Biol1007 Notes

Lecture 2 Notes

• Genetic material is shared through generations

• Encodes the molecules of life
• All species share common genes and cellular functionalities

Definition of life: Cell based, can reproduce, complex and organised, energy for growth and
reproduction, tend towards homeostasis (Maintenance of a relatively constant internal
environment), change over time, adapt to environment and respond to stimuli

Classification of living things

Essential elements for life: Hydrogen, carbon, oxygen, nitrogen, phosphorus, sulfur

Atom: smallest part of a chemical element, defined by number of protons, balanced by

number of electrons
• Covalent bond: shared electrons between bonded atoms (strong bond)

Molecules of life: Nucleic acids (DNA/RNA), proteins, fats/lipids, sugars and

carbohydrates
• All based on carbon
• Carbon can bond with itself and other elements
• All major biopolymers have a substantially carbon backbone
• “Sweet spot” of stability (stable but not too stable)
• Basis of life
• Carbon compounds are relatively inert or kinetically stable to hydrolysis and
oxidation
• In general, organic reactions tend to be under kinetic control rather than
thermodynamic control
• Often favourable but slow and good targets for enzymatic control

• Defined beginning and end

• Synthesised in one direction only, increasing the backbone
• Some of monomer is lost in polymerisation, leaving a “residue” incorporated in
growing chain
• Biopolymer synthesis relies on dehydration reactions and require energy input
 • 5’ end- N terminus/terminal for amino (H2N) terminal
• 3’ end- C terminus/terminal for carboxyl (COO-) terminal

Genome Expression and cell type

• Same DNA in all your cells
• Complete genetic information = genome
• Each cell uses a subset of expressed genes to achieve its structure and function
(transcriptome and proteome)

Bacterial Genomes
• Most prokaryotes (bacteria and archaea) have circular chromosomes
• Tend to be relatively small (12 kbp – 15 Mbp)
• Mycoplasma Genetalia 580,000 bp
• Escherichia coli, 5 million bp
Eukaryotic Genomes
• Tend to be big (10 Mbp – 150 Gbp)
• Linear chromosomes
• Condensed into chromatin
• Wrapped around histone proteins

Human Genome
• Eukaryotic
• Linear
• 6 billion bp
• 22 pairs of chromosomes (plus sex chromosomes)
• Encode approx. 20,000 proteins
• Often only one pair of copies of each genes (one on each chromosome pair = alleles)
• Genome (DNA): complete genetic composition of a cell or species
• Transcriptome (RNA): set of all RNA molecules in one cell or a population of cells
• Proteome (Protein): complete set of proteins expressed by an organism, cell or tissue
type
Lecture 3 Notes

Ion and electrostatic bonds

Ions: atoms that have lost or gained an electron and have become charged, like to be around
polar molecules and balanced by opposite charge

Polar or hydrophilic molecules: Atoms have permanent unequal sharing of electrons making
partial charges, like being around water and other polar molecules

Ionic bonds: Electrostatic attraction between oppositely charged ions/repulsion between like
charges, can be strong or weak depending on environment

Van der Waals interactions: attractions between partially charged atoms (permanent or
temporary), several different types, individually weak but together can be strong
DNA as source of genetic information
• Genetic inheritance was understood before it was known what genes were made up of
• Nuclei acids seemed too simple, too hard to purify from proteins, controversy about
what carried genetic information

Nuclei Acid polymers and building blocks

• Sugars, phosphate, bases/nucleobases
• Common sugar phosphate backbone
o Negative charge on phosphates
o Hydrophilic (sugars and phosphates)

Nucleotide: A base and sugar and phosphate

Nucleoside: A base and sugar
Bases/nucleobases = pyrimidines and purines
 no need to memorise chemical structure of bases

Mono-di-tri-nucleotides

DNA vs. RNA

• Thymine for DNA, Uracil for RNA
• Deoxyribose sugar for DNA, Ribose sugar for RNA
Properties of the sugar phosphate backbone
• Common, no matter what base is attached
• Phosphates (-ve charge)
• Sugars and phosphates (hydrophilic)
• Applications
o Electrophoresis: Nuclei acids migrating in electric field (as they are charged),
distance of migration depends on size
o Ethanol precipitation: nuclei acids become insoluble when mixed with salt (to
neutralise the charge) and ethanol
Aromatic molecules: cyclic, flat, conjugated molecules (alternating single and double bonds),
mostly hydrophobic, can react with positive charges

Hydrogen bonds: attraction between partially charged atoms, hydrogen and three
electronegative atoms (F, O, N), moderate strength
Nucleobases
• Aromatic ring structures
o Flat/planar, absorb at ~260 nm
• Pyrimidines (T,C,U) single ring
• Purines (A,G) double ring
• Hydrogen bonding potential (donor/acceptor)
Base pairing
• C and G complement each other ( 3 H bonds so stronger bonding)
• A and T/U complement each other ( 2 H bonds so slightly weaker)

• Chargaff's rules state that DNA from any cell of any organisms should have a 1:1
ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the
amount of guanine should be equal to cytosine and the amount of adenine should be
equal to thymine
• A=T
• C=G
• A + G = C + T = 50%
 • DNA double helix- B-DNA
o Strands run in opposite directions
o Flat bases stack on top of each other
o Negative phosphates repel each other
o Right-handed double helix
o Major and minor grooves
o Four bases seen from the grooves have different properties

Structure of RNA
• Does NOT form B-type structure
• Can base pair (C-G and A-U)
• Extra OH group on sugar stops RNA forming B-DNA-type helices
• This also makes it susceptible to degradation
 DNA vs. RNA
• Bases are generally stable
• C can spontaneously deaminate to U
• Happens 100 times per day per cell
• As DNA is meant to be stable genetic information, uracil in DNA is recognised as
wrong and repaired
• Tolerated by RNA (message, functional molecules, high turnover) so uracil in RNA is
not repaired

DNA as genetic store

• Double stranded: provides 2 copies and template for repair, obvious mechanisms for
replication/transcription via base-pairing
• Stable, not prone to degradation, cells can repair cytosine deamination

Properties of Nucleobases
• Aromatic ring structures
o Flat/planar
o Absorb at ~ 260 nm
o Bases have slightly different absorbance properties but purines are very
similar and pyrimidines are very similar
o Can monitor purity by checking ratios of absorbance values for likely
contaminating molecules
o A260:A280 (proteins)
o A260:A230 (carbohydrates/phenol)

Lecture 4 Notes

Proteins
• Amino acid sequence determines structure which determines function
• Proteins make up over 50% of the cell by dry weight
 • Proteins give cell shape, receptors, enzymes, hormones and growth factors, toxins,
transporters and antibodies

Alpha amino acid

• Non polar or hydrophobic molecules: equal sharing of electrons, don’t like being
around water and polar molecules
 • Hydrophobic interactions: tendency of hydrophobic molecules to stick together and
avoid water, can be strong or weak depending on environment

Peptide Bond Formation

• Two amino acids combine by condensation polymerisation to form a dipeptide
• Very energetically unfavourable; doesn’t happen spontaneously

• Partial double bond makes the peptide bond flat and rigid
• Partial charges encourage hydrogen bonding
• Can still rotate around other bonds
• Polypeptide backbone (under neutral pH conditions)

Amino Acid sidechains

• Hydrophobic aliphatic (chains of -CH2-)
• Aromatic, rings with conjugated bonds
• Polar non-ionic, side chains with -OH, -SH
• Acidic, side chains with carboxylate ion
• Basic, side chains with -N+
• Aromatic, basic, acidic and polar sidechains can form hydrogen bonds
• Aromatic sidechains have a characteristic absorbance of ~280 nm, used to
estimate protein concentration
Protein structure
• Needs to form an active structured molecule à protein folding
• Primary: amino acid sequence
• Secondary: local structures, alpha helix and beta sheet
• Tertiary: 3D arrangement of polypeptide chain
• Quaternary: organisation of subunits (many but not all proteins have multiple
subunits)

Secondary Structure
• Local features allow formation of structure
• Backbone-backbone hydrogen bonding interactions are very important
• Sidechain interactions help hold the structure together and form tertiary structure
• Helices, sheets and turns are regular repeating secondary structure – can have local
structure that isn’t one of these
• Backbone hydrogen bonding patterns and bond angles define structures
Tertiary Structure
• Held together by lots of different interactions/bonds
o Hydrogen, ionic/electrostatic, hydrophobic
o Driving force for protein folding is hydrophobic effect
o pH, solvents and temperature are really important to maintain structure

Quaternary Structure
Haemoglobin- 4 subunits (tetramer)
Myoglobin- monomer

• Disulfide bonds, a covalent bond, formed between cysteine residues when they form
cystine under oxidising conditions (mostly outside the cell)
• Can be very stabilising

Protein Folding
• Information encoded in amino acid sequence
• Burial of hydrophobic surfaces/sidechains in aqueous solvent
• Collapse of protein chain/formation of secondary structure
• Firming up tertiary structure by interactions between different parts of the protein

• Proteins and other structured biomolecules are not rigid but breathe as atoms move
around/bonds twist and lengthen/shorten within limits

Molecules, life and stability

• Most life of earth occurs under relatively mild conditions
• 5-50 degrees
• Atmospheric pressure
• Nearly neutral pH
 • Most biological macromolecules (proteins, nucleic acids) are unstable outside a
narrow range of environmental conditions
• Proteins can be hydrolysed, broken down into constituent amino acid residues- in very
acidic or basic conditions with added heat/pressure (easier to break peptide bonds
with enzymes)
• Proteins are much more easily unfolded- lose unique 3D shape if they are heated
• E.g. cooking an egg permanently unfolds ovalbumin and other proteins

• Alpha helices are perfect size to fit into the major groove of DNA
• Diameter of helix is on average 1.2 nm
• Major groove of B-DNA is 1.2 nm wide
• Common feature of DNA binding
• Sidechains must point right way to recognise either the backbone for general/non-
sequence specific binding, or bases for sequence specific binding

Lecture 5 Notes

Kinetics vs. Thermodynamics

• Need to break bonds (requires energy input) before you make bonds (releases energy)
• Substrate à Product will either be
o Favourable (give out energy, exergonic)
o Unfavourable (need energy, endogenic)
• Whether reaction takes place or not is determined by equilibrium state (at end of
reaction how much of substrate vs. product)
• Catalysts lower energy barrier
• Enzymes are biological catalysts
• Speed up reaction
• Enzymes increase reaction rates
• They do this by stabilising transition state complex
• Enzymes are specific
o Relatively big, highly functionalised binding pockets
o Specific
o Induced fit model, enzyme changes shape/conformation as it binds substrate
and stabilises transition state
 • Biological catalysts
• Mostly proteins (some RNAs are enzymes)
• Highly varied in terms of function, size, need for co-factors, ability to be regulated
• Enzymes required for metabolism, synthesis of cellular materials, communication
(signalling) etc
• Mutations that reduce activity/change specificity/increase activity/alter regulation can
cause disease
• Enzymes are partly regulated by compartmentalisation
o Inside or outside cells
o In particular, cellular compartments
• Enzymes in the wrong place can be a sign of a problem or can cause a problem
o Cardiac enzymes in blood stream (LDH)
• Increase the rates of reaction
• Are not used up in the reaction
• Highly specific for preferred substrate
• Can be regulated
• Can be localised in certain organelles
• Can be organised into pathways
• Mutations in enzymes (that affect activity/specificity) can cause disease

• Under same experimental conditions and high [substrate], doubling enzyme will
double rate

DNA/RNA polymerases
• Make a copy of DNA or an RNA copy of DNA from DNA template
• Always copy new strand 5’ to 3’
• Can only work in one direction
• Use nucleotide triphosphates as substrate
• Add nucleotide monophosphate to 3’OH end of growing chain
• Require a template
• Form a phosphodiester bond
• Release pyrophosphate (PPi)
Driving unfavourable interactions
• Biopolymer formation is intrinsically unfavourable
• Nucleic acids need to make high energy phosphodiester bonds between successive
nucleotides
Lecture 6 Notes

