Topic 1 Module 1: The cell and

its constituents

Ramesh Rajan, Scott Clarke

i
Topic 1 Module 1: The cell and its constituents

Ramesh Rajan, Scott Clarke

License: Copyright Monash University

Generated by Alexandria (http://localhost) on January 20, 2016 at 3:36 pm AEDT

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 10 Module 1: Test your knowledge

Contents
Title ............................................................................................................................................. i
Copyright ................................................................................................................................... ii
1 Overview ................................................................................................................................ 1
2 Module 1 Objectives ............................................................................................................ 3
3 The bodys uid compartments and their major ions .................................................... 4
3.1 The body contains mainly water ............................................................................. 5
3.2 Water in the body is distributed across four compartments ............................. 6
3.3 Water across body parts, and water usage in the body ..................................... 8
3.4 Dierences in ionic composition in body uids .................................................. 11
4 What denes a cell? ........................................................................................................... 13
5 Cellular organelles ............................................................................................................. 15
5.1 Nucleus ...................................................................................................................... 17
5.2 Endoplasmic reticulum ............................................................................................ 19
5.3 Golgi apparatus ........................................................................................................ 21
5.4 Mitochondria ............................................................................................................. 25
5.5 Lysosomes and peroxisomes ................................................................................. 27
5.6 Cyto-skeleton ........................................................................................................... 31
5.7 Microtubules and transport ................................................................................... 33
5.8 The major cell organelles summary and in song ............................................. 36
6 Structures that bind or link cells together in tissues and organs ............................. 37
7 The constituents of the cell membrane .......................................................................... 39
7.1 Membrane lipids ...................................................................................................... 41
7.2 Membrane proteins ................................................................................................. 43
7.3 Transport proteins ................................................................................................... 44
7.4 Membrane carbohydrates ...................................................................................... 45
7.5 Cell membrane revision .......................................................................................... 48
8 The uidity and dynamic nature of the cell membrane ............................................... 49
9 The roles of the cell membrane ....................................................................................... 53
10 Module 1: Test your knowledge .................................................................................... 54

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i
 1 Overview

1
Overview

It's all about cells.

(https://www.alexandriarepository.org/wp-content/uploads/2014/01/T1-lecture-1-4-
02-011.png)
(https://www.youtube.com/watch?v=Ao9cVhwPg84)

Points to be covered in this module:

Body uids and compartments

1
 1 Overview

What does a cell contain?

The main cellular organelles and their functions
The constituents and organization and role of the cell membrane
Linking cells together

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 2 Module 1 Objectives

2
Module 1 Objectives

Module 1: Objectives
1. Understand the distribution of water through the dierent body compartments and gain a general
knowledge of dierences in ionic composition across the body uids.
2. Learn the name and functions of the major cellular organelles, and the relative scale of their sizes.
3. Learn how cells are held together, especially the special junctions of tight junctions, desmosomes,
and gap junctions linking cells together.
4. Know the major constituents of the mammalian cell membrane and their functions, in particular:

Gain an understanding of the general structure of lipids, learn the meaning of amphipathic in
relation to lipids, and understand that the headgroups of lipids are polar and the fatty acid chains
are non-polar.
Understand how lipids self-assemble in water to orient the headgroups on the outside of the
structure and the fatty acid chains on the inside.
Gain an understanding of the general structure of proteins, understand the division and location of
membrane proteins into integral and peripheral proteins, and have an awareness of the four major
functions of membrane proteins.
Have an understanding of the general structure of carbohydrates, how they are associated with
lipids and proteins in the cell membrane, their relationship to the glycocalyx and the function of the
glycocalyx.

5. Learn the organization of the components as a cell membrane, how and why the cell membrane is
a dynamic structure, and its roles.

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 3 The bodys uid compartments and their major ions

3
The body's uid compartments and their major
ions
3.1 The body contains mainly water
3.2 Water in the body is distributed across four compartments
3.3 Water across body parts, and water usage in the body
3.4 Dierences in ionic composition in body uids

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 3.1 The body contains mainly water

3.1
The body contains mainly water
As the title says, the body contains mainly water.

It's the solvent for all body uids; it dissolves organic and inorganic solutes.

It makes up ~ 60%* of body mass and is a constant percentage of lean body mass.

e.g., 42 litres in "average" 70 kg male (60% of 70 kg)

It makes up a lesser % in females - because they have a higher fat content (and adipose tissue -
i.e., fat tissue - has less water)
A normal healthy young male has 10-15% body fat, a normal healthy young female has 20-25%
body fat

* - some times you'll see a value of 70% or even 75% being cited. Most reliably it's about 60%
but clearly this is going to vary with the amount of fat. So perhaps the values of 70-75% come
from the Bushmen of the Kalahari and the value of 60% comes from modern industrialised
societies?!

