Last Updated: 12/05/25 (addition of D3.1 - D4.

3)
GOOD LUCK EVERYONE!
A1.1 - Water - September 9 2024

Cohesive forces of Water Molecules

●​ In plants, cohesion allows water to be drawn up xylem, and fulfill other functions
for plants → there are continuous columns of water in xylem
●​ Water surfaces used as habitats
○​ Surface tension → water molecules more attracted to each other than air

●​ Adhesion: when hydrogen bonds form between water and the surface of a polar
material
○​ Capillary action: movement of water through adhesion through narrow
glass tubes → formation of bonds between water and glass
○​ Soil: Water is attracted to chemicals in soil → capillary action occurs in
dry, porous soil

Properties of Water
●​ Anything that dissolves is hydrophilic, anything that does not is
hydrophobic
​
Physical Properties of Water:
●​ Specific Heat Capacity/Temperature
○​ High specific heat capacity, preventing large fluctuations of
temperature in cells
○​ Aquatic environments don’t change temperature when the air
changes (stable environment)
○​ Frozen water is a platform for polar mammal

D2 3.1 - 3.11 - Water Potential

Osmosis - Passive movement (requires no energy), the net

movement across a membrane to the side with a higher
concentration
Lysis - the rupturing of an animal blood cell (phospholipid membrane) in a hypotonic
solution
Crenations - the shriveling/indentations in the membrane of a cell in a hypertonic
solution

*Bacterial and plant cells are less vulnerable to the effects of osmosis because the cell
wall protects them
●​ However, plant cells can become turgid (swollen) when in hypotonic
solutions, and flaccid in hypertonic solutions - the cytoplasm retracts from
the cell wall (plasmolysis)
○​ In plasmolysis, the plant becomes shriveled if the cell is
plasmolysed
○​ In turgid conditions, the plant becomes upright

Medical uses for isotonic solutions:

●​ Eye drops (isotonic)
●​ Saline fluid (9g of salt per cubic dm)
●​ Organ donor bags (isotonic solution)

Water Potential as a Potential Energy per Unit Volume (Ψ) (psi)

●​ Potential water energy per unit volume
●​ Rises or falls in hydrostatic pressure
●​ The sum of solute potential (osmotic potential) and pressure potential
○​ Solute potential: changes when solutes dissolve in it
 ○​ Pressure potential: hydrostatic pressure increases change the pressure
potential

Movement of Water from Higher to Lower Water Potential

●​ This action minimizes its potential energy, like a rock rolling down a hill
and atoms forming bonds
○​ Maximum water potential of 0 kPa in cells
○​ Can go negative (-200kPa in a leaf)
○​ Water will flow from a cell with a higher water potential to one with a
lower one (-200kPa ---> -300kPa)

Intercellular fluid: Lower water potential, lower pressure potential, lower osmotic
potential

B1.1.1 - B.1.1.3 - Organic Molecules

Chemical Properties of the Carbon Atom:

 ●​ The majority of all organic molecules in an organism are classified into four
biochemical groups: carbohydrates, lipids, proteins, and nucleic acids.
○​ Mirror images: Different groups attached to each of the four bonds
around carbon - 2 different ways of arranging those groups

Carbon-Oxygen Functional Groups:

Hydroxyl groups:
1.​ Alcohol - OH end that can form
hydrogen bonds (OH is a hydroxyl
group)

Carbonyl groups (do not form hydrogen

bonds)
1.​ Aldehyde - C with double bond O and single H bond

2.​ Ketone - C with double bond O (not at the end)

 3.​ Carboxylic Acid - COOH, double bond O single bond
OH

4.​ Esters - formed by condensation

reaction between acid and alcohol
(double bond O single bond O), single
bond O can form bonds

Carbon-Nitrogen Functional Groups

1.​ Amines - Nitrogen atom bonded with a lone pair (primary, secondary,
tertiary)

2.​ Amides - Formed by combining an acid and an amine, amine connected

to C=O bond
Macromolecules, Monomers, Polymers
●​ Macromolecules: large number of linked atoms. Main classes:
Polysaccharides, Polypeptides, Nucleic Acids. Made up of monomers.
○​ How are macromolecules made? Condensation reaction:
building blocks of macromolecules (monomers) creates
polymer chains by linking to each other, releasing water
■​ Opposite of condensation is hydrolysis

●​ In cell digestion, polymers break down so monomers can be reused to

build new polymers or as energy sources
○​ I.e. deconstruction of polysaccharides/polypeptides into
monosaccharides and amino acids
■​ “Decomposer” organisms release digestive enzymes to
break down polymers by hydrolysis to be absorbed

Introduction to Carbohydrates
●​ Consist of oxygen, hydrogen, and carbon - oxygen/hydrogen is found in a
2:1 ratio
○​ Monosaccharides: Single sugars made up of one substance
(glucose, fructose, ribose, etc) - TEND TO FORM RING
STRUCTURES BY REACTING WITH HYDROXYL GROUP
■​ Aldehyde group? Known as aldoses
■​ Ketone group? Known as ketoses
○​ Disaccharides: Sugars with two subunits joined together by a
condensation reaction
○​ Polysaccharides: Formed from long chains of monosaccharide
monomers

Introduction to Glucose
●​ Exists as two structural isomers - alpha and beta
 ○​ Alpha glucose chains make different molecules than beta glucose
chains

●​ Polar molecule that dissolves, is stable b/c carbon atoms in ring

structure have 4 covalent bonds
○​ Can be transported through plasma/broken down through
aerobic respiration to release energy

●​ Glucose can make covalent bonds with itself/other monosaccharides to

create disaccharides OR chain together to make polysaccharides

Disaccharides
●​ 2 monosaccharides linked by condensation reaction (produces WATER)
 ●​ Covalent bond formed is called ‘Glycosidic Bond’
●​ Sucrose, Lactose, Maltose
●​ Can be broken down into monosaccharides through hydrolysis (adding
water)

Polysaccharides
●​ Monosaccharides linked together (amylose, glycogen, cellulose)
○​ Used for energy storage in plants and animals (linked glucose)
○​ Some common polysaccharides below…

1.​ Starch
●​ Insoluble polysaccharide of glucose, major storage carb for most plants
●​ Can be hydrolyzed (add water) to form glucose
○​ 2 types…
■​ Amylose: unbranched chain of a-glucose molecules, contains 1,4
(carbon 1 and 4) glycosidic bonds
●​ Has a linear structure, but the glucose molecules’ bonds
bring it into a helix/coil formation (helix is stabilized by
hydrogen bonds between glucose molecules and the coil
makes the starch compact)

■​ Amylopectin: branched, shorter a-glucose chains - chains are

linked by a-1,4 glycosidic bonds. Branch points are at 1,6 glycosidic
bonds
2.​ Glycogen
●​ Similar to amylopectin but larger and more branched (same branch points
and everything)
○​ Carb storage for humans and animals (starch for plants and
glycogen for animals)
■​ Insoluble - no osmotic effects
■​ Stored in liver and muscles - able to be stored in small
volumes due to extensive branching

3.​ Cellulose
●​ Made from b-glucose molecules (every other polysaccharide is
a-glucose)
●​ Primary component of cell wall in plants (acts as structural support for
plant cells)
○​ Insoluble in water
○​ NOT an energy storage molecule (few organisms produce
cellulase enzyme, which digests cellulose)

●​ Straight and uncoiled; every other b-glucose is rotated 180 degrees to

create b-1, 4 glycosidic bonds
○​ Additional hydrogen bonds formed beside glucose molecules in a
strand and between strands (parallel cellulose strands form
microfibrils, of which tensile strength is compared to steel)
*END OF POLYSACCHARIDES*

Glycoproteins
●​ Membrane proteins with small chains of carbs attached to them
○​ Do not confuse with glycolipids (carb chain attached to
phospholipid head)
■​ Glycoproteins + glycolipids known collectively as
glycocalyx
■​ Again, glycocalyx serve as identifying markers between
cells

Glycoproteins and ABO blood types

●​ Glycoproteins on the surface of RBCs determine one’s blood type
○​ 2 types of glycoproteins: A and B (called antigens because they
trigger immune response)
■​ A: only A antigens
■​ B: only B antigens
■​ AB: A and B antigens
■​ O: no antigens
 ○​ Generate antibodies in the presence of antigens that are foreign. In
order to prevent this reaction, only certain blood types are
compatible with certain people
■​ Example: A blood type people cannot have B blood type
because they will produce anti B antibodies
●​ AB people can have everything because they have
every antigen
●​ O have no antigens, so cannot receive anything but O

B1.1.8 - B1.1.13 - Lipids

Lipids
●​ Fats (semi-solid) and oils (liquid) (hydrophobic and nonpolar)
○​ E.g. fats, waxes, oils steroids, phospholipids - but not true
polymers (will cluster b/c of hydrophobia)
■​ Carbon, oxygen, hydrogen

●​ Fatty Acids
○​ COOH group at the end (acidic)
○​ 14 to 22 carbon atoms long
■​ Long, hydrocarbon chain provides hydrophobic property

●​ Saturated: only single bonds between carbon atoms (as many hydrogen
atom bonds as possible

●​ Unsaturated: Double bonds BETWEEN CARBON ATOMS (not used at full

capacity)
○​ Monounsaturated: One double bond
○​ Polyunsaturated: 2 or more double bonds
 ●​ Unsaturated isomers
○​ Unsaturated fatty acids occur as isomers: either cis or trans config
■​ Trans: immediate hydrogen atom is on other side of double
bond
■​ Cis: Same side of the double bond

​
Triglycerides
●​ Glycerol and 3 fatty acid molecules (can be a combination of
saturated and unsaturated)
○​ Macro-composed subunits formed by condensation reaction
○​ HYDROPHOBIC AND INSOLUBLE
○​ MUST DRAW BELOW DIAGRAM FOR TEST
 ●​ More saturated fats? More solid

Hydrogenation
●​ Converts unsaturated fats to saturated fats by adding H2 (e.g. peanut
butter and margarine)

Lipids and Energy Storage

●​ Fantastic energy storage in plants/animals: WHY?
○​ Compact molecule, high in energy (1 gram of fat = twice as much
energy as 1g of carbs)
■​ Seeds/fish use unsaturated fats
■​ Endotherms use saturated fats (warm blooded animals)
Phospholipids
-​ Glycerol + phosphate + 2 fatty acids
(condensation reaction)
-​ Found in all cell membranes
(AMPHIPATHIC!)
-​ Phosphate head and fatty acid tails

​
​

Adipose Tissue
●​ Cells that form fat in the form of triglycerides (because they are insoluble
and won’t move from adipose storage sites)
○​ Undergo hydrolysis to supply energy when food is scarce
○​ Other functions than supplying energy storage:
■​ Metabolic water source: oxidation of fats + oils produces a
lot of water
■​ Thermal insulation: Subcutaneous fat = adipose tissue
stored under the skin
●​ Blubber: large layer of subcutaneous fat
○​ White adipose tissue: stores energy
○​ Brown adipose tissue: generates heat

Steroid Hormones
●​ Hormones: chemical messengers produced by adrenal cortex, testes, and
ovaries
○​ Steroids: group of hormones made from the lipid cholesterol
(hydrocarbon molecule found in plasma membrane)
■​ Steroid hormones pass through phospholipid bilayer
because they’re non-polar; then binds and gets carried by
 special receptors to the nucleus (they control which
proteins are made)

​ *(Estradiol: coordinates menstruation and secondary sex characteristics in

females) (Testosterone: secondary sex characteristics in males)
B1.2.1 - B1.2.12 - Proteins
●​ More than 50% of dry mass of the cell
○​ Speeding up reactions (enzymes), defense, storage, transport,
cellular communication, movement, structural support
○​ More than 10000 different proteins in humans (tens of thousands)

What are proteins?

●​ Unbranched polymers made from the same 20 amino acids
○​ Polymers of amino acids = polypeptide chain
○​ Proteins = 1 or more polypeptide chains folded into 3d structure

What are amino acids?

●​ Organic molecule possessing both amino and carboxyl group (common
structure)
○​ Central carbon is asymmetrical
○​ R group (side chain) differs with each amino acid (provides
unique properties e.g. polar and acidic)
○​ MUST BE ABLE TO DRAW THIS!

○​

Amino Acid Polymers (Polypeptides)

●​ Carboxyl group of one reacts with amino group of other through
condensation reaction (in the ribosome)
 ○​ Resulting covalent bond is called a peptide bond (water is a
byproduct)
○​ CAN BE WRITTEN AS amino acid 1 + amino acid 2 = dipeptide +
water

●​ Multiple amino acids can join together to form a polypeptide

(can fold to take a protein shape)
○​ # of amino acids in polypeptide can be anything from 4
to over 10000
○​ Each polypeptide will have a unique shape
○​ Genes store information about amino acid
sequence of a polypeptide, in the DNA

Notes from Textbook (more reliable)

B1.2.6 - Chemical Diversity in R-groups
●​ Out of the 20 amino acids, their R groups vary
widely
○​ Some are hydrophobic, some hydrophilic
○​ Of the hydrophilic groups, some are
polar and some become charged by
acting as an acid/base
○​ R-group diversity lets organisms
use/make wide range of proteins
 ●​ Sometimes, amino acids are modified after creation of polypeptide - this
creates another amino acid not included in the typical 20
○​ E.g. collagen - proline converted to hydroxyproline

Primary Structure in Proteins

●​ Primary structure = linear sequence of amino acids in a polypeptide (i.e.
glycine, alanine, valine)
●​ How does this impact protein conformation?
○​ Bond angles of amino acids are tetrahedral; the amine and
carboxylic acid can rotate around from the central carbon
○​ Allows polypeptides to fold into 3D shapes (conformation)
■​ Conformations of different proteins recorded in the Protein
Data Bank

Secondary Structure in Proteins

●​ In polypeptide chains, there are polar C=O and N-H groups from forming
the peptide bonds
○​ Oxygen: slight negative charge
○​ Hydrogen: slight positive charge
■​ The frequency of these polar groups allows many hydrogen
bonds to form; while weak alone, collectively they stabilize
conformational structures in proteins

Regular structures, stabilized by hydrogen bonds, are the secondary structure

of a protein.

There are 2 types of structure stabilized by hydrogen bonding:

1.​ ɑ-helix - polypeptide assumes helical structure (with hydrogen bonds
between adjacent turns of the helix)
2.​ 𝛃-pleated sheet - 2+ sections of polypeptides arranged in parallel with
hydrogen bonds in between (the parallel sections run in opposite
directions - forming a pleated (ribbed) sheet due to tetrahedral bond
angles
Tertiary Structure of Proteins
●​ The tertiary structure is the folding of a whole polypeptide chain into a
3-D structure - stabilized by interactions between R-groups

Four types of interactions:

1.​ Ionic bonds between positively and negatively charged R-groups; due to
involvement with protons/hydrogen ions, ionic bonds are subject to pH
changes
a.​ Amine groups become positively
charged by accepting protons

b.​ Carboxyl groups become negatively charged by donating protons

(COOH → –COO- + H+)

2.​ Hydrogen bonds between polar R-groups; hydrogen forms a link between
O or N, which are electronegative
3.​ Disulfide bonds - between pairs of cysteines (covalent, strongest of all
interactions)
4.​ Hydrophobic interactions - between the non-polar R-groups
 ●​ Tertiary structure develops while a
polypeptide is being made by the ribosome
●​ Within tertiary structures often lie secondary
structures
●​ Some polypeptides do not become folded i.e.
don’t have tertiary structures - these are fibrous
proteins with structural roles

Effect of Polar/Non-polar Amino Acids on

Tertiary Protein Structure
Amino acids are either non-polar (hydrophobic) or
polar (hydrophilic).
●​ Some globular proteins must be water-soluble to carry functions in the
cytoplasm/solution outside the cell
○​ These proteins have hydrophilic amino acids clustered on the
water-contacting surface
○​ Hydrophobic amino acids are clustered in the centre of the protein
○​ This maximizes hydrophobic interactions within the non-polar amino
acids and hydrogen bonding with the hydrophilic parts and
surrounding water

●​ Some proteins regularly making contact with non-polar substances have

hydrophobic amino acids on parts of their surface (i.e. integral proteins
having hydrophobic amino acids where they touch the nonpolar
hydrocarbon core of the membrane)
●​ Channel proteins serve as tunnels letting hydrophilic substances through
the hydrophobic core of the membrane bilayer - they have a hydrophobic
region sandwiched between 2 hydrophilic region
○​ Additionally, tunnel lined with hydrophilic amino acids are present
inside the tunnel

Quaternary Structure of Non-Conjugated/Conjugated

Proteins
●​ All proteins have at least 1 polypeptide, but many have 2+ linked together
with non-polypeptide components
 ●​ This arrangement of subunits is the quaternary structure

Non-Conjugated Protein:
●​ Only polypeptide subunits; they are linked by the same interactions as
tertiary structure
○​ I.e. insulin has 2 polypeptides linked by disulfide bonds
○​ Collagen has 3 polypeptides wound together

Conjugated Protein:
●​ 1+ non-polypeptide subunits in addition to
polypeptides
○​ I.e. Hemoglobin has 4 polypeptide chains
and 4 haem groups (non-polypeptide
components)
○​ Increases chemical/functional diversity of
proteins - haem group binds to oxygen,
allowing hemoglobin to transport it

Relationship of Form and Function - Globular and

Fibrous Proteins
The function of a protein depends on its form.
Fibrous:
●​ Elongated polypeptides, lacking tertiary folding
●​ No secondary structures i.e. alpha helices
●​ Quaternary structure is present; polypeptide chains are linked into
narrow fibres/filaments with hydrogen bonds in between
○​ E.g. Collagen: quaternary structure is 3 polypeptides wound into a
triple helix (P-G-X)
○​ Proline prevents a-helix formation, a small R-group of glycine
faces inward. Amino acid X’s R-group is variable and allows
variation of collagen. Rope-like structure provides tensile strength
Globular:
●​ Rounded (folding of polypeptides) - intricate shape, stabilized by
R-group interactions
○​ Conformation: precise position of each atom in a globular
protein - critical to its function
○​ E.g. binding site of active enzymes - only certain substrates can
bind, if active site shape changes this will not work anymore

​
Must memorize this special case on hemoglobin (4 of these because 4
polypeptide chains)

Insulin special case

●​ Hormone involved in blood-glucose regulation
○​ 2 polypeptide chains (a and b chain)
○​ Held by disulfide bridges, A chain has additional disulfide bridge
Collagen special case
●​ Most abundant protein in animals
○​ Quaternary structure consists of 3 left-handed helices twisted
into a right-handed coil
○​ The 3 left-handed helical polypeptide chains are held by
interchain hydrogen bonds (making tropocollagen)
○​ Helices lie parallel in a staggered pattern to make fibrils, which
form fibers
The Protein Shapes
●​ Proteins commonly described as fibrous or globular. Fibrous
proteins have structural roles whereas globular proteins are
functional

Effects of amino acid polarity on tertiary structure of protein

●​ Polar R-groups are hydrophilic
●​ Non-polar R groups are hydrophobic
●​ With globular proteins soluble in water, polar R-groups are clustered
in the middle (helps embed membrane proteins in the plasma
membrane) and non-polar R group are exposed to the cell

Protein Denaturation
●​ Denaturation: structural change in protein resulting in loss of
biological properties (occurs when temperature/pH range is off,
destroying protein structure
○​ In R-groups, increases in temperature and changes in pH
disrupt interactions between groups
■​ Specifically, increases in
temperature break
interaction between R groups
Amino Acids in the Diet
●​ Nutrient: chemical substance found in foods that is used by the
human body
○​ Essential nutrients: cannot be synthesized in the body, must
be eaten
○​ Non-essential nutrient: made in the body/replacement nutrient
that can fulfill the same purpose

●​ Out of 20 amino acids, 10 can be synthesized in the body

○​ Those that cannot are ESSENTIAL
○​ Liver contains enzymes that synthesize non-essential amino
acids
■​ They can be produced from other, essential amino acids
Malnutrition
●​ Proteins cannot be made if amino acids are scarce (protein
deficiency malnutrition)
○​ Kwashiorkor: results from protein deficiency malnutrition
■​ Cell function, growth, immunity are affected by lack of
amino acids
●​ Edema, stunted growth, impaired mental
development

○​ TAKEAWAY: All essential amino acids needed in a diet

■​ Meat is a good source of essential amino acids; vegan
diets not so much because of reliance on one source for
protein
●​ Rice and beans are lacking in respective amino
acids; combining them would get you all your
essential amino acids
B3.3 - Muscles and Mobility

Movement!
●​ 2 forms of movement of life
○​ Internal movement of systems (ventilation, peristalsis)
○​ Physical Locomotion/Movement

