3.2: Leaves - Biology

3.2: Leaves - Biology

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We see a massive amount of variation in the sizes and shapes of leaves. Plant leaves may be specialised to maximise light utilisation, to minimise water loss, to facilitate C4 photosynthesis or CAM photosynthesis, to resist damage due to water stress, or to float on water.

3.2: Leaves - Biology

Figure 1. Leaves are attached to the plant stem at areas called nodes. An internode is the stem region between two nodes. The petiole is the stalk connecting the leaf to the stem. The leaves just above the nodes arose from axillary buds.

Stems are a part of the shoot system of a plant. They may range in length from a few millimeters to hundreds of meters, and also vary in diameter, depending on the plant type. Stems are usually above ground, although the stems of some plants, such as the potato, also grow underground. Stems may be herbaceous (soft) or woody in nature. Their main function is to provide support to the plant, holding leaves, flowers and buds in some cases, stems also store food for the plant. A stem may be unbranched, like that of a palm tree, or it may be highly branched, like that of a magnolia tree. The stem of the plant connects the roots to the leaves, helping to transport absorbed water and minerals to different parts of the plant. It also helps to transport the products of photosynthesis, namely sugars, from the leaves to the rest of the plant.

Plant stems, whether above or below ground, are characterized by the presence of nodes and internodes (Figure 1). Nodes are points of attachment for leaves, aerial roots, and flowers. The stem region between two nodes is called an internode. The stalk that extends from the stem to the base of the leaf is the petiole. An axillary bud is usually found in the axil—the area between the base of a leaf and the stem—where it can give rise to a branch or a flower. The apex (tip) of the shoot contains the apical meristem within the apical bud.

Phyllotaxy (Arrangement of Leaves): Cyclic and Spinal Phyllotaxy

Phyllotaxy is the mode of arrangement of leaves on the stem. It is surprising how regular and strictly mathematical this is. There is a definite law according to which the leaves are arranged on the stem of a particular species. The arrangement is always regular and leaves are never placed on the stem in a haphazard manner.

The foliage leaves are usually spread about on the stem with long or short inter­nodes between them. This arrangement is called cauline. In some cases, however, the leaves arise as a cluster or a rosette from the very short stem just oh the top of the root.

This arrangement is called radical although the leaves do not actually arise from the root but from a very much condensed stem as in the case of radish.

In cauline leaves there may be one, two, three or more leaves at each node. When there is only one leaf the arrangement is spiral or alternate or a cyclic. This is by far the commonest type of phyllotaxy. When there are two or more leaves at each node the phyllotaxy is cyclic.

A. Cyclic Phyllotaxy:

In the cyclic type of phyllotaxy the leaves at each node form a whorl with the leaves placed on a circle in which the angles between adjacent leaves are the same.

Thus, if there be two leaves in a whorl, the two will be placed opposite (i.e., at an angular distance of two right angles) one another. If there be three leaves, the angle between leaves in the same whorl is 120° (i.e., one third of a circle), if four, it is 90° and so on.

When there are more than two leaves in a whorl the phyllotaxy is called verticillate.

(A) Opposite Phyllotaxy:

In opposite phyllotaxy the two leaves at each node are always opposite one another. If the successive pairs of leaves be placed at right angles to one another, the arrange­ment is termed opposite decussate .

In this case, when looked from the top, all the leaves will be found to be arranged along four vertical rows. This is found in Calotropis, Gardenia, Ixora, etc.

In some other plants it is found that the successive pairs are placed exactly on top of one another so that all the leaves lie in one plane and when viewed from above all the leaves are found to lie in two vertical rows.

This type of phyllo­taxy is known as opposite superposed . It should be noted that while the superposed type is found in many plants like Psidium guyava (guava), Quisqualis, etc., in many instances the phyllotaxy is initially decussate which later becomes superposed by the flattening out of the twig.

(B) Verticillate Phyllotaxy:

Nerium odorum shows three leaves forming a whorl at each node while Alstonia scholaris shows five or more leaves. These are instances of the verticillate type. Sometimes verticillate phyllotaxy is designated as whorled phyllotaxy.

B. Spiral or Alternate or Acyclic Phyllotaxy:

This is the commonest type of phyllotaxy and the mathematical regula­rity of the arrangement is astonishing. One can easily verify that (1) the angular distance (angular divergence) between any two consecutive leaves is constant (2) when looked from the top, all the leaves are found to lie in a fixed number of vertical rows or orthostichies (3) the orthostichies are evenly dispersed on a circle, the angle between adjacent orthostichies being cons­tant (4) although leaves look scattered, a close examination shows that leaves are evenly dispersed on all sides of the stem.

To correctly understand the plan of a spiral phyllotaxy one has to imagine a line touching the bases of successive leaves. It will be found that this line forms a spiral (hence the name spiral phyllotaxy) on the stem. This spiral is called the genetic spiral .

