Biology

What is life?​ - What defines a living being? There are 7 properties of life:
1. Homeostasis​ ​-​ ​the ability to maintain a relatively stable internal state that persists
despite changes in the world outside​ ​for example: The Skin helps in maintenance of
body Temperature.
2. Reproduction -
Sexual - happenes when two partners from opposite sexes share Gametes
(Ova \ sperm)
Asexual - When an individual duplicates in order to produce offsprings identical to the
parent.
3. Composed of Cell / Cells​ - Have an order.
4. Processing / Emission of energ​y =​ ​Metabolism​ ​- A butterfly obtaining fuel in the form
of Nectar from a flower
5. Evolutionary adaptation ​= Through Natural selection, species can differ from their
ancestors due to need for adaptation for their environment.
-Behavioural
-Physiological
-Structural
6. Response to environment = ​Organisms must respond to outside stimuli such as
temperature fluctuations.
7. The ability to grow and develop = ​The process of change resulting from genetic
information as the embryo ages. Unicellular usually only grow in size while
Multicellular undergo complex changes called development. Resulting from cell
division and selection, the Organism experiences changes in size and shape.
This process is slow in some organisms, while others express it in shorter periods.

Key Concepts:​ Emergent Properties - Properties which are​ present in a system,​ ​but lack in
an individual. Only become apparent after all fundamental structures are added.

System Biology - Used to ​study life at all levels​ through the process of
Reduction.

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Theme 1.1: The different Biological Organisations

1. The Biosphere
Consists of all life on earth:​ lands​, ​water, t​ ​he Atmosphere

2. The Ecosystem
Different Regions where all living things exist​, be it ​Forests​ / ​Deserts​ / Coral reefs. Organs
interact with other living or ​nonliving components​ of the environment such as ​soil​, ​water​,
atmospheric​ ​gases​, and ​light​.

3. Communities
All living organisms in a particular​ Ecosystem ​are called ​communities. ​They are the
different groups of animals, plants, Fungi, and even Microorganisms which inhabited that
specific Ecosystem.

4. Population
If we know a community is the identification of all living organisms in a certain area,
Population defines the individual groups which are being located.
For example: Population of Puffins in South of Iceland \ Squirrels in London

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 5. Organism
Specific individual composed of interdependent parts. Can be
composed of:
Producers
Consumers
Decomposers
They can live in soils, in the oceans, forests, some exist in the
human body such as Bacteria in the Human gut.

6. Organs​ and​ Organ System

An​ ​organ​ is an element, usually composed of Tissues, which serves an essential role for the
organism’s function. Each Organ has a different purpose. For example, the heart is an organ
which pumps blood.
​ Organ System​ is a group of Organs which work
simultaneously in order to perform one or more
functions.

*Some forms are formed by single cells, such as Bacteria

The Nervous System ​is composed of:

The Central Nervous System​ - ​The Brain​, ​The spinal Cord​ and
the ​Nerves
The Peripheral Nervous System​ - ​Neurons​, ​Ganglia​ and
Nerves​ which connect to one another as well as to the Central
Nervous System.

7. Tissues
Group of cells which work cooperatively for a specific role. A group of Tissues form ​Organs
There are Four types of functional Tissues:
Muscle Tissues
Connective Tissues
Epithelial Tissues
Nervous Tissues

In plants, there is a tissue located in the leaves which is responsible for ​Photosynthesis​.
The plants contain a layer (Epidermis) which allows CO2 to enter the ​cell​, where the gas,
with Sunlight, is used for transformation of Sugar.

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 8. Cell
Life’s fundamental unit of Structure and Function. Often called “​Building Blocks of Life”.
Some organisms are Single cells, which means they are a complete organism and able to
produce on their own, provide energy, metabolise and synthesize independently.
Multicellular Cells are Specialised Cells which work with other Specialised Cells to
perform differentiation, ​they receive nutrients from and expel wastes into their surroundings,
while adheres to and cooperates with other cells

Example:​ Blood cells which provide Oxygen to the rest of the body.

9. Organelle
A part / Component present in the cell. Usually is enclosed by a Membrane, and serves one
or multiple roles in the cell. ​Present only in Eukaryotic Cells.

Example:​ ​mitochondria and chloroplasts, which are responsible for obtaining Energy
by converting outside materials into simpler units and transferring it.

10. Molecule
Usually formed by chemical Structure made from one or more atoms, which is considered
the simplest unit.
Every combination of atoms is considered a Molecule, while a compound is a molecule
made from atoms comprised of different elements. A Compound is a Molecule, but not every
Molecule is a Compound.

Elements cannot be broken down into different chemical substances. (For example, Gold),
the same in terms of Properties.
The most important elements of life: ​Oxygen​, ​Carbon​, ​Hydrogen​, ​Nitrogen​.

