The Cell Theory Of Biology

1. Cells are the basic units of life

2. All organisms are constructed of cells. Every living organism on earth is at least a single cell or a
population of cells

3. Except for the origin of life itself, all cells arise from pre-existing cells. Cells arise only by division of living
cells, never by aggregation of cell parts and cell chemicals

4. Cells of multicellular organisms are sometimes interconnected, enabling the resultant populations to
function as single units

5. Cells of multicellular animals must stick to solid surfaces to divide, move, assume specialized shapes
and carry the necessary functions of life

A. Properties of Cells

1. Cells are complex and highly organized

1. They contain numerous internal structures

2. xSome are membrane bound (ex, organelles) while others do not

2. Cells contain genetic blueprint and machinery to use it

1. Genes are instructions for cells to create specific proteins

2. All cells use the same type of information

3. The genetic code is universal

4. The machinery used for synthesis is interchangeable

5. However, for this to function properly, the information must be error free ( errors are
called mutations)

3. Cells arise from the division of other cells

1. Daughter cells inherit the genes from the mother cells

2. Bacteria multiply by binary fission

3. Eukaryotic cells divide thru mitosis where the genetic complements of each daughter cell
is identical to the other and to the mother cell. This is asexual reproduction

4. Reproductive cells or gametes divide thru meiosis where the genetic complement of each
daughter cell is reduced by half and each daughter cell is genetically unique. This is used
in sexual reproduction
4. Cells acquire and utilize energy

1. Plant cells undergo photosynthesis; convert light energy and CO2 to chemical energy
(ATP and glucose)

2. Most cells respire

3. Release energy found in organic compounds

4. Convert organic compounds to CO2 and O2

5. Make ATP

6. Cells can perform a variety of chemical reactions

7. Transform simple organic molecules into complex molecules (anabolism)

8. Breakdown complex molecules to release energy (catabolism)

9. Undergo metabolism (all reactions performed by cells)

5. Cells can engage in mechanical activities

1. Cells can move

2. Organelles can move

3. Cells can respond to stimuli

4. Chemotaxis –movement towards chemicals

5. Phototaxis – movement towards light

6. Hormone responses

7. Touch responses

6. Cells can regulate activities

1. Cells control DNA synthesis and cell division

2. Gene regulation –cells make specific proteins only when needed

3. Turn on and off metabolic pathways

7. Cells contain the following structures

 1. Plasma membrane – separates the cell from the external environment

2. Cytoplasm-fluid-filled cell interior

3. Nuclear material –genetic information stored as DNA

8. Most cells are small, about 5 to 20 micrometers (0.00019 to 0.00076 in) in length

1. The smallest cell of the microorganisms, Mycoplasma are 0.2 micrometer (0.0000076 in)
but some giant cells are several centimeters long

9. All cells are of composed of similar chemicals and carry out the same biochemical processes

The Cell: Endomembrane System, Mitochondria,

Chloroplasts, Cytoskeleton, and Extracellular Components

The endomembrane system

The endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and vacuoles. Vesicle exchange between
compartments.

Introduction
Let’s imagine you are a pancreatic cell. Your job is to secrete digestive enzymes, which travel into the
small intestine and help break down nutrients from food. In order to carry out this job, you somehow have
to get those enzymes shipped from their site of synthesis—inside the cell—to their place of action—
outside the cell.
How are you going to make this happen? After a moment of panic in which you consider calling the postal
service, you relax, having remembered: I have an endomembrane system!
What is the endomembrane system?
The endomembrane system (endo- = “within”) is a group of membranes and organelles in eukaryotic
cells that works together to modify, package, and transport lipids and proteins. It includes a variety of
organelles, such as the nuclear envelope and lysosomes, which you may already know, and the
endoplasmic reticulum and Golgi apparatus, which we will cover shortly.
Although it's not technically inside the cell, the plasma membrane is also part of the endomembrane
system. As we'll see, the plasma membrane interacts with the other endomembrane organelles, and it's
the site where secreted proteins (like the pancreatic enzymes in the intro) are exported. Important note:
the endomembrane system does not include mitochondria, chloroplasts, or peroxisomes.
Let's take a closer look at the different parts of the endomembrane system and how they function in the
shipping of proteins and lipids.
The endoplasmic reticulum
The endoplasmic reticulum (ER) plays a key role in the modification of proteins and the synthesis of
lipids. It consists of a network of membranous tubules and flattened sacs. The discs and tubules of the
ER are hollow, and the space inside is called the lumen.
Rough ER
The rough endoplasmic reticulum (rough ER) gets its name from the bumpy ribosomes attached to its
cytoplasmic surface. As these ribosomes make proteins, they feed the newly forming protein chains into
the lumen. Some are transferred fully into the ER and float inside, while others are anchored in the
membrane.
Inside the ER, the proteins fold and undergo modifications, such as the addition of carbohydrate side
chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER
or those of other organelles—or secreted from the cell.
If the modified proteins are not destined to stay in the ER, they will be packaged into vesicles, or small
spheres of membrane that are used for transport, and shipped to the Golgi apparatus. The rough ER also
makes phospholipids for other cellular membranes, which are transported when the vesicle forms.

