BABS1201 Study Notes

Life
Universe = 13.8bya
Solar System = 4.6bya
Life = 3.8bya
1.8million species identified, thousands more each year, with 10-100 million species in
total, of which are arthopods

Characteristics of Life:
Reproduce
Grow and Develop
Metabolise
Respond to Stimuli/Environmental Changes
Have Cells (organizational units)
Possess the Chemicals of Life

o Carbohydrates
most abundant, chemically simple organic molecules
store/transport energy (mostly in plants, animals use lipids), structural
components
monosaccharides link to form oligosaccharides (2-6) or polysaccharides

o Proteins
Dependent on amino acid sequence, linked by peptide bonds
4 different levels of organisation (shape-dependent)

o Lipids
fats, oils, waxes, cholesterol, fat-soluble vitamins (A, D, E, K),
monoglycerides, diglycerides, phospholipids
energy storage, structural component of cell membrane

o Nucleic Acids
formed by linking nucleotides
store/transfer genetic information
DNA, RNA

Prions (proteinaceous infectious particles) are altered proteins that can change other
proteins through conformation.

Domains (classification), defined by Carl Woese (compared ribosomal RNA, formed

phylogenetic tree):
Eukarya (35 subdivisions) - plantae, fungi, animalia, 50-100 protist
kingdoms
Bacteria (19 subdivisions)
Archaea (16 subdivisions) - many are extremophiles (halophiles,
thermophiles, methanogens - swamps/marshes, anaerobic and produce
methane)
 Prokaryotes = bacteria + archaea; thrive almost anywhere, more in handful of
soil than the number of people who have ever lived

Viruses - 50-100nm (only seen with electron microscope)

Origin of Life:
1) Abiotic synthesis of small, organic molecules
2) Joining of these into macromolecules
3) Packaging into protobionts (perhaps by membrane, prokaryotic
precursors)
4) Origin of Self-Replicating Molecules

Fossil Record - biased for species that existed for a long time, were abundant and
widespread, and had hard parts. However it shows macroevolutionary changes (ones
youd be able to see, not genetic) in many species. Comparisons in common
structures, such as common DNA or the same structure of cilia in Paramecium (protist)
and windpipes are evidence for evolution (as with the pentadactyl limb, comparative
embryology, comparative biochemistry - comparing proteins like haemoglobin).

Darwins Theory of Natural Selection explained the duality of unity and diversity
through two main points:
species showed evidence of descent with modification from common ancestors
natural selection was the mechanism behind this

Cells
Bacteria and Archaea:
most numerous cells on the planet
no defined nucleus (DNA in cytoplasm)
very wide range of metabolic diversity
cell wall
10-20 times as many bacteria in/on the ;human body than there are human cells
(of which there are 1013)
Cell Membrane has a hydrophilic head and 2 hydrophobic tails (controls what
comes in and out of cell).
All cells contain:
plasma membrane
cytosol (semifluid)
chromosomes
ribosomes

Bacteria/Archaea Eukarya
no-membrane around organelles membrane-enclosed organelles
no nucleus nucleus (usually largest
organelle)
simple, small (1m; 0.5-5m) complex, larger (10-100m)
Bacterial Morphology and Colony
Formation

Bacteria and Archaea undergo binary fission (not

mitosis which involves nuclear division, which they do
not have, and instead chromosomes simply replicate)

Bacteria Archaea
Cell membrane contains ester Cell membrane contains ether
bonds linkages
Cell wall made of peptidoglycan Cell wall lacks peptidoglycan
One RNA polymerase Three RNS polymerases (like
eukaryotes - genes and enzymes
are more like this)
Bacterial ribosomes sensitive to Archaea (and Eukarya) are not
some antibiotics
Ubiquitous Typically extremophiles, also in
many marine environments

Whilst archaea are similar to bacteria in size, shape, lack of interior membranes (and
hence organelles), no nucleus (DNA in a single loop - plasmid), and they are both
usually bound by a cell wall, archaea are more genetically similar to eukaryotes.

Cell Theory:
 The smallest unit of life is a cell
All life forms are made of cells
Cells only arise from pre-existing cells
Major cellular components of eukaryotes:
cytoplasm - comprised of organelles and cytosol (gelatine-like aqueous
fluid containing salts, minerals and organic compounds)
nucleus - contains nucleoplasm in nuclear envelope (double membrane
system - two lipid bilayers) which has selectively permeable pores for RNA
and ribosome output; a nucleolus/nucleole (no membrane) composed of
protein and nucleic acids where ribosomal RNA transcription (ribosome
manufacture occurs); also houses chromosomes (DNA+histones), which
are condensed together into chromatin
ribosomes - (no membrane because in both eukarya and prokarya)
converts mRNA sequence into proteins by connecting amino acids to tRNA
which then complements the mRNA, catalysing some components of this
reaction (e.g. polymerisation of amino acids into polypeptide chain);
consists of large and small subunit; biochemically consists of rRNA
(ribosomal RNA) and ~50 structural proteins
endoplasmic reticulum - the endomembrane system modifies protein
chains into their final form, synthesises lipids and packages final proteins
and lipids into vesicles for export or use in the cell; continuous with the
other membrane of the nuclear envelope, forming a web or mesh of
interconnected membranes coming off the nucleus
o Rough ER - closest to the nucleus, contains ribosomes for
translation with mRNA coming out of nucleus, and is used for protein
synthesis and transport (through the channels formed)
o Smooth ER - lacks ribosomes, instead makes lipids (fatty acids,
phospholipids and sterols), and is also involved in cholesterol
metabolism and membrane synthesis; packages lipids into transport
vesicles (small membrane bound sacs) and sent to the Golgi body
Golgi body/apparatus - receives
transport vesicles on one side of the
organelle (the cis face), binding it to the
first layer, then modifying, sorting and
packaging the protein or lipid as they
pass through the various layers, and
pushing them out at the trans face;
molecular tags are added to the fully
modified substances, allowing the
substances to be sorted and
packaged, and then where they need to be shipped, to be then stored or
secreted; pinching off of membrane can produce other membrane-bound
organelles like lysosomes and vacuoles
lysosomes - small organelles that contain enzymes which breakdown
lipids, carbohydrates and proteins into small molecules that can be used
by the cell, and also to remove junk and clutter
cytoskeleton - network of protein filaments and microtubules, controls
cell shape, maintains intracellular organisation, acts as tracks for
transport, and is involved in cell movement; three types of fibres
o Microfilaments - (mostly actin, 7nm thick) maintain cell shape by
compression resistance, involved in membrane pinching in division,
forming pseudopodia, and in muscle contraction
 o Intermediate Filaments - (keratin, rope-like fibres, 8-12nm,
hollow) only in multiceullar organisms for cell structure and shape
(resist tension), anchoring of organelles, and may help hold
neighbouring cells together
o Microtubules - (- and -tubulin forming a heterodimer (two
different proteins making a polymer), 25nm, hollow) have +ve and
-ve end, forming a track for molecular motor proteins to move
organelles and other structures, powerhouse of flagella and cilia,
pull everything in mitosis, generatored from centrosomes/MTOC
(microtubule organising centres)
mitochondria - (1-10m) generate most of the cells ATP supply, also
used in signalling, cell cycle, growth and death; contain folds called cristae
and matrix within
chloroplast - found in plant, algae and some bacteria for photosynthesis,
contain granum (stacks of thylakoid discs), surrounded by the gelatinous
stroma and connected by stroma lamellae
membrane
Endosymbiosis - symbiosis in which one of the organisms lives inside another
(as with mitochondria and chloroplasts from cyanobacteria). Evidence includes:
double membrane (one from original cell, one from new packaging)
contain ribosomes more like prokaryotes
contain circular DNA (plastids), growing and reproducing independent of
the cell through binary fission
size of bacteria is the same as the organelles

