BOTANY / PHYTOLOGY

FLOWERING PLANTS

Flowering plants are plants that bear flowers and fruits and form the clade Angiospermae,
commonly called angiosperms. Non-flowering plants do not grow flowers, and use either
seeds or spores, which are very tiny parts of a plant that can be used to reproduce, to grow
more plants just like them.

CHARACTERISTICS OF FLOWERING PLANTS

Although flowers and their components are the major innovations of angiosperms, they are
not the only ones. Angiosperms also have more efficient vascular tissues. Additionally, in
many flowering plants the ovaries ripen into fruits. Fruits are often brightly colours, so
animals are likely to see and eat them and disperse their seeds. Brightly colour fruits attract
animals that may disperse their seeds.

PARTS OF A FLOWER

A flower consists of male and female reproductive structures. The main parts of a
flower are shown below.

They include the stamen, pistil, petals, and sepals.

 The stamen is the male reproductive structure of a flower. It consists of a stalk-like

filament that ends in an anther. The anther contains pollen sacs, in which meiosis
occurs and pollen grains form. The filament raises the anther up high so
its pollen will be more likely to blow in the wind or be picked up by an animal
pollinator.
 The pistil is the female reproductive structure of a flower. It consists of a stigma,
style, and ovary. The stigma is raised and sticky to help it catch pollen. The style
supports the stigma and connects it to the ovary, which contains the egg. Petals attract
pollinators to the flower. Petals are often brightly coloured so pollinators will notice
them.
 Sepals protect the developing flower while it is still a bud. Sepals are usually green,
which camouflages the bud from possible consumers.
 A flower includes both male and female reproductive structures

FLOWERS AND POLLINATORS

Many flowers have bright colours, strong scents, and sweet nectar to attract animal
pollinators. They may attract insects, birds, mammals, and even reptiles. While visiting a
flower, a pollinator picks up pollen from the anthers. When the pollinator visits the next
flower, some of the pollen brushes off on the stigma. This allows cross-pollination, which
increases genetic diversity.

HOW DO PLANT AND ANIMAL CELLS DIFFER?

Both plant and animal cells are eukaryotic, so they contain membrane-bound organelles like
the nucleus and mitochondria.
However, plant cells and animal cells do not look exactly the same or have all of the same
organelles, since each has different needs. For example, plant cells contain chloroplasts since
they need to perform photosynthesis, but animal cells do not.
Diagram of a typical animal cell:

ANIMAL CELLS
 PLANT CELL

 Both animal and plant cells have mitochondria, but only plant cells have
chloroplasts. Plants don’t get their sugar from eating food, so they need to make sugar from
sunlight. This process (photosynthesis) takes place in the chloroplast. Once the sugar is made,
it is then broken down by the mitochondria to make energy for the cell. Because animals get
sugar from the food they eat, they do not need chloroplasts: just mitochondria.

 Both plant and animal cells have vacuoles. A plant cell contains a large, singular vacuole
that is used for storage and maintaining the shape of the cell. In contrast, animal cells have
many, smaller vacuoles.

 Plant cells have a cell wall, as well as a cell membrane. In plants, the cell wall surrounds
the cell membrane. This gives the plant cell its unique rectangular shape. Animal cells
simply have a cell membrane, but no cell wall.
 EVOLUTION OF FLOWERING PLANTS

Flowering plants are thought to have evolved at least 200 million years ago
from gymnosperms like Gnetae. The earliest known fossils of flowering plants are about 125
million years old. The fossil flowers have male and female reproductive organs but no petals
or sepals.

Scientists noticed that the earliest flowers attracted insects and other animals, which spread
pollen from flower to flower, greatly increased the efficiency of fertilization over wind-
spread pollen, which might or might not actually land on another flower. To take better
advantage of this “animal Labour,” plants evolved traits such as brightly coloured petals to
attract pollinators. In exchange for pollination, flowers gave the pollinators nectar.

Giving free nectar to any animal that happened to come along was not an efficient use of
resources. Much of the pollen might be carried to flowers of different species and
therefore wasted. As a result, many plants evolved ways to “hide” their nectar from all but
very specific pollinators, which would be more likely to visit only flowers of the same
species. For their part, animal pollinators co-evolved traits that allowed them to get to the
hidden nectar. Two examples of this type of co-evolution are shown

CLASSIFICATION OF FLOWERING PLANTS

There are more than a quarter million species of flowering plants, and they show tremendous
diversity. Nonetheless, almost all flowering plants fall into one of three major
groups: monocots, eudicots, or magnolids. The three groups differ in several ways. For
example, monocot embryos form just one cotyledon, whereas eudicot and magnolid embryos
form two cotyledons. The arrangement of their vascular tissues is also different.

DIFFERENT BETWEEN FLOWERING AND NON- FLOWERING PLANTS

FLOWERING PLANTS
Flowering plants usually include the angiosperms. The angiosperms have their seeds
enclosed in a fruit. They are characterised by their flowers and seeded fruits. The flowering
organs of an angiosperm are specially modified to facilitate evolutionary advantage. Thus,
they become distinct from other seed plants.
Flowering plants produce flowers which ensure the fertilisation process. The male and female
gametophytes of flowering plants are much reduced. This allows for more rapid pollination.
After pollination and fertilisation, the embryo develops into a fruit containing seeds.

NON-FLOWERING PLANTS
Non-flowering plants do not produce seeds, fruits or flowers. They usually reproduce through
spores. They include the cryptogams and the gymnosperms. However, gymnosperms are a
seed-bearing group of plants. They have unenclosed or naked seeds that often produce onces.
Examples – Ginkgo and Conifers. The life-cycle of gymnosperms is sporophyte-dominant,
and their gametophytic phase is short-lived.

