General Biology

Chapter 2
Structure of the Cell

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General Biology

Introduction to the cells

The word cell comes from the Latin cellula, meaning "a small room". The cell is the basic
structural and functional unit of all known living organisms. It is the smallest unit of life that is
classified as a living thing, and is often called the building block of life. Some notes about
cells should be kept in mind:
§ Nothing less than cell can be called living: The vital functions of an organism occur
within cells. All cells come from preexisting. Like ourselves, the individual cells that form
our bodies can grow, reproduce, process information, respond to stimuli and carry out an
amazing array of chemical reactions. These abilities define life. Even simple unicellular
organisms exhibit all the hallmark properties of life, indicating that the cell is the
fundamental unit of life.
§ The Diversity: Organisms can be classified as unicellular (consisting of a single cell;
including most bacteria) or multicellular (including plants and animals). Cells come in an
amazing variety of sizes and shapes. Some move rapidly and have fast-changing
structures. Others are largely stationary and structurally stable. Oxygen kills some cells
but is an absolute requirement for others.
§ Similar basic chemistry: Despite the extraordinary diversity of plants and animals, all
living things are fundamentally similar inside. Cells resemble one another to an
astonishing degree in the details of their chemistry and sharing the same machinery for
the most basic functions. All cells are composed of the same sorts of molecules that
participate in the same types of chemical reactions.
§ Invention of the light microscope led to the discovery of cells: The descriptive term
for the smallest living biological structure was coined by Robert Hooke in a book he in
1665 when he compared the cork cells he saw through his microscope to the small
rooms. The name cell stuck even though the structures Hooke described were only the
cell walls that remained after the living plant cells inside them had died.

Types of cells:
The biological universe consists of two types of cells:

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§ Prokaryotic cells consist of a single closed compartment that is surrounded by the

plasma membrane, lacks a defined nucleus, and has a relatively simple internal
organization. Examples: Bacteria and Blue-green algae.
§ Eukaryotic cells: unlike prokaryotic cells, contain a defined membrane-bound nucleus
and extensive internal membranes that enclose other compartments. The region of the cell
lying between the plasma membrane and the nucleus is the cytoplasm, comprising the
cytosol (aqueous phase) and the organelles. Eukaryotes comprise all members of the
plant and animal kingdoms, including the fungi, which exist in both multicellular forms
(molds) and unicellular forms (yeasts).

Eukaryotes Prokaryotes
Complex in structure, with nuclei and more complex in structure, with nuclei and
membrane-bound organelles membrane-bound organelles
Large (100 - 1000 µm) Small (1-10 µm)
DNA in nucleus, bounded by membrane DNA circular, unbounded
Genome consists of several chromosomes Genome consists of single chromosome
Sexual reproduction common, by mitosis and Asexual reproduction common, not by mitosis
meiosis or meiosis
Mitochondria and other organelles present No general organelles
Most forms are multicellular Most forms are singular
Aerobic Anaerobic

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Biological Membranes
Membranes
Membranes are the outer boundary of individual cells and of certain organelles. Plasma
membranes are the selectively permeable outermost structures of cells that separate the
interior of the cell from the environment. Certain molecules are permitted to enter and exit the
cell through transport across the plasma membrane.

Components of biological membranes:

All cell membranes are composed of the same materials:
1. Lipids
Lipids are the most abundant type of macromolecule present. Plasma and organelle
membranes contain between 40% and 80% lipid. There are three types of lipids are found:
§ Phospholipids: The most abundant of the membrane lipids are the phospholipids. They
are polar, ionic compounds that are amphipathic (have both hydrophilic and hydrophobic
components). The hydrophilic or polar portion is in the “head group”. Within the head group
is the phosphate and an alcohol that is attached to it. The hydrophobic portion of the
phospholipid is a long, hydrocarbon (structure of carbons and hydrogens) fatty acid tail.
While the polar head groups of the outer leaflet extend outward toward the environment,
the fatty acid tails extend inward.
§ Cholesterol: Another major component of cell membranes
is cholesterol. An amphipathic molecule, cholesterol
contains a polar hydroxyl group as well as a hydrophobic
steroid ring and attached hydrocarbon. Cholesterol is
dispersed throughout cell membranes, intercalating
between phospholipids.

