When did life first appear on Earth?
3.6 billion years ago
The first life → simple cells (prokaryotes)
When did eukaryotic cells first appear, and how?
2.2 billion years ago
In the theory of symbiogenesis, a merger of an archaean and an aerobic bacterium created the eukaryotes, with aerobic mitochondria
When did Oxygen-producing photosynthesis first evolve, and in what organisms? How did our atmosphere change after that?
3.4 billion years ago → photosynthesis occurs in cyanobacteria
Oxygen enters the atmosphere as a waste product
Ozone layer formed; as ionizing radiation so terrestrial organisms don’t get fried (protects organisms from sun)
2.4 billion years ago → Great oxidation effect → significant rise in oxygen levels
Second merger 1.6 billion years ago adding chloroplasts
Origin of photosynthesis in eukaryotes was around 1.2 billion years ago
Where did chloroplasts come from (i.e., what is their evolutionary history), and what is the evidence for an endosymbiotic origin?
A second merger, 1.6 billion years ago, added chloroplasts, creating the green plants
Primary endosymbiosis → heterotrophic eukaryote engulfed cyanobacterium (prokaryote)
Evidence:
Structure of organelles
2 membranes (bacterial and host)
Antibiotics can block protein synthesis
Binary fission
Chloroplast DNA, rRNA, and ribosomes resemble cyanobacterial DNA
Circular organization
No histones
DNA sequence based phylogeny
How did multicellular algae make the transition to life on land (i.e., what kinds of features had to evolve?)
Adaptations for life on land:
Fungal associations
Plants moved onto land about 500 mya, accompanied by fungal partners to help absorb water and nutrients
Regional specialization
On land, resources are spatially segregated
Soil provides water and minerals to ROOTS, photosynthesis takes place in aerial SHOOT system
Transport
Vascular system → movement of water and minerals from roots to rest of plant (in xylem); of sugars from leaves to rest of plant (in phloem)
Water conservation
Waxy cuticle prevents water loss
Gas exchange
Stomata allows for gas exchange
Support
Support in herbaceous tissue provided by turgor pressure
In woody tissues, lignin (a hard material embedded in cellulose matrix of plant cell walls) provides support
Reproduction and dispersal
Reproductive structures protected from desiccation (moisture removal): gametes produced in gametangia (protective structure that produces and houses gametes); retention of the embryonic sporophyte within the female gametophyte → providing nutrients and protection
Dispersal by protected spores, and later, seeds
How do multicellular plants, animals, and fungi get their food?
Consumers
Animals are heterotrophs
They INGEST food; mostly internal digestion
Decomposers
Fungi are heterotrophs
They live inside their food; secrete enzymes that digest macromolecules into smaller molecules; they ABSORB nutrients
Producers
Plants and algae are autotrophs
They use CO2 and sunlight to MAKE their own food
Thanks to their endosymbiotically-acquired chloroplasts
How much of the tree of life is multicellular?
Eubacteria and archaea are almost entirely unicellular
Eukaryotes → multicellularity evolved independently in 6 eukaryotic linears, but overall mostly unicellular
Be able to explain the ‘Big picture’ of photosynthesis (summary slide in power-point): inputs, outputs, connections, locations (thylakoid, stroma)
Light reactions occur in thylakoid membrane
Inputs: H2O, light, NADP+, ADP
Outputs: O2
Connections → ATP and NADPH
Calvin cycle → stroma
Inputs: CO2, ATP, NADPH
Outputs: sugar (glucose, sucrose…)
Connections → NADP+, ADP
Why is photosynthesis so important (for plants, for you, for all life on earth?)
For plants → allows plants to produce their own food (glucose) and energy, allowing them to grow and produce
For you → oxygen to breathe and food that you eat (by consuming plants or indirectly consuming animals that eat plants)
For life on Earth → photosynthetic organisms form the base of the food chain, supporting other forms of life, removes CO2 from atmosphere,
Van Helmont experiment – what did he test, how did he do it, what did he conclude?
Took an earthenware vessel, placed in it 200 pounds of soil dried in an oven, soaked this with rainwater, and planted in it a willow branch weighing 5 pounds
At the end of five years, the tree grown from it weighed 169 pounds and about 3 ounces
He dried the soil in the vessel again, and the same 200 pounds were found, less than 2 ounces
Conclusion → 164 pounds of wood, bark, and root had arise from water only
What do we mean when we say that “trees are made of air”?
