1.

1 Introduction to the cell theory

Cell Theory
› All organisms are composed of cells
› Cells are the smallest unit of life
› Each cell arises from pre-existing cells

Exceptions to the cell theory

› Multinucleated cells (e.g., fungal cells in aseptate hyphae, striated muscle)
› Very large cells that are not compartmentalized (e.g., giant algae)
› Mature red blood cells that lack a nucleus

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Unicellular organisms carry out all functions of life including:

› Metabolism: the web of all enzyme catalyzed reactions
› Reproduction: all organisms produce offspring either sexually or asexually
› Homeostasis: the maintenance of all internal conditions
› Growth: all living things grow, change in size and shape
› Response: all living things respond to and interact with the environment
› Excretion: removal of metabolic waste
› Nutrition: all organisms consume food to obtain the essential nutrients and energy
for growth and survival.

As surface area to volume ratio decrease, the rate of the cells ability to exchange materials
decreases.
The greater surface area to volume ratio is, the faster the cell can remove waste and heat
and absorb nutrients essential for cell functions.
 Functions of life Paramecium Chlamydomonas
Metabolism Most metabolic pathways Most metabolic pathways
happen in the cytoplasm happen in the cytoplasm
and enzymes cause them with enzymes speeding
them up
Reproduction The nucleus supports cell Fuse to carry out sexual
division by mitosis reproduction
Homeostasis Contractile vacuoles fill up Contractile vacuoles fill up
with water and then they with water and then they
expel it through the plasma expel it through the plasma
membrane to manage membrane to manage
water content water content
Growth After obtaining the biomass After obtaining the biomass
from food, the cell grows from food, the cell grows
until it divides until it divides
Response The wave action of the cilia, The wave action of the
move the cell in response to flagella moves the cell, and
changes in the environment the sensitive eyespot allows
it to move toward light
Excretion Plasma membrane controls Plasma membrane controls
what goes in and out of the what goes in and out of the
cell cell
Nutrition Food vacuoles contain the Feeds through
food that the cell has photosynthesis that
already consumed happens in the chloroplasts

Differentiation is the process where a less specialized cell becomes a more specialized cell.
It changes, cell size, shape, membrane potential and metabolic activity.
Differentiation is controlled by gene expression; thus, some genes are turned on or turned
off in specific cells. For example, a nerve cell contains all the genetic information that other
cells have, however genes for the nerve cells are turned on while genes for other cells are
turned off.
When a gene is turned on it will produce specific proteins related to the specific function.
Some cells, when they differentiate, they lose their ability to reproduce (e.g., nerve cells,
muscle cells).
Stem cells, are cells that retain their ability to divide and differentiate into specific cell types.
Two main types of stem cells are adult stem cells, found in adult tissues (e.g., bone marrow)
and embryonic stem cells that come from undeveloped embryos. Pluripotent stem cells can
differentiate into any cell type.

Stargardt’s macular dystrophy is a genetic disease that develops in children 6-12 years old
and can cause blindness. It is due to a mutation of the gene ABCA4.
It affects a membrane protein of the retina causing the photoreceptive cells to
degenerate/destroy.
Embryonic stem cells are injected that can develop to retina cells. The cells attach to
the retina and begin to grow, improving vision.

Leukemia is a type of cancer. A mutation in the genes that control cell division, creates an
abnormal amount of white blood cells, which are produced in the bone marrow.
Using a large needle, stems cells are removed from the bone marrow.
The patient undergoes chemotherapy and radiation therapy to kill cancer cells in the
bone marrow.
After chemotherapy and radiation, hematopoietic (HS) cells are transplanted into the
bloodstream.
Stem cells go to the bone marrow, where they begin to reproduce and make new
healthy blood cells.

