General Biology 2 Comprehensive Practice Flashcards

100 vocabulary flashcards covering Photosynthesis, Systematics, Phylogeny, Taxonomy, Origin of Life, and Course Material from General Biology 2.

Photosynthesis Summary Equation

The chemical reaction represented by $6\text{CO}_2 + 12\text{H}_2\text{O} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{H}_2\text{O} + 6\text{O}_2$, where water is oxidized and light energy drives sugar synthesis.

Thylakoids

Disk-shaped membranous structures arranged in grana inside chloroplasts containing chlorophyll, photosynthetic pigments, and photosystems.

Granum

A stack of disk-shaped thylakoids located within the interior of a chloroplast.

Stroma

The fluid-filled interior space of a chloroplast surrounding the thylakoids where light-independent reactions (Calvin cycle) occur.

Light-dependent reactions

Photosynthetic reactions requiring light that capture energy from sunlight photons, produce ATP from ADP, and reduce $\text{NADP}^+$ to NADPH using electrons from water.

Light-independent reactions

Photosynthetic reactions (Calvin cycle) that do not require light and use ATP and NADPH to synthesize organic molecules such as glucose from $\text{CO}_2$.

Photon

A particle of light acting as a discrete bundle of energy with no mass.

Photoelectric effect

The removal of an electron from a molecule by light energy, boosting the electron to a higher energy level; discovered by Albert Einstein (1921 Nobel Prize).

Photosystem I

A multiprotein complex in the thylakoid membrane, designated as $P_{700}$, that absorbs light energy to pass excited electrons to ferredoxin and reduce $\text{NADP}^+$.

Photosystem II

A multiprotein complex in the thylakoid membrane, designated as $P_{680}$, that absorbs light, excites electrons, and uses a water-splitting enzyme to replace lost electrons.

Water-splitting enzyme

Membrane-bound Enzyme 1 inside Photosystem II that oxidizes water molecules to extract electrons, releasing oxygen and protons into the thylakoid space.

$b_6\text{-}f$ complex

Membrane-bound Enzyme 2 that receives electrons from plastoquinone, transfers them to plastocyanin, and pumps protons from the stroma into the thylakoid space.

NADP reductase

Membrane-bound Enzyme 3 that catalyzes the reduction reaction $\text{NADP}^+ + \text{H}^+ + 2e^- \rightarrow \text{NADPH}$ using electrons delivered by ferredoxin.

ATP synthase

Membrane-bound Enzyme 4, a large membrane complex acting as a channel that synthesizes ATP from ADP and $\text{P}_i$ as protons diffuse down their gradient back into the stroma.

Plastoquinone

A mobile organic protein electron carrier in the thylakoid membrane that transfers electrons from Photosystem II to the $b_6\text{-}f$ complex.

Plastocyanin

A mobile organic protein electron carrier that moves electrons from the $b_6\text{-}f$ complex to Photosystem I.

Ferredoxin

A mobile organic protein carrier that receives excited electrons from Photosystem I and passes them to NADP reductase.

Calvin cycle

The enzymatic pathway of light-independent reactions (also called $C_3$ photosynthesis) in the stroma that fixes $\text{CO}_2$ into organic molecules using ATP and NADPH.

Rubisco

Ribulose bisphosphate carboxylase/oxygenase, the enzyme that catalyzes the primary carbon-fixation reaction binding $\text{CO}_2$ to RuBP.

RuBP

Ribulose 1,5-bisphosphate, a 5-carbon organic molecule that combines with $\text{CO}_2$ during the initial step of the Calvin cycle.

PGA

3-phosphoglycerate, a 3-carbon intermediate compound formed immediately after $\text{CO}_2$ is fixed to RuBP by Rubisco.

G3P

Glyceraldehyde 3-phosphate, a 3-carbon sugar produced during the reduction phase of the Calvin cycle that serves as the direct output to form glucose and other sugars.

Photorespiration

An oxidation process where Rubisco binds $\text{O}_2$ instead of $\text{CO}_2$ to RuBP, favored when stomata close during hot, dry conditions.

Stomata

Microscopic openings on leaf surfaces through which water evaporates and gas exchange ($\text{CO}_2$ and $\text{O}_2$) takes place.

$C_3$ photosynthesis

Standard photosynthetic pathway where carbon is fixed directly into 3-carbon PGA molecules by Rubisco inside chloroplast stroma.

$C_4$ photosynthesis

A spatial solution to photorespiration where $\text{CO}_2$ is initially fixed by PEP carboxylase into a 4-carbon molecule in mesophyll cells before delivery to bundle-sheath cells.

PEP carboxylase

An enzyme in $C_4$ and CAM plants with a high affinity for $\text{CO}_2$ that binds atmospheric $\text{CO}_2$ to phosphoenolpyruvate (PEP) to form oxaloacetate.

Mesophyll cells

Leaf cells in $C_4$ plants where $\text{CO}_2$ is initially fixed into oxaloacetate and converted to malate by PEP carboxylase.

