BABS1201 Study Notes
BABS1201 Study NotesLife
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
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
Proteins
Dependent on amino acid sequence, linked by peptide bonds
4 different levels of organisation (shape-dependent)
Lipids
fats, oils, waxes, cholesterol, fat-soluble vitamins (A, D, E,
K), monoglycerides, diglycerides, phospholipids
energy storage, structural component of cell membrane
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/ArchaeaEukarya
no-membrane around organellesmembrane-enclosed organelles
no nucleusnucleus (usually largest 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
Bacterial Morphology and Colony FormationBacteria and Archaea
undergo binary fission (not mitosis which involves nuclear
division, which they do not have, and instead chromosomes simply
replicate)BacteriaArchaea
Cell membrane contains ester bondsCell membrane contains ether
linkages
Cell wall made of peptidoglycanCell wall lacks peptidoglycan
One RNA polymeraseThree RNS polymerases (like eukaryotes - genes
and enzymes are more like this)
Bacterial ribosomes sensitive to some antibioticsArchaea (and
Eukarya) are not
UbiquitousTypically 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 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) 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 Microfilaments -
(mostly actin, 7nm thick) maintain cell shape by compression
resistance, involved in membrane pinching in division, forming
pseudopodia, and in muscle contraction 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
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 membraneEndosymbiosis -
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
Macromolecules99% of living things are made CHON, with P&S
also abundant, which join to form macromolecules: a large molecule
formed by the joining of smaller molecules usually by a dehydration
reaction. Macromolecules (except for some lipids) are polymers of
similar or identical subunits (usually monomers) linked by covalent
bonds. Polymer breakdown is hydrolysis as a water molecule is added
to break the covalent bond.MacromoleculeSubunitBondExamples
CarbohydrateMonosaccharides (glucose, can form disaccharides
like maltose)Glycosidic BondStorage and Structure
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)
LipidFatty 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)Ester BondHydrophobic
(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
ProteinAmino Acids(20 different ones that form polypeptides
which fold into 3D structure)Peptide BondsAll 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 non-polar, polar or electrically charged (also
hydrophilic)
When polymerised they become a backbone with various side-chains
that determine how it folds and 3D structure (primary, secondary,
tertiary and quaternary levels of folding determine final
shape)Used as structure (keratin), storage (casein), transport
(haemoglobin), hormones (insulin), movement (actin), enzymes
(sucrase)Enzymes - catalytic proteins selectively speed up chemical
reactions without being consumed, allowing reactions to be fast
enough for a cell to survive
E (enzyme) + S (substrate) ES E + P (product)
Catalysis occurs at the active site
Enzymes lower the activation energy (EA) of a thermodynamically
favourable reaction, but do not affect the equilibrium or free
energy change (G - the difference in the energy between the
reactants and products) and cannot make a thermodynamically
unfavourable reaction favourable
Nucleic AcidsNucleotidesPhosphodiester BondsDNA or RNA, store
hereditary information, polymers also called polynucleotides
Cell IntegrityThe 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 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 combinationsSidedness is important for cell
recognition and adhesion
Membrane Permeability (selective nature maintains cell
integrity): small molecules can pass through (O2, CO2, H2O)
hydrophobic molecules will dissolve in the hydrophobic core and
diffuse across
ionised, polar and large molecules cannot cross without a
protein transporter
Animals prefer isotonic environments, die in hypotonicity
(lysis).
Plants prefer hypotonic environments, die in hypertonicity
(plamolysis).
Cellular TransportPassive 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
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)
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
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 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)
PhotosynthesisThe 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 NADPH2. 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 (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
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, CO2
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 RuBPThe 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
energy = lightChemotrophs
energy = chemicals
Autotrophs
carbon = CO2Photo-autotrophs
(photosynthetic bacteria, plants, some protists like
algae)Chemo-autotrophs
chemicals are inorganic
(some bacteria)
Heterotrophs
carbon = one or more organic compounds, e.g.
glucosePhoto-heterotrophs
(some bacteria)Chemo-heterotrophschemicals are organic(many
bacteria and protists, animals, parasitic plants)
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 ATPCatabolic processes in higher animals and other
organisms require O2 (they are aerobic). For example, respiration:
C6H12O6 + 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 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
FoodCellular 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 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). O2 is the terminal electron acceptor after this protein
complex, whilst the proton is transferred out of the mitochondria
and eventually back in by ATP synthase to produce an ATP from ADP
and Pi.Chemiosmosis (first proposed by Peter Mitchell in 1961) is
the theory that the proton gradient created by the respiratory
chain (as it pumps protons out of the mitochondria) provides a
means of free energy (a proton motive force) that can drive the
activity of ATP synthase to generate ATP (oxidative
phosphorylation). This can be shown experimentally as mitochondria
at pH 8 that are shifted to pH 4 have a burst of ATP synthesis
without any respiratory chain activity (no 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 gradientIn total
30-32 ATP equivalents (NADH 2.5ATP, FADH2 1.5ATP) are produced from
one glucose, which would only produce the initial 2NADH and 2ATP in
anaerobic fermentation.
