Notes Term 3 C14-C19

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CHAPTER 14: TAXONOMY AND BIODIVERSITY
Nomenclature Naming of organism
Taxonomy
Placing organism into
group (taxa) based on
Systematics certain relationship
between organisms
Importance of Taxonomy
1. Evolutionary pattern - To know the origin, evolutionary pattern and spread of beneficial and
harmful species
2. Newly discovered species – Predict the characteristics of newly discovered species
3. Record biodiversity – Classify the new species based on certain/ specific characteristics
4. Communication – Communicate efficiently among the scientists
5. Strategies – For endangered and threatened species by protection or conservation
6. Study – Anatomy, physiology, morphology etc.
Taxonomic Hierarchy
The taxonomic hierarchy and example as of human;
1. Kingdom (Animals)
2. Phylum (Chordata)
3. Class (Mammalia)
4. Order (Primates)
5. Family (Hominidae)
6. Genus (Homo)
7. Species (sapiens)
Ways to write the organism’s name:
- The name consists of only the genus and species
- The first alphabet of a genus is of capital letter
- The other alphabets are written in small letters
- If typed, the name is written in Italic or bold.
For example, Homo sapiens / Homo sapiens
- If hand-written, the name is underlined.
For example, Homo sapiens
5 Kingdom System
- First divided into Prokaryotes and Eukaryotes
- Prokaryotes are under kingdom Monera
- Eukaryotes are either under Protista, Fungi,
Plantae or Animalia
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Kingdom Protista
- The organisms are either unicellular (mostly) and some are multicellular
- They are either heterotrophs (eats other plants or animals for energy and nutrients) or autotrophs
(produce its own food using light, water, carbon dioxide, or other chemicals)
- They are widespread in damp habitats
- The subkingdoms which will be discussed are Algae and Protozoa
Algae Protozoa
Phylum Chlorophyta Differences Phylum Zoomastigina
Pear-shaped 1. Shape Spherical/Elongated
Made up by cellulose and 2. Cell wall Absent. Replaced by pellicle
mucilage
Central 3. Nucleus Not central
Pyrenoid (Starch stored) 4. Food storage Paramylum granules (Starch
stored)
Present, cup-shaped 5. Chloroplast Present
Present 6. Contractile Present, osmoregulatory in
vacuole function
A pair of flagella which extend 7. Flagella Not in pair. Only one and long
through the cell wall flagellum
Green algae, Chlamydomonas, 8. Example Euglena
Spirogyra
- Has more than 1 vacuole 9. Other - Unicellular
- Red stigma to detect light explanation - Heterotrophic
intensity changes - Has red stigma like algae
Kingdom Fungi
 Most are multicellular except yeast (unicellular)
 Lacks chlorophyll and non-photosynthetic
 Heterotrophic-saprotrophic = Digest foods outside the
body and absorb the digested food particles
 Body consists of mycelium = Network of fine tubular
filaments called hyphae. Hyphae have cell walls
containing chitin
 Non-motile, has no flagella and cilia to move around
 Carbohydrate store: Glycogen
 Asexual reproduction; produce spores
 E.g. Mucor
Kingdom Plantae
- Plants are autotrophic and derive energy by photosynthesis
- Dominant generation: Sporophyte (2n) or Gametophyte (n)
- From 2n to n, undergoes meiosis. From n to 2n, undergoes fertilisation
- Sporophyte (2n)  Spores (n)  Gametophyte (n)
- The FOUR PHYLA in kingdom Plantae are Bryophyta (e.g. Marchantia or moss),
Filicinophyta (e.g. Dryopteris or fern), Coniferophyta (e.g. Pinus or pine tree), and
Angiospermophyta (flowering plants)
Kingdom Plantae: Phylum Bryophyta

- E.g. Marchantia or moss
- Habitat: Damp and shady places
- Dominant generation: Gametophyte
- Body has thallus = Lack true roots, stems and leaves
- Only differentiated into simple leaves and stems
- Has rhizoid to anchor to substrate and absorb water
and nutrients
- Non-vascular plants (No xylem and phloem)
- May carry out sexual reproduction or asexual
reproduction
- Female organ (a) is called archegonia and its gamete
is oosphere
- Male organ (b) is called antheridia and its gamete is
antherozoid
- Gemma cup is used for asexual reproduction
- Bryophytes provide protection for seeds to germinate,
hold water in soil, capture and recycle nutrients
Kingdom Plantae: Phylum Filicinophyta
- E.g. Dryopteris
- Habitat: Terrestrial, tropical rainforests
- Dominant generation: Sporophyte
- Prothallus (gametophyte)
- Sporophyte has true leaves, stems and roots
- Vascular plants but not well developed (Xylem only consists of tracheid while Phloem only
consists of sieve tubes)
- Produce spores; Homosphore (Produce 1 type) or Heterosphore (Produce 2 types: Megaspore of
female and Microspore of male that form pollen grain)
- Organ for sexual reproduction is sporangia
Dryopteris
o Leaves are large and called as frond
o Leaf lets are known as pinnae
o Has underground stem called as rhizome
o Stem and petiole are covered with brownish scales called
ramenta
o Adventitious roots that grow profusely from rhizome
o Sporangia in cluster called sori on lower surface of leaves
o Mostly are homosporous (produce 1 type of spore)
Differences between Phylum Bryophyta and Phylum Filicinophyta
Phylum Bryophyta Differences Phylum Filicinophyta

Present 1. Thallus Present
Absent 2. Vascular tissue Present, not well developed
Gametophyte 3. Dominant generation Sporophyte
Sexual and asexual 4. Reproduction Sexual and asexual
Marchantia 5. Example Dryopteris
Kingdom Plantae: Phylum Coniferophyta

- E.g. Pinus or pine tree
- Dominant generation: Sporophyte
- Seeds are not protected by ovary
- Has vascular tissue which more developed than phylum Filicinophyta
- The xylem has tracheid with secondary thickening of lignin while the phloem has sieve tubes,
fibres and parenchyma. No companion cell in phloem
- The leaves are needle-like with thick waxy cuticle and sunken stomata to ensure less water is lost
- Mostly are heterosporous produce2 types of spore; megaspore and microspore
- Male cone has sporophyll and each sporophyll has 2 microsporangia. Microsporangia produce
microspores/ pollen grain which dispersed by wind and not water
- Female cone has sporophyll and each sporophyll has 2 ovules. Ovules have megasporangia.
Megasporangia produce megaspores
- Carry out sexual reproduction. The organ for reproduction is cone
Kingdom Plantae: Phylum Angiospermophyta
- Flowering plants. Dominant generation: Sporophyte
- Seeds are protected by ovary that will form fruit
- Highly developed vascular tissue
- Heterosporous: Megaspore (ovule) and microspore (pollen grain)
- Agents of pollination: Insects, birds, bats
- Carry out sexual reproduction. Flower is organ of reproduction
- 2 main classes are monocotyledoneae and dicotyledoneae
Monocotyledoneae Differences Dicotyledoneae

1 1. No. of cotyledon 2
Elongated, narrow, pointed, 2. Leaves Broad lamina,
parallel venation netlike/reticulate venation
- Scattered 3. Vascular bundle - In ring form
- No distinct cortex, no pith - Has distinct cortex and
- No vascular cambium pith
- No secondary growth - Has vascular cambium
- Has secondary growth
Perianth is not divided into 4. Flower Perianth is divided into
sepal and petal sepal and petal
Fibrous root system 5. Root Tap root system with
lateral roots
Comparison between Phylum Coniferophyta and Phylum Angiospermophyta

Phylum Coniferophyta Comparison Phylum Angiospermophyta
Not protected by ovary 1. Seeds Protected by ovary
Not produced 2. Fruit Produced
No companion cell 3. Phloem Has companion cell
Tracheid only 4. Xylem Tracheid and xylem vessel
Cone 5. Reproductive organ flower
Not carried out 6. Double fertilisation Carried out
By wind 7. Dispersal of seeds By insects, birds or bats
Sporophyte 8. Dominant generation Sporophyte
Mostly are heterosporous 9. Heterosporous Mostly are heterosporous
Kingdom Animalia
Few terms’ definition:
- Diploblastic = Has endoderm and ectoderm layers
- Triploblastic = Has endoderm, ectoderm and mesoderm layers
- Acoelomate = No body cavity
- Coelomate = Body cavity exists
- (Coelom provides space in which internal organs can grow, develop and function
- Pseudocoelom = Body cavity is not completely lined with tissues derived from mesoderm
Kingdom Animalia: Phylum Porifera
 E.g. Sycon or sponge
 Diploblastic, sessile (cannot move, not motile),
exists in colonial (in group), Plankton as their
foods
 Has no specialised tissue and not symmetrical
 The shape is hollow tube, single body cavity with
opening at the top called osculum
 Porocytes/ Pore cells/ Ostia in the body wall
 Body wall divided into outer layer and inner layer
 Outer layer:
- Covered by epithelial cells. Has mesohyle/ mesoglea between the outer and inner layer
- Amoebocytes secrete needles of calcium carbonate called spicules
- Spicules provide support and also protection against predator
 Inner layer:
- Consists mainly choanocyte (collar cells with single flagellum)
- Flagella beat at water to propel water, nutrients, oxygen through pores into body cavity and out through
osculum
 Are hermaphrodites where male and female develop at different times
 Carry out asexual reproduction by budding (outgrowth from body and separate) and
regeneration
 Carry out sexual reproduction by amoebocyte forming male gamete or female gamete and fuse
to form zygote
Kingdom Animalia: Phylum Cnidaria
 E.g. Hydra (Coral reef) and Obelia (Jellyfish)
 Diploblastic and has mesoglea (like phylum Porifera)
 Radially symmetrical
 Has epidermal, nervous, digestive, muscular and reproductive systems
 Gas exchange occurs through diffusion
 Its body cavity is called as coelenteron where a single opening is for ingestion and egestion
(function as mouth and anus)
 Use tentacles to catch food like fishes and crustaceans
 Tentacles have stinging cells called cnidocytes containing nematocyst (coiled thread + poison)
 Digestive system: Internal extracellular digestion
 Cells lining cavity wall release enzymes to break down food. Cells lining gut engulf food
fragments by phagocytosis
 Has 2 body forms or dimorphic:
i) Polyp: Shape (Cylinder), Movement (Sessile, cannot move), Has mouth and tentacles
ii) Medusa: Shape (Umbrella), Movement (Free), Has mouth and tentacles
 Carry out asexual reproduction by budding or strobilation and sexual reproduction which occurs
externally
Kingdom Animalia: Phylum Platyhelminthes

- E.g. Taenia or flatworm
- Bilaterally symmetrical, unsegmented and flattened
- Acoelomate/ has no body cavity
- The gut/enteron has only one opening as digestive cavity
- Digestion occurs by: Muscular contraction creates sucking force to help digestion. The cells
lining the gut engulf food particles by phagocytosis
- Excretory system:
~ Consists of network of fine tubules extend throughout the body
~ Ciliated flame cells on the side branches of tubule to move water
and wastes into tubule and exit through pores between epidermal
cells
- Has no excretory system. Gaseous exchange occurs by diffusion
- Flatenned body shape increase the surface area to volume ratio for gaseous exchange
- Has simple nervous system
- Have hermaphrodites and carry out internal fertilisation
Kingdom Animalia: Phylum Arthropoda
6 classes Example
- Triploblastic with body cavity exists (coelomate) Crustacea Penaeus (prawn)
- Body is bilaterally symmetrical and metamerically segmented Chilopoda Lithobius (centipede)
- Body is divided into head, thorax and abdomen Diplopoda Lulus (millipede)
- Some, the head is fused with thorax forming cephalothorax Insecta Periplaneta (cockroach)
- Body is covered by exoskeleton made up of chitin and protein Arachnida Lycosa (spider)
- Has compound eyes Merostomata Limulus (horseshoe crab)
- Has open circulatory system (no blood vessel) with haemolymph as body fluid (only found in
arthropods and molluscs)
- Heart is located at the back side (dorsal heart)
- Has nervous system which is more complicated than phylum Platyhelminthes
- Each body segment bears a pair of jointed appendages for locomotion, feeding or sensory
- Eliminate waste through Malpighian tubules
Kingdom Animalia: Phylum Mollusca
- E.g. snails, cockles, octopus and squids
- Habitat: aquatic and damp places
- Triploblastic with body cavity exists (coelomate)
- Some are bilateral symmetry while some are
asymmetrical due to torsion
- Soft body, head, ventral muscular foot, dorsal
visceral hump that has digestive, excretory and reproductive organs
- Mantle (special epidermal tissue) secrete shell made up of calcium carbonate
- Gills in cavity between mantle and body captures oxygen from water
- Has open circulatory system (no blood vessel) with haemolymph as body fluid (only found in
arthropods and molluscs)
- Heart has 3 chambers and the respiratory pigments are called as hemocyanin
- Has well-developed digestive system that consists of stomach and digestive glands
- Rasping organ; radula in mouth that used to break off plant material or bone into flesh of preys
- Nephridia (for excretory system) with tubular structures that gathers wastes from coelom and
discharged into mantle cavity
- Carry out external fertilisation except for terrestrial gastropods (like snails) which basically
oviparous (producing young by means of eggs)
Kingdom Animalia: Phylum Chordata Classes Example

