Chloroplasts

The sketch of the chloroplast above was made from an electron micrograph of a
chloroplast from a higher order plant (Levy). Plants use energy from the sun in tiny
energy factories called chloroplasts. Usingchlorophyll in the process
called photosynthesis, they convert the sun's energy into storable form in
ordered sugar molecules such as glucose. In this way, carbon dioxide from the air and
water from the soil in a more disordered state are combined to form the more ordered
sugar molecules.

Inside the chloroplasts are stacks of discs

called thylakoids. They are compared to
stacks of coins within the walls of the
chloroplast, and they act to trap the energy
from sunlight.

The stacks of thylakoids are called grana. They are connected with an extensive sytem
of tubules. The thylakoid membranes contain chlorophyll and other pigments arranged

in antenna arrays to capture light energy for two photosystems called Photosystem
I andPhotosystem II. In most plants, both photosystems are used in anelectron
transport process that yields energy in the form of ATP andreduced coenzymes to the
stroma of the chloroplast to be used in the synthesis of carbohydrates. The energy is
used in the Calvin cycle to fix carbon from atmospheric CO2 and construct sugars.
Order can be produced with an expenditure of energy, and the order associated with
life on the earth is produced with the aid of energy from the sun.

Chloroplast Structure
Index
Photosynthesis
Concepts
Second law
concepts
Reference
Levy
Ch 4
Moore, et al.
Ch 7

Plants use energy from the sun in tiny energy factories called chloroplasts. The
green color of leaves is attributable largely to these chloroplasts because they
contain chlorophyll for photosynthesis. Though obviously oversimplified, the
illustration depicts the somewhat elongated sausage type shape with large
dimension 5-10 m and smaller dimension 3-4 m. Moore suggests 40-200
chloroplasts per photosynthetic cell and about 500,000 per square millimeter of
leaf area.
There are two membranes, and inside the inner membrane is the gelatanous
matrix called the stroma. The stroma contains ribosomes, DNA, and is the
location for biochemical synthesis. Membranous sacs called thylakoids are
arranged in stacks called grana. The chlorophyll in the thylakoid membranes
carries out photosynthesis.

Energy and Order in Biological Systems

The concept of entropy and the second law of thermodynamics suggests that systems
naturally progress from order to disorder. If so, how do biological systems develop

and maintain such a high degree of order? Is this a violation of the second law of
thermodynamics?

Order can be produced with an expenditure of energy, and the order associated with
life on the earth is produced with the aid of energy from the sun.

For example, plants use energy from the sun in tiny energy factories
calledchloroplasts. Using chlorophyll in the process called photosynthesis, they
convert the sun's energy into storable form in ordered sugar molecules. In this way,
carbon and water in a more disordered state are combined to form the more ordered
sugar molecules.
In animal systems there are also small structures within the cells
calledmitochondria which use the energy stored in sugar molecules from food to form
more highly ordered structures.

Green leaves use the energy from the sun in tiny energy factories calledchloroplasts.
Using chlorophyll, they convert the sun's energy into storable form in
ordered sugar molecules. One of the electrons in chlorophyll is excited by energy
from the Sun. It transfers that energy through many steps in a process which finally
produces the highly ordered glucose structure.

Metabolism
If you burn wood, you liberate energy stored in the ordered cellulose molecules which
have been produced by the tree in a "disorder to order" process. In the burning, you
add oxygen and get carbon dioxide and water as combustion products along with the
liberated heat. The liberated heat comes from the energy stored in the ordered sugar
molecules which make up the cellulose.
The process by which animals use energy is a very similar process. They too need
oxygen to burn the starch in a way to produce CO2 and water with the liberation of
heat. When you are burning fat or burning sugars, you are producing about the same

things as if you were burning a wood fire. You do produce heat, which we warmblooded animals use to maintain our body temperature. But we also give off a lot of
heat as well. On a 24-hour average basis as a result of human energy, we may give off
about the same amount of heat as a 100 watt light bulb. For living things, only about
half the energy of the metabolic process is immediately released as heat - the rest is
trapped in a high energy molecule which is vitally important to all the processes of
life - the molecule adenosine triphosphate.
Obtaining energy from food molecule like glucose or carbohydrates involves breaking
them down into smaller molecules: this general process is called catabolism. By
contrast, the building up of complex molecules from simpler ones is called anabolism.