This genetic spiral can easily be projected on a flat surface to form a fiat spiral and the position of the leaves may be marked on this spiral. The angle subten­ded at the centre by two consecutive leaves is the angular divergence. In practice, the angular divergence may be denoted by finding out a leaf which is exactly above a particular leaf, then by counting the number of complete circles covered by the genetic spiral and the number of leaves beginning from the first to the one just before the last. The latter number of leaves -also gives the number of orthostichies. Thus,

Sometimes, only the above fraction is given without calculating the actual divergence in degrees.

A few instances will clarify the issue:

(1) Distichous or ½ Phyllotaxy:

In the family Gramineae (e.g., Cynodon, rice) the leaf on the second node is just opposite the leaf on the first node, the third leaf is above the first leaf, the fourth above the second and so on (Figs. 156A & 157A). Thus, the angular divergence is clearly 180° (straight angle) and all the leaves fall in two oppo­site orthostichies (hence, the name distichous). The genetic spiral covers only one circle and there are two leaves on the way in coming to the leaf exactly above the first leaf.

Hence, the angular divergence = of 360º = 180º. As only the fraction is usually given, the phyllotaxy is also called ½ phyllotaxy.

(2) Tristichous or 1/3 Phyllotaxy:

In the common sedge (Cyperus rotundus) the leaves are three-ranked (three orthostichies) the fourth leaf is above the first leaf, fifth above second, sixth above third and so on. Three leaves lie in one circle of the genetic spiral. Hence, angular divergence = 1/8 of 360° = 120° or 1/8 phyllotaxy.

(3) Pentastichous or 2/5 Phyllotaxy:

In many common plants like the china-rose and banyan, the 6th leaf is found above the 1st leaf, 7th above the 2nd and so on. The genetic spiral completes two circles in passing these five leaves or five orthostichies . Hence, angular divergence = 2/5 of 360° = 144° or 2/5 phyllotaxy.

(4) Octastichous or 3/8 Phyllotaxy:

In this case the ninth leaf is found above the first leaf and the genetic spiral completes three circles in this distance as in the case of the papaw (Carica papaya). Thus, there are eight orthostichies . The angular divergence is f of 360° = 135º.

It is rather interesting to note that in the common types of phyllotaxy the fractions of angular divergence lie in a series in which the numerator and the denominator in each
case are obtained by adding up the numerators and denominators of the two preceding phyllotaxies. Thus,

This series is called the fibonacci series or the Schimper-Brown series of divergence.

When the divergence becomes a big fraction it is not possible to count the orthosti­chies.

In plants showing these phyllotaxies, usually the internodes are very short so that the leaves are much crowded together. On date and other palms with persistent leaf bases showing such complex phyllotaxy one very close spiral of leaf bases is observed.

This type of phyllotaxy is called parastichous . The sporophylls on a pine cone are also arranged in the same way and the parastichous arrangement can be seen clearly when the cone is viewed from above .

Besides the fibonacci series, which is by far the commonest, there are possibly some other series of phyllotaxy. Two such rare series 1/4, 1/5, 2/8, 3/14…. and 1/2, 2/8, 2/5, 5/8, 8/18…The laws of phyllotaxy may sometimes be disturbed by some torsion of the stem or by incomplete development as towards the apex of a twig.

3.2 Cell Structures

Your body is made up of trillions of cells, but all of them perform the same basic life functions. They all obtain and use energy, respond to the environment, and reproduce. How do your cells carry out these basic functions and keep themselves—and you—alive? To answer these questions, you need to know more about the structures that make up cells.

A Tour of the Cell (Bozeman Science):


In some ways, a cell resembles a plastic bag full of Jell-O. Its basic structure is a plasma membrane filled with cytoplasm. Like Jell-O containing mixed fruit, the cytoplasm of the cell also contains various structures, such as a nucleus and other organelles. Figure below shows the structures inside a typical eukaryotic cell, in this case the cell of an animal. Refer to the figure as you read about the structures below. You can also explore the structures of an interactive animal cell at this link:


The plasma membrane forms a barrier between the cytoplasm inside the cell and the environment outside the cell. It protects and supports the cell and also controls everything that enters and leaves the cell. It works sort of like an international border. Only some things may enter the country (cell). The customs officials that choose what can and cannot come in are proteins. The plasma membrane allows only certain substances to pass through, while keeping others in or out. The ability to allow only certain molecules in or out of the cell is referred to as selective permeability or semipermeability. To understand how the plasma membrane controls what crosses into or out of the cell, you need to know its composition.

The plasma membrane is discussed at (6:16). The cell wall (see below) is also discussed in this video.

The Phospholipid Bilayer

The plasma membrane is composed mainly of phospholipids, which consist of fatty acids and alcohol. The phospholipids in the plasma membrane are arranged in two layers, called a phospholipid bilayer. As shown in Figure below (skip past the two root word alerts to see it), each phospholipid molecule has a head and two tails. The head “loves” water (hydrophilic),

and the tails “hate” water (hydrophobic).

The water-hating tails are on the interior of the membrane, whereas the water-loving heads point outwards, toward either the cytoplasm or the fluid that surrounds the cell. Molecules that are hydrophobic can easily pass through the plasma membrane, if they are small enough, because they are water-hating like the interior of the membrane. Molecules that are hydrophilic, on the other hand, cannot pass through the plasma membrane—at least not without help—because they are water-loving like the exterior of the membrane.

