Cell Biology Notes

Table of Contents
1.1 Introduction to Cells 3
Cell Theory 3
Exceptions of Cell Theory 3
MR SHENG Acronym 3
Differentiation 3
Use of Stem Cells 4
Location of Stem Cells 4
Microscopes 4
1.2 Ultra-Structure of Cells 5
Difference Between Prokaryotes and Eukaryotes 5
Prokaryotic Cell Features 5
Animal cell features 6
Plant cell features 7
Types of Bacteria 8
Differences Between Plant Cells and Animal Cells 9
1.3 Membrane Structure 9
Fluid Mosaic Structure (Singer-Nicolson Model) 9
What is a Phospholipid? 10
Characteristics of a Phospholipid Bilayer 10
Integral Proteins vs. Peripheral Proteins 10
Functions of Proteins in the Membrane 11
Cholesterol 11
Extracellular Matrix 11
Previous Theories on Cell Membrane Structure 12
1.4 Membrane Transport 12
Active Transport Vs. Passive Transport 12
Channel Proteins Vs. Carrier Proteins 13
Potassium Channel (example of facilitated diffusion in axons of nerve cells) 14
Active Transport 14
Sodium Potassium Pump (active transport) 14
Vesicular Transport 14
Bulk Transport 15
1.5 Origin of Cells 16
Abiogenesis 16
Biogenesis 16
 Origin of Eukaryotic Cells 17
RNA World Hypothesis 17
Oxygen Enrichment of the Atmosphere 18
1.6 Cell Division 18
The Cell Cycle 18
Interphase 19
Mitosis 19
Cytokinesis 21
Cyclins 21
The Development of Cancer 21
Difference Between Normal Cells and Cancer Cells 22
The Death of Cells 22
1.1 Introduction to Cells

Cell Theory
1. All living organisms are made of cells
2. Cells are the smallest unit of life
3. All cells are derived from pre-existing cells

Exceptions of Cell Theory

- Striated Muscle Fibres
- Large
- Multiple nuclei
- Giant Algae
- Large
- Fungal Hyphae
- 1 big uniform cell instead of many discrete cells

MR SHENG Acronym
Metabolism
Reproduction

Sensitivity - reacting to internal/external stimuli

Homeostasis
Excretion
Nutrition - similar to respiration
Growth

Differentiation
- Transform into specialised cells
- Differential gene expression
- Loses its ability to form/complete cell types
- Stem cells
- Self renewable
- Potency - able to differentiate
- Multipotent: less differentiability
- Totipotent: placental tissue, most potent
- Unipotent: Unable to differentiate
- Pluripotent: Found in embryos
Use of Stem Cells
- Stargardts disease - inherited genetically - causes blindness
- Parkinson's - nervous system - replace dead nerve cells
- Leukaemia - chemotherapy kills a lot of cells - stem cells can replace dead cells
- Paralysis - replacing nerve cells

Location of Stem Cells

- IVF - embryos (limitations: ethics)
- Umbilical cord/blood/placenta (limitations: costly to store)
- Adult tissue (limitations: less potent)

Microscopes
Light Microscope Electron Microscope

- Use lenses that bend light - Use electromagnets to focus on electrons

- Max magnification is roughly x100 - Gives a higher degree of magnification + a
better degree of resolution

- Used for living specimens in their natural - Used for dead specimens in monochrome
colour - Transmission electron microscopes
- Can use chemical dyes or fluorescent - Give you a cross section
labels - scanning electron microscopes
- Gives a 3D image

Relevant Size:
Plant cell: Between 10 and 100 micrometres long
Animal Cell: 10–20 μm in diameter
Organelle: Between 1 micrometre (μm) and hundreds of micrometres in diameter
Virus: 20 nanometres (nm; 0.0000008 inch) to 250–400 nm
Prokaryotic Cell: 0.1 to 5.0 micrometres (μm) in diameter

