The Anatomy

and
Regulatory Functions
Of Eukaryotic Cells

An Introductory Description for science students

By: Jesse Ruben



























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Audience and Scope

Starting in high school, students start to learn more complicated
sciences. Biology and biochemistry are the fundamental studies
of how life works both at a macro and micro level scale. From
the shape of leaves to the flagella on bacteria, science affects
everyone and everything. When people get sick from a bacterial
or viral infection it interrupts important functions inside the
body, but more specifically, within the body's cells.

The purpose of this technical document is to describe the
regulatory functions and the anatomy of a cell with specific
focus on the DNA structure and purpose, construction of
proteins, and regulation of transportation from the extracellular
matrix into the cell. In addition, attention will be given to highly
important side organelles, such as the mitochondria, and
chloroplast.

Introduction

The theory of evolution describes birth of the first cell through
the process of biopoiesis. The origin of life created a pathway
over billions of years, starting at the construction of the clump
of lipids called the proto-cell (Figure 1). As time moved forward
these proto-cells were able to incorporate small molecules that
it properly associated with, due to chemical charge and size of
the lipid membrane. Trillions of chemical reactions were set in
motion in the ocean full of proto-cells. In turn, one of the proto-
cells came to form a simple version on DNA that could replicate
itself, known as a cell and this was the start of life as we know it
today.

Throughout the cell's generational history, the DNA mutated
the offspring, thereby possibly leading to more complex
functions. Most mutations however ended in tragedy and select
positive mutations led to the survival of the cell which passed
on that DNA to their offspring. Some cells split into a separate
category called Eukaryotes, while others remained as
Prokaryotes and were able to survive and further mutate.

Modern cells make up everything we are, as well as all living
forms of life. Understanding the basic cell anatomy and
functions of these two forms of life are crucial for
understanding ourselves. In this document, we focus on the
Eukaryotes, since humans are primarily made up of these cells.

Flagella - whip -like Tail motor on cells
to improve motility.
Extracellular Matrix The chemical
environment surrounding a cell
Biopoiesis - The process of inanimate
to animate
Proto-cell - Lipid bilayer sheet
forming an interior compartment,
accessible for environmental uptake
Eukaryotes - Cells with a true Nucleus
Prokartotes- Cells without a true
Nucleus called a Nucleoid, the
absence of an envelope
* Nucleus is where the DNA is stored
and protected in the cell

Figure 1
Fatty acids / lipids
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DNA into you

DNA is a genetic code that describes to your cells how to form,
how to look, and how to function. In other words, DNA creates
a unique version of you. They determine if you have blonde
hair or brown hair, if you are a boy or a girl, and even if you
walk with a funny gait.

The structure DNA has is a helical shape made up of a
phosphate group and a deoxyribose sugar, forming a
phosphodiester "back-bone" with a nitrogenous base
protruding outwards. These components form a linear DNA
molecule called a template strand. Hydrogen is an element that
contributes a positively charged atmosphere that attracts
elements that contain a negatively atmosphere, like oxygen and
nitrogen. Each nitrogenous base contains these elements, in
which they attract and complement a different nitrogenous
base. This interaction of complementary molecules helps the
second strand of DNA anneal the two strands together. Four
different nitrogenous bases are found in a DNA, Cytosine which
complements a bond with Guanine and Adenine which
complements a bond with Thymine. This forms a base pair.

Genes are a combination of these four nitrogenous bases that
extend thousands of base pairs long and perform a unique
function known as a trait. The template DNA is coded by
transcriptional proteins forming a complementary RNA strand
(Figure 4a). RNA is a synthesis protein intermediate molecule
that is structured like DNA, except it replaces thymine with
uracil. The cell uses this mechanism to differentiate RNA from
DNA in order to translate the genetic code into proteins that
perform a specific task; the trait. Proteins are molecules that
provide a function; from how it metabolizes iron to creating the
color in your eyes (Figure 4b).


Anneal - Process of slowly cooling an object
to allow recombination of DNA strands
Trait - distinguishing quality or characteristic
Nucleoid
Nucleus
Deoxyribose
Sugar
Nitrogenous
base
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Membrane Structure



The membrane of a cell is a bilayer filament that surrounds the
cell made out of fatty acids. Fatty acids, known as lipids, are
molecules that have a hydrophobic tail and a hydrophilic head.
Hydrophobic molecules tend to interact with each other to
reduce the exposure to water. On the other hand, hydrophilic
heads tend to interact with water. Mass amount of lipids form a
sheet-like barrier containing an inside compartment known as
cytoplasm, and protect it from the Extracellular matrix (ECM)
environment (Figure 5).