Bundle-sheath cells

Specialized leaf cells surrounding veins in $C_4$ plants where malate is decarboxylated to supply concentrated $\text{CO}_2$ to Rubisco for the Calvin cycle.

CAM photosynthesis

Crassulacean Acid Metabolism, a temporal adaptation where stomata open at night to fix $\text{CO}_2$ into malic acid stored in vacuoles and close during daylight to run the Calvin cycle.

Aerobic respiration ATP yield

The metabolic oxidation process yielding $38\text{ ATP}$ per glucose molecule using oxygen in the Krebs cycle and oxidative phosphorylation.

Anaerobic respiration ATP yield

Fermentation pathways (alcoholic and lactic acid) yielding only $2\text{ ATP}$ per glucose molecule in the absence of oxygen.

Systematics

The branch of biology dealing with the classification, naming, and evolutionary relationships of organisms based on shared characteristics.

Bacillus anthracis

A Gram-positive, spore-forming bacterium causing anthrax, used in the September 2001 biological mail attacks.

Ames Strain

A highly lethal strain of Bacillus anthracis identified by DNA sequencing during the FBI investigation into the 2001 mailings.

Cladistics

An analytical method of classifying organisms based on shared derived characteristics (synapomorphies) to infer phylogenetic trees.

Derived characteristic

A trait or similarity that evolved in the most recent common ancestor of an entire group and was inherited by its descendants.

Ancestral characteristic

A trait or similarity that arose prior to the most recent common ancestor of a group, exhibited by the outgroup.

Outgroup

An evolutionary reference organism or group that diverged prior to the taxa being studied and possesses ancestral character states.

Synapomorphy

A shared derived character state that originated in the common ancestor of a clade and defines relationships among clade members.

Cladogram

A branching diagram depicting a hypothesized pattern of evolutionary relationships among species based on cladistic analysis.

Clade

A monophyletic group consisting of a common ancestor and all of its descendants, defined by synapomorphies.

Sister species

A pair of species or taxa that share a direct, immediate common ancestor with each other.

Homoplasy

A shared character state between species that was not inherited from a direct common ancestor, caused by convergent evolution or evolutionary reversal.

Convergent evolution

A form of homoplasy where similar traits evolve independently in unrelated lineages adaptively responding to similar selection pressures.

Evolutionary reversal

A form of homoplasy where a lineage re-evolves an ancestral character state, such as the loss of functional limbs in snakes.

Principle of parsimony

An analytical rule favoring the phylogenetic tree hypothesis that requires the fewest evolutionary changes, steps, or assumptions.

Monophyletic group

A taxonomic group that includes the most recent direct common ancestor and all of its descendants.

Paraphyletic group

A taxonomic group that includes the most recent direct common ancestor but excludes some of its descendants (e.g., traditional dinosaurs excluding birds).

Polyphyletic group

A taxonomic group that does not include the most recent direct common ancestor of all member species (e.g., grouping flying vertebrates like bats and hawks).

Binomial nomenclature

A two-part naming system instituted by Carolus Linnaeus consisting of a capitalized genus name and an uncapitalized specific epithet, both italicized.

Taxon

A named group or level of organisms at any tier in the hierarchical classification system (plural: taxa).

Class Mammalia synapomorphies

Diagnostic derived features defining mammals, specifically the presence of mammary glands and hair.

Order Carnivora synapomorphies

Diagnostic derived features defining carnivores, specifically the presence of carnassial teeth.

Family Felidae synapomorphies

Diagnostic derived features defining cats, including a skull with a short rostrum, short facial area, and short inflated braincase.

Genus Felis

A genus of small felines that cannot roar due to a unique throat structure, comprising six recognized species.

Felis margarita

A species of small wild cat inhabiting deserts of northern Africa and southwest/central Asia, characterized by large ear pinnae and reduced size.

Homologous structures

Structures derived from the same ancestral source that may perform different functions, such as dolphin flippers and bird wings.

Analogous structures

Structures performing similar functions that derived from different ancestral sources, such as vertebrate lungs (swim bladder) vs. land snail lungs (mantle tissue).

Sporophyll

A modified leaf that bears sporangia for spore production.

Megasporophyll

A specialized sporophyll that bears ovules, such as those covered in brown ramental hairs in Cycas.

Carpel

The female reproductive organ of a flower, formed by the evolutionary folding of a sporophyll, enclosing ovary, style, and stigma.

Cone scale

Reduced, shortened sporophylls that form the reproductive structures (cones) of gymnosperms.

Hadean Eon

The geologic eon ($4,500\text{ MYA} - 4,000\text{ MYA}$) marked by the formation of Earth as a hot mass of molten rock.

Archean Eon

The geologic eon ($4,000\text{ MYA} - 2,500\text{ MYA}$) during which chemically-rich oceans formed and life originated approximately $3.5\text{ billion years ago}$.

Proterozoic Eon

The geologic eon ($2,500\text{ MYA} - 600\text{ MYA}$) during which atmospheric oxygen accumulated and the first multicellular organisms appeared.

