DAT

Biology is the first and largest subtest of the Survey of the Natural Sciences: 40 of its 100 items, answered within the shared 90-minute block alongside General and Organic Chemistry. Questions span five content areas: cell and molecular biology; the diversity of life; the structure and function of organ systems; genetics; and evolution and ecology. Expect a mix of direct recall, mechanism-based reasoning, and experimental or data-interpretation items that ask what a result implies or what would happen if one step of a process were blocked.

Cell Theory and Cell Types

Cell theory holds that all living things are made of cells, the cell is the basic unit of structure and function, and all cells arise from pre-existing cells. Prokaryotic cells (bacteria and archaea) lack a membrane-bound nucleus; eukaryotic cells (animals, plants, fungi, and protists) have a nucleus and membrane-bound organelles.

Prokaryoticvs.Eukaryoticcells

Feature	ProkaryoticCells	EukaryoticCells
Nucleus	None;DNAliesinthenucleoidregion	Membrane-bound nucleus with a double-membrane
		envelope
Genome	Usuallyonecircularchromosome;	Multiplelinearchromosomespackagedwithhistones
	plasmidscommon
Ribosomes	70S(30S+50S)	80S (40S + 60S) in cytosol; 70S -like in mitochondria and
		chloroplasts
Organelles	No membrane-bound organelles	ER Golgi mitochondria lysosomes peroxisomes; , , , ,
		chloroplastsinplantsandalgae
Cytoskeleton	Simplehomologsofactinandtubulin	Microfilaments intermediatefilaments microtubules , ,
Transcriptionand	Coupledinthecytoplasm	Transcriptioninthenucleus;translationinthecytoplasm
translation
Size	Typically1–10µm	Typically10–100µm

Organelles and Their Functions

The plasma membrane is a phospholipid bilayer: hydrophilic phosphate heads face the aqueous environments on both sides, and hydrophobic fatty acid tails face inward. Embedded proteins act as channels, transporters, receptors, enzymes, and adhesion molecules. The fluid mosaic model describes lipids and proteins moving laterally within the bilayer; cholesterol buffers fluidity, and unsaturated (kinked) fatty acid tails increase it.

Structure	FunctionandKeyFeatures
Nucleus	HousesDNA;siteofreplicationandtranscription ChromatinisDNAwoundaroundhistoneproteins; .
	nuclearporescontroltraffic ThenucleolussynthesizesrRNAandassemblesribosomalsubunits . .
Ribosomes	Translate mRNA into polypeptides Free ribosomes make cytosolic proteins; ER -bound ribosomes .
	makesecreted membrane andlysosomalproteins , , .
RoughER	Ribosome-studded; co-translational insertion folding disulfide bonds and N -linked glycosylation of , , ,
	proteins .
SmoothER	Lipidandsteroidsynthesis carbohydratemetabolism detoxification(liver) andCa2+storage(the , , ,
	sarcoplasmicreticuluminmuscle) .
Golgiapparatus	Modifies (e .g O -linked glycosylation) sorts and packages proteins; receives vesicles on the cis face ., , ,
	andshipsfromthetransface .
Lysosomes	Acidic (pH ≈ 5) sacs of hydrolytic enzymes; digest engulfed material and worn-out organelles
	(autophagy) .
Peroxisomes	Oxidize very-long-chain fatty acids; produce and break down hydrogen peroxide with catalase .
Mitochondria	Siteofthecitricacidcycleandoxidativephosphorylation Doublemembrane;innermembranefolded .
	intocristae;owncircularDNAandribosomes(evidenceofendosymbioticorigin);maternally
	inherited .
Chloroplasts	Photosynthesisinplantsandalgae Doublemembraneplusinternalthylakoidsstackedintograna . ,
Centralvacuole(plants) Cellwall	surroundedbythestroma;ownDNA 1 . Storeswater ions andpigments;maintainsturgorpressure , , . Celluloseinplants chitininfungi peptidoglycaninbacteria;absentinanimalcells , , .

Element	Subunit	Roles
Microfilaments	Actin(≈7nm)	Cellshape cytoplasmicstreaming amoeboidmovement cleavagefurrow , , , ,
		musclecontractionwithmyosin
Intermediatefilaments	Keratin vimentin lamins(≈ , ,	Tensilestrength anchoringorganelles nuclearlamina , ,
	10nm)
Microtubules	α/β -tubulin dimers (≈ 25	Mitoticspindle vesicletracks(kinesin dynein) ciliaandflagella(9+2 , , ,
	nm)	arrangement);organizedbycentrosomes

Cell junctions link cells: tight junctions seal the space between epithelial cells, desmosomes anchor cells via intermediate filaments, and gap junctions (plasmodesmata in plants) form channels for direct cytoplasmic exchange.