Integrated proteins imbedded inside this bi-layered wall and
peripheral proteins are connected to the surface of the wall and
help the cell with bi-directional transportation of molecules in
and out of the cell. These proteins can act as signaling receptors
(Figure 6a) to relay messages to the nucleolus if a specific
protein is needed for translation(Figure 6b). An example of this
process is when bacteria sense an anti-biotic drug. It will signal a
message with other proteins to the nucleolus to produce a
resistant molecule that will degrade the drug. (Figure 6c)
Figure 5

X
figure 4a
figure 4
Figure 4b
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Intercellular Vesicular Traffic

Cells depend on signals from the environment to indicate a
function that the cell must perform in order to survive. Some of
these functions include absorption of nutrition, fusion of waste,
secretion, localization of proteins, and even destruction of
material. Endocytosis is the process in which the cell imports
nutrition or needed chemicals, as well as destroying and
recycling molecules. The Secretory pathway, known as
Exocytosis, is the process of exporting waste outside of the cell.
Transcytosis is a combination of both pathways whose function
is to bypass a molecule through the cell, often used by a barrier-
like cell (Figure) 7. For example, endothelial cells absorb the
glucose from the gut and secretes it into the blood. These
pathways of transportation are regulated by the Golgi
apparatus. This mechanism that allows these three pathways to
function as transports is an enclosed bi-layered membrane
called a vesicle.

- Ligand/ECM signal
- Signal molecule (GTP/ATP)
- Movement of protein


Figure 6
Figure 6a
Figure 6b
Figure 6c
Figure 7
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Two different Endoplasmic Reticulum (ER) layers the membrane
enclosing the nuclear envelope around the nucleus. One of the
layers that regulate protein synthesis from RNA is embedded by
proteins called ribosomes. This half of the ER is known as the
rough endoplasmic reticulum (RER). The second half is called
the smooth endoplasmic reticulum (SER), due to the lack of
embedded ribosomes. The responsibility of the SER is to
regulated lipid and carbohydrate metabolism (Figure 8) .


Skeleton of the Cell


Animal cells are organisms that are continuously motile and
have a dynamic outer and inner structure. Microtubules and
Actin are small molecules that form long fibrous-like filaments
that are continuously altered in stability. These are called the
Cytoskeleton. Signals from a chemical or concentration gradient
can be detected by the receptors on the membrane. These
signals from the extracellular matrix can cause the cell to either
attract or retract these filaments from the signaling beacon.
Specifically, actin or tubule monomers connect into a bridge
towards the receptors, while degrading the furthest end. This
process is called treed-milling (Figure 9a) .

Vesicles are compartments made by interactions from the Golgi
apparatus that travel through the cytoplasm of the cell. Vesicles
move along the microtubule filaments by proteins called Myosin
and Kinesin. Myosin and Kinesin are proteins that hold on to the
edge of a vesicle and move up or down the filament according
to the electrical charge of the microtubule. (Figure 9b)



Power Plant of the cell

All of the processes in the previous sections require energy to
operate. We know that in the cells that have been studied
today, a symbiotic relationship was formed by an aerobic and
an anaerobic cell where the small anaerobic cell fused inside the
larger aerobic cell. The small cell was given nutrition that the
larger cell absorbed through endocytosis. In turn, the cell was
able to produce waste that was considered to be energy for a
larger cell called ATP. This small cell became what is known as
the Mitochondria. This is the power plant of the cell (Figure
10a) .

Figure 9a
Figure 8
Figure 9b
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Mitochondria
This theory was supported by another incident that occurred
millions of years after that separated into another type of
eukaryotic cell. Plants have an extra subcomponent in their
cytoplasm called chloroplast. Chloroplast is another cell that is
able to absorb light and produce a waste that is used for energy
for a larger cell (Figure 10b). Plants have chloroplast as well as a
mitochondria, but no cell has a chloroplast without a
mitochondria. This unique relationship indicates that the same
symbiotic relationship occurred after the first relationship of the
mitochondria, and gave birth to plant cells that we see today.


Conclusion

This document described the broad functions and anatomy of a
cell. The first step explained the structure of DNA and the
function of its genetic code. The genetic code describes all the
cells from your hair to the proteins it produces. Next is the
description of the membrane around the cell that is used for
protection of the cell, as well as for relaying signals back to the
nucleus for transcription and translation. The translation of
proteins for RNA happens inside the RER on proteins called
ribosome. The proteins produced from this synthesis are
exported and localized through vesicles by the Golgi apparatus.
When the vesicles are released by the Golgi, they travel up and
down the microtubules of the cytoskeleton by proteins called
myosin and keisin. All of these functions use energy that is
produced in massive amounts by the mitochondria and
chloroplast.


Figure 10a
Figure 10b