BOTANY: CHAPTER 1
ORIGINS
Evidence
Earliest Evidence
Conditions
LUCA;
First identifiable algae: 1.6 BYA; First land plants: 600 MYA; First seed plants: 350 MYA; Flowering plants: 150 MYA.
Multicellular photosynthetic organisms; photosynthesis; plant cell; transition to land.
Life's principal currency: ATP;
Common genetic code: DNA and RNA
Transcription and Translation: DNA --> RNA --> Proteins
Tree of Life
Strata shows evidence of fossils, photosynthesis, descent, biological molecules.
Isotopes: C12 (most abundant), C13 (plant don't like to use it for photosynthesis), C14 (unstable).
Chemical reactions made life possible.
Ammonia and methane were thought to be the most abundant in the atmosphere.
Urey-Miller Experiment: simulated early Earth conditions in a lab and grew living organic molecules likes amino acids.
RNA World hypothesis: RNA preceded proteins and DNA throughout evolution.
EARLY METABOLISM
Chemosynthesis
Early Earth was much different from life today.
Photosynthesis only found on the uppermost branches of Bacteria tree.
Hyperthermophilic prokaryotes: cells lived in extremely hot environments. Most die in presence of oxygen.
They do not use oxygen during metabolic activities.
Chemosynthesis: Energy from inorganic molecules used to drive metabolism. Often found in extreme environments
Reducing power: Moves electrons around; OILRIG: Oxidation is a loss, Reduction is a Gain.
NADH: Nicotinamide adenine dinucleotide. Electron carrier. Strong reducing agent.
Protein motive force: through ETC. Generates ATP
ATP: Adenosine Triphosphate. ADP + P; high energy bond; primary energy source in all living things.
Glycolysis
Embden-Meyerhof-Parn Pathway; produce pyruvate; metabolic pathway; converts glucose into pyruvate; net of 2 ATP produced.
Steps: Uses two ATP for activation energy. Produces 4 ATP (Net 2). Glucose is the substrate. Pyruvate is the product. Pyruvate then enters into fermentation or aerobic respiration.
Fermentation: NADH recycled to NAD+, leads to lactic acid or ethanol.
Eukaryotes arose 1.8 BYA in anaerobic respiration.
Glycolysis is most ancient. It does NOT require oxygen. It connects with aerobic respiration.
Making Sugar
Carbon Fixation: Began with cehmosynthesizers. Described by the Calvin cycle.
Reverse TCA: Citric Acid Cycle. Precursor to stromal reactions of photosynthesis.
Glucose isomers: Alpha glucose - energy storage. Beta glucose - building and structure.
Starch: Amylose + Amylopectin; Alpha 1,4 bond and Alpha 1,6 bond.
CELLS
LUCA: Last Universal Common Ancestor
Prebiotic Soup of molecules
Membrane Bubbles: containing information molecule, performs limited number of metabolic reactions, able to divide, interact, fuse, and share genomes and metabolic activities.
Wet and Dry cycles: DNA and lipids, sandwich to lipid vesicle with DNA inside, spontaneously formed.
Plasma membrane: phospholipid, micelle, embedded proteins facilitate metabolism and are receptors for functions such as self identity.
Selection for complexity: essential nutrients depleted, impose selection pressure, favored cells capable of synthesizing limited molecules, origin based metabolic pathways, those less dependent on exogenous sources of nutrients,
Eukaryotes
evidence of eukaryotes 2.7 BYA; Geologically stable biomarker made predominantly by eukaryotes (sterol).
Endomembrane system: continuous connected membrane, forming multiple organelles - plasma membrane, golgi body, endoplasmic reticulum, nuclear envelope.
prokaryotes vs. eukaryotes: Membrane bound genetic material, circular DNA vs. Chromosomes, genome size, cytoskeleton, ribosome size.
Cytoskeleton: microfilaments - important for vesicle movement near membrane. Intermediate filaments - more permanent, fix things in place. Microfilaments - trackway for long range movement of transport vesicles.
Endosymbiotic theory
ancestral prokaryote, symbiosis becomes interdependent, mitochondria containing eukaryote eats a photosynthetic cyanobacterium but does not digest it, exchanges DNA.
Mitochondria and Plastids
mitochondrial structure: outer membrane, inner membrane, folded areas are called cristae, location of oxidative phosphorylation, the matrix is the location of the CAC.
Plastids: chloroplasts - typically green plastids used for photosynthesis. Chromoplasts - colored plastids for pigment synthesis and storage. Leucoplasts - colorless plastids. Amyloplasts - starch storage.
Chloroplasts: outer membrane, inner membrane, Grana, stack of thylakoids, thylakoid reactions with proteins embedded in thylakoid, stromal reactions inside aqueous stroma.
Cell Wall
Layer of additional protection, creates pressure along with large central vacuole, composed primarily of cellulose, hemicellulose, and pectin, remains flexible to permit growth.
Beta Glucose: monosaccharide, C1 hydroxyl group pointing towards floor, important for biological activity, major building block of cellulose.
Cellulose microfibrils: made of glucose monomers, beta glucose bonds through dehydration synthesis, hydrogen bonds make cellulose extremely strong, fiber in our diets.
Cellulose similarities: Chitin - insect exoskeleton, keratin - hair and fingernails
RESPIRATION
Complexity: becomes more complex and efficient over time, more specialized enzymes, compartmentalization.
Aerobic Respiration: uses the mitochondria to complete process, continue to strip energy from pyruvate in glycolysis, major steps - glycolysis, pyruvate oxidation, citric acid cycle, oxidative phosphorylation.