Other Molecules in the Plasma Membrane

The plasma membrane also contains other molecules, primarily other lipids and proteins. The green molecules in Figure above, for example, are the lipid cholesterol. Molecules of cholesterol help the plasma membrane keep its shape. Many of the proteins in the plasma membrane assist other substances in crossing the membrane.

Extensions of the Plasma Membrane

The plasma membrane may have extensions, such as whip-like flagella or brush-like cilia. In single-celled organisms, like those shown in Figure below, the membrane extensions may help the organisms move. In multicellular organisms, the extensions have other functions. For example, the cilia on human lung cells sweep foreign particles and mucus toward the mouth and nose.

The Cell Membrane (Bozeman Science):


The cytoplasm consists of everything inside the plasma membrane of the cell. It includes the watery, gel-like material called cytosol, as well as various structures. The water in the cytoplasm makes up about two thirds of the cell’s weight and gives the cell many of its properties.

Functions of the Cytoplasm

The cytoplasm has several important functions, including

  1. suspending cell organelles
  2. pushing against the plasma membrane to help the cell keep its shape
  3. providing a site for many of the biochemical reactions of the cell


Crisscrossing the cytoplasm is a structure called the cytoskeleton, which consists of thread-like filaments and tubules. You can see these filaments and tubules in the cells in Figure below. As its name suggests, the cytoskeleton is like a cellular “skeleton.” It helps the cell maintain its shape and also holds cell organelles in place within the cytoplasm.

The cytoskeleton is discussed in the following video (4:50).


Eukaryotic cells contain a nucleus and several other types of organelles. These structures are involved in many vital cell functions.

The Nucleus

The nucleus is the largest organelle in a eukaryotic cell and is often considered to be the cell’s control center. This is because the nucleus controls which proteins the cell makes. The nucleus of a eukaryotic cell contains most of the cell’s DNA, which makes up chromosomes and is encoded with genetic instructions for making proteins.


The mitochondrion (plural, mitochondria) is an organelle that makes energy available to the cell. This is why mitochondria are sometimes referred to as the power plants of the cell. They use energy from organic compounds such as glucose to make molecules of ATP (adenosine triphosphate), an energy-carrying molecule that is used almost universally inside cells for energy.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is an organelle that helps make and transport proteins and lipids. There are two types of endoplasmic reticulum: rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER). Both types are shown in Figure below.

  • RER looks rough because it is studded with ribosomes. It provides a framework for the ribosomes, which make proteins. Bits of its membrane pinch off to form tiny sacs called vesicles, which carry proteins away from the ER.
  • SER looks smooth because it does not have ribosomes. SER also makes lipids, stores substances, and plays other roles.


Ribosomes are small organelles where proteins are made. They contain the nucleic acid RNA, which assembles and joins amino acids to make proteins. Ribosomes can be found alone or in groups within the cytoplasm as well as on the RER.

Golgi Apparatus

The Golgi apparatus is a large organelle that processes proteins and prepares them for use both inside and outside the cell. It is shown in Figure below. The Golgi apparatus is somewhat like a post office. It receives items (proteins from the ER), packages and labels them, and then sends them on to their destinations (to different parts of the cell or to the cell membrane for transport out of the cell). The Golgi apparatus is also involved in the transport of lipids around the cell. At the link below, you can watch an animation showing how the Golgi apparatus does all these jobs.

This drawing includes the nucleus, RER, SER, and Golgi apparatus. From the drawing, you can see how all these organelles work together to make and transport proteins.

Vesicles and Vacuoles

Both vesicles and vacuoles are sac-like organelles that store and transport materials in the cell. Vesicles are much smaller than vacuoles and have a variety of functions. The vesicles that pinch off from the membranes of the ER and Golgi apparatus (see Figure above) store and transport protein and lipid molecules. Some vesicles are used as chambers for biochemical reactions. Other vesicles include:

  • Lysosomes, which use enzymes to break down foreign matter and dead cells.
  • Peroxisomes, which use oxygen to break down poisons.


Centrioles are organelles involved in cell division. They help organize the chromosomes before cell division so that each daughter cell has the correct number of chromosomes after the cell divides. Centrioles are found only in animal cells and are located near the nucleus (see Figure above).

Cellular Organelles (Bozeman Science)


Plant cells have several structures that are not found in animal cells, including a cell wall, a large central vacuole, and organelles called plastids. You can see each of these structures in Figure below. You can also view them in an interactive plant cell at the link below.

Cell Wall

The cell wall is a rigid layer that surrounds the plasma membrane of a plant cell. It supports and protects the cell. Tiny holes, or pores, in the cell wall allow water, nutrients, and other substances to move into and out of the cell. The cell wall is made up mainly of complex carbohydrates, including cellulose.

Central Vacuole

Most mature plant cells have a large central vacuole. This vacuole can make up as much as 90% of the cell’s volume. The central vacuole has a number of functions, including storing substances such as water, enzymes, and salts. It also helps plant tissues, such as stems and leaves, stay rigid and hold their shape. It even helps give flowers, like the ones in Figure below, their beautiful colors.