Ethics in therapeutic use of stem cells

› Embryonic stem cells have a higher risk of developing into tumors and the processes
involves the creation and destruction of embryos which is unethical.
› Cord blood cells are multipotent therefore have limited capacity to differentiate into
different cell types.
› Adult stem cells are difficult to obtain since they are small in number and can be
painful to extract. They are also multipotent thus limited capacity of differentiation.
In case of donation of adult stem cells there needs to be a close match in terms of
blood type so there is chance for the cells to be rejected by the immune system of
the patient.
1.2 Ultrastructure of cells
Eukaryotes in contrast to Prokaryotes have a compartmentalized structure. It is highly
beneficial since, damaging substances can be isolated, organelles can change shapes and
positions, ideal conditions as Ph can be maintained.

Prokaryotes Eukaryotes
Smaller in size Larger in size
70s ribosomes 80s ribosomes
Naked DNA DNA associated with histone proteins
DNA free floating in the cytoplasm DNA enclosed in a nuclear envelope
Has membrane bound organelles Does not have membrane bound organeles
Has a cell wall Has cell wall only in plants and fungi
DNA is circular DNA is linear

Electron microscopes have much higher resolution than light microscopes since light
microscopes are only limited on the wavelength of light.

Prokaryotes divide by binary fission. It is an asexual cell division that leads to the production
of two genetically identical daughter cells.
 Figure 1. Ultrastructure of a prokaryotic cell

i. Ribosomes: site of protein synthesis

ii. Cell wall: peptidoglycan layer that protects and maintains cell shape.
iii. Plasma membrane: phospholipid layer that controls what goes in and out of the cell
iv. Nucleoid: small region containing DNA
v. Plasmid: Protein filaments that facilitate conjugation
vi. Flagella: move the cell
 Figure 2. Ultrastructure of a eukaryotic cell

i. Ribosomes: site of protein synthesis. Free ribosomes produce proteins that will be
used inside the cell whereas ribosomes attached to the rER produce proteins that
will be secreted.
ii. Golgi Apparatus: Consists of flattened membrane sacs called cisternae, and is
located near the plasma membrane. It modifies proteins (collection  modification
 packaging  distribution)
iii. Nucleus: It regulates cell activities and contains DNA arranged in chromosomes.
Uncoiled chromosomes are chromatin and the nucleus is surrounded by a double
membrane called nuclear envelope.
iv. Mitochondria: site of ATP production (carry out aerobic respiration). It has a double
membrane, a folded inner one and smooth outer one. Folds are referred to as cristae
and increase surface area to enhance the ability to produce ATP. It is semi-
autonomous, has its own DNA and can divide independently.
v. Rough Endoplasmic Reticulum: site of protein synthesis (attached ribosomes) for
secretion out of the cell. It consists of flattened membrane sacs called cisternae.
vi. Lysosome: Contains hydrolytic enzymes that digest unwanted organelles, ingested
food and viruses or bacteria. It is formed from the Golgi Apparatus and has a single
membrane.
 1.3 Membrane structure
Cell membranes consist of phospholipids that have a hydrophilic (attracted to
water) head and a hydrophobic (repelled by water) tail.
The negatively charged phosphate group of the phospholipid is attracted to
water due to its polarity.
The hydrocarbon tail has no charge thus, repelled by water.
When placed in water, a double layer is formed with the heads facing outwards and
tails facing inwards. A stable structure is formed due to the interactions of heads to
the water and to each other and the hydrophobic interactions between tails. It is
fluid though since phospholipids move along the plane.

Functions of membrane proteins:

› Junctions: connects and joins cells together
› Enzymes: localize metabolic pathways
› Transport: responsible for facilitated diffusion and active transport
› Recognition: function as markers for cell identification
› Anchorage: attachment points for cytoskeleton and extracellular matrix
› Transduction: function as receptors

Properties of cholesterol
› Its hydrophilic group associates with phosphate
› The remainder of the molecule associates with tails
› Its hydrophilic properties prevent tails from crystallizing into solid
› Its hydrophobic properties prevent hydrophilic molecules from diffusing into the
membrane
› Regulates the fluidity and flexibility of the membrane

