Gen Bio Test 1

Biology is the study of living organisms and their interactions with each other and their environment. Despite huge diversity, living things share a set of defining properties:

• Order — complex, organized structure (cells, tissues, organs).

• Sensitivity / response to stimuli — reacting to changes in the environment.

• Reproduction — producing offspring.

• Growth and development — following specific genetic instructions.

• Regulation / homeostasis — maintaining a stable internal environment.

• Energy processing (metabolism) — using energy to carry out activities.

• Evolutionary adaptation — populations change over time in response to their environment.

Levels of biological organization

Biology can be studied at every scale, from a single atom to the entire planet. Each level is built from the one below it, and new ("emergent") properties appear at each step that aren't present in the parts alone:

atom → molecule → organelle → cell → tissue → organ → organ system → organism → population → community → ecosystem → biosphere

Why it mattersChapters 2–4 of this guide walk up the bottom rungs of this ladder in order: atoms and molecules (Ch. 2), the large biological molecules they build (Ch. 3), and the cell itself — the smallest unit that is actually "alive" (Ch. 4).

How biologists ask questions

The textbook distinguishes two complementary approaches to research. Discovery science is descriptive: collecting and analyzing data (often through observation) without necessarily testing a specific prediction — much of taxonomy and genome sequencing works this way. Hypothesis-based science follows a more structured cycle: make an observation → ask a question → form a hypothesis (a testable, falsifiable explanation) → predict what should be true if the hypothesis is correct → design a controlled experiment to test it → draw a conclusion and refine the hypothesis if needed. A good experiment isolates a single independent variable, includes a control group for comparison, and is repeated to check the result isn't due to chance.

Biology is also commonly divided by scale and specialty — e.g. molecular biology and biochemistry (the molecular level), cell biology and microbiology (the cellular level), physiology and anatomy (the organismal level), and ecology and evolutionary biology (populations and above) — mirroring the levels of organization above.

Ch. 2The Chemical Foundation of Life

Atoms, isotopes, ions, and bonds

Matter and elements

Matter is anything with mass that occupies space (solid, liquid, or gas). An element is a pure substance made of only one type of atom; there are 118 known elements (~94 occur naturally). Matter and energy are interchangeable (E = mc²); energy exists as potential, kinetic, chemical, or electrical forms.

About 96% of the mass of a living organism comes from just four elements: oxygen (~65%), carbon (~18%), hydrogen (~10%), and nitrogen (~3%). The rest is made up of mineral elements (Ca, P, K, Na, Cl, Mg, S) and trace elements (Fe, Zn, I, etc.).

Atomic structure

An atom is the smallest unit of an element that still has that element's properties. It has a central nucleus (protons, +; neutrons, neutral) surrounded by electrons (–) in shells/orbitals.

• Atomic number = number of protons — defines the element.

• Mass number = protons + neutrons.

• A neutral atom has equal protons and electrons; an ion has unequal numbers — a cation (+) has lost electrons, an anion (–) has gained them. Biologically important ions include Na⁺, K⁺, Ca²⁺, Mg²⁺, and H⁺ (cations) and Cl⁻, HCO₃⁻, and PO₄³⁻ (anions) — these drive nerve signaling, muscle contraction, and buffering throughout the body.

• Isotopes — atoms of the same element with different numbers of neutrons; same chemistry, different mass. Radioisotopes are unstable isotopes that decay, releasing energy (alpha/beta particles, gamma rays) at a constant rate (half-life).

Radioisotopes in practiceRadiometric dating uses a known half-life to estimate age: t = [ln(N/N₀) ÷ (–0.693)] × t½. Carbon-14 (t½ = 5,730 yr) dates material up to ~50,000 years old; Potassium-40→Argon-40 (t½ = 1.3 billion yr) and Uranium-235→Lead-207 (t½ = 710 million yr) date far older rock/fossil material.

Medical & other tracers: Iodine-131 (thyroid), Technetium-99m (bone imaging), labeled glucose (brain activity), Chromium-51 (red blood cells), Cobalt-60 (food irradiation), Americium-241 (smoke detectors). Radioisotopes are also mutagenic and can cause cancer.