Plastids are organelles in plant cells that carry out a variety of different functions. The main types of plastids and their functions are described below.

  • Chloroplasts are plastids that contain the green pigment chlorophyll. They capture light energy from the sun and use it to make food. A chloroplast is shown in Figure above.
  • Chromoplasts are plastids that make and store other pigments. The red pigment that colors the flower petals in Figure above was made by chromoplasts.
  • Leucoplasts are plastids that store substances such as starch or make small molecules such as amino acids.

Like mitochondria, plastids contain their own DNA.

Organization of Cells

Cells can exist as individual cells or as groups of cells. Cells in groups can be organized at several levels.

From One Cell to Many

The simplest level of cell organization is a single-celled organism, and the most complex level is a multicellular organism. In between these two levels are biofilms and colonies.

  • A single-celled organism floats freely and lives independently. Its single cell is able to carry out all the processes of life without any help from other cells.
  • A biofilm is a thin layer of bacteria that sticks to a surface. Cells in a biofilm are all alike, but they may play different roles, such as taking in nutrients or making the “glue” that sticks the biofilm to the surface. The sticky plaque that forms on teeth is a biofilm of bacterial cells.
  • Some single-celled organisms, such as algae, live in colonies. A colony is an organized structure composed of many cells, like the Volvox sphere in Figure below. Volvox are algae that live in colonies of hundreds of cells. All of the cells in the colony live and work cooperatively. For example, they can coordinate the movement of their flagella, allowing them to swim together through the water as though they were part of a single organism.
  • A multicellular organism consists of many cells and has different types of cells that are specialized for various functions. All the cells work together and depend on each other to carry out the life processes of the organism. Individual cells are unable to survive on their own.

Levels of Organization in Multicellular Organisms

There are multicellular organisms at all levels of organization, from the simplest, cell level of organization to the most complex, organ-system level of organization. Consider these examples:

  • Sponges have cell-level organization, in which different cells are specialized for different functions, but each cell works alone. For example, some cells digest food, while other cells let water pass through the sponge.
  • Jellyfish have tissue-level organization, in which groups of cells of the same kind that do the same job form tissues. For example, jellyfish have some tissues that digest food and other tissues that sense the environment.
  • Roundworms have organ-level organization, in which two or more types of tissues work together to perform a particular function as an organ. For example, a roundworm has a primitive brain that controls how the organism responds to the environment.
  • Human beings have organ system-level organization, in which groups of organs work together to do a certain job, with each organ doing part of the overall task. An example is the human digestive system. Each digestive system organ—from the mouth to the small intestine—does part of the overall task of breaking down food and absorbing nutrients.


  • The plasma membrane is a phospholipid bilayer that supports and protects a cell and controls what enters and leaves it.
  • The cytoplasm consists of everything inside the plasma membrane, including watery cytosol and organelles. The cytoplasm suspends the organelles and does other jobs. The cytoskeleton crisscrosses the cytoplasm and gives the cell an internal framework.
  • The nucleus is the largest organelle in a eukaryotic cell and contains most of the cell’s DNA. Other organelles in eukaryotic cells include the mitochondria, endoplasmic reticulum, ribosomes, Golgi apparatus, vesicles, vacuoles, and centrioles (in animal cells only). Each type of organelle has important functions in the cell.
  • Plant cells have special structures that are not found in animal cells, including a cell wall, a large central vacuole, and organelles called plastids.
  • Cells can exist independently as single-celled organisms or with other cells as multicellular organisms. Cells of a multicellular organism can be organized at the level of cells, tissues, organs, and organ systems.



1. Describe the composition of the plasma membrane.

2. List functions of the cytoplasm and cytoskeleton.

3. What is the role of the nucleus of a eukaryotic cell?

4. List three structures that are found in plant cells but not in animal cells.

5. Outline the levels of organization of cells in living things, starting with the simplest level, that of single-celled organisms.

Apply Concepts

6. Create a diagram to show how the cells of multicellular organisms may be organized at different levels, from the level of the cell to the level of the organ system. Give an example of a multicellular organism at each level of organization.

Think Critically

7. Explain why hydrophobic (“water-hating”) molecules can easily cross the plasma membrane, while hydrophilic (“water-loving”) molecules cannot.

8. Explain how the following organelles ensure that a cell has the proteins it needs: nucleus, rough and smooth ER, vesicles, and Golgi apparatus.


Cells carry out all the functions of life, and they use nutrients and oxygen and produce wastes. These substances must cross the plasma membrane.

Related Biology Terms

  • Stomata – Small holes on the bottom of plant leaves that are used for gas exchange.
  • Xylem – Tissue in plants that transports water and some nutrients from a plant’s roots to the rest of the plant.
  • Lenticel – A small pore in the bark of a plant.
  • Evapotranspiration – Evaporation of water from oceans, rivers and lakes, as well as from plants via transpiration.