Pyruvate oxidation: electrons stripped from pyruvate and given to NAD+, CO2 broken off - C3 to C2, Acetyl CoA.
CAC Steps: Acetyl CoA joins citrate, provide NAD+ with electrons, substrate level phosphorylation, provide FAD+ with electrons, complete cycle to C4.
Oxidative Phosphorylation: The Players - FAD: strong oxidizing agent, stands for Flavin adenine dinucleotide, Riboflavin base for construction.
Chemiosmotic electrochemical gradient: proton motive force, trapped protons creates a battery, on way through concentration gradient is through special protein complex, drives synthesis of ATP.
ATP Synthase: Catalyzes formation of ATP, molecular machine, driven by chemiosmotic electrochemical gradient across membranes, mitochondrial cristae, prokaryotic cell membranes, plant thylakoid membranes.
ETC: builds up proton motive force, regenerates electron carriers, consists of 4 large protein complexes.
Oxidative Phosphorylation: The Process
Major Steps: electrons dropped off by NADH and FADH2, electrons pass through ETC, protons are pumped across, oxygen is final electron acceptor, chemiosmotic electrochemical gradient runs ATP synthase, driving production of ATP.
PHOTOSYNTHESIS
Early thermophiles gave way to cooler environments. Photosynthesis limited by temperature and unknown above 74C
Stromatolites: important in understanding photosynthetic origins, they have layers of photosynthetic cyanobacteria, creates bands of sediment and dead bacteria.
Cyanobacteria: likely the oldest known fossilized organism, close to LUCA, chemical clues - 2-methylhopane almost exclusive in cyanobacteria cell walls.
Photosynthetic Pigments
Photosynthesis reverses Respiration: 2 stages: light reactions (thylakoid reactions) and dark reactions (CAC).
Likely started as sunscreens, chlorophyll similar to hemoglobin and like common ancestor.
Pigments: molecules that absorb different wavelengths of light energy and reflect others. Reflection, absorption, transmission.
Absorbed light energy causes electrons to become excited, electrons bump into the next orbital, electron is either passed to electron acceptor or back down to its original orbit. It releases heat energy and fluorescence.
Amount of energy absorbed depends on the pigment, electromagnetic spectrum holds much energy that cannot be used. The visible spectrum is used.
Chlorophyll A is most abundant in plants and its peak absorbance is 430 nm to 660 nm. Chlorophyll B is the second most abundant, with peak absorption at 450 nm to 650 nm.
Chlorophyll A and B also have accessory pigments.
Accessory pigments: carotenoids, beta carotene, helps broaden absorption spectrum, also acts as a sunscreen and is visible during the fall when the main pigments break down.
Resonance Energy
Energy absorption and excitation occurs in organized complexes of pigments & proteins called photosystems
Absorbed energy is moved around via resonance energy
Funnelled to reaction center
Photosystems
Consist of Antennal complex, accessory pigments, chlorophyll pigments, reaction center, and it embedded in the thylakoid membrane
controlled energy release
Energy of excited electrons released in a stepwise controlled manner
May have evolved initially as a way to dissipate excess energy
Some of the energy used to make stable, energy-rich molecules that can be used by living cells
Photophosphorylation
Cyclic
Flow of electrons does not directly create ATP
Electron flow coupled with flow of protons
Electron energy drops when flow through cytochrome complex
Drag protons across membrane
Electrons return to chlorophyll
Protons trapped in special internal chamber, thylakoids
PSI, plastoquinone, cytochrome b6f, plastocyanin.
Noncyclic
e- from PSII to NADPH
NADP+
is a great oxidizer
Final electron acceptor
Helps to build proton motive force
NADPH is a more powerful energy carrier than ATP
Photolysis
uses light energy to split water, oxygen evolving complex of PSII, oxygen and protons are released, oxygen diffuses out of stomata, protons are left behind.
Proton Pump
Plastoquinone & Cytochrome b6f
Both work in concert to bring protons from stroma to lumen
Builds up the lake of protons
Involved in both cyclic and noncyclic photophosphorylation
ATP synthase uses the proton motive force to run the molecular machine,
Stromal Reactions
RuBisCO: ribulose 1,5-bisphosphate carboxylase oxygenase
Fixation, Reduction, Regeneration
Photorespiration disadvantages - not as efficient, produces a toxic byproduct
Photorespiration advantages
High light tolerance
Reduce photo-inhibition
Provides metabolites for other processes, including stress protection proteins
Alpine environments
Drought prone environments
High salinity environments
Gluconeogenesis: production of glucose built from smaller molecules. Occurs in chloroplasts, amyloplasts, and cytosol.
Alternative Pathways
3 Major Pathways: C3 plant, C4 plants, CAM plants.
C4- restricted mainly to herbaceous forms, seasonally dry regions where fire is common, monocotyledons, dicotyledons.
CAM plants - more numerous than C4
Convergent evolution across clades and with multiple origins.
C4 Photosynthesis: RuBisCO is isolated in cells next to the bundle sheath. It is excluded from mesophyll cells. Carbonic anhydrase, pep carboxylase
C4 Advantages
Under low atmospheric CO2
Under high temperatures
When C3 photosynthesis is undergoing high photorespiration
Depends on the environmen
C4 Origins: It has evolved independently multiple times, the water availability declined and it became dominant.
CAM - Crassulacean Acid Metabolism, separates PEP carboxylase and RuBisCO temporarily, opens the stomata at night because it's cooler and less water is lost at night. During the day, malate moves out of vacuole and decarboxylated.
CAM advantages: similar selective pressure to C4, under high light conditions, under arid conditions, under high temperature conditions, likely diversified under low CO2 conditions.