- Triploblastic and body cavity exists
Chondrichthyes Carcharodon (Shark)
- Body is bilaterally symmetrical Osteichthyes Tilapia
- Chordates have post-anal which lost in some adults Amphibia Rana (Frog)
- Muscles are arranged in segmented blocks called Reptilia Naja (Snake)
myotomes on either body side to allow rapid and Aves Columba (Pigeon)
versatile movement Mammalia Rattus (Rat)
- Has distinct head with high degree of cephalization (location of sense organs and nerve cells in
anterior end of body)
- Has notochord
- Has tabular and hollow dorsal nerve cord
- Chordates have pharyngeal slit (visceral clefts). It presents in embryos and retained in primitive
chordates. Becomes gills in fish and lost in some adults
Characteristics of notochord:
 Slim, slender, stiff and flexible rod with vacuolated cells held together within a firm
sheath
 Originated from mesoderm. Located below the nerve cord
 Persists in primitive chordates but in most vertebrates, it is replaced by the vertebral
column (backbone)
Biodiversity
- The three main levels of biodiversity are; Genetic diversity, Species diversity (or taxonomic
diversity) and Ecosystem diversity (or community diversity)
i) Genetic diversity = Responsible for the variation/ different traits in a population
= Allows individual to adapt to different environment
ii) Species diversity = Responsible for richness of species in an area
iii) Ecosystem diversity = Complex interaction between biotic component (living
organisms like plants, animals and microorganisms) and abiotic component (non-living
organism like temperature, pH, light intensity and humidity)
Importance of Biodiversity
Importance Explanation
1. Maintaining the well- - Such as protect the water resources and natural
being of ecosystem resources
- Protect soils formation
- Protect nutrient storage and recycling
- Contribute to climate stability
2. Maintaining biological - Protect endangered species
resources - For food from animals and plants
- Medical and pharmaceutical resources
- Wood/timber products
3. Maintaining social - For research purpose
benefits - Recreation and tourism
- Education and awareness
STPM 2013 Q18(a) Describe the negative implications of human activities towards
i) Biodiversity [6 marks]
ii) Environment [4 marks]
i) Biodiversity:
- (Excessive/ over-exploitation of natural resources) (destroy the breeding grounds of many
species)
- and this (causes extinction of certain species)
- (Excessive use of pesticide/ herbicide/ insecticide/ fungicide) cause (loss of genetic diversity)
- (Illegal hunting/ overhunting/ fish bombing) cause (extinction of specific species)
- (Introduction of new species) cause (extinction of local species)
ii) Environment:
- Illegal logging causes global warming. More carbon dioxide accumulates in atmosphere
- Cleaning forest cause flood. Soil is being washed down the river and raising the riverbed. This
impedes the water flow due to erosion
- Unsustainable agricultural practices disrupt nutrient cycles. Eutrophication increases BOD
level in water. Leaching will lead to poor soil condition
- Indiscriminate discharge of industrial/ domestic waste/ open burning cause soil, water and air
pollution. Acid rain may occur which will change the soil pH. Toxic materials are introduced
into environment
- Industrialization and deforestation cause soil, water and air pollution. Acid rain may occur
which will change the soil pH. Toxic materials are introduced into environment
Biodiversity Conservation
- Conservation is used to describe the wise management of natural resources including
preservation of habitats and wildlife
- Conservation biology = scientific study of how humans impact biodiversity and how biological
diversity can be protected
- Conservation biology = a discipline that ranges from protecting populations of endangered
species to preserving ecosystem
Biodiversity Conservation: In-situ conservation
1. In-situ conservation maintains organism in their original habitats
2. Examples are Taman Negara, Turtle Sanctuary, Virgin Jungle Reserves, Royal Belum
3. Government law to protect and conserve the diversity of biological species
4. Establishment of restricted and protected areas to limit logging and hunting
5. The responsibility is taken by Department of Wildlife and National Parks, State Forestry
Department
6. To prevent loss of habitat and to protect endangered species
Biodiversity Conservation: Ex-situ conservation
1. Ex-situ conservation maintain organism outside their original habitats
2. Examples are Orang Utan Rehabilitation Centre, Sepilok, Penang Botanical Garden and
National Zoo
3. Established due to social responsibilities, commercial and research
4. Responsibilities taken by government, universities, research centre, commercial states or NGO
5. To save genetic materials of threatened and endangered species
6. To increase the number of animals and plants
7. Increases genetic variability
CHAPTER 15: ECOLOGY

Hierarchy in Ecosystem
1. Organism = Individual species of living organism
2. Population = A group of individuals of same species living in particular areas at one time
3. Community = Population of different species living in a demarcated geographical area at
any one time, interacting with each other
4. Ecosystem = Community (biotic) and non-living (abiotic) surroundings from ecosystem
5. Biomes = A major biotic community which is typically characterised by dominant
forms of vegetarian and climatic conditions
Niche = Is the role of an organism and how it fits in the environment. The environment here includes
food, competitor, predator and interaction with abiotic surroundings
There are 3 types of niche;
 Ecological niche = Sum of usage of biotic and abiotic resources

 Fundamental niche = Resources are used under ideal condition (maximum population,
abundant resources
 Realised niche = Resources that are actually can be used
Biogeochemical cycle
- Definition: Process whereby chemical elements/ inorganic substances are passed from the
environment through a sequence of living organisms and back into the environment
- Example: Producer  Primary consumer  Secondary consumer  Tertiary consumer 
Decomposers (Fungi and Bacteria), Detritivores (Millipede and Earthworm)  Producer
- Sedimentary cycle involves phosphorus and others that are not in gaseous form
- Geological uplifting occurs when solid nutrients are brought to land, to the seafloor and to dry
land later
Biogeochemical cycle: Carbon cycle
 Importance: Form biological molecules such as carbohydrates, lipids, nucleic acid and protein.
It is also important when carbon dioxide produced is used for photosynthesis
 Reservoir of carbon:
i) Fossil fuel; made up of ancient trees that were buried before being completely
decomposed
ii) Limestone; sedimentary in aquatic organism (matters settle at the bottom of the sea),
shell and bone of aquatic organism settle at the bottom of the sea then covered by
sediments and are thousands metre thick
 The processes that release carbon dioxide to atmosphere:

i) Respiration
ii) Combustion and manufacturing process of cements
iii) Weathering; cause erosion under adverse condition like strong wind, high temperature
and low humidity
iv) Decomposition; decomposers like fungi and bacteria feed on decaying matters and
waste
v) Shells of marine organisms  sink, sediments cover them  geological uplift 
weathering  release carbon dioxide
 Absorption in carbon cycle is carried out by plants (producers) by photosynthesis
 Dissolved carbon present in CO32- and HCO3-
 Carbon cycle involves movement of carbon between abiotic component and organisms (biotic)
Biogeochemical cycle: Phosphorus cycle
 Importance: incorporated with phospholipid, protein, nucleic acid, NADP and ATP
 In a sedimentary cycle and not in gaseous form
 Reservoir of phosphorus: Phosphate rocks (in rocks, phosphorus is bound to oxygen to form
phosphate)
 The processes that release phosphate:
i) Decomposition to soil (as phosphate) and
water
ii) Weathering of phosphate from rocks where
erosion occurs under adverse condition
iii) Farming activities use fertilizers (phosphate
ion)
iv) Leaching  Algae bloom (in aquatic habitats)
v) Algae  Zooplankton  Fishes and molluscs
 Birds eliminate faeces containing
phosphate ions  back to the soil
 When water flows over rocks, it erodes surface, carries
inorganic phosphate, PO43-, into the soil
 Animals feed on plants and take up phosphorus
Biogeochemical cycle: Sulphur cycle
 Importance: To synthesis amino acids, nucleic acid, protein, coenzyme A and biotin
 Reservoir: Iron pyrite found in sedimentary rocks
 The processes that release sulphur:
i) Combustion in mines and oil wells
ii) Volcanic eruptions
iii) Weathering of FeS = erosion of rock due to
adverse situation
iv) Decomposition form hydrogen sulphide, H2S
v) In waterlogged soil, organic sulphur is
reduced by sulphate-reducing bacteria namely
Desulphovibrio sp. to produce H2S
vi) H2S undergoes oxidation by Thiobacillus sp.
to form SO4
vii) H2S undergoes oxidation by Chromatium sp. to form S
 Some exists as sulphur dioxide in air

 Plant absorb sulphate ions, form amino acids and proteins
 Some bacteria use hydrogen sulphide as source of hydrogen for photosynthesis
 6CO2 + 12H2S  C6H12O6 + 6H2O + 12S
Energy Flow
 1st Law of Thermodynamics // Law of Conservation Energy states that energy can be converted
from one form to another but cannot be destroyed or created
 2nd Law of Thermodynamics // Law of Entropy states that at conversion of one form of energy
to another, energy is lost in the form of heat
Describe the energy flow in ecosystem
1. The source of energy is sunlight as solar energy
2. Green plants trap light energy and convert them to chemical energy
3. The process occurs in photosynthesis
4. Energy flows in one direction from producer to consumer
5. Energy is lost at each trophic level in the form of heat
6. Ecosystem can support up to 5 trophic level
7. Energy is lost to surrounding through respiration, excretion, reproduction and death
8. Energy loss is the result from metabolic activity
9. 10% of energy flow from producer to consumer. 10% of energy then flow from a consumer to
another consumer
Energy Flow: Terms, Definitions and Explanation
- Gross primary production (GPP) refers to the total rate at which producers synthesize organic
material which would be used in respiration or stored
- Net primary production (NPP) refers to rate at which producers store organic material
- NPP = GPP – Respiration (R) = x kJ m-2 y-1 // x kilojoule per meter squared per year
- Biomass refers to amount of organic materials in an ecosystem
- Only 10% of biomass produced by producers are transferred to primary consumers
- Secondary production refers to rate at which energy is used to make new consumers’ tissues
- Primary producers are autotrophic which can synthesize their own foods
- Consumers (animals, decomposers, detritivores) feed on the organism
- When producers and consumer die, they are broken down by decomposers which are fungi and
bacteria
- Food chain is sequence of organisms whereby one organism is the food of the next organism
and each organism represents one trophic level
- The two types of food chain; grazing food chain (begins with plants, living organism) and
detritus food chain (begins with dead organic matter)
- The grazing food chain can be further divided into
predatory food chain (size of organism is bigger in
chain) and parasitic food chain (size of organism is
smaller in chain)
- Detritivores are animals that feed on detritus or dead
organism. They break down detritus into smaller
particles. Examples of detritivores are earthworms,
millipedes and woodlouse
Tropical Rainforests
1. The rainfall is high
2. Floor receives about 2% of sunlight
3. Plants grow bigger and taller, stronger than plants in any other biomes
4. The soil is poor in minerals
5. The temperature is high and this makes the decomposers and detritivores decompose organic
matters rapidly
6. Very little matter accumulates in the soil
7. Wide/ vast network of roots makes the minerals are quickly absorbed from decomposing
materials. Thus, most mineral are withing the vegetation
8. Abundant solar energy and more rainfall captures large energy for photosynthesis
9. Since the GPP and NPP in tropical rainforests are high, energy transfer is more effective
10. Earthworms and fungi break down organic matter give feeds to plants of the rainforest. Plants
become adapted for maximum energy flow through diversity
11. The threat that tropical rainforest face is deforestation
Lakes
- A large lake has three zones which are littoral, limnetic and profundal zones
- At smaller lakes, profundal zone is absent
Littoral Limnetic Profundal

