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Biology 124

BIOCHEMISTRY
Life, Chemistry and Water
Atomic structure
-

-

Subatomic particles (neutrons, protons and electrons), energy levels, orbitals,
valence electrons and atomic structure
o Hydrogen: 1 proton in nucleus and 1 electron
o Carbon: 6 protons and 6 neutrons in nucleus with 2 then 4 electrons
Atoms more stable when outer shell/orbital/valence electrons full of electrons
(8)
o More stable configuration = chemical bonds between atoms

Chemical bonds – DNA and proteins
BONDS
Covalent
Ionic
Hydrogen
Van der Waal interaction

TYPE OF INTERATION
Sharing of electron pairs
Attraction of opposite charges
Share H-atom
Weak interaction between non-polar
molecules

STRENGH

Ionic chemical bonds (transfer)
-

Formed when ions with opposite charges (cations/anions) attract each other
o NaCl, MgCl2
Valence electrons (outer most electrons/last orbit) are completely transferred to
other atoms (either lost or gained)
o When losing an electron: it becomes a positive ion and proton number is
constant (sodium Na)
o When gaining an electron: it becomes a negative ion and proton number
is constant (chlorine Cl)
o Forms a crystal lattice

Covalent chemical bonds (sharing)
-

Formed when 2/more atoms share a valence electron pair (H2, O2, H2O2, CH4)
Binding capacity is determined by atoms valence
Strength depends on number of shared electrons
Bonds indicated by pair of dots/single line
Two types of bonds:
o Non-polar covalent bond – valence electrons shared equally (H2, O2, N2,
CH4)
▪ Symmetrical tetrahedral shape
▪ Angle between atoms (between H and H of methane) is 109,5
degrees
o Polar covalent bonds – valence electrons not shared equally (H20)

Biology 124

Asymmetrical shape
Angle between atoms (between H and H of water) is 104,5 degrees
Water: oxygen is slightly negative, and hydrogen is slightly positive
• Oxygen more electronegative than hydrogen so valence
electron spends more time closer to oxygen atoms = two
poles
Type of bond between atoms depends on electronegativity
When there is a triple bond (bonds increasing) it requires more energy to break it
▪
▪
▪

-

Hydrogen chemical bonds
-

-

Formed when a H atom (covalently bonded to an electronegative O or N atom) is
attracted by another electronegative O or N atom [ONLY]
Special dipole-dipole interaction with direction
Hydrogen bonds stabilise the secondary structures of proteins (helix structure)
Oxygen stronger than hydrogen therefore valence electron of hydrogen spends
more time by oxygen (same with nitrogen) creating slightly negative and positive
poles
1 water molecule can attract 4 other water molecules

Van der Waals chemical bonds
-

-

Forces is weak attractions between non-polar molecules over short distances
(temporary positive/negative bonds)
Constant motion of electrons = accumulation (by chance) in one part of
molecule
o Leads to zones of positive and negative charge
E
...
gecko toe, pads on seta and setae on toes

Properties of water with hydrogen bonds
-

-

Water molecule has a strongly polar covalent bond between O (negaitve0 and
the 2H (positive) atoms
Water forms hydrogen bonds with other polar molecules (therefore solvent of
life)
o Interaction with other water molecules = lattice
Manifold property of water is due to the ability to form hydrogen bonds

Ability of water to form hydrogen bonds gives it 5 properties:
COHESION (STICKINESS)
-

H20 attaches to any material to which it can form hydrogen bonds
Cohesion: formation of hydrogen bonds with other water molecules
Adhesion: formation of hydrogen bonds with other compounds (not H20)
Biological consequences of cohesion:
o Creation of surface tension by unbalanced hydrogen bonding
o Spider supported by water surface tension

Biology 124

-

Biological consequences of cohesion together with adhesion:
o Direction of water movement from roots to leaves – bark contains water
conducting cells and the water conducting cells contain cohesion
between the water molecules (as it is referring to water) and water
molecule to bark contains adhesion (as it is a hydrogen bonding not to
water molecules)

TEMPERATURE CONTROL
-

-

Hydrogen bonds needs a lot of energy to break the bonds and then needs a lot of
energy to evaporate
High specific heat: amount of energy (heat) which must be absorbed/released to
get a change of 1 degree per 1 g of substance
...
Biological
consequences:
o H20 stabilises body temperature and gives resistance to overheating
o Large volumes of water influence climate coastal regions and stabilise
ocean and coastal temperatures
High heat of vaporisation: amount of energy (heat) which is required to convert 1
g of fluid water to gas
...
Polar: water and non-polar: oil
Polar/charged molecules cause competing attraction
o Opens a cavity into which polar/charged molecules can move
Biological consequences:
o Biological membrane arounds cells and organelles are kept intact by
water

Biology 124

SERVES AS A SOLVENT
-

H20 is a good solvent – forms hydrogen bonds and a hydration layer
H20 sticks to polar molecules
o Hydrophilic = attraction by water (dissolve in water)
H20 repels non-polar molecules
o Hydrophobic = repelled by water (not dissolve in water – oil)
H20 is a good solvent because of its polarity and ability to form hydrogen bonds
(hydration layer)
Biological consequences:
o Bodily fluids (blood and saliva) contain water with different polar
components (proteins, sugar, DNA and ions) are dissolved – hydrophilic
▪ Ionic and polar regions on the proteins surface attract H20
molecules when purple lysozyme is in an aqueous environment

Water ionisation and pH
-

-

Water can dissociate:
o H20 – OH- + H+ (proton)
o [H+] = [OH-] in pure water so [H+] in pure water = 10-7 M (25°C)
▪ [H+] = [OH-] = 10-7 M therefore [H+] [OH-] = 10-14 M
pH scale describes how acidic or basic (alkaline) a solution is
o pH expressed in terms of [H+] therefore pH = -log[H+]/[H+] = 10-pH
o logarithmic scale of 0-14 (a pH unit = 10-fold different in [H+])

Acids and bases
-

-

Acid: substance which increases the solutions [H+] giving off H+ ions to the
solution and completely ionises
o HCl - H+ + Clo pH values are lower than 7 = acidic
Base: substance which decreases the solutions [H+] by binding H+ ions to the
solution or releasing OH- ions into the solution and completely dissociates
o NH3 (ammonia) + H+ - NH4+ (ammonium)
o
NaOH – Na+ + OHo
pH values are above 7 = basic

Biology 124

Buffers
-

-

Solution able to resist changes to pH when strong
acid or base is added
They reduce variability of the [H+] and [OH-] of the
solution (blood) by taking H+ ions out of the
solution (binding them) if there are too many or
giving H+ ions to the solution if there are too few to
prevent fluctuations
pH stays constant
E
...
stabilisation of blood pH by carbonic acid

Chemical bonds with C-atoms
-

Skeleton of biological molecules consists of C atoms
attached to other C atoms or other atoms (H, N, O and S)
Tetravalency of C atoms makes diverse structures
o Hydrogen: 1 valence electron
o Oxygen: 2 valence electrons

Functional groups
-

-

It is reactive groups of atoms that are coupled to a C atom framework
(backbone)
o Has specific chemical properties
o Properties are transferred to larger molecules to which it is coupled
Arrangement of C-atoms together with other molecular components gives
organics molecules properties

Molecules consisting of only C and H atoms:
HYDROCARBONS
-

-

Simplest is methane CH4
2-C hydrocarbons with single, double, or triple bonds
o Single bond: ethane (GET NOTES MORE FORMULAS)
o Double bond: ethene
o Triple bond: ethyne
Linear and branched hydrocarbon chains (when it becomes branched = yl)
Hydrocarbon ring (i
...
with double bonds) is a benzene ring (C6H6)
o The carbons are in a ring with double bonds alternating with single bonds
between them and a H atom branching off it

Molecules consisting of C, O and H atoms:
CARBOXYL GROUP (-COOH)
-

Carbonyl group (C=O) combined with hydroxyl group (OH)
Ionisable (pH dependant)

Biology 124

-

Has acidic properties

Molecules consisting of N and H atoms:
AMINO GROUP (-NH2)
-

Ionisable (pH dependant)
Has basic properties

Molecules consisting of P and O atoms:
PHOSPHATE GROUP (-OPO2-3 of -PO2-4)
-

Central P atom with 4 bonds to oxygen atoms
Ionisable (pH dependant)
Has acidic properties

Molecules consisting of S and H atoms:
SULFHYDRYL GROUP (-SH)
-

2 -SF groups can react (redox reaction) to form a disulfide
Disulfide bonds help maintain tertiary and quaternary structures of proteins

Isomers
-

It is 2/more molecules with the same chemical formula but different molecular
structures

Stereoisomers
-

Biological structures (amino acids) can exist as 2 stereoisomers
o Only 1 isomer occurs naturally
Importance of stereoisomers:
o Drug = Ibuprofen
...
Effective
stereoisomer = S-Ibuprofen
...
Condition = asthma
...
Ineffective stereoisomer = S-Albuterol

Structural isomers
-

Formed by the positional exchange of function groups (glucose and fructose)
o Glucose – aldehyde
o Fructose – ketone

Reactions involving function groups
-

Components of a water molecule (-H or -OH) are removed from/added to a
function group during chemical reactions
o During the assemble/degradation of macromolecules

Biology 124

Dehydration synthesis/condensation: smaller subunits (monomers) are combined to
form macromolecules (-H and -OH (H2)) is produced (removed)
Hydrolysis: macromolecules are broken down into monomers (-H and -OH (H2)) is
added
BIOLOGICAL MOLECULES
Carbohydrates, lipids, proteins, nucleic acid
Carbohydrates
-

-

They are macromolecules containing C, H and O in ratio 1:2:1 (CH20) n
Function: energy storage, structural role, cell recognition (most abundant
molecule)
Smallest subunit (monomer – building block) =
monosaccharide
o Glucose, fructose, and galactose
2 monosaccharides = disaccharide
o Sucrose, lactose, and maltose
Polymer (many) of monosaccharides = polysaccharide
o Starch and cellulose
3 carbon atoms with covalent bond = carbon chain

Monosaccharides
-

-

-

-

Carbon chain of at least 3 carbon atoms covalently bonded
to hydroxyl group/hydrogen and exception of 1 carbon
covalently linked to carbonyl group
Type of carbonyl group defines the monosaccharide
Differences are due to position of carbonyl group:
o Aldehyde has a terminal double bond O
o Ketone does not have a terminal bond
▪ They are structural isomers
Differences due to chain length and stereoisomers:
o Also structural isomers
Can occur in linear and ring form with 2 functional
groups
o Monosaccharides with 5/more carbons in
backbone can form a ring structure
2 functional groups react and form a closed ring
structure with 2 ring types:
o α stereoisomer = hydroxyl group at 1st
carbon is positioned downwards (af)
▪ More reactive
o β stereoisomer = hydroxyl group at 1st
carbon is positioned upwards (bo)

Biology 124

Disaccharides
-

-

2 monosaccharides linked to each other by a covalent bond
o Occurs by dehydration synthesis
Glycosidic bond: covalent bond linking monosaccharides
Formation of maltose: bonding between C1 of 1 glucose molecule and C4 of
another glucose molecule with linkage by means of a α glycosidic bond which is
covalent (consists of 2 alpha glucose molecules)
o If monosaccharide is an alpha (af = bottom) it will form a α glycosidic
bond

Formation of sucrose: bonding between C1 of 1 glucose molecule and C2 of a
fructose molecule by means of a α glycosidic bond

o

-

Formation of lactose: bonding between C1 of a galactose (hydroxyl – beta)
molecule and C4 of a glucose (hydroxyl) molecule by means of a β glycosidic
bond
o Monosaccharide is a beta (bo = top) it will form a β glycosidic bond

Polysaccharides
-

-

They are polymers of monosaccharides (100-1000s units) linked by glycosidic
bonds
o Linear and unbranched (cellulose)
o Contain 1/more branches (starch and glycogen)
o Consist of the same/different monosaccharides
Function is determined by the type of monomer and nature of glycosidic bonds:
o Storage polysaccharides (starch/glycogen) – alpha glycosidic bonds
(broken)
o Structural polysaccharides (cellulose and chitin) – beta glycosidic

STROAGE POLYSACCHARIDES

Biology 124

-

Plants store sugar as starch
o Polymers of glucose monomers
o Monomers linked by α glycosidic bonds
o Combination: amylose (linear/unbranched – coiled structured as alpha
therefore stored efficiently) and amylopectin (linear/branched)

-

Animals store sugar as glycogen – lover/muscle (food/energy)
o Polymer of α glucose monomers
o Monomers linked by α glycosidic bonds
o More branched than amylopectin
o Breaking bonds = glucose

STRUCTUAL POLYSACCHARIDES
-

Cell walls of plants consist of cellulose:
o Unbranched polymer of glucose monomers
o Monomers linked via β glycosidic bonds
o Microfibrils have hydrogen bonds between chains

-

Exoskeleton of arthropods (insects, spiders, crustaceans) have chitin (reenforcement)
o Unbranched polymer of modified glucose monomer (N-acetyl
glucosamine)
o Monomers linked via β glycosidic bonds
o Forms fibre like structure for protection

