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History of Cell Biology
29 September 2014

11:09

•
•
•
•

Young science
Early observations birthed cell theory
Electron microscopes demonstrated intricacy of cells
Discovery of DNA and subsequent decoding

Cell Theory
Very recently developed field
• Relied on development of compound mcroscopes
• Robert Hooke - Micrographia
○ Named cells
○ Looked at cork
• Antonie van Leeuwenhoek
○ Clothmaker, made lenses
○ Looked at semen
○ And found bacteria in water
• Next big leap with electron microscopy
○ Ernst Ruska and Max Knoll - proof of concept 1933
○ Albert Prebus and James Hillier - Made one 1939
• Matthias Schleiden and Theodore Schwann recognise similarities between all eukaryotic cells
• Hugo Mahl realised that all cells divide, while Albert von Kölliker saw that ova and sperm are cells
...
All organisms consist of one or more cells
2
...
All cells arise from pre-existing cells
...
)

DNA or Protein
• Chromosomes contain DNA and protein
...
coli to replicate
1
...
E
...
Radioactive protein transferred to surface of E
...
Radioactive DNA transferred inside the cell (for
replication)
5
...

○ i
...
artificial UUUUU RNA produced only Phe, so UUU = Phe

Biology of the Cell Page 1

Cell Communication
• Cells must communicate
○ Epinephrene outside cells triggers cAMP inside cells
• Entire new area of Biology

Studying Cells
01 October 2014

14:34

Light Microscope
• Can be alive
• Simple
• Contrast limited
○ Stains
 Fluoroglucinol shows lignin
 Stains kill cells
○ Darksource illumination
 Only light is refracted
around an opaque disc
 Alive
○ Phase contrast
 Two in phase beams
□ Reference beam, not
through the
specimen - phase
normal
□ Beam shone through
specimen, slowed by
density - phase
changed
 The beams cancel out, so
denser = darker
 Alive
• Resolution
○ Visible wavelength 380-750nm
Electron Microscope
• Wavelength of an electron is 0
...

• George Gey kept some cells
○ Realised they had no apparent Hayflick limit
• Standardised cell cultures made possible
○ Results could be compared
○ :( not normal cells

Biology of the Cell Page 2

Toxic Tools
• Many toxins interfere with cell processes
• Tetrodotoxin blocks sodium channels
• Effects show properties, e
...
which proteins are present
• Spindle toxins
○ Stop microtubules forming
○ We can see how important spindles are
 Shape, mitosis, etc
...
g
...

• Can be used to block receptors
○ HER2 receptors in breast cancer cells

Origins of Cells
06 October 2014

10:54

• Special creation
• Aliens
• Spontaneous generation

Law of parsimony
Simplest explanation is often the right one

Location
• Around 3-5bya temperature dropped to 50-90oC
○ Life appeared
• A reducing atmosphere (lacking in O2) is important - oxygen is harmful to macromolecules
• Shallow seas/shores
• Mud
• Deep sea vents
Stanley Miller and Harold Urey
○ 1953
○ Early Earth conditions simulated
 Hot water
 Lightning
 Methane and ammonia
○ Within one week 15% of the methane had incorporated into formaldehyde and HCN
○ Later formic acid and urea formed
 Capable of producing amino acids
○ Spontaneous generation possible
 Doesn't mean it happened
○ Very quick (initially)
○ Demonstrates the molecules are simple to form,
BUT
Self-replicating molecules and catalysts required
Self-replication - base pairing
Enzymes - Ribozymes: simple; protein based; combination

Prokaryotic past
• First 1
...
2bya first multicelluar eukaryotes
• Different from prokaryotes
○ Bigger
○ Nuclei
○ Complex internal membranes
Endomembranes

Organelles
○ Endosymbiosis
○ Not found in prokaryotes
○ Infolded membranes form some ^
○ Engulfing of aerobic heterotrophic prokaryotic
 Mitochondrion
○ Engulfing of photosynthetic prokaryote
 Chloroplast

Biology of the Cell Page 3

Membranes
• Hydrophobic molecules spontaneously form
bubbles
• Foaming sea edge or vents are perfect
locations for bubble formation
• Microsphere, protobiont, micelle, liposome
Louis Lermann's model
○ Volcanoes erupted undersea
 Gases in bubbles
○ Concentrated gases form organic gases
○ Reach surface and release gases
○ UV, lightning etc
...
5bya
• Bacteria-like
• Similar to first life
Methanococcus
○ Methanogenic Archaea
○ Hydrothermal vents
 88oC
 245 atmospheres
○ Genome sequenced in 1996
 Similar energy production to
eubacteria
 Other genes similar to eukaryotes
 67% unique
○ Archaea split from other life-forms
 3 bya

Plasma Membranes
08 October 2014

13:27

Phosphoglycerides
• Lipids with polar head group
• Glycerol backbone
• Major amphipathic lipids of the plasma membrane

Amphipathic lipids have a hydrophobic group and hydrophilic polar group
...