Vegetation - Plant, algae - Phytoplankton, Absence
- Emergent zooplankton
vegetation
Animal -Frogs, fishes, - Larger fishes Decomposer

insect larvae, water
strider, worms
Depth of water Shallow Depth is as far as light Light cannot
Light is abundant, can penetrate penetrate
receives nutrient from Plant and algae do
surrounding land, plant not live here
and algae growth is
stimulated
Photosynthesis The rate is high The rate is high The rate is low to
none
Population Ecology
The two types of growth curve are exponential curve and sigmoid curve
Exponential curve, J growth curve Sigmoid curve, S growth curve

Population tends to grow 1. Definition Growth rate of population is slow as
exponentially as long as there are fewer resources remain
available resources
2. Graph
Lag phase: Growth rate is low, only 3. Phases Lag phase: Natality is low
few numbers of individual are there
Exponential phase: Natality
Exponential phase: Growth rate increases and reach biotic potential.
increases, number or individual is Natality > Mortality
accelerating
Linear phase: Growth rate is low
But, food eventually runs out and due to limited resources. Size of
waste products begin to accumulate. population approaches carrying
Further growth is impossible capacity, K. Mortality > Natality
Equilibrium or Stationary phase:

Size of population becomes stable.
Mortality = Natality
 Natality = The birth rate of a population

 Mortality = The death rate of a population
 Emigration = Individual moves out of a population
 Immigration = Individual moves into the population
 Population = (Natality + Immigration) – (Mortality + Emigration)
 Biotic potential is the maximum reproductive capacity of organism under optimum condition
// Maximum number of offspring per birth
Survivorship
 Definition: Probability of individual can survive to certain age

 Percentage of survival = No. of survivors per No. of original population x 100%
 The 3 main survivorship curves are; Type I, Type II and Type III
 Birds exhibit Type III curve first and Type II later (2 survivorship curves)
Type I Type II Type III

Example Human Squirrel, Lizard Oyster, Cockroaches
Rate of survival - At young age, rate of - Have constant death - At young age, rate of
survival is high (mortality) survival is low
- Usually due to parental throughout the life - Due to high
care - Is rare in nature mortality,
- At later age, rate of - predators,
survival decrease - and absence of
- As decreases, it is due parental care
to aging-related - Only few can
problem survive and get
matured to later age
K-strategies and r-strategies
K- strategies r- strategies
1. Body size Large Small
2. Maturity Reach maturity slower Reach maturity faster
3. Life span Longer Shorter
4. Reproductive age Reach reproductive age late Reach reproductive age early
5. No. of offspring Few Many
produced
6. Probability of Most survive until their Most die before their
survivor of offspring reproductive age reproductive age
7. Parental care Exists, extensive Little or none
8. Environment Stable (usually stay in a Vary (may move to other
place) places)
9. Example Human, Tiger Insects
Carrying Capacity, K
 Definition: Maximum number that the environment can support with available resources
 Factors limiting the population size and distribution; Density-dependent factor and Density-
independent factor
Carrying Capacity: Density-dependent Factor
 Definition : Factors that are influenced by the number of organisms in given space
 Effect : Slow down the population growth when the population density is high
 Factors : Predation, Disease and Competition. Another one is overcrowding
 Predation : Involve Boom-and-Bust cycle where;
More prey and predator at beginning More predator, less prey  Less prey, less predator 
Less predator, more prey
 Disease : Population has high density may spread infectious disease easily
 Competition factor may be divided to intraspecific competition (between individual of same
species) and interspecific competition (between different species)
 In intraspecific competition, the same species compete by interference/contest competition or
exploitation/scramble competition
 Interference/contest competition; only dominant individual explores the resources at the
expense of others. Others are unable to compete and will die eventually
 Exploitation/scramble competition; every individual share limited resources equally
Carrying Capacity: Density-independent Factor

 Definition: environmental factors that can affect the size of a population and is not influenced
by population density
 Example: Severe frost/ ice crystal, blizzard/ snow storm, hurricane, flood, earthquake and forest
fire also change in weather conditions
Quantitative Ecology
- Sampling is used to collect part of data from the whole population when the are under study is
large, it is not possible to collect all the data from every area and when there is not enough time,
energy, manpower, money or equipment
- Sampling can be done by random, systematic or stratified
Quantitative Ecology: Sampling method: Quadrat
1. Frame : square frame made up of metal, wood or plastic with its area of 1 m 2
2. Point : frame with holes which “pin” can pass through
3. Three aspects of species distribution;
i) Frequency; measure of probability of finding a species in a quadrat
ii) Density; number of individuals of a species in a given area
iii) Cover; measure of proportion of ground occupied by the species
Aspects Formula
Percentage of frequency Percentage of frequency =
(unit = %) x 100%
Species density Species density =
(unit = individual per
meter2
Relative density Relative density =
x 100
Relative density Relative density =
x 100
Percentage of cover Percentage of cover =
(unit = %) x 100%
4. Advantages of quadrat sampling method:
i) Get to study the plants population that are spread out over large area
ii) Inexpensive
iii) Easy to design
iv) Harmless for organism
v) Can be adapted to study unevenly distributed populations
5. Disadvantages of quadrat sampling method:
i) Animals move out of the quadrat
ii) Physically demanding and tiring
Line transect Belt transect
- String is laid along 2 poles - 2 line transects
- Organisms touching the string is recorded - Density =
- Advantages: Reliable, versatile, easy to
- n = number of objects observed
implement and not time consuming
- L = total length of transect
Disadvantages: Just have the data of what
- w = width of transect
species are there and limited information
Capture-recapture Method
 Objective: Estimate the population of mobile animals
 Capture – Mark – Release – Recapture
 Ways of marking organism:
- Tag the operculum of fish with aluminium discs
- Attach rings to the legs of birds
- Use dye/ paint on small animals and insects
- Clip the fur in distinctive pattern
 Population size =
 Estimated population size is known as Lincoln index
 Assumptions made during the process:
- Organisms mix randomly within the population
- Sufficient time lapse between capture and recapture to allow random mixing
- Organisms are restricted geographically
- No change in population size due to births, deaths, immigration and emigration
- No hindrance to the movement of organism due to the marking
- The marking does not make organism conspicuous to predators
 Precautions should be taken:
- Dye should be waterproof
- Dye should not be toxic
- Dye should not be brightly coloured to not attract predators
Pattern of Distribution of Organisms
 Population distribution is the pattern of spacing/ dispersion relative to each other

 Population density is the number of individuals of a species per unit are or volume at a given
time
 The types of dispersion are random, clumped or uniform
Random distribution Clumped/Aggregated Uniform distribution

distribution or Patchiness
- Individuals are scattered - Individuals are - Individuals are evenly
- Distance between concentrated in a specific spaced
individual is different area - Distance between
- The distribution is - Distance between group is individual is equal or same
independent of one different - Help to reduce competition
another - Due to patchy distribution - Resource: Limited
- Resource: Many, of resources
unlimited - The grouping is due to
parental care or against
predator
- Resource: Unevenly
distributed
CHAPTER 16: SELECTION AND SPECIATION
Variation
 Definition: Differences between organisms of same species
 Importance of variation:
i) Our environment is constantly changing and give rise to new challenge. When there is
an outbreak of a disease, all the uniform organisms will die
ii) It is essential for survival of a species
 The 2 forms of variation are; Continuous variation and Discontinuous variation
Continuous variation Discontinuous variation

Individuals of population 1. Definition Individuals do not show
show gradation from one gradation
extreme to other
Height, weight, skin colour 2. Example Fingerprints, ability to roll
and hand span tongue and blood group
Environmental and genetic 3. Affected by factor Genetic only
Normal distribution / 4. Graph detained Discrete distribution
Gaussian curve
Exists 5. Intermediate Does not exist
characteristics
Polygene 6. Gene Single gene
 The similarities between continuous and

discontinuous variations;
i) Both cause differences between
individuals
ii) Both variations increase the
biodiversity in the population
iii) Both variations are important for
survival under changing
environment
iv) Both are caused by genetic
factors which can be inherited
Sources of Variation
- Variation may be caused by (genetic factors) that can be passed to the next generation or
(environmental factors) that cannot be passed
- Under genetic factors, (sexual reproduction) cause variation by (random fertilisation, crossing
over that produce new allele combination or by random assortment of homologous
chromosome)
- (Mutation) is also under genetic factor that cause variation when (chromosomal mutation occurs
or gene mutation (where there is sudden change on gene material)), (aneuploidy and euploidy)
- Under genetic factors too are (polygenes), (dominant and recessive gene) and (hybridisation)
that cause variation to occur
- Variation caused by environmental factors cannot be passed to the next generation
- Examples of environmental factors are climate (like temperature, humidity, light intensity), soil
condition (pH, oxygen, organic matter, water) and presence of nutrients
Selection
 Definition: A process whereby 1 or more factors acting on phenotypes (physical characteristics)
to favour the transmission of particular alleles or gene to the following generation
 Importance of selection;
i) Results in evolutionary change
ii) Avoid predator
 The 2 types of selection are: Natural selection (Stabilising selection, disruptive selection,
directional selection, sexual selection and polymorphism) and Artificial selection
Natural selection Artificial selection

- Process by which individual with - Process of intentional or unintentional
favourable traits are more likely to modification of a species through human
survive and reproduce action which encourage breed of certain
- Results in favoured traits being trait
represented - Can occur by selective breeding
Favourable traits that are better adapted will Desired traits are passed to next generation
be passed to next generation
No human interference. Natural environment Human interference involved
selects organism
Organisms survived and breed naturally Human breeds organisms by selective
breeding
Longer time is needed Shorter time is needed
Organisms chosen are with traits adaptable Organisms chosen are with desired traits as
to the environment preferred by humans
Selection: Natural Selection

**(when answering essay question on the first three below, the graph sketched need to put indicator of the arrow)
Graph detained Example

(1) Stabilizing selection - Birth weight of an infant
- Environmental forces baby
select against the 2 - If the weight is low, the
extreme phenotypes infant lose heat and get
- and favours the infections easily
intermediate - Average birth weight
phenotypes infant is more healthy
- High birth weight infant
will be difficult to deliver
(2) Disruptive selection - Deserts have black and
- Environmental forces white rocks
select against the - When a species with
intermediate black colour fur is there, it
phenotypes will survive from being
- and favours both 2 eaten by predators as they
extremes can hide at the black
- (is a driving force rocks
behind sympatric - Grey colour fur will be
speciation) seen by predator and not
survive
- White colour fur will
survive as they can hide at
the white rocks
(3) Directional selection - Long-neck giraffe

- Environmental forces - Bacteria resistant to drugs
select against one of - Pale/white moth live in
the extreme unpolluted are, hide at
phenotypes and trunks covered by lichen
intermediate - Melanic/ peppered moth
- only favours one live in polluted area, hide
extreme phenotype at trunks covered by
- Results in shift of carbon
mean either to right or (either to left of right, depends on
left extreme selected against)
- Certain allele has
greater fitness than
other. Frequency of
that allele increases
(4) Sexual selection

