2021

ACT II BIOLOGY

DR DAVID GIRGIUS
01273468684
INDEX
Chapter 1 Biological Processes Page 2
Chapter 2 Cell Structure Page 10
Chapter 3 Biochemistry Page 22
Chapter 4 Classical Genetics Page 35
Chapter 5 Molecular Genetics Page 44
Chapter 6 Photosynthesis & cellular respiration Page 58
Chapter 7 Cell division & Animal behavior Page 64
Chapter 8 Plant physiology Page 71
Chapter 9 Taxonomy & animal Physiology Page 84
Chapter 10 Ecology Page 95
Chapter 11 Evolution Page 107
Chapter 12 Human Physiology Page 118

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 Biological Processes
The scientific method has five main steps

I. Make an observation (notice the difference

between observation & conclusion)
 Making an observation about something that
interest you is the first step

II. Ask a question

 You must formulate a question about what
you have observed

III. Form a hypothesis or a testable

explanation
 A hypothesis is an idea that
suggested an explanation for a
natural event, a particular experience, or a
specific condition that can be tested
through definable experimentation.
 It states that the purpose of your
experiment, the variables used and the
predicted outcome
 A hypothesis isn’t necessarily right but it’s a best guess & the scientist must
test it to see if it’s actually correct
 Scientists test hypothesis by making prediction, then they do experiments or
make observation to see if the predictions are correct or not
 If they are correct, the hypothesis is supported. if they aren’t, it may be the
time for making new hypothesis

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IV. Experiment
 Once you have developed a hypothesis, you must design and conduct an
experiment that will test your hypothesis.
 You should develop procedures that state clearly how you plan to conduct
your experiment
 It’s important that you include and identify a controlled variable (dependent
variable) in your procedures
 Controls help us to test a single variable in the experiment because they are
unchanged
 So we can make comparison between controls & independent variables (things
that are changed in the experiment) to develop an accurate conclusion

Note: A controlled experiment is a scientific test done under controlled

conditions i.e. just one factor is changed over time, while the other factors are
constant (water is independent while plant is dependent variable)

V. Result
 The results are where you report what happened in the experiment. That
includes detailing all observations and data made during the experiment

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 Measurements in science (study conversions)

A. Qualitative measurements: have no associated

numbers e.g. the plant becomes blue
B. Quantitative measurements: have associated
numbers

Quantitative measurements are commonly used

by scientists

Assumptions about life

i. Nature is orderly
 The basic assumption of scientific approach is that there is a recognizable
regularity and order in the natural world. Events don’t occur randomly
e.g. sunset & sunrise , Day & night or four seasons

ii. Knowledge is superior to ignorance

 Knowledge should be pursued both for its own sake & for improving human
conditions
 The argument that knowledge is superior to ignorance does not mean that
everything in nature can or will be known.
 But it’s assumed that scientific knowledge is tentative and changing i.e. things
that are not known in the past, are known now, and the current knowledge
might be modified in the future

iii. All natural phenomena have natural causes

 The assumption that All natural phenomena have natural causes represent
scientific revolution
 It places the scientific approach on a head on collision with religious,
spiritualism & magic
 It rejects the counter assumption that forces other than those found in nature
operate to cause the occurrence of natural events

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Properties of life

 Although some nonliving organisms may show some of the following

characteristics, only living organisms can show them all

1)Organization
 Living organisms are highly organized or specialized
 All living organisms are composed of one of more cells (basic unit of life)
 Even Unicellular organisms are complex as each cell composed of atoms which
make up cell organelles & structures
 In multicellular organisms

Cells tissues organs organ system the organism

 Multicellular organisms such as humans are composed of many cells. These

cells are organized into tissues

Epithelial tissue Nerve tissue Muscle tissue Connective tissue

 Functions as a  Functions as  Functions in  Functions to
boundary messaging movement hold parts of
 It covers all of system  Controls the body
the inner &  Cells in nerve movements with & together
outer surfaces tissue carry without conscious  Tendons &
electrical ligaments
impulses

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2) Metabolism
 It’s the sum total of the biochemical reactions occurring in an organism
 It’s divided into
 Anabolism: organisms convert simple molecules into complex ones
 Catabolism: organisms convert complex molecules into simpler ones
 Anabolic processes consume energy while catabolic processes can make
stored energy available

3) Homeostasis
 Maintenance of a stable internal environment, even in the face of a changing
external environment
 Living organisms regulate their internal environment to maintain the relatively
narrow range of conditions needed for all cell functions e.g. Human body
temperature must be kept relatively close to 37 0C (98.6 0F)

4) Growth
 Growth depends on anabolic pathways that build large, complex molecules
such as proteins & DNA (genetic material)

5) Response
 Irritability means that they respond to stimuli or change in their environment
e.g. people pull their hands quickly from a flame
e.g. many plants bend toward light
e.g. bacteria move toward nutrient source

6) Evolution
 Evolution means that the genetic makeup of a population may change over
time
 Evolution involves natural selection, in which a heritable trait, such as darker
fur color lets the organisms survive & reproduce better in a particular
environment.

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 Over generations, a heritable trait that provides a fitness advantage may
become more and more common in a population, making the population
better suited to its environment which is known as adaptation

7) Reproduction
 Reproduction can be either
 Asexual “from single parent”

Fission Budding Fragmentation & Parthenogenesis

Regeneration
 Is the  Involves  Occur when a  Involves
separation of splitting off of single parent development of
an organism new individuals breaks into two an egg without
into two new from existing parts that fertilization. The
cells “amoeba ones “hydra” regenerate into resulting adult is
& bacteria” new individual haploid
“sponges, “honeybees &
planaria & sea some lizards”
star”

 Sexual “requiring two parent organisms that produce sperm & ova
containing half of the genetic material that fused together through process
called fertilization”

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 Viruses

 A virus (Acellular) is an infectious particle that reproduces by "commandeering" a

host cell and using its machinery to make more viruses.

 A virus is made up of a DNA or RNA genome inside a protein shell called a capsid.
Some viruses have an external membrane envelope.

 Viruses are very diverse. They come in different shapes and structures, have
different kinds of genomes, and infect different hosts.

 Viruses reproduce by infecting their host cells and reprogramming them to

become virus-making "factories."

Structure of the Virus

 Capsid : protect DNA

 DNA or RNA: gives the instructions
 envelope attach the virus to the host
cell

a. Capsid proteins are always encoded by the

virus genome, meaning that it’s the virus (not the
host cell) that provides instructions for making them.
b. Envelopes do, however, contain proteins that are specified by the virus, which
often help viral particles bind to host cells.
c. All viruses have genetic material (a genome) made of nucleic acid. You, like all
other cell-based life, use DNA as your genetic material. Viruses, on the other
hand, may use either RNA or DNA, both of which are types of nucleic acid.

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Viral replication: lytic VS Lysogenic

Viruses, Prion (which is a self-replicating protein that cause mad cow disease) &
self-replicating RNA enzymes also have some but not all of the properties of life

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 Cell Structure
 Anton Von Leeuwenhoek: invented the first microscope
 Robert Hooke: developed the microscope and named the cell “tiny room”
 Matthias Schleiden: concluded that all plants are made of cells
 Theodor Schwann: stated that all animals are made of cells

Cell Theory

1) All living things are composed of cells (except for virus)

2) Cells are the basic unit of all organisms
3) All cells arise from preexisting cells

Prokaryotic cells Eukaryotic cells

1) Smaller size less than 10 ϻm 1) Larger size 10-100 ϻm
2) Only bacteria and archaea 2) Animals, plants, protists and fungi
3) No nucleus or membrane bound 3) Has nucleus and membrane bound
organelles organelles
4) Smaller ribosome 4) Larger ribosome
5) Has only one circular chromosome 5) Many linear chromosomes

Note: Prokaryotes have “cell wall – cell membrane – cytoplasm – ribosome –

DNA”

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Theory of Endosymbiosis

o Eukaryotic cells containing organelles like mitochondria and chloroplasts

evolved when free-living prokaryotes took up permanent residence inside
other larger prokaryotic cells (proof: Mitochondria and chloroplasts have their
own DNA)

Structures of Plant and Animal cells

Cell wall, chloroplasts and large vacuole are only found in plant cell, while
lysosome and centrosome are only found in animal cell

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1) Nucleus
o The nucleus contains chromosomes made of
DNA wrapped with special protein called
histones
o The nucleus is surrounded by a double
membrane Nuclear membrane
 Function: control center and carry the genetic
material

2) Nucleolus
o Prominent region inside the nucleus of a cell that is not dividing
o One or two nucleoli are commonly visible in a non-dividing cell
o Formed tangles of chromatin and unfinished bits of ribosome
 Function: formation of ribosomes

3)Ribosome
o The site of protein synthesis
o A cell contains millions of Ribosomes that are made up of rRNA and proteins
o They are suspended freely in the cytoplasm or bound to the endoplasmic
reticulum
o Non-membranous (found in prokaryotic and Eukaryotic)

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 4) Endoplasmic Reticulum (ER)
“Is a system of a membrane channels that traverse the cytoplasm”
A. Rough ER: is studied with ribosome, therefore it’s the site of protein synthesis
as well as transport throughout the cytoplasm

B. Smooth ER: not covered with the ribosome but

i. Synthesize steroid hormones and other lipids

ii. Connects rough ER to Golgi apparatus
iii. Detoxifies the cell
iv. Carbohydrate (glycogen) metabolism

5) Golgi Apparatus
o Lies near the nucleus and consists of flattened sacs of membranes stacked
next to each other and surrounded by vesicles
Functions:
 Modify proteins, store and package
substances produced in the rough
endoplasmic reticulum
 Distributes these substances within
the cell and to other cells

6) Lysosome “found in animal cells only”

o A sac of hydrolytic “digestive” enzymes enclosed by a
single membrane (acts as garbage disposal)
o Site of intracellular digestion (food or bacteria)
o Help recycle old cell parts
o Apoptosis “programmed cell death”: is critical to
embryonic development of multicellular organisms and is
carried out by a cell’s own hydrolytic enzymes

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7) Mitochondria
o Is the site of cellular respiration, where glucose is broken down to release
energy
o All Eukaryotic cells have many mitochondria
o Mitochondria contain their own circular DNA and can self-replicate
(endosymbiosis)

8) Cell Vacuole
o Single membrane-bound structures that store substances for the cell
o Contractile vacuole: found in fresh water Protista, like amoeba and
paramecium. They pump excess water out of the cell by osmosis
o Plant cells and human fat (adipose) cells have large central vacuoles for
storage of food and water
o Isolating toxins

9) Vesicle
o Are tiny vacuoles that are found in many places in the cells, including the axon
of neuron, where they release neurotransmitter into the synapse.

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10) Cytoskeleton

o Complex network of protein filaments that extends throughout the cytoplasm

o It gives the cell its shape and
enable it to move

A. Microtubules: Formed from

protein tubulin
o Make up the cilia, flagella
and spindle fibers

Centrioles and Centrosome “Animal cell only”

o Lie outside the nucleus and organize the spindle fibers required for cell division
o Two centrioles, right angle to each other, make up one centrosome
o Centrioles and spindle fibers have the same structure “9 triplets of
microtubules arranged in a circle”
o Non-membranous

Cilia and Flagella (the figure)

o They have the same internal structure and made of microtubules

o Cilia are short while flagella are long
o Both consists of 9 pairs of microtubules organized around 2 singlet
microtubules

B. Microfilaments: Are made of protein actin

o Animal cells to form a cleavage furrow during the cell division
o Amoeba to move by sending out pseudopods
o Skeletal muscles to contract by sliding along myosin filaments

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 11) Plastids “in plants and algae only”

o Plastids have a double membrane

i. Chloroplast
 They are green (as they contain
chlorophyll)
 They are the site of photosynthesis
 Contain their own circular DNA and
can self-replicate
 They are found in green parts

ii. Leucoplasts
 They are colorless and store starch (leuco=white)
 They are found in roots, like turnips or tubers, like potatoes

iii. Chromoplasts
 Store carotenoid pigments (chromo = color)
 Are responsible for the red, orange, yellow color of carrots and tomatoes
 Are the bright pigments in petals and attract insects to pollinate the flower

12) Cell wall “in plants only”

o Formed of Chitin in fungi, peptidoglycan in bacteria and cellulose in plants

and algae
o Some plants develop secondary cell wall between the primary cell wall and cell
membrane
o When a plant cell divides, a thin gluey layer is formed between the two cell
walls, which becomes the middle lamella that keeps the two daughter cells
attached

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13) Cell membrane or plasma membrane (study the figure)

o Selectively permeable membrane that controls what enters and leaves the
cell according to cell needs and size
o Fluid Mosaic: formed of many particles that can move to control the
movement through the cell membrane
o Consists of phospholipid bilayer with proteins dispersed throughout.
o Cholesterol are embedded within the membrane, making it less fluid or more
stable
o Carbohydrate chains: attached to outer surface that are important for cell-to-
cell recognition

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 Transport into and out of the cell
Important Terminology

 Selectively Permeable: the substance that pass through a selectively

permeable membrane change with the needs of a cell
 Solute: the substance that dissolves
 Solvent: the substance in which the solute dissolves
 Hypertonic: having a greater concentration of solute than another solution
 Hypotonic: having a lower concentration of solute than another solution
 Isotonic: two solutions containing equal concentrations of solutes

Types of Transport

Passive transport Active transport

Doesn’t require energy require energy

First: Passive transport

i. Simple diffusion
o The movement of particles from higher concentration to lower concentration
o The steeper the gradient, the faster the rate of diffusion is
o Ex: humans obtain oxygen by simple diffusion across moist membranes in air
sacs called alveoli in the lungs / drop of ink into glass of water

ii. Facilitated diffusion

o Relies on special protein membrane channels to assist in transporting specific
substances across a membrane
o Ex: calcium ions to be transported by facilitated diffusion through calcium ion
channel within the axon membrane

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iii. Osmosis
o The diffusion of water across the membrane from
high water concentration to low water
concentration through semi-permeable
membrane till equilibrium (No Net movement)

Second: Active transport

“Movement of molecules against conc. Gradient, which requires energy, usually in

the form of ATP

1) Exocytosis: is the active release of molecules from a cell

2) Endocytosis

Pinocytosis Phagocytosis Receptor-mediated endocytosis

A. Pinocytosis: (cell drinking)

o The uptake of large dissolved molecules. The plasma membrane surrounds tiny
particles and encloses them in a vesicle

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B. Phagocytosis
o Is the engulfing of large particles or even small organisms by pseudopods. The
cell membrane wraps around particles and engulf them
Ex: this is the way the human white blood cells engulf bacteria and also the
way in which amoeba feed

C. Receptor-mediated endocytosis
o Enables a cell to take up large quantities of very specific substances
o Extracellular substances bind to specific receptors on the cell membrane and
are drawn into the cell into vesicles
Ex1: this is the way in which body cells take up
cholesterol from the blood
Ex2: Sodium – Potassium pump
 In nerve cells, carries sodium (Na⁺) and potassium
(K⁺) ions across the axon membrane to return the
nerve to its resting state after an impulse has
passed

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 Tools & techniques to study the cell:

Phase-contrast microscope Transmission electron Scanning electron

microscope (TEM) microscope (SEM)
 Light microscope  Electron microscope  Useful for studying the
 Useful in examining living, uses beam of surface of cells
unstained cells electrons instead of  The images have
beam of light to three-dimensional
produce magnification appearance
power over 100000x Disadvantages:
 Source of electrons is o Also kills the sample
tungsten filament o Complicated
within a vacuum preparations
column
 Studying anterior of
cells
Disadvantages:
o Tissue is no longer
alive after processing
o Preparation of
specimen is very
complicated
o High costs
When you use the microscope, remember that the image is upside-down &
backward from the actual specimen you placed onto the slide

To determine the magnification: multiply the magnification of the ocular lens of

eyepiece by that of objective lens

Ultracentrifugation

Enable scientists to isolate specific components of cells

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 Biochemistry
The Subatomic particles of the
atom:
A. Protons
 Protons are the positively
charged particles of the atom (+1)

B. Neutrons
 Neutrons have no electric charge

 Together protons & neutrons form the nucleus of the atom. The nucleus is at
the center of the atom
 The mass of the atom is concentrated in its nucleus
 The volume of the nucleus is very small compared to that of the atom

C. Electron cloud
 The negatively charged particles of the atoms are called electrons
 Electrons move around the nucleus very quickly
 It is not possible to determine the exact position & speed at the same time
 Compared with protons & neutrons, electrons have very little mass.

