Living organisms are composed primarily of few common types of molecules.

To study different processes occurring in living organisms we need to explore these

biological molecules.
Biological molecules are either organic or inorganic.
Inorganic molecules: they were existing even before life on earth like water
and minerals (Ca , Mg , Fe…..)
Organic molecules: they are Molecules that contain carbon and made in cells
of living organisms like: vitamins, carbohydrates, lipids, proteins, ATP, DNA.
Carbon is found in nature in three isotopes: carbon-12, carbon-13, and carbon-14. All
have six protons but their neutrons numbers: 6, 7, and 8 respectively.
 Isotopes are atoms of the same element that have different numbers of
neutrons but the same number of protons and electrons.
 Covalent bond: is a chemical bond that involves the sharing of electron pairs
between atoms.
 Ionic bond: is a type of chemical bond in which valence electrons are lost from
one atom and gained by another.

Water
The water molecule is Polar, meaning it has a positively charged side and a negatively
charged side. Each water molecule is composed of an atom of oxygen with 2 hydrogen
atoms attached at an angle by covalent bond. Oxygen draws the electrons in the
molecule towards itself, giving it self a partial negative charge, while the hydrogen
atoms are partially positive. The water molecule as a whole is not charged, but since

1
the molecule is bent, its unequal charge distribution makes one end positive and the
other end negative.
This makes the water molecule a polar covalent molecule. Water molecules are
attracted to each other by hydrogen bonds

Water is the only compound that exists in the earth's natural environment as a solid,
a liquid and a gas.
The unique properties of water all relate to its polar nature and hydrogen bonding.

Characteristics of water
1- Water has a high specific heat.
Specific heat is that amount of heat required to raise
the temperature of 1gm of a substance by 1 C0.
Benefits: providing a stable environment for marine
organisms, helps our bodies maintain their body
temperature constant.

2
2- Water has high adhesion properties
Adhesion is the clinging of one substance to another, it plays an important role
in plant survival as it helps water molecules flow up from roots of a plant to
the leaves because they stick to xylem tissue.

3- Water exhibits strong cohesion tension

Cohesion is the sticking of particles of the
same substance together. This character also
helps water to move up at all tree from the
roots to the leaves without the expenditure of
energy. Cohesion also results in surface
tension that allows insects to walk on water
without breaking the surface.

5- The solid form of water (ice) is less dense than its liquid form.
Unlike other substances, H2O has maximum density at 4CO, below this degree
the density of water decreases and its
volume increase that is why ice floats on
the top of the water. One of the many
benefits derived from this property is that
in winter , water freezes on top of lakes
first and insulates the layers below from
further cooling , allowing life to prosper in
the water beneath the ice.

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 6-Water has a high heat of vaporization.
This means that a relatively great amount of heat is needed to evaporate
water, which makes water a perfect cooling agent. Due to that, evaporation of
sweat significantly cools the body surface

7-Water is polar solvent

Due to high polarity of water, it

dissolves all polar and ionic substance

Organic molecules
(A)Vitamins
-They are organic molecules, needed in small amounts but very essential for the proper
functioning of an organisms metabolism as they act as coenzymes.
-They are not synthesized in the animal cell and must be obtained through the diet.
-They are not digested but absorbed directly.
-They are divided into:
1- Water soluble vitamins that are not stored in the body and must be taken daily,
ex: B and C vitamins.
2- Fat soluble vitamins that are stored in liver and fat tissue so no need to take
them daily ex: A and D vitamins.

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(B)Carbohydrates
 They consist of only: Carbon, oxygen, and hydrogen.
 They supply quick energy, 1 gram of any carbohydrate will release 4 calories of
heat when burned, and it is considered as the primary source of energy in
the body.
 There are 3 classes of carbohydrates:
Monosaccharaides, Disaccharides, Polysaccharides

1 – Monosaccharides
They are simple sugars that consist of formula C6 H12 O6
EX: glucose , fructose ,
galactose which are all
isomers of each other as
they have the same
chemical formula but differs
in their structures ,
therefore they have
different physical and
chemical properties.

2 – Disaccharides
They have the chemical formula C12 H22 O11 they consist of 2 monosaccharides joined
by a process known as dehydration synthesis, which is the process of joining two
molecules together following the removal of water.

5
Disaccharides are broken down during digestion by hydrolysis which is opposite to
dehydration synthesis.

3 – Polysaccharides
They are polymers of monosaccharide units joined together by dehydration
synthesis.

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There are 4 important polysaccharides you should know:
Cellulose: it is found in plants and makes up plant cell walls (structural
carbohydrates)
Starch: it is a polymer of glucose that is produced by most green plants as energy
storage.
Chitin: it is the major constituent in the exoskeleton of arthropods and cell walls of
fungi.
Glycogen: it is a polymer of glucose that is produced in animal cells as energy storage.

(C) Lipids
They are non-polar organic compounds that include fats, oils, and waxes.
Most lipids consists of one glycerol and 3 fatty acids. Each fatty acid consists of a
hydrocarbon chain with a carboxyl group (COOH) at one end.

The hydrocarbon chain may have only single bonds (saturated fats) or may contain one
or more double bonds (unsaturated fat):

7
 Saturated fats Unsaturated fats
Mainly come from animal source. extracted from plants

solid at room temperature liquid at room temperature

have no double bonds in its Have at least one double bond in

hydrocarbon chain its hydrocarbon chain thus, they
have fewer hydrogen atoms.

are linked to heart diseases when good dietary fats

ingested in large quantities
- ex: butter , cream - ex: olive oil

Lipid functions
1 – Energy storage: 1 gram of any lipid will release 9 calories of heat when burned, fats
are secondary source of energy in living organisms.
2 – Storing fat soluble vitamins
3 – Structural: enters in composition of myelin sheath in nerve cell, and cell membrane
4 – Endocrine: some lipids are hormones ex: sex hormones (steroids)
5 – Thermal insulators like in marine mammals and polar animals
6 – Buoyancy some animals like seals and whales can float in water because they have
thick layers of fats (fats are less dense than water).
7– Cushions organs like fat tissues that surround kidneys.
8– Water repellent ex: ear wax.

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(D) Proteins
They are polymers formed by joining simple units called amino acids together in a
process called translation that take place in the ribosome.
Amino acids consist of a carboxyl group, an amine group, and a variable R, all attached
to a central carbon atom. The R group differs with each amino acid.

Amino acid units are bonded together with peptide bond by dehydration resulting in
a chain called polypeptide chain

To continue adding amino acids to the same chain, the next amino acid will bond with
C atom in the acid end of the chain.

9
Proteins have many important functions: growth and repair, transport (hemoglobin),
hormones ( insulin ) , structural ( collagen ) , antibodies ( immune defense ) , enzymes
)amylase ).
The shape of a protein is the result of 4 levels of structure:
Primary, secondary, tertiary, and quaternary.

Enzymes
-They are large proteins with tertiary structure.
-They serve as biological catalyst as they speed reaction in the body by lowering the
energy of activation (the energy needed to begin a reaction).

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-Each enzyme has a specific shape that only fits to its own substrate (the chemical
molecule that the enzyme works on).
-Each enzyme has an active site , when the substrate binds to this active site , it induces
the enzyme to slightly alter its shape to fit better , this is called " the induced fit model"
( the old " lock and key " model was abandoned ).
-Enzymes are not degraded during a reaction and are reused.
-Enzymes function with the assistance of:
 Co factors which are minerals (inorganic)
 Co enzymes which are vitamins (organic)

The efficiency of enzymes is affected by temperature and PH :

Average human body temperature is 370C, if it rises above 400 C the enzyme will stop
functioning. High temperature causes denaturation (change in shape) of the enzyme
and it will be unable to fit to its substrate.

11
Each enzyme works at a specific pH changing its ph. range will also cause denaturation
of the enzyme.
pH is a measure of acidity and alkalinity of a solution. It is the negative logarithm of the
hydrogen ion concentration in moles per liter.
pH value varies from 1 to 7.

A change of 1 in pH is a ten times increase in acid or base strength

A change of 2 pH units means 100 times more basic or acidic.
Ex: a pH of 4 is 10 times more acidic than a pH of 5
Also a pH of 12 is 100 times more basic than a pH of 10

Biological systems regulate their pH through the presence of buffers, which are
substances that resist change in pH by absorbing excess hydrogen ions or donating
hydrogen ions when there are too few. Ex: bicarbonate ion (HCO3-).

Prions
They are infectious proteins that cause several brain diseases, including mad cow
disease. A prion is a misfolded version of a protein normally found in the brains of
mammals. If a prion gets into a normal brain, it causes all the normal proteins to
misfold in the same way.

12
The following table compares between the different biomolecules:

13
Steps to differentiate between biomolecules:
1- The molecule contains only C - H - O atoms (no N, no P) so: carbohydrate/
lipid
→If there is one or more ring structures so the molecule is
carbohydrate
→If there isn’t any ring structures, compare the number of C and O:
C≈O carbohydrate
C›O Lipids
2- The molecule contains only C – H – O – N atoms so: protein/ amino acid
→only 1 N atom amino acid
→more than 1 N atom protein
3- The molecule contains C- H – O – N – P atoms so: nucleic acids/ nucleotide
→only 1 phospate group and 1 nitrogen base and 1 pentose
 Nucleotide
→repeated nucleotides in one vertical chain:
 RNA
→repeated nucleotides in two vertical chains:
 DNA

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 The cell
The technological invention of microscopes allowed for development
of the cell theory.

Cell theory
- All living things are composed of cells.
- Cells are the basic unit of life.
- All cells arise from preexisting cells.

All living cells have:

1. Plasma membrane made of phospholipids
2. Cytoplasm
3. Chromosomes carrying the genetic material (DNA)
4. Ribosomes for protein synthesis

Living cells are divided into 2 varieties:

1- Prokaryotic cell has no nucleus, organisms with prokaryotic
cell are always unicellular, all bacteria and archea are
prokaryotes.
2- Eukaryotic cell has true nucleus, organisms with eukaryotic
cell are mostly multicellular, eukaryotic cell may be animal or
plant cell.

15
16
Structures of plant and animal cells:

Plant and animal cells have many cellular organelles in common

however, they also have organelles unique to their cell type.

17
The cell organelles

Nucleus:

Contains chromosomes made of DNA

wrapped on proteins (histones) into a
chromatin network.

The nucleus is surrounded by a

selectively permeable double
membrane that contains pores and
allows for the transport of large
molecules such as RNA.

Nucleolus:

It is a prominent region inside the nucleus where ribosomes are

synthesized, nucleoli are not membrane –bound structures.

Ribosomes:

They are particles made of rRNA and

protein that are found in the cytoplasm or
bound to rough endoplasmic reticulum.
Ribosomes are not membrane–bound
structures (present in both eukaryotic cell
& prokaryotic cell) and they are the site of protein synthesis.

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Endoplasmic Reticulum (ER):

It is a network of membrane channels that traverse the cytoplasm.

* Rough Er is studded with ribosomes, here protein is

synthesized and transported throughout the cytoplasm.

* Smooth Er has many roles:

1- Connects rough ER to Golgi apparatus.
2-Lipid synthesis.
3- Removes toxic substances.
4- Carbohydrate metabolism.

Golgi apparatus:

It lies near the nucleus and consists of flattened sacs of membranes

stacked next to each other and surrounded by vesicles. Primary
structure proteins (polypeptide chains) that were synthesized in
ribosomes are sent to Golgi apparatus in a vesicle to be modified,
stored, packed, and then secreted to other parts of the cell in
another vesicle.

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Lysosome:

It is a membrane bound sac that contain hydrolytic (digestive)

enzymes. It is the site of intracellular digestion, worn–out cell parts
are broken down (garbage disposal), also invading viruses and
bacteria are destroyed in lysosome.

In some cases, infected cells (cancer, leukemia…) undergoes

programmed cell death: apoptosis, in these cases lysosome is
opened and enzymes break down the cell components. Note that cell
death caused by injury is called necrosis. Lysosomes are not found
in plant cells.

Mitochondrion:

It is a double–membrane–bound organelle found in most eukaryotic

organisms. It is the site of aerobic cellular respiration; it can be
considered as the power generator of the cell as it converts oxygen
and nutrients into ATP. Mitochondria consist of:

20
1- An outer membrane that has many pores to allow the passage
of certain molecules.
2- Inter membrane space which is the area between inner and
outer membranes.
3- The inner membrane which has many foldings called cristae.
4- Matrix which is the space within the inner membrane.

Mitochondria contain their own DNA and ribosomes, which enable

them to self-replicate through binary fission, that is why it is
thought that mitochondria were free living prokaryotes that survived
inside another prokaryote in a symbiotic relationship, then evolved
(endosymbiosis theory).

Vacuole

They are single membrane–bound organelles that store substances

for the cell. In freshwater protists contractile vacuoles pump excess
water out of the cell.

Vesicles
They are tiny vacuoles found in many places in the cells, their role is
transporting and delivering their contents to certain destinations
within or outside the cell.

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Plastids
They have a double membrane and are only found in plants and
algae. They are the site of manufacture and storage of compounds
used by autotrophic eukaryotes in food synthesis.
The inner membrane forms a series of structures called grana, the
grana lie in liquid called stroma.

There are 3 main types of plastids:

1- chloroplasts they contain chlorophyll (green pigments), they are

the sites of photosynthesis.

Chloroplasts, like mitochondria, contain their own DNA and can

self-replicate, they are also thought that they arose from
endosymbiosis.

2- They are colorless and store starch, they are found

in roots like potatoes.

3- chromoplasts They store carotenoid pigments and are

responsible for the red, orange, and yellow coloring of many plants
like carrots and tomatoes.

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Cytoskeleton

It is a network of protein filaments that support the cell and gives it

an overall shape, it also aids in the correct positioning of organelles,
allows some cells to move, and provides tracks for transportation
inside the cell.

In Eukaryotes, there are 3 types of protein fibers in cytoskeleton:

micro filaments, intermediate filaments, and microtubules.

Microfilaments

They are the narrowest and made up of a protein called actin.

- serve as tracks for movement of a protein called myosin in the

muscles.

-Enable animal cells to form a cleavage furrow during cell division to

produce 2 daughter cells.

 Intermediate Filaments:
- They have an average diameter between that of microfilaments
and microtubules. They are composed of a variety of proteins.

 Microtubules:
They are the largest of the three. They are made up of tubulin
proteins arranged to form a hollow tube. Like actin filaments,
microtubules are dynamic structures, they play many important
roles and they make up the spindle fibers.

Microtubules are also key components of eukaryotic cell structures:

flagella, cilia, and centrosomes.

23
Cilia and flagella:
They have the same structure, both consist of 9 pairs of
microtubules organized around 2 singlet microtubules. They differ in
length; cilia are short while flagella are long, also a cell usually have
only one flagellum or just a few, while ciliated cells have many cilia.
Centrioles and centrosomes:
A centrosome consists of 2 centrioles oriented at right angles to
each other, they are present in animal cells only, they consist of 9
triplets of microtubules arranged in a circle.

Cilia and flagella centriole

Cell wall

It is a rigid covering that surrounds the cells of plants and fungi and
most prokaryotes. Cell walls in plants and algae are made from

24
cellulose, while in fungi they are made if chitin, and in bacteria
made of peptidoglycan. The primary cell wall is located outside the
plasma membrane, some cells have a secondary cell wall having
between them a gluey layer called middle lamella. A narrow thread
of cytoplasm passes through the cell walls of adjacent plant cells to
communicate between them

Cytoplasm and cytosol

The entire region between the nucleus and plasma membrane is

called cytoplasm. Cytosol is the semiliquid portion of the cytoplasm.
The streaming of the cytoplasm inside the cell is a process called
cyolosis.

Plasma membrane (cell membrane)

It encloses the cell and controls the passage of substances through

it according to the cell needs regardless to the charge or
concentration, this characteristic is called selective permeability.

25
Plasma membrane consists of:

- A phospholipid bilayer: It consists of 2 players of phospholipids

having a hydrophilic heads (phosphate group) directed to both the
inner surface and the outer surface of the cell, and 2 hydrophobic
tails (fatty acids) directed inwards.

- Proteins dispersed through the phospholipid bilayer that may

cross the membrane entirely or be loosely attached to its inside or
outside face. These proteins have channels inside them and they
play a vital role in transportation in and out the cell.

- Cholesterol molecules are embedded within the membrane

making it less fluid and more stable.

- Carbohydrate chains attached to only the outer surface of the

membrane, they serve in cell–to–cell recognition (cell ID) as the
shape of the chains differs from one cell to another.

Scientists described the cell membrane in a model called fluid

mosaic model because it is made of small particles that are able to
move around in all directions in order to control what enters and
leaves the cell.

26
27
 Cell transport
The movement of materials across cell membrane either doesn’t
require energy (passive transport) or require energy (active
transport).

In passive transport
materials are moving from
high concentration to low
concentration (with
concentration gradient) so
they do not need energy.

In active transport
materials are moving
from low concentration
to high concentration
(against concentration
gradient) so they need
energy.

A- Passive transport:

There are 3 types of passive transport: simple diffusion, facilitated

diffusion, osmosis.