• DNA polymerase
o Make a DNA copy from a DNA template
o Need a primer to start
o Proofread the last nucleotide added; often have 3’ to 5’ exonuclease activity
o Uses deoxynucleotide triphosphates (dNTPs: dATP, dGTP, dTTP, dCTP) as
substrate
o Often have nuclease activity (removing bases) as well as polymerase (adding
bases)
o Gives DNA polymerases an opportunity to proofread (check for mismatched
bases) and correct the newly copied sequence, AND allows DNA polymerase
to remove the RNA primer during replication
o Exonuclease activity is from end of strand
o Endonuclease activity is in the middle of sequence- usually to degrade DNA
o Some nuclease remove from 3’ end, others from 5’ end
• RNA polymerase
o Make a RNA copy from DNA template
o Don’t need a primer to start
o Limited proofreading, no 3’ to 5’ exonuclease activity
o Use ribonucleotide triphosphates (NTPs: ATP, GTP, CTP, UTP) as substrate
DNA Replication and Transcription
• Helical DNA needs to be unwound
• Pulling long helical strands apart causes supercoiling
• Topoisomerase enzymes cut strands, allow to unwind and stick back together
(religate)
• Bacterial DNA replication acts as a model
• Single Origin of Replication (ORI)
• Replication is bidirectional with both strands being copies at same time

• ORI sites are AT-rich (adenine and thymine), easier to pull strands apart because less
stable
• Multiple sites bound by DNA binding proteins
• DNA helicase unwinds part of the DNA
• DNA topoisomerase/gyrase stops supercoiling
• Forms replication forks
• Single-stranded binding proteins coat single stranded DNA (ssDNA) to keep strands
apart/stop small segments of base pairings (hairpins)/protect DNA
• Primase (RNA polymerase) makes a RNA primer
• DNA polymerase III makes a new strand of DNA
• DNA polymerase I removes RNA primer

• If there is a close template, DNA polymerase I also fills in the gap with DNA
• DNA ligase joins the DNA pieces

• Stops when it runs into the next strand of copied DNA (circular chromosomes)/
additional replication termination proteins help out
• Ends of the DNA (linear chromosomes)
 Leading Strands
• Primase makes a RNA primer to begin
• DNA polymerase III makes a DNA copy of the strand in the 5’ à 3’ direction
• Continuous copying
Lagging Strands
• Primase makes multiple RNA primers
• DNA polymerase III synthesises in 5’ à 3’ direction until it runs into the next primer
making Okazaki fragments
• When the two replication forks come together
o DNA polymerase I replaces RNA primer with DNA
o DNA ligase joints the pieces of DNA

Eukaryotic Replication
• Multiple ORIs on each linear chromosome
• Complexes form at each ORI (inactive forms)
• Get activated at the same time to replicate just before cell division
• Need to strip off nucleosomes before replication and reform nucleosomes
immediately afterwards
• Special mechanisms (telomerase) for the ends (telomeres) of the chromosomes

Transcription
• Challenges of Transcription include
o Only small sections of genome need to be transcribed
o Sections often have to be copied thousands of times
o Some sections are rarely copied in one cell but copied many times in another
cell

• RNA polymerase binds to a region of DNA known as the promoter, which sits just
upstream (past 5’ end) and starts transcribing downstream from that region
• Transcription stops at the terminator

• Only one strand of DNA is transcribed for each gene but which strand being copied
can vary, even in the same region of chromosome
• RNA polymerase is a multi-subunit enzyme, that associates with the DNA-bound
transcription factor (s)
• Transcription factor (s) (known as the sigma factor in bacteria) are proteins capable of
recognising a specific base sequence
• Promoter region where RNA polymerase must bind to transcribe the gene
• In bacteria this sequence is known as the consensus sequence, there are 2 regions, at
-10 and -35
• The -10 region often has the sequence TATA which is easy to melt
 • Initiation is relatively slow
• RNA is fast once started

Gene Expression Regulation

• Genes can be expressed at different frequencies (including at different
times/conditions) by
o Promotor strength, DNA sequence optimised for strong or weak sigma
factor/RNA pol binding
o Repressors
o Accelerators
Summary of nucleic acid synthesis
• Rely on base pairing for correct sequences in new chains
• Use polymerases and dNTPs to add nucleotides, hydrolysis of PPi to provide energy
• Need to separate out/unwind dsDNA
• Specific recognition of start sites by proteins
• DNA-whole genome copied once only, leading and lagging strands
• RNA- short segments copied at different frequencies, stop signals encoded in RNA
sequence, different types of regulation

Semi-conservative DNA replication- DNA contains one older and one newly replicated
strand

Protein Synthesis
• Translation converts nucleotide sequence to protein sequence
• 3 types of RNA
• Messenger RNA (mRNA)
o contains template for protein synthesis/information about which amino acids
to add in which order
• Transfer RNA (tRNA)
o matches the correct amino acids to the template
• Ribosomal RNA (rRNA)
o combines with proteins to form the machinery for protein synthesis/catalyses
peptide bond formation

Challenges of Protein Synthesis

• The need to convert a sequence of nucleotides to a sequence of amino acids
• The need to have the correct order of amino acids
• Peptide bond formation is very thermodynamically unfavourable

Possible Codes
• Singlet: 4 different bases and using only one position so you have 3 different
combinations: A, G, C or U
• Doublet- 16 possible pairs
• Triplet- 64 possible pairs
• There will be redundancy in the code i.e. some amino acids will have more than one
code

Codon
• Combination of 3 bases which codes for an amino acid is called a codon
• Triplet codon
• Quoted 5’ to 3’ from mRNA
• Codon will have same sequence as DNA strand that wasn’t copied (non-template
strand) except it will contain Us instead of Ts
 • Some amino acids have multiple codons
• Start codon is AUG
• Stop codons are UAA, UAG, UGA
• Some amino acids have one code only
• Because there are 3 positions, we have 3 reading frames

Reading the code

• Start codon determines the reading frame
• Stop codon doesn’t encode an amino acid
• Genetic code is degenerate or redundant (more than one codon can code for one
specific amino acid)
• Universal, used by all life forms (with a few exceptions)
• We can take genes from one organism and express them in another (biotechnology,
research, medicine, GMOs)
• How does cell know how to put Methionine in protein when it encounters an AUG in
the mRNA?

• Different aminoacyl-tRNA synthetases for each tRNA-amino acid combination

• Aa-tRNA synthetases
o Catalyse the activation of amino acids
o Use ATP hydrolysis to get the energy to make a high energy bond
o Attach the correct amino acid to its matched tRNA
o Recognise the anticodon and other parts of the tRNA
Ribosome
• Enzymes
• Riboproteins- made up of RNA (conventionally shown as blue/grey) and proteins
(purple)
 • Initiation, elongation, and termination (stages of protein synthesis)

Initiation
• Special Met-tRNA binds at start codon
• Modified Met (formyl-Met) in prokaryotes, special initiator tRNAi in eukaryotes
• Small subunit of the ribosome binds mRNA and Met-tRNA
• Large subunit of the ribosome binds
• A bit of extra sequence in mRNA helps to identify the start codon
Elongation
• AA-tRNA comes in, guided by anticodon/codon matching; activated amino acids are
positioned next to each other
• Peptidyl transferase in ribosome catalyses peptide bond formation using energy stored
in the aa-tRNA bond; first, Met is bound to second amino acid
• First-tRNA released, ribosome moves along to next codon on mRNA etc…
• No extra energy is required to make peptide bonds
• Extra energy from GTP hydrolysis used to get the correct aa-tRNA in, and move the
ribosome

Termination
• When stop codon is reached, no tRNA matches
• Protein release factor binds
• Peptidyl transferase adds water instead of an amino acid releasing the polypeptide
• Machinery disassembles and parts can be reused

Differences in Prokaryotic and Eukaryotic Translation

• Transcription/translation linked in bacteria, not in eukaryotes
• Ribosomes have slightly different sizes/makeup but same basic function
• Initiation uses different mechanisms to find the start site and different versions of
Met
• Different protein factors to help things along
• Applications of these differences in translation include
o Antibiotics can target bacterial and not eukaryotic translation because of
differences in molecules involved

Glossary
mRNA/tRNA/rRNA- messenger (encodes proteins), transfer (links mRNA to correct amino
acid) and ribosomal (forms the ribosome)
Aa-tRNA synthetase- enzyme that binds tRNA and charges it with correct, activated amino
acid
Anticodon- sequence in tRNA that recognises the codon in mRNA
Codon- sequence of 3 bases that specifies a given amino acid
Genetic code- set of codons and corresponding amino acids
Peptidyl transferase- enzyme component of ribosome that transfers the activated amino acids
from tRNA to growing peptide chain
Ribosome- RNA-protein complex that catalyses peptide bond formation and guides correct
sequence assembly in protein translation
Start codon- codon that signals the start of protein synthesis, encodes Met
Stop codon- codon that signals end of translation, no tRNAs recognise these codons
Release/terminal factor- protein that binds stop codon to terminate translation

Lecture 9 Notes

• Due to thermonuclear reactions, 13 x 10^23 calories energy reaching the earth’s

surface/year
• 1/3 reflected back to space
• 2/3 absorbed by earth’s surface (most converted to heat)
• 1% of energy converted to chemical potential energy by plants
• Plants form 80% of biomass on earth

• 2.5 billion years ago, earliest ancestors of modern plants caused the “Great Oxidation
Event”

The Great Oxidation Event

• Bacteria produced free oxygen in the atmosphere, via photosynthesis
• Cyanobacteria have chlorophyll and Rubisco (carbon-fixating enzyme)
 Endosymbiosis: evolutionary theory of the origin of eukaryotic cells from prokaryotic
organisms

• Prokaryoteà eukaryote

• First land plants, about 450 million years ago

o Oxygen reacted in upper atmosphere to produce ozone- UV protection
o Plants could start colonising the land
• 400 million years ago
o Plants are wide-spread on land, but still very simple morphology
o CO2 concentration in the atmosphere is low for the first time
o MAJOR PROBLEM for plants
o Biochemistry is aqueous, but plants needed to increase CO2 diffusion
o Leaves fixed this problem to increase CO2 diffusion (evolution!)
§ Large flat surfaces to capture light
§ Waterproof cuticles
§ Complex breathing structures
§ Plumbing to transport water and sugars
§ Stomata evolved to allow precise control of the diffusion of CO2 in
and the diffusion of water out of the leaves
§ Compromise between allowing CO2 in and not getting too much water
out
• Adenosine triphosphate (ATP)
• Adenosine diphosphate (ADP)
• Phosphate bonds are high energy bonds
• Cell’s energy carrier

• Nicotinamide adenine dinucleotide phosphate (NADP) reduces to NADPH

• Cell’s reducing agent

Photosynthetic electron transport

• In the chloroplast, there are thylakoid membranes that form up into stacks called
grana
 • 2 membrane layers and between membrane is lumen, thylakoid lumen and outside
membrane, outside the grana is the stroma
• One of the key roles of photosynthetic electron transport is to build up a proton
gradient across the membrane between the stroma and the lumen
1. Light hits photosystem two and is absorbed by quinone and this energises an
electron which passes down an electron transport chain, in the process water is
split into oxygen and hydrogen
2. Molecular oxygen diffuses off out of the cell and out of the plant, left with a
proton
3. Energised electron passes to plastoquinone which moves another proton across the
membrane, this passes the electron to cytochrome b6f which passes it to
plastocyanin and then it moves to photosystem one
4. Photosystem 1 also energies an electron (after absorbing light) and passes the
electron to ferredoxin and then FNR
5. FNR takes NADP, adds a hydrogen and makes NADPH
6. Higher concentration of hydrogen on lumen side of membrane rather than stroma
side
7. Proton gradient drives ATP, means we add a phosphate to ADP

Cyclic Photophosphorylation
• Light absorbed by Photosystem I
• Excited electron passed down the electron transport chain (PQ, B6F, PC)
• ATP is produced by ATPase
• Electron returns to PSI
• PSII not involved so no water splitting, oxygen or NADPH produced
• Most common in bacteria and isolated chloroplasts
• More common at low CO2 concentrations

