UNIT 1: Biodiversity in organisms

A3.2 Viruses A3.1 Diversity in organisms A3.2 Cladistics and classification B4.1 Adaptations to the environment A4.1 Evolution and speciation D4.1 Natural selection

Define a virus

An obligate intracellular parasite.

Why are viruses small and of fixed size?

Small to enter host cells; fixed size with fixed number of components; lack cytoplasm/complex structures so do not grow.

What genetic material do viruses have and why is it essential?

Viruses have nucleic acid (DNA or RNA); host translation machinery reads nucleic acid to make viral proteins—essential for replication.

Role and properties of the viral capsid

Protein shell giving symmetry; protects nucleic acid; shields from environmental hazards.

Why do viruses lack cytoplasm and most enzymes?

They rely on host metabolism; may carry specific enzymes (e.g., for genome replication in lytic cycle).

List structural features common to all viruses

Intracellular parasites; small/fixed size; nucleic acid genome; protein capsid; no cytoplasm; usually very few enzymes.

Positive-sense RNA virus

Genome acts as mRNA directly translated into viral proteins.

Negative-sense RNA virus

Genome must be transcribed into complementary (+) RNA before translation into proteins.

Retrovirus

RNA genome reverse transcribed to DNA, then transcribed/translated to make viral proteins.

Common capsid shapes with examples

Helical; icosahedral; complex (e.g., bacteriophages, some large enveloped viruses).

Differentiate enveloped vs non-enveloped viruses

Non-enveloped exit by lysis; more resistant to pH, heat, dryness, simple disinfectants. Enveloped acquire lipid bilayer by budding; more sensitive to harsh conditions.

Compare Bacteriophage Lambda, SARS-CoV-2, and HIV (host, structure, envelope, genome type)

Lambda infects E. coli; complex capsid; non-enveloped. SARS-CoV-2 infects mammalian epithelial cells; complex capsid; enveloped. HIV infects CD4+ cells; icosahedral; enveloped; retrovirus.

Main stages of the lytic cycle (phage)

Attach to specific host receptor; inject DNA via tail; linear DNA circularizes & replicates (rolling circle); host RNA pol transcribes phage genes; host ribosomes translate proteins; assemble new virions; lysis breaks cell wall; virulent phage released.

Why is the lytic cycle virulent?

It kills the host cell during lysis using enzymes that damage membrane/wall.

Selectivity of phage attachment

Phage tail fibers bind specific receptor proteins on bacterial membranes; compatibility determines host range.

What happens during lysis and why does it aid spread?

Host cell bursts rapidly releasing many virions to infect new hosts; if no hosts nearby, infection may die out; easy to detect.

How does the lysogenic cycle differ from lytic?

Phage DNA integrates into host genome (prophage) via integrase instead of immediately replicating/lysing; copied with host DNA during cell division.

Define prophage

Integrated phage DNA residing within the bacterial genome after lysogenic integration.

When can lysogenic switch to lytic?

Activation of prophage genes in response to internal/external stimuli triggers excision and entry into lytic cycle.

How can lysogeny benefit the host cell?

Integrated DNA may introduce new genes from previous hosts, increasing genetic diversity.

Why is lysogeny less detectable than lysis?

Temperate phage do not kill host; virus hidden in genome; cannot spread to new cells without induction; hosts may evolve defenses over time.

Main hypotheses for viral origins

First virus (predate or coevolved with cells); Progressive (escaped/modified cellular components); Regressive (reduced from cellular ancestors losing functions).

Regressive hypothesis & complex viruses (e.g., mimivirus)

Suggests convergent evolution of viruses via genome reduction from more complex ancestors in multiple independent lineages.

Evidence challenging first virus hypothesis

Viruses depend on cellular hosts for reproduction, implying cells likely existed before viruses.

How do high mutation rates drive rapid viral evolution?

Frequent changes in viral proteins can help evade host immunity; advantageous mutations spread quickly in large viral populations.

Role of natural selection in viral evolution

Huge offspring numbers + host defenses create strong selection; beneficial variants outcompete others.

Genetic recombination in influenza

Co-infection by multiple strains allows genome segment mixing (H/N antigen reshuffling) creating novel strains that evade immunity, driving pandemics; necessitates yearly vaccines.

Genetic recombination & mutation in HIV

Single-stranded RNA + error-prone reverse transcription without proofreading = rapid mutation; high genetic diversity in hosts selects advantageous strains.

Segmented genome & new influenza strains

Negative-sense ssRNA segmented genome enables reassortment among segments, boosting mutation & strain diversity.

HIV glycoprotein spikes & infection

Surface glycoproteins mediate binding/entry into CD4 cells, enabling infection.

Discrete vs continuous variation (with examples)

Discrete: qualitative categories, few genes/env (e.g., blood type). Continuous: quantitative range, polygenic + env (e.g., height).

Intraspecies vs interspecies variation

Intraspecies: heritable variation within a species. Interspecies: differences between species, typically greater than within-species variation.

Four processes generating genetic variation within a species

Mutation; gene flow between populations; meiosis (new allele combinations); sexual reproduction (random fertilization).