Flowering Plants Non-flowering Plants

They are commonly known as They include the cryptogams and the
angiosperms. gymnosperms.
They have seeds and flowers. They do not produce seeds and flowers
except for gymnosperms, which are seed-
bearing and non-flowering.
Most of the non-flowering plants do not
have true roots, leaves or stems.
They are highly evolved with true roots,
leaves and stems.
Examples – Orchids, Grasses, Sedges. Examples – Mosses, Ferns, Conifers

EXCRETORY PRODUCT OF FLOWERING PLANT

The removal of waste and hazardous compounds from the body is referred to as excretion in
plants. When you drink a lot of water, you know you’ll need to pee a lot sooner or later,
right? Do you know why this is the case? This is due to the fact that our kidney filters our
blood and gathers all waste products in our urine bladder, which we then expel. Excretion is a
vital action since it eliminates any poisons from our bodies as well as any surplus material,
such as water. Have you ever witnessed a plant pee? You haven’t, of course. But what
happens to the trash produced by plants? Even though they do not excrete it in the same way
that we do, they do defecate. How?

The removal of waste and hazardous compounds from the body is referred to as excretion.
Every living entity excretes waste. Plants, like mammals, lack a particular excretory
apparatus. They solely excrete through their vegetative sections.
 Oxygen is a byproduct of photosynthesis that is excreted by plant leaves, and Excess water
is expelled as water vapour through the transpiration mechanism. Plants store certain
excretory products in their leaves and get rid of them by losing them. Some plants retain
excretory products such as resins, gums, latex, and oils, and so on in their stems, leaves, and
bark. Plants eventually lose their components, resulting in excrement. Plants generate
secondary metabolites, such as alkaloids, that are utilised by animals but not by plants.
Alkaloids are nitrogenous chemicals that are stored in various areas of the plant. It is used as
a medication, as a sedative, and as an insecticide. In aquatic plants, excretion occurs by
diffusion.

DIFFERENT TYPES OF EXCRETION IN PLANTS

The following are the several forms of excretion in plants:

 Transpiration: Transpiration is the loss of water vapour from the plant’s surface, primarily
from the leaves. This water loss has the effect of ‘pushing’ water up the xylem. The quantity
of water lost by a plant as a result of transpiration can be surprising.
 Guttation: Guttation is the loss of water as water droplets from plant hydathodes. Water
droplets seep out of the leaf edges of several herbaceous plants. Water droplets seep out
through specific marginal structures called Hydathodes or Water Stomata when root pressure
is strong and transpiration is low.

Mineral salts, organic acids, carbohydrates, and nitrogenous substances abound in these
droplets. Garden nasturtium, grasses, tomatoes, potatoes, and colocasia all exhibit guttation.

 Bleeding: Bleeding is the exudation of sap from wounded plant parts. Due to root pressure,
xylem sap begins to flow out of an incision created in the stem of a plant growing in well-
watered soil.
 Respiration: Plants employ carbon dioxide, water, sunshine, and chlorophyll to synthesise
food in a process known as photosynthesis. As a byproduct of photosynthesis, oxygen is
produced. This oxygen works as an excretory product and is released through a mechanism
known as diffusion.

PLANTS ORGANS INVOLVED IN EXCRETION

1. Old Leaves: Waste materials are stored in the leaves as they age, and the leaves eventually
fall off the tree along with the waste products.
2. Old Xylem: Resins, gums, tannins, and other waste products are accumulated in the ancient
xylem, which quickly becomes non-functional, e.g., hardwood.
3. Bark: Bark is made up of dead cells that are stripped off by huge trees on a regular basis.
Tannins and other impurities accumulate in the bark of trees. Tannins, by the way, are the
basic ingredient used to make dyes and inks.
4. Central Vacuole: The core vacuole of a plant’s cell is where the majority of its waste
products are kept. Because of the presence of a selectively permeable membrane termed
tonoplast, they are unable to impact the functioning of cytoplasm.
5. Root Excretion: Some waste compounds are expelled by plants through their roots.
6. Detoxification: Toxic oxalic acid is detoxified by the creation of calcium oxalate, which
crystallises into needles (raphides), prisms (prismatic crystals), stars (sphaeraphides), and
 crystal sand. When there is an overabundance of calcium in plants, it precipitates in the form
of calcium carbonate crystals, such as cystolith.
7. Salt Glands: Plants expel excess salts from their environment.

PLANT EXCRETORY PRODUCT

The following are the primary products expelled by plants:

1. Carbon dioxide and oxygen: Carbon dioxide is produced during respiration. As a result of
photosynthesis, oxygen is produced and secreted by leaves.
2. Excess water: Excess water is expelled through stomata, a process called transpiration.
3. Excess salts: When there is a high level of salts present in water or soil and plants absorb
these salts, they are normally expelled by plants and deposited in plants as crystals.
4. Nitrogenous Waste Products (NWPs): They are by products of cellular metabolism in
general. Alkaloids, such as quinine, morphine, and atropine, are examples of prevalent
nitrogenous waste products. Diffusion is another name for this phenomenon.
5. Organic Acids: Organic acids serve as metabolic intermediaries. Some of them have no other
use. Rather, some organic acids, such as oxalic acid, can accumulate and become detrimental
and poisonous.
6. Tannins: Tannins are complex aromatic molecules produced as secondary metabolites.
7. Latex: Latex is a milky white liquid or fluid that is generated by blooming plants such as
rubber plants. It is an emulsion of varied compositions that is ejected by laticifers, which are
unique tubular cells.
8. Resins: As a result of oxidation, various aromatic oil compounds known as resins are
generated.
9. Gums: Gums are the breakdown products of cell walls.

MUNCH’S MASS FLOW OR PRESSURE FLOW HYPOTHESIS

The Mass Flow Hypothesis was first proposed by German plant physiologist Ernst Munch in
the year 1930. He theorised the movement of sap through the phloem tissue in plants. This
theory is also known as the Pressure Flow Hypothesis. A highly concentrated organic sugar
especially sugar in the cells of the phloem from a source like a leaf forms a diffusion gradient
which draws water into the cells of phloem tissue from the adjacent xylem. This develops
turgor pressure in the phloem, which is also called hydrostatic pressure.

Phloem movement occurs by mass flow from sources of sugar to sugar sinks. The phloem
movement is bidirectional but unidirectional in xylem cells. Due to this multidirectional flow,
it is not uncommon for sap in the sieve tubes besides to move in opposite directions based on
the fact that sap cannot travel easily between adjacent sieve tubes.

