Download Describing Matter

Name: _______________________
Date: ________________________
Flynt - _____ Period
___th Grade Science
Connection: What
are the 5 main gases
that make up the
atmosphere?
Main Idea: What
are 4 examples of
how nitrogen is
important to living
things?
Vocab: What is a
nutrient?
Connection: Can
you think of any
other nutrients?
Review: The prefix
“di-” means
_______.
Review: What are
eukaryotes?
Vocab: What is a
compound?
Connection: Can
you list any other
examples of
compounds?
Vocab: What is
Nitrogen Fixation?
Summary:
As you already know, ____________________ is the most abundant gas
in Earth’s atmosphere. You also know that nitrogen is essential to all living
things. Nitrogen is found in nucleic acids like DNA and RNA, which are
molecules that carry the genetic code and allow inheritable traits to be passed
down from one generation to the next. Nucleic acids also serve as the blueprints
of life, as they carry instructions for building proteins and enzymes, as well as
the directions for numerous cell structures and processes. Proteins and
enzymes, in turn, are also made up of nitrogen. Protein and enzymes serve as
the workhorses and building blocks of many cell structures and processes.
Therefore, all organisms need nitrogen in order to build cell structures, carry
out cellular processes, repair worn out cell parts, and make new cells (growth
and reproduction). In plants, nitrogen is also part of chlorophyll (klor-oh-fill),
the green pigment of the plant that is responsible for photosynthesis!
Nitrogen is a great example of a nutrient (noo-tree-int). A nutrient is a
substance that an organism must have in order to survive, but cannot make on
its own. So if organisms cannot make their own nitrogen, how do they get it?
Every time you take a breath, you are breathing in nitrogen gas (N2). In
fact, _____% of each breath that you take is composed of nitrogen gas.
Nitrogen gas in the atmosphere is made of two nitrogen atoms joined together;
thus, it is sometimes called di-nitrogen gas. It is also sometimes called
molecular nitrogen, since molecules are substances made of two or more
atoms joined together (even if they are the same type of atom). Unfortunately,
our bodies cannot absorb and use the di-nitrogen gas from the atmosphere. The
reason why has to do with the chemical properties of di-nitrogen gas. Molecular
nitrogen is often said to be inert, or unreactive. This is because of the strong
triple bond between the two nitrogen atoms; the triple bond
makes N2 molecules very difficult to break apart, and the
process of splitting molecular nitrogen is very “expensive”
energetically. Thus, while nitrogen is all around us in the
atmosphere, most organisms can’t “afford” to spend energy breaking dinitrogen molecules apart, and therefore never evolved the ability to do so.
Instead, all single-celled and multi-cellular eukaryotic organisms depend on
other organisms and natural processes to supply nitrogen compounds that CAN
be easily broken and recombined to form nucleic acids and proteins!
In order for organisms to obtain the nitrogen they need, the molecular
nitrogen first must be split so that each nitrogen atom can be recombined with
other atoms to form a nitrogen compound. A compound is a molecule made of
two or more different kinds of atoms joined together. The act of breaking the
triple bond in molecular nitrogen (N2) apart so that its atoms can combine with
other atoms to form new, biologically available nitrogen compounds is called
nitrogen fixation. And as you can imagine, breaking that triple bond requires
the input of a lot of energy; thus nitrogen fixation is very “expensive” in terms
of energy.
Page 2 of 9
Main Idea: What
are the three
methods of nitrogen
fixation?
NITROGEN FIXATION: Nitrogen fixation is the building up or “synthesis” part of the
nitrogen cycle! There are three ways that nitrogen can get fixed:
1. Atmospheric fixation (lightning fixation).
2. Biological fixation:
a. By symbiotic bacteria living in the root nodules of legumes
(Rhizobia).
b. By free-living bacteria in the soil or water (Azotobacter,
Cyanobacteria, and nitrifying bacteria).
3. Industrial/Anthropogenic Fixation (artificial fixation by humans).
Connection/Key
Concept: Which of
Earth’s “spheres”
interact in lightning
fixation?
Connection/Key
Concept: How is
the water cycle
connected to the
nitrogen cycle?
Micro =
Scopic =
Connect: What are
prokaryotic
organisms?
Main Idea: What is
the purpose of this
paragraph? (What
point is being
made?) 
