BABS1201 Study Notes

Life
Universe = 13.8bya
Solar System = 4.6bya
Life = 3.8bya
1.8million species identified, thousands more each year, with 10100 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 (26) or polysaccharides
o Proteins
Dependent on amino acid sequence, linked by
peptide bonds
4 different levels of organisation (shapedependent)
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, 50100 protist kingdoms
Bacteria (19 subdivisions)
Archaea (16 subdivisions) - many are extremophiles
(halophiles,
thermophiles,
methanogens
swamps/marshes, anaerobic and produce methane)

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Prokaryotes = bacteria + archaea; thrive almost anywhere,

more in handful of soil than the number of people who have ever
lived
Bacteria/Archaea
Eukarya
no-membrane around organelles
membrane-enclosed organelles
nucleus (usually largest
no nucleus
organelle)
simple, small (1m; 0.5-5m)
complex, larger (10-100m)
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

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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
Cell membrane contains ester
bonds
Cell wall made of peptidoglycan
One RNA polymerase
Bacterial ribosomes sensitive to
some antibiotics
Ubiquitous

Archaea
Cell membrane contains ether
linkages
Cell wall lacks peptidoglycan
Three RNS polymerases (like
eukaryotes - genes and enzymes
are more like this)
Archaea (and Eukarya) are not

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:

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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

Oliver Bogdanovski

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

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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.

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Macromole
cule

Subunit

Bond

Examples
Storage and Structure

Carbohydr
ate

Monosaccharid
es (glucose,
can form
disaccharides
like maltose)

Lipid

Fatty Acids
(In TAG, three
fatty acids
each join to a
glycerol by an
ester bond,
varying in
length, and
number and
positions of
double bonds)

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Glycosidic
Bond

Ester Bond

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

hydrolysis)
Glycogen (branched glucose) - stored by animals in liver and
muscle cells (cant sustain animal for long period of time)
Cellulose (flipping glucose) - structure, component of plant cell
walls
Chitin (glucose with nitrogen groups) - exoskeletons in arthropods
(insects, spiders, crustaceans)
Hydrophobic (non-polar)
Saturated - no double bonds in fatty acids between carbons
Unsaturated - 1+ double bonds in hydrocarbon chain of the fatty
acid, causing kinks
Phospholipids are two hydrophobic fatty acid tails connected to
glycerol, which is connected to a phosphate group which in turn is
connected to a polar group like choline (replacing one of the fatty
acids)
Energy Storage and Transport - triacylglycerols or TAGs
Structure - phospholipids, sterols
Chemical Messengers - steroids (cholesterol), glycolipids
Photoreceptors - carotenoids
Coverings - waxes

Oliver

All amino acids consist of:

central () carbon atom
amino group (NH3+)
carboxyl group (COO-)
hydrogen atom (H)
a variable side-chain (R) - determines whether they are nonpolar, polar or electrically charged (also hydrophilic)

Protein

Amino Acids
(20 different
ones that form
polypeptides
which fold into
3D structure)

Peptide
Bonds

Nucleic

Nucleotides

Phosphodies

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When polymerised they become a backbone with various sidechains 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
DNA or RNA, store hereditary information, polymers also called
Oliver

Acids

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Bogdanovski

ter Bonds

polynucleotides

Oliver

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 photobleaching) - 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

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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).
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

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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

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)

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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 NONbiological 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:
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

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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 (2H2O 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 proteinpigment 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.

Light-independent reactions occur in the stroma (outside the

thylakoids) in the Calvin cycle. It requires:

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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 3phosphoglycerate 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-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 6CO2, 18ATP, 12NADPH (1NADPH 3ATP in terms of

energy).
An Introduction to Metabolism

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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
Substrate-level Phosphorylation - an enzyme transfer a
phosphate group from a DIFFERENT substrate (which has a
phosphate group) to produce ATP

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Catabolic processes in higher animals and other organisms

require O2 (they are aerobic). For example, respiration: C 6H12O6 +
6O2 6CO2 + 6H2O. In many protists and bacteria catabolic
processes dont need O2. For example fermentation: C6H12O6
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

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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
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

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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 O2 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.
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)

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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 CO 2 and H2O (the
products of respiration). In cases of low O 2 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.

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

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Oliver Bogdanovski

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
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 antiparallel). Incoming nucleotides have 3 phosphate groups, and 2Ps
are released to provide energy for the reaction (as those are highenergy 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

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Oliver Bogdanovski

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. The reasoning for
triplets is that arranging our four base pairs gives 43=64
possibilities, which is enough for 20 amino acids plus stop (4 2=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

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Oliver Bogdanovski

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 Hbonds 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
P site - peptidyl-tRNA binding site (contains many
amino acids, hence peptide chain)
E site - exist site
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Oliver Bogdanovski

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.

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Oliver Bogdanovski

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). 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

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Oliver Bogdanovski

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:
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
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Oliver Bogdanovski

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
PCR and Individual Variation
In 2003, human genome project completed (based on the DNA
of several people including James Watson and Venter), and multiple
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Oliver Bogdanovski

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,
16220). As DNA polymerase is denatured at 90 oC,
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).
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
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Oliver Bogdanovski

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 greatgrandchild 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-19 th 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 105 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

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Oliver Bogdanovski

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 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
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Oliver Bogdanovski

(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
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.

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Oliver Bogdanovski

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 XaXa (rare) or XaY, but never
anyone with XA). Mitochondria are maternally inherited organelles
carrying their own genes, and an example of a disease is KearnsSayre 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).
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

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Oliver Bogdanovski

(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 sickleshaped, 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

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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 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).

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Oliver Bogdanovski