Electron micrographs showed a protein layer associated
...


In the 1960s x-ray crystallography led to the fluid-mosaic model
Embedded proteins - 1970s
Sphingolipids
 Amphipathic lipids which lack the glycerol, instead
having a sphingosine backbone

Sterols
• Cholesterol prevents cell membranes from
becoming too fluid
○ Binds between lipids
Membrane fluidity
• Temperature affects membrane fluidity
• Cells can alter membrane composition
○ Homoviscous adaptation
• Saturated lipids (C-C) can pack closer than
unsaturated

Membrane Synthesis
• Made in smooth endoplasmic reticulum
• Exocytosis
Membrane asymmetry
• New membrane is synthesised on the
cytosolic face of the ER and the new lipids
are added to just one side of the
membrane
...
g
...
Sugars synthesised in cytosol
2
...
Flippases flip it all to inside
4
...
passed back, trans to
cis
 Vesicular transport model
□ Material passed forwards by
vesicles, cisternae maintaining their
position and structure

Lysosomes
• Digest material taken in by endocytosis and damaged
organelles
• Contain hydrolitic enzymes active at low pH
• Protists expel residual bodies, but in animals they
accumulate
○ Lysosomes become less efficient as residual
bodies accumulate, so mitochondria remain and
cause damaging oxidative stress
• Different lysosomes are specialised for the materials
they digest
○ Microphagous lysosomes digest small debris and
have a single membrane

Cytoskeleton
Monday, October 20, 2014

9:56 AM

Proteins tubes and fibres that act as a scaffold for transport and organisation within the cell and allow
cells to change shape and move
...
g
...
g
...
g
...
g
...
g
...
eukaryotes
○ Eukaryotes
 ATP fuelled dynein
○ Prokaryotes
 H+ gradient generated
 They diffuse back across through a channel protein
□ Turns rotor protein
□ Spinning the flagellum

Practical - Bloodgroups, Lectins, and Haemoagglutination
21 October 2014

18:35

Determining ABO groups of two sample using the ability of lectins to distinguish between different
blood group antigens and to erythrocyteragglutination
Method
1
...
Label X and Y
3
...
Add blood
5
...
Tap to clear droplets
7
...
Score for agglutination or not

Results
Blood

Tube

Lectin

Sugar

Agglutinated?

X

1

-

PBS

No

2

UEA

PBS

Yes

3

UEA

D-glc

Yes

4

UEA

DgalNAc

Yes

5

UEA

L-fuc

No

6

HPA

PBS

No

7

HPA

D-glc

No

8

HPA

DgalNAc

No

9

HPA

L-fuc

No

PBS

No

Y

1

-

2

UEA

PBS

No

3

UEA

D-glc

No

4

UEA

DgalNAc

No

5

UEA

L-fuc

No

6

HPA

PBS

No

7

HPA

D-glc

Yes

8

HPA

DgalNAc

No

9

HPA

L-fuc

Yes

X=O
Y=A

Biology of the Cell Page 9

Haemoagglutination
03 November 2014

14:19

Method
This practical was performed in 3 stages, the first was to determine the efficacy of the method in detecting haemolysis; the second stage
was to determine the isotonic concentration of the erythrocytes; and the third was to determine the permeability of the erythrocyte
membranes to different solutes
...
edu/writingcenter/files/2012/06/TS-Bio-Lab-Report-3
...
neilstoolbox
...

4 drops of the defibrinated sheep's blood were added to each tube
...

After 5 minutes the tubes were held over newsprint
...

Result
Sample A (5ml of distilled water) had haemolysed
...