You can see the importance of water to human health here:

The Importance of Water to Human Health

(http://e-pao.net/epSubPageExtractor.asp?src=education.Health_Issue.The_Importance_of_Water_to_Human_Health)

And here to nd out how the body uses the water it ingests:

How our bodies use water (http://science.howstuworks.com/environmental/earth/geophysics/h2o3.htm)

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 3.2 Water in the body is distributed across four compartments

3.2
Water in the body is distributed across four
compartments
Water is distributed (unevenly) across four distinct compartments or spaces in the body:

1. Intracellular uids (64% of all body water): This is the uid found within cells. Just by virtue of its
existence, it has an important "passive" role as the site for metabolic processes including energy
production. However it also has a very important "active" (in the sense of actively participating in
the role) of acting as a "buer" to maintain constant the extracellular environment. A buer acts as
a buttress to block or prevent large changes in something happening; in the case of cells this
generally is taken to mean a large change in the composition of ions (charged particles).

Ions are particularly important everyday particles in the body, as you will see in
the next topic.

Because they are electrically charged, this is a property that can be exploited by
cells to carry out many functions, in particular that of signalling events.

2. Interstitial uids (25%): This is the uid that bathes non-blood cells. It is separated from plasma
(see next point) by single layer of epithelial cells, with H2O-lled pores. There is a rapid exchange
from this uid and plasma of all substances of all sizes up to the sizes of small proteins.

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 3.2 Water in the body is distributed across four compartments

3. Plasma (8%): This is the extracellular component of blood, i.e., the uid in blood outside the blood
cells.
4. Minor components (3%): This nal compartment consists of all the remaining transcellular uids
secreted by specialized cells and found in spaces surrounded by cells (CSF, synovial uid,
gastric/sweat secretions, intra-ocular uids).

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 3.3 Water across body parts, and water usage in the body

3.3
Water across body parts, and water usage in
the body
Intracellular water content varies between dierent tissues, as you can see below, which plots the
percentage of water in various tissues.

Percentage of Water in dierent tissues:

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 3.3 Water across body parts, and water usage in the body

(https://www.youtube.com/watch?v=rXXsOzQqEAs)

Hard tissues, such as bone and teeth, contain lower amounts of water in comparison to tissues such as
the lungs or brain.

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 3.3 Water across body parts, and water usage in the body

Water in the human body

The number of cells in the body is 50,000 billion and they contain about two thirds of the water
in our bodies (i.e. 2/3 of the 60% that water makes up of the body).

Although we can go without food for a month or longer, we cannot do without water for more
than 2-5 days. A loss of just 10-15% of our body water can kill us.

a) Water consumption consists of:

Drinking water (1.5 litres per day)

Water in food (0.9litres per day)

Water produced during the metabolism of food (0.6 litres per day)

b) Water disposal occurs through:

Respiration (0.5 litres per day)

Sweating and transpiration: 0.9 litres per day (and more in hot weather)

Urine (1.5 litres per day)

Feces (0.1 litres per day)

c) Water use in our body:

Saliva: about 1 litre per day

Gastric juice: between 2 and 2.5 litres per day

Bile: 0.5 litres per day

Pancreatic juice: 0.7 litres per day

Intestinal secretion: about 3 litres per day

Blood contains between 3-4 litres of water.

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 3.4 Dierences in ionic composition in body uids

3.4
Dierences in ionic composition in body uids

The most common intra- and extra-cellular ions

As we said earlier, ions are particularly important particles in the body, and this is because they are
electrically charged. Later topics will illustrate that this is an important property that is exploited by cells
to carry signals from outside the cell to cause changes within the cell, or to carry signals along the length
of the cell to then be transmitted to the next cell.

For now, we will just consider what is the distribution of the most common ions in the body. This actually
varies between dierent uid compartments.

The extracellular uid is normally high in Na+(142 mM) and in Cl-and low in other ions (< 5 mM; e.g., K+
= ~4 mM, Ca++ = 2.5 mM, Mg++ = 1 mM).

Almost the reverse applies to intracellular uid. It is high in K+(~150 mM), Mg++, Phosphate (HPO4-)
and proteins (which are not ions, but are included here because they are also often charged due to the
presence of charged particles making up the protein) and low in Na+ (10 mM) and very low in Ca++ (<1
mM).

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 3.4 Dierences in ionic composition in body uids

Summary of the distribution of ions

To simplify the situation for now, consider the extracellular uid to be high in Na+ among the cations
(positively charged ions) and Cl- among the anions (negatively charged ions) and the intracellular uid to
be high in K+ and Mg++ for cations (positively charged ions) and Phosphate and proteins for anions
(negatively charged ions).

FOOTNOTE:

Na+ = Sodium ion Cl- = Chloride ion Mg++ = Magnesium ion

Ca++ = Calcium ion

cations = positively charged ions (e.g., Na+)

anions = negatively charged ions (e.g., Cl-)

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 4 What denes a cell?

4
What denes a cell?
If you're interested in a detailed discussion of what is a cell, here is a link to a page giving a nice overview
of cells and their origins : What is a cell? - from the journal Nature
(http://www.nature.com/scitable/topicpage/what-is-a-cell-14023083).