●​ Motile: Organisms that move within their territory (like humans)​

Sessile: Fixed organisms - most plants rooted in soil

Sliding FIlament Model of Muscle Contraction

Muscle Fibre Structure

●​ Multinucleate - multiple nuclei
●​ Lots of mitochondria (need to synthesize lots of ATP)
●​ Specialized ER
○​ Sarcoplasmic reticulum
○​ Stores calcium ions

●​ Has tubular myofibrils (refer to previous chart) containing:

○​ Thin filament (actin)
 ○​ Thick filament (myosin)

●​ The membrane surrounding muscle fibre is known as sarcolemma

More on Sarcomeres
●​ Myofibrils contain contractile sarcomeres parts with myosin contain small
heads binding to actin
●​ A sarcomere is a repeating unit of a striated muscle cell
○​ A sarcomere is a FUNCTIONAL REGION of a myofibril

○​ Contractions lengthen/shorten sarcomere

●​ Each sarcomere is surrounded by Z discs (protein disks) holding

myofilament in place (recurring sarcomeres appear striated)

Center of sarcomere is darker b/c of

myosin/actin overlap (A band) (the top of this
diagram shows just the sarcomere region)

Could also have lighter central region due to

myosin (H zone)

Outside of sarcomere appear lighter due to

only actin present (I band)
Things to remember when Drawing:
■​ The myosin filaments are the thick filaments and should be represented as being thicker
than the actin filaments

■​ The myosin filaments should include protruding heads (myosin heads form cross-bridge
attachments with actin)

■​ The striated banding pattern should be identified (A band = dark region ; I band = light
region)

Role of ATP in Muscles

(HOW TO BUILD MUSCLE 101)
●​ ATP hydrolysis + cross-bridge formation are necessary for muscle
filaments to slide
○​ ONLY when muscles contract, ATP binds to myosin heads and
breaks down into ADP and phosphate, makes them break
cross-bridges by detaching from actin binding site
■​ (ATP=ADP+PI)

●​ Causes myosin heads to change angle, attach to actin binding site

further from sarcomere
○​ Moving myosin head moves actin a small distance (power stroke)
■​ Continued until motor neuron stop sending signals to muscle
fibre, and calcium ions are pumped back to sarcoplasmic
reticulum
■​ Everything is sliding and overlining
■​ ATP binds and moves myosin heads, Calcium ions unblock
those connections (calcium moved by SR)
Muscle Contraction
When muscle is relaxed…
●​ Protein called tropomyosin blocks binding sites on actin

When a signal to muscle is sent…

●​ Sarcoplasmic reticulum releases Ca++ ions
○​ These ions and ATP bind to the protein troponin, which causes
tropomyosin to move
■​ Thus, myosin heads can now bind to actin and cross-bridges
can form

●​ Each time myosin heads rebind farther from the sarcomere, they push
aside actin filaments a bit (8-10nm) towards the centre of the sarcomere.
This repeats itself, hugging the actin towards the sarcomere (ratchet
mechanism)

Antagonistic Muscles
●​ Skeletal muscles are antagonistic
○​ For movement, muscles work in antagonistic pairs (when one
contracts, another releases) because muscles can only provide
energy when contracting
■​ Lengthens the titin muscles, produces opposite movements at
a joint

Titin and Antagonistic Muscles in Muscles Relaxation

 ●​ Titin is a protein (largest in humans) and helps muscles recoil after
stretching
○​ Connects ends of myosin filaments to Z-discs
○​ Holds myosin in the right position (centered in 6 parallel actin
filaments)
○​ Prevents overstretching
○​ Releases counterenergy in recoil to add to force of contraction

Motor Units in Skeletal Muscles

●​ Skeletal muscles: striated muscle fibers, contracted when stimulated by a
motor neuron
●​ Neuron passes stimulus through synapse via neurotransmitter
acetylcholine (neuromuscular junctions)
○​ More muscle fibers than motor neurons in skeletal muscle; neuron is
branched and supplements multiple muscle fibers

Motor Unit
●​ A motor neuron and all the myofibers it innervates
(motor neurons + muscle myofibers)
○​ When stimulated, all fibers activated to
produce force (amt of force depends on size of unit)
○​ Usually hundreds of muscle fibers!
■​ These are not clumped together but
mixed with muscle fibers of other motor units (as few
motor neurons needed as possible)

Skeletons as Anchorage/Levers for Muscles

●​ Bones + exoskeletal structures provide anchorage for muscles/act as
levers
○​ In levers, there is effort force, pivot point (fulcrum) and resultant
force
○​ First class, second class, third class levers
●​ Endoskeletons: internal skeletons supporting surrounding muscles
 ●​ Exoskeletons: external skeletons surrounding/protecting most body
surface of animals
●​ Animals have skeletons of chitin (polysaccharide) held by joints

Movement of Synovial Joints (w/ examples)

●​ Bones meet at joints allowing for articulation/movement
○​ Synovial joints: Joints where ends of bones are encased
in cartilage, protected by capsule lined with synovial
membrane that produces synovial fluid
■​ Allow certain movements but not others

●​ Major components of synovial joints:

○​ Joint capsule (seals joint space, provides stability by
restricting range of motion)
○​ Cartilage (lines bones to facilitate smooth movement, absorb
shock, and prevent wear)
○​ Synovial fluid (provides oxygen + nutrients as cartilage,
lubricant)
○​ Ligaments (cords of tissue with collagen fibers - prevents
wrong movements/dislocation and holds capsule together)
○​ Muscles (forces to move the joint/attach to the bones above &
below joint)
○​ Tendons (attach muscle to bone)

Types of Synovial Joints

1.​ Plane joints - sliding movement (wrist, ankle)
2.​ Hinge joints - Flexion/extension in one place (elbow/ankle)
 3.​ Pivot joints - bone rotation about another bone (neck)
4.​ Condyloid joints - flexion, extension, abduction, adduction in wrist
5.​ Saddle joints - same movements as condyloid, combines with them to
make compound joints (thumb)
6.​ Ball & socket joint - All movements except gliding (shoulder/hip)

Internal + External Intercostal Antagonistic Muscles in Internal Body

Movements
●​ Alternating contraction in layers of intercostal muscles moves
ribcage oppositely
○​ External intercostal muscles contract, internal ones stretch
during inhalation
○​ During exhalation, internal intercostal muscles contract
because of stored potential energy in the titin

Reasons for Locomotion

●​ Foraging for food
●​ Escaping from danger
●​ Searching for a mate
●​ Migration
Adaptations for Swimming in Marine Mammals
●​ Streamlined body to minimize resistance to motion:
○​ Widest near the front, tapering towards the rear (less drag)
○​ Flippers, flukes, dorsal fin with teardrop profiles
○​ Smooth body surface (distribution of blubber, no hind limbs & ear
flaps)
●​ Locomotive adaptations, such as flippers and flukes on the tail for water
movement
●​ Airways (e.g. blowholes) allowing lung ventilation

C1.1 Enzymes and Metabolism

Enzymes
●​ Globular proteins that catalyze reactions in cells (substrate) by reducing
activation energy
○​ Destabilize existing chemical bonds in the substrate (enzyme
reactant)
○​ Randomly-moving substrates bind at a pocket in the enzyme
called active site, forming an enzyme-substrate complex (slightly
changes shape of the enzyme) like a hug!!!
○​ Active site: made from amino acids w/ shape matching the
substrate, gives site necessary properties for catalysis (binding
to substrate, holding on to it, lowering activation energy)
■​ Enzyme raised to high-energy transition state due to change
in shape; substrate undergoes reaction
○​ Finally, enzyme is released, unchanged and able to reuse
 ●​ Exergonic reaction: Products of a chemical reaction have less energy
than the reactants (tend to be catabolic)
●​ Endergonic reaction: Products of a chemical reaction have more energy
than the reactants (tend to be anabolic)

Metabolism
●​ Sum of all chemical reactions that occur within an organism
○​ 2 types of reactions…
○​ Anabolic: Reactions that build complex molecules from simpler
ones
○​ Catabolic: Reactions that break down complex molecules with the
release of energy

●​ Almost all metabolic reactions are catalyzed by enzymes and occur in

series
○​ Series are called metabolic pathways
○​ Straight chains: linear sequence
○​ Cyclic processes: circular sequence

○​ 2 categories of enzymes…
○​ Extracellular enzymes: secreted by endocytosis to work externally
 ○​ Intracellular enzymes: found inside organelles and imbedded in
organelle membranes

Immobilized Enzymes
●​ Substrate/Enzymes immobilized in a membrane are stable, more efficient
in catalysis
○​ Used in food, wastewater, pharmaceutical industries (don’t need to
memorize the below)

○​ Advantages:
■​ Enzymes easily separated from product
■​ Retrieved enzymes can be reused
■​ Increases stability of enzymes
■​ Substrates can be exposed to higher enzyme concentrations
(memorize this stuff)
Denaturation of Enzymes

●​ Weak intramolecular interactions between amino acid residues break with

changes in temperature and pH
○​ Changes shape of active site - no more substrate binding

Temperature to enzymes

●​ Must be able to draw this!

●​ Temperature to enzyme activity
chart
●​ Label a), b), c)
●​ Higher temperature = more kinetic
energy until denaturation

pH to enzymes
●​ Must be able to draw this!
●​ pH to enzyme activity chart
●​ Label a), b), c)
●​ a): Excess H+ interact with
exposed R groups, changing active
site shape
●​ b) optimum rate
●​ c) Active site also changes
shape
 Substrate concentration to enzymes
●​ Must be able to draw this!
●​ a): Increased chance of collision, increase in
rate of reaction
●​ b): Rate levels as active sites become
saturated
●​ c) Rate levels out to constant (full saturation)

NOTE: OPTIMAL CONDITIONS ARE DIFFERENT FOR DIFFERENT

ENZYMES (E.G. HUMAN ENZYMES VS THERMOPHILES)

Metabolic Efficiency
●​ In metabolic reactions energy transfer is not 100% efficient
○​ ~35% of the energy available to an organism (ATP) is used for cell
activities
○​ Remaining energy transferred to heat

●​ Endotherms: require heat to maintain constant body temperature

●​ Ectotherms: Cannot maintain body temperature, rely on other sources of
energy to moderate body temperature

Enzyme Inhibitors
●​ Substances that inhibit an enzyme’s activity by affecting the active site
○​ Can be formed in cells or absorbed from external environment
Competitive inhibitor: Built like a substrate and occupies the
active site, staying there +
not making products and
clogging the site

Statins: Special case,

competitive inhibitors
blocking essential
 enzyme-substrate complex in synthesis of cholesterol

Non-competitive inhibitor: does not interact with active site but something else
(allosteric site) that changes active site (e.g. cyanide)

End-Product Inhibition
●​ Enzyme in metabolic pathway is inhibited by the product of the pathway
○​ As product builds, assembly line is cut off
○​ Prevents cell from over-producing substance/wasting chemical
resources and energy
■​ As end product is used up, the enzyme is slowly
reactivated, triggering the pathway again
●​ In most cases, the product will be non-competitive inhibition
(different shape than substrate)
○​ Non-competitive inhibition that is reversible is called allosteric
regulation
 ■​ This type of enzyme is called allosteric enzyme, product is
called allosteric inhibitor

Mechanism-Based Inhibition
●​ Involves substrate analogue (molecule with similar structure to the
substrate)
○​ When substrate analogue binds to active site, it modifies to cause
irreversible binding through formation of covalent bonds
○​ Forms stable inhibitor-enzyme complex, enzyme cannot catalyze
any further reactions
○​ UNLIKE ALLOSTERIC REGULATION, IRREVERSIBLE
START OF UNIT 2: HEREDITY

D2.1.9 - Part 1
Homologous Chromosomes
●​ Each homologous chromosome (homolog) carries genetic information
○​ Individual genes have particular focuses
■​ In the two homologs genes will be found on same loci, but may
have different alleles

Re-introduction to Chromosomes
●​ Humans are diploid (2n) organisms & the diploid number is 46
 ○​ 23 maternal chromosomes and 23 paternal chromosomes

Process of Meiosis
1.​ Interphase
a.​ Chromosome is diploid and DNA in chromatin form
i.​ G1: Metabolically active period, synthesis of cell
components (protein, DNA)
ii.​ S: DNA replicates, making 2 daughter strands
(chromatids) held by the centromere
iii.​ G2: Cell prepares for meiosis

b.​ Meiosis I - Prophase I

i.​ Nuclear envelope breaks down into vesicles
ii.​ Centrosomes form microtubules (mitotic spindle), go to
cell poles
iii.​ Homologous chromosomes (tetrad) join & form a
bivalent (tetrad) - allowing for chiasmata (physical link
between 2 non-sister chromatids) to form and
crossing over (exchange of alleles) to occur
(Chiasmata: location where the fragments switch)

c.​ Metaphase I
i.​ Homologous kinetochores link, acting as one single one
 ii.​ Microtubules attach to kinetochores, align crossed over
chromosomes (bivalent chromosomes) on equator
(orientation is random per homologous pair)
iii.​ Chromosomes are lined up in pairs, line order random
(randomly to either pole) to be ripped apart

d.​ Anaphase I
i.​ Proteins are stuck onto the chromatic arms but not the
centromere; separates bivalents but keeps sister
chromatids joined
ii.​ Homologous pair is separated towards opposite poles;
microtubules are shortened by kinetochores

e.​ Telophase I
i.​ One homologous chromosome (sister chromatids
non-identical because of crossing over) per new cell
ii.​ Nuclear envelope reassembles, chromosomes
decondense and microtubules depolymerize
iii.​ Contractile/cleavage ring forms for cytokinesis, cytoplasm
divides (equal in spermatogenesis, unequal in
oogenesis)
iv.​ NO INTERPHASE FOLLOWS.

f.​ Meiosis II - Prophase II

i.​ Same as prophase I but without all the homologous
chromosome stuff

g.​ Metaphase II
i.​ Microtubules attach to sister chromatids
ii.​ Contraction and tension form microtubules, microtubule
motors align chromosomes along equator

h.​ Anaphase II
 i.​ Cohesion proteins at centromere are cleaved; separate
chromatids from each other, kinetochore shortens as
centrosomes move apart.
ii.​ New chromatids still referred to as chromosomes

i.​ Telophase II and Cytokinesis II

i.​ Nuclear envelope reassembles, chromosomes
decondense
ii.​ Microtubules depolymerize, cell divides
iii.​ Each cell, now gametes, have haploid nuclei, which will
specialize into sex cells

D2: 1.10-1.11 (Meiosis Part 2)

Genetic variation can result from:

●​ Mutation: changes in sequences in DNA
●​ Gene flow: movement of genes between different groups of organisms
 ●​ Meiosis: Formation of egg + sperm leading to the creation of new combinations
of genes
●​ Sexual reproduction: Random fertilization between egg and sperm

How does meiosis create variation?

●​ Synapsis (joining of homologous chromosomes forming bivalents)
●​ Crossing over (non-sister chromatids exchange random alleles along the
chromatics to become recombinants)
●​ Sister chromatids are now non-identical
●​ Number of independent gamete variations = 2^n (n=# of chromosomes in
haploid cell)
○​ For humans, more than 8388608 different arrangements

Nondisjunction
●​ Failure of separation of chromosomes during meiosis - one gamete too many
(trisomy) or one gamete too less (monosomy)
○​ Occurs in Anaphase I or Anaphase II

D3.2.1 - D3.2.7 Inheritance

●​ Gregor Mendel - discovered laws of inheritance through experiments with plants

○​ Tall x Short Plants: First generation 100% tall, second generation 2.84:1
ratio of tall to short plants

Genotypes
●​ Allele: different versions of genes (humans/other diploids have 2 alleles of most
genes, one from each parent)
○​ Homozygous: 2 copies of one allele
○​ Heterozygous: two different alleles

●​ Genotype: All possible combinations of alleles (e.. Dd, DD, dd)

○​ Homozygous genotype: two identical alleles from each
parental chromosome (same letters)) (e.g. 100%
homozygous)
 ○​ Heterozygous genotype: two different alleles of the gene

●​ Phenotype: Observable characteristics/traits of an organism (not always

100% genes)
●​ Carrier: Individual who has a recessive allele of a gene (no effect on the
phenotype)
Constructing a Punnett Grid
●​ Punnett grid: show how the allele of parents are split between gametes/how
new alleles show up in offspring
○​ Shows all possible combinations of genetic information (for a particular
trait in a monohybrid cross)
Key Terms:
●​ Dominant Allele (allele that dominates over the other one even if it’s different)
●​ Recessive Allele (won’t affect the phenotype by itself)

●​ Paternal (p) generation: The FIRST SET of parents crosses; alleles are known
○​ First filial generation (F1): First generation produced by parents
■​ Second filial generation (F2): Product of generation from the F1
generation

Phenotypic Plasticity
●​ Organism’s ability to adapt phenotype to the environment
○​ E.g. birds activating genes producing more maltase (digestive enzyme)
when fewer insects are available
○​ Freshwater snails can grow more rounded shells when sensing predator
signals, making them harder to crush - not mutations, but silencing and
activating of different alleles

Special Case: Phenylketonuria (PKU)

●​ Mutation in autosomal (involved with any chromosomes except sex
chromosomes) PAH gene causes low levels of enzyme phenylalanine
hydroxylase
○​ Phenylalanine hydroxylase converts amino acid phenylalanine into
tyrosine; phenylalanine, present in eggs/chickens/nuts is toxic at
high levels resulting in impaired brain development

3.2 Non-Mendelian Genetics

Single Nucleotide Polymorphisms (SNPS)
●​ Points in the genome (entire DNA code) that differ by 1 nucleotide pair between 1
population group and another
○​ E.g. SNPs can replace cytosine with adenine
○​ Occur once every ~1000 base pairs in a person, in both coding &
non-coding DNA
○​ In a gene pool, there can be multiple alleles from SNPs occurring in
the gene; however parents can only pass down two
○​ Can create alternate version of an allele/gene

Blood types and Multiple Alleles

𝐴 𝐵
●​ Blood types determined by 3 alleles of a gene: 𝐼 , 𝐼 , 𝑖
One person only has 2 of these 3

Codominance and Incomplete Dominance

●​ Alleles always exist as dominant or recessive
○​ Not all alleles show dominant/recessive expression patterns
■​ Codominance: Both alleles expressed in a phenotype
■​ Incomplete dominance: Dominant allele doesn’t fully mask effects
of recessive allele - resulting in heterozygous having an
intermediate phenotype (blend)
Chromosomes and Sex Determination
●​ In mammals, eggs have an X chromosome while half of sperm cells have X
and other half have Y
○​ Produces either XX or XY zygote
■​ At 2 months, gonads develop into testes (if Y chromosome is
present and makes the SRY [sex determining region of Y gene]):
else, makes ovaries
●​ SRY gene codes a protein that controls Y chromosome gene
expression
●​ In total, the Y chromosome has 78 genes coding for 25
proteins. The X chromosome has 1100. Genes on either
chromosomes are sex-linked genes (either Y-linked or
X-linked)

Male/Female Inheritance
●​ Fathers pass their X-linked alleles to their daughters but not sons (sperms have
Y chromosomes)
○​ However, mother passes X-linked alleles to sons and daughters
■​ Males only have 1 X-chromosome; any recessive allele that
causes disease on that chromosome (from the mother) will cause
the male to automatically have that disease
■​ Males will have more X-linked recessive disorders
■​ Only females can be carriers of X-linked disorders

●​ Special Case: Hemophilia

○​ Genetic disorder: blood doesn’t clot properly and people can bleed to
death from minor injuries
■​ Caused by a recessive allele: Queen Victoria passed this allele
to multiple descendants, spread worsened by inbreeding

3.2 - Inheritance - Pedigrees & Box-and-Whisker Plots

What is a pedigree?
●​ Flowchart that uses symbols to show inheritance patterns in family
generations - determines patterns of inheritance in certain traits
○​ Birth order is indicated left to right

Autosomal Dominant: Dominant disease-causing allele from autosome (1-22

chromosomes)
●​ Pedigrees usually have an affected individual every generation
●​ Unaffected parents won’t have an affected child
●​ No carriers

Autosomal Recessive: Recessive allele (2 alleles required for disease to show up) in
autosomes
●​ Unaffected parents can have affected children (if both parents are
heterozygous carriers)
○​ Disease can skip generations

Pedigree patterns in sex-linked genes

●​ X-linked dominant:
○​ Affected dad WILL have affected daughter
○​ Both sons and daughters affected
○​ Affected sons MUST HAVE affected mother

●​ X-linked recessive:
○​ Males more likely to be affected (only mother has to be a carrier since 1 X
chromosome)
○​ NEVER passed from father to son
○​ All daughters of affected fathers are carriers