1.2 Ultra-Structure of Cells

Difference Between Prokaryotes and Eukaryotes

Prokaryotes Eukaryotes

- Don’t contain nucleus - Contains a nucleus

- Belong to the monera kingdom - More complex than prokaryotes
- Monera have archaebacteria and - Compartmentalised by membrane-bound
 eubacteria
- No membrane-bound organelles
- 70s ribosome
- Lack compartmentalisation
- Binary fission
- Circular DNA is replicated in
response to a signal
- DNA attaches at the membrane
- The membrane elongates and then
‘pinches off’ to create two
separate cells
structures (organelles)
- Organelles perform specific roles
- Belong to: Protista, fungi, plantae,
animalia
- Protists are generally unicellular,
they can be multicellular but they
lack specialised tissue (eg
seaweed)
- Fungi have a cell wall made of
chitin + they obtain nutrients via
heterotrophic absorption
- Plantae, autotrophic absorption,
cell wall made from cellulose
- Animalia, no cell wall,
heterotrophic absorption

Prokaryotic Cell Features

Feature Purpose

Nucleoid - Contains DNA

- In the cytoplasm
- Looks like condensed squiggles

Cytoplasm - The fluid that is within a cell and contains

the other components

Cell wall - Made of peptidoglycan

- Maintains the shape
- Prevents bursting

70s ribosomes - Made of RNA + protein

- Help with synthesising polypeptides

Cell membrane - Barrier around the cell which selectively

allows things to enter/exit
- Semi-permeable

Flagellum - Helps the cell move (made of motor

protein)

Pili - Helps the cell stick to things

- Conjugation

Slime capsule - Outside the cell wall

- Made of polysaccharides
- Protection against drying out
 - Ingests things (phagocytosis)

Plasmid - Extra area of genetic material

- Usually circular
- Used for gene transfer between bacteria

Animal cell features

Features Purpose

Nucleus (contains nucleolus) - Contains the DNA

Cell membrane - Barrier around the cell which selectively

allows things to enter/exit
- Semi-permeable

80s ribosomes - Made of RNA + protein

- Help with synthesising polypeptides

Cytosol - The fluid that is within a cell and contains

the other components

Mitochondria - Energy/ATP synthesis

- This is where aerobic respiration occurs

Smooth/rough endoplasmic reticulum (ER) - Rough endoplasmic reticulum

- Has ribosomes attached
- Protein synthesis
- Smooth endoplasmic reticulum
- Produces lipids/fats

Golgi - Packaging of proteins

 - Takes proteins from the rough ER
- Packages + alters proteins (if needed)
- Sends off proteins in packages

Lysosome - Breaking down stuff

Peroxisome - Contains catabolic enzymes

- Breaking down toxic substances

Plant cell features

Features Purpose

Nucleus (contains nucleolus) - Contains the DNA

Cell membrane - Barrier around the cell which selectively

allows things to enter/exit
- Semi-permeable

80s ribosomes - Made of RNA + protein

- Help with synthesising polypeptides

Cytosol - The fluid that is within a cell and contains

the other components

Mitochondria - Energy/ATP synthesis

- This is where aerobic respiration occurs

Smooth/rough endoplasmic reticulum (ER) - Rough endoplasmic reticulum

 - Has ribosomes attached
- Protein synthesis
- Smooth endoplasmic reticulum
- Produces lipids/fats

Golgi apparatus - Packaging of proteins

- Takes proteins from the rough ER
- Packages + alters proteins (if needed)
- Sends off proteins in packages

Chloroplast - Contains chlorophyll and thylakoids

- The site of photosynthesis
- Energy production
- Absorption of light + converting to energy

Cell wall - Made of cellulose

- Maintains the shape
- Prevents bursting
- Prevents excess water uptake

Vacuole *(animal cells can have vacuoles but they - Large central ‘sack of water’
are small and temporary) - Store of water
- Turgidity
- Hydrostatic pressure

Peroxisome - Contains catabolic enzymes

- Breaking down toxic substances

Types of Bacteria
All Bacteria:
- Lacks compartmentalisation
- 70s ribosomes
- Naked DNA
- Lacks a nucleus

Differentiate
- Different shape
- Different things make up the cell wall
- Anaerobic vs aerobic
- Heterotrophic vs autotrophic
Differences Between Plant Cells and Animal Cells
Plant Cells Animal Cells

