Organismal Biology


Key Concepts


Chapter 8 - Plants




Plants, as well as some Protists and Monerans, can take small molecules from the environment and bind them together using the energy of light.  The incoming light energy is transformed into the energy holding the new molecules together, and the organisms use those molecules as an energy "fuel."  The basic process can be represented this way:

CO2    +    H2O      light   >    C6H12O6    +    O2
Carbon     Water                     Glucose       Oxygen
Dioxide                                     (sugar)                    


In the case of organisms that live in water, the carbon dioxide and water are from their immediate surroundings;  for most land plants, the water is absorbed from the soil and the carbon dioxide from the atmosphere.

The glucose is used for two major purposes:  1)  it serves as an energy reserve for periods of darkness (don't forget that photosynthesizers, like any living things, require energy and get it through respiration processes, commonly aerobic respiration; and 2)  it is used as a major component of structure:  the cell walls that surround almost all photosynthetic cells are made of starch-like carbohydrates called cellulose, huge molecules made up of hundreds, commonly thousands, of sugar molecules bound together.  This is why plant fibers are great sources of nutrition if you can break them down.  Breaking down plant fibers is chemically difficult - we humans can't, being limited to the more accessible starches put into seeds and fruits and tubers.  Plants use those starches as sources of sugar fuels, and so they build them into moleculse that are much easier to break down than the starch that holds them together.

Keep in mind that photosynthetic organisms are still living things, with protein-based chemistry, which means that they have nutritional requirements beyond carbon dioxide and water.  Proteins, unlike sugars and starches, contain a significant amount of nitrogen, which usually needs to be absorbed as nitrates (a nitrogen-oxygen molecule) to be usable.  For a very long time, plants have associated with nitrogen-fixing symbionts that can convert atmospheric nitrogen or decomposition-produced ammonia to nitrates.  Land plants absolutely could not have moved from the oceans without these symbionts, and most current species still rely on either prokaryote or fungal symbionts for their nitrates.

Plants convert the nitrates into amino acids, which are the components of protein molecules.  The production and use of glucose for energy also requires ATP as an energy carrier;  ATP contains phosphorus, usually absorbed as phosphates (a phosphorus-oxygen molecule).  Anyone who takes care of plants knows that nitrates and phosphates are important ingredients in fertilizers.  Most photosynthesizers have other nutrient needs, mostly various minerals:  they make a few critical molecules with materials such as iron, or need small ions, such as sodium, for some of their chemical processes.




Light can be understood as a combination of energy waves traveling outward from a light source, or as photons, small packets moving from that source at the speed of light (each wave peak would correspond to a single photon).  Light always travels at the speed of light, altering only for the material through which it's moving (it goes slower in water, for instance), so a segment of a light beam with wave peaks more separated (a longer wavelength) would have fewer peaks absorbed by a surface (a lower frequency) in any given amount of time, and would hit that surface with less energy.  This means short wavelength = high frequency = more energy,  long wavelength = low frequency = less energy.  The only reason that this is important is that sunlight contains a fairly wide range of energy frequencies, but only a few are absorbed and used by chlorophyll, the energy-capturing molecule of photosynthesis.

You can tell a few of the frequencies that are not absorbed by chlorophyll (and a few other light-absorbing molecules) by looking at a plant.  That green you see is part of the reflected frequencies of light.  For the most part, absorption of the other frequencies of light is used in an energy conversion process that "spits" electrons through a system from the "excited" chlorophyll molecules.

Although land plants absorb a variety of light frequencies, all frequencies are not equally powerful or useful:  while plants can absorb both red frequencies and purple frequencies, the purple have shorter wavelengths and carry more energy.  This is one of the reasons why "plant lights" may be distinctly purple.

It is not unusual for land plants to use molecular supplements to absorb some frequencies that chlorophyll can't, and feed more energy into the photosynthesis process;  these pigments are commonly types of carotenoids.  The colors of leaves in the autumn reveals the carotenoids that have always been there but have been covered by huge amount of chlorophyll.  

The many varieties of carotenoids can serve multiple roles:  they can be photosynthetic aids, but they may also minimize light damage (animals use pigments, like the human tan-producing molecule melanin, for similar protection) or even function in fighting disease.  Land plants may concentrate pigments, including carotenoids, in structures that need to stand out, such as the colors of flowers or mature fruits.  These colors signal animals that a food bribe is available, and then the animals are used to carry pollen or seeds.