28
1- Diffusion (simple diffusion): Happens through the
membrane without the aid of protein membrane channels, ex:
oxygen diffusion across alveoli
2- Facilitated diffusion: It is the transport of substances
through protein membrane channels, ex: calcium ions transport
through protein channels in axon membrane, glucose.
3- Osmosis:
It is the diffusion of water molecules across a membrane from
hypotonic solutions (↑water and ↓solute) to hypertonic
solution (↓water and ↑solute).

a- If a cell is placed in an isotonic solution water diffuses

continuously in and out but there is no net change in the cell.
b- If a cell is placed in a hypertonic solution, water will leave
the cell causing the cell to shrink which is known as plasmolysis.
c- If a cell is placed in a hypotonic solution, water flows into the
cell causing the cell to swell until it bursts.

29
 The 3 types of passive transport are illustrated in the following
diagram:

Active transport

Molecules move from low to high concentration, requires energy.

1- Exocytosis
The release of molecules from the cell to outside transported by
vesicles.
2- Endocytosis Molecules are brought into the cell, a vesicle is
formed to transport these molecules inside the cell. There are 3
type of endocytosis:
Pinocytosis (cell drinking)
It is the intake of liquid into the cell by budding a small
vesicle from the cell membrane.
Phagocytosis
The cell uses its plasma membrane to engulf a large particle
then encloses it (by pseudopod) forming a vacuole.
Ex: White blood cells engulf bacteria.

30
 Receptor-mediated endocytosis
The cell take up large quantities of very specific substances
that are drawn into the cell by vesicles.

3- Sodium-potassium pump
In nerve cells, sodium and potassium ions are carried across the
axon membrane against a gradient (From low concentration to
high concentration).

31
 Microscopy
Light microscope
This type of microscope uses visible light and a system of
lenses to magnify images of small objects.

To determine the magnification, multiply the magnification of

the Ocular lens by the magnification of the objective lens.

One big advantage of light microscopes is the ability to observe

living cells so we can observe biological activities.

32
Electron microscopes
They produce an image of a specimen by using a beam of
electrons rather than a beam of light.
They produce higher-resolution images and can be used to
examine even the subcellular structures.
One limitation, however, is that electron microscopy samples
must be placed under vacuum, this means that live cells cannot
be imaged.
The 2 main types of electron microscopes:
The transmission electron microscope (TEM)
Is used to view thin specimens (tissue sections, molecules,..)
Scanning electron microscopy (SEM)
A beam of electrons moves back and forth across the surface
of a cell or tissue, creating a detailed image of the 3D surface.

33
 Cell division
There are two types of cell division:

Mitosis: happens in somatic cells for growth and repair.

Meiosis: happens in germ cells to produce gametes.

We grow up by increasing the number of cells not by increasing the

size of the cells, this is because as cells become larger, it takes
longer to transport materials inside of them, and also it gets harder
for them to exchange enough nutrients and wastes with their
environment.

So, cells grow up until they reach surface–area–to-volume ratio

that is insufficient to their needs, at this point they divide.

The cell cycle of a somatic cell

The cell cycle is divided into 2 major phases: interphase, and mitotic
phase.

 Interphase is the longest part of the cell cycle and is divided

into 3 stages: G1, S, G2
 mitotic phase is divided into mitosis and cytokenesis

34
35
Mitotic phase:
A.Mitosis
This is where the cell divides its previously–copied DNA.

1. Prophase

2. metaphase

36
3. Anaphase

4. Telophase

37
B.Cyotkenesis
Here the cytoplasm splits in to and the cell divides. In animal cell
the plasma membrane of the parent cell pinches inward alone the
cell equator until 2 daughter cells form.
In plant cell a cell plate is formed and join to plasma membrane
then become a new cell wall, the 2 daughter cells keep attached by
middle lamella.

-Cancer is an uncontrolled cell growth.

-cell cycle is regulated by factors called checkpoints that helps the
cell to decide whether to move forward through cell cycle or to enter
a non-dividing state (G0) after exiting (G1) phase.
-nerve cells, heart cells, skin cells, and red blood cells do not
undergo mitosis (G0)
-Nucleus and nucleolus are the only cell organelles that disappear
for a while during cell cycle.

38
Meiosis:
It happens in germ cells. Meiosis purpose is to produce gametes (sex
cells).During meiosis 4 daughter cells are produced, each of which are
haploid (having half the number of chromosomes of the parent cell).

Meiosis I
In meiosis 1 the homologous pairs of chromosomes are
separated. Crossing over occurs in prophase I

39
Meiosis ll
In meiosis 2 the sister chromatids are separated.

Meiosis 1 is followed by meiosis 2 and the final yield is 4 cells having

half the number of chromosomes that was in the original cell:

40
Comparison between mitosis& meiosis:

41
 Cellular respiration & photosynthesis
Cells are constantly carrying out thousands of chemical reactions needed to keep the
cell, and the living organism as a whole, alive and healthy.
These chemical reactions are called: metabolism
Two metabolic processes are crucial to life on earth:
-building sugars: photosynthesis, an anabolic reaction
-breaking sugars down: respiration, a catabolic reaction

Cellular respiration
C6H12O6 + 6O2 → 6CO2 +6H2O + ENERGY
It is the process by which the cell converts the energy in glucose (chemical energy) to a
usable form of energy: ATP which is the energy currency of the cell.

42
-Note: ADP converts to ATP by adding phosphorus group using energy, this process is
called: oxidative phosphorylation.
-In a cell, this over all reaction is broken down into many smaller reactions.

 Respiration reaction is an oxidation reaction (glucose is oxidized)

 Water and carbon dioxide are waste products.
 Most of respiration reactions happens in mitochondria.
 There are 2 types of respiration: aerobic, and anaerobic respiration

(A) AEROBIC RESPIRATION

-It occurs in the presence of oxygen and consists of 3 processes:
Glycolysis, Krebs cycle, and ETC.

1-Glycolysis
-It is the anaerobic phase of aerobic respiration.
-One glucose molecule is broken into 2 molecules of pyruvic acid (pyruvate).
-Glycolysis happens in the cytoplasm.
-Glycolysis absorbs 2 ATP and release 4 ATP, resulting in a net gain of 2 ATP

43
Pyruvate oxidation
This step occurs in the matrix, 2 pyruvic acid (obtained from glycolysis) combine with
coenzyme A to form 2 acetyl-CoA each of which enters the Krebs cycle.

2-Krebs cycle (citric acid cycle)

-It occurs in the matrix of mitochondria.
-Krebs cycle happens twice.
-Each turn of the Krebs cycle produces:
1 ATP, 1 FADH2, 3NADH, and 2CO2 (waste product)
-NADH (cofactor) and FADH2 (coenzyme) carry protons and electrons from glycolysis
and Krebs cycle and deliver them to ETC.
-NADH translates 2 electrons to the production of 3 ATP while FADH2 translates 2
electrons to the production of 2ATP.

44
- Electron transport chain
-Aerobic phase (presence of oxygen).
-ETC happens in the inner membrane (cristae).
-In this process NADH and FADH2 enters ETC and the following process takes place:
 Proton are pumped from matrix to inner membrane creating a gradient to
produce ATP, this process is called chemiosmosis.
 Electrons are transferred from NADH and FADH2 to molecular oxygen, finally
oxygen accepts hydrogen atoms (e- + H+ ) to form water (note: water is a waste
product)

Note that: Aerobic respiration net yield is 30-32 ATP, 2 of them are made in glycolysis,
and another 2 ATP are made in Krebs cycle, and the remaining ATP all come from ETC.

(B) Anaerobic respiration (fermentation)

-It happens in the absence of oxygen and consists of 2 processes: glycolysis, and
fermentation.
- It occurs in the cytoplasm.

45
 1-Glycolysis
Glucose is broken and produces 2 pyruvic acid and 2 ATP
Pyruvic acid undergoes fermentation

2-Fermentation
There are 2 types of fermentation:
 Lactic acid fermentation that happens in yogurt bacteria and in the muscles and
produces lactic acid.
 Alcohol fermentation which happens in yeast fungi and produces alcohol and
CO2

Aerobic respiration vs. anaerobic respiration:

Aerobic respiration Anaerobic respiration

It is the breakage of glucose in the It is the breakage of glucose in the
presence of oxygen. absence of oxygen.
End products: CO2 and H2O End products: lactic acid or CO2 and
alcohol
Produces large amount of energy in Produces small amount of energy in
longer time shorter time
Occurs in cytosol and mitochondria Occurs in cytosol

46
 Photosynthesis
Photosynthesis is the process by which light (solar energy) is used to make glucose
(chemical energy). It happens in the chloroplast of plants and algae and in the
cytoplasm of some bacteria.

6CO2 + 6H2O C6H12O6 + 6O2

Overall, this process is a reduction reaction because carbon dioxide is gaining
electrons from the hydrogen in water.
Notes:
-we can measure the rate of photosynthesis performed by the plant by measuring the
rate of consumption or reactants (carbon dioxide and water) or the rate of production
of products (glucose and oxygen).
-oxygen is a byproduct in this reaction.
-glucose produced in photosynthesis is stored in the form of starch which turns blue in
the presence of iodine. Alcohol is added to the leaf before iodine to remove chlorophyl
-All green plant tissues can photosynthesize, but the majority of photosynthesis takes
place in the middle layer of the leaves which is called mesophyll.

47
Light and photosynthetic pigments
-Pigments are substances that absorb some wave lengths of light and reflect others,
the pigment appears with the color of the reflected wave lengths.
-A green plant reflects most green light and, therefore, green light is the least efficient
energy source for plants to make photosynthesis.
-Pigments that are involved in photosynthesis are:
 Chlorophyll a which plays a unique role in converting light energy to chemical
energy.
 Other pigments like chlorophyll b and carotenoids which absorb other wave
lengths that chlorophyll a cannot absorb, and pass these wave lengths to
chlorophyll a to perform photosynthesis. These pigments are called accessory
pigments or antennae.
(Note: carotenoids absorb the excess solar energy and convert it to heat.)

Photosynthesis can be divided into 2 stages: light dependent reactions, and light
independent reactions.

48
Light dependent reactions
-It takes place in the thylakoid and require continuous supply of light energy.
-Chlorophyll absorbs light energy, energy absorbed causes:
 Electrons of chlorophyll are excited and escape carrying energy to enter ETC
 Photolysis of water molecule which splits into: oxygen (↑) + hydrogen atoms
that complete in the reaction in the form of (H+) and (e-): Electrons (e-) enters
chlorophyll and replace escaped electrons, protons undergoes ETC.
Finally ETC produces:
1- ATP (this process is called phosphorylation)
2- NADPH (a reduced electron carrier).
-These 2 molecules are needed for the next stage of photosynthesis.

Light independent reaction

-It takes place in stroma.
-Electrons and protons carried on ATP and NADPH combines with carbon dioxide from
air, which is converted into sugar (carbon fixation).
-Carbon fixation occurs in a process called Calvin cycle, Rubisco enzyme catalyzes
carbon fixation by combining with CO2 as a substrate.

49
Photosynthesis can be summarized as follows

Notes:

-The light spectrum is the range of electromagnetic wave lengths that humans can see,
it ranges from the most energy and shortest wavelength (violet) to the least energy
and longest wavelength (red).
-Other invisible wave lengths may be important for other organisms:
 Ultraviolet has more energy than visible light and can be seen by some insects.
 Infrared has less energy than visible light and can be seen by some snakes.

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Photorespiration:
-In hot and dry conditions, Rubisco enzymes combines with O2 as a substrate instead of
CO2, and rather than fixing carbon, leads to the loss of already-fixed carbon. This
process is called photorespiration
-Plants are classified to 3 types according to their response to this condition:
 C3 plants: they have no special features to combat photorespiration, the
majority of plants are from this type.
 C4 plants: they exhibit modified anatomy which enable them to minimize
photorespiration and water loss and maximize sugar production, by
performing these steps in different cell types. As a result, they thrive in hot
and sunny environments where more typical plants would die.
 (CAM) plants minimize photorespiration and save water by separating
these steps in time, between night and day. They close their stomata during
day, and open them during night to obtain CO2.

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 Classical genetics
The human genome is made up of 23 chromosome pairs, each pair
consists of 2 homologous chromosomes that carry genes for the same
traits with different or same alleles.

-Allele: is one of two or more versions of a gene. An individual inherits

two alleles for each gene, one from each parent.
-Each gene (trait) is described by a genotype and a phenotype:

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The Genotype: is the genetic make-up of the individual.
The Phenotype: is the external appearance of the individual.
If the two alleles are the same, the individual is homozygous (pure) for
that gene.
If the 2 alleles are different, the individual is heterozygous (hybrid) for
that gene.
-Dominant: masking allele
-Recessive: masked allele

Mendel’s laws:
1-Law of dominance
Mendel’s first law is the law of dominance. It states that when two
organisms, homozygous (pure) for two opposing traits are crossed, the
offspring will be hybrid (carry two different alleles) but will exhibit only the
dominant trait. The trait that remains hidden is the recessive trait.

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 2-Law of segregation (separation)
The law of segregation states that during the formation of gametes, the
two traits carried by each parent separate

The cross that best exemplifies this law is the monohybrid cross:

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So you can deduce that:
If a phenotype wasn’t present in both parents but appeared in some
offspring so:
→→→ the genotype of the offspring having the new phenotype is pure
recessive, and →→→ the 2 parents were definitely heterozygous for this
trait.

- Note that if the generation resulted in the cross of the 1st law, is crossed
with each other, the resulted generation is the same that resulted in
second law, this illustrated in the following diagram:

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Test cross (backcross)
To determine whether an individual plant or animal showing the dominant
trait is homozygous dominant (BB) or heterozygous (Bb), the individual of
unknown genotype (B_) is crossed with a homozygous recessive individual
(bb). If the individual being tested is homozygous dominant (BB), all
offspring of the test cross will show the dominant trait and have the hybrid
(Bb) genotype. If the individual being tested is actually hybrid (Bb), we can
expect that the offspring, or at least one individual, will show the recessive
trait. Notice the following diagram:

3- Law of independent assortment

The law of independent assortment applies when a cross is carried out
between two individuals that are hybrid for two traits on separate
chromosomes.

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A cross between two yellow rounded seeds that are heterozygous for both
traits, yellow color (Y) is dominant over green color (y), rounded shape (R)
is dominant over wrinkled shape (r)
Only 4 phenotypes will result with a ratio of: 9 : 3 : 3 : 1

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Mendel’s rules in brief:
 Both parents heterozygous → offspring 75% dominant : 25%
recessive
 Pure dominant x pure recessive → offspring 100% heterozygous
 Heterozygous x pure recessive → offspring 50% : 50%

Notes about Mendel’s work:

 Mendel worked exclusively with true-breeder pea plants. This means
that the plants he used were genetically pure and consistently
produced the same traits.
 He used algebra to prove patterns of inheritance, and introduced
quantitative study.
 He studied the probability of traits transmission for more than one
generation.
 His work was limited to traits that show complete dominance.

Non mendelian cases:

Incomplete dominance
(blending)
It is when an allele does not
completely mask the effects of the
other allele, and the organism's
resulting physical appearance shows
a blending of both alleles. It is also
called semi-dominance or
partial dominance.

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Codominance
Codominance occurs when two alleles of
the same gene are both expressed.
Instead of one trait being dominant over
the other, both traits appear.

Multiple alleles
When there are more than two allelic forms of a gene,
we refer to that situation as multiple alleles. ex: blood
type is expressed by 3 alleles: A,B,O
Note that A, B alleles are codominant, while O is
recessive.

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Polygenic inheritance
Many characteristics such as skin color, hair color, and height result from a
blending of several separate genes. Two parents who are short carry
more genes for shortness than for tallness. However, they can have a child
who inherits mostly genes for tallness from both parents and who will be
taller than his/her parents.

Environmental influence
External environmental factors, like
temperature, influence gene
expression. Similarly, drugs,
chemicals, and light are among the
external environmental factors that
can determine which genes are
turned on and off, thereby
influencing the way an organism
develops and functions. Ex:
Himalayan rabbit

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Sex-linked genes
•Traits carried on the X chromosome are called sex-linked. X-linked genes
have different inheritance patterns than genes on autosomal
chromosomes. That's because these genes are present in different copy
numbers in males and females.
• If a sex-linked trait is due to a recessive mutation, a female will express
the phenotype only if she carries two mutated genes (X’X’). If she carries
only one mutated X-linked gene, she will be a carrier (X’X).
• Males (XY) inherit only one X-linked gene. As a result, if the male inherits
a mutated X-linked gene (X’Y), he will express the gene. There is no carrier
state for X-linked traits in males. If a male has the gene, he will express it.
• Common examples of recessive sex-linked traits are color blindness and
hemophilia.