Lecture 10 Notes
• Rubisco (ribulose bis-phosphate carboxylase/oxygenase), most abundant protein on
earth
• Found in chloroplast stroma
• 8 large sub-units, gene within chloroplast DNA
• 8 small sub-units, genes within nucleus DNA

Carboxylation
6CO2 + 12NADPH + 12H+ + 18ATP à 1 glucose + 12NADP+ + 18ADP + 18Pi +
6H2O

Rubisco fixes carbon

1. Carbon fixation produces 2 3-phosphoglycerate molecules, one is used in central

metabolic pathways
 2. Reduction, add a phosphate group to 3-phosphoglycerate using ATP (from electron
transport chain) to produce 1,3-bisphosphoglycerate
3. Use NADPH to remove a phosphate group and replace it with carbon to produce
glyceraldehyde 3-phosphate
4. Complicated biochemical reactions (phase 3), produces ribulose 5-phosphate that has
a phosphate group added using ATP to regenerate ribulose 1,5-bisphosphate

Calvin cycle named after Melvin Calvin, American biochemist who used radiocarbon to track
carbon through the cycle

• Rubisco evolved when oxygen concentration was low in atmosphere

• C4 plants evolved to deal with the fact that rubisco is also an oxygenase, concentrate
CO2 near rubisco
• Add an extra step, using PEPC and MDH to produce 4 carbon product, happens in the
mesophyll, produce malate, moved across to bundle sheath cell, around vascular
tissue, these have a suberin layer that means CO2 can not diffuse out of them
• Malate (MAL) is decarboxylated to yield CO2, CO2 cannot diffuse and enters calvin
cycle
• CO2 levels are very high within bundle sheath cell, unable to use up oxygen
• C4 plants have very high photosynthetic rates compared to C3 plants
CAM photosynthesis (Crassulacean acid metabolism)
• Plants that grow in arid environments use this
• Water is limited resource, close stomata to limit water loss during the day, CO2
cannot diffuse into the plant
• Uses temporal separation
• PEPC(PEP carboxylase) fixes CO2 during the night to produce malate, stores it in the
vacuoles, Calvin cycle occurs during the day
 • Increasing light and CO2 reaches saturation point where effect plateaus
• Enzymes have optimum temperatures, above this they denature, explains temperature
curve
• C4 plants have an advantage at high temperatures because oxygenase activity is
higher at higher temperatures so C3 plants would undergo more photorespiration at
high temperatures and C4 plants would not

Co-evolution of plants and the atmosphere

• CO2 levels used to be very high
• Became low 400 million years ago
• Plants evolved to allow more CO2 diffusion e.g. stomata
• Angiosperms (flowering plants) flourished 250-150 million years ago due to these
evolutionary features that helped increase CO2 diffusion
• Atmospheric CO2 levels became extremely low 50 million years ago, grasses and C4
plants flourished, hot, arid conditions as well, Savannah type landscape became
widespread
• In the last 800,000 years, CO2 levels have been very low, cycle between 180 and 280
ppm, due to glacial cycle, CO2 high in times of low glacial activity (warmer
conditions) and low in times of high glacial activity

Lecture 11 Notes
First 2 rules of thermodynamics
1) Energy can be changed from one form to another but not created or destroyed
2) In energy exchanges and conversions, potential energy of final state will always be
less than the potential energy of initial state (assuming no energy enters or leaves
system)
Potential energy is amount of energy released by conversion
Photosynthesis: radiant energy à chemical potential energy

• 120 in and 119-120 gigatons out (terrestrial)

• 90 in and 88 gigatons out (net ocean uptake)
• By burning fossil fuels we are moving carbon stored underground
• Known about link between atmospheric CO2 concentrations and temperature
for a long time (rising levels of CO2 lead to increase in global temperature as
CO2 traps heat)

• Loss of electron is oxidation

• Gain of electron is reduction
• In photosynthesis, electrons are transferred from H2O to CO2
o CO2 is reduced
o Formation of a mole of glucose stores 686 kilocalories of free energy
in the bonds within the glucose molecule
• In respiration, electrons are transferred from glucose to H2O
o Complete oxidation of a mole of glucose releases 686 kilocalories of
free energy
• Anabolism = synthesis of molecules
o Increase in atomic order
o Decrease in entropy
o Usually energy-requiring
o Involve NADPH (extra phosphate)
• Catabolism = breakdown of larger molecules
o Decrease in atomic order
o Increase in entropy
o Usually energy-liberating
o Involve NADH
• Glucose = sugar breakdown
o Glucose + 2NAD+ + 2ADP + 2Pi à 2 pyruvates + 2NADH + 2H+ +
2ATP + 2H2O
Krebs Cycle (Citric acid cycle) occurs in mitochondrion
• Produces 1 ATP molecule, 3 NADH molecules, and 1 FADH2 molecule
• Citrate molecule is reformed
• During glycolysis, glucose is broken down to pyruvate
• A two-carbon fragment of pyruvate (lets off one CO2 molecule) is used to form
Acetyl-CoA, NADH molecule is formed
• Acetyl-CoA enters the Krebs cycle, reacts with 4 carbon molecule to form a 6 carbon
molecule, CoA carrier molecule is released
• CO2 released to make 5 carbon molecule, NADH molecule is formed
• Oxidation and de-carboxylation then occur to produce a 4 carbon molecule, produces
ATP and NADH and CO2
• 4 carbon molecule is further oxidised to give starting material, FADH2 and NADH
are produced
 • 2 pyruvate molecules must go through process so cycle occurs twice to
breakdown products of glycolysis

Electron Transport Chain in the Mitochondria

• Build up proton gradient against the membrane
• 5 large protein complexes and 2 mobile protein complexes sit in the membrane
• There are four complexes composed of proteins, labelled I through IV in
Figure 1, and the aggregation of these four complexes, together with
associated mobile, accessory electron carriers, is called the electron transport
chain
• The electron transport chain is a series of electron transporters embedded in
the inner mitochondrial membrane that shuttles electrons from NADH and
FADH2 to molecular oxygen. In the process, protons are pumped from the
mitochondrial matrix to the intermembrane space, and oxygen is reduced to
form water.
• 1. Complex I: NADH -> NAD+, (NADH supplied from Krebs cycle), 4 H+
are transported across to intermembrane, electron released
• 2. Complex II: FADH2 -> FAD, occurs on the matrix side of the membrane,
electrons also release. Note; FADH2 is a redox cofactor.
• 3. Coenzyme Q picks up electrons from Complex I and II and transports them
to Complex III
• 4. Complex III:4 H+ released into intermembrane space, carrier Cyt C
transports electrons to Complex IV
• 5. Complex IV: 2H+ +1/2O2 -> H2O. Two protons pumped from matrix to
intermembrane space and forms water.
• 6. ADP + Pi + energy -> ATP. ATP synthase takes protons from
intermembrane space to matrix.
• Drives ATP synthesis
Lecture 12 Notes

• Largely composed of macronutrients and water, micronutrients present at very low

levels
• Biological molecules wear out, average protein has half-life of 20 minutes
• Damaged proteins are broken down for recycling and new ones are produced to
replace them
 • Proton is made on ribosome
• Inactive as they have hsp70 proteins (stress or chaperone proteins) attached, push
protein into inactive, compact position, allows vesicles to pack in lots of protein,
transported to other parts of the cell, hsp70 machinery goes away and protein is
correctly folded into its active form

Macronutrients
• Fats, proteins, carbohydrates
Micronutrients
• Vitamins and minerals

• Proteins are the only macronutrients that contain nitrogen, nitrogen has a bell-
shaped curve, if nitrogen levels are too high it becomes toxic, excreted by
kidneys
• Glycosidic bond formation
• Common carbohydrate is glycogen
o Stored in many cells, in liver and skeletal muscle
o Glucagon causes catabolism of glycogen, insulin causes anabolism

• When you eat a meal, villi in small intestine, bloodstream does not absorb protein, it
must be broken down into amino acids
• We have 20 amino acids, 11 of those we can make ourselves (non-essential), 9
essential

• Essential amino acids made from plants

 FATS

• Saturated or unsaturated
• Fats stored as glyceride (fatty acids bonded to glycerol)
• Fat is stored in adipose tissue

• Phosphate is a mineral micronutrient

• Gamma phosphate can dissociate and bond to R group of an amino acid and make
amino acid do work
• ATP à ADP + Pi plus energy!

• Fats, proteins and carbohydrates are interconvertible

Lecture 13 Notes
• Over 3.5 billion years, some cells have evolved complex structures and functions
• Endocrine cells that can respond to homeostatic signals and release hormones
• Voluntary muscle
• Fibroblasts that can repair wounds, secrete fibrin, covers wound and holds it
together, allows regeneration of tissues

• Cytoplasm is a gel, contains fibrous proteins (make up cytoskeleton), globular

proteins have charged surfaces (hydrophilic on outside, hydrophobic on
inside), gel like attraction between proteins and water, holds cell together and
gives it shape
• Rough ER is continuous with nucleus, synthesis, folding, modification, and
transport of proteins
• Smooth ER, makes cellular products like hormones and lipids.
• Golgi is sitting on top of ER (responsible for transporting, modifying, and
packaging proteins and lipids into vesicles for delivery to targeted destination
 • Mitochondria, make ATP through cellular respiration, biochemical reactions,
makes steroid hormones as well (from cholesterol), helps cell commit suicide,
apoptosis, triggering of enzymes that kill cell à triggered in cancer cells to
kill them before they grow, theory is that they sculpt e.g. a hand from a blob of
flesh
• Lysosome, digestion and waste removal, contain digestive enzymes, digest
excess or worn out organelles , food particles and engulfed bacteria and
viruses

• Theorised that we evolved from very simple cells

• Prokaryotic cells
o No membrane bound organelles
o Cell wall, made out of lattice of sugars and proteins
o Flagellum, long strings of protein, back and forth motion of
cytoskeletal fibres causes flagellum to move
o Do not reproduce sexually
o Plasmids (small bundles of DNA), use pili to make contact with
another bacterial cell, lock together and join cell membranes and
exchange plasmids

Prokaryotes- single cell, no membrane encircled nucleus

Bacteria- peptidoglycan (sugar and amino acid lattice), major constituent of cell wall
Archaea- do not have peptidoglycan as major constituent of cell wall, live in extreme
conditions

Eukaryotes: cells with membrane enclosed nucleus

Fungi, plants, animals
• Circle represents a phosphate group
• A phospholipid is a triglyceride (missing one of the fatty acid chains, replaced by a
phosphate group)
• Cholesterol stabilises the phospholipid bilayer, 4 ring structures

• Sidechain
• When cholesterol is taken up into the mitochondria, side chain is removed and
cholesterol is converted into pregnenolone, precursor of all steroid hormones
• Amphipathic molecule, hydrophilic and hydrophobic parts
• Transmembrane proteins can have carbohydrates attached
• Peripheral proteins (small circles)
• Glycocalyx
 • All cells have a plasma membrane

• If fatty acids have double bond (unsaturated) they can bend, allows
membrane to be thinner as it can stack together more closely
Formation of Phospholipid bilayer
• Lightening hit water, caused molecules to coalesce and form a micelle
• Proteins and cholesterol was wedged in between these micelles, stabilised the
phospholipids, able to form a bilayer

• Over time, internal membranes were formed to enclose organelles à

compartmentalisation which allows for specialisation

• Plants use cell wall of cellulose to stabilise their cell membrane

• Cytoskeleton, adds pieces of protein, fibre gets longer and longer, pushes nose of cell
forward, the cell ‘moves’, detaches fibres and on and on process repeats itself
• Can receive info, bacteria know when they bump into something

Evolution of the nucleus

• In ancient prokaryotic cell, DNA stuck to membrane, ribosomes bound as well
• Membrane started folding in, started forming a barrier around the DNA (takes
billions of years)
• Continuous barrier around DNA à nucleus
• Pockets form endoplasmic reticulum (transports and modifies proteins, another
function is that it stores calcium)
Evolution of the mitochondria
• Anaerobic pre-eukaryotic cells did not go further than glycolysis
• They took up a aerobic prokaryotic cell that uses the Krebs cycle (potentially
the bigger cell ate this smaller cell or the smaller cell pushed its way into the
bigger cell)
• Some of these smaller cells could have pinched off a bit of membrane that
protected them from digestive enzymes, performed Krebs cycle and let off all
the ATP it didn’t need into the engulfing cell, symbiotic relationship?
• Eventually cells evolved to have mitochondria and also performed the Kreb’s
cycle
• Cytoskeleton stabilises membrane
• Vacuole, stores molecules, can sometimes act like a lysosome
• Transcription takes place in the nucleus; RNA exits nucleus through
nuclear pores
• Translation occurs on rough endoplasmic reticulum (using ribosomes)
Lecture 14 Notes
• Contact site in mitochondria is where where outer and inner membrane touch