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Energy

Life needs ​energy, ​the sun is the main source of Energy for living beings.

The Transfer and Transmission of matter is a​ cycle process​.

: The sun provides energy which is converted as chemical energy in Plants, then into Sugar through
Photosynthesis. (Producers)
This sugar is passed to organisms feeding from the plant (Consumers).
The same chemical will be returned and broken down by decomposers such as Bacteria and Fungi into their
simple molecules, which in turn will be absorbed by the plant.

Energy is used in order to carry out activities, without energy source, the body will be
depleted of fuel necessary for daily tasks. For example, during muscle contraction energy is
being released in the form of Heat, therefore energy is required.

Interaction
In the Ecosystem - different organisms have different interactions between each other

Mutually Beneficial​ - When two organisms benefit

Example: A bird on top of an Hippopotamus which feeds on insects
Semi-Beneficia​l - When one organism is harmed while other benefits
Example: A lion hunting a Zebra for food
Non-Beneficial ​- When both organisms are harmed
Example: Two Plants competing for energy source from the soil when it is short on supply.

This interaction helps regulate the function of the Ecosystem as a whole. But it can also
affect it by using the resources available such as water and minerals and convert it to
different components like Soil and Oxygen.

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In a Molecule - Interaction is crucial for Homeostasis, it regulates and ensures that the body
can function properly.
​ For example: Glucose levels increase in the Bloodstream after a meal
Insulin is released from the Pancrea
Once it reaches a cell, more Glucose enters the cells through Diffusion and is formed to
Glycogene.

This process is called: Feedback Regulation.

There can be ​Positive Feedback​ or N
​ egative Feedback.
Positive: ​When a product speeds its own production
Negative: ​When production of a certain element is slowed due to its accumulation.

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Evolution
Can be classified into three main Domains: ​Bacteria​,​ ​Archaea​, ​Eukarya

Bacteria ​are grouped in Archaea​ ​are also Eukarya​ ​are all the
different kingdoms based grouped in different organisms which contain
on their shape and kingdoms, unlike an Eukaryotic Cell (Have
function. Bacteria, they are found a cell membrane)
in the earth’s most Distinguishing: Their
extreme environment. nutrition supply​.

The Eukarya include: Fungi, Plants, Protists (Unicellular Eukaryotes and simpler
Multicellular), and Multicellular organisms.

There is a certain Unity and Diversity that result from Evolution. All organisms are composed
from molecules which in turn form Organelle that form cells. But each cell has a different set
of structures which must be performed.

Evolution is also a factor for environment adaptation.

Charles Darwin and the Theory of Evolution

In his book: ​On the Origin of Species by Means of Natural Selection, D ​ arwin explains that
over time, species must adapt to their environment. As a result, a process of modification
called Neutral Selection occurs.
In each new generation, Organisms will have slightly different traits than their predecessors.

In nature, there are three ways in which it can be seen: Populations which reproduce use
more from the environment’s resources, consequently competition for survival.

Species must compete for mates in order to pass on their genes to offspring, sexual
selection.

Heritage - Many species vary from each other in traits.

Conclusion = Individual that has the most suited heritage

for the environment will survive and reproduce.

How does it happen?

During the coding process of the DNA, a mutation can

occur as a result of error during replication or repair, or
when exposed to chemical damage like radiation.

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These Mutations are then passed to daughter cells through cell division, as a result, the
genes are displayed in forms of physical traits.

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 Chapter 2 - Chemicals and Matter

All life is formed from Matter. They use space and contain a certain amount of mass.

Matter is made from ​Elements ​= Pure substances that cannot be broken down.
These elements ​create bonds​ (Molecular or Ionic)​ with elements of their kind /
different elements in order to form Compounds.

Every organism must acquire elements for his / her survival, but each group has
different amounts of elements needed. For example: Humans must obtain 25
elements, while plants only use 17.

Oxygen, Nitrogen, Carbon and Hydrogen make up most of living matter on earth.
(96%), while other elements, such as Phosphorus, Calcium, Sulfur, Potassium are
4%.
Certain Elements, called: ​Trace Elements ​are required only in small quantities by
the Organism / Only for certain groups of organisms.

Iodine is absorbed mainly by Vertebrate organisms and has a major role in production of a hormone responsible
for function of the Thyroid Glands. Lack of this elements results in abnormalities of the Thyroid Glands.

Elements can also be​ dangerous when exposed to certain Organisms in certain
amounts​.
Example: Arsenic which is highly toxic, found in minerals and groundwaters.
Can lead to a variety of illnesses, and even death.