Lipids
-

They are groups of molecules which are insoluble in water

Biology 124

-

-

o Primarily non-polar (hydrophobic)
o Contains hydrocarbons (C-H bonds) – covalently linked
Lipids in living organisms:
o Fatty acids (building blocks): triglycerides (fats/oils – neutral lipids),
waxes, and phospholipids
o Steroids (testosterone and oestrogen)
Fatty acids differ in length and number/position of double bonds
o Saturated fatty acids: internal C atoms at bonded to at least 2 H atoms
▪ Fatty acid is saturated with H
▪ Found in solid animal fats (butter) – linear structure and stack
▪ Solid at room temperature
Single hydrocarbon chain with carboxyl group -COOH (C double bond O and
single bond O) at one end (stearic acid) and is a saturated fat as all carbons are
covalently linked to hydrogen (also called acid as it has carboxylic acid)
▪ Hydrocarbon side is non-polar and carboxylic side is polar and
charged therefore hydrophilic interacting with water
o Unsaturated fatty acids: 1/more double bonds between adjacent C
atoms
▪ Fatty acid has a kink in carbon chain where there is a double bond
(cannot stack)
▪ Found in plant/fish oils
▪ Liquid at room temperature

Fatty acids
SATURATED FATTY ACIDS

UNSATURATED FATTY ACIDS (double bond)
Triglycerides
-

-

Composed of 2 types of smaller molecules linked by dehydration synthesis
o 1 glycerol molecule (3 carbon bonded to hydroxyl = alcohol) + 3 fatty acid
(length of hydrocarbon varies) molecules
Fats and oils: neutral lipids
Function: energy storage molecules
Water insoluble as lose hydrophilic head

Biology 124

Waxes
-

-

They are esters (between alcohol and acid)
formed when fatty acids combine with
long chain alcohols
Extremely hydrophobic
o Harder and less oily as fats
Function: protection, and lubricant

Phospholipids
-

-

Forms the core of all cell membranes
Consists of 3 subunits:
o 1 glycerol
o 2 fatty acids
o Phosphate group (bound to another polar unit)
2 ends of a phospholipid interact differently with water: forms a bilayer (double)
surrounding cells and organelles

Steroids
-

Lipids that consist of a C framework of 4 fused rings – cholesterol and sex
hormones
Absence of methyl group and presence of hydroxyl group and not carbonyl =
oestrogen

Biology 124

Protein
-

Most diverse macromolecule in structure and function
Functions:
o Support/structure
o Enzyme catalyst (chemical reactions)
o Transport
o Movement
o Regulation (transcription for genes)
o Cellular communication (receptor proteins)
o Defence/immunity (antibody proteins)
o Storage

Monomers
-

Proteins constructed of a combination of 20 (alpha) essential amino acid and
form unbranched chains
...
Rate
of forward reaction = rate of reverse reaction
...
Increases concentration of reactants in equilibrium it will favour the forward reaction
1
...
Endergonic reaction – energy added
∆G ≥ 0 (positive – adding)
Product more free energy (G) than reactant
Reaction not spontaneous (energy required for froward direction)
Free energy change (∆G) in exergonic

Free energy change in endergonic

Exergonic and Endergonic reactions
Individual reactions form part of a metabolic pathway with 2 types:
1
...
Anabolic pathway (biosynthetic)
Build-up of complex molecules from simpler compounds
Energy is used (endergonic)
Photosynthesis
Disaccharide formation
-

Formation of maltose involves:
o Breaking and making bonds (change in enthalpy ∆H is small)
o Turning 2 monosaccharides into 1 large disaccharide and 1 small water
(change in entropy ∆S is negative - ordered)
o Change in free energy ∆G is positive – require energy to proceed

ATP: energy currency of the cell
-

Cells supply energy to drive endergonic reactions in form of ATP (adenosine
triphosphate)

Biology 124

-

Purine nitrogenous base covalent to ribose sugar covalent to 3 phosphate
functional group
...
3 kcal/mol (30
kJ/mol) std cond)

Energy coupling
-

Without ATP a reaction is not spontaneous as ∆G will be positive: endergonic
o Glutamic acid + ammonia – glutamine (∆G = +3
...
3 kcal/mol)
Coupled with ATP hydrolysis, glutamine synthesis is spontaneous as ∆G is
negative
HARVESTING CHEMICAL ENERGY

Flow of energy (cellular respiration), cellular respiration (synthesis of ATP), oxidationreduction (redox) reactions, oxidation of organic molecule glucose, harvesting of energy
(NAD+ electron carrier)
Flow of energy
-

Living systems need energy to do work
Energy obtained from eating food containing organic molecules: proteins, lipids,
and carbohydrates

Sunlight (light energy) used in photosynthesis to produce glucose (chemical energy)
and oxygen is released
Glucose (contains electrons at high energy levels) used for cellular respiration and
oxygen produce carbon dioxide and water
ADP + P forms ATP
Cellular respiration
-

It is the collection of metabolic reactions that break organic molecules down to
produce energy
...
Substate level phosphorylation
ATP generated directly from intermediates of respiration process
- ATP produced directly by transferring a phosphate group (PO2-4) from a
phosphate containing substrate (phosphorylated donor molecule) to ADP (P – P
– Adenosine) to form ATP (P – P – P – Adenosine) + an unphosphorylated product
molecule
o Substrate – phosphoenolpyruvate (PEP) becomes dephosphorylated and
transferred to ADP = ATP
...
Oxidation phosphorylation
ATP generated indirectly through mechanisms using electrons produced in redox
reactions
- During breakdown of glucose, some intermediates undergo oxidation-reduction
(redox) reactions
o Oxidation (oxidised): electrons given off/loss of electrons (Na – Na+)
o Reduction (reduced): electrons taken up/gain an electron (Cl – Cl-)
- Breakdown of glucose and subsequent intermediates occur in steps that is
enzyme catalysed – electrons are released in redox processes during some
steps
o Electrons with protons (H+) are captured by electron carriers (NAD+)
o Final electron accepter is oxygen (oxygen must be present)
NAD+ as electron carrier
Oxidation of organic molecules
-

Electrons lose potential energy when transferred to oxygen
Electrons move to a lower energy level (oxygen has a high electronegativity)
o Energy released indirectly used for ATP synthesis

Stages of cellular respiration
Glycolysis (stage 1)
-

In the cytoplasm (cytosol)

Biology 124

It is the oxidation (break down) of the glucose 6-carbon ring (unstable) into 2
pyruvate 3-carbon ring molecule in a 10-step pathway with 2 phases:
1
...
Reaction 6-10: energy releasing phase where energy is released in the form of ATP
and electrons are transferred to NAD+
- Phosphofructokinase speeds up/slows down glycolysis for energy – phosphate
is transferred from ATP to glucose which is more reactive and traps glucose in
cell as it can’t cross membrane
-

ENERGY YIELD
-

Net energy yield from glycolysis per glucose molecule = 2 ATP + 2 NADH
Energy produced by hydrolysis of ATP = -30
...
5 = -61 kJ/mol
Energy content of chemical bonds in glucose = -2870 kJ/mol
Therefore glycolysis only yields 2
...
CO2 released from pyruvate (product: 2C acetate)
2
...
Coenzyme A (CoA) binds to 2C acetate (product: acetyl-CoA)
- Net energy yield per glucose molecule = 2 NADH
-

Citric acid cycle (CAC) – Creb’s cycle (stage 2b)
-

In the mitochondrial matrix
Completes glucose breakdown by oxidising
acetyl-CoA to produce oxygen
Oxidisation happens and is transferred to electron
transport chain
Net energy yield per glucose molecule = 2 ATP +
6 NADH + 2 FADH2

Oxidative phosphorylation: electron transport and chemiosmosis
-

In inner mitochondrial membrane
Accepts electrons from glycolysis, pyruvate oxidation and CAC via electron
carriers (NADH, FADH2)
o FADH2 and NADH electron carriers trasnport electrons to the elctron
trasnport chain where ATP is produced through oxidative phosphorylation

Biology 124

-

Go from higher energy level to lower energy level
Electron transferred to oxygen (final electron acceptor)
Forms a proton gradient = high proton concentration which
which represents stored energy (potential energy)
o Protons move down concentration gradient by channel protein (inner) –
ATP synthase
...
5 kJ/mol (std conditions)
Cellular respiration produces: 32 × -30
...
Glycolysis: glucose (6C) – 2 pyruvates (3C)
2
...
Substrate level phosphorylation: 2 ATP (glycolysis) and 2 ATP (citric acid cycle)
2
...
Complex I: flavoprotein combined with an iron-sulphur (Fe
...
Complex II: FAD combined with Fe
...
Complex III: cytochrome b (small heme containing protein) combined with Fe
...
Complex IV: cytochrome a combined with cytochrome a3
Transfer of electrons in ETC
-

Electrons from glucose go from a high energy state to a low energy state losing
electrons and chemical potential energy (used by complex 1, in each step as
energy is being released for ATP synthesis and oxygen is the final electron
acceptor used to pump H+ ions

How electron transfer and release of energy is coupled to ATP synthesis
ETC generates proton-motive force
-

-

During electron transfer the energy released is used to actively pump H+ protons
from the mitochondrial matrix to the intermembrane compartment
o Matrix is more negative
o Generates H+ gradient across the membrane (chemical/electrical
gradient)
The gradient constitutes stored/potential energy called proton motive force
(PMF)

PMF drives ATP synthesis
-

-

Energy stored in H+ gradient (PMF) is used by ATP synthase to synthesise ATP via
chemiosmosis (ATP synthase is an enzyme found in inner mitochondrial
membrane)
Chemiosmosis: chemical synthesis of ATP driven by energy stored in H+ gradient
generated across the inner mitochondrial membrane

ATP synthase
-

Functions as active ion transport pump in reverse (molecular motor)
o Motion catalysed ADP to ATP – turned by flow of protons
+
H gradient used to generate ATP instead of using ATP to pump H+ against a
gradient
Potential energy – kinetic energy which causes internal rod to rotate which goes
to catalytic knob for ATP

ATP yield
Amount of ATP generated from each electron carrier:
o 1 NADH – 2
...
5 ATP
1
...
NADH high
energy level therefore transfers to complex 1 = energy released to pump protons
-

Biology 124

inwards
...
Shuttle system (low energy level)
Electrons generated from glycolysis (cytoplasm) and carried by NADH must be
transported to mitochondrial matrix and require protein shuttle systems form the
transport as NADH cannot cross mitochondrial membrane
Important words
-

Aerobic respiration
Anaerobic respiration
Cellular respiration
Chemiosmosis
Fermentation
Oxidation/reduction
Substrate level phosphorylation
Oxidative phosphorylation

Fermentation
When oxygen is limited/absent (no final electron acceptor) ATP produced by
fermentation
- It is the partial breakdown of glucose to produce ATP in absence of oxidation
phosphorylation (no ETC) therefore no cellular respiration
- Consists of glycolysis and reactions that can regenerate NAD+ from NADH
produced during glycolysis
- No ETC is involved, no ATP produced from electron carriers, so electron carriers
are recycled producing reduced metabolites
1
...
In muscles
lactate acts as an electron store until oxygen is available (pyruvate reduced to
lactate directly)
2
...
5 kJ/mol
Fermentation produces: 2 × -30
...
1% of glucoses potential chemical energy
MEMBRANE AND TRANSPORT
Structure and function of cell membrane, fluid mosaic, passive/active transport,
exocytosis/endocytosis
Membrane Structure components
-

-

Lipids:
o Phospholipids (main)
o Sterols
Proteins:
o Transport
o Recognition
o Receptor
o Cell adhesion

Phospholipids
-

-

Membranes consist of a phospholipid bilayer (selectively permeable – certain
molecules to move due to hydrophobic nature) moving around in fluid
o Polar end (hydrophilic head): polar alcohol, phosphate group and glycerol
– interact facing aqueous environment
o Non-polar end (hydrophobic tail) – hydrocarbon combination
If membrane only consists of phospholipids, at low temperatures the bilayer
would freeze into semi solid and when shaken it’ll form into small vesicles
enclosing small drops of water

Sterols
-

-

Main sterol (steroid) is cholesterol
o Hydrophilic end – OH (hydroxyl)
o Hydrophobic end with hydrophobic tail
o Keeps membrane fluid
o Prevents freezing of phospholipid bilayer
Hydrophilic ends allow cholesterol to interact with polar heads of phospholipids
In plants it is phytosterols

Proteins
-

Membranes contain proteins that are inserted into the phospholipid bilayer
Each membrane has a characteristic group of proteins responsible for a
function:
o Transport/integral proteins (assisting in moving molecules – polar
molecules not diffusing embedded)
o Recognition proteins
o Receptor proteins (signally molecule – insulin hormone)
o Cell adhesion proteins

Biology 124

-

o Enzymes
o Peripheral proteins (membrane by non-covalent bonds – cytoplasmic
side)
Membrane protein: alpha helix on the membrane surface outside of the cell, a
channel, cytosol and COOH on the inside of the cell
Hydrophilic and hydrophobic surfaces: hydrophilic protein surface (above) and
hydrophilic channel with a hydrophobic protein surface embedded and
hydrophilic protein surface (below)

