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Bioenergetics

In the previous module, we learned about the origin of life, as well as

the theories that support certain hypothesis. Now, it is time to delve

deeper into the processes that perpetuate life. It is important to

understand how these processes occur at both a cellular and

organismic level. Learning these processes will arm you with the

knowledge needed to understand broader and deeper studies of life.

Bioenergetics concerns itself with studying the transfer of energy; that

is, how energy is converted into matter and other forms of energy.

The Cell as the Basic Unit of Life

The cell is the basic unit of life. Organisms may either be unicellular

(composed of one cell alone), or multicellular. Cells comprise both

animals and plants, although there are differences with regards to each.

However, the cell is the smallest unit of life. Cells may come together

to form tissues, which can come together to form organs. Organs make

up the human body, as well as the bodies of plants and animals.

The study of the cell is not possible without a microscope. Anton van

Leewenhoek constructed the first simple microscope. He was able to

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study the structure of bacteria, protozoa, spermatozoa, and red blood

cells. Robert Hooke, in 1665, coined the term “cell” that he used to

designate the small, honey-comb like structures that he was able to

view on a cork bottle. He was impressed with the little structures, as

they reminded him of rooms in a monastery. In 1838, Matthios

Schleiden proposed that all plants are made up of cells. Then, 1839,

Theodore Schwann proposed that all animals were also made up of

cells. Together, Schleiden and Schwann studied a wide variety of plant

and animal tissues, and proposed the Cell Theory in 1839. The theory

essentially stated that all organisms are made up of cells. However, the

theory was rewritten by Rudolf Virchow in 1858. In the succeeding

theory, Virchow wrote that, aside from all living things being made up

of cells, all cells arise from pre-existing cells. In 1861, Schulze found

that cells were not empty, as Hooke thought, but that they contained

material known as protoplasm.

It was during the 1950s that scientists were able to classify cells

according to eukaryotic cells and prokaryotic cells; with the latter

lacking a nucleus. Another important difference between prokrayotes

and eukaryotes is that prokaryotic cells do not have any intracellular

components. Prokaryotic cells include bacteria and blue-green algae,

while eukaryotic cells include plants, animals, fungi, and protozoa.

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Modern Cell Theory

Biologists today have made additions to the cell theory, which now

states:

1) All organisms are made up of cells;

2) New cells arise from pre-existing cells;

3) The cell is the structural and functional unit of all living things;

4) The cell contains genetic information that is passed from cell to

cell during cell division; and

5) All cells are basically the same in chemical composition and

metabolic activities.

The Structure of the Cell

Both prokaryotic and eukaryotic cells

posses a plasma membrane and a

cytoplasm. The plasma membrane is the

outermost surface of the cell and it

separates the cell from its environment.

The cytoplasm is the aqueous content of

the cell, in which the cell’s organelles

are suspended.

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The plasma membrane is semi-permeable membrane that is present in

all cells. The plasma membrane is composed of carbohydrates,

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proteins, phospholipids, and cholesterol. The plasma membrane

contains a lipid bilayer, which is termed as such because it contains

two layers of fat cells organized into two sheets. It is typically about

five nanometers thick and the surrounds all cells, providing the

membrane structure. The structure of the lipid bilayer explains its

function as a barrier. Lipids are fats, such as oils, that are insoluble in

water. There are two important regions of a lipid that are crucial for

the lipid bilayer. Each lipid molecule contains a hydrophilic region

(the polar head region) and a hydrophobic region (the non-polar tail

region). The hydrophilic region is attracted to water conditions while

the hydrophobic region is repelled from these conditions. Since lipid

molecules contain both regions, they are termed as amphipathic

molecules. The most abundant types of lipids found in the plasma

membrane are phospholipids. It has two nonpolar fatty acid chain

groups and a tail. The tail is composed of a string of carbons and

hydrogens. Due to its double-bond structure, the tail has a kink.

The bilayer is where the lipids organize themselves to hide their

hydrophobic region and to expose their hydrophilic regions. The

organization as such is a spontaneous process, which does not require

energy. The most important property of the lipid bilayer is that it is a

highly impermeable structure. This means that molecules cannot freely

pass across the lipid bilayer. Only water and gas can pass through. It

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also means that large molecules and small polar molecules cannot

cross the bilayer, and thus, the cell membrane, without being assisted

by other structures. Another important characteristic of the lipid

bilayer is its fluidity. The fluidity of the bilayer allows proteins to

move within it. The fluidity of the bilayer is also important because it

allows membrane transport. Fluidity is dependent on the temperature

as well as the specific structure of the fatty acid chains. Due to these

two properties, the lipid bilayer was summarized by Singer and

Nicholson (1974) as the Fluid Mosaic Model.