Define species (morphological perspective)

Group sharing characteristic external form & internal structure, recognizably distinct from others.

How Linnaeus’s classification organizes organisms

Taxonomy by morphological traits; hierarchical ranks: Kingdom, Phylum, Class, Order, Family, Genus, Species (also Domain above Kingdom in modern use).

Challenges using morphology to classify species

Cryptic divergence hard to detect; convergent evolution yields similar forms in unrelated taxa.

Rules of binomial nomenclature (example)

Genus capitalized; species lowercase; italicized when printed; underlined when handwritten; Genus may be abbreviated after first full mention (e.g., Homo sapiens → H. sapiens).

Why binomial system is globally essential

Reflects evolutionary relationships; provides universal scientific language for communication.

Biological species concept definition

Species = groups of actually or potentially interbreeding natural populations reproductively isolated from other such groups (geographic co-occurrence & timing matter); isolation due to geographic/behavioral/physiological/genetic barriers.

Limitations of biological species concept

Not for sterile hybrids; geographic variation blurs lines; gradual divergence complicates categorization; impractical/ethical to test crosses; unusable for fossils/extinct taxa; inapplicable to asexual organisms.

Define population & why boundaries blur

Population = organisms of same species in same area/time; gene flow between areas makes boundaries fuzzy.

Why is speciation gradual?

Accumulation of genomic mutations over long periods; divergence builds until reproductive isolation and infertile crosses mark separate species; more time since split → greater variation.

Examples where interbreeding blurs species lines

Phenotypically different populations interbreed partially; diverging populations during speciation; closely related post-speciation species difficult to distinguish.

Why diploid cells usually have even chromosome numbers

Chromosomes occur as homologous pairs from each parent; number characteristic of species.

Evidence human chromosome 2 formed by fusion

Internal telomere sequences mid-chromosome; banding & DNA match chimp chromosomes 12 & 13; shared genes indicate common ancestor.

Karyotype vs karyogram

Karyotype = number/types of chromosomes in nucleus; karyogram = visual arrangement by size, banding, centromere position, sex chromosomes/anomalies.

Four ways chromosomes classified in karyograms

By size; staining banding pattern; centromere position; presence/position of sex chromosomes & anomalies.

Steps to prepare a karyogram

Stain cells on slide; burst/spread chromosomes under coverslip; locate non-overlapping metaphase spread; cut/photo or digitally arrange stained chromosomes.

Define genome, gene, allele

Genome = complete genetic material of an organism; gene = DNA segment coding a protein/function; allele = variant form of a gene.

SNPs and genetic diversity

Single nucleotide polymorphisms are variable bases in genes; create allele differences influencing diversity, disease traits, drug responses.

Why same genes in same sequence within species?

Ensures homologous chromosome pairing & exchange (crossing over) during meiosis without losing or duplicating genes.

Why bigger genome ≠ more genes?

Large genomes may contain abundant non-coding DNA (introns, repetitive sequences, transposons) so size doesn’t equal gene count.

Vital genes in genome evolution

Essential genes change rarely; conserved across lineages; benchmarks for evolutionary studies.

How genomic differences reflect lifestyle adaptations

Gain/loss of genes; differences in gene number/type; small sequence changes accumulate as populations diverge—reflect ecology.

How genome sizes measured & what they show

Measured in base pairs; databases compile sizes; large size may include junk DNA so not a direct complexity indicator.

Whole genome sequencing definition

Determining the entire DNA base sequence of an organism.

Four uses of whole genome sequencing

Compare genomes to trace evolution; inform biodiversity conservation; control/prevent pathogen disease; enable personalized medicine via SNP/mutation prediction.

Why BSC not applicable to asexual organisms

They do not interbreed, so reproductive isolation criterion fails.

Define horizontal gene transfer (HGT) in bacteria

Movement of DNA between individuals by non-parental mechanisms (e.g., conjugation, transformation, transduction); means populations aren’t genetically isolated → BSC fails.

Why genetically isolated clones challenge BSC

No interbreeding; each clonal lineage would count as separate species under strict BSC, which is impractical.

How sexual reproduction maintains chromosome number

Meiosis halves chromosome number in gametes; fertilization restores diploidy, preserving species’ characteristic number.

Why are mules sterile & what does it show?

63 chromosomes (uneven) prevent proper homologous pairing in meiosis; illustrates hybrid sterility from parental chromosome differences.

Chromosome number as species trait

Species differ in chromosome counts; successful fertile breeding usually requires compatible numbers.

What is a dichotomous key?

Identification tool using paired, contrasting statements that guide stepwise to the correct organism.

Define environmental DNA (eDNA)

Genetic material obtained from environmental samples (soil, water, air) rather than directly from organisms; short standardized barcode sequences ID species.

Steps in DNA barcoding from eDNA

Collect environmental sample; extract DNA; PCR amplify barcode region; sequence; compare against reference database to identify species.

Three applications of eDNA barcoding

Biodiversity monitoring; invasive species detection; forensic/environmental investigations.

Purpose of biological classification & taxonomy

Group organisms by traits/evolutionary origins; taxonomy studies relationships; standardized naming improves scientific communication.

