Cytology: study of cells in terms of structure, function and chemistry (cytopathology,

cell biology)  general terms (talking about cells)  i.e. cells in blood
Histology: study of the fine detail of biological cells and tissues using microscopes to
look at specimens of tissues that have been carefully prepared using special
processes called "histological techniques" (talking about tissues and whole tissues)
History of cell biology
1665 Hooke used a primitive microscope to describe small pores in cork as ‘cells’
1838-9 Schleiden and Schwann propose the cell theory: the nucleated cell is the
universal building block of plant and animal tissues
1858 Virchow correctly asserted that cells arise only from other cells and that, as
the functional units of life, they are also the primary site of disease
1862 Pasteur disposed of the spontaneous generation theory of microbial
appearance
1952 Palade, Porter and Sjoestrand developed methods of electron microscopy that
enabled many intracellular structures to be seen for the first time

Cell theory

- all cells are membrane enclosed units filled with an aqueous solution of
chemicals (cytoplasm) and genetic instructions (DNA) - in higher organisms
cells contain cell organelles (bacteria sits in cytoplasm)
- organisms (‘living things’) consist of nothing but cells, transformed (i.e.
everything either made of cells, used to be cells, or secreted from cell) cells
and material produced by cells (apart from ingested materials and free fluid)
- all cells arise from pre-existing cells by division

Animals: epithelial on the outside, down gastrointestinal tract lined in epithelial tract.
(extra info)
Microscopes: used to visualise cells and cell organelles
Magnification: ratio of image to object size
Resolution: ability to produce separate images of closely positioned objects (“can
you discriminate two things between each other; is it blurry”)  “starting to lose
resolution)
Light microscope (light source, condenser, stage, objective lens, ocular
lens (or eyepiece))
Condenser focuses light to one specific point
Stage: place to put histological section, goes up and down
Objective lens; the one we change on microscope
When moving stage: moving the specimen until that point (red dot)  where focal
point of light (point where light is focused to) and focal point of optics of microscope
in same spot (that’s why the specimen needs to be thin sections)
0.2 micrometer / 200nm
40x objective = 400x magnficiation
Fluorescence microscopes (instead of visible light spectrum)
Light passes through 2 sets of filters: (stains
specimens with florophores  leads to flourenscen in
dark bg)
1. filter allows only wavelength to pass that
excites specific dye
2. Filer allows only those wavelength that are
emitted by specific dye
Objects appear bright on dark background
specific dyes bind with DNA
(blue), specific dyes bind with microtubule protein (green)

- Stains specific cells

 Whats happening in picture: undergoing constant
mitosis (cancer)

Confocal microscopy: specialised fluorescence

microscope, creating optical sections that can be combined to create a 3D image
(laser as light source)

- Shine light on one particular focal plane

Transmission electron microscopy: beam of electrons instead of light, use

magnets/magnetic coils to focus electrons instead of glass lenses to focus light
(1,000,000x magnification, resolution 1nm),

- Rough endoplasmic reticulum, ribosomes

Scanning electron microscopy (SEM: specimen coated with

thin layer of heavy metal is scanned by beams of electrons,
creates 3D images, resolution 3nm-20nm

- Instead of transmitting through, electrons bounce off

and is detected
 - Surface structure ONLY

Animal cells: no cell walls

Prokaryotes: mostly single celled organisms without nucleus (i.e. bacteria)  DNA in
cytoplasm
Eukaryotes: single celled/complex multicellular organisms (e.g. protozoa, animals
and plants)  have nucleus and cell organelles

- Different shapes sizes and functions, appearance and amount of cytoplasm

and/or their nucleus can identify them
Cell size: typically 5-20micrometers in diameter
Tissues: aggregation of cells and intercellular substances can assemble into a
variety of tissues. 4 types: 1. Epithelia, 2. Connective tissue, 3. Muscle tissue, 4.
Nervous tissue
Organs: consist various arrangements of four basic tissues
Gastrointestinal cells: lots of muscles for parastalysis
Movement across epithelium: absorption
How to define tissues: shape of cell and nucleus

Epithelia: closely adherent cells found on surfaces,

uniform and lined up
Epithelium lines respiratory and digestive system; vessels and ducts; body cavaties,
organs, body surfaces, nuclei in the bottom

- With light microscope, we can just about see Apical surface (outside part) in
gut
- Basal (connected part)

Types of epithelial cells classified by

- Function (absorptive cells, ciliated cells (can move, in respiratory tract),

secretory cells) example of secretory cells: mucous goblet secretory cells 
to lubricate gut for food. Secrete stuff into lumen (acids, enzymes that
breakdown  mucous to ensure gut doesn’t fully breakdown like foods)
- Location (epithelium, mesothelium, endothelium)
 - Shape (squamous, cuboidal, columnar)

- Arrangement (simple, pseudostratified, stratified)

Epithelial sheet: is polarized with apical (exposed

to air or fluid) and a basal surface (exposed to
other tissue)
Basal surface lies on a sheet of extracellular tissue
called basal lamina

Connective tissues (CONNECTS TISSUES, provides framework, supports the entire

body (“glues layers together”) via bones and cartilage). Consists of loosely
aggregated cells dispersed in intercellular material (aka extracellular matrix)
May be described as: dense, regular, irregular
Specialised connective tissues: cartilage, bone and fat
Two main types of extracellular protein fibre (in intercellular material): collagen and
elastin (so connective tissues are made up of collagen and elastin)

- Collagens: very fibre like: structure, so other layers can connect

Muscle cells: coordination, mechanical force by contraction, muscle cells =

fibres. Bundles of fibres aligned parallel to direction of contraction
Types: skeletal, smooth (in digestive), cardiac
Nervous: long lived highly specialised neurons (nerve cells) and their supporting
neuroglia (cells that help neurons in tissue)