Macromolecules
99% of living things are made CHON, with P&S also abundant, which join to form
macromolecules: a large molecule formed by the joining of smaller molecules usually
by a dehydration reaction. Macromolecules (except for some lipids) are polymers of
similar or identical subunits (usually monomers) linked by covalent bonds. Polymer
breakdown is hydrolysis as a water molecule is added to break the covalent bond.
Macromole
Subunit Bond Examples
cule
Storage and Structure

Starch (glucose) - stored by plants as granules (accessed by

Monosaccharid
hydrolysis)
es (glucose,
Carbohydr Glycosidic Glycogen (branched glucose) - stored by animals in liver and
can form
ate Bond muscle cells (cant sustain animal for long period of time)
disaccharides
Cellulose (flipping glucose) - structure, component of plant cell
like maltose)
walls
Chitin (glucose with nitrogen groups) - exoskeletons in arthropods
(insects, spiders, crustaceans)
Hydrophobic (non-polar)
Saturated - no double bonds in fatty acids between carbons

Fatty Acids Unsaturated - 1+ double bonds in hydrocarbon chain of the fatty

(In TAG, three acid, causing kinks
fatty acids Phospholipids are two hydrophobic fatty acid tails connected to
each join to a glycerol, which is connected to a phosphate group which in turn is
glycerol by an connected to a polar group like choline (replacing one of the fatty
Lipid ester bond, Ester Bond acids)
varying in
length, and Energy Storage and Transport - triacylglycerols or TAGs
number and Structure - phospholipids, sterols
positions of Chemical Messengers - steroids (cholesterol), glycolipids
double bonds) Photoreceptors - carotenoids
Coverings - waxes

Amino Acids All amino acids consist of:

(20 different central () carbon atom
ones that form Peptide amino group (NH3+)
Protein
polypeptides Bonds carboxyl group (COO-)
which fold into hydrogen atom (H)
3D structure)
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 a variable side-chain (R) - determines whether they are non-
polar, polar or electrically charged (also hydrophilic)

When polymerised they become a backbone with various side-

chains that determine how it folds and 3D structure (primary,
secondary, tertiary and quaternary levels of folding determine final
shape)
Used as structure (keratin), storage (casein), transport
(haemoglobin), hormones (insulin), movement (actin), enzymes
(sucrase)
Enzymes - catalytic proteins selectively speed up chemical reactions
without being consumed, allowing reactions to be fast enough for a
cell to survive
E (enzyme) + S (substrate) ES E + P
(product)
Catalysis occurs at the active site
Enzymes lower the activation energy (EA) of
a thermodynamically favourable reaction,
but do not affect the equilibrium or free
energy change (G - the difference in the
energy between the reactants and
products) and cannot make a
thermodynamically unfavourable reaction favourable
Nucleic Phosphodies DNA or RNA, store hereditary information, polymers also called
Nucleotides
Acids ter Bonds polynucleotides

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Cell Integrity
The membrane prevents unwanted nutrients and toxins from entering/leaving,
and hence maintains cell integrity. There were two proposed models for the
membrane:
Davson-Danielli Model (1935) - phospholipid bilayer with proteins above
and below
Fluid Mosaic Model (1972 by Singer and Nicholson) - integral membrane
proteins sat inside, peripheral proteins above and below, with a
cytoskeleton supporting it; had sidedness or asymmetrical distribution of
proteins, carbohydrates and lipids (like cholesterol) between each side as
many were formed inside the cell but cannot pass to the outside
o the fluidity refers to the rapid movement of lipids and proteins
laterally - shown by:
the fusing of mouse and human cells, and proteins were
mixed, not one-side human, the other mouse
microscopy with staining
FRAP (fluorescence recovery after photo-bleaching) - altering
DNA to produce proteins that lose colour after laser beam
exposure to one section of the membrane, and over time
colour comes back as this area is filled with non-zapped
proteins
Membrane members:
Lipids - of which 0-25% is cholesterol; lipid rafts are semi-solid molecules
that keeps proteins together or anchors them to the cytoskeleton
Proteins - both peripheral and integral that span the membrane and
shoot out either side but with different domains on each side
Carbohydrates (glycolipids and
glycoproteins) - the addition of the sugar
groups allow cells to be recognised by other
proteins or present different messages through a
variety of combinations

Sidedness is important for cell recognition and adhesion

Membrane Permeability (selective

nature maintains cell integrity):
small molecules can pass through
(O2, CO2, H2O)
hydrophobic molecules will
dissolve in the hydrophobic core
and diffuse across
ionised, polar and large molecules cannot cross without a protein transporter
Animals prefer isotonic environments, die in hypotonicity (lysis).
Plants prefer hypotonic environments, die in hypertonicity (plamolysis).

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Cellular Transport
Passive Transport (no energy required):
Diffusion - down concentration gradient
Facilitated Diffusion - down concentration gradient with assistance of transporter
protein (either for faster transfer or for molecules that could not otherwise cross
o Channels/Conduits - allow direct passage from one side to another
corridor for specific molecules or ions to cross
Example: aquaporins are the protein channel for water (water is
polar and travels quite slowly otherwise)
may be gated (require another molecule to be bound to a specific
site before they function)
o Carriers/Transporters
alternates between two shapes, moving the solute across in the
process in either direction (dependent on concentration gradient)
binding sites for activation show specificity
slower than channels
Active Transport - with a protein AGAINST the
concentration (uses energy from ATP), and hence they are
directional/irreversible (depends on protein;
multidirectional pass different proteins each way).
Concentration gradients are maintained by
active transport against the gradient (in addition to
chemical reactions).
Proton pumps:
electrogenic pumps which ensure H+ is
more concentrated in the extracellular fluid,
creating a stored energy in the form of a concentration gradient which is
used to drive other processes in the plants, fungi and bacteria
requires ATP to function (hence active transport), but can be used to drive
other processes
o Example: indirect active transport of sucrose by having H + move
down its own concentration gradient and bring sucrose with it
through the protein
Membrane potential:
potential difference across a membrane, created by differences in cation
and anion distribution (cytoplasm more negative, -50 to 200mV)
in animals, created by sodium-potassium pump (Na out, K in, both
AGAINST concentration gradient, overall more out than in)
favours passive transport of cations into the cell, anions out of the cell
diffusion is influenced by both concentration gradient and electrochemical
gradient
changes in membrane potential can also regulate voltage gated channels
o tracked by attaching non-functioning fluorescent tags to ions that
change shape and fluoresce when attached