When an atom losses or gains an electron or more, we refer to that atom as an

ion

How can we describe atoms?

I. By atomic number:
 The number of protons of the nucleus of an atom
 Give reason: hydrogen has atomic number of 1 Because it contains only one
proton

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II. By mass number:
 Mass number is the total number of protons & neutrons in atom’s nucleus
 The atoms of the same element always have the same number of protons but
not always have the same number of neutrons
 Isotopes are atoms of the same element having different number of neutrons

Note: There are 7 energy levels in the heaviest atom; the maximum capacity of
the first energy level is 2 electrons

Types of bonds

1) Ionic bond
2) Covalent bond
3) Coordinate bond
4) Hydrogen bond
5) Metallic bond

1) Ionic bond (transfer of electrons)

Metals Non-metals
 Large atomic size  Small atomic size
 Lose electrons & changes into  Gain electrons & changes into
cations (positive ions) anions (negative ions)

 Ionic bond is an electrostatic attraction occurs between the cations & anions
 Ionic bond has no materialistic existence

Ionic bonding & electronegativity:

In general, when the difference in electronegativity is more than 1.7 then the
formed compound is ionic

Give reason: sodium chloride has strong ionic properties

o Because the difference in electronegativity is more than 1.7

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2) Covalent bond (sharing of electrons)
 Covalent bond is – mostly – formed between atoms of non-metals with the
same electronegativity or those of close electronegativity

Classification of covalent bonds:

Pure covalent bond  Difference in electronegativity between the atoms

equals zero
Non-polar covalent bond  Difference in electronegativity between atoms is
between (zero & 0.4)
Polar covalent bond  Difference in electronegativity between atoms is
greater than 0.4 & less than 1.7

3) Coordinate bond:
“is formed between two atoms; one of them has a lone pair of electrons ( a
donor atom) while the other accepts a lone pair of electrons (an acceptor
atom)”
e.g.1) ammonium NH₄ ion (NH₃ + H⁺)
E.g. 2) hydronium ion (H₃O⁺)
 The coordinate bond is represented by an arrow
directed from the donor atom to the acceptor atom

4) Hydrogen bond
“is formed between hydrogen atom which binds with a polar bond with a high
electronegative atom (F, N & O)” (occurs between molecules)
e.g. between water molecules
 Hydrogen bond strength is far weaker than that of covalent bond because the
length of hydrogen bond is longer than that of covalent bond

5) Metallic bond
“is the bond produced from the electron cloud of valence electrons”
 As the number of valence electrons increases, the metal becomes more hard

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 Biological molecules

Inorganic molecules Organic molecules

 They Were existing even before life  They are made in cells of living
on earth organisms
 They don’t contain carbon atoms  They contain mainly carbon atoms
with exception of some compounds linked with hydrogen
link CO2  They also contain oxygen & other
 elements
 Their atoms are mainly bonded by  Their atoms are only bonded by
ionic & some covalent bonds covalent bonds
Ex: Ex:
 H₂O  Carbohydrates
 Minerals or salts  Proteins
 Lipids
 Vitamins
 ATP
 DNA

1) Vitamins
o Are organic molecules
o Needed in small amounts
o Act as co-enzymes
o Not synthesized In animal cells
o Not digested, but absorbed directly
o Are divided into water soluble : B & C needed daily
Fat soluble: A, D, E & K not needed daily, stored in fats

2) Carbohydrates CHO ( carbon hydrogen oxygen molecules)

Monosaccharide disaccharide polysaccharide

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A. Monosaccharide
“Is a monomer (single sugar)”
o General formula: C₆H₁₂O₆
o Ex: glucose, fructose and galactose
o The arrangement of the molecules makes different monosaccharide
o All monosaccharide are isomers

Note: isomers are molecules with same molecular formula, but different
structural formula

B. Disaccharide
“One molecule composed of two units (dimer)”
Dehydration Reactions: (H₂O is the product)
 Glucose + Glucose maltose + H₂O (in barley or malt)
 Glucose + Fructose Sucrose + H₂O (in fruits)
 Glucose + Galactose Lactose + H₂O (in milk)
Note:
 A+B C + H₂O (dehydration: building up)

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 C + H₂O A + B (hydrolysis: breaking down)

C. Polysaccharide
“One molecule composed of many units (polymer)”
Ex:
 Starch: a polysaccharide made in plant cell (polymer of glucose)
 Glycogen: a polysaccharide made in animal cell (in liver and muscles)
 Chitin: in the cell wall of fungi and exoskeleton of Arthropods
 Cellulose: in the cell wall of plant and algae cells

Note: Not All carbohydrates are energy storage used for respiration; some are
structural as cellulose and chitin

3) Lipids CHO compounds “sometimes P”

Lipids differ from carbohydrates in that oxygen in lipids is much less than carbon.
Lipids have the highest energy per gram, but it is not the respiratory substance
because it is harder to be broken down than carbohydrates

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 Types of lipids

Phospholipids Wax Steroids Triglycerides

(in cell membranes) (in ear & on leaves) (cholesterol, sex hormones) (main type)

Triglycerides

Fatty acids: Saturated – Unsaturated (study all) Saturated fatty acids

because all bonds are
Polar hydrophilic head
single and has more
hydrogen atoms

Unsaturated fatty acid

because it contains
double bond

Non-Polar hydrophobic tail

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 Fats Oils
 Saturated fatty acids  Unsaturated fatty acids
 Found in animals  Found in plants
 Solid at room temperature  Liquid at room temperature
 Cause heart diseases  Don’t cause heart diseases
Ex: butter & cream & ghee Ex: coconut oil & olive oil

Functions of lipids:

1. Storing energy
2. Storing fat soluble vitamins
3. Thermal insulation
4. Buoyancy
5. Enters in important compositions: cell membrane, some hormones and myelin
sheath in nerve cell
6. Cushions organs

4) Proteins CHO-N
“Polymer of amino acids (monomer)”

Structure of amino acid:

Variable that
determines the type of
amino acid

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Dimer (dipeptide):

Polypeptide: made by the same way as the dipeptide with dehydration reaction

Levels of proteins
A. Primary structure: a simple molecule made by several amino acids joined
together, very few proteins are found in this structure

B. Secondary structure: a coiled form of the primary structure, and hydrogen

bond held the shape

Advantages of secondary structure:

 Gives the molecule its elasticity

Elasticity: the ability of an object to restore its original shape after removing the
tension

 Needed for hair, muscles, walls of arteries, skin

 In order to help them dilate and restore its original shape

Ex: collagen & keratin

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C. Tertiary structure: when the secondary structure coiled around itself to make
a globular shape to fit with something
Ex: enzymes, hormones & antibodies

D. Quaternary structure: a chain of tertiary structure

Ex: hemoglobin

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Enzymes
“A biological catalyst, that speeds up the reaction without being involved”.
 Any chemical reaction requires activation
energy.
 Activation energy: the energy needed to
start the reaction
 An enzyme decreases activation energy, so
that the reaction can take place at body
temperature and with a lower energy
 Activation energy is lower with enzymes

Properties of enzymes:

1) Specific

2) Effect of PH: enzymes work at specific PH. It

becomes denatured if placed outside its PH range.

3) Effect of temperature: if placed at a higher

temperature than its range, the enzyme
becomes denatured and unfit for work again.

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Properties of water

1) Hydrogen bond: oxygen atom in

Polar molecule
one molecule binds with
hydrogen atom in another
molecule “between water
molecules”
2) Water is cohesive

Cohesion: attraction between

similar molecules

 Water molecules bind with similar molecules

 Biological benefit: this property facilitates the ascent of water in xylem vessels
against gravity
3) Water is adhesive: water molecules are attracted to different molecules

 Biological benefit: to keep water held in the xylem and prevent it from falling
down

4) Water has high specific heat capacity: water needs more amount of heat that
must be absorbed in order to rise the temperature of 1 gm of water by 1 :C

 Biological benefit:
 this helps bodies to maintain their body temperature constant
 provides constant thermal conditions for aquatic organisms

5) water has high heat of vaporization: a relatively great heat is needed to

evaporate water
 Biological benefit: water is perfect cooling agent

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6) Water is the universal Polar solvent: because water is a highly polar molecule,
it dissolves all polar and ionic substances
 Biological benefit: this frees the ions such that each can participate in its vital
role

7) Water has maximum density at 4 ⁰C: below 4 :C, the density of water
decreases, so ice floats on the top of the water.
General role: density = mass/volume
 As temperature ↑, volume ↑ , density ↓
 As temperature ↓, volume ↓ , density↑

Except in water (anomalous property)

 Biological benefit: so that ice (thermal insulator) and cold water will be on the
top of warm water where marine organisms live.

PH: is the negative logarithm of hydrogen ion concentration in mole/liter

As the concentration of H⁺ increases, the PH value decreases

A solution of PH 1 is 10 times more acidic than that of PH 2 & so on...

Buffer: substance that resist change in PH e.g. bicarbonate ion (HCO₃⁻)

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 Classical Genetics
Important genetics terminology

1. Diploid 2N: Cells in which chromosomes are found in pairs Ex: Body cells
2. Haploid cells N: cells in which chromosomes are single Ex: Gametes (sperms &
Ova) and bacteria
3. Chromosome: DNA + Histone Protein
4. Homologous chromosomes: pair of chromosomes
5. Gene (hereditary factor): a segment of DNA carries a code for certain
characteristic
6. Allele: Alternatives(forms) of the gene Ex: brown and blue eye colors
7. Homozygous: Pure “similar factors”
8. Heterozygous: impure or hybrid “different factors”
9. Dominant: masking allele
10.Recessive: masked allele
11.Phenotype: external appearance
12.Genotype: genetic make up

Note: Recessive individual is always pure

In case of recessive, phenotype indicates the genotype. While in case of

dominant, phenotype doesn’t indicate the genotype.

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 Heredity

Complete dominance (mendelian) Non-mendelian

The trait is controlled by a pair of genes _ incomplete dominance _ Multiple

The gene has two alleles. One is alleles _co-dominance _sex linkage

Dominant while the other is recessive sex influence _environmental

And the dominant appears influence _ polygeny

Mendel’s first law: law of segregation (monohybrid cross)

“States that when two pure organisms for two opposing traits are crossed, the
offspring will be hybrid but will exhibit only the dominant trait while the recessive
trait remains hidden”

P: T T x tt tall = T (dominant) short= t (recessive)

G: T T t t

F1: Tt Tt Tt Tt 100% hetero (impure) dominant

P: Tt x Tt

G: T t T t

F2: TT Tt Tt tt
3 (75%) : 1 (25%)
Note: if a trait appears in the offspring was not apparent in the parents, the trait
is recessive and the parents are heterozygous”

Homo + Homo = 100% hetero , Hetero + Hetero = 3:1 , Hetero + recessive= 1:1

36
Testcross or backcross

“A method to distinguish the genotype of the dominant individual whether it is

homo or hetero”

It’s made by crossing it with recessive

The Result of offspring

100% So the individual was homozygous
50% : 50% (1:1) So the individual was heterozygous

P: T T x tt P: Tt x tt

G: T T t t G: T t t t

F1: Tt Tt Tt Tt 100% F1: Tt Tt tt tt

1 : 1

Mendel’s second law: law of independent assortment (dihybrid inheritance)

“The genes for one trait are not inherited along with the genes for another trait”

The phenotype ratio is 9:3:3:1

Advantages of Mendel’s work:

 He studied the transmission of the traits for more than one generation
 He introduce quantitative study in biology

37
 Non-Mendalian

1. Incomplete dominance

“The trait is controlled by a pair of genes each of equal strength in heterozygous

and appear as a blend of 2 alleles”

Ex: Flower color in Japanese “4” clock

P: RR x WW RR = Red WW = White RW: pink

G: R R W W 3 phenotypes → Incomplete dominance

F1: RW RW RW RW 100% pink

P: RW x RW

G: R W R W

F2: RR RW RW WW Note: No needs for test cross as each

1 : 2 : 1 phenotype indicates a genotype
2. Co-dominance
“the trait is controlled by a pair of genes, each gene has 2 alleles, equal in
strength in the heterozygous state. Each gene expresses itself equally and
independently”
Ex: spotted animals as speckled chicken
3. Polygenes case of incomplete dominance with many genes
“the trait is controlled by many pairs of genes, the degree of the trait depends on
the number of each allele”
Ex: most human trait like skin color or body height
4. Multiple alleles

“The trait is controlled by a pair of genes; each gene has more than 2 alleles”

38
 Ex: ABO blood type
Blood phenotype genotype
Antigen Antibody group
A A AA( IᴬIᴬ ),
Special proteins Antithetic to antigene
AO (IᴬI:)
found on the surface found in blood plasma
of RBCs that B B BB (IᴮIᴮ),
determines the BO (IᴮI:)
blood group AB AB AB (IᴬIᴮ)
O O OO (I:I:)

Blood Group Antigen Antibody

A A Anti-b
B B Anti-a
AB A , B --
O -- Anti-a
Anti-b
Blood transfusion:

Blood Group A B AB O
Donates to A , AB B , AB AB Universal
Receive from A,O B,O Universal O

Denying Paternity
Case: The blood group of a baby is O , we want to know the baby belongs to
which parent. if the two wives have blood group O but the two fathers are
different, the 1st father has A blood group while the 2nd father has AB blood group
P: AA x OO P: AO x OO P: AB x OO
G: A A O O G: A O O O G: A B O O
F: AO AO AO AO F: AO AO OO OO F: AO AO BO BO
The baby may be O with 50% No babies are OO
So the baby belongs to the first parents.