Biological Molecules

Class	Monomer/Bond	KeyExamplesandFunctions
Carbohydrates	Monosaccharides;glycosidic	Roughly (CH 2O) n. Glucose , fructose , galactose; sucrose (glucose + fructose) ,
	bonds	lactose(glucose+galactose) maltose(glucose+glucose) Starch(plants) , .
		and glycogen (animals) store energy with α-linkages; cellulose (β-1 ,4) is
		structuralandindigestibletohumans;chitinformsfungalwallsandarthropod
		exoskeletons .
Lipids	Notruemonomer;ester	Triglycerides(glycerol+3fattyacids)storethemostenergypergram .
	bondsintriglycerides	SaturatedfattyacidshavenoC=Cbondsandpacktightly;unsaturatedhave
		oneormorecisdoublebonds Phospholipidsareamphipathicandform .
		membranes Steroids(fourfusedrings)includecholesterolandsteroid .
		hormones Waxeswaterproofsurfaces . .
Proteins	Aminoacids;peptide(amide)	Twenty standard amino acids differ in their R groups . Primary structure =
	bonds	sequence; secondary = α-helices and β -sheets held by backbone hydrogen
		bonds; tertiary = 3-D fold stabilized by R -group interactions (hydrophobic ,
		ionic , hydrogen bonds , disulfide bridges); quaternary = multiple subunits (e .g .,
		hemoglobin) Serveasenzymes receptors transporters antibodies . , , , ,
		hormones andstructuralcomponents , .
Nucleicacids	Nucleotides;phosphodiester	Each nucleotide = pentose sugar + phosphate + nitrogenous base . DNA:
	bonds	deoxyribose; A G C T; double-stranded and antiparallel RNA: ribose; uracil , , , .
		replaces thymine; usually single-stranded Purines (A G) have two rings; . ,
		pyrimidines(C T U)haveone , , .

Condensation (dehydration) reactions build all four polymers and release water; hydrolysis breaks them and consumes water. A–T pairs share two hydrogen bonds and G–C pairs share three, so DNA with a higher G–C content has a higher melting temperature.

Enzymes and Enzyme Kinetics

Enzymes are biological catalysts, almost always proteins (ribozymes are catalytic RNAs). They lower the activation energy (Ea) and speed up both forward and reverse reactions equally, so they change the rate but never ΔG or the equilibrium constant. Substrates bind the active site; the induced-fit model describes the enzyme changing shape as the substrate binds. Many enzymes require cofactors (metal ions) or coenzymes (organic molecules, often vitamin-derived, such as NAD+ and FAD).

Temperature: activity rises to an optimum (≈ 37 °C for most human enzymes), then falls sharply as the enzyme denatures.

pH: each enzyme has an optimum; pepsin works near pH 2, trypsin near pH 8.

Substrate concentration: velocity rises and then plateaus at Vmax when all active sites are saturated.

v = Vmax[S] / (Km + [S])

Km is the substrate concentration giving ½Vmax; a low Km means high apparent affinity. On a Lineweaver–Burk (double-reciprocal) plot, the y-intercept is 1/Vmax and the x-intercept is −1/Km.

Type	Binding	K m	V max	Overcomebymore substrate?
Competitive	Activesite(resemblessubstrate)	Increases	Unchanged	Yes
Noncompetitive Uncompetitive	Allostericsite;bindsEandESequally OnlytheEScomplex	Unchanged Decreases	Decreases Decreases	No No	1

Typesofenzymeinhibition(Continued)

Type	Binding	K m	V max	Overcomebymore substrate?
Mixed	Allostericsite;unequalaffinityforE	Increasesor	Decreases	No
	andES	decreases
Irreversible	Covalentmodificationoftheenzyme	—	Decreases	No
			(activeenzyme
			lost)

Allosteric enzymes have regulatory sites distinct from the active site and often show sigmoidal (cooperative) kinetics. In feedback inhibition, the end product of a pathway inhibits an enzyme near the start of the pathway, typically the committed step. Enzymes are also regulated covalently (phosphorylation by kinases, removal by phosphatases) and by proteolytic activation of inactive precursors called zymogens (e.g., pepsinogen → pepsin).

Membrane Transport

Small nonpolar molecules (O2, CO2, steroid hormones) cross the bilayer by simple diffusion; ions and polar molecules need proteins. Osmosis is the diffusion of water toward the side with higher solute concentration. In a hypertonic solution a cell loses water (animal cells crenate; plant cells plasmolyze); in a hypotonic solution it gains water (animal cells may lyse; plant cells become turgid); an isotonic solution causes no net movement.