On the other hand, cells also contain a cytoplasm, which is where

organelles are suspended. The cytoplasm contains living components,

which are cell organelles, and non-living components, which are

ergastic subsances and cytoskeletal elements. Without the organelles,

the cytoplasm is termed as cytosol. It is a jelly-like, semi-fluid matrix

that is found between the nuclear membrane and the cell membrane.

The cytoplasm often comprises up to 50% of the cell’s volume. Aside

from providing structural support for the cell, the cytoplasm is also

where protein synthesis occurs.

The cytoskeleton is another cell component that gives the cell its

structure. It also allows the cell to adapt. Thus, cells can reorganize

their cytoskeletal components in order to change their chapes. The

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cytoskeleton also has ‘tracks’ where it allows organelles to move

around the cell. The cytoskeleton can also move entire cells in multi-

cellular organisms. Therefore, the cytoskeleton is involved in

intercellular communication. The cytoskeleton is composed of three

different types of protein filaments: intermediate filaments,

microtubules, and actin. Briefly, actin is the main component of actin

filaments. They are double-stranded, thin, and flexible structures. It is

also the most abundant protein in eukaryotic cells. Microtubules are

long, cylindrical structures composed of tubulin. They are organized

around a centrosome. These filaments provide tracks upon which

organelles can move inside the cells. Intermediate filaments are rope-

like and fibrous. They have a diameter of approximately 10

nanometers. These filaments, however, are not found in all animal

cells, but only in those where they function to form the nuclear lamina.

The nucleus of the cell is one of the largest organelles found in cells. It

also plays an important biological role. It comprises close to 10% of

the cell’s volume and it is found near the center of eukaryotic cells.

The importance of the nucleus lies in its function as the storage space

for DNA. The cell nucleus is composed of two layers which form an

envelope around the cell and only allows selected molecules to enter

and leave the cell. The DNA that is found in cells is packaged in

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chromosomes. The nucleus directly comes into contact with the

endoplasmic reticulum. It is also the site of DNA and RNA synthesis.

The mitochondria, on the other hand, is a double-membrane structure

that is highly specialized. It generates adenosine triphosphate (ATP),

which provides organisms with energy. The outer membrane of the

mitochondria is smooth, while the inner membrane produces finger-

like infoldings called cristae. The inside of the mitochondria is filled

with the homogenous, granular mitochondrial matrix. This matrix has

mitochondrial DNA, RNA, lipids, proteins, enzymes, and 70s

ribosomes.

The endoplasmic reticulum is a network of tubular structures found in

the cystoplasm and is bound by a membrane. It extends from the

nuclear membrane to the cell membrane. The endoplasmic reticulum

exists as oval vesicles, unbranched tubules, and flattened sacs called

cisternae. There are two types of endoplasmic reticulum: smooth and

rough. The former does not contain ribosomes, while the latter

contains 80s ribosomes. The function of the endoplasmic reticulum is

that it helps in intracellular transportation. It also provides mechanical

support for the cytoplasmic matrix, and it helps in the formation of the

Golgi complex and nuclear membrane. It is also the storehouse of

lipids, carbohydrates, and metabolic wastes.

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Golgi bodies (Golgi complex) are a group of curved, flattened, plate-

like cisternae. The cisternae produce a netwrork of tubules from the

periphery. These tubules also end in vesicles. The Golgi complex is

also known as the packaging center of the cell. These bodies package

proteins, carbohydrates, etc. in their vesicles. They also produce

enzymes called lysosomes, which are “suicide bags” of the cell and

result in cell death. They secrete enzymes, hormones, and material

from the cell wall.

Plastids are found in plant cells and euglenoids. They are classified

based on the type of pigment that they contain. Chromoplasts contain

carotenoids. Leucoplasts store food materials and are colorless.

Chloroplasts are green in color and function in photosynthesis.

Vacuoles are single-membrane bound sacs that are present in the

cytoplasm. Plant cells have large vacuoles and animal cells have small

vacuoles. The tonoplast is the term for the membrane of the vacuoles.

It is filled with cell sap, which is watery. The cell sap has sugars, salts,

pigments, and enzymes. There are four types of vacuoles: contractile

vacuoles, food vacuoles, gas vacuoles, and storage vacuoles.