39
Notes:

 hetero (AO) + hetero (AO) = 25% O

 Rh factor is a protein found in blood plasma
 Rh⁺ means that it is present (dominant)
 Rh⁻ means that it is abscent (recessive)
 Rh⁺ Rh⁺ → positive , Rh⁺ Rh⁻ → positive , Rh⁻ Rh⁻→ Negative
 Rh⁻ cannot receive blood from Rh⁺ as he will produce antibodies
5. Linkage

Linked genes: are genes carried on the same chromosome

Ex: body color and wing shape of drosophila

G = grey g = black L = long wings l = short wings

P: GG LL x gg ll
G: G L gl
F1: GgLl 100% grey long winged
P: GgLl x GgLl
G: GL gl GL gl
F2: GGLL GgLl GgLl ggll
3 : 1
Notes:
 If he gave you 2 traits then check the ratio

If it is 9:3:3:1 if it is 3:1
Then independent assortment then linkage
 Linked genes can be separated during crossing over

40
6. Sex linkage
Sex determination in humans
Female: 44 + XX Meiosis 22 + x
Male: 44 + XY Meiosis 22 + X or 22 + Y
Types of cells
Somatic cells Reproductive cells
Body cells Sex cells (gametes)
Contain diploid no. of chromosomes Contain haploid no. of chromosomes
44+ XX or 44 + XY 22 + X or 22 + Y

Types of chromosomes

Autosomes (Somatic chromosomes) Sex chromosomes

Carries traits that are similar in male Carries sex determining genes
and female
The difference between X and Y chromosomes:

 X chromosome is bigger so it carries more genes

 X chromosome has other genes responsible for growth and development

Sex linked genes = X linked gene

Ex: Color blindness and haemophilia

Notes:

 X = Normal (dominant) , X’ = infected (recessive)

 In Females: X X = normal X X’ = carrier X’ X’ = infected
 In Males: X Y = normal X’ Y = infected
 No male carriers for X linked traits (has only one X)
 X linked recessive traits are more common in males than in females
 Sons cannot inherit Sex linked traits from the fathers because the sons inherit
Y chromosomes from their fathers

41
Ex: A woman normal to color vision whose father was a color blind, married a
man who is normal to color vision. What is the probability that they have a son
who is color blind?

P: X X’ x XY

G: X X’ X Y

F: XX XY XX’ X’Y 25% if a son is replaced by the or their sons then it will be 50%

7. Sex influence

“sex influenced traits are autosomal traits that are expressed based on the
influence of sex” Ex: Premature baldness

Male Female
HH Normal Normal
H’H’ Bald bald
HH’ Bald Normal
Because Testosterone hormone guides the baldness gene to be dominant

8. Environmental influence

“The environment can alter the expression of genes”

Ex: Fruit flies, in hot environment they develop long wings

Ex: white fur Himalayan rabbits, in cold temperatures, they develop black fur

Karyotype

“Is a laboratory procedure that analyzes the size, shape and number of
chromosomes & determine the gender“or “arrangement of chromosomes acc. To
their size”

Specialists photograph chromosomes during the metaphase of mitosis when they

are fully condensed.

42
Pedigree

“Is a family tree that indicates the phenotype of one trait being studied for every
member of a family”

 Females are represented by circles and males by a square

 The carrier state is not always shown but it is sometimes represented by a half
shaded in shape
 A shape is completely shaded in if a person exhibits the trait.

A&B C D
Genotype Both Tt tt Tt
Reason Trait is Recessive To have
recessive as traits only produced
both are expressed affected child
normal, yet when H, D must
have homozygous have
produced an inherited a
affected recessive
child (C ) allele from
either A or B

43
 Molecular Genetics
 Evidences
 Structure
 Duplication
 Gene expression
 Control of gene expression
 Gene technology
 Mutation

1. Evidences
A. Bacterial transformation: (Griffith)
“Ability of bacteria (R) to alter their genetic makeup by absorbing foreign DNA
molecules from other bacterial cells(S) and incorporating the foreign DNA into
their own” “DNA is the genetic material”
Pneumonia bacteria

R-strain (non-virulent) S-strain (virulent)

By injecting the bacteria into mice:

 R-stain Survived
 S-stain Died
 S-stain(heat killed) Survived
 R + S (heat killed) Died

B. Bacteriophage
“Proved that DNA, not the protein, is the genetic material by labeling the
bacteriophage (virus attacking bacteria), its DNA with radioactive ³²P and its
protein with radioactive ³⁵S”

44
2. Structure of DNA
“DNA is a polymer of nucleotides”

 DNA= Deoxyribonucleic acid

 RNA= Ribonucleic acid
 Purine(double ring) = A , G
 Pyrimidine(single ring) = T , C

Franklin carried out X-ray crystallography analysis of DNA that showed DNA to
be a helix with even width
Watson and Crick model of DNA
“DNA is described as antiparallel double helix”
 Base pairing rule: A=T , G≡C (stronger)
 The nucleotides of the opposite chains are
paired to one another by hydrogen bonds;
otherwise all other bonds are covalent bonds.
 H-bonds (weak bond) maintain the helix (spiral)
shape

45
3. DNA Duplication
“Is the making of an exact copy of DNA”

For a molecule to act as a genetic material, it has to be able to:

 Make a copy of itself

 Carry a code
“Semiconservative replication is the two new molecules of DNA that are
produced each consist of one old strand and one new strand”

Steps of replication:

A. Helicase enzyme unwinds the helices, breaks the H-bonds and separates the
two strands
B. Each strand acts as a template to make the complementary one
C. DNA polymerase joins the new nucleotides together makes a new strand.
Telomeres: “are special non-coding nucleotide sequences at the end of
chromosomes that are repeated thousands of times to protect against possible
loss of genes”

46
 4. Gene expression
“A gene is expressed when a certain protein is synthesized”
Gene expression = protein synthesis

RNA

“is a polymer of ribonucleotide”

Genetic codon

“A triplet of nucleotides carries a code for

an amino acid”

 1 gene = 1 protein
 A base sequence on DNA = amino acid
sequence on protein
Notes:

 4³ = 64 codons and we have 20 amino

acids
 Each amino acid may have more than
one codon
Types of RNA

I. mRNA : transfers information from the nucleus (DNA) to the cytoplasm

(ribosome)
II. rRNA : rRNA and protein enter in the structure of the ribosome (the translator)
that converts the base sequence to amino acid sequence
III. tRNA : brings the amino acids according to the codon on the mRNA

47
 DNA RNA
1) double stranded 1) single stranded
2) polymer of deoxyribonucleotide 2) polymer of ribonucleotide
3) the sugar is deoxyribose 3) the sugar is ribose
4) A,G,T,C 4) A,G,U,C
5) In nucleus of eukaryotes 5) In nucleus and cytoplasm
6) One type 6) Three types : mRNA , rRNA , tRNA
7) Carry genetic material 7) Helps in protein synthesis
8) Stable 8) Can be broken and resynthesized

Protein synthesis

Transcription Translation

A. Transcription: “formation of mRNA”

Steps:

1) The gene to be expressed opens

2) RNA polymerase binds to the promoter
”non-coding” (binding site)
3) The complementary nucleotides attach
4) The enzyme joins them in a strand
5) Introns ”non-coding” are removed by a
series of enzymes, that attach exons
“coding” to each other.

B. Translation: “converting the code sequence into amino acid sequence”

Steps:

1) At the ribosome, mRNA is translated as codons formed of three nucleotides

starting by AUG “start codon”
2) Amino acids present in the cytoplasm are carried by tRNA to the codons of the
mRNA strand at the ribosome

48
3) Each codon has anticodon found on the corresponding tRNA
4) The first tRNA brings methionine for AUG then remain attaching until the
second tRNA brings the next amino acid and a certain enzyme attaches the
two amino acids together then the first tRNA can leave and so on..
5) Till we reach to the stop codon or End codon which may be UAA , UAG , UGA
Note: if the protein consists of 50 amino acids, then there were 52 codons and
156 nucleotides, tRNA has two sites, anticodon site and a.a attachment site

Duplication Transcription
1) Helicase and DNA polymerase 1) RNA polymerase
2) Introns are not cut 2) Introns are cut
3) Occurs for The whole DNA 3) Occurs for the gene to be expressed
4) Each strand acts as a template 4) Only one strand acts as a template
5) A binds with T 5) A binds with U
6) Occurs Prior to cell division 6) Whenever a gene is needed to be
7) The product is a new molecule of expressed
DNA 7) The product is a new molecule of mRNA

49
 Transcription Translation
1) “it is the formation of mRNA” 1) “converting the code sequence into amino
2) Occurs in the nucleus of eukaryotes acid sequence”
3) RNA polymerase is the responsible 2) Occurs in the cytoplasm
molecule 3) Ribosome is the responsible molecule
Note: Amniocentesis is a procedure in which the doctor inserts a needle into
uterus of an expectant mother during fourth month of pregnancy and withdraws
few centimeters of amniotic fluid.

5. Control of gene expression

Ex: lac. Operon in E.coli

 Operon is formed of promoter, operator and functional (structural) genes

 The promoter is the binding site of RNA polymerase
 The operator is the binding site of the repressor
 TATA box (sequence of A&T) helps RNA polymerase bind to the promoter

 If there is a mutation in regulatory gene → always switched on→ continuous

production of lactase
 If there is a mutation in structural gene (sequence of nucleotides) → no
production of lactase or production of faulty (inactive) lactase

50
6. Gene technology
Human Genome “an organism’s genetic material” consists of about 3 billion base
pairs of DNA and about 50000 : 100000 genes. 97% of our DNA doesn’t code for
protein product called Junk as regulatory sequence and Introns.

Restriction enzymes

“They cut DNA at specific

recognition sites, such as GAATTC,
and are sometimes referred to as
molecular scissors”

Applications:

A. Recombinant DNA
B. PCR
C. Genetic fingerprint

A. Recombinant DNA
“means taking DNA from two sources
and combining them in one cell”
Ex: insulin

Notes:

 Plasmids: ring shaped DNA found in

prokaryotes
 Apply the same restriction enzyme to
Human and bacterial genetic material
 Gene is isolated by ultracentrifugation

51
B. Polymerase chain reaction (PCR)
“is a cell-free, automated technique by which a piece of DNA can be rapidly
copied or amplified”

We can have thousands of copies of DNA

in the test tube as large as you have these
three things:

 Original DNA
 Plenty of nucleotides
 DNA polymerase
Note: PCR is also described as DNA Amplification

C. Genetic fingerprint
“there is a part of DNA known to be unique for each individual”

Gel Electrophoresis

“separates large molecules of DNA on the basis of their rate of movement

through an agarose gel in an electric field”
 The smaller the molecule, the faster it runs through the gel

 Case study 1:
There is a crime, and in the scene, the police found a hair in the nail of the
victim (or saliva or blood drop or cells) for the
murder. There are three suspects Ahmed ,
Fares and Nadine

52
Steps of gel electrophoresis:

1) Take a sample of each suspect + DNA probe

2) For each sample apply all restriction enzymes
3) Apply electrophoresis
4) Take a photo for what you see

 Case study 2:
Proving paternity

7. Gene Mutation
“Sudden changes in the genetic material or primary source of genetic variations

Types Types

Somatic Germ cell Gene mutation chromosomal mutation

(Body cell) (Gametes or gonads)
Ex: cancer true mutation
As it is inherited
Notes: DNA repairing enzymes repair and correct damage to DNA molecules.
Cancer is caused by a mutation in protein involved in cell cycle regulation

53
 Gene Mutation

Deletion
Point mutation (substitution) frame shift
Insertion
A. Point mutation (substitution)
“a base-pair substitution, where one nucleotide converts to another”

Silent Mutation: “happens when the point mutation produces the same amino
acid or occurs in a non-coding area of DNA”

B. Deletion
C. Insertion

54
 Chromosomal Mutation (Chromosomal aberrations)

Inversion Translocation non-Disjunction (change in no.)

Non-disjunction

Polysomy Polyploidy

Aneuploidy: “having any abnormal number of chromosomes”

A. Polyploidy
“is due to inability of spindle fibers to separate the pairs of chromosomes that
results in producing extra set of chromosomes 3N or 4N”
N 2N
2N Normal gametes 2N abnormal
N
2N + N = 3N triploid zygote

Note: polyploidy is found in plants and leads to over expression of the traits but
we don’t see it in animals or humans

55
B. Polysomy
“Is due to inability of spindle fibers to separate one pair of chromosomes”
Female: 44 + XX meiosis 22 + X normal gamete

44 + XX 22 abnormal gametes

22 + XX
22 + XX + 22 + X → 44 + XXX trisomy “multiple sex gene”

A female with idiocy and infertility

22 + XX + 22 + Y → 44 + XXY trisomy “Klinefilter’s syndrome”

A male with feminine traits and infertility

22 + 22 + X → 44 + X monosomy “Turner’s syndrome”

A female with idiocy and infertility

22 + 22 + Y → 44 + Y monosomy “not liable”

If the extra chromosome is autosome not sex chromosome:

44 + XX 23 + X

21 + X
23 + X + 22 + X → 45 + XX trisomy “female Down’s syndrome”

23 + X + 22 + Y → 45 + XY trisomy “male Down’s syndrome”

Note: Down’s syndrome is a case of trisomy of chromosome pair no. 21

56
Chromosomal disorder Pattern of inheritance description
Down (Autosomes) Characteristic facial features,
syndrome 47 chromosomes mental retardation, prone to
Has an extra developing Alzheimer’s and
chromosome no. 21 leukemia

Multiple Sex Genes (sex chromosomes) A female with idiocy and

44 + XXX = 47 infertility
chromosomes

Klinefelter’s syndrome (Sex chromosomes) Have male genitals, but testes

44 + XXY = 47 are abnormally small and these
chromosomes men are sterile
A male with an extra X
chromosome
Turner’s syndrome (Sex chromosomes) A female with idiocy and
44 + X0 = 45 infertility
chromosomes

57
 Photosynthesis
6CO₂ + 6H₂O Sunlight/chlorophyll C₆H₁₂O₆ + 6O₂

It’s called reduction process as carbon in CO₂ is gaining electrons

The rate of any reaction can be measured by:

 The rate of consumption of the reactants

 The rate of formation of the products

Biochemical pathway: “series of reactions in which a product of one reaction

becomes a reactant in another reaction”

 A+B→C
 C+D→E
 E+F→G

Where does the photosynthesis take place?

 In the chloroplast (green plastids)

Pigments in the grana are divided into

Primary pigment Chlorophyll a (green)

Secondary pigments Chlorophyll b (green)
(accessory or antenna) Red pigment (phycobillins)
Brown pigment
Carotenoids (yellowish orange pigment)
Having many pigments, each pigment will absorb certain wavelengths, increasing
amount of light energy absorbed and increasing the rate of photosynthesis

58
 Reactions

Light reactions] Dark reactions

 Light dependent  Light independent or Calvin cycle
 Occurs in grana  Occurs in stroma
 Light is the limiting factor(controlling  Temperature and CO₂ concentration are
factor) the limiting factors
light
CO₂ + NADPH + ATP
Chlorophyll a (carbon fixation)

Sugar (PGAL)+ NADP⁺ + ADP

activated chlorophyll a

photolysis(hydrolysis) Burnt by O₂ converted into

(Cellular resp.) other compound
 H₂O 2H + ½ O₂ ADP + P + E Stored as starch
Note: the source of H₂ in the sugar is the
NADP⁺ water molecule while the source of O₂ in
ATP the sugar is the CO₂
NADPH

Notes
 Iodine is used for testing for the presence of Starch
(Yellowish Brown color → Blue color)
 As the rate of photosynthesis increases, the rate of production of starch
increases, so the blue color becomes darker
 Both reactions occur only when there is light

59
 Cellular respiration
“it is the process of releasing energy from organic substances”

C₆H₁₂O₆ + 6O₂ 6CO₂ + 6H₂O + Energy

Where does the respiration take place?

