Table of Contents:

Topic 1: The Chemistry of Life

Concept 1.1: How do we define life
Concept 1.2: The origins of life on Earth
Concept 1.3: Life and water
Concept 1.4: The elements of Nature (C,H,N,O)
Concept 2.1: Carbohydrates
Concept 2.2: Nucleic Acids
Concept 2.3: Proteins
Concept 2.4: Lipids
Concept 3.1: Early life and the classification of prokaryotes
Concept 3.2: The structure and composition of prokaryotes
Concept 3.3: The function and abundance of prokaryotes
Concept 4.1: What's the difference - Prokaryote versus Eukaryote
Concept 4.2: How the eukaryote cell evolved
Concept 4.3: Different types of eukaryotic cells
Concept 5.1: Cytoplasm
Concept 5.2: The endomembrane and secretory system
Concept 5.3: The structure and function of membranes in biological systems
Concept 6.1: Cell division and DNA replication
Concept 6.2: The prokaryotic cell cycle
Concept 6.3: The eukaryotic cell cycle

Topic 2: Cells and Energy

Concept 7.1: What is Energy?
Concept 7.2: The Chemistry of Energy
Concept 7.3: Speeding up chemical reactions
Concept 8.1: What is photosynthesis?
Concept 8.2: The light reactions
Concept 8.3: The dark reactions
Concept 8.4: Innovations in photosynthesis
Concept 9.1: Energy in the cell
Concept 9.2: An introduction to glycolysis
Concept 9.3: Anaerobic respiration
Concept 10.1: Energy in the mitochondria
Concept 10.2: The TCA cycle
Concept 10.3: Oxidative phosphorylation
Concept 11.1 Biomolecule creation and destruction
Concept 11.2 Enzymes and Energy - Reaction Rates
Concept 11.3: Enzymes and Energy - Inhibition and Allosteric Regulation
Concept 12.1: Cells detect a variety of signals
Concept 12.2: Receptors bind to signals
Concept 12.3: Mechanism to initiate a cellular response
Topic 3: Multicellularity
Concept 13.1 Origins & benefits of multicellularity
Concept 13.2 Diffusion limits & transport systems
Concept 13.3 Exchange surfaces
Concept 14.1 Homeostasis
Concept 14.2 Chemical cell-cell communication
Concept 14.3 Electrical cell-cell communication
Concept 15.1 Fundamental mechanisms of development
Concept 15.2 Animal development
Concept 15.3 Plant development
Concept 16.1 Animal tissue types
Concept 16.2 Animal organs
Concept 16.3 Plant tissue types & organs
Concept 17.1 Transport needs of plants
Concept 17.2 Transport of water through the xylem
Concept 17.3 Transport of sugars in the phloem
Concept 18.1 Diversity of animal circulatory systems
Concept 18.2 Mammalian circulatory system
Concept 18.3 Blood pressure & exchange in capillaries

Topic 4: Genes and Heredity

Concept 19.1 Transcription: DNA to RNA
Concept 19.2 The genetic code
Concept 19.3 Translation: mRNA to protein
Concept 20.1 How does mutation arise?
Concept 20.2 What are the effects of mutation?
Concept 20.3 Recessive and dominant mutations
Concept 21.1: Meiosis and the inheritance of genetic information via sexual reproduction
Concept 21.2: The law of Segregation and the inheritance of traits at a single locus
Concept 21.3: Diagramming genetic crosses and predicting outcomes
Concept 22.1: Sex determination and sex-linkage
Concept 22.2: Using different types of crosses to observe inheritance patterns
Concept 22.3: Pedigree analysis and inheritance of traits in families
Concept 23.1: The law of independent assortment and the inheritance of traits at different gene loci
Concept 23.2: Gene linkage and crossing-over
Concept 23.3: Determining the likelihood that traits will be inherited together
Concept 24.1: Horizontal gene transfer in prokaryotes
Concept 24.2: Bacterial genetics reveals DNA as the molecule of inheritance
Concept 24.3: Recombinant DNA
Topic 1.1
1. Define the characteristics of living organisms

Features common to all lifeforms:

➢ Composed of a common set of elements.

➢ Comprised of cells (unit of life is cell).

➢ Contain genetic information (allow coding of protein).

➢ Grow and change.

➢ Respond to the environment.

➢ Use molecules (from old) to make new molecules (in digestion/absorbtion/growth).

➢ Extract energy and use it (photosynthesis/respiration).

➢ Exist in population and can evolve.

Benefits and costs of virus:

Pro (alive): Cons (not alive):

➢ Contain nucleic acids (very small ➢ Not capable of independent

with protein coat acting as replication (require host cell
membrane). (virus-parasitic) cellular
machinary).
➢ Can replicate.
➢ Do not contain required metabolic
➢ Evolve and adapt to environment. processes to be considered alive
(no organelles).

➢ Not comprised of cells.

➢ Can not extract energy.

Evidence that DNA provide to explain evolution.

➢ Evidence - DNA → same genetic code (DNA/RNA), chemical composition (amino

acid - protein), and cellular structure (eukaryotic cell).

*Evolution → cells (fundamental unit of life, comprised to form living organisms) come from
pre-existing cells, evolved from a common ancestor (cell theory).

*Natural selection → fitter individuals survive and reproduce (variation → differential

reproduction → evolution).
Topic 1.2
1. Describe how life began on Earth and evaluate the evidence of early life on
Earth

Life arise on Earth (events 1-9)

➢ Life arose soon ater the appearance of liquid water (3.8 billion yrs).

Forces created life on Earth → hypothesis for life formation on Earth.

1. Life form spontaneously on Earth:

→ Miller-Urey experiment (-80°C over 30yrs – early conditions on Earth).
⇒ production of organic products (bases of DNA & RNA / amino acid in protein /
sugars / fatty acids……)

2. Life from other place arrived on Earth via meteorites:

→ sample of meteorite found amino acids / DNA bases / sugars / proteins.

Stromatolites (living fossils) → evidence for the beginning of life on Earth.

➢ Stromatolites → layers of limestone formed in hyper-saline water.

↳ as layers formed, it traps water and debris around (algae / bacteria). →
fossilization of bacteria.
→ provide evidence about when life arose.
Topic 1.3
1. Explain the connection between water and life

Water molecules interact with each other through hydrogen bonding (very strong
intermolecular force).

➢ High specific heat (heat capacity).

require huge amount of energy to incresae the tmep.

➢ High melting and boiling point (compared to other small molecules).

able to draw huge amount of energy when
turn into other fom
➢ High heat of vaporization.

➢ Cohesion (hydrogen bonding between water molecules).

➢ Adhesion (attraction of water to other molecules).

Interaction:

➢ Hydrophilic → polar (ionic) molecules attract to water.

➢ Hydrophobic → nonpolar molecules associate with one another than with water.

➢ Gas → no hydrogen bonding (H2O molecules move freely).

➢ Liquid → hydrogen bonding form and break as H2O molecules move.

➢ Solid → form hydrogen bonding in rigid state.

Water → act as acid (donate H+) and base (recieve H+).

Topic 1.4
1. List the major elements that comprise biological macromolecules and
describe the intermolecular forces that allow these molecules to form

Major elements of life:

➢ Hydrogen (H), Carbon (C), Oxygen (O), Nitrogen (N)
➢ Due to their abundance and significance in molecules and processes that are
crucial to life and living organisms (water, amino acid…).

Carbon → basic building block of life:

➢ Make up 18% of human body.
➢ Capable of forming up to 4 covalent bonds with other atoms simultaneously
(versatile).

Intermolecular Forces

Dipole-dipole Force:
➢ Attraction force between oppositely charged poles of two different molecules.
➢ Occur between polar molecules.
1. Large difference in electronegativity (uneven shared electron pair) → polar
bond.
2. Charge is asymmetrically distributed.
➢ Hydrophilic interaction.

*Dipole-dipole force (hydrogen bonding in this case).

Hydrogen Bonding:
 Dispersion Force:
➢ Type of van der Waals force.
➢ Any molecules can have dispersion force, but it is the only force between nonpolar
molecules.
➢ Electrons are shifting in the cloud around the atom, for a brief moment, more
electrons are on one side of the molecule, causing it to polarize.
➢ Bigger molecule (more atom), more electrons, higher chance of dispersion force.
➢ Hydrophobic interaction.

*Macromolecules (except lipids) → polymers (made up of monomers) contains thousands or

more atoms → functions depend on the specific (polarity) properties of the functional groups.
Topic 2.1
1. Recall the general structure of carbohydrate monomers and distinguish the
differences in carbohydrate polymer structure and function

Macromolecule → biological polymers, composed of long chain of repeating subunits

(monomers).

*Condensation reaction → hydroxyl monomers react to create polymer via covalent bond,
producing water.

*Hydrolysis → enzyme-assited reaction, covalent bond between polymer break to form

monomers, by adding water.

Ether → glycosidic linkage

Disacchardie (union of two monosaccharides) → release water (condensation):

➢ Glucose + fructose = sucrose
➢ Glucose + glucose = maltose
➢ Glucose + galactose = lactose

Polysaccharide: Chitin as well

➢ Glucose x many = glycogen (energy storage) / pectin (structural)

= starch (energy storage) / cellulose (structural)

Starch: Glycogen:
➢ Primary energy storage compound ➢ Primary energy storage compound
in plants. in animals, fungi, and bacteria.
*anaimal (energy storage → branched).

Similarity:
➢ Polymer of glucose (polysaccharide) with a-1,4 glycosidic bonds and a-1,6
glycosidic bonds, producing branching at carbon 6.
➢ Easily degraded by enzymes.

Plant

Starch: Cellulose:
➢ Branched (1,4 & 1,6) ➢ Linear (1,4) polysaccharide of
polysaccharide of glucose. glucose.
➢ Polymer of glucose ➢ Polymer of glucose
(polysaccharide) with a-1,4 (polysaccharide) with a-1,4
glycosidic bonds and a-1,6 glycosidic bonds.
glycosidic bonds, producing
➢ More chemically stable than starch.
branching at carbon 6.
Similarity:
➢ Polysaccharide of glucose.
Difference:
➢ Different enzymes are required to break starch and cellulose undergoing
hydrolysis, due to the different bonds.
➢ Enzyme for cellulose is lacked by most mammals.

*linear → form fibrils with hydrogen bonding between hydroxyl groups which provide
strength for cell wall (structural support).
*branch → readily digested for respiration / anabolism, making it useful energy source
(energy storage).
Topic 2.2
1. Recall the nucleotides in DNA and RNA and describe how these form nucleic
acids

Nucleotides → building blocks of nucleic acids (information storage).

Functional groups that link the nucleic acid sugar-phosphate backbone.

*hydrogen bond is more easy to break than covalent bond.

DNA and RNA direction:

➢ 5’ end has a free phosphate on 5th carbon in the sugar backbone of DNA.
➢ 3’ end has a free hydroxyl on 3rd carbon in the sugar backbone of DNA.
5’ ---> 3’ during DNA synthesis

*Pyrimides → C,T,U; Purines → A,G

Topic 2.3
1. Recognize the number of biological amino acids and communicate how these
assemble to form proteins

Functional groups that link amino acid monomers:

Various functions of proteins:

➢ Hormones (insulin)
➢ Enzymes (rubisco)
➢ Structural (keratin in hair)
➢ Contractile (myosin in muscles)
➢ Defence (antibodies)
➢ Storage (gluten)

Difference between primary, secondary, tertiary, and quaternary structures of proteins.

Disulfied bridge
Denatured protein:
➢ When protein structure changed through disruption / alteration of side-chains,
affecting its function.

Conditions affect secondary and tertiary structure protein:

➢ Temperature increase: energy added disrupt any hydrogen bonding, causing
polypeptides to move apart.
➢ pH change: alter the charge on the R groups for the acidic / basic amino acid.
➢ Addition of high concentration polar molecules: polar molecules interfere at high
concentration with the protein’s ability to make dipole-dipole and hydrogen bond
with its substrate.
➢ Addition of high concentration nonpolar molecules: nonpolar molecules deactivate
proteins through hydrophobic interaction being disrupted by the pressure of high
concentration nonpolar molecules.

*DNA →(transcription)→ RNA →(translation)→ amino acid chain →(folding)→ protein.

Topic 2.4
1. Describe the basic structures of fats, oils and phospholipids and explain the
importance of the relationship between lipids and water within cells

Physical and chemical properties of lipids:

➢ Insoluble in water.
➢ Nonpolar, held together by weak additive dispersion force.
➢ Dissolve readily in organic solvents (nonpolar).
➢ Composed mainly of C, H, O.
➢ Differ from carbohydrates, due to smaller proportion of oxygen.
➢ May contain other elements (P and N).

Lipids → mostly not water soluble.

➢ Lipids are nonpolar, so they are generally insoluble in water, since lipids are able to
form strong dispersion force with each other, therefore unable to form hydrogen
bond with water.

Difference between saturated and unsaturated fatty acids:

Saturated: Unsaturated:
➢ Palmitic acid. ➢ Linoleic acid.
➢ All bonds between carbon atoms ➢ Some bonds between carbon
are single, forming straight carbon atoms are double, forming kinks
chain, allowing molecules to peak (bends) in carbon chain,
tightly with other similar molecules. preventing molecules to peak
➢ Fat (solid, viscous) at room closely (double bond → inflexible).
temperature. ➢ Oil (liquid, fluid) at room
temperature.

Functional group in triglycerides:

Lipids: Phospholipids:
➢ Energy reserves.
➢ Insulation (heat).
➢ Increase buoyancy.
amphipathic
Topic 3.1
1. Explain the significance of cyanobacteria in the evolution of life and compare
the features of Bacteria and Archaea

Three domain of life:

1. Bacteria
2. Archaea
3. Eukarya
*Bacteria and Archaea → Prokaryotic

Archaea differ from bacteria:

➢ Over half of archaea genes are completely unique to eukarya and bacteria.
➢ The two central biological processes in archaea, genetic transcription (DNA →
RNA) and translation (RNA → protein), are more similar to those of eukarya than
bacteria (eukarya and archaea have several mRNA polymerase, while bacteria
only has can).
➢ Archaea lipids feature are quite unusual, archaea lipids are linked with ether
bonds, while other lipids are linked with ester bond.
➢ Archaea membranes and cell walls are unusual as well, due to lack of
peptidoglycan wall.
➢ Archaea have not been found to produce resting spores, while bacteria have.

Cyanobacteria → Great Oxygenation Event

➢ Photosynthesis cyanobacteria produce the majority of oxygen in the Earth, by
turning carbon dioxide from the old atmosphere into oxygen, which then allow an
ozone layer to form, and more complex life to evolve in the ocean, then on land.
Topic 3.2
1. Recall the structural features that characterise prokaryote cells

Prokaryote cells:

Ribosome in prokaryotic cell:

➢ Ribosomes: small structure, made of two subunits of ribosomal RNA and proteins,
carry out protein synthesis in two locations:
1. In cytosol (free ribosomes) → in both prokaryotic and eukayotic cells →
internal cellular use.
2. On outside of the endoplasmic reticulum (rough ER) or the nuclear
envelope (bound ribosomes) → in eukaryotic cells only → export into other
organelles / insert into membrane.
Differences between Gram-positive and Gram-negative bacteria:
→ common way to classify bacteria is through gram staining on cell wall.
Topic 3.3
1. Appreciate that prokaryotes are considered to be highly evolved and recall the
ways that certain bacterial species are used by humans

Prokaryotes are found everywhere.