Electron shells and the octet rule

Electrons fill the innermost shell first (max 2 electrons), then outer shells (max 8). Atoms with fewer than 8 electrons in their outermost shell are chemically reactive and tend to react to complete that shell — this is the octet rule. Atoms with ≤3 valence electrons tend to donate them; atoms with ≥5 tend to accept them.

Molecules, compounds, and bonds

A molecule forms when two or more atoms bond. If every atom is the same element it's a homonuclear molecule (O₂, N₂); if at least one atom differs, it's a compound (H₂O, CO₂). Bonds are classed as strong or weak:

Covalent bonds can share 1, 2, or 3 electron pairs (single, double, triple bonds). Ionic bonds form electrically neutral compounds; dissolved ions that conduct electrical current are called electrolytes (e.g. Na⁺, K⁺, Ca²⁺, Cl⁻ — essential in body fluids).

Free radicalsA free radical is an atom/molecule with a single unpaired electron in its outer shell — highly unstable. It reacts with other molecules to "steal" an electron, creating a new free radical and triggering a damaging chain reaction (oxidative stress), caused by radiation, toxins, inflammation, or normal metabolism. Antioxidants (vitamin C, vitamin E, flavonoids) can donate an electron to a free radical without themselves becoming reactive.

Water

Water (H–O–H) is a bent, polar molecule: oxygen pulls shared electrons closer, becoming slightly negative (δ–), while the hydrogens become slightly positive (δ+). This charge separation lets water molecules form weak hydrogen bonds with each other and with other polar molecules — individually fragile, but collectively very strong (they hold the shape of DNA and proteins).

Four life-sustaining properties of water

1. Temperature-stabilizing effects

   • High heat capacity — hydrogen bonds restrain molecular motion, so water resists rapid temperature change (thermal inertia). Water's specific heat (1 cal/g/°C) is roughly double that of most other common liquids, which is why large bodies of water buffer regional climate and why your body resists overheating or overcooling faster than it actually does.

   • High heat of vaporization — ~540 cal must be absorbed to evaporate each gram at 100 °C, which is why sweating is such an effective cooling mechanism.

   • High heat of fusion — raising water from 0→1 °C takes ~80 calories (vs. ~1 calorie for ice at –2→–1 °C), so ice stays cold far longer than liquid water at a similar temperature.

   • Ice is less dense than liquid water — bodies of water freeze top-down, and the ice layer insulates the water below, allowing aquatic life to survive winter.

2. Outstanding solvent properties — water is the "universal solvent." A solution = solvent (water) + solute. Polar/ionic compounds dissolve readily (hydrophilic); nonpolar compounds dissolve poorly (hydrophobic). This makes water the body's key transport medium (e.g. blood plasma).

3. Cohesion and adhesion — hydrogen bonds hold water molecules together (cohesion) and attract water to other polar surfaces (adhesion), together allowing water to be drawn upward through narrow plant vessels (capillary action/transpiration).

4. High surface tension — surface water molecules bond more tightly to each other than to the air above, forming an invisible "skin" strong enough to support small, nonpolar objects (leaves, water-striders).

Acids, bases, and pH

Water spontaneously ionizes: H₂O ⇌ H⁺ + OH⁻. Acids release H⁺ ions (sour, e.g. HCl); bases accept H⁺ or release OH⁻ (bitter, e.g. NaOH). The pH scale measures acidity: pH = –log₁₀[H⁺]. It is logarithmic — each whole-number change represents a 10-fold change in [H⁺] (pH 4 is 10× more acidic than pH 5).

pH affects the shape and function of molecules, reaction rates, binding between molecules, solubility, and the excitability of nerve and muscle cells — which is why organisms tightly regulate it (e.g. human blood: 7.35–7.45; living cells generally: 6.5–7.8).

BuffersBuffers are solutes that resist pH change by absorbing excess H⁺ or OH⁻. The main physiological buffer is the carbonic acid/bicarbonate system: H₂O + CO₂ ⇌ H₂CO₃ ⇌ H⁺ + HCO₃⁻ ⇌ 2H⁺ + CO₃²⁻ This same chemistry drives ocean acidification: rising atmospheric CO₂ dissolves into seawater, forms carbonic acid, releases H⁺, and lowers ocean pH — reducing the carbonate ions that corals and shelled organisms need to build CaCO₃ skeletons/shells.