Some species procure tolerance to this Toxicity, for example plant species which have
through evolution and neutral selection obtained tolerance to soil made with Serpentine
mineral, notably very toxic to most plants.

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 Element’s Properties

An Element is made from Atoms

Atoms are made from hundreds of Subatomic Particles

The most well known: Protons, Electrons, Neutrons

Protons - Have a Positive charge, packed in the Nucleus of an atom

Neutrons - Have a net charge of 0, packed with Protons in the Nucleus
Electrons - Have a Negative charge, orbit around the Nucleus as a result of attraction from
the opposite electric charge between Electrons and Protons.

Neutrons and Protons have a relative mass of 1.7 * 10-24.

Atomic number and Atomic Mass

Atomic Number - Represents the number of Protons.

Each element has a specific number of protons which define its property.
*With stable particles, Number of Protons = Number of Electrons

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Mass Number - Defines the number of Protons + Neutrons in the Nuclei.
Each element has same number of Protons, but can vary in number of Neutrons
(These are called Isotopes)

Atomic Mass = The average mass an Element has, calculated by abbreviating the Isotopes.
Atomic mass = [Atomic Number * %] + [Atomic Number * %].

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 Energy Levels
Energy = The capacity to cause change

Potential Energy = How much energy is obtained in terms of mass due to the element's
structure and position.

Electrons exist around the Nucleus in fixed places called Subshells, they can move between
subshells, or even to other atom’s Subshells, but only when the Potential energy required or
lost during the process equals the Potential energy level between the subshell it has been in
and the new subshell.

When an electron moves further from the Nucleus - Energy is absorbed.

When an Electron moves closer to the Nucleus - Energy is emissioned, mainly in form of
heat.

That is a result of the Energy Potential the Subshells obtain. The higher and further from the
Nucleus a subshell is, the higher and stronger is the Potential Energy.

There is a tendency for Energy to move from highest form to lowest form of Potential due to
the fact that it expands during the process.
In order to restore lost energy, energy must be obtained

This is called the Aufbau Principle.

Electron Distribution
Electrons, similar to energy, prefer to stay in the lowest Potential energy available. In the
periodic Table, this distribution is seen when moving from Higher to lower rows.
Hence, Hydrogen and Helium, which contain only one Valence shell, are located in the first
row of the Periodic Table.

Atoms with identical numbers of valence Electrons in their Valence shell exhibit similar
behaviour. For example, Fluorine and Chlorine, when come in contact with Sodium, form
Sodium Fluoride which prevents tooth decay and Table salt (NaCl).

According to the Octet rule: In order for an atom to become inert, in other words, be
considered complete, it must obtain 8 electrons in its Valence Shell. All atoms strive to be
stable.

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 Orbital Shells
In contrast to the fact that it may be unknown the exact location of an Electron relative to the
Nucleus, there is a model that shows the highest probable region where the Electron is
located.

These are called Atomic Orbitals. There are 4 different orbitals in them electrons move,

The S Orbital (1s) - A Spherical Orbital, closest to Nucleus, can contain up to 2 Electrons.

The P Orbital (2p) - Dumbbell shaped, can contain up to 6 Electrons. The Second shell
includes another 1s Orbital + 3p Orbitals.

The D Orbital (3d) - Usually is in the third Orbital, can contain up to 10 Electrons, it is clover
shaped.

The F Orbital (4f) - Can contain up to 14 Electrons.

Electrons which are in the same Orbital have similar Potential Energy, but move in different volumes of
space​.

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 Electron Bonding
How do Chemicals form?
How are Components made?
Why do atoms combine?

According to the Octet rule: In order to be considered stable, ​every atom must have a full
Valence shell​. To Clarify, 8 Valence electrons must be located in the Valence Shell.
Atoms with an incomplete Valence shell form bonds with other Atoms (whether metallic,
ionic, non metallic) through Ionic bonding, Covalent Bonding or Metal.
Usually Electron sharing is depicted​ through the Lewis dot Structure ​or S
​ tructural
Formula​.

Covalent Bonds​ - Interatomic linkage from sharing of two or more electrons between two
atoms in order to create a Molecule.

​ single Covalent bond​ - One pair of Electrons is shared in an

overlapped S Orbital.
​ Double / Triple Covalent bond
​ Sigma Bond​ - Strongest type of Covalent Bond. Can occur in any type
of Covalent bond, only if there is a direct overlap between two atom’s Nuclei.

Usually, the type of bond is affected by the number of Electrons needed for a complete
Valence Shell.

Two types of Covalent bonds

Polar Covalent = Share of two Electrons with a slight net charge between the atoms.
Occurs with Molecular and Ionic Atoms. It is a result of Electronegativity, one element has
higher Electronegativity than the other, this leads to the Electrons to be pulled slightly closer
to the Nucleus of the higher Electronegative element and spend more time around it.
Henceforth, that same atom gains a slight negative charge and its companion has a slight
positive charge.
Consequently, opposite charges attract, and a polar bond is formed.
Furthermore, a weak bond between other slightly polar components is also created.