And here take a really nice tour of cells:

(https://www.youtube.com/watch?v=1Z9pqST72is)

What denes a cell?

For our purposes, we rst have to establish what is it that denes the cell as an entity, and gives it an
identity separate from the surrounding uid and adjacent cells.

A TYPICAL CELL (and you know there ain't no such thing..!)

(https://www.alexandriarepository.org/wp-content/uploads/2014/01/T1-lecture-1-4-02-01.png)

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 4 What denes a cell?

The answer is: the cell membrane (also known as the "Plasma" membrane). This covers the entire cell
body (soma) and any cellular extensions.

This boundary isnt totally impervious (i.e., it is NOT a total barrier to everything) but is selective as to
what substances can get across from one side to the other.

This selective permability (a phrase we will encounter later in this Topic) is sucient to make the cell
membrane enough of a barrier to allow the cell to create and maintain an internal environment (a
cytoplasm) with a composition that can vary from the external environment (the extracellular uid) in
terms of uids, ions and molecules, and organelles.

The Intracellular components are mainly water (as you have seen previously: most water in the body is
within cells; conversely, most of a cell is water! ), with 0.66 grams H2O per gram of cell weight in human
red blood cells (RBCs) and 0.8 grams H2O per gram of cell weight in skeletal muscle.

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 5 Cellular organelles

5
Cellular organelles
In addition to water, cells contain a number of organelles, which are enclosed structures each bounded by
membranes. We will now consider these organelles.

You can get some idea of the size of these organelles by considering the enclosed box in the gure; that
box shows the range of sizes of cellular organelles and, as you can see, these range from a level visible
by light microscopy down to a level visible only by electron microscopy.

The membrane that denes these organelles is generally similar to the cell (plasma) membrane;
dierences include the fact that these membranes have greater uidity than the cell membrane (because
they have less cholesterol), are thinner (being ~ 4-5 nm whereas the cell membrane is close to ~10 nm)
and the organelle membrane has a low glycolipid content.

You'll see the signicance of cholesterol and glycolipids in membranes later in this modulke when we

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 5 Cellular organelles

consider the structure of cell membranes.

We will only briey consider some of these major organelles and you should read up on this material for
yourself. I've provided some material in the YouTube video below.

Material for revision

(https://www.youtube.com/watch?v=fKEaTt9heNM)

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 5.1 Nucleus

5.1
Nucleus

The Nucleus is the control centre of the cell

Let's start with the nucleus, which you know is the "control centre" of a cell.

The nucleus gains its separate identity by the fact of being surrounded by 2 membranes, which are
separated from each other by an inter-membrane space.

In the same way as a cell membrane gives the cell an identity separate from the surroundings, the
nuclear membranes give the nucleus an identity separate from the surrounding cytoplasm of the cell.

The nuclear membrane is not whole but contains pores. The pores are very important in allowing
substances produced in the nucleus to translocate into the cell's cytoplasm and thereby exert control of
metabolic and other processes occurring within the cytoplasm (which is where most metabolic processes
take place).

In addition the membrane pores allow substances (such as the steroid hormones and other "messengers"
to move from the cell's cytoplasm into the nucleus and exert eects on the controller elements found
within the nucleus.

The nucleus also contains a non-membrane bound structure called the Nucleolus: a small round body
composed of both proteins and ribonucleic acid (RNA). It is involved in protein synthesis as it is involved in
the production of a type of RNA known as ribosomal RNA (which is exported into the cytoplasm) where

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 5.1 Nucleus

proteins are synthesized under direction from DNA.

Finally, and critically, the nucleus also contains DNA, the genetic material that controls the cellular
activities. It is usually found in a highly condensed form (chromatin). The DNA starts the processes
(including the production of ribosomal RNA) leading to production of proteins (translation of RNA).

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 5.2 Endoplasmic reticulum

5.2
Endoplasmic reticulum

There are two types of ER which do dierent things: protein

synthesis or a range of other functions
The Endoplasmic Reticulum is an interconnected network of membranous tubules, vesicles
("pouches"), and cisternae ("sacs").

There are actually two types of these structures: the Rough (RER) and the Smooth ER (SER)

RER gets its spotty or studded appearance (under the electron microscope!) because it has
ribosomes dispersed across the outside surface which points towards the cytoplasm.

RER membrane is continuous with outer nuclear membrane and the RER is the site of protein
synthesis (on ribosomes) as well as some renement of the precursor protein products that are the
rst products of this synthetic process.

The SER has functions in several metabolic processes, including synthesis of lipids and steroids,
metabolism of carbohydrates, regulation of calcium concentration, detoxication of drugs,
attachment of receptors on cell membrane proteins, and steroid metabolism It is connected to the
nuclear envelope.

SER is also the site of production of substances that will be secreted into the cytoplasm or out from
the cell (secretory products).

In muscle, the SER has a special function where it stores Ca++ until required for muscles to contract,
and there it is called the sarcoplasmic reticulum, as you will see in a later topic.

