Module 1 Cells

CHEM233
Biochemistry for Nurses
Module 1: CELLS
Estimated Read Time: 1.5 HRS
Learning Objectives:
1. Compare and contrast prokaryotic and eukaryotic cells
2. Identify the main components of the cell
3. Discuss the structure and function of the different organelles
4. Identify cell organelles and the main cytoskeletal components in diagrams
Prepared by:
Engr. Eleazar Al T. Guzman
Department of Chemical Engineering
CIT – University
THE CONTENTS OF THIS MODULE ARE TAKEN FROM VARIOUS REFERENCES AND WILL BE USED FOR
EDUCATIONAL PURPOSES ONLY
What is Biochemistry?
Biochemistry is the chemistry of living organisms. It is the science concerned with the chemical basis of
life. Specifically, biochemistry is concerned with the structures and physical properties of biological
molecules including protein, carbohydrates, lipids, and nucleic acids. In addition, it also studies the
mechanism of enzyme action, chemical regulation of metabolism, chemistry of nutrition, molecular basis
of genetics, chemistry of vitamins, energy utilization in the cell, and the chemistry of the immune
response.
STRUCTURE OF A CELL
The cell, discovered by Robert Hooke in 1665, is the basic, living, structural, and functional unit of the
body. They are often called the building blocks of life. The cell is basically the structural and functional
unit of all living organisms.
Some organisms are unicellular such as bacteria, while some are multicellular (e.g. human cells). But on
the basis of structural differences, there are two types of cells: prokaryotes and eukaryotes. (Viruses also
bear some similarities to cells, but these are limited.) Prokaryotic cells are the simplest type of cells. Many
one-celled organisms are prokaryotes. The simplest way to distinguish these two types is that a
prokaryotic cell contains no well-defined nucleus, whereas the opposite is true for a eukaryotic cell.
PROKARYOTIC CELLS
The most primitive cell structure where there is an absence of nuclear membrane, nucleolus and
membrane bound organelles. The genetic material is stored in the form of nucleoid, found freely
distributed in the cytoplasm. Generally, this genetic material is made-up of one or more folded DNA stands
without presence of histone proteins. The bacteria, viruses and some of the fungi are good examples of
prokaryotic cells, which are significant in health sciences.
EUKARYOTIC CELLS
It is the most advanced cell, having a well-developed nucleus with nucleic membrane, nucleolus and
genetic material in the form of chromosomes. These cells are found in higher organisms such as human
beings. Structurally and functionally, eukaryotic cells are larger in size, advanced, developed and complex.
Some examples of eukaryotes are animals, plants, fungi, and protists. You are a eukaryote!
ANIMAL CELLS AND HOW THEY WORK
All animal cells (which are, as you now know, eukaryotic cells) have a number of components, most of
which are considered to be organelles. The primary components of animal cells are listed in Table 1-1.
(These components, and a few others, are also present in plant cells.) Figure 1-2 illustrates a simplified
animal cell.
See the human cell in 3D! (https://youtu.be/n_Jz9f7V6uA)
Can you identify the parts in the video?
COMPONENTS OF A CELL
The cells are too small to be seen with the naked eye. However, a microscope can be used to view a cell
and its components after staining with appropriate dyes. The cell and its components absorb the dye and
their structure and size may be clearly differentiated using a microscope. A typical eukaryotic cell consists
of the following components:
➢ Plasma membrane: Outer, limiting membrane separating the cell's internal components from the
extracellular materials and external environment.
➢ Cytosol: The thick intracellular fluid is termed as cytosol. The cytosol contains many dissolved
proteins and enzymes, nutrients, ions and other small molecules, which all participate in various
phases of metabolism. Organelles and inclusions are suspended in the cytosol. The term
cytoplasm includes cytosol, all organelles (except nucleus) and inclusions.
➢ Organelles: Highly organized structures with characteristic shapes that are specialized for specific
cellular activities. The organelle with the largest volume is the nucleus, which contains most of
the cell’s genetic material. The other major organelles are mitochondria, endoplasmic reticulum,
golgi apparatus, lysosomes, ribosomes, vacuoles and peroxisomes.
➢ Inclusions: These are the temporary structures in the cytoplasm that contain secretions and
storage product of the cell.
Now watch this! (https://youtu.be/URUJD5NEXC8)
COMPONENT OF THE CELL: PLASMA MEMBRANE
The plasma membrane not only defines the borders of the cell, but also allows the cell to interact with its
