Cell Biology- Chapter 1

1.1- Cell Theory, Cell Specialization and Cell Replacement

U1: According to the Cell Theory, Living Organisms are Composed of Cells
Cell Theory:
 All living things are made of one or more cells (proved by the light microscope)
 Cells are the smallest unit of life (components of cells cannot survive independently)
 All cells come from pre-existing cells

A1: Questioning the cell theory using atypical examples, including striated muscle, giant algae and aseptate
fungal hyphae
Exceptions to the Cell Theory:
 Striated Muscle Cells: Hundreds of times longer than regular cells and contain multiple nuclei
 Giant Algae: They grow very large (100mm) but remain unicellular
 Aseptate Fungi: There are no septa and each hypha are therefore uninterrupted with many
nuclei spreading across it

U2: Organisms consisting of only one cell carry out all functions of life in that cell
Functions of Life:
Metabolism Response Homeostasis (stable internal environment)
Growth Reproduction Excretion Nutrition
In unicellular organisms, the single cell will have to carry out all these functions, while in multicellular
organisms, different cells will work together and can carry out separate functions.

A2: Investigating the functions of life in Paramecium and one named photosynthetic unicellular organism’
Cells and Sizes:

 (smallest) Molecules- thickness of

membranes- viruses- bacteria- organelles, animal
cells- plant cells (largest)
 Magnification= Size of image / actual size
 Actual Size= Size of image / magnification
 Size of image= magnification X actual size

U3: Surface area to volume ratio is important in the limitation of cell size

Limiting Cell Size:

 The rate of metabolism of a cell is a function of its volume
 The rate of material exchange in and out of a cell is a function of its surface area
 As a cell gets larger, the surface area to volume ratio decreases
 This causes waste products to accumulate inside the cell as they are being produced faster than
they are being expelled and substances may not be able to enter the cell as fast as needed
(decreased rate of exchange)
 Moreover, if the ratio is small then cells may overheat since the metabolism produces heat
faster than it is lost over the cell’s surface
 Thus, it is more efficient for cells to copy and divide to be smaller than to grow large since it
maximizes the surface area to volume ratio

Exceptions to Cells Remaining Small:

 Regularly shaped large cells have greatly diminished surface area to volume ratios
 However certain large cells increase their surface area by:
 Changing their shape to be long and thin
 Having folds in the cell membrane

U4: Multicellular organisms have properties that emerge from the interaction of their cellular components

Emergent Properties:
 Emergent properties arise from the interaction of component parts (the whole is greater than
the sum of its parts)
 Multicellular organisms can complete functions that individual cells cannot due to the interaction
of cells to produce new functions.
 Using a holistic approach rather than a reductionist one allows us to see thing such as the
interaction of cells forming tissues, tissues forming organs and organ systems forming an
organism. This displays emergent properties at all levels.
U5: Specialized tissues can develop by cell differentiation in multicellular organisms
U6: Differentiation involves the expression of some genes and not others in a cell’s genome

Cell Differentiation:
 Cell differentiation allows for certain cells to carry out certain tasks (specialize) to carry out
their role more efficiently than if they had many different roles.
 Differentiation occurs due to gene expression:
 All (diploid) cells of an individual organism share an identical genome and contain the entire
set of genetic instructions for that organism. They can specialize in any way
 However not all the genes in the cell are expressed, allowing cells to be differentiated
 I.e., RBC’s will express what is necessary for their function (such as hemoglobin)
 Gene expression and its control is a key part of the development of a cell as the roles of
cells are determined. Thus, cell differentiation occurs due to gene expression.

U7: The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic
development. It also makes stem cells suitable for therapeutic uses.

