BioMax SAT 2 TO THE POINT Dr.

Amr Alaa 0567573420

Chapter1: Molecules of Biology (Biochemistry)
 Nitrogen: amino acid- proteins, nucleic acids
 Phosphorus: nucleic acid, ATP, membrane
 Sulfur: sulfide bridges in protein

Chemical Bonds
1. Non-polar covalent bond: equal electron share (CO 2- O2)
2. Polar covalent bond: unequal electron share (H 2O)
3. Ionic bond: electron transfer (NaCl)
4. Hydrogen bond: between H and O of 2 molecules (water – DNA-2nd structure of protein)
5. Water cohesion force (H-bond): rise of water in high trees

Polar molecules
 Charged, hydrophilic, and water soluble (proteins, sugars, salts, ions)

Non-polar molecules
 Not charged, hydrophobic, and fat soluble (lipids, CO 2, O2)

Oxidation - reduction reactions (transfer of electrons)

 Oxidation (electrons loss) - reduction (electrons gain)

Food energy (acc. To amount/gram): lipids(9 calories) > carbohydrates (4calories) = proteins (4calories)

Food energy (acc. To the use): Carbohydrate (Main Source) → Lipids → Protein

Minerals: inorganic nutrients such as Ca2+, Fe2+, Mg2+, K+ (promote the growth in plants = Fertilizers)

Vitamins
 Organic molecules act as co-enzymes and must be ingested
 Water soluble vitamins (B, C) and fat soluble vitamins (K, E, D, A)

pH: -log of H+ concentration (if H+ = 10-4, pH = 4)

 Water ionization: H2O →OH- + H+

pH Scale (0-14)
 Neutral solutions (pH = 7): OH - = H+ (water)
 Acidic solutions (pH < 7): H+ > OH - (gastric juice is 2)
 Basic (alkaline) solutions (pH > 7): OH- > H+ (blood: 7.4)
 Buffers keep pH constant such as HCO 3- or bicarbonate in plasma

Polymers
 Chains of similar subunits bonded together called monomers
 Carbohydrates, proteins, and nucleic acids
Metabolism: all chemical reactions in living organisms
1. Anabolism: building up (photosynthesis)
2. Catabolism: breakdown (respiration)
3. BMR: basal metabolic rate needed to survive
1
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Dehydration synthesis (condensation, building up, anabolism)
Monomers + Monomers → polymer + water

Hydrolysis (break down, catabolism)

Polymer + water → monomers

Enzymes
1. Large protein molecules that reduce activation energy and speed up chemical reaction (catalyst)
2. Not used up, not changed, and don't change products

Induced fit model

 Each enzyme has its specific substrate that fits in its active site

Factors affecting enzymes action

1. Optimum pH is 7.4, optimum temperature is 37cO
2. High temperature (over the optimum temp) denatures enzymes
3. Co-enzymes (vitamins) help enzymes to work faster
4. Inhibitors stop enzymes activity
5. Reactions stop when all active sites are saturated with substrates

Carbohydrates (C +H+O)
1. Monosaccharides (C6111206) C=O 2. Disaccharides (C12H22O11) 3. Polysaccharides
 Glucose, fructose, and galactose  Sucrose (glucose + fructose)  Glycogen: animal sugar
 Glucose is the main source of energy  Maltose (glucose + glucose)  Starch: plant sugar
 Lactose (glucose + galactose)  Cellulose: cell wall of plants
 Chitin: Cell wall of fungi and
exoskeleton of arthropods.

Lipids (C,H,O) (C, ↑H, ↓O)

Lipids are insulators and fuel reserve

1. Fat: animal origin, solid, saturated fatty acid (c-c)

2. Oil: plant origin, liquid, unsaturated fatty acid (c=c)
3. Wax: cover of leaves (cuticle) to prevent water loss
4. Steroid hormones: estrogen, testosterone
5. Cholesterol: structure in cell membrane, keep blood
vessel opens

2
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Proteins (C, H, O, N)
Amino acid
 Monomers of proteins (20 types)
 Bonded by peptide bonds forming polypeptides

Types of proteins
 Primary: 1 polypeptide chain (ultimately determine the function and shape of protein)
 Secondary : a helix bonded by hydrogen bonds
 Tertiary: 3 dimensional shape determines function. (R-group)
 Quaternary: 4 polypeptide chains –hemoglobin

Nucleic acids : Polynucleotides (C, H, O, N, P)

Nucleotide (monomer of nucleic acids)
 Phosphate group (PO4)
 Ribose sugar (RNA) or deoxyribose sugar (DNA)
 Nitrogenous bases
1. Purines (2 rings) 2. Pyrimidines (1 ring) Base pairs (bp)
• (A) Adenine (DNA and RNA) • (C) Cytosine (DNA and RNA) • A is attached with T by 2 hydrogen bonds
• (G) Guanine (DNA and RNA) • (T) Thymine (DNA only) • G is attached with C by 3 hydrogen bonds
• (U) Uracil in (RNA only) base

Monomer (Nutrients) Polymer

Monosaccharide (glucose) Carbohydrate
Amino Acids Protein
Nucleotide Nucleic acid.
Macromolecule but not Polymer
3 Fatty acids +1 Glycerol Triglycerides (Fats and oils)
2 F.A + 1 Glycerol +1 Phosphate Phospholipid (Cell memb)

In Blood cells, the enzyme carbonic anhydrase catalyses the

following reaction CO2 + H2O -------> H2CO3
Reactants: CO2 and H2O Products: H2CO3
Enzyme: carbonic anhydrase (Help in carry Co2 in plasma)

Molecules identification
a. Carbohydrate(momosaccahride)(Glucose): C,H,O C=O
b. Fatty acid: C,H,O C>O
c. Phosphate: PO4
d. Glycerol: 3 C connected to 3 (-OH)
e. amino Acid: Contain (NH2) + COOH+ R group
f. Nucleotide: 1 PO4 + 1 Sugar(pentose)+1 Nitrogen base.
g. ATP : 3 PO4 + 1 Sugar(pentose)+1 Nitrogen base
h. Lipid (fat or oil) : 3 F.A + 1 Glycerol.
i. Phospholipid: 2 F.A + 1 Glycerol + 1 Phosphate

3
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Water: All of the following characteristics of water
(A) Water can adhere to many kinds of surfaces.
(B) Water is an effective solvent.
(C) Water molecules have both a slightly positive and a
slightly negative charge. (polar)
(D) Water molecules have a strong attraction for each other.
(Hydrogen bond)

Nonpolar =don’t mix with water

Substance Polarity
Water Polar
Protein Mostly polar
Lipid Non Polar
Oxygen and Carbon dioxide Non Polar

Vitamin: Organic compound – Can’t be synthesized by animals-

must be ingested- Not all vitamins are required by the same quantity and types to all animals- have different
molecular formula.

 Biochemical cycling of nutrients are very important as the present with finite amount in nature.
 Molecular formula: Group of symbols of different elements shows:
a. Types of atoms. B. Number of atoms.
C. molecular weight. D. Numerical proportions of atoms in the molecule.

 To Change from polymer to monomer( Digestion) (add water)=Breakdown=Hydrolysis

 To Change from monomer to polymer (remove water)=dehydration or condensation or synthesis.

 During the purification of protein or enzyme, keep the sample cool to prevent denaturation.

 Indicators: substances that indicate the presence of a substance by changing in color or form.
Examples: a. Bromothymol blue indicates the presence of acid (blue becomes yellow)
b. Iodine solution indicates the presence of starch (yellow becomes blue)
c. Lime water: indicates the presence of CO2 (Clear becomes cloudy white)
 Starch and glycogen are excellent energy store molecules as:
a. insoluble in water: has no interference with osmotic pressure-abundantly stored.
b. Compact molecules: Doesn’t occupy much space.
c. Easily hydrolyzed to glucose that is easily burned releasing energy.
 Vitamins can be destroyed by heat.

4
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Chapter2: The Cell
Cell surface area/volume ratio - why cells are small?
 Cell surface area (cell membrane) increases by X2 ● Cell volume (cytoplasm) increases by X3
 Cell membrane can fulfill small cells requirements than large cells

Prokaryotic Cells (Bacteria) 0.1 – 1 μ

No nucleus - no membrane bound organelles
Plasmid: small circular DNA Plasma membrane Cytoplasm
Eukaryotic Cells (Fungi - Plants - Animals) 1- 10 μ (Nucleus - chromosomal DNA - all organelles)

5
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Organelles F u n c t i o n
Chromatin network, chromosomes, DNA, genes Nucleolus containing RNA
Nucleus
Membrane bounded Organelles

Mitochondria Cellular respiration, ATP (energy) production

Chloroplasts (Plastids) Chlorophyll for photosynthesis (plants and Algae only)

Golgi body Package, modify, shipping, secretion

Lysosomes Intracellular digestion, defense (animal Cell only)

Internal SER Synthesis of steroid hormones and lipids detoxification and storing Ca ions
transpor RER With attached ribosomes for protein synthesis
t
Vacuoles Store cell sap (water –nutrients- wastes)

Centrioles Produce spindle fibers for cell division (animal cell only)
Non Membrane
Bounded

Ribosomes (smallest) Protein synthesis

Cilia / Flagella Microtubules for movement (locomotion)

Microfilaments Small muscles for movement (locomotion)

Non-membranous Structures: (ribosome — chromosome – centrioles)

6
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Cell or Plasma Membrane

Transport of substances through cell membrane

Passive (diffusion) Active
Conc. gradient With Against
Energy required No Yes (pump)
Direction From high to low From low to high

Diffusion
Simple Facilitated
From Phospholipid bilayer Channel or Carrier protein
Substances (Non-polar) lipids, O2, CO2 Polar ions/a.a/Glucose
Examples Gas exchange/steroid hormones Dialysis
Osmosis: water movement from high water conc. to low water conc.
1- Hypertonic solution, higher (salt/sugar) conc.
 Water moves outside cells —> shrink —> plasmolysis in plants
2- Isotonic solution, equal (salt/ sugar) conc.
 No water movement, 0.9% salt conc. in human/ 5% glucose solution
3- Hypotonic solution, lower (salt, sugar) conc. Water moves inside cells —> swell —> lysis in animals and turgid in
plants
7
 BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
Respiration: a. Gas Exchange
 External Respiration: Exchange of gases between Alveoli and blood.
 Internal Respiration: Exchange of gases between blood and cells.
b. Cellular respiration: The process of releasing energy from organic compounds (Food) and
store it in the body in the form of ATP inside the cell. (Exothermic or Exergonic reaction)

 Oxidation and reduction reaction (redox) (transfer of electrons)

- Oxidation is a form of chemical reaction that involves loosing electrons
- Reduction reaction involves gaining electrons.
 Cellular respiration is an exothermic reaction (Exergonic) as it releases energy from food

Energy Carrying molecules

ATP NADH and FADH2
 Adenosine triphosphate  Reduced Coenzymes.
 Energy carrying molecules by the formation of covalent bonds  Energy carrying molecules by the
between PO4 molecules. (Substrate level phosphorylation) transfer of electrons. (Oxidative
 ATP formation: (Dehydration) (Cellular respiration) (release phosphorylation)
energy from food) (store ATP in the body)
ADP + Pi = ATP + H2O
 Breaking ATP (using ATP in the body):
ATP + H2O = ADP + Pi

Mitochondria (singular=mitochondrion)
The mitochondrion is enclosed by two membranes, an outer membrane and an inner cristae membrane that
is folded. This inner membrane divides the mitochondria
into two internal compartments, the outer compartment
and the matrix.

1
BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
Cellular Respiration

Aerobic Respiration (36ATP) Cellular Respiration

1. Glycolysis: the breaking down (lysis) of

glucose (glyco) to produce pyruvate (or pyruvic
Aerobic Anaerobic
acid) Respiration Respiration
36 ATP/Glucose 2 ATP/Glucose
 Site: Cytosol No oxygen is required
 2 ATP are added.
 2 NADH are produced. 1. Glycolysis
 4 ATP are produced. ( net = 2 ATP) 1. Glycolysis
 2 pyruvate are formed.
2. Krebs’
In summary, glycolysis takes 1 glucose and turns it 2. Lactic
cycle 2. Alcohol
into 2 pyruvate, 2 NADH, and a net of 2 ATP (made Acid Fermentation
or
4 ATP, but used 2 ATP). The process occurs in the Fermentation
cytosol. 3. ETC

2. Krebs’ Cycle: (citric acid cycle- Tricarboxylic acid cycle (TCA) )

a. From Pyruvate to Acetyl CoA ( Pyruvate decarboxylation)
 Mechanism: 2 pyruvates + 2 Co A (Coenzyme A) = 2 Acetyl CoA + 2NADH + 2 CO2
 Co A: Coenzyme A is derived from Vitamin A.

b. Acetyl CoA
 Site: Mitochondrial matrix. Requires no oxygen.
 Produce: 6 NADH, 2 FADH2, 2 ATP, 4 CO2 .
 The CO2 produced by the Krebs cycle is the CO2 animals exhale when they breathe.

Steps / Substances ATP NADH FADH2 CO2

Glycolysis 2 2 - -
Pyruvate to Acetyl CoA - 2 - 2
Krebs’ Cycle
Acetyl Co A 2 6 2 4
ToTal 4 10 2 6

2
BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
The Electron Transport Chain and Chemiosmosis
The electron transport chain (ETC) is located within the mitochondrial cristae membrane. Each ETC consists of a
series of carrier proteins that transport high energy electrons from the Krebs cycle. The energy from these high energy
electrons is coupled with and powers the pumping of protons across the cristae membrane into the outer compartment in
order to create a proton gradient. The potential energy in this proton gradient is then used to produce ATP through a process
called chemiosmosis or oxidative phosphorylation. Almost all the ATP produced during aerobic cell respiration is
produced by chemiosmosis.

PART I: A PROTON GRADIENT

The electron transport chain produces a proton gradient. NADH and FADH2 carry high-energy electrons from the Krebs
cycle and glycolysis to the electron transport chain (ETC). As these electrons are pulled along the ETC, they release energy
that is used to pump protons (H+) (active transport) across the cristae membrane, thus creating a proton gradient. This
gradient represents stored or potential energy that can be used to do work, just as water behind a dam can be used to
produced electricity.

PART II CHEMIOSMOSIS
Chemiosmosis uses the stored energy in the proton gradient to convert ADP into ATP. Chemiosmosis or oxidative
phosphorylation is the actual mechanism by which ATP is produced. It uses the energy stored in the proton gradient to
power the synthesis of ATP. Chemiosmosis depends on a very special molecule located within the cristae membrane called
ATP synthetase. This molecule is actually a proton channel structure that can spin like a turbine. As protons pour through
the ATP synthetase channel, part of the molecule turns and attaches phosphates to ADP molecules, forming molecules of
ATP.

Oxygen: final electron and proton acceptor in the ETC. When oxygen combines with protons and electrons at the end
of the ETC, water is formed as a waste product. This is the water vapor we constantly exhale.
 The ETC is a collection of carrier molecules (including cytochromes) embedded in the cristae membrane of
mitochondria.
 Every mitochondrion contains thousands of ETCs.

The ETC carries electrons through a series of redox reactions .

 Water is produced as a waste product as oxygen combines with protons and electrons that flow down the ETC
1
𝑂2 + 𝐻2 = 𝐻2𝑂
2

Hypothetically, each proton carried by an NAD molecule to the ETC produces 3 ATP molecules; while each proton carried
by an FAD molecule produces 2 ATP molecules.

3
BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
II. Anaerobic Respiration ( 2 ATP/Glucose )
1. Glycolysis
Glycolysis is the anaerobic phase of aerobic respiration. One molecule of glucose breaks apart into two molecules of
pyruvate. Pyruvate, or pyruvic acid.
Glycolysis occurs in the cytoplasm. (no oxygen)
 Glycolysis is the braking down of glucose
 Two molecules of ATP supply the energy of activation, the energy needed to begin the reaction.
 Glycolysis releases 4 ATP molecules, resulting in a net gain of 2 ATP.
 1 Glucose + 2 ATP →2 Pyruvate + 4 ATP + 2 NADH (net gain 2 ATP).