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 Large molecules (polysaccharides, proteins) cross the membrane in bulk through
vesicles by:
Pinocytosis (cellular drinking) - all outer solutes surrounded by
membrane which combines to cell membrane (but doesnt go straight in), then
transfer proteins choose which ones go through (no specificity)
Phagocytosis (cellular eating) - wrapping pseudopodia around solutes,
packaging in vesicle/vacuole, some absorbed, the rest thrown out (specific)
Receptor-Mediated Endocytosis - like pinocytosis, except receptor
proteins on membrane surface recognise and bind to specific molecules in
clustered regions called coated pits, and if all molecules are accepted then
they are all taken in (specific)

Photosynthesis
The physico-chemical process is used by
plants, algae (oxygenic) and photosynthetic
bacteria (anoxygenic; uses bacterial chlorophylls) to
produce organic compounds with light as oxygen (only
0.5% of the 21% is produced by NON-biological
processes, the main sources being cyanobacteria,
plankton and plants), whilst consuming the toxic CO2.
Photosynthesis supplies all food, petrol (and natural gas, coal and ethanol), and
clothing and building materials. In eukaryotes, photosynthesis occurs in chloroplasts
(green + form or entity), which are double membrane-bound flat discs 2-10m in
diameter and 1m thick, containing lots of small discs called thylakoid (thylakos =
sac) which consist of a thylakoid membrane surrounding a thylakoid lumen, and exist
as stacks called grana (Latin for stacks of coins), connected by intergrana or
stroma thylakoids. This is placed in a thick fluid called the stroma (the site of light-
independent reactions). The pigment chlorophyll is used to absorb light on the
thylakoid membrane, and green light is reflected whilst red and blue are mostly
absorbed (by chlorophyll a and b and carotenoids).
Photosynthesis occurs in two stages:
Page 10 Oliver Bogdanovski
 1. Light-Dependent Reactions - light captured, electron and proton
transfer reactions to make energy-carrying molecules, produces ATP and
NADPH
2. Light-Independent Reactions - ATP and NADPH used to convert CO2
into glucose
ATP (adenosine-5-triphosphate) is produced by either redox reactions or
photons. If it is done by photons (sunlight) it is called photophosphorylation
(phosphorylation simply means adding phosphate group). The light energy is
converted into electrical energy and packaged into chemical energy as ATP or NADPH
(nicotinamide adenine dinucleotide phosphate; considered energy couriers - provide
temporary storage of chemical energy). This process is performed by photosystems
(protein complexes that contain chlorophyll) found in thylakoid membranes. The
chlorophyll are bound to proteins which act as antennae that absorb photons and
transfer the excited electron to the reaction centre.
First a photon hits a chlorophyll molecule surrounding the Photosystem II (P680
as it absorbs a wavelength of 680mm - penetrated faster than longer wavelengths,
hence first), and the chlorophyll molecules transmit energy from the excited elections
in the antenna complex to a reaction centre. Each photosystem has one pair of
chlorophyll a molecules, but hundreds of chlorophyll b and carotenoid molecules.
Chlorophyll b and carotenoids absorb photons and pass excited electrons to each
other until it reaches the chlorophyll a, where the electrons can then be transferred
(by an electron transfer chain) to the primary electron acceptor (P.E.A.).
Electrons lost from the P680 are replaced by the splitting of water (2H 2O 4H+
+ O2 + 4e-), where the protons and oxygen are produced in the thylakoid space
(producing a proton gradient across the thylakoid membrane) whilst the electrons
continue in the membrane until they reach plastoquinone (Pq), the first mobile carrier,
where the electron carrier that holds the electron takes it to the cytochrome complex
(consists of several subunits like cytochrome f and cytochrome b6) back into the
thylakoid space. The electrons are then transferred to plastocyanin (Pc), until they
reach Photosytem I (P700; discovered first). This is another large protein-pigment
complex that contains light-absorbing antenna molecules where photons are absorbed
and electrons taken to reaction centres, then on to ferredoxin (Fd) outside the
thylakoid, which transfer the electron to Ferredocin NADP Reductase (FNR) which
catalyses NADP+ + H + 2e- NADPH in the case of non-cyclic
photophosphorylation.
In cyclic photophosphorylation ATP is produced (as this is sometimes needed
to power other activities in the chloroplast), where the electrons are recycled by being
transferred back to the cytochrome b6f complex (via Fd and Pq) to resume the cycle.

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 Light-
independent
reactions occur
in the stroma
(outside the
thylakoids) in
the Calvin
cycle. It
requires:
Ribulose-
1,5-

biphosphate carboxylase oxygen (RuBisCO) - which catalyses carbon fixation to

RuBP, probably most abundant protein on Earth
Ribulose-1,5-biphosphate (RuBP) - 5-carbon sugar chain, CO 2 acceptor in first
major step of carbon fixation
CO2 - used during fixation
ATP and NADPH - used in reduction phase to convert 3-phosphoglycerate to
glyceraldehyde-3-phosphate (three carbon precursor to flucose), and ATP is
used in regeneration phase where it converts this back into RuBP
The first stage is carbon fixation, where RuBisCO attaches CO2 to RuBP (6-
carbons), which breaks into two phosphoglyceric acids (3-PG as they have 3 carbons
each). This is phosphorylated (adds phosphate group) by ATP to form 1, 3-

Page 12 Oliver Bogdanovski

 biphosphoglycerate, then NADPH reduces this in the reduction phase into
glyceraldehyde-3-phosphate (G3P) - the ultimate goal of the Calvin Cycle. This is
composed of the simplest sugar known (D-aldotriose), which can be combined to form
organic molecules like fructose (which can then be rearranged into glucose, or other
molecules like sucrose and starch). In the regeneration phase G3P can be converted
back to RuBP by ATP. In total, one glucose molecule requires 6CO 2, 18ATP, 12NADPH
(1NADPH 3ATP in terms of energy).

An Introduction to Metabolism
Metabolism - the totality of an organisms chemical reactions (both catabolic
and anabolic pathways) to manage material and energy sources. A metabolic pathway
involves a starting molecule/s which undergoes several reactions catalysed by
enzymes to produce intermediates and eventually a desired product. Catabolic
pathways RELEASE energy (produce ATP) by breaking down complex molecules INTO
simpler ones (e.g. cellular respiration - break down of glucose in presence of O 2).
Anabolic pathways CONSUME energy (use ATP) to build complex molecule FROM
simples ones.
All organisms require both an energy and carbon source from the
environment:
Phototrophs Chemotrophs
energy = light energy = chemicals
Photo-autotrophs
Chemo-autotrophs
Autotrophs (photosynthetic bacteria,
chemicals are inorganic
carbon = CO2 plants, some protists like
(some bacteria)
algae)
Heterotroph
s Chemo-heterotrophs
carbon = one chemicals are organic
Photo-heterotrophs
or more (many bacteria and
(some bacteria)
organic protists, animals,
compounds, parasitic plants)
e.g. glucose
ATP is the energy shuttle of a cell,
composed of a ribose (sugar),
adenine (nitrogenous base) and
three phosphate groups. The bonds
between the phosphate groups of the
ATP tail can be broken down by
hydrolysis (addition of water), and the
lone inorganic phosphate becomes Pi,
producing G=-31kJ/mol of energy
and leaving adenosine diphosphate (ADP -
note only two phosphate groups now).
The ATP cycle allows energy from
catabolism (exergonic) to be
transported to areas where energy is
required and consumed
(endergonic). ATP can be
generated in two ways:
Oxidative Phosphorylation - addition of Pi to ADP to produce ATP powered by
redox reactions in the electron transport chain

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 Substrate-level Phosphorylation - an enzyme transfer a phosphate group
from a DIFFERENT substrate (which has a phosphate group) to produce ATP
Catabolic processes in higher animals and other organisms require O 2 (they are
aerobic). For example, respiration: C6H12O6 + 6O2 6CO2 + 6H2O. In many protists and
bacteria catabolic processes dont need O 2. For example fermentation: C 6H12O6
2C2H5OH + 2CO2 OR C6H12O6 C3H5O3- (lactate ion) + 2H+.
Fermentation also occurs in
eukaryotic cells, as glucose undergoes
glycolysis to to form pyruvate, in which
either fermentation can occur and only
2ATPs are produce, or respiration can
continue into the mitochondria and
produce a net energy of 36ATP.