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• In sex-linked inheritance, the father passes the trait to his daughters
only, sons cannot inherit a sex-linked trait from the father because the son
inherits the Y chromosome from their father.
Sex-influenced inheritance
Inheritance can be influenced by the sex of the individual carrying the
traits. An example can be seen in male pattern baldness in humans, where
hair is very thin on top of the head. This is not a sex-linked trait but rather
a sex-influenced trait. Males and females express the gene for pattern
baldness differently

Linked genes
Linked genes are genes for different
traits that are likely to be inherited together
because they are physically close to one
another on the same chromosome.
Note that linked genes can be separated
during crossing over in meiosis.

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Karyotype
Specialists prepare and photograph chromosomes during metaphase of
mitosis when they are fully condensed to analyze the size, shape, and
number of chromosomes. Of the 46 human chromosomes, there are 44
(22 pairs) autosomes and 2 sex chromosomes.

Pedigree
A pedigree is a family tree that indicates the phenotype of one trait being
studied for every member of a family. Geneticists use the pedigree to
determine how a particular trait is inherited.

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 Pedigree keys
Do all affected offspring have affected parent?

Yes: Dominant No: Recessive

-do all affected males -do all affected females
have affected mothers have affected fathers
and and
-all his daughters -all her sons are also
are also affected affected

YES: NO Yes: NO:

X-Linked Autosomal X-Linked Autosomal

Additional notes for pedigree:

Recessive traits skip generations.
Sex-linked traits are more common in males than in females.

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 MOLECULAR
GENETICS
Structure of deoxyribonucleic acid (DNA)
It is a polymer made of repeating units called nucleotides.
•Each nucleotide consists of 5-carbon sugar (deoxyribose), a phosphate
molecule, and a nitrogenous base.

•DNA is a double helix shaped, like a twisted ladder.

•DNA consists of two complementary strands running in opposite
directions
•Each nucleotide contains one of the four possible nitrogenous bases:
adenine (A), thymine (T), cytosine (C) guanine (G).
• (A) always bonds with (T), (C) Always bonds with (G)
•The nucleotides of opposite chains are paired to one another by
hydrogen bonds.

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 The three-dimensional structure of DNA model
was named: Watson and crick model
A chromosome is made up of a DNA molecule
coiled many times around proteins.

(DNA) Replication:
 It is making an exact replica of DNA, it occurs during s-phase in interphase,
this process is essential because, whenever a cell divides, the 2 new daughter
cells must contain the same genetic information as the parent cells.
 It is called semi-conservative replication because it produces two copies of
the original DNA molecule, each of which contains one
original strand, and one newly–synthesized strand.
 DNA polymerase is the enzyme that catalyzes the
replication, it proofreads each new DNA, fixing errors
and minimizing the occurrence of mutations.

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 Helicase enzyme unzips (separates) the 2 strands of the original DNA helix
by breaking the hydrogen bonds.

 Each strand of DNA serves as a template for the new strand according to
the base - pairing rule: (A) with (T) / (G) with (C)
 Each time the DNA replicates, some nucleotides from the ends of the
chromosomes are lost. To protect against this, some cells have special
nonsense nucleotide sequence at the ends of the chromosomes that repeat
thousands of times. These protective ends are called telomeres.

Chromosome before and after replication:

There are two types of nucleic acids in living cells:

Deoxyribonucleic acid DNA, and ribonucleic acids RNA

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 RNA
 It is a single – stranded helix.
 It is a polymer made of repeating units called nucleotides, each nucleotide
consists of 5-carbon sugar (ribose), a phosphate group, and a nitrogenous
base.
 The 4 possible nitrogenous bases in RNA are: adenine (A) uracil (U),
cytosine (C), and guanine (G).
(No thymine in RNA, uracil replaces thymine)
There are 3 types of RNA:
1- Messenger RNA (mRNA), its role is carrying the DNA code to the
Ribosomes where the message is translated.
2- Transfer RNA (tRNA), it is a clover–leaf–shaped molecule that carries
specific amino acid molecules to mRNA and ribosomes to form poly–
peptide chain.
3- Ribosomal RNA (rRna), it is a structural molecule that makes up part
of a ribosome. Each ribosome consists of a large unit and small subunit
each made of protein and rRNAs.

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How are the genes expressed?
The gene of any trait is responsible for making the protein that expresses
this trait (ex: skin color is expressed by synthesis of melanin).

Gene expression = protein synthesis

Protein synthesis:
The process by which DNA makes proteins, consists of 3 main steps:
transcription, RNA processing, and translation.
A- Transcription
A particular segment of DNA (gene)
is copied into mRNA, mRNA is
formed following the base – pairing
rules: (A) With (U), and (G) with (C).
Transcription begins when the enzyme
RNA polymerase binds to one strand of
DNA at the promoter region, uses this
strand as template to form mRNA.
When the newly formed mRNA strand reaches a stop codon, it terminates.

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 B- RNA Processing:
Before the newly formed strand of mRNA is shipped out of the nucleus to
the ribosome, it is edited by enzymes (snRNPs), these enzymes remove non
coding regions called introns, then reattach coding regions exons.

C- Translation of mRNA into protein:

It is the process by which mRNA sequence is converted into
an amino acid sequence. Every 3 nitrogenous bases (triplet)
carries a genetic code for an amino acid. The genetic code
is the language that genes are written in to encode proteins.
Since we have 4 nitrogenous bases so there are 64 possible codons (43).
There are only 20 amino acids but several codons code for the same amino
acid.

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Translation occurs at the ribosome in the cytoplasm. Amino acids present
in the cytoplasm are carried by tRNA molecules to the ribosome.
Each tRNA molecule has an anticodon to the corresponding amino acid,
then it binds to the mRNA strand where the amino acids are linked together
by peptide bond. Translation process begins at the start codon AUG and
stops when it reaches an end codon.

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 Steps of protein synthesis is shown in the following figure:

Gene regulation
We previously know that every somatic cell in the body contains all of the
genetic information (same genes) but different cells of the body serve
different functions, which means that different cells in the body need to

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express different genes. Also every gene in a cell is not turned on all the
time, but only when needed.
A simple model for gene regulation can be found in bacteria in a region of
DNA called operon.
The operon consists of functional genes responsible for making a certain
protein + the switches that turn them on and off.
There are 2 types of operons: inducible operon (ex: lac operon), which is
always turned off unless induced to turn on.
The other is repressible operon, which is always turned on unless it is
actively turned off.
Main parts of operon are the promoter, operator which is the binding site
for the repressor (that turns off the operon).
EX: lac operon which regulates the formation of lactase that digests lactose.

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 Mutations
They are changes in genetic material that can be caused by mutagenic
agents, including toxic chemicals and radiations, they are the raw material
for natural selection and the primary source of new genetic variation.
Mutations are either somatic or germline
 Somatic mutation: it happens in body cells and causes diseases that are
not inherited, ex: cancer which happens due to a mutation in the gene
that is responsible for cell division.
 Germline mutation: it happens in gametes or gamete producing cells
and it is called true mutation because it can be inherited.
There are 2 types of mutations:

A-Gene mutations
It is an alteration in the DNA sequence that makes up a gene, types of gene
mutations are:
1- Point mutations where one nucleotide is substituted by another
a- missense mutation: a single nucleotide change results in a codon
that codes for a different amino acid. ex: sickle cell anemia which is
caused by point mutations in the gene that codes for hemoglobin,
which can distort red blood cells into a sickle , or crescent, shape.
Sickle-shaped cells are not flexible and can stick to vessel walls, causing
a blockage that slows or stops the flow of blood. Also this makes blood
low in oxygen

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b- Silent mutation: point mutation that do not
have an observable effect on the organism's
phenotype. The codon formed after silent
mutation codes for the same amino acid, so the
polypeptide chain that will be translated
remains the same.

c- Nonsense mutation: is a change in DNA

that results in a stop codon, this causes a
protein to terminate or end its translation
earlier than expected, resulting in a
shortened or nonfunctional protein.

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2- Insertion or deletion it results from a loss or an addition of one letter
into the DNA sentence, both mutations result in a frameshift.
The effect of these changes can have disastrous results.

3-inversion mutation: it occurs when a section of DNA breaks away

and then reattaches to the same chromosome in reversed order.
An example of inversion mutation is shown in the following figure:

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B-Chromosome mutations:
They are alterations in chromosome that happens either in structure or in
number.
1-Chromosome mutations in structure:

2-chromosome mutations in number:

It is called aneuploidy and is mainly caused due to nondisjunction.
Nondisjunction
IT is an error that sometimes happens during meiosis in which homologous
chromosomes fail to separate as they should due to disability of spindle
fibers. When this happens, one gamete receives 2 chromosomes while the
other gamete receives none.

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 The embryo that receives at least one more chromosome than normal
is a case of polysomy.

- An example of polysomy in
autosomal chromosomes is Down
syndrome, this individual receives
third copy of chromosome 21 that
appears triplet in his karyotype
(trisomy-21).

- Examples of polysomy in sex

chromosomes: Klinefelter's
syndrome, Turner
syndrome.

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  Having entire extra sets of chromosome (ex: 3n,4n,5n….) is known as
polyploidy, Which is responsible of brilliantly colored flowers.
Example of polyploidy is an organism in which the cells have an extra set of
chromosomes is referred as triploid (3n).

The human genome

The human genome consists of 3 billion base pairs of DNA and about 20,000
genes. Only 3% of your DNA code for protein production and 97% are not!!!
These 97% of your DNA might be:
Regulatory sequence: genes that control the expression of other genes.
Repetitive sequence: they are base pairs that may repeat ten million
times and never get transcribed ex: telomeres.
Pseudogenes: they are accumulated mutations over a long time.

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Genetic engineering
It is the process of using recombinant DNA technology to alter
the genetic makeup of an organism.
Recombinant DNA
It means taking DNA from 2 sources (by restriction enzymes) then
combining them together in one cell.

Restriction enzymes:
They are enzymes isolated from bacteria. They cut DNA at specific
sequences called recognition sites (ex: GAATTC).These enzymes act as
molecular scissors, the pieces of DNA result are called restriction fragments.
Different restriction enzymes recognize different recognition sites.

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 Scientist use recombinant DNA technology in many purposes like:
- Gene therapy: inserting functioning genes into cells to replace non-
functioning ones in humans.
-Environmental cleanup: by altering genes of bacteria and use them to
degrade oil spills or in water treatment plants.
- Transgenic plants: Genetically modified plants to create new colors in
plants, and to create enhanced crops.
- Human insulin production:

Gel elctrophoresis
A technique that is used widely in genetic labs for many purposes such as
comparing DNA for genetic testing. DNA that will be analyzed is cut up by
restriction enzymes into pieces, gel electrophoresis separates these pieces
(fragments) according to their rate of movement as they flow through an
agarose gel in an electric field.
The rate of fragments movement depends on the size of the fragments.

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Polymerase chain reaction PCR
It is a method widely used in molecular biology to make several copies of a
specific DNA segment. Billions of copies are produced in a few hours, these
copies can be studied or used in a comparison with other DNA samples.
This process is also known as DNA amplification.

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  It is a system by which we name and classify all organisms, living and
extinct.
 In old classification scientists grouped living organisms into five
kingdoms: monera (bacteria & archea), Protista, fungi, plantae, and
Animalia.
 In modern classification scientists used the three domain system: Bacteria,
Archea, and Eukarya.

 Levels of classification are: domain → kingdom → phylum → class →

order → family → genus → species. (dear king Philip came over for
good soup)
 Carolus Linnaeus invented the binomial nomenclature system, the
first part name represents the genus and begins with a capital letter,
and the second part name represents the species and begins with a
small letter.
Example: Homo sapiens for humans, Panthera leo for lion.

 Species is a group of closely related organisms able to interbreed

giving a fertile offspring.

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Domain Bacteria
-All unicellular.

-All prokaryotes.

-Many are pathogens, some are useful.

-Some are autotrophic like cyanobacteria (blue green algae), others are

heterotrophic.

-Have no introns (non-coding regions) in their DNA.

-Play vital role in the ecosystem as decomposers (recycle dead organic

matter), and as nitrogen-fixing in the nitrogen cycle.

-Play vital role in genetic engineering.

Domain Archea
-All unicellular.
-All prokaryotes.
-Have introns in their DNA.
-Includes extremophiles, organisms that live in extreme environment, like:
1. Methanogens: obtain energy in a unique way by producing methane
from hydrogen.
2. Halophiles: thrive in environments with high salt concentration.
3. Thermophiles: thrive in very high temperatures.

Domain Eukarya
-All have nucleus, and internal membrane-bounded organelles.
-Eukarya include the remaining four kingdoms: Protista, fungi, Plantae,
Animalia.

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 DOMAIN EUKARIA
All have nucleus.

1.Protista 2. Fungi 3.Plantae 4.Animalia

1-some 1-some unicellular 1-All multicellular 1-All multicellular

unicellular (ex: yeast)/
(ex: amoeba,
Some multicellular
paramecium) /
(ex: bread mold,
Some
mushrooms)
multicellular(ex:
seaweed, kelp)

2-some 2-all heterotrophic, 2-All autotrophic. 2-All heterotrophic

heterotrophic / important role in
some ecosystem as
autotrophic decomposers
3-reproduce 3-some reproduce 3-Sexually/ 3-Most reproduce
sexually/ sexually, others asexually sexually
asexually asexually

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Kingdom Animalia was classified into 34 phyla according to the following
trends:

 Levels of organization of the body (cells, tissue, organs, systems)

 Cephalization (having head)
 Body layers (diploblastic, triploblastic)
 Body cavity (coelom)
 Body symmetry

We will discuss the main 9 phyla from kingdom Animalia:

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Kingdom Animalia
1- profirea (sponges)
- No symmetry, acephalized, acoelomate
-no true tissue (unspecialized cell layers)
-diploblastic: ectoderm + mesoglea (noncellular) + endoderm
-sessile

2-cnidaria
-radial symmetry new, acephalized, acoelomate
-diploblastic: ectoderm +mesoglea (noncellular) + endoderm
-sessile polyp (vase), motile medusa (inverted bowl)
-special cells (cnidocytes) contain stingers: nematocysts
-excrete ammonia NH2 without special structure

3-platyhelminthes- flatworms
-acoelomate, bilateral symmetry new, cephalization new
-Triploblastic new
-Digestive cavity with only one opening (no digestive system)
-exchange nutrients and wastes by diffusion due to thin body
-ex: planaria (free living), Tape worm (Parasitic) having
suckers
Note that: tape worm produce large number of offspring, and
Do not produce toxins
-excrete ammonia through flame cells
-nerve chord new
-Hydrostatic skeleton: closed body compartement filled with
Fluid whose shape is changed by muscles to enable worm to move.

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4-Nematodes (round worms)
-Cephalized, bilateral symmetry, triploblastic
-pseudocoelom new
-mouth and anus new
-hydrostatic exoskeleton

5-Annelids (segmented)
-Cephalized, bilateral symmetry, triploblastic
-coelomate new
-digestive tract new
-excrete urea through nephridia new
-diffusion of O2 and CO2 through moist skin
-hydrostatic skeleton

6-Mollusks
- Cephalized, bilateral symmetry, triploblastic, coelomate
-soft body with hard calcium shell
-open circulatory system new
-have specialized tissue called mantle that secretes the shell
-have tooth bearing tongue called radula
-have gills (respiration) and nephridia excretion

7-Arthropoda
-jointed legs, segmented body
-chitinous exoskeleton
-exoskeleton does not grow and must be
shed periodically
-classes: insecta, crustacean, arachnida,
myriapoda
-insects have wings, 1 pair of antenna,
and 3 body segments:
head (eyes), thorax (legs and wings), abdomen
-insects excrete uric acid through malpighian
tubules

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8-Echinoderms
-mostly sessile, slow motion
-embryo shows bilateral symmetry, but
adult shows radial symmetry
-water vascular system supports tube feet
-endoskeleton grows with body

9-chordates
-all have vertebral column (endoskeleton)
-dorsal nerve chord
-5 classes:

Amphibia Reptiles Birds (Aves) Mammals

Fish
Cold blooded; Cold blooded; Cold blooded; Warm blooded; Warm blooded;
ectothermic ectothermic ectothermic homeotherms homeotherms
(endothermic) (endothermic)
Excrete ammonia Excrete urea/ Excrete uric acid Excrete uric acid Excrete urea
Ammonia(in to reduce water To reduce water
water) loss loss
Cartilaginous Respiration Amniotic fluid Amniotic fluid Include: placental
(shark), through moist- In egg to prevent In egg to preventMonotremes,
Bony (gold fish) Skin / gills dehydration dehydration marsupials
Ex: shark, other Ex: frog, Ex: turtle, snake, Ex: dove, owl, Ex: marsupials,
Types of fish salamander Crocodile, lizard Eagle Kangaroo, cat

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Mammals charachteristics
 they have fur or hair
 all nourish their babies with milk (suckling)
 divided to 3 groups according to where embryo develops:
monotremes, marsupials, placental.