2. Alcohol Fermentation
Alcohol fermentation is the process by which certain cells convert pyruvic acid or pyruvate from glycolysis into eth yl
alcohol and carbon dioxide in the absence of oxygen.
 The bread-baking industry depends on the ability of yeast to carry out fermentation and produce the carbon
dioxide that causes bread to rise. Also, the beer, wine, and liquor industries depend on yeast to ferment sugar
into ethyl alcohol.

3. Lactic Acid Fermentation

Lactic acid fermentation occurs during strenuous exercise when the body cannot keep up with the increased demand for oxygen
by skeletal muscles. Pyruvic acid produced by glycolysis converts to lactic acid and builds up in muscles, causing fatigue and
burning. The expression, "No pain, no gain" refers to the pain caused by lactic acid buildup in skeletal muscles. When an increase
in blood flow restores proper oxygen levels, the muscle tissue reverts to the more efficient aerobic respiration and lactic a cid is
removed from the muscles. It is carried to the liver, where it is converted back to pyruvic acid .

4
BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
Summary
For Anaerobic respiration: The only ATP you get from
fermentation are the two net ATP from glycolysis. So instead
of a big 36 ATP per glucose from aerobic cellular respiration,
only two ATP per glucose are produced. Two ATP per glucose
is enough for yeast, a single-celled organism, to survive. And
it's enough for muscle cells to keep functioning for a short
while. But it is certainly not enough for large, multicellular
organisms like humans, other animals, and plants to survive.
This is why humans, other animals, and plants absolutely
MUST have oxygen to survive.

Cellular Respiration and Burning

Cellular Respiration Burning

Heat Production Both Both
O2 /requirement Both Both
Amount of energy Low High
released
Hydrocarbon formation NO Yes
Temperature required Low (body temp=37oc) High

 Krebs’ Cycle includes the following:

1. Carbon dioxide production (major step of CO2 production)
2. Energy released from this cycle in the form of NADH and FADH2 is used in ATP formation by chemiosmosis.
3. Specific enzyme is required of the reaction is found in mitochondrial matrix.
4. Hydrogen ion and NAD+ with high energy electron are required to form NADH>

 Lactic acid is produced in the muscle when oxygen is insufficient.

 Glucose is the initial reactant (substrate) of glycolysis.

 Indication of cellular respiration occurrence:

1. Decrease of oxygen level in the system (increase O2 consumption)
2. Increase CO2 production.
3. Increase Glucose consumption.
 Pyruvate is the intermediate chief product of cellular respiration.

5
BioMax Chapter4: Cellular Respiration Dr.Amr Alaa 0567573420
 Oxidation of Glucose = cellular respiration = formation of ATP
 Respiration, anaerobic respiration and photosynthesis form ATP.
 Process of ATP production by ATP synthase is called chemiosmosis.
 Fermentation produces no ATP
 Sliding of actin and myosin myofibrils (microfilaments) requires the usage of ATP.
 Krebs’ cycle produces the majority of CO2, While ETC (oxidative phosphorylation) produces the majority of ATP
(32 ATP).
 Number of moles = number of molecules = coefficient.

Alcohol Fermentation Lactic Acid Fermentation

Requirement (starts by) Pyruvate Pyruvate
Ethanol (alcohol) Lactic Acid
Products
CO2
Yeast (baking industry) Dairy industry (milk to yoghurt)
Alcoholic beverage Skeletal muscle. ( accumulation of
Example
lactic acid in the muscle causes muscle
fatigue.

How to detect the presence of CO2 (occurrence of Cell. Resp)

6
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

1
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Chapter 3: Cell Cycle and Division
Homologous chromosomes
 Same size, shape, and genes but different alleles
Chromosomal number in human somatic (body) cells
 46 (diploid - 2 copies of each chromosome - 2n)
 In female 44 autosomes (somatic chromosomes) + XX (sex chromosomes)
 In male 44 autosomes (somatic chromosomes) + XY (sex chromosomes)
Chromosomal number in human sex cells (gametes)
 23 (haploid - 1 copy of each chromosome - n)
 Male gametes (sperms) contain 22 autosomes + X or Y
 Female gametes (ova) contain 22 autosomes + X
Cell Cycle
Human cells divide, except muscle, Nervous tissues (brain and spinal cord
(CNS)), and gametes.
Interphase: (non-dividing) (DNA=Chromatin)
 Gl: duplication of organelles (longest phase)
 S: duplication of DNA (Chromatin)
 G2: preparation for cell division (Double check)
 Error (mutation) in cell division causes cancer
Mitotic/ Meiotic phase: (Division) (DNA+Histon=Chromosomes)
• Karyokinesis: nuclear division (Chromosomes)
• Cytokinesis: cytoplasmic division

2
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Mitosis Meiosis I Meiosis II

Function As. reproduction Growth Sexual reproduction (gametes) Spermatogenesis -
oogenesis
Chromosomes Identical Homologous Sister chromatids
Produced cells 2 (2n) 2 (2n) 4 (n)
Interphase   x
Crossing over x  x
Variation x  


3
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Diploid cells: Somatic cell (body cell) and Gametophyte (Gonads cells) = 2n (contain pairs of homologous
chromosomes that are structurally similar but differ in genetic content.
 Haploid cells: Gametes and spores in plant = n
 Offspring receives the half of chromosomes number vi gametes. Ex: Diploid cell contains 24 chromosomes so the
gametes contain 12 chromosomes or the offspring will receive 12 chromosomes from each parent.
 Duplicated Chromosomes = 2 chromatids. Ex: Chromosomes = 8 so chromatids = 16
 I: Meiosis II: Fertilization (sperm+egg) III & IV: Mitosis
Adult(2n)----gametes(n)----zygote(2n)---Embryo(2n)---adult (2n)
 Chromosomes move toward the poles of the spindle in animal cell
right after the centromeres in chromatid pair separate.
 Forms of Growth and tissue repairs:
a. Growth of embryonic tissues. b. Repair of damaged tissues. c. regeneration of
limbs.
 Anaphase I and Anaphase II:
Anaphase I: Homologous chromosomes are segregated (separate) to chromosomes. While in anaphase II chromosomes
are segregated to chromatids.
 Spindle fibers are attached to the centromeres so chromosomes move (transmit). No centromeres, no spindle
fiber attachment, no Chromosomes are transmitted.
 Spindle fiber can move in two directions (back and forth).
 Gametophyte –cells of gonads(testis and ovary) are diploid cells (2n) that divide by 2 steps meiosis to form
gametes.
 Undifferentiated cells (stem cells): cells with no specific type Ex: Zygote-morula. Differentiated cells are cells with
specific type. Ex: Skin, muscle, blood cells.
 Meiosis in higher plant form haploid spores.
 Sperm small motile cell by flagella. While egg (ovum) is large non-motile cell.
 After the completion of one cell cycle the number of cell is doubled. (1 → 2 → 4 → 8 → 16 → …ect)
 The cell plate is originated from the middle of the cell up to the cell wall.

4
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Chapter 4: Cellular Respiration

Aerobic cellular respiration
Exergonic reaction; releases energy from glucose C6H12O6 + 602 → 6CO2 + 6H2O + 36 ATP (energy)
Location Release
Glycolysis Cytoplasm 2 pyruvates, 2NADH+, 2ATP
Pyruvate oxidation Mitochondrial matrix 2NADH+ , 2Acetyl CoA, 2CO2
Krebs cycle Mitochondrial matrix 4CO2,6NADH+ 2FADH2,2ATP
Electron transport Inner mitochondrial Water (1/202+H2→H2O)
chain (oxidative membrane by NADH+→ 3ATP
phosphorylation) cytochrome C enzyme FADH2 → 2ATP
Chemiosmosis Inner mitochondria' H+ gradient is setup to form
membrane ATP by ATP synthase

5
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Respiration is measured by:
1. CO2 released by seedlings in that makes lime water turbid
2. Respirometer by measuring volume of 02 consumed by seedlings

Anaerobic respiration - fermentation

1. Alcoholic fermentation (yeast): glucose(2 Pyruvate) → Ethanol + CO2 + 2ATP
2. Acid fermentation (bacteria): glucose (2 Pyruvate)→ lactic acid + 2ATP

Cramp: accumulation of lactic acid in muscles during exercises

Cellular Respiration and Burning

Cellular Respiration Burning
Heat Production Both Both
O2 /requirement Both Both
Amount of energy Low High
released
Hydrocarbon formation NO Yes
Temperature required Low High
 Krebs’ Cycle includes the following:
1. Carbon dioxide production (major step of CO2 production)
2. Energy released from this cycle in the form of NADH and FADH2 is used in ATP formation by chemiosmosis.
3. Specific enzyme is required of the reaction is found in mitochondrial matrix.
4. Hydrogen ion and NAD+ with high energy electron are required to form NADH>

 Lactic acid is produced in the muscle when oxygen is insufficient.

 Glucose is the initial reactant (substrate) of glycolysis.
 Indication of cellular respiration occurrence:
1. Decrease of oxygen level in the system (increase O2 consumption)
2. Increase CO2 production.
3. Increase Glucose consumption.

 Pyruvate is the intermediate chief product of cellular respiration.

 Oxidation of Glucose = cellular respiration = formation of ATP
 Respiration, anaerobic respiration and photosynthesis form ATP.
 Process of ATP production by ATP synthase is called chemiosmosis.
 Fermentation produces no ATP
 Sliding of actin and myosin myofibrils (microfilaments) requires the usage of ATP.
 Krebs’ cycle produces the majority of CO2, While ETC (oxidative phosphorylation) produces the majority of
ATP (32 ATP).
 Number of moles = number of molecules = coefficient.

6
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Chapter 5: Photosynthesis
Photosynthesis
Endergonic reaction (absorb light energy by chlorophyll) Light energy + 6CO2 + 6H2O + C6H12O6 (glucose) + 6O2

1- Light reaction (Light Dependent) in grana

 Chlorophyll converts light energy into chemical energy (ATP)
 Light energy breaks down H2O into Electrons, hydrogen and released oxygen (Photolysis)
 Electrons lost by P.S I is compensated by electrons of P.S II
 Electrons lost by P.SII is compensated by electrons of water splitting
 H2+ NADP+ (hydrogen carrier) → NADPH.H+
2- Dark reaction - Calvin cycle – (Light independent) (Carbon Fixation) in stroma
 6CO2 + RUBP (Chief intermediated of Dark reaction)→ PGA (carbon fixation)
 PGA + (ATP, NADPH) from light reaction → PGAL + glucose
Important points for experiments
 Chlorophyll absorbs all colors except green
 Chlorophyll is removed by boiling alcohol
 Glucose is stored as starch which is detected by iodine (blue color)
 Rate of photosynthesis is measured by CO2 consumed or 02 released
 Oxygen is released from water
 The most photosynthetic tissue is palisade mesophyll in leaves

7
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Testing the presence of Starch:
Starch Test: Add Iodine-KI reagent to a solution
or directly on a potato or other materials such as
bread, crackers, or flour. A blue color results
if starch is present. If starch amylose is not
present, then the color will stay orange or
yellow. The degree of blue color is determine
according to the amount of starch. Dark blue
indicates the presence of high amount of starch
(long period of photosynthesis). While light blue
indicates the presence of few amount of starch
(short period of photosynthesis)
 Indications of photosynthesis occurrence:  Facts about Photosynthesis:
1. Increase CO2 consumption. 1. Happen in all Plants
2. Increase O2 production. 2. ATP consumed IS NOT more than ATP produced. 3. Requires
3. Increase Glucose (starch) production. CO2 and produce O2
4. Initiated by the absorption of energy.
5. RUBP is the chief intermediate of dark reaction (Calvin Cycle)
Feeding Pattern
A. Autotroph: self- feeder: make their own food (organic compound) using the energy of
 Light (Photoautotroph) Ex: Plant-Algae- Some bacteria as cyanobacteria
 Inorganic chemicals (Chemoautotroph) Ex: iron oxidizing bacteria – nitrifying bacteria
B. Heterotroph: non-self feeder: depends on other living organism for obtaining organic compounds.
 Consumer
 Decomposers
 Scavengers

 Chlorophyll plays important role in light dependent reaction of photosynthesis.

 Oxygen produced by photosynthesis is formed by the splitting of water molecules by a process is called Photolysis
during light reaction of photosynthesis.

 The sources of the oxygen in glucose that is formed by photosynthesis is CO2

 # of moles = # of molecules = coefficient

Light Dependent reaction Light independent reaction
Requirements/reactants Products Requirements/reactants Products
H2O NADPH CO2 C6H12O6
Chemicals
Light ATP NADPH
+
NADP O2 ATP
Site Thylakoid membrane Stroma of chloroplast
 ↑ Temperature → ↑ metabolic rate → ↑ water loss by cellular respiration.
In plants: plants become more flexible.
In animals: sweating and panting
 Photosynthetic bacteria contain chlorophyll but no chloroplast.

8
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Chapter 6: Classical Genetics
Introduction
1. Generation, progeny or offspring: F1 is 1st generation and F2 is the 2nd generation
2. Gene: sequence of DNA responsible for a certain trait
3. Allele: the form of gene, each organism has two alleles for each trait from his parents
4. Homozygous or pure or True: 2 identical alleles of a gene (AA, or aa)
5. Heterozygous, hybrid or impure: 2 different alleles of a gene (Aa)
6. Dominant allele: express itself in heterozygous individuals (A)
7. Recessive allele: cannot express itself in heterozygous individuals (a)
8. Aa Bb = 2X2= 4 different gametes / AA bb = 1X1= 1 gamete
9. Phenotype: an organism's appearance
10. Genotype: allelic or genetic composition

Gregor Mendel (father of genetics)

1. Experimental genetics on pea plant
2. Dominant/recessive inheritance.
3. Segregation of characteristics (1st law)
4. Independent assortment (2nd law)
5. True-breeding lines (parents and offspring have same genotype)
6. Cross-pollination and production of hybrid plants.
7. Quantitative measurement and analysis of results

1
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

2
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Sex determination 50% boys and 50% girls

Twins
1. Non identical (fraternal), 2 ova + 2 sperms
2. Identical, 1 ovum + 1 sperm

Sex linked inheritance (hemophilia and color blindness)

 "X" chromosome carries somatic traits while "Y" chromosome does not
 In male 1 recessive allele expresses a recessive trait (high probability)
 In female 2 recessive alleles are needed to express a recessive trait (rare)
Sex influenced traits (premature baldness)
 Female hormones prevent baldness from expression (heterozygous form)
Polygenic Traits
 More than 2 alleles (genes) controlling the trait. Ex: Skin, hair, eye color and tallness (Height) in human
Mutation
 It is an error in the genetic code on DNA (new allele)
 Most are recessive, harmful, and rare
I. Macro-mutation (chromosomal mutation)
1. Deletion: triplet code is lost.
2. Duplication: triplet code is repeated.
3. Inversion: triplet code is separated and inserted in a reverse order.
4. Translocation: triplet code is transferred to another chromosome.
5. Polyploidy (4n, 6n, 8n): artificial in fruits.
6. Chromosomal aberration: non-disjunction during anaphase of meiosis.
7. Down's syndrome (Trisomy) 45 + XX or 45 + XY - Retarded (extra somatic chromosome #21)
II. Micro-mutation (gene mutations
1. Point: substitution of single nucleotide (sickle cell anemia-Cystic fibrosis)
2. Frame-shift: addition or deletion of a nucleotide

3
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Summary

4
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Trait is controlled by single gene = Complete/simple dominance.
 Carrier
a. Autosomal trait: (carried on autosomes chromosomes) = Heterozygous (Aa)
b. Sex linked trait (X-linked): (carried on sex chromosomes (X)) = X-X
 During genotype expression, use the letters for the autosomal traits and (X) or (Y) for
sex liked traits.
The chance of any couple having male or female offspring= 50% male and 50% female.
 Mostly any trait is expressed by a gene. Each gene is located on same locus in a pair of
homologous chromosomes. Each locus contains an allele for the trait. These allelles may be
similar (homoaygous) or different (Heterozygous)
 Individual carries a single recessive allele = Heterozygous (Aa) or Homozygous recessive
(aa)

a A Gene of
Gene of
allele allele Fur
Fur
color color

A
allele
Gamete Homologous
(sex cell) chromosomes

Chapter 7: Molecular Biology and Genetics

DNA model - Watson and Crick
 The DNA is double helix (coiled ladder)
 The two DNA strands are anti parallel (3’-5' and 5'-3' directions)