Prokaryotic cells
• Peptidoglycan cell wall
• Little turbine machines that cause flagellum to spin around, powered by ATP

• ATP powers this molecular machinery

• Energy for ATP is taking food molecules in, energy is used in production of ATP

• Vesicles carry protein cargo

• Endoplasmic reticulum is very dynamic, molecules entering and leaving it
• Secretory vesicle goes to plasma membrane, fuses with membrane and releases its
contents by exocytosis
• Vesicles travel down microtubule proteins until reaches membrane
Cardiovascular Disease

• Immune cells eat so much cholesterol they become bloated (foam cells), form a
plaque underneath the endothelial cells lining the lumen
• Release cytokines, more immune cells come and begin eating the cholesterol, eating it
faster than they can digest it, calcium begins to build up (calcification)
• Smooth muscle cells begin to migrate in and eat the fat, expanding atherosclerotic
plaque
• As plaque gets bigger and bigger it pushes the endothelium inwards, narrows the
artery (at this point there is still no fat in the lumen
• Myocardial infarction (heart attack), not enough oxygen going to the heart

• When fats are travelling in blood, coated by phospholipids

lipoprotein molecule
• Low density lipoprotein (LDL)
• LDL Receptors in plasma membrane, interact with ligand, proteins are deposited
under circle of receptors, pulls into circle until indention folds in and becomes a
vesicle

• Vesicles congregate and form an endosome (receptors are sent back to surface)
• Endosome goes to organelle which breaks it down and recycles molecules,
lysosome
• Lysosome breaks down endosome, releasing cholesterol and triglycerides
• Cholesterol goes into mitochondria to make steroid hormones (steroidogenesis)
• Inner membrane touches outer membrane, so cholesterol can enter mitochondria
• Converted to pregnenolone, precursor of steroid hormones
• Process is called endocytosis

• Mitochondria can join together

• DNA?
 o Potential theory is that this is the remnant DNA of ancestral prokaryote
that needed its own DNA (before was engulfed by a eukaryote)
o Symbiotic relationship with host cell, proteins made by nucleus and
transported to mitochondria
• Mitochondria diagrams in textbooks are wrong, no contact sites shown
• Mitochondria can join together to form mitochondrial reticulum, complex of
cisternae

• Sperm cell has microtubules in its tail, linker proteins walk upon the microtubules
causing it to move back and forth and sperm is propelled forwards
• Uses ATP from mitochondrion

Three functions of Mitochondria

• Steroidogenesis
• Make ATP
• Apoptosis (e.g. cell death to sculpt hand from big blob of flesh)

Mitochondria are often attached to microtubules of the cytoskeleton

• Microtubules form “train tracks” for vesicles
• Proteins attached between mitochondrion and microtubule
• ATP is hydrolysed, these motor proteins change formation and “walk” along
microtubule
• This carries vesicles from one area of cell to another
• Also carry mitochondria to parts of the cell that require energy, apoptosis, position
them correctly for steroidogenesis
3 components of the cytoskeleton
• Microfilaments- made of actin
o Goes around outside of cell, running underneath the plasma membrane
• Microtubules- made of tubulin
o Way to identify is that they originate in nucleus and radiate out, towards
the edge of the cell
• Intermediate filaments- made of various proteins often keratin
o Rope-like, little pieces of protein twisted together like rope, very strong,
hold cell together
o Attach to junctions between cell, hold it together and reinforce it
o If it looks like a mesh going everywhere, it is intermediate filaments
Movement across membranes
• If a molecule reaches a passive tunnel and there is lots of one this
molecule on one side of the tunnel it will go through the tunnel to the
other side, with its concentration gradient
• Passive diffusion
• Sometimes molecules must be pushed against their concentration
gradient
Controlled channels
• Doorways that can open or close
• E.g. in nerve cells, first stimulus goes into a nerve cell, the
receptors open up, sodium comes rushing in
• Sodium ions rushing in provides voltage, opens up voltage-
dependent gates, allows more sodium to come in, spreads action
potential along axon of neuron
• They see something or come into contact with something and open
up
Powered transport
• Get molecule across membrane against its concentration gradient
• Powered by ATP
• ATP puts gamma phosphate onto protein, protein changes its conformation
• Funnels that can move in the membrane
• Sugar goes into active transport system , protein is phosphorylated, causes R groups
of protein to attract each other, puts tension down the bottom of the protein, bottom
opens up and sugar goes across membrane

• Protein is then de-phosphorylated and returns to regular conformation

Osmosis
• Where salt goes, water follows
• spontaneous net movement of water molecules through a selectively permeable
membrane into a region of higher solute concentration, in the direction that tends
to equalize the solute concentrations on the two sides
 • Endocytosis, bringing in of a molecule inside a cell
• If molecule is big enough à phagocytosis (a)
• If molecule is solute with some water, very small particles -à pinocytosis, cell is
“drinking”, small drops of extracellular fluid (b)

Exocytosis- export from the cell

Lecture 15 Notes
• Most multicellular organisms are made out of 4 major tissue types
o Epithelium
§ Epithelial tissue is water-proof
§ Is always present where cell comes into contact with water or gas
§ E.g. endothelial cells lining the inside of the lumen of blood vessels
o Connective
§ Has to have fibres, cells, ground substance
o Nervous
o Muscle
• Epithelium, forms covering of all body surfaces, line body cavities and hollow organs,
major tissue in glands
• You can see basal lamina underneath the cells, layer of extracellular matrix secreted
by epithelial cells, on which epithelium sits
• Lumen is the clear space in middle of each cell

simple epithelium

stratified epithelium

pseudo-stratified, nuclei at different levels so looks stratified

• Microvilli, increase surface area
• Squamous- flattened
• Cuboidal
• Columnar
• Epithelia is anchored to the basal lamina
• Active transport through apical membrane
• Passive transport through basal membrane

• Benign tumour, cancer cells do not proliferate at a fast rate

• Wart cancer cells can proliferate, break through basal lamina and lead to
cancerous tumours
• Basal lamina can hold back metastasis for a while
• Single primary tumour, cells can break through endothelium and go into
bloodstream and go everywhere
• Surgeons can cut around these tumours and remove them before they
become cancerous, excise out with a scalpel

Nervous tissue
• Allows the multicellular animal coordinated movement and behaviour

How a neuron polarises and depolarises

• Different regions have different densities of voltage and ligand-gated
channels
• High density of ligand-gated ion channels at dendrites
• High density of voltage-gated ion channels at axon hillock and along
axon to conduct action potentials
• Ligand binding to neurotransmitter receptor à opens channels and
begins depolarisation
• Many voltage gated sodium channels, explosive firing of AP, becomes
rapidly positive
• Passive spread to axon hillock
• Neuron at rest has concentration of sodium ions higher outside and
concentration of sodium ions inside
• Membrane potential is -65-70 mV
• negative charge inside cell
• Ligand gate opens when bound by specific molecule
• As ions enter cell, membrane potential moves away from resting
potential
• Membrane potential becomes more positive and less negative
(depolarisation)
• Eventually, membrane potential becomes positive (+30 mV), channels
become inactive and sodium ions stop flowing in
• Potassium ion voltage gated channels open and potassium flows out of
cell making it less positive and more negative (repolarisation)
Muscle tissue
• Sliding filament theory of muscle contraction, actin and myosin slide over each other
to give muscle contraction
• Striations in muscle, fibres lying over each other

• Round cells called myoblasts join together to make adult myofibril

• Has multiple nuclei
• Muscle fibers generally form from the fusion of myoblasts into multi-nucleated
fibers called myotubes
• Striated, fibres run in two dimensions, overlapping

• One nucleus per cell, very rarely 2

• It is thought that intercalated discs are there to hold cell together and withstand
the enormous pressure of heart contracting

• Fibres run in three dimensions so smooth muscle can contract in all directions e.g.
peristalsis
• Cells divide and replace themselves, new set of cells every 7 years (human)

• Cells can respond to signals e.g. in times of stress (any situation that changes
physiology from base level)
• In times of stress your body breaks down fats and protein to give you energy, undergo
Krebs cycle and produce ATP
• 2 types of hormone that signal in stressful situation

• Protein (green receptor in cell membrane) because proteins are hydrophilic

• Chemical signal going straight to receptor inside cell is a steroid hormone because
steroid hormones are hydrophobic
• Protein sends a signal to a series of enzymes and phosphorylates the enzymes
• If something phosphorylates enzymes its called a kinase
• Phosphatase is an enzyme that pulls phosphate off another enzyme
• Signal through the cell into the physiological machinery
• Protein hormone interacting with receptor in cell membrane, can send signals to
nucleus to make new proteins or switch on enzymes
• Cellular signals important in growth
• 3 types of hormones

Stress response
• Hypothalamus turns psychological signals into hormonal signals
• Connected to pituitary gland
• Adrenal glands on top of kidneys, made up of medulla which secrets
adrenaline and cortex
• Adrenal cortex secrets steroid hormones, cortisol helps you focus, cortisol
breaks down or metabolises fats and proteins, giving you energy in form of
ATP, fats and proteins fed into Krebs cycle
• Pituitary stimulates adrenal cortex by releasing a hormone called
adrenocorticotrophic hormone ATCH, travels to adrenal cortex
• Corticotrophic releasing hormone CRH
• In times of stress, brain picks up stress, signals to the hypothalamus to
release CRH
• CRH goes down infundibulum, down the hypophyseal portal system, goes
to the pituitary, stimulates release of ATCH, ATCH goes into the blood,
goes to adrenal glands and stimulates release of steroid hormones, e.g.
cortisol
History of Microbiology
• 1664- Robert Hooke described structure of blue moulds
• Hook’s microscope allowed observations of ~30x
• 1684- With more powerful microscopes, Antonie van Leeuwenhoek
discovered “wee animacules” -first recording of bacteria
• The theory of spontaneous generation
o Non-living objects can give rise to living organisms
o E.g. chopped hay with water boiled for 10 min, left uncovered
at room temperature, after a few days infusion becomes cloudy
(microscopy shows presence of bacteria) – John Needham’s
“life force” experiment
o Jean Baptiste Lamarck- creatures strive for greater perfection
and move up the “ladder”, new organisms arise by spontaneous
generation to fill vacant places
o 1748, John Needham, life force in organic matter including air,
causes spontaneous generation to occur
o 1768, Lazzaro Spallanzani, boiled broth and sealed flask-
microbes didn’t appear as long as material was sealed à
microbes move through the air and can be killed through
boiling, could still have life force in the air?
• 1861, Pasteur’s experiment with swan-necked flask
o Debate over spontaneous generation had become so heated,
Paris Academy of Sciences offered prize for any experiments
that could resolve conflict
 • Is there a means of allowing air, and thus “life force”, to
enter a container, but not the bacteria that are present in that
air?