Carbon — the segue into Chapter 3

Carbon forms 4 covalent bonds, making it an exceptionally versatile backbone for large molecules (allotropes like graphite, diamond, and nanotubes show this versatility even in pure carbon). Carbon chains can be linear, branched, or ringed, and can contain single, double, or triple bonds (e.g. ethane, ethene, ethyne).

Isomers share a molecular formula but differ in structure:

• Structural isomers — different bonding arrangement (e.g. butane vs. isobutane, both C₄H₁₀).

• Stereoisomers — same bonding, different spatial arrangement: geometric (cis–trans) isomers and optical isomers (enantiomers).

Organic molecules are further defined by their functional groups — small, reactive clusters of atoms attached to the carbon backbone:

Ch. 3Biological Macromolecules

All four classes of biomolecule are built the same two ways: dehydration (condensation) reactions join monomers by removing a water molecule; hydrolysis reactions break polymers apart by adding water back in.

Carbohydrates

General formula (CH₂O)ₙ. Function as an immediate energy source (converted to ATP), energy storage, and structural components; the most abundant organic molecules on Earth.

• Monosaccharides (monomer) — soluble, sweet; classified by carbon number (triose 3C, tetrose 4C, pentose 5C, hexose 6C, heptose 7C). Glucose and fructose are structural isomers of each other (aldose vs. ketose) and C₆H₁₂O₆ stereoisomers of other sugars.

• Disaccharides — two monosaccharides joined by a glycosidic bond via dehydration (glucose+fructose = sucrose; glucose+galactose = lactose). The bond is named for which carbons it links and their orientation — e.g. starch and glycogen are built almost entirely of α-1,4 linkages (with α-1,6 linkages at branch points), while cellulose's β-1,4 linkages produce straight, H-bonded chains that most digestive enzymes can't break — this single difference in bond geometry is why we can digest starch but not wood.

• Polysaccharides — long chains of monosaccharides; low solubility, not sweet.

  • Starch — plant energy storage (in amyloplasts), unbranched or branched.

  • Glycogen — animal energy storage, highly branched.

  • Cellulose — structural, found in plant cell walls; β-linkages make it indigestible by most animals.

Lipids

Nonpolar hydrocarbons, insoluble in water, and not true polymers. Roles include long-term energy storage, membrane structure, insulation, cushioning, and chemical signaling.

• Triacylglycerols (fats/oils) — glycerol + 3 fatty acids joined by ester bonds; the body's main long-term energy store.

• Fatty acids — saturated (no C=C double bonds, solid at room temp, e.g. butter) vs. unsaturated (one or more double bonds, usually cis, liquid at room temp, e.g. vegetable oil). Essential fatty acids (omega-3, omega-6, named for the position of the first double bond from the "omega" end) must come from the diet.

• Phospholipids — amphipathic (hydrophilic head, hydrophobic tails); the main component of the plasma membrane bilayer.

• Steroids/sterols — e.g. cholesterol, synthesized in the liver's ER; a precursor to vitamin D, bile acids, and sex hormones.

• Waxes — water-repellent, wear-resistant coatings.

Proteins

Monomer = amino acid (~20 naturally occurring). Each has a central carbon bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen, and a variable R group that gives each amino acid its unique chemistry. Amino acids are zwitterions (carry both + and – charges); pH changes alter this charge and therefore a protein's solubility and shape — every protein has an optimal pH.

Essential amino acids cannot be made by the body and must come from the diet. Animal proteins are generally "complete"; some plant proteins are low in specific essential amino acids (e.g. lysine, methionine, threonine, tryptophan) — combining sources (e.g. cereal + legume) yields a complete amino acid profile.

Amino acids are joined by peptide bonds (a dehydration reaction between the carboxyl group of one and the amino group of the next), building dipeptides, tripeptides, and polypeptides.

Four levels of protein structure

Proteins serve many roles: enzymes/hormones (metabolism), antibodies/toxins (defense), MHC proteins (cell recognition), hemoglobin/membrane transporters (transport), collagen/keratin (structure), actin/myosin (motion), albumin (osmotic regulation), and ferritin (storage).

Denaturation is the loss of protein structure from heat, pH, or chemical exposure. Misfolded proteins ("protein folding diseases") can result from defective chaperone molecules, and underlie conditions like prion disease, Alzheimer's, and cystic fibrosis.