●​ Y-linked genes:
○​ All sons of affected fathers have the trait

Continuous and Discrete Variation

●​ In traits with few alleles discrete
variation is demonstrated (distinct groups
with no transition between them) - mode,
but no mean b/c no central tendency
●​ In traits with lots of genes/alleles the number of possible genotypes increases
dramatically - hard to determine difference between a genotype in two very
similar phenotypes (thus this data is continuous with no distinct categories,
and has mean + central tendency)

●​ IB worked example: human skin

○​ A trait exhibiting continuous variation
■​ Skin color is determined by melanin levels, which is genetically
controlled
■​ 3-4 separately inherited genes on different chromosomes control
melanin production (polygenic inheritance: groups of genes that
together determine a characteristic)
●​ Skin color can also be determined by environmental
factors

Skewed Distribution
●​ Mean, median and mode do not align around one
value; values reduce in frequency faster on one side of
the curve than the other

Box-and-Whisker Plots
●​ Used to show difference in the mean and range
(difference between minimum & maximum values)
○​ Used with skewed data

●​ IQR = Q3 - Q1
○​ Indicates range of the middle half of scores

●​ Outliers: 1.5 * IQR above the third/below the first

quartile
○​ Can cause a data set to be skewed if not omitted
06 - Dihybrid Crosses
Segregation: during gamete formation, separation of the parental alleles so one is
inherited but not the other
●​ Diploid: 2 alleles of each gene
●​ Haploid: 1 allele of each gene

The Law of Independent Assortment

●​ Independent assortment: segregation of the alleles of two genes (where one
gene outcome (eye color) has no effect on the other outcome (hair color))
○​ Combination of alleles during meiosis is random for different genes

●​ Dihybrid Crosses: the crossing of two traits that create 16 possible

combinations in a gamete (9:3:3:1 ratio if both parents are heterozygous)

Y (yellow) is dominant​ ​ ​ ​ ​ ​ R (round) is dominant

y (green) is recessive​ ​ ​ ​ ​ ​ r (wrinkled) is recessive

9:3:3:1 ratio represents: 9 plants with 2 dominant traits

​ ​ ​ 3 plants with one recessive trait
​ ​ ​ 3 plants with the other recessive trait
​ ​ ​ 1 plant with both recessive traits

D.3.2.19 - D3.2.21 - Gene Linkage and Chi-Squared Tests

Automated Gene Linkage
●​ Genes located near each other on the same chromosomes tend to be
inherited together (not guaranteed) in genetic crosses

○​ Two vertical lines (representing homologous

chromosomes) are used to show the genes are linked
○​ The genes are read from top to bottom (example
showed would be ggll genotype)
○​ When linked genes are crossed, most of the F2
phenotype will be parental

Recombinants
●​ New allele combinations a a result of
crossing over (includes both gametes and
offspring)
○​ If the chiasma (crossing over) occurs
between 2 linked alleles,
recombinant gametes are formed
■​ In mendelian genetics, 50%
of offspring show a
recombinant phenotype

○​ Back-crossing: when a member of the F1 generation is crossed with an

individual genetically identical to one of the parents

2
Chi-Squared Tests (𝑋 )
●​ Used to determine if there’s a good fit between expected ratios and what’s
obtained that is statistically significant (in genetics)
○​ Before calculating X^2, state the null/alternative statistical
hypothesis
■​ Null hypothesis (Ho): No significant difference between observed
and expected results, with any variation due to chance alone
 ■​ Alternative hypothesis (H1): There is a significant difference
between observed and expected results - something more than
chance is likely causing the difference

How to calculate the chi-square value (X^2):

●​ Obtain the observed/expected values of the offspring
●​ Use the formula shown to calculate X^2:
2
2 (𝑜𝑏𝑠𝑒𝑟𝑣𝑒𝑑−𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑)
​ ​ 𝑋 = Σ 𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑

●​ Obtain the degrees of freedom (DF), the number of independent pieces of

information used to calculate a statistic
○​ Degrees of Freedom = # of categories (phenotypes) - 1

●​ Cross-reference with X^2 probability distribution table at a standard

deviation of 0.05 (standard in biology)
○​ When the calculated value of X^2 is lower than the critical value at the
0.05 probability level, the null hypothesis is accepted
Unit 3 - Metabolism
C1.2.1-1.2.6 - Cell Respiration
●​ Nucleotides: subunits of RNA and DNA consisting of:
○​ One nitrogen-containing base
○​ One 5-carbon sugar
○​ One or more phosphate groups

●​ ATP is a nucleotide (adenine with

nitrogenous base, ribose sugar, and 3
phosphate groups)
○​ The phosphate groups are in a chain -
each of them are negatively charged

What is ATP?
●​ “Energy currency of the cell”: used for temporary storage of energy and energy
transfer between processes and different parts of the cell
○​ This is because it’s soluble in water: can move freely through aqueous
solutions e.g. cytoplasm
○​ Stable at pH levels close to neutral (in cytoplasm)
○​ Cannot pass freely through phospholipid bilayer: movement can be
controlled within membrane-bound organelles
○​ The third phosphate group in ATP can be removed and reattached
via hydrolysis and condensation; this hydrolysis produces small
amounts of energy, enough for many processes within the cell (if any more
were released it’d be wasted through heat)

Cells need energy for 3 types of activity:

1.​ Synthesizing macromolecules
 a.​ Anabolic reactions linking monomers into polymers are endothermic; they
probably won’t happen without ATP to ADP conversion energy. 1+ ATP
molecules are used every time a monomer links to one polymer (e.g. DNA
synthesis, RNA during transcription, proteins in translation)
2.​ Active transport
a.​ Pumping particles against the concentration gradient requires energy from
ATP; this energy causes reversible changes in the shape of the pump
protein (when the pump is in one shape, the particle can enter from one
side of the membrane; when it’s in another shape the particle can exit from
the opposite side)
b.​ One of the 2 shapes is more stable; ATP is used to change shape to the
less stable one, which then changes back to the more stable one without
using energy
3.​ Movement
a.​ Cells use ATP for movement; i.e. components of cells, like chromosomes
moving to the poles and vesicles transporting materials. Larger amounts
of energy (more ATP) is needed to change a cell’s shape i.e. cytokinesis
and locomotion like phagocytes. Muscle cells also contract using ATP.

Energy Transfers in the Change from ATP to ADP

●​ ATP has more chemical potential energy than
ADP: energy is released when ATP is
converted to ADP + phosphate
○​ In cases, the last phosphate group of
ATP is linked to another molecule (e.g. a
protein pump or substrate in a metabolic
pathway); when the phosphate detaches
from this molecule, energy is released
causing a change in the molecule (e.g.
changing shape of membrane pump
or chemical change converting substrate into product)

●​ To convert ADP + Pi to ATP, energy is needed. This energy comes from:

○​ Cell respiration - oxidation of carbs, fats, proteins releases energy
○​ Photosynthesis - light energy converts to chemical energy
○​ Chemosynthesis - energy release by oxidizing inorganic substances
(sulfides)

●​ The quantity of ATP in a cell is small at any given time; if it’s all used up
processes that require energy can’t work
 ○​ Neurons can’t convey impulses and muscle cells stop working - eventually
without ATP everything dies
○​ This is prevented by continual regeneration of ATP through ADP + Pi

Cell Respiration and ATP

●​ All cells respire (carbon compounds or respiratory substrates are oxidized to
release energy, which is used to make ATP)
○​ E.g. Glucose, fatty acids - our food is the source of respiratory substrates
○​ Plants use carbs or lipids made by photosynthesis
●​ In many cells, respiration uses oxygen and produces CO2; oxygen must
enter through the plasma membrane while CO2 simultaneously exits (gas
exchange) but this isn’t 1:1 but instead them moving independently by simple
diffusion

*Gas exchange and cell respiration are different processes, but they are
interdependent.
●​ Without gas exchange cell respiration can’t work because of excess CO2 and no
O2
●​ Without cell respiration, gas exchange doesn’t work because the use of oxygen
and production of CO2 is what makes the concentration gradients the gasses
need to diffuse.
Difference between anaerobic and
aerobic cell respiration in humans
●​ Some pathways of cell respiration
are aerobic (use oxygen), while
others are anaerobic
●​ Anaerobic respiration is more
conservative: only carbs can be
used, 2 ATP is made per glucose
molecule, only waste substrates
are CO2 and either lactate or
ethanol

*Human lungs/blood system supply oxygen to most organs rapidly enough for
aerobic respiration; but sometimes anaerobic respiration is used in muscles

●​ Advantage: Can supply ATP rapidly over a short time (used to maximize muscle
contractions)
○​ I.e. short bursts of exercise are fueled by ATP from anaerobic respiration
 ●​ Disadvantage: Lactate (lactic acid) is a waste product of anaerobic
respiration: there is a limit of lactic acid the body can tolerate and this restricts
the amount of anaerobic respiration being done (why max muscle contractions
can only be handled for some time)
○​ The lactate must be broken down with oxygen after muscle contractions: it
takes minutes for all the oxygen needed to be absorbed, and this demand
for oxygen is known as oxygen debt

Ways to calculate cell respiration:

●​ Oxygen uptake
●​ CO2 production
●​ Consumption of glucose/other respiratory substrate

C1.2.7-1.2.10 - Cell Respiration/Glycolysis

●​ Oxidation and reduction: 2 chemical processes
occurring together
○​ Electron carriers: substances that accept and
lose electrons reversibly
■​ In cell respiration, the main electron
carrier is NAD (nicotinamide adenine
dinucleotide)

●​ NAD has one positive charge and exists as NAD+

○​ In respiration, substances are oxidized by
removing 2 hydrogen atoms (1 electron and 1
proton)
○​ NAD+ accepts 2 electrons and 1 proton from
the hydrogen atoms - becoming NADH (the other proton H+ is released)

*In its reduced form NAD is often shown as reduced NAD rather than NADH+H+...for
simplicity

●​ Thus, reactions involving NAD show that oxidation/reduction can be achieved by

losing/gaining hydrogen atoms

Oxidation/Reduction can also occur via loss/gain of oxygen (adding oxygen to a

molecule/ion is oxidation as oxygen atoms have high affinities for electrons -
draw them away from other parts of the molecule/ion)
 ●​ Some bacterias oxidize hydrocarbons using oxygen

●​ Others oxidize nitrite ions into nitrate

Glycolysis
●​ First part of aerobic respiration when glucose or a monosaccharide is the
substrate - happens in the cytoplasm
○​ Glucose is converted to pyruvate by a chain reaction (each is catalyzed
by a different enzyme)
○​ Glycolysis produces a bit of ATP without any oxygen consumption

How glycolysis works…

STAGE 1
1.​ Phosphorylation of Glucose
a.​ Phosphorylation: the addition of phosphate to a molecule, making
the molecule more unstable and likely to participate in subsequent
reactions (many phosphorylations are done by transfer of a phosphate
from ATP)
i.​ Glucose is phosphorylated with ATP
(glucose-6-phosphate means the phosphate is
linked to the 6th carbon atom of the glucose

2.​ Glucose is converted to fructose, creating a

symmetrical molecule that can be split

3.​ Phosphorylation of Fructose

 (At this point the fructose 1,6-bisphosphate is symmetrical)
STAGE 2: Lysis
1.​ Fructose bisphosphate is split into 2 molecules of triose phosphate

STAGE 3: Oxidation
1.​ Triose phosphates are oxidized through removal of 2 hydrogen atoms,
which are accepted by NAD
a.​ NAD becomes reduced NAD
2.​ Triose phosphate becomes biphosphoglycerate
a.​ Oxidation of a sugar produces an organic acid - in this case, glycerate
carrying 2 phosphates (energy released by triose oxidation allows a
second phosphate group to be attached)

Stage 4: ATP formation

1.​ ATP is formed from biphosphoglycerate
a.​ Biphosphoglycerate transfers its 2 phosphate groups to ADP, creating 2
molecules of ATP: 2 biphosphoglycerate molecules are produced making
2 ATPs each, so a total of 4 ATPs are produced
b.​ 2 molecules of biphosphoglycerate become 2 molecules of pyruvate

Conclusion: 2 NET ATPs are produced without the use of oxygen (4 produced, 2
used)
●​ If there is oxygen present pyruvate moves into mitochondria for aerobic
respiration; otherwise it begins anaerobic respiration in cytoplasm
●​ Glucose should not run out
●​ ADP will only run out of it’s all converted to ATP
- in which case glycolysis isn’t needed
●​ NAD will run out unless reduced NAD is
oxidized
 ○​ Several methods of regenerating NAD: in some human/animal/bacterial
cells hydrogen atoms are transferred from reduced NAD to pyruvate in the
cytoplasm
○​ The pyruvate is converted to lactate

○​ Since 2 molecules of glucose turned

into 2 molecules of pyruvate, 2 NADH
molecules are oxidized - so all the NAD
used in glycolysis is regenerated
■​ Thus, cells will never run out of NAD
so long as glucose is available and
lactate concentrations don’t go too
high
■​ This is called lactic fermentation - used in some foods as accumulating
lactic acid, which dissociates to form lactate, protects from bacteria and
fungi by lowering pH
●​ I.e. Yogurt, kimchi, sauerkraut

Anaerobic Cell Respiration in Yeast

●​ Instead of lactate, NAD from glycolysis can also be regenerated through converting
pyruvate to ethanol and CO2
○​ Stage 1: CO2 is removed from pyruvate (decarboxylation) to make ethanal
○​ Stage 2: 2 hydrogens are transferred from reduced NAD to ethanal, making
ethanol
■​ Since there are 2 pyruvate molecules, 2 reduced NADs are converted to
NAD
■​ Allows indefinite production of ATP through anaerobic respiration so long
as ethanol concentrations don’t rise too much
■​ This is called ethanol/alcoholic fermentation

Ethanol Fermentation - applications in food

 ●​ Bread: yeast is added to bread and undergoes anaerobic respiration, producing
CO2 through ethanol fermentation - the CO2 builds up and causes dough to rise
●​ Wine/Beer: Yeast is added to grape juice/barley grains and water and produces
ethanol through ethanol fermentation
●​ Bioethanol also produced using yeast and a plant matter

C1.2.11-1.2.12 - Krebs Cycle

Pyruvate in Aerobic Respiration - The Link Reaction
●​ Pyruvate can be oxidized to CO2 and water if oxygen is available
○​ Much higher ATP yield than anaerobic cell respiration
○​ Most of the reactions are in Krebs cycle, but the initial reaction is
converting pyruvate (from glycolysis) into a 2-carbon acetyl group
○​ This reaction forms a link between glycolysis and the Krebs cycle - thus
known as the link reaction

In the link reaction, 3 enzymes carry out 3 processes:

1.​ Decarboxylation of pyruvate by
removal of CO2, changing the 3
carbon pyruvate into a 2 carbon
molecule
2.​ Oxidation of pyruvate by removal of
2 electrons (i.e. hydrogen atoms) -
these electrons are accepted by
NAD
3.​ Binding of pyruvate’s acetyl group
to a carrier molecule “coenzyme
A” (the product is acetyl COA)

*Pyruvate is produced in the cytoplasm during

glycolysis, but transporter proteins in outer
mitochondrial membrane moves pyruvate into
the mitochondrial matrix (where link reaction
+ krebs cycle occur)

The Krebs Cycle

 ●​ Acetyl groups produced via link reaction (acetyl coenzyme A) are oxidized in a
reaction series happening in the mitochondrial matrix (The Krebs cycle)
Step 1: Acetyl groups are fed into the cycle via transfer from coenzyme A to
oxaloacetate - producing the organic acid citrate

●​ Oxaloacetate has 4 carbon atoms while citrate has 6; through a lot of

reactions citrate is converted back to oxaloacetate

Step 2: 2 decarboxylation reactions remove 2 CO2 molecules from citrate; in aerobic

respiration, all carbon in respiratory substrates (i.e. sugar, fat) are removed through
decarboxylation in the Krebs cycle - thus why CO2 is a waste product

*Four reactions in the Krebs cycle are oxidations and release energy; i.e.
electrons released during oxidation hold energy
●​ These electrons are transferred to either NAD or FAD (flavin adenine
dinucleotide); both molecules act as electron carriers/hydrogen carriers (as
they accept protons as well)
●​ Reduced FAD acts similarly to reduced NAD

The net effect of one Krebs cycle:

●​ One acetyl group is consumed
●​ 3 NADs are converted to reduced NAD - 1 FAD converted to reduced FAD
●​ 2 molecules of CO2 are released
●​ 1 ADP is converted to ATP

From the Khan Academy:

“The Krebs cycle harvests much of pyruvate’s bond energy in the form of
reduced NAD, reduced FAD, and ATP molecules; the reduced electron carriers
NAD and FAD will pass electrons into the electron transport chain and will
(through oxidative phosphorylation) generate most ATP produced in cellular
respiration)”

C1.2.13-1.2.17 - ETC and Chemiosmosis

Transfer of Energy Through NAD

●​ After the Krebs cycle, reduced NAD and FAD go to the inner mitochondrial matrix
- In the inner mitochondrial membrane, proteins acting as electron carriers exist -
they accept & pass on pairs of electrons
 ○​ This sequence of carriers forms the electron transport chain (ETC)

Steps of the Electron Transport Chain:

1.​ The first protein carrier accepts a pair of electrons from reduced NAD, changing
the carrier from an oxidized to a reduced state (the reduced NAD is converted
back to NAD)
a.​ Note: Cristae increase the area of membrane and thus the number of
ETCs it can accommodate
b.​ electrons transferred by reduced FAD have less energy than reduced
NAD; thus these electrons are accepted by a carrier somewhere along the
chain, which has a higher affinity for electrons than the 1st carrier

2.​ Electrons brought into the inner mitochondrial membrane by reduced NAD are
accepted by the first carrier in the chain; they pass along carrier to carrier,
releasing energy at every stage
a.​ The 3 main carriers in the ETC act as proton pumps; they use electron
flow energy to pump protons across the inner mitochondrial membrane
i.​ The first and second main electron carriers pump 4 protons per
pair of electrons; the third carrier pumps two per pair (total of 10
protons pumped from the matrix to inner membrane per pair of
electrons per reduced NAD
b.​ Electrons brought by reduced FAD are fed into the chain after the
first carrier - so only 6 protons pumped per pair of electrons
c.​ Energy is required to pump protons across the inner mitochondrial
membrane because they’re moving against the concentration gradient
(the energy is stored in the form of the proton gradient, which can then be
used to generate ATP)
In summary: The role of the ETC generates and maintains a proton gradient
across the inner mitochondrial membrane using energy from the flow of electrons
(brought to the inner mitochondrial membrane by reduced NAD and FAD)

Chemiosmosis and Making ATP in the mitochondrion

●​ ATP synthase: large + complex protein in the mitochondria phosphorylating
ADP to produce ATP
○​ This is an endergonic reaction so energy’s needed
○​ Energy is provided by the proton gradient created through the ETC
■​ The process of coupling the proton gradient to synthesis of ATP is
chemiosmosis
■​ *ATP production is coupled to the flow of protons.
The regions of ATP synthase
●​ Region 1: transmembrane subunits embedded in the inner mitochondrial
membrane (allowing protons to pass across the membrane)
●​ Region 2: Globular; projects into the
matrix. Has active sites using energy
released by the protons to catalyse
production of ATP

Chemiosmosis is the diffusion of

protons from the inner
mitochondrial membrane to the
matrix, facilitated by the
transmembrane enzyme ATP
synthase
●​ Protons move from a high concentration to low concentration area in the
intermembrane space → mitochondrial matrix
●​ This energy released is used to link a phosphate group to ADP (making
ATP)

ATP Synthase & Chemiosmosis

1.​ The drum-shaped part in ATP
synthase, located in the membrane,
has identical subunits (c), that have
binding sites for a proton
2.​ Next to it lies (a), a structure with 2
half-channels for protons
 a.​ One half channel allows internal protons from the intermembrane space -
to bind to a subunit of the ‘drum’
b.​ The other allows protons bound to a subunit to exit to the matrix; These
two half-channels are NOT aligned, they must rotate to allow protons to
pass through
3.​ The energy released by movement of protons down their concentration
gradient becomes kinetic energy; each proton’s carried by the drum for ~1 full
rotation before being released

4.​ The drum is connected to a stalk (Y on diagram): this stalk projects into the
matrix. Its tight connection causes the stalk to rotate at the same rate as the
drum (the drum & stalk are known as the rotor of ATP synthase)

5.​ In the matrix, the stalk is surrounded by the globular region of ATP synthase (a
ring of alternating subunits a and B).
a.​ Each B subunit has an active site for catalyzing the phosphorylation of
ADP to ATP
b.​ When the stalk in the ring of a and B subunits rotate, this causes
conformational changes to the B subunits