 In the Mitochondria

The inner membrane is folded to increase the surface area. As the surface area
increases, the rate of reaction increases. (Function of cristae)

Types of respiration

Aerobic respiration anaerobic respiration

 Oxygen is present  Oxygen is abscent
 Steps:  Steps
1) Glycolysis (in cytoplasm) 1) Glycolysis (in cytoplasm)
2) Krebs cycle (in matrix of mitochondria) 2) Fermentation (in cytoplasm)
3) Electron transport chain (in the cristae
of inner membrane)

60
 Anaerobic respiration

Glucose (6C) C―C―C―C―C―C

2NAD⁺ 2 ADP

2NADH 2ATP

2 pyruvic acids (3C)

Ethyl Alcohol + CO₂ (in yeast) Lactic acid (in muscles)

(Alcoholic fermentation) (Acidic fermentation)

Notes:

 lactic acid in muscles causes fatigue sensation

 NAD⁺ and FAD⁺ are enzymes that carry protons (H⁺) and electrons from
glycolysis and krebs cycle into the electron transport chain(ETC)
 The higher energy electrons are carried on NAD⁺ while lower energy electrons
are carried on FAD⁺
 1 NADH = 3 ATP , 1 FADH₂ = 2 ATP
 Oxidative phosphorylation: using the stored energy to convert ADP into ATP by
the aid of enzyme ATP synthetase
 Alcoholic fermentation used in bread-baking, beer, wine and liquor industries
 Bread-baking industries depend on the ability of yeast to carry out
fermentation and produce carbon dioxide that causes bread to rise
 During photosynthesis, reduction occurs (gaining of electrons) while during
respiration, oxidation occurs (losing of electrons)

61
 Aerobic respiration

Glucose (6C) C―C―C―C―C―C

2NAD⁺ 2 ADP

2NADH 2ATP

2 pyruvic acids (3C) C―C―C C―C―C

2NAD⁺

2NADH 2CO₂

Note: the cycle is repeated twice, one for each molecule of pyruvic acid

The net yield:

 4 ATP molecules
 2 FADH₂ molecules
 10 NADH molecules
 6 CO₂ molecules

62
 3. Electron transport chain

Occurs in the cristae of the inner membrane of the mitochondria

NADH NAD⁺ + 2 e⁻ + 3ATP

Then 10 NADH = 30 ATP

FADH₂ FAD⁺ + 2 e⁻ + 2 ATP

Then 2 FADH₂ = 4 ATP

The net yield for 1 glucose molecule:

 38 ATP in prokaryotes
 36 ATP in eukaryotes

The oxygen serves as the final electron

and proton acceptor in ETC

2 e⁻ + 2H⁺ + ½ O₂ H₂O

Notes:

•CO₂ is the by-product of Krebs cycle, while H₂O is the by-product of ETC

•During cell respiration, as electrons of NADH & FADH₂ are pulled along the ETC,
they released energy used to pump protons (H⁺) across the cristae membrane,
thus creating a proton gradient.

•The immediate result of ETC is that a proton gradient is created

Aerobic respiration Anaerobic respiration

1) In presence of Oxygen 1) In absence of Oxygen
2) 3 steps: glycolysis, krebs cycle and ETC 2) 2 steps: glycolysis and fermentation
3) Occurs in cytosol(cytoplasm) and 3) Occurs in cytoplasm only
mitochondria 4) Less energy ( 2 ATP)
4) More energy (38 or 36 ATP) 5) CO₂ and alcohol or lactic acids are the
5) CO₂ and water are the by-products by-products
6) Occurs in higher organisms 6) Occurs in primitive organisms like yeast

63
 Cell division
INTRODUCTION: Why do cells divide?

As the cell grows up, the S.A. increases, the volume increases but the ratio
S.A/VOL decreases till it reaches a level, the rate of exchanging materials through
it is no longer satisfying the cell demands, and so the cell needs to divide.

Cell Cycle:

 G: growth
 S: synthesis of new DNA (duplication) Interphase
 M: Mitosis (nuclear division)

Cytokinesis = cytoplasmic division (cell division)

In animal cell In plant cell

By cleavage furrow by formation of middle lamella (plate)

64
 Normal chromosome is a single chromatid but at division, it becomes in pairs
(duplicated chromosome)

1. Mitosis: “in growth and tissue repair” and “in unicellular reproduction”

Prophase Metaphase Anaphase Telophase

1) The nuclear 1) Chromosomes line 1) The centromere 1) Chromosomes
membrane up in one row of each are at cell
disintegrate 2) Spindle fibers chromosome poles
2) Chromosomes extend from the separate, and 2) Nuclear
condense and centrosome to the spindle fibers membrane re-
become visible centromere shorten and begin forms
3) Centrioles(centros to pull the sister 3) Spindle fibers
ome) migrate to chromosomes degenerate
the poles apart
4) Spindle fibers
begin to form

65
 Notes:

 during anaphase of mitosis “single chromosomes(chromatids)” are separated

 No. of chromosomes in the resultant cells equal to that of parent cell

2. Meiosis: “during gamete production”

Prophase I Metaphase I Anaphase I Telophase I

Extra: 1) Tetrads line 1) Chromosomes 1) Homologous
1) Synapse: up at the cell pairs(half of chromosomes pairs
Chromosomes equator tetrad) will move to cell poles
are arranged in separate and and the cell divides
Tetrads(two start to move to into two cells
homologous the opposite 2) Cells have half the
pairs) poles of the cell no. of
2) Crossing over: is chromosomes of
the process in mother cell
which 3) Resulting cells with
homologous unique genetic
chromatids structure(bec. Of
exchange genetic the crossing-over)
material(to
increase genetic
variety)

66
Notes:

 Interphase happens before meiosis I, while no interphase happens before

meiosis II
 Meiosis II is identical to mitosis, and happens to the two cells produced from
meiosis I producing four haploid cells
 Anaphase I separates the two homologous chromosomes, but Anaphase II
separates the sister chromatids

Mitosis Meiosis
1) Two daughter cells are produced 1) Four daughter cells are produced
2) Take place be most body cells 2) Take place by gonads only
3) 2N→ 2N (identical) 3) 2N→ N
4) No crossing over occurs 4) Crossing over occurs
5) So no genetic variations 5) Genetic variations
6) Occurs in growth, repair and 6) Occurs during gamete formation
asexual reproduction in unicellular 7) Two stages
organisms 8) In Metaphase I, chromosomes line
7) One stage only up in two rows
8) In Metaphase, chromosomes line
up in one row

67
 Animal Behavior

F.A.P (innate) Learned Social

 Cooperation
 Agonist
 Dominant
hierarchy
 Territorial
 Altruism
Habituation associative imprinting

Classical operant

1. Fixed action pattern “Tinbergen”

Innate (genetic born able to do it) during the whole life, stereotyped (unlearned)
behavior, once initiated it completes whatever silly or useless.

Sign stimulus: the sign that stimulate the action

2. Learned behavior “Acquired by experience”

It needs: complex nervous system and long life span

68
Types:

A. Habituation “ignoring a persisting stimulus”

B. Associative
 Classical “conditioning” ex: Pavlov dogs
saliva “observation”
 Operant “conditioning” trial and error
animal trainings “Skinner”

C. Imprinting “innate during the first period of life” (critical period)“Konrad Lorenz”

69
3. Social
A. Cooperation: “when the animal realizes that a certain action if done in groups
is better than in individual”
Ex: Hunting
B. Agonistic behavior: “aggression – submission ”
C. Dominant hierarchy
 ᾀ animal has the first choice in all resources
 ᵦ Animal that dominates all except ᾀ

D. Territorially
“The area defended by an animal by aggression as it contains all its resources”
E. Altruism
“When an animal sacrifice by himself for the survival of his kids”
Ex: motherhood

70
 Plant physiology
1) Plant classification

Byrophyta Tracheophyta “vascular”

“Non-vascular” as mosses

Non-seeded “reproduces by spore formation” as ferns

Seeded

Gymnosperm “conifers” Angiosperm

“Non-flowering” or cone-bearing “flowering”
E.g.: pine, oak, cedar & maple

71
Angiosperms are divided into monocotyledons & dicotyledons

Modifications enable plants to live on land

 Cell wall made of cellulose support the plant
 Roots & root hairs absorb water & nutrients from the soil
 Stomata open to exchange photosynthetic gases & close to minimize water
loss
 Cutin: waxy coating on the leaves, help prevents excess water loss from the
leaves
 Sporopollenin: tough polymers form the walls of spores & pollen

2) Plant tissues are classified into

Dermal tissues Vascular tissues Ground tissues
Any outer covering  Xylem & Phloem  Any other cells
tissues, usually consisting  It consists of three
of single layer of types of cells:
epidermal cells Parenchyma,
 Cuticle collenchyma &
 Tichomes: spike-like sclerenchyma
projections for
protection
 Guard Cells: are the
only dermal cells that

72
Parenchyma “filling cells” Collenchyma Sclerenchyma
 Normal cells without  Plant cells that have  Plant cells thickened
any further further thickening with
modification or with cellulose & gives  Leginin
further thickening “flexible support”  Suberin
 Found in leaves  Cutin
“rigid support”
 Found in xylem
contain chloroplasts

3) Plant Growth
Primary growth “vertical growth” Secondary Growth “↑ in width”
Cells in root tips & shoot tips called  The cells that are responsible for
apical meristem, are the only cells able root growth are pericycle cells
to divide to increase plant height or  The cells that are responsible for
depth in the soil “vertical growth” stem growth are cambium cells
 Zone of cell division: responsible for
producing new cells that grow down
into the soil.
 Zone of Elongation: cells elongate &
are responsible for pushing the root
cap downward and deeper into the
soil
 Zone of differentiation:
specialization into three tissue
systems in the plant; the epidermis,
ground tissues, xylem & phloem

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 Absorption (by roots)
4) Plant nutrition Photosynthesis (by leaves)
Taproot Fibrous roots Aerial roots Prop roots
 Large root that  Many thin  They grow in  Grow above
gives rise into roots that hold swamps or salt the ground &
lateral the plant firmly marches help support
branches in place  Stick up out of the plant
 It helps in fixing water & serve
the plants & to aerate the
also storage root cells

5) The transport system

The functions of the root:
 Absorb nutrients from the soil
 Anchor the plant
 Store food
Root structure

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A. Epidermis
 Covers the entire surface of the root & is modified for absorption
 Root hairs extend from epidermis to increase absorbing surface

B. Cortex
 Transport of water to xylem
 Aeration because it contains storage
 Storage of excess water
 Support as it surrounds the vascular bundle

C. Vascular cylinder
 It consists of vascular tissues (xylem & phloem) surrounded by one or more
layers of tissues called pericycle, from which lateral roots arise

D. Endoderm
E. Pericyle (meristem)
F. Xylem
G. Phloem
Adaptations of endoderm
 Phloem have cells that are completely suberized (covered by a waterproof
substance called suberin) to prevent water from leaking to the phloem & get it
into the xylem
 Xylem have cells that are suberized in the form of casperian strip (covered with
suberin on only four face) to allow only one passage of water to the xylem
Note: water pressure also help water get into the xylem

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Mechanism of water transfer through the cortex
 Through the cell wall (made of chitin, a polar molecule) & the intercellular
spaces. Water doesn’t enter the cell
 Through the vacuole of cortex cells (vacuolar pathway) by osmosis.
 The cell wall doesn’t cover the cell completely. The cell wall has some pores
that make the cytoplasm shared between the cell. This means of exchange
called plasmodesmata, which is also a mean of communication.
 So water may enter the cytoplasm in one cell which passes water to another
cell, this is called symplastic pathway
Notes:
 all these processes work together no separately
 Plasmodesmata is a narrow thread of cytoplasm that passes through the cell
walls of adjacent plant cells & allows communication between bundle sheath
cells & mesophyll cells.

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The Leaf

Upper epidermis  Adjacent for protection

 Barrel shaped to trap light rays
 Transparent to allow light to penetrate
 Thickened with cutin to prevent water loss
 No chloroplasts
Guard cells  Control the opening of stomata in response to change
in water pressure & have chloroplasts
Stomata  Allow gases exchange
 Responsible for transpiration
 When absorb water→ become rigid→ open
 When lack water→ become flaccid→ close to reduce
water loss
Palisade mesophyll  Contains the largest number of chloroplasts for
Photosynthesis
Spongy mesophyll  Photosynthesis
 Diffusion & exchange of gases
Veins “vascular  Carry water and nutrients from the soil to the leaves &
bundles” carry sugar, the product of photosynthesis, from the
leaves to the rest of the plant

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 Vascular bundle

Xylem Phloem

Vessels Tracheid sieve tubes companion cells

The Xylem
Vessels tracheid
 They are larger than tracheid & they  They are smaller than vessels & they
are the main conducting tubes of are the main conducting tubes of
water in angiosperm. They are water in gymnosperm. They are
covered with lignin (lignified) for lignified. They help in transporting
rigid support. water such that they may function in
 They are dead cells but functioning case vessels are blocked
 The holes in the xylem is called pits  They are elongated cells in the stem
only

Xylem carries water & nutrients from the soil up by:

 Cohesion: water molecules are attracted to each other
 Adhesion: water molecules adhere to walls of xylem
 Transpiration pull: a process of losing water through leaves which causes the
water column to be pulled up through xylem

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The phloem
Sieve tubes Companion cells
 The cytoplasm carries the  The movement of cytoplasm in sieve
manufactured food in the leaves & tubes requires energy (ATP) which is
distributes it to all body cells as it absorbed from the companion cells
goes from one sieve tube element to  Each sieve tube element has a
another companion cell

Important: translocation of manufactured food in

phloem is an active process because it’s assisted by
energy comes from companion cells
Note: sieve tube cells are living cells that don’t
undergo respiration

6) Plant sensitivity
Sensitivity: ability of an organism to detect a stimulus & respond to it
Examples of sensitivity in plants:
o Tropic movement (tropism)
o Nastic movement
o Photoperiodism
Tropism: movement of a part of a plant according to a stimulus either toward it
(positive tropism) or away from it (negative tropism)
Auxins are the responsible factors in plant movement. All tropic movement are
explained in terms of unequal distribution of auxins.
Auxins: are plant hormones, that stimulate growth, cell division, fruit ripening.
Auxins are found on root tip & shoot tip, which cause growth
Note: both shoot & roots need auxins to grow; they differ in concentration
needed for growth
 In shoot the ↑ auxins, the better the growth
 In roots the ↓ auxins, the better the growth

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A. Phototropism (light is the stimulus)
Auxins accumulate on the dark side
Shoot Root
 Auxins accumulate on the darker  Auxins accumulate on the darker
side so it grow longer & bent over side causing that side to have an
the other side inhibited growth. The other side
 The shoot grow toward the light (without auxins) grow faster & bent
 Positive phototropism  The root grow away from the light
 Negative phototropism

Notes:
 It’s beneficial for the plant to have positive phototropism in the shoot so that
the plant can easily absorb light rays
 It’s beneficial for the plant to have negative phototropism in roots so that the
root can grow deeper in the soil to absorb more nutrients

B. Gravitropsim (Geotropism)
Auxins accumulate in side towards gravity
Shoot (phmula) Root (radula)
 Auxins accumulate in the lower side,  Auxins accumulate in the lower side
so it grows more making the stem making the upper side grow more,
moves upward so the root moves downward
 Negative geotropism  Positive geotropism
Note: whatever the condition, the shoot grows up while root grows down

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C. Nastic movement
“The movement of a part of a plant according to a stimulus independent of the
direction of the stimulus
E.g.:
 Sleeping movement (nychtonastic)
 Touch movement (thigmonastic)

D. Photoperiodism
“Causes the plant to flower in certain season”

Notes:
 Abscisic acid: inhibit growth & enable the plant to withstand drought
 Ethylene: promotes ripening
 Cytokinins: promotes cytokinesis & cell division
 Gibberellins: promote stem & leaf elongation
 Phototaxis: is the movement of any motile organism (often animals) towards
light
Study the figure

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 7) Plant reproduction

I. Asexual reproduction

 By vegetative propagation where a vegetative part (root – stem – leaves)

produces genetically identical clone

II. Sexual reproduction

 The reproductive organ is the flower of cone “in non-flowering”

 Happens when the sperm “in the pollen grain” join egg “in ovum” & eventually
forms a seed
Parts of the flower:
A. Sepals: green typical leaves that encloses the flower before opening

B. Petals: colored leaves that attract pollinators

C. Pistil: female part that is formed of

a) Stigma: sticky upper part to capture pollen
b) Style: long thin stalk
c) Ovary: swollen part that produces ova produced from the ovule “the wall of
th ovary”

D. Stamen: male part that is formed of

a) Filament: thin stalk carrying anther
b) Anther: a sac that produces pollen

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Pollination & Fertilization
 Ovule becomes seed & the ovary becomes the fruit
 One pollen has three nuclei stich to the stigma & generate a pollination tube
reaching the ovary
 Two sperm nuclei enter the ovary; one fertilize the egg forming embryo (2N)
while the other nucleus fertilizes the two polar bodies forming the endosperm
(3N) “cotyledons”
The seed: formed of seed coat, embryo & cotyledons”stored food”
Self-pollination Cross pollination
 It’s the transfer of pollen grains from  The transfer of pollen grains from
the anther of a flower to the stigma the anther of flower to the stigma
of the same flower or to stigma of of a flower on another plant of the
another flower on the same plant same species
 The flowers are hermaphrodite  The flowers are hermaphrodite
where where
o The organs of two sexes must o The organs of one sex must be
be matured at the same time matured before the other sex
o The anther level must be organs
higher than the stigma level o The level of anther must be
lower than the level of stigma
o The flowers are unisexual

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 Taxonomy
Old classification

“Classifying organisms into groups according to

Modern classification

 Old classification: similarity in shape, mode of nutrition, habitat….