Autotrophic Heterotrophic

Cell wall made of cellulose No cell wall

Chloroplasts No chloroplasts

Always have vacuoles Rarely have vacuoles (small, temporary)

No centrioles Centrioles within centrosome

Excess glucose stored as starch Excess glucose stored as glycogen

Rigid form / shape Amorphous shape

1.3 Membrane Structure

Fluid Mosaic Structure (Singer-Nicolson Model)

(Animal Cell)
What is a Phospholipid?
- Amphipathic: some parts love water, some parts hate water
- Phosphate head, polar, hydrophilic
- Two fatty acid tails, non-polar, hydrophobic
- They arrange in the membrane spontaneously to form a bilayer
- Fatty acid tails face inwards
- Phosphate heads associate with either the cytoplasm or extracellular fluid

Characteristics of a Phospholipid Bilayer

- Semi-permeable
- Weak
- Individual phospholipids can move within the bilayer - fluidity/flexibility
- Fluidity allows for the cell membrane to break and reform to let certain things into and out of the
cell

Integral Proteins vs. Peripheral Proteins

- Integral proteins are permanent and transmembrane
- Integral proteins can come in two different structures
- Single helix/helix bundles
- Beta barrels
- Peripheral proteins are temporary - only associate with one side of the membrane
- All proteins can be polar or non-polar - attaches to whatever matches in polarity

Functions of Proteins in the Membrane

- Transport
- Active transport
- Facilitated diffusion
- Regulates the fluidity of the cell membrane
- Junction
- Helps to join two cells together
- Enzymes
- Recognition
- Proteins on a membrane may be a marker
- Anchorage
- Attachment
- Transduction
- Receiving peptide hormones
Cholesterol
- Only present in animal cells - absent in plant cells because cell wall provides this function
- Maintains integrity + mechanical stability in the cell membrane
- Amphipathic
- Has:
- Hydroxyl group - hydrophilic, near phosphate head
- Steroid ring and hydrocarbon tail - hydrophobic, near the fatty acid tails
- Reduces fluidity bye immobilising the outer surface of the membrane
- Makes the membrane slightly less permeable (specificity) - especially to very small water
molecules
- Separates the phospholipid tails
- Prevents crystallisation of the membrane
- Secures peripheral proteins

Extracellular Matrix
- Glycoproteins
- Protein fibres
- Etc (everything that exists outside of the cell membrane)
- Structural + biochemical support
- Can provide anchorage for cells
- Important for identification - signals, communicative structure, understanding what's around the
cell
- In plant cells, can also regulate water uptake and may provide strength and rigidity

Previous Theories on Cell Membrane Structure

Danielli and Davson model
- Lipoprotein sandwich
- Two layers of protein
- Lipids in between
- Limitations
- Assumes that it would have symmetrical and internal surfaces
- Assumes that they would all be uniform thickness throughout the whole membrane
- Did not account for the permeability of certain substances
- The temperature at which the membrane solidified and dissolved - didn’t match previous
knowledge on proteins
- Disproving Information / Experiments
 - Membrane proteins are insoluble + vary in size
- Able to tag membrane proteins in different colours - the colours showed that the
membrane proteins are mobile
- When tagged they fused two different cells and the markers were mixed throughout
- Freeze fracturing
- Split the membrane and revealed irregular rough surfaces that reveal a rough
irregular surface that was transmembrane
- Therefore, we now follow the Singer-Nicolson Model (i.e Fluid Mosaic))