➢ Ex. plants (legumes) → nitrogen-fixing bacteria, covert N2 to NH3 to absorb as
nutrients (symbiotic relationship); human (everywhere: skin, mouth, lungs…).
*Prokaryotes (include cyanobacteria) - major primary producer (photosynthesis),
have huge impact on Earth (Great Oxygenation Event).
➢ Archaea and some bacteria → extremophiles (live in extreme conditions of
temperature, pH, osmolytes) → able to maintain internal conditions.
○ Ex. hot sulphur spring (high temperature and low pH); hydrothermal vents
(high temperature).

➢ Recycle
○ Werribee sewage treatment plant, bacteria clean up wastes in water.
➢ Pharmaceuticals
○ Input specific gene code into bacteri genome, genetically modified bacteria
use its ribosome to make the corresponding pharmaceuticals (such as
human insulin, growth hormone, interferon).
➢ Genetically modified crops
○ Insert agrobacterium into crops gene, they cultured it and grew the traits of
interest within the plants.
Topic 4.1
1. Describe the basic structure of the nucleus, mitochondrion and chloroplasts

Features Prokaryote Eukaryote

Membrane bound organelles No organelles (simple). Have organelles that

undergo specific functions
for the cell.
➢ Nucleus
➢ Chloroplasts (plants)
➢ Mitochondrion

Cell wall Peptidoglycan (not archaea). Cellulose, hemicellulose,

pectin, lignin, soluble protein
(plants → able to change
shape).

*animal → no cell wall.

Plasma Membrane Yes Yes

Cytoplasm Yes Yes

DNA DNA clustered and loosely DNA packaged as

coiled in nucleoid. chromosome in the nucleus.

(free as nucleoid in
cytoplasm)
*Prokaryotes (simpler cell, adjust / mutate more quickly) have much higher diversity of
biochemical processes and environmental tolerances than eukaryotes (complex cell, specific
niches).

Mitochondria
➢ Surround by two membranes:
○ Outer membrane – control
internal environment (pH).
○ Cristae – hightly convoluted
(folded) inner membrane
(inward projections),
increase surface area to
volume ratio, allowing more
energy (ATP) produced.
➢ Carry out aerobic (with oxygen →
cellular respiration) respiration of all
eukaryotic cells.
Chloroplast
➢ Surround by two membranes:
○ Outer membrane – control
internal environment (pH).
○ Cristae – inner membrane,
complex internal network,
increase surface area to
volume ratio, allowing high
concentration of
photosynthetic pigments, to
produce more energy.
➢ Carry out photosynthesis,
converting light energy to chemical
energy (ATP).

*Root → not necessarily have chloroplast.

Leave → high concentration of chloroplast.

Nucleus
➢ Surrounded by double membrane /
nuclear envelope, allow mRNA to
move out and nucleotides to move
in the nucleus.
➢ Presence of nuclear (annular)
pores, allowing molecules / ions to
pass.
➢ Nucleolus, subregion of nucleus
containing transcribing ribosomal
genes, allowing transcription.
➢ Chromosomes in DNA in long
strands covered with histones
(protein, allow winding).
➢ Different organisms have different
numbers of chromosomes.
➢ RNA transcribed from DNA leaves
nucleus via pores and is translated
in the cytoplasm.
Topic 4.2
1. Justify how the nucleus may have evolved and explain the evidence that
mitochondria (all eukaryotes) evolved from the process of primary
endosymbiosis

Origin of the nucleus:

➢ Nucleus may have formed from invaginations of plasma membrane around the
nucleoid of ancient prokaryote.

Origin of the mitochondria:

➢ Mitochondria arose from primary endosymbiosis of purple bacteria.
➢ Own DNA (separate from nuclear DNA), mitochondrial DNA suggest it had a
bacterial origin ⇒ purple bacteria.
Origin of the chloroplast:
➢ Chloroplasts arose from primary endosymbiosis of photosynthetic cyanobacteria.

Evidence for the endosymbiotic origin of mitochondria and chloroplasts:

➢ These organelles appear morphologically similar to bacteria.
➢ They are surrounded by outer membrane similar to a cell membrane, while their
inner membrane invaginates to form lamellae (thylakoid) or cristae.
➢ They are semi-autonomous, retaining their own genome (DNA, RNA).
➢ They retain their own machinery for syntehsizing proteins, including ribosomes.
➢ Their metabolism is like existing prokaryotic organisms (cyanobacteria for
chloroplast, purple bacteria for mitochondrion).
➢ Chloroplast in some species still have bacterial peptidoglycan wall between the
inner and outer membranes (ex. cyanophora).
2. Compare chloroplasts (in land plants and algae) obtained by primary and
secondary endosymbiosis

Primary endosymbiosis: Secondary endosymbiosis:

➢ Where one organism eat another ➢ Where one eukaryote eat another
single cell, and that cell become like eukaryote that has a chloroplast in
mitochondria. it, and take the chloroplast.
➢ Double membrane. ➢ Triple / quadruple membrane.
➢ Ex. protist group: englenoids.
*Three source of genomes in the nucleus:
mitochondrial, chloroplastic, and nuclear.
Topic 4.3
1. Distinguish between plant and animal cells

Organelles of plant and animal cells ⇒ both eukaryotic cells.

*Differ in structure, nutrition, and functions.

3 major differences:
Cell wall
Chloroplast
Vacuole
Topic 5.1
1. Describe the structure and function of cytosol and the cytoskeleton

Structure and function of cytosol and cytoskeleton

Cytosol Cytoskeleton
➢ Metabolic heart. ➢ Maintains and control cellular
shape.
➢ Jelly-like fluid, mostly water, contain
large amount of raw materials that ➢ Facilitate movement of organelles,
can be used in production of ordered within the cell (particularly
macromolecules by the cell. after mitosis).
➢ Site if numerous biochemical ➢ Components of the cytoskeleton are
processes (ex. ribosomal protein composed of protein, not
creation, protein biosynthesis). membrane.
➢ Many biochemical intermediates are ➢ Cytoskeleton components (protein)
moved / shuttled and often act as a form of scaffolding or as
converted during transition. structural elements within the
cytoplasm of cells.
➢ Space between organelles and
endomembrane. ➢ Cytoskeleton (protein backbone)
organizes cellular structures and
➢ Cytoskeleton throughout.
activities, anchoring (held in place)
many organelles.
➢ Composed of three types of
molecular structures:
1. Microtubules
2. Microfilaments
3. Intermediate filaments

Components of cytoskeleton:

Microtubules Microfilaments Intermediate Filaments

(Tubulin Polymers) (Actin Filaments)
➢ Fibrous proteins
➢ Hollow tubes; wall ➢ Two intertwined strands supercoiled into
consists of 13 columns of of actin, each a thicker cables.
tublin molecules (protein). polymer of actin
➢ One of several
subunits.
➢ Tubulin, a dimer (protein different proteins of
with 2 different subunits) ➢ Actin. the keratin family,
consisting of a-tubulin depending on cell
➢ Maintenance of cell
and b-tubulin. type.
shape (tension-bearing
➢ Maintenance of cell elements). ➢ Maintenance of cell
shape shape
➢ Changes in cell shape.
(compression-resisting (tension-bearing
“girders”). ➢ Muscle contraction. elements).
➢ Cell motility (as in cilia or ➢ Cytoplasmic streaming ➢ Anchorage of
flagella). (free moving). nucleus and certain
other organelles.
➢ Chromosome movements ➢ Cell motility (as in
in cell division. pseudopodia). ➢ Formation of nuclear
lamina.
➢ Organelle movements. ➢ Cell division (cleavage
furrow formation).
Topic 5.2
1. Describe the function and interaction of the organelles within a eukaryotic cell
2. Recognise how complex macromolecules are synthesised within eukaryotic
cells and the pathway required to secrete them

Endomembrane and secretory system (eukaryotic cells)

→ all membrane-bound components (except mitochondria, chloroplast, microbodies).

Organelle Structure Function

Endoplasmic Reticulum ➢ Rough ER formed from ➢ Heart of endomembrane

(ER) – production invaginations of system.
ribosome-bearing plasma
➢ Rough ER produces
membrane around early
proteins (translation) and
nucleus.
lipids, smooth ER
➢ Consists of membrane produces majority of lipids,
cisternae that ramify through both make carbohydrates.
cytoplasm, forming internal
➢ ER provide surfaces for
compartments and channels.
synthesis of proteins,
➢ Dynamic structure, changing glycoprotein (sugar),
structure and function. carbohydrates, and lipids,
then secreted throughout
endomembrane either
used by the cell or
secreted into extracellular
space between cells.

Golgi Apparatus – collect, ➢ Consists of flattened stacks ➢ Functions in collections,

package, distribute of membrane / cisternae, packing, and distribution of
known as golgi stacks, and molecules, many being
collectively, all golgi stacks in secreted.
cell is known as golgi
➢ Functional extensions of
apparatus.
ER and constantly receive
➢ Polar (front and back side) vesicles from ER.
structures, vesicles arrive at
➢ Proteins, glycoproteins,
cis face (receiving) and
and other molecules
leave at trans face
formed in ER are
(shipping).
transported to golgi
apparatus in vesicles to be
biochemically modified
(ex. polysaccharides
formed).
➢ Many molecules
(hormones and digestive
enzymes) exit the golgi
apparatus in secretory
vesicles and then exit the
cell via exocytosis.
➢ Other molecules
(lysosomes) are packaged
into vesicles and remain
within the cell.
Plant Vacuoles (plant cells) ➢ Equivalent of lysosomes, ➢ Perform a diverse range of
surrounded by a single functions, including
membrane – tonoplast. storage of nutrients and
pigments, maintenance of
➢ Contain hydrolytic enzymes
cell turgor pressure
and serves as degradative
(osmosis), and break
compartments.
down of products.

Lysosome (animal cells) ➢ Surrounded by single ➢ Recycle bins of animal

membrane, as it is cells.
membrane bound, the ➢ Break down material
lysosomes are able to ingested by endocytosis /
maintain different internal phagocytosis or recycle
environment to the cytosol, old organelles
with a low internal pH of 4.5. (autophagy).
➢ Acidic interior, optimal ➢ Digest pathogens that
environment for hydrolytic enter the cells.
enzymes (specific pH),
approximately 40 different
hydrolytic enzymes derived
from rough ER and golgi
apparatus.

Microbodies (in both animal ➢ Similar in size to lysosomes ➢ Main organelle involved in
and plant cells) and also surrounded by a the removal of compounds
single membrane, but that are generated by the
contains enzymes derived cells.
from free ribosomes in
➢ Two main types of
cytoplasm, not rough ER,
microbodies:
thus not considered part of
the endomembrane system. 1. Peroxisomes
→ Breakdown amino
➢ Neutral pH, contain oxidative
acids.
enzymes that generate
hydrogen peroxide (H2O2) 2. Glyoxysomes
and enzyme catalase to → Breakdown fatty
break down H2O2. acids.

Pathway:
Topic 5.3
1. Explain the importance of the relationship between membrane phospholipids
and water for membrane structure and how this regulates molecular entry and
exit within a cell

Phospholipids → surfactants, structure allows formation of a semi-permeable membrane.

➢ Phospholipids have only two fatty acid chains attached to glycerol, the third carbon
is ester bonded to phosphate group.
➢ Phospholipidsnis hydrophobic (nonpolar fatty acid tails) and hydrophilic (polar
phosphate head, negatively charged).
➢ Polar phosphate head able to form electrostatic dipole interactions, nonpolar fatty
acid tail able to form London dispersion force.

➢ Fluid mosaic model – phospholipids form closed vesicles in water

○ Phospholipids form a bilayer, with two groups of tails sandwiched towards
the interior, one group of phosphate head toward the cytoplasm (aqueous),
other toward the cell’s exterior (aqueous).
○ Mobile, move laterally back and forth all the time, along the plane of
membrane.
○ Prevent free flow of liquids into / out of cells due to the hydrophobic middle
layer, protect cell’s interior.
○ Must be fluid to work properly, controlling the entry / exit of substances,
and maintaining internal chemical environment.
➢ Plasma membrane
○ Selectively permeable, regulating molecular traffic (exchange materials
with surrounding).
*nonpolar – hydrogencarbon, can dissolve and pass.
*polar – sugar, do not cross membrane easily.

Cholesterol – in plasma membrane

➢ Cholesterol reduce membrane fluidity, by packing fatty acid chains more closely.
➢ Cholesterol has a polar head and a large nonpoalr body, the nonpolar four ring
structure forms dispersion force with fatty acid chain on either sides of it, and the
polar hydroxyl group forms dipole-dipole / ion-dipole interaction with phosphate
head.
Isotonic, Hypertonic, and Hypotonic

➢ Osmosis – diffusion of water across selectively permeable membrane.

○ Water moves from low solute concentration to high solute concentration
across membrane.
○ Osmotic pressure prevent osmosis by resisting change in volume.
➢ Simple (passive) diffusion – based on concentration gradient.
○ Substance diffuse from high concentration area to low concentration area.
○ Uniform distribution, reach equilibrium (equal movement in all direction).

Facilitated diffusion vs. Active transport

Facilitated diffusion: Active transport:

➢ Down concentration gradient. ➢ Up concentration gradient.
➢ Transport protein, allow passage ➢ Carrier protein, move specific
of hydrophilic substances across substances across membrane
membrane. against concentration gradient.
1. Channel protein, hydrophilic ➢ Exchange pump, carrier move one
channel for ions and solute in one direction and another
hydrophilic substances. solute in opposite direction.
2. Aquaporins, channel for ➢ Factors affect rate: availability of
water. carrier protein, substrate, and ATP.
3. Carrier protein, bind to ➢ Substance involved: Na+, K+,
molecules and change Ca2+, Mg2+....
chape to shuttle across
membrane. *Primary active transport – use energy like
ATP to pump molecules against their
gradient.
*Secondary active transport – use energy
from one molecule’s gradient (established
by primary active transport) to transport
another molecule in / out the cell.
Endocytosis vs. Exocytosis
Topic 6.1
1. Recall the purpose and necessity of cell division
2. Recall and understand the features of DNA replication

DNA synthesis:
1. DNA helicase enzyme binds and move along the DNA strand unwinding and
separating the DNA, making a Y-shaped structure (replication fork, site of DNA
replication).
2. SSB protein bind to the single stranded DNA to inhibit rewinding, so that exposed
single stranded DNA can act as template for synthesis of daughter strand.

DNA polymerase → synthesize DNA in 5’ to 3’ direction.

Leading strand:
➢ Replication process is continuous and fast.

Lagging strand:
➢ Replication process is discontinuous, relatively slower, and start slightly later.
1. DNA primase synthesize multiple RNA primers on the lagging strand as DNA
unwinded.
2. DNA polymerase synthesize DNA onto the end of primer until encounter next
primer (short DNA fragment – Okazaki Fragments).
3. RNaseH remove RNA primers between the Okazaki fragments, while the other
DNA polymerase fill the empty spaces.
4. DNA polymerase can not fill the nicks between Okazaki fragments, DNA ligase join
3’ end of one fragment with 5’ end of another fragment, making continuous strand.
DNA replication

Prokaryotes Eukaryotes
➢ Often 1 DNA molecule in genome. ➢ Usually several DNA molecules in
genome.
➢ In S phase of the interphase.
➢ In replication phase.
➢ Only have a single origin of
replication along their DNA. ➢ Have multiple origins of replication
along the chromosomes.
Topic 6.2
1. Contrast prokaryotic and eukaryotic cell cycles and the complexity of these
steps in life
2. Describe the difference between the prokaryotic and eukaryotic cell cycles
and cell division

Binary Fission (asexual reproduction)

→ single-celled eukaryotes and prokaryotes.
Topic 6.3
1. Contrast prokaryotic and eukaryotic cell cycles and the complexity of these
steps in life
2. Describe the difference between the prokaryotic and eukaryotic cell cycles
and cell division
3. Model the stages of eukaryotic cell division and evaluate why mitosis is so
complex

Cyclin-dependent kinases → regulate checkpoints in eukaryotic cell cycle:

Mitosis → production of 2 genetically identical nuclei.