Plants, like all living things, are descended from ancient organisms that evolved and developed in the oceans.  The ocean-living plants that represent land plants ancestors are simple, so much so that they are often classified as Protistans - little multicellular complexity was needed to float in the light.

Even in the ocean, though, there are a number of different niches available for plants - in the shallows, many algae varieties exist that can attach to submerged objects, probably a feature that helped the land plants' direct ancestors to stick out of the water into the air.  But niches also exist in the deeper water, where there is a functional connection between the photosynthetic pigments used and the nature of how light interacts with water.

The surface of the water reflects some light, but the frequencies that get through get absorbed - you already know that the deeper you go, the darker it gets.  What you may not know is that not all frequencies get absorbed equally - the frequencies that "regular" green plants use don't get very far beneath the surface, but frequencies in the bluish and greenish ranges penetrate much further.  This has spurred the evolution of several classes of various-colored algae with different chlorophylls, capable of using these deeper-reaching frequencies to grow where the green algaes can't.  Red algaes especially can occupy greater depths than the others, although Golden algaes can occupy a bit of a middle zone between green and red.  The color of Brown algaes seems more to do with other pigments and is apparently not really depth-related.


Needs of Land Plants - Structure

The eukaryote plants that evolved in the oceans had very few structural needs;  the buoyancy of the water held them up near the light, and occasionally they needed to adhere to surfaces in the surf zones.  They remained fairly simple collections of cells, which is why they are considered protists.  The Kingdom Plantae are the land plants, showing adaptations to living in the air.

Early land plants may have just been plants that could withstand being left behind by the tide, coating the surfaces of the surf zone, but once such plants could function without being under water, spreading and supporting photosynthetic platforms became a very useful ability.  The bryophytes  are probably the best surviving example of early land plants.  There are indications that some materials that evolved to resist the action of waves may have been critical to the structures useful in the air.

Bryophytes include liverworts, which spread on very moist surfaces in flat sheets.  But mosses, also bryophytes, hold leaf-like surfaces on stem-like stalks ("true" leaves and stems have internal tubes not found in bryophytes).  This support ability appears to have come from modifications of the cellulose material of the cell walls, both making it stiffer and producing related materials that more strongly reinforce the force holding cells together.

Small green plants often have a structure inside their cells, a central vacuole, with a water-based solution that can build up pressure to reinforce the shape of the cells.  You've probably seen that plants, as they dry out, wilt as water is moved out of the vacuoles for photosynthesis and not replenished.

One main land-adapted structural component is a cuticle (also common in animals) whose main function is to provide a waterproof surface and reduce water loss to the air.  A material that acts as a waterproofing agent but which became critical in stiffening land plants is lignin, found in increasing amounts in larger land plants. It has the additional advantage of being somewhat protective against the more powerful effects of direct sunlight that land organisms have to deal with.  Later land plants evolved waxy materials as more efficient waterproofing - you can often tell how dry an environment a plant is from by the waxiness / shininess of its cuticle.

Many paleobotanists (who study plants of the distant past) believe that the Earth's coal and oil reserves stem from a time when lignin became a major component of land plants, but decomposers who could break it down had not yet evolved;  plants sank into the mucky sediments, and their organic materials slowly converted to the hydrocarbon-rich fuels we use today.

Needs of Land Plants - for Photosynthesis

Photosynthesis requires light, carbon dioxide, and water.  On the land, light is abundant from above, carbon dioxide is in the air, and water, with dissolved minerals, comes mostly from rain-soaked soil.

Light can be an issue, because as electromagnetic radiation it can interact with and damage cellular materials.  There are actually different types of photosynthesis:  plants from dry sunny areas use a somewhat different process to reduce damage from light and from high amounts of produced oxygen.