Lightning fixation happens in the atmosphere and probably contributes around
5– 8% of the total fixed nitrogen cycling in the biosphere. Lightning is able to
provide the enormous amounts of energy needed to break nitrogen (N2) molecules
apart, enabling their atoms to combine with oxygen (O2) molecules in the air,
forming nitrogen oxides. These nitrogen oxides dissolve in rain and cloud droplets
in the atmosphere, forming a new nitrogen compound called nitrate (NO3-). The
nitrate then gets carried by precipitation like rain and snow to the ground, where it
can infiltrate into and percolate through the soil. Once it has soaked into the soil,
the nitrate can be absorbed (soaked up) by the roots of plants.
However, not all of the nitrate ends up in the soil. Nitrate can also be carried
by surface runoff into rivers, lakes, canals, and even back to the ocean. The
nitrogen can also become part of the groundwater and flow into aquifers in a
process called leaching.
Lightning fixation only produces a tiny bit of the fixed nitrogen that living
things need. Instead, most fixed nitrogen is produced by bacteria. In fact, bacteria
play a key role in the nitrogen cycle and making soil fertile. They convert
molecular nitrogen gas (N2) in Earth’s atmosphere into compounds like ammonium
(NH4+) or nitrate (NO3-), both of which can be absorbed by plants and algae and
then converted into organic macromolecules like proteins.
For a long time,
microbiologists thought that
bacteria were the only organisms
that were able to carry out
nitrogen fixation. Today, there is
growing evidence that some types
of Archaea can fix nitrogen as
well! Still, most of the fixed
nitrogen that cycles through the
biosphere (and especially through
land-based ecosystems) is
contributed by the activities of
nitrogen-fixing bacteria.
So just what are bacteria? Bacteria are tiny, microscopic, prokaryotic
organisms that are made up of only one cell. They are so small that hundreds of
thousands of bacteria would fit on a rounded dot made by a pencil ().
Summary
Page 3 of 9
Key Concept: What
are the two main
types of “fixed”
nitrogen that plants
can use?
Key Concept:
Which types of
organisms CAN and
CANNOT fix
nitrogen?
Sym =
Biotic =
Key Concept:
Legumes include
peas, soybeans,
peanuts, clover,
alfalfa, and lupine.
Connection: What
are the other types
of symbiotic
relationships?
Bacteria are some of the oldest organisms on Earth. The earliest bacteria
probably lived about 3.5 billion years ago, long before humans or other plants and
animals! Today, bacteria live all around us and within us. Bacteria live in the
deepest parts of the ocean and deep within Earth. They are in the soil, in our food,
and on plants and animals. Even our bodies—inside and out—are home to many
different kinds of bacteria. Our lives are closely intertwined with theirs, and the
health of our planet depends very much on their activities. While it is true that a
few types of bacteria can be harmful to humans and other mammals, most bacteria
are in no way harmful and instead are extremely important to
keeping our planet healthy!
Some of the bacteria that fix nitrogen live in a mutually
beneficial symbiotic (sim-by-ah-tik) relationship with certain
plants. Symbiotic literally means “living things living together.”
Plants in the legume (ley-goom) family—which includes
beans, peas, and clover—have special root structures called
nodules (nod-yewls). Nodules are bumpy growths housing
tens of thousands of symbiotic bacteria called Rhizobia (rhyzōh-bee-ya). The Rhizobia bacteria in the nodules “fix”
nitrogen for the legume, turning nitrogen (N2) gas into
ammonium (NH4+) that the legume can use. In return, the
legume makes glucose (and other carbohydrates) using
photosynthesis and shares its food with the bacteria in the nodules.
The symbiotic relationship between legumes and Rhizobia is mutualistic
(both organisms benefit). The legumes receive nitrogen in a form that can easily be
converted into nucleic acids and proteins, and the Rhizobia receive carbohydrates
produced by the legume during photosynthesis. However, the relationship is
actually much more complex than what is described here. Legumes and Rhizobia
have coevolved for hundreds of thousands of years; each type of legume hosts its
own unique species of Rhizobia, and therefore each type of legume has evolved
unique root nodule structures that are specific to the needs of their particular
species of Rhizobia.