Semi-conservative replication of DNA (S phase)

 Helicase enzyme uncoils DNA and breaks hydrogen bonds
 DNA polymerase bind to primer and add nucleotides to growing strand
 Ligase enzyme binds nucleotides together
 Old strand/parental/template Vs new
strand/daughter/complementary
 Old: 3'-AGTCATGGAATCG- 5' →new: 5'-TCAGTACCTTAGC -3'

5
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Characteristics DNA RNA

Strands 2 1
Sugar group Deoxyribose Ribose
Bases A, T, C, G A, U, C, G
Function Genetic information Protein synthesis

Types of RNA
mRNA (messenger): carry triplet codons from DNA during transcription
tRNA (transfer): carry anticodon and the amino acid during translation
rRNA (ribosomal): location of protein synthesis in cytoplasm

Protein synthesis
I. Transcription of mRNA (nucleus)
 RNA polymerase binds to the promotor of DNA at the
start of a gene
 RNA polymerase assembles the mRNA from 5' to 3'
 DNA 3'TACTGCGAT5' 5'AUGACGCUA3' mRNA
II. mRNA processing (nucleus)
 Spliceosomes remove introns (non coding) and attach
exons (coding)
 Triplet codon: 3mRNA nucleotides amino acid
 Start codon is AUG and stop codons are UAG, UGA, or UAA
III. Translation (cytoplasm)
 2 ribosomal subunits (protein + rRNA) bind to mRNA ● tRNA anticodon binds with mRNA codon carrying amino
acid
 Each gene is translated into a poly peptide chain (protein)

Biotechnology: insertion of desired genes into bacterial colonies

1. Bacterial plasmid and human DNA are cut by same restriction enzymes
2. Plasmid and human gene will have complementary sticky ends
3. They combine forming recombinant DNA that is inserted into bacterial cell
4. Bacterial cell divides producing many copies of human gene
 Example: production of human insulin

Cloning: a genetic copy of an original

1. Unfertilized egg was obtained from a female frog
2. The nucleus was removed from the unfertilized frog egg
3. A donor nucleus (2n) was injected into the frog egg
4. The egg that received donor nucleus developed into normal frog Stem cells: undifferentiated embryonic cells for
cloning

6
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Polymerase Chain Reaction - PCR
 DNA polymerase amplifies a selected part of DNA
 DNA fingerprint in crime scenes and parental evidences
Restriction Fragments Length Polymorphisms (RFLPS)
 A restriction enzyme gives different lengths of DNA in different persons
 Crime scenes and parental evidences
Gel electrophoresis
 Separate DNA fragments by length and charge
 Protein is separated by electrophoresis or chromatography

7
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
1. DNA

2. Hydrogen Bonds

3. RNA polymerase

4. mRNA

5. Ribosome

6. tRNA

7. Polypeptide (protein)

1. Ribosome

2.mRNA

3. tRNA

4. Amino acids

5. Polypeptide

(A) : Nuclear envelop: bilayer of lipid.

Barrier to diffusion of large molecules from
nucleous to cytoplasm.

(B) RNA plymerase

(C) Ribosome

(D) Translated mRNA

(E) Polypeptide.

8
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 ↑G-C content in DNA → ↑ DNA stability (hydrogen bonds are hard to be broken)→ 2 strands become closer to each
other.
 (DNA) The molecule that carries the genetic information from one cell generation to the next.
 (mRNA) The product of transcription that determines the sequence of amino acids in a polypeptide chain.
 (tRNA) A nucleic acid that bonds temporarily with a specific amino acid during protein synthesis.
 (RNA polymerase) The protein that carries out transcription.
 Mutation is an error in DNA nucleotides.
 Mutation is the primary source of genetic variation.
 Mutation will be inherited if it is formed in the gamete forming cells (cells of gonads)
 What happen if an egg is fertilized by two sperms? Display abnormal number of chromosomes.
 tRNA positions amino acids for protein synthesis by paring with codons of mRNA.
 Chromatography is an alternative technique to gel electrophoresis.
 The production of different cell types of multicellular organism is regulated by specific sets of mRNAs that are produced
in a particular cell type.
 If Nitrogen base Guanine makes up 40% of the bases in DNA ,
% C=%G=40 % T and A = 100-(%G+%C)= 100-(40+40)=20% %A=10% %T=10%
 Genes ARE NOT unique to our species.
 Gene pool: The sum of all alleles present in a population in a given time.
 mRNA properties:
a. It receives genetic information from DNA
b. It consists of one nucleotide chain.
c. It is found in both the nucleus and cytoplasm.
d. It determines the order of amino acids in protein molecule.
e. It binds temporary with the tRNA during protein synthesis. (Translation)
 The human genome is estimated contain 30,000 expressed genes. This means that there are approximately 30,000
different possible proteins in a human.
 Although each body cell contain a full set of chromosomes (2n) with all the encrypted genes, but not all genes are
activated in each cell. (Example: insulin producing gene is present in all chromosomes in each body cells, but it is
activated only in cells of pancreases only.)
 Transformation: processes by which genetic material in the form of “naked” (DNA) is transferred between microbial cells.
 Transduction: e process by which foreign DNA is introduced into a cell by a virus. (Bacteriophage)
 Conjugation: he process by which one bacterium transfers genetic material to another through direct contact.
During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient

9
Biochemistry

Dr Alaa Badr
Bachelor of Medicine
01223306656
 Biochemistry

Basic Chemistry – Atomic Structure:

The atom consists of subatomic particles: protons, neutrons, and electrons
Subatomic Particle Charge Mass in amu Location
Proton +1 1 Nucleus
Neutron 0 1 Nucleus
Electron -1 0 Outside Nucleus

1. An atom in the elemental state always has neutral charge because the number of
protons (+) equals the number of electrons (-)
2. Electron configuration is important because it determines how a particular atom will
react to other element
3. Electron in the lowest available energy level are said to be in ground state
4. When an atom absorbs energy, its electrons move to a higher energy level. The
atom is then said to be excited state.
5. Isotopes: atoms of one element that vary in the number of neutrons in the nucleus.
They have same electrons. For example: carbon-12 and carbon-14, carbon-12 has 6
neutron while carbon-14 has 8 neutrons.
6. Radioisotopes: some isotopes are radioactive used to diagnose and treat disease
and to measure age of a fossil
Bonding:
A bound is formed when two atoms attract electrons. Energy is released when a bond is
formed. Energy must be applied to break a bond.
A. Ionic bond:
 Electrons are transferred.
 Atom gained electron  anion
 Atom loses electron  cation
B. Covalent bond:
 Atoms share electrons
 Resulting molecule called molecule
 Single covalent bond  two atom share 1 pair of electron
 Double covalent bond  two atoms share 2 pairs of electrons
 Triple covalent bond  two atoms share 3 pairs of electrons
 There are two types of covalent bond:
1. Polar covalent bond
2. Non polar covalent bond
Non Polar Covalent Bond Polar Covalent Bond
Electrons shared equally Electrons shared unequally
Formed between any two atoms that Formed between any two atoms that
are alike are unalike
Example: Example:
H2 (H-H) and O2 (O=O) CO (C=O) and H2 O (H-O-H)

Intermolecular Attraction:
 Molecules attract each other
 There are three types:
1. Polar-Polar Attraction:
 When two or more molecules form a bond, the entire resulting molecule is either
polar (unbalanced) or non-polar (balanced)
 Strong attraction exist between polar molecules
2. Hydrogen Bond:
 It's very important to living things
 It keeps the two strands of DNA bonded together forming a double helix
 It causes water molecule to stick together

3. Non-polar Molecules:
 Only the weakest attractions (van der Waals) exist between non-polar molecules.
Hydrophilic and Hydrophobic:
 Hydrophilic  loves water
 Hydrophobic hates water
 Polar substances dissolve in water while non-polar substances don’t dissolve in
water
Characteristics of Water:
ϖ Water is asymmetrical and very polar. It has strong intermolecular attractions. In
addition to polar attractions, it has strong hydrogen bond.
ϖ Characteristics:
1. water has high specific heat:
 Amount of heat needed to change the temperature of 1 gram of substance 1o
Celsius.
 It means that ocean absorb a lot of heat and resist change in temperature thus
providing stable life for the organisms
2. Water has high heat of vaporization:
 Great amount of heat needed to evaporate water
 As a result, evaporation of sweat cools body
3. Water has high adhesion properties:
 It plays an important role in plant survival as it helps water flow up from roots of
plant to leaves
4. Water is the universal solvent:
 It dissolves all polar and ionic molecules
5. Water has strong cohesion tension:
 That means molecules stick together and this helps in moving water up a tall
tree from the roots to the leaves without expenditure of energy
 It's also referred to as transpiration-pull cohesion tension
 It also result in surface tension that allows insect to walk on water without
breaking the surface
6. Ice floats because it is less dense than water
PH:
 It is the measure of acidity and alkalinity of a solution.
 It is the negative logarithm of the hydrogen ion concentration
 The internal PH of living cells is close to 7.
 Biological systems regulate their PH by the presence of buffers, substances that
resist change in PH. It works by absorbing excess hydrogen ions or donating
hydrogen ions when there are too few.
 The most important buffer in human blood is bicarbonate ion (HCO3)

PH Concentration of H+ Ion in mole/liter

1 1 x 10 -1 = 0.1 molar
2 1 x 10 -2 = 0.01 molar
3 1 X 10-3 = 0.001 molar
4 1 x 10-4 = 0-0001 molar
Organic compounds:
ϖ Organic compounds are compounds that contain carbon.
ϖ There are four classes: carbohydrates, lipids, proteins, and nucleic acid
1. Carbohydrates:
 It consists only of carbon, hydrogen, and oxygen
 It supply quick energy
 1 gram of carbohydrates release 4 calories
  There are three classes of carbohydrates: monosaccharide, disaccharides, and
polysaccharides
ϖ Monosaccharaides:
 Chemical formula C6 H12 O6
 Example: glucose, galactose, and fructose (all isomers of each other)

ϖ Disaccharides:
 Chemical formula C12 H22 O11
 They consist of 2 monosaccharide joined together by a process known as
dehydration synthesis
 Example:
1. Glucose + Glucose  Maltose + water
2. Glucose + Galactose  Lactose + water
3. Glucose + Fructose  Sucrose + water
 Hydrolysis: the breakdown of a compound. It is what happen during digestion
and it's the reverse of dehydration synthesis
ϖ Polysaccharides:
 They are polymers of carbohydrates
 They form as many monosaccharide joined together by dehydration synthesis.
 There are four important polysaccharides:
1. Cellulose: make up plant cell wall
2. Starch: the way plant store carbohydrates
3. Chitin: makes up the exoskeleton in arthropods and cell wall in mushrooms
4. Glycogen: it's the way animal store starch. It is stored in liver and skeletal
muscle
2. Lipids:
 It’s a diverse class include fats, oils, and wax.
 It's made up of 1 glycerol + 3 fatty acids
 Glycerol is an alcohol and fatty acids are hydrocarbon chain with a carboxyl
group at one end
  Fatty acids exist in two groups:
a) Saturated fats: it comes from animals. They are solid at room temperature.
They are linked to heart disease. An example is butter. It contains only single
bond between carbon atoms.
b) Unsaturated fats: it extract from plants. They are liquid at room
temperature. They have at least one double bond between carbon atoms in
the hydrocarbon chain. They have fewer hydrogen atoms

ϖ Lipid Function:
1. Energy storage: 1 gram of lipid release 9 calories per gram
2. Structural: phospholipids are a major component of cell membrane
3. Endocrine: some lipids are hormones
4. Cushing organs
3. Proteins:
 Proteins are polymers of repeating units called amino acids joined by peptide
bond
 Amino acids consist of carboxyl group, an amine group, and a variable (R). all
attached to a central carbon atom
 The R group differs with each amino acid
 1 gram of protein release 4 calories
 With only 20 different amino acids, cells can build thousands of different
proteins
 Enzymes are example of proteins
  Protein structure:

4. Nucleic acids:
ϖ The nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
ϖ They carry hereditary information
ϖ They are polymers of nucleotides
ϖ A single nucleotide consists of a phosphate, a 5-carbon sugar (either de-
oxyribose or ribose), and a nitrogenous base.
ϖ In DNA the bases are adenine, cytosine, guanine, and thymine
ϖ In RNA the bases are adenine, cytosine, guanine, and uracil
ϖ Adenine and guanine are purines
ϖ Cytosine, thymine, and uracil are pyrimidine
NOTE:
ϖ 1 gram of carbohydrates  4 calories 'most readily accessible in short time"
ϖ 1 gram of lipid  9 calories "in long time"
ϖ 1 gram of protein  4 calories "in VERY long time"
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420

THE SEARCH FOR INHERITABLE MATERIAL

 Griffith (1927)
 Avery, MacLeod, and McCarty (They provided
direct experimental evidence that DNA is the
genetic material.

 Hershey and Chase (1952) proved that DNA,

not proteins, is the molecule of inheritance
when they tagged bacteriophages.

 Rosalind Franklin (1950-53), carried out the X-

ray crystallography analysis of DNA that
showed DNA to be a helix.

 Watson and Crick received the Nobel Prize in

1962 for correctly describing the structure of DNA as a double helix.

 Meselson and Stahl (1953) proved Watson and Crick's hypothesis that DNA replicates in a
semiconservative fashion. Crick's theory.

1
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
STRUCTURE OF DEOXYRIBONUCLEIC ACID (DNA)
 DNA is a double helix shaped like a twisted
ladder.
 DNA consists of two complementary strands
running in opposite directions from each other.
 It is a polymer made of repeating units called
nucleotides.
 Each nucleotide consists of a 5-carbon sugar
(deoxyribose), a phosphate molecule, and a
nitrogenous base.
 Each nucleotide contains one of the four
possible nitrogenous bases: adenine (A), thymine (T),
cytosine (C), and guanine ( G).
 A always bonds with T; C always bonds with G.
 The nucleotides of opposite chains are paired to
one another by hydrogen bonds. G is bonded with C
with 3 hydrogen bonds, while A is bonded to T by 2
hydrogen bonds.
 Increasing %G-C makes DNA more stable. (Not easily broken by heat)

DNA REPLICATION IN EUKARYOTES

DNA replication is the making of an exact replica of DNA. The two new molecules of DNA that are produced
each consist of one old strand and one new strand. This is called semi-conservative replication as proved
by Meselson and Stahl.
 Replication occurs during interphase in the life cycle of a cell. (S Phase)
 Unwind the DNA molecules by breaking down Hydrogen bonds between two strands via DNA
Helicase.
 During DNA replication, the enzyme helicase unwinds the DNA helix, forming a Y-shaped replication fork.. As
helicase unwinds the DNA, it forces the double-helix in front of it to twist.

2
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
 DNA polymerase catalyzes the replication of the new DNA. (direction enzyme from 5’ end to 3’
end)
 DNA polymerase also proofreads each new DNA
strand, fixing errors and minimizing the occurrence of
mutations.
 DNA rewinds by forming new hydrogen bonds to
connect the two strands of the double helix.
 Each strand of DNA serves as a template for the new
strand according to the base-pairing rules: A with T and
C with G.
 If a strand of DNA to be copied is AAATCGGAC, then
the new strand is TTTAGCCTG .
 Each time the DNA replicates, some nucleotides from
the ends of the chromosomes are lost. To protect against
the possible loss of genes at the ends of the chromosomes, some eukaryotic cells have special
nonsense nucleotide sequences at the ends of chromosomes that repeat thousands of times. These
protective ends of the chromosomes are called telomeres. Telomerase: enzyme that restore the
length of chromosomes.