Mammals

Monotremes Marsupials Placental

Egg-laying mammals, Embryo born early and Embryo develops in uterus
embryo develops inside egg. completes development inConnected to his mother
It feed babies milk mother’s pouch by a placenta
Ex: platypus, anteater Ex: kangaroo Ex: primates

Primate
it is the highest order in placental mammals

Apes humans
Complex nervous system complex nervous system
Single birth Single birth
Nails instead of claws Nails instead of claws
Forward facing eyes Forward facing eyes
Most intense parenting Most intense parenting
Opposite thumb (legs and hands) Opposite thumb in hands only
Smaller brain cavity Bigger brain cavity
C- shape vertebral column S-shape vertebral column

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 Notes:
-Ectothermic: the animal depends on external sources of body heat.
-Endothermic / homeothermic: animal maintains a stable internal body temperature regardless
of external influence.
-Comparison between earthworm (Annelida) and grasshopper (arthropods – insecta)

digestion Mouth, esophagus, crop, gizzard (grind Mouth, esophagus, crop, gizzard (grind
with ingested sand), intestine, anus by chitinous plates), intestine, anus
excretion Excrete urea through nephridia Excrete uric acid - malpighian tubules
Gas exchange Diffusion through moist skin, Air enters tracheal tubes,
External respiratory surface Internal respiratory surface
Nervous Dorsal brain, ventral nerve cord Same
Circulation Closed circulatory system, blood Open circulatory system, hemocoels ,
Capillaries, hemoglobin hemocyanin
reproduction hermaphrodite Separate sexes

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Cladograms / phylogenic trees:
It is a diagrammatic representation of the evolutionary history of living organisms based on
DNA sequences. Phylogenic tree shows shared traits, and derived traits (traits that are not
shared with ancestor).
The root of the tree represents the ancestral lineage, and the tips of the branches represent
the descendants of that ancestor. As you move from the root to the tips, you are moving
forward in time.

Deductions from cladogram:

-The bird is more related to crocodile then to rabbit.
-The shark is most primitive, the bird is most advanced.
-There is no information about when these derived traits evolved or when the animals’
ancestors diverged from each other.
-If you were asked to provide a shared trait for all the animals shown: vertebrate.

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 Microorganisms
There are four types of microorganisms you should know about: protists,
fungi, bacteria, and viruses.

Protists
Protists are eukaryotes and contain organelles and a true nucleus. Most
are unicellular, and some are truly multicellular (algae). This kingdom can
be divided into three main groups, or phyla protozoa (animal-like protists),
algae (plant-like protists), except for cyanobacteria, the blue-green algae,
and a few fungus-like protists.

-euglena have red eyespot to locate light.

-Malaria is an example of diseases caused by protits, it is responsible for
the greatest number of death worldwide per year.
Fungi
 Most fungi are multicellular eukaryotes.
 Fungal cell walls are made of chitin.
 Fungi lack chloroplasts, therefore, they are classified as heterotrophs.

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 They are absorptive feeders. This means they secrete enzymes that digest
their food outside their bodies, this “predigested” food can then be easily
absorbed by the fungus. Many fungi feed on dead or decaying material,
helping to break it down; they are decomposers.
 Some fungi secrete substances that are toxic to bacteria that compete
with them for food. Scientists have used their knowledge of this ability of
fungi in order to produce antibiotics ex: penicillin.
There are many examples of fungi that you are familiar with: molds,
mushrooms, etc.
Fungi may cause some diseases like: athlete's foot

Bacteria
 Prokaryotes have no nuclei and no membrane-bound organelles
(they do have ribosomes, which are not membrane-bound). Because
they have no nuclei, their DNA is found in the cytoplasm.
 Bacterial DNA is usually found as a single, circular chromosome. It’s
still double-stranded, but the ends of the strand are joined in a circle.
This helps protect the DNA from damage.
 Bacteria also have a cell wall, which is made of peptidoglycan
(proteins and sugars)
 Some bacteria, the cyanobacteria, can perform photosynthesis,
which means that they’re autotrophs. Most bacteria, however,
cannot perform photosynthesis, and they’re heterotrophs.
 Bacteria reproduce in a process called binary fission.

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Bacteria can achieve genetic recombination (mix up the DNA) in three
different ways:
1. Transformation: In transformation, bacteria can pick up new DNA from
the extracellular environment. This is unusual and relatively rare in natural
environments but is often used in research for different purposes.
2. Conjugation: Conjugation means that a bacterium replicates its DNA and
donates some of it to another bacterium through a bridge called a pilus.
3. Transduction: In transduction, a virus carries DNA from one bacterium
to another bacterium during infection.

 Most bacteria need oxygen, they are known as obligate aerobes.

 Some bacteria are poisoned by oxygen, and these are known as
obligate anaerobes.
 Finally, there are some bacteria that will use oxygen if it’s available
but can survive by fermentation if it’s not. These bacteria are
facultative anaerobes.
An example of diseases caused by bacteria is sore throat caused by
streptococci

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Viruses
A virus isn’t really considered a cell, and it’s not even technically
considered to be alive.
Viruses causes many diseases ex: chicken pox.
Viruses has only two components: (1) a coat made of protein (only
protein) called the capsid and, inside the coat, (2) nucleic acid (the
genome). Depending on the virus, the genome might be DNA or RNA.

Viruses have none of the machinery required to reproduce themselves.

Therefore, they can reproduce only with the help of another cell, using
that cell’s enzymes as needed. Let’s consider a virus with a DNA genome.

The viral life cycle begins with the following two steps:
1. Attachment: The virus attaches itself to the host cell. This is a specific
interaction between the virus and the host cell; a virus can attach only to
its particular host.
2. Infection: The virus injects its genome into the host cell.

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Once inside the host, the viral genome enters into one of two possible life
cycles, the lytic cycle or the lysogenic cycle.

In the lytic cycle:

 The viral genome is first transcribed and translated using the host’s
RNA polymerases and ribosomes to make viral proteins (for example,
the capsid proteins).
 Host DNA polymerases then replicate the viral genome, and the new
viral genomes are packaged into the new viral capsids.
 Finally, the host is broken open (lysed) by a special viral enzyme and
the new viruses escape to infect new hosts.

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In the lysogenic cycle:
 The viral genome is not immediately transcribed, translated, and
replicated. Instead, it is inserted into the host’s genome, where it
remains dormant.
 Every time the host replicates its genome (during cell division) the
viral genome is replicated, too. Thus, every daughter cell of the
original infected host is also infected.
 The virus can remain in this dormant state for a long time until the
host cell experiences stress or illness, the virus can remove itself
from the host genome and begin the lytic cycle, being transcribed,
translated, etc.

Viruses with RNA genomes have a slight problem:

An RNA virus cannot use DNA polymerase of the host cell to replicate,
that’s because DNA polymerase copies only DNA.
Furthermore, the virus can’t use the host’s RNA polymerase for
transcription of its genome, because that enzyme makes RNA only by
reading a DNA template (transcription). The virus needs a special enzyme
that makes a strand of RNA by reading an RNA template.
Because this is a unique viral-only enzyme, the virus must either:
(a) Carry the enzyme with it in its capsid and inject it into the host along
with its genome, or
(b) Synthesize the protein during translation of the viral genome (a part of
the normal viral life cycle).
Retroviruses:
They are RNA viruses that go through the lysogenic life cycle.
It uses a special enzyme called reverse transcriptase to translate its genetic
information from RNA into DNA. That DNA can then integrate into the host

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cell's DNA. Once integrated, the virus can use the host cell's components
to make additional viral particles.

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 Plants

A-PLANT CLASSIFICATION
kingdom Plantae

Bryophytes tracheophytes
-No vascular tissue (primitive) vascular tissue (xylem, phloem)
-No transport (no roots or xylem)
-live in moist (absorb water by osmosis) seedless plants seed plants
-Tiny, no support -no seeds -reproduce by seeds
-Ex: mosses -reproduce by spores - gymnosperms or
-Ex: ferns angiosperms

Angiosperms
-Flowering plants
-the most diverse plants on earth
- divided into : monocotyledons,
and dicotyledones
-ex: roses, daisies, fruits, nuts
gymnosperms
-conifers plants (non flowering)
-modifications to dry conditions
including needle leaves, thick
cuticle
-ex: sedar, pines, redwoods

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Examples of monocots are the grasses: wheat, corn, oats, lawn grass, and rice.
Examples of dicots are cherry, roses, carrots, and most of other trees.

B-PLANT ANATOMY

Types of plant tissue:

1-Dermal tissue:
Single layer of epidermal cells, they do not contain chloroplasts except guard cells.

2-Vascular tissue:
Transports water and nutrients up & down the plant. It consists of xylem and
phloem:

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 xylem phloem
Type of cells Tracheids or vessel elements Sieve tube elements &
Dead cells at maturity companion cells (Living cells)
(wood)

Cell wall thickness Thick Thin

Cell wall material Lignin Cellulose
Permeability Impermeable Permeable
Transport & energy Water & minerals, no Food (sugar) made in leaves,
needed expenditure of energy, by requires energy, process is
Cohesion & transpiration called translocation.
pull
Direction of flow Up Up and down

3-Ground tissue:
 Parenchyma cells: thin and flexible, primary cell wall only, found in all parts of
plant, serve as storage sites for sugars, have one or two large vacuoles that
support the plant ex: mesophyll and epidermal cells.
 Collenchyma cells: thickened primary cell walls only (no secondary cell wall) ex:
string of celery.
 Sclerenchyma cells: very thick primary and secondary cell walls fortified with
lignin, their role is only support

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 Roots

 The function of root is: absorbing nutrients, anchor the plant, and store food.
Notes:
- root hairs function is to increase the absorption surface area.
- The absorption of water and nutrients from the soil occurs by :
 Apoplast and symplast:

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 Plants continue to grow as long as they live due to meristem tissue.
1. Primary growth (vertical)
It is the plant elongation (up and down) due to cell division in the apical meristem
which is located at the buds of shoots and the tips of roots.

2. Secondary growth (lateral):

New cells provided by the lateral meristem (cambium) making enlargement in the
trunk. Each year of growth another ring is added.

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Stem
Stem function is support and transport (water and nutrients)

Leaf

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The leaf is organized to maximize sugar production and minimizing water loss.
Stomata open and close according to plant needs to regulate gas exchange and
water loss (transpiration), during the day the plant need to open stomata for gas
exchange during photosynthesis, guard cells become turgid and stomata are open. At
night guard are shrunken causing stomata to close to reduce water loss

As the water is lost from the leaf surface by transpiration, more water molecules are
pulled up due to the tendency of water molecules to remain joined (cohesion), and
thus to produce a continuous column of water through the stem is called
transpiration pull.
The rate of transpiration through stomata increases by:
-low humidity, wind, and high intensity of light.

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C-PLANT REPRODUCTION

Asexual reproduction:
Occurs by vegetative propagation, a piece of root or stem or leaf produces an entirely
new plant which is genetically identical to the parent plant.

Sexual reproduction

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Steps of sexual reproduction in plants:
1-pollination: pollen grain containing 3 haploid nuclei sticks to the stigma.
2-one nucleus forms pollen tube that burrows down the style.
3- The two other sperm nuclei enter the ovule and make double fertilization:
 One nucleus fertilizes the egg and becomes the embryo (2n)
 The other nucleus fertilizes the 2 polar bodies of the ovule and becomes the
endosperm/cotyledon (3n), the food for growing embryo.

Notes:
- After fertilization the ovule becomes the seed and the ripened ovary becomes the
fruit.
- In monocots food remain in the endosperm, while in dicots it is transported to the
cotyledons; mature dicot seed lacks endosperm.
- The endosperm in coconut (monocot) is liquid.

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Alternation of generations: The sexual life cycle of plants is characterized by the
alternation of generation, in which haploid (n) and diploid (2n) generations alternate
with each other.

In mosses (bryophytes) life cycle, the

gametophyte generation is dominant. This
means that the organism is haploid (n) for
most of its life cycle, the gametophyte
performs photosynthesis and the sporophyte
(2n) depends on the gametophyte to obtain
nutrition.

In ferns (seedless tracheophytes), both sporophyte

and gametophyte obtain food by photosynthesis,
sporophyte generation is larger.

In seed plants (Angiosperms & gymnosperms):

gametophyte generation exist inside the sporophyte generation and is totally
dependent on it.

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Plant responses to stimuli
Plants cannot run away from a stimulants, but it still can respond to them by growing
either toward the stimulant (+) or away from it (-), this response is called Tropism.

Examples of tropism:
-Phototropism: plant response to light, and grow either toward light (positive
phototropism) which happens in stem, or away from light (negative phototropism)
which happens in root.

-Gravitropism or geotropism: plant response to gravity, shoot tip shows negative

geotropism, while root tip shows positive geotropism.

-Thigmotropism: plant response to touch, ex: climbing plants that attach to

surrounding objects to gain support.
Note that carnivorous plants, growing in poor soil, close their leaves when touched
by insects in order to provide themselves by nitrogen and other nutrients, this
response is not a growth response, it is called thigmonasty.

-Hydrotropism: plant response to water.

-Photoperiodism: plant response to the seasonal changes in day and night lengths.
 Critical night length: is the darkness period per 24 hours that is required to
inhibit flowering of long day plants and to induce flowering in short day plants.
 Long day plants (short night): plants that flower only after being exposed to
darkness period that is less than their critical night length.
 Short day plants (long night): plants that flower only after being exposed to
darkness period that is more than their critical night length.

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These responses are regulated by different plant hormones, auxins are hormones
that causes phototropism:

Auxins (+) (-):

 Auxin hormone stimulates the elongation of stem cells, and inhibits the
elongation of root cells.
 Phototropism in shoot tip and root tip occurs due to unequal distribution of
auxins, because auxins accumulate in the shaded side (away from sunlight).

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Evolution is the change in a population’s gene pool over time as a
response to the change in environmental conditions.
It happens because:
• Genetic variability within the same population allows some individuals
who have the adaptive traits to be better competitors than others. In
the “game” of natural selection, they win;
• The winners survive, reproduce, and pass their genes to their offspring;
• The offspring have genes like those of their parents. Hence, the gene
pool changes.
Gene pool: all genetic traits in a population
Population: all members of one species living in a particular geographic
area, ex: all lions in Kenya forest.
Microevolution: small changes that affect only one or a few genes in
populations over shorter time. The accumulation of these changes over
long time lead to macroevolution.
Macroevolution: is the formation of new species (speciation) due to
large-scale changes that occurred over extended time periods.
After speciation occurs, the 2 new species are said to have the same
ancestor
Note that: individuals never evolve, only populations do.

Sources of variations that results in diversity within same population:

1-Mutation: the raw material for evolutionary change (nonselective).
2-Gene flow: movement of alleles in or out a population due to migration of
individuals or gametes. (going out your country emigration, going in new
country immigration)
3-Genetic drift: change in gene pool due to chance.
 Bottleneck effect: a loss of genetic variation due to natural disasters.
 Founder effect: a small population breaks away from a larger one
to colonize a new area.

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Evidences of evolution
1-Fossil records
Fossils are preserved remains of once living organism. Only hard
structures like bones or teeth can be preserved in rock layers, the oldest
layer will be on the bottom and the youngest on the top.
The fossil records shows that:
 99%of all organisms that ever lived are now extinct
 Prokaryotes were the first organisms to develop on earth.
 Earth is about 4.5 billion years old, first living cell appeared 3.5
billion years ago. This was proved through studies of radioactive
dating and half-life.
Notes:
-Isotopes: two or more forms of the same element that contain different
numbers of neutrons, ex: Carbon-12 and Carbon-14
-Half-life: it is the time taken by a radioactive isotope to fall to half its
original amount.

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2-Comparative anatomy
 Homologous structures
Features with similar structure but different functions are an evidence of
common ancestor ex: the wing of the bat, the lateral fin of the whale,
and the human arm all have the same internal bone structure although
the function of each varies

 Analogous structures
Features with similar functions but different structures are evidence of
convergent evolution ex: a bat’s wing and a fly’s wing.

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  Vestigial structures
Structures that don’t function in an organism are evidence that the
anatomy of animals evolved ex: the appendix, limbs of snake, and hind
limbs in whale.

3-Comparative biochemistry
Organisms that have a common ancestor will have common
biochemical pathways ex: respiration.

4-Comparative embryology
Organisms that evolved from common ancestor go through similar
stages in their embryonic development ex: gill pouches in vertebrate
embryos develops in fish into gills and in humans into Eustachian tubes.

5-Molecular biology
Similarity in amino acid sequence in many organisms ex: cytochrome C
needed in aerobic respiration.

6-biogeography
The study of the geographical distribution of organisms, provides
information about how and when species may have evolved. Fossil
studies found that marsupials migrated from South Africa to Australia
before these 2 continents became separate 55 million years ago. As a
result all marsupials are isolated in Australia.

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Theories of evolution
1. Lamarck/ use and disuse (X)
He stated that individual organisms change their characteristics in
response to their environment. Ex: giraffes stretched their neck to reach
leaves of tall trees, then passed this acquired trait to offspring.
This theory was disproved because acquired traits are not inheritable.

2. Darwin’s theory of natural selection (√)

Populations tend to grow exponentially and overpopulate, when they
exceed their resources, they have to compete and struggle for
existence, the survival will be for the fittest (able to survive and
reproduce).