Interphase During S phase of interphase, nucleus

replicate its DNA and centrosomes.

Prophase Chromatin coils and supercoils, becoming

more and more compact and considering into
visible chromosomes. The chromosomes
consist identical paired sister chromatids
formed in S phase. Centrosomes move to the
opposite poles.

Prometaphase The nuclear envelope breaks down.

Kinetochore microtubules appear and connect
the kinetochore to the poles.

Metaphase The centromeres become aligned in a plane at

the cell’s equator.

Anaphase The paired sister chromatids separate, and

new daughter chromosomes begin to move
toward the poles.
Telophase The daughter chromosomes reach the poles.
As telophase concludes, nuclear envelopes
and nucleoli reform, the chromatin
decondenses. After cytokinesis, daughter cells
enter interphase once again.

Cytokinesis:

Animal cell: Plant cell:

*belt of actin microfilaments and myosin. *line of glogi vesicles fusing.

Topic 7.1

1. Recall the different types of energy in biological systems

Electrical Energy Electrical gradient across membrane, drive the movement of ions
through channels.

Chemical Energy Energy stored in chemical bonds, like covalent bonds in ATP.

Light Energy Sunlight captured by pigments in eyes or plants (photosynthesis).

Mechanical Energy Muscle movements and movements within cells.

Heat Energy Heat released by chemical reactions, alters internal temperature

of organism.

2. Explain how ATP stores energy

ATP stores energy by phosphorylating ADP, since the phosphate groups are
negatively charged, which requires a lot of energy for the phosphate groups to be
covalently bonded, thus these energies will be stored as potential energy.
Hydrolysis of phosphate releases energy because the free energy of the P~O
bond is higher than the free energy of the OH bond formed by hydrolysis.

3. Describe redox reactions and role of electron carriers in the cell

Redox reactions are reactions that involve the transfer of electrons between
chemical species.
Oxidation reaction is when chemical species lose electrons (more oxidized, less
energy stored in covalent bonds, less free energy)
Reduction reaction is when chemical species gain electrons (more reduced,
more energy stored in covalent bonds, more free energy).
The role of electron carriers (NADH and FADH2) in the cell is to provide energy
to mechanisms to undergo reaction.
Topic 7.2
1. Describe exergonic and endergonic chemical reactions
2. Describe catabolic and anabolic reactions

Exergonic

- Release energy.

- ΔG < 0 → spontaneous.

- Higner free energy in reactants than in products.

- Catabolic reaction:

- Break down bigger complex and ordered reactants into smaller

simple and randomly distributed products.

- Increase entropy.

- Hydrolysis of sucrose to fructose and glucose (used water).

Endergonic

- Input energy.

- ΔG > 0 → non-spontaneous.

- Lower free energy in reactants than in prodcuts.

- Anabolic reaction:

- Make single larger complex and ordered product from many

smaller and less ordered reactants.

- Decrease entropy.

- Synthesis of sucrose from fructose and glucose (release water).

Topic 7.3
1. Explain the role of enzymes in cellular processes

Enzymes acts as biological catalyst in cellular process, which lowering activation

energy, more particles have energy greater or equal to the activation energy to
react, so that less energy is required to start the reaction.

When substrate bind to enzyme, enzyme sightly changes the shape of its active
site to better fit the substrate (induced fit), enhancing / maximizing catalysis by
forming enzyme-substrate complex.

Enzyme-substrate complex creating an unstable transition state for reactants,

allowing reactions to proceed, without altering the reactants used and products
produced.

Substrate bind to enzyme through orientation, physical strain, and chemical

charge to catalyze reaction.
Topic 8.1
1. Explain the significance of the GOE (Great Oxygenation Event)

The Great Oxygenation Event has changed the Earth’s atmospheric composition
and lead to the evolution of multicellularity. During the GOE, photosynthesis
cyanobacteria produce the majority of oxygen in the Earth, by turing carbon
dioxide from the old atmosphere into oxygen, which then allow an ozone layer to
form, and more complex life to elove in the ocean then on land.

2. Recall location of photosynthesis in plants, algae, cyanobacteria

The location of photosynthesis is in chloroplasts, which is light-dependent

reaction happen in the thylakoid, while light-independent reaction (calvin cycle)
happen in the stroma.

*Anoxygenic photosynthesis - ex, purple sulfur bacteria use hydrogen sulfide

(H2S) as the electron donor, producing sulfur instead of oxygen.
Topic 8.2
1. Explain how light energy is converted to chemical energy in the light-dependent
reactions the cellular components and chemical processes involved

1. Light energy is absorbed by Light Absorption in PSII + Photolysis

pigments in the light-harvesting
complexes PSII and passed on to
the reaction center. The energy is
transferred to P680, which boost the
electron to high energy level. The
high energy electron is passed an
electron acceptor, and the pigment
is replaced with an electron from
water, by splitting the water, which
release O2. Photolysis:

2. The high energy electron travels Electrons Transport + Photon Gradient

down the electron transport chain
while losing energy. Some energy
released pump the H+ ions from the
stroma into the the thylakoid lumen,
building photon gradient, with H+
ions from the photolysis added into
the gradient.

3. The electron then arrives at PSI Light Absorption in PSI +Electron Transport
and joins the P700 in the reaction
center. When light energy is
absorbed by the pigment and
passed to the reaction center, which
boost the electron in P700 to high
energy level and transferred to an
electron acceptor, and the P700 is
replaced with an electron from PSII.

4. The high energy electron travels NADPH Production

down the electron transport chain
and transferred to NADP+
reductase, reducing NADP+ to
NADPH. (for noncyclic
photophosphorylation)
(for cyclic photophosphorylation, no
NADPH produced, electrons are
cycled respectively in PSII and PSI).
 5. The photon gradient that was ATP Synthase
created to be used by ATP
synthase. The H+ gradient has
potential energy. When H+ diffuses
through ATP synthase channel to
the stroma, this potential energy is
converted into kinetic energy,
causing the central subunit to rotate.
This rotation causes the lower
subunit to change its shape,
exposing the active site for ATP
synthesis, which allows ADP
phosphorylation to ATP to proceed
(chemiosmosis).

Photophosphorylation → on the thylakoid membrane

2. List the inputs and outputs of the light-dependent reactions

Inputs Outputs

- Sunlight (light energy) - O2

- H2O (oxidized) - NADPH
- NADP+ (reduced) - ATP
- ADP (phosphorylated)
Topic 8.3

1. Explain the light-independent reactions and the cellular components and

chemical processes involved

Carbon Fixation

1. CO2 molecules are fixed with RuBP (five carbon acceptor molecules) catalyzed by rubisco
enzyme, making a six carbon intermediate molecule. The six carbon molecule is then split into
two 3PG (three carbon molecule).

Reduction and Sugar Production

2. 3PG is reduced to G3P by using the energy from hydrolysis ATP to ADP and electron from
oxidize NADPH to NADP+. (about one-sixth of the G3P molecules are used to make sugar -
glucose).

Regeneration of RuBP

3. The rest of the G3P (about five-sixth) are recycled in the process to regenerate RuBP
acceptor with the energy from hydrolsis of ATP to ADP.

Calvin Cycle → Stroma

2. List the inputs and outputs of the light-independent reactions

Inputs Outputs

- 6 CO2 (reduced) - 1 Glucose (2 G3P)

- 12 NADPH (oxidized) - 12 NADP+
- 18 ATP (dephosphorylated) - 18 ADP

*The NADPH and ATP are fromed the light-dependent reaction.

*The NADP+ and ADP are regenerated for the light-dependent reaction.
*Photosysnthesis is an endergonic reaction (absorb light energy to proceed).
Topic 8.4
1. Compare and contrast C3, C4 and CAM photosynthesis

C3 plants C4 plants CAM plants

Calvin Cycle used? Yes Yes Yes

Primary CO2 Acceptor RuBP PEP PEP

Primary CO2 Fixing Enzyme Rubisco PEP carboxylase PEP carboxylase

First Product of CO2 3PG Oxaloacetate Oxaloacetate

Fixation (3-carbon) (4-carbon) (4-carbon)

Affinity of Primary CO2 Moderate High High

Fixing Enzyme

Photosynthetic cells of the Mesophyll Mesophyll Mesophyll

leaf Bundle Sheath Large Vacuoles

Photorespiration Extensive Minimal Minimal

Examples Wheat (most plants) Corn, Sugarcane Cacti, Pineapple

*Photoresperation: rubisco enzyme oxygenase → intermediates from calvin cycle are

degraded to CO2 and H2O → reduce photosynthesis efficiency, decrease glucose
production, affecting energy production during cellular respiration.
*Hot dry days - leaf stomata close to prevent water loss, increase O2 level relative to
CO2.

C3 plants Best for Wet & High CO2 conditions

CO2 is fixed by rubisco in the calvin cycle to

produce glucose.
 C4 plants Best for Hot & Low CO2 conditions

CO2 is initially fixed into a 4-carbon

compound (oxaloacetate) in mesophyll cells,
with the help of PEP carboxylase enzyme,
then converted to malate or other 4-carbon
compounds, which are transported into
bundle sheath cells deep in leaf (low oxygen)
where they are decarboxylated, releasing
CO2 around rubisco, minimizing the likelihood
of photorespiration and enhancing the
efficiency of carbon fixation, undergoing
calvin cycle and produce sugars - glucose)

CAM plants Best for Hot & Dry conditions

During the night, stomata opens, which

increase CO2 in the mesophyll cells,
minimizing the likelihood of photorespiration,
and the CO2 is fixed into a 4-carbon
compound (oxaloacetate) in mesophyll cells,
with the help of PEP carboxylase enzyme,
then converted to malate or other 4-carbon
compounds, which are stored in vacuoles
within the mesophyll cells, until the next day,
they are decarboxylated in the same
mesophyll cells, releasing CO2, enhancing
the efficiency of carbon fixation, undergoing
calvin cycle and produce sugars - glucose)

*CAM plants, carbon fixation happens at night (when stomata is open to minimize water loss due
to traspiration), while sugar synthesis happens during the day (when stomata is close), which the
two processes happen in the same cell, but at different times of the day; whereas C4 plants,
carbon fixation and sugar synthesis happen simultaneously but at different cells, carbon fixation
happens in the mesophyll cells, while sugar synthesis happens in the bundle sheath cells.

*CAM plants minimize the likelihood of photorespiration by oping stomata during night to increase
CO2 level than O2 level, enhancing the efficiency of carbon fixation; whereas C4 plants minimize
the likelihood of photorespiration by releasing the CO2 near rubisco to increase the chance of
rubisco binding to CO2, enhancing the efficiency of carbon fixation.

*C3 plants is more energy efficient compared to C4/CAM plants, since C3 plants directly fixed
CO2 into 3PG and produce glucose during calvin cycle, without additional energy needed for
other carbon fixation pathway; whereas C4/CAM plants need addition of energy to undergo initial
carbon fixation to oxaloacetate, then undergo calvin cycle for further carbon fixation to 3PG and
produce glucose, so in wet with high CO2 condition, C3 plants will be more efficient.
Topic 9.1
1. Diagram the cellular location of each step of cellular respiration within a cell

Cytosol (Cytoplasm) Mitochondria Matrix Inner Mitochondrial Membrane

(Cristae)
- Glycolysis - Pyruvate Oxidation
- Citric Acid Cycle - Oxidative Phosphorylation

Outside Mitochondria - Inside Mitochondria - Aerobic

Anaerobic

➢ Matrix - for citric acid cycle and pyruvate

oxidation. -

➢ Cristae (Inner membrane) - for oxidative

phosphorylation (electron transport chain) -

due to high surface area to volume ratio for

energy production (ATP synthase).

➢ Outer membrane - controls materials that go

in and out of the cell.

➢ Enzymes - catalyze reactions to proceed.

Topic 9.2
1. Explain the major steps in glycolysis
*Total of ten enzyme-catalyzed reactions.

Step 1 - 5: Energy Harvesting Phase (endergonic reactions)

***Step 1 (Hexokinase):
Glucose → glucose 6-phosphate
→ 1 ATP used

Step 2:
glucose 6-phosphate → fructose 6-phosphate

***Step 3 (Phosphofructokinase):
fructose 6-phosphate → fructose 1,6-bisphosphate
→ 1 ATP used

Step 4 & 5:
fructose 1,6-bisphosphate → 2 G3P
(six carbon sugar is break down into 2 three
carbon sugars)

Step 6 - 10: Energy Payoff Phase (exergonic reactions)

Step 6:
G3P → 1,2-biphosphoglycerate
→ 2 NADH produced (per glucose)

Step 7:
1,2-biphosphoglycerate → 3-phosphoglycerate
→ 2 ATP produced (per glucose)

Step 8:
3-phosphoglycerate → 2-phosphoglycerate

Step 9:
2-phosphoglycerate → PEP
→ 2 H2O released (per glucose)

***Step 10 (Pyruvate Kinase):

PEP → pyruvate
→ 2 ATP produced (per glucose = 2 pyruvate)
 Inputs Outputs

- 1 Glucose - 2 Pyruvates
- 2 ATP - 4 ATP
- 2 NADH

Net Outputs:

- 2 Pyruvates
- 2 ATP
- 2 NADH
*Phosphate on G3P is used to make ATP via phosphorylation
*H+ on G3P is used to produce NADH via reduction (NADH is send to
mitochondria for oxidative phosphorylation)

2. Describe where it takes place

Glycolysis take place in the cytosol.

3. Recall the control points in glycolysis

Phosphofructokinase acts as a control in glycolysis. Phosphofructokinase is an
enzyme that converts fructose 6-phosphate to fructose1,6-biphosphate by the
energy from ATP hydrolysis, while ATP can also inhibit phosphofructokinase, so
when ATP level is high, meaning that the cell have sufficient energy, not all ATP
are able to be hydrolyzed, these excess ATP will then act as inhibitors on
phosphofructokinase controlling glycolysis, preventing unnecessary ATP
production (maintain energy balance).

➢ Large amount of ATP or citrate

present, inhibit
phosphofructokinase.

➢ Large amount of fructose

6-phosphate substrates with large
amount of ADP/AMP, stimulate
phosphofructokinase.

*more example below

(Hexokinase and Pyruvate Kinase)
Topic 9.3
1. Describe how a cell can generate energy when oxygen is absent
When oxygen is absent, cells can either undergo anaerobic respiration or
fermentation to generate energy.

Anaerobic Respiration:
● Does have an electron transport chain, but it does not use oxygen as the final electron
acceptor at the end of the chain.
● Instead, it uses alternative electron acceptors such as sulfate (SO42-), iron (Fe3+), or carbon
dioxide (CO2) for many bacteria and archaea.
● Despite the absence of oxygen as the final electron acceptor, anaerobic respiration still
utilizes an electron transport chain to synthesize ATP, with lower efficiency compared to
aerobic respiration.