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 5.2 Endoplasmic reticulum

The RER and SER in a cell can quickly interchange from one type to the other, depending on the
metabolic needs and demands on the cell.

The Endoplasmic Reticulum (ER)

(a) The ER is a winding network of thin membranous sacs found in close association with the
cell nucleus. The smooth and rough endoplasmic reticula are very dierent in appearance and
function (source: mouse tissue). (b) Rough ER is studded with numerous ribosomes, which are
sites of protein synthesis (source: mouse tissue). EM 110,000. (c) Smooth ER synthesizes
phospholipids, steroid hormones, regulates the concentration of cellular Ca++ , metabolizes
some carbohydrates, and breaks down certain toxins (source: mouse tissue). EM 110,510.
(Micrographs provided by the Regents of University of Michigan Medical School 2012)

This content is available for free at https://cnx.org/content/col11496/1.7

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 5.3 Golgi apparatus

5.3
Golgi apparatus

The Golgi apparatus modies proteins and lipids for export via
vesicles
The Golgi apparatus is a series of cisternae (membranous sacs) located near the nucleus and the
ER.

(https://www.alexandriarepository.org/module/golgi-apparatus/image1-18/)

Functionally, it is linked to the RER because its roles are (a) to be the site where nal modications
are made to the proteins produced in RER, and (b) it organizes the proteins into membranous
vesicles for delivery to other organelles or to the cell membrane.

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 5.3 Golgi apparatus

(https://www.alexandriarepository.org/module/golgi-apparatus/image2-16/)

The Golgi apparatus consists of three sets of membrane stacks that

modify proteins and lipids in dierent ways
The Golgi apparatus stacks can be broadly divided into three sets of stacks ("networks" of stacks):

a. cis-Golgi network,
b. medial Golgi network, and
c. trans-Golgi network

Proteins and lipids move through the stacks, with modications (some examples of which are shown
in the text at the bottom of the gure above).

Finally, in the Trans-Golgi network the substances are sorted and stored in secretory vesicles for
release into cytoplasm. For release from the cell, vesicles fuse with cell membrane.

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 5.3 Golgi apparatus

The Golgi Apparatus

(a) The Golgi apparatus manipulates products from the rough ER, and also produces new organelles called
lysosomes. Proteins and other products of the ER are sent to the Golgi apparatus, which organizes,
modies, packages, and tags them. Some of these products are transported to other areas of the cell and
some are exported from the cell through exocytosis. Enzymatic proteins are packaged as new lysosomes
(or packaged and sent for fusion with existing lysosomes). (b) An electron micrograph of the Golgi
apparatus.

This content is available for free at https://cnx.org/content/col11496/1.7

Think of it like a production line conveyor belt - say for bottled water.

At one part of the production line, the bottle is lled with water. Then it
advances further along the conveyor belt to the part of the production line
where the cap is screwed on. Then it reaches the part of the production line
where the label is put on the bottle. Finally, it reaches the part of the
production line where it is boxed (and think of the boxes as vesicles) and
transported to the retail outlet.

Finally, for sale, the box has to be opened (fuse with the great ether of life) for
the bottle to be released, spread it's wings and y, y, little one - be free, grow
and be yourself. (OK OK that last bit was probably a leetle teeny weeny bit
over the top, but you've got to admit that up to then I was going ne with this
analogy.)

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 5.3 Golgi apparatus

Notice in the gure there are two such ways for fusion with the cell membrane: one which is
unregulated by any external factors (the CONSTITUTIVE SECRETORY PATHWAY) and which can
be regulated by external factors, such as hormones (the REGULATED SECRETORY PATHWAY).

ER and Golgi apparatus explained

(https://www.khanacademy.org/science/biology/cell-division/v/endoplasmic-reticulum-and-golgi-
bodies)

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 5.4 Mitochondria

5.4
Mitochondria

Mitochondria are the energy suppliers

Mitochondria (singular = mitochondrion) are elongated ovoid structures, found abundant in cells
where energy demands are high e.g., in cardiac muscle, in neurons (nerve cells).

As in the case of the nucleus, identity is conferred on the mitochondrion by the presence of 2
membranes and an inter-membrane space.
The outer membrane has pores while the inner membrane is highly folded to form the cristae.
The mitochondria are often referred to as the "powerhouse" of the cell because they produce the
molecule, ATP (adenosine triphosphate), the major molecule used by cells when energy is
required for metabolic processes (the energy is stored in the phosphate bonds to Adenosine).

Mitochondria use O2 to produce the energy molecule, ATP.

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 5.4 Mitochondria

Mitochondria damage in neurons may underlie many neurodegenerative diseases

While almost all cells need mitochondria to produce energy, post-mitotic neurons (nerve
cells) are particularly dependent on these structures.

Unlike replicating mammalian cells which have a metabolism that is essentially dependent
on glycolysis, post-mitotic neurons have an exclusive energy dependence on mitochondrial
metabolism. This is exacerbated by their particular distinctive shape which means
dierent parts of the neuron are eectively dierent compartments with distinct energetic
needs.