Micrograph and diagram of the endoplasmic reticulum. Micrograph shows the rough ER as a series of
membrane folds surrounding the nucleus. Diagram gives a 3D representation of rough ER and smooth
ER along with the cell nucleus.
_Image credit: left, "The endomembrane system and proteins: Figure 2" by OpenStax College, Biology
(CC BY 3.0), modification of work by Lousia Howard; right, modification of "Animal cell structure" by
Mariana Ruiz, public domain_
Since the rough ER helps modify proteins that will be secreted from the cell, cells whose job is to secrete
large amounts of enzymes or other proteins, such as liver cells, have lots of rough ER.
Smooth ER
The smooth endoplasmic reticulum (smooth ER) is continuous with the rough ER but has few or no
ribosomes on its cytoplasmic surface. Functions of the smooth ER include:
1. Synthesis of carbohydrates, lipids, and steroid hormones
2. Detoxification of medications and poisons
3. Storage of calcium ions
In muscle cells, a special type of smooth ER called the sarcoplasmic reticulum is responsible for storage
of calcium ions that are needed to trigger the coordinated contractions of the muscle cells.
There are also tiny "smooth" patches of ER found within the rough ER. These patches serve as exit sites
for vesicles budding off from the rough ER and are called transitional ER^11start superscript, 1, end
superscript.
The Golgi apparatus
When vesicles bud off from the ER, where do they go? Before reaching their final destination, the lipids
and proteins in the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the
right place. This sorting, tagging, packaging, and distribution takes place in the Golgi apparatus(Golgi
body), an organelle made up of flattened discs of membrane.
Micrograph of the Golgi apparatus showing a series of flattened membrane discs in cross-section
_Image credit: "The endomembrane system and proteins: Figure 3" by OpenStax College, Biology (CC
BY 3.0), modification of work by Lousia Howard_
The receiving side of the Golgi apparatus is called the cis face and the opposite side is called
the trans face. Transport vesicles from the ER travel to the cisface, fuse with it, and empty their contents
into the lumen of the Golgi apparatus.
As proteins and lipids travel through the Golgi, they undergo further modifications. Short chains of sugar
molecules might be added or removed, or phosphate groups attached as tags. Carbohydrate processing
is shown in the diagram as the gain and loss of branches on the purple carbohydrate group attached to
the protein.

Image showing transport of a membrane protein from the rough ER through the Golgi to the plasma
membrane. The protein is initially modified by the addition of branching carbohydrate chains in the rough
ER; these chains are then trimmed back and replaced with other branching chains in the Golgi apparatus.
The protein, with its final set of carbohydrate chains, is then transported to the plasma membrane in a
transport vesicle. The vesicle fuses with the plasma membrane, its lipids and protein cargo becoming part
of the plasma membrane.
_Image modified from "The endomembrane system and proteins: Figure 1" by OpenStax College, Biology
(CC BY 3.0), modification of work by Magnus Manske_
Finally, the modified proteins are sorted (based on markers such as amino acid sequences and chemical
tags) and packaged into vesicles that bud from the trans face of the Golgi. Some of these vesicles deliver
their contents to other parts of the cell where they will be used, such as the lysosome or vacuole. Others
fuse with the plasma membrane, delivering membrane-anchored proteins that function there and
releasing secreted proteins outside the cell.
Cells that secrete many proteins—such as salivary gland cells that secrete digestive enzymes, or cells of
the immune system that secrete antibodies—have many Golgi stacks. In plant cells, the Golgi apparatus
also makes polysaccharides (long-chain carbohydrates), some of which are incorporated into the cell wall.
Lysosomes
The lysosome is an organelle that contains digestive enzymes and acts as the organelle-recycling facility
of an animal cell. It breaks down old and unnecessary structures so their molecules can be reused.
Lysosomes are part of the endomembrane system, and some vesicles that leave the Golgi are bound for
the lysosome.
[Why don't lysosomes digest themselves?]
^{1,2}start superscript, 1, comma, 2, end superscript
Lysosomes can also digest foreign particles that are brought into the cell from outside. As an example,
let's consider a class of white blood cells called macrophages, which are part of the human immune
system. In a process known as phagocytosis, a section of the macrophage’s plasma membrane
invaginates—folds inward—to engulf a pathogen, as shown below.