 Modern classification: similarity in DNA sequence or protein
Levels of Classification

Kingdom Species
Phylum Class Order Family Genus
(least level) (last level)

Note: if two organisms are belonging to a

certain level, so they must belong to the
same previous level.

Species: “a group of closely related

organisms able to interbreed giving fertile
offspring

Binomial Nomenclature

Genus – species
1. Panthera leo is the scientific name of
the lion. leo represents the
a) Class 2. The correct way to write the name of
b) Order house fly is
c) Species a) Musca Domestica
d) Genus b) musca Domestica
e) Family c) musca domestica
d) Musca domestica
e) MUSCA domestica

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Bacteria Archaea Eukaryota

1) Unicellular 1)Unicellular  Protista

2) Prokaryotes 2)Prokaryote  Fungi
3) Some aerobic, others are 3)Have introns  Plantae
anaerobic 4)Called extremophiles  Animalia
4) Some are autotrophic  Methanogens All are eukaryotes (have
(cyanobacteria), and others are (↑O₂ Conc.) a nucleus)
heterotrophic (decomposers)  Halophiles
5) Some are useful, but most are (↑ Salt Conc.)
pathogens  Thermophiles
6) Play a role in genetic engineering (↑ Temp.)
7) Play a role in N-cycle
8) No introns
9) Peptidoglycan cell wall
10) Asexual reproduction, in
unfavorable conditions, they
undergo primitive sexual
reproduction (conjugation)
Resulting in formation of
zygospore (fertilized cell) having
thick-coated cell wall to withstand
harsh conditions

11) Virus is included

Kingdom Monera includes bacteria
and blue-green algae

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Domain Eukaryota

1) Kingdom Protista
 All are eukaryotes
 Some are unicellular as amoeba and paramecium, others are multicellular as
kelps
 Diversity (animal-like (plasmodium causing malaria), plant-like and fungus-like)
 Some are autotrophic while others are heterotrophic
 Different types of locomotion
 Some Protista carry out conjugation
Amoeba Paramecium Euglena
 Unicellular  Unicellular  Unicellular
 Animal-like  Animal-like  Plant-like
 Heterotrophic  Heterotrophic  Autotrophic (as it
 Locomotion by  Locomotion by cilia contains chloroplast)
pseudopodia  Locomotion by flagella

2) Kingdom Fungi
 All are eukaryotes
 Some are unicellular (yeast), others are multicellular (bread mold)
Note: spores can withstand harsh conditions for a long period of time

 All are heterotrophs (decomposers) but in Protista, some are autotrophs

 Some are edible (mushroom)
 Some have chitinous cell wall. Remember → bacteria has peptidoglycan cell
wall, while plants and algae have cellulose cell wall
 Fungi carry out extracellular digestion by secreting enzymes outside the body,
then absorb nutrients by diffusion

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 Reproduction: yeast by budding, bread mold by spore formation or
fragmentation
 Saprobes: organisms that obtain food form decaying organic matter
 Lichen: certain fungi that combine with algae in a mutualistic symbiotic
relationship

3) Kingdom Plantae
 All are eukaryotes
 All are multicellular
 All are autotrophs
 Their cell walls are made of cellulose, they store food in the form of starch
 Alternation of generation: sexual reproduction followed by asexual

4) Kingdom Animalia
 All are eukaryotes
 All are multicellular
 All are heterotrophs
 They are grouped in 35 phyla, but we commonly discuss 9 only

Evolutionary trends

1) Specialization
Unspecialized Simple specialized Specialized (most
(primitive) (advanced) advanced)

2) Cephalization
Acephalized (primitive) Cephalized (advanced)

3) Symmetry
Asymmetric Radial symmetric Bilateral (most
(primitive) (more advanced) advanced)

Sponges Jellyfish or Starfish Insects

87
4) Germ layers
Gastrula
Zygote blastula
Morula (group (ectoderm,
(ectoderm and
(cell) of cells) mesoderm and
endoderm)
endoderm)

Adult: 2 Layers Adult: 3 Layers

No organs Organs present

(diploplastic) (Triploplastic)

 Ectoderm: outermost layer, becomes the skin and the nervous system
 Endoderm: innermost layer, becomes the viscera (gut) or the digestive system
 Mesoderm: middle layer, becomes the blood, muscles and bones.

5) Coelomation (body shape)

 Coelom: “is a fluid-filled body cavity that is completely surrounded by
mesoderm tissue from both sides”

Acoelmates Pseudocoelomates Coelomates

 Acoelomates: don’t have body cavity, they are primitive as flat worms
 Pseudo-coelomates: they have a fluid filled tube between the endoderm and
the mesoderm
Note: A pseudo-coelomate is not completely lined by mesoderm
 Coelomates: are animals with a coelom and are the most complex in the
kingdom

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Nine Phyla of Kingdom Animalia

1. Sponges (porifera)
 No symmetry, Sessile mesoglea
Endoderm
 Diploplastic
 No true tissues
Central cavity
 Acephalized
 Reproduce asexually by fragmentation or sexually
 Hermaphrodite = bisexual Ectoderm

2. Cnidarians (Coelenterates)
 Radial symmetry
 Diploplastic
 extra or intracellular digestion Vase-like Inverted bowel-like
 Have string cells (nematocytes) “sensation”
 Secrets ammonia ( NH₃) “toxic” (polyp) (medusa)

Ex: hydra Ex: Jellyfish

Sessile motile

Gastrovascular cavity
Parasites ex: tape worm

3. Platyhelminthes (flat worms)

Free living ex: planaria

 Simple specialized
 Cephalized
 Bilateral symmetry
 Triploplastic
 Acoelomates
 Digestive system has one opening for ingestion and egestion
 No transport system (depend on diffusion)
 Hydrostatic skeleton

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 Un-segmented
Notes:

 planaria contains flame cells for excretion of ammonia

 Tape worm has suckers to attach to the walls of the intestine

4. Nematodes (round worms)

 Un-segmented worm
 Simple specialized
 Cephalized
 Bilateral symmetry
 Triploblastic
 Pseudo-coelomate
 Mostly parasite
 Transferred to human by eating uncooked pork
 Hydrostatic skeleton

5. Annelids ( segmented worms) Ex: leech and earthworm

 Specialized
 Bilateral symmetry
 Cephalized
 Triploplastic
 Coelomate
 hermaphrodite
 Little sensory apparatus
 Digestive tract with crop, gizzard and intestine
 Nephridia to excrete urea (alternative to kidney)
 Closed circulatory system
 Diffusion of CO₂&O₂ through moist skin
 Hydrostatic skeleton
 Ventral nerve cord

90
6. Molluscs (soft bodies)
EX: squid, octopus, slugs, clams and snails

 Specialized, cephalized, bilateral,

triploplastic and coelomate
 Open circulatory system with sinuses
 Hard calcium containing shells made in
the mantle

7. Arthropoda (arthro = joint , poda = legs)

 Specialized, cephalized, bilateral, triploplastic and coelomate
 All are invertebrates
 Have chitinous exoskeleton and Have segmented body
 Have jointed legs
 Greatest number of different species

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 Classes of phylum Arthropoda

Insecta Crustaceans Arachnida Myriapoda (many legs)

Ex: bee, ant, fly, Ex: shrimp, crab Ex: spiders and Divided into centipedes
grasshopper, cockroach, and lobster scorpions and millipedes
cricket, beetle and bug  Many  2 body 1) Centipedes:
 3 pairs of jointed legs segments segments  1 pair of legs per
 1 or 2 pairs of wings  Many pairs of (head- segment
 1 pair of antenna legs cephalothorax)  Scavenger (eat dead
 3 body segments:  1 pair of  4 pairs of organisms)
 Head: contains complex antenna jointed legs
and simple eyes  No wings  No antenna
 Throax: legs and wings  No wings
originate from thorax
 Abdomen: with
respiratory opening (to
cells directly by
diffusion), aslo excretory
and reproductive parts
 Open circulatory system
(white-blooded with no 2) Millipedes
hemoglobin)  2 pairs of legs per
 Digestive tract with crop, segment
gizzard  Free-living (eat
 Have malpigian tubules nutrients)
to excrete uric acid

Note: urea is soluble in water while uric acid is insoluble in water

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8. Echinodermata:
Ex: sea star, sea urchin, sea cucumber and sea horse
 Bilateral larva, radial adult (retarded evolution) “exception”
 Specialized, cephalized, triploplastic and coelomate
 Sessile or slowly moving
 They move by tube feet (with hydrostatic support)
 Sexual reproduction / external fertilization
 Endoskeleton of calcium plate

9. Chordates
 Specialized, cephalized, bilateral, triploplastic and coelomate
 Have notochord → spinal cord
 Endoskeleton (vertebrates)
 Dorsal nerve cord
 Ligaments: connect bone to bone , Tendons: connect muscle to bone
 Urea formed by the liver and excreted by the kidney

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 Classes of Chordates

Fish Amphibians Reptiles Birds mammals

Fish Amphibians Reptiles Birds Mammals

 Ammonia  Urea  Uric acid  Uric acid  Urea
 Divides into Ex: frog and Ex: snake  They give
 Cartilaginous salamander  Have  Have birth
(shark)  They have amniotic amniotic egg  They have
 Bony moist skin Can egg to to prevent external ear
(bolti) breathe prevent dehydration  Warm-
 Cold-blooded through dehydration  Warm- blooded or
ectotherm  Cold-blooded  Cold- blooded or homo-therm
(poikilothermic) ectotherm blooded homo-therm or
(poikilothermic) ectotherm or endotherm
(poikilothermic) endotherm
Class Mammalia

Monotremes marsupials Placental mammals

Ex: platypus Ex: Kangaroo and Kuala  the highest are the primates
 They lay eggs  Give birth but the (apes and humans) that
 But suckle their offspring complete differ from other placental
young its development mammals in that they have:
outside her body in  opposable thumb
the pouch  Complex N.S.
 single birth
 nails instead of claws

Humans Apes
1) Bigger brain cavity 1) Smaller brain cavity
2) S-shaped vertebral column 2) C-shaped vertebral column
3) Opposable thumb in hands only 3) Opposable thumb in hands and
legs
Temperature of cold-blooded changes by changing temperature of environment

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 Ecology
 Species: A group of closely related organisms able to interbreed and give
fertile offspring
 Population: A group of organisms of same species living together
 Community: different populations living together
 Ecosystem: biotic (living) + abiotic (non-living) factors interacting together
 Biome: many ecosystems
 Biosphere: the inhabited part of the planet
 Niche: includes what an organism eat and what it needs to survive
 Population size: the no. of individuals in the populations
 Population density: population size / area or volume
 Population dispersion

 Population growth

Exponential no limiting factor Logistic (sigmoid) Limiting factors

C
B
Pop. Size
Pop. Size

Time
Time
Ex: bacteria in lab and human population A: exponential, B: ↑ with Dec. rate

Increasing rate (b/c of the appearance of limiting factor)

C: carrying capacity (birth = death)

95
Carrying capacity: the max. no. of individuals can be supported by resources in
ecosystem. Carrying capacity is constant until any change occurs like declamation
or burning

Limiting Factors: “factors that limit the rate of the reaction”

Density dependent Density independent

Ex: predation, competition, disease Ex: any natural disaster as

Outbreak and toxins (wastes) Volcano, floods and drought

Species interactions

Predation Symbiosis Competition

Prey-predator “Mutualism” “Parasitism” “Commensalism” Intra-species
relationship: (+,+) (+,-) (+,0) “Inside the
 Adaptations Exchange Parasite - Ex: remora fish same species”
of the benefits host and shark
predator: Ex: Ex: bacteria
 Fast E. Coli and in your
 Strong human throat
 Canines Ex: lichens
 Camouflage
 Front facing Note: Note: successful
eye parasites parasite Inter-species
 Adaptations depend on flourishes inside “between
of the prey: host and not the host yet it different
 Fast feed on it allows him to species”
 Camouflage survive
 Lateral eyes
 Mimicry

96
 Notes:

 Camouflage: to hide by acquiring skin color similar to that of the background

 mimicry: is that a weak organism resembles another toxic one

Graphs

Prey increases first then the predator

Pop. Size

Pop. size of prey is greater

Time
 Prey
 Predator

Competition “Intra-species” “inter-species”

P.aurelia P.codatum P.aurelia

Pop. Size
Pop. Size

Pop. Size

P.codatum

Time Time Time

97
 Energy transfer

Mode of nutrition

Producer (autotrophic) Consumer (heterotrophic)

Make their own food by themselves

Photosynthetic Chemosynthetic

Carnivorous Scavenger

Herbivorous Omnivorous Decomposers

Note: scavengers eat the remains of prey; while decomposers (natural recyclers)
decay then absorb those remains

Food Chain: “A series that shows which organisms feed on which and how energy
transfers through the ecosystem”

Notes:

 Any food chain starts with a producer (tree – plant – grass – diatom –
phytoplankton “tiny plants”)
 Energy decreases to 10% in each trophic level and divided the previous level
by 10 if form the producer
 The closer you are from the producer, the more energy you get
 Food chain is always short
 Decomposers convert food chain into food cycle
 Food web is an interconnected food chains

Phytoplankton Zooplankton Small fish Large fish Human

Producer 1st consumer 2nd consumer 3rd consumer 4th consumer

(Herbivore – omnivore) (Carnivore – omnivore)
E: 100% 10% 1% 0.1% 0.01%

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Biological magnification

“The increase of concentration of a substance in the bodies

of organisms in food chain till it reaches a concentration
that is very toxic”

Ex: DDT, a non-biodegradable insecticide

Succession

“It is a series of steps in which the activity of each population changes the
environmental conditions such that it is suitable for more advanced populations”

wood land
lichens (pioneer mosses (pioneer
bare land ferns small trees climax
community) community)
community