Mitochondria

Mitochondrion structure

Mitochondria are the energy factories of the cells. The energy currency for the work
that animals must do is the energy-rich molecule adenosine triphosphate (ATP). The
ATP is produced in the mitochondria using energy stored in food. Just as
the chloroplasts in plants act as sugar factories for the supply of ordered molecules to
the plant, the mitochondria in animals and plants act to produce the ordered ATP
molecules as the energy supply for the processes of life.
A typical animal cell will have on the order of 1000 to 2000 mitochondria. So the cell
will have a lot of structures that are capable of producing a high amount of available

energy. This ATP production by the mitochondria is done by the process

of respiration, which in essence is the use of oxygen in a process which generates
energy. This is a very efficient process for using food energy to make ATP. One of the
benefits of "aerobic exercise" is that it improves your body's ability to make ATP
rapidly using the respiration process.
All living cells have mitochondria. Hair cells and outer skin cells are dead cells and no
longer actively producing ATP, but all cells have the same structure. Some cells have
more mitochondria than others. Your fat cells have many mitochondria because they
store a lot of energy. Muscle cells have many mitochondria, which allows them to
respond quickly to the need for doing work. Mitochondria occupy 15 to 20 percent of
mammalian liver cells according to Karp.

Adenosine Triphosphate
Adenosine triphosphate (ATP) is considered by biologists to be the energy currency of
life. It is the high-energy molecule that stores the energy we need to do just about
everything we do. It is present in the cytoplasm and nucleoplasm of every cell, and
essentially all the physiological mechanisms that require energy for operation obtain it
directly from the stored ATP. (Guyton) As food in the cells is gradually oxidized, the
released energy is used to re-form the ATP so that the cell always maintains a supply
of this essential molecule. Karp
quotes
an estimate that more than 2 x 1026molecules or >160kg of ATP is formed in the human body
daily! ATP is remarkable for its ability to enter into many coupled reactions, both those to food
to extract energy and with the reactions in other physiological processes to provide energy to
them. In animal systems, the ATP is synthesized in the tiny energy factories
called mitochondria by a process called glycolysis.

The structure of ATP has an ordered carbon compound as a backbone, but the part
that is really critical is the phosphorous part - the triphosphate. Three phosphorous
groups are connected by oxygens to each other, and there are also side oxygens
connected to the phosphorous atoms. Under the normal conditions in the body, each
of these oxygens has a negative charge, and as you know, electrons want to be with
protons - the negative charges repel each other. These bunched up negative charges
want to escape - to get away from each other, so there is a lot of potential energy here.
If you remove just one of these phosphate groups from the end, so that there are just
two phosphate groups, the molecule is much happier. Thisconversion from ATP to
ADP is an extremely crucial reaction for the supplying of energy for life processes.
Just the cutting of one bond with the accompanying rearrangement is sufficient to
liberate about 7.3 kilocalories per mole = 30.6 kJ/mol. This is about the same as the
energy in a single peanut.
Living things can use ATP like a battery. The ATP can power needed reactions by
losing one of its phosphorous groups to form ADP, but you can use food energy in the
mitochondria to convert the ADP back to ATP so that the energy is again available to
do needed work. In plants, sunlight energy can be used to convert the less active
compound back to the highly energetic form. For animals, you use the energy from
your high energy storage molecules to do what you need to do to keep yourself alive,
and then you "recharge" them to put them back in the high energy state. The oxidation
ofglucose operates in a cycle called the TCA cycle or Krebs cycle in eukaryotic cells
to provide energy for the conversion of ADP to ATP.