Examples for natural selection:

-Giraffe population in the past had different neck lengths → they
competed for limited food supply → only those were able to reach tall
trees survived → only long-necked giraffes existed.
-Before industrial revolution → light colored were able to
camouflage in their environment while dark colored moths were easy
prey for predators. After industrial revolution → environment became
darker and only dark moth were camouflaged and could survive while
light gradually disappeared.
-When antibiotics were discovered, only resistant bacteria could survive,
after few years (very rapid shift) the population of bacteria evolved to
be resistant to this type of antibiotic.
In all examples no single individual changed, but the population with
the adaptive advantage survived.

Types of natural selection:

The process of natural selection can alter the frequency of inherited
traits in population in 3 ways depending on which phenotypes are
favored:

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Directional selection, stabilizing selection, disruptive (diversifying)
selection.

3-Population stability theory/ Hardy-Weinberg

equilibrium
Allelic frequency does not change if the population is stable.
-Characteristics of a stable population:
 The population must be very large
 The population must be isolated
 There must be no mutation in the population
 Mating must be random
 There must be no natural selection

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-Hardy-Weinberg stated the following equation to calculate frequencies of
alleles in a population:

P + q = 1 or p2 + 2pq +q2 = 1
p= dominant allele, q= recessive allele, p2= homozygous dominant
genotype (AA)
q2= homozygous recessive genotype (aa), 2pq= heterogeneous genotype
2(Aa)

-Sample problem:
If 9% of a population has blue eyes, what percent of this population is hybrid
for brown eyes?
Blue eyes = q2 = 0.09
q = √0.09 = 0.3
p = 0.7 (p+q=1)
p2= 0.49
2pq = 1 – (p2 +q2)
2pq = 0.42
Percent of the population hybrid for brown eyes = 42%

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Isolation and new species formation:
Individuals in the same population may be isolated from each other
due to different circumstances.

1-Geographic isolation
Species are separated by mountains,
lakes, rivers,.. etc.

2-Polyploidy
Polyploid organisms cannot breed with
other organisms and therefore isolated from
them.

3-Habitat isolation
Two organisms live in the same area but different
habitats so they do not interbreed.

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4-Behavioral isolation
Two organisms become isolated from each other
due to some change in behavior, so they do not
interbreed.

5-Temporal isolation
Different plants of same species may become
functionally separated for some time because
some plants become sexually mature earlier
than the other plants.

6-Reproductive isolation
Individuals of closely related species may be unable
to mate due to anatomical incompatibility.

Patterns of evolution
Species evolve in 5 patterns:

Divergent evolution
A population becomes isolated and then exposed to new selective
pressures. Homologous structures are evidence of divergent evolution.

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Convergent evolution
Organisms not closely related (Unrelated species), evolve similar traits
as a result of having to adapt to similar environments or ecological
niches. Analogous structures are evidence of convergent evolution.

Parallel evolution
Two related species have made similar evolutionary adaptations and
show similar characteristics after their divergence from a common
ancestor.

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Coevolution
The evolution of one species in response to the
evolution of another. This includes the following
relationships: predator-pray, pollinator-plant, host-
parasite.

Adaptive radiation
The emergence of numerous species from a single
common ancestor introduced into an environment.
Ex: there are 14 species of finches each living in
different ecological niche and showing differences
to be adapted to their environment. All these species
evolved from a single ancestor.

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Theories about evolution
Gradualism (×)
Organisms descend from a common ancestor gradually, over a long
period of time in big changes occur by an accumulation of many small
ones.
This theory was disapproved by fossil records, because scientists rarely
find transitional forms or missing links.
This theory was abandoned to punctuated equilibrium.

Punctuated equilibrium (√)

The favored theory today. This theory proposes that new species
appear suddenly after long periods of no change.

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Spontaneous generation (×)
-It is the theory that living things emerge from non-living objects. This
theory was disproved by Redi and Pasteur.

The origin of life

 Life first appeared on this planet around 3.5 billion years ago. The
climate was hot, there was more lightning, and atmosphere
consisted of methane CH4, ammonia NH3, water vapor H2O, and
nitrogen N2, but lacked free oxygen O2.
 Under these conditions, amino acids and other building blocks of
life (like RNA) formed spontaneously.
 The first cell was produced from a multitude of chemical
reactions, energy source for these reactions was heat, lightning,
and U.V. radiation.
 heterotroph hypothesis: scientists believe that first cells on earth
were anaerobic heterotrophic prokaryotes.

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Ecology is the study of the interactions of organisms with their environment
and with each other. The environment includes abiotic (nonliving) factors such
as light, temperature, nutrients, and water, as well as biotic (living) factors
such as other organisms that inhabit the environment.
 A population: is a group of individuals of one species living in one area
who can interbreed and interact with each other.
 A community: consists of all the organisms living in one area.
 An ecosystem: includes all the organisms in a given area + the abiotic
factors with which they interact.
 A biome: ecosystems of the same type (same plants and animals)
inhabiting different areas that share the same climate.
 The biosphere: the global region (ecosystem) of planet occupied by
living organisms.
 A niche: includes what an organism eats and what it needs to survive.

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Population
Properties of populations
Size:
The total number of individuals in a population, which is limited by the number
of births, the number of deaths, and immigration.
Density:
The number of individuals in unit area or volume.
Dispersion:
It is the pattern of spacing of individuals within the area the population
inhabits.

a-Clumped: most common, for safety, resource

availability, or behavior. Fish travel in this pattern for
safety.

b-Uniform: influenced by social interactions such as

territoriality. Some plants secrete toxins to keep away
other plants that would compete for limited resources.

c-Random: occurs in the absence of any special

attractions or repulsions. Trees are spaced randomly
in a forest.

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Population growth
 Every population has its biotic potential which is the maximum rate at
which a population could increase under ideal conditions.
 Two types of population growth patterns may occur depending on specific
environmental conditions:
 An exponential growth (J curve): occurs in an ideal, unlimited
environment that is: no predation, parasitism, competition, wastes, and
resources are unlimited. Examples:
- A sample in a lab of bacteria inoculated onto a petri dish.
- Human population has been in the exponential growth phase for over
300 years although exponential growth is usually short-lived in nature.

 A logistic growth (S curve): occurs when environmental pressures slow

the rate of growth.

Classic population growth: after an initial period of slow growth when the
organism becomes accustomed to the new environment, the population
explodes and grows exponentially. The population grows (exponentially) until it
reaches the maximum that the environment can support (carrying capacity).
Carrying capacity: it is the limit to the number of individuals that can occupy
one area at a particular time which cause logistic growth (s-shape curve).

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Each environment has its own carrying capacity around which the population
oscillates.
The carrying capacity can change as the environmental conditions change.
After some undetermined amount of time, the population may crash.
Factors that cause a population crash: predation, parasitism, severe
competition, end of resources, and too much waste.

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Reproductive strategy
r-strategists: organisms that reproduce rapidly when the environment is
uncrowded and resources are vast.
k-strategists: organisms that tend to maximize population size near the
carrying capacity for an environment.
r- strategists k-strategists
Offspring quantity many few
Offspring size small large
Maturation rapid slow
reproduction Once in life time Many times
Example insect mammals

Limiting factors
They are the factors that limit population growth, they are divided into:
Density-dependent factors
Factors that increase directly as the population density increase. They include
competition of food, increase of wastes, predation and disease.
Density-independent factors
Factors that are unrelated to population density. They include earthquakes,
storms, fires, and floods.

Community and population interactions

1-Competition
Two species cannot coexist in a community if they share a niche, that is, they
compete for the same resources, and there are 3 possible outcomes for this
interspecies competition:

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 a) Competitive exclusion principle: one of the 2 species will become
extinct.

b) Resource partitioning: one species will evolve through natural

selection to use different resources.
c) Character displacement: one species evolves into many species
(ex: adaptive radiation in Galapagos islands finches)

2-predation
Predation can be either:
- Animal (predator) eating another animal (prey)
- Animal (predator) eating plant (prey)
Note: if two organisms are related in predator-prey relationship, the cycles in
predator’s population are caused by cyclic fluctuations in prey’s population.

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Adaptations of predator (for attack):
Fast, strong, camouflage (resembling background), and front facing eyes.
Adaptations of prey (for defense):
- Defense adaptations in plants: spines, thorns, and chemical poisons.
- Defense adaptations in animals:
 Active defenses (cost energy): such as hiding and fleeing.
 Passive defenses:
- Aposematic coloration: a sign in poisonous animals like bright red or
orange color to warn predators to avoid them.

- Batesian mimicry: one harmless animal mimics the coloration of another

that is harmful.

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 - Mullerian mimicry: two or more poisonous species resemble each other.

- Camouflage: resembling back ground.

3-Feeding:
Living organisms can be classified according their :
Heterotrophs include:
- Herbivores: feed on plants
- Carnivores: eat other animals
- Omnivores: eat plants or animals
- Detritivores and scavengers: eat large amounts of dead body and digest
them inside their bodies.
- Decomposers: fungi and bacteria decompose dead material externally
then absorb it.
Autotrophs include organisms that produce their own food using light
(photosynthetic) or chemicals (chemosynthetic).

Relationships based on feeding behaviors (symbiotic relationships):

A. Mutualism: (+ , +) both organisms benefits, an example is bacteria that
live in human intestine to feed and produce vitamins for the human.

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 B. Parasitism: (+ , -) one organism benefits (the parasite), while the host is
harmed, example: tapeworm in the human intestine. Note that parasites
do not directly kill their host.
C. Commensalism: (+ , 0) one organism benefits and one is neither helped
nor harmed, example: barnacles attach themselves to whales to gain
food, transportation and protection.

The food chain and energy transfer

 Living organisms feed on each other to obtain energy.
 The food chain is the pathway along which energy is transferred from
one trophic level to another.
 Energy, in the form of food, moves from the producers to the herbivores
to the carnivores.
 Only 10% of the energy stored in any trophic level is converted to
organic matter available for the next trophic level, 90% of energy is lost
as heat.
 Food web is an interconnected food chain.

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Different trophic levels in a food chain/pyramid:
Producers
- Have the greatest biomass of any trophic level
- Include photosynthetic organisms like plants, diatoms, and
phytoplankton.
- Most stable trophic level (least sensitive to fluctuations in other trophic
levels)
Primary consumers
- Eat producers
- Are herbivores or omnivores
- Ex: grasshoppers and zooplankton
Secondary consumers
- Eat primary consumers
- Are omnivores or carnivores
- Ex: frogs and small fish

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Tertiary consumers
- Eat secondary consumers
- Are carnivores or omnivores
- Top of the food chain
- Less biomass in the food chain
- Least stable (most sensitive to fluctuations in other trophic levels)
- Ex: hawk or larger fish

Note that decomposers are usually not drawn in any food chain however
without decomposers to recycle nutrients back to the soil to nourish plants,
there would be no food chain.

Biological magnification
Organisms occupying higher trophic levels have greater concentration of
accumulated toxins stored in their bodies than those of lower trophic levels.

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Ecological succession
Ecological succession is a series of progressive changes in the species that
make up a community over time.

Primary succession: the rebuilding begins in a lifeless area of rocks where

even soil not present or has been removed.
Pioneer organisms – lichens (symbiosis between algae and fungi) → mosses
are introduced into the area as spores by wind, pioneer community attract
more populations, final stage is the climax community.

Secondary succession: is a process started by an event (e.g. forest fire,

harvesting, hurricane, etc.) that reduces populations in an already established
ecosystem, secondary succession occurs on preexisting soil.

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BIOMES
Biomes are very large regions of earth whose distribution depends of the
amount of rainfall (humidity) and the temperature in an area.

Marine biome
 The largest biome
 The most stable biome, with temperatures that vary little.
 Provides most of earth’s food and oxygen
 Open oceans are nutrient-poor environment compared with land.

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Tropical rain forest
 This biome is found near the equator with abundant rainfall, stable
temperature, high humidity, and nutrient poor soil.
 Although these forests cover only 4% of earth’s land surface, they
account for more than 20% of earth’s net carbon fixation (food
production)
 It has the greatest plant and animal species diversity of any biome on
earth. Lush vegetation including tall broad leaved trees. Dominant trees
are very tall with interlacing tops that form a canopy (shading the floor of
the forest).
 Epiphytes (photosynthetic plants) grow on other trees rather than
supporting themselves, which may kill the trees by blocking light.

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 Desert
 It receives less than 10 inches of
rainfall per year, not even grasses
can survive.
 Desert biome is located at middle
latitude.
 The most extreme temperature
fluctuations of any biome
 Characteristic plants: drought
resistant cacti with modified leaves
(spines), sagebrush, and annual
plants that grow after hard rain then
die within a few weeks.
 Animals are active at night and
hiding in shade or burrowing during
the day.
Temperate grasslands
 Low total annual rainfall or uneven seasonal occurrence of rainfall
 Provides largest amount of food among terrestrial biomes.
 Grazing mammals include bison, antelope, and gazelle.
 Burrowing mammals such as prairie dogs and rodents.

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 Found in the northeast of North America,
south of the Taiga and have more plant
species than it.
 Characterized by trees that drop their
leaves in winter. Ex: maples.
 Shows vertical stratification of plants and
animals: some species live on the ground,
some in low branches, and some in the
treetops.
 Rich soil due to decomposition of leaf litter.
 Principal mammals include squirrels, deer,
foxes and bears that hibernate through the
cold winter.

 Found in northern Canada and much of world’s northern regions (high

latitudes) including Alaska,
Russia, and northern
Europe.
 Dominant by conifer
(evergreen) forests, dotted
with lakes and ponds.
 Abundance of rainfall, very
cold winters.
 Largest terrestrial biome.
 Heavy snowfall, needle like
leaves.
 Seasonal temperature
ranges of more than 700C.
 Large mammals include moose, black bear, lynx, elk, and porcupines.
 Flying insects and birds in summer.

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 Located in the far northern parts of North America, Europe, Asia, and
Alaska (highest latitude)
 Called the permafrost (permanently
frozen subsoil)
 Commonly referred to as frozen desert
because it gets very little rainfall, which
cannot penetrate the frozen ground.
 Treeless plains with many lakes, ponds,
and bogs in depressions.
 Insects, particularly flies, are abundant.
 Vast number of birds nest in tundra in
the summer to eat the insects and
migrate south in the winter.
 Mammals include reindeer, caribou, artic wolves, arctic foxes, arctic hares,
lemmings, and polar bears.
 Although number of individual organisms is high, number of species is
small.

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Ecosystems

The biogeochemical cycling of nutrients: Because raw materials on Earth

are limited resources (finite), nutrients are circulated through the biotic and
abiotic components of the ecosystem

The water cycle

Water is taken up into clouds by evaporation and transpiration, and returns

to the oceans, land, and lakes by rainfall or other types of precipitation.
Water that enters the soil returns to the oceans through runoff.

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Carbon cycle
Carbon enters from atmosphere to living organisms through photosynthesis
and returns to atmosphere through respiration and fossil fuel burning.

Nitrogen cycle

- Very little nitrogen enters ecosystems directly from the air (N2).
- Nitrogen fixing bacteria live in the nodules in the roots of legumes and
convert free nitrogen (N2) into ammonium ion (NH4+)
- Nitrifying bacteria convert the ammonium ion (NH4+) into nitrites (NO2-)
and then into nitrates (NO3-)
- Denitrifying bacteria convert nitrates (NO3-) into free atmospheric
nitrogen (N2)
- Decomposers are bacteria that break down dead organic matter into
ammonia (NH4+)

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HUMANS AND THE BIOSPHERE

1. Eutrophication of the lakes

1.Runoff from sewage and fertilizer increase nutrients in lakes → 2.excessive

growth of algae (algae blooming) → 3.prevent light to reach other plants →
4.other plants die → 5.dead material accumulates on the lake bottom→
6.detritivores and decomposers use up oxygen as they decompose dead
organic matter → 7.many fish die due to oxygen deplition → 8.decomposers
expand their activity and oxygen continue to decrease causing more deaths →
9.lakes disappears over centuries due to accumulation of decomposing matter
on the lake bottom.

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 2. Acid rain
The combustion of fossil fuels produce sulfur and nitrogen oxides causing the
pH of the rain to be less than 5.6, this causes the death of the organisms in
lakes and damages ancient architecture.

3. Global warming
It is the increase in the average temperature on earth caused by the increase
of carbon dioxide concentration in the air due to fossil fuel burning.
Carbon dioxide and water vapor absorb much of the infrared radiation
reflecting off of earth (greenhouse effect) causing the average temperature to
rise.
Global warming could have disastrous effects for earth: droughts, storms,
floods….
4. Ozone layer depletion
The accumulation in the air of chlorofluorocarbons CFC have caused the
formation a hole in ozone layer which allows more UV light to reach earth, this
responsible for an increase in the incidence of skin cancer.

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 5. Introduction of new species:
An introduced species is an organism that is not native to the place or area
where it is transported by human activity. They often dominate the ecosystems
they invade, upsetting the natural balance that existed prior to their
introduction.
Pesticides vs. biological control
Pesticides are chemicals used to kill undesirable organisms, but on the other
hand they can cause cancer in humans when exposed to them, also they lead
to the development of resistant strains of pests through natural selection.
An alternative to pesticides is biological control:
A method of controlling pests such as insects, mites, weeds and plant
diseases
using other organisms, examples:
 Use crop rotation change the crop planted in a field.
 Introduce natural enemies (predator, competitive) of the pests but not an
invasive species
 Use insect birth control by sterilizing male insect pets.