Getting carbon dioxide from the air seems simple, but carbon dioxide cannot be absorbed across a waterproofed surface;  anywhere it comes in, water vapor will be lost.  Water lost by plants into the air is called transpiration, and is a major contributor to the atmospheric water cycle.  Early land plants, who had pores to absorb carbon dioxide, were somewhat restricted to water-rich, humid environments.  For long periods of the distant past, they also benefited from higher levels of carbon dioxide in the atmosphere.  The bryophytes and later forms, the tracheophytes (ferns and their relatives), are still restricted in their ecological potentials by the limitations of their pores.   But later land plants, the gymnosperms (conifers and relatives) and angiosperms (flowering plants), developed pores that could be opened and closed.  These are called stomates (or stomata), and with them plants could "breathe" in a controlled manner.

The special-photosynthesis plants from desert systems mentioned above tend to open their stomates only at night;  they "charge" their leaves with carbon dioxide when it's cooler and transpiration is slower.  That's also why they need some chemistry to resist the activity of high oxygen levels, since lots of oxygen accumulates in the tissues during the day when the stomates are closed.

Water movement, as plant structure allowed for taller plants, became a major challenge.  For small plants, osmosis - movement of water from more-dilute situations (surfaces or in the soil) to less-dilute situations (inside the plants) could move water into and up a plant in a process called root pressure (even for plants without roots), but gravity counteracts that movement, making it useful only for fairly small (lower than your hip) plants.

For larger plants, special vascular (tube) structures were needed:  the water-using tops of the plant essentially "suck" the water (and nutrients) up special "straws" where the tendency of water to hold onto itself (and the water-sticky linings of the tubes) could help pull it to treetop heights.  These special straws are called xylem, and thinner tubes to take photosynthetic products to the lower / buried parts of plants are called phloem.  The tracheophytes, gymnosperms, and angiosperms are all vascular plants;  any large plant you see is in one of those groups.  Tracheophytes have vascular tissue in their stems and leaves, while the other groups have it in stems, leaves, and roots (technically, to be called stems, leaves, or roots, there has to be vascular tissue present).

Needs of Land Plants - for Reproduction

Organisms that evolved in watery environments had a fairly easy medium through which sperm could reach egg cells:  the water.  The further from water and wet environments organisms moved on land, the less viable using the environment for a passage medium became.

But first -


Chapter 1, in the discussion about sexual reproduction, it was mentioned that such reproduction does not require two separate parents or even male and female sources, although different genders (roles in sexual reproduction) are extremely common.  As we've just discussed, mosses can be male and female;  so can flower parts, pine cones, parts of a flatworm, and jellyfish.

You may think you know the basics of telling a male from a female, but you can't peek under a moss looking for noogies and a penis.  What makes a form male?

Gender is determined by the type of gamete produced.  A gamete is a sex cell - sperm is the male variety, ovum (we'll use the less-precise egg cell instead) is the female.  The differences in these cells will ultimately tell you if an organism or a reproductive organ is male or female, and it is the differences between the cells that really leads to the larger differences between males and females in any species that has genders...



...are produced in much much higher quantities.

...are produced in comparatively lower quantities.

...are much smaller than egg cells.

...are much larger than sperm, since they contain food for the embryo.

...are equipped to get from where they're made to where the egg cells are.

...pretty much wait in one place for the sperm to reach them.

...from each starting cell that divides by meiosis, four functional sperm are made.

...from each starting cell that divides by meiosis, one functional egg cell is made, with 3 tiny polar bodies used to discard "extra" sets of chromosomes.

Some things to remember:  don't assume that things always work the way that they do in humans, or even in animals.  In most gendered organisms, lots of egg cells are made (it's just that many more sperm are made), not just one (which is a commonly-known "fact" that isn't even really true for people).  And although many sperm types can swim or crawl, many (like in pollen) can't, even though they have evolved ways to get where they need to go.  And forget "XX" and "XY" chromosome mixes - gender is coded by chromosomes only in some animals, and most of the time there is no chromosomal difference between males and females.  In addition, many types of adult organisms are both male and female at the same time, a condition that used to be called hermaphroditism but is now called being monoecious.

The toughest problem to solve living on land, for both plants and many animal groups, concerned sexual reproduction that used swimming sperm, and this was true for plants:  long after the drying, support, and other problems were adapted to, the reproduction problem existed.  As also happened in the first vascular plants, bryophytes developed an alternation of generations pattern, with a sexual phase, the gametophyte, alternating with an asexual phase, the sporophyte.  Unlike the vascular plants, whose "main" (most obvious) form is the sporophyte, what we think of as "moss" is the gametophyte form.  A moss sporophyte is a small attached form that makes, not surprisingly, spores.