Stage 2 - Determining the concentration of 2 solutes which are isotonic with the erythrocytes
Two sets of tubes of various concentrations (shown below) were prepared, one set containing dilutions of CaCl2 and the other containing
dilutions of sucrose
...
50
(M)

0
...
40

0
...
30

0
...
20

0
...
10

0
...
02

0
...
50

2
...
00

3
...
50

3
...
00

4
...
5

4
...
90

5
...
50

2
...
00

1
...
50

1
...
00

0
...
50

0
...
10

0
...
00

3
...
40

3
...
80

4
...
20

4
...
60

4
...
92

5
...
25M
Sucrose (ml)

2
...
80

1
...
40

1
...
00

0
...
60

0
...
20

0
...
00

Once all dilutions had been prepared, 4 drops of blood were added to each tube
...

They were left to stand for 5 minutes
...

This data gave an approximation of the concentration within the erythrocytes
...
10M

0
...
075

0
...
275

Sucrose 0
...
32M urea was added to a test tube, 4 drops of blood were added
...

Using the same method as in stage 1 the time until haemolysis occurred was measured on the stop watch
...
This method was repeated 3 times for each solution
...
3

4
...
35

21
...
2

20
...
01

Glycerol

---

---

---

Did not haemolyse

---

Ethanol

4
...
8

3
...
53

1
...
2

3
...
6

3
...
46

Thiourea

Biology of the Cell Page 10

5
...
0

BR10310 Prac 2 model data

4
...
0

63
...
5

61
...
61

Biology of the Cell Page 11

Vesicle Transport
22 October 2014

13:34

• Exocytosis and endocytosis must be balanced to keep the plasma membrane's size constant
Exocytosis
• The process of exporting material from the cell by the movement of vesicles
• Adds material to the cell membrane
Evidence for Vesicle Transport
• Giant squid axons stretch for much of their body
• Vesicle transport is necessay to move material to the axon terminals
• You can squeeze the contents out
○ HUGE
• Vesicles and motor proteins can be seen
• Vesicle transport helps to keep organelles separate
○ Nocodazole destroys spindles
○ Vesicles don't move
○ Organelles collapse

•

SNARES
• SNARES are proteins responsible for correctly targeting vesicles to their
destination and fusing them with the membranes there

Endocytosis
• The opposite of exocytosis
• Can include phagocytosis
• Takes small segments of membrane

•

•

Synapses

• Study
○ Radioactively labelled molecules
○ Visible particles
○ Trace their passage
• Phagocytosis
○ Extends membrane
○ Microfilaments - actin
○ Forms endosome and later lysosome
• Pinocytosis
○ 2 types



 Clathrin-independent
 Clathrin-dependent

Calcium
• Ca2+ is critical
• The axon bulb membrane contains voltage sensitive calcium channels
• Calcium is let into the cell by the action potential, triggering the vesicles'
exocytosis

Clathrin

Exocytosis toxins
• Many animal toxins block neurotransmitter exocytosis
○ Flaccid paralysis
○ Loss of sensations
○ seizures

• Capable of spontaneously forming into cages (low pH and calcium ions)
• Coated pit formation:
○ Assembly particles bind the Clathrin to the membrane - if the Clathrin changes shape, so
does the membrane
○ Dynamin acts like a drawstring - pinches membrane into 2

Biology of the Cell Page 12

Cartilage and Bone
• During development chondrocytes deposit cartilage
• Much is converted to bone by impregnation of the ECM with hydroxyapatite
• Bone grows as cartilage is deposited and mineralised behind
○ Bone is reabsorbed in places - remodelling
 e
...
behind knee, to keep femur narrower than the knee

Extracellular Matrix
29 October 2014

13:20

Most animal cells are embedded in the ECM
Structurally similar to fungal and plant cell walls
It consists of fibres embedded in matrix
However, chemically very different to cell walls

Collagen
• Fibrous protein (cellulose is a polysaccharide)
• Triple helix
• 25 types
○ I, II, and III are most common
• Key component of all ECM tissue
• Brittle bone disease is a collagen issue - very important

Integrins
• Adhesion molecules
• Bind to other adhesion molecules
○ Heterophilic interactions
• Transmembrane proteins
• Bind to ECM and to cytoskeleton
○ Affecting inside can effect outside and vice versa

Elastin and Fibrillin
• Elastin
○ Protein
○ Allows ECM to stretch under tension
• Fibrillin
○ Basis for elastin

Junctions
• Tight junctions
○ Prevent even small molecules crossing cell layers
○ Force solutes to cross by transcytosis or transport across both apical and basement
membranes
○ They also restrict the movement of plasma membrane proteins
 Can be radically different on each side