Not all of the “fixed” nitrogen made by Rhizobia in the root nodules gets used
by the legume plant. Up until the time the legume begins producing flowers, the
root nodules my “leak” excess fixed nitrogen into the soil. When the legume plant
dies, any extra ammonium in the nodules or other plant tissues re-enters the soil,
making the soil more fertile (better for growing other plants).
Farmers often grow legumes like soybeans in order to build up the levels of
fixed nitrogen in their soil and make the soil more fertile. After harvesting the
Is corn a legume?
soybeans, the farmers plow the remnants of the soybean plants into the soil, so
Can it fix it’s own
that any left-over ammonium in the nodules or plant tissues will be released into
nitrogen?
the soil. Farmers can then plant crops like corn that DO NOT have symbiotic
bacteria living in their roots. Eventually the corn will use up all of the left over fixed
Connect: What does nitrogen in the soil, and the farmer will have to grow more legumes to replace the
it mean when soil is nitrogen. This is called crop rotation. Small-scale organic gardeners often grow
said to be fertile?
legumes simultaneously in and around other crops to help add nitrogen to the soil
throughout the growing season; this method is an example of companion planting.
Summary
Page 4 of 9
Key Concept: How
do practices like
crop rotation and
companion planting
impact soil fertility?
Connection:
Cyanobacteria (syan-oh-bak-teer-eeah) play a
significant role in
what other cycle of
matter?
Synthesize: How
many types of
bacteria have been
mentioned so far?
What are their roles
in the Nitrogen
Cycle?
Key Concept: Why
is nitrate leached
more than
ammonium?
Connect: Do you
think that nitrate
leaching is a
problem in Florida?
Comprehension
Check: What is
nitrate enrichment?
Summary
While the symbiotic relationship between legumes and Rhizobia plays an
important part in the nitrogen cycle, most plants do NOT have symbiotic bacteria in
their roots. Luckily there are also free-living bacteria that can “fix” nitrogen and
turn it into a form that plants can use.
Azotobacter (As-zōh-tōh-bak-ter) is a type of nitrogen-fixing bacteria that
lives freely in the soil. Like Rhizobia, Azotobacter can carry out chemical reactions
that transform molecular nitrogen into ammonium, but Azotobacter adds this
ammonium directly to the soil where it is available to all plants, not just legumes.
Cyanobacteria (sometimes mistakenly called blue-green algae) are another
type of free-living nitrogen-fixing bacteria. Like Azotobacter and Rhizobia,
Cyanobacteria also convert nitrogen to ammonium. Cyanobacteria are arguably the
most successful group of microorganisms on earth. They occupy a broad range of
habitats across all latitudes, and are widespread in freshwater, marine and
terrestrial (land-based) ecosystems. Thus, cyanobacteria play a critical role in
nitrogen fixation in a variety of habitats all over the world, including in aquatic
ecosystems.
Technically speaking, there are two distinct processes involved in turning
molecular nitrogen into a form that is biologically available: the transformation of
unfixed molecular nitrogen into ammonium (nitrogen fixation) and the
transformation of ammonium into nitrate (nitrification). Often times, both
processes are lumped together and referred to generally as nitrogen fixation.
All the bacteria discussed so far—Cyanobacteria, Azotobacter, Rhizobia—are
nitrogen-fixing bacteria that convert molecular nitrogen into ammonium. Nitrifying
bacteria are different; they take fixation one step further and perform
nitrification, a process that converts ammonium to nitrate! While both ammonium
and nitrate are biologically available and can be absorbed by plants, too much
ammonium can actually be toxic to many organisms. Thus, nitrifying bacteria and
the process of nitrification play a critical role in transforming toxic ammonium into
the less-toxic nitrates preferred by more plants.
Unfortunately, excess nitrate made by nitrifying bacteria does not last very
long in the pedosphere, especially in ecosystems that experience periods of heavy
rainfall. This is due to the fact that negatively charged nitrate (NO3-) compounds
are much more easily leached from soils than positively charged ammonium (NH4+)
compounds. Leaching occurs when runoff or groundwater percolating through
soils washes away critical nutrients like fixed nitrogen. The ammonium ions are
positively charged and therefore stick to (are attracted by) negatively charged clay
particles and organic matter in soil. This attraction between positively and
negatively charged ions—known as the Law of Attraction—prevents ammonium
from being leached out of the soil by groundwater flow. In contrast, the negatively
charged nitrate ions are actually repelled by negatively changed soil particles, and
so nitrates can be washed out of surface soils in ecosystems where there is heavy
rainfall, leading to decreased soil fertility. The leached nitrates don’t just disappear;
they are carried downstream by surface runoff, stream flow and groundwater flow,
leading to nitrate enrichment of ponds, lakes, aquifers and other downstream
bodies of water. Algae and aquatic plants often thrive in aquatic environments
enriched by nitrates that were leached from other ecosystems.