Moss spores, containing only one set of chromosomes (haploid), are carried by the wind from the parent sporophyte.  If they land somewhere with the right moisture content (remember, bryophytes don't do well if it's too dry), the spore begins to divide and produce very algae-like filaments that cover the surface it's on.  From that surface will sprout the gametophyte, with structures to anchor it called rhizoids (rhiz- is from a word for "root") and upward-growing "stems" with "leaves" that are only a single cell layer thick.  (they are not truly these structures because the "real things" always have vascular structures inside them - that's why they are being called "stems" in quotes, etc.)  The materials needed by the moss to grow are absorbed by the upper structures rather than the rhizoids, but this allows mosses to grow on fairly sparse surfaces.

Some of the moss gametophytes are male and some are female, and the very tips form sexual reproductive structures called antheridia (male) and archegonia (female).  The antheridia swell up and burst, and when the plants are wet with rain or heavy dew, release sperm that are splashed off and swim through the water coating nearby plants to the archegonia, where they fertilize waiting egg cells.  The fertilized egg, now a zygote containing two sets of chromosomes (diploid), grows into a small sporophyteSpores are eventually produced, and the tip of the sporophyte opens, releasing the spores into the winds, where they can travel great distances and still sprout even decades later.


Although the early vascular plants adapted new and better ways to rise above the bryophytes, they still had not quite solved the reproduction-on-land problem. Because of this, they, like the bryophytes, follow an alternation of generations life cycle. Unlike the bryophytes, however, the larger plant, the form we all think of when the word "fern" comes up, is the sporophyte. In ferns, the gametophyte is a relatively tiny thing, barely noticeable compared to the sporophyte.


As we did with the mosses, we'll start with a spore settling in a properly-moist environment. The haploid spores (cells with only one set of chromosomes) sprout and grow into small gametophytes that look like tiny heart-shaped leaves; these gametophytes contain male antheridia and female archegonia. Sometimes these are separate little plants, sometimes they're on the same small plant. When things get wet, such as in the rain, the antheridia release sperm that swim to and enter the archegonia, fertilizing the egg cells and forming diploid (2 sets of chromosomes) zygotes. The zygotes grow into the large, leafy sporophytes, which eventually generate spore-making packets called sori on the undersides of the leaves. In the sori, the haploid spores are produced by meiosis and released into the air.


The ferns are the best-known of this group but not the only seedless vascular plants, which includes horsetails and club mosses.


Seed-Bearing Vascular Plants - Gymnosperms 


The bryophytes and ferns did a relatively good job of invading the wetter parts of the land environment, but one critical weakness kept them from spreading farther:  the need for water to get sperm from male to female plants (or plant parts).  Both had developed wind-blown spores to spread asexually, but as we've seen, asexual reproduction limits the speed that organisms can adapt to new environment, and the land was full of new environments.  Still, it's quite likely that ancient forms of ferns and their relatives spread fairly widely - it's not easy to tell because such organisms don't fossilize easily.  We do know that, for a time, the landscape was very foresty, but the trees were really huge tree ferns.  How much the rest of the environment resembled modern versions is harder to guess at, but animals were spreading across the land very successfully, and that suggests lots of food choices, lots of plants to occupy the first level of the food chain.  Also, as often happens, there was apparently a major climate shift away from generally wet to widely drier, providing even more advantages to those best suited to the new conditions.

The adaptation that really led to an evolutionary leap was pollen, a tiny male gametophyte that, in its first versions, could be carried by the wind like spores to the female gametophytes and sprout a vascular-tube-like "tunnel" into them that a sperm could travel down.  No longer would the two genders have to be close to one another and need some sort of open water between them for the sperm to swim through.  Plants would still need water for their chemistry and specifically for photosynthesis, but they wouldn't be limited to environments where open water was periodically available.  These new types of plants could carry gametophytes high above the ground, where sporophyte embryos could be encased with some "starting off" food and also be set off in the wind.  The casings with little sporophytes in them were seeds, and all of the groups to evolve from pollen-bearing plants would also be seed plants.  