○
•

•

Proteoglycans
• Form the matric in the majority of ECM
• Very variable
• Can be used a guidance cues by migrating cells
• Attract water
• Cross-link with collagen
• Some are involve in plasma membranes
Fibronectin and Laminin
• Bind to collagen and to proteins on cell surfaces
• Links cells to ECM

Cadherins
• Adhesion molecules
• Only bind to other cadherins
○ Homophilic binding

• Gap junctions
○ Small pores between adjacent cells
○ Only solutes up to around 1200Da can cross
○ Like bad plasmodesmata

Adherens Junctions
• Cell to cell contacts are often clustered in junctions
• Adherens junctions are common epithelial adhesive junctions

○
•

•
Desmosomes
• Large clusters of cadherins bind cell to cell and linked to tension resisting intermediate
filaments within the cells
• Stretches across whole layers, resisting forces
○ Skin and heart
• At the bottom hemidesmosomes attach epithelial cells to the basement membrane
○ Epithelial cells must remain in their layer

•

Biology of the Cell Page 13

Cell Walls
27 October 2014

Function
Structural
• Protects against pathogens and wounding
• Supports entire plant
Defence
• Physical barrier and the source of defence elicitors
Permeability barrier
• 20kDa limit to permeation
• Growth factors are small

Structure
• Cellulose - microfibril - macrofibril
• 40% cellulose
• 20% hemicellulose
• 30% pectin
• 10% glycoprotein
• Middle lamella between cells
• Primary walls
○ Thin and flexible
○ Able to grow/expand
○ Microfibrils
• Secondary wall
○ After expansion
○ Multiple layers
○ Solid
○ Lignified
○ Cannot expand
○ Macrofibrils

Plant cell cytokinesis
• Division must occur within the cell wall
• Phragmoplast transports Golgi vesicles of callose (produces glucose) and cell wall proteins to the
division plane
• Vesicles fuse and form cell plate that grows outwards until it joins the cell membrane and a middle
lamella is formed
• Cell plate contents form the middle lamella, primary walls and plasma membrane

The Primary Walls
• The outermost of the cell wall is synthesised first
○ Lamella
• The primary cell wall is a 100-200nm unlignified mesh of cellulose microfibrils embedded in pectin
and hemicellulose and strengthened by extensins
• Cellulose is laid own fairly randomly by rosette protein complexes in plasma membrane

•

Cellulose
• Simple, long, unbranched chain
• 7,000 to 15,000 glucose per chain
• Embedded in a matrix of hemicellulose
Hemi-cellulose
• Structurally weak ad diverse
• Shorter than cellulose
• Easier to digest
• Xylose is the main component
Pectin
• Major component of the middle lamella
• Makes jam set
• Diverse and branches polypeptide
• Side-chains can stop it setting
Cell Walls proteins
• Extensins
○ Long proteins
○ Rod like
○ Hydrophobic and hydrophilic alternating domains
○ Give support
• Expansins
○ Inserted into the wall by exocytosis during growth
○ Disrupt cellulose-matrix interactions
○ Microfibrils can slide past each other
• Lignin
○ Immensely complex an variable
○ Randomly assembled monomers
○ Major component of secondary walls
○ Envelopes cellulose
○ Incredible hard to digest
○ Xylem walls entirely lignified

Biology of the Cell Page 14

Secondary Cell Walls
• Several layers of macrofibrils in lignin matrix
• Rosettes move in parallel
○ Lay down macrofibrils
• Once a layer is done the rosettes disassemble, re-orientate, and guide another layer
• Lignin monomers are exported into the cellulose mesh and joined by peroxidases
Like reinforced concrete
Tension bearing mesh
Solid matrix

Plasmodesmata
• Channels between adjacent plant cells allowing direct communication between cells
• Plasma membrane share between all linked groups
○ Desmotubule from ER
○ Shared ER lumen and contents
• Functionally one cell with multiple nuclei
○ Syncytium
• Formation
○ Phragmoblast remains after the cell plate is formed, between the original ends of the
starting cell
○ Tubules run between the two cells
• Close or are plugged as a defence response
• Movement proteins open them

Cell Signalling
03 November 2014

11:31

How do cells know where they are, what to become, and when to change?