Conversion from ATP to ADP

Adenosine triphosphate (ATP) is the energy currency of life and it provides that
energy for most biological processes by being converted to ADP (adenosine
diphosphate). Since the basic reaction involves a water molecule,
ATP + H2O ADP + Pi
this reaction is commonly referred to as the hydrolysis of ATP.

The structure of ATP has an ordered carbon compound as a backbone, but the part
that is really critical is the phosphorous part - the triphosphate. Three phosphorous
groups are connected by oxygens to each other, and there are also side oxygens
connected to the phosphorous atoms. Under the normal conditions in the body, each
of these oxygens has a negative charge, and as you know, electrons want to be with
protons - the negative charges repel each other. These bunched up negative charges
want to escape - to get away from each other, so there is a lot of potential energy here.
If you remove just one of these phosphate groups from the end, so that there are just
two phosphate groups, the molecule is much happier. If you cut this bond, the energy
is sufficient to liberate about 7000 calories per mole, about the same as the energy in a
single peanut.
Living things can use ATP like a battery. The ATP can power needed reactions by
losing one of its phosphorous groups to form ADP, but you can use food energy in the
mitochondria to convert the ADP back to ATP so that the energy is again available to
do needed work. In plants, sunlight energy can be used to convert the less active
compound back to the highly energetic form. For animals, you use the energy from
your high energy storage molecules to do what you need to do to keep yourself alive,
and then you "recharge" them to put them back in the high energy state.

Essential Amino Acids

Amino acids are organic compounds which contain both an amino group and a
carboxyl group. According to Tillery, et al., the human body can synthesize all of the
amino acids necessary to build proteins except for the ten called the "essential amino
acids", indicated by asterisks in the amino acid illustrations. An adequate diet must
contain these essential amino acids. Typically, they are supplied by meat and dairy
products, but if those are not consumed, some care must be applied to ensuring an
adequate supply. They can be supplied by a combination of cereal grains (wheat, corn,
rice, etc.) and legumes (beans,peanuts, etc.). Tillery points out that a number of
popular ethnic foods involve such a combination, so that in a single dish, one might
hope to get the ten essential amino acids. Mexican corn and beans, Japanese rice and
soybeans, and Cajun red beans and rice are examples of such fortuitous combinations.

The University of Arizona's Biology Project gives the following summary:"The 10

amino acids that we can produce are alanine, asparagine, aspartic acid, cysteine,
glutamic acid, glutamine, glycine, proline, serine and tyrosine. Tyrosine is produced
from phenylalanine, so if the diet is deficient in phenylalanine, tyrosine will be
required as well. The essential amino acids (that we cannot produce internally) are

arginine (required for the young, but not for adults), histidine, isoleucine, leucine,
lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino
acids are required in the diet. Plants, of course, must be able to make all the amino
acids. Humans, on the other hand, do not have all the the enzymes required for the
biosynthesis of all of the amino acids."
The failure to obtain enough of even 1 of the 10 essential amino acids has serious
health implications and can result in degradation of the body's proteins. Muscle and
other protein structures may be dismantled to obtain the one amino acid that is
needed. "Unlike fat and starch, the human body does not store excess amino acids for
later usethe amino acids must be in the food every day."(Biology Project)

Water, the Solvent for Life

The human body is 66% water by weight, according to Hill and Kolb. Water is the
universal solvent for life, referred to by Nobel Laureate A. Szent-Gyorgy as "the
matrix of life".That water serves as the solvent for sodium chloride (salt) and other
substances so that the fluids of our bodies are similar to sea water. This leads Hill and
Kolb to refer jokingly to us as "walking bags of sea water". Water serves to suspend
the red blood cells to carry oxygen to the cells. It is the solvent for the electrolytes and
nutrients needed by the cells, and also the solvent to carry waste material away from
the cells.
With water as the solvent, osmotic pressure acts to transport the needed water into
cells. With cells bathed in the interstitial fluid, diffusioncontributes to carrying needed
molecules into the cells. When more complex mechanisms control the transport of
molecules across the membranes into and out of cells, the presence of water as the
surrounding medium and solvent is essential.