Stem Cells:
 These are unspecialized cells that:
 Can Continuously divide and replicate
 Have the capacity to differentiate into specialized cell types
Types:
 Totipotent- Can differentiate into any type of cell
 Pluripotent- Can differentiate into many types of cells
 Multipotent- Can differentiate into a few closely-related types of cells
 Unipotent- Can regenerate but can only differentiate into their associated cell type (e.g. liver
stem cells can only make liver cells)

Embryonic Development:
 Embryonic stem cells are pluripotent and yet to commit to a pattern of differentiation
 The cell will then commit by deciding which pathway to differentiate on (whether to
differentiate as skin cells, liver cells etc.)
 Once committed, a cell can still divide, but they will differentiate in the same way and are no
longer stem cells

Therapeutic Uses:
 Embryonic stem cells can replace dead/damaged cells and tissues:
 Embryonic stem cells are most effective in their earliest stages for therapeutic uses as they are
yet to differentiate and can therefore replace all types of cells and tissues.
 Scientists grow embryonic cells and direct their differentiation so that they become a specific
tissue. such as regenerating skin for someone who has suffered burns
 Adult stem cells (unipotent) can also be used to regenerate new cells of the same type (liver
stem cells to make more liver cells.
 A3: Use of stem cells to treat Stargardt’s disease and one other named condition

Stargardt’s Disease:
 The Problem:
 Recessive genetic condition affecting around 1 in 10,000 children as active transport protein
on photoceptor cell malfunctions.
 The mutation causes photoreceptor cells to degenerate, causing a progressive and
eventually total loss of central vision.
 The Treatment:
 Embryonic stem cells are used to dive and differentiate to become retinal cells
 The retinal cells are injected and attach to the retina to become functional
 Central vision improves due to the new functional retinal cells
 The Future:
 Currently limited clinical trials, but will likely be more prevalent in the future

Leukemia:
 The Problem:
 Cancer of blood or bone marrow, causing abnormally high levels of malfunctioning WBC’s
 The Treatment:
 Hematopoietic Stem Cells (HSC’s) are harvested from the bone marrow
 Chemotherapy is used to destroy the diseased WBC’s
 HSC’s are transplanted back into the bone marrow and differentiate to form new healthy
WBC’s
 The Benefit:
 The use of the patient’s own HSC’s means there is far less risk of immune rejection than
bone marrow transplant.

A4: Ethics of the therapeutic use of stem cells from specially created embryos, from the umbilical cord of a new-
born baby and from an adult’s own tissues

Embryo Cord Blood Adult

Ease of Extraction Obtained from excess embryos Easily obtained and stored but Difficult as there are very few and
generated by IVF programs limited quantities available buried deep in tissues
Ethics of Embryo is destroyed Umbilical cord is removed at Adult patient can permit cell
Extraction birth and discarded either way extraction
Growth Potential Almost unlimited Comparatively reduced potential
Tumor Risk Higher risk of development Lower risk of development
Differentiation Any cell type Limited capacity to differentiate Limited capacity to differentiate
(wo/inducement only naturally
divide to blood cells)
Genetic Damage Less chance than adult stem cells Due to accumulation of mutation
through life, genetic damage can
occur
Compatibility Not genetically identical to the Fully compatible with the patient as stem cells are genetically identical
patient
Arguments for Therapeutic Cloning:
 Can cure serious diseases and disabilities with cell therapy (replacing bad cell w/ good ones)
 Transplants are less likely to be rejected as the cells are genetically identical to the parent and
do not require the death of another human
 Stem cells can be taken from embryos that have stopped developing and would have died
anyways (abortions)
 Cells are taken at the stage when embryos have no nervous system and cannot feel pain
 Saves the pain of someone suffering

Arguments Against Therapeutic Cloning:

 Involves the creation and destruction of human embryos (at what point do we afford the right
to life), are we creating life just to destroy it
 Embryonic stem cells are capable of continued division and may become cancerous
 More embryos are produced than needed, therefore excess embryos are killed
 With additional effort and cost, alternative technologies may fulfill similar roles
 Religious or moral objections due to the ‘playing god’ argument
 Cloning humans is not illegal everywhere, therefore there is the potential of a human being
cloned.
1.2- Ultrastructure of Cells

U1: Prokaryotes have a simple cell structure

Prokaryote Cell:
 Much smaller and simpler than eukaryotes (1-10 μm)
 Thought to have appeared on earth long before
eukaryotes
 Do not enclose their DNA in a nucleus (no nucleus)
 Do not have membrane-bound organelles
 DNA is a single loop and is not attached to proteins
 Divide by binary fission
 Examples include bacteria