- Neurons transmit electrical and chemical stimuli charaacterised

by their specialised processes: dendrites and axons

Histological techniques:
Staining (light microscopy): to contrast + differentiation of structures

- Acidic cell structures (e.g. DNA, RNA) stain well with basic dyes (hence
nucleus)  hematoxylin
 - Alkaline cell structures (e.g. cytoplasmic regions  i.e. rest of the cells) stain
well with acidic dye  eosin
Acidiophilia/eosinophilia: acidic dye lover (cytoplasmic)
Basophilia: tendency to bind basic dyes (DNA, RNA)
Periodic-acid Schiff stain (PAS)
- stains carbohydrate bright pink
van Giesen's stain
- muscle appears yellow and collagen red
Gomori's trichrome stain
- muscle appears red and collagen blue
Verhoeff stain
- elastic fibers stain black
Silver stain
- reticular fibers stain black

Cell membrane = plasma membrane = plasmalemma = fatty film surrounding the cell

- Membrane as lipids  membrane fluidity, can change shapes

- When things are secreted from cells, membranes can be reformed

Around 8nm thick (too thin to be seen in light microscope), but can be seen in
electron microscopes (1000nm in micron, cells are around 10 micrometers)
Cell membrane: made of phospholipids (hydrophobic and hydrophilic), cholesterols,
and proteins  phospholipid bilayer
cholesterol modulates fluidity
saturated: double bond (more kinks), increasing fluidity
(double bond increases fluidity
unsaturated: no double bond
outer membrane: unsaturated, lets a lot of things through
(loosely packed)
inner membrane: saturated, does not
cholesterol: hydrophobic, fat soluble, fits in between phospholipids  helps fluidity
Cell membrane structure: phospholipid bilayers formed sealed compartments. Cell
membranes behave more like fluids than solids & membrane proteins are not fixed
within lipid bilayer but move
Different type of membrane proteins

Types of membrane protein structure (secondary: alpha helixes (cork scew), beta
sheets (allow for transport))
Types of membrane proteins: 1. Transporters (e.g. carrier proteins, change
conformation to facilitate transport) or Channels (let proteins move
through, look at image), 2. Anchors (e.g. connects cytoskeleton to
adjacent tissues for structural integrity), 3. Receptors, 4. Enzymes

Most cells: a lot of carbohydrates attached to lipids

and proteins to form cell coat (called glycocalyx in
outermost cellular membrane)  for interaction of
cells and carbohydrates (cell-matrix interactions) and
cell-cell interactions, for protection (protects enzyme
like proteases from interacting with proteins)
Challenges of cell membrane: transporting correct proteins to correct organelles,
retrieving and degrading old components, controlling water flow and cell volume,
getting selected molecules through membranes, distribution of cell organelles in cell
division
Cell membranes receive information  import and export small molecules 
capacity of movement and expansion
Function of cell membranes: selectively permeable barrier to external medium,
(Controlled) transport through membrane for uptake of nutrients (absorption) and
secretion of waste products, capacity to move and grow, receptive to outside info
(receptor proteins), creates cell compartmentalisation

- Cell membrane formation: (material from outside of cell, secretion,

extracellular fluid, cytosolic face (vesicles), facilitated from fluid nature of
membranes)  look at the diagram below in terms of transport
Cell membrane – transport:
Diffusion: fat soluble molecules (like steroids) and small uncharged molecules pass
cell membrane by simple diffusion
Other molecules: a. highly selective membrane transport
proteins (carrier proteins that bind small organic
molecules or inorganic ions on one side of cell, change
conformation and release solute on other site of cell OR
channel proteins with hydrophilic pores for inorganic ions) b.
active transport by carrier proteins (aka pumps), required to
move against concentration and or electrochemical gradients
Cytosol = cytoplasm – cell organelles (water based gel
containing large and small molecules, location of chemical reactions)
Intracellular compartments & protein transport

- E.g. nucleus, ribosomes, ER (rough ER and smooth ER), golgi appar

Endomembrane system (nucleus, ER, golgi apparatus, endosomes, lysosomes,

peroxisomes)

- Membrane bound compartments in cells, derived from ancient invagination of

plasma membrane
Mitochondria & (a lil bit of chloroplasts)  derived from
endosymbiotic theory – aerobic and photosynthetic prokaryotes
engulfed by pre-eukaryotic cell overtime  into cellular organelles
Nucleus: stores genetic material, regulation of gene expression, assembly of
ribosomes (protein production). Largest organelle in eukaryotic cells (4-10microm)

- Includes nuclear envelope, chromatin and nucleolus

Nucleus: nuclear envelope: nucleus separated from

cytoplasm by membranous nuclear envelope (consists of
two concentric membranes separated by 25nm wide
perinuclear space)
Nuclear pores allow transport of large molecules
Outer nuclear membrane is connected to ER
Function: as physical barrier for compartmentalisation
Inside nucleus: Chromatin

- Consists of DNA, associated with histones

(structural proteins), globular and acid proteins
and RNA
o Interphase: chromosomes form a diffuse
network of elongated threats
(chromatins fill up entire space)
o Metaphase: chromatin is densely
packed in dividing cells to form chromosomes

Interphase chromatin (HE stain)  heterochromatin  part of cellular differentiation,

can be switched off, different structural (condensed, high stained active chromatin,
located with nucleolus), euchromatin (less density of staining, more spread out,
uncoiled, abundant in active cells)
Apotosis  blebbing (senescent cells  cant produce proper proteins)
Nucleolus: dense, basophilic nucleous (up to 4 micrometers), site of ribosomal RNA
production and initial ribosomal assembly (for protein production)