• Debunked theory of spontaneous generation

• In setup 1, bacteria trapped in skinny neck, no growth
• In setup 2, bacteria enter after neck is removed, growth
• In setup 3, liquid in neck contaminates liquid in flask,
growth
1876- The Germ Theory of Disease
• Robert Koch invented staining and purification methods including growth media and
agar
• His post-doc, Julius Richard Petri, invented the Petri dish
• Using these, identified the specific causative agents of tuberculosis, cholera and
anthrax
• Discovered spores à explained survival of anthrax for long periods in soil
• Work led to germ theory of infectious disease, microorganisms can lead to disease
• Koch’s postulates, to establish that an organism is the cause of a disease
o Found in all cases of the disease examined
o Isolated from the host with the disease and grown in a pure culture
o Capable of producing the same disease in a healthy, susceptible animal
o Re-isolated and identified as same organism infecting original host
o These postulates still underlie medical microbiology today

• 1928- History of penicillin

o Alexander Fleming cleaning up old Petri dishes, came across one with mould
growing on it
o All around mould, bacterial colonies were dead
o Published work but did not pursue it
• Worked discovered by Howard Flory and Ernst Chain, purified penicillin and found it
could cure mice of bacterial infectionà first effective antibiotic, greatly aided Allies
WW2 war effort
• Microbiology today
o Advanced molecular techniques
o Very sophisticated microscopy
o Enormous range of growth media
o Whole genomes available for hundreds of viruses, bacteria, fungi and protozoa
o New challenges include emerging diseases, drug resistance,
immunosuppression via HIV/AIDS and transplants, keeping food safe without
preservatives/cooking, global warming and bioterrorism

• Diversity of life is greatly dominated by microbes

• DNA sequencing, we have identified certain microbes but have not yet purified them
• Ubiquity of microbes
• Microbes are everywhere, in large numbers
• Only a tiny fraction cause disease à pathogens
• Many microbes live on and in us= normal flora (microbiota)
o Regularly found at anatomical site
o Highly specialised for different sites e.g. adapted to high salt on our skin, the
oil in our hair
o Mostly bacteria, also some yeasts and protists
o Commensal relationship, some benefits, bacteria get a place to live
o Acquired at birth or transiently through our environment
 • Gnotobiotic animals – either microbe-free or have a defined microbiota
• Usually more susceptible to pathogens which can establish themselves more easily
• Microbes prime the gastrointestinal immune system, does not function properly in
microbe-free animals
• Microbe-free animals resist tooth decay
• Delivered by Caesarean section, without any colonisation from their mother

Pathogens, infection and disease

• Pathogens are disease causing microorganisms
• Some pathogens are always harmful e.g. viruses

Other pathogens can range from benign to harmful

• Numbers, too many à damage
• Location, wrong place wrong time
• Host health, immune system may be compromised
• Virulence factors e.g. get new gene for toxins or drug-resistance
• Regular staphylococcus is found in nose and on skin, killed by our immune
system and can be treated with antibiotics
• Staphylococcus aureus, golden staph, superbug, gets into wounds and blood,
golden pigment shields cells from immune killing, resists many antibiotics

• New antibacterial craze, killing 99.99% of bacteria etc… could be harmful as we

have normal bacteria that boost immune system etc, without these we can’t
function properly
• Microbes could build resistance to antibacterial washes and antibiotics, super bugs
develop antibiotic resistance
One health idea

• Infectious diseases and major problems today

o New organisms (HIV, Zika, bird flu, ebola)
o Old organisms, new problems with diseases we thought we were controlling
well (due to antibiotic resistance etc…)

• Wildlife diseases caused by stresses on environment

• Running out of ways to treat old diseases

Tuberculosis (TB)
• Old disease, new problems
• Caused by mycobacterium tuberculosis, bacteria difficult to treat with antibiotics
• Spread person to person via infected droplets
• Can be latent, no symptoms for years but still there
• If you catch another disease, this can reactivate TB
• Damage to lungs, sweats, central nervous system
• 1/3 of people globally are infected with TB
• Disease of poverty, 14x more likely in Indigenous Australians
• TB has become more and more drug resistant
• First line and second line class drugs, front line class drugs are drugs you give to
someone who has TB and second line class drugs are used when these frontline
drugs fail (less effective and more toxic)
 • MDR TB developing around world, particularly prevalent in ASIA, low
socioeconomic conditions,
• Drug-resistant TB is extremely hard to treat
o 14,600 pills/person
o Of 19% that are treated, only ½ are cured

HIV/AIDS
• AIDs first observed in gay men and drug users in 1981
• Rare infections associated with very compromised immune systems
• Involved from viruses that attack chimpanzees and monkeys (SIV)
• Evolves very rapidly, moving target, difficult to treat
• HIV 2 less virulent than HIV 1
• Spread via sexual contact, contaminated blood, mother to embryo
• Infects and kills immune system cells à other microorganisms then attack
• Treatment= ART (active antiretroviral therapy), cocktail of drugs
• ART reduces but does not cure infection (came out in 90s)
• Lots of progress
• Peaked at 3.5 million new infections in 1997, now at 2 million per year
• Deaths peaked in 2005 at 2 million, now 1.1 million deaths per year
• Education and treatment are changing picture of HIV
• Still a problem
o Lack of education
o Lack of access to condoms
o Lack of access to ART
 o Social stigma
• Viral
o Very good at hiding from treatments
o Rapid mutation rate prevents vaccine development
o Resistance to ART is increasing

• Food supply is hugely complex à microbes can have devastating impacts on food
production
• Very globalised
• Microbes affect every point in the food production chain
• Microbes maintain soil health by
o Transforming and releasing important elements e.g. nitrogen,
phosphorous, iron, sulfur
o Breaking down soil to forms that can be used by plants
o Suppressing microbes that can cause plant and animal disease
o Breaking down toxic molecules like pesticides and pollutants
o Complex to simple substances that can be used by plants
• Vertebrates can’t digest cellulose and ruminants (cows, sheep, goats, llamas,
giraffes, deer etc..) completely depend on microbes to do this
• Rumen microbes are anaerobes, archaea living in extreme conditions, rumen of
the cow stomach
• Convert cellulose to sugars to acids, esters, CO2 and methane
• Microbes are then also digested
• Ruminants produce 15-20% of methane globally when they burp
 • Certain microorganisms can promote plant growth
• Mycorrhizal fungi increase water, mineral and nutrient uptake and receive
sugars from the plant
• Rhizobium bacteria in legumes fixes nitrogen for the plant and receives sugars
• Microbes grow in soil and interact with roots, promote root growth, break
down organic matter in soil
• Mutualistic relationship

• Production- fermentation
o Breaking a substance down into a simpler substance
o Yeast and bacteria are good at fermentation
o E.g. beer

• Barley is heated, dried and cracked and soaked in hot water à

releases sugars and activate the enzymes = “Wort”
• Hops are a natural preservative and provide bitterness
• Yeast converts the sugars into alcohol and CO2
• In bottle, yeast keeps making CO2 and making the beer fizzy

• Saccharomyces (yeast)
• Budding yeast because of how it divides

• You can see budding scars in above photo

• Also makes wine and cider and participates in many food fermentation
• Makes bread rise
 • Crop pathogens cause global food losses of 30-40%
• Bananas could be extinct in 5 years
o Genetically identical Cavendish bananas à one disease could kill them all
o Farmers apply fungicides 50 x per year
o Sigatoka complex, 3 fungal diseases in one à rapidly evolving resistance
• Animal pathogens cause about 20% of global food losses
• Food and Mouth Disease (FMD)
o Affects cows, pigs, sheep, goats
o Doesn’t infect people but causes huge economic losses
o 2001 outbreak in UK – 10 million animals were culled
o 2010-11 outbreak in Korea, 3 million pigs and 100,00 cows culled
o Ethical and environmental issues
• Microbial food spoilage
o Microbes and/or the enzymes that they release spoil food
o Mostly moulds, yeasts, and bacteria
o 20% of harvested food is lost to spoilage
o Can result in food poisoning
o 1 in 10 people fall ill every year, 420,000 die

• Important names to remember: Salmonella, E. coli. Listeria

• Importance of heat/cooking, kills microbes most of the time
• E coli, found in gut, often contaminates water
• Salmonella- carried by humans and animals
• Listeria, found in soil, water, cows, chickens, melons
• Campylobacter- found in the gut of chickens and cows
• Staphylococcus, found on the skin
• Food poisoning usually= diarrhoea/vomiting, cramps, fever, life-threatening
• Listeria can cause miscarriage

• Some food spoilage fungi can produce mycotoxins

• Fungi can grow on drier foods
• Mycotoxins are complex molecules, like antibiotics
• Highly toxic and carcinogenic
• Heat stable and not inactivated by cooking
• Secondary compounds, substances produced by fungi and bacteria not usually
produced by usual metabolism but produced under specific conditions e.g. human
host
• Aflatoxin is produced by many food spoilage fungi, natural most carcinogenic
substance

• Food contamination chain

o Food mishandled all along the food production chain
o Few initial pathogens can rapidly grow to a large number
o Some pathogens produce toxins that are not destroyed by heating
o Must manage microbes at every stage of production

• Gut microbiome depends on diet

• Bacteroidetes are associated with a healthier gut microbiota, firmicutes not so healthy
• Healthy gut microbiome means
o Good digestion, nutrient absorption, resisting pathogens, healthy gut lining,
immune functioning, mental health
• Unhealthy gut microbiome linked to chronic “western” diseases
o Allergy, irritable bowel disease (IBD), crohn’s disease, colorectal cancer,
osteo and rheumatoid arthritis
• Can gut microbiome influence obesity?
o Fat mice have distinct gut microbiome
o Transplanting ‘fat mouse’ microbes into a germ-free mouse makes it fat
o Link is not absolute, not sure about humans

• Vast majority of all biodiversity is microbes

o Taxonomic, metabolic, and niche diversity
• Most microbes cannot be isolated or cultured
• Biogeochemistry: where biology, chemistry and geology meet
• Biological processes that impact on chemistry at a global scale
• Most of these reactions are done by microbes
 • Carbon cycle (simplified)
• Autotrophs in carbon cycle
o Self feeder, uses CO2 as carbon source
o May use light as energy source (photoautotroph) and chemical energy
(chemoautotraph)
o Autotrophs convert inorganic C to organic C, act as sinks for CO2, act to
limit climate change (CO2 to solid forms)
o Algae perform 50% of photosynthesis worldwide
o Microbial processes (algal blooms) have impacts on global scales
o Methanogens- consume CO2 and H2 and produce methane
o Chemoautotrophs
o Act as CO2 sinks (good) but sources of CH4 (bad) / overall bad
o Example of archaea
o Anaerobic, killed by O2
o Breathe CO2 and exhale CH4, ancient mode of metabolism from pre
oxygen earth
o Limits methanogens to oxygen-free habitats (deep sediments, soil micro-
niches, animal gut)
o Rice paddies are large sources of methane due to presence of methanogens

• Heterotrophs = other feeders

o Methanotrophs: consume methane and produce CO2
o Traditional bacteria
 o Methane is their carbon source and energy source
o Impact on climate change, sink for methane (good) and source for CO2 (bad) /
goodish overall
o Can also attack other pollutants e.g. trichloroethene (TCE)

• Decomposers
o Eat other organisms, or other organic carbon sources, also supply energy
o All heterotrophs are sources of CO2, bad for climate change
o Decomposers” key group of heterotrophs, recycle dead matter back to CO2
• Protists (protozoa) predators of other microbes
o Ciliates, flagellates, amoebae
o Some protists are detritivores (scavengers) and some photosynthesise
• Pollutant degraders
o Hydro-carbon degrading bacteria are useful for bioremediation- clean up of
pollution by microbes
o Specialised enzymes that can attack hydrocarbons, eating ancient fossilised
carbon
o Clean up natural disasters e.g. oil spills
o Methane, hexadecane (fossil fuel, in crude oil) octane (fossil fuel, in crude oil)

Auto and heterotroph interactions

• Coral symbiosis
o Corals are primitive animals (Phylum Cnidaria) which rely on symbiotic
microscopic algae to supply them with food
o Algae: photoautotrophs, convert CO2 and light to sugars
o Coral: heterotrophs, convert sugars to CO2
o Algae live in poor nutrient waters (why water is so clear)
o Coral bleaching is when algae are expelled from coral, when temperatures
become too hot or cold, pollution, coral lose symbiosis and colour is lost (due
to algae dying)
o Coral symbiosis is like a miniature carbon cycle, carbon cycles between
organic and inorganic forms, biomass is produced, both parties are all g
• Lichen symbiosis
o Lichens are primary producers in some terrestrial habitats, especially in dry
environments
o Lichens are photosynthetic
o Symbiosis between heterotrophic fungus and autotrophic algae
o Algae photosynthesises, passes sugars to fungus which is able to provide algae
with a place to live