Replication of DNA in prokaryote and eukaryote are basically the same, with the following differences:
 Chromosome structure: A prokaryotic chromosome is circular and chemically made of DNA only.
While the chromosome of eukaryote is linear and chemically made of DNA and Histone protein.
The end of eukaryotic chromosomes contain telomeres.
 Origin of replications: A prokaryotic chromosome has one unique origin of replication. Eukaryotes
have multiple origins

DNA Repairing
1. DNA polymerase: checks that the new added nucleotides are correctly base-pair with the template strand.
2. Mismatch repair proteins: repairs errors that scape the proofreading ability of DNA polymerase.

3
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
Gene Expression (Protein Synthesis)

1. MESSENGER RNA (mRNA). It carries messages

directly from DNA in the nucleus to the cytoplasm
during the making of protein. The triplet nucleotides
of mRNA (such as AAC or UUU) are called codons.
2. TRANSFER RNA (tRNA). It is shaped like a cloverleaf
and carries amino acids to the mRNA at the ribosome in order to form a polypeptide. The triplet
nucleotides of tRNA are complementary to the codons of mRNA and are called anticodons.
3. RIBOSOMAL RNA (rRNA) is structural. Along with proteins, it makes up the ribosome

How Chromosomes Govern Protein Synthesis: Transcription and

Translation
 DNA contains genes, and genes tell your cells how to make
protein. The step in between is the production of RNA. RNA is the
“middleman” between DNA and protein.

 This is known as the “central dogma of molecular biology.” DNA to RNA

to protein. In other words, DNA directs the synthesis of RNA, and RNA
directs the synthesis of protein.
 When you switch from RNA (nucleotide language) to protein (amino
acid language), that’s a translation.

 RNA is transcribed from DNA, and protein is translated from RNA.

4
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
TRANSCRIPTION
 From DNA to mRNA
 By RNA polymerase
 Site: Eukaryote (in nucleus) Prokaryote (in cytoplasm)
RNA Processing (Post Transcription modification)
These noncoding regions that are removed are called introns (intervening sequences). The remaining
portions, exons (expressed sequences or coding regions), are pieced back together to form the final tran -
script. As a result of this processing, the mRNA that leaves the nucleus is a great deal shorter than the
piece that was initially transcribed. Mature mRNA contains only coding segments (Exons)

Here’s a summary of the differences between DNA replication and RNA transcription:

5
 BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
Codons of mRNA:
A sequence of three nucleotides is
called a codon, and the order of
codons on mRNA specifies the order
of amino acids in a protein.

Because there are four possible

nucleotide bases, and codons are
groups of three bases, there are 64 (4
× 4 × 4) possible codons. Because
there are only 20 different amino
acids, some of the amino acids are
coded for by more than one codon.

There are 4 special codons:

 1 Start (AUG)
 3 Stop (UAA) (UAG) (UGA)
All of the 20 amino acids are coded from 61 codons from the 64 codons possible.

So, for this piece of mRNA, the amino acid sequence would be:

Translation

6
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
GENE REGULATION (necessary for cellular differentiation: Change of no typed cells to specific types)
(inactive genes become active)
Every cell does not constantly synthesize every polypeptide it has the ability to make. For example,
cells in the pancreas are not always producing tons of insulin because it is not always needed. That
means that every gene in a cell is not turned on all the time. How does a cell know when to turn on a
gene or when to turn it off? This is actually a very complex process in humans and one tha t is not
understood well. However, a simple model for gene regulation can be found in bacteria in a region of
DNA called the operon.

Important Points:
 Promoter is the part of operon (gene)/site
where RNA polymerase binds.
 Structural genes are the parts of the
operon that codes for mRNA sequences for
amino acids.
 Terminator is the part of the operon where
transcription is stop.
 There are two types of operons:
a. Inducible operon: normally switched off.
b. Repressile operon: normally switch on.

7
 BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
Mutation
Mutations are changes in genetic material (DNA Nucleotides). They occur spontaneously and at random
and can be caused by mutagenic agents, including toxic chemicals and radiation. Mutations are the raw
material for natural selection. Mutation is inherited if it occurs in gametes or gametes forming cells.

Mutation

Gene mutation Chromosomal

(Point mutation) mutation

Change in
Change in
Substitution Chromosome
Chromosome
Number
structure
(Aneuploidy)
Insertion
Frame Inversion
Shift
Trisomy Monosomy Polyploidy
Deletion
Insertion

Deletion

Translocation

I. Gene mutation (change in base level)

Several types of gene mutations can occur: point mutations, insertions, and deletions. Both types can have deleterious effects on
the organism.

Substitution mutation (point mutation) Replacement of one base by another EX: Sickle cell anemia
Sickle cell is abnormal shaped RBCs
with low Hemoglobin content. The
abnormal RBCs may block small
blood vessels and low Hb content
will carry low level of oxygen in
blood (anemia).

8
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
Effects of Point mutation

1. A silent mutation occurs when the new codon still codes for the same amino acid. This occurs most often when
the nucleotide substitution results in a change of the last of the three nucleotides in a codon.
2. A missense mutation occurs when the new codon codes for a new amino acid.
3. A nonsense mutation occurs when the new codon codes for a stop codon.

NB: The position of a mutation in a gene and the location of an altered amino acid sequence in the corresponding
protein are in the same relative position.

II. Chromosomal mutation:

a. Change in the structure of chromosomes:
 Deletion: occurs when segment of the chromosome is lost.
 Duplication: occurs when segment of the chromosome is repeated. (antifreeze gene in fish)
 Inversion: occurs when a DNA segment is reversed.
 Translocation: occurs when a part of the chromosome is deleted and reinserted elsewhere in different
chromosome or in the same chromosome.

9
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
II. Chromosomal mutation:
B. Change in the number of chromosomes: (Aneuploidy)
 1. Trisomy: Number of chromosomes is increased by one. (Triplicated chromosome)
Ex: a. Down syndrome: Extra chromosome in pair number 21. (45, XX) or (45, XY)
b. Klinefelter syndrome: Male of Extra X chromosome. ( 44, XXY)
 2. Monosomy: Number of chromosome is decreased by one.
Ex: Turner Syndrome: Female missing one X chromosome (44, X0)
 3. Polyploidy: Organism in which his all cells have an extra set of chromosomes. Normal set of chromosomes
is (2n) or (n). Endosperms or the cotyledon of the seed is triploid (3n). Scientist breed plants to be polyploidy
as they will produce abnormally large flower or fruit.

The abnormal number of chromosomes is due to NONDISJUNCTION.

Nondisjunction is an error that sometimes happens during meiosis in which
homologous chromosomes fail to separate as they should. When this
happens, one gamete receives two homologues, while the other gamete
receives none. The remaining chromosomes may be unaffected and normal.
If either of these aberrant gametes unites with a normal gamete during
fertilization, the resulting zygote will have an abnormal number of
chromosomes.

10
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
THE HUMAN GENOME
The human genome (an organism's genetic material) consists of 3 billion base pairs of DNA and about 20,000 genes.
Surprisingly, 97 percent of our DNA does NOT code for protein product. Some of this DNA consists of regulatory
sequences that control gene expression. Some are introns that interrupt genes. Much of the DNA consists of repetitive
sequences that may repeat ten million times and never get transcribed. Some of the DNA are pseudogenes, former genes that
have accumulated mutations over a long time. Scientists are only beginning to understand the make-up of DNA.

GENETIC ENGINEERING AND RECOMBINANT DNA

Recombinant DNA means taking DNA from two sources and combining them in one cell.

Restriction Enzymes
Restriction enzymes are an important tool for scientists working with DNA. They cut DNA at specific recognition
sequences or sites. The pieces of DNA that result from the cuts made by restriction enzymes are called Restriction fragments
with sticky ends. Hundreds of different restriction enzymes have been isolated from bacteria.

Gel Electrophoresis (separation of DNA and Protein fragments according to the

molecular weight)
In order to run DNA through a gel, it must first be cut up by restriction enzymes into
pieces small enough to migrate through the gel. Once separated on a gel, the DNA
can be analyzed in many ways.

The DNA in lanes 1, 2, and 4 were previously cut with restriction enzymes; the DNA
in lane 3 was left uncut. Each sample is running in its own lane. The shorter pieces of
DNA run farther and faster through the gel. Lane 1 contains four bands of DNA, three
larger pieces and one short piece. Lane 2 contains two pieces of DNA, one large and one
tiny. Lane 3 contains one very large and uncut piece of DNA. Lane 4 contains two pieces
of DNA.

In another way:

11
 BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
The distance moved by a fragment within the electric field is influenced by:
 The number of amino acids in the fragments ( amount of nucleotide in DNA fragments) (molecular weight)
 The amount of electric current used in the apparatus (Current intensity)
 The porosity of the gel matrix

Polymerase Chain Reaction

Devised in 1985, polymerise chain reaction (PCR) is a cell-free, automated technique by which a piece of DNA can be rapidly
copied or amplified. Billions of copies of a fragment of DNA can be produced in a few hours. Once the DNA is amplified, these
copies can be studied or used in a comparison with other DNA samples.

Cloning:

 Developmental
genes not lost by
aging.
 Genes from older
embryo retain their
capacity to direct
normal
development.

12
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420

13
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
Summary

14
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420

1. DNA

2. Hydrogen Bonds
3. RNA polymerase

4. mRNA
5. Ribosome

6. tRNA

7. Polypeptide (protein)

1. Ribosome

2.mRNA
3. tRNA

4. Amino acids

5. Polypeptide

(A) : Nuclear envelop: bilayer of lipid. Barrier

to diffusion of large molecules from nucleous
to cytoplasm.
(B) RNA plymerase

(C) Ribosome
(D) Translated (matured) mRNA

(E) Polypeptide.

15
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420
 ↑G-C content in DNA → ↑ DNA stability (hydrogen bonds are hard to be broken)→ 2 strands become closer to each
other.
 (DNA) The molecule that carries the genetic information from one cell generation to the next.
 (mRNA) The product of transcription that determines the sequence of amino acids in a polypeptide chain.
 (tRNA) A nucleic acid that bonds temporarily with a specific amino acid during protein synthesis.
 (RNA polymerase) The protein that carries out transcription.
 Mutation is an error in DNA nucleotides.
 Mutation is the primary source of genetic variation.
 Mutation will be inherited if it is formed in the gamete forming cells (cells of gonads)
 What happen if an egg is fertilized by two sperms? Display abnormal number of chromosomes.
 tRNA positions amino acids for protein synthesis by paring with codons of mRNA.
 Chromatography is an alternative technique to gel electrophoresis.
 The production of different cell types of multicellular organism is regulated by specific sets of mRNAs that are produced in
a particular cell type.
 If Nitrogen base Guanine makes up 40% of the bases in DNA ,
% C=%G=40 % T and A = 100-(%G+%C)= 100-(40+40)=20% %A=10% %T=10%
 Genes ARE NOT unique to our species.
 Gene pool: The sum of all alleles present in a population in a given time.
 mRNA properties:
a. It receives genetic information from DNA
b. It consists of one nucleotide chain.
c. It is found in both the nucleus and cytoplasm.
d. It determines the order of amino acids in protein molecule.
e. It binds temporary with the tRNA during protein synthesis. (Translation)
 The human genome is estimated contain 30,000 expressed genes. This means that there are approximately 30,000
different possible proteins in a human.
 Although each body cell contain a full set of chromosomes (2n) with all the encrypted genes, but not all genes are activated
in each cell. (Example: insulin producing gene is present in all chromosomes in each body cells, but it is activated only in
cells of pancreases only.)
 Transformation: processes by which genetic material in the form of “naked” (DNA) is transferred between microbial cells.
 Transduction: e process by which foreign DNA is introduced into a cell by a virus. (Bacteriophage)
 Conjugation: he process by which one bacterium transfers genetic material to another through direct contact.
During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient

16
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420

Colored Atlas

17
BioMax Chapter7: Molecular Genetics Dr.Amr Alaa 0567573420

18
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Chapter 8:1 Evolution

BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Evidence of evolution
1. Fossils: Remains of living things, kept from decay in sedimentary rocks and Position of strata and radioactive C14
determine fossils age
2. Genetics and DNA: Crossing over, mutations, and universal T G A C bases
3. Biochemistry: Human use pigs insulin, horse anti-titanic serum, and cattle ACTH
4. Comparative anatomy:
a. Homologous structures (SS,DF) Wind of bat, Whale flipper, Human arm
b. Analogous structures: (DS,SF) Wing of bat and wing of insects.
C. Vestigial structures: Useless structures in present of importance in the past
 Appendix: digestion of cellulose in the past
 Horse splints: remains of eohippus(horse ancestor) 2 side toes
 Whale and snake hipbones: remains of 4 legs
6. Comparative anatomy
Homologous structures: Same structure and different function. Same origin (ancestor) then evolved divergently
Mammals have similar origin and different functions of forelimbs
Human hand Cat leg Whale flipper Bat wing
(Grasp) (Run) (Swim) (Fly)

Analogous structures Same function and different structure. Different origin (ancestor) then evolved convergently
Shark and dolphin have dissimilar origin and both swim

7. Biogeography: Continental drift: a single supercontinent (Pangaea) is separated into 7

 Koala and kangaroo (marsupials) in Australia are separated from Asia
 14 finches species in Galapagos islands are originated from one island
8. Embryology: Gill pouch in vertebrates embryo develops to gills in fish and Eustachian tube in human.

Origin of earth (Alexander Oparin)

Age of earth is 4.6 billion years
 1st organism was a prokaryote, 3.5 billion years ago (anaerobic)
 Eukaryotes appeared 1.5 billion years ago
 Early atmosphere: H2O, H2S, CH4, CO2, NH3, N2, and no O2
 The first cell appeared is heterotrophic
 Urey and Miller recreated early conditions of earth producing amino acids from early components.
Theory of spontaneous generation: Life appeared from non-living things. Denied by Louis Pasteur

Theory of use and disuse – Lamarck (Inheritance of acquired traits)

 Giraffes stretched their necks to reach high trees
 Evolution is the accumulation of acquired traits
 Criticism: Acquired characters are not inherited; are not carried on sex cells
Theory of mutation - Hugo de Vries: Evolution is due to accumulation of mutations
● Criticism: Mutation is harmful and recessive

Theory catastrophism fa special creation - George Cuvier

2
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Catastrophic changes resulted in death of all species followed by special creation of new species
 Criticism: Cells arise from pre-existing cells
Theory of natural selection — Charles Darwin
1. Overpopulation makes offspring more exposed to loss
2. Limited resources lead to competition and struggle for existence 4. Slight variations between individuals lead to
winners and losers (key)
3. Survival for the fittest as strong, fast individuals will reproduce and leave more offspring
4. Adaptive radiation of 14 different beaks of finches in 14 Galapagos Islands originated from 1 finch on 1 island
(divergent evolution due to competition for different foods)
● Criticism: Could not explain genetic basis and wrong definition of fitness
The equilibrium of population genetics - Hardy - Weinberg
 Population's gene pool is the total of alleles exists in a given population
 Fitness is the number of offspring
 Allele frequencies in a given population is p + q = 1 (p2 + 2pq + q2 = 1)
 p is frequency of dominant allele
 q is the frequency of recessive allele
 p2 is frequency of pure dominant genotype
 q2 is the frequency of pure recessive genotype
 2pq is the frequency of the heterozygous genotype
Stability of (maintain) gene pool Evolution (change)
1. Large size 1. Small size
2. No migration 2.Migration
3. No mutations 3. Mutation
4. Random mating 4. Isolation
5. No natural selection 5. Natural selection

Sources of Variations:
1. Mutation (main source) 2. Gene Flow: Migration 3. Crossing over
4. (genetic drift)

p
 Bottleneck: sudden reduction in population size leading to loss of alleles
 Founder effect: small populations isolated and form new population
Types of natural selection
A- Stabilizing selection
 Average phenotypic individuals are favored
 Extreme phenotypic individuals are selected against
 Average is not changed
B- Directional selection
• Individuals at one phenotypic extreme are favored
• Individuals at the other extreme are selected against (Average is changed)
C- Disruptive selection

3
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Individuals at both phenotypic extremes are favored
 Average phenotypic individuals are selected against
 2 new averages

Patterns of Evolution
1. Convergent evolution: Two species from different ancestors performing same function
2. Divergent evolution: Two species from a common
ancestor performing different functions
3. Parallel evolution: Species making similar evolutionary
changes.
4. Co- evolution: Evolution of a species depends on the
evolution of another species. (Insect and flower)
5. Adaptive radiation: Emergence of numerous species
from a single species (multiple divergence) (Finch birds)
6. Macroevolution
Large-scale evolutionary changes take place over a long
time that may lead the formation on a new species
(Speciation)

Evolution Rate Pattern:

1. Gradualism: Organisms descend from a common
ancestor gradually with slow rate (not supported by fossil
record)
2. Punctuated equilibrium: New species appear suddenly after long periods of no change.