This means that majority of trees mass comes from CO2 in the air, not soil or water
CO2 is converted into glucose using sunlight, and that glucose is then used to build cellulose/lignin/other organic molecules that make up plants mass
How is the H+ gradient built up inside the thylakoid space, and what is the consequence?
Transport of H+ into thylakoid during flow of electrons from PSII to PSI
Splitting of water inside thylakoid
Use of H+ to reduce NADP+ in stroma
Consequence: buildup of H+ ions in the thylakoid creates a proton gradient → H+ ions diffuse down their gradient → convert NADP+ to NADPH and ADP to ATP → these are used for sugar synthesis in the Calvin cycle
Why are plants green?
Contain chlorophyll, which absorbs red and blue light but reflects green light
Rubisco – what is it? What does it do? In what ways is it inefficient?
Rubisco is an enzyme that catalyzes the first step of the Calvin cycle, fixing CO2
Combines CO2 with RuBP to form 3-PGA, which is used to make glucose
Inefficient:
Slow: slow turnover rate of 2-3 reactions per second
Oxygenase activity: rubisco also catalyzes the opposing reaction (binding O2 for photorespiration instead of binding CO2 for the calvin cycle) causing it to reverse its own work
Rubisco has a 100x higher affinity for CO2 than O2, but the atmosphere has more O2 than CO2 → 20-50% of C fixed by photosynthesis is lost to photorespiration (even more in warm climates)
Photorespiration – problem and solutions
Pep Carboxylase, C3, C4, CAM
Problem: photorespiration occurs when the Rubisco enzyme binds O2 instead of CO2 during the Calvin cycle, wasting energy and reducing the efficiency of photosynthesis
C3: no adaptations, prone to photorespiration
Hot conditions → stomata close to decrease water loss → photorespiration increases → reduced efficiency
C4: spatial separation of photosynthesis stages
Mesophyll cell chloroplasts (light dependent reactions); PEP carboxylase turns CO2 into a 4 carbon compound
Bundle sheath cell chloroplasts: the 4 carbon compound is transported here and releases higher CO2 concentrations as Rubisco is sequestered from O2
CAM: temporal separation of light-dependent reactions and Calvin cycle
Night: plants open stomata → PEP carboxylase fixed CO2 into a 4 carbon acid → malate/aspartate builds up through the night until saturated with carbon → plant tissue becomes acidified
Day: stomata close → light reactions begin → malate is decarboxylated and the Calvin cycle operates
Growth is limited by how much CO2 can be stored
Why did I bring dry ice to class?
What is the composition of our atmosphere?
21% oxygen
78% nitrogen
0.9% argon
0.04% carbon dioxide
Where does your fat go when you lose weight?
Fat is broken down into CO2 and water when you lose weight
CO2 is exhaled and the water is excreted as urine or sweat
Fat goes into the air
How is plant nutrition similar to that of animals? Different?
Similar: amino acids, nucleic acids, sugars and with a few exceptions, and the same lipids (plants never use cholesterol). Small molecules such as ATP and vitamins perform same functions in both types of organisms
Different: plants make everything organic within their own bodies while animals have to digest
Selective uptake of minerals – how is it regulated?
Active transport (at a cost of ATP)
Difference between macro and micronutrients
Macronutrients: form the basic structure of plant cells and are involved in growth, energy storage, and metabolism
Primary nutrients are N, P, K
Secondary nutrients are Ca, Mg, S
Micronutrients: elements essential for plant growth that are needed in only very small (micro) quantities
B, Cu, Fe, Cl, Mn, Mo, Zn
Basics of N cycle – what kinds of organisms can process N2 in the atmosphere directly?
Nitrogen-fixing bacteria
Nitrogen fixation → N₂ → NH₃/NH₄⁺
By nitrogen fixing bacteria
Nitrification → NH₄⁺ → NO₂⁻ → NO₃⁻
By nitrogen fixing bacteria
Assimilation → NO₃⁻/NH₄⁺ → organic nitrogen in plants/animals
Plants absorb nitrogen for growth
Ammonification → organic nitrogen → NH₄⁺
Decomposers recycle nitrogen from dead organisms
Denitrification → NO₃⁻ → N₂
Done by bacteria to return nitrogen to the atmosphere
Mycorrhizae – what are they? How does each party benefit?