Cell Wall- Protects the cell and maintains its shape

Plasma Membrane- Controls the movement of materials into and out of the cell
Pilli- Allow bacterial cells to attach to each other and exchange DNA
Flagella- Present in some bacteria and are used for movement
Ribosomes- Site for protein synthesis and are found in large numbers for cells that produce lots of
protein
Nucleoid Region:
 The bacterial chromosome is a single, circular loop of DNA
 The DNA is not wrapped around proteins (naked DNA)
 It is not enclosed in a nucleus (unlike eukaryotes) but is found in a region called the nucleoid
region
 In addition to the single chromosome, most bacteria also contain plasmids
 Plasmids are DNA molecules that are not connected or associated with the regular
chromosome and are used to help the cell adapt to changes in its environment

Since prokaryote organelles are not compartmentalized, all cell processes occur in the cytoplasm. Since
chemical reactions are not separated, the efficiency is limited due to potential interferences.

U2: Prokaryotes divide by binary fission

 Prokaryotes divide (reproduce) asexually in a
process called binary fission
 In this process, the main chromosome is
copied and the two copies attach to different
sections of the plasma membrane
 Then the cell splits in half, producing 2
identical copies of the parent cell.
U3: Eukaryotes have a compartmentalized cell structure

Eukaryotic Cell:
 Larger cells (5-100 μm)
 Enclose their DNA in a nucleus
 Have membrane bound organelles that carry out specific functions
 Organelles compartmentalize so that normally incompatible chemical reactions can take place at
the same time. This increases the efficiency and capabilities of the cell

Cytoplasm:
 The cytoplasm is all the area within the cell except the nucleus
 This is where the organelles are found
 The fluid portion of the cytoplasm is called the cytosol
Endoplasmic Reticulum (ER):
 Network of tubes that extend from the nucleus to the plasma membrane
 It transports materials to different areas within the cell
 There are two types of ER: Smooth and Rough
Smooth ER:
 It has many enzymes on the surface
 Produces and transports lipids, some of which are used to make the plasma membrane
 Produces sex hormones (such as estrogen and testosterone)
 Transports lipid-based compounds (like cholesterol)
Rough ER:
 Has ribosomes on it
 Since ribosomes are involved in protein synthesis, the rough ER helps modify and transport
proteins
 Most cells have both types of ER’s
 The rough ER is usually closest to the nucleus
Ribosomes:
 No exterior membrane
 Found in both prokaryotes and eukaryotes
 Site of protein synthesis
 Found attached to the rough ER and throughout the cytoplasm (free ribosomes)
 Larger than the ribosomes found in prokaryotes (Eukaryotes= 80s Prokaryotes= 70s)
Lysosomes:
 Membrane-bound sacs that contain enzymes
 The enzymes are used to break down proteins, carbohydrates, lipids and other molecules
 Lysosomes find and fuse with old or damaged organelles so that they can ‘digest’ the broken-
down organelles and recycle their parts
 The enzymes within a lysosome can also break down the materials engulfed by cells
 Cells that are responsible for digestion (such as liver cells) have many lysosomes
Golgi Apparatus:
 Made of flattened sacs called cisternae
 Collects, packages and transports molecules (primarily proteins)
 One side of the Golgi is near the rough ER, It receives proteins and other materials and then
packages them in membrane sacs called vesicles
 The vesicles exit out of the other side of the Golgi
 The vesicles can be either transported within the cell or shipped out of the cell
 Cells that produce a lot of products for other areas of the body (like pancreas and other glands)
have a lot of Golgi bodies.
Mitochondria:
 Rod shaped organelles that are the site for cellular respiration- where chemical energy in food is
transferred into chemical energy in the form of ATP
 Have their own DNA and ribosomes
 Have a double membrane- one on the outside and one folded up in the inside. These inner folds
are called the cristae and they increase the surface area to speed up chemical reactions
 Cells that need a lot of energy (such as muscles) have many mitochondria
Nucleus:
 Bound by a porous membrane called a nuclear envelope
 The envelope’s pores allow communication, while the rest of it isolates the DNA from the
other reactions occurring in the cell
 Usually located in the center of the cell
 Most nuclei have a dark area called the nucleolus, where the ribosomes are made
Chloroplasts:
 Occur only in algae and plant cells
 Site of photosynthesis
 It has a double membrane and contains its own DNA and ribosomes
 Made of thylakoid disks (which contain chlorophyll and absorb light) and stroma (fluid portion)
Centrosomes:
 Occurs in all cells
 Helps with the movement of chromosomes during cell division
 Located near the nucleus
Vacuoles:
 Store materials such as water, salt and proteins
 Vacuoles in plants are often very large as they help the plant cell remain rigid