Nucleic acids

Monomer = nucleotide: a 5-carbon sugar + a nitrogenous base + a phosphate group. Nucleotides link via phosphodiester bonds into long polynucleotide chains.

• DNA — double-stranded helix; two sugar-phosphate backbones held together by hydrogen bonds between complementary bases; stores genetic information.

• RNA — usually single-stranded; several types: mRNA (messenger), tRNA (transfer), rRNA (ribosomal); found in both the nucleus and cytoplasm.

The nitrogenous bases fall into two chemical families: double-ringed purines (adenine, A; guanine, G) and single-ringed pyrimidines (cytosine, C; thymine, T in DNA; uracil, U in RNA). A purine always pairs with a pyrimidine — A–T (2 hydrogen bonds) and G–C (3 hydrogen bonds) in DNA, or A–U in RNA — which keeps the double helix a uniform width and is the chemical basis of complementary base pairing used in DNA replication and transcription.

Nucleotide derivatives also carry chemical energy (e.g. ATP, in its easily-hydrolyzed phosphoanhydride bonds) and act as intracellular signaling molecules (e.g. cyclic AMP).

Ch. 4Cell Structure

Cell theory: all living organisms are composed of one or more cells; the cell is the basic unit of structure and organization in organisms; cells arise only from pre-existing cells (Hooke, Schleiden, Schwann). A functioning cell needs three minimum things: an information-storage system (DNA), separation from the outside world (a membrane), and metabolic machinery to replicate, synthesize proteins, and extract energy/nutrients.

Why cells stay smallCell size is limited by the surface area-to-volume (S/V) ratio. Surface area (the membrane, which governs nutrient/waste exchange) increases with the square of size, while volume (which demands nutrients and produces waste) increases with the cube. As a cell grows, volume outpaces surface area — which is why cells specialized for absorption (e.g. intestinal cells) fold their membrane into microvilli to boost surface area.

Studying cells: microscopy

Most cells are between 1 µm and 1 mm — far smaller than the unaided eye can resolve (limit ~0.2 mm). Resolution is the minimum distance at which two points can still be seen as distinct; it depends on the numerical aperture of the lens and the wavelength of the illumination used.

Variants of light microscopy exploit differences in a specimen without staining it: brightfield, phase contrast, and differential interference contrast (DIC) all use changes in the phase of light passing through regions of different density. Fluorescence microscopy is more sensitive and specific — it can selectively illuminate labeled structures, including those tagged with GFP (green fluorescent protein), a 28 kDa protein originally from the jellyfish Aequorea victoria, which can be fused to a protein of interest to track it inside living cells.

Prokaryotic cells

Two domains: Bacteria (ubiquitous, some pathogenic, some photosynthetic or decomposers — important in carbon cycling) and Archaea (often found in extreme habitats — extreme pH, temperature, or salinity — and more closely related to eukaryotes). Prokaryotic cells are generally small (1–5 µm), structurally simple, and lack a nucleus and membrane-bound organelles, but are functionally complex.

Common bacterial shapes: coccus (spherical — arranged as diplococci, tetrads, sarcina, staphylococci, or streptococci), bacillus (rod-shaped), and spiral (spirochetes, spirilla, vibrio).

Key structures

• Nucleoid — region where the bacterial chromosome is located (no membrane).

• Ribosomes — protein synthesis.

• Plasma membrane — regulates molecule entry/exit.

• Cell wall — supports, shapes, and protects the cell; made of peptidoglycan in bacteria, polysaccharides + proteins in archaea.

• Glycocalyx — gel-like outer coating; a capsule if compact, a slime layer if diffuse.

• Flagellum — rotating filament for movement; fimbriae — hairlike bristles for surface adhesion; sex pilus — used for DNA transfer between cells.

• Mesosome — infolding of the plasma membrane that increases surface area.

• Inclusion bodies — stored nutrients for later use.

Gram-positive bacteria have a thick peptidoglycan wall with lipoteichoic acid; Gram-negative bacteria have a thinner peptidoglycan layer plus an outer membrane (with lipopolysaccharide and porins) and a periplasmic space. Archaeal membrane lipids are ether-linked with branched isoprenoid chains, distinct from the ester-linked, unbranched fatty acids of bacteria/eukaryotes.