Diagram of phagocytosis, in which the phagosome generated by engulfment of a particle fuses with a
lysosome, allowing digestion of the particle.
_Image credit: modified from "The endomembrane system and proteins: Figure 4" by OpenStax College,
Biology (CC BY 3.0)_
The invaginated section, with the pathogen inside, pinches off from the plasma membrane to form a
structure called a phagosome. The phagosome then fuses with a lysosome, forming a combined
compartment where digestive enzymes destroy the pathogen.
Vacuoles
Plants cells are unique because they have a lysosome-like organelle called the vacuole. The large
central vacuole stores water and wastes, isolates hazardous materials, and has enzymes that can break
down macromolecules and cellular components, like those of a lysosome.^33start superscript, 3, end
superscript Plant vacuoles also function in water balance and may be used to store compounds such as
toxins and pigments (colored particles).^44start superscript, 4, end superscript
Lysosomes vs. peroxisomes
One point that can be confusing is the difference between lysosomes and peroxisomes. Both types of
organelles are involved in breaking down molecules and neutralizing hazards to the cell. Also, both
usually show up as small, round blobs in diagrams.
However, the peroxisome is a different organelle with its own unique properties and role in the cell. It
houses enzymes involved in oxidation reactions, which produce hydrogen peroxide (\text H_2 \text
O_2H2O2H, start subscript, 2, end subscript, O, start subscript, 2, end subscript) as a by-product. The
enzymes break down fatty acids and amino acids, and they also detoxify some substances that enter the
body. For example, alcohol is detoxified by peroxisomes found in liver cells.
Importantly, peroxisomes—unlike lysosomes—are not part of the endomembrane system. That means
they don't receive vesicles from the Golgi apparatus. You can learn more about how proteins are shipped
to the peroxisome in the article on protein targeting.
What are mitochondria?
Mitochondria are often referred to as the powerhouses of the cell. They help turn the energy we take from
food into energy that the cell can use. But, there is more to mitochondria than energy production.
Present in nearly all types of human cell, mitochondria are vital to our survival. They generate the majority
of our adenosine triphosphate (ATP), the energy currency of the cell.
Mitochondria are also involved in other tasks, such as signaling between cells and cell death, otherwise
known as apoptosis.
The structure of mitochondria