Fermentation:
● Does not involve an electron transport chain.
● Use specific enzymes to oxidize NADH (produced during glycolysis) back to NAD+,
regenerating NAD+ for glycolysis to continue produce ATP.
● Fermentation pathways produce various end products such as lactic acid, ethanol, and
CO2, depending on the organism and the specific fermentation pathway.

Lactic Acid Fermentation: Alcoholic Fermentation:

*animal - red blood cell (lack of mitochondria) *yeast and alcoholic beverages (beer, wine)
skeletal muscles (strenuous exercise - low O2)
bacteria in yogurt
Topic 10.1
1. Describe the location and function of the TCA cycle and oxidative
phosphorylation in energy generation

Cytoplam Eukaryotic:
- Glycolysis
- Fermentation

Prokaryotic:
- Glycolysis
- Fermentation
- TCA
- Oxidation

Mitochondrial Matrix Eukaryotic:

- TCA
- Pyruvate Oxidation

Mitochondrial Inner Membrane Eukaryotic:

- Respiratory Chain

Inner Cellular Plasma Membrane Prokaryotic:

- Respiratory Chain
*no mitochondria in prokaryotic cells.

TCA Cycle Oxidative Phosphorylation

- Mitochondrial Matrix - Mitochondrial Inner Membrane (cristae)

- Input (per pyruvate): - Input:

- 1 Acetyl-CoA (oxidized) - NADH (oxidized)

- Output (per pyruvate): - FADH2 (oxidized)

- 3 NADH (reduced) - O2 (reduced)

- 1 GTP (can be converted into - Output:

ATP) (phosphorylated)
- H2O (by-product)
- 1 FADH2 (reduced)
- ATP (phosphorylated)
- 2 CO2 (waste product)

*double the amount of inputs and outputs for per glucose.

*about 30 to 32 ATP produced in oxidative phosphorylation.
Topic 10.2
1. Recall how energy is generated by the TCA cycle

Pyruvate Oxidation

Pyruvate oxidized
→ release 1 CO2
→ reduced 1 NAD+ to 1 NADH
→ 1 Coenzyme A added
→ produce 1 Acetyl CoA

2 Acetyl CoA were produced per glucose,

generated 2 NADH (energy) and released 2
CO2 (waste products).

*charged pyruvate enters mitochondria via

active transport and undergo enzymatic
reactions.

TCA Cycle (Citric Acid Cycle)

Acetyl CoA oxidized by combining with

oxaloacetate substrate
→ released 1 CoA, generating citrate
→ reduced 2 NAD+ to 2 NADH and released
2 CO2 (while converting a 6-carbon molecule
to a 4-carbon molecule)
→ phosphorylated 1 GDP to 1 GTP (can
transferred high-energy phosphate to form
ATP)
→ reduced 1 FAD+ to 1 FADH2 with 1 H2O
added into the cycle
→ reduced another 1 NAD+ to 1 NADH
→ regenerated oxaloacetate (acceptor
molecule) for next cycle.

6 NADH, 2 FADH2, and 2 GTP (energies)

were produced with 4CO2 (waste products)
released per glucose.

*redox reactions (pyruvate and acetyl-CoA oxidized; NAD+ and FAD+ reduced)
decarboxylation (CO2 released)
phosphorylation (GTP produced)
hydration (add H2O to generate intermediates)
Topic 10.3
1. Describe how the electron transport chain and chemiosmosis work together to
generate energy

Oxidative Phosphorylation (Electron Transport Chain + Chemiosmosis) — exothermic process

Electron released from the oxidation of NADH and FADH2 (electron donor / hydrogen carriers
generated during glycolysis, pyruvate oxidation, and citric acid cycle) to NAD+ and FAD+ →
passes through the complexes on the electron transport chain (progressively loses free energy
at each transfer in the respiratory chain) → pumping H+ ions into the intermembrane space
from mitochondrial matrix, creating proton gradient (electrochemical gradient)→ when the
electron reaches its lowest free energy level, it is used to reduced O2 (final electron acceptor,
removing de-energized electron from the electron transport chain) forming H2O (remove H+ n
the mitochondrial matrix to maintain the proton gradient)→ proton gradient has potential
energy, which when H+ diffuse through the ATP synthase down the proton gradient back to the
mitochondrial matrix, the potential energy is converted to kinetic energy, changing the shape of
the ATP synthase → activate site of ATP synthase exposed to synthesize ATP from ADP
through phosphorylation.

*absent of oxygen, electron will not be oxidized and pass through ETC, halting ATP production
as well as TCA cycle (no NAD+ and FAD+).
Topic 11.1
1. Describe catabolic and anabolic pathways that link carbohydrate, lipid and
protein metabolism

Carbohydrate Metabolism

1. Glycolysis
- Breaking down glucose to pyruvate, releasing ATP and NADH.
- Catabolic reaction.

2. Gluconeogenesis
- Synthesize glucose from non-carbohydrate molecules (pyruvate), requires energy.
- Anabolic reaction.
- Almost reversal of glycolysis (7 reversible steps with same enzyme).
- 3 steps that are not reversible (control pathway, prevent glycolysis and
gluconeogenesis happened simultaneously):
- Pyruvate to phosphoenolpyruvate occurs via oxaloacetate, by pyruvate
carboxylase enzyme and phosphoenolpyruvate carboxykinase enzyme.
- Fructose 1,6-bisphosphate to fructose 6-phosphate by fructose
1,6-biphosphatase enzyme.
- Glucose 6-phosphate to glucose by glucose 6-phosphatase enzyme.
***hexokinase, phosphofructokinase, pyruvate kinase (irreversible steps - changes in
free energy level, new enzymes needed to catalyze the new reactions) — control points
in glycolysis.

Lipid Metabolism

1. Beta-Oxidation
- Breaking down fatty acids (large molecule) into acetyl-CoA molecules (smaller
units), producing NADH and FADH2.
- Catabolic reaction.
- When energy is needed, fatty acid linked to coenzyme A in cytoplam, and then
transported into mitochondria to undergo beta-oxidation, which fatty acyl CoA is
oxidized into acetyl-CoA while NAD+ and FAD+ are reduced into NADH and
FADH2.
- Energy produced depends on the length of the fatty acid.

2. Lipogenesis
- Synthesize fatty acid and triglycerides from acetyl-CoA, requires energy to
convert carbohydrates into lipids.
- Anabolic reaction.
Protein Metabolism

1. Transamination
- Synthesize alpha-ketoglutarate to glutamate by adding amino group (from the
removal of amino group of alanine) → anabolic reaction.
- Breaking down alanine to pyruvate by removing amino group → catabolic reaction.

2. Oxidative Deamination
- Breaking down glutamate into alpha-ketoglutarate via glutamate dehydrogenase
enzyme, producing NADH.
- Catabolic reaction.
- Removal of an amino group (-NH2) from glutamate (amino acid), forming
alpha-ketoglutarate and ammonia (NH4+), while reducing NAD+ to NADH.

3. Urea Cycle
- Ammonia combine with CO2 to form urea.

Lipids vs. Carbohydrates:

Triglycerides (lipid) yield more than twice the

energy per unit mass when compared to
carbohydrates and proteins. Therefore, when
glucose levels are low, triglycerides can be
converted into acetyl-CoA molecules and used to
generate ATP through aerobic respiration.

*Triglycerides (glycerol + 3 fatty acids)

→ long-term energy storage.

*Lipolysis→ to obtain energy from triglycerides,

break down via hydrolysis in cytoplasm.
*Glycerol that is released from triglycerides after
lipolysis directly enters the glycolysis pathway as
DHAP; while fatty acids are oxidized by β-oxidation
into acetyl-CoA, which is used by the TCA.
Topic 11.2
1. Rationalise the speed of enzymatic reactions and what factors can affect these

Factors that affect the rate of enzymatic reactions

Temperature:

➢ Temperature below optimal temperature → less

molecules collide have enough energy to overcome
potential energy barrier → slower reaction rate.
➢ Temperature over optimal temperature → enzyme
denatured (increase kinetic energy leads to vibration
disrupting intermolecular interaction between R groups)
→ no reaction (loss of catalytic activity).

pH:

➢ pH below optimal pH (acidic) → enzyme denatured

(change in pH level affects acidic/basic R groups by
altering the charge, affecting electrostatic/ionic
interaction) → no reaction (loss of catalytic activity).
➢ pH above optimal pH (basic) → enzyme denatured
(change in pH level affects acidic/basic R groups by
altering the charge, affecting electrostatic/ionic
interaction) → no reaction (loss of catalytic activity).

Substrate concentration:

➢ Concentration of enzymes is usually much lower than

substrates.
➢ Increase substrate concentration generally increases the
rate of reaction, since at low substrate concentration,
more active sites of enzymes are available, but as
substrate concentration increase, more enzymes are
bound with substrate, leaving less enzyme with free
active site, until all enzymes are bounded to substrates—
at saturation, it is working at its maximum rate of reaction
(Vmax).

Enzyme concentration:

➢ Rate of reaction is directly proportional to the enzyme

concentration when substrate concentration is not the
limiting factor.
➢ When substrate is abundant, increase enzyme
concentration, increase rate of reaction, since more
enzyme-substrate can be formed.
➢ When substrate is limited, increase enzyme
concentration generally increases the rate of reaction,
since at low enzyme concentration, more free substrates,
but as enzyme concentration increases, more substrates
are bound with enzyme, leaving less free substrate, until
all substrates are bounded to enzymes— at saturation, it
is working at its maximum rate of reaction (Vmax).
*Most enzymes are proteins — biological catalyst, lowering activation energy,
accelerating reaction rate.
*Equilibrium constant in enzymatic reactions → association rate = dissociation
rate

*Lock and Key model → substrate precisely fit the shape of the active site (not
accurate)
*Induced Fit model → both active site and substrate undergo changes in their
shape to give the optimal fit for efficient catalysis. (modified from lock and key
model)

*Enzyme-substrate complex — amino acid R groups in active site of enzyme

interact with substrate, catalyzing reaction.
*When products of catalysis are released, the enzyme can bind to another
substrate, undergoing another catalytic reaction. (substrate binding → catalysis
→ product release → enzyme regenerate)

*Michaelis constant (Km) – measurement of affinity/attraction of enzyme for its

substrate (half of Vmax) → high affinity, low Km (require less substrates to reach
Vmax).

Cofactors:

Inorganic and/or organic molecules bind reversibly to enzymes (amino acid that can not
undergo redox reactions), catalyzing reaction by permanently attached to enzyme (prosthetic
groups - inorganic) / temporarily attached to enzyme (coenzymes, activators - organic).

Three groups of cofactors:

Prosthetic Groups: Coenzymes: Activators:

Inorganic (non-protein Organic molecules bind Molecules (can be inorganic

molecules - ions) bind tightly loosely to enzyme, do or organic - including protein)
to enzyme, do participate in participate in catalytic bind loosely to enzyme, do
catalytic reaction, reaction, but not permanently not participate in catalytic
permanently attached to (temporarily) attached to reaction but modify enzyme’s
enzymes. enzymes. structure/function to increase
catalytic efficiency, not
permanently (temporarily)
attached to enzymes.
Topic 11.3
1. Explain how inhibitors and allosteric changes in an enzyme can be used to
regulate flow through a metabolic pathway

Types of Inhibitors

Competitive Inhibitor:
- Have similar shape as the substrate.
- The inhibitor competes to bind to the active site of the enzyme.
- Overcome/reversed the inhibition by increase the concentration of substrate, since the
more substrate there is than the inhibitor, the higher chance of enzyme binding to the
substrate, allowing reaction to occur.

Noncompetitive Inhibitor:
- Does not have similar shape as the substrate.
- The inhibitor binds away from the active site of the enzyme, altering the shape of the
enzyme, affecting the enzyme’s function, so even if the substrate can bind, the active site
functions less efficiently.
- Inhibition can not be overcome/reversed by adding more substrate, since the inhibitor does
not compete to bind to the active site, instead the inhibitor alters the shape of the active
site, not allowing substrate to bind, so the only way is to remove the inhibitor by chemical
change.

Irreversible Inhibitor:
- Does not have similar shape as the substrate.
- The inhibitor forms covalent bond to the side chain in the active site of the enzyme.
- Inhibition can not be overcome/reversed by any ways, it is permanent.

Type of Allosteric Changes

Allosteric Inhibition — Feedback Inhibition (Noncompetitive Inhibitor!!!):

Enzyme in inactive form → allosteric inhibitor bind to regulatory site→ enzyme in stabilized
inactive form (unproper shape for substrate to bind), reduces the affinity of the enzyme for the
substrate, reducing enzymatic activity.

Negative feedback mechanism → high concentration of product can inhibit the action of the
enzyme that catalyze earlier reaction, which the product binds to a regulatory site on the
enzyme away from the active site, causing conformational change in the enzyme that prevents
it from binding to the substrate and continuing to catalyze the reaction, thereby slowing or
shutting down the reaction, to prevent excessibe buildup of substances in cell.
*When depletion of substances in the cell, the product no longer inhibits the enzyme, reaction
can proceed as usual.
Allosteric Activation — Feedback Activation:

Enzyme in active form → allosteric activator bind to regulatory site → enzyme in stabilized
active form (proper shape for substrate to bind), increases the affinity of the enzyme for its
substrate, increasing enzymatic activity.

Positive feedback mechanism → high concentration of product in one pathway can activate the
enzyme in another pathway via feedback activation, to speed up another reaction and to
prevent buildup of substances in the cell.

Cooperativity (Allosteric Activation):

Enzyme in inactive form → substrate bind to the active site of one of the subunit, locks all
subunits in active conformation → enzyme in stabilized active form.

Example. Inhibitors and Allosteric Changes in Enzyme that regulate glycolysis (control points)

Allosteric Changes — Feedback Inhibitor

(Non-competitive Inhibitor):

1. Hexokinase:

→ inhibited by high concentration of glucose

6-phosphate.

→ stimulated by high concentration of glucose.

2. Phosphofructokinase:

→ inhibited by high concentration of ATP and citrate.

→ stimulated by high concentration of AMP.

3. Pyruvate Kinase:

→ inhibited by high concentration of ATP and alanine.

→ stimulated by high concentration of fructose

1,6-bisphosphate.
Topic 12.1
1. Use the source and distribution mechanism of a signal to identify its type

Three stages of celular communication

1. Signal Reception:

When signal molecules (ligands, outside the cell) bind to receptor, signal (usually chemical
signals) is being detected by the target cell.

2. Signal Transduction:

Signal changes the structure of the receptor (protein), sending signals to intracellular
messengers, initiating the process of transduction, which is the conservation of signal from
extracellular to intracellular, transferring signal to cellular response by single/multiple sequence
of changes in different molecules.

3. Cellular response:

Signal triggers cellular specific response (can be any activity).

*cell-signalling process ensure crucial activities occur in the right cell that the right time,
maintaining homeostasis.
*Same signals can have different effects on different cell type by binding to different
cell-surface receptors, ex. Acetylcholine – nicotinic receptor → muscle cell (muscle
contraction); muscarinic receptor → cardiac muscle cell (decrease heart rate).
 Type of Signals (multicellular)

Juxtacrine Paracrine

Release signals (local mediators) to nearby

target cells through extracellular fluid (without
Release signals affect only adjacent cells (via direct contact).
direct contact).
Example: Synaptic (neurotransmitters)
Example: Contact-Dependent

Release signals (neurotransmitters) from

Release signals (membrane-bound signal) presynaptic neurons into synaptic cleft to bind
onto the surface of signalling cells to bind to to receptors on postsynaptic cells.
receptors on the target cell through physical
contact or flow directly through gap junctions *Bacteria (unicellular) → quorum sensing,
(animals) or plasmodesmata (plants) in detect the concentration of signaling ligands in
plasma membrane (small soluble signal). a colony and generate coordinated response.