Carbohydrates
-

Glycolipids: covalently linked to lipids
Glycoproteins: covalently linked to proteins

Fluid Mosaic Model
-

-

-

Fluid phospholipid bilayer = proteins freely move in bilayer
Phospholipids always move for membrane proteins to function, and the
membrane is fluid:
o Lateral in a layer/spin (hydrocarbons chains differ)
Membrane fluidity:
o Fluid – unsaturated hydrocarbons tails with kinks
o Viscous – saturated hydrocarbon tails
At high temperatures cholesterol prevents the membrane from becoming too
fluid
At low temperature it prevents hydrocarbons from coming too close and freezing

Transport
-

-

Membranes are selectively permeable (contents is regulated)
Movement across membranes are controlled by:
o Phospholipid double layer (hydrophilic barrier – prevents polar molecules
crossing)
o Transport proteins (movement of ions/polar molecules)
Direction of transport through membrane is determined by mechanism of
transport:
o Passive transport: diffusion down a concentration gradient (high – low)
o Active transport: transport against a concentration gradient (low – high)
and requires energy

Passive Transport
-

Form of diffusion: random movement of molecules causes a new movement
from areas of a high concentration to areas of a low concentration

SIMPLE DIFFUSION
-

Driven by a concentration gradient (potential energy)
Spontaneous process – no energy required

Biology 124

-

Movement continues until dynamic equilibrium is reached
Involves small molecules, only non-polar:
o Non-polar inorganic gasses (oxygen, nitrogen, and carbon dioxide) and
non-polar organic molecules (steroid hormones)

FACILITATED DIFFUSION
-

-

Passive diffusion of ions/polar molecules across a membrane with help of
transport proteins
o Diffusion down a concentration gradient
Polar and charged molecules (not pass hydrophilic bilayer)
2 types of transport proteins (membrane proteins)
o Channel proteins (gated/ungated)
▪ Ion channels, water pores
o Carrier proteins
▪ Glucose transporter, amino acid transporters

OSMOSIS
-

-

Diffusion of water across a selectively permeable membrane
o Allows passage of water (not solute) molecules
Passive movement of water in response to difference in solute concentration
o Moves from solution of a low solute concentration to solution of a high
solute concentration to establish equilibrium
Movement continues until dynamic equilibrium is reached
Hypertonic – solutions with a higher solute concentration
Hypotonic – solutions with a lower solute concentration
Isotonic – concentration of solute inside and outside are the same

Active Transport
-

-

Transport of molecules across a membrane against the concentration gradient
with help of transport proteins
o Requires energy input
o Creates differences in concentration of solutes/voltage across
membrane
Type of transport proteins used is called carrier proteins

PRIMARY ACTIVE TRANSPORT
-

Direct use of ATP (ATP hydrolysis) by transporter itself
o H+ pump, Ca2+ pump, Na+/K+ pump
Movement of 1/more sodium ions to outside = positive outer membrane =
difference in ion concentration and electric charge
Electrochemical gradient: potential energy as is combination as chemical and
electrical gradient
o Potential energy used by cell to drive transport of other molecules –
secondary

Biology 124

SECONDARY ACTIVE TRANSPORT
-

Transporter uses a favourable concentration gradient of ions created by indirect
use of ATP hydrolysis occurring in 2 ways:
o Symport/cotransport –
▪ Molecules move same direction as driving ion (glucose/amino
acids)
▪ Potential energy of electrochemical energy caused by driving ion:
driving ion diffuses allowing molecule to move against
concentration gradient
o Antiport/exchange diffusion
▪ Driving ion moves in 1 direction, other molecule moves in opposite
direction (ions – Ca2+)
▪ Provides energy to move against concentration gradient

EXOCYTOSIS (need energy)
-

Secretion of biological molecules by the fusion of vesicles with the cell
membrane

ENDOCYTOSIS (need energy)
-

Uptake of biological molecules by the formation of new vesicles from the cell
membrane
o Pinocytosis (bulk phase): uptake of water and solutes
o Phagocytosis: uptake of whole particles
o Receptor-mediated: uptake of specific molecules

CYTOLOGY
All about life, classification of life, origins of life, early experiments, development of first
cell
-

-

Cell: organised chemical system including specialised molecules enclosed
by a membrane making it the lowest level of biological organisation that lives
and reproduces
A cell is only alive when it remains organised as a cell, if it is damaged/broken
into components it is not alive (atoms/molecules)
Emergent property: characteristic that depends on the level of organisation
and does not exist at lower levels
o Life is an emergent property of the organisation of matter into cells

Characteristics of living organisms
1
...
Living organisms engage in metabolic activities
- Some genes code for specific molecules that play a role in metabolic activities
- Metabolism: ability of cells/organisms to extract energy from their
surroundings and use the energy to grow, reproduce and maintain themselves
o Photosynthesis: absorb electromagnetic energy from the sun and
convert it to chemical energy with some energy used to produce
biological molecules (cellulose) or stored (sugars and starch)
Glucose metabolism
-

Organisms use stored chemical energy through metabolic process cellular
respiration
Complex organic molecules broken down in presence of oxygen to produce
ATP

3
...
Living organisms detect changes and then compensate for them in the
environment
- Special receptors which are molecules on cell surfaces/structures on body
surfaces detect environmental changes
- Receptors trigger reactions for compensating the response
o Receptor (sensory neuron) to integrator (interneuron) to
effector/muscle (motor neuron) and the effector brings about the change
5
...
Populations of living organisms undergo changes from one generation to the
next
- Biological evolution/natural law/adaptation/social Darwinism/survival of the
fittest/Darwinian theory: individual may acquire a change in DNA = unusual
traits which they pass to offspring
- Adaptation: favourable mutations produce traits that help an organism
survive longer/reproduce more under certain environmental conditions
Biodiversity and the tree of life – classification
-

-

-

Species: group in which the individuals are so similar in structure,
biochemistry, and behaviour that they can successfully interbreed
Genus: group of similar species sharing characteristics and recent common
ancestry
o Similar species – genus – related genera are grouped into a family –
related families into an order – class (Mammalia) – phylum – kingdom
(animal)
o Domains were then added to be the most inclusive grouping
Nucleotide sequences in the DNA of organisms are used to determine
evolutionary lineages therefore constructing phylogenetic trees
o Phylogenetic trees: illustrations of evolutionary pathways through
which species appeared
Phylogenetic trees provide more information than traditional hierarchical
classification as they reveal:
o Evolutionary events occurring and which ancestors gave rise to
descendants

Biology 124

-

Prokaryote: DNA is suspended inside the cell (nucleoid) without being
separated from other cellular components therefore no nuclear envelope
Eukaryote: DNA is enclosed in a nucleus by the nuclear envelope therefore
the nucleus is a separate structure inside the cell

Phylogenetic tree (tree of life) has 3 domains: bacteria, archaea and eukarya
-

Each domain represents a major trunk and includes a group of organisms with
unique characteristics

Bacteria (prokaryotic)
-

Unicellular (one celled) organisms
Only visible under microscope
Live as producers, consumers, or decomposers
Simple cellular organisms (internal structure and DNA)
Metabolically the most diverse group
Some groups have unique structural molecules and mechanisms of
photosynthesis

Archaea (prokaryotic)
-

Unicellular and live as producers/decomposers
Achaeans inhabit extreme environments (hot springs, extreme salty ponds, or
habitats with little/no oxygen)
Some with distinctive structural molecules and primitive form of
photosynthesis
Some molecular and biochemical traits of a eukaryote (DNA, RNA/protein
synthesis)

Eukarya (eukaryotic)
PROTISTS (algae and protozoans)
-

Not a kingdom as the organisms do not share a common ancestor
Diverse group of single celled and multi-cellular eukaryotes
Protozoans (common) are primarily unicellular, and algae can be
unicellular/large multicellular seaweeds
Protozoans are consumers/decomposers and algae are photosynthetic
producers

KINGDOM PLANTAE (flowering plants, conifers, and mosses)
-

Multi-cellular
Carry out photosynthesis and are producers
Stationary organisms (except pollen and seeds)

KINGDOM FUNGI (yeast, mould, and fungi)
-

Highly varied group of unicellular/multi-cellular species

Biology 124

-

Most live as decomposers that absorb nutrients from dead organisms and
then break complex molecules into raw materials
Fungi do not carry out photosynthesis
Cell walls contain chitin

KINGDOM ANIMALIA (sponges, worms, insects, fish, amphibians, reptiles, birds,
mammals)
-

Multi-cellular
Feed on protists and other kingdom organisms
Unique characteristic of being able to move between places at a stage in life
cycle

Origins of life
-

Protocells (primitive cell-like structures with properties of life) were earliest
precursors of cells
Geological evidence shows prokaryotes lived during the Archaean eon 3
...
Extra-terrestrial origins – Panspermia which is testable but not done but
meteorites have been shown to carry organic molecules
2
...
Life may have developed near hydrothermal vents on ocean floor – black
smokers
o Reducing conditions are present in these areas with abundance of
chemical molecules with vents containing high levels of H2, CH4 and
NH3
o Bursts of mineral rich water superheated to 400 degrees by marine
volcanoes – temperature may be too high (extremely hot and acidic)
o Complex ecosystems found in their vicinity
2
...
Some organic compounds may have an extra-terrestrial origin
o Many of compound made in Miller Urey experiments exist in outer
space – amino acid and nucleic acids
Development of the first cells
Development of molecular replicators and molecules that store/reproduce genetic info

Biology 124

-

Monomers of organic molecules assembled to form polymers: proteins,
nucleic acids, carbohydrates, and lipids
...
Concentration of monomers by evaporation of water
...
Condensation reaction (dehydration synthesis) = monomers assembling
into larger molecules through removal of water molecule
...
Reproduction of genetic information is key – genetic information is stored
in form of nucleotide sequences in DNA and this information is read to
determine the properties of cells through genes that are transcribed and
translated to produce RNA and proteins which in turn make up structures
4
...
7 billion years ago
Stromatolites: fossils that formed as layers of phototropic bacteria grew and
died then their remains were filled by Ca carbonate or silica dated to 3,4 billion
years ago

Biology 124

-

Biosignature: specific organic molecules that were formed by cellular activity
(steroid-like molecule only formed by cyanobacteria) dated to 2
...
Nuclear envelope (membrane): separates DNA from cytoplasm and other
organelles evolved through endocytosis (folding in of plasma membrane) then
closed genetic material and formed Golgi and endoplasmic reticulum
2
...
Engulfed bacteria are endosymbionts as they live inside host and
relationship between the cells = endosymbiosis
Endosymbionts benefit by living in a protected environment and received
nutrients from host, host benefits as the endosymbionts provide products
from metabolic processes
Overtime some genes were lost from the genomes of the mitochondria and
chloroplasts therefore no longer exist on own
Some genes were deleted from endosymbiont genome because there were
copies in hosts genome
Other genes were transferred from chromosome of endosymbiont to nuclear
genome of host and become dependent on host

Discoveries
-

-

1674: Royal Society of London received a package at a gentleman scientists lab
from Holland and it came from a man who built the world’s most powerful
microscope (hidden kingdom)
...
Royal society had a microscope but
never saw the organisms, so they thought the Dutchman was crazy
Antony Van Laden Hoek was not a scientist (linen-merchant) he inspected cloth
with magnifying glass and was obsessed with lenses (microscope)
...
He looked at water and saw moving
creatures/bugs/Protozoa
17th century: he assumed he saw miniature everyday animals with muscles and
hearts and called them animalcules
...
Looking through a microscopic he saw single celled amoeba (first to
see individual living cells)
...
Hoek wrote an important book that he saw and described
things (micrographia - first book)
...
Hoek thought he saw narrow channels carrying
sap up and down plant
...
He
improved magnification and saw animals which confirmed VLH
- Royal society made VLH a fellow and formally declared discover of little animals
- Most famous in Holland and royalties visited him to view his machine
- VLH scraped teeth and found more animals such as bacteria plaque and round
things in blood such as globules (red blood cells)
- He used his own semen and saw tiny animalcules with tails
...
He believed the sperm contained a tiny male and when in womb
it grew (never saw the male)
- Spontaneous generation: living organisms sprung from inanimate objects (van
Helmond) and he wrote a protocol of a mouse
- Plants have a structure made of cells: Scottish botanist Robert Brown brought
exotic plants and studied it (orchid has cells that are large, and he was
interested in sex life pollen grains to eggs)
...
He
was first to describe it and give it the name
...
Known for physics for the movement of particles in pollen
...
He met with a friend and both used nuclei to identify building blocks
...
Cells work together to make a large organism (founder of cell theory)
o Half of the theory is wrong as they believed new cells were spontaneous
and grew like crystals from tiny nucleus material

Biology 124

-

-

-

-

French Louis Pasteur convinced spontaneous generation didn’t occur
...