Ribosomes: small electron dense particles (not visible in light microscope,

15x25nm), protein synthesis. Consist of two subunits (translation)

- mRNA and tRNA + large + small ribosomal subunit join together to

synthesise the new protein during translation (N to C terminus)
- Groups of ribosomes that translate the same mRNA are called
polyribosomes
Free ribosomes: synthesise intracellular proteins
ER signal sequence directs ribosome to ER : ER bound ribosomes synthesise
proteins for plasma membranes, lysosomes and secretory vesicles  directly sent to
lumen (transported some place)

Ribosomes = basophilic, nerve cells basophilic aggregation of ribosomes called nissl

bodies
Endoplasmic reticulum: network of membrane bound channels (cisternae, tubules,
vesicles)  connected to outer nuclear membrane

- Rough ER (where ribosomes are associated) smooth ER (not much ribosome

o Rough ER: protein transport, Smooth ER: lipid biosynthesis and transp
- Synthesis and trasports of lipids and some proteins

- Storage of calcium

- Detoxification

sER: enzymes at lumen surface to synthesise lipids (e.g. phospholipids for

membrane formation)

- Storage and release of Ca2+ (=sarcoplasmic reticulum in muscle cells)

- Enzyme mediated drug detoxification

sER found in large amounts in liver and adrenal cortex cells, show no
basophilia due to lack of ribosomes (acidophilia-eosin)  HARD TO SEE
rER: membrane, lysosomal (digestive enzyme) and secretory proteins
synthesised by membrane bound ribosomes (basophilic) ribosomes cause
basophilic stain
cytosolic face (outside face of ER)  see budding off little
spheres of membranes (hollow, mini cells have lipid bilayer
and lumen)  within the hollow we see lipids and proteins
 they move to golgi apparatus  bud off  secreted or
fused with endosome (modified vesicle with material from
outside cell)  END UP WITH LYSOSOME
Transport vesicles carry soluble proteins and membrane between
compartments (This is how molecules move around)  vesicular transport
of molecules
Different types of transport vesicles with distinctive surface proteins
shuttle between various organelles

Protein (red circles): associated with

certain site  buds off  pinched off by
motor proteins  sphere of membrane
with molecule transported inside

Golgi apparatus (stains with silver nitrate and osmium, negative golgi
image in conventional stains)

- Network of cisternae (fold like bundles)

- Several layers of cisternae (3-20) with network of tubules and

vesicles  for transport of proteins nad lipids
Functions: For modification Golgi complex receives proteins and lipids from
ER for
1. Chemical modification
a. glycosylation, phosphorylation and sulfation of proteins
b. Enzymatic proteolysis (e.g. prohoromes broken down to active
forms)
c. Removal of sugars
2. Packaging of secretoy proteins prtoeins
3. Routing of proteins to correct cellular compartments
Transport Vesicles: through to endosomes to form lysosomes or (transport =
within cell)
Transport Vesicles: FOR plasma membrane, NOT OUSIDE: (via secretory
pathway to plasma membrane)
Secretory Vesicles: to the outside: in response to extracellular stimulus to
plasma membrane  EXOCYTOSIS (i.e. insulin from increased blood sugar)
 Formation of endosome: start with vesicle
from outside of cell (with bacteria or
molecules)  fusion of vesicle and early
endosome  late endosome  lysosome
Endosome: polymorphic membrane
bounded tubes and vesicles  for transport
between early and late endomes through
vesicular transport

Early endosome: located close to plasma membrane

3 life paths of early endosome: recycling, degradation
and transcytosis

- Sorting compartment for endocytic vesicles

(pinocytosis: cell taking in liquids)
o Receptor bound molecules dissolve and
empty vesicles including receptors go
back to plasma membranes
o Receptor bound molecules get transported
through for transcytosis (release outside of
cell via vesicles to adj cells)
o Receptor bound molecules get transported
to late endosome to be degraded in
lysosomes
Late endosomes: located close to golgi complex 
receive endocytic material for digestion from early endosomes  fuse with
heterophagosomes or autophagosomes  fuse with transport vesicles
containing lysosomal enzymes  become lysosomes  pH decreased to 5
Heterophagosomes and autophagosomes (contain particulate matter like worn
out cell organelles (e.g. mitochondria), damaged cells, senescent)
Phagosome = vesicle (vesicle formed
when engulfed by phagocyte)

Lysosomes: repeatable structure. Much of

the time, material inside broken down cell
can be recycled by cells (proteins broken
down to amino acids)
 in neurons a lot of accumulation of cells (called senility pigment). If
lysosomes fail to function  lipofuscinosis/lysosomal storage disease  buildup
of lysosomes in brain neural regulation  brain atrophy
Peroxisomes: small membrane-bound spheres: contain enzymes (urate oxidase
that produce H2O2  contains catalase that uses H2O2 to oxidise substances
(break down of lipid and toxic material)  in cells of liver and kidney

Mitochondria
Mitochondria (site of chemical energy generate)

- 0.2micrometers – 12micromet diameter

- Double membrane (inner membrane

folding, impermeable) outer membrane
permeable
- Contain DNA (cytoplasmic inheritance)

- Divide

- Size and shape are highly variable

- Move in cell

High number in active cells (~800 in mammalian hepatic cell, few in

lymphocytes), contribute to staining in cytoplasm
Outer membrane: contains large, channel-forming proteins. permeable to
molecules 5000 daltons or less (smaller molecules like peptides)
Intermembrane space: kind of like concentration of molecules in cytoplasm.
Contains several enzymes that use the ATP passing out of matrix to
phosphorylate nucleotides. Also contains proteins released during
apoptosis (separates inner and outer membrane)
Inner membrane: folding, cristae increases surface area for function of cell. A
lot of membrane spanning proteins in inner membrane. Carry out oxidative
phosphorylation, ETC, and ATP synthase. Contains transport proteins
that move selected molecules into and out of matrix
Matrix: highly concentrated mixture of hundreds of enzymes, including those
to oxidation of pyruvate and fatty acid for citric acid cycle/krebs (energy).

