Cell Biology

1.1 Cell Introduction

The Cell Theory:

1. All living things are composed of cells.

2. The cell is the smallest unit of life.
3. Cells only arise from pre-existing cells.

Certain types of cells / tissues do not conform to a standard notion of what constitutes a cell:

Striated Muscle Fibres Aseptate Fungal Hyphae Giant Algae

Fuse to form fibres that may be Fungi are not separated by Unicellular algae may grow to
very long, multiple nuclei even septa so have a continuous be very large sizes, almost 7cm
with one plasma membrane. cytoplasm. in length.

Functions of Life:

1. Metabolism – Undertake essential chemical reactions.

2. Reproduction – Produce offspring.
3. Sensitivity – Responsive to internal and external stimuli.
4. Homeostasis – Maintain a sustainable internal environment.
5. Excretion – Exhibit removal of waste products.
6. Nutrition – Exchange materials and gases with the environment.
7. Growth – Move and change in shape or size.

Emergent Properties:

“The whole is greater than the sum of its parts”

When the interaction of individual components produces new functions.

Surface Area: Volume Ratio

= rate of material exchange: rate of metabolism

Cells need to produce chemical energy (via metabolism) to survive, requiring the exchange of
materials with the environment.

As a cell grows, volume increases faster than surface area, leading to a decreased ratio.

Cells and tissues that are specialized for gas or material exchanges will increase their surface area to
optimize material transfer.
Cell Differentiation:

Newly formed cells become more specialized and distinct from one another as they mature.

All cells of an organism share an identical genome – each cell contains the entire set of genetic
instructions for that organism.

The activation of different genes through chemical signals will cause it to differentiate.

DNA is packaged with proteins to form chromatin.

 Active Genes: packaged in an expanded form called eurochromatin.
 Inactive Genes: packaged in a more condensed form called heterochromatin.

Stem Cells:

Unspecialized cells that can continuously divide and replicate and have the capacity to differentiate
into different cell types.

Totipotent: can form any cell type along with extra-embryonic tissue.
Pluripotent: can form any cell type.
Multipotent: differentiate into several closely related cell types.
Unipotent: cannot differentiate but are capable of self-renewal.

Use of Stem Cells:

Necessary for embryonic development as they are an undifferentiated cell source from which all
other cell types may be derived, also a viable therapeutic option.

Biochemical solutions to trigger differentiation -> surgical implantation -> suppression of host
immune system to prevent rejection -> monitoring of cells.

Stargardt’s Disease Replacing dead cells in the retina with functioning ones.
Parkinson’s Replacing dead nerve cells with living, dopamine-producing ones.
Disease
Leukemia Bone marrow transplants for patients who are immune compromised.

Stem cells can be derived from 3 sources:

1. Embryos. Requires destruction of potential living organism.
2. Umbilical cord blood or placenta. Need to be stored and preserved at a cost.
3. Specific adult tissues (e.g., Bone marrow). Limited in scope of application.

Artificial Stem Cell Techniques

 Somatic Cell Nuclear Transfer Nuclear Reprogramming
Therapeutic cloning – fusing a diploid nucleus Change in the gene expression profile – trans
with an enucleated egg cell. differentiation.
More embryos are created than needed. Use of oncogenic retroviruses, risk of health
consequences.

1.2 Cell Structure

Prokaryotic Cells:

Organisms whose cell lacks a nucleus.

 Archaebacteria: found in extreme environments.
 Eubacteria: traditional bacteria.

Cytoplasm Internal fluid component.

Nucleoid Location of DNA.
Plasmids DNA transferred between
bacteria.
Ribosomes Polypeptide synthesis.
Cell Semi-permeable and selective
Membran barrier of the cell.
e
Cell Wall Maintains shape and prevents
bursting.
Slime Protection against dessication.
Capsule
Flagella Enables movement.
Pili Adhere to surfaces.

Prokaryotes divide by Binary Fission: Asexual Reproduction

1. Replication Signal -> circular DNA is copied.
2. Two DNA loops attach to the membrane.
3. Membrane elongates and pinches off.

Eukaryotes:

Organisms whose cell contains a nucleus. Compartmentalized in membrane-bound structures that

perform specific roles.
Organelles:

Specialized sub-structures within a cell that serve a specific function.