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Its polarhydroxyl group is near the polar head groups of the

phospholipidswhile the steroid ring and hydrocarbon tails of
cholesterol areoriented parallel to those of the
phospholipids. Cholesterolfits into the spaces created by
the kinks of the unsaturatedfatty acid tails, decreasing the
ability of the fatty acids to undergomotion and therefore
causing stiffening and strengthening of themembrane.
§ Glycolipids: Lipids with attached carbohydrate (sugars), glycolipidsare found in cell
membranes in lower concentration than phospholipids and cholesterol. The carbohydrate
portion is always oriented toward the outside of the cell, projecting into the environment.
Glycolipids help to form the carbohydrate coat observed on cells and are involved in cell-
to-cell interactions.
2. Proteins
While lipids form the main structure of the membrane, proteins arelargely responsible for
many biological functions of the membrane. The types of proteins within a plasma membrane
vary depending on the cell type. However, all membrane proteins are associated with
membrane in one of three main ways:
§ Transmembrane proteins: They are embedded within the lipid bilayer of the membrane
with structures that extend from the environment into the cytosol. All trans membrane
proteins contain both hydrophilic and hydrophobic components. These proteins are
oriented with their hydrophilic portions in contact with the aqueous exterior environment
and with the cytosol and their hydrophobic portions in contact with the fatty acid tails of the
phospholipids.
§ Lipid-anchored proteins: They are attached covalently to a portion of a lipid without
entering the core portion of the bilayer of the membrane. Both trans membrane and lipid-
anchored proteins are integral membrane proteins since they can only be removed from a
membrane by disrupting the entire membrane structure.
§ Peripheral membrane proteins: These proteins are located on the cytosolic side of the
membrane and are only indirectly attached to the lipid of the membrane; they bind to other
proteins that are attached to the lipids.

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Structure of biological membranes:

The proteins and lipids of a cellular membrane are arranged in a
certain way to form a stable outer structure of the cell. The
membrane components, including lipids and proteins, are not
fixed rigidly into a particular location. Both can exhibit several
types of motions. Membrane proteins can also move laterally and
can rotate.
Despite its fluidity, the membrane structure is very stable and supportive for the cell. The
arrangement of the phospholipids provides the basic structure which is then augmented by
cholesterol, with functional roles played by proteins. The biological membranes have the
following characters:
§ Bilayer arrangement: Membrane phospholipids are oriented with their hydrophobic fatty
acid tails facing away from the polar, aqueous fluids of both the cytosol and the
environment. The hydrophilic portions of the phospholipids are oriented toward the polar
environment. Two layers of phospholipids are required to achieve this structure.
§ Asymmetry: The fatty acid tails of all the phospholipids are structurally very similar to
each other. Some phospholipids are found on the outer leaflet while others are more
commonly seen on the inner leaflet. In addition, glycolipids are differentially arranged as
well and are always on the outer leaflet with their attached carbohydrate projecting away
from the cell.
§ Fluid mosaic model: The membrane is described as a fluid, owing to the ability of lipids to
diffuse laterally. The overall structure is likened to a flowing sea. Membrane proteins are
dispersed throughout the membrane. Many of the membrane proteins retain the ability to
undergo lateral motion and are likened to icebergs floating within the sea of lipids.

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General Biology

Organelles
Organelles are complex intracellular locations where processes necessary for eukaryotic
cellular life occur. Most organelles are membrane-enclosed structures. Their membranes are
composed of the same components asplasma membranes that form the outer boundaries of
cells. Together with the cytosol (liquid portion of the cytoskeleton), the organelles help to form
the cytoplasm, composed of all materials contained within the boundaries of the plasma
membrane. Organelles do not float freely within the cytosol but are interconnected and joined
by the framework established by proteins of the cytoskeleton. Each organelle carries out a
specific function.

Nucleus (plural = nuclei):

All eukaryotic cells except mature erythrocytes (red
blood cells) contain a nucleus where the cell’s
genomic DNA resides. The outermost structure of
the nucleus is the nuclear envelope. This is a
double-layered phospholipid membrane with nuclear
pores to permit transfer of materials between the
nucleus and the cytosol. The interior of the nucleus
contains the nucleoplasm (the fluid in which the
DNAs are found). Within the nucleus there is a
suborganelle called the nucleolus. The nucleolus is
the site of ribosome production.

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Ribosomes:
Ribosomes are the cellular machinery for protein synthesis. They are composed of proteins
and ribosomal RNA (rRNA) with approximately 40% being protein and 60% rRNA.
Ribosomes are found within the cytosol either free or bound to the endoplasmic reticulum.

Endoplasmic reticulum (ER):

ER is often observed to surround the nucleus. The outer
layer of the nuclear envelope is actually contiguous with the
ER. The ER forms a maze of membrane-enclosed,
interconnected spaces that constitute the ER lumen
Regions of ER where ribosomes are bound to the outer
membrane are called rough endoplasmic reticulum
(rER). Bound ribosomes and the associated ER are
involved in the production and modification of proteins.
Smooth endoplasmic reticulum (sER) refers to the regions of ER without attached
ribosomes. Both rER and sER function in the glycosylation (addition of carbohydrate) of
proteins and in the synthesis of lipids.

