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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

Bacteria/Archaea Eukarya Viruses


- 50- 100nm
no-membrane around organelles membrane-enclosed organelles
(only seen
no nucleus nucleus (usually largest organelle)
with
simple, small (1m; 0.5-5m) complex, larger (10-100m)
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

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

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 bonds Cell membrane contains ether
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 some Archaea (and Eukarya) are not
antibiotics sensitive to 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: a large molecule formed by joining smaller molecules by dehydration reaction


99% of living things are made CHON, with P&S also abundant, which join to form macromolecules.
They (except for some lipids) are polymers of similar or identical subunits (monomers) linked by
covalent bonds.
Polymer breakdown is hydrolysis as a water molecule is added to break the covalent bond.
Macromolecu
Subunit Bond Examples
le
Storage and Structure

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


(glucose, can form Glycosidic Glycogen (branched glucose) - stored by animals in liver and muscle cells (cant
Carbohydrate
disaccharides like Bond sustain animal for long period of time)
maltose) 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


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

All amino acids consist of:


Amino Acids central () carbon atom
(20 different ones amino group (NH3+)
that form carboxyl group (COO-)
Protein Peptide Bonds
polypeptides hydrogen atom (H)
which fold into 3D a variable side-chain (R) - determines whether they are non-polar, polar
structure) 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
Phosphodieste
Nucleic Acids Nucleotides DNA or RNA, store hereditary information, polymers also called polynucleotides
r Bonds
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 (O 2,
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 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)

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:
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.
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-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
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 O2). 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)
Heterotrophs Photo-heterotrophs Chemo-heterotrophs
carbon = one or (some bacteria) chemicals are organic
more organic (many bacteria and protists,
compounds, e.g. animals, parasitic plants)
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
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 O2. For example fermentation: C 6H12O6 2C2H5OH + 2CO2 OR C 6H12O6 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 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 CO 2, 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 CO2 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). O 2 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 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 P i, 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 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 H 2O
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
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. 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 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
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). 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:


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
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, 162 20). As DNA polymerase
is denatured at 90oC, the DNA polymerase from the thermophile Thermus aquaticus (Taq) is used,
which is stable at 98oC, 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 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-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 10 5 bases, leading to
incorrect base-pairing, however DNA repair enzymes reduce this to 1 in 10 10)

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 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
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 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 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).
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 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).