Botany Exam 2 Flashcards (2nd generation)

What happens in the thylakoid membranes and in the stroma of a chloroplast?

Light reactions happen in the thylakoid membranes (pigments embedded there). Carbon fixation (Calvin cycle) occurs in the stroma. Daytime carbohydrate is stored temporarily as starch grains in the stroma.

Where are PSII, PSI, ATP synthase, and cytochrome b₆/f located in the thylakoid membrane?

PSII – mainly grana (stacked) thylakoids. PSI + ATP synthase – almost entirely stroma thylakoids and grana margins. Cyt b₆/f – evenly distributed. So mobile carriers (plastoquinol, plastocyanin) must shuttle electrons between them.

What do PQ, PC, Fd, and FNR stand for, and what is their order in linear electron flow?

H₂O → PSII → PQ (plastoquinone) → cyt b₆/f → PC (plastocyanin) → PSI → Fd (ferredoxin) → FNR (ferredoxin–NADP⁺ reductase) → NADPH

What is cyclic electron flow, and what does it produce?

Uses only photosystem I; electrons cycle back through cyt b₆/f to PSI. Makes ATP (cyclic photophosphorylation, chemiosmotic). No O₂ released, no NADPH made.

What is the higher-energy state of an electron after chlorophyll absorbs light called?

Excited state (10/09 quiz).

In a tobacco leaf, what moves through the stomata, and what is the hair-like projection called?

Stomata on the lower surface of a tobacco (Nicotiana tabacum) leaf, SEM; most open. CO₂ diffuses in, O₂ diffuses out. Projection = a trichome (leaf hair).

What gases make up air, and which is most abundant?

N₂ 78%, O₂ 21%, Ar 0.93%, CO₂ ~0.0428% = ~428 ppm. Most abundant gas = nitrogen (quiz).

On the Mauna Loa CO₂ graph, what do the red and black lines represent?

Atmospheric CO₂ (Mauna Loa). Red = monthly means (zig-zag = seasonal cycle). Black = same data corrected for the seasonal cycle (trend). Steady rise over recent decades.

What are the three stages of the Calvin–Benson–Bassham cycle?

1. Fixation – CO₂ + RuBP → (6C intermediate) → 2 PGA (Rubisco). 2. Reduction – PGA → 1,3-bisphosphoglycerate → G3P (uses ATP, NADPH). 3. Regeneration – 5 of 6 G3P → 3 RuBP (5×3C → 3×5C).

What molecule accepts CO₂ in the Calvin cycle, and what are its features?

Ribulose 1,5-bisphosphate (RuBP) — 5-carbon sugar with 2 phosphates; the starting AND ending compound of the Calvin cycle; CO₂ acceptor.

What is Rubisco, what reaction does it catalyze, and why is it notable?

Rubisco = ribulose 1,5-bisphosphate carboxylase/oxygenase. Catalyzes CO₂ fixation onto RuBP. World’s most abundant enzyme — up to ~40% of soluble leaf protein.

What do the two main bands on a barley flag-leaf protein gel represent?

Rubisco large subunit (~50 kD) and small subunit (~15 kD). Shows how abundant Rubisco is compared with all other soluble leaf proteins (and its degradation as leaves age).

What happened in the Calvin-cycle “lollipop” experiment, and what was the first stable product?

Algae in the “lollipop” were briefly given ¹⁴CO₂, then dropped into hot (boiling) ethanol to stop reactions; labeled compounds separated by 2-D paper chromatography. First stable product – 3-phosphoglycerate (PGA) → “C₃” photosynthesis; ¹⁴C appears in one of the two PGA.

Which two enzymes carry out the reduction stage of the Calvin cycle, and what does each use?

(a) 3-phosphoglycerate kinase – ATP → PGA becomes 1,3-bisphosphoglycerate. (b) Glyceraldehyde 3-phosphate dehydrogenase – NADPH → G3P. Trap – in glycolysis the same dehydrogenase uses NAD⁺/NADH.

How many Calvin-cycle turns, ATP, and NADPH are needed to produce one exported G3P?

3 turns (3 CO₂), 9 ATP, 6 NADPH. 3 RuBP + 3 CO₂ → 6 PGA → 6 G3P; 1 exported, 5 regenerate 3 RuBP.

What are the five enzymes in glycolysis’ payoff phase, and what is the total yield?