Page 5 of 9
NITROGEN AND THE FOOD CHAIN
Herbivore =
Carnivore =
Omnivore =
Once nitrogen enters a plant, it becomes part of the food chain. The fixed
nitrogen absorbed by the plant is used to make proteins, amino acids and DNA
(nitrogen-containing organic macromolecules). If the plant gets eaten by an
herbivore (or other primary consumer), the herbivore will digest the nitrogencontaining organic macromolecules stored in the plant and use that nitrogen to
make new nitrogen-containing organic macromolecules. Through predation,
herbivores pass on the nitrogen in their bodies to carnivores (secondary
consumers). Omnivores can get the nitrogen they need from both the plants and
the animals that they eat. Thus, the only organisms that actually absorb fixed
nitrogen from the surrounding environment and allow it to enter the food chain are
producers like photosynthetic plants and algae.
Decomposers, the final step in the food chain, also play a vital role in the
nitrogen cycle. Decomposers are often called “Nature’s recycling system” because
of the role they play in the cycling of nutrients like fixed nitrogen back into the
abiotic (non-living) environment. Decomposers—which include some types of fungi,
mold, mushrooms, earthworms, and even our old friends bacteria—can break down
the nitrogen-containing organic compounds stored in the bodies of dead organisms
and release that nitrogen back into the soil. The process by which these organic
compounds (like proteins, amino acids, and DNA) are chemically changed back into
ammonium is called ammonification. Usually, the nitrogen released (produced) by
decomposers is ammonium (NH4+). This fixed nitrogen then can be re-absorbed by
plants and enter the food chain again. In other words, ammonification returns
valuable fixed nitrogen back to the soil (abiotic environment) where it can re-enter
to food chain (biotic environment) through uptake by plants.
Organic farmers sometimes use decomposers to help create natural soil
fertilizer for their crops. Autumn leaves, grass clippings, weeds, fruit and vegetable
trimmings, egg shells, coffee grounds, and manure from horses, chickens and cows
can be mixed with special decomposing bacteria in a compost bin or compost pile.
The decomposing bacteria break down the proteins and other organic nitrogen
compounds and turn them back into ammonia. After a certain amount of time, the
“mature” compost can then be applied to gardens and fields to enrich the soil, thus
turning “garbage” and “waste” into a valuable resource for growing crops.
The inert (unreactive) nature of the N2 molecule (remember that triple bond?)
means that biologically available (fixed) nitrogen is often in short supply in natural
ecosystems. Thus, the availability of fixed nitrogen in an ecosystem can be an
important limiting factor. A limiting factor is an environmental factor that is
essential for life that is absent or depleted below the critical minimum, or that
exceeds the maximum tolerable level for the species. When fixed nitrogen is in
short supply, the growth of plants and other producers is restricted, and this
cascades up through the entire food chain, limiting biomass growth throughout the
entire ecosystem. However, population sizes of organisms in natural ecosystems
have evolved in balance with the limited availability of fixed nitrogen sources in
each ecosystem. Disrupting the balance of nitrogen, either through addition or
removal, therefore can have significant negative consequences on the health of an
ecosystem.
Summary
Page 6 of 9
HUMAN IMPACTS: BURNING FOSSIL FUELS
Sometimes plants and animals die and their
bodies do not get decomposed. Instead, their bodies
may quickly become
buried along with
other plants and
animals. Over millions
of years, the remains
of these organisms can
be turned into fossil
fuels like oil, coal, and
natural gas. If humans
extract (dig up) these
fossil fuels and burn
them, the combustion
reactions produce harmful nitrogen compounds like NO (nitric oxide), N2O (nitrous
oxide), and NO2 (nitrogen dioxide) that enter the atmosphere where they are
considered pollutants.