6.​ Changes in the B subunit cause ADP and a phosphate group to bind to the
active site; they then make the phosphate link to the ADP; finally the new ATP is
released into the matrix

7.​ Rotation of the ring of a and B subunits is prevented by a structure adjacent to it

- the rotor arm (b2 and S) linked to the proton channel a2 [the blue thing in the
inner mitochondrial membrane]

With an understanding of chemiosmosis one can predict rates of ATP production

per reduced NAD/FAD:
●​ 3 B subunits in ATP synthase make 1 ATP EACH per turn of the rotor
●​ ONE proton must pass through EACH of the 10 c subunits in the rotor of ATP
synthase to cause ONE rotation
●​ Each pair of electrons from the reduced NAD passing along the ETC results in
TEN PROTONS pumped into the intermembrane space - each pair of electrons
from reduced FAD results in 6 protons
○​ In total (factoring glycolysis, link reaction, and Krebs cycle, and ETC) amt
of ATP produced per glucose molecule is 32 (2 + 0 + 2 + 28 - glycolysis, link
reaction, Krebs cycle, ETC)

Oxygen as a Terminal Electron Acceptor

 ●​ ATP production by mitochondria can only continue IF there is electron flow/proton
pumping
○​ Each electron carrier in the ETC has a stronger
affinity for electrons than the last - removal of
electrons from the last carrier can only be done
by something with a high affinity for electrons
○​ Most organisms use molecular oxygen O2
(the terminal electron acceptor)
■​ Molecules of oxygen accept electrons
from the final electron carrier and
hydrogen ions from the matrix,
producing water
○​ Use of oxygen = last stage in aerobic cell
respiration

*IF OXYGEN RUNS OUT, ELECTRONS ARE NOT

REMOVED FROM ETC AND BUILD UP IN THE CARRIERS
●​ Reduced NAD accumulates - when ALL NAD in the
mitochondria is converted to reduced NAD, link reaction
and Krebs cycle stop
○​ Anaerobic respiration can continue in the
cytoplasm but ATP yield is far smaller…only
2 ATP per glucose

Lipids vs. Carbs as Respiratory Substrates

●​ Both lipids & carbs can be used as respiratory substrates; but there are different
metabolic pathways & energy yield per gram

○​ Carbs: Anaerobic respiration is present & energy yield (per gram) is 17

kilojoules - energy is released from a substrate through oxidation of
carbon & hydrogen, and carb mass is more than 50% oxygen

○​ Lipids: Fatty acids must first be broken down into acetyl groups in the
mitochondrial matrix: these are then fed into the Krebs cycle (only possible
with oxygen, so anaerobic respiration NOT possible) but the energy
yield is 37 kJ per gram - 90% of the mass of lipids is carbon + hydrogen
Photosynthesis
●​ Organisms need complex carbon compounds to build cell structure and carry out
life processes
○​ Using photosynthesis, some can make all carbon compounds with just
light energy and simple inorganic compounds

Photosynthesis: An energy conversion process that turns light energy into chemical
energy (in carbon compounds)
●​ Main groups of carbon compounds: carbohydrates, proteins, lipids, nucleic
acids
●​ Supplies most of the chemical energy needed for life processes in ecosystems

How Does Photosynthesis Work?

●​ Plants convert carbon dioxide + water into carbohydrates by photosynthesis!

●​ Hydrogen is needed for the reduction reaction converting CO2 to glucose (from
photolysis or splitting of water - only happens when light is
available. Oxygen is a waste product)

●​ Photolysis increases the concentration of oxygen in

chloroplasts, causing it to diffuse out of them, and then
the leaf cells, to air spaces outside said leaf

Chromatography
●​ Chloroplasts have different types of chlorophyll - along with
other pigments (accessory pigments)
○​ These pigments absorb different ranges of light
wavelengths (they look different to us)
○​ Pigments can be separated through chromatography
(shown is thin layer chromatography)
■​ Pigments from leaf tissue is placed at one end of a
plastic strip (coated with thin layer of porous
material)
■​ Solvent runs up the strip to separate the pigments
Photosynthetic Pigments and Specific Wavelengths of Light
●​ 1st stage in photosynthesis is absorption of sunlight (involves pigments, which
absorb light)
●​ The colour of the pigment depends on what wavelengths of light it absorbs
○​ White/transparent substances aren’t pigments (white reflects everything,
transparent allows all light to pass through)
○​ Pigments that absorb everything are black

●​ Photon: A particle/unit of light (discrete quantity of energy)

○​ The longer a wavelength, the less energy a photon holds
○​ Photons are absorbed by pigments if the photon energy causes an
electron in a pigment molecule’s atom to become excited (jump to a
higher energy level)
■​ Specific amount of energy
required for this to happen; this
energy is only supplied by certain
wavelengths of light
○​ The main photosynthetic pigments are
chlorophylls (reflect green light)
■​ Red and blue wavelengths can
excite chlorophyll electrons, but
not green; thus green is reflected

■​ Absorption spectrums: graphs showing the % of

light absorbed at each wavelength - by a
pigment/group of pigments (Y = absorption of light)

■​ Action spectrums: graphs showing rate of

photosynthesis at each wavelength of light (Y =
percentage of maximum photosynthesis rate)

*Photosynthesis only occurs in wavelengths of light that can be absorbed by the

pigments.

Carbon Dioxide Enrichment

●​ In high light intensities/warm temperatures photosynthesis rates are limited by
CO2 concentrations
○​ In greenhouses CO2 is raised to increase the rate of plant growth (from
natural gas boilers or compost)
 ○​ Free-air-carbon dioxide enrichment experiments (FACE): experiments
increasing CO2 concentrations in open conditions to monitor effect on
photosynthesis

Photosystems
●​ A photosystem is a
pigment-protein complex in the
thylakoid membranes of
chloroplasts
●​ A typical photosystem has ~100
chlorophyll molecules and 30
accessory pigment molecules (e.g.
carotene, xanthophyll) in a
molecular array (but variation
exists)

●​ Photosystems have core complexes connected to light-harvesting antenna

complexes (containing pigments)

●​ In a light-harvesting complex, when an excited electron emits energy, this energy

is just absorbed by an electron in the adjacent pigment molecule (excitation
energy transfer)
○​ Repeated across light-harvesting complex
○​ Energy jumps from pigment to pigment,
reaching reaction centre in the core complex
(whole process only takes ~few femtoseconds)
○​ For this energy transfer to happen pigment
molecules must be held in a precise array
(both distance and relative orientations)
■​ This is achieved by the protein subunits in a light-harvesting
complex
●​ Once reaching the core complex, light energy reaches a pair of chlorophyll
molecules in the reaction centre
○​ These molecules can donate a pair of excited electrons to electron
acceptors (completing photosystem task - light energy has been
absorbed, generating excited electrons)
○​ Excited electrons are emitted from the photosystem - carrying
energy needed for later stages of photosynthesis
■​ In low light conditions this process is efficient - in high-light
conditions some factors make harvesting less efficient
 ●​ There are two types of photosystems: Photosystem I and Photosystem II

Advantages of the Array of Pigment Molecules in a Photosystem

●​ Photons of light are scattered (combining pigment molecules increases # of
photons absorbed/second)
●​ Combination of pigments allows more wavelengths to be absorbed
●​ Close proximity of pigment molecules allows energy transfer and prevents loss of
light energy via fluorescence
●​ Structured array ensures absorbed energy is funnelled to photosystem’s reaction
centre
●​ Individually, pigment molecules cannot perform photosynthesis; together
they harvest light energy very efficiently allowing photosynthesis

Photolysis of Water in Photosystem II

●​ When photosystem II absorbs light, a special chlorophyll (P680) in the reaction
centre oxidizes by emitting excited electrons
●​ After oxidation, P680 (a powerful reducing agent) gains electrons from water in
the oxygen evolving complex (OEC) of photosynthesis II

○​ OEC contains a group of manganese, calcium, and oxygen atoms - it is in

the core of photosystem II next to the thylakoid space
○​ In the OEC, it binds 2 water molecules before splitting them
(photolysis), releasing 4 electrons & 4 protons
■​ Remaining 2 oxygens bind, producing a molecule of O2

●​ 4 electrons transferred to the reaction centre, while protons released into

the thylakoid space (contributing to a protein gradient in thylakoid
 membrane) - O2 is a waste product, diffusing from thylakoids into
chloroplast stroma, cytoplasm, and out of cell

ATP Production by Chemiosmosis in Thylakoids

●​ Excited electrons from photosystem II are passed to plastoquinone (an
electron carrier in the thylakoid membrane)
○​ Plastoquinone accepts 2 electrons and 2 protons from the stroma (fluid in
chloroplast) to become plastoquinol

●​ Through the thylakoid membrane, plastoquinol moves to the cytochrome b6f

complex, passing 2 electrons to the complex & releasing 2 protons into the
thylakoid space
○​ Creates a proton gradient across the thylakoid membrane
○​ Plastoquinol converts back to plastoquinone and returns to photosystem II

●​ Cytochrome b6f complex contains electron transport chains - transferring

electrons from plastoquinol to another electron carrier plastocyanin
○​ Plastoquinone is hydrophobic and remains in the thylakoid membrane;
plastocyanin is water soluble and free-moves in the fluid inside the
thylakoid
○​ Plastocyanin transfers electron from b6f complex to reaction centre
of photosystem I - this electron has less energy; some of it was used
to pump protons into thylakoid space
■​ Proton gradient stores potential energy; ATP synthase can
generate ATP with the gradient through passive movement
■​ Similar to animal cell production - ATP is released into the stroma

Reduction of NADP by Photosystem I

●​ Making carbon compounds via photosynthesis requires electron supply, provided
by NADP (nicotinamide adenine dinucleotide phosphate)
 ○​ Identical to NAD but has 1 extra phosphate group

●​ Reduced NADP is produced by photosystem I; energy from photons of light is

absorbed by pigment molecules & passed to the reaction centre with chlorophyll
pair P700 (the primary electron donor)
○​ 1 electron in each chlorophyll molecule is excited then emitted from
reaction centre
○​ Passed via chain of electron carriers to the enzyme NADP reductase -
positioned on stroma side of the thylakoid membrane, where it
receives electrons from photosynthesis I
■​ When NADP reductase has 2 excited electrons, it can convert 1
molecule of NADP (in the stroma) to reduced NADP
■​ Electrons used to reduce NADP in photosystem I are replaced by
electrons carried from plastocyanin
●​ If all the NADP in a chloroplast is
reduced to reduced NADP, excited
electrons from photosynthesis I
diverted to plastoquinone
●​ Causes proton pumping, which
allows ATP production by
chemiosmosis:
●​ Some of the energy from the excited
electrons of photosynthesis II are
used to pump protons from the
matrix into thylakoid space, creating
a proton gradient and chemiosmosis
●​ Non-cyclic phosphorylation: When
ATP is produced with energy from the electrons flowing from PSII to PSI and
NADP reductase enzyme
○​ Somewhat of a passive process
●​ Cyclic phosphorylation: When energized electrons rejoin the electron transport
chain at the cytochrome complex because NADP supply runs out
●​ Allows ATP to be produced when a plant can’t make any more reduced NADP

Thylakoid Structural Adaptations

●​ Thylakoid: sac-like vesicle performing
light-dependent reactions of photosynthesis
○​ In chloroplasts…
 ■​ Disc-shaped thylakoids are arranged in stacks called grana
■​ Unstacked thylakoids (stroma lamellae) form connections
between thylakoids in grana

●​ Individual components of a thylakoid cannot carry out

photosynthesis; a thylakoid is a system
○​ Thylakoid membrane: separates the fluid inside the
thylakoid (lumen) from outside fluid (stroma), maintaining proton
gradient
○​ ATP synthase: synthesizes ATP on stroma side (dur)
○​ OEC: splits water in the lumen by photolysis
○​ Photosystem II: Uses light energy to excite electrons
○​ Plastoquinone & cytochrome b6f complex: use excited electron energy
to pump protons from stroma into lumen
○​ Plastocyanin: Transfers electrons to photosystem I from cytochrome b6f
complex
○​ Photosystem I: Absorbs light energy, using that energy to excite
electrons, of whose energy is used to reduce NADP on the stroma side

*Photosystem II and cytochrome b6f complexes are mostly in the grana; photosystem I
and ATP synthases are mostly in stroma lamellae; synthesis of ATP and reduced NADP
is easier due to greater stroma exposure.
Carbon Fixation by Rubisco
●​ CO2 is the carbon source for all photosynthetic organisms (water-soluble, passes
through cell walls/membranes - diffuses from atmosphere into photosynthetic
cells)
○​ Diffusing of CO2 out of photosynthetic cells is prevented by carbon
fixation
■​ In carbon fixation, CO2 is converted into a more complex carbon
compound
■​ Occurs in the stroma (fluid surrounding thylakoids)
■​ Product: glycerate 3-phosphate (3-carbon compound)
●​ CO2 is attached a 5-carbon compound ribulose
bisphosphate to produce 2 molecules of
glycerate-3-phosphate
●​ Catalyzed by the enzyme ribulose 1,5 bisphosphate
carboxylase oxygenase (Rubisco)

●​ Rubisco is inefficient - only fixes 3 CO2 molecules per second

○​ To compensate, there are very high concentrations of Rubisco in stroma
(the most abundant enzyme in the world)
Synthesis of Triose Phosphate using Reduced NADP + ATP
●​ Normally in sugars/other carbs the ratio of hydrogen to
oxygen is 2:1
○​ When ribulose biphosphate is converted to
glycerate-3-phosphate, carbon and oxygen is
added but not hydrogen
○​ Ratio is less than 2:1; hydrogen must be added to
glycerate-3-phosphate (reduction reaction)
■​ The carboxyl group in glycerate-3-phosphate is
replaced with an aldehyde
●​ This reduction involves ATP and reduced NADP; ATP provides
energy needed to perform the reduction, reduced NADP
provides the electrons (hydrogen ions)
○​ Product of this reduction: triose phosphate
○​ This reduction occurs in the stroma (part of
light-independent reactions)

Calvin Cycle & Regeneration of RuBP

●​ 1st carb produced by light-independent photosynthesis reactions
is triose phosphate
○​ 2 triose phosphate combine, forming 1 hexose phosphate
○​ Hexose phosphates can combine (by condensation) to form starch (a
polysaccharide of glucose)
○​ Thus, when conditions are suitable for photosynthesis, starch accumulates
in chloroplasts

●​ But…if all triose phosphates are used up, the supply of

ribulose bisphosphate would be as well
○​ Some triose phosphate must be used to
regenerate RuBP (conversion of 3 carbon
sugar into a 5 carbon one)
○​ This requires ATP - triose phosphate converts
to ribulose phosphate, which converts to RuBP
■​ Cycle where RuBP is consumed and
produced is The Calvin Cycle
●​ As much RuBP must be
produced as it is consumed
●​ In Rubisco reaction, only 1 of the 6
carbon atoms are newly fixed - so
 1/6th of the triose phosphate molecules can be taken out of
the cycle

Synthesis of Carbs, Amino Acids, & other Carbon Compounds using Calvin Cycle
Products + Mineral Nutrients
●​ 6 turns of calvin cycle needed for 1 molecule of glucose (each turn contributing to
a fixed carbon atom in glucose)
○​ Glucose is sometimes produced faster than it can be converted to
sucrose & transported from the leaf; it is converted to starch & stored
within the chloroplast
■​ At night, this starch is broken down & carbs are exported from leaf
○​ Chloroplasts can convert triose phosphate from the Calvin cycle to fatty
acids (using enzymes of glycolysis + link reaction to produce acetyl
coenzyme A, linking together 2-carbon acetyl groups)
○​ Glycerol can also be made from triose phosphate and linked to fatty
acids to make triglycerides (drops of stored oil visible in chloroplasts)
●​ Many other carbon compounds can be produced through photosynthesis -
starting with either glycerate 3-phosphate or triose phosphate from the Calvin
cycle (or intermediates from aerobic respiration pathways)
○​ Mineral nutrients - phosphate/sulfate - also needed to make
compounds with elements other than carbon/hydrogen/oxygen (e.g.
amino acids)
Interdependence of light-dependent and light-independent reactions

●​ Each reaction cannot occur without the other

○​ Light intensity is a factor in carbon compound production - in low light
intensity, production of ATP and reduced NADP are restricted
○​ In high-light intensity, carbon fixation is the limiting factor

Consolidation: (Know where everything occurs!)

Unit 4: Molecular Genetics

A1.2 - Nucleic Acids

What is genetic material/hereditary information?
●​ A store of information that can be copied & passed between cells (as well
as parent to offspring); organisms use DNA to store hereditary
information
●​ Genetic material comes in large polymers of nucleotides. 2 types…
○​ DNA = Deoxyribonucleic acid
■​ Used by all living organisms
○​ RNA = Ribonucleic acid
■​ Used by some viruses, which are not considered living
organisms

Nucleotides consist of 3 parts:

●​ A pentose sugar (5
carbon atoms)
●​ A phosphate group
(acidic + negatively
charged)
●​ A base containing
nitrogen with 1 or 2
rings of atoms in its
structure

*In Figure 4, the base and phosphate are linked by

covalent bonds to the pentose sugar; the carbon atoms
are numbered*

The Sugar-Phosphate “Backbone”

●​ To link nucleotides into polymers, phosphate
groups and sugars form covalent bonds through
condensation reactions between nucleotides
 ○​ This ‘chain’ of sugars and phosphates creates a ‘backbone’ in
DNA/RNA molecules
Bases in DNA/RNA
●​ 4 nitrogenous bases in DNA/RNA - each nucleotide has one base
○​ 3 are the same, the fourth is different
○​ Any two nucleotides can be linked together: thus any base
sequence is possible (almost infinite possibilities)
■​ This sequence is how information is stored

What is RNA?
●​ A single, unbranched polymer of nucleotide
monomers
○​ Number of nucleotides is unlimited, but they
are always linked via condensation
(elimination of water)
○​ Hydroxyl groups (OH) of the phosphate and
pentose sugar are combined, forming one
oxygen molecule (combines with the
pentose’s hydrogen) and water
What is DNA?
●​ DNA consists of polymers of nucleotides - with the nitrogenous bases
adenine, cytosine, guanine, thymine
○​ A DNA molecule has 2 strands of nucleotides linked together
○​ Bases are linked via hydrogen bonds
■​ IMPORTANT:
●​ Adenine only forms H bonds with thymine (AT)
●​ Guanine only forms H bonds with cytosine (GC)
■​ This is called complementary base pairing

●​ The two strands are antiparallel: they run in opposite directions but are
parallel, and form a double helix shape (coiled structure w/ constant
diameter of 2 nanometres)
○​ This is to allow the bases to form bonds
 Differences between DNA and RNA
3 important differences…
●​ The polymer number: 2 nucleotide polymers in
DNA, only 1 in RNA (DNA is double-stranded)
●​ The bases: RNA has uracil instead of thymine as a
base
●​ The pentose sugar: Deoxyribose in DNA and ribose
in RNA (deoxyribose has one less oxygen atom)

How does complementary base pairing help gene

expression?
●​ Complementary pairing allows exact copies of DNA
molecules to be made via replication
○​ In replication, the two strands of the double helix
separate; each strand becomes a guide/template for
the genesis of a new one
○​ I.e. new strands form by linking specific nucleotides
one-by-one: the new strand will be the exact same as
the old. This is called semi-conservative
replication

●​ Genetic information is sections of DNA, called genes

○​ When gene information has effects on the cell, this is gene
expression
Transcription:
1.​ To express a gene, first the base sequence is copied - but this copy is
made of RNA (only 1 DNA strand is used as a template for this)
2.​ Adenine pairs with uracil instead of thymine - this copying process is called
transcription

●​ RNA produced by transcription can have regulatory/structural roles in the

cell or may be used in protein synthesis (the base sequence in RNA is
translated to the amino acid sequence of the protein)
Sequencing of Bases
●​ Many possibilities of base sequences in one strand of a DNA molecule are
possible
○​ I.e. AAA, AAC, GTA
𝑛
○​ With n bases per DNA strand, there are 4 possible combinations
■​ DNA molecules can be any length! Sequencing is infinite

●​ DNA diameter is just 2 nanometres - so immense lengths can be stored in

a small volume. DNA is quite economical!