MECHANISM
When the movement of minerals and water via the xylem is driven mostly by negative
pressure and movement via phloem is driven by hydrostatic pressure. This process is called
translocation and is accompanied by a process known as phloem loading and unloading. Cells
in sugar sources load a sieve tube by osmosis developing pressure that pushes the sap low.
The cells deliver solutes out of the elements of sieve tube and produce opposite effects. The
sugar gradient from the source creates pressure-flow via the sieve tube towards the sink.
  Glucose is formed by photosynthesis in the cells of mesophyll and some glucose is
utilized in the cells during respiration. The leftover glucose is transformed into non-
reducing sugar.
 Sucrose is delivered to the neighbour cells of minute veins of the leaves.
 Sucrose diffuses from neighbour cells to the elements of the sieve tube via
plasmodesmata. Hence, the amount of sucrose rises in the elements of the sieve tube.
 Water travels from the close xylem to the leaf vein by osmosis and raises the
hydrostatic pressure of the elements of the sieve tube.
 The Hydrostatic pressure shifts the sucrose along with other substances via the cell of
the sieve tube towards the sink.
 In storage sinks, sucrose is eliminated into the apoplast before entering the sink’s
symplast.
 The water travels out of the cells via osmosis and lowers the hydrostatic pressure in
them. Hence, a gradient of pressure is developed as a result of the entry of sugar at the
source and elimination of sucrose at the sink.
 The phloem sugar is eradicated by the cortex of the root and stem and utilized by
cellular respiration. The starch is insoluble and does not exert any osmotic effect.
Ultimately, pure water is left and drawn into xylem vessels by transpiration pull.

TRANSPORT SYSTEM
Transport systems in plants Plants may not have blood vessels and a heart, but they
nevertheless have transport systems of cells which form tubular vessels to transport
molecules and ions in solution from one place to another. The xylem tissue carries
water and dissolved ions from the roots to the aerial parts of the plant. In the tallest
trees this can be over 100 metres. Phloem carries water and dissolved food molecules
from the leaves to all parts of the plant. For more about the solvent properties of water
see Soil water

TURGOR AND PLASMOLYSIS

The shape of plant cells is defined by their cell wall. This is normally slightly stretched and
rigid, due to the uptake of water by osmosis. Water will move from a less concentrated
solution into a more concentrated solution through a partially permeable membrane, as there
will be a diffusion gradient from where there is more water to where there is less water. The
ability of water to move from one place to another is called water potential. Water will move
from higher to lower water potential

THE TRANSPIRATION STREAM

Transpiration is the evaporation of water from the surface of the mesophyll cells (especially
spongy mesophyll) in leaves. It diffuses out into the atmosphere through the stomata. The
transpiration stream is the flow of water and dissolved inorganic ions from the roots up to the
leaves. As water evaporates in the leaves, more water is pulled through the plant, in a
continuous stream from the roots up through the xylem and into the leaves, due to the
cohesion of the water molecules.

TRANSLOCATION
Food molecules that have been synthesised in the leaves have to be moved to all the other
parts of the plant in a process called translocation. Nutrients like sugars (glucose and starch
are converted to sucrose for translocation) and amino acids are moved up and down in the
plant in the phloem. Meristems (growing regions), fruits and seeds, and root storage systems
in particular need good supplies of nutrients. When necessary, molecules must be retrieved
from storage and redistributed. The place of origin of a nutrient is called its source and its
destination is called the sink.

THE PHLOEM

Phloem is found in vascular bundles, closely associated with the xylem. It is a living tissue.
Translocation requires energy. If phloem cells are killed, translocation will cease. Phloem
tissue contains sieve tube cells which lie end to end to form continuous tubes. The cellulose
cells walls at the ends of the cells are perforated to form sieve plates that allow cytoplasm to
run from one cell into the next. These cells translocate nutrients, but lose their nuclei and
most of their organelles when they mature. Companion cells run alongside the sieve tube
cells. These are connected to them by plasmodesmata. They do not translocate nutrients, but
control the activity of the sieve tube cells. They have cytoplasm with many cell organelles.

ROOTS

The xylem is found in a vascular bundle in the centre of roots. Here it provides resistance to
stretching forces, thereby helping to anchor the plant in the ground. A sheath of specialised
cells called the endodermis surrounds the vascular bundle. Each cell is bound to its
neighbours by a strip of corky material (suberin) forming the Casparian strip. This forces all
the water that passes into the xylem in the root to pass through selective cell membranes that
control which inorganic ions reach the xylem. Important ions that are transported include
nitrates, phosphates, potassium and magnesium. Protein carrier molecules in the cell
membranes use energy from ATP to actively transport inorganic ions through the
endodermis. This lowers the water potential of the cells inside the endodermis, so water
follows by osmosis

XYLEM

Xylem is one of the two types of transport tissue in vascular plants, the other being phloem.
The basic function of the xylem is to transport water from roots to stems and leaves, but it
also transports nutrients.
Movement of Water up the Xylem against Gravity

How is water transported up a plant against gravity, when there is no “pump” or input of
cellular energy to move water through a plant’s vascular tissue? There are three hypotheses
that explain the movement of water up a plant against gravity. These hypotheses are not
mutually exclusive, and each contributes to movement of water in a plant, but only one can
explain the height of tall trees:

1. Root pressure pushes water up

2. Capillary action draws water up within the xylem
3. Cohesion-tension pulls water up the xylem
We’ll consider each of these in turn.

Root pressure relies on positive pressure that forms in the roots as water moves into the
roots from the soil. Water moves into the roots from the soil by osmosis, due to the low solute
potential in the roots (lower Ψs in roots than in soil). This intake of water in the roots
increases Ψp in the root xylem, “pushing” water up. In extreme circumstances, or when
stomata are closed at night preventing water from evaporating from the leaves, root pressure
results in guttation, or secretion of water droplets from stomata in the leaves. However, root
pressure can only move water against gravity by a few meters, so it is not sufficient to move
water up the height of a tall tree.