How taxonomy helps predict traits

Known group traits allow predictions about newly discovered members.

Taxonomy & evolutionary insight

Shared taxonomic groups imply common ancestry.

Taxonomic hierarchy & domains

Largest rank domain (Archaea, Eukarya, Eubacteria); Eukarya → Protista, Fungi, Plantae, Animalia; then Phylum, Class, Order, Family, Genus, Species; subspecies optional.

Limitations of traditional taxonomy

Arbitrary rank limits; hard to resolve diverging species; convergent morphology misleads; emphasizes naming over evolutionary relationships (contrast cladistics).

How cladistics improves grouping

Uses evolutionary ancestry; all group members descend from common ancestor.

Four advantages of cladistics

All members share common ancestor; share homologous (synapomorphic) traits; allows trait prediction across group; flexible nested hierarchies without forced ranks.

Define clade & cladogram

Clade = ancestor + all descendants (incl. extinct); cladogram = branching diagram depicting evolutionary relationships.

Evidence used to build cladograms

Molecular sequence homology (DNA bases, amino acids); morphological similarity (esp. fossils); best practice uses multiple evidence sources.

Mutation rate & clade divergence timing

Mutations accumulate gradually; more sequence differences = longer time since common ancestor; mutation frequency per nucleotide per division underlies molecular clock.

Factors affecting molecular clock reliability

Generation time; population size; selection intensity; other rate-variation factors—clock gives estimates, not exact times.

Why DNA/amino acid data preferred over morphology in cladistics

Morphological convergence/gradual divergence can mislead; molecular data are more objective/testable.

Role of bioinformatics & parsimony in cladograms

Align homologous sequences; software finds tree needing fewest changes (parsimony criterion); compare multiple genes/proteins for robustness.

Interpret root, nodes, taxa, outgroup in cladogram

Node = divergence from hypothetical ancestor; root = common ancestor of all taxa; taxa = terminal branches (species/groups); outgroup = most distantly related comparator.

How molecular data improved cladistics vs anatomy

Revealed that some anatomical similarities were analogous; sequence data increased accuracy and prompted reclassification (e.g., figwort family split into multiple families).

Figwort reclassification lesson

~5000 species reassigned after gene sequencing showed no single common ancestor; demonstrates classification is falsifiable and subject to change with new data.

Two-domain vs three-domain systems

Old: Prokaryotes vs Eukaryotes. New: Eubacteria, Archaea, Eukarya (Archaea closer to Eukarya than to Eubacteria).

Why Archaea closer to Eukaryotes than to Eubacteria

Despite prokaryotic form, molecular differences greater between Archaea & Eubacteria than between Archaea & Eukaryotes.

rRNA evidence for three-domain system

Comparisons of ribosomal RNA base sequences show early split yielding Eubacteria and a lineage that later diverged into Archaea + Eukarya.

Define habitat (with example)

Physical conditions/place an organism/population/community lives (e.g., Emperor penguin habitat = Antarctic landfast ice: climate, physical features, resources, other organisms).

Define adaptation

Trait that improves survival & reproduction in a specific environment.

Abiotic vs biotic factors

Abiotic = nonliving (temperature, soil, water, air); Biotic = living (other organisms).

Marram grass adaptations to sand dunes

Waxy cuticle (reduce water loss); stomata in hair-lined pits (retain moisture); rolled leaves (reduce wind, humid chamber, lower transpiration); tough sclerenchyma (drought resistance); upward rhizomes for stability; root fructans increase osmotic water uptake.

Mangrove tree adaptations to coastal intertidal zones

Salt-expelling glands; cork-coated roots block salt; shallow roots access CO2; pneumatophores/cable roots for gas exchange & stability; high mineral roots enhance osmosis; large buoyant seeds disperse by sea.

High-altitude shrub adaptations

White woolly hairs reflect UV & insulate; small/stunted leaves reduce water loss & wind exposure; thick fleshy leaves store water/nutrients from permafrost soils.

Three abiotic factors influencing animal distribution (examples)

Water availability (elephants); temperature (polar bears); life-stage habitat shifts (salmon life cycle).

Abiotic factors affecting plant distribution

Water; temperature; light intensity; soil pH; mineral content; salinity.

Define range of tolerance

Span of an abiotic factor within which a species can survive; shapes distribution.

Adaptations, distribution & tolerance relationship

Adaptations expand/define tolerance limits; species occur where abiotic conditions fall within tolerance; outside range survival/reproduction drop.

Line transect vs belt transect

Line = record organisms at points along a line gradient; Belt = wider strip along line to record all within area (better abundance data).

How quadrats assess abundance vs abiotic factors

Place square frames (systematic/random), count/estimate cover; measure abiotic variables (light, pH, etc.) concurrently; analyze abundance vs environment.

Coral–zooxanthellae mutualism & reef importance

Algal symbionts photosynthesize providing energy; coral provides habitat; relationship determines tolerance limits essential for reef formation.

Abiotic conditions required for coral reefs

Shallow clear water (light for algae); proper salinity; alkaline pH (CaCO3 skeleton formation); suitable temperature (enzyme function); moderate wave action (nutrient/oxygen circulation, prevents smothering).