Phylogeny (phylogenetic tree)

 The relatedness patterns among different species
 The most related taxa are C and D
 Node is where divergence (split) occurs
 Lines represent DNA, RNA, or amino acid sequences
 Phylogeny represent linage of species

Degree of relatedness between species is determined by

1. DNA, RNA, or amino acid sequences
2. Embryology
3. Anatomy
4. Fossil record

Old Humans Australopithecus species, Homo habilis, Homo erectus, and Cro-Magnon
 Brow ridges and massive jaw ●Less brain capacity

Modern Human Homo sapiens evolved 100,000 years ago

 Migration →↑ gene flow →↑ exchange of alleles between different gene pools of different population →↑evolution
adaptation.
4
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Parasite successfully evolves, when it flourish allowing the host to survive.
 Convergent evolution results when two or more species become resemble to each other even though they are
phylogenically dissimilar.
 Great Difference between human skull and ape skull of same locality, that the apes’ skull has small brain cavity.
 The determining factor in the natural selection is the number of individuals that reproduce.
 Phylogeny biology: the evolutionary history of a group of organisms.
 Paleontologists: scientist who studies fossils.
 The best evidence that the individuals in a population are of the same species would be that they can mate producing
fertile offspring (progeny).

 Bone adapted for flying must be small and light

(2,3)
 Bones adapted for swimming must be strong and
fully extended. (1).
 Bones for grasping well defined fingers (6).

 Evolution time line for animals:

Sponge → cnidarian (hydra/jelly fish) →
Helminthes (worms) → Mollusca (snail/octopus) → arthropods (insects) → Echinoderms (Star fish) → Fish →
Amphibian (frog) → Reptiles → Birds → mammals.
 ↑ Hardness of a structure → ↑ chance to be fossilized.
 First organisms were anaerobic. (as ancient atmosphere contained NO OXYGEN)
 Adaptive radiation refers to the evolution of single ancestral species inter several species adapted to various
environment.
 Sexual reproduction has an evolutionary importance as it results in genetic variation among offspring.
 Key point in Darwin’s theory of evolution that slight variations among individuals significantly affect the chance that a
given individual will survive in the environment and able to reproduce.
 Radioactive carbon dating is not an evidence of evolution by itself, but it is used in establishment of fossil record that is
used as an evidence for evolution.
 Mutation is the main source of variation and it will be inherited if it takes place in gametes producing cells.
 Prokaryotes are thought to be similar to the first form of cellular life as it lacks of nuclear membrane.
 A geologic era is a subdivision of geologic time that divides an eon into smaller units of time. The Phanerozoic Eon is
divided into three such time frames: the Paleozoic (era of insects, fish, and amphibian), Mesozoic (conifers and
reptiles), and Cenozoic (birds and mammals) represent the major stages in the macroscopic fossil record. These eras
are separated by catastrophic extinction boundaries.
 Human and chimpanzees are divergently evolved from a common ancestor.
 Hot spot: is an area in the mantle from which heat rises as a thermal plume from deep in the Earth (middle of plate not
at the boundaries).
5
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 The evolution of an organism will not be related to the mechanism of the formation of geological features if this feature
is formed before the existence of the organism itself.
 Forms of fossils: 1. Mold: solidified sand makes the shape of the organism. 2. Cast: the superficial remains of nonliving
parts (leaves) 3. Print: the superficial remains of living parts. 4. Whole body fossil: Mammoth whole body fossil in ice.
 All development are consider as evolution, while not all evolutions are development.

 Golden moles: are underground animals-marsupial mammals- their eyes are not developed by mutation giving rise to
more successful variation of moles.
 Adaptive characters ↑ evolutionary fitness.
 Non Random mating , Mutation, migration, and natural selection are factors the likely change the frequency of alleles in
a population,
 Modern theory of evolution suggests that sexual reproduction is necessary for evolution to happen as it is a source of
genetic variation.
 Speciation happens when two species are not able to produce fertile offspring.
 Dolphin flippers (Bones) and sharks (cartilage) fin are analogous strictures.
 Evolution by nature selection will occur when the following are present:
a. Heritable trait.
b. Genetic variation.
c. Differential reproductive success.
 Little evolutionary changes for long period of time in a species indicate that species exist in environment niche that has
remain stable.
 Adaptation → new variation → natural selection → evolution.
 Heterotrophic prokaryotes (no chlorophyll) are thought to present before autotrophic prokaryotes (chlorophyll) as they
requires fewer evolutionary steps..
 Mass extinctions are followed by adaptive radiation.
 Porpoise is a mammal.
 Weevil is an insect
 Apes skull is smaller than human skull.

6
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

7
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Chapter 9: Taxonomy
Old system kingdoms
 Kingdom Monera: all bacteria
 Kingdom Protista: unicellular animals and plants
 Kingdom Fungi: cell walled multicellular heterotrophs except yeast
 Kingdom Planta: multicellular autotrophs
 Kingdom Animalia: multicellular heterotrophs
Modern system
1. Domain Archaebacteria: prokaryotes with some genes from eukaryotes
2. Domain Eubacteria: prokaryotes
3. Domain Eukaryota: eukaryotes (Protista, Fungi, Plant, Animalia)

Series of taxonomy Domain, Kingdom, phylum, class, order, family, genus, species

Same species Interbreed and give fertile offspring

Binomial system 1st name is genus and 2nd name is species (Homo sapiens)Both must be Italic

1. Kingdom Archaea
 Unicellular prokaryotes having some genes from eukaryotes
 Extermophiles, live in high temperature and salt
2. Kingdom Bacteria
 Unicellular prokaryotes
 Reproduce by binary fission and conjugation
 Parasitic, saprophytic, mutualistic
 Photosynthetic (blue green algae - cyanobacteria)
3. Kingdom Protista Unicellular and multicellular (mostly unicellular) eukaryotes

I. Animal-like protista (Protozoa)

1. Ameba move by pseudopodia (false feet)
2. Paramecium move by cilia
3. Plasmodium move by spores and cause
malaria
4. Trypanosoma move by flagella and cause
African sleeping sickness

II. Plant -like Protista: Algae and planktons

III. Fungal like Protista: Slime mold

4. Kingdom Fungi
1. Unicellular heterotrophs reproduce by budding (Yeast)
2. Multicellular heterotrophic hyphae reproduce by spores
Decomposers (bread mold and mushroom) or Parasites (athletic foot)
Penicillium is used as a source of antibiotics
8
 BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

5. Kingdom Planta
• Multicellular and photosynthetic autotrophs
Phyla Example Vascular Tissue Seeds Flower
Bryophyta Mosses x X xs
Pterophyta Ferns  X x
Gymnosperms Pines (conifers)   (cone) x
Angiosperms Flowering plants   

Angiosperms Monocotyledons Dicotyledons

Seed lobe (cotyledon) 1+ 1 embryo leaf 2 + 2 embryo leaves
Leaf venation Parallel Net
Flower Group of 3 or multiple Group of 4,5
Stem (vascular tissue) Scattered Arranged
Root Fibrous Tap (wood)

6. Kingdom Animalia: Multicellular heterotrophic aerobic organisms. Mostly motile with no cell wall and chloroplast.
1. Phylum Porifera: no symmetry 3. Phylum Flatworms (Platyhelminthes) (non-segmented)
No true tissue Ex: Sponge Tapeworm, planaria (head)- Bilateral symmetry-No coelom-No systems-
3 layers- Head.
2. Phylum Cnidarians (movement)
 Jellyfish, hydra, corals 4. Phylum Roundworms (Nematodes) (non-segmented)
 2 Germ layers – Radial symmetry Filaria, hookworms-C. elegens –Pseudocoelom – 3 Layers -Head
5. Phylum Segmented worms (Annelids) 6. Phylum Mollusks
Earthworm, leeches  Open circulation
Ventral nerve cord- Coelom  No shell: squid, octopus
Closed circulatory system- Complete digestive system  With shell: slugs, clams, snails, mussels (shell is
(2 openings) (Bilateral) (3 layers) secreted by mantle)
7. Phylum Arthropods: Largest phylum-Segmented body-Jointed appendage - Chitin exoskeleton-Open circulation
Metamorphosis and molting
Class Crustaceans Class Insecta Class Arachnida
 Shrimp, crab, lobster, crayfish ● Grasshopper, ants, bees  Spiders, scorpions, ticks
 Gills  3 pairs of legs and wings  4 pairs of legs
 5 pairs of legs  Pair of antennae  2 body parts (cephalothorax) and
 2 pairs of antennae Butterfly (complete metamorphosis) abdomen
● 3 body parts (head-Thorax- Grasshopper (incomplete metamorphosis):
Abdomen) egg, nymph, adult
● 3 body parts (head-Thorax-Abdomen)

8. Phylum Echinoderms: Starfish - sea urchins - sea cucumber -Tube feet- Water vascular system- Radial Adult –
Bilateral larva.

9
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
9. Phylum Chordata- Dorsal nerve cord (spinal cord)- Notochord (vertebral column)- Endoskeleton

Fish Amphibian Reptiles Birds Mammals

Aquatic Organisms ●These animals are well ●Develop completely on ●Birds are tetrapods with
●Mammals endothermic,
● Cold-Blooded - adapted to both land and land (no water role in the forelimbs modified as ● have hair or Fur,
Poikilothermic) water. (Complete part of development) wings. ●They breathe ●Nourish their young the
milk from mammary
● External their life cycle in water and ●Their eggs with shells through lungs and lay glands.
Fertilization other on land) ●They breathe through shelled eggs. ●They breathe through
lungs.
● Two Groups ●Their eggs lack shells and lungs ●They are endothermic. ●Examples are rodents,
(Bony Fish) must be laid in the water. ●Has leathery egg and ●Have no teeth kangaroos, antelope, and
humans.
Cartilaginous Fish: ●They have an aquatic watertight skin. ●High metabolic rate. Types:
(Shark) larval stage and undergo a ●Examples are Snake – ●Light weighted ● Monotreme (Ley egg ,
Ex: Platypus –Anteater)
● Lateral Line metamorphosis into a turtle- lizard – crocodile- endoskeleton. ●Examples ● Marsupial (Give birth to
(sensation) terrestrial adult. alligator are owls, eagles, sparrows, an incompletely
developed offspring that
● Gills ●They breathe through and penguins develops inside a pouch)
● Ectothermic lungs and/or skin. (Ex: Kangaroo- Koala)
● Placental (eutherians)
(Poikilothermic) ●Examples are frogs and (Give birth to a
salamanders. completely developed
offspring. ( Human-Cow-
●Ectothermic Cats-Horse)
(Poikilothermic)

Excretion Nitrogenous wastes

a. Sponge: vacuoles b. Planaria: flame cells • Aquatic animals: ammonia (water soluble)
c. Earthworm: nephridia d. Insects: malpighian tubules • Mammals / amphibians: Urine (liquid)
e. Reptiles / birds: slat gland f. Mammals: kidneys (Nephron) • Reptiles / birds: uric acid (solid)
Circulatory system Colors
 Fish: nucleated RBCs and 2 chambered heart  Human visible color (red to violet)
 Amphibians: nucleated RBCs and 3 chambered heart  Insects detect landing position on flower
 Reptiles: nucleated RBCs and 4 chambered heart (mixed blood) by ultraviolet rays
 Aves/ mammals: RBCs (no nucleus)and 4 chambered heart (separated)  Snakes detect prey by infrared rays
Asexual reproduction Body temperature regulation
(thermoregulation)
 Fission: split into two equal-sized organisms (bacteria, ameba) 1. Cold blooded (ectotherms)
 Budding: split into two unequal-sized organisms (yeast, hydra)  Variable temperature
 Fragmentation: development of the missed part into an adult (Worms)  All organisms except birds and mammals
Sexual reproduction
2. Warm blooded (endotherms/
 Conjugation homeotherms)
 External fertilization: eggs lack shell for fertilization (aquatic animals)  Constant temperature.
 Internal fertilization: male deposits sperm in female (Land animals)  Birds and mammals
 Parthenogenesis: egg develops into adult without fertilization (bees)
 Hermaphrodite: Contains both male and female parts.
10
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

11
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Organism Pro/Eu(karyoe) Number of cells Pattern of feeding Cell wall Examples
Autotroph/Heterotrop E. Coli
Bacteria Prokaryote Unicellular Peptidoglycan
h
Plant like: Algae
Uni/multicellular Autotroph: Plant like
Cellulose Amoeba/Parameci
Protista Eukaryote Mostly Heterotroph: Animal
Protozoa: NO um
unicellular and fungal like.
Fungal like: Chitin Slime mold
Uni/multicellular Yeast
Heterotroph
Fungi Eukaryote Mostly Chitin Mushroom
(saprophyte)
multicellular
Plant Eukaryote Multicellular Photoautotroph Cellulose Next table
Animal Eukaryote Multicellular Heterotroph NO Next Table

Phylum Common Name Germ Symmetry opening Coelom Embryonic

layers development
Profera Sponge 2 NO NO NO -
Cndidaria Hydra/Jelly fish 2 Radial 1 NO -
Platyhelminthes Tape worm 3 Bilateral 2 Acoelomate Protostome
(non-
segmented)
Nematode Rotifer Bilateral 2 Pseudocoelom- Protostome
(round) Trichinella ate
Nonsegmented C. elegans
Annelida Earth worm 3 Bilateral 2 Coelomate Protostome
(segmented) Leech
Polychaete
Arthropods Insects/Scorpion/Spider/Crab/ 3 Bilateral 2 Coelomate Protostome
Lobster/mites/ticks/flees/Weevil
Mollusca Snail/Octopus/Squid 3 Bilateral 2 Coelomate Protostome
Echinoderms Star fish/Sea urchin/ 3 2 Coelomate Deuterostome
Sea cucumber/Sand dollars
Chordate Fish/Amphibian/Reptile/Birds/mammals 3 Bilateral 2 Coelomate Deuterostome

12
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 RBCs of vertebrates: Nucleated: fish-Amphibian-Reptiles-Birds Non-nucleated: Mammals

 Adaptions found in reptiles that enable them to be completely terrestrial (live on land) are a leathery
amniotic egg and watertight skin.
 Amniotes are reptiles, birds, and mammals that lay their eggs on land or retain the fertilized egg within the
mother. They are distinguished from the Anamniotes, which typically lay their eggs in water (Fish and
amphibians)
 Examples of:
Fish: Salmon-Trout-Shark (cartilage)-Cray fish-Eel
Amphibian: Frog – Toad – Salamander.
Reptiles: Alligator – Turtle – crocodile-Lizard-Snake.
Birds: Sparrow- Ostrich.
Mammals: Squirrel-Dolphin-Porpoise-Whale-Bat-Seal
 Fish gills and vertebrates lung share all the followings:
● Moist Respiratory surfaces. ● Large diffusion surface area. ● Proximity to blood vessels. ● Access to oxygen.

 Countercurrent exchange is a unique property for fish.

