BIODIVERSITY AND EVOLUTION

Population is a group of living things within a certain area that are all the
same species.
Biodiversity refers to the variety of life in the area
Limiting factors are anything that limits the size of the population like certain
environmental conditions.

Formula of Index of
Diversity:

Formula of Density:

 Endangered means when the population becomes so low that only a

few remain.
 Threatened means when a particular species that declines so fast that
it becomes endangered.
 Extinct means the disappearance of species when the last of its
members are dead.

Causes of extinction:

Deforestation is one of the country’s environmental problems in the rapid

rate at which trees are cut down.

Kaingin farming Conversion of agricultural lands to housing project

Illegal logging Forest fires Typhoons

Water pollution happens when the concentration of organic nutrients that

come from domestic garbage are thrown in bodies of water, increases rapidly
one of the effects of water pollution. It is supposed to be a slow process, but
man activities fasten it up.

Air Pollution happens when pollutants enter the air gases, liquids or soil. Cars
burn fuel and produce harmful gases like carbon dioxide, nitrogen oxides and
hydrocarbons.

Destruction of Coastal resources, coral reefs, and coastal mangrove forests in

the Philippines serves as the breeding grounds and nourishes fishes. But due
to man’s activities, coastal areas are getting destroyed through the years.

Deforestation, agricultural activities, and mining activities

Dynamite fishing, and muro-ami

Coastal areas conversion to beach resorts, or residential areas

Overharvesting

Acid Precipitation is commonly known as acid rain. Rain is normally acidic,

because carbon dioxide is normally present, other pollutants, mostly sulphur
and nitrogen oxides, make rainwater even more acidic, with a plt of 5.6 or
lower. Emissions from factories and from exhausts of motor vehicles are
some examples of pollutants. Acid rain can be harmful on living things, it
causes yellowing of leaves and causes leaves to fall.

ANATOMY OF A LEAF
A leaf is a flattened, lateral (meaning growing from the side) outgrowth from
the stem of a vascular plant in most cases, leaves are green and contain
chlorophyll which makes them the primary site of photosynthesis. Beyond
photosynthesis, leaves also play other roles in the plants life, such as
transpiration (releasing water vapour), gas exchange, and protection from
sunlight and food for the herbivores.

Parts:

A cuticle is waxy layer of covering the upper epidermis of the leaf, made of a
substance called cutin. The cuticle acts a waterproof barrier, reducing water
loss from the leaf’s surface.

Mesophyll is the tissue between the upper and lower epidermis of the leaf,
responsible for photosynthesis. It contains chloroplasts for capturing sunlight
and carrying out photosynthesis. It’s further divided into two types of cells.
Which are:

 Palisade cells are tightly packed cells that contain a high number of
chloroplasts. They specialize in photosynthesis due to their abundance
of chloroplasts for capturing sunlight.
 Spongy mesophylls are irregularly shaped cells in the lower region of
the mesophyll, containing air spaces between them which allows for
gas exchange.

Chloroplasts are specialized organelles within the plant cells containing

chlorophyll, the green pigment responsible for capturing sunlight during
photosynthesis. Chloroplasts convert sunlight energy into chemical energy
(glucose) through photosynthesis.

Guard Cells are a pair of specialized cells surrounding each stomata,

responsible for opening and closing the pore. By changing their shape
(inflating or deflating), guar cells control the size of the stomata opening,
regulating gas exchange and water loss.

Stomata are microscopic pores on the leaf surface, allows for gas exchange
(carbon dioxide intake and oxygen release). Controlled by guard cells,
stomata open and close to regulate gas and water loss.

Lower Epidermis is the single layer of cells covering the underside of the leaf.
Similar to the upper epidermis, it provides protection and contains more
stomata for gas exchange.

Vascular Bundles are networks of tubes within the leaf, transporting water,
nutrients, and sugar throughout the plant.

Xylem vessels transport water and minerals.

Phloem vessels transports sugar

PHOTOSYNTHESIS

Photosynthesis is a chemical process by which plants create carbohydrates

using light energy. Photosynthesis is also responsible for balancing oxygen
and carbon dioxide levels in the atmosphere. Plants absob carbon dioxide
from the air and release oxygen during the process of photosynthesis. In the
process of photosynthesis, the absorbed light energy converts carbon dioxide
and water into glucose, with oxygen released as a by-product.
Process:

1. Water is absorbed by the roots and passes through vessels in the stem
on its way to the leaves.
2. Sunlight is absorbed by a green chemical called chlorophyll. Sun’s
energy is used to split water molecules into hydrogen and oxygen.
3. Carbon dioxide from the air passes through small pores in the leaves.
These pores are stomata.
4. Hydrogen and carbon dioxide are used to form glucose or food for
plants.