1. Which is NOT a type of transpiration?
A. Lenticular transpiration
B. Mesarchal transpiration
C. Cuticular transpiration
D. Stomatal transpiration

2. When temperature increases, what happens to the rate of transpiration?
A. Transpiration increases.
B. Transpiration decreases.
C. Transpiration stays at the same rate.

3. When _____________ increases, the rate of transpiration decreases.
A. Wind
B. Moisture in soil
C. Moisture in air
D. Temperature

3.2: Leaves - Biology

Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs) and leaving as heat during energy transformation between trophic levels. Rather than flowing through an ecosystem, the matter that makes up organisms is conserved and recycled. The six most common elements associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and may exist for long periods in the atmosphere, on land, in water, or beneath Earth’s surface. Geologic processes, such as weathering, erosion, water drainage, and the subduction of the continental plates, all play a role in the cycling of elements on Earth. Because geology and chemistry have major roles in the study of these processes, the recycling of inorganic matter between living organisms and their nonliving environment are called biogeochemical cycles.

The six aforementioned elements are used by organisms in a variety of ways. Hydrogen and oxygen are found in water and organic molecules, both of which are essential to life. Carbon is found in all organic molecules, whereas nitrogen is an important component of nucleic acids and proteins. Phosphorus is used to make nucleic acids and the phospholipids that comprise biological membranes. Lastly, sulfur is critical to the three-dimensional shape of proteins.

The cycling of these elements is interconnected. For example, the movement of water is critical for the leaching of sulfur and phosphorus into rivers, lakes, and oceans. Minerals cycle through the biosphere between the biotic and abiotic components and from one organism to another.

Head to this website to learn more about biogeochemical cycles

The Water Cycle

The hydrosphere is the area of Earth where water movement and storage occurs: as liquid water on the surface (rivers, lakes, oceans) and beneath the surface (groundwater) or ice, (polar ice caps and glaciers), and as water vapor in the atmosphere.The human body is about 60 percent water and human cells are more than 70 percent water. Of the stores of water on Earth, 97.5 percent is salt water (see Figure 1 below). Of the remaining water, more than 99 percent is groundwater or ice. Thus, less than one percent of freshwater is present in lakes and rivers. Many organisms are dependent on this small percentage, a lack of which can have negative effects on ecosystems. Humans, of course, have developed technologies to increase water availability, such as digging wells to harvest groundwater, storing rainwater, and using desalination to obtain drinkable water from the ocean. Although this pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water continues to be a major issue in modern times.

Figure 1. Only 2.5 percent of water on Earth is fresh water, and less than 1 percent of fresh water is easily accessible to living things.

The various processes that occur during the cycling of water are illustrated in Figure 2 below. The processes include the following:

  • evaporation and sublimation
  • condensation and precipitation
  • subsurface water flow
  • surface runoff and snowmelt
  • streamflow

The water cycle is driven by the Sun’s energy as it warms the oceans and other surface waters. This leads to evaporation (liquid water to water vapor) of liquid surface water and sublimation (ice to water vapor) of frozen water, thus moving large amounts of water into the atmosphere as water vapor. Over time, this water vapor condenses into clouds as liquid or frozen droplets and eventually leads to precipitation (rain, snow, hail), which returns water to Earth’s surface. Rain reaching Earth’s surface may evaporate again, flow over the surface, or percolate into the ground. Most easily observed is surface runoff: the flow of freshwater over land either from rain or melting ice. Runoff can make its way through streams and lakes to the oceans.

In most natural terrestrial environments rain encounters vegetation before it reaches the soil surface. A significant percentage of water evaporates immediately from the surfaces of plants. What is left reaches the soil and begins to move down. Surface runoff will occur only if the soil becomes saturated with water in a heavy rainfall. Water in the soil can be taken up by plant roots. The plant will use some of this water for its own metabolism and some of that will find its way into animals that eat the plants, but much of it will be lost back to the atmosphere through a process known as transpiration: water enters the vascular system of plants through the roots and evaporates, or transpires, through the stomata (small microscope openings) of the leaves. Ecologists combine transpiration and evaporation into a single term that describes water returned to the atmosphere: evapotranspiration. Water in the soil that is not taken up by a plant and that does not evaporate is able to percolate into the subsoil and bedrock where it forms groundwater.

Groundwater is a significant, subsurface reservoir of fresh water. It exists in the pores between particles in dirt, sand, and gravel or in the fissures in rocks. Groundwater can flow slowly through these pores and fissures and eventually finds its way to a stream or lake where it becomes part of the surface water again. Many streams flow not because they are replenished from rainwater directly but because they receive a constant inflow from the groundwater below. Some groundwater is found very deep in the bedrock and can persist there for millennia. Most groundwater reservoirs, or aquifers, are the source of drinking or irrigation water drawn up through wells. In many cases these aquifers are being depleted faster than they are being replenished by water percolating down from above.

Head to this website to learn more about the world’s fresh water supply.

Rain and surface runoff are major ways in which minerals, including phosphorus and sulfur, are cycled from land to water. The environmental effects of runoff will be discussed later as these cycles are described.