 Any respiratory surfaces (skin-gills-lung) must be a moist surface.
13
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
 Notochord presents only in chordate (as vertebrates)
 If two organisms share the same taxonomic level, they also share all the previous levels. Example if organism
A and organism B belong to same order, they also share the same kingdom, Phylum and class.
 The basic principle in designing modern cladogram (phylogenetic tree) is the sequences of nucleic acid
nitrogen bases. C D E

 Line age leading to A is separated from that leads to E at mode 1

 Line age leading to C is separated from that leads to E at node 2 A B ●
 B evolves after A and D evolves after C Node 2
 Organism is closely related to what evolves after it not what evolves before it. ● Line
And equally related to what evolves before it age1
Node
Example: C is equally related to A and B.
 Influenza (flu) is caused by influenza virus.
 Malaria is caused by protozoa. (human parasite)
 Penicillin is the first antibiotic was isolated from pencillium fungi.
 Hemolytic toxin: Toxin that breaks RBCs.
 A dichotomous key is a tool that allows the user to determine the identity of items in the natural world, such
as trees, wildflowers, mammals, reptiles, rocks, and fish. Keys consist of a series of choices that lead the user
to the correct name of a given item. "Dichotomous" means "divided into two parts"
Ex: Identify the organism shown using the following dichotomous key.
Abdomen has distinct
1a Go to 2
A. Acari segments
Abdomen lacks distinct
B. Araneae 1b Go to 3
segments
C. Opiliones Pedipalps (large “pincers”)
D. Scorpiones
2a in front of shorter legs
Go to 4
E. Pseudoscorpiones Long and slender, leg, no
2b pedipalps
Opiliones
Body is divided into two
3a main parts
Araneae
Body is not divided into two
3b parts and is oval in shape
Acari
No stinger is present at the
4a end of the abdomen
Pseudoscorpiones
A stinger is present at
4b the end of the abdomen
Scorpiones

 All animals from Annelida to mammals have a segmented body.

 Most Diverse kingdom is Protista.
 Huddling, Shivering, and countercurrent are mechanisms for Thermal regulation.
 Factors affection the BMR (basal metabolic rate) are:
1. Temperature. 2. Mass 3. Level of oxygen consumption/concentration 4.Other: Thyroid gland activity.
 Ectothermic organisms maintain their metabolism in low temperature, by decreasing oxygen consumption.

14
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420

Worm

Hydra

Star fish

Jelly fish

Metamorphosis
 The process of transformation from an
immature form to an adult form in two or
more distinct stages.
 Developmental process. ( Meta: Change
morph: Shape sis: process )
 Types of Metamorphosis
a. Complete metamorphosis: includes different forms
than egg and adult.
Ex: Butterfly: Egg- Lava- Pupa- adult.
b. Incomplete metamorphosis: includes limited
development from egg to adult.
Ex: Grass hopper: Egg- Nymph (small version of the
adult)- Adult

15
BioMax SAT 2 TO THE POINT Dr. Amr Alaa 0567573420
Metamorphosis in Frog:
a. Egg.
b. Tadpole: tail (no hind limb) – 2 chambered heart- gills.
c. Froglet: Disappearance of tail and hind limbs start growing.
d. Adult Frog: No tail – Lung instead of gills- 3 chambered heart.

16
 BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Plants are multi-celled, eukaryotic, photosynthetic autotrophs. Their cell walls are made of cellulose, and they store
carbohydrates as starch. Biologists believe that modern, multi-celled plants evolved from the green algae (Chlorophyta) that lived
in fresh water.

Classification of plants

Bryophyta Trachephyta
Non Vascular Vascular
Seedless Trachephyta
● Primitive Seedless Vascular Seed Trachephyta
●Non true plants (no root-no Seed Vascular
stem-no leaves) ● Vascular plant
● Live in moist area. ● True plants
● No vascular tissues. ● Spore forming.
● Absorb water by Diffusion. ● Ex: Ferns-Club mosses Gymnosperm Angiosperm
●Tiny ( No lignin for support) ● Leaves of ferns is called
●Sperms swim in water to Fronds
fertilize the egg.
●Non Flowering (conifers) ●Anthrophyta
●Carpet like in forest, fallen logs
● reproduce by forming naked seed. ●Flowering plants.
● Ex: mosses/Liverworts/
● Reproductive organ: cones. ●Rep.Structure: Flowers
Hornworts
●Needle shaped leaves. ●Seeds are covered by fruits
●Thick cuticle to reduce water loss ●Most diverse and plentiful.
by transpiration. ●Ex: grasses-corn-wheat-
● Cone bearing seeds. oat-lawn grass-rice-roses-
●Ex:Pine-cedar-cycads-redwoods- carrots-oak-peanut
junipers.

Monocotyledon ( Eudicot) dicotyledon

Derived traits: vascular tissue, seeds, and flowers

Monocot seed: one embryo leaf

Dicot seed: two embryo leaf

Monocots provide the food for most of the world.

1
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
EVOLUTIONARY DEVELOPMENTS THAT ENABLED PLANTS TO MOVE TO LAND

1. Cell wall: support the plant against watery environment and maintain the plant cell shape. (made of cellulose)
2. Roots and Roots hair: Absorption of water and nutrients from the soil, store food, and anchoring (fixing) plants in soil.
3. Stomata: Tiny open that play role in gas exchange in plant.
Opened stomata: exchanging photosynthetic gases (CO2 in and O2 out) and cellular respiration gases (CO2out and O2 in)
Closed stomata: minimize water loss via transpiration.
4. Cuticle: Waxy layer made of cutin wax covers the green parts of plant to prevent water loss via transpiration.
5. Gametangia: Protective jacket around gametes and zygote to prevent them from dehydration.
6. Sporopollenin: A tough polymer that is found in the wall of spores and pollen) for protection from dehydration.
7. Reduction of gametophyte generation (n) : because it’s a primitive generation.
8. Seed coat: protection of embryo and has a role in seed dispersal.
9. Stem: Support the upright growth and contains the vascular Tissues (xylem and Phloem) that transport material across the
plant and allows leaves to receive most of light.

Plant Growth
Primary Growth (Vertical) Secondary Growth (horizontal)
↑ Length- By apical meristems in buds of shoots ↑ Width- By Lateral meristems- in woody
and root tips- in both herbaceous and woody plants. plants. (cambium)

ROOT CAP: Protects the tip of root from friction during

soil penetration.

ZONE OF CELL DIVISION (area of cell division)

This zone contains meristem cells that are actively
dividing and are responsible for producing new cells
that grow down into the soil. This is the region you
observed under the microscope in lab when you were
studying cells undergoing mitosis.

ZONE OF ELONGATION
Cells in this zone elongate and are responsible for pushing
the root cap downward and deeper into the soil. (By water
diffusion→ Heavier cells→ roots get deeper in the soil)

ZONE OF DIFFERENTIATION (maturation)

Cells in this zone undergo specialization into three primary
meristems that give rise to three tissue systems in the
plant: the epidermis, ground tissue, and xylem and phloem

2
 BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Roots (Structures and Functions)
Dicot root Monocot root

● Epidermis: outer covering protecting Single layer of cells- ↑ root hairs to ↑ surface are of absorption of water-protection-not
covered by impermeable cutin (wax).

● Cortex: Modified parenchyma cells contain plastids-Support and starch storage-↑ air between cells (aeration)-water absoption.

● Endodermis: (Last layer of cortex) surround vascular cylinder (xylem and phloem)- cells are surrounded by casparian strip
(impermeable to water).

●Vascular cylinder, or stele, makes up the tissues inside the endodermis. The outer part of the vascular cylinder consists of one
to several layers of cells called the pericycle, from which lateral roots arise. Inside the pericycle is the vascular tissue.

Roots have multiple functions: Storage of food-mineral absorption- cell reproduction (apical meristem)- anchorage)

Types of Root
A. Underground roots:
1. Fibrous Root: Monocot (grasses make fine ground cover because they minimize soil erosion)
2. Tap Root: Dicot (carrots, beets, and turnips, are modified for storage)
B. Adventitious Roots: Above ground roots:

1. AERIAL ROOTS. Trees that grow in swamps or salt marshes like mangroves have aerial roots that stick up out of the
water and serve to aerate the root cells. English ivy has aerial roots that enable the ivy to cling to the sides of buildings.
2. PROP ROOTS. Some tall plants like corn have prop roots that grow aboveground out from the base of the stem and
help support the plant. (upper part ˃ lower part) (start from stem base to down)

3
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420

Absorption of Nutrients and Water

Plants use their roots to absorb nutrients and water from the soil. These then must be absorbed by the cells themselves

APOPLAST, SYMPLAST and TRANSCELLULAR (VACOULAR)

The movement of water and solutes across a plant, called lateral movement, is accomplished along the symplast and
apoplast.
●Symplast (slow movement) is a continuous system of cytoplasm of cells interconnected by plasmodesmata by the effect
of osmosis then imbibition (special type of diffusion when water is absorbed by solids-colloids causing an enormous
increase in volume).
●Apoplast (Fast movement by cohesion and adhesion) is the network of cell walls and intercellular spaces within a plant
body that permits extensive extracellular movement of water within a plant.
●Vacuolar: Through vacuoles. (Osmosis)

MYCORRHIZAE
In mature plants of many species where older regions of roots lack root hairs, mycorrhizae supply the plant with water and
minerals. Mycorrhizae are symbiotic structures consisting of the plant's roots with the hyphae (filaments) of a fungus
((recycle nutrients into the soil) that greatly increase the quantity of nutrients that a plant can absorb.

RHIZOBIUM
Rhizobium is a symbiotic bacterium that lives in the nodules on roots of specific legumes. It fixes nitrogen gas from the air
into a form of nitrogen the plant requires.

4
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Stems (Structures and Functions)
Monocot stem Dicot stem

1. The epidermis (outer covering protecting) contains epidermal cells covered with a waxy (fatty) substance called cutin.
The cutin forms a protective layer called the cuticle. Other epidermal cells include various specialized cells such as guard
cells and stinging cells.
2. The cortex (Support and storage) is ground tissue types that lie between the epidermis and the vascular cylinder. Many
of these contain chloroplasts.
3. The vascular cylinder consists of xylem, phloem, and pith (Modified parenchymal cells for support and storage).
The phloem is arranged on the outside of each bundle, while the xylem occupies the inside. In addition, a single layer of
cells between the xylem and phloem may remain undifferentiated and later divides become the vascular cambium
producing new tissue layers.

Position of xylem and phloem in leaves, stems, and roots

Cambium
Cells
PH X PH
Xylem UP Xylem Phloem
Inside outside X X
To the To the
Phloem Down center edges PH X PH
Phloem Phloem
Leaf DownStem
Down Root

5
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Leaves (Structures and Functions) (go to chapter 5)

Parts of Leaf Function

Epidermis—upper and Protection/Cuticle to
lower prevent water loss
Waxy cuticle—made of Minimizes water loss
cutin cells—
Guard Control the opening of
modified epidermal the stomates
cells, contain Photosynthesis
Palisade mesophyll—
chloroplasts
tightly packed
Spongy mesophyll— Photosynthesis
loosely packed
Diffusion and exchange
of gases into and out of
Veins—located in the these
Carrycells
water and
mesophyll nutrients from the soil
to the leaves and
carry sugar, the
product of photo-
Stomata (Stoma) synthesis, from the
When plants carry outleaves to the
cellular rest of
respiration,
they take in oxygen and give off carbon diox ide cells and when they carry
the plant.
out photosynthesis, however, they take in carbon dioxide and give off oxygen and water vapor. Plants exchange these
gases between air spaces in the spongy mesophyll and the exterior of the leaf by opening their stomata. So why do
plants ever close their stomata? If stomata were kept open all the time, the plant would lose so much water through
transpiration (loss of water from the leaf) it could not survive. To minimize excessive water loss, when the sun is
shining brightly and photosynthesis is running at top speed, stomata are open. At night, though, most plants close
their stomata. Plants must keep their stomata open long enough to allow photosynthesis to take place but not so long
that they lose too much water.

Guard cells are modified epithelial cells that control the opening and closing of the stomata (Control Gas exchange)
in response to changes in water pressure. When guard cells absorb water by osmosis and become turgid
(Hypotonic), they curve like hot dogs, causing the stomata to open. When guard cells lose water and become flaccid
(isotonic), the stomata close. (K+ ions and water that are absorbed by guard cells play important role control stomata )

6
 BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Plants Tissues

Dermal Tissues Vascular Tissues: Ground Tissues

Transportation of water and food
Supportive Tissues
●The outer protective tissues Phloem Xylem 1. Parenchyma cells:
● Vascular tissue that is responsible for ● Vascular tissue that is responsible for ●Thin, flexible, primary cell
●Made up of single layer of cells.
the food (sugar) (carbohydrate) the water transportation in vascular
wall only, 1 or 2 vacuoles.
●Special protective structures: plant
transportation (translocation) in ●Modified parenchyma:
● Highly lignified. (↑ lignin)
① Cuticle. vascular plant ● Made up of dead cells (contains no ①Cortex ②Pith.
● No lignin organelles or cytosol) still functional Support and storage.
②Trichomes: modified dermal ①Tracheids(Wood/Lignin/2nd cell wall)
● Made up of living cells
②Vessel elements. 2.Collenchyma cells:
tissue for leaves protection.
①Companion cells ●Water is transported via xylem
●Rigid, flexible, primary cell
●Transparent ②Sieve tube. passively and unidirectional (from
wall, uneven thickening,
roots to other parts) (relay on pores to
●Water is transported via Phloem
●No Chloroplast speed water movement) around vascular bundle and
actively and bidirectional (from leaves Mechanism of water transport: leaf (no break by wind).
●No photosynthesis.
to other parts up and down) 1. Osmosis (soil to root)
2. Capillarity (through root) 3. Sclerenchyma cells:
3. Cohesion and Adhesion (inside ●Tough, rigid, ↑ Lignin, very
Several factors affect the rate of transpiration and loss of water from a leaf. xylem)
thick , Primary and secondary
4. Transpiration (negative pressure to
 High humidity slows down transpiration, while low humidity speeds it up. cell wall, Woody plants.
pull water up for higher distance
 Wind can reduce humidity near the stomata and thereby increase through the evaporation of water)
The transpiration pull-cohesion II. Growth tissue (meristem)
transpiration.
tension theory states that for each Apical meristem (bud): ↑length
 Increased light intensity will increase photosynthesis, thereby increasing both the (tips of shoot and root)
molecule of water that evaporates from
amount of water vapor to be transpired and the rate of transpiration. a leaf by transpiration, another Lateral meristem (cambium):
↑width (diameter) (Between
 Closing stomata stops transpiration molecule of water is drawn in at the
root to replace it. xylem and Phloem)

7
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
PLANTS REPRODUCTION
Plants can reproduce both asexually and sexually.
Asexual Reproduction
Plants can clone themselves or reproduce asexually by vegetative propagation. In this process, a piece of the vegetative
part of a plant, the root, stem, or leaf, produces an entirely new plant genetically identical to the parent plant. Examples
are grafting, cuttings, bulbs, and runners.

Sexual Reproduction: ALTERNATION OF GENERATIONS

The sexual life cycle of plants is characterized

by the alternation of generations in which
haploid (n) and diploid (2n) generations Sporophyte (2N)
alternate with each other. The gametophyte (n)
produces gametes by mitosis that fuse during
fertilization to yield 2n zygotes. Each zygote
develops into a sporophyte (2n) that produces
haploid spores (n) by meiosis. Each haploid
spore forms a new gametophyte, and the cycle
continues. Zygote/
1. Fertilization Embryo Spores (N)
2. Mitosis (Growth) (2N)
Rolled up
3. Meiosis
fronds
4. Mitosis
Gametophyte (N)

Mosses and Other Bryophytes

The gametophyte generation dominates the life cycle. This means that the organism is haploid (n) for most of its life
cycle, and the sporophyte (2n) is dependent on the gametophyte. The gametophyte obtains nutrients by photosynthesis. The
sporophyte obtains its nutrients from the gametophyte.

Ferns
The sporophyte generation is larger and is independent from the gametophyte. Both the gametophyte and the sporophyte
sustain themselves by photosynthesis.

Seed Plants
In the flowering plants (angiosperms), the gametophyte generation exists inside the sporophyte generation and is totally
dependent on the sporophyte.
In a gymnosperm (cone-bearing plant) like the pine tree, the gametophyte generation develops from haploid spores that
are retained within the sporangia.