The nitrogen/oxygen compounds produced by the burning of fossil fuels can
cause serious environmental and health-related hazards, including acid rain,
photochemical smog, and high levels of tropospheric ozone (remember good up
high, bad nearby). Acid rain—also known
as acid precipitation— is rain or any other
form of precipitation that is unusually
acidic, meaning that it has a low pH.
Precipitation becomes acidic when
combustion products (mainly gasses)
from the burning of fossil fuels enter the
atmosphere and form condensation nuclei
for cloud droplets. Acid rain can have
harmful effects on plants, aquatic
animals, and infrastructure. The picture
shown here illustrates a spruce forest that
was destroyed by acid precipitation.
Ozone forms when harmful nitrogen compounds released by the combustion
of fossil fuels enter the atmosphere and react with oxygen (O2) gas molecules.
According to the American Lung Association, your lungs and heart can be
permanently affected by ozone pollution and smog. While the young and the elderly
are particularly susceptible to the effects of ozone, anyone with both short and long
term exposure can suffer ill health effects. Problems include shortness of breath,
coughing, wheezing, bronchitis, pneumonia, inflammation of pulmonary tissues,
heart attacks, lung cancer, increased asthma-related symptoms, fatigue, heart
palpitations, and even premature aging of the lungs and death.
N2O is also a dangerous greenhouse gas, with 310 times the ability per
molecule of gas to trap heat in the atmosphere. Thus, increased levels of N2O in the
atmosphere are exacerbating global warming.
Summary
Page 7 of 9
HUMAN IMPACTS: ANTHROPOGENIC FIXATION
Besides the burning fossil fuels, the application of nitrogen-based fertilizers is
another human activity that can significantly impact the nitrogen cycle. Farmers use
man-made fertilizers to increase crop yields per acre (more productive harvest on
same amount of land), which lowers food prices for consumers. Thus, the use of
man-made, nitrogen-based fertilizers is an accepted and common agricultural
practice that is of great significance both to farmers and to people like you and me
that want to be able to purchase inexpensive food for our families.
The nitrogen-based fertilizers used in agriculture are man-made in a process
generally referred to as industrial fixation (anthropogenic fixation). More
specifically, the Haber-Bosch process produces synthetic fertilizers by causing N2 to
react with H2, resulting in the production of ammonium. As second step converts
the ammonium to ammonium-nitrate. Industrial fixation using the Haber-Bosch
process has increased significantly over the past several decades as agricultural
demands have increased. In fact, today, nearly 80% of the nitrogen-containing
organic macromolecules found in human tissues originated from the Haber-Bosch
process rather than natural atmospheric or biological sources of fixation!
The current methods used to apply fertilizers are incredibly inefficient. Not
only must fertilizer must be repeatedly added to the soil after each harvest (before
the next planting), but very little of the fertilizer added to a field ever actually gets
absorbed by the intended target plants. As mentioned earlier, fixed nitrogen can be
easily leached from the soil, and so much of the fertilizers used in agriculture
ultimately make their way into our rivers, lakes, estuaries and oceans. Nitrates can
even end up in our drinking water when runoff carrying fertilizers infiltrates and
percolates through the bedrock and contaminates our aquifers.
The inefficient use of man-made fertilizers in agriculture is dramatically
increasing the amount of biologically available nitrogen in the Earth’s natural
ecosystems, even hundreds of miles away from agricultural lands. In fact, human
activity has doubled the amount of global fixed nitrogen in the biosphere, and this
is becoming a significant environmental issue. Since fixed nitrogen is often a
limiting factor, you might think that increasing the amount of fixed nitrogen in an
ecosystem would be a good thing. However, the biological communities in an
ecosystem co-evolve over millions of years and develop a balance based on the
available resources provided by the various cycles of matter (nitrogen cycle, carbon
cycle, oxygen cycle, etc.). A change in any one component in any part of one of the
cycles of matter can ripple throughout an ecosystem and cause disruptions in other
cycles of matter as well.
In terrestrial (land-based) ecosystems, the addition of nitrogen can lead to
nutrient imbalance in trees, changes in forest health, and declines in biodiversity.
As the availability of fixed nitrogen increases, tree growth may temporarily explode
and strip the soil of other, non-nitrogen-based nutrients, basically starving other
plants with less extensive root systems. As the plant diversity shrinks, a similar
collapse occurs in populations of consumer organisms that depend on the impacted
plant species. In addition, since trees absorb and store huge amounts of carbon for
much longer periods of time than other forest organisms, rapid tree growth can
disrupt the cycling of carbon, thus impacting more than just the nitrogen cycle.