Louis said microbes and dust came from outside and went into flask then
accumulated = cloudy
New flask: let air in and keep out microbes and dust from outside like a swan
neck flask (microbes stick at bottom of curve) therefore sterile and free of
microbes
...
So he took 2 flasks,
one neck open and one with a swan neck with broth inside
...
Romack used a chick embryo (easily accessible
and can view easier under microscope) and took some blood in a pipette
...
Rudolf thought the research was rare and only to red
blood cells to only chicks
...
Saw cell
division after egg fertilized and 2 cells = 4 = 8 = 6 which then formed all tissues
and then the frog (key stone to theory)
...
5 billion years ago

EUKARYOTIC
Eu = after, karyon =
nucleus
1
...
Diseasecausing bacteria: presence/absence of capsule determines
whether the strain is infective/virulent or not
Plasma membrane:
o Transport materials in and out of the cell
o Contains molecular structures responsible for metabolism and
production of ATP (similar to eukaryotic mitochondrion)
o Photosynthesising prokaryotes: absorbs light energy and converts to
chemical energy in ATP (similar to eukaryotic chloroplasts
Genetic material is found in nucleoid, mass of highly folded DNA

Biology 124

-

-

-

o DNA is a single circular molecule unfolding from a chromosome when
released from the cell
o Genes are in the DNA code for proteins and RNA of cell
o Code is first copied to mRNA molecules
o Ribosome use mRNA to assemble amino acids into proteins
o Contains chromosomes & plasmids (small circles of DNA) in cytoplasm
– contain complementary genes, genes coding for antibiotic resistance
and replicate independently from nucleoid
o Prokaryotic ribosomes are smaller than eukaryote ribosomes – contain
less rRNA molecules and proteins
Move: swim through liquids/wet surfaces using thread protein fibres – flagella
o Flagellum: helical shape and rotates in socket in plasma
membrane/cell wall
Attachment: pili (protein shafts) extending from cell walls help them attach to
surfaces/other cells
o Sex pilus: specialised pilus that attaches one bacterium to another
during conjugation (mating) and DNA is transferred between cells
Metabolically versatile: utilise variety of substances as energy and carbon
sources
o Synthesis most of organic molecules from simpler inorganic
compounds therefore outnumber other organisms and inhabit all
regions

CARBON DIOXIDE
CARBON
SOURCE
ORGANIC
MOLECULES
-

-

ENERGY SOURCE
Oxidation of molecules
Light
Chemoautotroph:
Photoautotroph:
bacteria and some
photosynthetic bacteria,
Archaean’s
some protists, and plants
Chemoheterotroph:
some bacteria and
Chemoheterotroph: some
Achaeans, protists,
photosynthetic bacteria
fungi, animals, and
plants

Oxygen differentiation:
o Aerobes: require oxygen for cellular respiration and is final e- acceptor
o Anaerobes:
▪ Obligate: oxygen is poisonous and live via fermentation (organic
molecules final e- acceptor) or process where inorganic
molecules (NO3) final e- acceptor
▪ Facultative: use oxygen when present and fermentation in
absence of oxygen
Fix and metabolize nitrogen (Azotobacter and Rhizobium):
o N vital for amino acids and nucleotides
o Prokaryotes fix atmospheric N2 (convert N2 – NH3)

Biology 124

-

o Plant fixing nitrogen: microbes fix nitrogen in nodules on roots of pulse
crop by taking nitrogen from the air and converting it to carbohydrates
o Cells use NH4+ to produce amino acids and nucleotides
o N-fixation: prokaryotic process and way to replenish N sources needed
by plants/animals (all organisms use N fixed by prokaryotes)
Reproduction:
o Binary fission: parent cell divides to form 2 daughter cells (exact
copies)
o Conjugating (some): 2 parent cells mate and exchange plasmids
therefore genes carried on plasmid is transferred (sex pilus – strand
attaching the 2)
o Endospores (not many): dormant cell that can survive adverse
environmental conditions and carry bacterial genome and some
cytoplasm

Domain Bacteria
GRAM POSITIVE BACTERIA (purple)
-

-

Live as chemo heterotrophs
Human pathogens – Bacillus anthracis (anthrax), Staphylococcus aureus
(pimples, pneumonia, meningitis), Streptococcus pyogenes (strep throat,
scarlet fever)
Many beneficial spp
...
coli, Salmonella enterica
typhi
o Delta proteobacteria: slime bacteria
o Epsilon proteobacteria which is a small group in animal digestive tracts:
Campylobacter and Helicobacter

Domain Archaea
-

Inhabiting extreme environments – hot springs, hydrothermal vents, and salt
lakes therefore extremophiles
Some live in normal environments therefore mesophiles
Chemoautotrophs and chemoheterotrophs = obtain energy from oxidising
inorganic or organic molecules
Some are pathogenic to humans

CHARACTERISTICS

ARCHAEA

Membrane lipids with branched
hydrocarbons
Grow at temperatures greater than 100
Chromosomes are circular
Lack nuclear envelope
Lack membrane enclosed organelles
Methionine is initiator amino acid for
protein synthesis
Lack peptidoglycan in cell wall
Growth not inhibited when responding to
antibiotics streptomycin and
chloramphenicol
Histones associated with DNA
Contains many RNA polymerase

X

-

ARCHAEA AND
BACTERIA

ARCHAEA AND
EUKARYA

X (some)
X
X
X

Why do antibiotics kill bacteria (prokaryotes) and not body cells? Antibiotics
affect certain structures and processes unique only to prokaryotic cells
Bacteria can become resistant against antibiotics – they acquire the ability
(adapt) to combat the effect of antibiotics
Why do antibiotics affect prokaryotes and not eukaryotes? Antibiotics only
target components found exclusively in bacteria cell walls to prevent
growth/replication

X
X
X
X
X

Biology 124

-

Do antibiotics affect viruses? Viruses are surrounded by a protective protein
coating; they don't have cell walls that can be attacked by antibiotics like
bacteria does
...
Vacuole in plants is similar
Formed from budding off Golgi complex and enzymes are formed in rough ER

Biology 124

Mitochondrion and cytoskeleton
MITOCHONDRION
-

-

Organelles where most reactions of cellular respiration occur
o Cellular respiration: energy rich molecules (sugars/fats) are broken
down = carbon dioxide, water, and energy ATP – mitochondrial reactions
Structure: enclosed by 2 lipid bi-layer membranes
o Outer membrane – smooth and covers outside
o Inner membrane – expanded by folds (cristae) and more electron
transport chains as the surface area is increased
o The 2 mitochondrial membranes enclose the mitochondrial matrix
(enzymes)
o Cellular respiration reactions occur mostly in matrix/cristae – generate
ATP
o Mitochondrial matrix – DNA and ribosomes (like bacteria) and thought
to have originated from aerobic heterotrophic bacteria (endosymbiont)

CYTOSKELETON
-

Supports and moves cell structures with each cell having own characteristic
shape and internal organisation (kept in place by cytoskeleton)
Interconnected system of protein fibres that run through the cytoplasm
Animal cells: cytoskeletons well developed and supports the plasma
membrane and helps with the movement inside the cell and the cell as a whole
Plant cells: cytoskeletons less prominent as these cells are supported by cell
wall and large central vacuole (turgor pressure = shape)
Cytoskeleton has 3 types of structural elements:

Microtubules (largest) – tubulin proteins
-

Microscopic tubes and function like scaffolding (hollow tubes)
13 tubulin protein filaments arranged side by side (alpha - and beta +)
Occur in animal cells – they form and radiate out from centrosome near
nucleus with key functions:
o They anchor cell organelles: ER, Golgi complex, lysosomes, secretory
vesicles, and mitochondria (motor proteins carries vesicle)

Biology 124

o Provide tracks from vesicles to be transported from cell interior to
plasma membrane and back
o Separate and move chromosomes in cell division
o Maintain shape of animal cells
o Enable movement in animal cells – muscle cells (myosin’s, dynein’s,
and kinesins) and sperm cells (movement of tails)
Intermediate filaments – intermediate filament proteins
-

Fibres with 8-12 nm diameter occur singly, parallel bundles or interlinked
network
IFs are tissue specific in protein composition
Animal epidermis: nucleus held in by basket shaped network of IFs made of
keratins
Found in anchoring junctions between cells – button like spots/belts that keep
neighbouring cells together with IFs
Common in tissues that stretches frequently (heart muscle, skin, cell payers
covering organs and body cavities)

Microfilaments (smallest) – actins proteins (thin and small)
-

Thin protein fibres with 5-7 nm diameter consisting of 2 polymers
of actin molecules wound round each other
Functions:
o Transports nutrients, proteins and organelles in animal and plant cells
o Responsible for diving the cytoplasm in cell division
o Amoeboid movement

FLAGELLA – enables cells to move and are elongated, slender, motile structures that
extend from the cells surface
...
Found in protozoa,
algae, plants, and animals (sperm cell and reproductive cells of plants)
...
Vertebrates – occur in all body tissues (HEART MUSCLE
TISSUE)
o Pulp of teeth (not normally in nerve cells)

ECM (extra cellular matrix)
-

-

Organises the cells exterior
Animal cells are embedded in an ECM (ECM depends on tissue type) made of
proteins and polysaccharides
Function:
o Protection and support = mass of skin, bones, and tendons
o Forms high specialised EC structures (cornea and filtering network in
kidney)
Collagen is most abundant protein (tendons – tough/elastic, bone, and
cartilage)
Proteoglycans: determine consistency of matrix (soft and jelly/hard and
elastic)

Biology 124

-

Fibronectins: organise ECM and helps cells attach to it and bind to receptor
proteins (integrins)
Integral proteins: bind to cytoskeleton on inside of membrane and
communicate changes outside and inside

Plant cells
-

Unique and contain specialised structures

PLANT CELL
Chloroplast
Vacuole
Cell wall

-

-

BOTH
Nucleus
Cytoplasm
Ribosomes (80S)
Mitochondria, ER and Golgi
body

ANIMAL CELL
No chloroplast
No vacuole (lysosomes)
No cell wall
Flagella

Chloroplasts: site of photosynthesis
o Lens/disc shaped with an outer and inner boundary membrane
o Membranes completely enclose an inner fluid compartment (stroma)
o Stroma: flattened closed sacs (thylakoids – 3rd membrane system)
▪ Thylakoid membranes contain molecules (chlorophyll – green
pigment) that absorbs light energy converting it to chemical
energy through photosynthesis
...
DNA is similar to modern cyanobacteria
with identical genes
Central Vacuole:
o Large vesicles of plant cells recognised as distinct organelles
o 90% of mature plant cells volume may be occupied by 1/more large
vacuoles
o Pressure in the central vacuole supports the cell
o Tonoplast: membrane surrounds the central vacuole, and it contains
transporter proteins that move substances into and out the vacuole
o Plant growth – pressure and volume increases
o Functions:
▪ Stores salts, organic acids, storage proteins, pigments, and
waste
▪ Enzymes break down biological molecules (properties of
lysosomes)
▪ Chemical defences against plant pathogens
▪ Cell sap: high osmotic concentration = high uptake of water and
turgor pressure providing the plant with shape and strength
Cell Wall: extracellular structure
o Functions:
▪ Provides support for cells
▪ Contains pressure of central vacuoles
▪ Provides protection against pathogens
o Consists of cellulose fibres embedded in highly branched
carbohydrate network
o Initial cell wall laid down is primary cell wall – soft and flexible
...
Not change allele frequencies but genotype
frequencies
Individuals with similar genetically based on phenotypes mate and there will
be more homozygous offspring than expected under HWE (like mates with like)
o Finches: females have preference for males with same face colour (like
prefer like) = shift genotypes so genotype frequencies shifted to
homozygotes
All females prefer same male (one phenotype all mating) forms sexual selection
which will change allele frequencies

Sexual selection (certain phenotype selected):
1
...
Intrasexual selection – interactions between members of same sex where
males produce weapons (horns) to compete with other males for mates
- Sexual selection = sexual dimorphism, which is phenotypic differences between
sexes, so allele frequencies change dramatically over time
NATURAL SELECTION
-

Drives evolutionary change where there is no differentiate success/fitness

Biology 124

-

-

Relative fitness = variants contribute different members of offspring to the
next generation which leads to a variation in phenotypes and genotypes
(change) and acts on the phenotypes and through selection on phenotypes
alters allele frequencies (genotype)
o Allowing reproductive success (reproduce high number of offspring)
o Those with favourable traits (advantageous in competing for resources)
therefore have a high relative fitness
o Variation must be heritable to influence future generations
When individuals reproduce, all (favourable/unfavourable) alleles are
transferred to next generation so natural selection acts on all traits at all
stages and has minimal effect on traits that appear after reproductive life
(Huntington disease) so it cannot cure i
...
cancer that happens later in life so it
must occur in germ life
o Can be slow as have extra/negative alleles (unfavourable) are also
inherited

Natural selection = change in phenotypes (average trait between generations):
Directional selection (one direction)
-

-

-

Moegistorhynchus longirostris and Lapeirousia anceps – moving towards
creating a long tongue to get the nectar in the long tubes therefore higher
success
One side of the bell curve so one extreme has the highest fitness, mean shifts
from left to right
Select the most extreme phenotype have highest relative fitness (smallest
dog/fastest horse) and through time the trait value increases towards 1
extreme
o Force alleles to one side = lower the alleles
Artificial selection – hotter and hotter chilis