N.B: Flower is a modified leaf.

8
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Sexual Reproduction in flowering plant

Colored, attracts pollinators

1. Pollination: Landing of pollen grain (male gametophyte) on the stigma

(sticky).Each pollen grain is made of 1 tube nucleus + 2 sperm nuclei .
2. As pollen matures: a pollen tube is formed along the style by the tube
nucleus that opens in the ovule by micropyle.
3. Double Fertilization occurs:
a. 1 sperm nucleus (n) + Egg (n)= Embryo (2n)
b. 1 sperm nucleus (n) + 2 polar bodies (n-n)= Cotyledon/Endosperm (3n)
4. Ovule (female gametophyte)Embryo 2n + Cotyledon/Endosperm 3n) = Seed
A. Monocot seed: Food is stored in endosperm Ex: Coconut has liquid
endosperm.
B. Dicot seed: Food in endosperm transported to cotyledon. (Mature seed lack of endosperm)
5. Ripened Ovary = Fruit (fleshy part)
● For seed germination water is required as it activates
series of hydrolytic enzymes that are responsible for
cracking seed coat. (Germination begins)
Seed Structures:
a. Seed Coat: Protection
b. Embryo: 1. Radical : embryonic root (First part develop)
2. Hypocotyl: Lower embryonic stem
3. Epicotyl: Upper embryonic stem
c. Food: a. Endospore (monocot) b. Cotyledon (Dicot)

9
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Plant Hormones

Plant hormones help coordinate growth, development, and response to environmental stimuli. They are produced in
very small quantities. However, they have a profound effect on the plant because the hormone signal is amplified. A
plant's response to a hormone usually depends not so much on absolute quantities of hormones but on relative amounts

Auxin: (IAA)
 Phototropisms occur due to an unequal distribution of auxins.
 Auxins enhance apical dominance, the preferential growth of a plant upward (toward the sun) rather than laterally. The
terminal bud actually suppresses lateral growth by suppressing development of
CYTOKININS
axial buds.
 Auxins stimulate stem elongation and growth by softening the cell wall. Cytolcinins stimulate cytokinesis
 The first plant hormone discovered was auxin. and cell division.
 A human-made auxin, 2,4-D, is used as a weed killer. They delay senescence (aging) by
 Auxins are used as rooting powder to develop roots quickly in a plant cutting. inhibiting protein breakdown. (Florists
 A synthetic auxin sprayed on tomato plants will induce fruit production spray cut flowers with cytokinins to keep
without pollination. This results in seedless tomatoes. them fresh.)

10
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
Summary

11
BioMax Chapter10: The Plants Dr.Amr Alaa 0567573420
 Photoperiodism: The response to the photoperiod, or day length (Day hours and dark hours). Short-day plants flower when

day length is below a certain threshold, while long-day plants flower when day length is above a certain threshold. Plants

generally fall into three photoperiod categories: long-day plants, short-day plants, and day-neutral plants. Long-day plants

generally flower during the summer months when nights are short and days go longer. Examples of long-day plants are

carnations and oats. Short-day plants flower during seasons that have longer periods of night. They require a continuous

amount of darkness before flower development can begin. Some examples of short-day plants are cotton, soybeans, and

rice. However, some plants referred to as day-neutral plants do not flower based on a particular photoperiod.

 Fertilizers contains minerals as N, P, K. Fertilizer is balanced if all its components are nearly equal.

 Palisade mesophyll is the highest region in plants’ leaf containing Chloroplast.

 The transport system in both higher plant and higher animal shares that both transport fluids containing dissolved

substances. (Blood in animals –Water containing nutrients in pants) .

 The cytoplasmic communication across plant cell walls occurs by the means of plasmodysmata (look Chapter 2).

 Seed dispersal (distribution) by wind, water, animals as birds.

 Increasing the number of stomata specially on the upper surface of the leaves will increase the

transpiration rate.

 The rate of water movement up in a tall vascular plant is depends mostly on transpiration pull.

 Plant respiration is mostly aerobic.

 Dandelion fruit (as shown and figure) that is small light weighted and milkweed seeds are

examples form seed dispersal by wind.

 Flower with bright color and strong fragrance is likely to be pollinated by pollinators. While flower with no bright color or

no fragrance is likely to be pollinated by wind.

 Bushy: highly dense. Removal of terminal buds makes plant especially woody plants, develop to bushier forms.

 Plants tropism take place due to plant hormones.

 Plants grow vertically from the tips of roots and buds of stems only. (apical meristem)

 Sensation is a property of animals, not for plants. Plants respond to stimuli only.

 Annuals - Plants that perform their entire life cycle from seed to flower to seed within a single growing season.
 Biennials - Plants which require two years to complete their life cycle.
 Perennials - Plants that persist for many growing seasons.

12
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
Reproduction: is the process by which organisms are able to produce offspring (progeny) of the same species.

Most animals show definite cycles of reproductive activity, often related to changing seasons. The periodic nature of this
process allows animals to conserve resources and reproduce when environmental conditions favor the survival of
offspring. Reproductive cycles are controlled by a combination of hormonal and environmental cues.

Types of reproduction:
I. Asexual reproduction: (no transfer of genetic materials between different organisms)
 Includes the production of High number of genetically identical offspring.
 In a mother organism: Genetic material is duplicated and cytoplasm is divided and distributed to new daughter
cells.
 There is no expenditure of energy maintaining elaborate reproductive systems or hormonal cycles.
 No Genetic variation (suitable for an organism live in a stable environment).
 Examples:
a. Binary fission: Bacteria. (Equally distribution of cytoplasm in daughter cells)
b. Multiple fission: at the cellular level occurs in many protists, e.g. sporozoans and algae). The nucleus of the
parent cell divides several times by mitosis, producing several nuclei. The cytoplasm then separates,
creating multiple daughter cells.
c. Budding: Yeast-Hydra
d. Fragmentation: Planaria : The process of breaking up of parent animal into small parts, each of which can
grow into a new complete individual.
e. Regeneration: Star Fish: The ability of an organism to grow its lost parts.
f. Parthenogenesis: Honey bees. A process in which the egg develops without being fertilized and adult males
that result are haploid. This is characteristic of honeybees, where haploid individuals are male drones and
diploid individuals are female workers. (Male bees (XO) female bees (XX) No Y chromosomes)
g. Vegetative propagation: In plants

1
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
II. Sexual reproduction: (Transfer of genetic materials between different organisms)
 Includes the production of few numbers of that are NOT genetically identical
offspring(share the characters of both parents)
 Shuffling of alleles or Genetic recombination
 Play important role in Genetic variation (suitable for an organism live in an
unstable environment).
 There is an expenditure of energy maintaining elaborate reproductive
systems or hormonal cycles.
 Hermaphrodite: A special case of sexual reproduction animal can mate with
any animal of their species. Both animals act as male and female, and both
donate and receive sperm. (Worms)
 Conjugation in bacteria is sorted as sexual reproduction as the genetic
material is transferred from one species to another.
 During sexual reproduction in most of organisms, a small flagellated haploid sperm (n) fertilizes a larger,
nonmotile haploid egg (n) to form a diploid (2n) zygote.

Types of Fertilization and Development

Animal Fertilization Development Number of Eggs Parental Care

Fish External External Many None

Amphibian External External Many None

Reptiles Internal External (inside the egg) Few Some

Birds Internal External (inside the egg) Few Much

Mammals Internal Internal Few Much

Human Reproductive Anatomy

I. Female Reproductive System
The female reproductive system consists of the following structures:
1. Ovary. This is the organ where ova (singular, ovum), or eggs, are
produced. Each female has two ovaries.

2. Oviduct (or fallopian tube). Eggs move from the ovary to the uterus
through the oviduct. There are two oviducts, one for each ovary.
Oviduct is the site of fertilization.
3. Uterus. A fertilized ovum implants (attaches) on the inside wall, or
endometrium, of the uterus. Development of the embryo occurs here until
birth.
4. Vagina. (Birth canal; during labor and delivery) At birth, the fetus passes
through the cervix (an opening in the uterus), through the vagina, and out
of the body.

2
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
II. Male Reproductive System:
The male reproductive system consists of the following structures:

1. Testis (plural, testes). Each of the two testes consists of

seminiferous tubules for the production of sperm and interstitial
cells which produce male sex hormones (testosterone and other
androgens). The two testes are contained in a Skin, the scrotum,
which hangs outside the body (Outside the abdominal cavity). The
external scrotum provides a temperature of about 2° C below that of
the body cavity, a condition necessary for the development of sperm.

2. Epididymis. This coiled tube, one attached to each testis, is the site
for final maturation and storage of the sperm.

3. Vas deferens (plural, vasa deferentia). Each of these two tubes

transfers sperm from one epididymis to the urethra. Sperm exit the
penis through the urethra.

4. Seminal vesicles. During ejaculation, these two glands secrete into

the vas deferens mucus (which provides a liquid medium for the sperm), fructose (which provides energy for the
sperm), and prostaglandins (which stimulate uterine contractions that help sperm move into the uterus).

5. Prostate gland. This gland secretes a milky alkaline fluid into the urethra and serves to neutralize the acidity of urine
that may still be in the urethra, as well as the acidity of the vagina

6. Bulbourethral glands (or Cowper’s glands). These two glands secrete a small amount of fluid of unknown function
into the urethra.

7. Penis. The urethra passes through the penis and serves to transport semen, the fluid containing sperm and
secretions, into the vagina. It also serves in the transport of urine out of the body.

Sperm Structures
Sperm are compact packages of DNA specialized for the effective delivery of the male genome. They consist of the
following structures:
1. Sperm head. The head of the sperm contains the haploid nucleus with
23 chromosomes (in humans). At the tip of the sperm head is the
acrosome, a lysosome containing enzymes which are used to penetrate
the egg. The acrosome originates from Golgi body vesicles that fuse to
form a single lysosome.

2. Midpiece. The midpiece, is characterized by mitochondria that spiral

around the flagellum and supply ATP for flagellar movement.

3. Tail. The remainder of the flagellum, behind the midpiece, is the tail. Sperm are propelled by whiplike motion of the
tail and midpiece.

3
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
Hormonal Control of Human Reproduction
The human female reproductive cycle is characterized by events in the ovary (ovarian cycle) and the uterus (menstrual
cycle). The purpose of these cycles is to produce an egg and
prepare the uterus for the implantation of the egg, should it
become fertilized. The activities of the ovary and the uterus are
coordinated by negative and positive feedback responses involving
gonadotropin releasing hormone (GnRH) from the hypothalamus,
follicle stimulating hormone (FSH) and luteinizing hormone (LH)
from the anterior pituitary, and the hormones estrogen and
progesterone from the follicle and corpus luteum.

The menstrual cycle (menses) is a series of changes in the ovary

and uterus that is controlled by the interaction of hormones.
Human females release a gamete at intervals that average about
every 28 days from puberty until menopause. The release of an egg
(really a secondary oocyte) is one of four stages of the cycle. Then
the thickening of the endometrium of the uterus in preparation for
implantation of a fertilized egg and the shedding of the
endometrium if implantation does not occur.

The menstrual cycle is controlled by both positive and negative

feedback mechanism.

1. FOLLICULAR PHASE
Several tiny cavities called follicles in the ovaries
grow and secrete increasing amounts of estrogens
in response to follicle-stimulating hormone (FSH)
from the anterior pituitary. Growing follicle
produces estrogen.

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

3. LUTEAL PHASE
After ovulation, the corpus luteum (the cavity of the
follicle left behind) forms and secretes estrogen and
progesterone that thicken the endometrium (lining)
of the uterus. New blood vessels are formed.

4. MENSTRUATION
If implantation of an embryo does not occur, the
buildup of the lining of the uterus breaks down ,
new blood vessels are shed. Tissue and some blood
are discharged from the vagina. This bleeding is
commonly called the period.

4
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420

The male reproductive cycle is regulated by the same hormones that regulate the female reproductive cycle. In
response to GnRH from the hypothalamus, the anterior pituitary in males secretes FSH and LH. (In males, LH is also
called ICSH, interstitial cell stimulating hormone). LH stimulates the interstitial cells in the testes to produce
testosterone and other male sex hormones (androgens). Under the influence of FSH and testosterone, Sertoli cells
promote the development of sperm. In contrast to females, however, hormone and gamete production are constant
during the reproductive life of the male.

In addition to influencing the production of sperm and eggs, testosterone and estrogen stimulate the development of
the secondary sex characteristics in males and females, respectively.

Spermatogenesis (At puberty till the end

of life)
Note that each spermatogonium cell undergoes meiosis to produce
four active, equal-sized sperm.

Oogenesis (From birth till menopause)

5
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
EMBRYONIC DEVELOPMENT

1. Fertilization. Fertilization occurs when the sperm penetrates egg.

2. Cleavage. The zygote now begins a series of cleavage divisions, rapid cell divisions without cell growth. As a result,
each of the resulting cells, called blastomeres, contains substantially less cytoplasm than the original zygote.

3. Morula. Successive cleavage divisions result in a solid ball of cells called a morula.

4. Blastula. (2 germ layers) As cell divisions continue, liquid fills the morula and pushes the cells out to form a circular
cavity surrounded by a single layer of cells. This hollow sphere of cells is called the blastula, and the cavity is the
blastocoel. Stage of implantation in uterus

5. Gastrula. Formation of the gastrula, or gastrulation, Three germ layers. The ectoderm, mesoderm, and endoderm
(outside, middle, and inside layers, respectively) are the primary germ layers from which all subsequent tissues develop.

6. Organogenesis. As cells continue to divide after gastrulation, they become different from one another (cell
differentiation), taking on characteristics of specific tissues and organs. This development of organs is called
organogenesis. (Stage of differentiation)
 The ectoderm will become the skin and the nervous system.
 The endoderm will form the viscera, including the lungs, liver, and digestive organs.
 The mesoderm will give rise to the muscle, blood, and bones. (ligaments and tendons)

7. Extraembryonic membrane development. In birds, reptiles, and humans, collectively called the amniotes,
extraembryonic (outside the embryo proper) membranes develop, as follows:

Organism Chorine Allantois Amnion Yolk Sac

Cavity filled with fluid
External membrane Store wasters (uric
Reptiles/Birds cushions embryo Nutrition
Gas exchange acids)
(protection)
Transport products to
Cavity filled with fluid
Form Placental with placenta. (Gases-
Human cushions embryo Empty
maternal tissues. nutrients-wastes)
(protection)

6
BioMax Chapter12: Reproduction Dr.Amr Alaa 0567573420
Summary
 Eggs All Terrestrial animals that lay eggs, are sounded by shell to the protect the eggs from
dehydration.
 Estrogen hormone has the following functions
a. It controls the secondary sex characters in female
b. It inhibits the production of some hormones of anterior pituitary (FSH by negative feedback)
c. It presents in females at variables levels within menstrual cycle.
 Main process during the formation of egg (ovum) and sperm is meiosis.
 A woman whose ovulation is normal, can be infertile because:
a. Her fallopian tubes are blocked.
b. Sperm movement is inhibited by an incompatible pH of fluids in vagina or uterus.
 Using exogenous sources (external) of sex hormones (Testosterone -estrogen) may cause that the
gonads become small or atrophy.
 Separation of homologous chromosomes is essential step in the formation of sperm and egg in
animals.
 An important advantage of sexual reproduction over asexual reproduction is that sexual
reproduction gives the chance to alleles to be shuffled into new combinations.
 Woman can conceive (got pregnant) shortly after the release of egg.
 Sexual reproduction is evolutionary important because it results in genetic variation among
offspring.
 Meiosis in male takes place in seminiferous tubules of testis.
 One egg is released from female ovaries per cycle.
 Urethra function a common tract for both urine and sperms in male only.
 Placenta of female human has no role in conveying nerve impulses.

7
BioMax Chapter 13: Immune System Dr.Amr Alaa 0567573420

Immunity: 1. Fight infection 2. Prevent infection.

Pathogens: (patho=disease / gem= produce) agents that can cause diseases. Ex: virus–bacterial-Fungi-
Protozoa)

NONSPECIFIC DEFENSE
The nonspecific immune system consists of two lines of defense.