Example: H2O (Water Molecule)

Nonpolar Covalent = Equal share of Electrons between two atoms with the same Electron
Affinity. They are from the same Elements.
The stronger the electron Affinity = Stronger attraction [Usually with Gases and diatomics].

Example: H2 (Hydrogen Gas)

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Ionic Bonding = Interatomic linkage between two atoms as a result of transfer of Valence
Electrons due to different Electronegativity each atom possesses.
Usually occurs between Metals and Nonmetals, and the result is Ionic Compound or Salt.

​ [Before an Ionic Bonding starts, the Atoms are not charged, Protons = Electrons]

When two such atoms are exposed to each other, the Electrons of the lower
Electronegative element will be pulled by the Electronegativity of the other element. This
results in two complete Valence shells, but due to the difference in number of Electrons, the
element which has lost Electrons becomes a Cation while the element which gains electrons
becomes an Anion.

They obtain Positive and Negative Charge respectively, and because opposite charges
attract, an Ionic bond is formed between the two atoms.

When many atoms form an Ionic compound, an organised three dimensional Lattice
Structure is built.

*When there is an unequal number of Cation and Anions, there is a multiplication of the missing element.
For example: in order to have MgCl2, there must be 2 Cl atoms in order to satisfy the Octet rule. Because
Cl must gain 1 Valence Electron while Mg must lose 2 Electrons.

Environmental Effects: When exposed to dry locations, the bonds are stronger than when
exposed to liquid. This is due to the fact that in Liquid molecules, such as water,the positive
side will connect to an Anion and the Negative side will connect with a Cation of each Ion.

Weak Bonding
There are Three types of Weak Bonds -

Hydrogen Bond
Considered the Strongest. When paired with a higher Electronegative atom in an Ionic bond,
it gains a slight positive charge that allows it to interact with other electronegative elements.
Example: NH3

Van der Waals

Interaction between two molecules in Gases, Liquid or solid states. Or between one atoms in
a larger molecule. Considered a weaker bond than of a Covalent, but when formed
simultaneously the bond strengthens.
Maintain a lower melting point and softer. Occurs only when an overlap of two atomic
orbitals is present, and when the atoms are very close to each other.
As a result, the three dimensional structure of a molecule is reinforced.
Example: ​RCH(NH2)COOH (Protein)

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 Dipole

Can result from three resources:

- Permanent electric Dipoles:​ when one atom is slightly positive and the other
slightly negative due to change in electric field. The axis tends to rotate with the direction of
the Electric field, [undergoes a Torque]. The stronger the electric field the greater the
Torque.

- Permanent Dipole affecting the nearby Polar / Nonpolar molecules.

Can result in more Polarization due to the electric charge the Dipole maintains. Which pulls
the nearby molecules closer. An interaction between the permanent Dipole and neighbouring
molecules occurs.

- When an electric force between non Dipole molecules is present. Most if not all
covalent bonds are not coinciding, this means - the share between electrons is not evenly
distributed. This fluctuation causes constant change between the electric charge of the
shared atoms, which leads to a bond.

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 Molecular Shape / Function

Molecular shape is determined by Orbital’s Position and is what allows the bond between
molecules and their surroundings.
It shows a match between structure and function.

Example: when a bond between morphine and the brain is created, it is a result of
complementary shape of the Morphine molecule which binds to a specific receptor for
Endorphins. The Morphine mimics the Endorphins structure [molecular mimic], hence
connection.

A Tetrahedron shape: In a covalent bond, there is an overlap between electron shells.

This affects the orbitals in a way that four new identical hybrid Orbitals are formed.

Example: CH4 [Mathene]

Chemical reaction

A result of change in chemical composition due to interaction between atoms.

In a reaction, atoms cannot be destroyed or created, only distributed.

An example of a chemical reaction happens during Photosynthesis.

6 CO2 + 6 H2O - C6H12O6 + 6 O2

The Carbon Dioxide and water molecules are converted, with an input energy from the
sunlight, in order to form Oxygen and Glucose.
The amount of matter which has been absorbed = the amount that is being released.

Reactions can also be reversible - Ammonia is formed from 3 H2 + N2, but it can
decompose into its original components.

When a reaction between reactants with a resulting product = reaction between products
resulting in reactants in terms of rate and relative concentration, the reaction undergoes
Chemical equilibrium.
​The concentration has been stabilised in a certain percentage, thus a reaction still occurs,
but the amount of Products and Reactants being produced is in the same ratio.

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