Capillary action (or capillarity) is the tendency of a liquid to move up against gravity when
confined within a narrow tube (capillary). You can directly observe the effects of capillary
action when water forms a meniscus when confined in a narrow tube. Capillarity occurs due
to three properties of water:

1. Surface tension, which occurs because hydrogen bonding between water molecules is
stronger at the air-water interface than among molecules within the water.
2. Adhesion, which is molecular attraction between “unlike” molecules. In the case of
xylem, adhesion occurs between water molecules and the molecules of the xylem cell
walls.
3. Cohesion, which is molecular attraction between “like” molecules. In water, cohesion
occurs due to hydrogen bonding between water molecules.
On its own, capillarity can work well within a vertical stem for up to approximately 1 meter,
so it is not strong enough to move water up a tall tree.

LEAF ANATOMY

Epidermis covers the upper and lower surfaces of the leaf. Usually a single layer of tightly-
packed cells, the epidermis mediates exchanges between the plant and its environment,
limiting water loss, controlling gas exchange, transmitting sunlight for photosynthesis, and
discouraging herbivores.

Leaf tissues are composed of layers of plant cells. Different plant cell types form three main
tissues found in leaves. These tissues include a mesophyll tissue layer that is sandwiched
between two layers of epidermis. Leaf vascular tissue is located within the mesophyll layer.
 MORPHOLOGY OF LEAF

EPIDERMIS
The outer leaf layer is known as the epidermis. The epidermis secretes a waxy coating called
the cuticle that helps the plant retain water. The epidermis in plant leaves also contains
special cells called guard cells that regulate gas exchange between the plant and the
environment. Guard cells control the size of pores called stomata (singular stoma) in the
epidermis. Opening and closing the stomata allows plants to release or retain gases including
water vapor, oxygen, and carbon dioxide as needed.
MESOPHYLL
The middle mesophyll leaf layer is composed of a palisade mesophyll region and a spongy
mesophyll region. Palisade mesophyll contains columnar cells with spaces between the cells.
Most plant chloroplasts are found in palisade mesophyll. Chloroplasts are organelles that
contain chlorophyll, a green pigment that absorbs energy from sunlight for
photosynthesis. Spongy mesophyll is located below palisade mesophyll and is composed of
irregularly shaped cells. Leaf vascular tissue is found in the spongy mesophyll.
Vascular Tissue
Leaf veins are composed of vascular tissue. Vascular tissue consists of tube-shaped
structures called xylem and phloem that provide pathways for water and nutrients to flow
throughout the leaves and plant.

COMPOUND LEAF
 GASEOUS EXCHANGE

Flowering plants exchange gases through their leaves:

• In the light there is a net intake of carbon dioxide for photosynthesis and a net output of
oxygen from respiration

• In the dark there is a net intake of oxygen for respiration and a net output of carbon dioxide

In the dark the plant's potassium pumps stop and potassium ions diffuse back out of the guard
cells, they lose turgidity and the stomata close. Sufficient oxygen for respiration can still get
into the leaf cells by diffusion. Gas exchange is achieved by diffusion. This is a process by
which particles move naturally from a region where they are in high concentration to a region
where they are in lower concentration. They move down a concentration gradient: the steeper
the gradient, the faster the rate of diffusion.

With the stomata open, production and consumption of oxygen and carbon dioxide in the leaf
is sufficient to maintain a concentration gradient steep enough to facilitate gas exchange with
the atmosphere. In potential drought conditions, a mechanism triggered by the plant hormone
abscissic acid (ABA), causes potassium ions to be pumped out of the guard cells into adjacent
cells. This reduces turgidity in the guard cells and causes the stomata to close which reduces
the rate of gas exchange. Plants living in areas prone to drought usually have adaptations to
cut down water loss or even store water.

There are many layers that make up a plant’s cell, which all serve their own purpose.

Gas exchange in the leaves occurs through the stomata on the lower epidermis. Most plants,
including dicotyledonous plants, use the stoma for gas exchange.

Stoma (singular) is openings which allow for the exchange of carbon dioxide and oxygen.
They are opened by ions (mainly K+) which move in via active transport, which allows
water loss, something that needs to stay balanced.

Stomata open in response to guard cells bending due to becoming turgid (and uneven
thickness in the walls). Water moves in via osmosis due to the water potential being
decreased.

Unlike other organisms, plants are reliant on both oxygen and carbon dioxide for processes
such as photosynthesis and respiration:

1. During photosynthesis, which occurs in most plants during the day (favourable
conditions), plants take in carbon dioxide through the open stoma and release oxygen
into the environment.
 2. During respiration, which occurs in most plants at night, plants take in oxygen
through the closed stoma and release carbon dioxide into the environment?
3. Both carbon dioxide and oxygen enter and exit through the stoma by simple diffusion
down their concentration gradients

WHAT IS GAS EXCHANGE IN PLANTS?

Gas exchange in plants refers to the process by which plants take in carbon dioxide and
release oxygen through tiny pores called stomata.

HOW DOES GAS EXCHANGE TAKE PLACE IN PLANTS?

Gas exchange occurs in plants through tiny pores called stomata, which are found on the
leaves. Carbon dioxide enters the plant through the stomata, and oxygen is released.

WHAT IS THE ROLE OF STOMATA IN GAS EXCHANGE?

Stomata play a critical role in gas exchange as they allow carbon dioxide to enter the plant
and oxygen to be released. The opening and closing of stomata are regulated by the plant to
maintain a balance between the uptake of carbon dioxide and the release of oxygen.

WHAT FACTORS INFLUENCE THE OPENING AND CLOSING OF STOMATA?

The opening and closing of stomata are influenced by various factors, including light,
temperature, and the availability of water. In bright light, stomata open to allow for greater
gas exchange, and in low light conditions, they close to conserve water.
HOW DOES THE RATE OF PHOTOSYNTHESIS AFFECT GAS EXCHANGE IN
PLANTS?

The rate of photosynthesis affects gas exchange in plants as it influences the opening and
closing of stomata. As the rate of photosynthesis increases, the demand for carbon dioxide
also increases, and the stomata open to allow for greater gas exchange.