environment in a controlled way. Cells must be able to exclude, take in, and excrete various substances,
all in specific amounts. In addition, they must able to communicate with other cells, identifying themselves
and sharing information.
To perform these roles, the plasma membrane needs lipids, which make a semi-permeable barrier
between the cell and its environment. It also needs proteins, which are involved in cross-membrane
transport and cell communication, and carbohydrates (sugars and sugar chains), which decorate both the
proteins and lipids and help cells recognize each other.
The currently accepted model for the structure of the plasma membrane, called the fluid mosaic model,
was first proposed in 1972. This model has evolved over time, but it still provides a good basic description
of the structure and behavior of membranes in many cells.
According to the fluid mosaic model, the plasma membrane is a mosaic of components—primarily,
phospholipids, cholesterol, and proteins—that move freely and fluidly in the plane of the membrane. In
other words, a diagram of the membrane (like the one below) is just a snapshot of a dynamic process in
which phospholipids and proteins are continually sliding past one another.
Interestingly enough, this fluidity means that if you insert a very fine needle into a cell, the membrane
will simply part to flow around the needle; once the needle is removed, the membrane will flow back
together seamlessly.
The principal components of the plasma membrane are lipids (phospholipids and cholesterol), proteins,
and carbohydrate groups that are attached to some of the lipids and proteins.
• A phospholipid is a lipid made of glycerol, two fatty acid tails, and a phosphate-linked head group.
Biological membranes usually involve two layers of phospholipids with their tails pointing inward,
an arrangement called a phospholipid bilayer.
• Cholesterol, another lipid composed of four fused carbon rings, is found alongside phospholipids
in the core of the membrane.
• Membrane proteins may extend partway into the plasma membrane, cross the membrane
entirely, or be loosely attached to its inside or outside face.
• Carbohydrate groups are present only on the outer surface of the plasma membrane and are
attached to proteins, forming glycoproteins, or lipids, forming glycolipids.
The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary between different
types of cells. For a typical human cell, however, proteins account for about 50 percent of the composition
by mass, lipids (of all types) account for about 40 percent, and the remaining 10 percent comes from
carbohydrates.
Confused? No, worries! Watch this! (https://youtu.be/ipa1vmQ7H_4)
Phospholipids
Phospholipids, arranged in a bilayer, make up the basic fabric of the plasma membrane. They are well-
suited for this role because they are amphipathic, meaning that they have both hydrophilic and
hydrophobic regions.
The hydrophilic, or “water-loving,” portion of a phospholipid is its head, which contains a negatively
charged phosphate group as well as an additional small group (of varying identity, “R” in the diagram at
left), which may also or be charged or polar. The hydrophilic heads of phospholipids in a membrane bilayer
face outward, contacting the aqueous (watery) fluid both inside and outside the cell. Since water is a polar
molecule, it readily forms electrostatic (charge-based) interactions with the phospholipid heads.
The hydrophobic, or “water-fearing,” part of a phospholipid consists of its long, nonpolar fatty acid tails.
The fatty acid tails can easily interact with other nonpolar molecules, but they interact poorly with water.
Because of this, it’s more energetically favorable for the phospholipids to tuck their fatty acid tails away
in the interior of the membrane, where they are shielded from the surrounding water. The phospholipid
bilayer formed by these interactions makes a good barrier between the interior and exterior of the cell,
because water and other polar or charged substances cannot easily cross the hydrophobic core of the
membrane.
Thanks to their amphipathic nature, phospholipids aren’t just well-suited to form a membrane bilayer.
Instead, this is something they’ll do spontaneously under the right conditions! In water or aqueous
solution, phospholipids tend to arrange themselves with their hydrophobic tails facing each other and
their hydrophilic heads facing out. If the phospholipids have small tails, they may form a micelle (a small,
single-layered sphere), while if they have bulkier tails, they may form a liposome (a hollow droplet of
bilayer membrane
FUNCTIONS OF THE PLASMA MEMBRANE
Following are the major functions of the plasma membrane of a cell:
▪ Semi-permeable: The plasma membrane regulates the entry and exit of materials inside the cell.