Coordination
• The immune system, for example has 7 types of cell, and 21 different chemical signals
• Each cell has to select one of a number of possible responses at the right time and in the right place
Signal problems
• Hormones such as steroids are lipophilic and easy to synthesise
• Lack diversity
• Peptide hormones are much more diverse
○ 34 human interleukins
But are expensive to make and cannot cross the plasma membrane
• Peptide signals are at low concentrations and cannot enter the cell
• Receptors
○ Receptors are proteins which bind and respond to signals
○ Many sit on the cell surface
○ Respond to low concentration, hydrophilic, peptide signals
○ Characteristics:
 Transfer information from outside to inside
 Specific
□ Distinguish between closely related signals
 Sensitive
□ Detect at low concentration
 Interactions are reversible
□ End stimuli
 Can be controlled (on/off)
 Coupled to a response
○ Types:
 Ligand-gated
□ Ionotropic
□ e
...
nicotinic, ACh
 G-Protein-coupled
□ Metabotropic
□ Secondary messengers
□ e
...
muscarinic
□ Another type of on/off switch which depends on the binding of GDP or GTP
□ G proteins are heterotrimeric signal receptors

Secondary Messengers
• A secondary messenger as a signal generated within
a cell in response to an extracellular signal

□
•

□ There are also lots of small monomeric GTP binding proteins that act as on/off switches or
regulate decisions between two states
 Kinase-linked receptor
□ Often long-term changes
□ Cytokine receptors
□ Protein kinases transfer a phosphate from ATP to an amino acid
...


• Another type of secondary messenger system yes
membrane phospholipids as a source of 2 internal
signals
□

 Nuclear receptors
□ Affect gene transcription
□ e
...
Oestrogen receptors
□ Used for steroid hormones
 Can cross plasma membrane
□ Testosterone passes through p
...
This causes a conformational change, unbinding hsp's, and allowing the
androgen to pass into the nucleus and bind to DNA, triggering change in expression
...




• Atherosclerosis

Biology of the Cell Page 17

•

• Atherosclerosis

○

○ Positive feedback between macrophages and more endothelial damage, as ROS are produced
• Cancer
○ ROS can damage DNA
 Mutations
○ Even when repair occurs, mistakes can be made and the subsequent change then become fixed
in the genome

○

Biology of the Cell Page 18

Chloroplasts and Mitochondria
10 November 2014

13:23

Mitochondria
• Most eukaryotic cells
• Aerobic respiration
• Believed to have originated as free prokaryote
• Structure
○ Double membrane
○ Ribosomes
○ DNA loop
• Membrane

○

○ Massive electrochemical gradient
○ ATP-synthase
 H+ follows gradient through synthase
 Massive efficiency
○ Inner membrane is less permeable
○ Outer membrane has lots of porins
 Intermembrane space is pretty full
• Division and growth
○ Mitochondria grow by acquiring nutrients and divide like
simple cells
○ Cells cannot produce mitochondria
○ They can trigger their replication and autophagocytosis

Endosymbiosis
• Schimper (1883)
○ 1st proposed
• Meresclonsky (1905)
○ Chloroplasts
• Wallin (1920s)
○ Mitochondria
• Margulis (1980s)
○ Championed concept
○ Cilia and flagella
• Evidence
○ Chloroplasts and mitochondria share features characteristic of a prokaryotic past
○ Ribosomes are different
○ DNA loop
○ Double membrane
 Bacterial and eukaryotic
 Chemical composition
○ F1 F0 ATPsynthase
 Same as bacteria

Protein import into the mitochondria
• Many mitochondrial proteins are encoded in the nuclear genome and must be imported

○

Chloroplast
• All photosynthetic cells
• Number of chloroplasts in cell is related to photosynthesis and
light intensity
• Structure
○ Double outer membranes
 Inner isn't folded - differ from mitochondria
○ Third membrane within
 Thylakoid
○ Ribosomes and DNA
• Membranes
○ Inner membrane forms a strong permeability barrier
○ Outer membrane is very permeable
○ Thylakoid membrane is key to photosynthesis

•

○

Plastids
• Chloroplasts are very specialised plasmids
• Proplasmid precursors can mature into various organelles

•

Protein import into the chloroplast
• Translocase of the outer chloroplast membrane (TOC)
• Translocase of the inner chloroplast membrane (TIC)
• But there is a third membrane
○ Once across the inner membrane, some must cross the thylakoid
○ How depends on the protein