Stabilising selection (optimal)
-

-

In the middle (higher and narrow) of the bell curve have highest relative fitness,
even on both sides, variation decreases, mean doesn’t change so frequency of
alleles frequencies decreases
Intermediate phenotypes have highest selection therefore have middle value
between both extremes
Selection against both extremes: eggs too small not have offspring and too big
cannot be laid – stabilise
Wasp’s parasite more flies in small galls so selecting for bigger and bigger galls
and birds consume more flies in large galls so selecting for smaller and smaller
galls

Biology 124

-

Extremes from both sides become less (premature child and overweight child)
– wants the optimum

Disruptive selection (changes everything)
-

-

Cactus finches (Geospiza conirostris)
On the left and right side only (not middle) of the bell
curve – both extreme phenotypes are favoured
therefore both have high relative fitness
...
Those that do not meet this requirement are
unsuccessful
...
Right traits have a high relative fitness
(tallness) passing through to next generation
It is strong as there are a lot of individuals that are selected
MAINTENANCE OF VARIATION

Variation exists despite genetic drift and stabilising selection eliminating alleles
1
...
Balanced polymorphisms – 2/more phenotypes stable over generations and
therefore maintained by natural selection
...
Heterozygous advantage: heterozygotes have a higher relative fitness
than homozygotes therefore both alleles retained still allowing variation and
no elimination of alleles – Malaria and sickle cell disease which is
heterozygous therefore preventing blood cells from Malaria (HbSHbS
individuals die, HbAHbA have a high mortality during infections and HbAHbS
likely to survive)
b
...
Frequency dependant selection: common forms eliminated at
disproportionately high rate and uncommon forms at disproportionately
low rate
...
Selectively neutral alleles: different forms of a protein (coded by different alleles)
function equally well
...
More than 85% of living species
disappeared – trees, trilobite/marine species, reptiles, and insects at the end
of the Permian-Triassic-Jurassic period (sharp decrease)
CRETACEOUS (145-65 mya) mass extinction caused by asteroid impact where
dust clouds blocked the sunlight for photosynthesis
...
Major animal phyla evolved – end of Cambrian and beginning of Paleozoic
2
...
After Permian extinction, immediate ancestors of modern fauna evolved
Vascular plant diversity
1
...
Diversification of angiosperms resulted in decline of other plant groups in
Mesozoic
era and Cretaceous period – they had key innovations (flower and fruit
novelties)
-

-

-

Over lineage evolution change (time): horses have gone through the reduction
of toes (now long and narrow limbs), increased in body size, metacarpals of foot
have become one unit and increased grinding surface of molar teeth (different
habitats)
Hyracotherium (first horse species) did not change gradually into Equus
(modern horse) along a linear path – evolutionary branches
...
It is disordered and
overlaps
Dating of geology of the Rising Star places Homo naledi 200 000 – 300 000
years ago when other hominin species were alive as well as archaic forms
Homo sapiens
o 4 million years ago – Australopithecines (Australopithecus afarensis)
adapted to climbing as well as bipedalism and then had more specialised
diets of tough fibrous foods
...
africanus/robustus/sediba (2
mya)
o From 3 million years ago – Homo habilis – H
...
sapiens where
lower legs adapted to walking/running and smaller teeth with larger

Biology 124

brains (process more information) indicates they hunted and ate more
meat
o From 1 mya – H
...
Mutations can be eliminated or used for
advantageous purposes
o In humans, mice, and fruit flies – all have a functional Pax6 gene in the
eyes where the pupil is seen and a dysfunctional Pax6 gene where the
pupil is not seen
...
When extinction occurs, species/ancestors move into
new niches to radiate out species
Major morphological novelties (open new adaptive zones) punctuate history
of life – result quickly as a result of altered patterns of development in
regulating homeotic genes

HISTORY OF EVOLUTION
Evolution is the change in the population or species over time
...
All forms of life are related and descended from
shared ancestors through evolutionary change
Evolution provides:
1
...
Competition: a few survive with favorable traits
3
...
Selection: over generations there is a change in allele frequencies
What is evolution?
- Natural selection: natural mechanisms produce and transfer the diversity of life in
earth so individuals in a population best suited to environment will survive and
produce offspring therefore genes spread in future generations
- Darwin said biological species change over time and mechanism for change is
evolution which is driven through natural selection (Wallace helped with this)
History of evolution:
- Aristotle said that all things (from simple to complex forms) have fixed character
arranged on ladder of life through hierarchy

Biology 124

-

-

Pre-Darwin: natural theology in which everything is static (unchanged) as everything
was God’s creation which led to taxonomy (classification system = species, genus,
family, order, class, phylum, kingdom, and domain)
Organisms were fixed and unchanged: extinction impossible so organisms can’t
form through time and that the earth was young
Realization of evolutionary change (1500-1700)
o Biogeography: study of global distribution of organisms – adaptation based
on changes in environment
o Comparative morphology (Leclerc): all have digits, carpals, radius, ulna,
humerus (same structure) even if different in shape/size/function and same
attachment/embryos
o Fossil record: sedimentary rocks have different fossils in different layers –
bottom layers have simple life forms and upper have complex life forms but
through catastrophism there is an abrupt change in fossils which mark
environmental catastrophes
o Geological change: geological features on earth produced over time –
gradualism from James Hutton and uniformitarianism from Charles Lyell

Lamarckism: law of use and disuse - giraffe
- Used parts (stretched) became stronger and grew through time to become better
suited to environment and parts not used shrank and disappeared
...
Ancestors from South American diverged on the
island
...
Species change over time and share a common ancestor
1
...
Survival of the fittest (Thomas Malthus): human populations exceed food supply
available and people with resources and access food in natural population survive
Observations
1
...
Individuals within populations exhibit variability in many characteristics and many
variations appear to be inherited by subsequence generations therefore hereditary
characteristics may allow some individuals to survive longer/reproduce more
3
...
Adaptation by natural selection –
- When mosquitos were exposed to DDT, few resistant and insecticide killed most as
there was variability of traits being resistant and not resistant
- Resistant individuals survived/reproduced so passed genes for resistance to
generations
- Over time half pollution was resistant and the same concentration killed half
population
- Over time majority of population was resistant and same concentration killed a few
2
...
First contradicted Darwin as not gradual as there was a
change in next generation but it’s because there are many traits being dealt with
- Modern Synthesis (1900) from Haldane: consistency between genetics and
evolutionary changes
- Molecularly revolution: genome sequencing and PCR for how genes control traits
(natural selection) change phenotypes
- Misinterpretation: humans evolved from chimpanzees/gorillas they rather share an
ancestor and evolution is goal orientated (change happens between environment
and phenotype – response)
MACROEVOLUTION
-

Large scale changes in diversity and morphology over 3
...
Formation through
chemical replacement of minerals and fossil impression of external anatomy
only
Amber: no oxygen = decay is prevented so soft tissues are preserved
(invertebrates)
Fossils can be mummified in acidic and icy environments (peat bogs) allowing
external, internal and DNA analysis (genome – diseases) providing many details
Preserved in tar, dried saps, rock, amber, peat bogs – animals, plants (leave
impression – changes in shapes/pattern), wood (petrified wood – cells
mineralised)
o Pollen fossils – pollen grains have a hard exterior that fossilises greatly
Fossil record is incomplete because:
o Soft bodied things do not fossilize easily
o Rare and locally restricted species are unlikely to fossilize easily
o Fossils form in certain habitats
o Fossils are destroyed by geological processes (erosion expose fossils)
Fossils provide only direct information about the past such as trilobites:
o Appearance of organisms
o Change is traits through time
o Proliferation and extinction of lineages
o Past geographical distributions
o Indirect data about behaviour, physiology, and ecology
o Dating the history of life
▪ Relative dating: oldest sediments have the oldest fossils and
compare to environmental disasters
▪ Radiometric dating (isotopic decay) so unstable radioisotopes
decay into stable molecules: in newly formed rock 100% of the
parent isotope is present, after 1 half-life only 50% remains and
after 2 half-lives 25% remains (exponential decay)
• Radiocarbon dating (recent), uranium isotopes (older)
▪ Geological time scale: sedimentary strata & distinct fossil
assemblages – relative dating
• Hadean eon – formation of earth and crust (4600 mya)
• Archean eon – prokaryotes (unicellular) and oxygen started
to accumulate (3850 mya)
• Proterozoic eon – eukaryotic cells (2500 mya)
• Cambrian period – animal phylum and vertebrates
appeared (542 mya)

Biology 124

Mesozoic era in Triassic period – Pangea broke up (>201
...
6
mya) – gymnosperms, terrestrial habitats and dinosaurs and then Cretaceous period –
angiosperms (145
...
01 mya) [Oligocene period
– ape-like]
Earth history
-

-

-

Continental drift: Late Cambrian (514 mya) which is one land – Late Permian
(255 mya) where Pangaea identified super continent – Late Jurassic (152 mya)
where Gondwana (South America, India, and Africa) and Laurasia (North
America/Asia) identified – Late Cretaceous (66 mya) where oceans and
continents were identified
Plate tectonics (crossed plates floating on semi-solid mantel with currents =
slow movement across globe, built at oceanic ridges and absorbed into mantel
at oceanic trenches) and climate change (continental drift): circulation in
oceans and earths orbit has changed – dry spells where water is locked up with
ice and connectivity of land masses
...
The organisms have similar morphology across the continents
Endemism:

Convergent evolution: similar adaptations in distantly (separate land masses)
related organisms that occupy similar habitats/niches (not recent ancestors)
o Similar morphologies – large predators, burrowers (common
mole/marsupial mole), terrestrial seed eaters (house mouse/marsupial
mouse) have similar natural section
o Euphorbia in Africa and Cactus in North America (succulent plants with
spikes) – unrelated lineages converged to same adaptation

Evolutionary departmental biology
-

Molecular revolution – tools to understand morphology
MICROEVOLUTION

-

Evolution within a population: variants in phenotypes of individuals in a
population is critical for evolution and variation/structure results from life
experienced by individuals (nature of conditions)
...

- Therefore, diversity exists because of different evolution creating different
populations (phenotypes) and different areas/environments
- Qualitative variation is discrete and no intermediates (striped/not striped appeared or not) so when phenotypes are discrete, they are polymorphism

Biology 124

-

-

Quantitative variation is individuals that differ is small ways which is
continuous and measurable (frequency histogram = broad low curve shows
lots of variation and high narrow curve shows little variation)
Phenotype variation is dependent on genotype (genes are expressed produce
phenotype) and environment (size determines by nutrition or conditions)
Heritable genetic traits: different genotypes in same environment (variation
passed through generation)
...
Multiple variants = more combination of alleles
(blood types)
- Expression is determined on dominant alleles (always expressed) and
recessive are expressed if homozygous
- Population: localized group of interbreeding individuals (same
species/habitat)
- Gene pool: collection of alleles for a gene in a population
- Allele frequencies: how common a particular allele is in a population which is
the relative abundance (amount of A vs a)
Evolutionary change in populations
- Evolution is the change in allele frequencies in a population (micro-evolution)
- When allele frequencies are constant/not change or evolving = null model:
1
...
No migration of genes in and out so no gene flow
3
...
Random mating so no sexual selection
5
...
Testable model (null hypothesis): natural

Biology 124

-

-

-

populations are virtually never in HW equilibrium and is used to determine
which forces are causing micro-evolutionary changes in populations
...
Sum of allele frequencies must equal 1 (p + q
= 1)
BB = p2 and pp = q2 and Bb = pq (know p and q are you can find the genotype
frequencies) but p + q = 1 and p2 + 2pq + q2 = 1
...
If there are 100 flowers with 84 yellow and 16 red: q2 (bb) =
16/100 = 0
...
4 – recessive and p (B) = 0
...
So p2 =
0
...
16 therefore Bb (pq = 0
...
6) but 2 so = 0
...
THIS IS HW
EQUILIBRIUM
If genotype frequencies collected differ from HW equilibrium (expected) then
the population for a trait is evolving therefore changing through generations

Forces of micro evolution (not in HW equilibrium)
- Mutation
- Gene flow in or out
- Non-random mating
- Genetic drift (loss alleles)
- Natural selection (favorable conditions survive/fittest)
SPECIATION
-

-

The process in which over time (gradualism) populations change = new
species so population will diverge in allele frequencies by gene flow
It is the evolution of reproductive isolation
Microevolution occurs and then speciation (difficult to observe) which cause
macroevolution (large scale changes over time to be able to recognise)
Speciation: evolution of reproductive isolation mechanism preventing gene
flow linking small microevolution to large macroevolution – promoting
diversity
Species Panthera: lion, leopard, cheetah, and jaguar

Morphological species – observable traits so species differ in diagnostic traits
-

Birds of paradise
Sudden change of an aspect in the phenotype between species that produce
distinguishing diagnosis traits
o Yellow/white throat and flat/upright tail