Why don’t plants defecate?
Symbiotic association between plant and fungus
Important for uptake of phosphorus
Fungus collects water, N, P for plant
Plants pay fungus with sugar
Plants don’t defecate because they efficiently recycle or remove waste through leaves, bark, root, and gases
Carnivory in plants - function? Mechanisms of prey capture? Evolution?
Function: carnivorous plants augment their N by eating insects
Mechanism of prey capture:
Snap traps: rapid leaf movement triggered by sensory hairs snaps shut on prey
Flypaper traps: sticky glandular hairs trap and digest insects
Suction traps: vacuum like bladders in small aquatic organisms
Evolution: Convergent evolution and adaptation to specific ecological niches
Water movement – how does water get to the top of a tree?
Water is pulled, under tension, through plants in a continuous stream from soil out through leaves
Water movement can be explained by water potential
Water moves from an area of less to more solute (osmosis) → passive transport
Plant cells have walls, so pressure is also involved
Structure and function of endodermis?
Function: Prevents water and solutes from passing through this layer via the apoplastic pathway
Structure: Tightly packed cells and casparian strips
Relationship between gas exchange, water loss, photosynthesis, stomata
SUMMARY:
Uptake of water and minerals by root hairs and/or mycorrhizae
Diffusion through cortex to xylem (must pass through membrane)
Vertical transport through xylem (bulk flow) into stems and leaves
Cuticle/bark reduces evaporation from above ground parts
In leaves, water used in photosynthesis, enters phloem, or evaporates (most water lost by evaporation (transpiration))
Water vapor passes from intercellular spaces in mesophyll through stomates, which regulate loss of water and CO2 uptake
Transpiration-to-photosynthesis ratio
The amount of water lost per gram of CO2 assimilated into organic material created by photosynthesis
Transpiration rate / photosynthesis rate
C4 plant ratio is 300:1 vs C3 ratio is 600:1
Can close stomata when losing too much water but stockpile CO2 inside
Why do plants 'drink' so much more than animals?
Photosynthesis → key reactant, and especially important since plants lose water through transpiration
Nutrients → dissolve and transport nutrients absorbed through the roots
Root pressure → as water flows upward, need constant intake through the roots
Structural support → plants hold their shapes through turgor pressure
Water potential - solute, pressure potential
Potential of water to do work; incorporates solute concentration and pressure
Solute potential + pressure potential = water potential
Which way will water move?
Water moves across the membrane from solution with higher to lower water potential (down the water potential gradient)
Water under pressure has a positive pressure potential
Water under tension has a negative pressure potential
Flaccid cell has pressure potential of 0
Turgid cell has a positive pressure potential
Be able to solve basic WP problems
Water potential gradients in a living plant
Water moves down water potential gradient from less negative to more negative
Water always moves from regions of higher water potential (less negative) to regions of lower water potential (more negative)
How is water potential involved in the opening and closing of stomata?
Water potential changes within the guard cells, driven by osmotic movements of water, are crucial in controlling the opening and closing of stomata
Presence of solute → less free water available for movement → water potential is more negative
Opening: negative water potential in guard cells → water moves into guard cells
Closing: less negative water potential in guard cells → water moves out of guard cells
Turgor and wilting – causes?
Turgor pressure → water in vacuole pushes the cell membrane against the cell wall
Wilting → empty vacuole causes the cell walls to shrink and to pull away from the neighboring cells
Results in droopy appearance
Causes:
Water loss from transpiration
Dehydration
Root damage
High temperature and increased transpiration
How is sugar translocated from source to sink?