6 G3P dehydrogenase, 7 phosphoglycerate kinase, 8 phosphoglycerate mutase, 9 enolase, 10 pyruvate kinase. Yield – 4 ATP + 2 NADH.

What happens to most fixed carbon, and where are sucrose and starch made?

Little free glucose. Exported G3P → sucrose in the cytosol (major transport sugar). G3P kept in chloroplast → starch in the stroma (major storage carbohydrate). At night starch → sucrose → exported via vascular bundles.

What is sucrose made of, and what are its formula and molar mass?

Disaccharide of glucose + fructose; C₁₂H₂₂O₁₁; 342.30 g/mol; chemically relatively inert; table sugar.

What are Rubisco’s two activities, and what conditions favor each one?

Carboxylase (RuBP + CO₂ → 2 PGA) – high CO₂, low O₂. Oxygenase (RuBP + O₂ → PGA + phosphoglycolate) – low CO₂, high O₂ — i.e., normal air.

What is photorespiration?

It is where rubisco oxygenase activity + the phosphoglycolate salvage pathway, which together consume O₂ and release CO₂ (in the light).

Which three organelles work together during photorespiration?

Chloroplast, peroxisome, mitochondrion — often seen pressed together in EM.

Where is O₂ consumed and where is CO₂ released during photorespiration?

O₂ is consumed twice in the chloroplast (Rubisco oxygenase) and peroxisome (glycolate → glyoxylate). CO₂ is released once in the mitochondrion (2 glycine → serine).

What are the seven steps of photorespiration, and where does each occur?

1 phosphoglycolate → glycolate (chloroplast); 2 glycolate → glyoxylate (peroxisome); 3 glyoxylate → glycine (peroxisome, transamination); 4 2 glycine → serine + CO₂ (mitochondrion); 5 serine → hydroxypyruvate (peroxisome); 6 hydroxypyruvate → glycerate (peroxisome); 7 glycerate → PGA (chloroplast)

Why can peroxisomes have a crystalline core when viewed with an electron microscope?

Their most abundant enzymes (e.g., catalase) become so concentrated they aggregate into a crystal.

In the C₄ pathway, which enzyme fixes carbon, what molecules does it use, and what product forms?

PEP carboxylase adds bicarbonate (HCO₃⁻), NOT CO₂, to phosphoenolpyruvate (PEP) → oxaloacetate (4C), then reduced to malate or aminated to aspartate.

What happens in the mesophyll and bundle-sheath cells of a maize leaf with Kranz anatomy?

Kranz anatomy (“wreath”). Mesophyll cells (outer ring) – C₄ pathway (PEP carboxylase). Bundle-sheath cells (around vascular bundle) – CO₂ released, Calvin cycle. = spatial separation.

Why do maize bundle-sheath cells produce no O₂, and how do they make ATP?

Their chloroplasts lack photosystem II (no water splitting). PSI is present → ATP by cyclic electron flow.

Why are C₄ plants especially productive in hot, bright, and dry conditions?

CO₂ is “pumped” into bundle-sheath cells → high CO₂ –O₂ at Rubisco → little photorespiration. Net photosynthesis 2–3× that of C₃ grasses; higher temperature optimum; evolved in the tropics; arose independently many times in monocots and dicots.

What photosynthetic pathway does purple nutsedge (Cyperus rotundus) use?

It uses a C₄ plant.

What happens in CAM plants at night and during the day?

Night – stomata open; starch → PEP; HCO₃⁻ + PEP → oxaloacetate → malate, stored as malic acid in the vacuole. Day – stomata closed; malic acid decarboxylated → CO₂ + pyruvate; CO₂ refixed by Rubisco (Calvin cycle).

When is the pH of CAM leaf sap at its lowest?

At dawn — after a night of malic acid accumulation (quiz 10/16).

What type of separation do C₄ and CAM photosynthesis use?

C₄ – spatial (different cells, same time). CAM – temporal (same cells, night vs day). Both feed CO₂ into the Calvin cycle.

What is the scientific name and family of the jade plant, and what photosynthetic pathway does it illustrate?

Jade plant, Crassula ovata (Bryophyllum was the other example) — family Crassulaceae, origin of the name “crassulacean acid metabolism.”

When are stomata open in C₄ plants compared with CAM plants?

C₄ – open by day, closed at night. CAM – closed by day, open at night.

Besides carbon, which two macronutrients must plants reduce and assimilate, and in what forms are they absorbed?