• Most of global biogeochemistry is microbial

 • Traditional biotechnology: fermentation
o To preserve foods or make alcohol
o Early fermentations used mixed cultures of naturally-occurring bacteria and
fungi
o Sugar into ethanol
o We have much better control over conditions nowadays
o Fermentation could be defined as cellular biotechnology
§ Need some biology skills (microbiology)
§ Don’t need understanding of DNA, RNA, proteins
• Modern methods are molecular biotechnology
o Need high-level biology skills (microbiology)
o Need understanding of DNA, RNA, proteins

Viruses
• Vectors to carry genes into new hosts
• Source of enzymes e.g. T4 ligase (converts genome from linear to circular, DNA
joining ability)
• Move DNA from one place to another
• Hack T4 phage genome, put other information into it, deliver it into a bacterial cell,
bacteria will be modified
• In the genome of viruses, there are lots of useful genes for code for enzymes

Archaea
• Useful ones for biotechnology live in hot habitats, hyperthermophiles
• E.g. live in deep sea vents, enzymes can tolerate very high temperatures
• Source of thermostable polymerase enzymes for copying DNA sequences
• Very stable and have high activity

Bacteria
• Excellent hosts for cloning DNA and expressing proteins
• Empty shell that we can put info into, molecular machinery makes proteins, give it
new DNA, read and make RNA, turns into protein
• Easy to modify genome of bacteria, make useful products or change behaviour
• Change proteins that the cell makes
 • E coli is used for this

Algae
• Photosynthetic
• Conversion of CO2 and light into biofuels (ethanol and H2)
• Eukaryotic algae (true algae) and cyanobacteria
• Can make biomass, convert into more useful products
• Source of biofuels
• H2 is a negative net carbon fuel

Fungi
• Eukaryotic
• Split into yeasts (single-celled) and moulds (filamentous)
• Moulds used in antibiotic synthesis
• Yeasts are excellent cloning and overexpression hosts

Problems with E.coli

• Sometimes, genes from eukaryotic organism (e.g. human) do not work properly, as
final product requires post-translational modifications, protein encoded by bacteria is
not sufficient to get the function you want
• Eukaryotic genes would work better in a yeast
GRAS (genetically recognised as safe)
• Legal definition that means organism is able to go into food chain and not cause harm
• No pathogenic strains recorded
• Host cell contains machinery for biosynthesis of high value products from simple raw
materials

• Ribosomes, convert RNA to proteins

• Converts nitrogen from ammonia into amino acids, builds them up into a peptide
chain or a protein
• Proteins act as enzymes
• Provides metabolic pathways

• Host cell factory needs instructions or a blueprint to tell it which products to make
• Instructions = DNA
• Plasmids: circular DNA elements found in microbes, replicate independently of the
chromosome(s)
• A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a
cell's chromosomal DNA
• Most commonly used vector for delivery of foreign DNA into target host cell
• Viruses can also be used as vectors
• Wild plasmids found in nature allow microbes to swap genes
• Plasmids are main way antibiotic resistant genes are passed between microbes
• Core genome and accessory genomes in the forms of plasmids
• Plasmid-borne genes are not essential but are useful under specific conditions
• If you get rid of all the antibiotic resistance genes à simple structure
 • Wild plasmid
• Plasmid has to be able to replicate in the host
• Has to have an ORI region, origin of replication, able to replicate independently of
chromosome
• Must be a way to keep it in cells, a selectable marker that enables us to force cells
to take up plasmid, lets you keep the plasmid in cells over times
• Cloning site or multiple cloning site, add foreign genes at cloning site, where you
put foreign DNA that you introduce into the cells, restriction enzymes which chop
DNA
• Cloning: to make many copies of a biological entity
• Either creating identical organisms or making copies of a bit of DNA by adding it
into a plasmid and then replicating the plasmid

• We need 3 tools for DNA cloning

• Way of copying DNA

o Thermostable polymerase
o Copy DNA very specifically
• Cutting DNA
o Restriction enzyme, allows for specificity, recognises specific sequences,
usually 6 bases in length, leave sticky ends that can be re-joined to each
other by joining enzyme T4 ligase

DNA cloning
• Digestion and ligation
• We have an organism of interest with useful phenotype, jellyfish that has green
fluorescent protein
• Extract or copy the DNA, then cut it into pieces (‘digestion’)
• Get plasmid and cut it with same restriction enzyme (so ends have same sequences
and can be joined together)
• Join vector and source DNA using ligase in a process known as ligation
• In ligation mixture
o Starting plasmid that has escaped ligation, non-recombinant
o Non-ligated parts of foreign DNA
o Hopefully some plasmids that are recombinant (contain bits of foreign DNA)

• Transformation and screening (removing recombinant from non-recombinant)

• Sequence based techniques involve PCR and hybridisation, take longer and more
effort
• Promoter, switch that turns on gene, in order for foreign gene to be expressed you
need the right switch, bacteria recognises promoter and switches on transcription and
translation (expression) process
• Switches are organism specific

• Foreign protein may itself be end product (HepB vaccine) or it could make the
end-product (metabolic enzymes)

Example of recombinant products: vaccines

• Primary defence against infectious diseases
• Some of these diseases have no cure…therefore prevention is only way to fight
them
• Work by training the immune system to recognise antigens associated with
invader
• May consist of live attenuated microbes, killed microbes, antigens (proteins)
produced in a GMO host
Hepatitis B vaccine
1. Isolate antigen gene (Surface protein antigen HBsAg)
2. Use recombinant methods, selectively copy DNA using thermostable
polymerase to attain HBsAg gene
3. Cloning of antigen gene
 Lecture 22 Notes

• Coping mechanism = morphology + physiology + behaviour

• Behaviour = part of how organisms respond to biotic and abiotic environment

• Wolf has pronounced canine teeth that allow animal to shear meat off the animal it
has killed
• Simple gut, small cecum, relatively small large intestine
• Koalas have long flat teeth, well developed incisors to snip leaves, flattened molar
teeth that allow them to grind plant material to extract the cellular contents
• Koalas have elaborate gut, cecum is greatly enlarged, houses microbes that break
down plant’s cellular material before it is passed into very large colon
• Links between morphology and diet and their physiology as well
• Behaviour has to be coupled with these other 2 aspects
• Behaviour is not about choice, it must be linked to other components of biology, e.g. a
koala would not have the digestive machinery to eat a steak and a wolf to eat lettuce
• Behaviour is fundamental

• It has small, sturdy fingers adapted for pulling grass and narrow, small incisors
adapted for chewing it.
• Shuffle gait, uses when feeding, squats bipedally and moves by sliding feet without
changing posture, rump is hidden beneath and unavailable for display

• Behaviour affects fitness

• Fitness- individual’s relative contribution to next generation’s gene pool
• Plant-insect interactions
o Insect herbivores consume vegetative parts of plants (e.g. leaves)
o Insects pollinate ~2/3 of all plants, often with food rewards (e.g. nectar)
• Food quality affects butterfly reproductive success, foraging on high quality food
provides a fitness advantage, butterflies have the behaviour to forage on high quality
food instead of low quality food
• Experimental evidence proves this, 2012 study by Cahenzli F, Erhadt A, nectar amino
acids in female butterflies (Coenonympha pamphilus)
Behaviour is ecologically significant because
• Link between individuals and environment
• Affects interactions among species (community level outcomes)
o Larger population of herbivorous insects, more pressure put on plants
• Affects demographics (population level outcomes)
o Small heath butterfly, if they choose to eat high quality food, their fitness is
improved, population of this species goes up
Evolutionary significant because
o Has some genetic basis (nature v.s. nurture)?
o Affects fitness
o Can be selected (benefits must exceed costs)
 We know this because of
o Observations: inter and intra specific comparisons
o Manipulative experiments that test hypotheses

Behaviour in relation to (1) abiotic environment

• Fringe Lizard cooling feet on hot Namib desert sand
• Fringe toed, front and hind feet, elaborate scales, maximises SA, allows them to not
sink into sand
• Rhythmically lifts front and hind feet, allows it to lose excess heat and remain on
sandy surface

Behavioural responses to biotic environment

(1) Obtain food
• Foraging strategies linked with morphology and physiology
 • Huge variety of foraging strategies, defined by
o What they eat: frugivore, herbivore, nectivore, granivore, granivore,
insectivore, carnivore, omnivore
o How they get it: ambush vs. active
o Diet breadth: specialist vs. generalist
• Foraging and food choice is non-random, individuals make foraging choices
• Optimal foraging theory
o Assumed that foragers would move about in an environment that was non-
depleting
o Predicts foragers should maximise net rate of food intake
• Marginal value theory
o Assumed that if animals keep on eating at a food patch, becomes depleted
o That animal should make a decision at a point when amount of food was
marginal compared to amount of food in environment
o Models when an animal should leave a food patch in a depleting
environment
o Predicts that foragers should lead food patches when capture/harvest rate
at patch < average capture/harvest rate
• Foraging ecology tests makes predictions about foraging behaviour
• Honey bees
o Do they return to hive with crop load of nectar that maximises
o Net rate of energy delivered (energy gain per unit time)
o Efficiency (energy gain per unit spent)
o Test with individually marked worker bees and artificial flowers

• Optimal foraging theory is heavily debated as energy is the only currency examined
(no proteins etc…)
• Must incorporate a range of theories into foraging models
• Key thing is to maximise efficiency with energy not being the only currency
• Optimal foraging theory focuses on efficiency of energy gain
• But most foragers are also prey
 • Foraging strategies are linked to predator avoidance strategies
• Trade-off between food and fear

(2) Avoid becoming food

• Dead don’t reproduce, being eaten is ultimate fitness cost
• This leads to strategies to decrease predation risk
• Relevant to most of food chain

• Costly, act or be not very energetically favourable for a predator to eat

• Evidence for 6…
 • The further you get away from cover that acts as protection from predation, the
less likely you are to find Pademelons

• For anti-predator strategies to evolve, benefits > costs

(3) Reproduction
• Courtship and mating
o Relevant to sexual reproduction
o Male-male competition
o Female choice
o Results in non-random mating and non-random offspring, sexual selection
• Peacock’s tail seems evolutionarily stupid (increases risk of predation because it is
so big and colourful, costly to maintain)
• Darwin reasoned that high cost of such a tail is because it confers from benefits
• More likely to be chosen by females, access to mates if they have a more
colourful tail
• Peacock tail arises from natural selection via selective pressure associated with
sexual reproduction
• Intrasexual selection
o Competition, usually from sexual dimorphism (hefty vs. slight, weaponry
like antlers)
• Intersexual selection, mate choice (often chosen by females), owing to sexual
dimorphism
• Parental care, requires lots of effort, some animals just lay eggs and take off
o Extended parental care
o For parental care to evolve, benefits must outweigh the costs
o Benefits: increased survival and growth of offspring (fitness benefits)
o Costs: missed opportunities (to reproduce again)
• You don’t need a brain to express behaviour, just need to detect environment and
respond in a meaningful way
• Higher preference for low cost, high quality food, eventually you deplete the safe
patch, at the same time a risky patch that had a lower relative preference, increases in
preference due to the availability of high-quality food
• Equivalence point is where risky = safe, trade-off between finding food and safety has
been reached ,where many optimal foraging models predict you will find organisms
foraging for food
 • Group: multiple organisms occupying a common space (can be multi-species)
• Ephemeral or consistent
• Can aggregate because of social (positive or negative) factors, resource availability
(indirect) or accidental (random chance)
• Difference between population and group
• Population: a number of organisms of same species in defined geographical area
• Properties of population
o Number of individuals or population size
o Area they occupy
o Age structure
o Sex ratio
• Shapes and drive diversity of life
• Populations: composition and structure are influenced by life history, mobility and
habitats (can be sessile or mobile)
• Ecology
o Distribution and abundance of individuals
o Density
• Evolution
o Population of organisms evolve, not individuals
o Gene flow
• Conservation and management
o Invasive species
o Defining threat status of taxa
o Translocations and restoration
• Where is the line between group and population?
• Dynamics, which change through time, are relevant to deciding this distinction, what
are processes involved (e.g. is there reproduction), how cohesive is aggregation?