Role of cholesterol in membrane fluidity:

› Restricts the movement of phospholipids and other molecules, reducing fluidity
› It disrupts the regular packing of hydrocarbon tails
› Reduces the permeability to hydrophilic molecules and ions
Davson and Danielli model:
It was the first model suggested, it was trilaminar and was called a lipoprotein sandwich
since a lipid layer was sandwiched between two protein layers.
Problems of the model were that it assumed that all membranes were that it assumed that
all membranes were of the same thickness and had a constant lipo-protein ratio. It also
assumed that all membranes had symmetrical internal and external surfaces and finally the
temperatures at which the membrane solidified was different from reality.

Falsification evidence:
› Improved biochemical techniques were used to isolate proteins and discover that
they are insoluble in water and varied in size.
› Fluorescent antibody tagging proved that proteins were mobile and not fixed.
› Freeze-fracturing techniques were used to open membranes and find irregular rough
surfaces.

The new model suggested was the Singer and Nicolson model where proteins were
embedded within the membrane.

1.4 Membrane transport

Methods of transportation:
› Passive transport: no use of ATP, substances move from high to low concentration
o Simple diffusion
 Only small non polar substances move through the phospholipid
bilayer from a high to low concentration until equilibrium is reached.
o Facilitated diffusion
 Polar substances move through channel protein of the plasma
membrane from a high to low concentration until equilibrium is
reached.
 o Osmosis
 Net movement of water molecules across a semi-permeable
membrane from low to high concentration until equilibrium is
reached.

› Active transport: requires the use of ATP, substance move against the concentration
gradient from low to high concentration.
o Endocytosis:
 External substances are engulfed and enclosed by the membrane.
 A vesicle is formed containing the substances and moves to the
cytoplasm
 The vesicle pinches off the plasma membrane and it is possibly fused
with lysosomes whose digestive enzymes break down the content of
the vesicle.
o Exocytosis:
 A vesicle from the Golgi apparatus containing a modified substance
fuses with the plasma membrane and the membrane opens towards
the extracellular space and releases the substance.
o Sodium-Potassium pump:
 A sodium potassium pump opens towards the intracellular space and
3 sodium ions are loaded in and attach to the protein.
Phosphorylation takes place when the energy released causes a
conformational change to the pump which then opens towards the
extracellular space and releases the ions. During this time 3 potassium
ions are loaded in which causes the dephosphorylation the pump
which then once again opens towards the intracellular space and
releases the ions.

A hypertonic solution has a higher osmolarity (solute concentration) than the other
solution. If cells are placed in a hypertonic solution they will most probably shrink.
A hypotonic solution has a lower osmolarity (solute concentration) than the other solution.
If cells are placed in a hypotonic solution they will most probably swell.
An isotonic solution therefore chosen.

1.5 Origin of cells

Organic molecules must have existed, and macromolecules were formed from them. Some
molecules must have been able to replicate themselves and thus, membranes were formed
from mixtures of larger molecules.

Endosymbiotic theory
› About two billion years ago, a bacterial cell entered a eukaryotic cell.
› The eukaryotic cell, acted as a “predator” letting the bacterial cell inside.
› Both cells formed a symbiotic relationship were both organisms were in contact with
one another.
› The bacterial cell, underwent some changes and developed into, mitochondria and
chloroplasts.
o Mitochondria and chloroplasts are indeed about the size of a bacterial cell
o They both have two membranes
o They divide independently by fission
o They have their own 70s ribosomes
o They have their own circular chromosomal DNA

Pasteur’s experiment
He wanted to test whether cells only arise from pre-existing cells.
He prepared nutrient broth and boiled it so as to kill any microorganisms. He divided
the broth into two flasks, a one with a straight neck and the other bent in an S shape. The
flasks were incubated for a period of time. After a few weeks, Pasteur observes that the one
with straight neck was discolored and cloudy whereas the other did not have any changes.
Thus, growth only occurred when the flask was exposed to external contaminants.
Consequently, bacterial growth did not occur spontaneously
Miller – Urey Experiment
It tested the non-living synthesis of simple organic molecules, recreating the conditions of
pre-biotic earth.
Water was boiled so as to evaporate and reflect the high temperature. The vapor
was then mixed with gases except for oxygen to recreate the no-oxygen earth. The mixture
was then exposed to electrical discharge to reflect lightning and then was left to cool for a
week. Once it was analyzed, organic molecules were discovered.