Summary
Page 8 of 9
When nitrogen-enriched runoff reaches a body of water—be it river, lake,
spring, estuary, or ocean—the sudden increase in biologically available nitrogen can
trigger a population explosion in aquatic algae, an event known as an algal bloom.
The rapidly reproducing algae quickly use up important nutrients needed by other
aquatic plants and animals (resource depletion). Often the affected water becomes
cloudy, typically colored a shade of green, yellow, brown, or red (depending on the
species of algae). As the algal bloom grows, it can block sunlight and prevent it
from reaching other photosynthetic organisms that live in deeper waters.
Eventually, the algae population itself collapses due to exhaustion of resources. As
the algae die, they sink to the bottom where they are decomposed. The increase in
dead algae causes a spike in the decomposition process, which in turn uses
precious amounts of dissolved oxygen, leading to anoxic (no oxygen) or hypoxic
(low oxygen) conditions that can kill fish, shellfish (mussels, oysters, crabs,
crawfish), amphibians (frogs and salamanders) and other aquatic organisms. This
entire process—from algae bloom to the creation of “dead zones” due to polluted
runoff—is known as eutrophication. About half of all the lakes in the United States
are now eutrophic, while the number of oceanic dead zones near inhabited
coastlines is also increasing.
There are many different types of algae that can “bloom” suddenly and lead
to eutrophication events. Algae is also known as phytoplankton (which literally
means “plant-like floaters”) and includes many different kinds of tiny, plant-like,
photosynthetic organisms that drift near the surface of the water. Dinoflagellates
(dy-nōh-FLAJ-jell-ates) are one of the most important types of phytoplankton. They
are small single-celled organisms, which swim freely in water with a forward
spiraling motion propelled by two flagella: one flagellum oriented around the cell,
and the other directed backwards (like a tail). These single-celled protists have
plates covering their cells, and numerous internal
cellular structures, including chloroplasts, mitochondria
and a nucleus. Many dinoflagellates are important
primary producers in aquatic food webs.
When certain species of dinoflagellates reproduce
in great numbers, the water may appear golden or red,
producing and algae bloom known as a "red tide". Red
tides sometimes occur naturally; long before the
invention of anthropogenic fixation, seafarers and
coastal dwellers in certain places would report occasional colorful “blooms” during
the warm months of summer. However, over the last several decades, many areas
of the world, including the United States and Florida, have experienced a growing
trend in the frequency and size of toxic dinoflagellate blooms. There is growing
evidence linking red tides to runoff polluted with anthropogenic fixed nitrogen.
During a red tide event, many kinds of marine life suffer, and not just
because of hypoxic/anoxic conditions and resource depletion. For in additional to all
of the typical hazards associated with algal blooms, the dinoflagellate blooms carry
an additional threat, since many dinoflagellates produce a neurotoxin which affects
muscle function in some organisms. Because of these toxins, red tides have been
associated with high mortality (death) rates in populations of fish, shellfish, birds,
sea turtles, and even marine mammals like manatee and dolphin.
Summary
Page 9 of 9
When consumed, the dinoflagellate toxins can be quickly carried up the food
chain and passed onto secondary consumers and apex predators—including
humans—via fish and shellfish consumption. The human health risks associated
with the consumption of fish and shellfish contaminated by red tides include
gastrointestinal illness, permanent neurological (nerve/brain) damage, and in rare
cases, even death.
As the size and frequency of algal blooms like red tides and their associated
dead zones continue to increase, socio-economic concerns grow due to the impact
on commercial fisheries, human health, and coastal tourism near the affected
areas. For our wildlife, the end results potentially include organism death,
decreasing biodiversity, and the potential loss of certain species in the local
ecosystem (local extinction). In extreme cases, such events may even lead to such
drastic changes in food-web structure that an entire ecosystem fails.
Because of these concerns, as of 2006, the application of nitrogen-based
fertilizer is now increasingly controlled in Britain and the United States. Still, even if
eutrophication can be reversed, it may take decades before the accumulated
nitrates in groundwater that feeds local rivers and lakes can be broken down by
natural processes.
Summary