Advantages
-

Useful for recognising species
Applied to extinct fossilized organisms

Biology 124

Disadvantage
-

Difficult to apply to morphologically variable/similar species
Doesn’t tell you about process which gave rise to species

Biological species – Ernst Meyer – 2 species reproductively isolated
-

-

Similar: groups of interbreeding natural populations that are reproductively
isolated from one another
If there is speciation for reproductive isolated species, they cannot produce
fertile offspring if given opportunity to interbreed – reproductive barrier or they
can’t interbreed as they are separated geographically – geographical barrier
Reproductive isolation prevents gene flow

Advantages
-

Species defined on basis of evolutionary concepts
Species easy to diagnose
Clear indication of process

Disadvantage
-

Doesn’t work for life that doesn’t reproduce sexually (asexual)
Doesn’t work for extinct life

Phylogenetic species – species have different evolutionary species
-

Group of populations that share a recent evolutionary history
o Panthera leo, Panthera pardus, Panthera tigris

Advantages
-

Can be applied to any group of organisms (sexual/asexual)
Can include extinct organisms
Distinctiveness of branches reflects lack of gene flow – reproductive
isolation of biological species

Disadvantages
-

Evolutionary history of only a few groups is known
Level of genetic distinctiveness used to define species is arbitrary – there are
different levels

Variation within species
-

Subspecies: morphically identifiable in different landscapes but can interbreed
Ring species: reproductively isolated on opposite sides of the ring but around
the ring it is not reproductively isolated which allows for gene flow
Clinical variation (body size decrease with increasing temperatures) – gene flow
can occur there is no barriers
o Continuous variation in traits along environmental gradients

Biology 124

o Neighbouring population adapting to different environ exchange genes
o Phenotypes different at end of gradients
Reproductive isolation
-

Biological species concept: ability of species to interbreed under natural
conditions
Reproductive isolating mechanism: biological characteristic that prevents
gene pools of two species mixing
...
Courtship – fireflies with light
signals
This causes no interbreeding with other species

Mechanical isolation
-

-

Different structure of reproductive organisms prevents successful mating
(genitals) allowing only certain animal organs to interlock with other animal
organs
Does allow interbreeding of the wrong species therefore only allowing same
species

Gametic isolation
-

Gametes don’t recognise each other as eggs and sperm are not compatible –
surface proteins which is common in sea urchins
Sperm needs to locate eggs of the right species and stigmas chemically
recognise pollen of the same species

Biology 124

POSTZYGOTIC ISOLATION (offspring are born and offspring reproduce)
Hybrid inviability
-

Species A and B (different phenotypes) can’t develop a proper zygote so dies
early because of mismatch which does not create hybrid offspring (F1) – sheep
and goats

Hybrid sterility
-

-

Species A and B (different phenotypes) create a zygote which leads to hybrid
offspring (F1), but those offspring are sterile because different in structure of
chromosome between the parent species which prevents meiosis in the
offspring
Horse and a donkey mate producing a mule that is infertile and cannot produce
fertile offspring

Hybrid breakdown
-

-

Species A and B (different phenotypes) create a zygote which leads to hybrid
offspring (F1) but the F1 offspring cannot create F2 hybrids – hybrids become
less fit
Hybrids produces viable gametes, but the viability breaks down through time

Geographic isolation preventing interbreeding leading to speciation
Allopatric speciation (continuous population) – different homeland
-

Geographical isolation creating 2 populations (barrier or long-distance
dispersal)
Genetic and phenotypic divergence based on the different environments
Secondary contact – barrier lifted or revert back
o Merging of populations – if there is no reproductive isolation
o Hybrid zones/reinforcement – reproductive isolation evolved = infertile
▪ Direct selection favouring prezygotic isolation through same
species
o Coexistence of reproductively isolated species

PHYSICAL BARRIER (Panama)
1
...
Geographical change (river changing course) separates the original populations
which creates a barrier to the gene flow
3
...
When river change course again allowing the species to come into contact, they do
not produce and therefore not allowing fertile offspring as there could have before
(secondary contact)
...
A few individuals of a species from the mainland arrive on isolated islands A and B
– geographically isolated populations on edge of range
2
...
e
...
Founder effects: populations diverge from the range centre and from one another
4
...
There are
nested hierarchy clades (clades within clades): node (ancestor) – straight

Biology 124

-

-

-

line – branches at node (ancestor) into descendants (clades have 2/more
ancestors)
o Sister species: closely related species to other species (share recent
common ancestor)
...
Moving
closes to root increases DNA difference
Anagenesis: change along the branch (continues “straight”) – even if straight
there is still change (mutations)
Cladogenesis: change related to speciation event – change at nodes
(branches off)

Systematics = classification of evolutionary history
-

-

-

Monophyletic taxon comprises of 1 clade and includes an ancestral species
and all the descendants with no other species throughout the tree with there
being many new ancestors for certain descendants (contains the most recent
ancestor)
Polyphyletic taxon comprises of species from different clades but not the
common ancestor of these clades (most recent ancestor not included), so
species form different evolutionary lineages
...

Helarctos

Traditional classification and paraphyly
-

Traditional systematics are based on morphology but does not always reflect
branching patterns of evolution
Reptiles: paraphyletic so all descendants of ancestor but exclude birds
o Birds are most closely related to crocodiles
o Reptiles are lizards, snakes, tortoises, and crocodiles
o But Class Reptilia is paraphyletic because it does not include Class Ave
(birds)

Data for phylogenetic analysis

Biology 124

-

-

-

-

Homologous characters = phenotypic characters with heritable genetics
which arose in common ancestors – similar due to presence in ancestors
(human, cat, whale, and bat)
o Similar in anatomical details/surrounding structures but slightly
different due to differences in selection pressure therefore suited for
different functions: phalanges, ulna and radius, humerus, ball & socket
movement
o Developed from the same embryonic tissue is similar ways
Homoplastic characters = phenotypic similarities that evolved
independently in different lineages, they are not similar because they were
present in a common ancestor but rather as result of convergent evolution
(skin and feathers)
o Similar selective pressures not common ancestors
o Forelimbs in flying vertebrates: wing surface have large surface area for
flight
Morphology = these differences are genetic and can be used to compare
extinct and living organisms but is not enough on its own to reveal
evolutionary relationships
Behaviour = when morphology is similar you can use behavioural traits –
prezygotic characters is what animals use to recognise each other
(calls/pollen)
Molecular DNA data = similar DNA sequences with chromosomes, histones,
DNA double helix and base pairs therefore creating similar proteins (only
variable characters used for relationships): extraction of DNA and sequences of
DNA
o Fewer changes of base pairs between species = more recently related
species
o Advantages = produces lots of data as each base pair is an
independent character, useful in distantly related groups/closely
related organism and not influenced by environment (no plasticity)
o Disadvantage = only 4-character states (A, C, T, G) – homoplasy by
change (same base at locus) is a problem as bases may be the same but
not because of their presence in a shared ancestor

Cladistics analyses
-

-

Cladistic methods are based on shared derived characters because in direct
common ancestors and not ancestors deeper in time = synapomorphies
o Morphological similarity is not good enough unless similarities reflect
descent with modification – needs characters with 2/more character
states (which evolved first – distance ancestors and which was derived –
direct ancestors)
Characters and character states:
o Character – eye colour and character states – blue, brown, or green
o Molecular characters – nucleotide bases and states – A, C, T, G

Biology 124

o Character – number of bones and states – 0, 2, 4, 6, 8
Synapomorphy (shared derived character states)
-

Serve as markers for monophyletic groups
Only defined when comparing character states among species – character is
derived (different compared to ancestor) in relation to ancestral state in other
organisms

Ancestral character (character state ancestor)/Apomorphy (derived character
descendent)
-

To distinguish – use fossil record to see transition between traits – ancestor
(distant)/derived (recent) but some fossils not present
Use of outgroups – characters of ingroup (derived) are compared with those of
a closely related species which is not in the clade studied
Characters of the outgroup (species related to clade) serve as ancestral
characters

Analysis
-

-

Cladistic: construction of phylogenetic trees by grouping
species with shared derived characters (synapomorphies)
Cladogram which illustrates the distribution of character
states and hypothesised sequence of evolutionary
branching
Common ancestors indicated by each node and
synapomorphies define each monophyletic group

Using phylogenetic trees – molecular clocks
-

Mitochondrial DNA (mtDNA) has high mutation rates therefore good for dating
over last million years (recent events) – point in time when branching occurred
Chloroplast DNA (cpDNA) and ribosomal RNA mutate slowly so good for
dating over 100s of million years (older events)
Molecular clocks/mutation rates need to be calibrated against fossils or
biogeographical breaks (marked)
o Use dates of developed of islands to calibrate nodes of molecular clocks

Testing evolutionary hypotheses
-

-

Similarity in species and a common ancestor = convergent evolution which
forms part of sympatric speciation
o Lake Tanganyika and Lake Malawi have similar species of fish – species
are closely related (relatives) so need to build phylogeny then shows all
fish are closely related so share common ancestor RECENTLY
...
Prophase (no thread chromosomes = condensed, nucleus starts to disintegrate,
spindles)
On the surface of the nucleus double chromosomes condense and centrosomes
generate the spindle as they separate
...
Centrosomes split and form
centrioles when they move to the opposite end of the poles with
branched microtubules
In S phase there are duplicated centriole pairs which forms an
aster (looks like a star) leading to early prophase where there is the
old centriole and new centriole that pair up
...
Centrosomes = centrioles and microtubules
2
...
There is a pair of centrioles at each spindle pole (opposite ends) with

Biology 124

kinetochore microtubules attaching the kinetochores (proteins) to the centrioles (actin
filaments are the middle fibres)
Non-kinetochore microtubules are tubules (spindle fibres) that are not attached to
any kinetochore
3
...
Anaphase (kinetochore microtubules pull)
Spindle separates the 2 daughter chromatids and
moves them to opposite spindle poles
5
...
Plasma membranes that
line the 2 surfaces of cell plate are derived from vesicle membranes

Biology 124

Result of mitosis
-

2 daughter cells with genetic duplicates of each other and to the parent cell
(G1)
Chromosomes different through cycle: count chromosome by centromere
o 1 chromosome (single – gamete) with 1 chromatid = double (2
chromatids)
o Homologous pairs (double stranded)
o Homologous pairs separate to ends (double stranded)
o Anaphase 2: back to single stranded – gamete

Defects of regulation of cell cycle
-

-

Cancer: normal cells = abnormal cells = multiply = malignant cancer
o Grows own blood vessels (angiogenesis) and invade surrounding tissue
o Overactive cell cycle forms abnormal growth (cancer)
Wounds that do not heal have a defective cell cycle

3 checkpoints for the regulation of the cell cycle:
1
...
G2/M transition: DNA replication and commits cell to
mitosis (cell will not enter point in DNA replication
incomplete/defective)
3
...
Describe cell cycle: G1 for growth of cell, S phase for DNA replication, G2 for
growth and preparation for mitosis which is all interphase and then it is Mitosis
for cell division
2
...

3
...

Spindle fibres are made up of microtubules which form a protein structure that
divides the genetic material in a cell and is necessary to equally divide the
chromosomes
4
...
Diploid multicellular organism (46 chromosomes) undergoes meiosis
(ovary/testes)
2
...
Fertilisation occurs when 2 haploid gametes fuse (1 maternal and 1 paternal)
4
...
Humans are diploid – 2 alleles at each
genetic locus with 1 allele inherited from each parent

Meiosis
1
...
Replication during premeiotic interphase
3
...
Chromosome pairing during prophase 1 of meiosis – nuclear membrane
dissolves and centrioles to poles
5
...
Metaphase 1: they line in the middle and Anaphase 1: they are pulled by the
homologous chromosome whereas Anaphase 2: they pulled by centromere
7
...
MEIOSIS 2: each of the 2 cells split into 4 cells where the sister chromatids
are separated therefore creating single chromosomes (haploid)
Equational division of n – n
9
...
Genetic recombination – crossing over in prophase 1 between non-sister
chromatids
Structure is tetrad with one original allele and the other allele recombinant
If no crossing over, it will inherit the same alleles from parents
2
...
Random joining of male and female gametes in fertilisation – random fertilisation
Male/female gametes by meiosis are genetically diverse and joins by chance
Summary
-

-

-

Meiosis: production of haploid gametes where there are 4 daughter cells
genetically different with half the number of chromosomes as the original cell
First division (meiosis 1) is 2n to n where there is replication of chromosomes
(mitosis), recombination (crossing over of homologues) and separation of
homologues (anaphase) – WHOLE CHROMOSOMES
Second division (meiosis 2) is n to n where there is separation of sister
chromatids (similar to mitosis) – SINGLE CHROMOSOMES
Generate diversity: recombination (crossing over), independent assortment
and random segregation of homologues and sister chromatids, and random
joining of female and male gametes
Mitosis (diploid end): daughter cells have same chromosome number as
parent, 2 nuclei formed and genetically identical to each other and parent cell
whereas Meiosis (haploid end) has half the number of chromosomes as
parents, 4 nuclei formed and genetically different to each other and parent cell
with crossing over