It is therefore not surprising to learn that there is mounting evidence that changes in
quality control of neuronal mitochondria are associated with many devastating human
neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease,
Huntington's disease, and amyotrophic lateral sclerosis (motor neuron disease).

Progressive mitochondrial failure is tightly associated with the onset of many age-related
human pathologies not only because of the production of ATP but because mitochondria
also produce reactive oxygen species (ROS) and these are toxic to the cell. Mitochondrial
damage results in ooding of the cell with the ROS, leading to death.

Thus, quality control of mitochondrial proteins is one of the mechanisms that protect
mitochondrial integrity.

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 5.5 Lysosomes and peroxisomes

5.5
Lysosomes and peroxisomes

Lysosomes and Perioxisomes are really good cleaners

Lysosomes and Perioxisomes are organelles involved in the breakdown and digestion of material
within a cell, generally waste or toxic material.

Lysosomes: vesicles containing enzymes for breakdown of material. They digest waste intra-
cellular material & recycle cell components, & extra-cellular material.
Peroxisomes: vesicles also containing enzymes that break down O2. They reduce the damaging
eect of alcohols, etc, through their actions in destroying free radicals within the cell.

Digestive functions of Lysosomes

The lysosome is an acidic organelle that functions as the cell's major recycling system. In neurons,
lysosomes are also critical for tracking and recycling of neurotransmitters and their receptors.

This gure below shows the three major digestive functions of Lysosomes:

Phagocytosis (eating up of nasty things from outside the cell) into phagocytotic vacuoles
Endocytosis (internalization of nasty things from outside the cell) into small vesicles called
endosomes
Autophagy (eating up of self - i.e., nasty or decaying things from inside the cell - the example
here being of a decaying mictochondrion) being internalised into an autophagic vacuole or
autophagic vesicle. Autophagy is part of the cellular recycling system, and is a process whereby
organelles or cellular "waste" are engulfed in a membrane to form autophagosomes or autophagic
vesicles (AV). AVs are rarely seen under normal conditions because they rapidly fuse with
lysosomes, where lysosomal enzymes degrade them and their contents.

The Lysosome goes through various stages, incorporating acid hydrolases which have been
produced in the Golgi apparatus and packaged in vesicles.

The Lysosome has a highly acidic enviroment (pH of about 5.2 versus pH of about 7.2 in the
cytoplasm), which allows the hydrolases to operate optimally and digest the internalised contents.

Notice that the digested contents are recycled into the cytoplasm for use by the cell; undigested
matter is expelled through Exocytosis (the opposite of Endocytosis)

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 5.5 Lysosomes and peroxisomes

Peroxisomes
Peroxisomes are membrane-bound organelles that contain an abundance of enzymes for detoxifying
harmful substances and lipid metabolism.

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 5.5 Lysosomes and peroxisomes

Peroxisome
Peroxisomes perform a couple of dierent functions, including lipid metabolism and chemical
detoxication. In contrast to the digestive enzymes found in lysosomes, the enzymes within
peroxisomes serve to transfer hydrogen atoms from various molecules to oxygen, producing
hydrogen peroxide (H2O2). In this way, peroxisomes neutralize poisons such as alcohol.

Some things about Reactive Oxygen Species

Reactive oxygen species (ROS) such as peroxides and free radicals are the highly
reactive products of many normal cellular processes, including the mitochondrial reactions
that produce ATP and oxygen metabolism.

Examples of ROS include the hydroxyl radical OH, H2O2, and superoxide ( O2 ).

Some ROS are important for certain cellular functions, such as cell signaling processes and
immune responses against foreign substances.

Free radicals are reactive because they contain free unpaired electrons; they can easily
oxidize other molecules throughout the cell, causing cellular damage and even cell death.

Free radicals are thought to play a role in many destructive processes in the body, from
cancer to coronary artery disease. Peroxisomes, on the other hand, oversee reactions that
neutralize free radicals.

Peroxisomes produce large amounts of the toxic H2O2 in the process, but peroxisomes
contain enzymes that convert H2O2 into water and oxygen.

These byproducts are safely released into the cytoplasm.

Like miniature sewage treatment plants, peroxisomes neutralize harmful toxins so that
they do not wreak havoc in the cells.

The liver is the organ primarily responsible for detoxifying the blood before it travels
throughout the body, and liver cells contain an exceptionally high number of peroxisomes.
Defense mechanisms such as detoxication within the peroxisome and certain cellular
antioxidants serve to neutralize many of these molecules.

Some vitamins and other substances, found primarily in fruits and vegetables, have

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 5.5 Lysosomes and peroxisomes

antioxidant properties.

Antioxidants work by being oxidized themselves, halting the destructive reaction

cascades initiated by the free radicals. Sometimes though, ROS accumulate beyond the
capacity of such defenses.

Oxidative stress is the term used to describe damage to cellular components caused by
ROS.

Due to their characteristic unpaired electrons, ROS can set o chain reactions where they
remove electrons from other molecules, which then become oxidized and reactive, and do
the same to other molecules, causing a chain reaction.