Nitrogen — as nitrate (NO₃⁻), sometimes ammonium (NH₄⁺). Sulfur — as sulfate (SO₄²⁻). Energy – light reactions in leaves; respiration of phloem-delivered sucrose in roots.

Which nutrients are macronutrients, micronutrients, and beneficial elements?

Macro – N, P, S, K, Mg, Ca. Micro – Fe, Mn, Zn, Cu, B, Mo, Cl, Ni. Beneficial – Na, Si, Co (±); I, V. Fungi exceptions – no Ca, no B.

Who proposed the three-domain system, and what molecule did they use?

Carl Woese (Univ. of Illinois, 1970s) — small-subunit ribosomal RNA. Domains – Bacteria, Archaea, Eukarya.

How do the three-domain and two-domain trees differ in the placement of eukaryotes?

Three-domain (Woese) – Eukarya = sister clade to Archaea. Two-domain – Eukarya arose from within Archaea (near Asgard archaea) — quiz answer “Archaea.”

What do LUCA and LECA mean, and what features did each have?

LUCA – last universal common ancestor of all domains; had a cell membrane, genetic code, ribosomes. LECA – last eukaryotic common ancestor of all supergroups; had a nucleus, mitochondria, peroxisomes.

How do Bacteria, Archaea, and Eukarya differ in their cell structures and molecular features?

See table. Unique to Bacteria – peptidoglycan, 1 RNA polymerase, formyl-methionine, no introns, inhibited by streptomycin/chloramphenicol. Unique to Archaea – some branched lipids. Unique to Eukarya – nucleus, organelles.

How do streptomycin and chloramphenicol affect bacterial cells?

Streptomycin – binds bacterial ribosome, blocks binding of formyl-methionyl-tRNA (initiation). Chloramphenicol – blocks chain elongation. Neither affects Archaea or Eukarya.

What is a supergroup, which kingdoms remain, and what does “protist” mean?

A rank between domain and kingdom. Surviving kingdoms – Plantae, Fungi, Animalia. Protists = all other eukaryotes; an informal, non-natural (non-clade) grouping.

Which groups are most closely related

animals and fungi, animals and plants, or fungi and plants?

What organisms belong to Chloroplastida, Opisthokonta, and SAR?

Chloroplastida = green algae + plants. Opisthokonta = animals, fungi + unicellular relatives. SAR = Stramenopiles, Alveolates, Rhizarians.

What is the taxonomic classification of maize, from domain to species?

Eukarya → Archaeplastida → Plantae → Anthophyta → Monocotyledoneae → Poales → Poaceae → Zea → Zea mays.

What is the difference between a taxonomic category and a taxon?

Category = the rank/level (e.g., genus). Taxon = the actual group at that level (e.g., Zea).

What is the biological species concept, who proposed it, and what are its limitations?

Ernst Mayr – populations that interbreed with each other but not (usually) with other groups; key = genetic isolation. Fails for fossils, asexual and highly self-fertilizing organisms; hard to test in nature.

What is the morphological species concept?

Species recognized by structural/anatomical distinctness — how most species are actually named; assumes isolation → genetic → visible differences.

What pigments do cyanobacteria contain, and what colors are the two phycobilins?

Chlorophyll a, carotenoids, phycobilins – phycocyanin (blue), phycoerythrin (red).

What is Anabaena cylindrica, and what does it store?

Cyanobacterium Anabaena cylindrica (freeze-fracture EM) – thylakoids, nucleoid; storage = glycogen.

Why is the term “blue-green algae” inaccurate for cyanobacteria?

Only ~half are blue-green, and they are prokaryotes — algae are eukaryotes.

How does Oscillatoria reproduce?

It reproduces only by fragmentation of the filament.

What is Calothrix, and what is its basal cell called?

it is a genus of filamentous cyanobacteria, basal cell is a basal heterocyst (N-fixing); forms akinetes just above the heterocysts.

What does a Nostoc colony look like?

The colony looks like many filaments in a mucilaginous sheath; freshwater.

What are stromatolites, and how do they form?

Stromatolites (“layered rock”) – cyanobacterial colonies bind calcium carbonate into domes. Common as fossils; forming today in few places, e.g., Hamelin Pool, Western Australia.

What is the difference between a heterocyst and an akinete in Anabaena?

Heterocyst – N₂ fixation → NH₄⁺. Akinete – thick-walled resting spore resistant to heat and desiccation.