Oxidation is the loss of electrons

(or H atoms as often e- is attached to a
proton), whilst reduction is the gain,
however these two reactions are done simultaneously.
Catabolism is generally oxidation, whilst anabolism is
generally reducation. When a metabolic fuel is
oxidised, electrons are collected by a
coenzyme/cofactor like NAD+
(nicrotinamide adenine dinucleotide - two
nucleotides joined together at their
phosphate groups) which becomes NADH
with the enzyme dehydrogenase.
Metabolism can be regulated by
feedback inhibition, where a product of the
pathway inhibits an enzyme earlier in the pathway, and hence when enough product
is formed the enzyme stops and no more is produced
until there isnt enough product. Enzymes with
allosteric properties (activity that changes
through binding an effector molecule at an allosteric
site - different to the active site) are
commonly involved in control of metabolic
processes. Alternatively, allosteric regulation
could stimulate enzyme activity instead of inhibiting
it. Enzymes will often oscillate between an active
and inactive state, so a stabiliser can help it stay
either active or inactive.
Catabolic pathways are often inhibited
by ATP, whilst activated by ADP or AMP (mono-,
one phosphate group). Anabolic pathways are
inhibited by ADP or AMP, whilst activated by ATP.
Generally all metabolic pathways are activated
by earlier reactants and inhibited by later products.
Cells are compartmenalised, and cellular
structures help bring order to metabolic
pathways. In eukaryotes, some enzymes reside in
specific organelles, like those for glycolysis (glucose

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 breakdownpyruvate) are located in the cytosol whilst those for the TCA cycle are in
the mitochondria.

Extracting Energy from Food

Cellular respiration - the process by which cells
break down organic compounds using various
catabolic pathways for the purpose of generating ATP
Glycolysis consists of 10 enzyme-catalysed
reactions (found in all organisms), where glucose (6C) is
oxidised into 2 pyruvate molecules (3C each). The
pathway has to stages - an energy investment and
energy payoff - overall yielding 2ATP per glucose and
producing the reduce cofactor NADH. The pyruvate
could then be fermented anaerobically (and produce
wastes) or undergo respiration in which it is
converted to acetyl-CoA by pyruvate dehydrogenase
that produces CO2, converts NAD+ to NADH and adds
Coenzyme A in the mitochondria in preparation for
the TCA cycle.
The TCA (or citric acid) cycle occurs inside the
mitochondria and is where the acetyl- group (from
acetyl-CoA) is broken down. The 3C from the
pyruvate are broken down to produce 3 more CO 2
molecules, 4NADH and 1FADH are produced, and one
ATP is formed.
Cellular respiration also involves a controlled
energy release whilst the reaction 2H2 + O2 2H2O
occurs. This is done by the respiration chain, where
reduced cofactors transfer their reducing power (H
atoms and/or electrons) to oxygen through a series of
redox reactions with a G=217kJ/mol. The
components of this electron transport chain are all
proteins (except Coenzyme Q) located in the inner
mitochondrial membrane within or between protein
complexes I (proton comes from NADH), II (proton
comes from NADH), III (proton comes from I or II) and IV
(from III). O2 is the terminal electron acceptor after this protein complex, whilst the
proton is transferred out of the mitochondria and eventually back in by ATP synthase
to produce an ATP from ADP and Pi.
Chemiosmosis (first proposed by Peter Mitchell in 1961) is the theory that the
proton gradient created by the respiratory chain (as it pumps protons out of the
mitochondria) provides a means of free energy (a proton motive force) that can drive
the activity of ATP synthase to generate ATP (oxidative phosphorylation). This can be
shown experimentally as mitochondria at pH 8 that are shifted to pH 4 have a burst of
ATP synthesis without any respiratory chain activity (no O 2 is used, so it is the protons
that matter). If the inner membrane is made permeable to protons, no ATP is
synthesised as no gradient is produced.
Page 15 Oliver Bogdanovski
 ATP synthase includes integral membrane
proteins (located in mitrochondrial and chloroplast
membranes in eukaryotes, or the plasma membrane in
bacteria). ATP synthase has membrane-spanning
domains that form a rotor which is driven by the
movement of protons down the H+ concentration
gradient (think of it as electric charges in a DC motor).
Rotating the motor shaft in head piece causes
conformational changes in the active sites that bind ADP
and Pi, and provides energy for this synthesis.
The mitochondrial membrane is important for ATP
synthesis as it is:
fluid - allows H atoms/electrons/protein
components to move and interact
asymmetric - monodirectional proton pumps
drive ATP synthesis through gradients
impermeable to ions - maintains proton gradient
In total 30-32 ATP equivalents (NADH 2.5ATP, FADH 2 1.5ATP) are produced
from one glucose, which would only produce the initial 2NADH and 2ATP in anaerobic
fermentation.

(becomes part of
6)

Respiration
is controlled
by allosteric
enzymes. For example, phosphofructokinae (PFK) catalyses the third step in
glycolysis, however it is inhibited by citrate (from the citric cycle) and ATP, whilst
being stimulated by AMP.
Amino acids from proteins are broken down to acetyl-CoA or intermediates
within the glycolysis or TCA cycle, whilst carbohydrates and fats are both broken down
aerobically into acetyl-CoA (allows for recycling of some materials, which is what
occurs when eating food). Ultimately it will form CO2 and H2O (the products of
respiration). In cases of low O2 supply, such as intense exercise in skeletal muscle cells
and red blood cells, carbohydrate catabolism involves fermentation, and the glucose
is converted to lactate (lactic acid), which causes cell death if oxygen supply is
interrupted.