Mitochondria: food molecules from cytosol and

oxygen transformed into CO2 and ATP
 Cell inclusions (no activity in cells)

- Transitory or permanent structures

- Membrane bound: e.g. secretory and pigment granules (in cytoplasm,

surrounded by membranes, as) aggregate
- Non-membrane bound e.g. lipid and glycogen (in cytoplasm, no
membrane)
- Exogenous (e.g. phagocytosed material, from external) or endogenous
origin (glycogen, lipid, pigments, from inside cell)
(Cell inclusion) Glycogen (leads to increase in blood glucose, carb stores,
dissolves in H&E stains, characteristic unstained patterns in cell, stains pink
in PAS stains)

- Glycogen storage diseases (due to inability to degrade glycogen  cells

become enlarged  functional loss of glycogen (less cell energy and as
blood glucose buffer)  pompe disease in Brahman and Shorthorns
(poor growth, incoordination, muscle weakness, eventual recumberence)
(Cell inclusion) Lipid: energy reserve, abundant in adipocytes and steroid
hormone-producing cells. Present as unstained gaps in most histologic
techniques. Special techniques involve osmic acid fixation (brown/black) or
Sudan III stained frozen sections (stain fat red)
(Cell inclusion) Melanin: dark brown/black pigment. Occurs in basal layer of
epidermis. Found in external root sheath and hair matrix of hair follicles,
epithelium of retina

- Membrane bounded granules. Melanocytes: big elongations  penetrate

tissue of epidermis and release melanin pigments (phagocytized by
surrounding cells e.g. keratinocytes)
o Ability to absorb UV light, prevent mutations when UV light fuses
with DNA
Hemosiderin: from hemoglobin degradation, contains iron

- Golden brown pigment. Occurs as granular cytoplasmic inclusion (after

phagocytosis or erythrocytes) in spleen, liver bone marrow.
- Specf.stains allow distinction of similar coloured pigments (e.g. lipofuscin)

- If iron increases beyond normal levels, excess hemosiderin is deposited in the

liver and heart. can reach the point that the impaired organ function
Pathological hemosiderin deposits occur in
- Hemosiderosis (disorder by excessive iron deposits –multiple blood transfusions)
z Hemochromatosis (inherited iron-storage disease)
z Local hemorrhage (bruising)

Lipofuscin: from buildup of lysosomes (digestive)

end product of lysosomal activity (indigestible residues of heterophagy, autophagy
and crinophagy (phagocytosis of secretory vesicles)
- golden brown pigment +stainable with fat and lysosomal dyes
more abundant in non-dividing cells (neurons; skeletal, smooth, and cardiac muscle)
andincrease with age
Other Pigments inclusions
Pigments
- naturally coloured (colour may be altered by stains)
- exogenous and endogenous pigments

- carotenoid - yellow pigment carotene found in green leaves, carrots etc

and can be deposited in the skin when excessive quantities of the
pigment are ingested – skin will appear pale yellow-red and resembles
jaundice
Dusts  Coal dust will accumulate in macrophages.
Crystals are occasionally observed in cells - little is known of their significance

Cytoskeleton (intermediate filaments, microtubules, microfilaments (actin

filaments), proteins that interconnect filaments to cell)  for structural integrity
Function: mechanical strength, control shape, guide movement, major role in
cell division
1. Microfilaments = actin filaments: (7nm diameter, thinnest filaments)
a. Helical polymers of identical globular actin molecules (rope
like structure)
b. Assemblage and disassemblage
c. Throughout cell, but most abundant beneath plasma
membrane
d. Linear bundles, 2D networks, 3D gels
e. Facilitate structure from cell type + actin binding proteins
(cross-linking, side binding proteins etc.)
f. Microvilli on brush border (A), contractile bundles (e.g. muscle cells
(B), protrusions in crawling cells (e.g. migrating neutrophils) (C),
contractile ring in cell division (D, mitosis, splitting off), cell cortex (E)
How actin function works (contractile
movement)  movement of vesicles within
cell – cytoplasmic streaming (A)  movement
of atin filaments against plasmamembrane (in
phagocytosis C)  actin filaments slide
against myosin filaments (muscle contraction,
B)
Myosin = motor proteins

Proteins dragging along actin in

both directions  bring actin
filaments together

Intermediate filaments (roplelike

fibres, great tensile strength 
form
network throughout cytoplams- anchored to plasma
membrane at CELL-CELL JUNCTION),
strengthens nuclear envelope via nuclear lamina

- Helical arrays of tetramers of fialmentous

protein monomer 
- Energy minimised conformation: hydrophilic towards water (polarity in
proteins in filaments)
Microtubules

- Long hollow cylinders, made of tubulin, rapidly disassemble and

reassemble
- one end attached to single microtubule-organizing centre (centrosome or
basal body), organise the cell interior
 - alpha and beta tubulin to form dimer tubulin  linear chains of dimers
form protofilaments  13 linear protofilaments form wall of cylindrical
microtubule
- polar structure (negative end attached to microtubule-organizing centre
(centrosome or basal bodu), continuous state of polymerisation at + end
(growing) and depolymerisation at – end
- Position organelles (guide transport of organelles, vesicles and macro
molecules in nerve cells)
- Mitosis (mitotic spindle)

- Cila (reproductive or respiratory)  facilitate movement of material 

respiratory: lining of cilia towards lumen (mucous blanket  secreted by
goblet cells)  particulates captured by mucous as we breath in  cilia
push mucous back out (wave like contraction)

Cytoskeleton continued
Cell surface: movement of cells, detection of movement in extrcellular material
Cillia & Flagella

- Hair like cilium and whip like flagellum projections of cell surface.