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Scientific inquiry refers to the different ways in which scientists study the
natural world and propose explanations based on the evidence derived
from their work.
There was never one standard method. The most common steps that may
be included in a scientific inquiry:
1. Make an observation.
2. Ask a question.
3. Form a hypothesis.
4. Plan an experiment.
5. Data are collected, analyzed, and illustrated.
6. conclusion

1. Make an observation.
It is receiving knowledge of the outside world through our senses, ex: bean
plants growing in different ways.

2. Ask a question
The question must be specific and testable, i.e. there must be a way to
find the answer, ex: will different types of fertilizer affect the growth of a
bean plant in different ways?

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3. Form a hypothesis
A hypothesis is a prediction of what will happen. It is a specific answer to
the question, ex: fertilizer A is the most likely to affect the growth rate of
bean plants
4. Plan an experiment
An experiment is performed to test our hypothesis, this experiment must
include:
a. Experimental design:
The experimental design consists of a list of materials, and a series of steps
(procedures) that must be followed.
b. Independent variable (manipulated):
It is changed by the person conducting the experiment in order to see
what the effect will be, ex: the four types of fertilizer.
c. Dependent variable (responding):
What happens as a result of independent variable, and is measured by the
scientist in the experiment, ex: the height of the plants
d. Controlled variable:
Factors that are kept the same to make sure the results are accurate, ex:
the type of seeds used, the amount of soil, the amount of light received by
the plant, the amount of water per day, the amount of fertilizer.
Note: Controlled experiment is an experiment in which only one variable is
changed
5. Collecting and analyzing data
After the experiment is conducted, scientist gather data.
Quantitative data: observations and facts that can be easily measured, ex:
the heights (in cm) of the plants.
Qualitative data: observations that cannot be easily measured, ex:
comparisons about how strong and healthy the bean plants seem to be.
The data then are analyzed and illustrated by graphs, tables, etc.

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 6. Conclusion statement
A statement that summarizes some or all of the findings of an experiment
or investigation, e.g., fertilizers with high concentrations of ammonia
nitrate increase the growth rate of bean plants while maintaining a strong
stem and leaf system.

149
 Basic assumptions in sciences

1.Nature is Orderly
Natural events have a pattern of regularity and order in their occurrence.
Even when there appears confusion in the ecosystem as seen during
floods, drought, famine, earthquakes, and disease epidemics, human
interference has always been the cause.
Take for example:
- The sun rises daily in the east and sets in the west within the
tropics.
- Seasons of spring, winter, autumn and summer always follow
that order.
- The rainfall periods of long rains and short rains in the tropics
always follow a known order and time.
- Heavy clouds are always a sign of coming rains.
- Seeds when plated will germinate and grow to yield their fruits
before the plant dies.
2. Humankind can know nature
This assumption is based on the premise that human beings as living
organisms are part of the natural world. So if we can understand how the
natural world functions using scientific inquiry, then we can also use
scientific inquiry to understand human nature.

3. Knowledge is superior to ignorance

In science, knowledge (truth) is relative to evidence, method used to
generate it and theories used to support its universality.

150
4. All natural phenomena have natural causes
This assumption argues that there is a natural cause for any natural event.
This opinion dismisses the belief that a supernatural power exists, which
controls natural events and order. This approach has also been the source
of conflict between religious fundamentalists who believe in the existence
of God and scientists of the Darwinian philosophy who believe in the
process of evolution.
5. Nothing is self-evident
Truth or knowledge must be derived through scientific method, and is not
self-evident or taken to be obvious.

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 Reproduction and development
-It is the process by which an organism produces its offspring, providing
for the continued existence of his species.
-Reproduction is either asexual or sexual.
Asexual reproduction Sexual reproduction
Involves one parent only (advantage Involves 2 organisms (male and
in isolation) female)
Offspring are genetically identical to Offspring show genetic variation,
the parent (except if mutation an advantage in a changing
occurs), this is an advantage when environment, leads to greater
environment is favorable and reproductive success (offspring
stable more fitting for natural selection)
Gametes are not produced (except Gametes are produced by parents
parthenogenesis)
The cell division are only mitotic Gametes are produced by meiotic
divisions and zygote develops by
mitotic division
No expenditure of energy High biological cost (expenditure of
(advantage), no hormonal cycles or energy)
reproductive systems
Large progeny (offspring number) Smaller progeny
Faster Slower

Types of asexual reproduction

1- Binary fission
- It is the separation of an organism into
two new cells. Ex. Amoeba, bacteria.
Results in equal division of the
cytoplasm and symmetrical daughter
cells.

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 2- Budding
A new organism develops from an
outgrowth or bud due to cell
division at one particular site. It
involves an unequal division of
the cytoplasm and asymmetrical
daughter cells.
Ex. Yeast, hydra

3- Spore formation
Spores are protected through the formation of a thick cell
wall and can withstand harsh conditions such as drought
or extreme temperatures.
Ex. Bread mold, mosses.

4- Regeneration
It is the ability of a simple organism
to re-grow its lost parts. Ex starfish,
flat worms.

5- Schizogony (multiple fission)

It occurs in some protozoa, in which,
after a varying number of nuclear
divisions, the cell divides into a number
of daughter cells.

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 6- Parthenogenesis

Reproduction from an ovum

without fertilization, that
divides mitotically and
become new individual. Ex.
Some plants, some bees.

Sexual reproduction
During sexual reproduction, a small flagellated haploid sperm (n) fertilizes
a larger, nonmotile haploid egg (n) to form a diploid (2n) zygote. The
zygote then undergoes cleavage, gastrulation, and organogenesis.

Types of Fertilization and Development:

Animal fertilization development Number Parental
of eggs care
fish external external many none
amphibian external external many none
Reptiles internal External (inside the egg) few some
Birds internal External (inside the egg) few much
mammals internal internal few much

Note: Animals that practice external fertilization and external

development must produce many eggs and sperm in order to ensure
survival of the species,
Because they are subjected to environmental factors and predators.

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Sexual reproduction in humans
1- Male reproductive system

• Testes: (testis, singular): male gonads; composed of seminiferous

tubules which are the site of meiosis (sperm formation)
•The epididymis: is a long, coiled tube that stores sperm and transports it
from the testes
• Vas deferens: the duct that carries sperm during ejaculation from the
epididymis to the penis
• Prostate gland and seminal vesicle: add their secretions so that the
sperms are in a fluid which makes their transport easier and this fluid also
provides nutrition.

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• Scrotum: the sac outside the abdominal cavity that holds the testes; the
cooler temperature there enables sperm to survive
• Urethra: the tube that carries semen secreted from prostate, also
carries urine. A fluid is secreted before semen to neutralize any acid
residue in the urethra left over from urine.
Production of seminal fluid:
1- Sperms are made by meiosis in seminiferous tubules in the testis
2- Sperms are stored in epididymis.
3- Sperms are ejaculated to vas difference.
4- Fluid is secreted from prostate gland and seminal vesicle and added
to sperms.
5- Seminal fluid is ejaculated into urethra

2-Female reproductive system

• Ovary: where meiosis occurs and where the secondary oocyte forms
prior to birth
• Oviduct or Fallopian tube: where fertilization occurs; after ovulation, the
egg moves through the oviduct to the uterus
• Uterus: where the blastula stage of the embryo will implant and develop
during the nine-month gestation, should fertilization occur

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• Vagina: the birth canal; during labor and delivery, the baby passes
through the cervix and into the vagina
• Cervix: the mouth of the uterus
• Endometrium: lining of the uterus

Menstrual cycle
The female reproductive system not only has to produce gametes, it also
has to prepare itself for pregnancy. That means we have to consider two
organs: the ovaries (which produce the gametes) and the uterus (which
sustains a pregnancy).

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 Ovarian cycle Uterine cycle
day 1 to 13 follicular phase: About 5 days of
FSH from the anterior menses, then Estrogen
pituitary gland secreted by mature
stimulates a follicle to follicle promotes
mature and produce thickening of the
estrogen. uterine lining to
support an embryo if
fertilization occurs.
day 14 Ovulation: Uterine lining is
When the follicle is maintained and
mature, a surge in LH enhanced.
secretion from the
anterior pituitary
causes ovulation (the
release of the ovum
from ovary)

Day 15 to 27 luteal phase: Progesterone and

the remains of the estrogen enhance
follicle in the ovary lining formation in the
create the corpus uterus in preparation
luteum which produce for implantation of the
progesterone and fertilized egg.
estrogen
Day 28/1 If no fertilization has Progesterone and
occurred, LH estrogen levels fall,
production is blocked, and the uterine lining
corpus luteum degenerates and sheds
degenerates. off, marking the
beginning of the next
cycle.

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Problems that may prevent fertilization:
 Fertilization occurs in fallopian tube (oviduct), if it is blocked no
fertilization occurs.
 An egg lives for about 12-24 hours after being released.
For pregnancy to happen, the egg must be fertilized by a sperm
within this time. Sperm can live for up to 7 days inside female's body.
 An imbalanced pH level in the cervix or vagina can damage sperm
enough to prevent it from fertilizing an egg.

If fertilization occurs:
1. The developing placenta produces hCG hormone, which maintains
the corpus luteum.
2. The corpus luteum then continues to make progesterone and
estrogen for about 3 months.
3. Progesterone prevents menstruation and ensures that the uterine
wall is thickened so pregnancy can continue.
4. With time, the placenta develops and takes over the production of
estrogen and progesterone for the duration of pregnancy.
5. Placenta provides oxygen and nutrients to the fetus and removes
waste products from his blood. Placenta never pass nerve impulses
to fetus.

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Oogenesis and spermatogenesis
Oogenesis
Occurs in ovaries except last stage
Unequal division of cytoplasm
1 gamete (and 2 or 3 polar bodies)
In embryo stage, all primary
oocytes are produced by mitosis,
the rest of the process occurs
monthly after puberty until
menopause.
Note: meiosis 2 occurs after sperm
penetration.
Spermatogenesis
Occurs entirely in testis
Equal division of cells
4 gametes produced
Begins at puberty and occurs
continuously until death (reduces
with age)
Note: LH hormone induces testis to
produce testosterone, FSH and
testosterone stimulate sperm
production in the testes.
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 Embryonic development
After fertilization, a zygote (2n) is formed, embryonic development passes
through several stages. Here are the basic steps and events:

Process fertilization cleavage Differentiation/ growth

embryonic stage
Stage Zygote Morula blastocyst gastrula neurulation fetus
Time 1 day 4 days 6 days 10 days 20 days till
birth
where Fallopian Fallopian Uterine Uterine wall Uterine
tube tube wall wall
Details The nuclei While Cells the inner Every organ The
of both travelling continue cell mass in the body organs
gametes down the to divide divides is formed simply
fuse and oviduct, cells and start into three during this mature
form perform hollowing layers, period, by and
zygote that rapid mitosis out making called the the end of grow
has a full with no cell a fluid- primary this stage all larger.
set of growth, it filled ball germ the organs
chromoso- becomes a of cells layers and
mes (2N) solid ball of called a endoderm structures
cells called a blastula mesoderm are formed.
morula. which is and
implanted ectoderm
in uterine
wall
The 3 main layers are formed in gastrulation stage, while different organs
arise from these layers in neurulation stage.
-The ectoderm: develops into the skin, the nervous system, and the eyes,
hair, and teeth.
-The mesoderm: develops into the muscles, the skeleton, the circulatory
system, the kidney, and the gonads.

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-The endoderm: develops into the lining of the digestive and respiratory
tracts, and the lining of the bladder, pancreas, and liver.

Note that:
Initially, the fertilized embryo divides into many undifferentiated
(unspecialized) cells, also the zygote divides but maintains its size (no cell
growth). Morula is 16-cells stage.

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Extra embryonic membranes:
The four membranes that arise outside the embryo are known as the
extraembryonic membranes. They consist of the chorion, yolk sac, amnion,
and allantois.

Birds and reptiles human

chorion (the lies under the shell and encloses all the other
outermost allows for diffusion of membranes, forms the
membrane) respiratory gases embryo’s part of the
placenta
Yolk sac (encloses A lot of yolk to provide Very little yolk,
the yolk) the food of the of because human
embryo that develops embryos develop
outside mother’s body inside the mother’s
body and receive their
nutrition from a
placenta. Human yolk
is the source of the
first blood cells
Amnion Clear membrane that Clear membrane that
surrounds the surrounds the
developing embryo developing embryo
and is filled with and is filled with
amniotic fluid. Protects amniotic fluid. This
bird and reptile fluid acts as a shock
embryo from absorber
dehydration. This fluid
acts as a shock
absorber
Allantois Disposal site for solid Becomes the umbilical
wastes (nitrogenous cord, which connects
waste accumulates the embryo to the
until the chick hatches) placenta.

163
164
 Digestive system
The human digestive system has two important functions:
1- Breaking down large food molecules into smaller, usable molecules.
2- Absorbing these smaller molecules.
Note: vitamins and minerals are small enough to be absorbed without being digested
The digestive tract (alimentary canal) is about 30 feet long made of smooth
(involuntary) muscle that pushes the food along the digestive tract by a process
called peristalsis, these muscles are controlled by autonomic nervous system.

165
Mouth
 Mechanical and chemical digestion begins here (bolus)
 Starch digestion begins (from polysaccharide to disaccharide) by salivary
amylase in saliva secreted from salivary glands.
 pH neutral is neutral (7)
 Type of teeth is related to dietary habits:
Omnivores (like humans) have three types of teeth incisors for cutting, canines for
tearing and molars for grinding.
Esophagus
 No digestion occurs here
 After swallowing, food is directed into the esophagus and away from windpipe
by the epiglottis.
Stomach
 It has a thick muscular wall that churns food mechanically and secrets gastric
juice which contain hydrochloric acid and enzymes
 Both mechanical and chemical digestion occurs here
 Protein digestion begins here: HCL kills microbes, break down muscles (meat),
and activates the inactive enzyme pepsinogen to become pepsin
 The enzyme renin aids in the digestion of the protein in milk
 pH acidic (2-3)
 the cardiac sphincter at the top of the stomach keeps acidified food from
backing up into esophagus and burning it, the pyloric sphincter at the bottom
of the stomach keeps the food in the stomach long enough to be digested
 Mucus secreted in stomach protects it from acid, excessive acid can cause an
ulcer to form in the esophagus, the stomach, and the duodenum (upper
intestine), also a particular bacterium called helicobacter pylori is a common
cause of ulcers.
Small intestine
 All digestion is completed and nutrients are absorbed here.
 It is 6 meters long and pH is 8
 All digestion is completed in the duodenum (first 10 inches of intestine).
 Proteases (secreted by intestine and pancreas), continue to break down
protein.

166
  Nuclease (secreted by pancreas) hydrolyze nucleic acid into nucleotides.
 Lipase (secreted from pancreas) break down fat emulsion.
 Disaccharidases (secreted by intestine) break down disaccharides
 millions of fingerlike projections called villi line the small intestine and absorb
all nutrients that were previously released from digested food
 each villus contains capillaries, which absorb amino acids, vitamins, and
monosaccharaides directly into the bloodstream, and a lacteal, which absorbs
fatty acids and glycerol into the lymphatic system and also have microvilli that
increase the rate of absorption

Liver
 associated organ (not a part of the alimentary canal)
 Produces bile (salts) that emulsifies fats (mechanical digestion)
 Bile = pH 11 neutralizes chime (acidified food from stomach) entering small
intestine
 Sends bile to the gallbladder until its release into the small intestine
 Liver has other functions besides associating digestion:
1- Breaks down and recycles red blood cells
2- Detoxifies blood; removes alcohol and drugs
3- Produces cholesterol necessary for structure of cell membrane
4- Produces the nitrogenous waste urea from protein metabolism
Gallbladder
 Associated organ (not a part of the alimentary canal)

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  Stores bile that is produced in liver
 Bile emulsifies fats in small intestine, body can function well without a
gallbladder but needs to avoid fatty and greasy foods in his diet.

Pancreas
 Associated organ that is not a part of the alimentary canal.
 A gland that produces enzymes and secretes them into small intestine to
break down: Carbohydrates (amylases), proteins (peptidases), lipids (lipases),
and nucleic acids (nucleases).
 Also pancreas produces sodium bicarbonate, a base that neutralizes stomach
acid enabling intestinal enzymes, which require a basic environment to be
effective
Large intestine or colon
 No digestion occurs here
 Major functions:
1) Egestion: removal of undigested waste (not excretion because wastes didn’t
enter our cells)
2) Vitamin production: bacteria symbionts living in the colon produce vitamin K
and vitamin B (folic acid)
3) Reabsorption of water: if amount of water reabsorbed from intestine to the
body is inadequate it causes constipation or diarrhea
Rectum
Last 7 to 8 inches stores feces until their release through the anus.
-----------------------------------------------------------------------------------------------------------------
----
Notes:
Humans do not obtain any energy from eating cellulose because the required enzyme
necessary to hydrolyze cellulose is lacking.
All the digestive system is controlled by involuntary muscles except mouth pharynx,
and anus.