Ribosomes produce proteins in cells. These are granular,

nonmembraneous structures inside the cells. They are present in the

cytoplasm, mitochondria, and chloroplast. Eukaryotes have 80s

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ribosomes in the cytoplasm and 70s ribosomes in the plastids and

mitochondria. Centrosomes form spindles during cell division. They

are surrounded by a denser type of cytosol called the centrosphere.

Centrosomes have two cylindrical structures called centrioles at the

center.

Photosynthesis

Photosynthesis is the process by which

plants that contain chlorophyll covert

energy from the sun into photochemical

energy. This energy is stored in the form

of carbohydrates. Carbohydrates provide

food for man and other heterotrophic

organisms. Aside from this,

photosynthesis also produces oxygen as

a by-product that is essential for all life

on earth. The photosynthetic activity

from previous eras in geology have

provided us with large deposits of fuel.

Lately, however, the by-products

produced through photosynthesis is

undergoing scrutiny, in part because it is

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in danger of being inadequate for animal

and human survival. Thus,

understanding the process of

photosynthesis will help us gain an

underastanding of how its efficieny can

be improved, and in devising artificial

sources of photochemical energy based

on it. In addition to this, many

biochemical processes, such as electron

transport, can be understood through

photosynthesis.

In the photosynthetic activity of green

plants, CO2, H2O, and light energy react

with each other, producing O2 and

carbohydrates (CH2O) as its products.

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Molecules of pigment, especially chrolophyll, various enzymes, and

electron carriers act in a manner that is catalytic in this reaction. The

overall bioenergetics of this reaction can be summarized as follows: C,

H, and O in CO2 and H2O are converted from a very stable

arrangement of atoms to less stable arrangement of the same electrons

and nuclei (CH2O + O2). In order for this process to occur, light energy

is needed. The total energy stored is 112kcal/mole difference. The

difference is supplied by the energy from light. Photosynthesis is

considered as an oxidation-reduction reaction.

In addition to green plants, certain kinds of bacteria (e.g. purple and

green) are capable of photosynthesis. Photosynthetic bacteria are

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different from plants in that they are not capable of oxidizing H2O.

Consequently, no oxygen is involved in the photosynthesis of bacteria.

Primary Events in Photosynthesis

Light absorption is the first step in photosynthesis. There are three

main groups of pigments involved in light absorption: chlorophylls,

phycobilins, and carotenoids. These pigments function as a means for

plants to absorb light through the visible sprectrum. The energy is then

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transferred to reaction centers, where it is used for photochemical

reactions. The bulk of the pigments involved in absorbing light are

called light-harvesting pigments.

There are two kinds of chlorophyll in plants and green algae:

chlorophyll A (Chl a) and chlorophyll b (Chl b). These pigments are

soluble in organic solvents. On the other hand, carotenoids are yellow

and orange pigments that are found in almost all photosynthetic

organisms. They are also soluble in organic solvents. There are two

kinds of carotenoids: carotenes, of which beta-carotene is the most

common, and carotenols, or alcohols. Phycobilins are water-soluble

pigments, which are present in blue and red algae. They are open-

chain tetraphyroles. There are also two kinds of phycobilins:

phycocyanins, which are primarily found in blue-green algae, and

phycoerythrins, which are found in red algae.

Light emission is the second step in photosynthesis. The Chl a

molecule becomes excited due to direct light absorption. These

molecules undergo fluorescence. After fluorescence, delayed light

emission occurs. Photosynthetic organisms emit light for short periods

of time.

The third step is energy transfer and migration. Through a maze of

several hundred Chl a molecules, energy migration occurs until the

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energy reaches the reaction center where it can be converted into

chemical energy. There are two processes in energy transfer and

migration: heterogenous, when the energy is transferred to other Chl a

molecules, and homogenous, when energy is transferred through the

same kinds of molecules.

The fourth step is the reaction at reaction centers. This is the process

by which energy reaches reaction centers and is converted into

chemical energy. This reaction produces an oxidizing and reducing

equivalent. The primary electron in this process is reduced and the

reaction center undergoes oxidation. In turn, this receives an electron

from the primary electron donor. This transfer of electrons is

summarized in the Calvin cycle. After electrons are transferred, the

products of oxygen and carbo

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hydrates are created.

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References

Reece, J.B., Urry, L.A., Cain, M.L…& Jackson, R.B. (2013).

Campbell Biology 10th ed. Pearson.

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