Mechanism	Energy	FeaturesandExamples
Simplediffusion	None	Downthegradientdirectlythroughthebilayer;rateriseslinearlywiththegradient .
Facilitateddiffusion	None	Downthegradientviachannels(ionchannels aquaporins)orcarriers(GLUT ,
		glucosetransporters);carrierssaturate .
Primaryactivetransport	ATPhydrolysis	Against the gradient . Na+/K+-ATPase pumps 3 Na+ out and 2 K+ in per ATP; Ca2+ -
		ATPase;H+pumps .
Secondaryactive	Storediongradient	Couplesuphillmovementofonesolutetodownhillmovementofanother(usually
transport		Na+) Symport: Na+ –glucose (SGLT) in the intestine and kidney Antiport: Na+/Ca2+ . .
		exchanger .
Endocytosis	ATP	Phagocytosis (particles) pinocytosis (fluid) receptor-mediated endocytosis via , ,
		clathrin-coated pits (e .g LDL uptake) ., .
Exocytosis	ATP	Vesiclesfusewiththeplasmamembranetosecretecontents(neurotransmitters ,
		hormones enzymes) , .

Secondary active transport uses no ATP directly. If the Na+/K+ pump is poisoned (for example, by ouabain), the Na+ gradient collapses and Na+-coupled glucose uptake stops, even though the SGLT protein itself is undamaged.

Signal Transduction

Cells respond to extracellular signals through a three-stage process: reception (a ligand binds a receptor), transduction (a relay cascade amplifies the signal), and response (a change in enzyme activity, gene expression, or cell behavior). Hydrophilic ligands (peptide hormones, most neurotransmitters) bind cell-surface receptors; hydrophobic ligands cross the membrane and bind intracellular receptors.

Receptor	Mechanism	Examples
G protein–coupled	Seven-pass receptor activates a heterotrimeric G protein (GDP	Epinephrine (β -adrenergic) ,
receptor(GPCR)	exchanged for GTP on Gα) . Gs stimulates adenylyl cyclase → cAMP	glucagon ADH manyodorant , ,
	protein kinase A; Gi inhibits adenylyl cyclase; Gq activates →	receptors
	phospholipase C which cleaves PIP into IP (releases ER Ca2+) and , 2 3
	DAG(activatesproteinkinaseC) .
Receptortyrosinekinase	Ligandbindingcausesdimerizationandautophosphorylationof	Insulin EGF growthfactors , ,
(RTK)	tyrosines;phosphotyrosinesrecruitrelayproteins activatingRas(a ,
	smallGprotein)andtheMAPkinasecascade orthePI3Kpathway , .
Ligand -gated ion channel	Ligandbindingopensachannel;ionflowchangesmembrane	Nicotinicacetylcholinereceptor ,
	potentialwithinmilliseconds .	GABA A
Intracellular(nuclear)	Lipid -soluble ligand diffuses in binds a cytoplasmic or nuclear ,	Steroidhormones(cortisol ,
receptor	receptor; the complex acts as a transcription factor at hormone-	estrogen testosterone) thyroid , ,
	responseelementsinDNA Sloweronset longerlasting . , .	hormone vitaminD ,

Signal cascades amplify: one activated receptor activates many G proteins, each adenylyl cyclase makes many cAMP molecules, and each kinase phosphorylates many targets. Signals are terminated by GTP hydrolysis, phosphodiesterase (degrades cAMP), and phosphatases. A cholera toxin–type defect that locks Gαs in the GTP- bound state therefore produces continuous cAMP signaling.

Bioenergetics and Thermodynamics

Living systems obey the laws of thermodynamics. Energy is conserved (first law), and every spontaneous process increases the entropy of the universe (second law); cells maintain order by releasing heat and disorder to their surroundings.

ΔG = ΔH − TΔS   |   ΔG = ΔG°′ + RT ln Q

ATP hydrolysis to ADP + Pi releases about 7.3 kcal/mol (−30.5 kJ/mol) under standard conditions and more under cellular conditions.

Energy coupling: an endergonic reaction proceeds when paired with a more exergonic one; the free-energy changes of coupled reactions add. Coupling usually works by phosphorylating a substrate or protein to form a reactive intermediate. Redox: oxidation is loss of electrons (often loss of H); reduction is gain. NAD+, FAD, and NADP+ are electron carriers; NADH and FADH2 carry high-energy electrons to the electron transport chain.

Metabolic pathways are catabolic (break down molecules, release energy) or anabolic (build molecules, consume energy).

Cellular Respiration

Aerobic respiration oxidizes glucose completely: C6H12O6 + 6 O2→ 6 CO2 + 6 H2O, ΔG ≈ −686 kcal/mol, captured as roughly 30–32 ATP per glucose.

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Cytosol; glucose → 2 pyruvate;

Matrix; pyruvate → acetyl-CoA +

Matrix; per turn 3 NADH, 1

Inner membrane; ETC +

net 2 ATP, 2 NADH

CO2 + NADH

FADH2, 1 GTP, 2 CO2

chemiosmosis; O2→ H2O

Stage	ATP/GTP (substrate-level)	NADH	FADH 2	CO 2
Glycolysis	2net(4made 2invested) ,	2	0	0
Pyruvatedehydrogenase(×2) Citricacidcycle(×2turns) Total	0 2 4	2 6 10	0 2 2	2 4 6	1

In the electron transport chain, NADH donates electrons to complex I and FADH2 to complex II; electrons pass via ubiquinone, complex III, cytochrome c, and complex IV to O2, the final electron acceptor. Complexes I, III, and IV pump H+ from the matrix into the intermembrane space. The resulting proton-motive force drives H+ back through ATP synthase (chemiosmosis). Each NADH yields about 2.5 ATP and each FADH2 about 1.5 ATP. Key regulatory points: phosphofructokinase-1 (PFK-1) in glycolysis is inhibited by ATP and citrate and activated by AMP.