- Movement due to dynein/ATP

o Flagella = movement of cell
o Cilia = create currents in overlying cell (think mucous)
- Microtubules grow from basal body
o Arranged in 9+2 array (9 outer doublets = 13 protofilaments)
+ incomplete microtubule (10 protofilaments)
o 2 central microtubules are separate and complete
o Doublets carry rows of dynein molecules and connective
proteins
Movement: motor proteins that
crawl along actin filamets form
ovement (muscle contraction)
Dynein + ATP causing sliding of
isolated microtubules
Dynein is anchored to one
microtubule doublet crawl along the
other
 - Effectively slide across eachother (only one side moves)

- Linking proteins for bending  to facilitate wave like motion

CILIA: regular synchronous undulating movement of rows of cilia

to create wave across epithelium (rapid forward rigid stroke
followed by flexible slower recovery stroke)

Flagella; represents single long cilium (100 micrometers long) 

rapid successive waves of bening form the attached to free end
Eg. Each spermatozoa (sperm) possesses a single flagellum
Microvili: bleb like projections, closely packed, uniform projections supported by
20-30 parallel actin filaments for rigidity.

- Actin filament anchor to plasma membrane at the tip and sides of

microvillus and extend into the apical cytoplasm, where they interact with
horizontal network of actin filaments (terminal web)
- Found in apical (TOP) surface of epithelia

Filopodia (finger like) and lamellipodia (irregular

cell protrusion that allow crawling of cells)

- E.g. mgrating white blood cells, growing of

axons in nerve cells
Example of growing filopodium

- actin polymerisation pushes forward cell

surface in sheetlike (lamellipodia) or thin
microvilli (filiopodia) protrusions
- Protrusions stick to favourable surfaces via
integrins
- Cell body dragged towards attachment via actin
and myosin action (muscle contraction)
o Protrusion and contraction “drags” cell
check image below
LAD (leukocyte adhesion deficiency)  defects of
neutrophil adhesion  cells can’t latch on  cannot
move well (caused by poor neutrophilchematacis and
pahgocytosis)  prone to bacterial infection
Lateral and Basal cell surface folds

- Tortuous boundary due to infoldings or interdigitations (folding of

membranes) of each cell with its neighbour or extracellular matrix
- Folds prominent in places with clear epithelial layers (kidney and salivary
gland tubules)
Interceullular junctions in epithelia

- Epipthelial sheets: compartmentalisation , selectively permeable barrier

(stuff moves through, selective absorption/transport e.g. gastrointestinal)
- Does not allow things out

- Polarised (apical surface exposed to air/fluid) and basal surface (exposed

other tissues)
- Basal laminar: sheet of extracellular matrix below basal surface (collagen
laminin proteins)
- Cells connected via cell junctions (tight junctions, adherens junctions,
desmosomes &hemidesmosomes, gap junctinos)
Tight junctions
Only in epithelial cells, continuous belt of transmembrane
proteins of neighbouring cells (links)  link outer leaflets
of adjacents membranes (stops “leakage”, separates
apical and basal lsuraface to maintain cell polarity),
transcytosis  so that the right transporters work.
Cytoskeleton-linked junctions
To other cells/ECM

- Types: cell2cell contact (adherens junction,

desmosome) + cell to basal lainal
(hemidesmosome)
 Adherens junction
Belit like struction below tight junction in epithelial cells
Connected via transmembrane linker proteins
(cadherins) linked to linker proteins which are attached
to intracellular actin filaments

Adheren junc (continu.)

Actin network = contractile (for embroyonic development as
epithelia sheets bend to form)  tubes e.g. neural tube
(central nervous system) or vesicles (e.g. lens vesicle (lens))
Desmosome:
Disc linke junction between cells.
Connected via cadherins linked to
intracellular linker proteins which are
attached to intracellular intermediate
filaments (e.g. keratins)
Links cytoskeleton of neighbouring
cells to maintain integrity of tissue (tensile strength, for
stretching)

Hemidesmosome: disc like cytoskeleton-linked junction between extracellular

matrix (basal lamina). Transmembrane linker proteins
(integrins) link the extracellular matrix protein at the
outside of the cell via linker proteins to intracellular
intermediate filaments (KERATIN)
JEB (junctional epidermolysis)  defect in protein
involved in hemidesmosomes
Gap junction:
Pore like structure between cells: direct passage of inorganic ions/small water
soluble molecules to synchronise function and metabolic cooperation 
coordinated function (via electrical and metabolic coupling)
- six transmembrane protein form connexon, two connexons of neighbouring
cells form hydrophilic channel

Small molecules, energy and biosynthesis

Polysaccharides (made of sugars), Fats and lipids (made of fatty acids), proteins
(made of amino acids), nucleic acid (made of nucleotides, small org.buildingblox
Water ionisesthis ability is essential to biochemical lreactions)
Minimised conformation (lowest energy)  elements of protein that are
hydrophilic hydrophobic (minmal repulsion)  change pH change conformation
Sugars: organic molecules (C, H, O)  energy source, subunits of
polysaccharides (carbohydrates)