Biology 124

Questions:
1
...
What is recombination and where does it occur?
Exchange of genetic material between organisms leading to offspring with a
combination of traits (alleles) creating genetic diversity occurring in the nucleus
during prophase 1
3
...
Helps maintain a
constant number of chromosomes to avoid over duplication
4
...
True breeding: when self-fertilised it only produces offspring with the
same traits and true breeding is genetically identical and have identical
alleles for a trait (homozygous)

Dominant and recessive alleles
-

-

Trait that disappeared was present but masked by the stronger/dominant
allele
Mendel’s conclusion:
1
...
If a pair of alleles of gene consists of different alleles
(hybrid/heterozygous) – one is dominant, and the other is recessive
(masked)
In a homologous chromosome, one chromatid will be purple (P) and other
chromatid will be white (p) – gametes
Phenotypes: observable trait which is the appearance presented by a
genotype (dominant alleles shows which trait will show)
Genotype: genetic composition of alleles of a gene
Homozygotes/true breeding: both alleles of the gene are the same (PP or pp) –
pure bred can only produce 1 gamete (P, P or p, p)

Biology 124

-

Homozygous: it is an individual that is homozygote – homozygous for a particular
allele of the gene (homozygous recessive or homozygous dominant)
Heterozygotes: alleles of the gene are different (hybrid) – produces 2 types of
gametes (Pp = P and p)
Heterozygous: it is an individual that is heterozygote – heterozygous for the pair
of different alleles of a gene
Hybrid: offspring of parents with different traits
Dominant allele (uppercase): determine trait expressed when paired with
recessive allele (Pp/PP)
Recessive allele (lowercase): expresses trait only when 2 copies of allele is
present (pp)

Mendel’s monohybrid crossings
-

-

He studied a variety of characteristics one at a time (seed form/cotyledon,
flower colour, pod form/colour, stem place/size)
He focussed on alternative forms (alleles) which is the trait of phenotypes
(flower colour – white/purple)
1
...
F2 generation will always be in ratio of 3:1 when self-fertilisation
happens (75:25%)

3rd conclusion – Principle of segregation: Mendel’s first law of heredity
-

The pairs of alleles separate/segregate in meiosis during gamete formation so
that half the gametes carry one allele and the other half carry the other allele and
that each gamete only consists of 1 allele for each gene

Testcrosses
-

It is a test to determine/predict the genotype (homozygous/heterozygous) of an
organism with a dominant phenotype for a trait by looking at offspring
1
...
If half offspring shows recessive trait and half shows dominant trait
(50:50), then the unknown genotype is heterozygous (Pp)
3
...
F2
generation (self-fertilisation) is 9:3:3:1

4th conclusion – Principle of independent assortment:
-

Segregation of different genes carrying different traits occurs independently
during gamete formation – alignment of homologous pairs in metaphase can
occupy different positions and in anaphase they separate independently

Later modification and addition to Mendel’s hypothesis
1
...
Co-dominance: alleles have approximately the same effect in individual (both
combined and equal) – RR with WW = RW (red and white spots)
3
...
+ or – on blood group = presence or not of antigen (- mother with +
child = body produce antibodies and attack foetus)

Biology 124

Antigens (A and B) communicate with white blood cells
4
...
Polygenetic inheritance: multiple genes responsible for a trait (enviro
responsible)
Steroids/not, bird colour with many different colours, height, and skin tone

6
...
How can a trait skip a generation and appear in the next?
The recessive trait was masked as the parents were homozygous dominant and
recessive therefore the dominant trait showed up and the recessive trait was just
present but not showing/masked
...
Phenotype, genotype, heterozygous, homozygous, dominant, and recessive
definitions:
Phenotype: observable physical properties determined by the genotype and
environmental conditions affect the phenotype
Genotype: it is the set of genes organisms have after genetic material has been
passed that consist of a combination of alleles
Heterozygous: 2 different alleles for a particular gene
Homozygous: 2 identical alleles for a particular gene – dominant or recessive
Dominant: an allele of a gene on a chromosome masking another allele and is
produced even if it has one copy of the allele
Recessive: phenotype does not appear if there is a dominant allele therefore
often being masked and is produced only if it has 2 copies of the recessive allele
Monogenic inheritance: characteristics controlled by single gene at a single
position (locus) on chromosomes
Polygenic inheritance: characteristics controlled by more than one gene found
at different positions (loci) on one/more chromosomes
3
...
Therefore two alleles of a gene separate so each gamete contains one
of the factors
Independent assortment: factors controlling different characteristics are
separate entities not influencing each other and sorting themselves out
independently during gamete formation – metaphase and anaphase
4
...
Incomplete and co-dominance, epistasis, and pleiotropy definitions:
Incomplete: no allele is dominant so there is no recessive or dominant allele –
when in combination the alleles produce a third phenotype (phenotype is
intermediate)
Co-dominance: both alleles are equally dominant – when in combination both
alleles affect phenotypes (partial)
Epistasis: expression of one gene is affected by expression of one/more
independent genes
Pleiotropy: one gene influence two or more unrelated phenotypic traits which is
a gene that exhibits multiple phenotypic expressions

Biology 124

GENES, CHROMOSOMES & HUMAN GENETICS
Genetic linkage
-

Mendel: genes assort independently (not inherited together)
TH Morgan: genes located on the same chromosomes may be inherited
together

Drosophila melanogaster (model organism – fruit fly)
-

-

4 pairs of chromosomes not 23 pairs (small genome)
Easy to maintain and inexpensive
Shares 60% with human genes
Short generation time – 10 days
High fecundity (reproduction) – 100 eggs/day and can be genetically modified
There are many mutants
Red eyes and normal wings = wild type and purple and vestigial = mutant type
Wild type: a phenotype, genotype or gene that predominates in natural
population of organisms/strain of organisms in contrast to a natural/laboratory
mutant form
o Wild type is most common in populations and wild type allele is
dominant
Garden peas = 1 generation per a year of drosophila = 36
...
6% - highest recombination therefore greatest distance
between the gene a and b (most cross overs)
o a and c = 8% (possible cross overs)
o b and c = 2% - lowest recombination therefore smallest distance between
the gene b and c (cross over might not occur)

Sex chromosomes in humans
-

-

Diploid cells in female parent (homogametic) of XX and diploid cells in male
parent (heterogenic) of XY undergoes meiosis = eggs and sperm gametes
which fuses in a punnet square to form an F1 generation with 50% male: 50%
female
Sex chromosome is chromosome 23 (22 autosomes and 1 gonosome)
The y gamete is smaller/shorter in the karyotype
Sex-linked genes are on sex chromosomes so XX-XY arrangement causes sex
linkage:
o 2 copies of alleles on X chromosome in females (XX)
o One copy of the alleles on the X chromosome in males (XY)
o Alleles on the Y chromosome are absent in females
o XY – father Y and mother X and XX – consists of father X and mother X

X linked and other gene inheritance patterns and pedigree analysis
-

-

Family tree/Pedigree: examines the way a trait occurs in a family
Pedigree analysis: some symbols used in human pedigrees
o Used to identify patterns of inheritance of traits/diseases and
interpretation of genotypes/phenotypes a whether it is X linked or Y
linked
o Males are squares and females are circles
o Marriage/reproduction are horizontal lines (line between 2 shapes)
o Offspring are shown by a line from marriage and is vertical
o Shaded shapes – trait, unshaded do not and heterozygous half-shaded
(carry)
Haemophilia is an X-linked recessive disease/royal disease: blood lacks
ability to clot as 1/more plasma proteins is absent
...
Daughter of a haemophilic male will always inherit his mutation
and then to have the disorder depends on if the mother’s recessive/dominant
allele is transferred whereas a son will always have the disorder if the recessive
allele is transferred from the mother as there is no masking with another X

Biology 124

allele as a male has one X as the other is a Y
...
Both
chromosomes of one pair are separated to the same pole of
the spindle and 2 gametes have an extra chromosome and 2 have a missing
chromosome
Non-disjunction in Meiosis 2 – separation of sister chromatids failed
Aneuploidy: produces 2 normal gametes (2 cells) and 1 with an extra chromosome
and 1 with a missing chromosome
-

-

Trisomy 21: non-disjunction of chromosome 21
in meiosis = down syndrome
o 3 chromosomes on chromosome 21 not 2
o Live to 60
Trisomy 13: Patau syndrome (early death)
Trisomy 18: Edwards syndrome (early death)

Questions:
1
...
Use a dihybrid cross
for 2 different genes
2
...
Infer the relative order of genes based on observed recombination
frequencies
Further away the chromosomes are the more cross overs therefore half the
gametes will have recombinant chromosomes and the other half will have nonrecombinant chromosomes (same as the parents) = 4 different gametes
...
Autosomal dominant and recessive inheritance:
Autosomal dominant – cannot be recessive as two affected parents can not
have an unaffected offspring (parents must be heterozygous) = Aa * Aa
Autosomal recessive – cannot be dominant as two unaffected parents can
not have an affected offspring (parents must be heterozygous) = Aa * Aa
5
...
If only one gene in the pair is abnormal, the disease does
not occur
6
...
Non-Mendelian inheritance: any pattern of inheritance in which traits do not
segregate in accordance with Mendel's laws (mitochondria, cytoplasm DNA and
genomic imprinting)
8
...
Variations in chromosome number: aneuploidy (abnormal chromosome
number where there is a loss/addition of chromosome sets), monoploidy (loss
of chromosome set – less than 1 set), polyploidy (more than 2 sets), trisomy 21:
non-disjunction of chromosome 21 in meiosis = down syndrome, trisomy 13:
Patau syndrome (early death), trisomy 18: Edwards syndrome (early death)
10
...
They are
then coiled to form a 5’ and 5’ (top and bottom on left) and 3’ and 3’
(bottom to top on right)

Complementary nitrogenous base pairs: adenine pairs with thymine/uracil (2
hydrogen bonds) and cytosine pairs with guanine (3 hydrogen bonds – more stable)
therefore double rings (purines) always pair with single rings (pyrimidines)
Antiparallel: the 2 strands of double helix run in opposite directions – the 3’ end of
one strand is opposite the 5’ end of the other strand (both at the top but on opposite
strands)
Bond strengths:
1
...
Phosphodiester bonds – covalent bond (sharing of electrons) in phosphate
molecule therefore intramolecular forces
3
...
Van der Waals forces – weak bonds
DNA replication – Watson and Crick model:
-

-

-

DNA is double stranded helix shape, and strands are complementary (consists
of complementary base pairs A-T and G-C by hydrogen bonds) being antiparallel
Two strands unwind and unzip with the hydrogen bonds breaking between
bases
Replication: each old strand (now 2) serves as a template for new nucleotide
bases to join and form a new strand
...
DNA double helix opens: initiator proteins bind to replication origin (3’), helicases
unwind helix, SSB proteins stabilise single strands and topoisomerase relieve
torque/twisted generated by winding creating a fork
2
...
Elongating complementary strands: DNA polymerase III binds both sides of
replication fork, moves down parental double strand (5’ to 3’) and complementary
sequences on both parent strands synthesise simultaneously – leading is made
continuously by the 5’ to 3’ direction by adding nucleotides but the lagging strand
is made discontinuously by Okazaki fragments and each fragment strands with
RNA primer and DNA polymerase adds DNA bases in 5’ to 3’ then another primer
is further down
4
...
Joining the Okazaki fragments: DNA ligase seals nick (phosphodiester bonds) =
continuous (semi-conservative = one old and one new strand)

Biology 124

Replication bubble
-

Each of the replication forks move away
from the origin (3’ OH) replication

DNA is fast and accurate
- Many replication origins

Repairs of errors in DNA made by DNA polymerase
-

-

Proofreading: DNA polymerase adds nucleotides to new chain and builds 5’
to 3’ according to base pairing rules, it rarely adds mispaired nucleotides,
when it does it recognises the mistake, so it reverses (3’ to 5’) and removes the
mispaired molecule
...
Describe the 3D structure of DNA:
Double helix twisted/winded structure with a sugar-phosphate backbone attached
to a deoxyribose sugar and a nitrogenous base, there are complementary base pairs
attaching by hydrogen binds to each other, the strands of DNA run antiparallel so
the 5' end of one DNA strand is parallel with the 3' end of the other DNA strand
2
...
The N bases (purines and pyrimidines):
Adenine and guanine are purines (double ring), and cytosine and thymine are
pyrimidines (single ring)
...
Describe DNA replication steps:
Recognition of origin – the replication fork/bubble begins; RNA polymerase and
initiator proteins initiates the synthesis of RNA primer for formation of DNA chain,
nicks (discontinuity/no attachment/cut open) are produced by endonuclease
enzyme, helicase unwinds helix, SSB proteins stabilise single strands and
topoisomerase relieve torque/twisted generated by winding
RNA primer – RNA polymerase synthesizes RNA primer on template DNA
(complementary)
Chain elongation – new DNA strand is formed due to DNA polymerase III enzyme
...
Polymerizing activity of
polymerase III enzyme takes place in 5’ to 3’ direction
...