When you see a pine tree, or a spruce, or a cone-bearing shrub, the "main plant" is a sporophyte;  the gametophyte form is confined to the cones, which commonly have male and female versions.  In many pine trees, the males cones are smaller and located at the tree tops, while the female cones are larger and found farther down.  The sizes relate to the needs of the two genders:  the female cones will generate seeds, and will need to be bigger, while the male cones just produce tiny wind-carried pollen (and even though a lot of pollen is made, not much room is needed for it).  The location on the trees reflects how the pollen is wind-spread, with the male cones as high as can be for best wind access, and the female cones lower since much of the pollen will settle eventually.

Pollen from the male cones makes contact with the sticky surface of a female cone and adheres there.  It sprouts and grows down into the female cone, forming what is known as a pollen tube;  this may take as long as a year-and-a-half.  The pollen tube eventually makes contact with the part of the female cone, the ovule, that holds the egg cells, and the sperm from the pollen moves down the tube and fertilizes the egg cell.  Many pollen produce pollen tubes and fertilize many egg cells in  a female cone.

The fertilized egg cell, the zygote, grows into an embryo which is encased in a seed.  The seeds have "wings" and are light enough to be carried off in the wind, once the female cone "opens" to release them.  The seeds that settle in hospitable places sprout and grow into new sporophytes.  The sporophytes have true roots, and true stems, and true leaves, although the leaves are usually needles.  These long thin leaves are more effective than flat leaves at conserving water and supporting snow.  They also commonly produce a cuticle, to reduce evaporation from the inside of a needle.

Much of the patterns and even structures in gymnosperms are found again in the angiosperms, with a few exceptions and several additions.

Angiosperms - Flowering Plants 

There is a very good chance that the vast majority of the plants you can see out your window are angiosperms.  They have taken over the land since their rise during the Age of Dinosaurs, pushing the other groups to the ecological fringes.  Gymnosperms still have an advantage in systems that are too cold and/or dry (they become more common with higher altitude and higher latitude), or have nutrient-poor soils, and so haven't been completely pushed out of business.

Reproduction in angiosperms follows a course similar to that in conifers, with the gametophytes confined to a periodically-made part on the main sporophyte.  These gametophytes are parts of the characteristic feature of the group:  flowers.  Although some species have separate male and female flowers, most have both male and female gametophytes in each flower.  Many angiosperm flowers don't look like what you might expect of a flower - this is discussed below in the section on coevolution.

Angiosperms get their name from the fact that the seeds (which are sporophyte embryos packaged with some fuel to sprout with) are produced inside a fruit, a structure used to move seeds away from the parent plant.  All angiosperms produce fruit, although some might not be things you would see as fruit:  fruits can be built to fly through the air (maple trees and dandelions make this type), float across the water (coconuts), stick to passers-by (burrs), as well as be eaten by animals.  Even edible fruit is almost never meant to act as a food source for the seeds inside. 


 As was true in the gymnosperms, the "main plants" in angiosperms are sporophytes, while the gametophytes are confined to the flowers, usually male and female together.  Male gametophytes are called stamens, female gametophytes are pistils.  The pollen from the stamen has to reach the pistil and make a pollen tube to the base of the flower, the ovary, and the ovules, where the egg cells are.  Once the egg cells are fertilized, the embryos are sealed up with food in a seed and the ovary is converted into a fruit.

The seeds often wait for some environmental cue, such as warmth, moisture, or light periods shifts, before germinating, sprouting.  A type of growth hormone known as auxins, which settled to the bottom of the sprouting root and stem as they emerge, have different effects on those parts:  auxin-soaked root cells grow more slowly, making the top of the root grow faster and curve the root downward;  auxin-soaked stem cells grow faster, curving the stem up.

In a mature plant, auxins migrate away from the sunlit side of the plant - if the light is coming in from the side, the migration causes the stem to curve toward the light as it grows and better orient the leaves to catch light.  Plants produce many different types of hormones that can affect reproduction, overall growth, defenses, fruit ripening, and other features.