Photosynthesis takes place primarily in the leaves of plants, specifically

within the specialized cell structures called chloroplasts. Chloroplasts are
organelles that contain chlorophyll, the green pigment that captures light
energy from the sun. Chloroplasts are most abundant in the mesophyll cells
of leaves, where they are well positioned to receive light.

CHLOROPHYL
Outer Membrane is a semi-porous membrane and is permeable to small
molecules and ions which diffuses easily. The other membrane is not
permeable to larger proteins.

Stroma is the colourless fluid surrounding the grana within the chloroplast.
The light-independent reactions of photosynthesis take place within the
stroma.

The inner membrane forms a border to the stroma. It regulates the passage
of materials in and out of the chloroplast.

Thylakoids are tiny compartments that contain the chlorophyll. Their role is
to help absorb sunlight for photosynthesis to occur during the light-
dependent reaction.

Granum or grana (plural) the site of light reaction photosynthesis. Increases

the surface area of the thylakoid membranes thereby elevating the sugar
production of plants through the process of photosynthesis.
Lamella act as the skeleton of the chloroplast. They increase the efficiency of
photosynthesis by keeping grana at a distance so that they do not clutter
together.

MITOCHONDRIA

Matrix is the outermost layer of the mitochondrion, smooth and permeable to

small molecules and ions. Serves as the protective barrier and regulates the
entry and exit of ions and molecules between the cytoplasm and
intermembrane space.

Intermembrane Space is the space between the outer and inner membranes.
Plays a crucial role in the electron transport chain by allowing protons (H +
ions) to accumulate and create a gradient, which is essential for ATP
production.

Inner Membrane are highly folded into structures called cristae to increase
the surface area. Responsible for the electron transport chain and ATP
production. The increased surface area due to cristae enhances the
mitochondrion’s ability to produce ATP.

Cristae are the folded extensions of the inner membrane. Increase the inner
membranes surface area, allowing for a greater number of electron transport
chain complexes and ATP synthase molecules tp be present, which enhances
ATP production efficiency.

Matrix is the innermost compartment of the mitochondrion, enclosed by the

inner membrane. The matrix is the site of the Krebs cycle, where acetyl-CoA
is oxidized to produce high-energy electrons, which are then used in the
electron transport chain.

ATP Synthase is an enzyme complex embedded in the inner membrane. Uses

the proton gradient created by the electron transport chain to produce ATP
from ADP and inorganic phosphate. This process is known as chemiosmosis.

1. Glycolysis is the first stage of cellular respiration that occurs in the

cytoplasm, where glucose is broken down into two molecules of
 pyruvate, yielding ATP and NADH. Glycolysis is the process in which
glucose is broken down to produce energy. It produces two molecules
of pyruvate, ATP, NADH and water. The process takes place in the
cytoplasm of a cell and does not require oxygen. It occurs in both
aerobic and anaerobic organisms.
2. Krebs Cycle (Citric Acid Cycle) is the second stage, occurring in the
mitochondrial matrix, where acetyl-CoA is oxidized to produce NADH,
FADH2 and CO2.
3. Electron Transport Chain (ETC) is a series of protein complexes in the
inner mitochondrial membrane that transfer electron, creating a proton
gradient that drive ATP production.

Take note:

 ATP (Adenosine triphosphate) is the primary energy carried in

cells, produced in large amounts during cellular respiration.
 NAD+ or NADH (Nicotinamide Adenine Dinucleotide) is an electron
carrier molecule. NAD+ accepts electrons during glycolysis and
Krebs cycle to form NADH which then donates electrons to ETC.
 FAD or FADH2 is another electron carrier similar to NAD +, FAD is
reduced to FADH2 in the Krebs cycle and also donates electrons
to the ETC.
 Acetyl-CoA is a molecule that enters the Krebs cycle, derived
from pyruvate, fatty acids, or amino acids, providing fuel for the
cycle.
 Oxidative Phosphorylation is the process in which ATP is
produced using energy derived from the redox reaction in the
electron transport chain.
 Chemiosmosis is the movement of protons (H + ions) across the
inner mitochondrial membrane, powering ATP synthase to
produce ATP.
  Pyruvate is the end product of glycolysis which is converted to
acetyl-CoA before entering the Krebs cycle.
 The Proton Gradient is the difference in proton concentration
across the inner mitochondrial membrane, which drives ATP
synthase during chemiosmosis.