Distinguish ETC inhibitors from uncouplers. Cyanide or carbon monoxide blocks complex IV: electron flow, O2 consumption, and ATP synthesis all stop. An uncoupler (such as 2,4-dinitrophenol or thermogenin in brown fat) makes the inner membrane leaky to H+: O2 consumption rises, ATP synthesis falls, and the energy is released as heat. Oligomycin blocks ATP synthase directly.

Fermentation

Without O2, the ETC stops and NADH accumulates. Fermentation regenerates NAD+ so glycolysis can continue, yielding only the 2 ATP per glucose made in glycolysis.

Pyruvate is reduced directly to lactate by lactate

Pyruvate is decarboxylated to acetaldehyde (releasing CO2),

dehydrogenase. Occurs in skeletal muscle during intense

which is reduced to ethanol. Occurs in yeast and some

exercise, in red blood cells (no mitochondria), and in some

bacteria. Yeast are facultative anaerobes.

bacteria used to make yogurt.

Photosynthesis

Photosynthesis converts light energy into chemical energy: 6 CO2 + 6 H2O + light → C6H12O6 + 6 O2. Isotope labeling shows that the O2 released comes from water, not from CO2.

Chlorophyll in photosystem II (P680) absorbs light; excited

Fixation: RuBisCO adds CO2 to ribulose-1,5-bisphosphate

electrons are replaced by splitting water (photolysis), releasing

(RuBP), giving two 3-phosphoglycerate. Reduction: ATP and

O2 and H+. Electrons flow through plastoquinone, the

NADPH convert these to glyceraldehyde-3-phosphate (G3P).

cytochrome b6f complex, and plastocyanin to photosystem I Regeneration: ATP regenerates RuBP. Three turns fix 3 CO2

(P700), then to NADP+ reductase, forming NADPH. H+

and export one G3P, using 9 ATP and 6 NADPH.

accumulates in the thylakoid lumen and drives ATP synthase (photophosphorylation). Cyclic electron flow through PSI makes ATP but no NADPH or O2.

Photorespiration occurs when RuBisCO fixes O2 instead of CO2, wasting fixed carbon; it worsens in hot, dry conditions when stomata close and O2 builds up in the leaf.

C3,C4,Andcamplants

Type	FirstFixationProduct	SeparationStrategy	Examples
C 3	3 -phosphoglycerate	None;pronetophotorespiration	Wheat rice soybeans , ,
	(RuBisCO)
C 4	Oxaloacetate(PEP	Spatial: CO 2 fixed in mesophyll cells , released to	Corn sugarcane ,
	carboxylase , no O 2 affinity)	the Calvin cycle in bundle-sheath cells
CAM	Oxaloacetatestoredasmalic	Temporal: stomata open at night to fix CO 2;	Cacti pineapple succulents , ,
	acid	Calvincyclerunsbydaywithstomataclosed

The Cell Cycle

The cell cycle consists of interphase (G1, S, G2) and the M phase (mitosis plus cytokinesis). In G1 the cell grows and makes proteins; in S phase DNA replicates, so each chromosome becomes two sister chromatids joined at the centromere; in G2 the cell prepares for division. Nondividing cells (most neurons, mature muscle) exit into G0.

Cyclins and cyclin-dependent kinases (CDKs): cyclin levels rise and fall each cycle; cyclin–CDK complexes phosphorylate targets that drive the cell past checkpoints. MPF (mitosis-promoting factor) is the cyclin B–CDK1 complex that triggers mitosis.

G1/S checkpoint: the main commitment point; checks size, nutrients, growth factors, and DNA damage. p53 halts the cycle (via p21) or triggers apoptosis if DNA is damaged; Rb protein restrains entry into S until phosphorylated.

G2/M checkpoint: confirms complete, undamaged DNA replication.

Spindle (M) checkpoint: anaphase begins only when every kinetochore is attached to spindle microtubules.

Cancer arises when proto-oncogenes become gain-of-function oncogenes (e.g., RAS) and tumor suppressor genes suffer loss-of-function mutations (e.g., TP53, RB1). Tumor suppressors usually require loss of both alleles.