168
Digestion in brief:

169
170
 Respiratory system and gas exchange

In humans, air enters the nasal cavity and is moistened, warmed, and filtered. From
there air passes to pharynx then through the larynx and down the trachea and
bronchi into the tiniest bronchioles which end in microscopically tiny air sacs called
alveoli (air sac). Here diffusion of respiratory gases occurs.

Gas exchange process:

Humans have an internal respiratory surface because respiratory gases are
exchanged deep inside the body. The rib cage expands and the diaphragm contracts
and move downward, thus expanding the chest cavity and decreasing the internal
pressure.

Air is drawn into the lungs by negative pressure because the internal pressure inside
the chest cavity is lower than the air pressure surrounding the body.

171
The medulla in the brain sets the breathing rhythm by monitoring carbon dioxide
levels in the blood and by sensing changes in the pH of the blood. A blood pH lower
than 7.4 triggers autonomic nerves from the medulla to increase the breathing rate
to rid the body of more carbon dioxide. The concentration of oxygen in the blood
usually has little effect on the breathing control centers.

172
Transport of Oxygen and Carbon Dioxide:
Oxygen is carried in the human blood by the respiratory pigment hemoglobin, which
combines loosely with oxygen molecules to form the molecule oxyhemoglobin.
Carbon dioxide, the by-product of cell respiration, is released from every cell and
dissolves in the blood.
 Some CO2 is carried in the plasma as part of the reversible blood-buffering
carbonic acid-bicarbonate ion system, which maintains the blood at a constant
pH of 7.4
 Very little CO2 is transported by hemoglobin forming carbohemoglobin.

Notes:
- Alveoli of the lung and villi of the intestine are alike in:
 They increase the surface area for exchange of materials
 They have a thin layer of epithelial cells
 They have extensive blood vessels
 They are extremely numerous.
- Different organisms have different gas exchange organs (gills, lungs, skin) but they
are alike in having moist respiratory surface.
- Emphysema is a disease characterized by the destruction of the alveolar walls. This
results in reduced elasticity of the lungs, making exhalation difficult. Most cases can
be traced to cigarette smoking.

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 Circulatory system
The circulatory system transports needed materials to the cells and carries away
waste materials. Human circulation consists of a closed circulatory system

1- Blood vessels
They transport blood through the body. They consist mainly of: arteries, veins, and
capillaries. Arteries and veins are designated as arteries or veins based only on the
direction they are carrying the blood—either away from or toward the heart.

174
 2- Blood
Blood consists of several different cell types (45%) suspended in a liquid matrix called
plasma (55%). The average human body contains 4 to 6 liters of blood
Blood component Scientific name properties
Plasma none -Liquid portion of the
blood
-Contains clotting factors
(plasma minus clotting
factors = serum),
hormones, antibodies,
dissolved gases, nutrients,
and wastes.
90% water
Red blood cells Erythrocytes -Biconcave disc-like cells
-No nucleus
-Contains hemoglobin that
transports oxygen from
lungs to body parts
-Live about 120 days
-Formed in bone marrow
and recycled in the liver

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 White blood cells Leukocytes -Fight infection
-Formed in bone marrow
-Die fighting infection and
are one component of pus
-Main types:
Lymphocytes that produce
antibodies to destroy
microorganisms
Phagocytes that engulf
bacteria and
microorganisms

Platelets Thrombocytes -Cell fragments that are

formed in the bone
marrow from a mother
cell called megakaryocyte
-Clot blood

The mechanism of blood clotting

Anticlotting factors constantly circulate in the plasma to prevent the formation of a
clot or thrombus, which can cause serious damage in the absence of injury.

After an injury, platelets and damaged tissue release thromboplastin and Ca++

Here is the pathway of normal clot formation:

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 3- The heart

The heart is located beneath the sternum and is about the size of your clenched fist.
It beats about 70 beats per minute and pumps about 5 liters of blood each minute.
Two atria receive blood from the body and two ventricles pump blood to the body.

177
The heart itself has its own pacemaker where the electrical impulses are generated,
the sinoatrial (SA) node, which sets the timing of contractions of the heart. Electrical
impulses travel through the cardiac and body tissues to the skin, where they can be
detected by an electrocardiogram. The heart’s pacemaker is influenced by: nervous
system, hormones such as adrenaline, and body temperature.

Blood pressure is lowest in the veins and highest in the arteries when the ventricles
contract. The average blood pressure for all normal resting adults is 120/80

The systolic number (120) is a measurement of pressure when the ventricles

contract, while the diastolic number (80) is a measure of the pressure when the
heart relaxes.

The pathway of the blood

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Heart → lungs → heart = pulmonary circulation.

Heart →body → heart = systemic circulation.

Remember that: pulmonary artery is the only artery that carries deoxygenated blood,
and pulmonary vein is the only vein that carries oxygenated blood.

Blood circulates through: coronary circulation (heart), renal circulation (kidneys),

hepatic circulation (liver), and pulmonary circulation (lungs)

Note: animals of different classes in chordates have different heart chambers: 2 in

fish, 3 in amphibian and reptiles, and 4 in birds and mammals.

Diseases related to blood:

 Anemia is low hemoglobin count due to lack of iron in the diet of the patient.
 Leukemia is cancer of the blood-forming tissues; it usually involves white blood
cells.
 Hypertension is high blood pressure, hypotension is low blood pressure.
 Having infection, inflammation, and fever lead to an increase in white blood
cells count.
 The decrease in white blood cells leads to low immunity and high susceptibility
to infections
 Sickle cell anemia is an inherited red blood cell disorder that causes blockage in
blood vessels and low oxygen content in the blood.

The lymphatic system

The lymphatic system, is part of the circulatory system and the immune system. It is
made up of a large network of lymphatic vessels, lymphatic organs or lymph nodes,
the vessels carry a clear fluid called lymph towards the heart.

Lymph nodes are small structures that work as filters for harmful substances.

Its main functions:

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 The removal of excess fluids from body tissues and return them to blood,
which keeps the blood volume from decreasing.

 Production of immune cells (such as lymphocytes, monocytes)

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 EXCRETION
 Excretion is the removal of metabolic wastes from blood and body cells.
 This includes:
 removing carbon dioxide and water from cell respiration
 Nitrogenous wastes from protein metabolism.
 The organs of excretion in humans are the skin, lungs, liver, and the kidneys.
 Skin excretes sweat consisting of water and salts, including urea.
 Lungs excrete water vapor and carbon dioxide from the Krebs cycle.
 The liver does not excrete any substances from the body, but it is the site of
deamination of amino acids and the production of urea.
 The kidneys excrete excess water and urea.
THE HUMAN KIDNEY

 The kidney adjusts both the volume and the concentration of urine depending
on the animal’s intake of water and salt and the production of urea.
 Humans have two kidneys supplied by blood from the renal artery.
 The kidneys filter about 1,500 liters of blood per day and produce, on average,
1.5 liters of urine.
 Like all terrestrial animals, we need to conserve as much water as possible, but
we must balance the need to conserve water against the need to rid the body
of soluble poisons.

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  The kidney is able to respond quickly to the changing requirements of the body
because it is under hormonal control.
 Antidiuretic hormone (ADH) regulates the water level in blood, it is
released by the posterior pituitary and targets the collecting tube of the
nephron. ADH regulates blood pressure by controlling how much water
is reabsorbed by the kidneys. Note that lacking this hormone causes
excess loss of water through urine which leads to dehydration.
 Aldosterone hormone is secreted by adrenal cortex and can increase the
amount of sodium the body sends into the bloodstream or the amount
of potassium released in the urine.

THE NEPHRON
 The nephron is the basic functional unit of the kidney.
 It consists of:
 a cluster of capillaries, known as the glomerulus—which sits inside a
cuplike structure called Bowman’s capsule
 a long narrow tube called the tubule
 The loop of Henle.

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  Each human kidney contains about 1 million nephrons.
 The nephron carries out its job in four steps:
1. Filtration
2. Secretion
3. Reabsorption
4. Excretion.
1-Filtration
- Filtration occurs in the glomerulus and creates a plasma like filtrate of the blood.
- Filtration is passive and nonselective and occurs by diffusion.
- The filtrate contains everything small enough to diffuse out of the glomerulus and
into Bowman’s capsule, including glucose, salts, vitamins, wastes such as urea, and
other small molecules.
- From Bowman’s capsule, the filtrate travels into the loop of Henle and then the
collecting duct or tubule.
- From the collecting tubule, the filtrate trickles into the ureter and the urinary
bladder for temporary storage and then to the urethra and out of the body.

2-Secretion
Secretion is the active, selective uptake of molecules that did not get filtered into
Bowman’s capsule. This occurs in the tubules of the nephron.

3-Reabsorption
-Reabsorption is the process by which most of the water and solutes (glucose, amino
acids, and vitamins) that initially entered the tubule during filtration are transported
back into the capillaries and thus back to the body.
-This process occurs in the tubule, the loop of Henle, and the collecting tubule.
-The longer the loop of Henle, the greater is the reabsorption of water.

4-Excretion
-Excretion is the removal of metabolic wastes, for example, nitrogenous wastes.
-Everything that passes into the collecting tubule is excreted from the body.

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THE SKIN

 The skin and all of its associated structures, such as hair, nails, sweat glands, oil
glands, and sensory receptors, are collectively considered an organ.
 The skin is made of three layers of tissue: the epidermis, the dermis, and the
hypodermis.
 The epidermis is a thin layer of cells at the body surface, most of which
are dead. It contains melanin pigment that gives skin color and protects
from UV radiation
 The dermis is a relatively thick layer of connective tissue underneath the
epidermis that contains blood vessels, nerves, hair follicles, and glands.
 The hypodermis is a deep layer of fat that helps protect and insulate the
body. The hypodermis varies in thickness from person to person.

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  The skin’s primary job is to protect the body from:
 Abrasion (friction)
 Heat loss
 Water loss
 Infection
 UV radiation
 vitamin D production
 sensation
 Thermoregulation (body temperature control).

Thermoregulation (too hot / too cold)

When your body temperature rises, receptors in your skin and body core monitor
the change. They send information to your brain, and your brain sends messages to
your body that cause it to cool.
1. Blood vessels in the dermis dilate (Vasodilation), allowing more blood to come
close to the surface of the skin. This allows more heat to leave the body. (It also
produces the characteristic red flush of an overheated person.)
2. Sweat glands in the skin become active, secreting sweat. As the sweat evaporates,
the body temperature lowers.

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 When your body temperature falls, receptors in the skin and body core monitor the
change and send the information to the brain, and the brain sends commands to the
body to increase warming.
1. Blood vessels in the dermis constrict (vasoconstriction), keeping the blood from
the surface of the body. This retains more heat near the body core. (It also produces
the characteristic bluish color of a very cold person.)
2. Sweat glands in the skin are inactivated.
3. Shivering is initiated. Shivering is rapid, involuntary muscular contractions. Muscle
contraction generates a lot of heat, so shivering is an excellent way to raise body
temperature.
Notes:
-The camel can tolerate a wide range of body temperatures because of its hump
which is a protective fat layer.
-Other animals adaptations for thermoregulations: Hiding in shade, huddling, bees
swarming, dogs pant and sweat by tongue, elephants flap their ears, Humans shiver
or jump around.

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 Endocrine system

The Endocrine system secretes hormones, the nervous system secretes

neurotransmitters and both systems work together to maintain homeostasis.
In one case, epinephrine (adrenaline) functions both as the fight-or-flight hormone
and as a neurotransmitter that sends a message from one neuron to another
(synapse).
 Hormones are produced in ductless (endocrine) glands and move through the
blood to a specific target cell, tissue or organ.
 Hormones can produce either an immediate short-lived response (ex: fight-or-
flight response caused by adrenaline) or a dramatic long-term development of
an entire organism (ex: ecdysone controls metamorphosis in insects)

 Trophic hormones are hormones that stimulate other glands to release

hormones. For example the anterior pituitary in the brain releases thyroid-
stimulating hormone (TSH) which stimulates the thyroid in the neck region to
release thyroxin.
 Pheromones are chemicals secreted outside the body to impact the behavior
of other organisms, ex: pheromones in the urine of dogs carry a message to
other dogs.
 Nitric oxide gas in vertebrates is produced by one cell and diffuses to and
affects only neighboring cells before it is broken down
.
 The hypothalamus is the bridge between the endocrine and nervous system. It
acts as an endocrine gland when it produces oxytocin and antidiuretic
hormone. In times of stress, the hypothalamus acts as a part of the nervous
system by sending electrical signals to adrenal gland to release adrenaline.
The Hypothalamus also contains the body’s thermostat and centers of regulating
hunger and thirst.

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The following table states the other glands and hormones of the endocrine system
and their effects:

Gland Hormone Effect

• Growth hormone -Stimulates growth of bones.
(GH)

•Luteinizing hormone -Stimulates ovaries and testes.

(LH)

Anterior • Thyroid-stimulating -Stimulates thyroid gland

hormone (TSH)
pituitary
• Adrenocorticotropic -Stimulates adrenal cortex to
(ACTH) hormone secrete glucocorticoids.

• Follicle-stimulating -Stimulates gonads to produce

hormone (FSH) sperm and ova.
• Oxytocin -Stimulates contractions of uterus
and mammary glands
Posterior
pituitary • Antidiuretic hormone -Promotes retention of water by
(ADH) kidneys
Thyroid • Thyroxin (T4), (T3) -Controls metabolic rate

• Calcitonin -Lowers blood calcium levels

Parathyroid •Parathormone -Raises blood calcium levels
Adrenal cortex •Glucocorticoids -Raises blood sugar levels

• Epinephrine -Raises blood sugar level by

(adrenaline) increasing rate of glycogen
Adrenal breakdown by liver
medulla
• Nonepinephrine
(noradrenaline)
Pancreas— islets • Insulin Lowers blood glucose levels
of Langerhans
• Glucagon Raises blood glucose levels

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Thymus (in neck) •Thymosin Stimulates T lymphocytes as part of
the immune response
Pineal (in brain) •Melatonin Involved in biorhythms, sleeping
rythm
Ovaries • Estrogen Stimulates uterine lining, promotes
development and maintenance of
primary and secondary
characteristics of female
Promotes uterine lining growth
• Progesterone
Testes • Androgens Support sperm production and
promote secondary sex
characteristics

How hormones trigger a response in target cells

There are 2 types of hormones:
 Steroid (lipid) hormones: they diffuse directly through the plasma membrane
and bind to a receptor inside the cell that triggers the cell’s response
 Non steroid (protein) hormones: they cannot dissolve in the plasma
membrane so they bind to a receptor on the surface of the cell. Once the
hormone (the first messenger) binds to a receptor on the surface of the cell, it
triggers a secondary messenger such as c-AMP which converts the extracellular
chemical signal to a specific response inside the cell.

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Feedback mechanism
A feedback mechanism is a self-regulating mechanism that decreases or increases an
action or a level of a particular substance.
Positive & negative feedback
Positive feedback is a process in which the end products of an action cause more of
that action to occur in a feedback loop, this amplifies the original action. It is

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contrasted with negative feedback, which is when the end results of an action inhibit
that action from continuing to occur.
An example of positive feedback is contractions in child birth and the ripening of
fruit.

An example of negative feedback is how glucose levels in blood is regulated:

Some disorders of endocrine system:

Growth hormone:
Hypersecretion → gigantism

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Hyposecretion → dwarfism
Thyroid hormones:
Hyposecretion → low metabolic rate; they can gain weight and become
sluggish
Hypersecretion → a higher than normal metabolic rate, accompanied by
symptoms such as weight loss and a fast heart rate.
Note that lack of iodine causes hypothyroidism
Calcitonin / parathormone:
Inadequate level of calcium in blood affects many different situations like
nerve impulse conduction, heart contraction, and blood clotting.
Antidiuretic hormone (ADH)
Hypersecretion → excess fluid building up in the body (water retention)
Hyposecretion → excessive urination, ADH deficiency may be caused by
diabetes, drinking alcohol and caffeine products.

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 NERVOUS SYSTEM
The vertebrate nervous system consists of:
 Central nervous system (CNS)
 Peripheral nervous system (PNS)

The central nervous system (CNS)

Consists of the brain and spinal cord.

Note that the hypothalamus:

 Maintains body homeostasis which means a constant internal
environment regardless of changing external conditions.
 It monitors things like hormone levels, electrolyte balance, and
temperature.
 It also controls the pituitary gland.

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The peripheral nervous system (PNS)
Consists of all nerves outside the (CNS), here is an outline of the
peripheral nervous system:

Note that:
 Somatic System Controls the voluntary muscles (skeletal
muscles)
 Autonomic System Controls involuntary muscles (smooth and
cardiac muscles)
 Sympathetic responses:
-Fight-or-flight response
- Increases heart and breathing rate
- Liver converts glycogen to glucose (energy is required)
- Bronchi of lungs dilate and increase gas exchange
- Adrenaline raises blood glucose levels
 Parasympathetic (Opposes the sympathetic)
- Calms the body
- Liver store glucose as glycogen (energy isn’t required)
- Decreases heart/breathing rate
- Enhances digestion

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The neuron

It is the basic functional unit of the nervous system

The reflex arc

A reflex is an involuntary instantaneous action in response to a
stimulus, aiming to protect the body.