Figure 2. Water from the land and oceans enters the atmosphere by evaporation or sublimation, where it condenses into clouds and falls as rain or snow. Precipitated water may enter freshwater bodies or infiltrate the soil. The cycle is complete when surface or groundwater reenters the ocean. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

The Carbon Cycle

Carbon is the second most abundant element in organisms, by mass. Carbon is present in all organic molecules (and some molecules that are not organic such as CO2), and its role in the structure of biomolecules is of primary importance. Carbon compounds contain energy, and many of these compounds from dead plants and algae have fossilized over millions of years and are known as fossil fuels. Since the 1800s, the use of fossil fuels has accelerated. Since the beginning of the Industrial Revolution the demand for Earth’s limited fossil fuel supplies has risen, causing the amount of carbon dioxide in our atmosphere to drastically increase. This increase in carbon dioxide is associated with climate change and is a major environmental concern worldwide.

The carbon cycle is most easily studied as two interconnected subcycles: one dealing with rapid carbon exchange among living organisms and the other dealing with the long-term cycling of carbon through geologic processes. The entire carbon cycle is shown in Figure 3 below.

Figure 3. Carbon dioxide gas exists in the atmosphere and is dissolved in water. Photosynthesis converts carbon dioxide gas to organic carbon, and respiration cycles the organic carbon back into carbon dioxide gas. Long-term storage of organic carbon occurs when matter from living organisms is buried deep underground and becomes fossilized. Volcanic activity and, more recently, human emissions bring this stored carbon back into the carbon cycle. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

The Biological Carbon Cycle

Organisms are connected in many ways, even among different ecosystems. A good example of this connection is the exchange of carbon between heterotrophs and autotrophs by way of atmospheric carbon dioxide. Carbon dioxide (CO2) is the basic building block that autotrophs use to build high-energy compounds such as glucose. The energy harnessed from the Sun is used by these organisms to form the covalent bonds that link carbon atoms together. These chemical bonds store this energy for later use in the process of respiration. Most terrestrial autotrophs obtain their carbon dioxide directly from the atmosphere, while marine autotrophs acquire it in the dissolved form (carbonic acid, HCO3 – ).

Carbon is passed from producers to higher trophic levels through consumption. For example, when a cow (primary consumer) eats grass (producer), it obtains some of the organic molecules originally made by the plant’s photosynthesis. Those organic compounds can then be passed to higher trophic levels, such as humans, when we eat the cow. At each level, however, organisms are performing respiration, a process in which organic molecules are broken down to release energy. As these organic molecules are broken down, carbon is removed from food molecules to form CO2, a gas that enters the atmosphere. Thus, CO2 is a byproduct of respiration. Recall that CO2 is consumed by producers during photosynthesis to make organic molecules. As these molecules are broken down during respiration, the carbon once again enters the atmosphere as CO2. Carbon exchange like this potentially connects all organisms on Earth. Think about this: the carbon in your DNA was once part of plant millions of years ago perhaps it was part of dinosaur.

The Biogeochemical Carbon Cycle

The movement of carbon through land, water, and air is complex, and, in many cases, it occurs much more slowly than the movement between organisms. Carbon is stored for long periods in what are known as carbon reservoirs, which include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil, rocks (including fossil fuels), and Earth’s interior.

As stated, the atmosphere is a major reservoir of carbon in the form of carbon dioxide that is essential to the process of photosynthesis. The level of carbon dioxide in the atmosphere is greatly influenced by the reservoir of carbon in the oceans. The exchange of carbon between the atmosphere and water reservoirs influences how much carbon is found in each. Carbon dioxide (CO2) from the atmosphere dissolves in water and reacts with water molecules to form ionic compounds. Some of these ions combine with calcium ions in the seawater to form calcium carbonate (CaCO3), a major component of the shells of marine organisms. These organisms eventually die and their shells form sediments on the ocean floor. Over geologic time, the calcium carbonate forms limestone, which comprises the largest carbon reservoir on Earth.

On land, carbon is stored in soil as organic carbon as a result of the decomposition of organisms or from weathering of terrestrial rock and minerals (the world’s soils hold significantly more carbon than the atmosphere, for comparison). Deeper underground are fossil fuels, the anaerobically decomposed remains of plants and algae that lived millions of years ago. Fossil fuels are considered a non-renewable resource because their use far exceeds their rate of formation. A non-renewable resource is either regenerated very slowly or not at all. Another way for carbon to enter the atmosphere is from land (including land beneath the surface of the ocean) by the eruption of volcanoes and other geothermal systems. Carbon sediments from the ocean floor are taken deep within Earth by the process of subduction: the movement of one tectonic plate beneath another. Carbon is released as carbon dioxide when a volcano erupts or from volcanic hydrothermal vents.

Click this link to read information about the United States Carbon Cycle Science Program.

The Nitrogen Cycle

Getting nitrogen into living organisms is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the atmosphere (where it exists as tightly bonded, triple covalent N2) even though this molecule comprises approximately 78 percent of the atmosphere. Nitrogen enters the living world through free-living and symbiotic bacteria, which incorporate nitrogen into their organic molecules through specialized biochemical processes. Certain species of bacteria are able to perform nitrogen fixation, the process of converting nitrogen gas into ammonia (NH3), which spontaneously becomes ammonium (NH4 + ). Ammonium is converted by bacteria into nitrites (NO2 − ) and then nitrates (NO3 − ). At this point, the nitrogen-containing molecules are used by plants and other producers to make organic molecules such as DNA and proteins. This nitrogen is now available to consumers.