Golgi complex:
It appears as flat, stacked, membranous sacs. Three
regions are described within the Golgi complex: the cis,
which is closest to the ER; the medial; and the trans Golgi,
which is near the plasma membrane. Each region is
responsible for performing distinct modifications to the
newly synthesized proteins, such as:
§ Glycosylations (addition of carbohydrate)
§ Phosphorylations (addition of phosphate)
§ Proteolysis (enzyme-mediated breakdown of protein)

Mitochondrion (plural = mitochondria):

Complex organelles, mitochondria have several important functions in eukaryotic cells. Their
unique membranes are used to generate ATP (greatly increasing the energy yield from the

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breakdown of carbohydrates and lipids). The very survival of individual cells depends on the
integrity of their mitochondria.
One characteristic feature of mitochondria is the double
phospholipidbilayer membranes that form the outer
boundary of the organelle. The inner mitochondrial
membrane forms folded structures called cristae that
protrude into the mitochondrial lumen known as the
mitochondrial matrix.

Lysosomes:
Lysosomes are membrane-enclosed organelles of various sizes that havean acidic internal
pH (pH 5). Lysosomes containpotent enzymes known collectively as acid hydrolases.
They function within the acidic environment of
lysosomes to hydrolyze or break down macromolecules
(proteins, nucleic acids, carbohydrates and lipids).
Nonfunctional macromoleculesbuild up to toxic levels if
they are not degraded within lysosomes andproperly
recycled for reuse within the cell.In addition, lysosomal
enzymes also degrade materials that have beentaken
up by the cell through endocytosis or phagocytosis.

Peroxisomes:
Peroxisomes resemble lysosomes in size and in structure. They havesingle membranes
enclosing them and contain hydrolytic enzymes. It helps in:
§ Break down of fatty acids and purines (AMP and GMP).
§ Detoxification of hydrogen peroxide (a toxic by-product of many metabolic reactions).
§ Synthesis of myelin (the substance that forms a protective sheath around many neurons).
§ In liver cells, peroxisomes participate in cholesterol and bile acid synthesis.

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General Biology

Cytoskeleton
The cytoskeleton is a complex network of protein filaments that establish a supportive
scaffolding system within the cell. Cytoskeletal proteins are located throughout the interior of
the cell, anchored to the plasma membrane and traversing the cytoplasm. Organelles reside
within the framework established by the cytoskeleton. The cytoskeleton is not simply a
passive internal skeleton but is a dynamic regulatory feature of the cell. These components of
the cytoskeleton work together as an integrated network of support within the cytoplasm.

Actin:
Actin helps to establish a cytoplasmic protein framework known as microfilaments visualized
radiating out from the nucleus to the lipid bilayer of the plasma membrane. Some forms of
actin are found only in muscle cells, while other forms of actin are found within the cytoplasm
of most cell types. Functions of actin in the cytoplasm of non muscle cells include:
§ Regulation of the physical state of the cytosol
§ Cell movement
§ Formation of contractile rings in cell division
§ Within the nucleus, actin is involved in the regulation of gene transcription.
§ Regulators of the gel/sol of the cytosol: One characteristic of a cell is the physical
nature of its cytosol. It can be described either as gel, a more firm state, or sol, a more
soluble state. The more structured the actin, the firmer (gel) the cytosol. The less
structured (more fragmented) the actin, the more soluble (sol) the cytosol. Actin is
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continuously tread-milling in both the gel and sol states, contributing to the character of
the cytoplasm.

Intermediate filaments:
They are larger than actin microfilaments and
smaller than microtubules. Most intermediate
filaments are located in the cytosol between
the nuclear envelope and the plasma
membrane. They provide structural stability
to the cytoplasm, somewhat reminiscent of
the way that steel rods can reinforce
concrete. There are six categories of
intermediate filaments, grouped by their
location. Examples include keratins, vimentin
and neuroflaments

Microtubules:
Microtubules are the last type of predominant structure
observed in the cytoskeleton. The structure of a
microtubule resembles a hollow cylindrical tube. They
are involved in:
§ Chromosomal movements during nuclear divisions
§ Formation of cilia and flagella in certain cell types
§ Intracellular transport

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General Biology

Extracellular Matrix
A substantial part of tissue volume is an extracellular space largely filled by the intricate
network of macromolecules of the extracellular matrix (ECM). The ECM is specialized to
perform different functions in different tissues. For example, the ECM adds strength to
tendons and is involved in filtration in the kidney and attachment in skin.
The physical nature of the ECM also varies from tissue to tissue. Blood is fluid, while cartilage
has a spongy characteristic owing to the nature of extracellular materials in those tissues.
Three categories of extra cellular macromolecules make up the ECM:
1. Proteoglycans:
Proteoglycans are aggregates of glycosaminoglycans (GAGs) and proteins. GAGs arealso
known are composed of repeating disaccharide chains where one of the sugars is an amino
sugar and the other is an acidic sugar. They are organized in long, unbranched chains. GAGs
contain multiple negative charges and are extended in solution. The most prevalent GAG is
chondroitin sulfate. Other GAGs include hyaluronic acid, keratin sulfate, dermatan sulfate,
heparin and heparan sulfate.
Because of their net negative surface charges, GAGs
repel each other. In solution, GAGs tend to slide past
each other, producing the slippery consistency we
associate with mucous secretions. The bones of the joint
are cushioned by the water balloon–like structure of the
hydrated GAGs in the cartilage. When compressive
forces are exerted on it, the water is forced out and the
GAGs occupy a smaller volume. When the force of
compression is released, water floods back in,
rehydrating the GAGs, much like a dried sponge rapidly
soaking up water.