The simple reflex arc is the simplest nerve response, an example is

the knee-jerk reflex which consists of only a sensory and a motor
neuron, the spinal cord is not involved in this type of reflex.

The complex reflex arc consists of 3 neurons: sensory, motor, and

interneuron or association neuron. A sensory neuron transmits an
impulse to the interneuron in the spinal cord which sends one
impulse to the brain for processing and also one to the motor neuron
to effect change immediately (at the muscle). This the type of response
that quickly jerks your hand away from a hot iron before your brain
has figured out what occurred.

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Types of effectors: muscle or gland (controlled by motor neuron)

Types of sensors (receptors that stimulate sensory neuron):

How a neuron functions:

1-RESTING POTENTIAL
A neuron at rest or unstimulated is polarized, that means a difference
in electrical charge between inside the cell and extracellular fluid. The
sodium-potassium pump maintains this polarization by actively
pumping ions out of the cell that leak inward. (Remember selective
impermeability of plasma membrane)

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2-ACTION POTENTIAL
An action potential, or impulse, can only be generated in the axon of a
neuron. When an axon is stimulated sufficiently to overcome the
threshold:
- The permeability of a region of the membrane suddenly changes.
- Sodium channels open and sodium floods into the cell, down the
concentration gradient.
- In response, potassium channels open and potassium floods out of
the cell.
- This rapid movement of ions or wave of depolarization reverses the
polarity of the membrane and is called an action potential.

3-Repolarization (refractory period)

- The action potential is localized and lasts a very short time.
- The sodium-potassium pump restores the membrane to its original
polarized condition by pumping sodium and potassium ions back to
their original positions. This period of repolarization, which lasts a few
milliseconds, is called the refractory period, during which the neuron
cannot respond to another stimulus.
- The refractory period ensures that an impulse moves along an axon
in one direction only since the impulse can move only to a region
where the membrane is polarized.

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Note: action potential is like a row of dominoes falling after the first
one is knocked over. The transmission of nerve impulse through axon
can be described as a wave of depolarization and repolarization.

4-The synapse
-The site of transmission of impulses between two nerve cells
(neurons) or between a neuron and a gland or muscle cell (effector).
-Although an impulse travels along an axon electrically, it crosses a
synapse chemically.
-The cytoplasm at the terminal branch of the neuron contains many
vesicles, each containing thousands of molecules of neurotransmitter.

The impulse is transmitted through a synapse as follows:

1- Ca++ ions rush into the terminal branch through calcium-gated

channels.
2- This sudden rise in Ca++ levels stimulates the vesicles to fuse
with the presynaptic membrane and release the neurotransmitter
by exocytosis into the synapse, which sets up another action
potential on the adjacent cell.
3- Shortly after the neurotransmitter is released into the synapse, it
is destroyed by an enzyme that stops the impulse at that point.

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The human eye

• Cornea: tough, clear covering that protects the eye and allows light
to pass through
• Humor: fluids that maintain the shape of the eyeball
• Iris: colored part of the eye that controls how much light enters the
eye • Lens: focuses light onto the retina
• Pupil: small opening in the middle of the iris
• Retina: converts light into nerve impulses that are carried to the
brain, it contains 2 types of photoreceptors (nerve cells):
1-Rods: photoreceptors in the retina that are extremely sensitive,
receive dim light vision but do not distinguish different colors or
details.
2-cones: photoreceptors in the retina that receive bright light
vision, colors and details are distinguished.

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The human ear
• Auditory canal: ear canal, where sound enters
• Cochlea: fluid-filled part of inner ear, sends nerve impulses to brain
Note: cochlea is a receptor that converts vibrations into an impulse,
cochlea contain basilar membrane.
• Ear bones: hammer, anvil, and stirrup; transmit vibrations from
eardrum to oval window
• Eustachian tube: equalizes pressure between environment and
inner ear
• Oval window: sends waves of pressure to the cochlea
• Semicircular canals: fluid filled, helps you maintain your balance
• Tympanum/ear drum: vibrates as sound waves hit it

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The cochlea analyzes sound frequencies (distinguishes pitch) by
means of the basilar membrane, which exhibits different degrees of
resonance, along its length. High-frequency sound waves (high pitch)
cause maximum vibration of the area of the basilar membrane nearest
to the base of the cochlea; medium-frequency waves affect the centre
of the membrane; and low-frequency waves (low pitch) stimulate the
apex of the basilar membrane.

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 Skeletal and muscular systems
Both systems work together and provide support, stability, shape, and movement to
the body.

Skeletal system
Humans like all vertebrates (phylum chordate) have an endoskeleton as a framework
for the attachment of skeletal muscles. All voluntary movement involves muscle
contraction bringing bones together.

There are two main types of tissue found in the skeletal system

Bones
A rigid substance made up of cells (osteocyte) embedded in a solid calcium-
phosphate matrix. Bones have many functions:
 Body support
 Provide protection for many organs; for example brain, spinal cord, heart, and
lungs.

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  Production of blood cells in bone marrow
 supply of calcium that can be dissolved and released into the plasma if the
body needs it.

 Bone cell is called osteocyte

Cartilage
It is a relatively rigid substance, more flexible than bone, found on the ends of all the
bones and at the joints
 Acts as a shock absorber to protect the bone ends from rubbing together.
 Some structures, such as the end of the nose, the external ear, and the
anterior portions of the ribs, are completely made of cartilage.

Bones are connected with other bones by ligaments

Bones are connected with muscles by tendons

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 Muscular system

There are actually three different types of muscle tissue in the body: skeletal muscle,
cardiac muscle, and smooth muscle.
smooth cardiac skeletal
location found in the walls of hollow found only in the Found attached to
organs such as the stomach, heart bones
blood vessels, and bladder.
Cell Nonstriated Striated Striated
characteristics one nucleus One nucleus Multinucleated

Control Involuntary Involuntary Voluntary

Action Produces peristalsis contracts Pumps blood out of Produces movement at
and relaxes slowly the heart, self- joints, stimulated by
excitatory but nervous
influenced by
nervous system and
hormones

-Muscle tissue is mostly made up of two types of proteins: actin and myosin.
- Actin molecules form long, thin chains, while myosin molecules bundle together to
form thick fibers. In a muscle cell, actin and myosin are arranged in structures called
sarcomeres.
-Actin and myosin → sarcomere → myofibril → muscle cell → fascicle → whole
muscle

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When a muscle contracts, it gets shorter. The first component of the muscle that
actually contracts is the sarcomere which become shorter during contraction and
shorter during muscle relaxation. Actin and myosin fibers do NOT change length
during muscle contraction. The myosin heads bind to actin and cause
the actin filaments to slide.

Notes:
-Muscle contraction requires calcium.
-Calcium helps build and maintain bones, while vitamin D helps your body effectively
absorb calcium.
-Some structures, such as the end of the nose, the external ear, and the anterior
portions of the ribs, are completely made of cartilage.

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 Immunity
Immunity is the capability of multicellular organisms to resist harmful
microorganisms (pathogens). Immunity involves both specific and nonspecific
components.

Nonspecific defense
The nonspecific immune system consists of two lines of defense.
First Line of Defense
The first line of nonspecific defense is a barrier that helps prevent pathogens from
entering the body. The body has several different types of barriers:
• Skin that blocks pathogens
• Mucous membranes that release mucus to trap microbes
• Cilia in the respiratory system that sweep out mucus with its trapped microbes
• Stomach acid that kills germs that enter through the nose and mouth

Second Line of Defense

Microbes that get into the body encounter the second line of nonspecific defense. It
is meant to limit the spread of invaders in advance of specific immune responses.
There are three types:
1. Inflammatory response:
It is characterized by swelling, redness, soreness (pain), and increased warmth in
the area. The purpose of this process is to increase the blood supply to the area,
thus increasing nutrients including oxygen and white blood cells to fight disease.
The inflammatory response works in several ways:
 Histamine triggers vasodilation (enlargement of blood vessels), which
increases blood supply to the area, bringing more phagocytes to
gobble up germs. Histamine is also responsible for the symptoms of
the common cold: sneezing, coughing, redness, and itching and runny
nose and eyes all an attempt to rid the body of invaders.
 Increased body temperature speeds up the immune system and
makes it more difficult for microbes to function.

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 2. Phagocytes: These gobble up invading microbes. Macrophages (“giant
eaters”) are a type of white blood cell that extend pseudopods and engulf
huge numbers of microbes over a long period of time.

3. Interferons: are a group of signaling proteins made and released by host cell
(virus-infected cell) causing nearby cells to heighten their anti-viral defenses.

Specific defense (third line of defense):

The third line of defense is specific and consists of lymphocytes. There are two
types of lymphocytes, B lymphocytes and T lymphocytes.
 Both originate in the bone marrow. Once mature, both cell types circulate in
the blood, lymph, and lymphatic tissue: spleen, lymph nodes, tonsils, and
adenoids.
 Both recognize different specific antigens (germs) (an antigen is anything
that triggers an immune response).
B lymphocytes. These produce antibodies against a specific antigen in what is
called a humoral response.
T lymphocytes. These fight pathogens by hand-to-hand combat in what is called
a cell-mediated response.
Antibodies
 Antibodies are part of the third line of defense (the specific immune
response).
 Each antibody has the ability to bind to only one particular antigen.
 Antibodies neutralize antigens by binding to them and by forming an antigen-
antibody complex that can then be gobbled up by a phagocyte.

Clonal Selection
Antigens that have entered the body bind to specific B or T lymphocytes. Once a
lymphocyte has been selected, it becomes very metabolically active, proliferates
(clones thousands of copies of itself), and differentiates into plasma cells and
memory cells.

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PLASMA CELLS
These fight antigens immediately in what is called the primary immune response.
They do not live long.

MEMORY CELLS
These fight the same antigens that plasma cells do, but they remain circulating in
the blood in small numbers for a lifetime. You have memory cells circulating in your
blood that are specific for every viral infection you have ever been ill with and
against every disease against which you have been vaccinated.
The capacity of the immune system to generate a secondary immune response is
called immunological memory. The immunological memory is the mechanism that
prevents you from getting any specific viral infection, such as chicken pox, more
than once.

Types of immunity
Passive immunity
It is temporary.
• Antibodies are borrowed and do not survive for long.
• Examples are maternal antibodies that pass through the placenta to the
developing fetus or that pass through breast milk to the baby.
Active immunity
It is permanent.
• You make the antibodies yourself.
• An individual makes his or her own antibodies after being ill and recovering or
after being given an immunization or vaccine.

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ABO Blood Types
− ABO antibodies circulate in the plasma of the blood and bind with ABO
antigens in the event of an improper transfusion
− Blood type O is known as the universal donor because it has no blood cell
antigens to be clumped by the recipient’s blood.
− Blood type AB is known as the universal recipient because there are no
antibodies to clump the donor’s blood.

Notes:
•AIDS stands for acquired immune deficiency syndrome. People with AIDS are
highly susceptible to opportunistic diseases, infections, and cancers that take
advantage of a collapsed immune system. The virus that causes AIDS, HIV (human
immunodeficiency virus) mainly attacks helper T cells.

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• Allergies are hypersensitive immune responses to certain substances called
allergens. They involve the release of excessive amounts of histamine, an anti-
inflammatory agent, which causes blood vessels to dilate. A normal allergic reaction
involves redness, runny nose, and itchy eyes. Taking antihistamines can normally
counteract these symptoms. However, sometimes an acute allergic response can
result in a life-threatening response called anaphylactic shock that can result in
death within minutes.
• Antibiotics: are medicines that kill bacteria or fungi. Antibiotics are administered
after a person is sick. They cure the disease.
• An immunity serum: is a serum containing naturally or artificially produced
antibodies to a given antigen, obtained from human or animal sources. This is an
example of passive immunity.

• Vaccine: it prevents viral infections, a weakened microbe or virus is introduced to

the body to create antibodies for this type of virus. There is no medecines for viral
infections as there is for bacterial infections. To develop a new antiviral drugs,
researchers study the mechanism used by the virus to infect cells.
Vaccine is an example of active immunity.

• Autoimmune diseases: is terrible mistake of the immune system. The system

cannot properly distinguish between self and nonself. Instead, it perceives certain
structures in the body as foreign and produces antibodies to attack them.

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 Animal behavior
Behavior is defined as the way an organism responds to changes in its
internal or external environment. A behavior can be innate (inborn), such
as running for shelter upon hearing a loud noise. It can also be learned.

(A) Fixed action pattern (innate)

(FAP) is an innate, highly stereotypical behavior that, once begun, is
continued no matter how useless or silly looking. FAPs are initiated by
external stimuli.
An example of a FAP is the stickleback fish, which attacks other males that
invade its territory. The releaser for the attack is the red belly of the
intruder. The stickleback will not attack an invading male stickleback
lacking a red belly, but it will attack a nonfishlike wooden model as long as
a splash of red is visible.

Other examples:
 Suckling behaviors
 Newly hatched ducks swim when they enter the water
 A baby bird opens its mouth, a mother bird will put food in it.
 A goose sees its eggs outside its nest, it rolls them back in using its
beak, also it rolls back any other object resembling to the egg.

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 (B) Learning
Learning is a sophisticated process in which the responses of the organism
are modified as a result of experience. The capacity to learn can be tied to:
length of life and complexity of the brain.

1- HABITUATION
Occurs when a non-harmful stimulus is repeated over and over again and
the organism learns to ignore it.

2- Associative learning
It is one type of learning in which one stimulus becomes linked to another
through experience.
 Classical conditioning
Two stimuli are linked together to produce a new learned response in a
person or animal. Ex: Pavlov’s dogs.

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  Operant conditioning
It is also called trial and error learning, is another type of associative
learning. An animal learns to associate one of its own behaviors with a
reward or punishment and then repeats or avoids that behavior.

3-Imprinting
Imprinting is learning that occurs during a sensitive or critical period in the
early life of an individual and is irreversible for the length of that period.
Konrad Lorenz investigated the principle of imprinting and how
birds imprint on their mothers.

4- Insight learning / reasoning

The highest form of learning is insight learning. Insight refers to the ability
to approach new situations and figure out how to deal with them.

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C- Social behavior
It is any kind of interaction between two or more animals, usually of the
same species. Types of social behaviors are cooperation, agonistic,
dominance hierarchies, territoriality, and altruism.
1- Cooperation
Cooperation enables the individuals to carry out a behavior, such as
hunting, which they can do as a group more successfully than they can do
separately. Ex: cooperative hunting in lions.

2- Agonistic behavior
It is aggressive behavior to settle disputes between
individuals over access to food, mates, or shelter. It
involves both real aggressive behavior as well as
ritualistic (symbolic) behavior such as 'teeth baring'. One
combatant does not have to kill the other.
If the aggressor succeeds in scaring the opponent, the
loser (submissive) engages in submissive behavior that
says, “You win, I give up.”

3- Dominance Hierarchies

Dominance hierarchies are pecking order behaviors that

dictate the social position of an animal in a culture. This is
commonly seen in hens where the alpha animal (top-ranked)
controls the behaviors of all the others. The next in line, the
beta animal, controls all others except the alpha animal.

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 4- Territoriality
A territory is an area an organism defends and from which other members
of the community are excluded. Territories are established and defended
by agonistic behaviors. They are used for capturing food, mating, and
rearing young.

5- Altruism
It is acting out of concern for the well-being of other people, which
reduces an individual’s reproductive fitness (the animal may die) while
increasing the fitness of the group or family. When a worker honeybee
stings an intruder in defense of the hive, the worker bee usually dies, but it
increases the fitness of the queen bee that lays all the eggs. This is called
kin selection. Altruism evolved because it increases the number of copies
of a gene common to a related group.

Another innate behavior is taxis:

Taxis is a form of movement behavior that involves movement towards or
away from a stimulus. This movement can be in response to light, known
as phototaxis; chemical signals, known as chemotaxis; or gravity, known as
geotaxis.

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 Index
Biochemistry………………………………………………………….1
The cell…………………………………………………………………..15
Cell transport…………………………………………………………28
Cell division……………………………………………………………34
Cellular respiration & photosynthesis…………………….42
Classical genetics…………………………………………………..52
Molecular genetics………………………………………………..65
Taxonomy……………………………………………………………..83
Microorganisms……………………………………………………. 92
Plants………………………………………………………………….100
Evolution……………………………………………………………112
Ecology………………………………………………………………125
Biology process………………………………………………….147
Reproduction ……………………………………………………152
Digestive system…………………………………………………165
Respiratory system………………………………………………171
Circulatory system……………………………………………….174

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Excretion………………………………………………………………181
Endocrine system………………………………………………… 187
Nervous system…………………………………………………… 193
Skeletal system……………………………………………………. 202
Immunity…………………………………………………………….. 206
Behavior……………………………………………………………… 211

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