Note: Lichen = algae and Fungi mutualistic relationship

Types of Succession

Primary Secondary

If the area was not inhabited before If the area was inhabited before

99
Natural Cycles or biological cycles: they are important because the resources are
finite

Combustion Decay

Respiration

100
Note: lightning allows nitrogen and oxygen to react together forming nitrate so it
can increase the nitrate concentration

Biome

“Very large areas of Earth, which differ according to temperature and rainfall”

1.Marine Biome
 Largest biome (75%) of earth
 The most stable biome (water has high specific heat)
 Provides most of earth’s food and oxygen
 Subdivided into different regions classified by the amount of sunlight they
received, distance from shore, water depth and whether open water or ocean
bottom
 Open oceans has less nutrients

2. Tropical rainforest
 Found near the equator with abundant rainfall,
stable temperature and high humidity
 4% of Earth’s land, but produce 20% of food made
by photosynthesis “second source of food”
 Largest plant diversity on Earth
 Largest animal diversity on Earth
 Characterized by lush vegetation, including all
broad-leaved trees & nutrient poor soil
 Large tress are very tall and their branches keep it always dim at the forest
floor
 Rain doesn’t fall directly at the floor, its dripped constantly on leaves
 Many tress are covered with epiphytes (photosynthetic plants that grow on other
trees for support), they may kill them by blocking light

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3. Desert
 It receives less than 10 inches of rainfall per year; not even grasses can survive
 Daytime surface temperature can be high as 70 :C. with no moderating
influence of vegetation, heat is lost rapidly at night
 Characteristic plants are drought-resistant cacti,
sagebrush, creosote bush and mesquite
 There are many small annual plants that are stimulated
to grow only after a hard rain, but die in few weeks
 Most animals are active at night or during a brief early-
morning period or late afternoon
 During the day, animals remain cool by burrowing underground or hiding in
the shade
 Characteristic animals include rodents, kangaroo rats, snakes, lizards,
arachnids, insects and a few birds

4. Temperate grasslands
 Cover huge areas in both the temperate and tropical
regions of the world
 Low total annual rainfall or uneven season
 Principal grazing mammals include bison and pronghorn
antelope in the United States and wildebeest and gazelle in Africa. Also some
rodents are common

5. Temperate deciduous forest or boreal forest

 Found in Northeast of North America, south of Taiga and
characterized by trees that drop their leaves in winter
 Shows vertical stratification of plants and animals (some
species live on ground, some in low branches and some in
treetops)
 Rich soil due to decomposition of leaf litter
 Principal mammals include squirrels, deer, foxes and bears that are dominant
or hibernate through the cold winter

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6. Conifer Forest-Taiga “the largest terrestrial Biome”
 Found in Northern Canada and much of the world’s
northern regions
 Dominated by conifer (evergreens) forests
 Landscape is dotted with lakes, bonds and bags
 Characterized by trees with needlelike leaves and a
short growing season
 Has very cold winters with heavy snowfall, trees are shaped with branches
directed downward to prevent heavy accumulations of snow from breaking
their branches
 Has greater variety in animal species than does the tundra, moose, black bear,
lynx, elk, wolverines, martens and porcupines

7.Tundra
 Found in Northern parts, at high elevations or latitudes
 Characterized by small trees that grow near the ground
 Called the permafrost, permanently frozen subsoil in the
farthest point north, including Alaska
 Commonly referred to as the frozen desert because it
gets very little rainfall
 Few species of mammals and birds that feed on insects and most birds
migrate in winter

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 Humans and the Biosphere

1. Eutrophication of the lakes

 Runoff from sewage and manure from pastures increase nutrients in lakes
 This cause excessive growth of algae and other plants
 Shallow areas become choked with weeds and swimming and boating become
impossible
 Large populations of photosynthetic organisms die, two things happen
 First, organic material accumulates on the lake bottom and reduces the depth
of the lake
 Second, decomposers use up oxygen as they decompose the dead organic
matter
 This kills the fish also and increase activity of decomposers
 Ultimately, the lake disappears

2. Acid Rain
 PH of acid rain to be less than 5.6
 Caused by pollutants in the air from the
combustion of fossil fuels
 Nitrogen and sulfur pollutants in the air turn into
nitric, nitrous, sulfurous and sulfuric acid
 This causes the death of the organisms in lakes
and damages ancient stone architecture

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3. Toxins
 Most cattle and chicken feeds contain antibiotics and hormones to accelerate
animal growth
 Any carcinogens or teratogens (causing birth defects) that get into the food
chain accumulate and remain in our body’s fatty tissues

4. Global warming
 Excessive burning of fossil fuels caused high
levels of carbon dioxide in the air
 Greenhouse effect: carbon dioxide and water
vapor in the air absorb much of the infrared
radiation reflecting off of Earth
 This cause the increase of Earth’s average
temperature (Global warming)
 Starting from melting polar ice caps, raising
the level of the seas and ending with burring
many coastal cities under water

5. Depleting the ozone layer

 Chlorofluorocarbons, chemicals used for
refrigerant and aerosol, cause a hole in the
ozone layer (that blocks most of the UV rays)
and responsible for skin cancer

6. Introduction of new species

 “the killer honeybees” : aggressive African
honeybees brought to Brazil and caused death of
ten people

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7. Pesticides VS. Biological control
 Pesticides include insecticides, herbicides, fungicides, mice and rat killers
 Pesticides save lives by increasing food production and by killing animals that
carry and cause diseases like bubonic plague (diseased rats) and malaria
(anopheles mosquitoes)
 Exposure to pesticides can cause cancer in humans
 Spraying with pesticides ensures the development of resistant strains of pests
through natural selection. The pests came back stronger than before

 The Biological Control

1) Use crop rotation “change the crop planted in a field”
2) Introduce natural enemies of the pests “so you must be careful”, however
that you don’t disrupt a delicate ecological balance by introducing an invasive
species
3) Use natural plant toxins instead of synthetic ones
4) Use insect birth control (male insect pests can be sterilized by exposing them
to radiation and then releasing them into the environment to mate
unsuccessful with females

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 Evolution
 Evolution
 Evidence of evolution
 Theories of Evolution
 New species formation
 Patterns of Evolution
 Theories about Evolution
 How life began
 Heterotroph hypothesis
 Adaptations for life land

1) Evolution

“Change of gene of population over time”

Types:

 Microevolution: small changes that accumulate over time that make great
change
 Macroevolution: A new Species is formed

Notes:

 Evolution is any change in organism even making the organism become worse
in contrary to improvement
 It doesn’t occur at the same rate in all living organisms
 It doesn’t always cause organisms to become more complex
 It is not always a slow process
 It occurs in population, not individuals
 It is directed by changes in environment

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 2) Evidences of Evolution

A. Fossil Records Fossil remains of

living organisms

Condition of fossilization: presence of hard

structure (as bones)

Types of fossils:

i. Entire fossils (mammoth, insects and amber)

ii. Mold
iii. Cast

Transitional fossils: link older extinct fossil to modern species Ex: Archaeopteryx,
flying fish

B. Comparative anatomy
 Homologous structure: features with
similar structure but with different
function (common ancestor)
Ex: fore arm in vertebrates

 Analogous structure: Features with similar

function but with different structure
Ex: wings in bats, moth and birds or fins in fish
and flippers in whales

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 Vestigial Structure: Structures that don’t function in
organisms
Ex: hair in human skin, appendix (in human not
herbivores), limbs of snake and hind limbs in whales
(common ancestor)

C. Comparative Biochemistry

Similarity in biochemistry pathways Ex: Cellular

Respiration or photosynthesis

D. Comparative Embryology

Similarity in early embryos of

vertebrates Ex: gill pouch

E. Molecular biology

Similarity in amino acid sequence in many organisms

Ex: Cytochrome C, Universal Gene Code

F. Biogeographic

206 million years ago, all continents were one part (Pangaea). 55 million years
ago, marsupials migrate from South Africa to Austria

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 3) Theories of Evolution

I. Lamarck

“Use and disuse” living organisms respond to environment

Lamarck believed acquired characteristics could be passed on to offspring. The

classic example is the giraffe, it stretches its neck to reach higher branches and
then when it has offspring they have a longer neck as a result. Of course this
doesn’t happen, phenotypes can change in an individual’s life but the genotype
stays the same (acquired traits aren’t inherited). (Disuse = vestigial)

II. Darwin

“Natural selection” : the process by which traits become more or less common in
population due to consistent effects upon the survival or reproduction of their
bearers. It’s a key mechanism of evolution. He had no knowledge of genetics, for
example, so had no idea what the mechanism was for the variation and
hereditability on which his theories depend

Postulates of Darwin:

a) Large population
b) Variation
c) Competition (struggle for survival)
d) Survival for the fittest

Fittest: ability of organism to survive and reproduce a large no. of offspring

Adaptive advantage: the trait that allows the organism to accommodate the
change in environmental conditions.

Case study:

- Piston P.tularia moth - Antibiotic resistant bacteria

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 In an early age, light moth was able blind trees, rocks and
sand for having the same color. When the industrial
revolution occurs, trees, rock and sand color changed to
moths were able to hide. Now, dark moths can camouflage
with the environment to hide.

Types of Natural Selection:

Stabilizing Disruptive Directional

selection selection selection
 Eliminates the  Increases the  One
numbers of number of phenotype
extremes and extreme types replaces
favors the in a population another
more common at the expense  Ex: ant
intermediate of intermediate eaters (new
forms forms species of
 Ex: body  Ex: snails on ant dig
height in beach and wild deeper)
lizards (prey- birds
predator)

III. Hardy-Weinberg
 Population is a unit of evolution
 Gene pool: all genetic traits in a population
 Allele frequency: ratio of certain allele to the no. of alleles
 Phenotype frequency: the ratio of a certain phenotype to
the total no. of individuals

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 Genotype frequency: the ratio of a certain genotype to the total no. of
individuals
 Equilibrium: The state in which allele frequency and phenotype are constant
generation after generation
 Gene flow: movement of alleles into and out of a population
Ex: pollen from one valley can be carried by the wind to another valley
 Gene drift: is the change in the frequency of a gene variant (allele) in a
population due to random sampling

Conditions for equilibrium:

 No natural selection
 Random mating (except for human)
 No Mutation
 Large population
 No gene flow

Hardy-Weinberg Equation:
A a
 P+q=1 A AA Aa
 P² + 2Pq + q² = 1 a Aa aa
 P = dominant allele frequency (%) , q = recessive allele frequency (%)
 P² = homozygous dominant (%) , q² = homozygous recessive (%)
 2Pq = heterozygous

Ex: if 9% of the population has blue eyes, what percent of population is hybrid for
brown eyes and Homozygous for brown eyes?

 bb = q² = 9% → into decimal = 0.09 → q² = 0.09 → q = 0.3

 p + q = 1 → p = 1 – q = 1 – 0.3 → p = 0.7
 hybrid = 2pq = 2 (0.7 x 0.3) = 0.42 → % = 0.42 x 100 = 42%
 Homozygous = p² = (0.7)²= 0.49 → % = 0.49 x 100 = 49%

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4) New species formation (cause reproductive isolation) “speciation”

A. Polyploidy
Triploid (3N) or tetraploid (4N) or octaploid (8N), polyploidy organisms cannot
interbreed with organisms that are not polyploidy to five fertile offspring

B. Geographic isolation
Occurs when species are separated by things like
mountain ranges, canyons, rivers and lakes

C. Habitat isolation
Occurs when two organisms live in the same area but
encounter each other rarely
Ex: two snakes live in the same area; one inhabits water while
the other is mainly terrestrial

D. Behavioral isolation

E. Temporal isolation
It refers to time. Different plants of one species living in the
same area become functionally separated into two
populations because some plants become sexually mature
earlier

F. Reproductive isolation
Closely related species may be unable to mate because of
anatomical incompatibility. For example, a small male dog
and a large female dog cannot mate because of the enormous
size differences between the two animals.

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5) Patterns of evolution

A. Divergent evolution describes two or more species that

evolved from common ancestor
Ex: homologous structures A
A B

B. Convergent evolution describes two or more unrelated species that have

adopted similar adaptations to their environment
Ex: whale (mammal) and fish both have streamline appearance while their
ancestors are different A
NB: all analogous are convergent A B

C. Parallel evolution describes two or more species that have continued to

evolve similar characteristics even after their divergence from common
ancestor
Ex: grey wolf of North America (mammal)
and Tasmanian wolf of Australia (marsupial)

D. Coevolution describes the evolution of

one species in response to the evolution
of another.
Ex: pollinator – plant
Ex: prey – predator relationship

E. Adaptive radiation is the emergence of

numerous species from a single ancestor
introduced into an environment
Ex: finches on Galapagos Island

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 6) Theories about Evolution

I. Gradualism: is a theory that organisms descend from a common ancestor

gradually, over a long period of time, in a linear or branching fashion

II. Punctuated: this theory proposes that new species appear suddenly after a
long period of No change

III. Spontaneous Generation: is the theory that living things emerge from non-
living things or inanimate objects
Disproving this theory
a) Francesco Redi

b) Spallanzani

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 c) Louis Pasteur

7) How life began

After the big bang formed the planets, the Earth’s surface cooled and solidified to
form the crust. The environment consisted of methane, ammonia, vapor and
nitrogen. Intense heating, lightening and UV radiation made several reactions till
the first cell was produced.

i. Oparin: he said that under the conditions of early earth, organic molecules
could form. He stated that in the absence of corrosively reactive molecular
oxygen that would react with and degrade them, organic molecules could form
and persist

ii. Urey and Miller: they proved that almost any energy source would have
converted inorganic molecules in the early atmosphere into a variety of
organic molecules, including amino acids. They used electricity to mimic
lightning and UV light that must have been present in great amounts in the
early atmosphere. (they only supported oparin)

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iii. Sidney Fox: carried out similar experiments. He was able to produce
membrane-bound, cell-like structures he called proteinoid microspheres,
which would last for several hours in a lab.