 Definition: selection favours the trait to help animal to increase the chance of mating ad allow
transmission of genes to the next generation
 Traits of male animals;
i) Sing song – cricket
ii) Protect territory
iii) Building elaborated structure – e.g. bowerbird builds nest
iv) Display prominent features – e.g. peacock
(5) Polymorphism
 Definition: many different phenotypes or forms in population of same species
 The 2 types are; Balanced polymorphism and Transient polymorphism
 Balanced polymorphism:
- Definition: Favour 2 or more alleles of a gene to be maintained
- Cause: Environmental force
- Example: genotype HH of normal haemoglobin will be dead where malaria is endemic,
genotype Hh of carrier of sickle cell anaemia will survive while genotype hh of sickle cell
anaemia patient will die due to anaemia
 Transient polymorphism:
- Definition: A morph is in process of spreading in a population
- Cause: Environmental force
- Example: Pale/white moth live in unpolluted are, hide at trunks covered by lichen.
Melanic/ peppered moth live in polluted area, hide at trunks covered by carbon. In
Manchester, England, due to industrialization, melanic moth lives there as the place
becomes polluted
Selection: Artificial Selection

 Definition: Process of intentional or unintentional modification of a species through human
action encourages the breeding of certain traits
 Gene bank: Collect, process, store and distribute specimens of animals (eggs, sperms, embryo,
coral fragment), plants (cuts, seeds, spores) and human (sperm, ovum) for scientific
investigation
 Importance of human sperm bank:

- Artificial insemination
- Male cancer patient before radiotherapy or chemotherapy
- Male patient taking certain medications
- Vasectomy that decide to have child later
- Working in high radiation area
- Gene defects can be controlled
 Importance of animal sperm bank:
- Breed animals with desirable traits
- Survival of endangered animal
- Transport to other part of world
- Gene defects can be controlled
Speciation
 Definition: Evolutionary process to form new species from previously existing species
 When 2 species give rise to 1 new species, it is known as interspecific speciation/ hybridisation
 Species is a group of individuals which can interbreed with each other
 There are 2 modes of speciation which are; Allopatric speciation and Sympatric speciation
Explain the mode of speciation type allopatric [9 marks] **refer to STPM 2016 Q18(a)
- Population of same species live in a same geographical area

- Allopatric speciation occurs due to geographical isolation and dispersal
- For example, mountain range that separates members of population
- Interbreed is inhibited by geographical isolation
- Both group members are unable to meet and reproduce
- No gene flow occurs between the species
- For dispersal, a group of individuals from original population migrate to other places
- This group is exposed to different environment force
- Population is physically separated
- The separated members diverge through changes in mating tactics or use of habitats
- They become reproductively separated, cannot interbreed and no exchange of gene
Extra:
- Geographical barrier/isolation also knows as vicariance
- Separation of group of organisms by geographical barrier leads to isolation. This results in
differentiation of the original group into new species over a period of time
- Dispersal is the movement of a few members of a
species to a new geographical area
Explain the mode of speciation type sympatric [5 marks]
- Sympatric speciation is caused by evolution in the
same geographical area
- Population of same species live in the same
geographical area
- Members of the population occupy different niche
- Interbreed is inhibited by reproductive isolation
- This results in genetic divergence
- For example, maggot flies lay eggs either at the
hawthorn or in the apple (same geographical area,
different niche)
Formation of new species
 A new species can be formed by 4 methods

 Isolation, Genetic drift, Hybridisation and Adaptive radiation
Formation of new species: Isolation
 Definition: Species are isolated by reproductive barriers to prevent successful reproduction

occurs or reproduction occur but fail to produce fertile offspring
 There are 2 reproductive barriers; Prezygotic barrier and Postzygotic barrier
Prezygotic barrier Explanation Example

1. Geographical barrier - 2 species never encounter Aquatic snakes and terrestrial
(Extrinsic isolation) each other in same snakes
geographical area
- Occupy different habitats
2. Ecological barrier - 2 species are in the same Mosquitoes breeding at
(Intrinsic isolation) geographical area stagnant water or running water
- Separated by short distance
- Different niche/ preference
3. Seasonal/ Temporal - Plants have different Skunks either mate in late
barrier flowering seasons, no summer or late winter
(Intrinsic isolation) pollination occurs
- Animals have different
mating seasons, no
copulation/mating occurs
4. Behavioural barrier - Different species show Blue-footed Booby dances to
(Intrinsic isolation) different courtship display attract female
or mating ritual
5. Mechanical barrier - Reproductive structures are Snail with shell clockwise or
(Intrinsic isolation) incompatible anticlockwise
- Prevent copulation/mating
6. Gamete incompatibility - Gametes are incompatible Red or purple sea urchins.
(Intrinsic isolation) physically or chemically Protein on eggs and sperms are
- Male gamete fails to fuse incompatible
with female gamete
- No zygote is formed
Postzygotic barrier Explanation

1. Hybrid inviability - Hybrids do not develop normally
(reduced hybrid viability, incapable to - Does not reach sexual maturity
live)
2. Hybrid sterility/infertility - Hybrids do not have homologous
(reduced hybrid fertility) chromosome
- No meiosis occurs
- No gamete or normal gamete
produced
3. Hybrid breakdown - Hybrid of 1st generation, F1, is
fertile and viable
- When F1 cross with F1, hybrid of 2nd
generation is sterile or infertile
Formation of new species: Genetic drift
 Definition: A random change in allele frequency by chance occurrence/event in a small

population
 Occurs slowly, significant in small population
 Change allele frequency substantially. May reduce or increase genetic variation
 2 circumstances result in genetic drift; Bottle neck effect and Founder effect
STPM 2014 Q18(a) Describe bottleneck effect phenomena that contribute to the changes is allele
frequency [9 marks]
- Bottleneck effect occurs when there is a sudden change in environment that kills a large number
of individuals in a population
- For example, earthquake, flood, forest fire, volcanic eruption, hurricane, outbreak of disease,
overhunting and drought (lowers food supply)
- Large number of individuals die. This reduces the gene pool
- Some alleles are under-represented
- Some alleles are also over-represented and even absent
- Only a few individuals are left to contribute to the gene pool of the entire populations
- It reduces the genetic variation
- This change the allele frequency substantially in small population
- When genetic drift occurs, the small population form new species
- The newly formed species is very different from the original population as the frequencies of
alleles change
STPM 2015(U) Q20(a) Describe how founder effect could lead to genetic drift in a population
[8 marks]
STPM 2018 Q19(a) Explain the founder effect and relate it with genetic drift during the formation
of a new species [6 marks]
- Founder effect occurs when a small population is dispersed from the original population due
to migration
- The smaller the population, the greater the effect of genetic drift
- It has a gene pool which is slightly different from the original population
- The new population grows from a small number of pioneer individual
- **Continuous interbreeding in the new population changes the genotype and allele frequency
- Some alleles are under-represented, over-represented and even absent
- Reproductive barriers prevent them from breeding with other population
- The new population becomes a new species
Formation of new species: Hybridisation
 Definition: Mating between 2 closely related species which are genetically different
 Speciation can occur if hybrid;
i) receives a genome that enables it to breed with other hybrids
ii) does not breed with parental species
iii) escape to a habitat where it does not have to
compete with parent
iv) adapt to live under new condition
 Colchicine is used to induce formation of polyploids in
plants by interfering with spindle formation
 Allopolyploid = derived from 2 different closely related
species, produce sterile/infertile F1 hybrids. When 2 sets
of chromosomes of F1 doubles, produce fertile hybrid
Formation of new species: Adaptive radiation
 Definition: Gradual change of an ancestral species to a number of diverse species. Each species
occupies new habitat
 A group of individuals of a species invade different habitats
 Expose to different selection pressures (types of food)
 Adapt to different habitats
 Form many new species
 E.g. finches in Galapagos island
By using a specific example, explain the concept of adaptive radiation [7 marks]
- Adaptive radiation is the gradual change of an ancestral species to a number of diverse species.
Each species occupies new habitat
- Example: Darwin’s finches in Galapagos Island
- The original population of Darwin’s finches are mainland finches that had short and straight
beak to crush seeds
- As the population increases, intraspecific competition increases
- Some of the finches went to different new habitats
- New ecological niches were found and occupied by 14 species of finches to reduce competition
- Due to the changes in gene pool and natural selection, the finches became adapted to the various
food resources available in the different new areas
- Ground finches eat seeds and cactus, tree finches eat insects, warbler finches eat insects, fruits
and nectar
- Adaptive radiation of Darwin’s finches shows divergent revolution
Population Genetics
 **Gene pool is the sum total of all alleles of all the genes in a sexually reproducing population at
a given time
 Hardy-Weinberg equation; p + q = 1
 where p is the dominant allele frequency and q is the recessive allele frequency
 Example;
Given from 10 000 population size, 5000 are with tall homozygous dominant 3000 are with tall
heterozygous and 2000 are with dwarf homozygous recessive. Calculate the value of p and q.
Total alleles = 10 000 x 2 = 20 000

p = Number of dominant alleles per Total allele q = Number of recessive alleles per Total allele
=[(5000 x 2) + 3000] per 20 000 = [(2000 x 2) + 3000] per 20 000
=0.65 = 0.35
Alternatively, p + q = 1. Substituting p=0.65, we will get 0.35 as the value of q
Hardy-Weinberg Equilibrium
 Hardy-Weinberg Law states that the frequencies of dominant allele and recessive allele in a
population remain constant from generation to generation
 under following conditions;
1) The population size is large. Any change in allele frequency is negligible
2) Random mating and fertilization. This provide equal chance to mate freely
3) No natural selection. All alleles have the same level of reproductive advantages and
disadvantages
4) No net mutation. Mutation can change allele frequency
5) No migration, no gene flow in or out of the population. Gene flow may change the allele
frequency
6) No overlapping of generation
 p + q = 1. By squaring both sides, we will get p2 + 2pq + q2 = 1
 where p2 is the frequency of homozygous dominant, 2pq is the frequency of heterozygous and q2
is the frequency of homozygous recessive ((note that they are not the allele frequency as in original
equation))
Changes in genotype frequencies in relation to evolution
 Agent of change: Selection

 Selection favors certain phenotypes and cause the transmission of certain gene to the next
generation
 The phenotypes which are not selected and genes which control the phenotypes will be wiped
out
 It changes the allele and genotype frequencies and result in evolution
DNA Replication
Experiment to prove DNA is the genetic material by Avery, MacLeod and McCarty
 Material used is Streptococcus pneumoniae
 2 strains of bacteria involved; S strain (produce smooth colonies, virulent, and cause death to
mouse) and R strain (produce rough colonies, avilurent, and does not cause death to mouse)
 Procedure:
1) Use heat to kill bacteria with S strain. DNA will survive in the heating process
2) Avery and his colleague isolated and purified different substances from dead bacteria S strain
3) They inject each substance into the mice with R strain
 Results obtained:
Treatment Outcome to mice
1. DNA (S) + live R strain Dead
2. Protein (S) + live R strain Live
3. RNA (S) + live R strain Live
4. Lipid (S) + live R strain Live
5. Polysaccharide + live R strain Live
 Conclusion: DNA is the genetic material which can cause transformation
 But not many scientists believe as they thought that the DNA might be contaminated with protein
or the theory is only true for bacteria
Hershey and Chase Experiment
 Material: T2 bacteriophage (virus infecting bacteria)
 Mechanism of T2 bacteriophage:
i) Attach to cell wall of bacteria E. coli, inject DNA into the bacteria and leaves its protein
coat on the outside
ii) T2 DNA control the metabolism of bacteria. It synthesizes T2 DNA and protein coat
iii) Assemble T2 DNA and protein coat to form new T2 virus. Bacteria is lysed and release new
T2 viruses
 Procedure:
1) Label viral DNA (T2) with radioactive
isotope of phosphorus (32P)
2) Label protein coat (T2) with isotope of
Sulphur (35S)
3) Add virus T2 to cultured E. coli
4) Use blender to shake the mixture
vigorously to separate viral coats (T2)
from infected bacteria E. coli
- The experiment set of 32P + E. coli; E. coli bacteria are detected to be radioactive
- The experiment set of 35S + E. coli; E. coli bacteria are not radioactive. Only the viral coats
are radioactive
 Conclusion: E. coli become radioactive because they contain DNA with radioactive 32P Viral DNA
(T2) transform the DNA of E. coli
3 Models of DNA Replication proposed by Watson and Crick
 DNA replication is the process where DNA carries inherited genetic information and able to copy
exactly to be passed to the next generation
 Conservative model: Use the whole original DNA as template to
form another new DNA (daughter DNA)
 Semiconservative model: Original DNA unwind and each DNA
strand acts as a template. New DNA consists of one original DNA
strand and one new strand
 Dispersive model: New DNA is a mixture of original and new DNA
Meselson and Stahl Experiment