1.4 Membrane Transport

Active Transport Vs. Passive Transport

Active Transport Passive Transport

Requires energy Doesn’t require energy

Goes against the concentration gradient Goes with the concentration gradient

Primary/Direct Facilitated diffusion

- Direct use of ATP to mediate the transport
Secondary/Indirect
- Molecules are grouped together to move
along an electrochemical gradient
Osmosis
Simple/Passive diffusion
- Large and polar molecules
- Pass through passively with the use of
proteins within the membrane
- Used by molecules that would otherwise
be unable to freely cross the phospholipid
bilayer
- Makes use of channel proteins and carrier
proteins
- The net movement of water molecules
across a semipermeable membrane
- Occurs from an area of low solute
concentration to high solute concentration
- Movement of small nonpolar molecules
- The net movement of molecules from
high concentration to low concentration
- Non-polar = lipophilic (loves fats)
Polar = lipophilic (hates fats)
- Factors that influence rate of diffusion:
- The higher the kinetic energy /
temperature, the faster diffusion
will occur
- Molecular size; the larger a
particle is, the harder to diffuse
 - The steepness of the gradient

Channel Proteins Vs. Carrier Proteins

Channel Proteins Carrier Proteins

Integral proteins Integral proteins

Lipoproteins Glycoproteins

Has a channel which allows the solute to cross Undergo a conformational change to allow the
solute to translocate/cross the membrane

Ion selective - sometimes they have gates on the Will only ever bind to specific molecules that they
pore to regulate the amount of ions allowed to are designed for
pass through in response to certain stimuli

Molecules pass through the channel according to Can move molecules against the concentration
the concentration gradient gradient, and therefore are sometimes used for
active transport

Much faster than carrier proteins Much slower than channel proteins

Potassium Channel (example of facilitated diffusion in axons of nerve cells)

- One example of an integral channel protein
- Allows for potassium ions to be transported
- Voltage gated
- Will cycle between opened and closed depending on whether they receive a
transmembrane voltage from the brain

Active Transport
- Carrier proteins are called protein pumps when used for active transport
- Molecule will bind to protein pump on one side of the membrane
- Hydrolysis of ATP will cause a conformational change in the shape of the protein pump which
allows the molecule to be translocated across the membrane
- Hydrolysis = ATP being broken down into adenosine diphosphate + phosphate
- The release of the third phosphate (the breaking of the chain) is what actually
provides energy
Sodium Potassium Pump (active transport)
- Located in the axon of nerve cells
- Integral proteins (carrier proteins/pump)
- 3 sodium ions will bind to the intracellular sites on the sodium potassium pump
- A phosphate is transferred to the pump via the hydrolysis of ATP
- Which causes the pump to undergo its conformational change - as a result the 3 sodium
ions are able to move across the membrane
- Exposes 2 potassium binding sites which allows 2 potassium ions to bind
- The phosphate from the ATP gets released
- Returns back to its original shape
- The potassium has now gone in

Vesicular Transport
Anything that a cell produces and needs to secrete will be transported in vesicles
1. Starts in the endoplasmic reticulum
- Rough ER synthesises proteins - Smooth ER synthesises lipids
- The ER membrane will bulge and then cut off to create a vesicle around the proteins +
lipids which the cell has produced

2. Golgi apparatus
- The vesicle will be transported to the golgi apparatus
- Fuses to the internal face of the golgi - cis face
- Move from the cis face to the external/trans face
- As they move across it gets changed/modified + packaged
- Gets sent to either the lysosome or to the cell membrane
- If the proteins are sent to the lysosome they are consumed internally
- Can be sent immediately (constitutive secretion) or stored to wait to be released in
response to a stimulus (regulatory secretion)

3. Cell membrane
- Fuse with the cell membrane
- Expelled into the extracellular fluid (exocytosed)

Bulk Transport
- how we get materials i.e vesicles in and out of the cell
- All bulk transport is active
- Endocytosis
- Ingestion or entering of large substances into the cell
- They are able to enter the cell without having to cross the membrane
 - Cell membrane will invaginate - forms a depression which envelopes the material that is
trying to be brought in
- The invagination will seal off to form an intracellular vesicle which contains the material
- 2 main types of endocytosis
- Phagocytosis
- For solid substances
- Pinocytosis
- For liquids or dissolved substances
- Generally faster than protein channels
- Exocytosis
- The process where cells secrete/expel large substances without crossing the membrane
- The vesicle will generally move from the golgi to the plasma membrane
- It will fuse with the plasma membrane
- It'll expel the contents once it fuses