Organic nitrogen is especially important to the study of ecosystem dynamics because many ecosystem processes, such as primary production, are limited by the available supply of nitrogen. As shown in Figure 4 below, the nitrogen that enters living systems is eventually converted from organic nitrogen back into nitrogen gas by bacteria (Figure 4). The process of denitrification is when bacteria convert the nitrates into nitrogen gas, thus allowing it to re-enter the atmosphere.

Figure 4. Nitrogen enters the living world from the atmosphere via nitrogen-fixing bacteria. This nitrogen and nitrogenous waste from animals is then processed back into gaseous nitrogen by soil bacteria, which also supply terrestrial food webs with the organic nitrogen they need. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

Human activity can alter the nitrogen cycle by two primary means: the combustion of fossil fuels, which releases different nitrogen oxides, and by the use of artificial fertilizers (which contain nitrogen and phosphorus compounds) in agriculture, which are then washed into lakes, streams, and rivers by surface runoff. Atmospheric nitrogen (other than N2) is associated with several effects on Earth’s ecosystems including the production of acid rain (as nitric acid, HNO3) and greenhouse gas effects (as nitrous oxide, N2O), potentially causing climate change. A major effect from fertilizer runoff is saltwater and freshwater eutrophication, a process whereby nutrient runoff causes the overgrowth of algae, the depletion of oxygen, and death of aquatic fauna.

In marine ecosystems, nitrogen compounds created by bacteria, or through decomposition, collects in ocean floor sediments. It can then be moved to land in geologic time by uplift of Earth’s crust and thereby incorporated into terrestrial rock. Although the movement of nitrogen from rock directly into living systems has been traditionally seen as insignificant compared with nitrogen fixed from the atmosphere, a recent study showed that this process may indeed be significant and should be included in any study of the global nitrogen cycle.

The Phosphorus Cycle

Phosphorus is an essential nutrient for living processes. It is a major component of nucleic acids and phospholipids, and, as calcium phosphate, it makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in aquatic, particularly freshwater, ecosystems.

Phosphorus occurs in nature as the phosphate ion (PO4 3- ). In addition to phosphate runoff as a result of human activity, natural surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus sending phosphates into rivers, lakes, and the ocean. This rock has its origins in the ocean. Phosphate-containing ocean sediments form primarily from the bodies of ocean organisms and from their excretions. However, volcanic ash, aerosols, and mineral dust may also be significant phosphate sources. This sediment then is moved to land over geologic time by the uplifting of Earth’s surface. (Figure below)

Phosphorus is also reciprocally exchanged between phosphate dissolved in the ocean and marine organisms. The movement of phosphate from the ocean to the land and through the soil is extremely slow, with the average phosphate ion having an oceanic residence time between 20,000 and 100,000 years.

Figure 5. In nature, phosphorus exists as the phosphate ion (PO43-). Weathering of rocks and volcanic activity releases phosphate into the soil, water, and air, where it becomes available to terrestrial food webs. Phosphate enters the oceans in surface runoff, groundwater flow, and river flow. Phosphate dissolved in ocean water cycles into marine food webs. Some phosphate from the marine food webs falls to the ocean floor, where it forms sediment. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

Excess phosphorus and nitrogen that enter these ecosystems from fertilizer runoff and from sewage cause excessive growth of algae. The subsequent death and decay of these organisms depletes dissolved oxygen, which leads to the death of aquatic organisms such as shellfish and fish. This process is responsible for dead zones in lakes and at the mouths of many major rivers and for massive fish kills, which often occur during the summer months (see Figure 6 below).

Figure 6. Dead zones occur when phosphorus and nitrogen from fertilizers cause excessive growth of microorganisms, which depletes oxygen and kills fauna. Worldwide, large dead zones are found in coastal areas of high population density. (credit: NASA Earth Observatory)

A dead zone is an area in lakes and oceans near the mouths of rivers where large areas are periodically depleted of their normal flora and fauna. These zones are caused by eutrophication coupled with other factors including oil spills, dumping toxic chemicals, and other human activities. The number of dead zones has increased for several years, and more than 400 of these zones were present as of 2008. One of the worst dead zones is off the coast of the United States in the Gulf of Mexico: fertilizer runoff from the Mississippi River basin created a dead zone of over 8,463 square miles. Phosphate and nitrate runoff from fertilizers also negatively affect several lake and bay ecosystems including the Chesapeake Bay in the eastern United States.