The other strand having 5’ to 3’ polarity (below) gets synthesis of DNA in small
fragments (okazaki fragments) therefore it is the discontinuous/lagging strand
...

Ligation is when RNA primers are exited out once the replication is finished
...

5
...
Proofreading and mismatch/base pair excision repair that corrects DNA
replication mistakes:
DNA polymerase I and polymerase III act as proof-readers of the newly formed DNA
...
Repair enzymes
scan DNA for distortions due to
mispairing and break backbone on each side of mismatch, remove mismatch and
adjacent nucleotides, DNA polymerase I fills the gap using template as a guide and
then ligase joins the nicks to complete repair

GENE EXPRESSION: TRANSCRIPTION
Gene expression for protein synthesis
-

-

-

Flow of genetic information from gene to protein involves transcription &
translation
DNA is replicated and the DNA template is used for transcription in which
mRNA is formed on the template (transcribed) to create a single stranded
complementary copy, but uracil replaces thymine – translation occurs where
a protein is formed due to a polypeptide composed of amino acids (RNA used
and converted to amino acid)
The template strand is read as 3’ to 5’ and the non-template strand
(complementary strand) is built 5’ to 3’ which becomes the mRNA
Transcription: RNA polymerase (II) reads the DNA template as 3’ to 5’ to
create an mRNA strand
...
Role of transcription in protein coding gene expression:
It allows the DNA sequence to be copied/transcribed into a mRNA molecule so that
it can be used in translation in order to create proteins by the building blocks of
amino acids so that our bodies can function – it is the key step in using information
from a gene to make a protein
2
...

Elongation: RNA polymerase II moves along the DNA (RNA transcript) to form mRNA
and RNA polymerase is released
...
Difference between prokaryotic and eukaryotic protein coding gene
transcription:
PROKARYOTES
PROKARYOTES
Transcription and translation in
Transcription in nucleus and translation in
cytoplasm
cytoplasm
DNA/RNA in cytoplasm
DNA in nucleus and RNA travels out/in
nucleus
RNA poly binds directly to
RNA poly binds to TATA box and transcription
promoter
factors
Transcription makes mRNA (not
Transcription makes pre mRNA – RNA
processed)
processing – mRNA
No introns
Exons and introns (cut out)
4
...
Processing of pre-mRNA:
RNA polymerase transcribes the DNA molecule starting at the promotor, 5’ cap
(UTR) with G – guanine added, and transcription continues past the end of the gene
and stops at cleavage site by the 3’ tail end (UTR) where there is polyadenylation
signal and an addition of poly (A – adenine) tail to the 3’ tail end
...
Mechanisms of splicing:
Introns are recognized, looped, degraded, and removed by a protein (snRNPS) and
RNA complex called the spliceosome as they are non-coding proteins only there to

Biology 124

increase the area of binding
...
Role of alternative splicing:
Introns provide protein variability and increase coding capacity without increasing
genome with a single gene coding for many proteins (more than one mRNA can be
made from the same gene)
GENE EXPRESSION: TRANSLATION
Translation: polypeptide synthesis
-

mRNA: 5’ cap, 5’ UTR, the start codon, coding region, stop codon, 3’ UTR,
poly(A) signal and then the poly(A) tail
Ribosomes: have a large subunit and a small subunit with the small subunit
combining to the mRNA
tRNA: codon (mRNA 5’ to 3’) i
...
GCC attaches to an anticodon (CGG) at the
bottom of the tRNA molecule, there is then intramolecular base pairing and at
the top the required amino acid is attached by an ester bond to the tRNA
molecule at the 3’ end (amino acid is based on the mRNA sequence)
o Amino acid: amino group (NH2), a variable chain (R) and a carboxylic
acid group (C double bond at top – OH)

Process (ALL HAPPENING ON/IN RIBOSOME):
-

-

mRNA translated into amino acid in ribosomes to produce polypeptide
(cytoplasm)
o Ribosomes facilitates the binding of tRNAs to codons on the mRNA and
the formation of a peptide bond at the 5’ to 3’ end so a ribosome moves
codon by codon in 5’ to 3’ direction
o Anticodons are attached to the tRNA which attach to the mRNA so then
tRNA reads the codon and introduces the next amino acid after which
tRNA are released with no amino acids – starts at the A site – P site then
E site
o A polypeptide chain is made from N-terminal (at Met with H3N+) to Cterminal end (COO-) with the first amino acid/codon being Met (Acyl)
mRNA associates with a ribosome and tRNAs bring a specific amino acid
o tRNAs (amino acid & anti-codon) bind to exposed codon (5’ to 3’) on
mRNA via complementary anti-codon (3’ to 5’) with attached amino
acid (3’ to 5’)
o Wobble hypothesis: pairing with 3rd nucleotide of codon is more flexible,
the same tRNA can read C/U and inosine allows for pairing with C, T, or
U
o Ribosomes read mRNA codons and moves 5’ to 3’ direction
o Amino acid is based on the mRNA codon
▪ Aminoacyl-tRNA complex is when amino acid being AA attached
to 3’ on tRNA formed through aminoacylation/charging

Biology 124

-

▪ Enzyme responsible to aminoacyl-tRNA synthetases
E – exit, A – aminoacyl and P – peptidyl site on large subunit of a ribosome and
the small subunit of a ribosome situated on the mRNA: aminoacyl-tRNA
carrying the next aa to be added to polypeptide binds at A site on mRNA, tRNA
caring growing polypeptide chain bound at P site and tRNA without aa binds
to E site before exiting ribosome (RIBOSOME MOVES ON MRNA and reads
codon as moved from 5’ to 3’ and join amino acid)

Stage 1: initiation
-

-

-

Methionine (AUG) amino acid attaches to the initiator tRNA at 3’ (GTP) and has
an anticodon attached to start the codon at the bottom, the anti-codon
attaches the mRNA codon on the small subunit of the ribosome
Initiation complex: components assemble on the start codon of the mRNA
which is situated on the P site of the large subunit of the ribosome after
scanning has taken place from the 5’ cap on the smaller subunit
GTP is released as GDP and a phosphate molecule
Base-pairing: binding of tRNA & mRNA through
scanning

Biology 124

Stage 2: elongation – assembled complex reads string of codons in mRNA 1 at a time
while joining amino acids in the polypeptide
-

-

-

Ribosome with initiator Met-tRNA bound to the P site and the A site is empty
(mRNA at the peptidyl site) with GTP converted to GDP + phosphate group
released
Aminoacyl-tRNA with AA2 binds at the A site (aminoacyl) with GDP hydrolysed
There is a creation of a peptide bond between Met and AA2 with GTP converted
to GDP + P as it uses energy – peptidyl transferase binds aa and forms peptide
bonds
A tRNA attaches to the E site without an amino acid (exit) and the empty tRNA
is released from the E site

Stage 3: termination
-

Ribosome reaches a stop codon after enough scanning is done (UAG, UUA or
UGA)
There is no tRNA for a stop codon – RF (release factor/terminal factor) binds to
A site as its shape mimics tRNA including region like anticodon for stop codon
RF stimulates peptidyl transferase to cleave polypeptide off the tRNA from P
site, no aminoacyl-tRNA is in the A site and the polypeptide is released
Uncharged tRNA & RF released, and ribosomal subunits dissemble
(small/large)

Biology 124

Polypeptides are processed and folded into final forms
-

Certain amino acids are removed and there is addition of carbohydrate/lipid
groups
Proteins need helper proteins (chaperones) to fold into 3D shapes
Some proteins are processed into initial/inactive form (pepsinogen) which is
later activated by removal of segment of amino acid chain (different location
in cell/certain time) – digestive enzyme
pepsinogen

Finished proteins are sorted to where they function
in cells
1
...
Endomembrane system: ER, Golgi,
lysosome, secretary vesicles, nuclear
envelope, plasma membrane
3
...
Pathway from gene to protein: transcription and translation
5’ cap with a G, 5’ UTR, the start codon, coding region, stop codon, 3’ UTR,
poly(A) signal and then the poly(A) tail
...
Ribosomes read
mRNA codons and moves 5’ to 3’ direction
...

Aminoacyl-tRNA complex forms with the first amino acid being AA at the 3’ end
(as the mRNA is 5’ to 3’) through aminoacylation/charging via aminoacyl-tRNA
synthetase
...
Organisation of genetic code in triplets
On the mRNA from the 5’ to 3’ end there are codons which consist of 3
nitrogenous bases/nucleotides (triplets) and each codon codes for 1 amino acid
which is brought by a tRNA through the base complementary attachment of the
anticodons
...
Process of translation: how amino acids are assembled in polypeptides
occurring on the ribosomes, tRNA molecules with an attached anticodon and
amino acid attach to the mRNA codon via the complementary anticodon which
is in the 5’ to 3’ direction therefore the attaches amino acid is on the 3’ end
...
Peptide bonds form between amino
acids to form a polypeptide chain (composed of an N-terminal end and a Cterminal end)
4
...

Energy is used so GTP = GDP + P
...
There is a
formation of a peptide bond between Met and AA2 (peptidyl transferase binds aa
and forms peptide bonds)
...
RF stimulates peptidyl transferase to cleave
polypeptide off the tRNA from P site as the add a water molecule (hydrolyse) to
last amino acid, there is no aminoacyl-tRNA in A site and polypeptide released
...
Polypeptides are not finished proteins

Biology 124

Certain amino acids need to be removed and addition of a carbohydrate/lipid
group, to become a protein, helpers (chaperones) need to fold the chain into a
3D structure
...
They then need to be
sorted to function – EMS/membrane organelles
REGULATION OF GENE EXPRESSION – PROKARYOTES
Importance of regulation of gene expressions
-

The series of divisions eventually produce all the specialised cell types
Structural and function differences are determined by patterns of gene
expression that result in different sets of proteins
Determines if the genes are expressed or not

Transcriptional regulation determines which genes are transcribed into mRNA
Prokaryotic cells – short term response (switch on/off)
-

-

Rapid alterations in biochemical pathways allow them to adapt quickly to
changes in their environment
o Turn off genes for metabolic process not needed (HCl not activated in
eyes)
o Turn on genes for metabolic process needed (HCl activated in stomach)
When lactose is present, E
...
This allows
transcription/translation to occur for production of lactose catabolism
enzymes (repressor acts as a lactose sensor) so lac operon structural genes
activated
Lac operon: promoter (RNA polymerase), operator (repressor), transcription
initiation site, 3 structural genes (lacZ, lacy, lacA), transcription terminal site

Positive regulation: RNA polymerase does not bind efficiently and needs help
to achieve high levels of transcription via a CAP (produced in inactive form) and
cAMP (cyclic AMP – hunger) (high transcription = glucose is low)
o cAMP (in promotor) activates CAP if glucose is low
o CAP binds to the CAP site (in promotor)
o Bound CAP helps RNA polymerase bind to promotor for genes
expression
Lactose present & glucose low/absent: structural genes expressed at high
levels
• Active lac repressor with allolactose inducer = inactive repressor
(structure change) so transcription will take place, lots of cAMP, active CAP
attaching to the CAP site (in the promotor) with RNA polymerase at the
binding site (in the promotor), transcription occurs for the formation of
mRNA after which is translation
...

HIGH LEVEL OF GENES
• Positive regulation: lactose + glucose (decreases) then structural gene
increase
Lactose present & glucose present: structural genes expressed at low levels
• Active lac repressor with allolactose inducer = inactive repressor so
transcription will take place, no/very low cAMP, inactive CAP attaching to
the CAP site so RNA polymerase cannot bind efficiently to the binding site
(both in promotor) so there is low level of transcription
...
Why regulation of gene expression is necessary
Divisions produces specialised cell types; it determines structural and
functional differences and determines if genes are expressed or not (regulation
conserves energy and space as it would require a significant amount of energy
for an organism to express every gene at all times, so it is more energy efficient
to turn on the genes only when they are required) and makes sure the correct
proteins are made
...
Transcriptional control in prokaryotes: transcription factors/proteins =
activator/CAP (increase transcription – help DNA polymerase bind to promotor)
and repressor (binds to operator and blocks RNA polymerase = no synthesis)
...
Features of an operon
Contains 3 genes (lacZ, lacY and lacA) that are transcribed as mRNA by control
of the promotor that helps cell utilize lactose, DNA sequences – regions where
regulatory proteins bind, promotor – binding site of RNA polymerase, operator –
negative regulatory site where the repressor binds to (binds when lactose is not
present) which overlaps the promotor so when the repressor binds the RNA
polymerase cannot bind to promotor (no transcription), CAP binding site –
positive regulatory site bound by CAP which promotes transcription and allows
RNA polymerase to bind
4
...
Positive regulation of Lac operon by activator
Lactose present – receptor loses DNA binding ability, but DNA polymerase
cannot bind on its own to the lac operon promotor, so it gets help from CAP to
attach to promotor in which the CAP is binded to the CAP site (region before the
lac operon promotor) = high transcription
Low glucose: cAMP (made by E
...
Inducible system
The lac operon is considered an inducible operon because it is usually turned
off (repressed) but can be turned on in the presence of the inducer allolactose
...
coli – lac operon
Translate this information into humans/animals



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