 Materials: E. coli, heavy isotope of 15N and normal isotope of 14N
 Procedure:
1) Set up one controlled experiment
2) Grew E. coli in medium containing 15N (parental generation)
3) Some E. coli were transferred to medium containing 14N (produce F1 generation). Some E.
coli from 1st generation were transferred to medium containing 14N (produce F2 generation)
4) Extracted DNA from parental, first and second generations were mixed with cesium chloride,
CsCl
5) Place the mixture in density dependent centrifugation and centrifuged at high level for 48
hours. DNA molecules were separated according to density
6) Expose tubes to ultraviolet light at 260nm. DNA absorbs the wavelength ray and appear as
dark band
Generation Medium DNA produced Type of DNA
15 15
Parental/Zero N N 15N Heavy DNA
14 15
First, F1 N N 14N Hybrid DNA
14 15
Second, F2 N N 14N and 14N 14N Hybrid DNA and Light DNA
- The first generation, F1 results dispelled the conservative model
- The second generation, F2 result dispelled the dispersive model
 Conclusion: DNA replication use semiconservative model
Mechanism of DNA Replication
- DNA replication occurs during the S phase of interphase before nuclear division
- DNA replication starts at specific base sequence where the replication bubbles are formed and
eventually fuse at the end of the process
- Helicase unwind/separate doble helix to form replication fork by breaking the hydrogen bonds
- The DNA now has 2 antiparallel DNA strands
- Single strand binding protein stabilize the 2 strands separated during replication
- RNA primase synthesizes and attaches the RNA primer to one of the DNA strands
- RNA primase eaves specific site so DNA polymerase can bind to RNA primer
- DNA polymerase III adds DNA nucleotides to RNA primer from 5’3’
- A new DNA strand is polymerized continuously in the same direction as the movement of
replication fork. The strand is called as leading strand
- RNA primase attaches RNA primer to the second DNA strand
- DNA polymerase III adds DNA nucleotides to RNA primer in 5’3’ direction
- Short new DNA strands are polymerized discontinuously in the opposite direction of movement of
replication fork. The fragments are called as Okazaki fragment. The strand formed is called as
lagging strand
- DNA polymerase I removes the RNA primer.Ligase joins the lagging strands of Okazaki fragments
- Two new daughter double helix DNA are formed. Each double helix DNA consists of one parental
strand and one new DNA strand. The model is called as semiconservative model
Gene Expression
 Gene expression is the activation of gene to synthesize protein
Experiment of Beadle and Tatum
 Material: Neurospora crassa (pink mold)
 Features of pink mold:
- Easily cultured in minimal medium
- Bred in large number in a confined space
- Short life cycle of 10 days
- 7 pairs of chromosomes, gene loci can be easily determined
- Produce haploid spores asexually
 Procedure:
1) Asexual spores (F1) of Neurospora were irradiated with X-ray to increase the frequency of
mutations
2) Irradiated spores were grown in complete medium (contain all 20 amino acids) to produce
enough second generation, F2 spores
3) 2nd generation spores were placed in minimal medium. If the spores grow, they were not
mutant and produce enzymes normally. Enzymes can synthesize carbohydrates, fats, proteins
and nucleic acids
4) If the spores didn’t grow, they were mutant which contain 1 or more mutated genes
5) Add 20 different amino acids to minimal medium to determine the mutated gene. For example,
if the mutated gene is to produce arginine, spores are unable to grow in minimal medium but
grow when arginine is added
6) Isolate few genes on chromosome synthesizing arginine. Mutation can occur in 3 loci on
chromosome
 Conclusion: One gene, one enzyme hypothesis is revised to one gene, one protein hypothesis then
revised to one gene, one polypeptide hypothesis
Characteristics of genetic code
- Gene is sections of DNA that contain genetic information
- Genetic information is encoded by triplet code. Triplet code consists of 3 bases
- Triplet code encodes for 1 amino acid
- Genetic code is universal
- Genetic code is degenerate. More than 1 triplet code codes for the same type of amino acid
- The genetic code is not overlapping
- The code is read from 5’3’
- Genetic information carried by triplet code = Genetic information carried by anticodon

- Triplet code (on DNA) undergoes transcription at the nucleus to form codon (mRNA) then
undergoes translation on ribosome to get anticodon (tRNA)
- **To determine what type of protein is produced, refer to its codon produced
- UAA, UAG and UGA are the stop codons. They do not code for any amino acids
- AUG is the start codon
- Both start and stop codons are called as punctuation codon
Protein Synthesis
1) Gene on the DNA is activated. Promoter site is of the TAC triplet code
2) Genetic information on DNA is transcribed to form 1 strand of mRNA
3) mRNA moves from nucleus to ribosome in cytoplasm
4) translation occurs in ribosome to synthesize polypeptide chain
Protein Synthesis: Transcription
- Transcription is a process where the base sequence of a section of DNA representing a gene is
converted into complementary base sequence in nucleus of a cell
- RNA polymerase unwinds the double-stranded DNA
- RNA polymerase attaches to promoter site with triplet code TAC to initiate transcription
- The template DNA strand is called as antisense strand
- The other DNA strand which not used for transcription is called as sense strand
- RNA polymerase moves along DNA in 5’3’ direction while adding ribonucleotides to form
mRNA
- DNA polymerase join the ribonucleotides by phosphodiester bonds
- Double helix of DNA reform behind the RNA polymerase when RNA polymerase moves to
another region
- Upon reaching the “terminator”, RNA polymerase detaches. mRNA moves from the nucleus to
ribosome in cytoplasm
Extra info:
- Pre-mRNA transcribed from DNA contains intron and exon
- In eukaryotes, introns are removed before mRNA leaves the nucleus. After that, exons are
spliced to form real mRNA
- Sense strand has the same base sequence as mRNA except T is replaced by U
Differences between DNA replication and Transcription
DNA replication Transcription (Protein synthesis)

Present 1. Helicase Absent
DNA polymerase III and DNA 2. Polymerase RNA polymerase
polymerase I
5’  3’ 3. Movement of 5’  3’
polymerase
Both DNA strand 4. Template Only one called as antisense
strand
2 new daughter DNA double 5. Product at end mRNA
helix of process
Differences of Transcription between Prokaryotes and Eukaryotes

Prokaryotes Eukaryotes
Absent 1. Introns - Does not code for amino
acid
- Cut at pre-mRNA
Absent 2. Exon Code for specific amino
acid
Does not occur 3. Splicing Exons are joined/ spliced to
form mRNA
Cytoplasm 4. Site of transcription Nucleus
mRNA, tRNA and rRNA

- mRNA has 1 polynucleotide strand which is linear. mRNA functions in transcribe of genetic
information from DNA
- tRNA molecules are made by transcription of special genes in the nucleus
- tRNA has 1 polynucleotide strand with clover-leaf shape. It has a site of attachment for anticodon
- tRNA functions in transferring amino acids. It needs to be activated by aminoacyl-tRNA
synthetase. Charged tRNA/ activated amino acid carries the amino acid
- rRNA is a major component of ribosomes other than proteins
- Large subunit of ribosome is the binding site for tRNA while the small subunit binds to mRNA
Structure of tRNA Structure of a ribosome

Protein Synthesis: Translation
- Translation is a process where information needed within mRNA is used to make specific
polypeptide chain at the ribosome
- The 3 stages of translation are the Initiation stage, Elongation stage and Termination stage
1) Initiation stage:
- mRNA bind to the small subunit of ribosome
- Small subunit recognizes the start codon AUG on mRNA
- Charged tRNA (by aminoacyl-tRNA synthetase) with anticodon UAC binds to codon AUG
- Large subunit caps to small subunit to form RNA-ribosome complex
- RNA-ribosome complex has 3 sites; E, P and A sites
- First charged tRNAmet occupies the P site. Next charged tRNA occupies the A site
2) Elongation stage:
- Ribosome moves along mRNA in 5’  3’ direction
- When first amino acid is formed, it detaches from the P site. The detached amino acid form
peptide bond with second amino acid at the A site by condensation reaction
- Covalent bond between amino acid and tRNA is broken
- Free tRNA leaves the ribosome at the E site to be charged again
- These steps are repeated
3) Termination stage:
- Ribosome recognizes the stop codon (UAA, UAG or UGA) on mRNA
- Release factor will bind to the A site
- mRNA, ribosome and tRNA will separate
- Polypeptide chain is released
- Protein synthesis is accelerated by formation of polysomes

- Polysomes is a condition where 5 to 50 ribosomes read the same mRNA strand and synthesize
the polypeptide chain repeatedly
- Large number of polypeptide chain can be synthesized from 1 strand of mRNA
- On leaving ribosome, polypeptide chain is processed according to its destination. This include
folding and adding chains to form secondary, tertiary or quaternary structure protein
Differences between Transcription and Translation
Transcription Translation
Nucleus 1. Site Ribosome in cytoplasm
mRNA 2. End product Polypeptide chain
RNA polymerase 3. Enzyme Aminoacyl-tRNA synthetase
Regulation of Gene expression

 Gene expression is the activation of gene to synthesize protein
 In eukaryotes, regulation of gene expression is done by start codon (AUG) and stop codons (UAA,
UAG, UGA)
 In prokaryotes, regulation of gene expression is done by operon system
Regulation of Gene expression: Operon
 An operon consists of promoter, operator and structural genes

 Promoter (P) is the binding site for RNA polymerase to start transcription by structural genes
 At operator (O), when repressor bind to the operator, this switch off the operator and block the
RNA polymerase from binding to the promoter. No transcription occurs, no mRNA produced, no
translation, no amino acid and no protein synthesis may occur
 When the operon is switched on, structural genes are activated and transcription may occur
 Regulator (R) is not a part of an operon unit
 Regulatory gene produces protein named repressor. Repressor will bind to the operator to switch
off the operator
 Protein synthesis occurs when;
- No repressor binds to the operator hence the operon is switched on
- RNA polymerase binds to the promoter
- Transcription may occur, mRNA is produced, translation occurs, amino acid is produced and
protein synthesize may take place
Regulation of Gene expression: Operon: Lac Operon
- Lactose operon is a unit of transcription in bacteria which consists of promoter, operator and
structural genes
- Lactose operon in E. coli has 3 structural genes; Lac Z, Lac Y and Lac A
- All structural genes are transcribed as a unit producing 1 mRNA
- Transcription of lac operon is controlled by promoter, operator and regulatory gene
- Regulatory genes code for repressor protein
- Operator is the binding site of repressor protein
- Promoter is the binding site of RNA polymerase
Mechanism of Lac operon:

- Lac operon is important to break down lactose by enzyme β-galactosidase to glucose and
galactose
- When lactose is absent (glucose is present), regulator synthesize repressor molecule
- Repressor binds to the operator and block the RNA polymerase from binding to the promoter
- Operon is switched off
- When lactose is present, lactose forms its isomer namely allolactose
- (allolactose is an inducer// inactivator repressor in an operon by binding to it)
- Allolactose binds to the repressor molecule and form allolactose-repressor complex
- This changes the configuration of repressor allosterically
- Repressor cannot bind to the operator
- RNA polymerase will bind to the promoter to initiate transcription
- The operon now is switched on
- Structural genes are activated to produce mRNA
- Translation occurs
- Lac Z gene will synthesize enzyme β-galactosidase to hydrolyze lactose to glucose and
galactose
- Laz Y gene will produce enzyme lactose permease. This enzyme allows more lactose to pass
through the plasma membrane easily. This increases the uptake of lactose
- Lac A gene will produce enzyme transacetylase. This enzyme transfers acetyl group to enzyme
β-galactosidase
- Glucose and galactose are absorbed by E. coli
Extra notes:
- Inducible enzyme: Only produced in the presence of specific substance. E.g. β-galactosidase,
lactose permease and transacetylase
- Constitutive enzyme: Produced consistently regardless the presence or absence of certain
substance. E.g. hexokinase, aldolase and enolase
- Repressible enzyme: regularly produced but its production can be disabled by certain condition
like excess amount of end product as in tryptophan operon
Regulation of Gene expression: Operon: Tryptophan Operon
- Tryptophan operon is important to produce tryptophan synthetase, a type of repressible enzyme
- Tryptophan synthetase is used to produce tryptophan, an amino acid
- The operon unit consists of promoter (P), operator (O) and 5 structural genes
- Regulator gene produce inactive repressor (cannot bind to the operator)
- RNA polymerase binds to the promoter (P)
- Operon is switched on
- Transcription of 5 structural genes occur to produce mRNA
- Translation then takes place to produce 5 enzymes collectively known as tryptophan synthetase
- Tryptophan synthetase synthesizes tryptophan
- When there is excessive tryptophan, tryptophan will act as corepressor
- It binds to the repressor
- and change the configuration of repressor
- Repressor binds to the operator (O), block the RNA polymerase from binding to the promoter
(P) and the operon is switched off
Mutation
Definition: Abnormal change in genetic material (gene or chromosome) and lead to change in the
function of protein
Types; Spontaneous (occurs naturally in environment) and Induced (caused by mutagens like
ultraviolet light, ionizing radiation or α, β, γ and x rays and chemicals like colchicine)
The ionizing radiation cuts the DNA and cause error. Chemicals have the same structure as DNA
bases and cause error
Mutant (gene, cell or organism) undergoes changes in genetic material due to mutation
The 2 main types of mutation are Gene mutation and Chromosomal mutation
Mutation: Gene mutation
Gene mutation occurs when there is a change in bases of a gene
4 types of gene mutation; Substitution, Insertion, Deletion and Inversion
Mutation: Gene mutation: Substitution
Definition: Substitution of bases pair of a gene (2 alleles) will cause missense mutation, non-sense
mutation or silent/neutral mutation
Missense mutation:
- Altered codon will produce different amino acid
- For example, normal DNA (CTT) changed to mutant DNA (CAT). The base T is substituted
by base A. The normal codon produced is supposed to be GAA (amino acid glutamate) but
changed to GUA (amino acid valine)
- It occurs at the 6th amino acids of β globin
- This cause sickle-cell anemia where normal red blood cell is pulled to form sickled-shape
- Sickled-shape red blood cells are brittle, fragment easily and clog the blood capillaries
- This lowers the transport of oxygen
- HbS HbS (sickle cell), HbA HbS (codominance, suffer from mild anaemia) and HbA HbA
(produce normal haemoglobin)
Non-sense mutation:
- Altered codon is stop codon (UAA, UAG or UGA)
- Translation of mRNA will stop prematurely
- It often results in non-functional protein
Silent/ neutral mutation:
- Altered codon codes for the same type of amino acid
- It has no significant effect
Mutation: Gene mutation: Insertion
 Definition: Insert nucleotide base pair in a gene
 For example;
Normal mRNA AUG AAG UUU GGC
Altered mRNA AUG AAC GUU UGG C
 Cause frameshift mutation where sequence of bases is changed after the insertion point and change
the sequence of amino acids. Results in non-functional protein
Mutation: Gene mutation: Deletion
 Definition: Delete the nucleotide base pair of a gene
 For example;
Normal mRNA AUG AAG UUU GGC
Altered mRNA AUG AGU UUG GC
 Cause frameshift mutation where sequence of bases is changed after the insertion point and change
the sequence of amino acids. Results in non-functional protein
 For example; Thalassaemia major. It caused by deletion of base pair encodes for α or β globin.
Non-functional globin will cause deformed red blood cells
Mutation: Gene mutation: Inversion
 Definition: Inversion of nucleotide base pair in a gene

 For example;
Normal mRNA CCU AGG CUA AGG
Altered mRNA CCU AGC GUA AGG
 Change the sequence of amino acid and may cause production of non-functional protein
Mutation: Chromosomal mutation
 Chromosomal mutation occurs when there is a change in the number of chromosome or change
in the structure of chromosome resulting in change in the characteristic of organism
 4 types of chromosomal (structure) mutation; Inversion, Translocation, Deletion and Duplication
 2 types of chromosomal (number) mutation; Aneuploidy and Euploidy
Mutation: Chromosomal mutation: Inversion
 Segment of chromosome detaches and reattach to the same
chromosome at the same position
 in reverse orientation
 Form spiral loop or inverted loop
 Effect:
- Alters the position and order of gene BUT
- No increase or decrease in genetic material
- No significant effect
Mutation: Chromosomal mutation: Translocation
 Segment of chromosome detaches
 and attach to same chromosome at different position or at non-homologous chromosome
 Effect:
- No increase or decrease in genetic material
- No significant effect
- But if inherited, may cause abnormalities to offspring
Mutation: Chromosomal mutation: Deletion

 Loss of segment of chromosome and cause
genetic disorder
 It may form a deletion loop on the
chromosome after synapsis
 For example, Cri-du-chat disease which
caused by loss of chromosome number 5.
The symptoms are mental retardation and
physical defect
Mutation: Chromosomal mutation: Duplication
 Extra copy of chromosome segment
 Effect: Homologous chromosomes cannot pair/ synapsis during meiosis
Types of chromosomal mutation involving changes in number

1) Aneuploidy diploid organism gains/losses 1 or more chromosome
2) Euploidy diploid organism gains 1 or more haploid set of chromosomes
Mutation: Chromosomal mutation: Aneuploidy
Types Example Explanation

-2 Nullisomy (2n - 2) (1 2 3 4) (1 2) 2 different chromosomes from
non-homologous chromosome
are missing from complete
diploid set of chromosomes
-1 Monosomy (2n - 1) (1 2 3 4) (1 2 3) 1 chromosome is missing from
complete diploid chromosome
set
+1 Trisomy (2n +1) (1 2 3 4) (1 2 3 4) (1) 1 extra chromosome is added
to complete diploid
chromosome set
+1 +1 Double trisomy (2n + 1 + 1) (1 2 3 4) (1 2 3 4) (1 2) 2 extra different chromosomes
of non-homologous
chromosome are added to
complete diploid chromosome
set
+2 Tetrasomy (2n + 2) (1 2 3 4) (1 2 3 4) (1 1) 2 extra same chromosomes are
added to complete diploid
chromosome set
+3 Pentasomy (2n + 3) (1 2 3 4) (1 2 3 4) (1 2 3) 3 extra different chromosomes
are added to complete diploid
chromosome set
Aneuploidy is caused by non-disjunction

Non-disjunction: chromosome or chromatid fail to separate during the meiosis (Anaphase I or
Anaphase II)
Normal meiosis I – Anaphase I:
- Chromosomes are pulled to the opposite poles
- Chromosomes are separated
 Non-disjunction in Anaphase I:
 Spindle fibers are not formed during Anaphase I
 Conclusion made are non-disjunction at Anaphase
I of meiosis I will produce 50% gametes with
chromosome n+1 and another 50% gametes with
chromosome n-1
 Non-disjunction in Anaphase II:

 Conclusion can be made; when non-disjunction
takes place at Anaphase II of meiosis II, 50%
gametes (n), 25% gametes (n+1) and 25% gametes
(n-1)
 Non-disjunction involving sex chromosome in Meiosis I:

 Non-disjunction at Anaphase I of meiosis
I will produce 50% gametes with
chromosome n+1 and another 50%
gametes with chromosome n-1
 One abnormal ovum will have 22+XX
chromosomes (n+1) and the other one
with 22 chromosomes (n-1)
 When abnormal egg cell (22+XX) is
fertilized by normal sperm (22+X),
offspring produced has 44+XXX
chromosomes, a triple-X female
 When abnormal egg cell (22+XX) is
fertilized by normal sperm (22+Y),
offspring produced has 44+XXY
chromosome, a male with Klinefelter’s
syndrome
 When abnormal egg cell (22) is fertilized
by normal sperm (22+X), offspring
produced has 44+XO chromosomes, a
female with Turner’s syndrome
 44+Y chromosome, the offspring is not
viable and unable to live
 Non-disjunction at Anaphase I of meiosis

I will produce 50% gametes with
chromosome n+1 and another 50%
gametes with chromosome n-1
 One abnormal sperm will have 22+XY
chromosomes (n+1) and the other one
with 22 chromosomes (n-1)
 When abnormal sperm (22+XY) is
fertilized by normal egg cell (22+X)
offspring produced has 44+XXY
chromosomes, a male with Klinefelter’s
syndrome
 When abnormal sperm (22) is fertilized
by normal egg cell (22+X) offspring
produced has 44+XO chromosomes, a
female with Turner’s syndrome
 Non-disjunction involving sex chromosome in Meiosis II:

 When a sperm undergoes non-disjunction
at meiosis II, gametes formed are XX
(n+1), YY (n+1) and 2 O gametes (n-1)
 When abnormal sperm (22+XX) is
fertilized by normal egg cell (22+X), the
offspring produced has 44+XXX
chromosomes, a Triple-X female
 When abnormal sperm (22+YY) is
fertilized by normal egg cell (22+X), the
offspring produced has 44+XYY
chromosomes, a super-male
 Abnormal sperms with 22 chromosomes
when fertilized with normal egg cell
(22+X) will produce offspring with
44+XO chromosomes, a female with
Turner’s syndrome
 Aneuploidy: Changes in number of chromosomes
Types of abnormality Genetic constitution Characteristic

Abnormality in number of sex
chromosome Male, small testis, fail to form sperm.
a) Klinefelter’s syndrome XXY Large breasts and voice like a female
b) XYY XYY Male, Psychopathic
syndrome/Super-male
c) Triple-X XXX Female, slight mental retardation
d) Turner’s syndrome XO Female, barren, ovaries and breasts are not

developed. No menstrual cycle and no
ovulation. Dwarves, deaf, has heart
abnormalities and low IQ
Types of abnormality Genetic constitution Characteristic

Abnormality in number of
autosomes Drooping eyes, low resistance to
a) Down’s syndrome 3 chromosome 21 infections and mentally retarded
b) Trisomy-13/Patau 3 chromosome 13 Polydactyl, heart abnormalities, cleft lip
syndrome and mental imbalance
c) Trisomy-18/Edwards 3 chromosome 18 Organs incomplete, small nose, mental
syndrome deficiency and U-shaped kidneys
Mutation: Chromosomal mutation: Euploidy

 Euploidy diploid organism gains 1 or more haploid set of chromosomes
 Caused by non-disjunction where no spindle fiber is formed during nuclear division and also
caused by use of chemicals like colchicine (inhibits formation of spindles)
 Euploidy is more common in plants
 2 types of euploidy; Autopolyploidy and Allopolyploidy
 Autopolyploidy:
- Double 2 same genome from the same species (AA cross with A to form AAA)
- Produce bigger flowers and fruits. Produce greener leaves and darker flowers
- No gamete is formed so no homologous chromosome. Meiosis fail to occur
- Carry out asexual reproduction by vegetative or through self-pollination
 Allopolyploidy:
- Double 2 different genome from 2 different species
- For example, plant A form gamete A and plant B form gamete B. When fertilized, produce
hybrid AB (2n) which is infertile as it has no homologous chromosome
- When it undergoes non-disjunction and the genome is doubled, it becomes AABB (4n) called
as tetraploids
- When genome AABB undergoes meiosis, gamete AB is formed which can be used to form
fertile offspring
- Important example of allopolyploidy;
 AABB (allopolyploidy) is better than AAA (autopolyploidy) because AABB can form similar
gametes and able to reproduce sexually and form new species
CHAPTER 18: GENE TECHNOLOGY