Conservation of the Genetic Code

●​ DNA and RNA sequences contain information in a coded form - this is
decoded during protein synthesis
○​ Groups of 3 bases are called codons and have meanings in the
code (i.e. ACT, GGA)
○​ There are 64 codons, each of which have meaning:
■​ Most specify one particular amino acid
■​ One signals protein synthesis should start
■​ Three signal protein synthesis should stop

●​ All living organisms/viruses use the same genetic code (it is the universal
genetic code)
○​ All living organisms are related

Directionality of DNA and RNA

●​ All strands of DNA/RNA are linked in the same way; the strand as a whole
has directionality and two strands are antiparallel
 ●​ This directionality affects enzyme/ribozyme processes:
○​ Replication of DNA by DNA polymerase/other enzymes
○​ Transcription of RNA from DNA base sequence
○​ Translation at a ribosome with an RNA base sequence, that
determines the amino acid sequence of a polypeptide

●​ DNA/RNA strands and nucleotides must face the correct direction for them
to fit enzymatic/ribozymatic active sites
○​ Replication, transcription, and translation happen in the same
direction
■​ Replication: DNA nucleotides are always
added to the 3’ side of the polymer - DNA
replication is 5’ to 3’ in terms of the
pentose sugar carbons
■​ Transcription: Just like replication but
with RNA nucleotides
■​ Translation: An RNA molecule has
sequencing information for making a
polypeptide by linking amino acids
together - the ribosome carrying out
translation moves this RNA molecule
towards the 3’ end, working in a 5’ to
3’ direction

●​ During replication, both DNA strands are used as

templates: the two strands are antiparallel, so on one strand replication
moves in opposite directions
○​ Consequently, there are differences in what happens on the 2
template strands

Purine-to-Pyrimidine Bonding
●​ The nitrogenous bases in DNA are in 2 chemical groups:
○​ Adenine and guanine are purine bases (2 rings of
atoms)
○​ Cytosine and thymine are pyrimidine bases (1 ring of
atoms)
 ●​ Purines bind with pyrimidines - base pairs are always the same width &
require the same distance between backbones, stabilizing DNA

Structure of a Nucleosome
●​ Under an electron microscope, eukaryotic DNA looks like a bead string
(each bead is a nucleosome)
○​ At the core of a nucleosome are 8
histone proteins (2 copies of 4
types of histones make up a
disc-shaped structure)
■​ DNA molecules are wound
twice around this protein
structure
■​ An additional histone protein
molecule H1 reinforces this
binding (also helps
package chromosomes
during mitosis)
■​ While plants/animals/other
eukaryotes have nucleosomes, bacteria do not - their DNA is
‘naked’

Hershey-Chase Experiment
●​ Until the 1940s scientists believed proteins were responsible for genetic
material
○​ In the 50s, scientists Hershey and Chase madeT2 bacteriophages
radioactive
○​ T2 bacteriophages had proteins with sulfur and DNA with
phosphorus
○​ They cultivated some with radioactive phosphorus (radioactive DNA)
and radioactive sulfur (protein)
■​ During infection of bacteria and after centrifugation (separation
with medium) more radioactive components were found in the
supernatant (the liquid lying above the cell material)
●​ I.e. In phosphorus, the radioactive DNA was in the
bacteria so it did not transfer to the supernatant
○​ Thus they discovered DNA was responsible for genetic material
Chargaff’s Data
●​ Before the structure of DNA was known, scientists thought it would be a
repeating sequence of the four bases
○​ To test this, Chargaff analysed DNA samples from many
animals to find their nucleotide composition
 ●​ I.e. Nucleotide composition is not the same in every animal/human

D1.1.1 - D.1.1.5 - DNA Replication

●​ DNA replication is the production of new

DNA, with exact identical base
sequences to existing DNA
●​ DNA replication is needed for two
biological processes:
○​ Reproduction: Offspring need
copies of their parents’ base
sequences, so parents must
replicate DNA
○​ Growth and Tissue
Replacement: Each cell in a
multicellular organism needs a
full set of the organism’s base
sequences (i.e. cells must
replicate DNA before it divides)

Semi-Conservative Nature of DNA Replication + Complementary Base Pairing

●​ When DNA gets replicated, double helix strands separate and are used to guide
the polymerization of new strands
○​ The site of replication is called the replication fork
○​ DNA replication is semi-conservative because of complementary base
pairing - only certain nucleotides (AT, CG) can bond with each other during
replication
○​ The two DNA sequences resulting from replication are identical to parent
molecule - very low error in replication

Role of Helicase and DNA Polymerase in DNA Replication

●​ DNA replication is a multi-step process, carried out by an assemblage of
functional subunits called replisomes
○​ Helicase and DNA polymerase are 2 proteins that are essential parts of
replisomes

●​ Helicase
 ○​ Ring-shaped protein separating the 2
strands of a DNA molecule to act as
templates (i.e. a zipper)
○​ As it moves along a strand, helicase
breaks hydrogen bonds between
bases - 1 strand is pulled through
the helicase’s hole & another passes
to the side
■​ This uncoils the double helix
■​ Tensions during unwinding may cause DNA to
supercoil - parts of the replisome prevent this

●​ DNA Polymerase
○​ Assembles new strands of DNA using the original ones as
templates
■​ Two separate DNA polymerases move along the template strands,
adding 1 nucleotide at a time (free nucleotide are available where
DNA is being replicated)
●​ Once the polymerase detects hydrogen bonds have formed
between bases, it links the new nucleotide to the end of the
new strand (condensates phosphate group and sugar of
each nucleotide)

Polymerase Chain Reaction + Gel Electrophoresis to Amplify/Separate DNA

●​ Polymerase chain reaction (PCR) is an automated
method of DNA replication
○​ PCR machines follow repeated steps to
double DNA (the process of making more
DNA with a specific sequence is DNA
amplification)
○​ The steps in a PCR cycle are triggered by
temperature changes

●​ 3 steps of a PCR cycle:

○​ Melting: Heating to 95 C for 30-60 seconds breaks the hydrogen bonds
holding DNA strands together - but not covalent bonds within the
nucleotide (DNA polymerase is not denatured)
 ○​ Annealing: Cooling to 54 C for 30-60 seconds allows primers to bind;
Different primers needed for the 2 separate strands. An excess of primers
(short single strand of DNA, designed to bind to a part of the original DNA)
ensures rapid binding, preventing single strands from pairing up again
○​ Elongation: Heating to 72 C provides optimum temperature for DNA
polymerase - which binds to the DNA strand next to the primer and works
at very high speeds to assemble new strands (~1000 nucleotides/minute)

●​ DNA polymerase, and the four bases, are needed for PCR
○​ With the help of DNA polymerase, PCR allows huge production of copies
in a short time

Sometimes, DNA molecules must be separated by length; this can be done with gel
electrophoresis
1.​ In a 3-4 mm sheet of gel, close to the ends are rectangular holes (wells)
2.​ An electrolyte solution is poured over the gel to cover it
3.​ One DNA sample is pipetted into each well
4.​ A voltage is applied across the electrodes to create an electric field, causing
charged molecules to move through the gel
5.​ DNA has negative charges due to phosphates in the sugar-phosphate backbone,
so it moves towards the positive anode
6.​ As DNA travels to the positive anode, mesh filaments in the gel resist the
movement of molecules - smaller molecules move further than larger ones, so
DNA fragments can be separated by
length
7.​ The voltage is turned off and gel
treated with a dye to make DNA
visible - number of ‘bands’ in the gel
determines how many different
lengths of DNA were in the sample
8.​ The bands are compared with an
existing band of DNA with known
length to determine their length

Applications of Polymerase Chain Reactions/Gel Electrophoresis

1.​ Coronavirus Testing
●​ Viral RNA from a nose swab is rinsed in a saline solution to produce a
liquid sample
 ●​ RNA is converted to DNA using the enzyme reverse transcriptase
●​ PCR amplifies viral base sequences, markers of the coronavirus (~35
cycles of PCR are used)
●​ PCR attaches fluorescent markers to any DNA that is produced - if above
a target level the test is positive
○​ Advantages: It is very sensitive and specific to 1 strain of virus
○​ Disadvantages: Requires expensive material and time lag
between results

2.​ DNA profiling for paternity testing

●​ DNA profiling distinguishes individuals using base sequences called
short tandem repeats (sequences of 2-7 bases repeated consecutively)
○​ Helps to distinguish between individuals (very unlikely 2 would have
the same number of tandem repeats)
1.​ A sample of DNA is obtained
2.​ Selected tandem repeats are copied by PCR - AT LEAST 13
3.​ DNA produced by PCR is separate by fragment length - and therefore # of
repeats
4.​ A pattern of bands is produced on the gel, identical to the DNA taken from
one individual - this is their unique DNA profile

●​ How does this help with paternity testing?

○​ If any bands in the child do not occur in the profile of either the mother or
the father, another person is the father

HL Content
Directionality of DNA Polymerases
●​ Nucleotides are linked to form strands of
DNA or RNA with covalent bonds; terminal
nucleotides either have a sugar or
phosphate group
○​ One terminus - the 3’ end - has the
3rd carbon of the sugar (linking site)
○​ One terminus - the 5’ end - has the
phosphate group of the nucleotide
(that is linked to the 5th sugar
carbon)
○​ There will always be a 5’ end and a 3’ end
DNA Polymerase
●​ Assembles new DNA strands by linking existing strands with complementary
bases (using covalent bonds between the sugar and phosphate)
○​ DNA Polymerase can either link the free nucleotide’s sugar to the
phosphate (3’ to 5’) or the phosphate of a free nucleotide to the sugar (5’
to 3’)
○​ In practice, DNA polymerase always works 5’ to 3’: phosphates are
always linked to sugars
■​ To add nucleotides to DNA on a template strand, there has to be a
3’ terminal present

Leading and Lagging Strands

●​ The two strands formed when helicase separates DNA are antiparallel - their 5’
to 3’ directions are opposites
●​ DNA polymerase always moves 5’ to 3’
○​ On one strand, DNA polymerase adds nucleotides moving towards the
replication fork - this replication is continuous so it’s quicker (leading
strand)
○​ On the other strand, DNA polymerase adds
nucleotides moving away from the replication
fork - they are added in lengths, as the
replication fork exposes more template strand -
restarting replication of DNA polymerase makes
the process slow, so this is the lagging strand
■​ The short lengths of DNA formed are
Okazaki fragments
Functions of DNA primase, DNA polymerase I, DNA polymerase III and DNA ligase
Besides helicase, many proteins have a role in DNA replication.

DNA Primase: A type of RNA polymerase. During DNA replication, assembles ~10
RNA nucleotides on the template strand - to provide a site where DNA polymerase III
can start binding/adding nucleotides to the 3’ end
●​ An RNA primer is needed only once on the leading strand - but primers are
inserted every 100-200 nucleotides on the lagging strand

DNA Polymerase III: The principal polymerase in DNA replication. Binds to the
template strand (on 3’ side of RNA primer) and assembles complementary DNA
nucleotides, adding 5’ to 3’ until either end of template strand or another RNA primer
●​ Additionally, proofreads each nucleotide after it’s added

DNA Polymerase I
●​ An exonuclease; breaks bonds between nucleotides and a polymerase because
it can link nucleotides. On the lagging strand, DNA polymerase I binds to the
junction (point of joining) between 3’ end of Okazaki fragment and 5’ start of a
primer; DNA polymerase cannot connect 3’ to 5’, so DNA polymerase I leaves
gap in the chain of nucleotides that makes up the new DNA strand (where a
sugar-phosphate bond between 2 nucleotides is missing)

DNA Ligase: Connects the gap in the chain nucleotides left by DNA polymerase I by
making sugar-phosphate bonds between two adjacent nucleotides (ligation is joining
things together)
DNA Proofreading
●​ Proofreading corrects errors in DNA replication
●​ Immediately after a nucleotide is mistakenly connected with the template strand,
DNA polymerase III excises the incorrect nucleotide and moves back by 1
nucleotides to insert one with the correct base

Protein Synthesis

What is transcription?
●​ The synthesis of RNA, using DNA as a template
○​ Transcription occurs alone 1 strand of DNA - genes can be transcribed
repeatedly to provide lots of base sequence copies

RNA Polymerase
●​ Multiple roles in transcription:
○​ Binding to DNA at the start of the gene subject to transcription
○​ Unwinding the double helix, separating it into 2 strands (template &
sense)
○​ Moving along the template strand and positioning RNA nucleotides on it
(with complementary bases to the template strand)
○​ Linking the RNA nucleotides (sugar-phosphate bonds) to produce a strand
of RNA
○​ Detaching the new RNA from the template strand, allowing the previous
double helix to reform

●​ Transcription stops when a sequence indicating the end of the gene is

released - releasing the RNA molecule
○​ This RNA is identical to the sense strand except for that uracil replaces
thymine (AU not AT)
Hydrogen Bonding and Complementary Base Pairing in
Transcription
●​ Each nucleotide added to the RNA strand must have a complementary base to
the template DNA strand
○​ Transcription copies one of two base sequences (the sense strand)

Stability of DNA Templates

●​ The template and sense strand only part for a short time as RNA polymerase
moves along the gene - bases are only briefly vulnerable to chemical
changes
●​ This stability is essential; DNA may be transcribed many, many times and errors
must be avoided

Transcription for Expression of Genes

●​ Gene expression: process by which gene
information has observable effects on an
organism
○​ The base sequence in genes doesn’t
determine observable characteristics - they
code for proteins, which do that
○​ Transcription and translation are needed
to produce these polypeptides
○​ Not all genes are transcribed; e.g. insulin
gene is only expressed in the pancreas
○​ The full range of RNA types made in a
cell is its transcriptome, which changes
over time

Translation as Synthesis of Polypeptides from mRNA

Translation is the synthesis of polypeptides from mRNA.

●​ To make a polypeptide, amino acids must be linked together in the right

sequence
○​ This information is held in the base sequence of an RNA molecule
copied through transcription (through the genetic code) - mRNA
○​ The code is translated from the base sequence (translation)
○​ This process happens in the cytoplasm (RNA produced in nucleus,
moves to cytoplasm via nuclear pores)
 ■​ In prokaryotes, they happen in different parts of the cell

mRNA, Ribosomes, and tRNA

What are their roles in translation?

These components work together to synthesize polypeptides by translation.

mNRA:
●​ Has a site that ribosomes can bind to, and a codon sequence specifying the
amino acid sequence of the polypeptide
●​ Includes start and stop codons indicating where translation should begin and
end
○​ One mRNA molecule can be translated many times - but is broken down if
it’s damaged or we don’t need more of the polypeptides

tRNA (transfer RNA)

●​ Translates the base sequence of mRNA into the amino acid sequence of a
polypeptide (the translator)
●​ Each molecule has a distinctive shape - recognized by a dedicated activating
enzyme which attaches the correct amino acid onto the tRNA
●​ To do this…
○​ At one end, tRNA has an anticodon consisting of 3 bases
○​ At the other end, an attachment point for the amino acid corresponding
to the anticodon
●​ Ribosomes (complex structures with small and large subunit) binds tRNA on a
binding site (small subunits has 1 binding site, large subunit has 3 and a
catalytic site making peptide bonds between amino acids)
Complementary Base Pairing between tRNA and mRNA
●​ The 3 bases of an anticodon
on tRNA must complement
the 3 bases of the mRNA
codon for the tRNA to bind to
the ribosome and deliver
amino acids
Genetic Code Features
●​ DNA is well suited to data storage as it can hold long base sequences in any
order
●​ This data, which codes for amino acid sequences, is stored in coded form
○​ ALL living organisms use a universal triplet code - groups of 3 bases code
for amino acids (16 combos of 2 and 64 combos of 3)
○​ A sequence of 3 bases on the mRNA is called a codon
■​ One start codon - codon AUG (starts translation)
■​ Three stop codons (UAA, UAG, UGA) (ends translations)
Stepwise Movement of Ribosomes along mRNA + Linkage of
Amino Acids to Polypeptides via Peptide Bonding

●​ Translation is done by a repeating cycle of steps (each cycle adds 1 amino acid
to a polypeptide chain)
●​ In each cycle:
1.​ An activating enzyme with an active site fitting the tRNA binds to it,
attaching the specific amino acid corresponding to the tRNA anticodon to
the tRNA
2.​ The tRNA binds to the A (amino acyl) site on the ribosome - its anticodon
links (through complementary base pairing) to the next codon on mRNA
3.​ The amino acid linked to tRNA is attached to the growing polypeptide by
formation of a peptide bond
4.​ The tRNA, holding the polypeptide and bonded with the mRNA, moves
from the A to the P (peptidyl) site
5.​ The ribosome moves along mRNA by one codon (3 bases)
6.​ The polypeptide held by tRNA is transferred to another tRNA at the A site
7.​ The tRNA moves from the P to E (exit) site as the ribosome moves along
mRNA by one more codon
8.​ The tRNA anticodon separates from the mRNA codon, allowing tRNA to
separate from ribosome
9.​ Repeat. (A, P, E)
Mutations Changing Protein Structure

●​ A gene mutation is a change to the base sequence of a gene, changing a codon

○​ This changed codon may code for another amino acid especially if the
1st/3rd base in the codon is changed
○​ One amino acid changes in the polypeptide produced - this may or
may not affect the protein

Sickle Cell Disease

●​ An example of single base substitution
●​ The mutated gene codes for the beta-globin
polypeptide in hemoglobin (Hb)
○​ Most humans have allele HbA; if a base
substitution mutation occurs, the 6th codon of
the gene turns from GAG to GTG
○​ A new allele is formed called HbS and it can
be inherited if it occurs in a cell of the
ovary/testis that develops into an egg/sperm
●​ The 6th codon turns from glutamic acid to valine
○​ Causes hemoglobin molecules to link into
chains and form bundles distorting the red
blood cells into a sickle shape (in tissues w/
low oxygen concentrations)

○​ These sickles block capillaries, reducing

blood flow and damaging tissues
■​ Hemoglobin bundles break up when
returning to high oxygen concentrations
in the lung; this grueling cycle repeats
■​ The plasma membrane and hemoglobin
are damaged - life expectancy of RBC
can be as little as 4 days
●​ The body can’t replace these
damaged cells quickly enough
- anemia develops
●​ 2 copies = severe anemia
●​ 1 copy = mild anemia
D1.2 - Protein Synthesis HL

Initiation of Transcription at the Promoter

●​ The promoter is the section of DNA initiating gene transcription (100-1000 bases
long)
●​ Located adjacent to genes on chromosomes - allows RNA polymerase to bind
along with transcription factors
○​ In the promotor, repressor sequences let transcription factors preventing
RNA polymerase bind - transcription is prevented

●​ Gene expression depends on the transcription factors - some are expressed

together, some only become active after binding with another molecule (e.g.
testosterone)

What if a sequence doesn’t code for DNA?