This (a) satellite image shows the Chesapeake Bay, an ecosystem affected by phosphate and nitrate runoff. A (b) member of the Army Corps of Engineers holds a clump of oysters being used as a part of the oyster restoration effort in the bay. (credit a: modification of work by NASA/MODIS credit b: modification of work by U.S. Army)

The Chesapeake Bay has long been valued as one of the most scenic areas on Earth it is now in distress and is recognized as a declining ecosystem. In the 1970s, the Chesapeake Bay was one of the first ecosystems to have identified dead zones, which continue to kill many fish and bottom-dwelling species, such as clams, oysters, and worms. Several species have declined in the Chesapeake Bay due to surface water runoff containing excess nutrients from artificial fertilizer used on land. The source of the fertilizers (with high nitrogen and phosphate content) is not limited to agricultural practices. There are many nearby urban areas and more than 150 rivers and streams empty into the bay that are carrying fertilizer runoff from lawns and gardens. Thus, the decline of the Chesapeake Bay is a complex issue and requires the cooperation of industry, agriculture, and everyday homeowners.

Of particular interest to conservationists is the oyster population it is estimated that more than 200,000 acres of oyster reefs existed in the bay in the 1700s, but that number has now declined to only 36,000 acres. Oyster harvesting was once a major industry for Chesapeake Bay, but it declined 88 percent between 1982 and 2007. This decline was due not only to fertilizer runoff and dead zones but also to overharvesting. Oysters require a certain minimum population density because they must be in close proximity to reproduce. Human activity has altered the oyster population and locations, greatly disrupting the ecosystem.

The restoration of the oyster population in the Chesapeake Bay has been ongoing for several years with mixed success. Not only do many people find oysters good to eat, but they also clean up the bay. Oysters are filter feeders, and as they eat, they clean the water around them. In the 1700s, it was estimated that it took only a few days for the oyster population to filter the entire volume of the bay. Today, with changed water conditions, it is estimated that the present population would take nearly a year to do the same job.

Restoration efforts have been ongoing for several years by non-profit organizations, such as the Chesapeake Bay Foundation. The restoration goal is to find a way to increase population density so the oysters can reproduce more efficiently. Many disease-resistant varieties (developed at the Virginia Institute of Marine Science for the College of William and Mary) are now available and have been used in the construction of experimental oyster reefs. Efforts to clean and restore the bay by Virginia and Delaware have been hampered because much of the pollution entering the bay comes from other states, which stresses the need for inter-state cooperation to gain successful restoration.

The new, hearty oyster strains have also spawned a new and economically viable industry—oyster aquaculture—which not only supplies oysters for food and profit, but also has the added benefit of cleaning the bay.

The Sulfur Cycle

Sulfur is an essential element for the molecules of living things. As part of the amino acid cysteine, it is involved in the formation of proteins. As shown in Figure 7 below, sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is found in the form of sulfur dioxide (SO2), which enters the atmosphere in three ways: first, from the decomposition of organic molecules second, from volcanic activity and geothermal vents and, third, from the burning of fossil fuels by humans.

Figure 7. Sulfur dioxide from the atmosphere becomes available to terrestrial and marine ecosystems when it is dissolved in precipitation as weak sulfuric acid or when it falls directly to Earth as fallout. Weathering of rocks also makes sulfates available to terrestrial ecosystems. Decomposition of living organisms returns sulfates to the ocean, soil, and atmosphere. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and geothermal vents. Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere, sulfur is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly from the atmosphere in a process called fallout. Also, as sulfur-containing rocks weather, sulfur is released into the soil. These rocks originate from ocean sediments that are moved to land by the geologic uplifting of ocean sediments. Terrestrial ecosystems can then make use of these soil sulfates (SO4 2- ), which enter the food web by being taken up by plant roots. When these plants decompose and die, sulfur is released back into the atmosphere as hydrogen sulfide (H2S) gas.

Sulfur enters the ocean in runoff from land, from atmospheric fallout, and from underwater geothermal vents. Some ecosystems rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine ecosystems in the form of sulfates.

Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large quantities of fossil fuels, especially from coal, releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls through this gas, it creates the phenomenon known as acid rain, which damages the natural environment by lowering the pH of lakes, thus killing many of the resident plants and animals. Acid rain is corrosive rain caused by rainwater falling to the ground through sulfur dioxide gas, turning it into weak sulfuric acid, which causes damage to aquatic ecosystems. Acid rain also affects the man-made environment through the chemical degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial in Washington, DC, have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects of human activities on our environment and the challenges that remain for our future.

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Biogeochemical Cycles by OpenStax is licensed under CC BY 4.0. Modified from the original by Matthew R. Fisher.

Section Summary

Leaves are the main site of photosynthesis. A typical leaf consists of a lamina (the broad part of the leaf, also called the blade) and a petiole (the stalk that attaches the leaf to a stem). The arrangement of leaves on a stem, known as phyllotaxy, enables maximum exposure to sunlight. Each plant species has a characteristic leaf arrangement and form. The pattern of leaf arrangement may be alternate, opposite, or spiral, while leaf form may be simple or compound. Leaf tissue consists of the epidermis, which forms the outermost cell layer, and mesophyll and vascular tissue, which make up the inner portion of the leaf. In some plant species, leaf form is modified to form structures such as tendrils, spines, bud scales, and needles.

Watch the video: Leaves on Roads - Tue on (May 2022).


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