Individuals
• Populations may consist of a number of individuals that grow, survive, and reproduce
• Individuals may be unitary or modular
• Unitary
o Develop from zygote, genetically distinct
o Form is determinate
o Development and growth predictable
• Modular
o Grow by addition of modules (e.g. leaves or length of stems), genetically
identical (clones)
o Individuals are highly variable in number of modules (some plants, aquatic
invertebrates)
o Modular individuals are often difficult to count
o Lemna sp. (duckweed)
o Hydra sp. (cnidarian)
o Trifolium arvense (clover)
o Penmaria sp. (cnidarian)
o Buchloe dactyloides (buffalo grass)
o Campanularia sp. (cnidarian)
o Festuca octoflora (fescue grass)
o Cryptosula sp. (bryozoan)
o Quercus sp. (oak tree)
o Gorgonia sp. (sea fan coral)

• Studies of population are important because

o Understanding of temporal dynamics of populations
o Understanding of spatial distribution of populations
o Natural selection occurs within populations

• Population growth
o Populations change in numbers over time
o Change can be positive or negative
o Rate (‘r’) = change/unit time
o Populations grow at different rates

• Birth, death, emigration, immigration, growth (individual), age at maturity, and sex
ratio all drive changes in population size
• Birth and death rates
o Fundamental to population growth
o Balance between additions (births) and losses (deaths) determines growth rates
o Inherent to all types of population growth models
Population growth in “closed” systems
• Population growth rate is the change in numbers of individuals over time
 • Where there is no emigration/immigration, population is closed (isolated
areas, islands, mountain tops)
• N(t) = number of individuals in the population at time t
• N(t + 1) = N(t) + Birth – Deaths
o Number next year (t + 1)

Exponential growth
• Population’s per capita growth remains the same irrespective of pop size, populations
grow faster as they get bigger (exponential growth)
• Dynamic over time and depends on life history of organism
• Discrete- reproduction occurs periodically
• Continuous- reproduction occurs year-round

Estimating birth rates

• Common methods
o Histology of reproductive organs
o Capture/counting of fertilised gametes
o Counting of newly born individuals

Resource limited growth

• Population growth is often resource limited (e.g. food, space, water, nesting sites)
• Numbers cannot increase without bound
 • Carrying capacity (k)- maximum population size of a species that environment
can sustain indefinitely, bound by resource availability
• Estimating death rates (mortality)
o Challenging
o Tagging (follow individuals if sessile, probability if organisms more
motile)
o Changes in size structure, mortality extrapolated from this data

Population growth in “open” systems

• If individuals move in and out of the population, then it is open
• N(t + 1) = N(t) + Births – Deaths + immigrants – emigrants
• Estimating demographic rates
o Tagging (physical, GPS, radio telemetry, acoustic)
o Genetics
§ Genetic similarity occurs with only very low levels of interbreeding
between populations
§ Genetic differences = no movement between populations
§ Common chimpanzee tested in this way
§ Genetic analysis of microsatellites
§ 3 definitive sub species
§ No evidence for fourth distinct population (vellerosus) as suggested by
others (green on map
§ Eastern and central populations more closely related
Spatially structured populations
Metapopulations
• Local populations, but individuals move
• Demographic rates vary spatially
• Large scale dynamics dependent on local dynamics and connectivity
• A metapopulation is a group of spatially separated populations of the same species
which interact at some level
• Individual populations have finite lifespans, metapopulation as a whole is often stable
because populations from one population are likely to recolonise a habitat which has
been left open by the extinction of another population
• May emigrate to a small population and save it from extinction, rescue effect
• Glanville Fritillary butterfly (Melitaea cinxia)
o Periodic local extinctions
o Recolonisation from nearby populations
o Metapopulation level extinction prevented
• Mayfly
o Larval stages mature in local pools
o Adults disperse between pools
o Mortality variable from pool to pool
o Some pools are sources (low mortality) while others are sinks (high mortality)

Estimating population size

• Common tools
o Counts (visual, auditory, acoustic)
o Mark and recapture
• Mark release recapture (MRR)
o MRR method estimates total population size from sample proportion of
mobile species
o Uses proportion of recaptures to estimate whole population size
o Assumptions often hard to satisfy
§ Closed population
§ All individuals equally likely to be marked
§ Marked individuals do not lose their mark
o Technique used on whales, lizards, small mammals
 Estimating growth and age
• Trees- tree rings
• Perennial plants- rings in the tap root
• Mammals- teeth e.g. Grey-headed flying fox
• Fish- otoliths
• Dendrochronology is the dating and study of annual rings in trees

Age determination in grey-headed flying fox

• Sources of mortality
o Shooting, electrocution, barbed wire, nets, heat events
• Colonies- many thousands of bats
• Located in gullies of eucalypt forests or in mangrove forests
• Sydney colonies at Ku-ring-gai Chase, Gordon, Cabramatta Creek,
Centennial Park
• Urban parks- royal botanic gardens (no longer there)
• Diet
o Nectar, pollen of native trees, gum trees
o Native fruits, rainforest trees
o Orchard fruits when preferred foods not available
o May travel up to 50 km each night from their camp to feed
• Low reproductive rate
• Listed as vulnerable species in NSW
• Orchards are issued permits to shoot animals
• Impact of this additional mortality is unknown
• Use cementum rings in teeth to estimate age
• Aging fish with otoliths
Understanding age and size-structured population dynamics
• Age and/or size of individual affects
o Fecundity (probability of giving birth)
o Survival
• Treating all members of a population as identical? Unrepresentative of natural
population structure
• Imbalanced initial age structure à age and number cycles
• Life tables: show survivorship probability at each age, long term studies are key to
understanding population dynamics
• Australia’s human population dynamics
o Changes in human population size, mostly due to behavioural changes
o Economists need to know future age structure to plan: more nursing homes,
more schools
o Current trend: ageing population
o Growth rate of many western countries
§ Below replacement rate
§ So population numbers will level out and then fall

• Extinction
o Loss of all populations of a species
o Processes of chance that contribute to extinction event
o Genetic stochasticity (small populations)
o Demographic stochasticity (random nature of births and deaths)
o Environmental stochasticity (variability)
o Catastrophes (cyclones, epidemics, fire)
o Human impacts (habitat loss, fragmentation, over exploitation, hunting,
pollution, introduction of new pest species, other environmental changes e.g.
climate change)
o Dodo, Stellar sea cow, great auk, Tasmanian tiger

• Eastern Quoll
o Small cat-sized marsupial carnivore
o Occurs in 2 colours (black or fawn) with white spots
o Distinguishable from larger spotted-tailed quoll by absence of spots on tail
o Small colony survived in Nielsen Park until 1963/64
o Eastern Quolls are still present in Tasmania…only just

Population viability analysis (PVA)

• PVA is a tool to model population dynamics over time
• Uses basic population data
• Includes environmental variation in these values
• Can change values to reflect human impact
• Population size and carrying capacity needed
• Fecundity needed
• Mortality of adults and juveniles needed
• Inter-annual variation in parameters needed
 Long-nosed bandicoots PVA
• North head, Sydney
• Endangered population
• Remnant population, cut off by urban development
• ~100 individuals, must be self sustaining
• At risk from cars, habitat loss and isolation
• Monitored for ~12 years
• We have learnt their population size, fecundity and mortality
• Use PVA to understand effects of habitat loss, increased mortality rates, non
native predators such as foxes and multiple impacts

• PVA only as good as the data

• Test robustness of conclusions using sensitivity analysis of parameters based on
known or hypothesized variance in data used to estimate the parameters
• Fundamental to PVA

Variation within a species

• Groups within species can be defined as being of a taxon hierarchically lower than a
species
• In zoology, only subspecies is used
• In botany, variety, subvariety and form are used
• In conservation biology, concept of evolutionary significant units (ESU) is used,
which may define either species or smaller distinct population segments
• In horticulture there are cultivars
• Breeds of domesticated animals, dogs, cats etc…

Species
• Species is one of basic units of biological classification and a taxonomic rank
• Species is often defined as a group of organisms capable of interbreeding and
producting fertile offspring
• "groups of actually or potentially interbreeding natural populations, which are
reproductively isolated from other such groups”
• Limitations of biological species concept
o Not relevant to organisms capable of asexual reproduction (bacteria)
 o Organism that does not interbreed is outside of definition
o Fossils
o Clonal species
o Asexual species
o Organisms may also breed beyond notional definition of species
§ Interspecific hybrids
§ Ring species
Other species concepts

Interspecific hybrids, some species are capable of forming hybrids – problem with defining
the term species e.g. a Liger, Corymbia x 'Summer Beauty’ (A cross between Corymbia
ficifolia and Corymbia ptychocarpa), promiscuous proteaceae (hybridisation between native
Australian Lomatia species)
Why does hybridisation occur?
1. Breakdown of reproductive isolating barriers which usually prevent gene flow
between closely related species
2. Potential causes of hybridisation in Lomatia include
a. Habitat disturbance, species in closer proximity
b. Secondary contact, increased migration distances (pollinator change, or
dispersal)
c. Altered phenology, leading to overlap in flowering times (and pollen transfer)
d. Altered genetics, breakdown in pollen incompatibility system
3. Potential evolutionary outcomes
a. Sterile
b. Speciation
c. Enhanced variation

Ring species- a parental population expands around an area of unsuitable habitat in such a
way that when the two fronts meet they behave as distinct species while still being connected
through a series of intergrading populations
• "The Caribbean slipper spurge”
• Most mammals, birds, fish and plants have been described but the other groups
remain poorly known
• About 300, 000 species of fossil organisms have been described. Thus the number of
known fossil species is less than 2 percent of the probable total number of species.
(Rosenzweig 1995)
• "The actual number of living species is probably at least 10 million (and possibly as
high as 50 million)
• but there are probably more than 10 million species in existence. The total number is
uncertain because estimates are based on extrapolations from samples of species
richness taken from only a few environments
• Insects comprised about 57% of all named species Beetles comprised 25% But most
non-insects have probably been discovered and described. Most insects never will.
• Estimation of number of species is based off extrapolations
• 13.5% of beetles (162 spp) live only on this one tree species, there are ~50 000
species of tropical trees
• Implies 8.1 million species specialising on single tree species
• +2.7 million beetle species live on more than one tree species
• 10.8 million species of canopy beetles
• If beetles are 40% of all tropical arthropod species
• This implies 27 million arthropod species in tropics and 3 million temperature
species= 30 million arthropod species in the world today
• World is full of insects
• Beetles are the most diverse

Using higher taxonomic classification of species to estimate number of species

• Phylum, class, order, family and genus follows consistent and predictable
pattern from which the total number of species in a taxonomic group can be
estimated
• Method predicts 8.7 million eukaryotic species globally with 2.2. million of
these marine
• After 250 years of taxonomic classification and >1.2 million species, 86% of
existing species on earth and 91% of species in ocean still await description
• Cryptic speciation is a biological process that results in a group of species (which, by
definition, cannot interbreed) that contain individuals that are morphologically
identical to each other but belong to different species.