Source: where sugar is made and stored
Sink: where the sugar is sent to
Translocated: organic material synthesized in leaves but most of it is stored or used elsewhere
Organic materials transported in living phloem cells
Largely transported as sucrose (also amino acids and other compounds)
Pressure-flow hypothesis
Active uptake of sucrose from source into phloem (“loading”)
Water follows (enters sieve cells from xylem by osmosis)
At sink, sugar is transported out of sieve cell, water follows (diffuses out)
Flow created by water entering sieve cells at source and leaving cells at sink
Movement of sugars can be bi-directional
Changes in sources and sinks over the seasons
Spring → active growth phase
Source: storage organs
Sink: leaves, shoots, flowers
Summer → peak photosynthesis
Source: mature leaves
Sink: developing fruits, seeds, storage organs
Fall → preparation for dormancy
Source: leaves
Sinks: storage organs
Winter → dormancy
Source: minimal photosynthesis
Sink: few active sinks
Differences between sugar and water transport
Location:
Sugar in the phloem
Water in the xylem
Direction:
Water is upward from roots to leaves
Sugar is bi-directional
Mechanism:
Phloem is alive → doing active work → sieve tube elements
Xylem → made up dead, hollow cells
Transport:
Water is mostly a passive process
Sugar is an active process that requires ATP
Plants vs animals - differences in type /mode/ timing of growth and development
Type:
Animal growth → determinate
Plant growth → indeterminate
Mode:
Animals → growth is more uniform and occurs throughout the body
Plants → growth occurs at meristems (root and shoot tips)
Timing:
Animals → Specific life stages
Plants → seasonal/continuous
Determinate vs indeterminate growth
Determinate: overall shape of adult animal is genetically determined from its earliest development stages
Indeterminate: retain tiny regions of embryonic tissue (meristems) that are capable of developing into new parts of the plant, so that the plant grows new shoots and roots for as long as it is alive
Overall shape of plant is not determined in advance
Meristems – SAM and RAM, vascular cambium
Meristems: regions of undifferentiated cells capable of continuous cell division
Plant growth:
Primary growth - elongation
Shoot apical meristem (SAM)
Root apical meristem (RAM)
Secondary growth - thickening
Vascular cambium
Why/how do beet and carrot greens grow from the top of a cut-off root in a 'trash garden'?
Beet and carrot greens regrow from top of a cut-off root due to meristematic tissue that remains active
Stored nutrients in the root provide energy for new leaf growth, while water absorption and hormonal signals trigger shoot regeneration
Plant cannot grow its taproot → will eventually stop once energy reserves are depleted
Process used in trash gardens to regrow edible greens from vegetable scraps
Primary and secondary growth
Plant growth:
Primary growth - elongation
Shoot apical meristem (SAM)
Root apical meristem (RAM)
Secondary growth - thickening
Vascular cambium
Modular growth – implications for diversification of function?
Implications:
In animals, the rudiments of all organs form in the embryo and so are all the same age
Plants add organs at their tips for as long as they live, so the modules of a plant vary in age, in proportion to their distance from the SAM
Youngest organs are near the shoot tip while older organs are farther away
Because plants can make many copies of their organs, they can vary in functions
Alternative functions of structures – leaves, stems, roots
Modified leaves:
Water storage
Defense
Reproduction
Modified stems:
Photosynthesis
Water storage
Defense
Modified roots:
Support
Climbing
Storage
How can you tell a simple leaf from a leaflet on a compound leaf?
Simple leaf: a single blade attached to a stem, one petiole
Leaflet on a compound leaf: Multiple leaflets, one petiole, bud at base of whole leaf
Plant ‘immortality’ – what, how?
Meristems: active meristems provide the ability to keep growing indefinitely as long as the environment allows
Perennial growth: some plants can grow back each year from same root system
Grocery store botany – what’s what?
Look at a variety of plants, each used for different purposes
Cabbage → leaf
Brussels sprouts → bud
Celery → petiole
Cloves → flower
Capers → flower
Pollination
Plant: reproduction and genetic diversity
Animal: food (nectar and pollen)
Seed and fruit dispersal
Plant: spread offspring, reduce competition
Animal: Food (fruit and seeds)
Defense
Plant: protection from herbivores, improved health
Ant: food (nectar, food bodies), and shelter
PLANT SENSES AND BEHAVIOR
Categories of behavior – e.g., foraging, reproduction, defense, etc.
Foraging: for light, nutrients, water
(host/victims for parasitic plants)
Reproduction: germination, pollination, sex change
(functional gender)
Defense: physical and chemical induced responses
Kin recognition: role of modular construction and dispersed mechanisms
What do plants forage for?
Light, nutrients, water
(Host/victims for parasitic plants)
How is plant behavior similar to / different from animal behavior?