Autocrine Endocrine

Release signals (hormones) into the

bloodstream by endocrine cells, and travel
Release signals that affect the cells that made
toward distant target cells.
them.
*hormones → travel to distant cells, usually
via the circular system.
*Signals detected by adjacet cell is much faster in synaptic signals than in endocrine
signals, but synaptic signals are more complicated than endocrine signals.
*Both synaptic signals and endocrine signals use chemical message (neurotransmitter
and hormones), and have target cells.
Topic 12.2
1. Explain how specificity is achieved in a signal transduction pathway

Signal Transduction Pathway:

Signal travels toward the target cell → binds

to the specific receptor protein on the cell
surface (hydrophilic, large molecule) or in the
cell (hydrophobic, small molecule) → changes
the conformation / three-dimensional shape of
the receptor → activates the receptor by
exposing its active site to allow interact with
other molecules within the cell → activates
signal transduction pathway (cascade — relay
signal molecules through series of proteins)
→ activates cell response.

*Short-term response → enzyme activation,

cell movement.

*Long-term activation → altered DNA

transcription.

Type of Receptor (Signal Pathways)

Enzyme-Linked Receptor:

1. Signal (ligand) binds to the receptor (integral

protein) on the plasma membrane (extracellular).

2. Conformational changes in the receptor

protein (receptors dimerize — paired up), lead to
autophosphorylation of the receptor's intracellular
domain, to transmit signal to the cytoplasm.

*cell-surface (memebrane) receptor has three

components: 1. extracellular (external
ligand-binding) domain; 2. transmembrane
(hydrophobic membrane-spanning) domain; 3.
Intracellular domain.

3. Activates the receptor’s protein kinase domain

(amplify signals) in the cytoplasm leading to
phosphorylating other intracellular proteins,
triggering a protein kinase cascade (series of
proteins are sequentially activated), resulting in
strong cellular response.

*EGF, Insulin receptors

 G-Protein Coupled Receptor (GPCR):

1. Signal (ligand) binds to the G protein-linked

receptor on the plasma membrane (extracellular),
leading to conformational changes in the receptor
which activates the associated G protein by
exchanging GDP for GTP.

2. Activated G protein dissociates from the

receptor and moves to activates the effector
protein, leading to downstream signaling to
generate second messenger to trigger cell
response, which then GTP on the G protein is
hydrolyzed to GDP to deactivate the G protein
and the signal on the receptor comes off for
another round of signaling.

*Epinephrine receptor

Ligand-Gated Ion Channel:

1. Signal (ligand) binds to channel receptor on

the plasma membrane (extracellular), causing
changes in the shape of the channel, opening the
channel.

2. The channel is lined with charged amino acids,

allowing ions to flow into the cell.

3. The ions buildup in the cell which initiate

downstream signaling, triggering cellular
response.

*Acetylcholine receptor

Intracellular Receptor (nuclear receptor):

1. Signal (ligand — small nonpolar/hydrophobic

can diffuse through hydrophobic plasma
membrane) enters the cell and binds to the
intracellular receptor in the cytoplasm or nucleus.

2. Changes the shape of the receptor and

undergo dimerization, allowing ligand-receptor
complex to enter the nucleus, increasing or
decresing the transcription of specific gene,
leading to long-term cellular response.

*Estrogen receptor
*nonpolar signal can diffuse directly across the lipid bilayer of the cell membrane to encounter the
receptor in the cytoplasm or nucleus; polar/large signal cannot diffuse through the cell membrane,
it encounter the receptor embedded in the membrane (membrane-bound receptor → both
extracellular and intracellular regions connected by hydrophobic region, which allows
signal/ligand to fit the receptor at the extracellular region).
Topic 12.3
1. Explain how and why different cells respond to different chemical signals

Signal transduction pathways have different effects:

1. Simple Relay→ simply relay the signal onward, help spread the signal
through the cell.

2. Amplify → amplify the signal received, making the signal stronger, so that
few extracellular signal molecules are enough to evoke large intracellular
response.

3. Integrate → detect signals from more than one intracellular signaling

pathway, and integrate the signals before relaying a signal onward.

4. Distribute → distribute the signal to more than one effector protein,

creating branches in the information flow diagram, evoking complex
response.

Example in animal cell — epinephrines (G Protein Coupled Receptor)

See prey (fight-or-flight response)→ brain signals adrenal gland to release

epinephrine (hormone) into the bloodstream (endocrine signaling) to target cell
→ epinephrine bind to receptor of muscle cell (signal reception) → relay
molecules transmit the signal via G protein, activating an enzyme (signal
transduction) → enzyme break down glycogen, releasing glucose (ATP) to fuel
leg muscle (cellular response).

Example in plant cell — ions (Ion Channel)

Change in environmental factors (CO2, air humidity, temperature, light) → trigger

alterations of ion concentration in leaf tissue surrounding the guard cells (signal
reception) → changes in ion concentration activate specifc ion channels on the
guard cell to open, allowing specific ions to enter or leave the cell (signal
transduction) → the buildup or depletion of ions in the guard cell cause osmotic
water movement into or out the cell, changing the size of the guard cell by
swelling or shrinking, causing open or closed stomatal pore (cellular response).
Topic 13.1
1. Describe how multicellularity might have evolved with the benefits of cell
specialisation and increased body size

Volvocine Green Algae (transition to multicellularity - evolution)

Unicellularity Transition to multicellularity — results in individuals cell

losing the ability to live independently.

Aggregation of cells into a cluster Intercellular Specialization of Organization of

communication some cells within specialized cells
with the cluster the cluster into groups
(cooperation) (tissues)

Benefits of Multicellularity

Chlamydomonas Volvox

Single cell → switches between two cellular Multicellular colony with two cell types (no
phases (can not occur together): phase switching):

1. Swimming phase — flagellum movement. 1. Outer cells — for coordinated flagella

2. Reproductive phase — cell division. movement, and create an inner space to
protect reproductive cells.

2. Inner cells (big) — for reproduction.

Size → Volvox become larger shift in position (avoid being prey).

Functional Specialization → perform delicate task (reproduction or mortality —

specialization cell), and work in unison (beating of flagella → efficient phototaxis, more
rapid movement).

*Multicellularity enables (specialisation) cells to dedicate their energy to one task rather
than multiple taks → increase efficiency.
Topic 13.2
1. Describe diffusion as movement of molecules down a concentration gradient

● Passive movement of substances down their concentration gradient (from high

concentration area to low concentration area), at constant exchange rate (random
motion), until achieve dynamic equilibrium, when no net movement (molecules move back
and forth with no overall change in concentration).

● Require no expenditure of cellular energy (spontaneous → concentration gradient)

● Rate to cross membrane depends mostly on the molecule’s relative hydrophobicity:

1. Lipid, soluble, nonpolar (O2, CO2, vitamins) → readily diffuse

2. Uncharged, polar (H2O, glucose) → slower rate but still diffuse

3. Charged ions, non-lipid, soluble → repelled by lipid bilayer, require mechanism to

cross.

2. Explain how osmosis is a special case of diffusion of water molecules across

a semi-permeable membrane

● Movement of only water across a semi-permeable membrane, driven by the difference in

solute concentrations on either side of the membrane.

● Solute or any dissolved substances cannot cross the plasma membrane.

● Water moves down the concentration gradient:

Less solute, more water (low osmolarity – greater ratio of water to solute) →
more solute, less water (high osmolarity — smaller ratio of water to solute)

3. Explain why the surface-area:volume ratio necessitates transport systems in

big bodies

As organism increase in size, the surface area to volume ratio decrease and the distance
between internal cells to external environment increase → less of the interior is exposed to
the exterior contact with the environment, decreasing the opportunity to exchange substances
— CO2, O2, nutrients, and wastes → diffusion is not sufficient to meet the metabolic
demands of the cell efficiently → transport systems are needed to overcome the problems, by
having specialized cells with high surface area to volume structure and have internal aqueous
environment for substances to be effectively exchange throughout the cell.
 Multicellularity

Problems Solutions

1. Surface area to volume ratio of 1. Features — small and thin or highly

multicellular organism is small. branched/folded or hollow/porous →
→ not sufficient contact with external increase surface area to volume ratio, and
environment to meet the exchange needs of all cells are close to the external
multicellular organism. environment for diffusion.

2. Distance of internal cells to external 2. Specialized cell have barrier that help
environment is large. create internal environment, stabilized by
→ to far to undergo effective exchange with homeostasis (sense changes in
environment due to the time takes for gas to surrounding, optimize cellular functions),
diffuse over the distance. and meet their exchange needs through
exchange with an internal aqueous
environment, since extracellular fluid
enables exchange of respiratory gases,
nutrients, and wastes from exchange
organs reach cells of the body — maintain
high concentration gradient for diffusion and
pressure gradient for bulk flow.

*Animal - active processes (circulatory systems)

Plants - passive processes (vascular systems)
Topic 13.3
1. Explain the features of exchange surfaces using Fick's law

𝑠𝑢𝑟𝑓𝑎𝑐𝑒 𝑎𝑟𝑒𝑎 𝑥 𝑝𝑎𝑟𝑡𝑖𝑎𝑙 𝑝𝑟𝑒𝑠𝑠𝑢𝑟𝑒 𝑔𝑟𝑎𝑑𝑖𝑒𝑛𝑡 𝑥 𝑑𝑖𝑓𝑓𝑢𝑠𝑖𝑜𝑛 𝑐𝑜𝑒𝑓𝑓𝑖𝑐𝑖𝑒𝑛𝑡

𝑅𝑎𝑡𝑒 𝑜𝑓 𝐷𝑖𝑓𝑓𝑢𝑠𝑖𝑜𝑛 = 𝑑𝑖𝑓𝑓𝑢𝑠𝑖𝑜𝑛 𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒

➔ Surface area → greater area for more diffusion to happen simultaneously.

➔ Partial pressure gradient → greater difference in pressure concentrations,

forming gradient, drives diffusion (gas move down the gradient).

➔ Diffusion coefficient → greater solubility of gas in liquid/air, easily diffused.

➔ Diffusion distance → shorter distance for gas to travel to undergo diffusion.

Animals - Lungs Plants - Leaves

➢ Large surface area → branches, air ➢ Large surface area → flat and thin
sacs. surface, with numerous stomata and
branching veins.
➢ Maximize partial pressure gradient →
well vascularized, lots of capillaries in ➢ Maximize partial pressure gradient →
blood around air sacs, forming pressure stomata, microscopic pores, forming
gradient between O2 and CO2. pressure gradient between H2O and
CO2.
➢ Maximize diffusion coefficient →
minimise diffusion in aqueous medium ➢ Maximize diffusion coefficient →
(film of moisture on the air sacs are kept minimize diffusion in aqueous medium
thin), which lead to higher diffusion (thin cell wall and and air spaces within
coefficient in air than liquid. leaf mesophyll), which lead to higher
diffusion coefficient in air than liquid.
➢ Minimize diffusion distance → thinner
barrier (air sacs close to capillaries). ➢ Minimize diffusion distance → thinner
barrier (thinness of leaf wall and air
spaces within leaf mesophyll).
Topic 14.1
1. Explain stimulus-response and negative feedback as a mechanism for
maintaining internal homeostasis

Homeostasis → maintain stable internal condition in response to changing

external environment (including temperature, pH, and nutrient level), enables
optimal cellular function effeciently on narrow range condition, to survive and
growth.

Negative Feedback: Positive Feedback:

→ products of the process reduce initial → products of the process stimulate
stimulus, leading to decrease respond. further increase in its production,
leading to increase respond.

Ex. Blood glucose level Ex. Blood clotting

When blood glucose level is too high Cut in blood vessel wall act as
(hyperglycaemia), it stimulate beta-islet cell in stimulus that trigger nearby
pancreas to release insulin (hormones via platelets to release chemical signals
bloodstream — endocrine signaling), which (paracrine signaling), activating
triggers liver cell to take up glucose and stored several clotting factors, while
as glycogen, reducing blood glucose level until attracting platelets to the site of the
it is at a normal level, maintaining homeostasis, injury, and release more signal to
which stop pancreas from producing insulin, attract more platelets, initiating a
prevent excessive hormones level. blood clot until the wound is sealed.

When blood glucose level is too low *does not directly maintain
(hypoglycaemia), it stimulate alpha-islet cell in homeostasis, instead is an essential
pancreas to release glucagon (hormones via physiological process for the body.
bloodstream — endocrine signaling), which
triggers the liver cell to break down glycogen
and release glucose, increasing blood glucose
level until it is at a normal level, maintaining
homeostasis, which stop pancreas from
producing insulin, prevent excessive hormones
level.
Topic 14.2
1. Compare the different types of chemical signals between cells using
examples

Animal Hormones:
➢ Complex organic substances (hydrophilic - extracellular or lipophilic - intracellular).
➢ Transport through bloodstream.
➢ Act on distant target cells/tissues.
➢ Produced by specific cell/glands → specific effect.
➢ Included various types — ex. protein, steroid, amine…

Insulin → binding to insulin receptor Glucagon → binding to glucagon receptor

Insulin receptor → enzyme-linked receptor Glucagon receptor → G protein coupled receptor
Effects: Effects:
➢ increase the glucose transporter in ➢ activates glycogen phosphorlase in the cell.
membrane.
➢ inactivates glycogen synthase (enzyme),
➢ activate glycogen synthase (enzyme), prevent converting glucose to glycogen,
converting glucose to glycogen, increasing blood sugar level.
reducing blood sugar level.

Plant Hormones:
➢ Simple organic substances.
➢ Transport through vascular tissues (xylem and phloem) or diffusion.
➢ Act on nearby target cells/tissues.
➢ Can be produce by each plant cells throughout the plant→ diverse effect (can work
synergistically or antagonistically)
➢ Six types — abscisic acid, cytokinins, auxins, ethylene, brassinosteroids, gibberellins.

Abscisic acid → bind to the receptors on/in the guard cells

Under dry condition, change in water potential (water stress) stimulate cells in roots and leaves
to produce abscisic acid (hormones), which translocated to the receptors on/in the guard cells
through xylem, changing osimotic potential due to activation of potassium and anions efflux
channels (complex signal transduction pathway), causing net loss of potassium ions and
anions out the guard cells, forming higher water potential than surrounding, resulting water
move out the guard cells, reducing the pressure (loss turgor), which the guard cell become
flaccid, closing the stomata, stoping transpiration → negative feedback homeostasis.

*Communication with hormones is slower than with electrical signals, but longer
lasting.
Topic 14.3
1. Explain how action potentials provide a faster cell-cell signalling mechanism in
animals.

Resting Potential Threshold of Depolarization Repolarization &

Excitation (Active Potential) Hyperpolarization

Greater sodium ions Some voltage More sodium Voltage gated potassium
concentration outside gated sodium ions flow down channels open.
of neurons, and greater channels open its gradient into
potassium ions for membrane the neurons Potassium ions flow down its
concentration inside of potential to rapidly, causing gradient out the neurons
neurons. reach the the membrane rapidly, which the membrane
threshold of potential to potential to quickly become
Resting potential is around 50mV, quickly become negative. (outflow of
typically around allowing more more positive. potassium briefly
60-70mV. voltage gated hyperpolarized the neuron,
sodium channels Voltage gated making the membrane
All voltage gated closed to open. sodium channel potential even more negative
with leak of potassium then closed (at than resting potential —
channel to create peak). reduce action potential until
resting potential. resting potential is restored).