WHAT ARE THE LIMITATIONS OF GAS EXCHANGE IN PLANTS?

The main limitations of gas exchange in plants are water availability and temperature. If a
plant doesn’t have access to enough water, its stomata will close to conserve water, limiting
the exchange of gases. High temperatures can also lead to the closure of stomata to prevent
water loss.

PLANT METABOLISM

Plants are responsible for incredible feats of molecular transformation.

 Photosynthesis
Photosynthesis is the process by which light energy is captured, converted and stored in a
simple sugar molecule. This process occurs in chloroplasts and other parts of green
organisms. It is a backbone process, in the sense that all life on earth depends on it’s
functioning. The following equation sums up the process:

6CO2 (carbon dioxide) + 12 H2O (water) + light energy -> C 6H12O6 (glucose) +
6O2 (oxygen) +6H2O (water)

As you see from the equation, this process is vital to us as humans, because it transforms
carbon dioxide into oxygen—which we enjoy with every breath!

Carbon Dioxide (CO2)

The earth’s atmosphere contains approximately 79% nitrogen, 20% oxygen, and the
remaining 1% is a mixture of less common gases—including 0.039% carbon dioxide. Carbon
dioxide in the atmosphere reaches plant mesophyll via the stomata. The carbon dioxide
dissolves on the thin film of water that covers the outside of cells. The carbon dioxide then
diffuses through the cell wall into the cytoplasm in order to reach the chloroplasts. The
oceans hold a large reservoir of carbon dioxide, which keeps the atmospheric levels
essentially constant. Although there are some indicators that the atmospheric levels of
CO2 are rising and adding to the global warming issue. That is a whole other topic though.

WATER

Water is plentiful on earth; however, it may or may not be plentiful at the location of each
individual plant. Therefore, plants will close their stomata, if need be, which reduces the
CO2 supply to the mesophyll. Not even 1% of the water that is absorbed by plants is used in
photosynthesis, the remainder is either transpired or incorporated into protoplasm, vacuoles
or other cell materials. The water utilized in photosynthesis is the source of oxygen released
as a photosynthetic byproduct.

Enzymes generally operate in the presence of water, and reduced water in a plant will reduce
the rate of respiration. Seeds usually have a water content of less than 10%, while mature
living cells usually are in excess of 90% water. Seeds keep better if they are kept dry as the
respiration rate remains quite low. However, if a seed comes into contact with water and via
imbibition swells, the respiration rate will skyrocket. The temperature could increase to the
point of killing the seeds. Spontaneous combustion can occur from the respiration generated
heat when a fungus or bacterium is permitted to grow on wet seeds. Kind of a neat little
trivial fact to tuck away.

LIGHT

Light has a dual nature, in that it exhibits properties of both waves and particles. The energy
from the sun comes to earth in various wavelengths, the longest being radio waves and the
shortest are gamma rays. Approximately 40% of the radiant energy the earth receives from
the sun is visible light. Visible light ranges from red, 780 nanometers to violet, 390
nanometers. The violet to blue and red to orange ranges are the most often used in
photosynthesis. Most light in the green range is reflected.

Of the visible light that reaches a leaf, approximately 80% is absorbed. Light intensity varies
widely. Time of day, temperature, season of year, altitude, latitude, and other atmospheric
conditions all play roles in the intensity of the radiant energy that will reach the earth and its
organisms. High-intensity light isn’t necessarily a beneficial thing for plants. In high-intensity
light, photorespiration may occur, which is a type of respiration that uses oxygen and releases
carbon dioxide but differs from standard aerobic respiration in the pathways that it utilizes.

CHLOROPHYLL

A few things to know about chlorophyll before we get into the nitty- gritty of photosynthesis
and respiration. There is more than one type of chlorophyll; however, they all have one atom
of magnesium in the center. In some ways, the chlorophyll is quite analogous to the heme
structure in hemoglobin (the iron-containing pigment that carries oxygen in the blood).
Chlorophyll has a long lipid tail that anchors the molecule in the lipid layers of the thylakoid
membranes—recall that thylakoids are coin-like discs in stacks within the stroma of the
chloroplasts. The chloroplasts of most plants contain two types of chlorophyll embedded in
the thylakoid membranes. The formula for bluish-green chlorophyll a is C55H72O5N4Mg and
the formula for yellow-green chlorophyll b is C55H70O6N4Mg. In general, most chloroplast has
about three times as much chlorophyll a than b.

The main role of chlorophyll b is to broaden the spectrum of light available for
photosynthesis: chlorophyll b absorbs light energy and transfers the energy to a chlorophyll a
molecule. Other pigments are contained in chlorophyll c, d, and e and take the place for
chlorophyll b in some cases. Note that all the chlorophyll molecules are related to each other
and differ only slightly in molecular structure. Light-harvesting complexes contain 250 to
400 pigment molecules and are referred to as a photosynthetic unit. There are countless
numbers of these units spread throughout the grana of a chloroplast. In the chloroplasts of
green plants, two types of these harvesting units operate together in order to bring about the
first phase of photosynthesis.

The photosynthetic process occurs in two successive processes: the light reactions and the
carbon-fixing reactions.

THE LIGHT REACTIONS

The light reactions involve light striking the chlorophyll molecules embedded in the
thylakoids of chloroplasts. The subsequent reaction results in the conversion of some light
energy to chemical energy. In the light reactions, water molecules are split apart into
hydrogen ions and electrons and oxygen gas is released. In addition, ATP (adenosine
triphosphate) molecules are created and the hydrogen ions derived from the water molecules
are involved in “loading” NADP which carries the hydrogen as NADPH. NADPH is integral
in providing the hydrogen ions used in the second series of major photosynthetic reactions:
the carbon-fixing reactions.