It permits the passage of certain substances and restricts the passage of others. This property of
membrane is known as “selective permeability.”
▪ Receptor: The plasma membrane proteins can identify and attach to a specific molecule such as
hormones, neurotransmitter or a nutrient, that is important for some cellular function.
▪ Communication: The plasma membrane functions in cellular communication. This includes
interactions with the other body cells, foreign cells, hormones, neurotransmitters, enzymes,
nutrients and antibodies in extracellular fluid.
▪ Electrochemical gradient: The membrane maintains an electrical and chemical gradient, called an
electrochemical gradient, between the inside and outside the cell. The electrochemical gradient
and the resulting membrane potential are important for proper functioning of most the cells.
See it in 3D! (https://youtu.be/dCfcwmmBy6Q)
COMPONENT OF THE CELL: CYTOSOL
Chemically, cytosol is 75 to 90% water plus solid components. Proteins, carbohydrates, lipids and
inorganic substances comprise most of the solids. Inorganic substances and smaller organic substances,
such as simple sugars and amino acids are soluble in water and are present as solutes.
Larger organic compounds, like proteins and polysaccharides, glycogen, are found as colloidal particles
that remain suspended in the surrounding medium although they are not dissolved. The colloids bear
electrical charges that repel each other and thus remain suspended and separated. The cytosol contain
enzymes that catalyze catabolic and anabolic reactions, ATP is produced in glycolysis reactions.
COMPONENT OF THE CELL: ORGANELLES
An organelle (think of it as a cell’s internal organ) is a membrane bound structure found within a cell. Just
like cells have membranes to hold everything in, these mini-organs are also bound in a double layer of
phospholipids to insulate their little compartments within the larger cells. You can think of organelles as
smaller rooms within the factory, with specialized conditions to help these rooms carry out their specific
task. These organelles are found in the cytoplasm, a viscous liquid found within the cell membrane that
houses the organelles and is the location of most of the action happening in a cell. Below is a table of the
organelles found in the basic human cell, which we’ll be using as our template for this discussion.
Guided tour of the cell in 3D! (https://youtu.be/rKS-vvhMV6E)
1) NUCLEUS
The nucleus is the control center of a cell and is generally situated at the center of the cell, covered with
a double layered membrane (nuclear membrane) and contains all of the cell’s chromosomes, nucleoplasm
and nucleolus. Chromosomes carry the genetic material of the cell and nucleolus serves as site for
ribosome synthesis.
Most of the cells contain a single nucleus, some cells have more than one nucleus (such as some liver
cells). Long muscle cells have hundreds of nuclei. However, red blood cells during their maturation lose
their nucleus.
2) ENDOPLASMIC RETICULUM
Endoplasmic means inside (endo) the cytoplasm (plasm). Reticulum comes from the Latin word for net.
Basically, an endoplasmic reticulum is a plasma membrane found inside the cell that folds in on itself to
create an internal space known as the lumen. This lumen is actually continuous with the perinuclear space,
so we know the endoplasmic reticulum is attached to the nuclear envelope. There are actually two
different endoplasmic reticuli in a cell: the smooth endoplasmic reticulum and the rough endoplasmic
reticulum. The rough endoplasmic reticulum is the site of protein production, the smooth endoplasmic
reticulum is where lipids (fats) are made.
Rough Endoplasmic Reticulum
The rough endoplasmic reticulum is so-called because its surface is studded with ribosomes, the
molecules in charge of protein production. When a ribosome finds a specific RNA segment, that segment
may tell the ribosome to travel to the rough endoplasmic reticulum and embed itself. The protein created
from this segment will find itself inside the lumen of the rough endoplasmic reticulum, where it folds and
is tagged with a (usually carbohydrate) molecule in a process known as glycosylation that marks the
protein for transport to the Golgi apparatus. The rough endoplasmic reticulum is continuous with the
nuclear envelope, and looks like a series of canals near the nucleus. Proteins made in the rough
endoplasmic reticulum as destined to either be a part of a membrane, or to be secreted from the cell
membrane out of the cell. Without a rough endoplasmic reticulum, it would be a lot harder to distinguish
between proteins that should leave the cell, and proteins that should remain. Thus, the rough