Universal Organelles
Ribosomes Polypeptide synthesis. Larger in eukaryotes (80S) and (70S) smaller in
prokaryotes.
Cytoskeleton Provides internal structure
Plasma Membrane Semi-permeable layer and selective barrier surrounding the cell.
Eukaryotic Organelles
Nucleus Stores genetic material as chromatin, nucleolus is site of ribosome
assembly.
Endoplasmic Reticulum Transports materials between organelles (smooth ER; lipids, rough
ER; proteins).
Golgi Apparatus Sorting, storing, modification and exporting of secretory products.
Mitochondrion Site of ATP production.
Peroxisome Catalyzes breakdown of toxic substances.
Centrosome Contributes to cell division.
Plant Cells Only
Chloroplast Site of photosynthesis.
Vacuole Maintains hydrostatic pressure.
Cell Wall Provides support and mechanical strength.
Animal Cells Only
Lysosome Hydrolysis of macromolecules.

1.3 Membrane Structure

Phospholipid Bilayer:

Phospholipids from bilayers in water due to amphipathic properties of phospholipid molecules.

  Polar head (hydrophilic) composed of a glycerol and a
phosphate molecule.
 Two non-polar tails composed of fatty acid hydrocarbon
chains.
 Hydrophilic + hydrophobic = amphipathic.
 They spontaneously arrange into a bilayer.
 The hydrophobic tail regions face inwards and are
shielded from the surrounding polar fluids, while the two
hydrophilic head regions associate with the extracellular
fluids.

 Bilayer is held together by weak hydrophobic

interactions.
 Restrict the passage of many substances.
 Individual phospholipids move around the bilayer,
allowing for membrane fluidity and flexibility.
 Fluidity allows for breaking and reforming of membranes.

Membrane Proteins:

Bilayers are embedded with proteins, which may either be permanently or temporarily attached to
the membrane.

 Integral Proteins: permanently attached to the membrane, span across the bilayer.
 Peripheral Proteins: temporarily attached to non-covalent interactions and associate with
one surface of the membranes.

The amino acids of a membrane protein are localized according to polarity:

 Non-polar: associate directly with the lipid bilayer.
 Polar: located internally and face aqueous solutions.

Transmembrane proteins typically adapt one of two tertiary structures: single helices or beta barrels.

They serve a variety of functions:

 Serve to connect and join cells.
 Fixing to membranes to localize metabolic pathways.
 Responsible for facilitated diffusion and active transport.
 Markers for cellular identification.
 Receptors for peptide hormones.

Cholesterol:

Component of animal cell membranes, it functions to maintain integrity and mechanical stability.
 Amphipathic molecule: hydroxyl group is hydrophilic, aligning towards the phosphate heads
while the steroid ring and hydrocarbon tail is hydrophobic, associating with the tails.
Phospholipid bilayers are fluid = in constant movement relative to one another.

Cholesterol interacts with the fatty acid tails of phospholipids to moderate the properties of the
membrane:
 Makes the membrane
less permeable.
 Reduces fluidity by
immobilizing the outer
surface of the
membrane.
 Prevents crystallization
of the membrane by
separating
phospholipid tails.

Fluid Mosaic Model:

Membrane Models:

The first model that attempted to describe the position of proteins within the bilayer was proposed by
Hugh Davson and James Danielli in 1935
When viewed under a microscope, membranes exhibit a characteristic 'trilaminar’ (two dark outer
layers and a lighter inner region) appearance.
  The model was described as a 'lipo-protein sandwich’, as the lipid layer was sandwiched
between two protein layers
However, there were a number of problems with this model, such as it assuming that:
 There was a constant lipid-protein ratio.
 Symmetrical internal and external structures.
 Did not recognize the need for hydrophilic pores.

Falsification Evidence:

Membrane was insoluble in water and varied in size.

Fluorescent antibody tagging of membrane proteins showed they were mobile and not fixed in place
 Membrane proteins from two different cells were tagged with red and green fluorescent
markers respectively
 When the two cells were fused, the markers became mixed throughout the membrane of the
fused cell
 This demonstrated that the membrane proteins could move and did not form a static layer (as
per Davson-Danielli)

Freeze fracturing was used to split open the membrane and revealed irregular rough surfaces within
the membrane 
 These rough surfaces were interpreted as being transmembrane proteins, demonstrating that
proteins were not solely localised to the outside of the membrane structure

New Models:

In light of these limitations, a new

model was proposed by Seymour
Singer and Garth Nicolson in 1972
According to this model, proteins
were embedded within the lipid
bilayer rather than existing as
separate layers