- Monosaccharide Formula: (CH2O)n, 2 or morme hydroxyl group,

aldehyde and ketone groups
- Aldoses: aldehyde group, ketoses: ketone group

Ring formation (in aqueous solution) from linear to ring  due to

sollubilisation and energy minimised state in aq

- Isomerisation  many monosaccharides differ in spatial

arrangement of atoms  important in drugs can
dramatically affect purpose/function
HOW SUGARS LINK
Alpha and beta link: bond arrangement
Hypoglycaemia (not enough glucose
 weakness, muscle spasm, coma),
Lactic acidosis (blood pH decrease 
weakness, staggering, death),
Ketosis (ketone bodies, not a lot of
carbs, no glucose cannot metabolise
loss of production), Diabetes (elevated blood glucose  hypothermia
and coma)
Fatty acid (composed of C, H, O, less oxygen than sugars), components of cell
membranes as lipids + energy reserves in cells

- Lipids e.g. triacylglycerols (fat droplets in cells), phospholipids

(mebranes), sphingolipids (membrane)
- Hydrophobic (hydrocarbon chain), hydrophilic (carboxylic acid)
o When ionises in solution (--COO- )  reactive

Saturated: no double bonds (animals), Unsaturated: double bonds (plants)

Unsaturated: double bond = kink: phospholipid and membranes  how tightly
they can pack will change  cant fit together as close (affects membrane
fluidity). ALSO less energy can be liberated from hydrocarbon tail (from
oxidation) because energy is needed to be invested to get rid of kink (less
energy/gram)
Significance fo fatty acids: Obesity (accumulation of fat in internal reserves
and subcutaneous tissue) Fatty acid deficiencies (disrupt cell function by
affecting cell membrane)
Amino acids: subunits of proteins (enzymes, horomnes), structural proteins
(collagen)

- Carboxylic + amino group

Familiesi of amino acids (based on side chains (R group)

Acidic (second carboxyl group, net negative charge at pH 7.0) acid = proton
donor
Basic: net positive charge at pH 7.-0 (base = proton acceptor)
Uncharged polar: hydrophilic forms H bonds with water
Nonpolar: hydrophobic (biggest group)
Folded conformation in aqueous
environment (from linear) energy
minimsed
Hydrophilic side chains outside,
hydrophobic on inside
Leucine deficiency: significantly smaller  amino acid imbalance (amino acid
deficiency, antagonism, toxicity)

Nucleotides: subunits of DNA and RNA, short term carriers of ATP

- Nitrogen containing ring compounds linked to 5-C sugar with

one or more phosphate group. Sugar can be ribose or
deoxyribose (RNA, DNA)

Types of nucleotides
Pyrimidines (6 membered ring) 
Cytosine, Thymine (DNA), Uracil (RNA)
Purines: (5 membered ring + 6 membered
ring): Guanine, adenine

Significance clinical: Cancer, genetic

disorders, disorders of nucleotide metabolism (disruption of cell division, transfer
of energy, enzyme catalysis, often result in death of embryo)
Biological order and energy
First law of thermodynamics: Total energy in universe is constant
Second law of thermodynamics: Entropy of universe will spontaneously
increase
Cells not isolated systems (energy taken from environments)  liberation from
heat
Photosynthesis (utilise sunlight) + cellular respiration (utilise chemical energy)
ADP is less complex than ATP
= ADP G < ATP G = - deltaG (energetically favourable, decrease in free energy
 complex to simple (Second Law of thermodynamics))  from ATP  ADP is
-ve delta G (releases energy)
ATP (3 phosphate groups), ADP (2 phosphate groups)
Coupled
reactions
(e.g.
oxidation
and reduction)  oxidation is energetically favourable (as long as NET delta G
is negative  it will happen)

Why are all molecules not broken down to CO2  energetically

favourable reactions still need an energetic push (Enzyme
catalysis)  spontaneous reaction (high  low energy state)
Energetically favourable: Release of electron = OXIDATION
(release of energy)
Most energetically favourable: CO2 and H2O
Formic acid CHOOH  carbon dioxide (2 protons are lost from central carbon =
2 electrons are lost from central carbon)
As number of electrons must be conserved  oxidation and reduction
occur simultaneously (e.g. metabolism)

- Cell respiration: sugar + O2  H2O + CO2, sugar oxidise to CO2, but O2

gained electrons to form H2o and therefore O2 is reduced
- Practically: we need a temporary storage of energy. Rather than
simultaneously oxidising and reducing at the same time when energy is
needed
Activated carrier molecules: temporary storage in the form of chemical
bonds in carrier molecules, which are able to diffuse rapidly throughout
the cell (smaller so diffusion happens quickly)
Oxidation: release electrons 
release energy
Reduction: gain electron 
absorb energy
Chemical bond energy is in
easily exchangeable forms 1.
Transferable chemical group
2. High energy electrons
Example of high energy linkage: 1. ATP (Phosphate) 2. NADH, NADPH, FADH2
(e-, H), Acetyl CoA (acetyl group)
Coenzymes: enzymes for energetically unfavourable reactions
ATP in water readily undergoes hydrolysis
(ionising ability of water, breaking down
covalent bond)  to form ADP and inorganic
phosphate (Pi)  spontaneous  energy for
cells and biochemical reactions

If a lot of energy is needed  ATP is oxidised to form AMP

Activated molecules
NADH and NADPH (electron carriers, closely related)  reduced form