*Action potential is regenerated at each node of Ranvier along the myelinated axon → allowing
signals to be rapidly and reliably (strong and undiminished) transferred over a long distance,
enabling rapid and efficient cell-to-cell communication signaling → myelinated axon allows
action potential to transfer from node to node (saltatory conduction), rather than propagating
continuously along the entire axon.
Topic 15.1
1. Explain common features of development: Cell specialisation, division,
growth, morphogenesis.

Determination → Cell fate establishment arises during the early stages of

embryogenesis.

→ Cells become increasingly more restricted in their fate,

changing in cell potency.

→ Pattern of cell fate is highly ordered and reflects the position

of cells in the developing embryo – instructive cues
(cytoplasmic factors / cell signalling molecules).

Differentiation → Cell specialisation, process by which determine the

properties of a cell and is associated with the subset of genes
that are active (cells from zygote are genetically equivalent –
same genome), by expressing different genes (gene
regulation), specialized cell are being developed (perform
specific function).

● House-keeping genes — genes expressed in all cells

○ Actin — elements of cytoskeleton.

○ Tublin — elements of cytoskeleton.

○ Histone — protein associated with DNA.

● Cell-specific genes — genes expressed in one cell

type but not another (differential gene expression)

○ Myosin H11 (smooth muscle cell)— protein

associated with muscle contraction.

○ Lactase (enterocyte) — enzyme hydrolyze lactose

to monosaccharide.

○ Synapsin (neuron) — protein associated with

neurotransmitter release and express in neuron.

Morphogenesis Process by which cells and tissues organise and arrange to

create the final form of the body (shape) of the organism.

● Cell division

● Changing shape (expansion)

● Movement of cells (animal embryogenesis only)

● Adhesion of cells (animals embryogenesis only)

● Cell death (apoptosis)

*embryogenesis → formation of multicullular organism from a zygote, zygote undergoes

multiple rounds of cell division producing specific cell types in precise pattern along major
spatial axes (organization of cells is not random, cell types arranged according to body plan).
Animals Plants

➢ Determinate growth: ➢ Indeterminate growth

○ Predetermined body form (develop ○ Flexible body form (develop

parts of bodies just once). leaves/flowers continuously
through lifetime)
○ Increase in size.
○ Increase in size
➢ Morphogenesis and body plan:
➢ Morphogenesis and body plan:
○ Cell divisions more random but can
still be oriented. ○ Cell divisions is oriented.

○ Cell shape change. ○ Cell shape change (expansion).

○ Cell movement (specialized call ○ Apical/basal axis established.

moving sound and electrically
active).

○ Cell adhesion and de-adhesion.

○ Anterior/posterior axis established.

○ Formation of segments.
Topic 15.2
1. Describe how a fertilised egg develops into an adult body and the role of stem
cells in ongoing maintenance of that body.

Embryonic Development in Animals:

Fertilisation
→ a sperm fertilising an egg to produce zygote (first cell of embryo).

Cleavage
→ zygote divided into many cells (with no growth phases) to produce the blastula (simple
arrangement of undifferentiated cells surrounding a fluid filled cavity).

Gastrulation
→blastula undergo rearrangement whereby some cells move into embryo, establishing
body plan and forming three germ layers gastrula.

1. Determination: establishment of three distinct cell identities (germ layers) occurs

early during embryogenesis.

2. Inward bludge formation: cells at the base of the blastula change shape.

3. Mesoderm formation: some cell break free and migrate into the cavity.

4. Endoderm formation: cells invaginated, (extend, flatten, and undergo arrangement

to form a long thin tube – gut)

5. Gastrula formation: future sites for mouth and anus determined, with different types
of tissue arise from the germ layers.

Organogenesis
→ complex processes which tissues and organs of the body are formed, having the end
product of development.

Metamorphosis
→ some species has this as final stage where lava form transforms into adult form.
Three Germ Layers

Ectoderm → outer layer (external surface of animals)

Mesoderm → middle layer (rest of organs)

Endoderm → inner layer (lining of gastrointestinal tract)

Triploblastic Diplobastic

→ three germ layers (ectoderm, mesoderm, → two germ layers (ectoderm and
and endoderm) endoderm, lack of mesoderm)

→ most animals → cnidarians (jellyfish / hydra)

→ bilateral symmetry (single plane through → radial symmetry (any plane along the
anterior-posterior midline divides the animal central body axis divides the animal into
into mirror-image halves) similar halves)

Stem cells
→ undifferentiated cells that can divide indefinitely forming new cells.
→ division produce a new stem cell and a daughter cell that can subsequently differentiate
into other cell types (potency)

Totipotent → potential to produce all cell types of an organism

→ zygote

Pluripotent → can produce all cell types of the body but not cells of extraembryonic
tissue like placenta
→ embryonic stem cells, induced pluripotent stem cells

Multipotent → can produce several cell types

→ intestinal stem cells

Unipotent → can produce only one cell type (can only produce daughter cells of the
same type)
→ skin cells
Topic 15.3
1. Describe embryonic development in plants and the subsequent role of
meristems in continuous development.

Embryonic Development in Plants:

Establishment of the apical-basal axis and polarity of the embryo:

1. Zygote undergo asymmetric cell division into apical daughter cell and basal
daughter cell in two-cell stage.

2. Apical daughter cell (smaller upper cell) form embryo (later form shoots), whereas
basal daughter cell (larger lower cell) form suspensor (extra embryonic structure
that tethers the developing embryo to the storage materials, which will later form
roots).

*determination occurring — cell fate being specified (determined by cytoplasmic factors

that are unevenly distributed).

Formation of the spherical embryo and a linear suspensor:

1. Embryo and suspensor undergo orientated cell divisions in the octant stage which
generates spherical embryo and a long thin suspensor (which nutrients and signals
are conducted to the developing embryo).

Embryo becomes bilateral symmetrical (cotyledon outgrowth), radial pattern of tissue types
established and formation of the shoot and root meristems:

1. The spherical embryo and a linear suspensor undergo further orientated cell
divisions, which is an expansion resulting in the formation of heart stage embryo,
from having radial symmetry to bilateral symmetry caused by emergence of two
cotyledons.

*morphogenesis occurring — creation of form (bilateral shape).

*some plants (grasses) only have one cotyledon (not bilateral symmetry).

Embryo becomes cylindrical in shape and tissue begin to differentiate:

1. Elongation of the cotyledons (some function as storage) and the main axis,
developing shoot meristems and root meristems in torpedo stage.

2. By the end of embryogenesis, the cylindrical shape of the embryo is well

established, with root and stem retaining the shape throughout plant’s life

*differentiation occurring.
*three tissue systems of the embryonic plant are arranged concentrically are now apparent
with own characteristic features.
*after extensive cell divisions, expansion, and differentiation, mature seed is formed
(inactive for seed dispersal, and active when receive signals).
*combination of determination, morphogenesis and differentiation → cell with distinct fates are
created at particular locations in plant’s embryo, forming body plan.
 Primary Growth (Apical Meristems) vs. Secondary Growth (Lateral Meristems)

Primary Growth
→ increase the length of the plant.

Apical Shoot Meristems Apical Root Meristems

Protoderm ● epidermis ● epidermis

➢ dermal tissue

Ground Meristem ● cortex ● cortex

➢ ground tissue ● pith

Procambium ● primary xylem ● primary xylem

➢ vascular tissue ● primary phloem ● primary phloem

Secondary Growth
→ increase the thickness of the plant.

● Vascular cambium
○ Secondary xylem
○ Seconday phloem
● Cork cambium
○ Periderm (phelloderm and cork)
*meristem → plant tissues containing undifferentiated cells that can perpetually divide.
*Tree ring (secondary growth) → estimate the age of a tree (1 tree ring per year)
(early wood (light) – larger diameter and thinner wall (spring); late wood (dark) (summer)).
- thin ring (cold or dry year – less growth)
- thick ring (warm and wet year - more growth)
Topic 16.1
1. Compare and contrast the four different tissues found in animals.

Epithelial tissue Composed of single or multiple cell layers that cover external body
parts, line internal body surface and form different glands.

Ex.
Cell-cell junctions

Tight junctions
→ prevent substances from moving through the space between
cells, as well as maintain distinct faces of surface from one face
to the other, resulting certain function being conducted to one
region of the cell surface.

Desmosomes
→ hold neighboring cells firmly together, but materials can still
move around in the extracellular matrix, providing mechanical
stability for tissue.

Gap junctions
→ channels that run between membrane pores in adjacent cells,
allowing substances to pass between cells.

Connective tissue Contain cells in various matrix of extracellular fibers, provide

structural support, transport nutrients, and serve as fat reservoirs.

Ex.
● Bones
● Adipose tissue
● Blood cells
● Ligaments and tendons

Muscle tissue Consist of specialized contractile cells that facilitate body

movements.

Ex.
● Cardiac muscle
● Smooth muscle
● Skeleton muscle
 Muscle contraction
→ activated by electrical signals (action potential), which
ATP-dependent motor protein comprised of myosin filaments
pulling on actin filaments, shortening sarcomere.

Muscle → composed of bundles of muscle fibres , which is

multinucleate cell with many myofibrils (highly ordered
arrangements of myosin (thick) and actin (thin) filaments in
striated appearance).

Nervous tissue Consists of neurons that respond to stimuli by generation electrical

signals, help coordinates various body activities.

Ex.
Electrical signal transmission:
→ gather information about the external and internal
environment then processing information to control physiology
and behavior of the body.

Neurons Glial cells

Transmit electrical signals Provide mechanical and

(action potentials) nutritional support for neurons,
do not generate action
potential (Schwann cell)

● Sensory Neurons→ ● Schwann cell

generate electrical signals ● Oligodendrocytes
based on different stimuli ● Astrocytes
and output to neurons. ● Microglia
● Interneurons → take input
from neurons and output to
other neurons.
● Motor Neurons → Take
input from neurons and
output to muscles.
Topic 16.2
1. Explain how different tissue types combine to form a functional organ.

Mouth/Tongue/Teeth → breaks food up into smaller parts to aid digestion.

Salivary gland → secrete enzymes (amylase) that begins the breakdown of carbohydrate.
Stomach → secretes enzyme to breakdown proteins.
Liver → involved in detoxification and the control of blood glucose levels.
Gallbladder → secretes bile that aids the digestion of fats.
Pancreas → secrete digestive enzymes and hormones.
Small intestine → absorbs most nutrients.
Large intestine → absorbs water, ions, and vitamins.
Topic 16.3
1. Compare and contrast the three tissue types found in flowering plants.

Vascular tissue Dermal tissue Ground tisse

→ complex tissue that → simple permanent tissue → makes up the main bulk
enables the transport of that forms the outer of the plant and plays
water and minerals through protective covering (first several roles including
the plant (composed of two line of defense against photosynthesis, support and
specialised conducting pathogens and physical storage (responsible for
vessels – xylem and damage) as well as most metabolic functions of
phloem). promote gas exchange. plants, and provide structural
support to stem).

● permanent tissues → terminally differentiated and can no longer divide.

2. Describe how the three tissue types are integrated into a functioning leaf.

Vascular ➢ vein (highly branched to support water and nutrients, with

bundle sheath cell facilitates transfer to the leaves)
○ xylem (transport water and mineral from roots to shoot,
by the help of tracheid and vessel elements)
○ phloem (transport sugar and nutrients from shoot to
roots by the help of companion cells and sieve tube)

Dermal ➢ upper / lower epidermis

➢ cuticle (waxy → limit water loss, gas impermeable, protect
external damages)
➢ guard cell

Ground ➢ parenchyma (thin primary cell wall, round shape, large vacuole,
abundant, inside plant’s stems and leaves, storage and
transport)
○ palisade mesophyll cell (most photosynthesis
happened)
○ spongy mesophyll cell (protect leaf, non-photosynthetic)
➢ collenchyma (thick primary cell wall, outer layer of plant’s stems
and leaves, structural support, bendable)
➢ sclerenchyma (secondary cell wall, outer layer of plant’s stems
and leaves, rigid, hydrophobic)
*Primary cell./ wall has a thick and flexible structure, allow plant and cell wall to expand during
cell growth, after plant cell matures and stop growing, secondary cell wall may deposit
between primary cell wall and plasma membrane, secondary cell wall is thick and rigid which
provide protection and support. Middle lamella (outermost layer) allow cells to adhere to one
another and form plant tissue.
Topic 17.1
1. Explain the transport needs of plants.

From roots to shoot From shoot to roots

● Transport water ● Transport sugars

○ Shoot requires water from soil via roots. ○ Non-photosynthetic
○ Required for photosynthesis in leaves, transport tissue require sugars
solutes between plant organs, cooling plant and other materials
(latent heat loss as transpiration occurs), and from photosynthetic
structural support (turgor pressure). tissue.
○ Most water loss through transpiration. ○ Transport in phloem
as phloem sap
● Transport nutrients (source – shoot to
○ Main macronutrients (nitrogen and phosphorus) sink – root).
○ Main micronutrients (iron)
○ Shoot requires macro/micronutrients from roots
which accumulate nutrients from soil.

Water potential:
→ determine the direction of water movement.
→ water moves in and out of cells by osmosis (passive process).

Ex. Plant cell

● turgor pressure is equivalent to pressure potential.
● low turgor pressure → water enter plant cell by osmosis due to low solute potential.
● turgor pressure balance solute potential → no net flow of water in/out the plant cell.
 Apoplast Symplast

→ spaces between cell walls and plama → spaces within the cell membrane
membrane (interconnected cell wall and (interconnected cytoplasm via
intercellular spaces between cells) plasmodesmata).

→ water and dissolved nutrients passively → water enter the symplast via osmosis
diffuse into apoplast. across cell membrane.

→ blocked from entering the stele by → nutrients are taken up via active
Casparian strips. transport.

→ movement is rapid and unregulated. → able to move freely toward the center of
the root through cell to cell connections
crossing cell membrane.

Root
*Water and solutes that move via apoplast travel as far as the endodermis (inner layer of root
cortex).
*Casparian strip (diffusion barrier) → layers of water-impermeable (hydrophobic) suberin in
the cells of the endodermis, which surrounds the stele, this structure block the passage of
potentially undesirable / toxic elements (elective uptake of solute to protect plant).
Topic 17.2
1. Discuss how transpiration, cohesion and tension draw water into the roots
past the Casparian strip and up through the non-living xylem cells

Xylem (transport of water)

➢ composed of long tubular vessels of dead cells
➢ sap forms a continuous column in the xylem vessels due to cohesion and adhesion
○ Cohesion → interaction of water molecules with other water molecules via
hydrogen bond
○ Adhesion → interaction between water molecules and the xylem wall
(capillary action)

Tracheids Vessel Elements

→ spindle shaped cells with cavity (pits). → larger in diameter than tracheid.
→ in secondary cell wall, water can move → meet end to end.
with little resistance from one tracheid to its → partially break down the end wall to form
neighbor. an open pipeline for water conduction.

Transpiration - cohesion - tension - mechanism:

1. Transpiration occur which water vapor diffuse out of the stomata down the concentration
gradient (concentration of water vapor in atmosphere is lower).

2. Water evaporate from the surface of mesophyll cells, creating surface tension.

3. Increased surface tension pulls water out of the veins into the apoplast of mesophyll
cells.

4. Tension in the veins pulls on the column of water in the xylem of the stem, the cohesion
between water molecules in the xylem passively draws water up through the xylem
vessels.