1.5 Origin of Cells

Abiogenesis
Miller & Urey experiment
- Mimicked the environment of early earth; water being boiled at high temperatures, the water
vapour was mixed with other gases to create an atmosphere with no oxygen
- The mixture was exposed to electricity to mimic lightning
- Condensed the gas into a liquid
- Let it sit and cool down for a week
- Analysed the condensed mixture
- Found simple organic molecules
What does this mean for cell theory? (Why now, do cells only come from preexisting cells)
- The chemical processes identified in the Miller and Urey experiment are extremely rare and
specific.
- I.e reducing atmosphere + high temp (>100 degrees) + electrical discharge
- Where might these conditions have been present in the past?
- Volcanoes
- Shorelines / ocean
- Extra-terrestrial origins
- Hydrothermal vents

Biogenesis
Louis Pasteur
 - Proving the law of biogenesis (cell theory; cells only come from preexisting cells)
- Disproving spontaneous generation

Origin of Eukaryotic Cells

Endosymbiotic theory:
- The first eukaryotic cells evolved from prokaryotes that engulfed other prokaryotes via
phagocytosis
- The engulfed prokaryotic cell wasn’t digested because it contributed beneficially to the cell
- As cells continued to evolve, the digested cell lost its ability to function independently and
became a supplementary organelle
Evidence:
- Mitochondria and Chloroplasts share certain features with prokaryotic / independent cells
- contain their own (different) dna
- Double membrane bound
- Susceptible to antibiotics / develop antibiotic resistance
- They divide / undergo replication
- Contain their own ribosomes

RNA World Hypothesis

- Life on Earth began from self-replicating RNA
- precursors to current life forms that uses DNA
- RNA can store genetic information
 - It can undergo processes such as replication, mutation, and natural selection, which are essential
for the evolution of life
- RNA have the ability to act as both genetic material and enzymes
- RNA-based organisms evolved to use DNA for more stable genetic storage and proteins for more
efficient enzymatic functions

Oxygen Enrichment of the Atmosphere

- Initially Earth had a reducing atmosphere
- There is an exponential increase in the amount of oxygen in the atmosphere dating back 4 billion
years ago
- Why?
- Increased breakdown of chemicals in the atmosphere and ocean with oxidised compounds
as a product
- As more organisms have evolved, they have become more capable of breaking down
oxygen-rich agents
- The formation of the ozone layer - protects from UV radiation, allowing for greater
growth of organisms such as plants

1.6 Cell Division

The Cell Cycle

Cell division / mitosis must be controlled
-
Interphase
- The stage between two divisions
- G1 stage
- The first break after the division where the cell undergoes growth and prepares
for DNA replication
- G1 checkpoint: check for appropriate conditions for growth and that DNA hasn’t
been damaged (may enter G0 phase which is resting state)
- S stage
- Synthesis stage - DNA is replicated
- G2 stage
- Final growth and preparation before the division
- G2 checkpoint: check that cell is big enough for division and make sure no
replication faults
The M phase (mitosis phase)
- The cell + contents are dividing to create 2 genetically identical daughter cells
 - Mitosis
- DNA is separated into 2 identical nuclei - nuclear division
- Cytokinesis
- Cellular contents are separated and the cell splits into 2 - cytoplasmic division

Interphase
- Active period - metabolic reactions must occur in order to prepare thc ell for a successful division
- Cell growth
- DNA replication
- Organelles need to be duplicated
- Transcription and translation
- Must obtain nutrients
- ATP production via cellular respiration

Mitosis
𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑐𝑒𝑙𝑙𝑠 𝑖𝑛 𝑚𝑖𝑡𝑜𝑠𝑖𝑠
Mitotic index = 𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑐𝑒𝑙𝑙𝑠
; indicator of the proliferation status (how active are the cells in
the organism with regards to division, can be an indicator of certain things). Mitotic index should be
elevated in certain events such as growth and cell repair. It can be used to predict the response of cancer
cells to chemotherapy. 4 reasons why an organism might go through mitosis; growth, repair, embryonic
growth, and asexual reproduction.