Eukaryotic Chromosomes:

 Chromosome number varies with species

 Chromosomes are only present during cell division
 When the cell is not actively dividing, the DNA is in the form of chromatin
 Chromatin is DNA wrapped around proteins called histones

Prokaryotic Vs. Eukaryotic Cells:

 Similarities:
Both: have a plasma membrane carry out all functions of life have DNA have ribosomes

 Differences:

Prokaryotic Cells Eukaryotic Cells

DNA in a loop form with no proteins (naked) DNA wrapped around proteins
DNA free in the cytoplasm DNA enclosed within the nucleus
No membrane bound organelles Has membrane bound organelles
70s ribosomes 80s ribosomes
Size less than 10μm Size greater than 10 μm
 U4: Electron microscopes have a much higher resolution than light microscopes

Electron Microscopes:

 Electron microscopes have two key advantages when compared to light microscopes:
 They have a much higher range of magnification (can detect smaller structures)
 They have a much higher resolution (can provide clearer and more detailed images)

 A disadvantage is that they cannot display living specimens in natural colors

A1: The structure and function of organelles within exocrine gland cells of the pancreas (animal cell)
A2: The structure and function of organelles within palisade mesophyll cells of the lead (plant cell)

Plant Cell Vs. Animal Cell:

 Similarities:

Both have: Cytoplasm Plasma Membrane Ribosomes Vacuoles Centrosome

Nucleus Golgi ER Mitochondria

 Differences:

Plant Cells Animal Cells

Cell wall No cell wall
Chloroplasts No chloroplasts
Large central vacuole Vacuole absent or small
Carbohydrates stored as starch Carbohydrates stored as glycogen
No centrioles within the centrosome area Has centrioles within in centrosome area
Cell has a fixed, angular shape due to cell wall Cell has more flexible and rounded shape as there is no cell wall

Outermost Layers of Cells:

 Bacteria: Cell wall of peptidoglycan
 Fungi: Cell wall of chitin
 Algae: Cell wall of cellulose
 Plants: Cell wall of cellulose
 Animals: No cell wall; has an extracellular matrix instead

Cell Wall Function:

The cell wall helps to maintain shape and help regulate water uptake

Extracellular Matrix:
It is a network of collagen fibers, proteins and sugars on the outside of the cell wall that strengthen the
plasma membrane and provide the cell with support and structure.
1.3- Membrane Structure

U1: Phospholipids form bilayers in water due to the amphipathic properties of phospholipid molecules

Phospholipid Bilayers:

Hydrophilic- Polar molecules that are attracted to water (such as salt)

Hydrophobic- Non-polar molecules that are not attracted to water
(such as oil)

Phospholipids are amphipathic- part of the phospholipid is hydrophilic

and part of it is hydrophobic
 The hydrophilic part of the phospholipid is referred to as the
phosphate heads
 The hydrophobic part of the phospholipid is referred to as the
lipid tails

 When phospholipids are mixed with water, the phosphate heads are attracted to the water
 However, the lipid tails are not attracted to the water and are therefore attracted to
themselves
 This causes the phospholipid to arrange into double layers
 The hydrophobic lipid tails face inwards to each other.
 The hydrophilic phosphate heads face the water on either side of the lipid tails.
 These double layers formed by the phospholipids in water are called phospholipid bilayers, they
are stable structures that form the basis of all cell membranes

U2: Membrane proteins are diverse in terms of structure, position in the membrane and function

Membrane Proteins:
 Integral Proteins:
 They are permanently embedded in the membrane and have amphipathic properties
 This allows them to go all the way through the surface of the protein- polytopic (poly=many,
topic=surface), while some just penetrate one surface of the membrane and are monotopic
 Integral proteins are useful for facilitating the movement of molecules across the membrane

 Peripheral Proteins:
 Usually have temporary association with the membrane
 Do not protrude into the hydrophobic region, they stay on the surface of a membrane and
are usually anchored to an integral protein
 Many of these proteins are glycoproteins