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Chromatin condenses;

Nuclear envelope breaks

Chromosomes align at

Cohesin cleaved; sister

Nuclear envelopes

spindle forms; nucleolus

down; kinetochores

the metaphase plate

chromatids move to

reform; chromosomes

disappears

attach

poles

decondense

Cytokinesis divides the cytoplasm: in animal cells an actin–myosin contractile ring pinches a cleavage furrow; in plant cells Golgi-derived vesicles build a cell plate that becomes the new wall. Prokaryotes divide by binary fission, without a mitotic spindle.

Meiosis

Meiosis produces four genetically distinct haploid (n) cells from one diploid (2n) cell through one round of DNA replication followed by two divisions. Meiosis I is reductional: homologous chromosomes pair (synapsis) to form tetrads (bivalents), exchange segments by crossing over at chiasmata during prophase I, line up as pairs at metaphase I, and separate at anaphase I. Meiosis II is equational and resembles mitosis: sister chromatids separate. Genetic variation arises from crossing over, independent assortment of homologs at metaphase I (223≈ 8.4 million combinations in humans), and random fertilization.

Mitosisvs.Meiosis

Feature	Mitosis	Meiosis
Purpose	Growth repair asexualreproduction , ,	Productionofgametes(animals)orspores(plants fungi) ,
Divisions	One	Two(meiosisIandII) afteroneSphase ,
Daughtercells	Two diploid geneticallyidentical , ,	Four haploid geneticallydistinct , ,
Synapsisandcrossingover	Donotoccur	OccurinprophaseI
Metaphasealignment	Individualchromosomeslineup	Homologouspairslineup(metaphaseI)
Anaphaseseparation	Sisterchromatids	Homologs(anaphaseI);sisterchromatids(anaphaseII)
Humanexample	46 chromosomes two cells of 46 →	46 two cells of 23 (duplicated) four cells of 23 → →

Track chromosome number and DNA content separately. A human cell in G2 has 46 chromosomes but 4c DNA (92 chromatids). After meiosis I, each cell is haploid (23 chromosomes) but still 2c because each chromosome has two chromatids. Nondisjunction in meiosis I makes all four gametes abnormal; nondisjunction in meiosis II makes two of four abnormal.

Experimental Cell Biology

DAT items frequently describe an experiment and ask which technique fits the goal or what a result implies. Know what each method separates or detects.

Microscopy

Method	PrincipleandBestUse
Light (bright-field)	Visiblelight;resolution≈02µm;canimagelivingcells;stainsaddcontrast . .
Phase-contrast / DIC	Convertsdifferencesinrefractiveindexintocontrast;viewsunstainedlivingcells .
Fluorescence/confocal	Fluorescent tags (antibodies GFP fusions) localize specific molecules; confocal rejects out-of -focus ,
	light for optical sections and 3-D reconstruction .
TransmissionEM(TEM)	Electronspassthroughthinsections;highestresolution(≈02nm)ofinternalultrastructure; .
	specimensaredead .
ScanningEM(SEM)	Electrons scan the surface; detailed 3-D surface images .

Technique	WhatItDoes
Differentialcentrifugation	Homogenized cells are spun at increasing speeds; larger , denser components pellet first: nuclei →
	mitochondria and chloroplasts microsomes (ER fragments) and small vesicles ribosomes; the → →
Density-gradient centrifugation	finalsupernatantiscytosol . 1 Separates particles by buoyant density (e .g sucrose or CsCl gradient); the Meselson–Stahl ., experimentusedCsCltoshowsemiconservativereplication .

Separationanddetectiontechniques(Continued)

Technique	WhatItDoes
Gelelectrophoresis	Nucleicacids(negativelychargedphosphatebackbone)migratetowardthepositiveelectrode
	(anode);smallerfragmentsmovefarther AgaroseforDNA;polyacrylamideforproteins . .
SDS-PAGE	SDSdenaturesproteinsandcoatsthemwithuniformnegativecharge soproteinsseparatebymass ,
	alone .
Chromatography	Separatesbysize(gelfiltration:largemoleculeselutefirst) charge(ionexchange) orspecificbinding , ,
	(affinity) .
Westernblot	SDS-PAGE transfer to a membrane then probing with a labeled antibody: detects a specific protein , ,
	anditssize .
Southern/Northernblot	LabelednucleicacidprobesdetectspecificDNA(Southern)orRNA(Northern)sequences .
ELISA	Antibodylinkedtoanenzymeproducesacoloredproductinproportiontotheantigenorantibody
	present;quantitativeandusedfordiagnostictesting .
Flowcytometry	Counts and sorts cells by size and fluorescent labeling; measures DNA content per cell (G 1 vs . G 2) .

For experimental items, identify the independent variable, the dependent variable, and the control. A valid control differs from the experimental group in only one variable. A radioactive pulse-chase (e.g., 3H-leucine followed by unlabeled leucine) traces secretory proteins in order: rough ER → Golgi → secretory vesicles → exterior.

Prokaryotes have 70S ribosomes, no nucleus, and no

Glycolysis yields net 2 ATP and 2 NADH; full aerobic

membrane-bound organelles; mitochondria and chloroplasts

respiration yields about 30–32 ATP; O2 is the final electron

retain prokaryote-like DNA and ribosomes.

acceptor.