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From Gene to Function
The genetic language must be accurately copied and passed on and readily
accessed for the information contained. Proteins had greater complexity and 20
building blocks, whilst DNA had a regular structure and only 4 building blocks so it was
believed proteins would the means of inheritance, however like binary the simpler
language still allowed for complexity. Experimental data in the 1940s-early 50s
suggested that DNA may be genetic material. For example, in 1953 Hershey and
Chase grew two batches of bacteriophage T2 (virus that infects bacteria, one with
radioactive sulfur (present in two amino acids) which labelled proteins, the other with
radioactive phosphorus which labelled DNA. Mixing these with bacteria infected the
bacteria with the genetic material of the virus, and upon centrifuging to separate the
bacteria from the viruses they found it was the DNA inserted into the bacteria.
In 1953 Watson and Crick published the structure of DNA using molecular
models from X-ray diffraction patterns, proving it was a
double helix (they knew it had the nucleotide bases
adenine, thymine, cytosine and guanine
which stood on sugars, each linked by a
phosphate group after an H2O has been
taken out). DNA is deoxyribonucleic acid,
whilst RNA is ribonucleic as it has an extra O.
Combined with a phosphate group and
base, it becomes a nucleotide.
A & G are double-rings (purines), so
an A & G would produce a strand to wide (to
be consistent with X-ray data). T & C are
single-ringed (pyrimadines - smaller size
compensated for by longer name), and would
produce a strand too close for DNA. Hence one
pyramidine had to be paired with one purine. In
addition, A & T have two hydrogen bonds,
whilst C & G have three, so they can only match like
AT and CG. It forms an alpha helix (follows
right-hand grip rule), and being a helix (not
spiral) the strands are not evenly distributed but
close then far then close then far, which
produces almost a spiral shape with the
resulting ribbon (but as the two strands are
separate it is not a spiral). Each strand is
considered antiparallel (running in opposite
directions - the phosphates charges face
opposite directions and the carbons sit on the
opposite sides). The 5 phosphate end (the top)
finishes with a phosphate, whilst the 3 hydroxyl end
finishes with the OH from the sugar.
Humans have 3.2109 base pairs (2m long, 0.01mm wide), and this is
complexed with histones (proteins) to form nucleosomes, solenoids and eventually
chromatin. Histones maintain structure of the chromosome and help regulate gene
expression/activity. It is folded, coiled and condensed in preparation for cell division.
Mitochondria also have their own circular DNA within their matrix (the part
inside the folds (cristae), not the tissue itself), which codes for proteins essential for
normal mitochondrial function.

DNA Replication
Page 17 Oliver Bogdanovski
 First, at the origin of replication helicase unwinds the strands and forms a
small bubble. Multiple origins are needed to ensure replication occurs as quickly as
possible (in human cells there are 6 billion base pairs all copied within a few hours).
DNA polymerase then catalyses the addition of new nucleotides in opposite directions
on each strand (as the two strands are anti-parallel). Incoming nucleotides have 3
phosphate groups, and 2Ps are released to provide energy for the reaction (as those
are high-energy bonds). DNA polymerase must have a 3 OH group to add on to, and
hence will move along the template strand from 35, producing a new growing
strand and elongating it in the 53 direction (as the DNA polymerase can only exist
at the 3 end). DNA synthesis cannot initiate unless a primer (short piece of RNA that
contains a 3 OH) to continue building off.
After a primer has been made in leading strand synthesis DNA polymerase III
(which consists of a sliding clamp ring and boxing glove) starts synthesising the
leading strand right after the helicase continues to unwind (otherwise it will join back)
and forming a replication fork. However in the lagging strand, as it moves in the
opposite direction to the helicase (anti-parallel), it must do so in small fragments,
called Okazaki fragments. First, primase joins RNA nucleotides into a primer on the
template, then DNA polymerase III adds DNA nucleotides to the primer, forming
Okazaki fragment 1, then a new primer is added slightly before and the polymerase
attaches to this once finishing its fragment, forming a second fragment until it reaches
the original primer and detaches. DNA polymerase I replaces the RNA with DNA (by
adding to the 3 end of fragment 2), then DNA ligase forms a bond between fragment
2 and fragment 1.
Replicating the ends
of chromosomes is
difficult as there are no 3
OH ends to build off, and
hence with every
replication the 5 end
becomes shorter on the
lagging strand (but not
on the leading as it runs
until the end as thats
a 3). To counter this,
telomeres are
sequences (10, 000 base
pairs at each end)
produced by
telomerase (which also
has RNA within the
enzyme, not just amino acids, to produce remaining base pair sequence) extending
the ends of the sequences. Telomerase in inactivated in post-embryonic cells (and
many cancers involve reactivating telomerase).
To treat disease, nucleotide analogues can be used. For example, thymidine (the
nucleotide with thymine) can be replaced with AZT, which swaps the OH group on the
sugar for a triangle of nitrogens, and hence no OH group is present for DNA
polymerase to continue constructing off and blocking DNA replication. This is how
AIDS (HIV) is treated.

Gene Expression: Transcription

To express a gene, it undergoes transcription into mRNA (which is
complementary through base pairing - hydrogen bonding; thymine is replaced with
uracil), and then each codon (triplet of base pairs) is translated into an amino acid.
Page 18 Oliver Bogdanovski
 The reasoning for triplets is that arranging our four base pairs gives 4 3=64
possibilities, which is enough for 20 amino acids plus stop (42=16 isnt enough),
however much of this code is redundant as it doubles up (which provides some
protection). To crack this code they synthesised strands of just specific codons (e.g.
AAAAAA) then observed the protein in vitro (outside a cell). The code was also found
to be genetic, as the gene coding from the firefly luciferase protein (which makes it
glow) was inserted into a mouse embryo, and the mouse was able to produce a
functional fluorescent protein.
Transcription has three stages:
1. Initiation - RNA polymerase binds to the promoter region upstream of the
gene, DNA strands unwind, RNA synthesis is initiated by the RNA
polymerase
2. Elongation - the polymerase complementary copy downstream, adding
to the 3 in the mRNA (moving away from 5), unwinding the DNA and
elongating the mRNA transcript; the mRNA does not stay bound to the
DNA, but sits parallel to it, and once the RNA polymerase has been
through the DNA reforms a double helix
3. Termination - upon reaching a termination point the RNA polymerase
transcribes a terminator sequence which signals the end of the gene, and
the RNA polymerase and transcript are released
This process is vital, shown by the toxin -amanitin produced by the death cap
mushroom. The toxin binds to RNA polymerase, preventing transcription and inhibiting
protein synthesis, often resulting in kidney and liver failure.
Prokaryotic cells have no nucleus, so the mRNA is immediately translated into a
protein. The mRNA is formed as pre-mRNA in the nucleus, and this is extensively
modified before being exported to the cytoplasm for protein synthesis by adding a 5
cap and poly(A) tail (to the 3 end) which package it for protection against
exonucleases used to kill virus RNA (signals it as eukaryotic) and labels it for correct
cellular course. Intervening sequences (introns) are also spliced out leaving just the
expressed sequences (exons). Exons can be spliced in different ways to produce
different proteins from the same gene sequence. For example, the muscle protein -
tropomyosin has 12 exons which can be used to produce striated muscle, smooth
muscle, fibroblasts (for connective tissue) or brain cells.
Initiation in eukaryotes begins with transcription factors (proteins) that mediate
the initiation of transcription by blocking the promoter sequence.