ROS can cause permanent damage to cellular lipids, proteins, carbohydrates, and nucleic
acids.
Damaged DNA can lead to genetic mutations and even cancer. A mutation is a change in
the nucleotide sequence in a gene within a cell's DNA, potentially altering the protein
coded by that gene.
Other diseases believed to be triggered or exacerbated by ROS include Alzheimer's
disease, cardiovascular diseases, diabetes, Parkinson's disease, arthritis, Huntington's
disease, and schizophrenia, among many others. It is noteworthy that these diseases are
largely age-related.

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 5.6 Cyto-skeleton

5.6
Cyto-skeleton

The cell gets a structure from its cyto-skeleton ("cell

skeleton")
The cell is not a oppy bag containing organelles and molecules bathed in water, but has a dened
structure provided by a series of interlinked laments.

These laments are collectively called the cytoskeleton, i.e., the skeleton of the cell, because they
give the cell form and rigidity in the same way as our skeleton does for our body.

The laments can be grouped according to size as:

Thin laments:
Mainly Actin (with associated proteins)
Size: 5-8 nm
Role: Structural support & motility
Intermediate laments:
Family of related proteins (Keratins, Laminins, Neuro-laments, etc)
Size: 8-10 nm
Role: Structural support, esp. in areas of tensile stress
Microtubules:
Mainly a protein called Tubulin
Size: 12-15 nm
Role: Maintain cell shape, Movement & motility, (interact with thin laments)

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 5.6 Cyto-skeleton

The Three Components of the Cytoskeleton

The cytoskeleton consists of (a) microtubules, (b) microlaments, and (c) intermediate laments.

The cytoskeleton plays an important role in maintaining cell shape and structure, promoting cellular
movement, and aiding cell division.

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 5.7 Microtubules and transport

5.7
Microtubules and transport
Microtubules are elongated, hollow cylinders, made up of protein (tubulin) & various associated
proteins. Their role is multi-faceted and ranges from helping form motile extensions called cilia and
agella, in being involved in movement of substances within the cell (e.g., of chromosomes in mitosis; in
expelling foreign particles in the pulmonary pathways), and in transporting organelles through the
cytoplasm.

The transport can in the direction away from the cell body (where often the organelles and other
substances are synthesized), or towards the cell body (where often the organelles and other substances
are destroyed/metabolized).

Away from the cell body is called Anterograde Transport; Towards the cell body is called Retrograde
Transport

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5.7 Microtubules and transport

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5.7 Microtubules and transport

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 5.8 The major cell organelles summary and in song

5.8
The major cell organelles - summary and in
song
Learn from the journal Nature: The organelles of a cell
(http://www.nature.com/scitable/ebooks/essentials-of-cell-biology-14749010/114010457#bookContentViewAreaDivID)

and have some fun too:

(https://www.youtube.com/watch?v=KzMviiBoRtA)

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 6 Structures that bind or link cells together in tissues and organs

6
Structures that bind or link cells together in
tissues and organs
In the last section, we will consider the properties of the cell membrane, a structure whose properties
will feature in the next few Modules of this Topic (and in later Topics).

Before doing so, while we are still considering cell structures and organelles, let us look, in passing, at the
structures (membrane junctions) that hold many cells together as tissues and organs (not all - e.g.,
blood cells are free oating in the blood uids).

Cells are held together by three dierent means, and we will very briey consider only the last of these
means. You will see these structures in body structures such as the digestive system, or the vascular
system.

1. The extracellular matrix (the "glue" between cells) which is a mesh of brous proteins + watery
gel-like substance (the interstitial uid) made of complex carbohydrates.
2. Cell adhesion molecules which are protein bres (Collagen, Elastin and Fibronectin) in the cells'
plasma membranes, and which play a role in holding cells together (that's why they are called
adhesion molecules).
3. Specialized junctions between cells, known as Desmosomes, Tight junctions and Gap
junctions.

Tight junctions seal the gaps between cells to make a sealed sheet and are the most impervious /
impenetrable of the three types of junctions between cells. Here the plasma membranes are tightly
apposed. This can provide a continuous barrier within a tissue, eg lining of the gut. Substances have to
pass through cells and not between them.

Desmosomes link adjacent cells without sealing them into a sheet. They are a region where the plasma
membranes of adjacent cells become closely apposed (but with a nite gap of ~20 nm.) They are made

37
 6 Structures that bind or link cells together in tissues and organs

up of dense protein material that lies immediately adjacent to and between cells. Protein bres extend
across the cell. They function to hold cells together in tissues that are subject to stretching, eg skin.

Gap junctions connect the insides of two cells through a hollow structure (a protein channel) that
spans the gap between two cells. The protein channels are ~1.5 nm internal diameter and link the
internal uid contents in adjacent cells. Gap junctions allow small molecules and ions to move between
cells but prevent movement of large molecules, e.g., in heart muscle cells.