Enzymes lower Ea and change rate, never ΔG or Keq.

Fermentation exists to regenerate NAD+; C4 plants separate

Competitive inhibition raises Km; noncompetitive inhibition

fixation in space, CAM plants in time.

lowers Vmax.

Meiosis I separates homologs (reductional); meiosis II

Primary active transport uses ATP; secondary active

separates sister chromatids.

transport uses an ion gradient that ATP-driven pumps

Differential centrifugation pellets nuclei first; DNA runs

created.

toward the anode, and small fragments travel farthest.

GPCRs signal through G proteins and second messengers (cAMP, IP3/Ca2+, DAG); RTKs autophosphorylate; steroid receptors act as transcription factors.

Diversity of Life

This area tests the defining characteristics of viruses, the three domains, and the major groups of eukaryotes, with emphasis on features that distinguish one group from another.

Classification and Phylogeny

Taxonomy is hierarchical: domain, kingdom, phylum, class, order, family, genus, species. Binomial nomenclature names each species by genus and specific epithet (Homo sapiens). Modern systematics builds phylogenetic trees that reflect evolutionary history. Cladistics groups organisms by shared derived characters (synapomorphies); a monophyletic clade contains an ancestor and all its descendants, whereas polyphyletic groups (such as "protists") do not share a single recent common ancestor. Comparisons of small-subunit ribosomal RNA sequences established the three-domain system.

Feature	Bacteria	Archaea	Eukarya
Nucleus	Absent	Absent	Present
Cellwall	Peptidoglycan	Nopeptidoglycan(pseudopeptidoglycan	Cellulose(plants) chitin ,
		or protein S -layer)	(fungi) ornone(animals) ,
Membranelipids	Ester-linked unbranched ,	Ether-linked branched isoprenoid chains ,	Ester-linked unbranched fatty ,
	fattyacids		acids
RNApolymerase	Onesimpletype	Several eukaryote-like ,	Several(I II III) , ,
Histones	Absent	Presentinmany	Present
Initiatoraminoacid	Formyl -methionine	Methionine	Methionine

Archaea look like bacteria but share many molecular features with eukaryotes (histones, multiple RNA polymerases, methionine initiator). Archaea and Eukarya are therefore more closely related to each other than either is to Bacteria.

Viruses

Viruses are noncellular, obligate intracellular parasites. A virion consists of a nucleic acid genome (DNA or RNA, single- or double-stranded, never both DNA and RNA) inside a protein capsid; many animal viruses also carry a lipid envelope taken from host membrane. Viruses lack ribosomes and metabolism, so they use host machinery to replicate. Host range is set by attachment proteins that bind specific host receptors (for example, HIV gp120 binds CD4 on helper T cells). Bacteriophages infect bacteria.

Attachment → injection of the genome → synthesis of viral

The phage genome integrates into the host chromosome as a

components using host enzymes → assembly → lysis of the

prophage and is copied with every cell division. Stress (e.g.,

host, releasing many new virions. Virulent phages such as T4

UV light) can trigger excision and entry into the lytic cycle.

use only this cycle.

Temperate phages such as lambda can do both.

Retroviruses (e.g., HIV) have a single-stranded RNA genome and carry reverse transcriptase, which makes DNA from the RNA template; integrase inserts this provirus into host DNA. Reverse transcriptase lacks proofreading, so mutation rates are high.

Positive-sense (+) RNA viruses can be translated directly; negative-sense (−) RNA viruses must carry an RNA- dependent RNA polymerase to make mRNA first.

Prions are misfolded proteins that induce normal proteins to misfold (no nucleic acid); viroids are small circular RNAs that infect plants.

Antibiotics target bacterial structures and do not work on viruses; antivirals target viral enzymes such as reverse transcriptase or protease.

Bacteria

Bacteria are classified by shape (cocci, spherical; bacilli, rods; spirilla and spirochetes, spirals), Gram reaction, oxygen requirement, and metabolism. They reproduce asexually by binary fission and gain genetic variation through mutation and horizontal gene transfer.

Gram-Positivevs.Gram-Negativebacteria

Feature	Gram-Positive	Gram-Negative
Peptidoglycan	Thicklayer;retainscrystalviolet	Thinlayerbetweentwomembranes;stainspinkwith
	(stainspurple)	safranincounterstain
Outermembrane	Absent;teichoicacidspresent	Present containinglipopolysaccharide(LPS endotoxin) , ,
Periplasmicspace	Minimal	Prominent
Examples	Staphylococcus Streptococcus , ,	Escherichiacoli Salmonella Neisseria , ,
	Bacillus

Process	Mechanism
Transformation	UptakeofnakedDNAfromtheenvironment(Griffith'sexperiment) .
Transduction	AbacteriophagecarriesbacterialDNAfromonecelltoanother .
Conjugation	DirecttransferthroughasexpilusfromanF+donor(carryingtheFplasmid)toanF−recipient;Hfrstrains
	transferchromosomalgenes .
Transposition	Transposons ("jumping genes") move within or between genomes and can carry antibiotic-resistance
	genesontoplasmids .