Similarities:
Both plants and animals respond to environmental stimuli and external cues
Both communicate with other organisms
Both exhibit behaviors related to reproduction, survival, and defense
Differences:
Movement
Plants → growth based movement
Animals → rapid, locomotion based movement
Nervous system
Plants → no nerves
Animals → complex nervous system
Reproduction
Plants → typically stationary
Animals → active mating
Communication methods
Plants → chemical signaling
Animals → vocalization
Having read the Light Eaters, what do you think about the ‘intelligence’ (agency? consciousness?) of plants? Are these concepts useful? Misleading? What surprised you the most?
Intelligence: Plants exhibit complex behaviors and problem-solving abilities (e.g., foraging for resources, defending against herbivores), but this is not the same as consciousness or agency. The concept of plant "intelligence" can be useful for understanding their adaptive capabilities but may be misleading if it implies human-like cognition.
What surprised me: The extent to which plants can communicate with each other and other organisms (e.g., releasing volatile compounds to warn neighbors of herbivores) and their ability to remember past experiences (e.g., exposure to stress).
YAMASHITA and WHITE paper
How do plants sense their environments? (ie, what sensory modalities do they use?)
Sight → 3 kinds of photoreceptors
Taste → response to compounds dissolved in water
Smell → response to volatile compounds
Touch → response to touch, vibration
Hearing → CONTROVERSIAL!!!!!!!
Response to gravity
Ability to keep time → daily (circadian) and yearly (photoperiodic) cycles
Pollan article → 15-20 distinct senses
Tropisms and nastic responses - examples
Thigmotropism:
Response to touch
Tendrils detect contact via sensory epidermal cells called tactile blebs
Tendrils coil around objects they touch
Phototropism:
Stems grow toward light (positive) while roots grow away from light (negative)
Gravitropism:
Roots grow downward (positive) while stems grow upward (negative)
Nastic responses: Non directional movements in response to stimuli
Nyctinasty: leaf movements in response to day/night cycles
Thigmonasty: rapid movements in response to touch
Gravitropism in roots vs shoots; how do roots sense gravity?
Stems are negatively gavitrophic
Roots are positively gavitrophic
How roots sense gravity: Starch filled plastids called amyloplasts sink towards the gravitational field. This stimulates the release of the growth hormone auxin
Camouflage plant – Observations? Evidence? Do you buy it?
Observation/evidence: various instances of plants mimicking other plants
Farmers pulled out rye weed to keep crops healthy
So rye weed took on a form similar to wheat to avoid the selective pressure
I buy it → solid defense mechanism
What parts of plants get eaten?
Leaves → eaten by herbivores
Stems → eaten by insects
Roots → eaten by insects
Flowers and seeds → eaten by insects
Who eats plants?
Mammals: Deer, rabbits, elephants, etc.
Insects: Caterpillars, beetles, aphids, etc.
Birds: Some birds eat seeds, fruits, and leaves.
Other herbivores: Snails, slugs, and even some fish.
How do plants defend themselves? Physical / chemical?
Spines/thorns
Hairs
Toxic chemicals
Latex
Crypsis or mimicry
Mutualistic relationships with ants
Help from predators or parasitoids
Chemical communication between plants and animals
Direct / indirect defenses
Direct defenses: constitutive (always present) or induced (produced following herbivory)
Physical → spines, hairs, thorns, waxes, latex
Chemical → toxic chemicals, digestibility reducers, egg killers
Indirect defenses: constitutive or induced
3rd trophic level → EFNS, mutualism with ants, domatia, release of volatiles
Detection of eggs
Chemical detection: plants recognize specific chemical compounds left behind when insects lay eggs
Mechanical detection: some plants sense physical presence of eggs via changes in leaf pressure or local cell damage
Light detection: some plants can sense light pattern changes caused by eggs blocking sunlight
Pollination
What, broadly, is the role of a flower?
Attract and reward pollinators
Facilitate reproduction in angiosperms
Be able to describe the process of pollination
Pollen production: anther produces pollen grains
Pollen transfer: pollen is carried by wind, water, or pollinators to another flowers stigma
Pollen adhesion: pollen sticks to the sticky stigma of the flower
Pollen tube formation: a pollen tube grows down the style to reach the ovary
Fertilization: sperm cells travel through the tube to fertilize the ovule, forming a seed
Significance of POLLEN, FLOWERS (innovations in Angiosperms)
Pollen: Allows for the delivery of sperm without water, enabling seed plants to colonize diverse habitats.