- Prophase: DNA supercoils, chromosomes condense. First point that chromosomes are visible
under a microscope. Before prophase occurs, DNA is loosely packed in the nucleus as chromatin.
During prophase, chromatin condenses into chromosomes - tightly bound and condensed,
supercoiled. While in chromosomes DNA is able to be easily separated into two identical copies,
however it is unable to be used for transcription. Paired centrosomes move to the opposite sides of
the cell and begin forming microtubule spindle fibres. The nucleus will also dissolve.

- Metaphase: the fibres connect from the centrosome to the centromere, they will then shorten in
length and contract (microtubule depolymerisation) causing the chromosomes to line up at the
equator (centre) of the cell.
 - Metaphase Checkpoint: make sure centromeres of chromosomes are attached to spindle
fibres

- Anaphase: In anaphase the fibres continue to contract causing the genetically identical sister
chromatids to split apart. The result is that there are now identical chromosomes on each side.

- Telophase: Chromosomes are now at the poles, therefore the spindle fibres can dissolve. The
chromosomes then decondense, unravel the supercoiling (they will become progressively less
visible under the microscope). The nuclear membrane will then reform around the chromosomes
which leads into the process of cytokinesis.
Cytokinesis
The cytoplasm is divided into two to create two identical daughter cells. Cytokinesis is different in animal
cells and plant cells.
Cytokinesis in animal cells (centripetal):
- After anaphase, microtubule filaments form a concentric ring around the centre of the cell
- The microfilaments will constrict which forms a cleavage furrow
- The microfilaments will construct so much that the furrow meets in the centre
- At this point the cell becomes completely pinched off and forms two cells

Cytokinesis in plant cells (centrifugal):

- During anaphase, carbohydrate-rich vesicles get produced at the centre of the cell in a line
- The vesicles fuse together to form a cell plate at the middle of the cell
- The cell plate will continue to grow until it meets the cell wall
- It then divides the cell into two cells

Cyclins
The family of proteins which regulate the rate of mitosis. Cyclins work by activating CDK’s (cyclin
dependent kinases) - a process which is dependent on the presence of cyclin. If cyclin and CDK join to
make a complex (combination of two different things), the cyclin allows for the complex to bind to
specific target proteins. When the target protein binds to the complex it gets modified and becomes
activated (commonly via phosphorylation). The activated target protein will then trigger a specific event in
the cell cycle. The cyclin then gets degraded so that CDK can no longer bind to target proteins. More
cyclins = more divisions. Cyclin concentrations must be tightly regulated to ensure that the cell cycle
occurs in a proper sequence and at a proper level.
The Development of Cancer
Cancer = uncontrolled cell division, leading to the formation of tumours (abnormal growths)
Main reasons why this may occur;
1) Genetic change due to carcinogens / mutagens (eg x-rays, radiation, virus, age etc)
2) Oncogenes - genes that have the potential to cause cancer
a) Proto oncogene - too many proto oncogenes may result in uncontrolled cell growth
b) Tumour Suppressor Genes - these normally limit tumour growth and cell division, so
some people can lack these
Cancer normally occurs in one location, however it may metastasise (spread from one location to
another). Primary = where it starts, secondary = where it spreads to.

Difference Between Normal Cells and Cancer Cells

Normal cells Cancer cells

Small and uniform. Very organised Large with lots of variation in size and shape, they
are disorganised

Mostly cytoplasm Very low cytoplasm

Able to carry out differentiated processes Lose the ability to perform specialised features

Low mitotic index High mitotic index

Aren’t detected by the immune system because

they aren’t an infection or virus.

The Death of Cells

Cells die in 2 ways;
Necrosis Apoptosis

Uncontrolled - unplanned or unwanted Programmed - intentional

Premature, normally caused by some sort of Controlled event, certain signals will tell the
disruption - injury, toxins, nutrition deprivation etc organism when to undertake this process

The cell loses functional control and becomes There is a catabolic reaction which causes the cell
unstable contents to be digested

The cell will swell and then burst which can cause Results in blebbing, everything is repackaged into
inflammation in the tissue small shrunken fragments / bodies and are
digested