Five alternative functions:
●​ Production of tRNA
●​ Production of rRNA
●​ Production of promoters, enhancers, silencers
●​ Production of telomeres
●​ Production of introns - base sequences edited out of mRNA

Post-transcriptional Modification in Eukaryotic Cells

●​ In eukaryotes, new RNA is changed into mRNA before transcription in the
nucleus
○​ This is why eukaryotes need a nuclear membrane
●​ How does modification work?
Modification stabilizes the mRNA ends from nuclease enzyme digestion.
○​ Five-prime caps - a modified nucleotide with 3 phosphate groups and a
methylated guanine base - is added to the 5’ end
○​ Poly (A) tails - 100-200 adenine nucleotides added to the 3’ end.
○​ Ribosomes will never touch a poly A tail

●​ There are two types of sequences in mRNA: exons (translated into amino acid
sequence) and introns (not expressed).
○​ Introns are 20-200 nucleotides long
○​ mRNA contains alternating exons/introns - introns are removed and
digested into nucleotides while exons are spliced
What is alternative splicing?
Alternative splicing is a type of change allowing many polypeptide variants to be
produced from one gene. It increases diversity of the proteome (all protein variants).
●​ Transcription is unchanged; post-transcriptional modifications are different
○​ Exon skipping: whole chunk of base sequence is edited out to produce
polypeptide variants, but remains in the mRNA
●​ Example: troponin T gene
○​ The protein tropomyosin has 11 exons in its code
○​ Pre-mRNA, it’s spliced differently in different tissues resulting in 5 different
protein forms (i.e. exon 2 missing in skeletal muscle, exons 3 and 10
missing from the smooth muscle)
●​ Example: Fruit flies
○​ In the Dscam protein, over 38 000 different mRNAs

Initiation of Translation
mRNA translation begins with special steps and then repeating steps.
These steps initiate the process:
●​ An activating enzyme attaches amino acid methionine to an initiator tRNA with
anticodon UAC (methionine is from start codon code)
●​ The initiator tRNA binds to the ribosome’s small subunit (producing a ternary
complex, composed of 3 parts - small ribosomal subunit, initiator tRNA, amino
acid)
●​ Ternary complex binds to the 5’ end of the mRNA & slides along it (uses UAC
anticodon to search for start codon AUG)
●​ UAC anticodon links to AUG; small subunit stops moving
 ●​ Large subunit binds to small subunit - with the initiator codon on the P site
●​ New tRNA with complementary anticodon binds to the A site
●​ Peptide bond forms between the new amino acids - A tRNA holds the dipeptide
●​ Initiator tRNA exits through E site as ribosomes move in a 5’ to 3’ direction

Modifying Polypeptides into their Functional State

●​ Modifying polypeptides after translations turns them into functional proteins. The
main types of changes are:
○​ Removal of methionine (start codon) from the 5’ end
○​ Changes to the amino acid side chains (phosphorylations, carbohydrates)
○​ Folding the polypeptide to make tertiary structure via intermolecular
interactions
○​ Removing part of the chain
○​ Combining 2+ into quaternary structures
○​ Combining non-polypeptides into quaternary structures

Turning Preproinsulin to Insulin

The insulin gene INS on chromosome 11 becomes transcribed in pancreatic beta cells
into mRNA.
●​ The resulting polypeptide is preproinsulin (110 amino acids)
●​ It passes into the lumen (membrane) of the RER - 24 amino acids (signal
peptide) are removed from the N terminal (start) by a protease enzyme
recognizing 3 adjacent alanines
●​ The resulting chain, proinsulin, folds into a tertiary structure with 3 disulfide
bonds
○​ Proteases break peptide bonds at 2 locations, excising 33 amino acids
and leaving 2 chains (held together by disulfide bonds)
■​ A-chain: 21 amino acids
■​ B-chain: 32 amino acids
 ●​ A pair of amino acids is removed from the C-terminal (end) of the B chain by a
protease, finally getting insulin

Proteasomes Recycling Amino Acids

●​ Proteins have short cell lives because…
○​ Cell activities may change i.e. the
protein isn’t needed
○​ Free radicals/reactive chemicals
easily change protein structure
○​ Protein can become
misfolded/denatured

●​ In this case, they are broken down by

proteasomes in the cytoplasm
○​ Proteasomes use proteases to break
down proteins into chains of 2-20
amino acids
○​ Proteins are identified for
degradation with a chain of small proteins called ubiquitin
 ■​ They are unfolded and fed into the central chamber by an
ATP-consuming subunits at either end
●​ In the central chamber, they are broken down by proteases
●​ Finally, the amino acids can be used for new proteins

D1.3 - Mutation and Gene Editing

D1.3.1 - Gene mutations as structural changes to genes at the

molecular level
Usually, DNA is stable and base sequences are copied with great accuracy…

●​ Sometimes, changes occur to a gene’s base sequence - called a gene mutation

(random occurrences)

3 types of gene mutations…

1.​ Substitution - a base in the coding sequence is replaced by a different
base (i.e. adenine replaced by cytosine)
a.​ Occur due to chemical changes to bases or mispairing during
replication (commonest example: G to T)
2.​ Insertion - a nucleotide is inserted/extra base in the sequence of the
gene…more major change as it requires breaking sugar-phosphate
backbone
3.​ Deletion - nucleotide is removed from the gene - requires 2 breaks in
sugar-phosphate backbone

Note: Multiple can occur where 2+ consecutive nucleotides are added/removed.

D.1.3.2 Consequences of base substitutions

In some cases neutral, in some cases lethal.
●​ In non-coding DNA, unlikely to have any effect
●​ Same-sense mutations: one codon for amino acid A is changed to another
codon that codes for the same amino acid A
 ●​ Nonsense mutations: Changes a codon coding for an amino acid into a stop
codon ATT, ATC, ACT). Translation terminated before a polypeptide has been
completed - the resulting protein does not function properly
●​ Mis-sense mutations - alters 1 amino acid in a polypeptide. May or may not
have bad or good effects (i.e. sickle cell disease)

●​ SNPS: Single-nucleotide polymorphisms - large numbers of base substitutions

D.1.3.3 - Consequences of Insertions and Deletions

Insertions/deletions are less likely than substitutions to have beneficial consequences.

1.​ Major insertions/deletions almost always result in the coded polypeptide ceasing
to function
2.​ Minor insertions/deletions of 1-2 nucleotides can result in total loss of
polypeptide function - they change the reading frame for every codon onwards
(frameshift)
3.​ Insertions/deletions of multiples of 3 aren’t frameshift - but they can still have
severe consequences due to more/less amino acids changing protein structure
What is BRCA1? (Bracker-one)
●​ Gene coding for the BRCA1 protein in humans
●​ Over 20 000 alleles - including base substitutions, deletions, insertions
○​ Referred to as a tumour suppressor gene - actual function is DNA repair
(mends double strand breaks, corrects base pairing mismatches)
○​ If BRCA1 mutates, the risk of other mutations increases due to lack of
DNA repair
■​ Increased risk of tumour formation & cancer (particularly breast,
ovarian, prostate)

Causes of Gene Mutations

The chance of mutations are normally low as DNA resists chemical change
●​ Increased risk during replication - base-pairing errors sometimes made, not
corrected by DNA repair
●​ Frequency of mutation is affected by two types of mutagen: radiation and
chemicals
 1.​ Radiation
​ Increases mutation rate if it has enough energy causing chemical changes in
DNA i.e. is mutagenic (gamma rays, X-rays, alpha particles from radioactive sources,
UV from the sun)

2.​ Chemicals
Some mutagenic chemical substances cause chemical changes in DNA
(polycyclic aromatic hydrocarbons, nitrosamines found in tobacco smoke,
mustard gas)

Mutation Randomness
Mutations can be described as random changes i.e. unpredictable - but some chemical
changes happen easier than others, so some bases change more often

What are the consequences of mutations?

●​ Depends on whether it occurs in a germ cell or somatic (body) cell
○​ Germ cells: give rise to gametes, can be passed to offspring
■​ I.e. new alleles from mutations can be inherited (most times a
genetic disease)
○​ Somatic (body) cells: Eliminated when the person dies - mostly limited
consequences
■​ The consequences of mutations in a group of genes is much
greater - i.e. roles in cell cycle/cell division
■​ These are proto-oncogenes and can be mutated into oncogenes
- cancer causing genes
●​ Cancer is due to loss of control of the cell cycle -
uncontrolled cell division & tumour formation

Mutation as Genetic Variation

An allele is a variant of a gene - differing in 1+ bases from other alleles
●​ So, mutation changes one allele into another
○​ I.e. mutation increases the # of different alleles in a gene in a population,
increasing genetic variation
○​ Meiosis/sexual reproduction also increase variation through generating
new combinations of alleles
■​ Regardless, mutation is original source of genetic variation
■​ Without mutation, genetic variation declines over time leading to
extinction. We need mutation (although the effects are mostly bad)!

Gene Knockout
We can predict which base sequences in a genome are genes (i.e. what they do) using
characteristic base sequence patterns!
●​ These are called open reading frames (ORFs)
●​ I.e. RNA transcribed from them has start and stop codons
○​ Albeit gene function is not immediately obvious upon discovery, gene
knockout is a technique that changes that

How to do gene knockout?

1.​ DNA is prepared with a base sequence letting it be inserted in a genome of
embryonic mouse cells - replacing a target gene which is deleted (using
CRISPR-Cas-9)
2.​ Cells surviving the procedure grow into adult mice - they only have 1 copy of the
target gene
3.​ Males/females with 1 copy of the target gene mate - 25% of offspring have no
copies of the gene (knockout mice)
4.​ The phenotype of the knockout mice are investigated - determine which traits
have been altered by target gene deletion
Note: entire libraries of knockout genes/organisms exist!

Using CRISPR sequences and enzyme Cas9 for gene editing

What is CRISPR?
●​ Acronym for “clustered, regularly interspaced, short palindromic repeats”
●​ Or…
 ○​ Repeats - the same base sequence occurs several time in the genome
○​ Short - # of base pairs in the repeat is between 23-47
○​ Clustered - repeats are clustered in one part of the genome
○​ Regularly interspersed - repeats are separated by other base sequences
of a similar length (spacers). Spacers are unique - there can be 2 or >120
in a CRISPR locus (derived from viruses infecting prokaryotes, allowing
viral DNA sequences to be recognized in reinfection)
○​ Palindromic - repeated sequences have parts reading the same forwards
& backwards (dyad symmetry)

●​ Prokaryotes make guide RNA by transcribing one repeat + an adjacent spacer -

this repeat side binds to Cas9 & the spacer side searches for viral base
sequences in DNA

What is Cas9?
●​ Enzyme Cas9 can find specific DNA base sequences in the genome - using the
guide RNA (gRNA) bound to it
○​ Guide RNA is made by transcribing 1 spacer + 1 repeat from a CRISPR
array (spacer forms variable 17-20 base sequence at the 5’ end, which is
complementary to the target DNA being searched for)
■​ The repeat side forms other parts of the gRNA (partially double
stranded) - generates loop & distinctive shape that promotes
binding to Cas9

●​ Cas9 moves along and uncoils DNA - then it brings it adjacent to the spacer’s
variable base sequence
○​ Cas9 has two endonucleases.

■​ If the target sequence is

recognized, the
endonucleases cut one
sugar-phosphate bond in
both DNA strands
(double-strand break)
 ■​ Thus, prokaryotes can recognize + destroy foreign (viral) DNA

Cas9-CRISPR in gene editing

Gene editing is long sought, and the Cas9-CRISPR system can help!
●​ To edit genes, we must find a base sequence in the genome & replace it with a
desired sequence
○​ Biologists can modify a Cas9-CRISPR system to find & make changes to
it

Prime Editing as an Approach to Gene Editing

1.​ Prime-editing guide RNA (pegRNA) is prepared - at its 5’ end it has the usual
guide sequence, and the base sequences allowing binding to Cas9
2.​ 2 extra sequences added beside each other at the 3’ end of peg RNA
a.​ Primer binding site
b.​ RNA copy of the desired replacement base sequence for the gene being
deleted i.e. the RT template
3.​ A new version of Cas9 is made:
a.​ A reverse transcriptase enzyme is attached to it, so it assembles a
polypeptide complementary to the RT template
b.​ One endonuclease is deactivated - only cuts one DNA strand now

4.​ The Cas9 and pegRNA, introduced into cells, form a complex & begin editing
genes
a.​ Cas9 moves along the DNA molecule for the target sequence (identified
with the guide sequence at the pegRNA’s 5’ end)
b.​ When recognized, the complementary strand is cut (makes 3’ and 5’ ends)
c.​ The 2 sense & antisense strands are separated - guide RNA links to target
sequence by base pairing
d.​ The primer binding site on
pegRNA binds to the
complementary strand on the 3’
side (initiated reverse
transcription)
 e.​ Reverse transcriptase adds DNA nucleotides to extend the nicked DNA
strand from the 3’ side according to the primer
f.​ The 2 DNA strands pair again - new sequence from reverse transcriptase
displaces old sequence (which becomes a single-stranded flap :(
g.​ Single-stranded flaps’ nucleotides are removed
h.​ If there are mispairing of bases at the reform site, because of
replacement/original base sequence differings, they are corrected by DNA
repair enzymes

Hypotheses Accounting for Conserved/Highly Conserved

Sequences in Genes
Conserved sequences = identical/nearly identical sequences across a species or
group of species
Highly conserved sequences = identical/similar over long periods of evolution (i.e.
occurs along wider range of species)

●​ Many conserved sequences are in protein-coding parts of genome

○​ Alternatives: Genes for making ribosomal/transfer RNA and regulation of
gene expression
○​ Some sequences are found in all mammals

●​ Non-coding elements also conserved in many organisms’ genomes

○​ Functions are unknown, but widespread conservation suggests they have
functions
○​ Alternative hypothesis: Conserved elements may be in regions where
mutation rates are low
■​ E.g: HACNS1 gene has 546 base pairs - highly conserved among
birds and mammals
●​ However, shows fast rate of change in human evolution

D2.2 - Gene Expression

D.2.2.1 How Genes Influence Phenotype

The genotype of an organism is all its genetic information.
The phenotype is the structural/functional aspect of the organism i.e. characteristics.
●​ Gene expression: turning the genotype into the phenotype.
Gene expression happens in stages:
●​ Transcription: Genes in the genotype are selected/used in RNA production
○​ The gene’s DNA base determines the RNA’s base sequence
○​ RNA made by transcribing protein-coding genes is messenger RNA
(mRNA) (i.e. goes to the cytoplasm & ribosomes)

●​ Translation: mRNA is used in polypeptide synthesis: its base sequence is

translated into the amino acid sequence i.e. the polypeptide
●​ Protein Function: The protein changes the phenotype (albeit not all are
physically visible e.g. lactose intolerance)
Gene expression can be controlled by measuring protein/gene quantity.

How is transcription regulated?

Transcription is selective - enzyme RNA polymerase will bind to a sequence close to the
wanted sequence (promotor)
●​ Regulation of transcription includes the TATA box:
○​ Short base sequence (TATAAAA) that’s part of the promoter
○​ On the DNA, a general transcription factor binds to the TATA box,
indicating to RNA polymerase where transcription should start
●​ Every organism’s gene has a shared promoter - but only some genes are used
for transcription
○​ Selection is based on DNA-binding proteins or transcription factors,
which locate & reversibly attach to specific base sequences in DNA along
2 grooves in the double helix where proteins can bind - these binding sites
are upstream of the target gene:
■​ Major groove (more common spot)
■​ Minor groove
○​ Binding sites have variable base sequences, enabling regulation of
gene/genes
●​ Transcription factors can bind to enhancers and silencers - turning genes on or
off
○​ Enhancers are sequences increasing the rate of transcription when
bound with activators
○​ Silencers are sequences decreasing the rate of transcription when bound
with activators
Controlling mRNA Degradation to Regulate Translation
After transcription, degradation of mRNA is one way to curb it.
●​ After transcription is done, a long sequence of adenine nucleotides gets added
to the 3’ end of the mRNA molecule (poly-A-tail)
●​ Increases stability, but gets shorter over time (the shorter the tail, the less likely
the mRNA gets translated, the more likely to be degraded by a nuclease
enzyme)

●​ Rate of shortening varies vastly, but average tail length is 200 nucleotides (i.e.
mRNA survives 5 minutes - 1 week)
○​ Regulating the lifespan of an mRNA molecule influences the amount of
protein produced - i.e. for proteins needed temporarily or continuously
(casein)
■​ Hormones + chemical signals also influence degradation rates -
i.e. vitellogenin (egg yolk) is under hormonal control in chickens
■​ When estrogen levels are higher, mRNA guiding vitellogenin
production lasts 3.5 times longer than low levels

Epigenesis
The concept that a multicellular organism (plant, animal) develops from undifferentiated
cells.
●​ Structures/functions appear that weren’t present at the start of life
●​ Differentiation is achieved through activating/silencing certain genes through
chemical modifications to DNA/proteins (epigenetic tags)
○​ Epigenetic modification doesn’t influence the genotype, but the
phenotype - no altering base sequences
Difference between the Genome, Transcriptome, and Proteome
●​ A genome = all genetic information (coding + non-coding)
●​ Transcriptome = entire set of mRNAs transcribed in a cell (less than an RNA
copy of each protein-coding gene, subject to change with time)
●​ Proteome = entire set of proteins produced by a cell - isn’t proportional to the
quantity of the mRNAs (i.e. # proteins from one mRNA varies)

Methylation of the Promoter/Histones in Nucleosomes as

Epigenetic Tags
Methylation of DNA is the replacement of a hydrogen with a CH3 methyl group in a
base.
●​ Cytosine methylation is frequent - converts it to methylcytosine (also happens
with adenine)
○​ Pattern of methylation changes during a cell’s lifetime - it’s affected by
environmental factors (but genome is unaltered as base pairing is
unaffected)
○​ This methyl group is an epigenetic tag - has roles in gene expression
■​ I.e. methylation of cytosine in the promotor causes resistance in
transcription

●​ DNA combines with histone proteins to form nucleosomes (8 histones with DNA
wound twice) in almost all organisms
○​ The histones have tails extending from the compact nucleosome - they
interact with other nucleosomes causing tight bonding during chromosome
condensation
○​ Nucleosomes also regulate gene expression - in the histone tails
modifications can occur to the amino acids (i.e. methylation, acetylation,
phosphorylation)
 ■​ These are also epigenetic tags
■​ Methylation of amino acids in histone tails decreases/increases the
accessibility to transcription factors - and transcription

Epigenetic Inheritance Via Heritable Changes to Gene Expression

The chemical modifications just described are called epigenetic tags - they have
impacts on gene expression i.e. phenotype
●​ The sum of all epigenetic tags in a cell/organism is the epigenome
●​ When cells divide, they pass on their unique epigenetic patterns: as a result
environmental changes to epigenome are preserved
○​ Reprogramming: when a pattern of epigenetic tags is erased upon
forming haploid gametes
■​ Note: a few epigenetic tags cannot be removed
(transgenerational epigenetic inheritance)
■​ The environment encountered by parent can impact the offspring’s
gene expression (however, this can be reversed)

How does the environment affect gene expression?

●​ Air pollution: damages tissue and decreases DNA methylation, causing greater
proteins to be made that increase risk of heart disease, inflammation, asthma
○​ Can also affect methylation affecting gestation & early life - bad for
pregnant women

What are the consequences of removing most (not all) epigenetic

tags from ovum/sperm?
●​ 99% of epigenetic tags are removed during sperm/egg production in humans
(some tags persist, which has an effect on phenotype)
○​ This is non-Mendelian inheritance called genomic imprinting - epigenetic
tags are “imprinted” in the gametes and maintained through cell division
○​ One allele is silenced, other allele is expressed (no matter dominant or
recessive)
●​ I.e. if the mother is homozygous recessive and the father is
homozygous dominant, the child may still be homozygous
recessive if the dominant allele is silenced

●​ Lions and tigers interbreed in

zoos sometimes: the cross
outcome depends on whether the
mother or father is a lion
 ○​ Female lion: Tigon
○​ Male lion: Liger

Monozygotic Twin Studies

Twins happen when 2 eggs are released during ovulation and both are fertilized
(dizygotic twins) - 50% genetic information in common
●​ Identical twins: cells of an early embryo separate and each develops into a
person

External Factors Affecting Gene Expression

Environmental factors have an impact on gene expression.
●​ Genes responsible for lactose absorption/metabolism are only expressed in E.
coli if lactose is present (the repressor protein is deactivated)

●​ Each cell in a multicellular organism expresses only some genes - regulation is

important in cellular differentiation and development (e.g. seen in life cycles and
embryonic development)
○​ Hormones affect gene expression - e.g. receptors only bind to some
promoters if estrogen is bound to it
■​ E.g. receptor for production of progesterone - estrogen makes
the endometrium more responsive to progesterone
Unit 5: Ecology
C.4.1.1 - C.4.1.6
●​ Population: a group of individual organisms (of the same species) living in
a given area
○​ Members of like species usually interbreed
○​ Interactions within individuals in a population include competition
for food, or cooperation (avoid predation)
○​ In the world, there can be many populations of species (separated
by geographical barriers)
●​ Size of population = total # of individuals in it (normally impossible to
count)
○​ Estimated (based on evidence) using multiple samples (a small
portion of something)
○​ Random Sampling: every member of the population has equal
chance of being selected - i.e. avoid unconscious bias
■​ Random #s used for this purpose
■​ Sampling error: difference between sample statistic & the
equivalent value for the whole population (random sampling
reduces sampling error i.e. everyone has an equal chance)

●​ Random Quadrat Sampling (for populations of sessile organisms)

○​ Quadrats = square sample areas (marked with a quadrat frame) -
where quadrat frames are placed randomly throughout random
positions in a habitat + recording # organisms present
○​ Procedure:
1.​ Measuring tape used to mark base lines along the edge of the
habitat
2.​ Random numbers are generated
3.​ The first random number is used to determine the distance
along the measuring tape
4.​ Second random number is used to determine the distance
across the habitat (at right angles to the tape)
5.​ Quadrat is placed where the spot is marked
●​ Note: this only works for SESSILE (NON-MOVING) ORGANISMS
Capture-Mark-Release-Recapture & Lincoln Index for Motile Organisms
●​ Procedure:
1.​ Capture as many individuals in the occupied habitat possible -
netting, trapping, careful searching
2.​ Mark each individual (without making visible marks for predators)
3.​ Release all marked individuals, allowing them to settle in
4.​ Recapture as many individuals possible - count how many are
marked, how many are unmarked
5.​ Calculate estimated population size using the Lincoln Index