Biology of the Cell Page 19



• Plastid division
○ Binary fission
○ Similar to mitochondria

○

Biology of the Cell Page 20

The Nucleus
12 November 2014

14:09

Most cells have a single nucleus
• Red blood cells have no nucleus
○ Start with one and then it breaks down
• Phloem cells
○ Companion cells

Structure
• Nuclear envelope
○ Outer continuous with ER
○ Perinuclear space continuous with ER lumen
○ Inner membrane anchored to lamina
○ At mitosis the membrane breaks into chunks
○ Membrane tubules penetrate and cross
• Nuclear lamina
○ Lattice of nuclear lamins
○ Lamins bind to inner membrane proteins
○ Heterochromatin binds to lamina
○ Internal nuclear scaffold
• Nucleolus
○ 2 types
 Compact
 Reticular
 *DFC – dense fibrillar centre, FC – fibrillar centre, GC – granular centre



 rRNA transcription
 Ribosome assembly
 Stretches of rRNA genes may induce spontaneous nucleolus formation
 Nucleolus formation does not depend on DNA associated proteins
• Nuclear pore
○ 3000-4000 per nucleus
○ Regulate protein and nucleic acid movement

○

○ Molecules diffuse through channels
○ Cytosol and nucleoplasm are continuous
○ Transporter regulates
 Export of RNA species and ribosome subunits
 Import of proteins

Biology of the Cell Page 21



□ Ran(GDP) = outside nucleus
□ Ran(GTP) = inside nucleus
 Common for both
• Nucleosome
○ DNA around histone core
 Histones are arganine and lysine rich proteins with strong positive charge
 ~200 base pair per histone
○ The histones have tails that help regulate packing
 Acetyl groups can be added to them
○ Nucleosomes block transcription
 Nucleosome structure is disrupted by the addition of acetyl groups
 Become less attractive
□ Complexes break up
 Polymerase moves along
○ Nucleosomes have a compaction ratio of 5
○ Nucleosomes wind with each to a ratio of 40
• Heterochromatin
○ Transcription active chromatin is euchromatin
○ Inactive chromatin is heterochromatin
○ Found in telomeres
○ Methyl groups not acetyl
○ Silences whole regions of DNA
○ Proteins interact with methylated tails to form heterchromatin

Biology of the Cell Page 22

Enzymes
26 November 2014

13:45

• Macromolecular biological catalysts
• Many key reaction impossible without enzymes
• Most are proteins
○ Ribozymes
 Make all other enzymes
• Function depends on sequence and 3D structure
• Structure
○ Sequence
 Key catalytic amino acids
3D structure
○
 3D cleft brings reactants together
 Enzymes are selective
 Other regulatory sites
□ e
...
activation sites
○ Co-factors, co-enzymes, prosthetic groups
 Crucial to function
 Co-factors
□ Inorganic ions
 Co-enzymes
□ Organic molecules
 Prosthetic groups
□ Tightly bound co-factor/enzyme
 Haem
□ Permanently bound prosthetic
□ Inorganic ion in organic framework
• Role
○ Many reactions are slow/don't happen
○ Enzymes increase rate by 105 to 1014 times
○ Bring reactants together
 Substrates enter site and are held there
□ Interaction more likely than when free floating
 Interaction stabilised
□ H, ionic, covalent bonding
 Product is formed and released
○ Take intermediate routes
○ Makes even unfavourable reactions possible
• Activation energy
○ Lowered
• Michaelis-Menten kinetics
○ Relationship between [S] and rate in enzyme catalysed reactions
○ Vmax = maximum turnover
○ Km = [S] at 1/2Vmax
 Measure of [S] at which enzyme is active
○ Gives a clue to the [S] at which saturation occurs

Biology of the Cell Page 23

○

• Inhibition

○

Biology of the Cell Page 24

Transcription
24 November 2014

13:43

Central dogma of biology
DNA -> RNA -> protein

Genes
• 3 main types
○ rRNA genes encode rRNA
○ tRNA genes encode tRNA
○ Protein genes encode proteins (via mRNA)
• The process of transcribing mRNA from DNA and translating into a protein is gene expression
...
g
...
g
...