THE CARBON-FIXING REACTIONS

The carbon-fixing reactions used to be called dark reactions because light does not play a
direct role in their functioning. The reactions take place in series outside of the grana in the
stroma of the chloroplast. These reactions only occur if the end products of the light reactions
are available for use. Depending on the plant involved, the carbon-fixing reactions may
develop or progress in different ways. The most common type of carbon-fixing reactions in
plants is the process called the Calvin cycle. In the Calvin cycle, carbon dioxide from the
atmosphere is combined with a 5-carbon sugar—RuBP, or ribulose bisphosphate. The
combined molecules are converted via several steps into a 6-carbon sugar, such as glucose.
The ATP and NADPH molecules from the light reactions provide the energy and resources
for the reactions. Some of the sugars produced are further combined into polysaccharides
(strings of simple sugars) or are stored as starch within the plant. There are other variations,
including the 4-carbon pathway which is usually found in desert plants (C4 plants).

Before getting into respiration let’s take a closer look at what happens in both the light
reactions and the carbon-fixing reactions.

Nitty-gritty of Light Reactions

Einstein called the discrete particles of light photons. Particles (photons) and waves are both
currently accepted aspects of light. The quantum (energy) of photons is different depending
on what kind of light they are in. Longer wavelength light has lower photon energies; while
light with shorter wavelengths have higher photon energies. As mentioned earlier, every
pigment color has a different distinctive pattern of light absorption—called the pigment’s
absorption spectrum. The energy levels of some of the pigment’s electrons are raised when
the pigment absorbs light. If energy is emitted immediately upon absorption, the effect is
called fluorescence. The red part of light does this characteristically, as demonstrated when
chlorophyll is placed in light it will appear red. If the absorbed energy is emitted as light after
a delay, then the effect is called phosphorescence. The energy may be converted to heat or
stored, as in photosynthesis within chemical bonds.

OXIDATION-REDUCTION REACTIONS

OIL RIG, a cute little mnemonic device to remember that oxidation is loss and reduction is
gain. Perhaps better put, oxidation results in the net loss of an electron or electrons, while
reduction results in a net gain of an electron or electrons. The electrons come from
compounds within the process or donated in from previous processes. These types of
chemical reactions are found scattered throughout the processes within photosynthesis and
respiration.

PHOTOSYSTEMS
The two types of photosynthetic units in most chloroplasts are what constitute photosystem I
and photosystem II.

Photosystem I contains photosynthetic units with 200 or more molecules of chlorophyll a,

small amounts of chlorophyll b, protein saddled carotenoid pigment and a pair of specialized
reaction-center molecules of chlorophyll called P700. All pigments in a photosystem are
capable of absorbing photons, however, only the reaction-center molecules can really utilize
the light energy. The other pigments aren’t worthless in the system, as they act sort of like an
antenna in gathering and passing light energy along to the reaction-center. Iron-sulphur
complexed proteins initially receive electrons from P700 and serve as primary electron
acceptors for the unit.

Photosystem II contains chlorophyll a, protein saddled beta-carotene, a small amount of

chlorophyll b and special pair of reaction-center molecules of chlorophyll a otherwise called,
P680. The photosystem has a primary electron acceptor called pheophytin or Pheo.
For the record, the 680 and 700 in the names of the reaction-center molecules stand for the
peaks in the absorption spectra of light waves of 680 nm and 700 nm.
PHOTOLYSIS

A photon of light strikes the photosystem II reaction center, the P680 molecule to be exact
near the inner surface of a thylakoid membrane. The received light energy excites an electron
(boosts it to a higher energy level) which is an unstable reaction and thus most of the energy
is lost to heat. Up to four photons at a time can strike the P680 molecule, however, it can only
accept one electron at a time. The molecule of pheophytin picks up the excited electron,
which then crosses the thylakoid membrane and is passed along to another acceptor called
plastoquinone or Pq near the outside surface of the thylakoid membrane. Protein Z extracts
electrons from water and replaces the ones lost by the P680 molecule. Protein Z contains
manganese which is required in order to split water molecules. Simultaneously, as two water
molecules are split and a molecule of oxygen and four protons are produced. This enzyme-
mediated water splitting process is called photolysis.

PHOTOPHOSPHORYLATION

The acceptor molecule, releases the excited electron into the care of an electron transport
system that is sort of like a downhill bucket brigade. The transport system moves electrons
extracted from water temporarily to a high-energy storage molecule called nicotinamide
adenine dinucleotide phosphate (NADP+). NADP+ is an electron acceptor for the
photosystem. The transport chain is essentially iron-containing pigments, cytochromes, a
copper-containing protein called plastocyanin and other electron transferring molecules. As
electrons are passed through the chain and protons are being shuffled through a coupling
factor, ATP molecules are assembled from ADP and phosphate in a process called
photophosphorylation.

A similar series of events occurs in photosystem I. After a photon of light strikes a P700
molecule, the resulting excited electron is passed along to an iron-sulphur molecule Fe-S
which in turn passes it to another acceptor molecule ferredoxin, (Fd). The ferredoxin
molecule releases the electron to a carrier molecule called flavin adenine dinucleotide (FAD)
and then eventually on to NADP+. A reduction occurs and NADP+ becomes NADPH.
Electrons from photosystem II and the activities of the electron transport system replace any
electrons removed from the P700 molecule. Because the electrons move in one direction, the
movement of electrons from water to photosystem II to photosystem I to NADP+ are said to
be part of noncyclic electron flow. Any ATP that is produced is designated noncyclic
phosphorylation.
It should be noted that photosystem I can operate independently of photosystem II. When this
occurs, the electrons boosted from P700 reaction-center molecules (photosystem I) are passed
through an intermediary acceptor molecule called P430 and then on to the electron transport
chain. This is rather than to the ferredoxin and NADP+. After being passed through the
electron transport chain, the electron is dumped back into the reaction-center of photosystem
I. This process demonstrates cyclic electron flow and any ATP generated by cyclic electron
flow are termed cyclic phosphorylation. Note, that no water molecules are split and no
NADPH or oxygen is produced.

CHEMIOSMOSIS

Earlier we mentioned in passing a coupling factor. The enzyme necessary for the mediation
of the splitting of water molecules is on the inside of the thylakoid membrane. As a result of
this, a proton gradient form across the membrane and the movement of these protons is
thought to be a source of energy for generating ATP. The motion is thought to be similar to
molecular movement during osmosis and has hence been termed chemiosmosis. As the
protons move across the membrane, they are assisted in crossing by protein channels called
ATPase or coupling factor. Because of the proton movement, ADP and phosphate combine
which produces ATP.