1.4 Membrane Transport

Types of Transport:

Cellular membranes possess two key qualities:

1. Semi permeable.
2. Selective.

Movements of materials across a biological membrane may occur either actively or passively.
Passive Transport:
Passive transport involves the movement of material along a concentration gradient (high
concentration ⇒ low concentration)
Because materials are moving down a concentration gradient, it does not require the expenditure of
energy (ATP hydrolysis)
There are three main types of passive transport:
 Simple diffusion – movement of small or lipophilic molecules (e.g. O2, CO2, etc.)
 Osmosis – movement of water molecules (dependent on solute concentrations)
 Facilitated diffusion – movement of large or charged molecules via membrane proteins (e.g.
ions, sucrose, etc.)

Simple Diffusion

The rate of diffusion can be influenced by a number of factors, including:

 Temperature  (affects kinetic energy of particles in solution)

 Molecular size  (larger particles are subjected to greater resistance within a fluid medium)
 Steepness of gradient  (rate of diffusion will be greater with a higher concentration gradient)

Osmosis

 Because solutes cannot cross a cell membrane unaided, water will move to equalise the two
solutions
 At a higher solute concentration there are less free water molecules in solution as water is
associated with the solute
 Osmosis is essentially the diffusion of free water molecules and hence occurs from regions of
low solute concentration

Osmolarity

The measure of solute concentration, as defined by the number of osmoles of a solute per liter of solution.

 Hypertonic: Solutions with a relatively higher osmolarity (high solute concentration ⇒ gains

water).
 Hypotonic: Solutions with a relatively lower (low solute concentration ⇒ loses water)
 Isotonic: Solutions that have the same osmolarity (same solute concentration ⇒ no net water
flow)

Tissues or organs to be used in medical procedures must be kept in solution to prevent cellular
desiccation. This solution must share the same osmolarity as the tissue/organ to prevent osmosis
from occurring.

Uncontrolled osmosis will have negative effects with regards to cell viability:
 In hypertonic solutions, water will leave the cell causing it to shrivel (crenation)
  In hypotonic solutions, water will enter the cell causing it to swell and potentially burst (lysis)

In plant tissues, the effects of uncontrolled osmosis are moderated by the presence of an inflexible
cell wall
 In hypertonic solutions, the cytoplasm will shrink (plasmolysis) but the cell wall will
maintain a structured shape
 In hypotonic solutions, the cytoplasm will expand but be unable to rupture within the
constraints of the cell wall (turgor)

Facilitated Diffusion

Utilised by molecules that cannot freely pass the phospholipid bilayer.

Carrier Proteins Channel Proteins

Are used in active transport. Are not used in active transport.
Only move molecules against a concentration Only move molecules along a concentration
gradient. gradient.
Slower rate of transport. Faster rate of transport.

Potassium channels.

Active Transport:

Active transport involves the movement of materials against a concentration gradient (low

concentration ⇒ high concentration)
Because materials are moving against the gradient, it requires the expenditure of energy (e.g. ATP
hydrolysis)
There are two main types of active transport:
 Primary  (direct) active transport – Involves the direct use of metabolic energy (e.g. ATP
hydrolysis) to mediate transport
 Secondary (indirect) active transport – Involves coupling the molecule with another moving
along an electrochemical gradient

Active Transport:

FINISH

Vesticular Transport:

FINISH

Bulk Transport:

FINISH
1.5 Origin of Cells

Non-living Synthesis:

Abiogenesis, the theory that living cells arose from non-living matter.

1. There was non-living synthesis of simple organic molecules 

2. These simple organic molecules became assembled into more complex polymers
3. Certain polymers formed the capacity to self-replicate 
4. These molecules became packaged into membranes with an internal chemistry different from
their surroundings

Miller-Urey Experiment:

 Water was boiled to vapour to reflect the high temperatures common to Earth’s original

conditions
 The vapour was mixed with a variety of gases (including H 2, CH4, NH3) to create a reducing
atmosphere (no oxygen)
 This mixture was then exposed to an electrical discharge (simulating the effects of lightning
as an energy source for reactions)
 The mixture was then allowed to cool (concentrating components) and left for a period of ~1
week
 After this time, the condensed mixture was analysed and found to contain traces of simple
organic molecules

Biogenesis:

The chemical processes that contributed to the initial formation of biological life required specific
conditions to proceed
 This included a reducing atmosphere and high temperatures (>100ºC) or electrical discharges
to catalyse chemical reactions

The law of biogenesis is largely attributed to Louis

Pasteur, who demonstrated that emergent bacterial
growth in nutrient broths was due to contamination
by pre-existing cells
 Broths were stored in vessels that contained
long tubings (swan neck ducts) that did not
allow external dust particles to pass
 The broths were boiled to kill any micro-
organisms present in the growth medium
(sterilisation)
  Growth only occurred in the broth if the flask was broken open, exposing the contents to
contaminants from the outside
 From this it was concluded that emergent bacterial growth came from external contaminants
and did not spontaneously occur

Endosymbiosis:

A cell which lives inside another cell with mutual benefit.

1.6 Cell Division

Mitosis is the division of the nucleus into two genetically identical daughter nuclei.

Interphase:
The active period in the cycle when many metabolic reactions occur.

 DNA replication – DNA is copied during the S phase of interphase

 Organelle duplication – Organelles
must be duplicated for twin daughter
cells
 Cell growth – Cytoplasmic volume must
increase prior to division
 Transcription / translation – Key
proteins and enzymes must be
synthesised
 Obtain nutrients – Vital cellular
materials must be present before division
 Respiration (cellular) – ATP production is needed to drive the division process

DNA Supercoiling:

Chromosomes condense by supercoiling during mitosis.

A chromosome is the condensed form of DNA which is visible during mitosis (via microscopy)
As the DNA is replicated during the S phase of interphase, the chromosome will initially contain two
identical DNA strands.

These genetically identical strands are called sister chromatids and are held together by a central
region called the centromere.

When these chromatids separate during mitosis, they become independent chromosomes, each made
of a single DNA strand.

Mitosis:

Prophase -> Metaphase -> Anaphase -> Telophase

Prophase:
 DNA supercoils and chromosomes condense (becoming visible under microscope)
 Chromosomes are comprised of genetically identical sister chromatids (joined at a
centromere)
 Paired centrosomes move to the opposite poles of the cell and form microtubule spindle
fibres

Metaphase:

 Microtubule spindle fibres from both centrosomes connect to the centromere of each
chromosome
 Microtubule depolymerisation causes spindle fibres to shorten in length and contract

Anaphase:
 Continued contraction of the spindle fibres causes genetically identical sister chromatids to
separate
 Once the chromatids separate, they are each considered an individual chromosome in their
own right
 The genetically identical chromosomes move to the opposite poles of the cell

Telophase:
 Once the two chromosome sets arrive at the poles, spindle fibres dissolve
 Chromosomes decondense (no longer visible under light microscope)
 Nuclear membranes reform around each chromosome set
 Cytokinesis occurs concurrently, splitting the cell into two

Cytokinesis:

Process of cytoplasmic division.

Animal Cells – Microtubule filaments form a concentric ring -> form a cleavage furrow,
Centripetal making the cell pinch off.
Plant Cells – Vesicles fuse together to form a cell plate -> extends and fuses with cell
Centrifugal wall, dividing the cell.

Mitotic Index:

cells∈mitosis
total number of cells

Used to measure the proliferation status of a cell population.

Cyclins:
Family of regulatory proteins that control the progression of the cell cycle.

Cyclins activate cyclin dependent kinases (CDKs), which control cell cycle processes through
phosphorylation
 When a cyclin and CDK form a complex, the complex will bind to a target protein and
modify it via phosphorylation
 The phosphorylated target protein will trigger some specific event within the cell cycle (e.g.
centrosome duplication, etc.)
 After the event has occurred, the cyclin is degraded and the CDK is rendered inactive again
 Cyclin levels will peak when their target protein is required for function and remain at lower
levels at all other times

Cancer Development:

Tumours are abnormal cell growths resulting from uncontrolled cell division and can occur in any
tissue or organ.

Mutagens:

A mutagen is an agent that changes the genetic material of an organism.

Mutagens may be physical, chemical or biological in origin:

 Physical – Sources of radiation including X-rays (ionising), ultraviolet (UV) light and
radioactive decay
 Chemical – DNA interacting substances including reactive oxygen species (ROS) and metals
(e.g. arsenic)
 Biological – Viruses, certain bacteria and mobile genetic elements (transposons)

Mutagens that lead to the formation of cancer are further classified as carcinogens.