38
 7 The constituents of the cell membrane

7
The constituents of the cell membrane
As a prelude to discussing the organization of the cell membrane (and then to consider the roles of the
cell membrane) we'll rst consider the molecules that make up this membrane. These molecules are
shown in the gure here and the main ones we need to consider are the sugars, the proteins, and the
lipids in which the sugars, proteins and other molecules are embedded (the double layered structure that
is the actual cell membrane).

The sugars, proteins and lipids are not dispersed randomly across the cell membrane but found in
particular locations or congurations as they each have dierent and specic roles to play in the function
of the cell membrane.

Learn from the journal Nature: What is the cell membrane?

(http://www.nature.com/scitable/topicpage/cell-membranes-14052567)

39
7 The constituents of the cell membrane

40
 7.1 Membrane lipids

7.1
Membrane lipids
Lipids are long chains of Carbon & Hydrogen (long-chain fatty acids) that can be attached to another
molecule (the head group). Common membrane lipids consist of:

Glycero-phospholipids (phospholipids)
Sphingolipids
Sterols (Cholesterol)

Here's a link to a nice page dening lipids: Classifying lipids

(http://www.biologyexams4u.com/2012/10/classication-of-lipids.html). It also denes saturated and unsaturated fats, a
concept you'll need to understand in a couple of pages from here.

Membrane lipids have a special property of being amphipathic - they consist of polar (charged) & non-
polar parts. The fatty acid chains are non-polar and the headgroup is polar.

The property of being amphipathic is very important in the way that the membrane lipids are then
oriented in a uid environment.

Since the polar molecules are hydrophilic & uncharged molecules are hydrophobic, lipids can self-
assemble in water to form structures with a hydrophobic interior & a hydrophilic surface - such as micelles
and lipid bilayers.

41
 7.1 Membrane lipids

As you'll see later in this module, the second gure is the one relevant to our present consideration of cell
membranes.

The inside and outside of cells are lled with water.

Thus, it won't surprise you to know that the cell membrane is a lipid bilayer - i.e., it consists of
two layers of lipids, like that shown in the lower gure.
Both layers are organised so that their hydrophilic polar heads face the water, and their long
hydrophobic tails face each other, to form the bulk of the cell membrane.

42
 7.2 Membrane proteins

7.2
Membrane proteins
Proteins are, in essence, a long sequence of amino acids (C, H O & N) which are folded in some
particular complex ways.

There are three types of membrane proteins:

1. Integral trans-membrane protein: extends through entire membrane.

2. Integral outer/inner membrane protein: extends part way through membrane, with portion
exposed on outer surface (outer membrane protein) or on cytoplasmic side of membrane (inner
membrane protein).
3. Membrane-associated protein (peripheral): not inserted into membrane, but associates with
membrane itself or another membrane protein

43
 7.3 Transport proteins

7.3
Transport proteins

Membrane proteins carry out many functions

These functions are summarised in the gure below. You'll see many of these functions through the rest
of these topics as well as in any other biomedical material you study.

We'll discuss the dierent functions as we encounter them in this particular set of Topics so we won't look
at them in any detail now. It's best to see these functions in context rather than have an
incomprehensible exposition about them now. However, one important function of relevance right now is
the role of proteins in transport of substances across the cell membrane.

Of all the functions listed in the gure, in this module and this subject generally we are going to see a lot
of Transport proteins. So, for now, here is some information about this category of proteins.

Transport proteins are Integral proteins and come in two categories.

1. Carrier proteins which bind a substrate (the chemical that they can interact with), undergo a
conformational change and through that change transport substrate across membrane. These proteins
can be inner or outer membrane proteins depending on the face of the cell membrane on which they are
located.

2. Channel proteins are aqueous (water-lled) pores that allow a substrate through from one side of the
cell membrane to the other (i.e., they are trans-membrane proteins).

44
 7.4 Membrane carbohydrates

7.4
Membrane carbohydrates

Carbohydrates form a coat across the cell surface

Carbohydrates are chains of carbon, hydrogen & oxygen. On the outer surface of the cell membrane
are found carbohydrates as strands of mono-saccharides bound to lipids or proteins (glycolipids &
glycoproteins).

They form a coat, called the glycocalyx, across the cell surface. The sugar molecules are involved in
immunological responses such as cell recognition (to prevent them being attacked by the self
immune system).

45
 7.4 Membrane carbohydrates

Material for revision

46
 7.4 Membrane carbohydrates

(https://www.youtube.com/watch?v=q3YUKnz_ezM)

47
 7.5 Cell membrane revision

7.5
Cell membrane revision

(https://www.youtube.com/watch?v=Mv247P8ufCA)

OR

(https://www.youtube.com/watch?v=moPJkCbKjBs)

48
 8 The uidity and dynamic nature of the cell membrane

8
The uidity and dynamic nature of the cell
membrane

The cell membrane is a uid lipid bilayer

As we noted earlier, in essence, the cell membrane is primarily a lipid bilayer i.e., two layers of
lipids.