Flowers: Innovations in angiosperms that attract pollinators and increase reproductive efficiency. Flowers provide rewards (e.g., nectar, pollen) and have co-evolved with pollinators to ensure successful pollination.
Biotic and abiotic pollination
Biotic - by insects, birds, mammals, etc
Pollination ‘syndromes’
Abiotic - wind, water
Thought to be a secondary reduction or loss of petals and rewards
Cheating by plants and animals in pollination 'mutualisms'
Nectar robbing: insects remove nectar from flowers without contacting sexual structures
Plants cheat: Flowers look and smell like rotting meat, attract carrion flies
Floral mimicry: a non-rewarding flower resembles a rewarding one
Seed and fruit dispersal
In what groups of plants are seeds found (i.e., what are the SEED plants?)
Gymnosperms: seeds not enclosed in a fruit, they develop on the surface of cones or other structures
Angiosperms: seeds are enclosed inside a fruit, which develops from the ovary of a flower
What are the 3 main components of a seed?
Seed coat → protective outer layer
Embryo → developing plant
Endosperm → provides nutrients / cotyledons → in dicots, are modified leaves that store nutrients for the growing plant, initial food source during germination
Evolutionary innovations of seed plants
Seeds: Protect and nourish the embryo, allowing dispersal in space and time.
Pollen: Enables sperm delivery without water, expanding habitat range.
Flowers: attract pollinators
Fruits: help seed dispersal
Further innovations of angiosperms
Flowers → specialized reproductive structures
Increase pollination efficiency
Fruits → enhanced seed dispersal
Seeds are enclosed within fruits (aid in protection and dispersal)
Double fertilization → energy efficiency
One sperm fertilizes the egg (forming the embryo) and another sperm fertilizes polar nuclei
Xylem with vessel elements → faster water transport
Wider/more efficient at transporting water
Distinction between fruit and seed; function and developmental origin of each
Seed: Develops from a fertilized ovule; contains the embryo and food supply. Function: Protects and nourishes the embryo, aids dispersal.
Fruit: Develops from the ovary; protects seeds and aids in their dispersal. Function: Enhances seed dispersal through various mechanisms (e.g., wind, animals).
Orchid seeds vs coconuts – different strategies; how does each embryo get its start?
Orchid seeds: Tiny, dust-like, and lack food reserves. They rely on mycorrhizal fungi to provide nutrients for germination.
Coconuts: Large, with a significant food reserve (endosperm). The embryo uses this stored energy to germinate and grow.
What does it mean to say that seeds can travel in time and space?
Traveling in space refers to the movement of seeds across different locations, enabling plant species to expand and adapt to new environments.
Traveling in time refers to seeds’ ability to remain dormant and survive through unfavorable conditions, effectively allowing them to "wait" until the right time to germinate.
Selective advantages of seed dispersal (departure and arrival benefits)
Departure benefits:
Avoid competition with the parent plant.
Escape from natural enemies (e.g., herbivores, pathogens).
Arrival benefits:
Colonize new habitats.
Reach microsites favorable for germination and growth.
Modes of seed dispersal – biotic, abiotic, inside or outside of animals
Biotic: Dispersal by animals (e.g., birds, mammals) either inside (e.g., ingested fruits) or outside (e.g., hitchhiking on fur).
Abiotic: Dispersal by wind (e.g., winged seeds), water (e.g., drift seeds), or explosive mechanisms (e.g., seed pods).
Indehiscent / dehiscent fruits
Dehiscent fruits: Split open at maturity to release seeds (e.g., pea pods).
Indehiscent fruits: Do not split open; seeds are dispersed within the fruit (e.g., acorns).
Simple vs accessory fruits
Simple fruits: Develop from a single ovary (e.g., peach, tomato).
Accessory fruits: Develop from tissues other than the ovary (e.g., apple, strawberry).
4 red fruits; what is the reward in tomatoes, strawberries, pomegranates, raspberries?
Tomato: Fleshy pericarp (fruit tissue) is the reward.
Strawberry: The fleshy receptacle (not the ovary) is the reward.
Pomegranate: The juicy arils (seed coverings) are the reward.
Raspberry: The aggregate of drupelets (small fleshy fruits) is the reward.