What four features of heterocysts protect nitrogenase from oxygen?

1 Thick walls rich in glycolipid (block O₂); 2 Lack PSII → cyclic photophosphorylation only, no O₂; 3 Low phycobilins; 4 Remaining O₂ reduced by H₂ (by-product of N fixation); Nitrogenase is O₂-sensitive → anaerobic process.

How do heterocysts exchange materials with neighboring cells?

Through microplasmodesmata – fixed N (NH₄⁺) out, photosynthetic products in.

What is Trichodesmium, and why is it important in tropical oceans?

Free-living N-fixing cyanobacterium of tropical oceans; ~¼ of the nitrogen fixed there (blooms off the Great Barrier Reef).

What allows Asian rice terraces to be farmed for centuries without fertilizer?

Anabaena azollae, a N-fixing cyanobacterium living in the water fern Azolla floating in the paddies.

What makes prochlorophytes different from other cyanobacteria?

They have chlorophyll a AND b (+ carotenoids) but no phycobilins — like green-algal/plant chloroplasts.

What are the three prochlorophyte genera, and which is the smallest and most abundant photosynthetic organism?

Prochloron (symbiont in sea squirts), Prochlorothrix, Prochlorococcus (~0.6 µm, smallest genome; most numerous on Earth).

Which prokaryote lives inside the sea squirt Didemnum molle?

Prochloron, on tropical seashores, inside colonial ascidians (Didemnum molle).

What pigments do purple and green bacteria use, and how many photosystems do they have?

Bacteriochlorophylls; one photosystem; no O₂ produced; grow in light only anaerobically (O₂ represses pigment synthesis).

Which plant photosystem is evolutionarily related to purple bacteria, and which to green sulfur bacteria?

Purple bacteria (type II RC) → PSII. Green sulfur bacteria (type I RC) → PSI.

What is the photosynthesis equation for purple and green sulfur bacteria, and what replaces water as the electron donor?

CO₂ + 2 H₂S + light → (CH₂O) + H₂O + 2 S; H₂S replaces water as electron donor. Nonsulfur bacteria use organic donors (alcohols, fatty acids).

What are the vesicle-like structures in Rhodospirillum rubrum, and how does light affect their abundance?

Rhodospirillum rubrum (purple nonsulfur). Vesicles = plasma-membrane intrusions with bacteriochlorophyll — extensive in dim light, fewer in bright light.

What are the main parts of chlorophyll, and how do chlorophyll a and b differ?

Porphyrin (tetrapyrrole) ring with central Mg; hydrophobic hydrocarbon tail. Chl a – methyl (–CH₃); chl b – formyl (–CHO) at same position.

Who was Lynn Margulis, and what theory did she champion?

Serial Endosymbiotic Theory – mitochondria and chloroplasts descend from engulfed bacteria; mitochondria came first.

What were the bacterial ancestors of mitochondria and chloroplasts?

Mitochondria – an alpha-proteobacterium. Chloroplasts – cyanobacteria. Land plants got theirs from green algae.

What evolutionary changes allowed an early host cell to take up and retain endosymbionts?

Wall-less heterotrophic prokaryote → phagocyte – flexible membrane + cytoskeleton (endocytosis), lysosomes; internal membranes → endomembrane system; then prey adopted, not digested.

In the Vorticella–Chlorella relationship, what does each partner provide?

Vorticella (protozoan) with green alga Chlorella in perialgal vacuoles. Host – protection + minerals. Alga – carbohydrates.

Why do mitochondria and chloroplasts have small genomes?

Endosymbiont DNA and functions were transferred to the host nucleus; wall was lost. Organelles still self-replicate.

What is primary endosymbiosis, how many plastid membranes result, and which groups have these plastids?

it is where eukaryote engulfs a cyanobacterium; 2 membranes; red algae and green algae (→ plants).

What is secondary endosymbiosis, how many plastid membranes result, and which groups have these plastids?

Secondary — eukaryote engulfs a plastid-containing eukaryote; 3 or 4 membranes; haptophytes, most cryptomonads, many euglenoids, dinoflagellates, stramenopiles.

What is tertiary endosymbiosis, and in which organisms does it occur?

Plastid from a eukaryote that itself had a secondary plastid (cryptomonad, haptophyte or diatom); >2 membranes; in several dinoflagellates.

What is Grypania spiralis, and why is it important?

It is the oldest fossil interpreted as a eukaryotic (multicellular) alga; up to ~2.1 billion years.