- Dinucleotides, nicotinomide ring which electron is

taken up and imparted  movement of electron 
subsequent uptake of proton
- NADH: intermediate reactions to generate ATP
(catabolic) ETC
- NADPH: biosynthesis (anabolic)
o Extra phosphate group, binds to different
enzymes
- Acetyl CoA  transfers energy within chemical bonds by
exchanging an acetyl group
o Important in oxidation of amino acids and alcohols,
fatty acid and carbohydrate metabolism
Roles of activated carrier molecules 1. Oxidation of food
molecules and biosynthesis, 2. muscle contraction, 3. active
transport across membranes, 4. nerve cell function
Biosynthesis required for (some energy is required)
1. Interconversion between different small molecules (one amino acid to
another)
2. Synthesis of macromolecules from small molecules
3. Synthesis of macromolecules of greater complexity or
interconversion from other molecules
Interconversion between small molecules (glutamic acid  glutamine

Synthesis of macromolecules from small molecules (glycogen

from glucose)

Synthesis of macromolecules of greater complexity or

interconversion from other molecules (e.g. phosphorylation,
glycosylation of proteins or lipids)

Protein synthesis: Rough ER

Carbohydrate synthesi: cytoplasmic matrix
Lipid synthesis: smooth ER
DNA synthesis: nucleus
Activation of carrier molecules: mitochondria
Indirect pathway to allow biosynthesis
1. Activation step: e.g. hydrolysis of ATP to form high energy
intermediate
2. Condensation step: e.g. high energy intermediate reacts directly with
molecule which it is added (covalent bond formed, energetically
unfavourable)
Head polymerisation: reactive bond (high energy intermediate)carried by
growing polymer (proteins and lipids
Tail polymerisation: reactive bond (high energy intermediate)carried by the
monomer (DNA, RNA, polysaccharides)

Why do cells need energy, and why do cells

need to build larger molecules? Second law
of thermodynamics: without maintenance, cells will undergo deterioration
spontaneously

Macromolecules
Proteins: macromolecules from amino acids, cell functions, structure
Enzymes: catalysation, Structural proteins: collagen actin, Transport proteins
(hemoglobin in blood), motor proteins (myosin in muscle), storage proteins
(casein in milk), Signalling proteins (peptide hormones), receptor proteins
(hormone receptors), gene regulatory proteins (DNA binding proteins), special
purpose proteins (GFP in jellyfish)
Protein functionality dependent on 3D shape (defined by amino acid
sequence)  hence look at properties of amino acids covalently linked by
peptide bond (amide bond between 2 amino acids) into chain making up protein
Covalent peptide bonds may allow rotation
between amino acids (depends on amino
acid)
Similarly, noncovalent bonds (ionic, H-bond,
dispersion) may form between atoms in

- Polypeptide backbone, side chains

- These noncovalent bond will affect

3D

structure of proteins
Polypeptides are in a folded conformation in aqueous environment. Unfolded is
linear (energy minimised states)

Secondary Structure: Tertiary structure: confo

Conformation: final folded structure (where energy is minimised) 

conformation may change slightly interacting with molecules within cell. Usually
consistent guided by chaperone proteins (in ER)
Primary structure: amino acid sequence
Secondary: folds due to noncovalent bonding

- Alpha helix: single polypeptide chain turns around to make rigid cylinder,
H bond between every 4th peptide bond. Complete turn every 3.6 amino
- Beta sheets : neighbouring polypeptide chains run in same orientation
OR polypeptide chains folds back and forth upon itself
o Formed by H-bonds

Tertiary: 3D conformation (energy minimised conformation)

Quaternary structure: structure formed by more than one polypeptide
(more than one protein) e.g. ribosomes = aggregation of ribosomal
units
Alpha helices may wrap around each other to form
coiled-coils (e.g. keratin)  side chains hydrophobic 
2 peptides coil around each other (hydrophobic
towards centre)

Parts of proteins can fold differently (Protein

domains)  part of polypeptide chain that
fold independently into compact stable
structure (30-350 amino acids with different functions)
1. Theoretically with 20 common amino acids there are
20^n possible proteins that could be made.
(where n = peptide length).
Most of these would not have stable conformation and
therefore would be relatively useless in a biological system.
2. Proteins may be classified into two major sorts:
Fibrous proteins: arranged in long chains or sheets
Globular proteins: tightly folded into spherical or
globular shapes
3. Extracellular proteins often stabilised by covalent cross linking.
Because they are exposed to extracellular conditions that
require additional stabilisation (e.g. disulphide bonds, linking -SH
groups of cysteine)
Protein Function: biological activity dpending on proteins binding to
other molecules  some proteins bind very tightly or weakly (known as
AFFINITY for a ligand)

- Specificity: how selective protein binding is to array of molecules

- Ligand: molecule protein binds

- Binding site: part of protein ligands is binded

Due to thermal energy, cell in constant motion. Proteins encounter

molecules at random and if specificity is high, many non-covalent
bonds will form (high affinity)  slower to release, reduce rate of
reaction

- Binding is reversible, often ligands and proteins dissociate

Antibodies: multiple domains, quaternary structure, extracellular

(multiple disulfide bonds), particular binding site (antigen)
Motor proteins: role in movement of other molecules (use shape
changes from ATP to facilitate movement)

- Myosins (in mucles for contraction)

- Kinesins (moves chromosomes during mitosis)

- Change in conformation of protein (big one) move protein along.