Production of new cells in plants happens in a type of tissue called the meristem.  Meristems can be, and usually are, at the growing tips of the plants, where they are called apical meristems.  Most plants add new cells from the tips out, not evenly all over and not from the bottom up - in the other parts of the plant, the cells grow but do not divide.  Leaves, branching stems or roots, and flowers all are produced by apical meristems.  Some growth may also occur along the sides of the plants, such as is found in the rings of trees - these are called lateral meristemsThese make tree ring patterns in ecosystems with growing seasons,  where good growth produces big, "light" cells, alternating with seasons of less growth (cold winters or dry periods), which produce smaller, "darker" cells - each light/dark zone is a ring, and the wider, lighter the ring, the better the growth season, leaving a record of year-to-year climate. 


Since a significant part of any organism's ecosystem is the other organisms it shares that system with, it should come as no surprise that much of evolution is driven by interactions between individuals of different species, sometimes driving long-term relationships between the species.  The interactions can be cooperative, as happens in a symbiosis, or more of an ongoing battle, as happens between predator and prey or plant-eater and plant.  The evolutionary process where two species adapt to each other over time is called coevolution.

Coevolution is obvious throughout the angiosperms.  The most well-known is the use of animals as pollinators, carriers of pollen from the male parts of a flower to the female parts of another flower.  These angiosperms have evolved ways to make their flowers stand out in the environment to their pollinators, both visually and with smells, and often present "rewards" such as food to bring pollinators back over and over.  The construction of a flower is often a clue to its pollinators.  Many flowers without pollinators have no colors or odors, and pollen bearing and catching parts stick out in the air:  these are wind-pollinated, common in many grasses.  Some flowers are broad, with stumpy parts:  these are often pollinated by crawling insects.  Some flowers are tall and narrow, with a central platform:  these are commonly pollinated by flying insects, who press past the anthers on the way in and pick up pollen, then land on the next flower's pistil, leaving pollen there.  Flowers can give clues about their pollinators:  the reason that red flowers rarely use bees (and often use beetles) as pollinators was a clue toward the discovery that bees don't see red as a color (although they can see ultraviolet as a color, and some bee-pollinated flowers are ultraviolet-colored).  Fruits also have often evolved to use particular types of animals as seed-carriers, although the relationships are rarely as carrier-specific as those that have developed with pollinators.

Other types of coeveolution exist in angiosperms:  many defenses, such as thorns and poisons, are set against particular types of enemies.  Many of the drugs that humans use recreationally are derived from the poisons plants have developed to fight their insect enemies:  the active ingredients in tobacco, cocaine, and marijuana are all neurotoxins, natural equivalents of RaidTM.  

One of the lesser-known theories about the decline of the dinosaurs hypothesizes that the plants that served as the basis of their food chain adapted defenses against them and effectively put them "out of business."  It seems very unlikely, especially given that our plant-eating relatives haven't been fought off as well. 


Informational Links


A very weird thing:  Photosynthesis the Movie.

And The Photosynthesis Song.

Some links to pages from a New Hampshire Colleges herbarium, which has more-or-less local examples of gymnosperms.

How to get many different seed varieties to germinate. 


Click on term to go to it in the text.
Terms are in the order they appear.


Basic Reaction of Photosynthesis
Uses for Glucose
Cell Walls
Plants & Aerobic Respiration 
Other Nutritional Requirements  
Nitrogen Needs 
Nitrogen-fixing Symbionts
Mineral Needs
Light:  Wavelength and Frequencies 
Light Absorption and Reflection  
Plant Pigments 
Types of Algae

Bryophyte types
Central Vacuoles

Photosynthesis-Based Needs
Water Cycle


Vascular Structures

Gender is determined
Male / Female Differences

Alternation of Generations
Moss Life Cycle
Evolution:  Plants, Seed
Seed Plants

Conifers:  Life Cycle
Cones:  Male vs Female
Gender Differences:  Cones
Pollen, Pine
Pollen Tube
Seed, Conifer
Zygote, Conifer
Embryo, Conifer

Gymnosperm-Dominated Environments

Angiosperm Seeds
Life Cycle
Pollen Tube
Fruit Formation
Auxins & Sprouting
Auxins and Light
Hormone Effects
Apical Meristem
Lateral Meristem
Tree Rings
Using Tree Rings as Climate Record
Flower Form & Function
Plant Defenses




Organismal Biology

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