units of life; all cells arise from pre-existing cells; all living things composed of cells.
• Prokaryotic vs. Eukaryotic cells:
  • Prokaryotes: smaller (1–10 μm), no membrane-bound organelles, nucleoid region containing DNA.
  • Eukaryotes: larger (5–100 μm), nucleus enclosed by a membrane, membrane-bound organelles.
• Endomembrane system in eukaryotes: nucleus, ER, Golgi, lysosomes, vacuoles, plasma membrane; vesicle-mediated transport.
• Organelles and functions:
  • Nucleus: houses DNA, transcription occurs here; chromatin = DNA + histones; nucleolus = ribosome synthesis site.
  • Endoplasmic reticulum (ER): Rough ER has ribosomes for protein synthesis; Smooth ER synthesizes lipids and processes toxins; stores calcium.
  • Golgi apparatus: modifies, sorts, and ships proteins; vesicle trafficking.
  • Lysosomes: digest cellular waste and ingested materials.
  • Mitochondria: site of cellular respiration; energy production (ATP).
  • Chloroplasts: site of photosynthesis in plants/algae.
  • Vacuoles: storage and maintenance; central vacuole in plants.
  • Peroxisomes: breakdown of fatty acids and detoxification.
  • Ribosomes: synthesize proteins; composed of rRNA and proteins; can be free or bound to ER.
• Cytoskeleton: three types of filaments provide structure and transport:
  • Microfilaments (actin): support cell shape, enable movement and contraction.
  • Intermediate filaments: provide tensile strength and anchor organelles.
  • Microtubules: tracks for vesicle movement; form spindle apparatus during cell division; form cilia and flagella.
• Cellular junctions in animal tissues: tight junctions (seal sheets), desmosomes (anchor cells), gap junctions (cytoplasmic channels).
• Plant cells have cell walls (cellulose) and plasmodesmata (cytoplasmic channels between plant cells) that facilitate intercellular communication.

The Cell as a System: Membranes and Transport

• Phospholipid bilayer: phospholipids with hydrophilic heads and hydrophobic tails form a bilayer; membranes are fluid and permeable selective barriers.
• Membrane proteins: transport, receptors, enzymes; integral and peripheral proteins contribute to function.
• ECM (extracellular matrix) in animals: glycoproteins (collagen, laminin) and proteoglycans; integrins connect ECM to the cytoskeleton; ECM regulates cell behavior and tissue integrity.
• Cell walls and plasmodesmata in plants provide structural support and intercellular communication.

Cells and Tissues: How Form Fits Function

• Plant vs. animal cells: plants have cell walls, chloroplasts, large central vacuoles; animals rely on ECM and cell junctions for tissue integrity.
• The plasma membrane as a selective barrier: controls entry/exit of substances; surface area-to-volume ratio governs exchange efficiency.
• The size of cells: smaller cells have higher surface area-to-volume ratios, enabling efficient exchange with the environment.
• Mitochondria and chloroplasts as energy processors: mitochondria harvest chemical energy; chloroplasts convert light energy to chemical energy via photosynthesis.

Evolutionary Connections and Human Relevance

• Lactase persistence as an example of recent human evolution; variations in LCT and regulatory regions allow adults to digest lactose in certain populations.
• Climate change context: human activities (fossil fuel burning) increase CO₂, leading to climate changes that affect ecosystems and species distributions.
• Ethical and practical implications: science informs public health, conservation, and policy; critical thinking about data and evidence is essential.

Summary of Key Equations, Concepts, and Structures

• Central Dogma: ext{DNA}
  ightarrow ext{RNA}
  ightarrow ext{Protein}
• pH: ext{pH} = -
  \log [H^+]
• Dehydration synthesis (polymers formed): ext{Monomer}1 + ext{Monomer}2
  ightarrow ext{Polymer} + H_2O
• Hydrolysis (polymers broken): ext{Polymer} + H2O ightarrow ext{Monomer}1 + ext{Monomer}_2
• ATP hydrolysis energy release: ext{ATP} + H2O ightarrow ADP + Pi + ext{energy}
• Energy in fats: E_{ ext{fat}} \approx 9 \, \text{kcal/g}
• DNA base pairing: A↔T, C↔G; bases pair via hydrogen bonds; antiparallel strands with 5' to 3' orientation; double helix ~ 3.4 nm per turn, 10 bp per turn.
• Glycosidic linkages in carbohydrates: α-1,4 vs β-1,4 linkages determine starch/glycogen vs cellulose structure.
• Major macromolecule classes and monomers: Carbohydrates (monosaccharides), Proteins (amino acids), Nucleic acids (nucleotides), Lipids (not polymers but include triglycerides, phospholipids, steroids).
• Four levels of protein structure: Primary → Secondary (α-helix, β-pleated sheet) → Tertiary (R-group interactions) → Quaternary (subunits).

Quick Reference: Taxonomy and Evolution

• Tree of life: Bacteria, Archaea, Eukarya; domains reflect major lineage differences.
• Binomial nomenclature: genus and species (e.g., Homo sapiens).
• Taxonomic ranks mnemonic: Did King Phillip Come Over For Good Soup (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species).
• Emergent properties: new properties appear at each higher level of organization due to interactions among components (e.g., properties of water emerge from H and O bonds).

Note on the Exam-Prep Perspective

• Be able to explain how evolution accounts for both unity and diversity of life, give examples of adaptations, and describe how natural selection operates on genetic variation.
• Be able to describe the central dogma, transcription/translation steps, and the role of ribosomes.
• Understand the four major biomolecule classes, their monomers/polymers, and how dehydration and hydrolysis reactions build/destroy polymers.
• Explain cell theory, differences between prokaryotic and eukaryotic cells, and the roles of organelles in the endomembrane system.
• Understand the structure-function relationship across biological scales, from molecules to ecosystems, including energy flow and matter cycling in ecosystems.
• Be able to discuss origins of life experiments (Miller-Urey), RNA world hypothesis, and endosymbiotic theory for mitochondria and chloroplasts.
• Recognize the scientific method, hypothesis testing, and experimental design concepts (independent/dependent variables, controls).
• Recognize how plants and animals differ at the cellular level (cell walls, ECM, junctions) and how membranes and lipids contribute to cellular compartmentalization and homeostasis.