The nitty-gritty of carbon-fixing reactions

Both ATP and NADPH are important products of the light reactions and both of them play
roles in the synthesis of carbohydrates from atmospheric carbon dioxide. Although the
carbon-fixing reactions do not require daylight, they generally are conducted during daylight
hours as there is some indication that some of the enzymes required for the processes in
carbon-fixing may require some level of light. These reactions take place in the stroma of the
chloroplast.

Three known mechanisms of converting carbon dioxide to sugar: (1) Calvin Cycle, (2) 4-
Carbon pathway, and (3) CAM photosynthesis.

The Calvin Cycle or the 3-carbon pathway—The Calvin cycle is the most common of the
three mechanisms and has four main results:

1. With the assistance of the enzyme rubisco (RuBP carboxylase), six molecules of
atmospheric carbon dioxide combine with six molecules of ribulose 1, 5-bisphosphate
(RuBP)
2. The result of the first step is six unstable 6-carbon complexes, which immediately
split into two 3-carbon molecules of 3-phosphoglyceric acid or 3PGA. This is the first
stable compound in photosynthesis.
3. NADPH and ATP from the light-reactions, supply the energy required to convert the
3PGA to 12 molecules of glyceraldehydes 3-phosphate (GA3P), which is a 3-carbon
sugar phosphate complex.
4. Finally, of the 12 molecules formed; 10 are restructured into six 5-carbon molecules
of RuBP—the sugar that the process started with.

The sugars produced can either add to an increase in the sugar content (carbohydrate content)
of the plant or they can be used in pathways that lead to the production of lipids and amino
acids.
 4-CARBON PATHWAY

C4 plants are plants that use a 4-carbon molecule called oxaloacetic acid in place of the 3-
carbon 3-phosphoglyceric acid in step two of the Calvin cycle. Oxaloacetic acid is produced
from a 3-carbon compound PEP—phosphoenolpyruvate and carbon dioxide. This process is
enzyme-mediated and occurs in the mesophyll cells of the leaf. Some species will convert the
resulting oxaloacetic acid to aspartic, malic or other acids.

Note that the acids do not substitute for 3PGA. The 4-carbon acids migrate to the bundle
sheaths surrounding the vascular bundles, where they are further converted to pyruvic acid
and carbon dioxide. In returning to the mesophyll cells and interacting with ATP molecules,
the pyruvic acid molecules are able to produce additional PEP. In the bundle sheath cells, the
carbon dioxide formed converts into 3PGA and other molecules, by combining with RuBP.
The other molecules formed are similar to the other ones formed in the Calvin cycle. The C4
cycle furnishes carbon dioxide to the Calvin cycle in a more roundabout way than the C3
pathway, but there is an advantage to this extra pathway.

The extra pathway greatly reduces photorespiration in C4 plants, and this is a good thing
because photorespiration is in direct competition with the Calvin cycle and even takes place
in the light while the Calvin cycle is functioning. During photorespiration, RuBP reacts with
oxygen to create carbon dioxide; in contrast, during photosynthesis RuBP and carbon dioxide
are used to form carbohydrates. C4 plants are able to pick up carbon dioxide in very low
concentrations via the mesophyll cells.

The Calvin cycle occurs in the bundle sheath where carbon dioxide is readily available.
Because of the location, the enzyme rubisco will be in a prime spot to catalyze the reaction
between RuBP and carbon dioxide, rather than oxygen. As a result, C4 plants have
photosynthetic rates that are two to three times higher than C3 plants. There are a few other
characteristic features of C4 plants worth noting:

C4 plants have two types of chloroplasts and an alternate pathway for using carbon dioxide.
C3 plants only have one type of chloroplast and one pathway. Chloroplasts with starch grains
and are large with very little grana, and sometimes none, in the bundle sheath cells. In the
mesophyll, the small, but numerous chloroplasts have no starch grains and contain highly
developed grana.

PEP carboxylase is found in high concentration in the mesophyll cells which permits ready
conversion of carbon dioxide to carbohydrate at lower concentrations than does rubisco (in
bundle sheath cells) of the Calvin cycle.

The temperature ranges for C4 plants are much higher than C3 plants that enable C4 plants to
live well in conditions that would likely kill a C3 plant.

CAM photosynthesis

Crassulacean acid metabolism is a modified photosynthetic system that is somewhat similar

to C4 photosynthesis in that 4-carbon compounds are produced during the carbon-fixing
reactions. CAM plants accumulate malic acid in their chlorenchyma tissues at night, which is
converted back to carbon dioxide during the day. In the daytime, malic acid diffuses out of
the vacuoles and is converted to carbon dioxide for use in the Calvin cycle. PEP carboxylase
is responsible for converting the carbon dioxide plus PEP to malic acid at night.

This modification allows for a greater amount of carbon dioxide to be converted to

carbohydrate during the day than would be otherwise converted given the conditions CAM
plants generally grow in. CAM plants generally close their stomata during the day in order to
reduce water loss. There are more than 20 families that contain CAM plants, including cacti,
stonecrops, orchids, bromeliads, and many succulents growing in regions of high light
intensity. There are some succulents that do not have CAM photosynthetic capabilities, as
well as non-succulents that do have the ability.

RESPIRATION
Respiration is the group of processes that utilizes the energy that is stored through the
photosynthetic processes. The steps in respiration are small enzyme-mediated steps that
release tiny amounts of immediately available energy; the energy released is usually stored in
ATP molecules which allow for even more efficient use of an organism’s energy. Respiration
occurs in the mitochondria and cytoplasm of cells.

There are several forms of respiration: aerobic—which requires oxygen, anaerobic—which

occurs in the absence of oxygen, and fermentation—which also occurs in the absence of
oxygen.

Aerobic respiration is the most common form of respiration and cannot be completed without
oxygen gas. The controlled release of energy is the main event in aerobic respiration.