 Glycoproteins:
 They are proteins with an oligosaccharide (oligo=few, saccharide= sugar) chain attached
 They are important for cell recognition by the immune system and as hormone receptors
Functions of Membrane Proteins:
 Channels for passive transport to allow hydrophilic particles across by facilitated diffusion
 Cell-to-cell communication, for example receptors for neurotransmitters at synapses
 Cell adhesion to form tight junctions between groups of cells in tissues and organs
 Hormone binding sites (hormone receptors)- such as the insulin receptor
 Immobilized enzymes with the active site on the outside- such as in the small intestine
 Pumps for active transport which use ATP to move particles across the membrane

U3: Cholesterol is a component of animal cell membranes

Cholesterol:
 The main components of animal cell membranes are phospholipids, proteins and cholesterol
 Cholesterol is a liquid from a group of substances called steroids
 Most of the cholesterol molecule is hydrophobic, so it is attracted to the hydrophobic
hydrocarbon (non-polar) tails in the center of the membrane.
 However, one end of the molecule has a hydroxyl (polar) group which is hydrophilic and is
attracted to the phosphate heads on the periphery of protein
 Thus, cholesterol molecules are positioned between phospholipids in the membrane

A1: Cholesterol in mammalian membranes reduces the membrane fluidity and permeability to some solutes

Membrane Fluidity:
 The hydrophobic hydrocarbon tails usually behave as a liquid and the hydrophilic phosphate
heads act more like a solid
 This makes it hard to determine whether the membrane is truly either a solid or liquid,
however it can be said to be fluid as all its components are free to move

Importance of Regulating Fluidity:

 Membranes need to be fluid enough for the cell to move
 Membranes need to be fluid enough that the required substances can move across the
membrane
 However, if too fluid, the membrane cannot effectively restrict the movement of substances
across

Role of Cholesterol:
 The presence of cholesterol in the membrane restricts the movement of phospholipids and
other molecules- this reduces membrane fluidity
 The presence of cholesterol disrupts the regular packing of the hydrocarbon tails of
phospholipid molecules- this increases the flexibility as it prevents the tails from crystalizing and
hence behaving as a solid
 Cholesterol also reduces the permeability to hydrophilic/ water soluble ions such as sodium and
hydrogen
S1: Drawing the Fluid Mosaic Model

S2: Analysis of evidence from electron microscopy that led to the proposal of the Davson-Danielli model

The Evidence for Davson-Danielli Model:

 In high magnification electron micrographs membranes appeared as two parallel lines with a
lighter colored region in between
 Proteins appear dark in electron micrographs and phospholipids appear light- possibly indicating
protein layers either side of a phospholipid core

The Model:
 A protein-lipid sandwich- proteins coating the outer surface without permeating the lipid bilayer
 Lipid bilayer composed of phospholipids (hydrophobic tails inside, hydrophilic tails inside)

This explained that despite membranes being very thin, they are an effective barrier to the movement of
certain substances

S3: Analysis of the falsification of the Davson-Danielli model that led to the Singer-Nicolson model

Freeze-etched Electron Micrographs:

 Involves rapid freezing of cells and then fracturing them, with fractures occurring along lines of
weakness, including the center of membranes
 Globular structures scattered through freeze etched images of the center of membranes were
interpreted as transmembrane proteins

Structure of Membrane Proteins:

 Proteins were found to be varied in size and globular shape, therefore unable to form
continuous layers on the periphery of the membrane as the model suggests
 Also, part of the proteins were hydrophobic on part of their surface, which would be attracted
to the hydrocarbon tails of the phospholipids in the center of the membrane
Fluorescent Anti-Body Tagging as Evidence:
 Red or green markers attached to antibodies which would bind to membrane proteins
 The membrane proteins of some cells were tagged with red and other cells with green
 The cells were fused together and within 40 minutes the red and green markers were mixed
throughout the membrane of the fused cell
 This showed that membrane proteins are free to move within the membrane rather than being
fixed in a peripheral layer

Singer-Nicholson Fluid Mosaic Model:

 Phospholipids form a bilayer- phospholipids are fluid and move laterally
 Peripheral proteins are bound to either the inner or outer surface of the membrane
 Integral proteins- permeate the surface of the membrane
 The membrane is a fluid mosaic of phospholipids and proteins in a dotted pattern
 Proteins can move laterally along the membrane
1.4- Membrane Transport

U1: Particles move across membranes by simple diffusion, facilitated diffusion, osmosis and active transport

Passive Transport:

 Particles move from an area of higher concentration to an area of lower concentration

 The movement occurs along/down the concentration gradient
 It does not require energy
 Involves simple diffusion, facilitated diffusion and osmosis

Simple Diffusion:
 Diffusion is the passive net movement of particles from areas of high concentration to low
concentration, often through a partially permeable membrane.
 Simple diffusion across membranes involves particles passing between phospholipids in the
membrane
 For example, if the concentration of oxygen inside a cell is less than outside of the cell, then
oxygen will pass through the membrane by passive diffusion.
 Simple diffusion is more difficult for polar molecules as the center of membranes is hydrophobic.

Facilitated Diffusion:
 Since ions and some large particles cannot diffuse through phospholipids, they diffuse through
protein channels (transmembrane proteins) on the membrane.
 The diameter and chemical properties of protein channels ensure that only one type of
particle can pass through, i.e. sodium or potassium ions through a channel, not both

Osmosis:
 The movement of water molecules from an area of low solute concentration to an area of high
solute concentration, often through a partially permeable membrane.
 Even though the center of the membrane is hydrophobic, water molecules are small enough to
pass through the phospholipid bilayer.
 Aquaporin is an integral protein that acts as a pore in the membrane, increasing the membrane
permeability and speeding the movement of water molecules. (seen in kidney and root hair cells)
Types of Solutions (tonicity):
 Hypotonic: A solution with higher solute concentration and less water concentration
 Hypotonic: A solution with lower solute concentration and more water concentration
 Isotonic: A solution in which water molecule and solute molecule concentration is equal

Active Transport:
 Particles move from an area of low concentration to high concentration
 Movement is against/up the concentration gradient
 Requires energy (ATP)
 Involves protein pumps, endocytosis and exocytosis

Protein pumps:
 Active transport is carried out by globular proteins in membranes called protein pumps
 Integral protein pumps use the energy from the hydrolysis of ATP to move ions or large
molecules across the cell membrane against their concentration gradient

 The molecule or ion enters the protein pump and a conformational change of the protein takes
place using energy from ATP
 After this, the ion or molecule can pass to the opposite side of the membrane and the protein
pump can return to its original conformation

U2: Vesicles move materials within cells

Intracellular Vesicle Transport:

 They are small sacks of membrane that bud off the rER and the Golgi apparatus
 They carry proteins produced by ribosomes on the rER to the Golgi, where they are prepared
for export from the cell via another vesicle
U3: The fluidity of membranes allows materials to be taken into cells by endocytosis or released by exocytosis

Endocytosis:
 The taking in of external substances by an inward pinching of the plasma membrane, forming a
vesicle
 Proteins in the membrane use energy from ATP to allow the inward pinching
 It is done to allow larger molecules that are needed by the cell but cannot pass through the
plasma membrane
 Pinocytosis: “cell drinking” Phagocytosis: “cell eating”

Exocytosis:
 The release of substances from a cell (secretion) when a vesicle-from the Golgi- fuses with the
plasma membrane.
 Both processes create temporary holes in the cell membrane. However, the hydrophobic nature
of the phospholipid tails lets it immediately rejoin to fill the holes and avoid contact with water.
 The fluidity of the cell membrane allows structures surrounded by the membrane to change
shape and move, which allows both processes to occur since the membrane changes (slight
changes in size)

A1: Structure and function of sodium-potassium pumps for active transport and potassium channels for
facilitated diffusion in axons

Sodium Potassium Pump:

1. A specific protein binds to specific sodium ions inside a cell
2. The energy in ATP is released by breaking the third phosphate bond
3. The energy from ATP causes the protein to change its shape, which releases the sodium ions to
the outside of the cell
4. Potassium ions outside of the cell bind to a different region of the same protein, which causes
the release of the phosphate group
5. The loss of the phosphate group causes the protein to go back to it’s original shape, which
causes the potassium ions to be released into the cell