1.6 Cell division

During cell division a cell divides into two genetically identical daughter cells.

Interphase
G1 phase:
› It is the main and longest phase
› The cell grows in size and expresses genes required
› There is a checkpoint at the end of G1 that checks several parameters. If everything
is okay the cell will proceed to the S phase. If not it will remain at Go in order for all
internal and external conditions to become optimal.
S phase:
› DNA replication takes place.
› The cell duplicates the genetic material in order to have one copy for each daughter
cell.
G2 phase:
› The cell produces proteins required for cell division
› Some organelles duplicate
› There is a checkpoint at the end of G2 in order to ensure that all conditions are
optimal for mitosis.

Mitosis
Prophase:
 › Nuclear envelope and nucleolus disappear
› Chromatin starts condensing into chromosomes
› The two centrosomes start organizing microtubules into the mitotic spindle
Metaphase:
› The mitotic spindle is fully formed
› Chromatin has fully condensed into chromosomes
› Each chromosome is attached to the spindle with the two spindles being in opposite
sides
› The spindle apparatus moves chromosomes at the equator level and aligns them in a
single line
› There is a checkpoint at the end which ensures that all chromosomes are attached to
the spindle
Anaphase:
› The poles pull the chromosomes until the centromere breaks and the two sister
chromatids move to opposite sides.
Telophase:
› Nuclear envelope and nucleolus reappear
› Chromatin decondenses into chromosomes
› The mitotic spindle degenerates

Cytokinesis:
› In animal cells, at the equator level actin filaments create clewage furrow
› In plant cells, at the equator level, a series of vesicles form the cell plate

Cyclins are proteins that regulate the cell cycle. The bind to cyclin dependent protein kinases
and through phosphorylation they activate other proteins enabling them to act as enzymes.
Cyclin D: triggers the cell to move from Go to G1 and from G1 to S
Cyclin E: prepares the cell for replication during the S phase
Cyclin A: responsible for replication
Cyclin B: causes the mitotic spindle to form and other tasks needed for mitosis
a. They retain their ability to divide and replicate and can differentiate into specialized
cell types.
b. A multicellular organism consists of cells that all arise from the same cell the zygote.
During differentiation each cell specializes into specific properties and produce and
express the proteins related to their functions. Some genes are expressed and are
turned on whereas others can be turned off. For example, a neuron has all genes of a
cell but only the genes needed for the neuron to function are turned on.

Active transport is a method of transportation that uses ATP to move substances against
a concentration gradient, through protein pumps. It includes, endocytosis, exocytosis
and sodium potassium pump.

Endocytosis and exocytosis are a form of active transport which requires ATP to move
substances against a concentration gradient through protein pumps. In endocytosis a
substance is engulfed by the cell and stored in a vesicle from the rER. The vesicle then,
will possibly fuse with lysosomes whose digestive enzymes will break down the content
of the vesicle. In exocytosis the vesicle coming from the Golgi apparatus with the
modified substance will fuse with the membrane and open towards the extracellular
space and release it.

In active transport substances move against a concentration gradient through

membrane proteins using ATP. In active transport they are included endocytosis,
exocytosis and sodium potassium pump. In passive transport no ATP is required and
substances move across a concentration gradient from high to low concentration. It
included, osmosis, simple and facilitated diffusion. An example of passive transport is
the transport of oxygen across the alveoli and an example of active transport is glucose
absorption in ileum.