HISTORY OF ATOM

Solid Sphere Model – John Dalton – 1803

His theory stated that atoms are indivisible, those of

a given element are identical, and compounds are
combinations of different types of atom

Plum Pudding Model – J.J. Thompson – 1904

Thomson discovered electrons which he called

‘corpuscles’ in atoms in 1897, for which he won a
Nobel Prize. He subsequently produces the ‘plum
pudding’ model of the atom. It shows the atom as
composed of electrons scattered throughout a
spherical cloud of positive charge.

Nuclear Model – Ernest Rutherford – 1911

Rutherford fired positively charged alpha particles

at a thin sheet of gold foil. Most passed through
with little deflection, but some deflected at large angles. This was only
possible if the atom was mostly empty space, with the positive charge
concentrated in the centre: the nucleus.

Planetary Model – Niels Bohr – 1913

Bohr modified Rutherford’s model of the atom by

stating that electrons moved around the nucleus
in orbits of fixed sized and energies. Electron
energy in this model was quantised; electrons
could not occupy values of energy between the
fixed energy levels.

Quantum Model – Erwin Schrodinger – 1926

Schrodinger stated that electrons do not move in

set paths around the nucleus but in waves. It is
impossible to know the exact location of electron;
instead, we have; ‘clouds of probability’ called
orbitals, in which we are more likely to find an
electron.

OCTET RULE

The octet rule dictates that atoms are most stable when their valence shells
are filled with eight electron. It is based on the observation that the atoms of
the main group elements have a tendency to participate in chemical bonding
in such a way that each atom of the resulting molecule has eight electron in
the valence shell. The octet rule is only applicable to the main group of
elements.
The molecules of the halogens, oxygen, nitrogen, and carbon are known to
obey the octet rule. In general, the elements that obey this rule include s-
block elements and the p-block elements (except hydrogen, helium and
lithium).

CHEMICAL BONDING

Remember that every atom has a certain number of electron, which orbit the
nucleus in the electron cloud. These electrons orbit in different energy levels,
which are known as electron shells. The first shell can house two electrons,
and it must be full before any electron can move to the next shells, which
can house eight electrons.

Valence Electron are the electron in the outermost shell of an atom.

In chemical reactions, the electron in the outermost shell are the most
important. We can represent elements using Lewis dot diagrams, which
visually emphasize those electron over the others.

When atoms form bonds with other atoms, it is known as chemical bonding.
Atoms will form chemical bonds with each other in order to fill their electron
shells and gain stability.

Some elements have atoms with the ideal number of electron needed by
others. This makes certain pairs of elements more compatible for bonding.
There are two main types of chemical bonds: ionic and covalent.

Ionic bonds are formed when a metal and non-metal react. Metal atoms
become positively charged ions by losing electron. Non-metal atoms become
negatively charged ions by gaining electron. The oppositely charged ions are
very strongly attracted to each other. This is known as an electrostatic
attraction.

 Forming positive ions – metal atoms lose electrons to form positively

charged ions with a full outer shell of electrons.
 Forming negative ions – non-metal atoms gain electrons to form
negatively charged ions with a full outer shell of electrons.

Example:

Sodium Chloride

Chlorine gains an electron from sodium to become

a negative ion. Sodium loses an electron to
become a positive ion. Both ions now have a full
outer shell of electron and the ionic compound
sodium chloride is formed.

Ionic lattice is when an ionic compound is a regular repeating structure of

ions known as a giant ionic lattice. The lattice is composed of repeating
pattern of oppositely charged ions held together by strong electrostatic
attractions.

Conduction, Ionic compounds can conduct electricity when they are either
melted or dissolved in water to form an aqueous solution. In these states, the
ions are free to move from place to place. Ionic compounds cannot conduct
electricity whenc solid as their ions are in fixed positions.

Melting and Boiling points, Ionic compounds consist of oppositely charged

ions held together by strong electrostatic attractions. A lot of energy is
required to overcome these strong attraction, hence the high melting and
boiling points.
Covalent Bonds is formed when two atoms share a pair of electrons. The
electron which contribute towards a covalent bond, are found in the outer
shells of the atoms. Usually each atom contributes on electron, but some
atoms can react make multiple covalent bonds.

Example:

Hydrogen Fluoride

Fluorine has 7 electrons in its outer shell and needs to achieve 8 to have a
full outer shell. Hydrogen has one electron. As this electron is in the first
shell, hydrogen needs to achieve 2 electrons to have a full shell. The simple
covalent molecule of hydrogen fluoride is made by sharing electrons.

Conduction, simple covalent substances cannot conduct electricity. This is

because charged particles and free movement are required for electrical
conduction to occur. Covalent bonds are fixed and the electrons cannot
move.

Melting point, covalent bonds are very strong but there are weak
intermolecular forces between molecules which do not require a lot of
thermal energy yo be overcome. This means that simple covalent substance
have low melting points and are often liquid of gas at room temperature.