Phanerozoic Eon

The current geologic eon ($600\text{ MYA} - \text{Present}$) marked by abundant visible animal and plant life beginning with the Cambrian explosion.

Cambrian explosion

A dramatic diversification event approximately $500\text{ million years ago}$ in aquatic environments establishing major invertebrate phyla and primitive chordates.

Atmospheric oxygen concentration

The current percentage of oxygen gas in Earth's atmosphere, which is approximately $21\%$.

Oxygen lag hypothesis

The $200\text{-million-year}$ delay between the origin of cyanobacteria and atmospheric oxygen accumulation, explained by oxygen reacting with iron in oceans to form iron oxide.

Ozone layer ($\text{O}_3$)

An atmospheric layer created when $\text{O}_2$ interacts with UV radiation, protecting life on Earth by reducing UV-induced mutation rates.

Endosymbiosis hypothesis for mitochondria

Theory stating that mitochondria evolved when a primitive eukaryote engulfed an aerobic Alphaproteobacteria (like Rickettsia or purple non-sulfur bacteria).

Endosymbiosis hypothesis for chloroplasts

Theory stating that chloroplasts evolved when an eukaryotic cell engulfed a photosynthetic cyanobacterium, leading to red and green algae.

Secondary endosymbiosis

The process wherein a eukaryotic cell engulfed a eukaryotic red alga, resulting in brown algae chloroplasts surrounded by four membranes.

Three Domains of Life

The top-level monophyletic clades into which all life evolved: Eubacteria, Archaea, and Eukaryotes.

Dr. Ortega's course extra credit policy

Grants $4\text{ extra credit points}$ per exam for reflection surveys, up to $15\text{ points}$ on the second lowest exam for 100% clicker participation, and $6\text{ points}$ for the Gateway survey.

Exam score dropping policy

The single lowest grade among the four course exams (including the final exam) is dropped when calculating the final exam average.

Weekly quiz weight

Weekly quizzes account for $5\%$ of the final grade, with the three lowest quiz scores dropped.

Exam grade rounding rule

Final calculated numeric course grades are rounded up by adding $0.6\text{ points}$.

Cell phone & device exam rule

During exams, cell phones must be disconnected inside bags, and smartwatches, earphones, calculators, food, and drinks are strictly prohibited.

Course email requirement

Students must communicate with Dr. Ortega exclusively using their official FIU email address or through the Canvas portal.

Inhalational anthrax mechanism

Inhaled Bacillus anthracis endospores germinate and release toxins in lymphatic system nodes and alveoli, circulating eventually to the brain.

Bruce E. Ivins

A biodefense researcher at Fort Detrick, Maryland who was the primary suspect in the 2001 anthrax mailings before committing suicide in 2008.

Oldest Homo sapiens fossil

The oldest known fossil of Homo sapiens, discovered in Morocco and dated to approximately $300,000\text{ years old}$.

Ape clade synapomorphy

The shared derived character state defining the common ancestor of all apes, which is tail loss.

Bipedalism

The shared derived character state (synapomorphy) defining the genus Homo relative to knuckle-walking apes.

Cetacean flipper origin

A modified mammalian limb adapted for swimming through convergent evolution, sharing structural homology with bird wings.

Snake limb loss reversal

An evolutionary reversal wherein snakes lost functional limbs possessed by tetrapod ancestors, forming a synapomorphy defining snakes.

Archosauria clade

A monophyletic group containing crocodilians, pterosaurs, dinosaurs, and their direct descendants (birds).

Traditional Dinosaur group classification

A paraphyletic grouping because it historically excludes birds, which are direct descendants of dinosaur ancestors.

Flying vertebrates grouping

A polyphyletic assemblage combining bats (mammals) and hawks (birds) that does not share a single direct flying common ancestor.

Euphorbia handiensis and Cactaceae convergence

Plant taxa exhibiting homoplasy via convergent evolution for CAM physiology, succulent stems, and modified leaf spines in separate deserts.

Land snail colonization

At least 10 independent land colonization events from marine environments, representing convergent evolution of lungs in terrestrial snails.

Terrestrial arthropod colonization

Four independent land colonization events occurring around $400\text{ million years ago}$ by spiders, millipedes/centipedes, crustaceans, and insects.

Aquatic ancestor of insects

The ancestral aquatic lineage of insects identified through phylogenetic analysis as crustaceans.

Alphaproteobacteria

The bacterial group (including Rickettsia and purple non-sulfur bacteria) that gave rise to mitochondria via endosymbiosis.

Cyanobacteria

Photosynthetic prokaryotes originating $\sim 3.7\text{ billion years ago}$ that generated atmospheric oxygen and became chloroplasts via endosymbiosis.

Mitochondrial DNA

Circular DNA contained inside mitochondria whose nucleotide sequence closely matches Alphaproteobacteria.

Lichen

A symbiotic organism resulting from the intimate interaction between two distinct phylogenetic lineages (a fungus and a photosynthetic partner).

Respiration gene localization

In humans, most of the genes that control cellular respiration are located in the cell nucleus rather than in the mitochondria.