*tension on the water column causes water to flow from the roots to the leaves.
*water enters the root and then the xylem by osmosis.
*cohesion transmits the tension from the leaf to the root, which the water flows upward.

A gradient of negative pressure potential lift the water column by bulk flow (fluid move from
high pressure potential area to low pressure potential area)

*difference in pressure potential need strong xylem wall (lignin) to withstand the force.
Topic 17.3
1. Explain how active transport and bulk flow move phloem sap via the living
companion cells and sieve tube elements of the phloem.

Phloem (transport of sugar)

➢ composed sieve tube elements which a tubular network of living cells (differ from
xylem).
➢ sieve tube elements received metabolites and proteins from an associated
companion cell (life support).
➢ sugar is transported from sugar source (produce more sugar than consume) to
suga sink (roots, stems, fruits — sugar consumers) in phloem sap via phloem →
translocation – process that distribute products of photosynthesis to other plant
tissues.

Sieve Tube Elements Companion Cells

→ join end to end. → connected to sieve tube elements via

large plasmodesmata.
→ end walls retained (differ from xylem).
→ free diffusion between cells.
→ plasmodesmata connect neighboring
cells together (the diameter of → contain nucleus.
plasmodesmata increase allow easy
movement of phloem saps between cells). → cytoplam perform all metabolic functions
for sieve cells.
→ associated closely with companion cell.

→ lack of nucleus, ribosomes, golgi, and

cytosketelon (flow out the cell via large
pores).

Bulk Flow:
→ phloem sap move from high pressure potential area to low pressure potential area (from
one sieve tube elements to the next).
→ the difference in solute concentration between source and sink create difference in
pressure potential along the sieve tubes, resulting in bulk flow.

Mass Flow Hypothesis (explaned how bulk flow is generated):

1. Sucrose and other solutes (protein, RNA, hormones..) in the sugar source are actively
(requires ATP – require for living cells, unlike xylem transport) transported into companion
cells and then flow into the sieve tube cells via plasmodesmata → loading (apoplastic and
symplastic pathways)

- Apoplastic pathway (extracellular space): from mesophyll cells to phloem then

actively transport into sieve tubes.

- Symplastic pathway (cytosol): taken up by companion cell and move via

plasmodesmata into sieve tubes.

2. Sucrose accumulation make water potential more negative (more negative solute
potential — higher sucrose concentration than surrounding cells) in sieve tube elements
causing water to enter the cells by osmosis from adjacent tissue (xylem, occur in leaves
where water can move out of the xylem easily).
3. Increase in hydrostatic pressure (more positive pressure potential at source end of the
sieve tube) causes mass in the phloem to move away from the pressure (pushing the
phloem sap toward the sink end of the sieve tube where has lower pressure potential –
down pressure gradient).

4. Transport of sucrose into sink cells (both passively and actively from companion cells,
lowering the solute concentration in the sieve tube) cause increase in the water potential of
the sieve cell tube elements (solute potential become less negative and water potential is
greater than the surrounding tissue).

5. Water leaves the phloem by osmosis, reinforcing the water gradient (pressure gradient
and solute gradient).
Topic 18.1
1. Compare and contrast open and closed circulatory systems and the
evolutionary progression of vertebrate circulatory systems.

Circulatory system in animals:

→ transport substances (nutrients, wates, gasesm hormones, blood cell) around animal
body.
→ move heat (to or from the surface of the animal) to maintain physiological temperature.
→ transmission of force (for locomotion in many worms/mollusks, and for reproduction in
vertebrates).

Components needed in animal’s circulatory system:

➢ muscular pump (one or more) to provide the force to drive the flow of circulating
fluid that moves through a system of (open-ended or closed) tubular vessels (that
form a circuit).
➢ in order for the diffusion distance to kept small, circulatory system need to be
slightly branched, breaking down into smaller and finer vessels, so that it is close
enough to all cells.

*large animal need a specialised gas exchange organ to meet the demand of getting
oxygen in and carbon dioxide out.

Open Circulatory System Closed Circulatory System

simple hea Advantages:

● More rapid fluid flow, allowing faster
metabolism.
● Direct (control) flow to where needed.
● Specialised content by retaining cells
and large molecules.
*no circulatory system → organisms (thin, small, hollow, porous) with all cells that have short
distance from the external environment (rely on diffusion).

Evolution of vertebrate circulatory systems:

➢ 4-chambered heart.
➢ Gas exchange with ➢ 3-chambered heart. ➢ 4-chambered heart.
water. ➢ Gas exchange with air. ➢ Gas exchange with air.
➢ Single circuit ➢ Partial double circuit ➢ Double circuit circulatory
circulatory system. circulatory system. system (can have
➢ Low blood pressure ➢ Pulmonary and systemic different pressure).
in vessels leading to circuits partially separated ➢ Low blood pressure in
the body (slow flow). → mixed blood. vessels leading to the
➢ Deoxygenated blood lungs.
primary transport to ➢ High blood pressure in
pulmonary circuit, while vessels leading to the
oxygenated blood primary body (rapid flow, to meet
transport to systemic high nutrients demand).
circuit (mixing blood is ➢ Blood can not mix, thus
limited due to anatomical systemic circuit receive
features of ventricles). blood with highest
oxygen content.
Topic 18.2
1. Describe how the structure and function of the mammalian heart and
circulatory system facilitates efficient blood flow through the body.

Mammalian circulatory system

→ complex network of blood vessels and heart to transport nutrients, gases, and wastes
throughout the body via three circuits, which is coronary (heart), pulmonary (lungs), and
systemic (entire body).

Different type of blood vessels in Heart structure and blood flow pathway:
mammalian circulatory system:
- Artery
- Arteriole
- Capillary
- Venule
- Vein

1. Deoxygenated blood enters right atrium

via the superior and inferior vena cava.
2. Blood flows through the tricuspid valve
into the right ventricle.
3. Right ventricle pumps the blood through
the pulmonary valve into the pulmonary
artery, which takes it to the lungs.
4. In lungs, blood is oxygenated and returns
to the left atrium via pulmonary veins.
*blood flow is controlled by body’s needs, 5. From left atrium, blood passes through
can be regulated by neurological signals. the bicuspid valve into the left ventricle.
ex. exercising 6. Left ventricle pumps oxygenated blood
→ blood target muscle due to vasodilation. through the aortic valve into the aorta,
→ blood away from digestive system due to which distributes it to the body.
vasoconstriction (to where blood is needed).

Cardiac cycle at systole (contraction) and diastole (relaxation):

Topic 18.3
1. Explain how blood pressure varies in the circulatory system and dictates the
flow of fluids in and out of capillaries.

Blood pressure changing in circulatory system:

Left ventricle → high oxygen partial pressure (100 mmHg), high hydrostatic pressure with
huge change in hydrostatic pressure (120-0 mmHg), and high fluid flow rate (40 cm/s).
Aorta → high oxygen partial pressure (100 mmHg), high hydrostatic pressure with slight
change in hydrostatic pressure (120-80 mmHg), and high fluid flow rate (40 cm/s).
Lung/Alveoli → high oxygen partial pressure (100 mmHg).
Artery/Arteriole → low fluid flow rate (0.03 cm/s), high oxygen partial pressure (90 mmHg),
and hydrostatic pressure around 40 mmHg.
Vein/Venule → low fluid flow rate (0.03 cm/s), low oxygen partial pressure (40 mmHg), and
hydrostatic pressure around 16 mmHg.
Superior/inferior vena cava → low oxygen partial pressure (40 mmHg) with normal fluid
flow rate (15 cm/s).
Interstitial fluid → no fluid flow rate (0 cm/s) due to no blood, and low oxygen partial
pressure (40 mmHg).

Lungs → maximize respiratory gas exchange between alveoli and associated capillaries.
Alveoli are covered by network of fine capillaries, when air enters the lung and fill the
alveoli, alveoli has high O2 and low CO2 while blood inside the capillary has low O2 and
high CO2, thus diffusion occur, allowing gas exchange across thin alveoli and endothelial
cells, which O2 diffuse out of the alveoli and into the blood, whereas CO2 diffuse out of the
blood and into the alveoli, converting the blood from deoxygenated to oxygenated back to
the heart.
Efficient exchange of substances between capillaries and interstitial fluid:
→ in capillaries, substance exchange down concentration gradient between blood plasma
and interstitial fluid across capillary wall.
→ O2 and nutrients diffuse out of the capillaries to supply cells.
→ CO2 and nitrogenous waste diffuse into the capillaries from the cell.

mig
Topic 19.1
1. Describe the three major steps in transcription and the cellular components
involved and recognise the key differences between eukaryotes and
prokaryotes

Three major phases of transcription (process of synthesizing RNA from DNA)

Transcription (DNA gene act as template for RNA synthesis) → pre-mRNA undergo
splicing (removal of non-coding intron sequences, leaving coding exons, and add 5’ cap
and 3’ poly-A-tail to form mRNA) → mRNA travels to ribosome to undergo translation
(tRNA translate three nucleotides codons in mRNA into amino acid squence) →
polypeptide chain undergo processing into functional protein.

Initiation
→ RNA polymerase binds to the promotor and starts to unwind the DNA strands.

Elongation
→ RNA polymerase moves along the DNA template strand from 3’ to 5’ and produces the
RNA transcript by adding nucleotides complementary to the DNA template to the 3’ end of
the growing RNA.

Termination
→ when RNA polymerase reaches the termination site, the RNA transcript and polymerase
are released from the template.

*complementray (coding) strand → serve as reference for sequence of RNA molecule.

*template strand → act as base for RNA synthesis.
 Prokatyotes Eukaryotes

➢ Does not contain nucleus and introns, ➢ In nucleus, transcription occur which
thus transcription and translation are produced pre-mRNA, then by splicing
directly coupled and occur introns with addition 5’ cap and 3’
simultaneously. poly-A-tail to form RNA for RNA to
➢ Has only one RNA polymerase, which remain intact while traveling from
responsible for transcribing all types of nucleus to cytoplasm.
RNA, including mRNA, rRNA, and ➢ In cytoplasm, translation occurs to form
tRNA. amino acid sequence by the help of the
➢ Contains sigma factors (protein), by ribosome on rough ER.
work with RNA polymerase to initiate ➢ Has three RNA polymerases (RNA
transcription. polymerase I, II, and III), each
responsible for transbring different type
of RNA, allowing more complex
regulation of gene expression.
○ RNAP I transcribe rRNA
○ RNAP I transcribe mRNA
○ RNAP III transcribe tRNA
➢ Contains general transcription factors,
by assist with recruiting RNA
polymerase to the promoter.

*mRNA → carry genetic information from DNA to ribosome for protein synthesis.
tRNA → deliver amino acid to ribosome during translation.
rRNA → form the structural and functional core of ribosomes, where protein synthesis occur.
Topic 19.2
1. Identify an open reading frame and understand the significance of degeneracy
in the genetic code

Open reading frame (mRNA in translation)

★ Region of DNA sequence that correspond to mRNA transcript that can be translate by
ribosome into continuous polypeptide sequence.

★ Begin with start codon (AUG) and end with stop codon (UAA, UAG, UGA) with
intervening sequence that is multiple of three nucleotides.

*incorrect reading frame affect the translation, by altering amino acid sequence, producing
non-functional or aberrant protein.

Significance of degeneracy in genetic code

There are four nucleotides (A, U, G, C), and a codon consists of three nucleotides, which 43
equals to 64 types of codons, but there are only 20 types of amino acid (including start
codon AUG — for initiation of translation), thus causing the degeneracy in genetic code,
which some amino acids are coded by more than one codon while there are also three stop
codons — for termination of translation.

Advantage:
★ Error tolerance → change in nucleotide of a codon (slient/synonymous mutation) but
still produce the same amino acid, without influencing the function and structure of the
end protein.
Topic 19.3
1. Describe the three major steps in translation and the cellular components
involved and recognise the key differences between prokaryotes and
eukaryotes

Three major phases of translation (process of synthesizing protein from RNA)

Initiation

1. The small ribosomal subunit binds to its

recognition sequence on MRNA.

2. Methionine-charged tRNA binds to the

AUG start codon, completing the initiation
complex.

3. The large ribosomal sununit joins the

initiation complex, with methionine-charged
tRNA now occupying the P site.

Elongation:

1. Codon recognition – the anticodon of the

income tRNA binds to the codon at the A
site.

2. Peptide bond formation – the amino acid

is linked by peptidyl transferase acitivty of
the large subunit.

3. Elongation – the ribosome shift down one

codon, moving the uncharged tRNA to the E
site, and the tRNA carrying the growing
polypeptide chain to the P site, opening up
the A site. A new charged tRNA enters the
A site and the uncharged tRNA is released
from the E site. The polypepetide is
transferred to the amnio acid on the A site
tRNA.The ribosome shifts down one codon,
moving the tRNA with the polypeptide to the
P site, and opening up the A site. The
process then repeats.

Termination

1. A release factor binds to the complex

when a stop codon enters the A site.

2. The release factor disconnects the

polypeptide from the tRNA in the P site.

3. The remaining components (mRNA and

ribosomal subunits) separate.
 Prokatyotes Eukaryotes

➢ Utilize the Shine-Dalgarno sequence ➢ Use the 5' cap structure for ribosome
for ribosome binding, have binding, scan for the start codon in the
formylmethionine (fMet) as the initiator mRNA, have methionine (Met) as the
amino acid. initiator amino acid, and involve
initiation factors.
➢ Bacteria does not have 5’ cap to
initiate translator, instead each ➢ Initiator tRNA contains conserved
bacterial mRNA contains nucleotides that are recognised by
Shine-Dalgarno sequence (upstream eukaryotic initiation factors (EIF), with
of the first start AUG codon), which EIF and GTP, the initiator tRNA binds to
serves as the ribosomal binding site by the P-site of the small ribosomal subunit
base pairing with a complementary forming eukaryotic preinitiation complex,
sequence on the rRNA of the small which recognises the mRNA by
ribosomal subunit, with initiator tRNA interacting with initiation factors that
binds to the start AUG codon, allowing binds to the 5’ cap and 3’ poly-A-tail on
the large ribosomal subunit to bind to the mRNA, with the power by ATP
the initiation complex with complete hydrolysis, the eukaryotic preinitiation
ribosome to begin translation. complex move from the 5’ to the 3’
direction with the tRNA anticodon
searching for the start AUG codon on
the mRNA, when codon and anticodon
recognise, GTP is hydrolyzed and the
initiation factors are dissociated allowing
large ribosomal subunit to join forming
complete ribosome to begin translation.
*tRNAs help ribosomes introduce correct amino acid to protein by carrying specfic amino
acids and matching them with coreesponding mRNA codons through complementary base
pairing.
Topic 20.1
1. Explain how de novo and induced mutations can occur and describe the
outcomes of somatic and germline mutations.

Spontaneous Mutation:

Deamination → affect pyrimidine bases (C to U, loss of amnio group and present in water
lead to conversion).

Depurination → loss of purine bases due to cleavage of bond between the base and
deoxyribose, leaving an apurinic site in DNA.

*water is present abundantly in cells, which can cause hydrolytic (spontaneous) damage to
DNA (bases).

Replicative Transposition → transposon from a part of the DNA is copied and inserted into
another part of teh DNA, altering the mRNA produced.