endoplasmic reticulum helps cells specialize and allows for greater complexity in the organism.
See it in 3D! (https://youtu.be/DDsH0B5MdaA)
Smooth Endoplasmic Reticulum
The smooth endoplasmic reticulum makes lipids and steroids, instead of being involved in protein
synthesis. These are fat-based molecules that are important in energy storage, membrane structure, and
communication (steroids can act as hormones). The smooth endoplasmic reticulum is also responsible for
detoxifying the cell. It is more tubular than the rough endoplasmic reticulum, and is not necessarily
continuous with the nuclear envelope. Every cell has a smooth endoplasmic reticulum, but the amount
will vary with cell function. For example, the liver, which is responsible for most of the body’s
detoxification, has a larger amount of smooth endoplasmic reticulum.
See it in 3D! (https://youtu.be/HD5gT3n4-9k)
3. GOLGI APPARATUS (AKA GOLGI BODY AKA GOLGI)
We mentioned the Golgi apparatus earlier when we discussed the production of proteins in the rough
endoplasmic reticulum. If the smooth and rough endoplasmic reticula are how we make our product, the
Golgi is the mailroom that sends our product to customers. It is responsible for packing proteins from the
rough endoplasmic reticulum into membrane-bound vesicles (tiny compartments of lipid bilayer that
store molecules) which then translocate to the cell membrane. At the cell membrane, the vesicles can
fuse with the larger lipid bilayer, causing the vesicle contents to either become part of the cell membrane
or be released to the outside.
See it in 3D! (https://youtu.be/ady9okEbweg)
Different molecules actually have different fates upon entering the Golgi. This determination is done by
tagging the proteins with special sugar molecules that act as a shipping label for the protein. The shipping
department identifies the molecule and sets it on one of 4 paths:
1. Cytosol: the proteins that enter the Golgi by mistake are sent back into the cytosol (imagine the
barcode scanning wrong and the item being returned).
2. Cell membrane: proteins destined for the cell membrane are processed continuously. Once the
vesicle is made, it moves to the cell membrane and fuses with it. Molecules in this pathway are
often protein channels which allow molecules into or out of the cell, or cell identifiers which
project into the extracellular space and act like a name tag for the cell.
3. Secretion: some proteins are meant to be secreted from the cell to act on other parts of the body.
Before these vesicles can fuse with the cell membrane, they must accumulate in number, and
require a special chemical signal to be released. This way shipments only go out if they’re worth
the cost of sending them (you generally wouldn’t ship just one toy and expect to profit).
4. Lysosome: The final destination for proteins coming through the Golgi is the lysosome. Vesicles
sent to this acidic organelle contain enzymes that will hydrolyze the lysosome’s content.
4. LYSOSOME
The lysosome is the cell’s recycling center. These organelles are spheres full of enzymes ready to hydrolyze
(chop up the chemical bonds of) whatever substance crosses the membrane, so the cell can reuse the raw
material. These disposal enzymes only function properly in environments with a pH of 5, two orders of
magnitude more acidic than the cell’s internal pH of 7. Lysosomal proteins only being active in an acidic
environment acts as safety mechanism for the rest of the cell - if the lysosome were to somehow leak or
burst, the degradative enzymes would inactivate before they chopped up proteins the cell still needed.
See it in 3D! (https://youtu.be/pF0jPXtULd4)
5. PEROXISOME
Like the lysosome, the peroxisome is a spherical organelle responsible for destroying its contents. Unlike
the lysosome, which mostly degrades proteins, the peroxisome is the site of fatty acid breakdown. It also
protects the cell from reactive oxygen species (ROS) molecules which could seriously damage the cell.
ROSs are molecules like oxygen ions or peroxides that are created as a byproduct of normal cellular
metabolism, but also by radiation, tobacco, and drugs. They cause what is known as oxidative stress in
the cell by reacting with and damaging DNA and lipid-based molecules like cell membranes. These ROSs
are the reason we need antioxidants in our diet.
6. MITOCHONDRIA
Just like a factory can’t run without electricity, a cell can’t run without energy. ATP (adenosine
triphosphate) is the energy currency of the cell, and is produced in a process known as cellular respiration.
Though the process begins in the cytoplasm, the bulk of the energy produced comes from later steps that
take place in the mitochondria.
Like we saw with the nuclear envelope, there are actually two lipid bilayers that separate the