Oxygen requirement: obligate aerobes need O2; obligate anaerobes are killed by it; facultative anaerobes respire when O2 is available and ferment when it is not; aerotolerant anaerobes ignore it.

Nutrition: photoautotrophs (cyanobacteria, which produce O2), chemoautotrophs (oxidize inorganic compounds such as NH3 or H2S), photoheterotrophs, and chemoheterotrophs (most bacteria, including pathogens and decomposers).

Endospores (e.g., Bacillus, Clostridium) are dormant, highly resistant structures, not a form of reproduction.

Growth in culture follows lag, log (exponential), stationary, and death phases.

Bacteria act as decomposers, nitrogen fixers (Rhizobium in legume root nodules), gut symbionts, and pathogens.

Archaea

Many archaea are extremophiles: thermophiles (hot springs), halophiles (high salt), and acidophiles (low pH). Methanogens are strict anaerobes that produce methane from CO2 and H2; they live in swamps and in the digestive tracts of cattle and humans. Archaea are also abundant in ordinary soils and oceans. No archaea are known to cause human disease.

Protists

Protists are the eukaryotes that are not plants, animals, or fungi, a polyphyletic assemblage that is mostly unicellular.

Group	Characteristics
Greenalgae	Chlorophyllsaandb starchstorage cellulosewalls;theclosestrelativesoflandplants , , .
Redalgae	Mostlymarine;phycoerythrinpigmentsabsorbbluelight allowinggrowthatdepth , .
Brownalgae	Multicellularmarinealgae includinggiantkelps , .
Diatoms	Unicellular algae with two-part silica shells; major marine and freshwater primary producers .
Dinoflagellates	Twoflagella;somecausetoxic"redtides";othersarecoralsymbionts .
Amoebas	Moveandfeedwithpseudopodia .
Ciliates	Ciliaformovementandfeeding;macronucleusandmicronucleus;conjugation(eg Paramecium) . ., .
Flagellates	Movebyflagella;includeTrypanosoma(sleepingsickness)andGiardia .
Apicomplexans	Nonmotileparasiteswithanapicalcomplex;Plasmodiumcausesmalariaandistransmittedby
	Anophelesmosquitoes .
Slimemolds	Plasmodialorcellular;aggregateintomulticellularfruitingbodieswhenfoodisscarce;decomposers .

Fungi

Fungi are heterotrophic eukaryotes that secrete digestive enzymes and absorb nutrients. Walls contain chitin; they store glycogen. Most are multicellular, built of filaments called hyphae (septate or coenocytic) that form a mycelium; yeasts are unicellular and bud. The life cycle is usually haploid-dominant, with a dikaryotic (n + n) stage in many groups after plasmogamy and before karyogamy. Fungi are more closely related to animals than to plants.

Group	KeyFeatures Examples
Chytrids	Aquatic;theonlyfungiwithflagellatedspores Batrachochytrium(amphibian
	decline)
Zygomycetes	Coenocytichyphae;resistantzygosporangia Blackbreadmold(Rhizopus)
Ascomycetes	Sexualsporesinsacs(asci) Yeasts morels Penicillium , ,
1 Basidiomycetes Sexual spores on club -shaped basidia; long-lived dikaryotic Mushrooms rusts smuts , , mycelium cologically fungiarekeydecomposers formmycorrhizaethatimproveplantmineraluptake andformlichenswith , , , lgaeorcyanobacteria Somecausedisease(eg Candidaintheoralcavity) . . ., .

Ecologically, fungi are key decomposers, form mycorrhizae that improve plant mineral uptake, and form lichens with algae or cyanobacteria. Some cause disease (e.g., Candida in the oral cavity).

Plants

Plants are multicellular photosynthetic eukaryotes with cellulose walls, chlorophylls a and b, and starch storage. Their evolution on land shows four major innovations: embryos protected in the parent (all land plants), vascular tissue (xylem carries water and minerals; phloem carries sugars), seeds with pollen, and flowers and fruits. All plants show alternation of generations: a multicellular haploid gametophyte makes gametes by mitosis, and a multicellular diploid sporophyte makes haploid spores by meiosis.