Respiration is controlled by allosteric enzymes. For example,
phosphofructokinae (PFK) catalyses the third step in glycolysis,
however it is inhibited by citrate (from the citric cycle) and ATP,
whilst being stimulated by AMP.Amino acids from proteins are broken
down to acetyl-CoA or intermediates within the glycolysis or TCA
cycle, whilst carbohydrates and fats are both broken down
aerobically into acetyl-CoA (allows for recycling of some
materials, which is what occurs when eating food). Ultimately it
will form CO2 and H2O (the products of respiration). In cases of
low O2 supply, such as intense exercise in skeletal muscle cells
and red blood cells, carbohydrate catabolism involves fermentation,
and the glucose is converted to lactate (lactic acid), which causes
cell death if oxygen supply is interrupted.From Gene to FunctionThe
genetic language must be accurately copied and passed on and
readily accessed for the information contained. Proteins had
greater complexity and 20 building blocks, whilst DNA had a regular
structure and only 4 building blocks so it was believed proteins
would the means of inheritance, however like binary the simpler
language still allowed for complexity. Experimental data in the
1940s-early 50s suggested that DNA may be genetic material. For
example, in 1953 Hershey and Chase grew two batches of
bacteriophage T2 (virus that infects bacteria, one with radioactive
sulfur (present in two amino acids) which labelled proteins, the
other with radioactive phosphorus which labelled DNA. Mixing these
with bacteria infected the bacteria with the genetic material of
the virus, and upon centrifuging to separate the bacteria from the
viruses they found it was the DNA inserted into the bacteria.In
1953 Watson and Crick published the structure of DNA using
molecular models from X-ray diffraction patterns, proving it was a
double helix (they knew it had the nucleotide bases adenine,
thymine, cytosine and guanine which stood on sugars, each linked by
a phosphate group after an H2O has been taken out). DNA is
deoxyribonucleic acid, whilst RNA is ribonucleic as it has an extra
O. Combined with a phosphate group and base, it becomes a
nucleotide.A & G are double-rings (purines), so an A & G
would produce a strand to wide (to be consistent with X-ray data).
T & C are single-ringed (pyrimadines - smaller size compensated
for by longer name), and would produce a strand too close for DNA.
Hence one pyramidine had to be paired with one purine. In addition,
A & T have two hydrogen bonds, whilst C & G have three, so
they can only match like AT and CG. It forms an alpha helix
(follows right-hand grip rule), and being a helix (not spiral) the
strands are not evenly distributed but close then far then close
then far, which produces almost a spiral shape with the resulting
ribbon (but as the two strands are separate it is not a spiral).
Each strand is considered antiparallel (running in opposite
directions - the phosphates charges face opposite directions and
the carbons sit on the opposite sides). The 5 phosphate end (the
top) finishes with a phosphate, whilst the 3 hydroxyl end finishes
with the OH from the sugar.
Humans have 3.2109 base pairs (2m long, 0.01mm wide), and this
is complexed with histones (proteins) to form nucleosomes,
solenoids and eventually chromatin. Histones maintain structure of
the chromosome and help regulate gene expression/activity. It is
folded, coiled and condensed in preparation for cell
division.Mitochondria also have their own circular DNA within their
matrix (the part inside the folds (cristae), not the tissue
itself), which codes for proteins essential for normal
mitochondrial function.
DNA ReplicationFirst, 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: TranscriptionTo 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 (42=16 isnt enough), however much of this code is
redundant as it doubles up (which provides some protection). To
crack this code they synthesised strands of just specific codons
(e.g. AAAAAA) then observed the protein in vitro (outside a cell).
The code was also found to be genetic, as the gene coding from the
firefly luciferase protein (which makes it glow) was inserted into
a mouse embryo, and the mouse was able to produce a functional
fluorescent protein.Transcription has three stages:1. Initiation -
RNA polymerase binds to the promoter region upstream of the gene,
DNA strands unwind, RNA synthesis is initiated by the RNA
polymerase2. 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 helix3.
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 releasedThis
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: TranslationThe 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. Elongationa.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
anew3. 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 ReproductionIn 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 G1 -
growth
S - DNA synthesised (replicated/duplicated)
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)
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
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 cellsTo 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 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 Metaphase I - chromosomes have
untwined (are clearly two dyads) and line up in two rows, with
homologous pairs next to each other Anaphase I - homologous
chromosomes are pulled to opposite sides by kinetochore
microtubulues Telophase I - chromosome homologues are at opposite
poles, and begin to reform a nuclear membrane
Cytokinesis (not exactly part of meiosis) - produces two DIPLOID
cells (basically back to square one, but with crossing over)
Meiosis II Interkinesis (Interphase II) - no DNA replication
(however still centrosome replication) Prophase II - as with
mitosis (includes prometaphase)
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)
Anaphase II - as with mitosis
Telophase II and Cytokinesis - as with mitosis
PCR and Individual VariationIn 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, 16220). 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.MutationA mutation is a change in the nucleotide
sequence of an organisms DNA, ultimately creating genetic
diversity. They can also occur in virus DNA or RNA. Mutations lead
to diversity which is critical to the survival of life. For
example, the British Peppered Moth had a mutation resulting in some
light, some dark, which were better at camouflage in either
lichen-covered trees or soot-covered industrial areas during the
Industrial Revolution of the mid-19th C when pollution was being
produced. They will only be inherited in offspring if they occur in
gametes.Mutations can occur as:
point mutations (changes single base)
insertions
deletions
duplications of sequences
chromosomal rearrangements (like fusion, fission, inversion and
translocation)
Mutations can be caused by:
errors in DNA replication (DNA polymerase makes 1 error in 105
bases, leading to incorrect base-pairing, however DNA repair
enzymes reduce this to 1 in 1010)
mutagens chemicals (nicotine, asbestos, free radicals, oxidising
agents, nucleotide analogues) which damage DNA
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 stopFrameshift -
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 HeredityGenetics - 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
locusHeterozygote - 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
PopulationsGenetic 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). EMBED PBrush
(becomes part of 6)
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Oliver Bogdanovski