Not always unicellularUp to ~80% of bacterial and archaeal cells live in organized, multicellular-like communities called biofilms, rather than as free-floating single cells.

Eukaryotic cells

Larger and more complex than prokaryotic cells, with DNA enclosed in a true, membrane-bound nucleus. Compartmentalization into membrane-bound organelles lets eukaryotic cells grow larger and isolate chemical reactions from one another — though organelles still communicate via chemical signaling, vesicular transport, and membrane contact sites. The fluid surrounding the organelles is the cytosol.

Organelles and structures

• Plasma membrane — phospholipid bilayer with embedded proteins; regulates transport, provides a surface for reactions, and mediates sensitivity/protection.

• Cell wall (plants, fungi, some protists — not animals) — cellulose + other polysaccharides + proteins; maintains shape, protects from mechanical damage.

• Nucleus — the cell's "command center"; double membrane (nuclear envelope) with pores that regulate exchange with the cytoplasm; contains chromatin and a nucleolus (rRNA synthesis / ribosome assembly).

• Ribosomes — rRNA + protein, made of a large and small subunit; free in the cytoplasm (singly or as polyribosomes), bound to rough ER, or found in mitochondria/chloroplasts.

• Rough ER — ribosome-studded; folds/sorts proteins, adds carbohydrates (glycosylation) or lipids, synthesizes phospholipids.

• Smooth ER — no ribosomes; synthesizes/modifies lipids, carbohydrates, and hormones; detoxifies; stores Ca²⁺.

• Golgi apparatus — modifies and packages proteins/lipids into vesicles; receives from the ER at the cis face, ships from the trans face (within the cell, or out via secretion/exocytosis).

• Lysosomes — membrane-bound sacs of hydrolytic enzymes (low pH, ~5) that break down cellular debris, misfolded proteins, defective organelles (autophagy), or ingested pathogens (phagocytosis).

• Vacuoles — storage, osmoregulation (contractile vacuoles), or lytic functions; the plant central vacuole can occupy up to 90% of a cell's volume and maintains turgor pressure.

• Peroxisomes — oxidize fatty acids (α/β-oxidation), generate and break down hydrogen peroxide via catalase, and neutralize reactive oxygen species. (Zellweger syndrome results from an absence/reduction of peroxisomes.)

The endosymbiont theoryMitochondria and chloroplasts are thought to have originated as free-living bacteria engulfed by an ancestral eukaryotic cell, which escaped digestion and evolved in symbiosis with their host. Evidence includes their own DNA and the fact that both organelles still divide independently by fission. Mitochondria likely derive from purple (α-proteo-)bacteria; chloroplasts from cyanobacteria.

• Mitochondria — double membrane; inner membrane folds into cristae (↑ surface area); the matrix holds respiratory enzymes; the main site of cellular respiration/ATP production, also involved in molecule synthesis/degradation and heat generation (brown fat).

• Chloroplasts — double membrane; stacks of disc-like thylakoids (a stack = granum) suspended in the stroma; contain chlorophyll (green, photosynthetic pigment); the site of photosynthesis.

The cytoskeleton

A dynamic network of protein fibers that maintains cell shape and assists movement of the cell and its organelles — assembling and disassembling as needed. Three fiber types:

Centrioles are made of 9 overlapping microtubule triplets (one pair per animal cell) and separate during mitosis. Cilia and flagella share a "9+2" arrangement of microtubules (9 outer pairs + 2 central singles); cilia are shorter and move in coordinated waves, while flagella are longer and move like a propeller.

How cells connect to each other

Multicellular eukaryotic cells also physically link to their neighbors and to the extracellular matrix. Animal cells use three main junction types:

• Tight junctions — press adjacent membranes tightly together, blocking fluid from leaking between cells (e.g. lining the bladder and gut).

• Desmosomes — act like rivets, anchoring intermediate filaments between cells to resist mechanical stress (abundant in skin).

• Gap junctions — channels that directly connect the cytoplasm of neighboring cells, allowing ions and small molecules to pass between them (important in cardiac muscle, for coordinated contraction).

Plant cells, which have rigid walls, instead use plasmodesmata — channels through adjoining cell walls that connect the cytoplasm of neighboring cells, functionally similar in role to animal gap junction