Remember:

There was No free Oxygen in the ancient Earth’s atmosphere

8) Heterotroph hypothesis

This theory states that the first cells on Earth were unicellular, prokaryotic,
heterotroph and anaerobic, simply they absorbed organic molecules from the
surrounding primordial soup to use as a source

9) Adaptations for life land

Animals Plants
 Lungs  Roots that fix them into the soil and
 Skin to keep them from drying out absorb water
 Limbs to move  Supporting cells that enable them to
 Mechanisms for internal fertilization compete favorably for light
 Shell to protect their eggs and to  Vascular tissue (cutin) to protect
keep them from drying out leaves from dehydration
 Seeds, a protective package for
embryo and its food

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 Human Physiology
I. Digestive system
Digestion

“The breakdown of large, complex & insoluble substance into small,

simple & soluble substance to be easy to be absorbed”

Types of digestion

Mechanical digestion Chemical digestion

 Large → small “↑ S.A”  Complex → Simple
 Without chemical reaction  Insoluble → soluble
(no change in chemical structure) (change in chemical structure)
 It takes place by teeth & peristalsis  It is carried on by enzymes
Teeth:

 Incisors → cutting
 Canines → tearing
 Molars & premolars → crushing
Peristalsis

“The movement of food by series of contraction and relaxation of the muscular

wall of the esophagus, besides, the movement also crushes the food. It is found in
every stage in digestion”

The system responsible for digestion is the digestive system

Alimentary canal Associative organs

 The canal through which the food  Organs or glands that pour digestive
passes juices on the food while it is in the
 Mouth → pharynx → esophagus → alimentary canal
stomach → small intestine → large  Pancreas, liver & salivary gland
intestine → rectum

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1) Mouth (PH 7-7.2)
Teeth Salivary glands Tongue
(mechanical) (chemical) (mechanical)
 Breakdown of  Starch contains glycogen which is a  Food
food polymer of glucose made by manipulation
dehydration  Taste sensation
 Saliva contains water and amylase
enzyme
 Starch disaccharide (maltose)
Note: each enzyme has a PH that can work best at. In saliva, amylase works only
on glycogen not protein or lipid etc…

2) Pharynx
“It transfers food from the mouth to the esophagus (common organ)”
Note: during swallowing, the breathing stops because the trachea elevates and
closes the air tract with the epiglottis, so it will have only one way to the
esophagus

3) Esophagus
“A narrow tube through which food moves to the stomach, it has a muscular
wall for peristalsis”
Notes:
 Esophagus doesn’t secret any enzyme, so the amylase still works there
 Any body part that has a cavity has a mucus membrane
Peristalsis: rhythmic contraction & relaxation of the muscles in the walls of
alimentary canal

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4) Stomach (PH 1.5 – 2.5)
“Is a sac-like structure with a muscular wall that digests food”

The stomach secrets gastric juice which includes:

 H₂O, HCl & Pepsin enzyme

Functions of HCl:

 create acidic medium which stops action of amylase

 activates gastric enzyme ( Pepsinogen HCl Pepsin)
 kills harmful bacteria
Pepsin enzyme: secreted in an inactive form called pepsinogen, it becomes active
by action of HCl, catalysis the hydrolysis of proteins

Proteins + Water Pepsin (HCl) Polypeptide

This reaction breaks the cross links between the polypeptide chains

Important:

 If the stomach produces a protein-breaking enzyme, why doesn’t it digest itself

given that the cells (in the stomach) are mainly proteins?
 The enzyme pepsin is secreted in an inactive form, activated in an acidic PH
1.5 – 2.5, so it gets activated in HCl in the stomach cavity. Gastric juices,
moreover, are only secreted if there is food
 The mucus isolated the muscle layer from the reaction occurred in the
stomach
Notes
 gastro → stomach , cardo → heart, hepat → liver
 Ulcer could be formed in stomach, esophagus & intestine due to excessive acid
 Helicobacter pylori is a type of bacteria that causes ulcer & is treated using
antibiotics
 Risk factors: smoking, eating spicy food & prolonged stress

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5) Small intestine (PH 8)
“Is divided into duodenum (first 25 cm) and the ileum”
Three Juices help digest food in small intestine:
A. Bile (liver juice)
B. Pancreatic Juice
C. Intestinal Juice

A. The Bile: (stored in gallbladder) secreted by the liver through the bile duct
 Bile plays an important role in digestion of fats. Bile has no enzymes but it has
bile salt which plays the following role:
 Water and fat aren’t mixed together, so the enzymes from the pancreas
can’t work on fats
 Bile breaks the fats into fat droplets, not dissolved, but spread throughout
water (O/W emulsion). In other words, bile decreases the surface area of
fats in contact with water. The chemical structure of fat & water is still the
same, so it’s a mechanical digestion
Note: if too much salts concentrate, hepatic duct will be blocked resulting in
severe pain & food isn’t digested well. So it is broken by laser or extracted in
surgery
B. The Pancreatic juice:
1-Sodium bicarbonate: neutralizes HCl and makes the medium alkaline
2-Pancreatic amylase: starch amylase maltose
3-Trypsinogen: inactive enzyme, activated into trypsin.
Proteins trypsin Polypeptide
4-Lipase: Emulsified Fats Lipase Fatty acids + Glycerol
C. Intestinal juice: secreted by certain cells in the wall of small intestine
especially the ileum, it contains:
1-Peptidase Enzyme: Polypeptides Peptidase amino acids
2-Enzymes hydrolyze disaccharides into mono-saccharides
 Maltose Maltase 2 Glucose
 Sucrose Sucrase glucose + fructose
 Lactose lactase glucose + galactose

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Absorption
“Is the transfer of digested food into the blood by villi
Adaptations of small intestine for digestion:
 Very large surface area
 Very thin wall for fast diffusion
 Huge network of transport
system (lymph – veins –
arteries)
the inner epithelial lining of ileum
has many folds called Villi (is a Mucosa
single projection on the lining of
small intestine that functions in
absorption of digested food by Submucosa
increasing the surface area for Muscle layer
absorption). The small food
molecules can be absorbed directly into cells of villi, food molecules then diffuse
into blood vessels of villus then into the blood stream. (Villus is a link between
digestive system and circulatory system)

6) Large Intestine
“It surrounds the small intestine, and the undigested food passes through it.
Water and minerals are absorbed by blood vessels that surround the large
intestine by diffusion (colon)

Presence of E.Coli: a) synthesize some B vitamins and vitamin K

b) Stop harmful bacteria from colonizing

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 II. Respiratory system
The pass of the respiratory system: nose→ pharynx→ larynx→ trachea→
bronchus→ bronchioles→ alveoli

1) Nose
“The organ through which the air enters the lungs, and the wastes are
released”
Adaptations of the nose:
 Cilia to filter the air
 Mucus to cool hot air before it enters the lungs and trap dusts
 Capillaries to warm cold air, because the capillaries carry blood with the
body’s normal temperature, so the air gets warmed

2) Pharynx
“Common organ between the digestive and respiratory system, the air tract is
closed during swallowing”

3) Larynx
“Contains the vocal cords, air passes through it to the trachea”

4) Trachea
“A hollow tube through which air passes to the lungs”
Adaptations of the trachea:
 Hollow tube lined with mucus
 Contains cilia to filter the air
 Surrounded by cartilaginous rings to prevent it from collapsing
Then the trachea is divided into two branches called bronchi, each bronchus is
divided into several smaller bronchioles

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5) Lungs
The lungs are the main organs of respiration. They have very fragile structure and
they have the site of exchanging of gases.

Adaptations of respiratory surfaces

 Large
 Thin walls
 Large surface area
 Moist
Alveoli: they are the air bags in the lungs

Transport of oxygen and carbon dioxide

 Hemoglobin in blood combine loosely with oxygen (oxide ion) to form

oxyhemoglobin
 Carboxyhemoglobine carry the carbon dioxide (carbonic acid-bicarbonate ion)
Mechanism of breathing

P.O.C Inhalation Exhalation

diaphragm Contracts relaxes
So it moves Downward upward
Inter costal muscles Contracts relaxes
Ribs Move outward Move inward
Chest cavity Increases decreases
Lung volume Increases decreases
Inter-pulmonary pressure < P. atm. > P. atm.
Air Move to the lungs Move out of the lungs

 ↑ CO₂ conc. → PH ↓ → ↑ Acidity → inhalation

 The medulla in the brain sets the breathing rhythm by monitoring the carbon
dioxide levels in the blood and by sensing changes in the PH of the blood

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 III. Excretion
Excretion is the removal of metabolic wastes. This includes removing of carbon
dioxide and water from cell respiration and nitrogenous wastes from protein
metabolism

Remember: Egestion is the removal of undigested food

The organs of excretion:

 Skin excrete sweat consisting of water and salts including urea “thermo
regulation”
 Lungs excrete water vapor and carbon dioxide from krebs cycle
 The liver is the site of deamination of amino acids and production of urea
The human Kidney

o The kidney adjusts the volume and concentration of

urine depending on the animal’s intake of water & salts
and the production of urea
o Humans have the two kidneys supplied by blood from
the renal artery
o Kidney filters 1500 L of blood per day
o Antidiuretic hormone (ADH) is released by the posterior
pituitary gland and targets the collecting tube of the
nephron
o ADH regulates the blood pressure by controlling how much water is
reabsorbed by the kidney
The Nephron

“The basic function unit of the kidney” (one million nephrons per kidney)

A. Glomerulus: a cluster of capillaries inside Bowman’s capsule at which filtration

occurs

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B. Proximal convoluted tubule: a small, twisted tube
that’s close to glomerulus
C. Loop of Henle: in which a lot of water is reabsorbed,
that’s why some desert rodents and lizards have very
large loop of henle
D. Distal convoluted tubule:
 Small, twisted-up tube that’s farther from the
glomerulus.
 Reabsorption and secretion occur
 Aldosterone hormone increases the amount of sodium
that’s reabsorbed into the blood by the distal tubule

E. Collecting duct:
 Where hormone ADH has its effect (makes the walls permeable to water)
 ADH level is high when the body is dehydrated Ex: after running
 ADH level is low when the body is well hydrated Ex: after drinking

1) Filtration occurs by diffusion: the filtrate contains everything small enough to

diffuse out of glomerulus and into Bowman’s capsule, including some glucose,
salts, vitamins, wastes as urea….etc

2) Secretion: is the active & selective uptake of molecules that didn’t get filtered
into Bowman’s capsule.

3) Reabsorption: is the process by which most of water and solutes (glucose,

amino acids & vitamins) that initially entered the tubule during filtration are
transported back into the capillaries and thus back to the body

4) Excretion: is the removal of metabolic wastes, everything that passes into the
collecting tubule is excreted from the body.

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 IV. Circulatory System

Cardiovascular system lymphatic system

Heart blood lymph nodes lymph

Blood vessels lymph vessels

Cardiovascular system
“It is the system responsible for transporting deoxygenated blood from the body
to the lungs and transporting oxygenated blood back to the body”

First: The Heart

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Blood circulations
1) Pulmonary circulation: Right ventricle P.A. lungs P.V. left atrium
 This circulation for the blood to be oxygenated and releasing wastes

2) Systemic circulation: Left ventricle aorta body cells veins right atrium
 This circulation transports oxygen to all body cells, nutrients for digestion &
removes wastes
3) Hepatic portal circulation:
Left ventricle aorta small intestine H.P.V liver renal vein right atrium

The liver plays a role in homeostasis. Glucose is stored in the form of glycogen in
the liver & muscles. Excess amino acids are broken down into urea by the liver
which is extracted by the kidney. The function of the liver is to make the
concentration of glucose and amino acid normal & detoxification.

 Heart Beats: 70→72 heart beat per minute in normal adult at rest
 Blood pressure: 120/80 in aorta (120→ systolic “ventricular contraction” &
80→ diastolic “ventricular relaxation”)
 Lower than normal → hypotension & higher than the normal → hypertension

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Control of Heart Beat

The heart is myogenic, which means that the heart is self-beating muscle. The
nervous system doesn’t control the heart pump.
Sino-atrial Node (SA Node) is the pace maker. If the heart beats, it’s found in the
muscles of the walls of the right atrium. It initiates the electric excitation which is
captured by the atrio-ventricular node. The AV node then passes the charges to
the septum, to the walls of the ventricles making the ventricles contract.
This is why the atrium contracts first then the ventricles. The electric charge
comes from the atrium causes it to contract, then the charges are received by the
ventricles making them contract.

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Blood Vessels

Artery Vein Capillary

  

 Thicker muscle layer  Thinner muscle layer  Capillaries are the end
(has elastic fibers) (has no elastic fibers) of the artery and the
beginning of the vein.
 Any blood vessel that  Any blood vessel that  It is the site of
carries a blood away carries blood to the exchange of nutrients
from the heart heart to and from body cells
 Adaptations:
 Carries oxygenated  Carries deoxygenated  Large surface area
blood except blood except  Thin walled
pulmonary artery pulmonary vein
What ensures the return
 High blood pressure,  Low blood pressure, of vein blood to the
so it has thicker so no need for thick heart?
muscle layer muscle layer  Valves prevent back
flow
 Has no valves bec.  contains valves  Veins are connected
High blood pressure because Of low blood to arteries by
allows no back flow pressure capillaries, so blood in
arteries pushes blood
 Sunken deeply, so it  sunken deeply & in veins
cannot be injured due found superficially  Contraction of skeletal
to high pressure muscles presses on
the veins, so the blood
moves forward
 Posture helps in blood
circulations

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Blood (5~6 liters)

Plasma Cells
54% of the blood Red blood cells White blood cells Platelets
It consists of: “Erythrocytes” “leucocytes” “Thrombocytes”
 90% H₂O  5 million cells /  3000→7000  250000 cells /
 Amino acids, mmᶟ cells / mmᶟ mmᶟ
glucose…etc  Found in bone  Found in bone  Found in
 Antibiotics marrow marrow & lymph bone marrow
 Hormones  No nucleus nodes  For blood
 Urea, uric acids  Filled with  Increase during clotting
& other wastes hemoglobin infection
 Plasmatic  Elastic to  Elastic (to engulf
proteins squeeze in the microbes)
finest capillaries  Last few days
 120 days life
span Types of WBCs:
 Destroyed in the a) Phagocyte:
liver and spleen  Engulf microbes
The liver destroys b) Lymphocyte:
the RBCs & remove  Secret
them with bile in antibodies
the form of
undigested food,
but the hemoglobin
(iron) is stored in
the liver to be used
again by the bone
marrow
Mechanism of blood clotting
a) blood platelets + destroyed cells clotting factors thromboplastin

b) Prothrombin thromboplastin + calcium thrombin

c) Fibrinogen thrombin fibrin

(soluble protein) (insoluble protein)

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Lymphatic system
 The lymphatic system is another system for transportation of nutrients in the
body.
 The lymph, alternative of blood, has all blood components except the red
blood cells.
 The lymph nodes make the white blood cells.
 If there is an infection, the nodes produce more white blood cells.
 So it has two functions:
 Transport function: transport fatty acids, glycerol & water insoluble vitamins
 Immune function: produces WBCS in response to infections

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 V. The Human Immune System

1) Non-specific Defense

A. First-line defense: “Barriers”

 Skin that blocks pathogens
 Mucus membranes that release mucus to trap microbes
 Cilia in the respiratory system that sweep out mucus with its trapped microbes
 Stomach acids that kill germs that enter through the nose & mouth

B. Second-line defense:

I. Inflammatory response
 Characterized by swelling, redness, soreness & increased warmth in the area
 Aims to increase the blood supply to the area carrying more oxygen & white
blood cells to fight the infection
Histamine Increased body temperature
o Nitrogenous compound secreted o Speeds up the immune system &
as part of inflammatory response makes it more difficult for
o It triggers vasodilation microbes to function
“enlargement of blood vessels”,
which increases blood supply to
the area, bringing more
phagocytes to engulf microbes
o Responsible for symptoms of
common cold: sneezing, coughing,
redness, itching & runny nose and
eyes (to get rid of invaders)

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 II. Phagocytes
 Macrophages “giant eaters” are one type of white blood cells that extend
pseudopods and engulf huge number of microbes over a long period of time

III. Interferon
 Chemicals released by immune system fight viral infections

2) Specific response “third-line defense”

 Formed of two types of lymphocytes B-lymphocytes & T-lymphocytes

 Both are made inside the bone marrow & then are moved with the blood to
the lymphatic tissue including spleen, lymph nodes, tonsils & adenoids

I. Humoral response II. Cell-mediated response

 Includes production of  Including the T-lymphocytes the secrets
antibodies by B-lymphocytes chemicals to kill invaders
triggered by specific antigen Antibodies secreted by B-cells neutralize
antigens by binding to them & by formation
of an antigen-antibody complex that can be
engulfed by the phagocyte

III. Clonal selection

 After a B-cell or T-cell binds to an antigen, it starts to create thousands of
copies of itself, that will later differentiate into plasma cells or memory cells
A. Plasma cells “primary immune B. Memory cells “secondary immune
response” response”
o Immediately fight pathogens by o Can fight antigens as plasma cells,
secreting antibodies. (don’t live but they live for a lifetime
long) circulating the blood to fight every
pathogen that your body has ever
fought of vaccinated for

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Notes:

 Passive immunity: is temporary like maternal antibodies that pass through the
placenta to the fetus or that pass through breast milk to the baby
 Active immunity: made by the baby after being ill or vaccinated with dead or
weak virus or even parts of virus coat

Immunity diseases

AIDS Virus

 HIV is the virus that cause AIDS

 It attacks mainly the helper T-cells and uses some enzymes to make the cell
produce million copies of its own DNA
Allergies

 Hypersensitive immune responses to certain substances that are called

allergens
 They involve the release of excessive amounts of histamine
 Taking antihistamines can normally counteract these symptoms
Autoimmune disease

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  The immune system cannot properly distinguish between self & non-self
 If identifies body cells as foreign & starts to attack them
Antibiotics

 Used after infections

 Medicines that kill bacteria & fungi
Vaccine

 Used to prevent the infection

Immune
System

Acquired Innate

B-cell immunity Physical

T-cell immunity Bloodbourne
"humoral" barriers
"cell-mediated"

1. skin
Antigen Phagocytes
Whole T-cells released 2. mucus
exposure membrane
into
3. saliva
1. Neutrophils 4. Flushing
Lymphoblasts action of
Supressor Helper T- Cytotoxic 2.Macrophages urine &
T-cell cell T-cell 3. Basophils tears
Death of the body’s
4.Eosinophils 5. Stomach
cells that are infected Plasma Clonal B- acids
cells cells 5. Natural killer Stops
with a virus or
cells infection
otherwise damaged
Death of before it
dangerous enters the
Memory body
Antibodies organisms
B-cells

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 VI. Muscles
Skeletal Smooth Cardiac
 Voluntary muscles  Involuntary muscles  Involuntary muscles
 Striated  Un-striated  Striated
 Multinucleated  Makes up the walls of  Found in the heart
 Very large blood vessels and the  It generates its own
 They work in pairs, digestive tract action potential
one muscle contract  It is under the control
while the other of the autonomic
relaxes nervous system

The Sliding Filament Theory

 Within the cytoplasm of each

skeletal muscle cell are
thousands of fibers called
myofibrils
 Myofibrils consist of thin &
thick filaments
 Each thin filament is composed
of actin protein
 Each thick filament is composed of myosin proteins
 Muscles contract as thick & thin filaments slide over each other

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 VII. Endocrine System
Importance of this system

 Coordination & adjustment

 Endocrine Glands
 Negative Feedback
 Mode of Recognition

Types of glands

Exocrine glands Endocrine glands Mixed glands

Any gland that secret into Secrets hormones directly A gland that has cells for
a duct then goes to a into the blood “ductless” both exocrine &
cavity “ducted” Ex: All hormones are endocrine secretion
Ex: Salivary glands & gall secreted endocrinally Ex: liver & pancreas
bladder

The Endocrine glands

1) Pituitary gland (master gland)

2) Pineal gland
3) Thyroid gland (activity gland)
4) Parathyroid gland (bond gland)
5) Thymus gland
6) Pancreas (sugar gland)
7) Adrenal gland (emotional gland)
8) Gonads (reproductive gland)

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I. Endocrine glands

1) Pituitary gland “the maestro”

It is divided into two lobes:

Anterior lobe Posterior lobe

1. Growth hormone (GH) 1. ADH (Anti-Diuretic Hormone) or
 Hypo secretion: Dwarfism Vasopressin
 Hyper secretion: Gigantism  Stimulates reabsorption of water
from the renal tubules “osmo-
2. Stimulating hormones: regulation”
 TSH  So, the kidney is not only an
 ACTH excretory organ, but also it’s a
 FSH / LH → stimulate gonads homeostatic organ
 Prolactin → stimulate milk 2. Oxytocin
production  Stimulates uterine contraction
during labour
These two hormones are made by the
hypothalamus & stored inside the
posterior lobe of pituitary gland

2) Pineal gland

 It secrets melatonin hormone that controls sleeping rhythm

 It’s found also in the brain
 Hyper secretion of melatonin causes more sleeping & inability to wake up
 Hypo secretion of melatonin causes lack of ability to sleep

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3) Thyroid Gland

 It secrets two hormones

Calcitonin Thyroxin
↓ blood calcium level by taking it into  It stimulates metabolic activities &
bones or urine production of energy
 Iodine enters in its structure

What are the symptoms of hyper thyroiditis & Hypo thyroiditis

Hyperthyroiditis Hypothyroiditis
 High BMR  Low BMR
 Increased heart rate, heart beats &  Decreased heart rate, heart beats &
blood pressure blood pressure
 Sweating & thin body  Obesity
 Heat intolerance (↑ body temp.)  Cold intolerance (↓ body temp.)
 Nervous & exophthalmus

4) Parathyroid gland

 It’s found on the surface of thyroid gland, its function is the inverse of thyroid
 It secrets Parathormone hormone which regulates calcium level in blood by
increasing its concentration
 It withdraws Ca⁺ from bones to blood “raises blood calcium level”
 Hyper secretion of this hormone leads to osteoporosis (weak bones)

5) Thymus gland

 It secrets thymosin hormone that stimulates the lymphocytes production by

the lymph nodes
 It has immune function specially at childhood

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6) Pancreas

 Cells of islets of Langerhans secret

Insulin “from β cells” Glucagon “from α cells”
 Stimulates the liver to convert  Stimulates liver to convert glycogen
excess glucose into glycogen into glucose
 Stimulates cells to absorb glucose  This leads to ↑ blood glucose level
from the blood
 This leads to ↓ blood glucose level

The sugar level remains in homeostasis by the antagonistic action of insulin &
glucagon hormones

7) Adrenal gland “supra-renal gland”

 The gland is divided into adrenal cortex & adrenal medulla

Adrenal cortex Adrenal medulla
 It secrets cortisol → that controls  This hormone is secreted in critical
the salt balance “Na⁺, K⁺, Cl⁻” in situations “fear, fight, flight”, so
blood adrenaline helps us face critical
situations by increasing heart beats,
lung movement & conversion of
glycogen into glucose
 Side effects of Adrenaline:
 When heart beats increase, blood pressure also increases, so weak
capillaries may burst leading to blood clotting
 Stops salivation
 Causes hairs to lose pigments
 Severe doses may cause heart to stop

Note:

141
 Adrenaline increases sugar levels in case of strong emotions
 Glucagon increases sugar level in case insulin decreases it

8) Gonads
Testes Ovaries
Secret Testosterone & androgen Secret Estrogen & progesterone

Negative Feedback

Counteracting any change back to the normal value to maintain homeostasis

Examples:

 Insulin & glucagon

 Calcitonin & parathormone
Types of hormones

Steroid-based hormones Amino acid-based hormones

 Because the hormone & the  Once the hormone enter, cAMP
membrane are lipid in nature, the takes place & the cell responds to
hormone can directly penetrate the the message
membrane

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 VIII. Nervous System

Central Nervous System Peripheral Nervous System

“Nerve branches from brain & spinal cord”

Brain Spinal cord

Motor Sensory

For movement For sensation

Somatic Autonomic

Carrying order of Carrying an order of

movement to a movement to an
voluntary muscle involuntary muscle

Sympathetic Parasympathetic

↑ movement ↓ movement

The Nerve cell

Sensory Connector Motor

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Motor Neurons

The Brain

 Cerebrum: center of higher activities

 Cerebellum: balance center
 Medulla oblongata: center of movement of involuntary muscles
 Pons: transfer impulse from or to cerebrum

The Spinal Cord

“Responsible for reflex action: rapid involuntary response”

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Transmission of nerve impulse (Electric Nature)

1) Through the axon

A. Polarization
 Net Charge in axon: -70 mV
 During the resting potential,
Na doesn’t enter the axon
due to selective permeability
of the membrane

B. Depolarization
 Membrane loses selective permeability due to a stimulus, so Na⁺ gets in the
axon until equilibrium (Na⁺ out = Na⁺ in). until this happens, the Na⁺ in would
be more than K⁺
 Net charge in axon= +40 mV
 Potential difference = 70 + 40 = 110 mV
C. Repolarization

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 Membrane restores its permeability, pushing Na⁺ out of the axon
 Hyperpolarization occurs when the membrane pushes more sodium that the
net charge in the axon is less than -70 mV, but it restores the sodium within
0.001 → 0.003 sec
 The disturbance in a region is a stimulus for the neighboring region.
 We can describe the transmission of the electric impulse through the axon as a
wave of action potential

146
2) Through synapse at terminal endings

Events occurring at synapse

 An arriving action potential depolarizes the synaptic knob

 Calcium ions enter the cytoplasm, after a brief delay, acetylcholine is released
during the exocytosis of synaptic vesicle
 Acetylcholine binds to the sodium channel receptors on the post synaptic
membrane, producing a graded depolarization
 Depolarization ends as acetylcholine is broken down into acetate & choline by
acetylcholinestrase enzyme (AChE)
 The synaptic knob reabsorbs the choline from the synaptic cleft & uses it to
synthesize new molecules of acetylcholine (ACh)
Notes:

 Nerve cells don’t touch each other

 Post-synaptic cells can be nerve cells, muscle cells or gland cells

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 IX. The Eye

1) Cornea
 Tough, clear covering that protect the eye & allows light to pass through
2) Iris
 Colored part of the eye
 It can expand or shrink to control the amount of light entering the pupil
3) Lens
 Main site of refraction “focuses light onto the retina”
4) Pupil
 Small opening in the middle of iris
5) Retina
A. Rods: responsible for vision in dim light “photoreceptors”
 No details
 No colors
 Distributed all over the retina
B. Cons: responsible for vision in bright light
 Detailed
 Colored
 Concentrated in fovea

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 X. The Ear

1) Outer Ear: gather the sound & funnel it into the auditory canal
2) Auditory canal: ear canal through which the sound enter
3) Tympanum: ear drum, vibrates as the sound waves hit it
4) Ear bone: hammer, anvil & stirrup; transmit vibrations from ear drum to the
oval window
5) Semicircular canal: fluid filled, helps you maintain your balance
6) Oval window: sends waves of pressure to the cochlea
7) Cochlea: fluid filled part of the inner ear, distinguish the sound intensity &
sends nerve impulse to the brain
8) Eustachian tube: equalizes pressure between environment & inner ear

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 XI. Reproduction & Development
Asexual Reproduction

“Results in individuals that are identical to the parents. This is an advantage when
the environmental conditions are stable”

Fission Budding Fragmentation & Parthenogenesis

Regeneration
 Is the  Involves  Occur when a  Involves
separation of splitting off of single parent development of
an organism new individuals breaks into two an egg without
into two new from existing parts that fertilization.
cells “amoeba ones “hydra” regenerate into The resulting
& bacteria” new individual adult is haploid
“sponges, “honeybees &
planaria & sea some lizards”
star”

Advantages of Asexual over sexual reproduction:

1) It enables animals living in isolation to reproduce without a mate

2) It creates numerous offspring quickly
3) There is no expenditure of energy maintaining elaborate reproductive systems
of hormonal cycles
4) Asexual reproduction is advantageous when the environment is stable &
favorable
Sexual Reproduction

 Hermaphrodite: organisms with both male & female sex organs

 The main advantage is increasing variation within population
Sperm + Egg → Zygote → Gastrula → organogenesis

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Types of Fertilization & Development

Animal Fertilization Development No. of eggs Parental care

Fish External External Many None
Amphibians
Reptiles (inside the Some
Birds internal eggs) Few Much
Mammals Internal

The Human Male Reproductive System

 Testes: male gonads; the site of sperm formation

 Vas deferens: the duct that carries sperm during ejaculation from the
epididymis to the penis
 Prostate gland: large gland that secret semen “alkaline solution” directly into
the urethra
 Scrotum: the sac outside the abdominal cavity that holds the testes; the cooler
temperature there enables sperms to survive
 Urethra: common tube inside the penis for both semen & urine

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The Female Reproductive System

 Ovary: where meiosis occurs & 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 blastula stage of the embryo will implant & develop during the
nine-month gestation
 Vagina: the birth canal; during labor & delivery, the baby passes through the
cervix then into the vagina
 Cervix: the mouth of the uterus
 Endometrium: lining of the uterus
The menstrual Cycle of Human Female

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1) Follicular phase
 Several tiny cavities called follicles in the ovaries grow & secret increasing
amounts of estrogen hormone in response to FSH from the anterior pituitary
gland

2) Ovulation
 The secondary oocyte ruptures out of the ovaries in response to a rapid
increase in LH from the anterior pituitary. Ovulation occurs on or about the
14th day after the menstruation

3) Luteal Phase
 After ovulation, the corpus luteum “the cavity of the follicle left behind” forms
& secrets estrogen and progesterone that thicken the endometrium “lining of
the uterus”

4) Menstruation
 If implantation of an embryo does not occur, the buildup of the lining of the
uterus breaks down and is shed. Tissues & some blood are discharged from the
vagina. This bleeding is commonly called the period

Hormonal control of the menstrual cycle

Hypothalamus Releases gonadotrophic releasing hormone that

stimulates the pituitary gland releasing FSH & LH that stimulate the ovary
releasing Estrogen & progesterone that thicken the lining of the uterus

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Spermatogenesis

“The process of sperm formation (4

sperms) , is a continuous process that
begins at puberty & can continue into old
age”

1) Luteinizing hormone (LH) induces the

testes to produce testosterone
2) FSH & testosterone stimulate sperm
production in the testes
3) Spermatogonium cell (2N) divides by
mitosis to produce two primary
spermatocytes (2N)
4) Spermatocytes undergo meiosis I to
produce two secondary spermatocytes
(N)
5) Each secondary spermatocyte
undergoes meiosis II, which yield four
spermatids (N)
6) Spermatids differentiate & move to the
epididymis where they become motile

Oogenesis

“The production of ova begins prior to birth. A female baby is born with all the
primary oocytes she will ever have” (one ovum)

1) Within the embryo, each oogonium cell (2N) undergoes mitosis to produce
two primary oocytes (2N) that remain inactive until puberty
2) After puberty meiosis I occurs, producing secondary oocytes (N) that are
released monthly at ovulation

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3) During meiosis I & meiosis II, the cytoplasm divides equally. Almost all the
cytoplasm remains in the egg, leaving two tiny polar bodies that have very
little cytoplasm & which will disintegrate
Embryonic Development

“A small flagellated, haploid sperm (N) fertilizes a larger, non-motile, haploid egg
(N) to form a diploid (2N) zygote”

1) Cleavage
 The rapid mitotic cell division of the zygote that begin immediately after
fertilization
 The end of cleavage to be characterized by the production of a fluid-filled wall
of cells called a blastula
 The individual cells of the blastula are called blastomeres, and the fluid-filled
center is a blastocoel

2) Gastrulation
 Involves differentiation; the rearrangement of the blastula to produce a three
layered embryo called a grastula
 These three layers are the ectoderm, endoderm & mesoderm
 The ectoderm will become the skin & nervous system
 The endoderm will become the viscera; the lungs, liver & digestive system
 The mesoderm will become the muscle, bones & blood

3) Organogenesis
“The process by which cells continue to differentiate, producing organs from the
three embryonic germ layers

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Extra-embryonic Membranes of the Bird Embryo

1) Chorion: a membrane that lies under the shell & allows for the diffusion of
respiratory gases between the outside environment & the inside of the shell

2) Yolk Sac: store the food needed by the embryo

3) Amnion: it encloses the embryo in protective amniotic fluid

4) Allantois: in mammals, it is the conduit for respiratory gases to & from the
embryo. It is also the place where the nitrogenous wastes “uric acid”
accumulate until the chick hatches

156