●​ ASSUMPTIONS MADE:
○​ NO migration in/out of the population
○​ No deaths/births
○​ Marked individuals mix back into the unmarked population i.e. equal
chance of being captured on occasion #2
○​ The marks are visible
○​ The marks do not increase
predation/other threats to survival

Carrying Capacity & Competition

●​ If a larger population exists it needs more
resources, which can be limited by amount
available/production rate
○​ Individuals compete for scarce
resources - some die if they can’t get
enough (reduction of population size)
 ●​ The maximum size of a population an environment can support is the
carrying capacity
○​ One resource (or small #) is likely to limit population size i.e.
determine carrying capacity

Controlling Population using Negative Feedback + Density Dependent

Factors
●​ If a population is successful/fills in unoccupied ecological niche, there can
be long-term population increase
●​ Long-term decrease is also possible (i.e. ecological changes have
negative impacts on the population)
○​ More commonly, populations fluctuate but remain stable over
time due to negative feedback control

2 Factors:
1.​ Density-Independent Factors - same effect on population no matter the
size; (i.e. seawater flooding killing all plants intolerant of salinity whether
population is large or small)
2.​ Density-Dependent Factors - increasing effect as the population gets
larger (reduce larger populations, allow smaller ones to increase; basis for
negative feedback mechanisms)

3 Groups of Density-Dependent Factors:

●​ Competition - limited resources i.e.
water, food, light
●​ Predation - I.e. if prey becomes
denser/easier they are predated more, if
population becomes scarce this happens
less
●​ Infectious disease/parasitism/prey
infestation - these increase w/ population
as it’s easier for parasites to spread
host-host
C.4.1.7 - C.4.1.10

Population Growth Curves

●​ Reproduction = exponential growth in populations (positive feedback)
○​ If density-dependent limiting factors are absent, populations increase
exponentially (i.e. species spreads, finds new ecological niche -
resources are abundant)
●​ Example: Eurasian Collared Dove
○​ Originally native to Asia; spread to Europe in 20th century
○​ Thrived in suburban areas/farmland
■​ Population growth has stopped where there was previously
exponential growth - exponential growth can’t continue
indefinitely (finite resources, carrying capacity reached - or
another density-dependent factor i.e. parasites)

○​ As a result, population growth changes from a J shape to an S shape

(sigmoid curves)
■​ Exponential phase, Transitional phase, Plateau phase
 ■​ Not all populations reach plateau phase - some cycle between
“booms/busts” - population exceeds carrying capacity then drops
below it before repeating
■​ Other populations may crash after reaching maximum - i.e. some
populations produce toxins which are harmful if accumulated

Modelling the Sigmoid Population Growth Curve

●​ Using duckweed/yeast, sigmoid population growth can be modelled
experimentally
○​ Small number of organisms introduced initially - resources abundant, no
other organisms present
○​ I.e. Duckweed fronds (stemless, photosynthetic water plants) and yeast
(saprotrophic fungus w/ ovoid cells) reproduce asexually (yeast produces
by budding i.e. producing cells by mitosis)

Communities and Interacting Organisms

●​ All species depend on relationships with other species for survival - 1 species’
population cannot survive in isolation
○​ A group of populations living together in an area + interacting with
one another is a community
■​ Can have 100-1000+ species living together

Intraspecific Relationships
●​ Intraspecific Relationships: a relationship existing between individuals of
the same species (usually same population)
●​ 2 types of intraspecific relationships:
1.​ Competition
-​ Individuals (same species)
compete for the same resources -
stronger individuals get the
resources and survive/reproduce
(natural selection)
-​ Species compete for light,
pollinators, food, breeding sites,
etc.
2.​ Cooperation
-​ Individuals of a population cooperate in many ways - less in plants, more
in social animals
-​ Advantage: all individuals benefit
-​ I.e. Communal roosting, hunting in groups, defence against
predators, communal parental care
C.4.1.11 - 4.1.18 (not 4.1.14-4.1.15)
●​ Interspecific relationships: relationships between species in a
community
6 categories of interspecific relationships:
1.​ Herbivory
a.​ Primary consumers eating producers - i.e. bison grazing
2.​ Predation
a.​ One consumer species (predator) kills and eats another consumer
species (prey)
3.​ Interspecific Competition
a.​ 2+ species competing for the same resource - amount used by 1
species reduces the amount available to the other one

4.​ Mutualism
a.​ 2 species live in close association - both benefit from association
i.e. nitrogen-fixing bacteria living in root nodules of Fabaceae family,
exchanging materials with the plant
5.​ Parasitism
a.​ One species (parasite) lives inside/outer surface of another
species (host), obtaining food from them
6.​ Pathogenicity
a.​ One species (pathogen) lives inside another species (host), causes
host disease

Mutualism
●​ Mutualisms = close association between species where both species benefit
from the relationship
Examples:
1.​ Root Nodules in Fabaceae
a.​ Plants require nitrogen for amino acids + other compounds; they need
fixed nitrogen i.e. ammonium, nitrate, cannot use nitrogen in the air
b.​ Plants in the Faabaceae family (peas, beans/legumes) develop mutualistic
relationship w/ Rhizobium bacteria
c.​ The plants’ root nodules act as shelter for bacteria from consumer +
suitable low oxygen conditions + supplies sugars from photosynthesis for
the bacteria
 d.​ Rhizobium absorbs nitrogen (N2), fixes it to produce ammonium, which it
supplies to the plant - prevents nitrogen deficiency giving it competitive
advantage
2.​ Mycorrhizae in Orchidaceae
a.​ Mycorrhizal relationships: roots of most plants forming association with
fungi in the soil
b.​ Orchids depend on these relationships - their seeds don’t have food
reserves
c.​ During germination, fungal hyphae penetrate the orchid seedling’s root -
forms a sheath around hypha (does not bust root cell’s plasma
membranes)
d.​ Initially the fungus supplies orchid w/ carbon compounds, mineral
nutrients; once orchid begins photosynthesis 2-way exchange of materials
begins

3.​ Zooxanthellae in hard corals

a.​ Hard corals secrete calcium carbonate - forms a skeleton where
individual zooxanthellae (polyps) can live
b.​ Coral reefs built from these skeletons
c.​ Zooxanthellae supplies carbon compounds & oxygen to the coral,
coral provides polyps with safe environment/source of light/CO2
Resource Competition - Endemic vs. Invasive Species
●​ Endemic species: occur naturally in an area
●​ Alien species: introduced by humans (deliberately or accidentally)
○​ If an alien population grows rapidly (lack of limiting factors), it is invasive
●​ Competitive exclusion principle: No 2 species can occupy the same ecological
niche indefinitely
○​ Invasive species compete with endemic species for resources - endemic
species can decline, lose niche, or become extinct

Examples
1.​ Lionfish
a.​ Endemic to Indo-Pacific: some escaped from
aquariums in Florida, become invasive species
by claiming territory
2.​ Salvinia
a.​ Endemic to Brazil: spread worldwide due to
being kept as ornamental plants - eliminates
endemic species through competition for light
as it spreads on ponds quickly

Predator-Prey Relationships as Density-Dependent Control

●​ Usually, populations of prey don’t change much when being hunted by predators
- for every prey killed one is usually born at the same rate
○​ In some communities this equilibrium is absent, replaced by cyclical
oscillations
■​ Prey population increases → food availability increases for
predators. Predator numbers increase
■​ Increase in predators causes decrease in prey population - more
prey is being hunted
■​ Predator numbers decrease (food availability decreases)
■​ Falling predator numbers increase prey population
Example: hunters hunting red foxes and hares

●​ 4 cycles of population rises/falls occurred before 1980

○​ After 1980, sudden outbreak of mange decreased fox population - hare
population skyrocketed
○​ After outbreak ended, normal oscillations returned

●​ Cyclical oscillations are more often seen where weather conditions vary year
to year (i.e. warmer than average spring causes more plant growth, which starts
the cycle of oscillation)

Top-down and Bottom-up Control of Populations

●​ In many communities interactions between trophic
levels are the basis for population control (direct
[feeding] and indirect [population size]
interactions)
●​ Such interactions operate in 2 directions
○​ Top-down control: Acts from a higher
trophic level to a lower one (i.e. increase in
predator population decreases prey
population)
○​ Bottom-up control: Acts from a lower
trophic level to a higher one (i.e. limited
producer population due to availability of
nutrients in soil/water)
Allelopathy and Secretion of Antibiotics
●​ Living organisms share many cell growth metabolic pathways
○​ Substances made by these pathways are primary metabolites (include
both intermediate and end products)

○​ Secondary metabolites: substances produced and released by pathways only

existing in some taxonomic groups: not essential for cell growth but have other
functions
■​ Antibiotics: secreted by microorganisms to kill/prevent growth of other
microorganisms
■​ Allelopathic agents: secreted into soil by plants, preventing growth of
neighbouring plants

Example: Antibiotic production in Penicillium

●​ Penicillium: genus of saprotrophic fungi inhabiting natural
environments i.e. soil, foods
○​ Has hyphae: hyphae secrete enzymes, which
digests carbs, proteins, etc. in the environment
○​ Also absorbs sugars, amino acids, general
products of digestion
●​ Saprotrophs compete for these digested foods; some
species of Penicillium secrete the antibiotic penicillin
○​ Penicillin interferes with cross-linking of
peptidoglycan molecules in the cell walls of
Gram-positive bacteria
■​ Walls become weak, bacteria bursts and
dies - less competition for food resources
in the environment

Example: Allelopathy in Ailanthus altissima

●​ Tree of heaven (ailanthus altissima) is an invasive species in North America
○​ Releases an allelopathic chemical ailanthone - similar to the Eastern
black walnut tree, which releases the chemical juglone
C.4.2.1 - 4.2.11
Ecosystems as Open Systems
●​ An ecosystem (i.e. lakes, forest) is
composed of all of the organisms in an
area together with their abiotic
environment
●​ Two main types of systems:
○​ Open systems: resources can
enter/exit, including chemical
substances/energy
○​ Closed systems: energy can
enter/exit, chemical resources
cannot

Sunlight as Energy
●​ Initial source of energy for most ecosystems = sunlight (energy harvested by
photosynthesis)
○​ 3 groups carry out photosynthesis (producers):
■​ Cyanobacteria
■​ Plants
■​ Eukaryotic Algae (i.e. seaweeds growing on rocky shores)
○​ The percentage of light harvested by producers varies by ecosystem
- i.e. deserts (little producers, little energy), forests (high producers, high
energy)

●​ In marine/freshwater ecosystems, light must pass through water (not 100%

transparent) - shorter wavelengths penetrate further i.e. violet-blue
○​ Photosynthesis uses light with wavelengths from 400nm (violet) to 700nm
(red)
■​ Living organisms/matter in marine/freshwater ecosystems reduce
light penetration
■​ Coastal waters are
turbid (cloudy) due
to suspended
clay/silt/phytoplankton
- little light below 50m
○​ Deep-water ecosystems
therefore rely on other
sources of energy
 ●​ In dark caves, ecosystems also exist; streams entering caves have dead organic
matter (energy source)
○​ I.e. dead leaves contain energy from photosynthesis
●​ Some caves are isolated - no energy flows in

Movile Cave, Romania (2 sealed/isolated ecosystems present)

●​ The producers in sealed caves are called archaebacteria
○​ Archaebacteria gain energy from chemical reactions using
methane/sulfides/inorganic compounds as substrates
●​ Energy from these reactions used to
synthesize carbon compounds - this
process is metabolism known as
chemosynthesis
○​ Microscopic invertebrates feed on
chemosynthetic archaebacteria →
other invertebrates feed on them

Flow of Chemical Energy Through Food Chains

●​ Food chain: sequence of organisms in which each feeds on the previous one
(2-5 organisms)
○​ Producers photosynthesis light into chemical energy
○​ Consumers get energy from the carbon compounds of the organisms they
eat
■​ Producers, primary consumers, secondary consumers, tertiary
consumers

●​ In an ecosystem, multiple food chains exist providing organisms with energy

supply - for example tara shrubs being eating by guanaco and then pumas
Constructing Food Chains/Webs Representing Feeding Relationships in a
Community
●​ Trophic relationships in ecological communities are complex/web-like
(consumers eat more than 1 species, are eaten by more than 1 species)
○​ Food webs show all known feeding relationships

●​ Some organisms feed at more than 1 trophic level, thus not everyone can be
on the same trophic level as on their food chain

Supplying Energy to Decomposers using Carbon Compounds in

Dead Organisms
●​ The body of a dead organism can be used as sources of organic energy
○​ Exoskeletons, fallen leaves, undigested feces
○​ Some organic matter is eaten by certain animals (earthworms, vultures),
other decomposed by saprotrophs (bacteria and fungi)
○​ Saprotrophs (decomposers) secrete digestive enzymes into organic
matter, digesting it externally, before absorbing the products (through
active transport/facilitated diffusion)
●​ I.e breaking complex insoluble carbon compounds into
simpler soluble ones
●​ This is why dead matter softens and crumbles away
 ← Shown is a fungal
hypha burrowing its way
into dead matter &
absoring broken down
simple soluble carbon
compounds

Autotrophs Synthesizing Carbon Compounds from Inorganic

Substances
●​ Autotrophs (self-feeding): Organisms that can make essential carbon
compounds (amino acids, sugars, fatty acids, nucleic bases, etc) using carbon
dioxide (CO2) or hydrogen carbonate (HCO3-)
○​ They can build these carbon compounds from inorganic simple
substances (anabolic reactions)
○​ External energy source needed: either light or chemical reactions
■​ Carbon in CO2, HCO3 is oxidized - reduction and anabolic
reactions are endothermic, so external energy source is needed

Autotrophs are Divided according to the External Energy Source they

Use:
1.​ Photoautotrophs - use light
●​ Sunlight is the main energy source used in most ecosystems
●​ Plants, eukaryotic algae, cyanobacteria - photoautotrophs

2.​ Chemoautotrophs - use exothermic inorganic chemical

reactions
●​ Bacteria, archaebacteria
●​ A reduced substrate (sulfur, hydrogen sulfide, iron, hydrogen, ammonia) is
oxidized, the released energy is used to synthesize carbon compounds
Iron-Oxidizing Bacteria
●​ Iron sulfide (FeS2) found in sedimentary rocks in low-oxygen environments
○​ When these rocks are exposed to air, iron sulfide becomes Fe2+ ions,
sulfate ions, sulfuric acid

●​ Iron-oxidizing bacteria remove electrons from the iron ions (converting

them to Fe3+)
○​ The electrons, carrying energy from the oxidation of iron, are
accepted by electron carriers in the bacterial plasma membranes
○​ Electrons used to reduce NAD

●​ Some energy from electrons are used for proton pumping (increase the
proton gradient across the plasma membrane, formed by sulfuric acid
produced from iron sulfide)
○​ Proton gradient allows ATP production by chemiosmosis
○​ At the end of the pathway, electrons are accepted by oxygen with
hydrogen ions to produce water
■​ The end products of iron-oxidizing bacteria are Fe3+, H2O

●​ Reduced NAD, ATP are finally

used to fix carbon dioxide &
produce carbon compounds -
through the Calvin cycle

○​ Many iron-oxidizing
bacteria are adapted to
acidic conditions due to
the production of
sulfuric acid from iron
sulfide
Heterotrophs
●​ Organisms that get nutritional requirements by getting
carbon compounds from other organisms (i.e. feeding on
them)
○​ Foreign carbon compounds are digested before
products of digestion are used to build larger, more
complex carbon compounds
○​ The process of absorbing carbon compounds/making
them part of the body is assimilation

●​ Assimilation requires absorbing carbon compounds into

cells; molecules must be small/soluble to pass through
cell membranes
○​ Heterotrophs are subdivided according to
whether they digest food internally or externally
■​ Saprotrophs: external
■​ Consumers (unicellular/multicellular):
internal

Both autotrophs and heterotrophs get ATP through cellular respiration,

which is made possible through either making carbon compounds or getting it
from another source

Trophic Levels
●​ Levels organisms are classified in depending on how they obtain energy/carbon
compounds - therefore where they are in food chains
○​ Some animals can occupy 2+ trophic levels (e.g. foxes eating both
primary consumers and producers)
Reductions in Energy per Successive Trophic Level
Energy is lost between trophic levels - less energy is available to each successive
trophic level. There are 3 main forms of energy loss:

1.​ Incomplete Consumption

a.​ Not all of an organism is consumed - i.e. bones, hair: this energy is lost to
saprotrophs
2.​ Incomplete Digestion
a.​ Not all parts of ingested food are digested/absorbed - i.e. fibrous plant
matter containing cellulose
b.​ Energy within feces is lost from the food chain to saprotrophs
3.​ Cell Respiration
a.​ Waste products of cell respiration (CO2, water) can’t supply energy to the
next trophic level
b.​ Energy flowing to each successive trophic level gets smaller per level -
smaller amounts of carbs, proteins, energy-containing substances

Heat Loss in both Autotrophs and Heterotrophs

●​ In ecosystems, all chemical energy is transformed into heat
○​ Energy is always lost during cell respiration, in the form of heat
■​ Chemical energy also converted to heat when ATP used in cellular
activities
○​ Thus, heat energy flows through ecosystems, cannot be recycled -
organisms emit heat into their surroundings, this energy can’t be
converted back to chemical energy

Trophic Level Restrictions Due to Energy Loss

●​ Number of stages in a food chain varies; so much energy is lost at each stage of
the chain, eventually there isn’t enough energy to support successive
trophic levels
○​ In higher trophic levels, there is just not enough prey available. It isn’t
anything to do with the energy levels

Primary Production
●​ Production in ecosystems: the accumulation of carbon compounds in biomass
(i.e. the mass of all living biological organisms)
○​ Autotrophs, heterotrophs produce biomass through growth, reproduction
 ○​ Autotrophs are primary producers; they synthesize carbon compounds
from simple substances
■​ Gross Primary Production (GPP): total biomass of carbon
compounds made in plants through photosynthesis
■​ Net Primary Production (always lower than GPP): GPP minus
biomass lost due to respiration of the plant: biomass available to
consumers
●​ Both measured over long time intervals, in units of grams of
carbon accumulated per square meter of ecosystem

Secondary Productions by Heterotrophs

●​ Secondary production: accumulation of carbon compounds in biomass by
animals, other heterotrophs
○​ I.e. sugars, amino acids are ingested from food, built up into proteins/other
macromolecules
○​ Biomass is lost through cell respiration; more loss of biomass in every
trophic level
■​ I.e. hectare of plant farmland would feed more humans than
hectare of livestock
Constructing Carbon Cycle Diagrams
●​ Carbon pool: a reserve of carbon, whether organic or inorganic (i.e. CO2 in the
atmosphere is inorganic, biomass in an ecosystem is organic)
●​ Flux: the transfer of carbon from one pool to another
○​ Photosynthesis: absorption of CO2 from air/water, and its conversion to
carbon compounds
○​ Feeding: gaining carbon compounds from other organisms
○​ Respiration: releasing CO2 into the atmosphere through respiration
(includes saprotrophs during decomposition)
●​ In diagrams text boxes = pools, labelled arrows = fluxes

Ecosystems as Carbon Sinks, Carbon Sources

●​ As ecosystems are open systems (matter, energy can
move freely) - carbon enters/exits mostly through
carbon dioxide (through photosynthesis, respiration)
○​ If photosynthesis exceeds respiration; there
is net uptake of carbon, the ecosystem is a
carbon sink
○​ If respiration exceeds photosynthesis: there
is net release of carbon, the ecosystem is a carbon source
 ■​ I.e. saprotrophs releasing CO2 during digestion → acidic/anaerobic
conditions in waterlogged habitats prevent decomposition, carbon
becomes coal
■​ Sequestration: removal of carbon from the carbon cycle
■​ Ecosystems also become carbon sources during forest fires, when
CO2 released through combustion of living organisms (i.e. carbon
compounds)

Combustion of Biomass, Peat, Coal, Oil, Natural Gas

These are carbon sinks, as carbon within them can remain sequestered for long times.