Induced Mutation:

- Nitrous acid → cause deamination

- Benzopyrene → add chemical group to guanine
- Radiation → break sugar-phosphate backbone of DNA (x-ray, gamma ray), and
cause colvent bond between adjacent thymine bases (UV).

Somatic Mutation Germline Mutation

→ occur in body cells (non-reproductive → occur in cells that give rise to gametes,
cells), passed to daughter cells in mitosis, passed to offspring at fertilization.
but not to offspring.
→ mutation happened prior to fertilization.
→ mutation happened after fertilization.
→ entire organism (every cells) carries
→ specific cells carry the mutation. mutation.

→ none of the gametes carry somatic → half of the gametes carry germline
mutation. mutation.
*Mutation → a change in the nucleotide sequence that can be passed on from one cell or
organism to another.

Common DNA Repair Mechanism

Base excision repair Nucleotide excision repair Mismatch repair

→ focus on fixing → can fix damage caused → fix faulty base

endogenous DNA damage by ultraviolet light or certain incorporation by DNA
(hydrolytic damage – chemical carcinogens. polymerase during
deamination / depurination) replication.
Topic 20.2
1. Contrast synonymous versus non-synonymous mutations, and missense
versus nonsense mutations.

Synonymous Mutation Non-synonymous Mutation

→ a change of one nucleotide to another in → a change of one nucleotide to another in

a codon triplet that does not affect the a codon triplet that does affect the amino
amino acid specified. acid specified.

Non-synonymous Mutation

Missense Mutation Monsense Mutation

→ a change of one nucleotide to another in → a change of one nucleotide to another in

a codon triplet cause change in the amino a codon triplet cause change in the amino
acid specified to another new amino acid. acid specified to a stop codon.

→ mutation could either lead to loss of → mutation often lead to loss of function
function (codes for nonfountional protein) or (incomplete protein).
gain of function (codes for new protein).

*Frameshift mutation → when reading frame (set of three nucleotides are grouped into
codons) is shifted due to insertion / deletion of nucleotides, resulting in new series of codons
encoding for different amino acids, creating different (abnormal) protein.
Small Mutation Large Mutation
→ more common but have less significant → less common but have significant effects.
effects.

CNV SNPs

→ structural variations in DNA segments if → random, single-base substitutions

more than one kilobase pair (large through the genome (not all qualify).
distance).
→ only one nucleotide variation, found in
→ if chromosomal segment contains a more than 1% of the population.
gene, the CNV can either increase or
decrease the copy number of that gene by → confer various diseases (ex. diabetes /
duplication and insertion or deletion. cancer)

→ can affect phenotype that depend on the → ex. Sickle cell anemia → A to T in
number of functional gene copies beta-globin gene cause sickle-shaped red
(ex. AMY1) blood cells.
Topic 20.3
1. Describe dominance, incomplete and co-dominance at the molecular level

Dominance Imcomplete Dominance Co-dominance

One allele's effect masks the No dominant alleles, thus Both alleles are dominant,
other's, thus heterozygotes heterozygotes expressed thus heterozygotes
only expressed dominant neither allele completely, expressed both alleles fully,
allele, resulting dominant resulting an intermediate resulting in a phenotype that
phenotype being showed. phenotype being exhibited. shows both traits distinctly.

RR → red RR → red RR → red

Rr → red Rr → pink Rr → red and white
rr → white rr → white rr → white

*blood type
*allele → variants of gene, one from each parent (diploid → two alleles at same locus),
combination of allele is known as genotype.
Topic 21.1
1. Describe and contrast stages of mitosis and meiosis and describe the
segregation of genetic information

Mitosis Meiosis

➢ Somatic cell. ➢ Germ cell.

➢ Equational division, where each diploid ➢ Reductional division, where each

parent cell produces two identical diploid parent cell produces four
dipold daughter cells. non-identical haploid daughter cells.

➢ Four stage processes (prophase, ➢ Eight stage processes (prophase I,

metaphase, anaphase, telophase). metaphase I, anaphase I, telophase I,
prophase II, metaphase II, anaphase II,
➢ Shorter prophase stage, no pairing of telophase II), without an intermediate
homologous chromosomes and no DNA synthesis phase (S phase – DNA
crossing over happening, thus all replication).
daughter cells are genetically identical.
➢ Prophase one is the longest phase,
➢ Less error. consisting five sub stage to form pairs
of homologous chromosomes with
crossing over happening, thus
daughter cells are genetically diverse.

➢ More error (aneuploid cells – down

syndrome).

X-shaped I-shaped

→ after DNA replication (interphase - after S → before DNA replication.

phase). → incomplete replication.
→ chromosome containing two identical → structural abnormalities.
sister chromatids. → chromosome containing one chromatid.
Meiosis I Meiosis II

➢ Reduce number of chromosome ➢ Maintain the number of

from diploid (2n) to haploid (n). chromosome (haploid — n).

➢ Undergo crossing over (prophase I) ➢ Only undergo independent

and independent assortment assortment (metaphase II).
(metaphase I) → provide different
genetic combination. ➢ Separate individual chromosomes
into individual chromatids.
➢ Separate homologous
chromosomes to individual
chromosome.
Topic 21.2
1. Use Mendel's first law of allelic segregation to explain how traits at single
gene locus are passed on from one generation to the next

Law of Segrgation:

➢ Allele Pairs Separate: Each individual organism contains two alleles for each trait,
one inherited from each parent. These alleles segregate (separate) during the
formation of gametes (egg and sperm cells), so that each gamete carries only one
allele for each trait.

➢ Random Combination: During fertilization, gametes combine randomly to form

offspring, with each parent contributing one allele for each trait. This results in the
offspring having two alleles for each trait, one from each parent.

Inheritance:

➢ First Generation (F1): If starting with pure-breeding (homozygous) parents, AA

(dominant) and aa (recessive), all F1 offspring will be heterozygous (Aa) and
display the dominant phenotype.

➢ Second Generation (F2): When F1 individuals (Aa) are crossed, the Law of
Segregation ensures that the alleles separate so that each gamete carries only one
allele. This results in a 3:1 phenotypic ratio (dominant to recessive) in the F2
generation, demonstrating the predictable patterns of inheritance according to
Mendel's first law.
Topic 21.3
1. Use genetic diagrams and nomenclature to illustrate how traits are inherited
and predict the outcomes of a genetic cross

➢ Chi-squared test → to check whether there is a significant difference (p<0.05)

between the expected value and observed value.

➢ Null Hypothesis: assume no real difference between expected and observed

values, and any difference between is due to chance.
Topic 22.1
1. Distinguish between the transmission of traits carried autosomes and the
X-chromosome

Autosomes Dominant Autosomes Recessive

X-chromosome Dominant X-chromosome Recessive

*Since females have two copies of x-chromosome while males have only one copy of
x-chromosome, a recessive mutation on x-linked gene will often affect males more than
females, who may have a normal gene on the other copy of x-chromosome (carrier but does
not display the trait) to compensate the loss.
Topic 22.2
1. Describe the utility of different types of genetic crosses in determining
inheritance patterns

Hybrid cross

→ cross between two genetically distinct homozygous parents, typically differing in one or
more traits, to produce heterozygous offspring (hybrids) and study the inheritance patterns
of specific traits.

→ crossing a pure-breeding plant with green pods (YY) with a pure-breeding plant with
yellow pods (yy). The F1 generation will all be heterozygous (Yy) and typically display the
dominant phenotype (green pods).

Monohybrid Cross

→ varients of one gene locus.

→ law of segregation.

Dihybrid Cross

→ varients of two gene locus.

→ law of segregation and the law of independent assortment.

Test cross
→ to determine the genotype of organisms expressing dominant trait.
→ by crossing the unknown genotype expressing dominant trait with homozygous
recessive genotype to test.
→ useful in identifying the arrangement of alleles of linked genes in dihybrid.

→ if the outcome contains recessive phenotype, the unknown genotype is heterozygous; if

the outcome is all dominant phenotype, the unknown genotype is homozygous.

*recessive lethal allele → produced 1:2 ratio of (AA) and (Aa), which does not align with
Mendel’s monohybrid cross, this is because the one with (aa) is dead, suggesting (a) is
recessive lethal allele.
Topic 22.3
1. Demonstrate how information can be assembled into pedigrees and
interpreted in order to describe how traits are inherited in humans

Pedigree:

➢ Dominant trait observed in every generation of pedigree because individuals

carrying the dominant allele will express the dominant phenotype.

➢ Recessive trait may skip generations of pedigree because carrier of recessive

allele can pass it without expressing the trait, leading to trait being expresseed only
when two copies of recessive alleles are inherited.
Topic 23.1
1. Use Mendel's law of independent assortment to explain and calculate
genotype and phenotype ratios across multiple loci

Characteristic ratio of a dihybrid cross for two genes that assort independently.

➢ Mendel’s second law (law of independent assortment) ⇒ 9:3:3:1

● 9 → both dominant (A-, B-)

● 3 → 1 dominant & 1 recessive (A-, bb)
● 3 → 1 dominant & 1 recessive (aa, B-)
● 1 → both recessive (aa,bb)

Some crosses result in a modified 9:3:3:1 ratio.

➢ Epistasis → one gene masking or interfering with the expression of another.

➢ Gene linkage → tendency of genes located close to each other on same

chromosome to be inherited together.

Identify if two genes are assorting independently.

➢ By using dihybrid cross, if the observed ratio is 9:3:3:1, then the two genes are
independently assorted.

Dihybrid cross.

➢ Breeding between two organisms that are identically hybrid for two traits.
➢ Demonstrate the principle of independent assortment (9:3:3:1).
Topic 23.2
1. Contrast genetic linkage with independent assortment and explain how
crossing over can result in recombinant outcomes

Dihybrid Cross Test Cross

(9:3:3:1) (1:1:1:1)

➢ To determine if two genes are linked or not is by observing the phenotypic ratio in
dihybrid cross and see if it fit the expected Medel’s ratio of independent assortment
(9:3:3:1).

➢ Two genes can be on he same chromosome but appear to be genetically unlinked,

because when the proximity of the gene is ≥ 50%, it appears to be genetically
unlinked (independent assortment), which the likelihood of crossing over events
during meiosis increase, resulting in equal frequency between parental and
recombinant gamete.
Topic 23.3
1. Explain how data from genetic crosses can be used to determine the location
of genes on chromosomes and use genetic maps to determine the likelihood
that two traits will be inherited together

Parental arrangement of alleles.

➢ Specific combination/sequence of alleles (inherited from parental generation)
present on chromosome before undergo crossing over in meiosis (where
recombinant arrangement formed).

The parental arrangement of alleles in an individual come from the combination of alleles
present in parental gametes.

Recombinant arrangement of alleles.

➢ Combination/sequence of alleles on a chromosome that had been recombined
through crossing over during meiosis, which produce combination of alleles that
were not presented together in original parental chromosomes.

Parental arrangement of alleles observed more frequently for linked loci, because linked
loci / linkage gene (alleles close to each other on the same chromosome) has higher
tendency of to be inherited together, less likely to undergo crossing over during meiosis.

There is no difference in frequency of parental and recombinant alleles when genes are on
different chromosomes because the alleles segregate independently (no crossing over
between non-homologous chromosome, no linkage).

Test cross is more useful in linkage analysis than dihybrid cross, because test cross only
generate homozygous recessive gamete, which directly show the genotype that receive
parental and recombinant of alleles.

Difference between cis and trans arrangement of alleles.

Cis arrangement Trans arrangement

➢ Parental alleles have both ➢ Parental alleles have one wild-type

wild-type / mutant alleles on the and one mutant allele on same
same chromosome. chromosome.
Difference in observed progeny phenotypes → allow to distinguish between the cis and
trans arrangement of alleles in a test cross.
Topic 24.1
1. Explain how bacteria acquire DNA from the environment from other bacteria
or via bacteriophages, and its implications for bacterial evolution by horizontal
gene transfer

Horizontal gene transfer:

➢ When genetic material from one organism is introduced to another organism of the
same generation (can be same / different species).

Three mechanism which bacteria can gain genetic material:

➢ Transformation
➢ Transduction
➢ Conjugation

Bateria take up exogenous DNA that comes from outside the cell (in the environment) via
transformation, which bacteria must either be naturally competent to take up extracellular
DNA from the environment or chemically treated in lab to make the cell wall permeable to
DNA.

Plasmid
➢ Circular DNA fragment.
➢ Mostly found in bacteria.
➢ Allow ro replicate independently.

Differences between the lytic and lysogenic cycles of transduction:

Lytic Lysogenic
➢ Reproduction by taking over ➢ Reproduction without killing host.
bacterium cellular machinery and kill ➢ Phage attach to the host cell and
the host. inject the DNA, phage DNA
➢ Phage attach to the host cell and recombine and integrate with
inject the DNA, phage DNA destory bacterial genome forming
the host DNA and forcing it to prophage (not active, does not
produce viral DNA and components produce new phage), whe host
undergoing self-assembly, the cell divide the prophage replicate
phage degraded the cell wall with host DNA.
allowing water to enter causing cell
burst, which phages released to
infect new nearby bacteria.

DNA is directly transferred from one cell (donor) to another cell (recipent) via sex pilus,
which then the transferred plasmid may integrate into the genome.
*not sexual reproduction, no gametes exchanged, no offspring produced.
Topic 24.2
1. Describe how experiments using bacterial transformation and transduction
identified DNA as the molecule of inheritance

Enzymes:

➢ Protease → degrade protein

➢ RNase → degrade RNA
➢ DNase → degrade DNA

Griffith’s experiment:

➢ Traits of virulence transmitted between bacteria, which virulent strain had been
introduced into non-virulant strain, making the strain lethal (non-virulent bacteria
become virulent).

Avery’s experiment:

➢ Identify DNA as the molecule of inheritance.

Hershey-Chase experiment:

➢ Radioactive P only label the DNA, which prove that DNA is the molecular of
inheritance.

Orthogonal replication:

➢ Replication process that operates independently and does not interfere with host
cell’s natural replication mechanism.

➢ Separation between synthetic and natural function, prevent affecting host’s

replication due to cross-interaction.
Topic 24.3
1. Explain how bacterial genetics is applied in recombinant DNA techniques

Recombinant DNA
➢ DNA construct from different sources.
➢ DNA (donor) + DNA (vector).

Transformation used in recombinant DNA technology by recombinant DNA inserted into

host organism (bacteria) and replicate, creating many copies of gene of interest.

Antibiotic selection:

➢ Identify and isolate bacteria that have successfully taken up the recombinant
plasmid, ensure maintenance of plasmid in bacteria population and eliminate
non-transformed cells.

*used following transformation of a recombinant plasmid.

Function of enzymes:

➢ Restriction enzyme (restriction endonucleases) → derived from bacterial defence

system destory foreign DNA by recognising and binding to specific DNA
sequences and break the phosphodiester bond across both DNA strands at the
recognition site.
*restriction sites are palindromic → read the same in 5’ to 3’ direction on both DNA
strands.
 ➢ DNA ligase → repair the joint by building phosphodiester bonds over the nicks.
*restriction enzyme + DNA ligase → make new recombinant plasmid.

➢ DNA polymerase (heat-resistence) → responsible for DNA replication.

➢ Cas nuclease → direct to matching sequences in viral DNA, lead to cleavage and
destruction of viral DNA.

Three features of plasmids used as DNA vectors:

➢ Ori → sllow plasma replication within bacterial host cell.

➢ Antibiotic resistance gene → potential driver for horizontal gene transfer, and
selection for cells that have been transformed with recombinant plasmid.

➢ Recognition site for restricted enzyme.