Gene Expression: Translation

The ribosome is the protein synthesis factory, and
where the tRNA (carrying amino acids) base pairs
(hydrogen bonds) with the mRNA, ensuring amino acids
are placed in the correct mRNA (and hence DNA)
sequence. tRNA (transfer) is single stranded
(however intramolecular H-bonds make it fold to look
sort of double-stranded). The amino acid attaches to the
3 end of the tRNA, and partway between the 3 and 5
is the anticodon (at the bend) that H-bonds to the codon in the mRNA. Each amino
acid has a different tRNA, joined by aminoacyl-tRNA synthetase (this is done by the
enzyme first binding ATP and the amino acid by one P and releasing the other two (but
adenosine still attached, so AMP), and then the tRNA replaces the AMP).
The ribosome has two subunits (small and large), and three sites:
A site - aminoacyl-tRNA binding site

Page 19 Oliver Bogdanovski

 P site - peptidyl-tRNA binding site (contains many amino acids, hence
peptide chain)
E site - exist site
The stages of translation are:
1. Initiation - the small subunit binds the mRNA, and the initiator
tRNA (complement to AUG with methionine) binds to it, then the larger subunit
binds to the initiator tRNA in the P site (uses energy from GTPGDP, not A)
2. Elongation
a. Codon Recognition - next tRNA binds to A site codon (requires
2GTP2GDP)
b. Peptide Bond Formation - peptide bond forms between amino acids
(catalysed by enzymes in the ribosome itself; the peptide chain is joining
onto the new amino acid)
c. Translocation - then the mRNA moves along, putting the tRNAs into the
E and P site (requiring another GTP) and the tRNA is ejected and recycled
at the E site, and then the cycle begins anew
3. Termination - a stop codon is recognised in the mRNA by a release
factor (protein), allowing the last tRNA and new protein to leave, the
ribosome units to separate (for recycling) and mRNA released (to be
broken down or reused)
Many antibiotics target bacterial transcription and translation (which is
sufficiently distinct in prokaryotes from eukaryotes that it is possible to specifically
inhibit them). For example, RNA polymerase can be blocked with rifampin, and protein
synthesis with 30S inhibitors like tetracycline and streptomycin, or 50S inhibitors like
erythromycin and chloramphenicol.
In prokaryotes control of gene expression occurs at the level of transcription
(whether a gene is transcribed), as once the mRNA is formed it is immediately
transcribed (which allows them to respond immediately to their environment). In
eukaryotes, the most important stage of gene expression occurs during transcription
(initiating), however also occurs at processing, transport and degradation of mRNA. At
the protein level, proteins can be modified, transported and degraded.
By

activating eye genes on a Drosophila larvae leg, the adult grew an

eye on its leg. However as no neurons connected it to the brain it
was not functional.
The size of a genome varies amongst organisms, a more
base pairs generally but doesnt always mean more genes.
Organism complexity doesnt necessarily determine how many
genes you have (as worms, water fleas and plants have more
genes than a human, although most have fewer base pairs).
Humans have 20, 000 genes, with each gene having an
average of 27, 000 base pairs (ranges from 1000 to 2.4 million).

Page 20 Oliver Bogdanovski

 99.9% of the genome is the same in all people. Genes are not evenly distributed
amongst chromosomes (chromosome 1 has 2968, Y has 231). The function of many
genes is still unknown.

Cell Division and Reproduction

In prokaryotes, cell reproduction occurs by binary fission, in which DNA
replication commences at the origin of replication until each chromosome has been
completely replicated, and each origin becomes separately attached to the plasma
membrane. Once replication is complete, the plasma membrane grows inwards to
produce two daughter cells and a cell wall is deposited.
In humans there are 1 billion cells/gram of tissue, all derived from a fertilised
egg, so this cycle must be regulated precisely. Most cells replicate between 10-30
hours (whilst E. coli is 20mins). Cell replication has two major phases (basically 2n4n
(two of each individual single chromosome)2n):
Interphase - growth and replication of cellular components, gathers
materials and ensures enough for replication
o G1 - growth
o S - DNA synthesised (replicated/duplicated)
o G2 - cell components replicated (including centrosomes, which have
perpendicular centrioles - smaller component)
Mitotic Phase - nucleus divides and chromosomes are distributed to
daughter cells (mitsosis) and the cytoplasm divides into two daughter
cells (cytokinesis)
o Mitosis
Prophase - chromosomes condense, centrosomes separate
and form mitotic spindle
Prometaphase - nuclear membrane breaks down, further
condensing, centrosomes move to spindle poles where they
anchor, microtubules connect to centromeres (centre of
duplicated DNA) by binding to kinetochores (also made of
microtubule)
Metaphase - each chromosome attaches to a spindle pole
(equal pressure each way - if not properly attached one cell
will have an extra copy, the other missing one; NOT trisomy,
as this isnt meiosis)
Anaphase - protease chews through protein holding sister
chromatids together and they are pulled apart causing cell
elongation
Telophase - nuclear membrane reforms and chromosomes
decondense
o Cytokinesis - cleavage furrow (contracting ring of microfilaments in
animals, cell plate made of vesicles in plants which becomes part of
cell wall) separates the two cells

To ensure DNA is being replicated correctly, there are multiple checkpoints:

Page 21 Oliver Bogdanovski
 G1 Checkpoint - sufficient nutrients,
nucleotides, starts choosing to get ready for
mitosis
G2 Checkpoint - checks all DNA for mitosis has
been replicated properly
M (metaphase) Checkpoint - ensures all
chromosomes are connected to spindles before anaphase commences
Apoptosis is programmed cell death which removes unwanted cells (webbing
between digits during embryo development, shedding of leaves provides protection
against cold and recycles nutrients, removal of damaged cells, disintegration of
tadpoles tail for recycling).
Human somatic cells have 46 chromosomes (2n - diploid) whilst gametes (sperm
and ova) have 23 (n - haploid) so when they fuse during fertilisation they make 2n.
The process of producing a haploid cell is meiosis, which has two stages, the second
of which is near identical to mitosis (2n4n (a tetrad of each chromosome
pair)2n2n):
Interphase - as with mitosis, however instead of one dyad (duplicating
each chromosome) a tetrad (two dyads) is formed
Meiosis I
o Prophase I - homologous chromosomes (as dyads) come together
and synapse (closely apply themselves to each other); the
chromosomes shorten and thicken, and within the tetrad a
ladderlike protein structure (synaptonemal complex) aligns the pair
and they cross over to form chiasma (swaps genes, increases
genetic diversity); the centrioles move to opposite poles of the
nucleus and the nuclear membrane breaks down
o Metaphase I - chromosomes have untwined (are clearly two dyads)
and line up in two rows, with homologous pairs next to each other
o Anaphase I - homologous chromosomes are pulled to opposite
sides by kinetochore microtubulues
o Telophase I - chromosome homologues are at opposite poles, and
begin to reform a nuclear membrane
o Cytokinesis (not exactly part of meiosis) - produces two DIPLOID
cells (basically back to square one, but with crossing over)
Meiosis II
o Interkinesis (Interphase II) - no DNA replication (however still
centrosome replication)
o Prophase II - as with mitosis (includes prometaphase)
o Metaphase II - as with mitosis (except each chromosome is made
of one of each homologous pair so splitting changes genetic
diversity, rather than a duplication of each single chromosome and
splitting doesnt change genetic diversity as already the same)
o Anaphase II - as with mitosis
o Telophase II and Cytokinesis - as with mitosis