A basic diagram of a mitochondrion

Mitochondria are small, often between 0.75 and 3 micrometers and are not visible under the microscope
unless they are stained.
Unlike other organelles (miniature organs within the cell), they have two membranes, an outer one and an
inner one. Each membrane has different functions.
Mitochondria are split into different compartments or regions, each of which carries out distinct roles.
Some of the major regions include the:
Outer membrane: Small molecules can pass freely through the outer membrane. This outer portion
includes proteins called porins, which form channels that allow proteins to cross. The outer membrane
also hosts a number of enzymes with a wide variety of functions.
Intermembrane space: This is the area between the inner and outer membranes.
Inner membrane: This membrane holds proteins that have several roles. Because there are no porins in
the inner membrane, it is impermeable to most molecules. Molecules can only cross the inner membrane
in special membrane transporters. The inner membrane is where most ATP is created.
Cristae: These are the folds of the inner membrane. They increase the surface area of the membrane,
therefore increasing the space available for chemical reactions.
Matrix: This is the space within the inner membrane. Containing hundreds of enzymes, it is important in
the production of ATP. Mitochondrial DNA is housed here (see below).
Different cell types have different numbers of mitochondria. For instance, mature red blood cells have
none at all, whereas liver cells can have more than 2,000. Cells with a high demand for energy tend to
have greater numbers of mitochondria. Around 40 percent of the cytoplasm in heart muscle cells is taken
up by mitochondria.
Although mitochondria are often drawn as oval-shaped organelles, they are constantly dividing (fission)
and bonding together (fusion). So, in reality, these organelles are linked together in ever-changing
networks.
Also, in sperm cells, the mitochondria are spiraled in the midpiece and provide energy for tail motion.
What do mitochondria do?
Mitochondria are important in a number of processes.
Although the best-known role of mitochondria is energy production,
they carry out other important tasks as well.
In fact, only about 3 percent of the genes needed to make a
mitochondrion go into its energy production equipment. The vast
majority are involved in other jobs that are specific to the cell type
where they are found.
Below, we cover a few of the roles of the mitochondria:
Producing energy
ATP, a complex organic chemical found in all forms of life, is often referred to as the molecular unit of
currency because it powers metabolic processes. Most ATP is produced in mitochondria through a series
of reactions, known as the citric acid cycle or the Krebs cycle.
Energy production mostly takes place on the folds or cristae of the inner membrane.
Mitochondria convert chemical energy from the food we eat into an energy form that the cell can use. This
process is called oxidative phosphorylation.
The Krebs cycle produces a chemical called NADH. NADH is used by enzymes embedded in the cristae
to produce ATP. In molecules of ATP, energy is stored in the form of chemical bonds. When these
chemical bonds are broken, the energy can be used.
Cell death
Cell death, also called apoptosis, is an essential part of life. As cells become old or broken, they are
cleared away and destroyed. Mitochondria help decide which cells are destroyed.
Mitochondria release cytochrome C, which activates caspase, one of the chief enzymes involved in
destroying cells during apoptosis.
Because certain diseases, such as cancer, involve a breakdown in normal apoptosis, mitochondria are
thought to play a role in the disease.
Storing calcium
Calcium is vital for a number of cellular processes. For instance, releasing calcium back into a cell can
initiate the release of a neurotransmitter from a nerve cell or hormones from endocrine cells. Calcium is
also necessary for muscle function, fertilization, and blood clotting, among other things.
Because calcium is so critical, the cell regulates it tightly. Mitochondria play a part in this by quickly
absorbing calcium ions and holding them until they are needed.
Other roles for calcium in the cell include regulating cellular metabolism, steroid synthesis, and hormone
signaling.
Heat production
When we are cold, we shiver to keep warm. But the body can also generate heat in other ways, one of
which is by using a tissue called brown fat.
During a process called proton leak, mitochondria can generate heat. This is known as non-shivering
thermogenesis. Brown fat is found at its highest levels in babies, when we are more susceptible to cold,
and slowly levels reduce as we age.
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Mitochondrial disease
If mitochondria do not function correctly, it can cause a range of
medical problems.
The DNA within mitochondria is more susceptible to damage
than the rest of the genome.
This is because free radicals, which can cause damage to DNA,
are produced during ATP synthesis.
Also, mitochondria lack the same protective mechanisms found in the nucleus of the cell.
However, the majority of mitochondrial diseases are due to mutations in nuclear DNA that affect products
that end up in the mitochondria. These mutations can either be inherited or spontaneous.
When mitochondria stop functioning, the cell they are in is starved of energy. So, depending on the type
of cell, symptoms can vary widely. As a general rule, cells that need the largest amounts of energy, such
as heart muscle cells and nerves, are affected the most by faulty mitochondria.
The following passage comes from the United Mitochondrial Disease Foundation:
"Because mitochondria perform so many different functions in different tissues, there are literally
hundreds of different mitochondrial diseases. [...] Because of the complex interplay between the hundreds
of genes and cells that must cooperate to keep our metabolic machinery running smoothly, it is a hallmark
of mitochondrial diseases that identical mtDNA mutations may not produce identical diseases."
Diseases that generate different symptoms but are due to the same mutation are referred to as
genocopies.
Conversely, diseases that have the same symptoms but are caused by mutations in different genes are
called phenocopies. An example of a phenocopy is Leigh syndrome, which can be caused by several
different mutations.
Although symptoms of a mitochondrial disease vary greatly, they might include:
1. loss of muscle coordination and weakness
2. problems with vision or hearing
3. learning disabilities
4. heart, liver, or kidney disease
5. gastrointestinal problems
6. neurological problems, including dementia
Other conditions that are thought to involve some level of mitochondrial dysfunction, include:
1. Parkinson's disease
2. Alzheimer's disease
3. bipolar disorder
4. schizophrenia
5. chronic fatigue syndrome
6. Huntington's disease
7. diabetes
8. autism