What is the body form of Volvox, and how do daughter colonies form?

The body form is hollow sphere colonies in a gelatinous matrix; daughter colonies form from specialized cells dividing repeatedly.

What is zygotic meiosis, and which organisms use this life cycle?

A type of meiosis there a zygote is the only diploid cell. Fungi, some algae (Chlamydomonas).

What is gametic meiosis, and which organisms use this life cycle?

In this type of meiosis, gametes are the only haploid cells. Most animals, some protists, some green & brown algae.

What is sporic meiosis, and which organisms use alternation of generations?

Sporic meiosis = alternation of generations. Meiosis makes spores; multicellular n gametophyte and 2n sporophyte. Plants, some brown, red, green algae. (Quiz answer – option C.)

What is the difference between a spore and a gamete?

Spore – divides by mitosis directly into a multicellular haploid organism. Gamete – develops only after fusing with another gamete.

What is the difference between isomorphic and heteromorphic alternation of generations?

Isomorphic – generations look alike (most red, many green, a few brown algae). Heteromorphic – they differ (plants, some brown and red algae).

How many cells are typically found in angiosperm female and male gametophytes?

Female – typically 7 cells; male – 3 cells; both dependent on the sporophyte — extreme gametophyte reduction.

Into which two clades did green algae split, and which clade includes land plants?

Chlorophyte clade (most green algae) and streptophyte clade (charophyceans incl. Coleochaetales, Charales, zygnemataleans + bryophytes and vascular plants).

What are desmids, and what is the narrow connection between their two half-cells called?

They are two half-cells joined by the isthmus. Freshwater, related to Spirogyra, no flagellated cells, love nutrient-poor peat bogs.

What is Xanthidium armatum?

It is a desmid

What is a phragmoplast, and what is its role in cell division?

System of microtubules perpendicular to the plane of division — scaffold for forming the cell plate. Shared by Coleochaetales, Charales and plants.

What traits link Coleochaetales and Charales to land plants?

Phragmoplast, oogamy, sperm like bryophyte sperm, branched apical growth, plasmodesmata, retention of egg. Plants came from an extinct charophycean like them.

What is the body form of Coleochaete, and what chloroplast feature does it share with hornworts?

The body form is a parenchymatous disk, one cell thick (big cells = zygotes). Each cell has one large chloroplast with a pyrenoid, like hornworts. Name = “sheathed hair.”

What is Chara commonly called, and why?

It is commonly called stonewort, because some have heavily calcified walls. Nodes with whorled branches, internodes; apical growth.

What are the two gametangia of Chara, and how can you distinguish them?

Oogonium (elongate, wrapped in twisted cells) (female). Antheridium (round) (male) — most complex of any protist. Sperm = only flagellated cells.

What is sporopollenin, and where is it found?

Very resistant wall polymer in Chara zygote walls and plant spores and pollen → why spores/pollen fossilize so well.

What material makes up the characteristic cell walls of diatoms?

Silica (10/23 quiz). Note – diatoms are not in your uploaded slides — review in textbook.

What are the three bryophyte phyla, and how are they related to other land plants?

Marchantiophyta (liverworts) — sister to all other land plants. Bryophyta (mosses). Anthocerotophyta (hornworts) — share most recent ancestor with vascular plants.

What evolutionary innovations appear on the embryophyte cladogram, in order?

All – multicellular embryo, sporopollenin spores, antheridia/archegonia with sterile jackets (>450 Mya) → stomata (not liverworts) → sporophyte persistent (hornworts+) → sporophyte independent, branching → vascular tissue with tracheids.

Which generation is dominant in bryophytes, and which is dominant in vascular plants?

Bryophytes – gametophyte larger and free-living; sporophyte attached and dependent. Vascular plants – sporophyte larger and free-living.

Are rhizoids unicellular or multicellular in mosses, liverworts, and hornworts, and what do they do?

Mosses – multicellular (a row of cells). Liverworts & hornworts – unicellular. Mostly anchorage (absorption occurs over whole gametophyte).

What is a Marchantia thallus pore, and how does it work?

Pore — barrel-shaped, 4–5 tiers of 4 cells, leads to an air chamber; bottom tier closes when dry, opens when moist → stomata-like function (but NOT a stoma).

How can you distinguish a leafy liverwort leaf from a moss leaf?

Leafy liverwort leaves lack a midrib; moss leaves have one.