Page 22 Oliver Bogdanovski

 PCR and
Individual
Variation
In 2003,
human
genome
project
completed
(based on the
DNA of several
people
including
James Watson
and Venter), and multiple human genomes have now been fully sequenced. A single
gene is one-millionth of the DNA, and a virus may inject its own DNA (although in only
a few out of millions of cells), so the challenge is to detect the gene or viral DNA in the
presence of billions of bases, and this is completed using PCR (polymerase chain
reactions). PCR requires:
DNA polymerase
single-stranded DNA template - pattern to synthesise from
primers - short pieces of DNA to add on to (one for upstream, different one
for downstream)
free nucleotides - to add to the growing chain
(dNTPs=deoxyribunucleotide triphosphate)
heat - separates DNA strands (although can denature enzyme)

Note that
arrows without lines within them only cover the exactly
length of the gene. Each cycle (production of new
copies) resulting in a doubling of molecules (2, 4, 8, 16
20 o
2 ). As DNA polymerase is denatured at 90 C, the DNA
polymerase from the thermophile Thermus aquaticus
(Taq) is used, which is stable at 98 oC, but optimal at
70oC, allowing extending to be done at a higher temperature than annealing (now
72oC - diagram shows for normal DNA polymerase).
We now have automated PCR machines that can do 96 samples at once using
solid states to rapidly increase and decrease temperature (as common in a molecular
lab as a photocopier is in an office). PCR is incredibly sensitive and specific, targeting
only certain genes, and the electrophoresis can be applied (as DNA is slightly negative
moves to positive electrode, smaller molecules can move through gel mesh more
easily and hence move further, only those replicated will be potent enough to see
after staining with fluorescent that glows in UV when bound to DNA).
Page 23 Oliver Bogdanovski
 Simple sequence repeats (SSR) are short base pair sequences that repeat many
times, with a different number for different people. With around 120, 000 SSRs, and
each being unique, it is easy to identify a person by their DNA. PCR is used to amplify
each specific SSR being analysed using primers designed for those SSRs and then
these bands are compared (only identical twins should have identical patterns). Using
this, we can identify people after disasters (as in 9/11, comparing to kin), paternity
testing (particularly with celebrity heirs), deduce crime suspects (13 used by FBI), or
prove historical truths (Anastasia and the Romanovs). However, this evidence can only
be used for EXCLUSION, as you can prove that the SSRs dont line up. If they do line
up, inclusion cannot be proved as this may be by happenstance. Mitchondria also
have their own DNA which comes entirely from the mother, which was used in cases
like identifying if Anastasia was still alive by comparing to another great-grandchild of
Queen Victoria. Hair cannot be used (as it is just protein, no DNA), however hair
follicles can be.

Mutation
A mutation is a change in the nucleotide sequence of an organisms DNA,
ultimately creating genetic diversity. They can also occur in virus DNA or RNA.
Mutations lead to diversity which is critical to the survival of life. For example, the
British Peppered Moth had a mutation resulting in some light, some dark, which were
better at camouflage in either lichen-covered trees or soot-covered industrial areas
during the Industrial Revolution of the mid-19th C when pollution was being produced.
They will only be inherited in offspring if they occur in gametes.
Mutations can occur as:
point mutations (changes single base)
insertions
deletions
duplications of sequences
chromosomal rearrangements (like fusion, fission, inversion and
translocation)
Mutations can be caused by:
errors in DNA replication (DNA polymerase makes 1 error in 10 5 bases,
leading to incorrect base-pairing, however DNA repair enzymes reduce
this to 1 in 1010)

mutagens
o chemicals (nicotine, asbestos, free radicals, oxidising agents,
nucleotide analogues) which damage DNA
o radiation (natural radiation like uranium, nuclear waste/bombs,
medical X-rays, UV - 20, 000 pyrimidine dimers (e.g. T-T)/hour/cell
are caused at 12pm in Sydneys Summer) which damages DNA
transposable DNA (jumping genes)
Damaged DNA (like the thymine dimers caused by UV -adjacent thymines that
bend towards each other through H-bonds - which causes DNA to buckle due to their
pull towards each other and hence interfere with replication) can be repaired to
ensure transcription is not problematic and gene expression occurs correctly. Repair is
done using a nuclease enzyme that cuts the damaged DNA at two point around the
area of damage, and then this is removed. DNA polymerase then fills in the remaining
nucleotides (from the OH of the previous one), and DNA ligase seals this to the
following strand.
Xeroderma pigmentosum (CP) is an inherited defect in a DNA damage repair
enzyme, resulting in individuals that are hypersensitive to sunlight (cant correct
Page 24 Oliver Bogdanovski
 thymine dimers), which can result in silencing tumour suppression genes and lead to
skin cancer.
Most DNA changes are outside of genes, which often doesnt have any effect on
the final result, however there are many regulatory genes outside coding regions and
hence they can still have large effects on gene expression. These changes can have
three outcomes within exons:
No effect - results in different codon that results in same amino acid
Missense - changes amino acid
Nonsense - changes amino acid to stop
Frameshift - insertion/deletion of amino acids not a multiple of three will change
all amino acids downstream (may introduce missense or nonsense); if it is a multiple
of three, it is simply the gain or loss of amino acids. This could result in changing the
tertiary structure of the protein depending on the side chain properties of the amino
acid (charge, shape) and how different this is to what it was before; otherwise there
may be no change. Those that do change may lose some or all functionality, or could
gain a new activity. If the amino acid is where the substrate or cofactor binds it will
likely have a greater effect than if elsewhere on the protein.
Single base changes are the most common variants (~85%) un the human
genome, and two unrelated individuals have ~1 in 1000 base pairs that are difference
(for a total of 3.2 million differences). There are over 10, 000 gene defects in humans,
most of which are rare but have multiple variants. For example, Phenylketonuria (PKU)
results in a defective phenylalanine hydroxylase, making a person unable to convert
phenylalanine into tyrosine, which can result in death by 30-40 years of age. To avoid
this, avoid foods with phenylalanine in them (people are screened at birth to check for
this). Cancer is also the result of genetic mutations, from either overstimulation or a
lack of inhibition of the cell cycle due to faulty proteins. The classic Irish/Scottish fair
skin and hair (blonde or red) results from a mutation in the Mcr1 gene, which results in
sunburning instead of tanning and increasing susceptibility to skin cancer. The most
common genetic disorders are haemochromatosis (too much iron absorption, 1 in
200), cystic fibrosis (Cl+ imbalance, 1 in 400), thalassemia (reduced production of
haemoglobin, 1 in 25 in some areas) and sickle cell anaemia (haemoglobin variant
with one amino acid different (GAAGUA, GluVal), allows haemoglobin to form fibres
and changes shape; blocks blood flow but also protects against malaria - regions of
high malaria are also regions of high sickle-cell anaemia due to natural selection).
DNA viruses can correct mistakes that occur during their own replication, whilst
some RNA viruses cannot do so and make DNA copies of their genome using an error-
prone polymerase which generates mutants easily. HIV is one such virus, and as such
can develop resistance to drugs rapidly.
Whether good or bad, mutations provide genetic variation for natural selection
through evolutionary fitness (the ability of an organism to survive to reproduction).