This lipid bilayer is made up of phospholipids which have their polar groups facing outwards and
the non-polar tails facing inwards towards the non-polar tails of the other half of the bilayer.
Cholesterol is interspersed throughout the membrane, between the fatty acid tails of
phospholipids, and oriented towards the polar headgroups.

A consequence of this organization is that the cell membrane is not rigid but actually quite a uid
structure. Often the cell membrane is described as being a rather viscous gel, but one with uidity
(like olive oil).

You will often hear the term uid mosaic being used to describe the cell membrane in recognition
of the fact that is a "uidy" structure that is always dynamically changing as things like

49
 8 The uidity and dynamic nature of the cell membrane

phospholipids keep moving around within the membrane and even ipping from one side to the
other, as you will see discussed at the end of this section.

Cell membrane uidity depends on three main factors

1. Lipid composition (Length and branching of, and number of unsaturated bonds in, fatty acid tails:
Shorter lipids - and those with double bonds create a more uid membrane)
2. Amount of cholesterol (more cholesterol makes it rigid by reducing phospholipid movement)
3. Temperature (higher temperatures more uidity)

You can see the eect of these factors in the following drawing:

The rst two factors, i.e., lipid composition and the cholesterol content, can vary across the
membrane, and between the two surfaces of the membrane. (e.g., less cholesterol in inner leaf of
organelles with curved membranes such as mitochondria reduces the rigidity of this inner membrane
allowing it to be curved). Thus the membrane surface is not uniform; as well, the two surfaces are
not identical.

Kinks in the membrane increase the "permeability" of the

membrane
A membrane with no 'kinks' makes it harder for substances to get across. Look at the drawing above
- which would you expect to be able to cross more easily - the viscous membrane or the uid
membrane?

As you saw in the drawing above, kinks are due to presence of unsaturated fatty acids (i.e., the

50
 8 The uidity and dynamic nature of the cell membrane

number of double bonds in the fatty acid chains).

Thus a lipid bilayer with more unsaturated fatty acids is more permeable to substances (i.e., more
readily traversed). So, of the top two membranes in the drawing, the one on the left is more
impermable than the one on the right.

This property of permeability is a core concept in Physiology and you will see it emphasized in the
next few modules in this Topic.

Cell membrane structure changes dynamically

Finlally, it is important to note that the cell membrane structure should not be conceived of as a rigid
one - it is a highly dynamic one.

There are no covalent bonds between phospholipids or between phospholipids and proteins. This
means that the molecules can move independently, in the plane of the membrane.
Thus there is a lot of lateral movement of the phospholipids within the membrane (as shown in the
gure below) - and, much more rarely, even "ip-op" motion where phospholipids ip from facing
one side of the membrane to the other (e.g., ip from facing the extracellular environment to
facing the intracellular environment).

51
 8 The uidity and dynamic nature of the cell membrane

When lipid asymmetry can be lost

Normally the phospholipids are not the same on the two faces of the lipid
bilayer of the cell membrane. This asymmetry of the plasma membrane is
important for the dierent functions inside the cell versus outside the cell.

However this asymmetry can be lost under conditions of injury.

For example it is lost in nerve cells after cutting of the axon of the nerve cell
(you'll see this term "axon" dened later, when you study nerves, as a long
extension / process of the nerve cell used to transmit electrical information -
think of it as a long electrical cable extending from the nerve cell body).

Cutting of the axon by injury causes the membrane lipid phosphatidyl serine
(PS), which is normally restricted to the cytoplasmic leaet, to be externalised.
The PS functions as a 'save me' signal for recognition between the regrowing
axon and its separated fragment.
This is part of the process of allowing axons to regenerate after injury. It is
very ecient in the peripheral nervous system but not in the central nervous
system (brain and spinal cord) because the latter contains an inhibitory micro-
environment.
Now if you're wondering why the vertebrate CNS would have pathways that
inhibit regeneration - it's worth noting that these same inhibitory pathways
are important in the uninjured nervous systems to inhibit aberrant growth of
neurons so that the CNS can be a stable, functional system.

52
 9 The roles of the cell membrane

9
The roles of the cell membrane

A major function of the cell membrane is to act a barrier to

permeability of substances
As I said before we'll discuss the dierent functions as we encounter them.

For now, for the coming modules in this topic, just be aware that we'll be focusing on the role as a
permeability barrier. This has implications for how substances needed by the cell can get across, as well
as how substances move in the opposite direction.

These are topics we shall be looking at in the next two modules but you'll see them recur throughout this
content as these properties play important roles in allowing nerve cells and muscle cells to function
properly.

A very nice summary of all we've looked at so far on the cell membrane:

(https://www.youtube.com/watch?v=y31DlJ6uGgE)

53
 10 Module 1: Test your knowledge

10
Module 1: Test your knowledge
The quizzes found below test your knowledge of module 1 of topic 1.

Start Quiz (https://www.alexandriarepository.org/app/WpProQuiz/33)

Start Quiz (https://www.alexandriarepository.org/app/WpProQuiz/34)

Start Quiz (https://www.alexandriarepository.org/app/WpProQuiz/35)

54