2. Fibrous proteins:
Fibrous proteins are extended molecules that serve structural functions in tissues. There are
two types of fibrous proteins:
§ Collagen: The most abundant protein in the human body, collagen forms tough protein
fibers that are resistant to shearing forces. Collagen is the main type of protein in bone,

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tendon and skin. In the ECM, collagen is dispersed as a gel-like substance and provides
support and strength. Collagen is a family of proteins, with 28 distinct types. However,
over 90% of collagen in the human body is in collagen types I, II, III, and IV. Together the
collagens constitute 25% of total body protein mass.
§ Elastin: The other major fibrous protein in the ECM is elastin. Elastic fibers formed by
elastin enable skin, arteries and lungs to stretch and recoil without tearing. The structure
of elastin is that of an interconnected rubbery network that can impart stretchiness to the
tissue that contains it. This structure resembles a collection of rubber bands that have
been knotted together.

3. Adhesive proteins:
The last category of ECM components consists of proteins that join together and organize the
ECM and also link cells to the ECM. Fibronectin and laminin are adhesive glycoproteins
secreted by cells into the extracellular space. Both are considered multifunctional proteins
because they contain three different binding domains that link them to cell surfaces and to
other components of the ECM, including proteoglycans and collagen. Through their
interactions with fibronectin or laminin, proteoglycans and collagen are linked to each other
and to a cell’s surface. Thus, adhesive proteins join ECM components to each other and link
cells to the ECM.

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Cell Adhesion
A growing tissue is able to form because the member cells remain attached and do not travel
elsewhere. Cell junctions are important in maintaining the structure of a tissue as well as its
integrity. They are composed of a collection of individual cell adhesion molecules.
Cell adhesion molecules mediate selective cell-to-cell and cell-to-ECM adhesion. These are
all transmembrane proteins that are embedded within the plasma membranes of cells. They
extend from the cytoplasm through the plasma membrane to the extracellular space. In the
extracellular space, they bind specifically to their ligands, which may be:
§ Cell adhesion molecules on other cells
§ Certain molecules on the surface of other cells
§ Components of the ECM
Four families of adhesion molecules function in cell-cell adhesion: the cadherins, the
selectins, the immunoglobulin super family, and the integrins. The integrins also function in
cell-to-ECM adhesion.

Cadherins:
The cell adhesion molecules that are important in holding
cells together to maintain the integrity of a tissue are
called the cadherins. These transmembrane linker
proteins contain extracellular domains that bind to a
cadherin on another cell. Cadherins also have intracellular
domains that bind to the actin cytoskeleton.
Therefore, when two cells are linked together via cadherins, their actin cytoskeletons are
indirectly linked as well. Calcium is required for cadherin binding to another cadherin.
Adhesion mediated by cadherins is long-lasting and important in maintaining the tissue
structure.

Selectins:
Selectins mediate more transient cell-to-cell adhesions.
They are particularly important in the immune system in
mediating white blood cell migration to sites of
inflammation.

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Selectins are named for their “lectin” or carbohydrate-binding domain in the extracellular
portionof their structure. A selectin on one cell interacts with a carbohydrate-containing ligand
on another cell.

Immunoglobulin superfamily:
They are named because they share certain structural
characteristics of immunoglobulins (antibodies). These
members of the immunoglobulin superfamily of adhesion
molecules regulate cell-to-cell adhesions. Some
immunoglobulin superfamily members facilitate adhesion
of leukocytes to endothelial cells lining the blood vessels
during injury and stress.

Integrins:
Both cell-to-cell and cell-to-ECM adhesions are mediated
by integrins. Members of this family of transmembrane
proteins bind to their ligands with relatively low affinity;
multiple weak adhesive interactions characterize integrin
binding and function.
Integrins consist of two transmembrane chains, α and β. When integrins mediate cell-to-cell
adhesions, their ligands are members of the immunoglobulin superfamily. When integrins join
a cell to the ECM, collagen and fibronectin commonly serve as their ligands. Therefore,
Integrins mediate interactions between the cytoskeleton within the cell and the ECM
surrounding the cell.

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