Mendels Laws of Heredity

Genetics - study of heredity (inheritance); how biological information (DNA base
sequence) is passed onto offspring. A genome is the complete genetic composition of
an organism, cell or just organelle. In eukaryotes, genomes are comprised of linear
chromosomes, usually with multiple chromosomes per genome. In prokaryotes, their
genome consists of circular chromosomes, and often plasmids (circular DNA molecules
that self-replicated and carry genes).
Locus (loci) - the position on a chromosome a gene/sequence is located
Allele - form/variant of a gene at a given locus
Genotype - the alleles an individual has
Phenotype - the physical traits of an organism

Page 25 Oliver Bogdanovski

 We use superscripts of + and - to show if a particular protein is produced by a
gene (e.g. in bacteria, leu + can synthesis leucine, but leu - cannot and required leucine
in the medium to grow). Variation in a gene may also not have an effect, for example
single nucleotide polymorphism (SNP) is a region of DNA in the introns.
In asexual reproduction, offspring are identical to parks, mostly in prokaryotes
(binary fission), but also some eukaryotes like some plants, aphids (plant lice) and
hydra (simple freshwater animals). In sexual reproduction, offspring are a combination
of parents. Humans have 22 pairs of autosomes and one pair of sex chromosomes,
which halve through meiosis (which introduces variation by independent assortment
of chromosomes and crossing over/recombination) and combine into a zygote in
fertilisation. In diploids we also have:
Homozygote - genotype with two like alleles at a locus
Heterozygote - genotype with two different alleles at a locus
Dominant allele - the allele that determines the phenotype (as opposed to the
recessive allele)
In 1865, Mendel made inferences on gene activity before we knew what genes
were. His theory of dominance was superior to blended inheritance as that would only
lead to identical populations. In his experiments he measured a ratio of 3.15:1
(approximately 3:1), and explained in terms of factors. A test/back cross can be used
to determine which allele is dominant and if heterozygous or homozygous organisms.
Mendels First Law: diploid individuals carry two copies (alleles) of a gene,
which segregate in the formation of gametes, and individuals inherit one copy from
each parent (explains 3:1 ratio)
Mendels Second Law: for two genes on separate chromosomes, the pairs of
alleles assort independently into gametes (explained 9:3:3:1 in dihybrid crosses)

Mechanisms of Inheritance
Huntingtons disease (neural degeneration) is an example of an autosomal
dominant (50% of inheritance if one parent has it, affects both sons and daughters),
whilst an X-linked recessive would be haemophilia (which can only occur in X aXa (rare)
or XaY, but never anyone with XA). Mitochondria are maternally inherited organelles
carrying their own genes, and an example of a disease is Kearns-Sayre syndrome,
which causes a short stature and retinal degeneration.
Occasionally homologous chromosomes dont separate during meiosis (non-
disjunction), resulting in n-1 or n+1 haploids and aneuploidy in the diploids (2n-1 or
2n+1 chromosomes). For example, Down syndrome (trisomy-21), Klinefelter syndrome
(XXY generally fairly normal, the
second X being turned off as if they
were female producing a male), and
Turner syndrome (monosomy X
severe in humans, not so much in
mice).
Mendels second law of
independent assortment was
formulated without the
knowledge that genes occur on
chromosomes, so if two genes are
near each other on the same
chromosome, the law breaks down
(evidenced by a dihybrid
testcross of drosophila producing a
phenotypic ratio of 5:5:1:1
instead of 1:1:1:1).
Page 26 Oliver Bogdanovski
 Recombination is just the rearrangement of genetic material, particularly by
crossing over or artificial joining of DNA segments.
This ratio occurs because the loci/genes are linked on the same chromosome
and the closer the loci, the lower the chance of recombination. We can reverse this
(the fewer recombinants in a testcross, the closer the genes), with the percentage of
offspring being recombinants being the relative distance (in the above example 17%).
The maximum recombination is 50% (after which point it is more likely the genes are
on separate chromosomes and the complementary percentage is the percentage of
recombination). So a 0% chance of recombination means recombinants are
impossible, whilst 25% recombination would be 12.5% of each type of recombinant
(as there are two when looking at two genes), and 50% would be 25% (at which point
it is as likely as independence). This principle is used to map genes that cause disease
in many species.
Incomplete dominance is when two alleles both contribute to the phenotype,
like codominance in Snapdragon (CR + CW = pink), and often occurs in multiple
alleles like blood groups (where IA and IB are codominant over io). However this is still
not blended inheritance as they dont all come out the same. In pleiotropy, one gene
affects more than one trait (for example a gene may encode a protein that forms part
of more than one protein complex, or if homozygous for the recessive sickle-cell allele
then during low oxygen content red blood cells crystallise and become sickle-shaped,
causing the phenotypes anaemia, brain damage and spleen damage, all from the one
gene). Epistasis is the interaction of loci or dependence of one gene upon another
(for example, enzyme pathways that require one to happen before the other which
can affect mouse colour (cc stay white, cannot become brown, those with C become
brown, and if bb stay brown but if they have a B then go black). Environment can
also influence phenotype, like hydrangeas that change colour depending on the
acidity of the soil (this is the reason monozygotic twins are not entirely identical
physically). Polygenic traits are those influence by many genes, each having a
smaller effect on the phenotype and producing a continuous scale, like height, weight,
skin colour and learning ability. They are called quantitative traits as they are
measured on a scale rather than being binary (yes or no). Some traits are called
complex/multifactorial as they depend on many factors (like environment,
epistasis, polygenesis, etc.) and are difficult to map (like diabetes, heart disease,
alcoholism).

Genes in Populations
Genetic variation comes from mutations, sexual reproduction (independent
assortment and random pairing) and recombination/crossing over. The gene pool is
the collection of genes amongst an entire population. Variation at a locus means there
are at least two alleles, which may exist at different allele frequencies (a proportion
that can be studied over space (mapping sickle-cell anaemia) and time).
The Hardy-Weinberg Law/Principle states that assuming you have an infinite
population size, no mutation and no migration, no natural selection and random
mating, alleles have an equal chance of survival, and hence will maintain their
frequency throughout generations, unless an assumption is not met.
In small populations, chance events lead to fluctuations in allele frequencies,
with the smaller the population the larger deviation from the law. This is called
genetic drift (the changes in allele frequencies due to chance events in small
populations which can lead to the fixation (the only gene left) of a particular gene). A
bottlenecking event (drastically reduces size of surviving population limits the gene
pool, and hence makes them susceptible to further environmental changes). The
founder effect is when there is a high frequency of an allele in a small population
that continues that species elsewhere (essentially bottlenecking), such as Clinodactyly
Page 27 Oliver Bogdanovski
on the island of Tristan da Cunha, where a small number of British troops who
happened to have curved little fingers led to a high frequency in the population.
In natural selection, some genotypes will have a higher probability of surviving
due to their higher fitness, and can lead to fixation in the population for fitter alleles,
called adaptation. However there is not always biological perfection, as in the case of
the peacock whose long a brightly coloured tailed makes it slower and easier to spot
(whilst also being good at scaring predators), however its primary advantage is that it
makes it more attractive to mates, and this sexual selection has not necessarily lead
to a better fitness. Similarly, natural selection ahs lead to increased levels of sickle-
cell anaemia in some African countries as it is resistant to malaria, however also has
negative effects upon health. Adaptive evolution is also limited by historical
constraints, like the epiglottis which chooses lungs or stomach but can result in
choking, or standing up in humans which can cause back problems. Microbes also
evolve to escape the immune system (those that arent recognise survive) or
antibiotics (by developing resistance).

Page 28 Oliver Bogdanovski