• Prions
○ Incorrect protein folding
• Folding is spontaneous but must be controlled
○ Pre-folding and binding with other proteins
○ Folding during synthesis
○ Folding whilst being transported through membranes
• Chaperone proteins
○ Bind to polypeptides using ATP
○ Prevent inappropriate folding
○ Can rescue some misfolded proteins
○ Mis-folded proteins targeted for degradation
 Or can be re-linearised
• Disulphide bonds
○ Form in ER
 More oxidising conditions
○ Catalysed by protein disulphide isomerase (PDI)
○ PDI is also a chaperone
 Quality control
 Ensures correct disulphide bonds form



Protein Degradation
• Persistence measure as half life
• Some very stable
• Some unstable
• Proteins also degraded when damaged, mis-processed or to maintain a constant level of protein
• Ubiquitin molecules attached
○ Ubiquitin markers bind to lysine
○ If marked they are degraded by a proteosome

Biology of the Cell Page 31

The Cell Cycle
03 December 2014

13:07

• Newly formed cells enter the cell cycle
• There are several potential fates
○ Divide
 Proliferating ells
 G1 short
○ Enter G0
 Doesn't enter S phase
 Quiescent
 Waiting for signal to divide
 Can re-enter cycle
○ Exit cycle
 Terminal differentiation
 Neurons

G1
• Variable phase
• Can be very short/non-existent
• In interphase (along with S and G2)
○ Chromatin not condensed

Restriction Point
• Cell division is a major step
○ Must be controlled
• Restriction point is main check
• Checked for
○ Size
○ Nutrient availability
○ Undamaged DNA
○ Permission
• End of G1
○ If failed then G0
• If DNA too damage programmed cell death (PCD) triggered
• G2:M checkpoint
○ After DNA replication
○ DNA checked for damage
○ If tests fail a G0-like state is entered
M phase
• Final checkpoint can halt mitosis if potential problems with disjunction (chromosome
separation)
• Check for
○ Attachment to spindle
○ Correct number of chromosomes
• Failure can result in abnormal separation (nondisjunction)
○ This can lead to aneuploidy (change in chromosome number)

Biology of the Cell Page 32

•

• Cytokinesis in animals
○ Cleavage furrow
○ Contractile ring of actin microfilaments
○ Interaction with myosin tightens contractile ring

Phosphorylation
• Addition of phosphate to an amino acid
• Can cause a protein to undergo conformation change

○

• Cyclin dependent kinases
○ CDKs
○ Control cell cycle
○ CDKs bind cyclins and become active
○ Cyclin b and CDK 1 form mitosis promoting factor
 Cyclin b concentration rises, forms complex
 Mitosis happens
 Cyclin b degraded
Biology of the Cell Page 33

 Cyclin b degraded
 CDK1 remains, inactive
○ Retinoblasma protein
 Rb
 Restriction point
 Rb protein bound to E2F (transcription factor) needed for expression of genes
which are required for DNA synthesis
 CDK phosphorylation of Rb releases E2F, and allows DNA replication to begin
○ Cyclin levels rise --> bind to and activate CDK1 --> binds to Rb --> E2F released --> DNA
replication
Telomeres and the Hayflick limit
• Telomeres on end of chromosomes
• Every time chromosome copied the end is lost
• Telomeres can be lost with chromosome being damaged
• Telomeres shorted each cycle
• Eventually telomeres are lost
○ Limit of replication
○ Hayflick limit
• Stem cells
○ Endless reproduction
○ Embryos and adult tissues
○ Telomerase replaces lost telomeres
 Cancer cells often express telomerase
DNA damage
• Repair requires the cell cycle to pause
• p53 tumour suppressor
○ Cause p21 expression
○ Rb phosphorylation blocked
○ E2F not released
○ DNA replication cannot start
• Serious damage
○ P53 activates expression of Puma
○ Puma inhibits anti-PCD protein, Bcl-2
○ PCD triggered
• If Rb or p53 not expressed
○ Cancer
○ 70% bowel cancer due to lost p53

Biology of the Cell Page 34

Programmed Cell Death
08 December 2014

11:21

Limbs
• Vary between organism
○ Chicken vs
...


Death Signals
• T-cell death ligands
• Fibroblasts
• P53 protein, activates Puma
...
g
...
g
...
g
...
g
...
5mm diffusion is insufficient
• This limits tumour growth
• In order to successfully grow to a stage at which metastasis is possible the tumour must grow
a blood supply
○ Angiogenesis
 Outgrowth from existing vessels
○ Vasculogenesis
 Growth of new vessels
○ These are normal developmental and homeostatic processes
• Inhibitors of angiogenesis should suppress tumours

Biology of the Cell Page 41



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