Lipid structure: water insoluble, composed of fatty acids (function: stores of
chemical energy (triacylglycerols), components of cell membranes (polar lipids),
hormones (steroids), lipoproteins (blood plasma), secreted waxes (lanolin in
wool))

- Fatty acid = hydrophilic carboxylic head, hydrophobic carbon skeleton

- Fats, triglycerides: most abundance lipid in cells, esters of alcohol

glycerol (triglycerides, triacylglycerol)
Lipid: nonpolar, contain 3x same fatty acid (simple triglycerols) contain 2 or more
fatty acids (mixed triglycerol)
Triacyglycerol

- Undergo antioxidation (oxygen attack double bonds) in unsaturated fatty

acid to form rancid fats
- Adipocytes (fat cells) specialise in storage of triglycerols (in skin,
mammary gland, abdomen)
- Yield 2x more energy g/g than carbohydrates

Polar lipids: phosophlipids sphingolipids (within cell mebranes)

Phospholipid: (most common in membranes as phosphoglycerides)

- 2 fatty acids esterified with glycerol)

- Phosphate group binds to second alcohol group (amphipathic to form

lipid bilayers) like water
Sphingolipids: polar head 2 nonpolar tails

- 1 fatty acid and long chain amino alcohol sphingosine

Steroids: fat soluble molecules with 4 fused rings most

abundant are sterol (steroid alcohols) e.g. cholesterol
Lipoproteins: aggregates of polar lipids, triacyglycerols
and sterols (how they move around)

- Hydrophilic polypepetide chains and polar lipids on surface

- Hydrophobic polypeptide chains, triacylglyerols and sterols

inside
o Lipoproteins: method to transport water insoluble lipids around
body
4 classes of lipoproteins in blood plasma: based on density
1. Chlyomicrons
2. Very low density lipoproteins (VLDL), low density (LDL) high density
(HDL)  high VLDL level and low HDL level important in atherosclerosis
Waxes: esters of fatty acids (14-36 carbon atoms) and long chain
alcohol (16-22 carbon atom)  secreted from skin gland for
lubrication, waterproofing, pliability (skin, feathers, fur, wool, hair etc.)
Trans fats: add H to vegetable oil  longer shelf life. WHY?

- Double bonds are trans rather than cis configuration (=H on

opposite sides)  resulting in straighter rather than kinked shape. Less
fluid and hence higher melting point (reduces rancidity, less
autooxidation)
- Increases risk of heart disease change lipoprotein profile (decrease HDL)

Carbohydrates: classification depending on number of sugar units

Functions: stores of chemical energy (starch, glycogen), lubrication skeletal
joints (mucopolysaccharides)

- Monosaccharides

- Oligosaccharides (“few” short cahin monosaccharides)

o Disaccharides (covalently bonded, abundance in nature,
example: sucrose, lactose, maltose)
o Lactose (galactose +glucose), maltose (glucose + glucose)
Sucrose (glucose + fructose)
Found in many plants, formed when glucose transported around plants (more
stable than glucose), cannot be absorbed by animals, must first be cleaved
before entering SI

- Polysaccharides (long chain monosaccharides)

o Carbohydrates in nature, function: storage of sugars/energy, cell
structure (plants), specialist function
o Homopolysaccharide (single monosaccharide type), heteropolysa

Starch (carbohydrate continued): storage polysaccharide (plants), occurs

intracellularly in granules, contains 2 types of glucose polymer:

- α-amylose (long glucose chains up to 50,000) & amylopectin (branched)

Glycogen: storage polysaccharide (animals), occurs intracellularly in granules

(not membrane bound), branched polysaccharide of glucose, abundant in liver
and skeletal
Structural polysaccharides
Cellulose: -fibrous, water insoluble, cell walls of plants (cotton, wood)

- linear unbranched glucose (homopolysaccharide)

Peptidoglycan: - bacterial cell walls, -peptide/polysaccharide hybrid, -penicillin

(antibiotic) inhibits peptidoglycan synthesis
Glycoproteins: proteins covalently attached to carbohydrates, extracellular
location or function (e.g. membrane proteins like glycophorin, fibronectin)
Mucopolysaccharide: glycoproteins where carbohydrate % higher than
protein component, formed of recurrent disaccharide units in a framework of
polypeptides -> Heparin: abundant in arterial blood vessels, inhibitor of
blood clotting
Glycaemic index of foods: High GI = more effect on blood glucose
DNA: nucleus of cell distributed among set of chromsomes, each consists
of a linear DNA molecule and assocated protein, complete genetic info =
genome

- Consist 2 polynucleotide chains (strands), held by H bonds (ATCG),

deoxyribose = sugar
- Polynucleotide chains formed by interlocking sugar and phosphate
components of nucleotides  align in same orientation  polarity (5’to3’)
 - AT (2H-bonds), CG(3H-bond)

- Double helix because sugar phosphate = hydrophilic, bases hydrophobic

 hydrophilic out + hydrophobic inside (energy minimized conformation)
RNA: similar to DNA structure (linear, polymer of 4 different nucleotide subunits,
linked by phosphodiester bonds)

- Nucleotide sugar is ribose (not deoxyribose), uracil replaces thymine

Enzymes
Substrate: thing that enzymes bind to
Come in contact randomly to increase the rate of contact…
How enzymes lower activation energy of reaction?
Binding of enzyme alters shape or chemical characteristics of substrate
molecules: may result in
1. Changes in proximity/orientation of substrates
2. Changes in charge stabilisation of substrate
3. Changes bond angle of reactive group in substrate
4. Covalent bond formation to form an
enzyme/substrate complex that is more reactive
Enzyme: special binding site (active site) to fit contours
substrate
Rate of Catalysis step is influenced by the
factors that effect rate of reaction

First product = enzyme-substrate

complex
Enzymes influence the direction of metabolism (what product it produces,
reduces Ea for reaction path 1)

Enzymes and Activated Carrier Molecules

Reactions that require an activated carrier molecule to impart
energy (e.g. biosynthesis) will also be directed by an enzyme

- Activated carrier molecule will often bind to enzyme so

high energy bond from activated carrier molecule will form
correct energy intermediate