Lecture Notes: Phylogeny, Prokaryotes, Protists

A set of Question-and-Answer flashcards covering key concepts from Phylogeny, Prokaryotes, and Protists based on the provided notes.

Why are snake lizards not considered snakes, and what are some characteristics unique to snake lizards and to snakes?

Snake lizards (amphisbaenians) are a separate lineage of squamates from snakes. They share a limbless body with snakes but differ in anatomy such as ringed scales (annuli) and burrowing adaptations in many amphisbaenians, whereas snakes have highly specialized skulls and other features like the loss of external ears. Snakes and snake lizards are not the same lineage.

Define biodiversity.

The variety and variability of life in all its forms, levels, and combinations within a habitat or on Earth.

Define taxonomy.

The science of naming, describing, and classifying organisms into a hierarchical framework.

How is binomial nomenclature written, and who developed this system?

Binomial nomenclature uses genus name capitalized and species name lowercase, both italicized (e.g., Homo sapiens). It was developed by Carl Linnaeus.

How has binomial nomenclature helped science?

It provides universal, standardized names for organisms, enabling clear communication and consistent classification across disciplines and languages.

List the Linnaean hierarchy from most inclusive to least inclusive.

Domain (or Kingdom in older usage) > Kingdom > Phylum > Class > Order > Family > Genus > Species.

What were the drawbacks of the old Linnaean system and how does the modern phylogenetic system address these issues?

The old system grouped by overall similarity without reflecting evolutionary relationships. Modern phylogeny uses clades and ancestry (monophyly) to classify organisms based on evolutionary history.

What is phylogeny?

The evolutionary history and relationships among a group of organisms or their lineages.

What are the main parts of a phylogenetic tree?

Root, internal nodes (ancestral splits), branches (lineages), and tips (taxa). Branch lengths may indicate time or amount of change.

Define apomorphy.

A derived character state that is new relative to the common ancestor.

Define plesiomorphy.

An ancestral character state shared by an ancestor and its descendants.

Define synapomorphy.

A shared derived character state that defines a clade.

Define autapomorphy.

A derived character state unique to a single lineage.

Define homoplasy.

A similarity due to convergent evolution or reversal, not due to shared ancestry.

Differentiate homology and analogy with examples.

Homology: similarity due to shared ancestry (e.g., forelimbs of humans and whales). Analogy (homoplasy): similarity due to convergent evolution, not shared ancestry (e.g., wings of birds and bats).

Define monophyletic, paraphyletic, and polyphyletic groups.

Monophyletic: includes a common ancestor and all its descendants. Paraphyletic: includes a common ancestor and some, but not all, descendants. Polyphyletic: includes taxa from multiple ancestors and excludes the most recent common ancestor.

What is an outgroup and why is it important in understanding ancestral and derived characters?

An outgroup is a taxon outside the group of interest used to root the tree and infer which character states are ancestral vs derived.

What domains of life are prokaryotes part of?

Bacteria and Archaea.

How did prokaryotes become the most abundant species on Earth?

Rapid reproduction, diverse metabolisms, small size, widespread distribution, and horizontal gene transfer.

Describe the general structure of prokaryotic cells.

Lack a nucleus and membrane-bound organelles; typically small; cell wall present (peptidoglycan in bacteria); ribosomes; sometimes flagella.

What happens to a prokaryotic cell in a hypotonic solution?

Water enters the cell, causing it to swell; the cell wall helps resist lysis, but excessive influx can lead to bursting.

What happens to a prokaryotic cell in a hypertonic solution?

Water leaves the cell, causing it to shrink (plasmolysis) and potentially impair function.

What color do Gram-positive and Gram-negative bacteria stain, and why?

Gram-positive stain purple due to thick peptidoglycan in the cell wall; Gram-negative stain pink/red due to thinner peptidoglycan and the presence of an outer membrane.

Name key prokaryotic adaptations and their functions (capsules, endospores, fimbriae, pili, flagella).

Capsules protect from desiccation and immune attack; Endospores are dormant, resistant forms; Fimbriae aid adhesion; Pili enable conjugation and DNA transfer; Flagella provide motility.

What is binary fission and why is it important for prokaryotes?

Binary fission is asexual reproduction yielding two genetically identical daughter cells, enabling rapid population growth.

Describe the three types of horizontal gene transfer.

Transformation: uptake of free DNA from the environment. Transduction: gene transfer via bacteriophages. Conjugation: direct transfer of DNA between cells via a pilus.

Define photosynthesis-based and chemical-based energy sources (phototrophs vs chemotrophs) and autotrophs vs heterotrophs.

Phototrophs obtain energy from light; chemotrophs obtain energy from chemical compounds. Autotrophs fix carbon from inorganic sources (e.g., CO2); heterotrophs obtain carbon from organic compounds.

Name and define the main categories of oxygen reliance in prokaryotes.

Obligate aerobes (require O2); Obligate anaerobes (poisoned by O2); Facultative anaerobes (can use O2 but grow without it); Microaerophiles (require low O2).

Are bacteria all bad? Are there good bacteria?

No—many are beneficial, such as gut microbiota, nitrogen fixation, decomposition, and production of foods.

Give examples of pathogenic bacteria and the diseases they cause (E. coli, V. cholerae, B. burgdorferi).

E. coli can cause gastroenteritis and UTIs; Vibrio cholerae causes cholera; Borrelia burgdorferi causes Lyme disease.

What is unique about archaea compared to bacteria?

Archaea have distinct membrane lipids and molecular machinery; shares some features with eukaryotes; many are extremophiles and occupy unique ecological niches.

What are the two types of extremophiles and what environments do they prefer?

Thermophiles prefer hot environments; halophiles prefer high-salt environments.

Why are decomposers important for ecosystems?

They break down dead organic matter, recycle nutrients, and sustain ecosystem productivity.

Name the three types of symbiosis and give an example of each.

Mutualism (both benefit; e.g., gut microbiota and host), Commensalism (one benefits, other unaffected), Parasitism (one benefits, host harmed).

What is a protist, and why is the group so diverse?

Protists are eukaryotes not classified as plants, animals, or fungi; the group is extremely diverse with many lineages, lifestyles, and morphologies.

What are the major protist supergroups and what is notable about their subgroups?

Major supergroups: Archaeplastida, SAR, Excavata, Unikonta; each contains diverse subgroups with unique traits.

Diplomonads lack mitochondria; what do they have instead?

Mitosomes (mitochondria-derived organelles).

Trypanosoma can cause which diseases?

African sleeping sickness (Trypanosoma brucei) and Chagas disease (Trypanosoma cruzi).

What is alternation of generations and what do haploid and diploid mean?

A life cycle that alternates between haploid (n) and diploid (2n) stages; haploid has one set of chromosomes, diploid has two sets.

Malaria is caused by Plasmodium and is carried by which vector?

Anopheles mosquito.

The holdfast in brown algae is analogous to which structure in land plants?

Roots.

Volvox is the __ form of chlorophytes.

Colonial.

Which supergroup does red algae belong to?

Archaeplastida.

Which organisms are responsible for creating the White Cliffs of Dover in England, among the options provided?

Foraminiferans.

Ciliary beating is a feature of which group?

Ciliates.