Measuring Biodiversity
• Species richness =number of species
• Species turnover = difference between samples
• Evenness = equitability of individual abundance among species
• Diversity indices
• How many species we find often depends on how hard we look
• Few samples – mostly find common species
• Many samples needed to encounter rare species
• Species composition also responds to environmental conditions
• Many ecological communities are made up of a few common species and many rare
species
• Rank abundance curves can be used to compare community composition
• Steeper slope indicates that the commoner species are a greater total proportion of the
community
• Alpha diversity is quantified with diversity indices
• Combines number of species and relative abundance of individuals within species
• Many types that emphasise either common or rare species and have different types of
bias
• Comparisons should be made using same index
• Simpson’s index
• Shannon-Weiner index
 Autotrophs
• Producers
• Make it themselves (synthesise organic from organic compounds)
• Green plants, phytoplankton, algae and chemosynthetic bacteria

Heterotrophs
• Consumers, degraders, decomposers
• Get it from others
• Animals are heterotrophs
• Food chains describe energy flow between organisms among trophic levels

• Food webs describe more complex interactions

• Food chains are usually short
• Energy loss between trophic levels

• but food chains often short, whether energy base (1(o)productivity) is low OR
high
Dynamic stability hypothesis
• Longer food chains less stable because fluctuations at low trophic levels
magnify at high levels so top predators more likely to go extinct
• Predicts predictable (stable) environments should have longer chains

• Observations among ecosystems useful but may confound factors

• E.g. tropical forests v.s. grasslands
• Not just differences in productivity
• 1o producers have very different life forms
• Some experimental evidence supporting both hypotheses
• Hypotheses are not mutually exclusive
• Relative importance of one hypothesis may depend on ecosystem
 • Ecological interactions are exchanges and flows of energy and matter
• Within and between trophic levels
• Intimately linked with trophic ecology
• Mutualism: 2 organisms in close association, both benefit
• Competition: both do not benefit
• Predation e.g. herbivory, carnivory, parasitism
• Commensalism [+, 0]
• Amensalism [0. -]
• No interaction

Mutualism
• Obligate and facultative mutualism
• Obligate, one organism cannot survive without the other
• Facultative mutualism , both species benefit but do not depend (life or death) on each
other

Competition
• For resources
Communities: 2 or more species that occur together in space and time
• In addition to co-occurring, community members interact with each other as an
ecological unit
• Sometimes taken to be just vegetation, but should include all biota that occur together
• Assemblages, less well defined, group of species that live together with no
assumptions made about how or whether they interact with each other

Ecotones
• Gradual transitions are norm, rather than abrupt and hard edges (marine-terrestrial
transition is an exception)
• Usually a transitional area between 2 different communities, such as woodland and
heath

Communities over time

• Change in composition
• Local colonisations and extinctions
• Classic models driven by succession
• Predictable patterns of change in response to a disturbance
• New communities assembled by human activity
• New communities often homogeneous in many parts of the world

Succession
• Trees fall down in forest à light gap
• Light unsuitable for certain species (shade tolerant), creates high quality
environment for other species
• Changes in species composition and abundance, growth rates in lower canopy
stratum
• Dominant species etc.. in system change over time
• Various biogeochemical processes associated with presence of certain species also
changes
• New dominants move in
• Equivalent changes often seen with animals, fungi etc
• Primary succession
o Bare area without soil e.g. sand dune, bare rock
• Secondary succession
o In a habitat modified by other species e.g. forest gaps, abandoned
agricultural fields
• Facilitation
o Early arriving species make environment more favourable for later
species
• Tolerance
o Neither negative nor positive interactions between early and late
species
• Inhibition
o Early species inhibit later species
• Pioneer species grow in sun, fix nitrogen, good dispersal, small seeds, rapid growth,
short generation time, poor competitors
• Climax species are shade tolerant, slow growth, long-lived and good competitors
• Climax community is final community in successional series
• Self-perpetuating, no replacement
• Keep getting reset by disturbances. Natural and anthropogenic

Competition’s role in succession

• Limited resources
• One organism deprives another organism of a resource (resources are sometimes,
but not always, in short supply).
• Exploitation and interference competition
• Intraspecific competition leads to density dependence and population regulation
• Interspecific competition leads to competitive exclusion and niche differentiation
• Intraspecific competition is an interaction in population ecology, whereby
members of the same species compete for limited resources. This leads to a
reduction in fitness for both individuals. By contrast, interspecific competition
occurs when members of different species compete for a shared resource

Rock platforms: competition and successional niches

• Great range and distribution of species
• Tide shifts, changing conditions
• Competition over limited resources
• E.g. barnacles

• Removal and transplant experiments

• Chthamalus was able to extend its range down in the absence of Balanus, mortality
not caused by subermergence but by interspecific competition
• Balanus not affected by presence/absence of Chthamalus
• Balanus distribution affected by intraspecific competition or predation?
• Balanus competes directly by smothering, undercutting or crushing
• Disturbance is a driver of community structure and diversity
• Intermediate disturbance

• Derived from observations of storms on tropical rainforests and coral reefs

• Resilience: how long before a community returns to equilibrium after disturbance
• What objective and non-arbitrary criteria for determining pre and post disturbance
conditions do we have?
• Ecosystem- community of living organisms considered in conjunction with abiotic
components of their environment, interacting as a system

• In ecology, productivity refers to the rate of generation of biomass in an ecosystem

• Energy flows through biosphere

• Materials are recycled
• Ecosystem productivity is controlled by efficiency of recycling as well as by energy
available
• Materials transported in atmosphere (water, carbon, nitrogen and sulfur) à global
cycles
• Phosphorus, potassium, calcium, magnesium move through soil à local ecosystem
cycles
• Productivity in ecosystems may change through time
o Young ecosystems have more actively growing tissue but older systems have
more biomass
o If resources are limited, regeneration of original ecosystem may be
impossible, cleared rainforest may revert to open grassland
• Marine systems relatively unproductive
• Nutrients (especially nitrogen and phosphorus) tend to accumulate at great depths and
are unavailable to phytoplankton
• Major fishing grounds in upwelling zones where nutrients are forced up

• 2/3 of mainland Aus is desert

• Rainfall highly variable
• Desert ecosystems productive in pulses when rain falls, or from utilisation of reserves
at other times
• Consumers must adopt ‘pulse and reserve’ pattern e.g. grasshoppers, budgies, desert
rodents
• Eat reserves of other organisms
• Adopt opportunistic feeding habits
Anthropocene- proposed geological epoch dating from the commencement of significant
human impact on Earth's geology and ecosystems, including, but not limited to,
anthropogenic climate change

• Bioaccumulation- occurs when organism absorbs toxic substance at rate greater

than that at which substance is lost à accumulation
• Persistent and mobile
• Accumulation occurs in body tissues
• Particularly in higher predators at top of food chains and webs
• 2,4-D and 2,4,5- T (herbicides
• DDT, dieldrin, lindane (organochlorine insecticides)
• PCBs (polychlorinated biphenyls, chlorinated organic compounds used as
insulation in electrical equipment)
• Heavy metals (mercury, lead cadmium)
• Problem transcends international borders
• PCBs are now banned worldwide
• Monitoring and regulation needed
• Bioaccumulation has effects on growth and development

• Habitat fragmentation: classic ideas from theory of island biogeography

o Habitat loss is one of the major contributors to biodiversity loss
o Fragment size and isolation are primary drivers of diversity
o Edge effects are prevalent
o Shape matters
o Connectivity and corridors enhance landscapes
o Role of matrix- hospitable or not
Climate change
Extinction Crisis- mass extinction events
• More than 28,000 species are threatened with extinction
• Rate of extinction 10-100.000 times higher than background rates
• Should be only 1 species every few years
• Australia has lost ~33 species in last 200 years
• Non-flying mammals in the critical weight range (CWR)
• 35g to 5.5 kg…arid species experienced most loss
• >30% of nation’s mammals are extinct or threatened
• Western NSW: case study of mammal loss
• Faunal losses 41% of marsupials, 65% of rodents

Conservation biology is a response to extinction crisis

Aims to
1. Describe problems and understand processes
2. Predict impacts of threats
3. Develop solutions
4. Ultimately: stop more species, communities, ecological processes going extinct
Paradigms of conservation biology
Small population
• Effect of small numbers on a population’s persistence
• I.e. stochastic influences (demographic and environmental, genetic drift, inbreeding
depression)
• How or why it is small is not the issue
Declining population
• Why population has declined to low numbers, what might be causing it and how to
reserve decline
• Diagnose causes of declines and treat them

• Evil quarter of extinction forces

o Alien species
o Over-hunting
o Habitat loss
o Co-extinction
o HIPPO
§ Habitat destruction
§ Invasive species
§ Pollution
§ Human over Population
§ Over harvesting

Alien species
• 56 introduced species of vertebrates
• Annual economic and biodiversity costs estimated at 800 million to 1 billion
managing pest animals
• 4 billion managing weeds (direct control and lost production)
• New Zealand has more alien plant species (>24,000) than native ones (6,700)
• New megafauna
o Cattle, sheep, goats, pigs, buffalos, donkeys, deer, hoses, camels, now all feral
o Many are major pests
• Microfauna
o Cats, rats, mice arrive with early explorers
o Rabbits, hare, foxes, cane toads and others released
o Bees, wasps, new plants (blackberry, lantana, gorse, buffel)
o Ants etc…
• Invasion
o Deliberate introduction
§ Acclimatisation societies (comfort/familiarity)
§ Ornamentals
§ Agricultural
§ Domestics
§ Biological control
o Human traffic
§ Trade routes
§ Ease of global travel
§ Poor quarantine
 o Native invaders
o Tens rule
§ 1/10 of plant and animal species brought into a region will escape to
appear in the wild
§ 1/10 of those escaped species will become naturalised
§ 1/10 of those will become invasive
o Invasive species that characteristics that maximise or enable high
reproduction, enable great ecological dispersal, enable species to be greatly
ecologically flexible
o 20 mammal, 25 bird, several amphibians, 30 freshwater fish, 1000s of
invertebrates
o Red fox
§ Competes with carnivorous marsupials
§ Local fauna are naïve to it
§ Preys on everything, some have even learned to climb trees to look for
baby koalas
§ Linked to 12 extinctions of mammals and threats to 48 mammals, 14
birds, 12 reptiles, 2 amphibians
§ Fox distributions limited by and facilitated by rabbit distribution
• Continental scale, except far north
• Suppressed by dingo over large areas
§ all states except Tasmania and it is widespread throughout the country
with the exception of tropical areas of northern Queensland, the
Kimberley and the Top End of the Northern Territory

• Overhunting
o Humans over-exploiting wildlife
§ >50,000 bounties paid on brush-tailed rock wallabies in NSW where
species is now endangered
§ 27 million kangaroos, wallabies, bandicoots killed in QLD 1877-1930
by government decree, marsupial destruction acts
§ Fisheries management
§ Overseas as bushmeat, wild meat
§ Overexploitation risks higher in data-deficient systems

• Habitat loss and the extinction debt

o Major cause of species extinctions
o Island biogeographic theory suggests that
§ Reducing habit area to 10% of its former extent will eventually cause
about 50% of species dependent on natural habitat to disappear,
predictions not always matched by observations
o Extinction debt reflects the future ecological cost of current habitat destruction
§ Extinctions occur generations after fragmentation
o Moderate habitat destruction is predicted to cause time-delayed but inevitable,
deterministic extinctions
 Co-extinction
• Critical ecosystems functions lost when species are lost
• Loss of engineer digging species from Australia’s rangelands
• Haast’s eagle in NZ went extinct after its main prey, moa, were hunted to
extinction
• Cassowaries are only vector of large rainforest fruits, their decline puts
these fruits at risk
• Hawaiian hibiscus close to extinction because of loss of honeyeater
pollinators due to alien species
• Passenger pigeon, one the most numerous bird on the planet, >5 billion
birds
o Hunted to extinction in USA
o Last wild specimen seen in 1900
o Co-extinction of 2 species of bird louse

• Alien predators have twice the impact of native ones

• Predation examples (removal/supplementation) and meta-analyses (towards general
pattern across experiments and studies)
• Fox control and native mammal conservation
• Endangered black footed rock wallaby in WA wheatbelt
• Operation Western Shield
o 1080 poison used
o Brush-tailed bettongs removed from endangered list, numbats, rock wallabies,
possums, bandicoots and chuditch also more common
• Models of population dynamics are useful to predict impacts and to identify
management options
• PVA
o Most effective at comparing management options
o MVP minimum viable population size
o Data hungry process, helpful and effective
o MVPS must be large (10000-100000) for long term persistence
Long-nosed bandicoots at North Head, Manly
• Endangered population under NSW threatened species conservation act now
biodiversity conservation act
• Remnant population, cut off by urban development
• ~100 individuals, must be self sustaining
• At risk from cars, habitat loss, isolation

Legislation
• Federal and NSW listing
• Biodiversity conservation ACT 2016
• Identify critical habitat
• List species, populations, communities
o Provides for recovery plans
• List threatening processes
o Threat abatement plans

• “Ecological restoration is the process of repairing damage caused by humans to the

diversity and dynamics of indigenous ecosystems”
• Restoring ecosystems to some pre-impact or reference state
• Enhancing habitat quality
• Restoring ecosystem functions via reintroductions