Genetic Engineering using Recombinant DNA Technology
 Recombinant DNA Technology is the process of extracting useful genes from an organism to
be inserted into another organism of different species
 Uses of genetic engineering using recombinant DNA technology:
- Extract human gene and to be inserted into unicellular organism (yeast, bacteria)
- Use them as chemical factory to produce; hormone, vitamin, antibiotic and interferon (a
glycoprotein to prevent viral replication)
 Advantage: Get to join donor DNA with recipient DNA to produce recombinant DNA (where
donor species ≠ recipient species)
Genetic Engineering
 Techniques:
1) Remove the desired gene// Get a copy of gene
2) Place the gene into a vector (a plasmid or bacteriophage)// Insertion
3) Use vector to insert the gene into host cell// Transformation
4) Screen the host cells that took up the gene
5) Cloning the gene//Amplification
Stage 1: Remove the desired gene/ useful gene from a donor
 3 methods to get the target gene:
i) Using restriction enzyme/ endonuclease
ii) Reverse transcription
iii) Synthesize the target gene artificially
 i) Using restriction enzyme/ endonuclease
- Where the enzyme can be found? =In bacteria
- There are how many of them? =2000 types
- Function of enzyme? =To cut the DNA at a specific site
- Specific site is a short base sequence (4 to 6 bases) which is palindromic (when the sequence of
base is read from 5’3’ on the complementary strand, they are the same)
- The restriction enzyme cut the DNA to produce either sticky end fragment or blunt end fragment
- Restriction enzymes that cut DNA to produce sticky end fragment:
- Restriction enzymes that cut DNA to produce blunt end fragment:

- Electrophoresis:
 Used to separate the DNA fragments obtained after being cut by restriction enzyme
 Gel used are either agarose (for longer and bigger DNA fragment) or polyacrylamide (for
shorter and smaller DNA fragment)
 Electric field consists of negative and positive electrodes
 Since DNA fragments are negatively charged (due to phosphate group), longer fragment
and higher negative charge fragment will move to the positive electrode
- Once the different lengths of DNA fragment have separated, a gene probe is added to locate the
desired gene.
- The gene probe is a single strand DNA that has the sequence of base which complementary to
the bases of the desired gene
- For example; Desired gene C G G T T A C G T
Gene probe GCCAATGCA
- Gene probe is attached with a radioactive marker
- Expose the gel (containing desired gene) to the autoradiography. Radiation blackens the fil and
form black band
 ii) Reverse transcription
- mRNA undergoes reverse transcription to produce DNA
- Use probe to identify the correct mRNA
- mRNA undergoes reverse transcription catalysed by enzyme reverse transcriptase to form single
strand DNA
- Then, enzyme DNA polymerase is added to form second single DNA strand and eventually
produce complementary DNA, cDNA
 iii) Synthesize the target gene artificially
- Identify the correct sequence of amino acid and synthesize the target gene artificially
- For example; Amino acid A Amino acid B
tRNA ACG UAU
mRNA UGC AUA
DNA ACG TAT
Stage 2: Place the gene into a vector// Insertion
 The 2 types of vector used are either Plasmid or Bacteriophage/Phage lambda/ X phage
 Plasmid is a simple and circular piece of DNA. It is found in bacterial cell and it can accept small
piece of DNA fragments
 A plasmid has a Lac Z gene that act as a selectable marker and
produce enzyme β-galactosidase
 Plasmid also has an antibiotic resistance gene which is ampicillin
resistance gene, ampR gene also act as a selectable marker
 Properties of Plasmid:
i) Small - easy to purify
ii) Known DNA sequence, Contain selectable gene markers
iii) Has many unique restriction sites - ease cloning process
iv) Rapid replication - higher yields
v) Origin of replication - may replicate on its own
 Bacteriophage is a type of virus that attack bacteria and it can accept a large piece of DNA fragment
 Properties of Bacteriophage:
i) Known DNA sequence, Replicates independently
ii) Accept large piece of DNA, Efficient in transformation
iii) In-vitro packaging – can be easily reconstituted in tubes
iv) Extensively engineered
 How to insert the target gene into the plasmid?

- Use the same type of restriction enzyme/ endonuclease
(with the one used to cut the DNA) to cut the plasmid
- Use enzyme DNA ligase and ATP energy to join the
DNA fragment with the plasmid
- The results formed might contains DNA fragment,
plasmid or recombinant plasmid (cut plasmid with the
target gene)
 There’s complimentary base pairing occurs where A pairs
with T and C pairs with G by hydrogen bonding
Stage 3: Use vector to introduce the gene into the host cell// Transformation
Recombinant plasmid + E. coli (host cell) Bacteriophage infects the E. coli
Calcium ions in calcium chloride are added,

followed by brief heat shock.
Attach to the wall of E. coli
This makes holes in the E. coli plasma
membrane
Recombinant plasmid enters the E.coli Inject target DNA into the nucleus of E. coli
- At last, only about 1% of the E. coli has taken up the target gene
- The host cells that has taken up the target gene are called to undergo transformation and now are
transformed
- Properties of host cell:
i) Able to receive DNA transformation process
ii) Able to maintain the structure of new DNA from one generation to another generation
iii) Able to amplify the desired gene and replicates rapidly
iv) Able to take a large amount of foreign DNA
v) Relatively small genome for easy handling
vi) Able to grow in aerobic and anaerobic conditions
Stage 4: Screen the host cells that took up the target gene
 Type I screening is called as antibiotic screening and Type II screening is called as blue-white
screening or X-gal screening
 About 99% of the host cells are untransformed and another 1% are transformed (but might
transformed by plasmid or recombinant plasmid)
 Screening I: Ampicillin
- Grow the E. coli in the medium containing ampicillin
- The results are; 99% untransformed host cell will die while the 1% transformed host cell
survive as they have the plasmid/ recombinant plasmid (some has normal plasmid without
target gene and some are recombinant) containing ampR gene
 Screening I: X-gal (colourless sugar)

- Grow the survived E. coli in a medium containing X-gal sugar
- The colourless sugar will be transformed to blue compound by enzyme β-galactosidase (if the
plasmid is normal and not recombinant)
- E. coli with normal plasmid will form blue colonies as they have plasmid with functioning
Lac Z gene
- E. coli with recombinant plasmid will form colourless colonies as the recombinant plasmid
has no functioning Lac Z gene
- The colourless colonies will be selected as they contain the target gene
Stage 5: Cloning the gene// Amplification
 Industrial fermenter:
- For bacterial cells taken up the recombinant plasmid
- All conditions are under control like temperature, pH and nutrients
- Bacteria cell E. coli reproduce asexually
- Produce product in vast amount in a short time period
 Polymerase Chain Reaction, PCR
- For DNA
- PCR material required; double helix DNA, primer, DNA polymerase and DNA nucleotides
- Heat up to temperature above 1000℃ to separate the double helix DNA
- Cool down the 2 separated DNA strands
- Add primer to each DNA strand that acts as template
- Primer will attach to single strand DNA by forming hydrogen bonding where base A pairs
with base T and base C pairs with base G
- Add DNA polymerase. DNA polymerase will add DNA nucleotides to the primer to
synthesise new DNA strand
- Produce thousand copies of double-stranded DNA
 Reverse transcription:
- For example, used for human insulin production
- Probe is used to identify the correct mRNA
- Reverse transcriptase is added and mRNA undergoes reverse transcription to produce single
strand DNA
- DNA polymerase is added to form second single strand DNA and eventually produce
complementary DNA, cDNA
- In human insulin, mRNA is used first so gene/ cDNA only consists of exons because bacteria
cannot cut pre-mRNA transcribed directly from human cistronic gene
Application of Genetically Engineered Organisms
Genomic Library cDNA library

Genome (complete set of genes 1. Starting material mRNA (undergoes reverse
of particular species) transcription to form cDNA)
Present 2. Introns (does not code Absent
for any amino acid)
Present 3. Exons Present
Stage 1  Stage 2 (Plasmid)  4. Cloning process Reverse transcription  Stage 2
Stage 3  Stage 4  Stage 5 (Bacteriophage)  Stage 3 
Stage 4  Stage 5
Restriction enzyme, DNA ligase 5. Enzyme Reverse transcriptase, DNA
polymerase
Large 6. Size of library Small
Clone both eukaryotes and 7. Function Express eukaryotic gene in
prokaryotes prokaryotic cells
- cDNA library can be considered as collection of bacterial clones that have recombinant plasmids
- cDNA library consists of clones of bacteria or phage that have only exons from an organism
Extra notes:
 Why same restriction enzyme is used for Stage 2 Insertion?
= So sticky ends DNA fragments and cut plasmid have complementary bases to allow hydrogen
bonds being formed
 Recombinant plasmid/Recombinant DNA is a DNA that has foreign gene from other source
incorporated into it by genetic engineering
 Proof of human insulin effectiveness; No side effect, no antibodies produced
CHAPTER 19: BIOTECHNOLOGY

Biotechnology
 Definition: Application of organism or biological processes (like reproduction, respiration) in
manufacturing process (where raw materials are converted to products)
Application of Biotechnology: 1) Food and Beverage
1) Bakery:
- Flour is added with yeast (Saccharomyces cerevisiae) to produce carbon dioxide and bread
- Saccharomyces cerevisiae produces mixture of enzymes and break down the starch. It also
encourages proving where aerobic and anaerobic produce carbon dioxide to rise the dough
2) Wine:
- Grapes + Yeast  Wine + Ethanol by alcoholic fermentation
3) Yoghurt:
- Milk + Lactate-producing bacteria  Lactic acid + Yoghurt by lactate fermentation
- Lactobacillus bulgaricus produces lactic acid, methanoic acid and ethanal
- Streptococcus thermophilus adds creamy flavour
4) Vitamin-enriched egg:
- Hen (+ Feed) to produce vitamin-enriched eggs
- Vitamin D to improve development of bones in children
- Omega 3 has double bon, can be oxidized but affect health
- Vitamin A, C and E help by acting as antioxidants
- Omega 3 helps to build cell membrane
- Vitamin B6, B12 and vitamin E increase the vitamins in eggs
- Choline is added for brain development
Application of Biotechnology: 2) Agriculture
 Organisms that have been genetically altered using genetic engineering are called as transgenic
organism
 Advantages of transgenic plants and transgenic animals:
- Increase the yields and have higher growth rate
- Improve the quality of foods
- Resistance to pest, disease and herbicide
- Resistance to environmental stress – drought, cold, heat, tolerance to wind damage, acid, salty
soils and waterlogged soils
1) Hybrid rice:
- Crossing 2 genetically different species
- F1 generation has improved quality (hybrid vigour/heterosis), higher yields, higher resistance
and more efficient in use of soil nutrient
- But F2 generation are not fertile because hybrid vigour is lost
2) Herbicide resistant plant:
- Introduce genes which confer resistance to herbicide in plants
- When weed-killer is used, only weeds are killed
- E.g. corn, wheat, sugar beet and cotton tree
3) Transgenic fish:
Process to insert new DNA into fish;
- Use micro syringe/ gene gun to insert the gene (fluorescent genes
extracted from jellyfish or firefly), or, Subject fishes’ eggs to electrical
pulse to form pores. Insert the vector carrying gene into the fish egg
- Vectors are lentivirus transferring gene into the fish
Advantages of transgenic fish:

-Higher growth meat, more meat and higher resistance to disease
-Ornamental fish industry e.g. zebrafish with bright red, green or orange fluorescent colour
-Research in genetics, pharmaceutical application and health
-Genetically modified zebrafish can detect aquatic pollution by detecting the pollutants and
radiate green/red light
Disadvantages of transgenic fish:
- Gene for resistance to disease cause fish to absorb toxic substances like heavy metals and
mercury
- Allergies, health risks if consumed raw or uncooked
- Breed faster, lowers the genetic diversity of native population
- Short life span. If interbreed with native population, this decreases the life expectancy of native
population
- Compete with native population for food, resources and habitat
4) Temperature tolerance in plant:
- Insert gene that regulates extreme temperature
Application of Biotechnology: 3) Medicine and Forensic
1) Human growth hormone, extracted pituitary gland of dead humans to treat dwarfism
2) Human insulin, extracted from pancreas to treat diabetic patient
- Extract **mRNA** (not DNA) from pituitary gland (for human growth hormone) or pancreas
(for human insulin)
- Use enzyme reverse transcriptase to form single stand DNA by reverse transcription
- DNA polymerase is added to form second single strand of DNA and form double stranded
complementary DNA or cDNA
- Extract plasmid from a bacterial cell
- Use the same type of restriction enzyme to cut the cDNA and plasmid
Continuation for human insulin:
- Insert the gene for insulin into the plasmid to
form recombinant plasmid by using DNA
ligase and energy form ATP (Insertion)
- Insertion may take place in a medium
containing calcium chloride, CaCl2
- Recombinant plasmid introduces the gene for
insulin into the bacteria cell/ host cell
(Transformation)
- Plasmid replicates in the host bacteria
- Screen for target gene for human insulin using antibiotic screening and X-gal screening
- Amplification using industrial fermenter to produce vast amount of insulin
- Separate and purify the gene for insulin (Separation and purification of human insulin)
- Inject the insulin into diabetic patients
3) Gene therapy:
- Gene therapy works by using genetic engineering to overcome genetic disorder
- There are 2 types; Gene replacement (normal gene replace faulty gene) and Gene
supplementation (does not remove pre-existing faulty gene but add more normal genes and will
mask the effect of faulty gene)
- Gene therapy can be applied at Sperm/Ovum (germ-line gene therapy that can be inherited) or
at Body cell (somatic-cell gene therapy that cannot be inherited
Cystic fibrosis
- Definition: Disease affect epithelial cell lining trachea
and block pancreatic duct
- Normal gene codes for cystic fibrosis transmembrane
protein (CFTP)
- CFTP transport chloride ions out of epithelial cells into
the mucus and later makes the epithelial smooth and
moist while the mucus is watery
- Mucus traps dust and microorganism to prevent lungs infection
- Effect of mutant gene on CFTP:
 Sticky mucus clogs the airway of lungs, lungs become prone to infection
 Salty sweats to remove excessive chloride ions
 Affect digestion as it may block the pancreatic duct
 Breathing difficulty and coughing
 Affect the cells secreting sweat, mucus, hormone and enzyme
- Stages of cystic fibrosis gene therapy
 Extract normal gene for CFTP and extract plasmid from bacteria
 Use the same type of restriction enzyme to cut DNA for target gene and plasmid
 Use DNA ligase to join the gene fragment with the cut plasmid to produce recombinant
plasmid
 Use recombinant plasmid to introduce gene for CFTP in bacterial host cell
 Recombinant plasmid will replicate in the host cell
 Screening for transformed host cell
 Cloning/ Amplification to increase output
 Insert recombinant plasmid into liposome (a lipid that passes through the plasma
membrane easily)
 Spray liposome into the nose
 Liposomes enter the lung tissue
 Normal genes are expressed and effect may last for few weeks. Epithelial cell will shed
off
Severe combined immunodeficiency disorder, SCID

- SCID is caused by adenosine deaminase (ADA) deficiency in infants
- The gene for ADA in SCID infants is not functioning
- ADA is used by white blood cells to produce antibodies
- Extract normal ADA gene and vector. Use the same type of restriction enzyme to cut both
- The normal gene for ADA joined to the vector by DNA ligase and ATP energy
- Vector containing ADA gene is introduced into a retrovirus that had been inactivated to become
non pathogenic
- Produce recombinant virus
- ADA gene incorporated into the DNA of the retrovirus
- A small amount of bone marrow is isolated from the SCID infant and cultured in the lab
(medium containing nutrient and carbon dioxide)
- The bone marrow cells are infected with the retrovirus that contains ADA genes
- The retrovirus integrates the normal ADA gene into the bone marrow cells
- Bone marrow cells with the normal ADA gene are reintroduced into the SCID infant
- Normal ADA gene will be transcribed, translated and produce ADA
4) Forensic science- DNA fingerprinting

 Definition: Technique used to identify individual from the sample of DNA using non-coding
regions of DNA
 95% of the DNA do not code for any amino acid
 Unknown sample is compared against the known sample
 By comparing the non-coding parts of DNA
 The non-coding parts of DNA is repetitive. It is known as variable number tandem repeat
(VNTR)
 Polymerase chain reaction (PCR) is used to amplify the small sample
 Stages in DNA fingerprinting:
 Collect the DNA sample. If the sample is small, amplify it using PCR
 Extract the DNA from the sample
 Use restriction enzyme/endonuclease to cut the DNA into fragments (sticky end/blunt end)
 Fragments are called as restriction fragment length polymorphism, RFLP
 Separate the DNA fragment using electrophoresis (using agarose gel, electrical field and
buffer solution of pH 7)
 Add alkaline to split the double strand DNA into single stands
 Perform Southern blotting where the single strand is transferred from the gel to a
nitrocellulose membrane/ nylon membrane
 Probe with radioactive marker (process known as hybridisation) to identify the target gene
on single strand DNA with complementary base
 Autoradiography; place an x-ray film over the
nylon membrane with phosphate substrate
 Alkaline phosphatase removes the phosphate,
cause substrate to fluoresce and fogging the x-ray
film
 Develop the x-ray film and the fogging parts will
appear as dark band
 Compare the repetitive non-coding region with
another sample’s result
 Extra notes:
- Probe attach to specific base sequence in DNA fragments, process called as hybridisation
- Complementary base pairing during hybridisation occurs between probes and DNA of
sample
- During Southern blotting, DNA deposited on nylon membrane by capillarity action
- DNA fixed with the membrane by being exposed to short wavelength of light
 DNA fingerprinting is used to convict criminal suspects, establish paternity, determine the
identity of a dead body and to identify defective gene by genetic screening
Application of Biotechnology: 4) Public Health
1) Genetic screening
 Definition: Procedure to examine genetic disease
 When?
- Foetus- Prenatal diagnosis
- Carrier- Carrier diagnosis
- Future genetic disease- Predictive diagnosis
 Screening technique:
i) Amniocentesis
- Insert a fine sterile needle into the uterus. Use ultrasound to monitor the position of the
foetus and needle
- Withdraw sample of amniotic fluid (living cell e.g. skin cell of foetus)
- Sample is centrifuged to separate cells and supernatant fluid. Cells are cultured
- Analyse karyotype for abnormality
- DNA analysis/ biochemical analysis is done to detect metabolic disorder
- When? 4th month of pregnancy/15-16 weeks of pregnancy
ii) Chorionic villus sampling
- Insert needle through abdomen or insert catheter (flexible tube) through vagina and cervix
- Along with ultrasound scanner
- Get cells from chorionic villus
- Analyse the karyogram
- When? 2-3 months of pregnancy/8-12 weeks of pregnancy
- Has higher chance causing miscarriage than amniocentesis
iii) Pre-implantation diagnosis
- In-vitro fertilization/test tube baby
- Embryo at 8 cells stage, Take sample of cell
- Carry out on the embryo before it implants in the uterus
2) Diagnostic kit
 Definition: Electronic monitoring device uses biological material like cell, enzyme or
antibody to detect or measure chemical compound
 Biological material + Substrate
- Change in heat, light, pH, mass, flow of electron, new chemical
- Transducer converts change into electrical signal
- Amplify electrical signal to give digital display
 Example: Diagnostic kit to detect blood glucose
- Glucose oxidase in immobilized form + glucose generate electrons
- Enzyme oxidizes glucose in blood to release electrons
- Electrons are collected and converted into electrical current
- Amount of glucose is directly proportional to the current
- Digital display to get the result in 20 seconds
 Advantages of diagnostic kit:
- Low risk of error in diagnosis
- Lower cost
- Less time
- Less expertise, need no hospital laboratories
- Less chance of sample being mishandled, lost or contaminated
3) Oil-decomposing bacteria
 Source of oil pollution:
- Collision of oil tanker
- Seepage of offshore installation
- Flashing of tanker holds (lover cavity part of ship)
 Effect of oil pollution:
- Kill seaweeds, marine invertebrates (mussels, cockles, crustacean, and fishes)
- To bird, it will mat the feathers impair flight, cause swimming difficulty and heat insulation
is lost cause bird to be under hypothermia, lower body temperature
- When taken into stomach during preening, it causes gut irritation and poison the bird
- Lower the economic value of fish as flesh is tainted with oil
 Oil decomposing bacteria:

- Pseudomonas can break down 4 main groups of hydrocarbons in oil
- Relevant genes occur on plasmid Pseudomonas
- But no single strand contains all four plasmids
- Now, all 4 are introduced into single “super bug”
- This bacteria type is strayed onto oil-polluted surfaces
- Bacteria only able to work at oil-water interface as they need oxygen
- So, they can clean the oil better on thin surfaces rather than thick
- They function slowly at low temperature, thus, might be unsuitable for use in cold climates
- To clean oil spill, genetically engineered Pseudomonas bacteria are used
Advantages of using human insulin:
- Identical to human insulin in body, Less side effect
- Cheaper to produce
- Rapid response, Pure and uncontaminated
- Not dependent on livestock
Gene therapy
- Ex vivo (outside the body) e.g. to treat severe combined immunodeficiency disorder, SCID
- In vivo (inside the body) e.g. to treat cystic fibrosis or viral delivery system

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CHAPTER 14: TAXONOMY AND BIODIVERSITY

Nomenclature Naming of organism

Kingdom Plantae: Phylum Bryophyta

Differences between Phylum Bryophyta and Phylum Filicinophyta

Phylum Bryophyta Differences Phylum Filicinophyta

Kingdom Plantae: Phylum Coniferophyta

Monocotyledoneae Differences Dicotyledoneae

Comparison between Phylum Coniferophyta and Phylum Angiospermophyta

Kingdom Animalia: Phylum Platyhelminthes

Kingdom Animalia: Phylum Chordata Classes Example

CHAPTER 15: ECOLOGY

 Ecological niche = Sum of usage of biotic and abiotic resources

 The processes that release carbon dioxide to atmosphere:

 Some exists as sulphur dioxide in air

Littoral Limnetic Profundal

Animal -Frogs, fishes, - Larger fishes Decomposer

Exponential curve, J growth curve Sigmoid curve, S growth curve

Equilibrium or Stationary phase:

 Natality = The birth rate of a population

 Definition: Probability of individual can survive to certain age

Type I Type II Type III

K-strategies and r-strategies

Carrying Capacity: Density-independent Factor

 Population distribution is the pattern of spacing/ dispersion relative to each other

Random distribution Clumped/Aggregated Uniform distribution

CHAPTER 16: SELECTION AND SPECIATION

Continuous variation Discontinuous variation

 The similarities between continuous and

Natural selection Artificial selection

Selection: Natural Selection

Graph detained Example

(3) Directional selection - Long-neck giraffe

(4) Sexual selection

Selection: Artificial Selection

 Importance of human sperm bank:

- Population of same species live in a same geographical area

Formation of new species

 A new species can be formed by 4 methods

 Definition: Species are isolated by reproductive barriers to prevent successful reproduction

Prezygotic barrier Explanation Example

Postzygotic barrier Explanation

Formation of new species: Genetic drift

 Definition: A random change in allele frequency by chance occurrence/event in a small

Formation of new species: Adaptive radiation

Total alleles = 10 000 x 2 = 20 000

 Agent of change: Selection

Meselson and Stahl Experiment

- Genetic information carried by triplet code = Genetic information carried by anticodon

Differences between DNA replication and Transcription

DNA replication Transcription (Protein synthesis)

Differences of Transcription between Prokaryotes and Eukaryotes

mRNA, tRNA and rRNA

Structure of tRNA Structure of a ribosome

Protein Synthesis: Translation

- Protein synthesis is accelerated by formation of polysomes

Regulation of Gene expression

 An operon consists of promoter, operator and structural genes

Mechanism of Lac operon:

 Definition: Inversion of nucleotide base pair in a gene

Mutation: Chromosomal mutation: Deletion

Types of chromosomal mutation involving changes in number

Types Example Explanation