1.​ Natural gas

●​ Formed over past 550 million years through burial of decomposed organic matter
under sediments; high temps cause chemical changes, produced oil/natural gas
in porous rocks

2.​ Coal
●​ Formed 325-250 million years ago; accumulation of wood, plant matter in
swamps where it was buried

3.​ Peat
●​ Formed in the past 10 000 years; incomplete decomposition of dead plant matter
(waterlogged habitats prevent decomposition, bogs/swamps)

4.​ Biomass
●​ Wood in trees, etc: plant biomass derived from photosynthesis, transferring
along food chains to animal biomass
*Today, the balance of CO2 production and uptake has been shifted due to fossil fuels.
The Keeling Curve
A curve plotting atmospheric carbon dioxide concentrations. 2 trends are present:

1.​ Annual fluctuations

●​ Each year, CO2 concentrations increase between October and May, falling
the remaining year
○​ Photosynthesis is higher during summer - plants consuming more
carbon dioxide

2.​ Long-term trend

●​ The full Keeling Curve shows carbon concentrations are increasing over
time; i.e. increases in CO2 are not balanced by decreases per year
○​ Burning of fossil fuels, deforestation, etc.
Codependence of Respiration & Photosynthesis
●​ Oxygen released through photosynthesis allows for aerobic respiration;
heterotrophs are dependent on autotrophs
●​ However, heterotrophs cause CO2 concentrations to rise in the atmosphere,
without heterotrophs these concentrations would be limiting factor to
photosynthesis; autotrophs are dependent on heterotrophs

Recycling of Vital Chemical Elements in Ecosystems

Living organisms need certain chemical elements:
●​ Carbon, hydrogen, oxygen to make carbon compounds (carbs, lipids, etc)
●​ Nitrogen, phosphorus (nitrogenous bases, phospholipid bilayers)
●​ ~15 other trace elements

These chemical elements can be endlessly

recycled
●​ Nutrient Cycle: Organisms absorb elements
from abiotic environment and return them to the
environment
○​ Often passed organism by organism
○​ Complex carbon compounds broken
down by decomposers back into simple
elements (i.e. NH3 to N)
D4.2.1 - 4.2.11
●​ Stability of an ecosystem: how long it can persist due to mechanisms operating
within it
○​ Daintree Rainforest (Northern Australia): 180 million years
■​ Contains species from ancient plant families
○​ Borneo Lowland Rainforest: 140 million years
○​ Namib Desert (Southern Africa): 55-80 million years old

●​ Stability: The absence of change

●​ Resistance: the ability of an ecosystem to remain unchanged despite
disturbance
●​ Resilience: the ability of an ecosystem to rebound from change

Requirements for Stability

Ecosystems must meet the following structural/functional requirements:
●​ There is a steady supply of energy
●​ Nutrient cycling should have no leakages i.e. nutrients leaving the system
●​ Individual species should have high genetic diversity (so populations can
survive environmental selectivity)

Disruptions can interfere with an ecosystem’s stability:

●​ Harvesting/removing materials, disrupting nutrient cycles
●​ Erosion causing loss of nutrients
●​ Eutrophication - nutrient enrichment of a body of water (can cause population
imbalances)
●​ Selective removal of species (poaching, epidemics) → disrupts ecosystem
structure

●​ If the genetic diversity of a population drops below certain threshold, the

population becomes less resilient
○​ I.e. high biodiversity = stable ecosystems
○​ Climate of an area also contributes to ecosystem structure
Deforestation of Amazon Rainforest - Loss of Ecosystem
Stability
●​ With enough disturbance systems can cross an ecological threshold that is
difficult to reverse (tipping point)
○​ Tipping point = abrupt change rather than gradual change
○​ Decreases in forest cover (deforestation) reduces plant transpiration
■​ Decrease in cloud formation, reducing rainfall - further loss of forest
→ forest fires increase forest loss
■​ These changes can result in tipping point; Amazon may
transform from stable forest to stable grassland ecosystem

Models to Investigate Effect of Variables on Ecosystem Stability

●​ Mesocosms: small experimental areas used as ecological experiments
○​ I.e. mesocosms replicating natural environments - water tanks, fenced-off
grassland enclosures
■​ Ecological experiments can be done in mesocosms - explore the
effects of varying 1+ ecological conditions (i.e. lack of fish,
testing sustainability)

Keystone Species
●​ Keystone Species: one whose activity has a disproportionate effect on
ecological community’s structures
○​ Species diversity decreases if keystone species is lost - i.e. keystone
species is a highly important predator, if it it lost other species will be
negatively affected

Sustainability of Harvesting Natural Resources

There are 3 requirements for sustainability in ecosystems:
1.​ Nutrient availability - nutrients can be recycled indefinitely, there shouldn’t be a
lack of it (i.e. using saprotrophic bacteria, fungi)
2.​ Detoxing Waste Products - waste products used as a resource by another
species, in the process being detoxified (i.e. ammonium ions)
3.​ Energy availability - continued energy supply through the Sun

How to harvest sustainably?

●​ Plants: When harvesting plants, leave some seeds to germinate/grow into new
plants
 ●​ Fish: Follow sigmoid growth curve; only harvest
at a maximum yield equal to the maximum
population growth rate of fish

Measures to restore Cod stocks in the North Sea

(biomass has tripled since 2005):
●​ Exclusion zones in nursing areas
●​ Increase net hole size (allows smaller cod to
escape)
●​ Decommissioning certain boats (reducing fishing fleet size)
●​ Monitoring cod population and setting fishing quotas based on this

Sustainability of Agriculture
●​ Intensive farming overuses finite resources, is not sustainable & contributes to
climate change. Ways agriculture has become unsustainable:
○​ Tillage (preparing soil for a crop): soils become loosened by
plowing/cultivation, soil structure degrades causing soil erosion
○​ Nutrient depletion of soils: as water drains through depleted soils,
nitrogen fertilizers cause eutrophication in streams/rivers; requires
constant applications of chemical fertilizers
○​ Monoculture: encourages pests & weeds; when treated with
pesticides/herbicides this can cause pollution
○​ Mechanical Tillage: Requires power from diesel oil

Eutrophication of Aquatic, Marine Ecosystems

Nutrient enrichment of water is known as eutrophication

●​ When it rains on agricultural land, water-soluble nutrients added to crops dissolve

in the draining water through the soil
○​ Resulting groundwater pollutes lakes, seas - nutrients (particularly nitrate,
phosphate) cause algal blooms
○​ Unicellular algae, photosynthetic bacteria explode in number & float to
surface
■​ Algae blooms block light to plants below -
as algae and shaded plants die, they are
decomposed by saprotrophic bacteria
■​ These bacteria are aerobic; greatly
increased biochemical oxygen demand
●​ Fish death occurs
Biomagnification of Pollutants in Natural Ecosystems
●​ Some natural ecosystems are polluted with low concentrations of chemicals; but
these chemicals accumulate by the end of food chains (DDT and
falcons+ospreys+otters)

●​ Bioaccumulation: an increase in the concentration of a toxin in an animal’s body

tissues over its lifetime
○​ Problematic with fat-soluble toxins i.e. mercury, which are hard to excrete

●​ Biomagnification: an increase in the concentration of a chemical at each

successive trophic level
○​ Predator consumes large quantities of prey, chemical toxin accumulates
○​ Toxin can also be taken up from the abiotic environment

Microplastics and Macroplastics in the Oceans

●​ Oceans contain lots of non-biodegradable plastic waste
○​ Toxic carbon compounds released into the oceans or when ingested by
marine organisms - they can bioaccumulate, biomagnify toxic
compounds

●​ Macroplastics: large visible debris (nets, ropes, bottles, caps)

○​ Often ingested by marine wildlife
○​ Degradation of macroplastics releases microplastic fragments

●​ Microplastics: smaller than 5mm - globular or fibrous in shape

○​ Found in animal tissues

Rewilding to Restore Natural Processes in Ecosystems

The consequences of natural ecosystem degradation include biodiversity loss, species
extinction, loss of ecosystem services (carbon sequestration, purification of air/water)

●​ Rewilding: as little intervention by humans to ecosystems as possible in efforts

to restore natural processes
○​ Stop human activities - agriculture, logging
○​ Distribute plant seeds that have eroded
○​ Reintroduce apex predators, keystone species
○​ Control alien species
Hinewai Reserve (New Zealand):
●​ 1 250 hectares of farmland has been returned to native forest
○​ Alien mammals (goats, possums, deer) heavily controlled
○​ Minimal human interference otherwise

D.4.2.12 - 4.2.15 - Ecological Succession

●​ Ecological succession: sequences of changes progressively transforming

ecosystems (both biotic and abiotic
changes)
○​ Changes in an ecosystem
trigger other changes,
eventually leading to one
ecosystem replacing
another (interdependence
between organisms and
abiotic factors)
○​ Climax community: stable,
persistent ecosystem that
develops & does not undergo
further significant change

Primary and Secondary Succession

There are two categories of ecological succession: primary and secondary.

Primary succession
●​ Begins in environments with mostly absence of living organisms
○​ Succession occurs on bare rock or deposits of clay/silt/sand - no soil
○​ Only bacteria, lichens, mosses colonize these inorganic substrates -
generating small amounts of soil (making way for herbs to root)
■​ More soil = successively larger plants = diverse animal populations

●​ General principles of primary succession:

○​ Species diversity increases - more species join the community than
eliminated
○​ Primary production of biomass increases - larger plants colonize the
area, more photosynthesis per unit area
○​ Food webs become complex
○​ Nutrient cycling increases as dead organic matter increases
Cyclical Succession in Ecosystems
●​ Some ecosystems undergo cycles of change - i.e. species replace each other
repeatedly over time
○​ I.e. Oak-dominated forests can’t regenerate as oak is intolerant to shade;
oak gets succeeded by other tree species but then oak is now able to
grow due to less shade, dominates the forest again
●​ Cyclical succession also occurs:
○​ When a community’s changed by recurring events
■​ I.e. coastal chaparral ecosystem of California - fires occur every
10-15 years but the climax community (deciduous shrubs,
evergreens) can regrow
■​ I.e. North Island, New Zealand: barnacles settle on bare rock; algae
and mussels colonize, forming a dense carpet; when the mussels
detach bare rock, becomes available for the cycle again

Climax Communities and Arrested Succession

●​ Nature of climax communities depends on environmental circumstances
○​ In well-drained steep slopes, climax community in Glacier Bay ecosystem
is a forest of western hemlock trees
○​ In poorly drained soil on shallow slopes, the climax community is muskeg
swamp

●​ Arrested Succession: when human activity alters natural processes of an

ecosystem
○​ Plagioclimax: an alternative stable community that develops due to
human action

There are two main human activities causing Plagioclimax:

1.​ Grazing by farm livestock

●​ Trees, shrub seedlings are killed by grazing
●​ Areas meant to develop into forests remain grasslands
●​ Grazing animals are not regulated in terms of population; they maintain
grassland ecosystems naturally (i.e. prevent tree growth)
 2.​ Drainage of wetlands
●​ Swamps: ecosystems developing on waterlogged sites; species adapted
to the anaerobic conditions of soil
○​ No saprotrophic fungi due to lack of oxygen: decomposed plant
matter accumulates forming peat
●​ Lots of peat can increase waterlogging, create acidic conditions (peat
bogs); trees cannot grow
●​ Peat bogs sequestrate large amounts of
carbon - reduce airborne CO2
concentrations
○​ Drains are constructed to remove water
from wetlands + aerate soil (open
ditches/porous pipes)
■​ As soil dries, plants adapted to
drier conditions colonize i.e. trees
■​ If the drains fail over time, the
ecosystem can cycle back to peat
bogs

D.4.3.1 - 4.3.8 - Climate Change

​
Anthropogenic Causes of Climate Change

Greenhouse Gases
●​ While some short-wave radiation (i.e. UV) from the Sun is reflected, most is
absorbed and reemitted as long-wave radiation
○​ Gas in the atmosphere that retain this radiation heat keep the Earth warm

Anthropogenic sources of climate change: greenhouse gases released due to

human activities
●​ Carbon dioxide (combustion of fossil fuels, cellular respiration)
●​ Methane (marshes, landfills, fossil fuels, melting permafrost)

Oxygen, nitrogen are NOT greenhouse gases (don’t absorb long-wave radiation)
Weather
●​ Consists of temperature, humidity, precipitation, visibility, wind,
atmospheric pressure
○​ Consistent increases in atmospheric heat content influences long-term
weather patterns/climate
●​ Water Vapour: formed through ocean evaporation/plant transpiration
○​ These processes accelerated by global heating; atmospheric water acts
as a heat sink
○​ Water in atmosphere (i.e. clouds) absorbs heat energy, radiates it back to
Earth

Positive Feedback Cycles in Global Warming

●​ Albedo: solar radiation snow+ice reflects into

space
○​ Light-coloured matter has more albedo;
dark-coloured matter has less
○​ As polar/sea ice melts, darker exposed
water absorbs more radiation
■​ More infrared radiation emitted at
the poles due to new darker
water in polar regions

●​ Permafrost: ground that is frozen all-year round

○​ If global heating increases, permafrost melts
■​ Waterlogged detritus decays, releasing the greenhouse gas
methane
■​ Methane accelerates global heating

●​ Solubility of gas decreases with temperature

○​ As CO2 levels rise (with global temperature), ocean temperatures rise
releasing more CO2 into the atmosphere

●​ Frozen methane in oceans capping stored methane can dissolve due to higher
ocean temperatures
○​ Sudden release of large amounts of methane

●​ Increased droughts/forest fires due to climate change

○​ Reduced carbon capture of the excess carbon as forest has been
destroyed
Tipping Points: Boreal Forests
●​ Tipping points: environmental changes/positive feedback cycles overwhelm an
ecosystem’s resilience
○​ Ecosystem shifts from 1 stable form to another

●​ Boreal Forests:
○​ Cold reduces cellular respiration, so detritus composition is slower
compared to accumulation rates
○​ Trees in boreal forests store carbon dioxide - carbon sinks
■​ Climate change has caused more predisposition of boreal forests to
fires - detritus releases excess carbon dioxide & forest cannot
store it
■​ Tipping point: forest goes from carbon sink to carbon source
■​ After fires, new species arise within the forest

Melting Landfast Ice and Sea Ice

●​ Landfast ice: attached to the shore, doesn’t move with ocean currents
●​ Pack ice: drifts with wind/ocean currents

Example 1: Emperor Penguins

●​ Penguins hunt from landfast ice edges (into open ocean)
○​ Depend on stable landfast ice for breeding - flat surface needed for
nesting
○​ Climate variability: disrupts ice formation/break-up: habitat is unreliable
■​ Changes in nesting site distances impact chick survival
■​ Ross Island: break-up of landfast ice in 2018 caused mortality
event in penguin chicks

Example 2: Walruses
●​ Walruses use pack ice to birth/rest between
feeding trips
○​ They are benthic feeders (eat from ocean
floor in shallow waters)
○​ Melting pack ice: walruses must use
land-haul outs
■​ Risk of trampling pups
■​ Must travel farther for food
■​ Lose more heat in water, making
trips energy-wasteful
Changes in Ocean Currents & Nutrient Upwelling
●​ Ocean stratification: when an ocean has layers of less salty and more
salty/dense water
○​ Layers mix as heat seeps into the ocean from currents/winds/tides
●​ Warming climates increase ocean stability
○​ Surface ocean is made less dense through heating, which expands its
volume
○​ Melting ice adds freshwater, which decreases salinity of surface water
○​ Climate change increases ocean stratification
■​ Transport of heat/oxygen/CO2 from surface to deeper layers is
inhibited

Ocean Stratification as a Positive Feedback Loop

●​ Increased stratification = less CO2 absorbed by surface ocean
○​ Increases atmospheric CO2, causing further warning
●​ Warmer water absorbs less oxygen
○​ Harder to mix oxygen with deep waters; harms deep marine life
●​ Warmer water = coral bleaching

●​ Surface ocean = most active biological zone (top 100m)

○​ Sunlight only penetrates this far
○​ Carbon from photosynthesis enters into marine food chains
■​ Also includes carbon in detritus/feces - can sink, circulate through
deep ocean mixing
●​ Upwelling: deep currents reach continental shelves, bringing nutrients to
surface waters
○​ This supports primary production, energy flow in marine ecosystems
○​ Climate anomalies like El Nino reduce upwelling → lower ocean
productivity

Poleward/Upslope Range Shifts of Temperate Species

●​ Montane species: species who live on mountains
○​ Climate change leads to warmer temperatures at high elevations
○​ Montane species go upslope tracking optimal climates - cannot go higher
if they live at highest elevations
●​ Competitive exclusion results in species seeking new marginal niches - as
new competition arrives escaping the heat
○​ More species will occupy higher elevation habits of mountains
○​ Tropical montane species will be more sensitive to temperature changes
than temperate species
 ●​ More species are shifting in latitude ranges due to deaths/colonizations in the
southern/northern boundaries
○​ European butterflies: >60% shifted north (>240km) in the 20th century

Threats to Coral Reefs and Ecosystem Collapse

●​ Due to man-made carbon dioxide emissions ocean acidification is occurring
○​ Marine animals i.e. reef-building corals need carbonate ions to make
calcium carbonate for their skeletons
●​ CO2 reacts with water to make H2CO3 (carbonic acid)
○​ Carbonic acid dissociates into hydrogen, hydrogen carbonate ions
○​ Hydrogen ions react with carbonates, reducing concentration of pure
carbonates

●​ With less carbonate ions, reef-building corals cannot make proper skeletons &
existing ones dissolve
○​ Mutualism between hard corals, zooxanthellae (photosynthetic algae)
exist
■​ Coral provides algae place to attach to
and get sunlight, algae gives corals
carbohydrates
■​ If ocean water becomes too warm,
coral ejects zooxanthellae - coral
becomes bleached (not enough nutrients)
■​ Loss of coral would devastate
surrounding ecosystem

Afforestation, Forest Regeneration, Peat-Forming Wetlands

●​ Carbon sequestration: capture/storage of carbon occurring naturally through
geological/biological processes
○​ Biological: carbon fixation in photosynthesis, growth in vegetation/wood
biomass storage, buried detritus
●​ Afforestation: Planting trees in areas where they don’t currently exist
○​ Many countries make pledges to tree planting targets
 ●​ Forest regeneration/reforestation: Restocking forests
that have been depleted (forestry practices,
clearcutting)
○​ Following forest harvest, tree seedlings are
replanted

●​ Peat: partially decayed organic matter from

waterlogged ecosystems
○​ Peatlands are carbon sinks (sequestrate
carbon): restoring peatlands means restoring
water levels, blocking drainages, restoring native
species

Phenology and Timing of Biological Events

●​ Phenology: study of seasonal biological events in plants, animals (tree leaf
opening, egg-laying)
○​ Can provide evidence of climate change
●​ Photoperiod (day length): duration of light exposure in 24 hours (unaffected by
climate change)
○​ Varies near poles, remains mostly stable yearly
●​ Plant Responses to Photoperiod
○​ Short-day plants (chrysanthemums, poinsettias): flower when day length
is short
○​ Long day plants (lettuce, spinach, beets): flower when day length is long
●​ Bud Set/Budburst in Deciduous Trees
○​ Bud set (tree growth stops before winter): triggered by shorter day length
in some species and cold temperatures in others. Bud forms, encloses
ends of branches (apical meristems)
○​ Budburst (new leaves in spring): controlled by temperature & lesser
extent day length
●​ Bird Migration/Photoperiod
○​ Birds migrate to find food/nesting
■​ Migration cue: day length changes
Climate Change Disrupting Phenological Events
●​ Due to climate change affecting biological life cycles, the timing of
phenological events is disrupted
●​ Interactions (plant-herbivore, predator-prey, pollinator-plant) become mismatched
○​ Birds synchronize migration to maximum food availability - but climate
change alters periods of peak food availability
■​ I.e. Great Tit Bird: relies on caterpillars to feed young
●​ Due to warmer springs, peak caterpillar biomass occurs
earlier
●​ Reproductive timing of tit birds remains unchanged; birds
give birth after caterpillar peaks
○​ As a result, less chicks survive & less mean mass
■​ I.e. Greenland Caribou: time spring migration with emergence of
essential food plants
●​ Climate change leads to mismatch between plant
development and caribou migration
○​ Caribou get less plants = less nutrition

Increase in Insect Life Cycles from Climate Change

●​ Climate events exasperated by climate change puts stress on trees (i.e. drought)
○​ Warm temperatures encourage faster pest reproduction (Spruce bark
beetles: 2 → 1 years of development)
■​ Development is synchronized after 1 year, beetles attack trees in
large, greater numbers
■​ Weakened trees + synchronized beetle generations = danger
Chi-Squared Tests for Interspecific Competition
●​ Chi squared test for species association (observational study):
●​ How many times species A occurs alone
●​ How many times species B occurs alone
●​ How many times they occur together

H0 = two species are distributed independently

H1 = two species are associated (doesn’t necessarily mean they’re competing)
●​ Further investigation needed (field manipulation, mesocosms, labs)
●​ If chi-square value is higher than critical value, accept H1
Observed value ​ ​ ​ ​ ​ ​ ​ ​ Expected values

Calculating X^2 (chi-squared):

*Add together the last column to get the chi-squared (X^2) value.

Critical Value Table:

●​ P = 0.05
●​ Degrees of freedom =

○​ I.e. if ur comparing the association between 2 species, degrees of

freedom will always be 1