Study Guide for OpenStax General Biology II exam #1

Taxonomy and systematics

Taxonomy is the science of naming, describing, and classifying organisms. Systematics studies evolutionary relationships and includes taxonomy.

Phylogenetic trees and cladistics

Phylogenies are diagrams (trees) that show evolutionary relationships. Cladistics classifies organisms by common ancestry using shared derived characteristics (synapomorphies).

Shared traits and common ancestry

Organisms with a recent common ancestor share more derived traits. Homologous traits come from common ancestors, while analogous traits come from convergent evolution.

Reading and interpreting evolutionary trees

Trees can be rotated at nodes without changing relationships. The order of branching indicates the recency of common ancestry, not progression or complexity.

Limitations and challenges in phylogenetics

Horizontal gene transfer, incomplete fossil records, and convergent evolution can make it hard to build accurate trees.

Structure of viruses

Viruses consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat (capsid), and sometimes a lipid envelope.

Lytic cycle

Virus replicates quickly and destroys the host cell.

Lysogenic cycle

Virus integrates into host DNA and replicates with the cell until triggered.

Classes of viruses

DNA viruses have stable genomes (e.g., herpes). RNA viruses mutate quickly (e.g., COVID-19). Retroviruses use reverse transcriptase to turn RNA into DNA (e.g., HIV).

Viral diseases

Examples include HIV, influenza, HPV, and coronavirus. They affect various tissues and use host machinery to replicate.

Vaccines and viral evolution

Vaccines prepare the immune system to recognize and fight viruses. Rapid viral mutation can reduce vaccine effectiveness, requiring updates.

Characteristics of Bacteria and Archaea

Both are unicellular, lack a nucleus, and have circular DNA. Archaea differ in cell wall and membrane structure.

Prokaryotic structure

Includes a cell wall (peptidoglycan in bacteria), cell membrane, ribosomes, and sometimes flagella or pili.

Metabolism and nutrition types

Autotrophs make their own food (photoautotrophs, chemoautotrophs). Heterotrophs get food from others. Obligate aerobes need oxygen; obligate anaerobes cannot tolerate it.

Horizontal gene transfer

Conjugation is direct transfer between cells. Transformation is the uptake of DNA from the environment. Transduction is DNA transfer by viruses (phages).

Roles in environment and human health

Bacteria and archaea act as decomposers, nitrogen fixers, and microbiome members. Some cause disease; others are used in biotechnology.

Defining protists and their diversity

Protists are eukaryotes that are not plants, animals, or fungi. They include algae, protozoa, and slime molds.

Origins of eukaryotic cells

Endosymbiosis explains the origin of mitochondria (from aerobic bacteria) and chloroplasts (from cyanobacteria).

Major groups of protists

Excavata includes Giardia. SAR includes diatoms, brown algae, and ciliates. Archaeplastida includes red and green algae. Unikonta includes amoebas and slime molds.

Ecological roles and human relevance

Protists are producers (algae), parasites (Plasmodium), and decomposers. They form plankton and are crucial to food chains.

Plankton

They form plankton and are crucial to food chains.

Life cycles and reproduction

May be asexual or sexual. Some have complex life cycles with alternation of generations.

Green algae and the move to land

Green algae share features with land plants (chlorophyll, starch storage). Land plants evolved from charophytes.

Bryophytes

Non-vascular plants (mosses, liverworts, hornworts). Require water for fertilization and have dominant gametophyte stage.

Seedless vascular plants

Include ferns, club mosses, and horsetails. Have xylem and phloem for transport. Sporophyte stage is dominant.

Adaptations to land

Waxy cuticle to prevent water loss, stomata for gas exchange, and vascular tissue for support and transport.

Levels of organization in animals

From cells → tissues → organs → organ systems. Each level increases complexity and specialization.

Homeostasis and feedback loops

Negative feedback brings system back to set point (e.g., body temperature).

Positive feedback

Enhances change (e.g., childbirth).

Epithelial tissue

Covers surfaces and lines organs.

Connective tissue

Includes bone, blood, fat.

Muscle tissue

Enables movement (skeletal, cardiac, smooth).

Nervous tissue

Sends electrical signals.

Surface area and volume in physiological processes

Smaller organisms or organs often have higher surface area-to-volume ratios to help with exchange (e.g., lungs, intestines, root hairs).

Taxonomy

Organizes organisms into a hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

Systematics

Combines taxonomy with the study of evolutionary relationships.

Phylogenetic trees

Represent hypotheses about evolutionary history based on physical traits, DNA, behavior, etc.

Clades

Groups of organisms that include a common ancestor and all its descendants (monophyletic groups).

Homologous traits

Come from shared ancestry.

Analogous traits

Result from convergent evolution (similar function, different origin).

Synapomorphies

Shared derived traits used to identify clades.

Outgroups

Closely related species not part of the group being studied, used to infer trait evolution direction.

Branch points (nodes)

Show common ancestors.

Virion

Virus outside a host cell (inactive).

Tissue tropism

Viruses target specific cell types (e.g., HIV infects CD4+ T cells).

Vaccines

Prime the immune system.

Antiviral drugs

Target reverse transcriptase, protease, or entry/fusion.

Prokaryotes

Organisms that lack a nucleus and membrane-bound organelles; DNA is in a nucleoid.

Binary fission

A method of reproduction in prokaryotes that occurs rapidly.

Cell walls

Structures that differ between Bacteria (peptidoglycan) and Archaea (pseudopeptidoglycan or proteins).

Gram-positive

Bacteria with a thick peptidoglycan layer that stain purple.

Gram-negative

Bacteria with a thin peptidoglycan layer and an outer membrane that stain pink.

Autotrophs

Organisms that make food from CO₂, including photoautotrophs and chemoautotrophs.

Heterotrophs

Organisms that obtain carbon from other organisms.

Obligate aerobes

Organisms that require O₂ for survival.

Obligate anaerobes

Organisms that are poisoned by O₂.

Facultative anaerobes

Organisms that can switch their oxygen use depending on O₂ presence.

Conjugation

A method of horizontal gene transfer where a plasmid is transferred through a pilus.

Transformation

A method of horizontal gene transfer where DNA is taken from the environment.

Transduction

A method of horizontal gene transfer where DNA is transferred via a phage.

Eukaryotic cells

Cells that contain a nucleus and organelles, originating from endosymbiosis.

Endosymbiosis

The theory that mitochondria and chloroplasts originated from aerobic bacteria and cyanobacteria, respectively.

Protists

Mostly unicellular eukaryotes not classified as animals, plants, or fungi.

Haplontic

A life cycle where the haploid stage is dominant.

Diplontic

A life cycle where the diploid stage is dominant.

Haplodiplontic

A life cycle where both haploid and diploid stages alternate.

Homeostasis

The maintenance of internal balance in organisms, such as temperature and pH.

Negative feedback

A mechanism that reverses changes to maintain homeostasis.