mitochondrial contents from the cytoplasm. We refer to them as the inner and outer mitochondrial
membranes. If we cross both membranes we end up in the matrix, where pyruvate is sent after it is
created from the breakdown of glucose (this is step 1 of cellular respiration, known as glycolysis). The
space between the two membranes is called the intermembrane space, and it has a low pH (is acidic)
because the electron transport chain embedded in the inner membrane pumps protons (H+) into it.
Energy to make ATP comes from protons moving back into the matrix down their gradient from the
intermembrane space.
Mitochondria are also somewhat unique in that they are self-replicating and have their own DNA, almost
as if they were a completely separate cell. The prevailing theory, known as the endosymbiotic theory, is
that eukaryotes were first formed by large prokaryotic cells engulfing smaller cells that looked a lot like
mitochondria. Instead of being digested, the engulfed cells remained intact and the arrangement turned
out to be advantageous to both cells, which created a symbiotic relationship.
See it in 3D! (https://youtu.be/inJKNDN4u1s)
6. RIBOSOMES
All living cells contain ribosomes, tiny organelles composed of approximately 60 percent ribosomal RNA
(rRNA) and 40 percent protein. However, though they are generally described as organelles, it is important
to note that ribosomes are not bound by a membrane and are much smaller than other organelles. Some
cell types may hold a few million ribosomes, but several thousand is more typical. The organelles require
the use of an electron microscope to be visually detected
Ribosomes are mainly found bound to the endoplasmic reticulum and the nuclear envelope, as well as
freely scattered throughout the cytoplasm, depending upon whether the cell is plant, animal, or bacteria.
The organelles serve as the protein production machinery for the cell and are consequently most
abundant in cells that are active in protein synthesis, such as pancreas and brain cells. Some of the
proteins synthesized by ribosomes are for the cell's own internal use, especially those that are produced
by free ribosomes. Many of the proteins produced by bound ribosomes, however, are transported outside
of the cell.
See it in 3D! (https://youtu.be/1cwtnwUbQ80)
So far we’ve discussed organelles, the membrane-bound structures within a cell that have some sort of
specialized function. Now let’s take a moment to talk about the scaffolding that’s holding all of this in
place - the walls and beams of our factory.
Cytoskeleton
Within the cytoplasm there is network of protein fibers known as the cytoskeleton. This structure is
responsible for both cell movement and stability. The major components of the cytoskeleton are
microtubules, intermediate filaments, and microfilaments.
Microtubules
Microtubules are small tubes made from the protein tubulin. These tubules are found in cilia and
flagella, structures involved in cell movement. They also help provide pathways for secretory
vesicles to move through the cell, and are even involved in cell division as they are a part of the
mitotic spindle, which pulls homologous chromosomes apart.
Intermediate Filaments
Smaller than the microtubules, but larger than the microfilaments, the intermediate filaments are
made of a variety of proteins such as keratin and/or neurofilament. They are very stable, and help
provide structure to the nuclear envelope and anchor organelles.
Microfilaments
Microfilaments are the thinnest part of the cytoskeleton, and are made of actin [a highly-
conserved protein that is actually the most abundant protein in most eukaryotic cells]. Actin is
both flexible and strong, making it a useful protein in cell movement. In the heart, contraction is
mediated through an actin-myosin system.

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CHEM233

Biochemistry for Nurses

Estimated Read Time: 1.5 HRS

ANIMAL CELLS AND HOW THEY WORK

See the human cell in 3D! (https://youtu.be/n_Jz9f7V6uA)

Can you identify the parts in the video?

Now watch this! (https://youtu.be/URUJD5NEXC8)

COMPONENT OF THE CELL: PLASMA MEMBRANE

Confused? No, worries! Watch this! (https://youtu.be/ipa1vmQ7H_4)

FUNCTIONS OF THE PLASMA MEMBRANE

Following are the major functions of the plasma membrane of a cell:

See it in 3D! (https://youtu.be/dCfcwmmBy6Q)

COMPONENT OF THE CELL: ORGANELLES

Guided tour of the cell in 3D! (https://youtu.be/rKS-vvhMV6E)

See it in 3D! (https://youtu.be/DDsH0B5MdaA)

See it in 3D! (https://youtu.be/HD5gT3n4-9k)

See it in 3D! (https://youtu.be/ady9okEbweg)

See it in 3D! (https://youtu.be/pF0jPXtULd4)

See it in 3D! (https://youtu.be/inJKNDN4u1s)

See it in 3D! (https://youtu.be/1cwtnwUbQ80)

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