Oncogenes:

An oncogene is a gene that has the potential to cause cancer

Most cancers are caused by mutations to two basic classes of genes – proto-oncogenes and tumour
suppressor genes
 Proto-oncogenes code for proteins that stimulate the cell cycle and promote cell growth and
proliferation
 Tumour suppressor genes code for proteins that repress cell cycle progression and promote
apoptosis. Known for preventing cancer.

Metastasis:
Tumour cells may either remain in their original location (benign) or spread and invade neighbouring
tissue (malignant)
Metastasis is the spread of cancer from one location (primary tumour) to another, forming
a secondary tumour
Secondary tumours are made up of the same type of cell as the primary tumour – this affects the type
of treatment required

Molecular Biology

2.1 Metabolic Molecules

Molecular Biology

Is a field of study that focuses on investigating biological activity at a molecular level. Biological
processes are tightly regulated by enzymes, whose expression is controlled by gene activation.

Organic Compounds:

A compound that contains carbon and is found in living things.

Carbon forms the basis of organic life due to its ability to form large and complex molecules through
covalent bonding.

There are four principal groups of organic compounds that contribute to much of the structure and
function of a cell.

Complex macromolecules may commonly be comprised of smaller, recurring subunits

called monomers
 Carbohydrates, nucleic acids and proteins are all comprised of monomeric subunits that join
together to form larger polymers
 Lipids do not contain recurring monomers, however certain types may be composed of
distinct subunits
Carbohydrates

 Most abundant organic compound found in nature, composed primarily of C,H and O

 Principally function as a source of energy.
 Also important as a recognition molecule and as a structural component.

Lipids

 Non-polar, hydrophobic molecules which may come in a variety of forms

 Lipids serve as a major component of cell membranes
 They may be utilised as a long-term energy storage molecule (fats and oils)
 Also may function as a signalling molecule
 Fatty acids are long chains of hydrocarbons that may or may not contain double bonds
(unsaturated vs saturated)
Nucleic Acids

 Genetic material of all cells and determines the inherited features of an organism
 DNA functions as a master code for protein assembly, while RNA plays an active role in the
manufacturing of proteins

Proteins

 Make over 50% of the dry weight of cells; are composed of C, H, O and N atoms
 Major regulatory molecules involved in catalysis
 May also function as structural molecules or play a role in
cellular signalling

 Each amino acid consists of a central carbon connected to an

amine group (NH2) and an opposing carboxyl group
(COOH)
 A variable group (denoted ‘R’) gives different amino acids
different properties (e.g. may be polar or non-polar, etc.)

Falsifying Vitalism:

Vitalism was a doctrine that dictated that organic molecules could only be synthesised by living
systems
 It was believed that living things possessed a certain “vital force” needed to make organic
molecules

Vitalism as a theory has since been disproven with the discovery that organic molecules can be
artificially synthesised
 In 1828, Frederick Woehler heated an inorganic salt (ammonium cyanate) and produced urea
 Urea is a waste product of nitrogen metabolism and is eliminated by the kidneys in mammals
Metabolism:

The web of all enzyme-catalyzed reactions in a cell or organism.

 They provide a source of energy for cellular processes (growth, reproduction, etc.) 
 They enable the synthesis and assimilation of new materials for use within the cell

Anabolic/Catabolic:

Anabolic reactions describe the set of metabolic reactions that build up complex molecules from
simpler ones
- The synthesis of organic molecules via anabolism typically occurs via condensation reactions
- Condensation reactions occur when monomers are covalently joined and water is produced as
a by-product

Catabolic reactions describe the set of metabolic reactions that break complex molecules down into
simpler molecules
- The breakdown of organic molecules via catabolism typically occurs via hydrolysis reactions
- Hydrolysis reactions require the consumption of water molecules to break the bonds within
the . polymer

2.2 Water

Water is made up of two hydrogen atoms covalently bonded to an oxygen atom.

Oxygen, because of its higher electronegativity, attracts the electrons more strongly.

2.3 Carbohydrates and Lipids

2.4 Proteins

2.5 Enzymes

2.6 DNA/RNA Structure

2.7 DNA -> Protein

Genetics

3.1 Genes

3.2 Chromosomes
 3.3 Meiosis

Human Physiology

6.1 Digestion

6.2 The Blood System

6.3 Disease Defences

6.4 Gas Exchange

6.5 Neurons and Synapses

6.6 Homeostasis