Group	Dominant Generation	VascularTissue	SpermTransport	OtherFeatures
Bryophytes	Gametophyte	None	Swimsinwater	Small growinmoisthabitats;sporophyte ,
(mosses liverworts , ,				dependsonthegametophyte
hornworts)
Seedlessvascular	Sporophyte	Xylemand	Swimsinwater	Independent free-living gametophyte;
(ferns horsetails , ,		phloem		sporesinsori
clubmosses)
Gymnosperms	Sporophyte	Xylem	Pollen;nowaterneeded	"Naked"seedsoncones;windpollination
(conifers cycads , ,		(tracheids)and
ginkgo)		phloem
Angiosperms	Sporophyte	Xylem(vessels)	Pollentube	Flowers fruits anddoublefertilization: , ,
(floweringplants)		andphloem		one sperm + egg → 2n zygote; one sperm
				+ two polar nuclei → 3n endosperm

Monocots have one cotyledon, parallel leaf veins, scattered vascular bundles, and floral parts in threes; eudicots have two cotyledons, net veins, vascular bundles in a ring, and parts in fours or fives.

Transpiration (evaporation from leaves) pulls water up xylem by cohesion and tension; phloem moves sugar from source to sink by pressure flow.

Plant hormones: auxin (phototropism, apical dominance), gibberellins (stem elongation, germination), cytokinins (cell division), abscisic acid (stomatal closure, dormancy), ethylene (fruit ripening).

Animals

Animals are multicellular heterotrophic eukaryotes without cell walls that ingest food and usually develop from a blastula. Major body-plan distinctions include tissue organization, symmetry (radial vs. bilateral), germ layers (diploblastic vs. triploblastic), body cavity (acoelomate, pseudocoelomate, coelomate), and developmental pattern. In protostomes the blastopore becomes the mouth and cleavage is spiral and determinate; in deuterostomes (echinoderms and chordates) the blastopore becomes the anus and cleavage is radial and indeterminate.

Phylum	Symmetry	BodyCavity	DistinguishingFeatures	Examples
Porifera	None	None(notrue	Choanocytes(collarcells)filterwater	Sponges
Cnidaria	Radial	tissues) Gastrovascular cavity(one opening)	throughpores Diploblastic;cnidocytes(stingingcells); polypandmedusaforms;nervenet	1 Jellyfish corals , , hydra

Majoranimalphyla(Continued)

Phylum	Symmetry	BodyCavity	DistinguishingFeatures	Examples
Platyhelminthes	Bilateral	Acoelomate	Flattened;cephalization;incompletegut;	Planaria ,
			flamecells	tapeworms flukes ,
Nematoda	Bilateral	Pseudocoelomate	Completegut;cuticle whichtheymolt ,	Roundworms C , .
				elegans
Mollusca	Bilateral	Coelomate	Muscularfoot visceralmass mantle;most , ,	Snails clams , ,
		(reduced)	havearadula	octopuses
Annelida	Bilateral	Coelomate	Segmentedbody;closedcirculation;	Earthworms ,
			nephridia	leeches
Arthropoda	Bilateral	Coelomate	Chitinexoskeleton jointedappendages , ,	Insects ,
		(hemocoel)	opencirculation;largestphylum	crustaceans ,
				arachnids
Echinodermata	Radialadults ,	Coelomate	Deuterostome;watervascularsystemwith	Seastars sea ,
	bilaterallarvae		tubefeet;endoskeleton	urchins
Chordata	Bilateral	Coelomate	Deuterostome;notochord dorsalhollow ,	Tunicates lancelets , ,
			nerve cord pharyngeal slits post-anal tail , ,	vertebrates
			atsomestage

Group	KeyFeatures
Jawlessfishes	Nojawsorpairedfins;lampreysandhagfishes .
Cartilaginousfishes	Cartilageskeleton jaws placoidscales;sharksandrays , , .
Bonyfishes	Bone skeleton swim bladder operculum over gills; two-chambered heart , , .
Amphibians	Aquatic larvae and terrestrial adults; moist permeable skin; three-chambered heart .
Reptiles	Amnioticeggandscaly dryskin;ectothermic;birdsarepartofthereptileclade , .
Birds	Feathers hollow bones four-chambered heart endothermic; air sacs give one-way airflow , , , .
Mammals	Hair mammary glands four-chambered heart endothermic; monotremes lay eggs marsupials have , , , ,
	pouches eutherianshaveplacentas , .

Three domains: Bacteria (peptidoglycan), Archaea (ether-

Transformation, transduction, and conjugation transfer genes

linked lipids, histones), and Eukarya; Archaea are closer to

horizontally between bacteria.

Eukarya.

Fungi absorb food, have chitin walls, and are closer relatives

Viruses have DNA or RNA in a capsid, lack ribosomes, and

of animals than of plants.

replicate only inside host cells; retroviruses use reverse

Bryophytes are gametophyte-dominant and nonvascular; all

transcriptase.

other plants are sporophyte-dominant; angiosperms have

Lytic cycles kill the host immediately; lysogenic cycles

double fertilization.

integrate a prophage that is copied with the host genome.

Deuterostomes (echinoderms, chordates): blastopore

Gram-positive bacteria have thick peptidoglycan; gram-

becomes the anus; arthropods are the most diverse phylum.

negative bacteria have an outer membrane with LPS.