Certain types of bacteria and other organisms without oxygen gas carry on anaerobic
respiration and fermentation. Compared to aerobic respiration the amount of energy released
is quite small. The main difference between aerobic respiration and fermentation is in the
way hydrogen is released and combined with other substances. Two very common forms of
fermentation are summed up by the following equations:

(Equation 1) C6H12O6 (glucose) -> (with enzymes)-> 2C2H5OH (ethyl alcohol)+

2CO2 (carbon dioxide) + energy (ATP)

(Equation 2) C6H12O6 (glucose) -> (with enzymes) -> 2C3H6O3 (lactic acid) + energy
(ATP)

Note the first equation is particularly valuable to the brewing industry.

Major Steps in Respiration:

GLYCOLYSIS

 4 molecules of ATP +2 molecules of NADH (which yields 4 ATP in the ETS) = 8

molecules of ATP net
 8 molecules of ATP net – 2 ATP molecules to start the glycolysis process = 6 ATP
molecules

Conversion of pyruvic acid to acetyl CoA:

  2 molecules of NADH (yields 6 ATP in the ETS)

The first step does not require oxygen gas (O 2) and takes place in the cytoplasm. The
glycolytic phase is subdivided into three main steps and several smaller ones. Each step is
mediated by an enzyme. A small amount of energy is released and hydrogen atoms are
removed from compounds derived from glucose. The main gist of the steps is:

 The glucose molecules go through several steps and become a double phosphorylated
fructose molecule.
 The 6-carbon fructose molecule is split into two 3-carbon fragments, each with a
phosphate, GA3P
 Hydrogen, energy, and water are removed from the GA3P molecules leaving pyruvic
acid.

Glycolysis requires two molecules of ATP to get the process started. In the processes, four
ATP molecules are created, with a net gain of 2 ATP molecules at the end of glycolysis. The
hydrogen ions and electrons that are released are held by an acceptor molecule called NAD—
nicotinamide adenine dinucleotide. The overall end product of glycolysis is: 2-ATP
molecules, 2-NADH molecules, and pyruvic acid.

The next step depends on the kind of respiration involved—aerobic, true anaerobic or
fermentation. In aerobic respiration (with oxygen present), the next steps are Krebs
Cycle and Electron Transport Chain.

The Krebs cycle (or citric acid cycle)

The Krebs cycle takes place in the fluid matrix of the cristae compartments of the
mitochondria. It is called the citric acid cycle because of all the intermediate acids in the
cycle. The pyruvic acid product of glycolysis is re-structured, some of the CO 2 is lost and
becomes acetyl CoA which then dumps into the Krebs cycle. During the restructuring of
pyruvic acid, a molecule of NADH is produced. The Krebs cycle removes energy, CO 2, and
hydrogen from acetyl CoA via enzyme-mediated reactions of organic acids.

The hydrogen removed during the Krebs cycle is picked up by FAD and NAD acceptor
molecules. The end result of the metabolizing of two acetyl CoA molecules in the Krebs
cycle is two ATP molecules, oxaloacetic acid (to further drive the cycle), six
NADH2 molecules, two FADH2 molecules, and two CO2 molecules.

The NAD and FAD molecules and the hydrogens that they carry will be dumped into the next
step in respiration in order to extract the energy from the molecules.

THE ELECTRON TRANSPORT CHAIN

The electron transport chain (ETC) is a bit like a bucket brigade in that the chain passes the
molecules along until the job is done. Energy is released as the hydrogen and electrons from
the NAD+ and FAD+ carrier molecules are dumped into the system. When the electrons
reach the end of the chain they pick up oxygen and water is released. ATP is produced by
oxidative phosphorylation during the action of the electron transport chain. This occurs
essentially like chemiosmosis.

Aerobic respiration yield

As a whole, from glycolysis to finish aerobic respiration yields the following:

KREBS CYCLE:

 2 molecules of ATP + 2 molecules of FADH 2 (which yields 4-ATP in the ETS) + 6

molecules of NADH2 (which yields 18-ATP in the ETS) = Total ATP yield: 36

The 36 resulting ATP molecules represent approximately 39% of the energy in a molecule of
glucose. Compared to each other, aerobic respiration is about six times as efficient as
anaerobic respiration.

Anaerobic respiration and fermentation result in a net gain of 2 ATP molecules from
glycolysis. It should be noted, that the by-products of these processes, lactic acid, and
alcohol, will eventually kill the organism if the products are not digested.

Factors regulating the rate of respiration

TEMPERATURE

To a point, the higher the temperature the faster respiration occurs. At some temperature,
enzymes will become inactivated, although there are thermophilic (heat-loving) organisms
that do quite well in high-temperature environments. Energy from sugar is released faster as
the rate of respiration increases which results in a net weight loss. Plants offset the weight
loss by increasing photosynthetic production of sugar. Note that during respiration, some of
the energy is lost as heat, which results in an overall increase in organism temperature—not
necessarily detectible by human hands.

OXYGEN

Oxygen is an important regulator of respiration. If oxygen is drastically reduced, respiration

may drop off to the point of retarding growth or death. Low oxygen concentrations can lead
to the onset of fermentation processes.

ASSIMILATION AND DIGESTION

Assimilation is the conversion of the sugar produced by photosynthesis to fats, proteins,
complex carbohydrates, and other substances. While digestion is the breakdown of large
insoluble molecules by hydrolysis to smaller soluble forms that can be transported to various
parts of the plant.

PHOTOSYNTHESIS VS RESPIRATION
Summary of key differences between photosynthesis and respiration:

PHOTOSYNTHESIS

 Energy stored in sugar molecules

  Carbon dioxide and water used
 Increases weight
 Requires light
 Occurs in chlorophyll
 In green organisms, produces oxygen
 With light energy, produces ATP

RESPIRATION

 Energy released from sugar molecules

 Carbon dioxide and water released
 Decreases weight
 Can occur in light or darkness
 Occurs in all living cells
 Uses oxygen (aerobic respiration)
 With energy released from sugar, produces ATP.

THERE ARE TWO TYPES OF RESPIRATION:

 Aerobic respiration occurs in the presence of oxygen and in most cells most of the time.
 Anaerobic respiration occurs without oxygen and much less frequently than aerobic
respiration.