First Line of Defense

The first line of nonspecific defense is a barrier that helps prevent pathogens from entering the body. The body has several
different types of barriers:

 Skin that blocks pathogens

 Mucous membranes that release mucus to trap microbes
 Cilia in the respiratory system that sweep out mucus with its trapped microbes
 Stomach acid that kills germs that enter through the nose and mouth
Second Line of Defense
Microbes that get into the body encounter the second line of nonspecific defense. It is meant to limit the spread of
invaders in advance of specific immune responses. There are three types.
1. INFLAMMATORY RESPONSE. It is characterized by swelling, redness, soreness, and increased warmth in the area. The
purpose of this process is to increase the blood supply to the area, thus increasing nutrients—including oxygen and
white blood cells to fight disease. The inflammatory response works in several ways.
 Histamine triggers vasodilation (enlargement of blood vessels), which increases blood supply to the area, bringing
more phagocytes to gobble up germs. Histamine is also responsible for the symptoms of the common cold: sneezing,
coughing, redness, and itching and runny nose and eyes—all an attempt to rid the body of invaders.
 Increased body temperature speeds up the immune system and makes it more difficult for microbes to function.
2. PHAGOCYTES. These gobble up invading microbes. Macrophages ("giant eaters") are a type of white blood cell that
extend pseudopods and engulf huge numbers of microbes over a long period of time. (antigen presenting cell)
3. INTERFERONS (from liver). These chemicals are released by the immune system to block against viral infections.

SPECIFIC DEFENSE THIRD LINE OF DEFENSE

The third line of defense is specific and consists of lymphocytes. There are two types of lymphocytes, B lymphocytes and T
lymphocytes. Both originate in the bone marrow. Once mature, both cell types circulate in the blood, lymph, and lymphatic
tissue: spleen, lymph nodes, tonsils, and adenoids. Both recognize different specific antigens (germs) (Strictly speaking, an
antigen is anything that triggers an immune response).
1. B LYMPHOCYTES. These produce antibodies (immunoglobulin) against a specific antigen in what is called a
humoral response.
2. T LYMPHOCYTES. These fight pathogens by hand-to-hand combat in what is called a cell-mediated response

1
BioMax Chapter 13: Immune System Dr.Amr Alaa 0567573420

Antibodies
Antibodies are part of the third line of defense—the specific immune response. Each antibody has the ability to bind
to only one particular antigen. For example, antibodies against influenza bind to and neutralize only influenza virus;
they have no effect on the polio virus, for example. Antibodies neutralize antigens by binding to them and by
forming an antigen-antibody complex that can then be gobbled up by a phagocyte.

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

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

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

TYPES OF IMMUNITY
Passive immunity (without the exposure of disease-causing agents) is temporary.

 Antibodies are borrowed and do not survive for long.

 Examples are maternal antibodies that pass through the placenta to the developing fetus or that pass through breast
milk to the baby. The first milk that a newborn receives from mother is called colostrum(first mother’s milk) and is 100
percent antibodies.

Active immunity (by the exposure to the disease-causing agents) is permanent.

 You make the antibodies yourself.
 An individual makes his or her own antibodies after being ill and recovering or after being given an immunization
or vaccine. A vaccine contains either dead or live viruses or enough of the outercoat of a virus to stimulate a full
immune response and to impart lifelong immunity.

2
BioMax Chapter 13: Immune System Dr.Amr Alaa 0567573420
ABO Blood Types
ABO antibodies circulate in the plasma of the blood
and bind with ABO antigens in the event of an
improper transfusion. Certain danger from a
transfusion comes when the recipient has antibodies
to the donor's antigens. However, before someone
receives a transfusion of blood, samples of the
recipient's and the donor's blood must be mixed in
the lab to determine and ensure compatibility. This
is called a cross-match.
Blood type O is known as the universal donor
because it has no blood cell antigens to be clumped
by the recipient's blood. Blood type AB is known as the universal recipient because there are no antibodies to clump the
donor's blood.

There are four different human blood types: A, B, O, and AB. Blood types are inherited, and your blood type does not
change during your lifetime. Agglutination of of blood will take place if wrong blood transfusion happens.

AIDS Virus
AIDS stands for acquired immune deficiency syndrome. People with AIDS are highly susceptible to opportunistic
diseases, infections, and cancers that take advantage of a collapsed immune system. The virus that causes AIDS, HIV
(human immunodeficiency virus) mainly attacks helper T cells. HIV is a retrovirus. Once inside a cell, it transcribes itself
in reverse. That means that the viral RNA uses the enzyme reverse transcriptase to make DNA. This is the opposite of the
typical DNA transcribing mRNA. The host cell then integrates this newly formed DNA into its own genome.

ALLERGIES, ANTIBIOTICS, VACCINES, AND AUTOIMMUNE

DISEASES
 Allergies are hypersensitive immune responses to certain substances that normally cause no disease called
allergens. They involve the release of excessive amounts of histamine, an anti-inflammatory agent, which causes
blood vessels to dilate. A normal allergic reaction involves redness, runny nose, and itchy eyes. Taking antihistamines
can normally counteract these symptoms. However, sometimes an acute allergic response can result in a life-
threatening response called anaphylactic shock that can result in death within minutes.
 Antibiotics are medicines that kill bacteria or fungi. While vaccines are given to prevent illness caused by
viruses, antibiotics are administered after a person is sick. They cure the disease.
 Vaccines prevent viral infections. There is no cure for viral infections as there is for bacterial infections. New
vaccines and treatments are always being developed. In fact, a new vaccine against the human papilloma virus (HPV)
that causes cervical cancer is now available. It is the first vaccine designed to prevent cancer. It is recommended for
girls between the ages of 11 and 12.
Autoimmune diseases such as multiple sclerosis, lupus, rheumatoid arthritis, and juvenile diabetes are caused by a
terrible mistake of the immune system. The system cannot properly distinguish between self and nonself. Instead, it
perceives certain structures in the body as foreign and produces antibodies to attack them. In the case of multiple sclerosis
(attach myline sheath of nerves), the immune system attacks the myelin sheath surrounding certain neurons. Treatment for
these varies with the disease. In the case of juvenile diabetes, the treatment is shots of insulin. In other diseases, the goal is to
reduce symptoms by suppressing the immune system while maintaining the body's ability to fight disease

3
BioMax Chapter 13: Immune System Dr.Amr Alaa 0567573420
Summary
 Blood cells are made is bone marrow of long bones as Humorous and femur.

 Antibiotic sensitivity test is used to determine the most suitable antibiotic killing a specific kind of bacteria.
Procedures: 1. Use a petri dish to cultivate a special strain of bacteria.
2. Add paper discs containing the samples of an antibiotic in each discs.
3. Put the petri dish in the incubator for 24 hours at suitable temperature.
4. Findings: Look to the diagram below.
5. Result: Antibiotic in disc C is best for killing this strain of bacteria (shows the greatest zone of
Inhibition).

If this result above appears,

means that this strain of bacteria
builds an antibiotic resistance to
the antibiotic in disc B
4
BioMax Chapter 13: Immune System Dr.Amr Alaa 0567573420
• Rh antigen is found on the red blood cells of 95 % of organisms ( Rh+)
• If blood containing the ( Rh-) is mixed with blood containing (Rh+) agglutination occurs
• The most serious problem is when a mother with Rh- marries an Rh + father the baby will inherit the
dominant Rh+
• On delivery some of the fetus blood will pass to the mother resulting in the production of antibodies
against Rh+
• During the 2nd pregnancy the fetus will receive from the placenta the antibodies of the Rh+ and he may
day
To solve this problem the mother should be injected with antibodies of Rh+ before her body develops normal
antibodies to destroy the passing antigens from the baby

5
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
Behavior is defined as the way an organism responds to changes in its internal or external (stimuli) environment.

Difference between irritability and behavior:

 Irritability: sensing stimuli and respond to it. (Done by all living organism)
 Behavior: is the way or pattern of response.
 Usually behaviors are carried out in response to a stimulus, a change in the environment. A monkey eats a
banana (behavior) in response to hunger (stimulus).

Types of behavior:
1. Innate (inborn) (Instinctual), such as running for shelter upon hearing a loud noise.
2.Learned, (based on experience) such as one child sharing her toys with another child.

Importance of behavior: An organism's behavior is important for its survival and for the successful production of
offspring.

Ethology: Studying behavior

 Karl von Frisch: Von Frisch is known for his extensive studies of honeybee communication and his famous
description of the bee waggle dance.
 Konrad Lorenz: famous for his work with imprinting.
 Niko Tinbergen: is known for his elucidation of the fixed action pattern,

I. Innate behavior:
1. A fixed action pattern (FAP) is an innate, highly stereotypical behavior that, once begun, is continued to completion no
matter how useless or silly looking. FAPs are initiated by external stimuli called sign stimuli. When these stimuli are
exchanged between members of the same species, they are known as releasers. An example of a FAP studied by Tinbergen
involves the stickleback fish, which attacks other males that invade its territory. The releaser for the attack is the red belly of
the intruder. The stickleback will not attack an invading male stickleback lacking a red underbelly, but it will readily attack a
non-fish like wooden model as long as a splash of red is visible.
Other examples of FAP
 Baby bird opens its mouth, a mother bird will put food in it.
 Newly hatched ducks swim when they enter the water.
 Mating rituals,
 Displays of territoriality
 Suckling behaviors.
 Graylag goose sees an egg outside her nest, she will methodically roll the egg back into the nest with a series of
maneuvers using her beak.

II. Learning behavior:

Learning is a sophisticated process in which the responses of the organism are modified as a result of experience. The
capacity to learn can be tied to length of life and complexity of the brain. If the animal has a very short life span, like a fruit
fly, it has no time to learn, even if it has the ability. It must therefore rely on fixed action patterns. In contrast, if the animal
lives a long time and has a complex brain, then a large part of its behavior is dependent on prior experience and learning.
1. Habituation:
One of the simplest forms of learning in which an animal comes to ignore a persistent non harmful stimulus. If you tap the
dish containing a hydra, it will quickly shrink and become immobile. If you keep tapping, after a while the hydra will begin
to ignore the tapping, elongate, and continue moving about. It has become habituated or used to the stimulus.

1
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
2. Associative learning
a. Classical conditioning, a type of associative learning, is widely accepted because of the ingenious work of Ivan Pavlov
in the 1920s. Normally, dogs salivate when exposed to food. Pavlov trained dogs to associate the sound of a bell with food.
The result of this conditioning was that dogs would salivate, an automatic response, upon merely hearing the sound of the
bell even though no food was present.
b. Operant conditioning, also called trial and error learning (Reward and punishment, Training), is another type of
associative learning. An animal learns to associate one of its own behaviors with a reward or punishment and then repeats or
avoids that behavior. The best-known studies involving operant conditioning were done by B. F. Skinner in the 1930s. In
one study, a rat was placed into a cage containing a lever that released a pellet of food. At first, the rat would depress the
lever only by accident and would receive food as a reward. The rat soon learned to associate the lever with the food and
would depress the lever at will. Similarly, an animal can learn to carry out a behavior to avoid punishment. Such systems of
rewards and punishment are the basis of most animal training.
c. Spatial learning is another form of associative learning. It occurs when an animal associates attributes of a location
(landmarks) with the reward it gains by being able to identify and return to that location. Nikolaas Tinbergen observed that
wasps were able to associate nearby markers (pinecones) with the location of their nests. When Tinbergen removed the
markers, the wasps were unable to locate their nests.
3. Imprinting is learning that occurs during a sensitive or critical period in the early life of an individual and is irreversible
for the length of that period. When you see ducklings following closely behind their mother, you are seeing the result of
successful imprinting. Mother-offspring bonding in animals that depend on parental care is critical to the safety and
development of the offspring. If the pair does not bond, the parent will not care for the offspring and the offspring will die. At
the end of the juvenile period, when the offspring can survive without the parent, the response disappears. (innate program
for learning)

Classic imprinting experiments were carried out by Konrad Lorenz with geese. Geese hatchlings will follow the first thing
they see that moves. Although the object is usually the mother goose, it can be a box tied to a string or in the case of the
classic experiment, it was Konrad Lorenz himself. Lorenz was the first thing the hatchlings saw and they became imprinted
on the scientist. Wherever he went, they followed.

4. Insight: The highest form of learning is insight learning. Insight refers to the ability to approach new situations and
figure out how to deal with them. As animals go, human beings are pretty good at insight, and so are some other animals,
like cows. Another word for insight is reasoning.

5. Observational learning occurs when animals copy the behavior of another animal without having experienced any prior
positive reinforcement with the behavior. Japanese monkeys usually remove sand from a potato by holding the potato in one
hand and brushing sand away with the other hand. One monkey discovered that she could more easily brush the sand away if
she held the potato in water. Through observational learning, nearly all of the other monkeys in the troop learned the
behavior.

2
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
In general, inherited (Innate) behaviors and learning capabilities of animals have evolved because they increase
individual fitness.

Associative learning allows individuals to benefit from exposure to unexpected (or novel) repeated events. Once they form
an association with the event, they can respond to the next occurrence more efficiently. Habituation allows individuals to
ignore repetitive events which, from experience, they know are inconsequential. As a result, the animals can remain focused
on other, more meaningful events.

Observational learning and insight provide a mechanism to learn new behaviors in response to unexpected events without
receiving reinforcement. This reduces the time required for new behaviors to be acquired.

SOCIAL BEHAVIOR

Social behavior is any kind of interaction between two or more animals, usually of the same species. It is a relatively new
--
field of study, only developed in the 1960s. Types of social behaviors are cooperation, agonistic, dominance hierarchies,
Territoriality, and altruism.
1. Cooperation enables the individuals to carry out a behavior, such as hunting, which they can do as a group more
successfully than they can do separately. Lions or wild dogs will hunt in a pack, enabling them to bring down an animal
larger than an individual could ever bring down alone.
2. Agonistic behavior is aggressive behavior. It involves a variety of threats or actual combat to settle disputes between
individuals. These disputes are commonly over access to food, mates, or shelter. It involves both real aggressive behavior
as well as ritualistic or symbolic behavior. One combatant does not have to kill the other. The use of symbolic behavior
often prevents serious harm. A dog shows aggression by baring its teeth and erecting its ears and hair. It stands upright to
appear taller and looks directly at its opponent. If the aggressor succeeds in scaring the opponent, the loser engages in
submissive behavior that says, "You win, I give up." Examples of submissive behaviors are looking down or away from
the winner. Submissive dogs or wolves put their tail between their legs and run off. Once two individuals have settled a
dispute and established their relationship by agonistic behavior, future encounters between them usually do not involve
combat or posturing.
3. Dominance hierarchies are pecking order behaviors that dictate the social position of an animal in a culture. This is
commonly seen in hens where the alpha animal (top-ranked) controls the behaviors of all the others. The next in line, the
beta animal, controls all others except the alpha animal. Each animal threatens all animals beneath it in the pecking
order. The top-ranked animal is assured of first choice of any resource, including food after a kill, the best territory, or
the most-fit mate. (must not lead to death or serious injuries)
4. A territory is an area an organism defends and from which other members of the community are excluded. Territories are
established and defended by agonistic behaviors. They are used for capturing food, mating, and rearing young. The size of
the territory varies with its function and the amount of resources available. Territories insure their owners adequate food and
a place to mate and rear their young

5. Altruism is a behavior that reduces an individual's reproductive fitness (the animal may die) while increasing the fitness
of the group or family. When a worker honeybee stings an intruder in defense of the hive, the worker bee usually dies.
However, it increases the fitness of the queen bee that lays all the eggs. How can altruism evolve if the altruistic individuals?
The answer is called kin selection. When an individual sacrifices itself for the family, it is sacrificing itself for relatives (the
kin), which share similar genes. The kin are selected as the recipients of the altruistic behavior. They are saved and can pass
on their genes. Altruism evolved because it increases the number of copies of a gene common to a related group (natural
selection).

3
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
Communication in Animals

Communication in animals is commonly used in species recognition, in mating behavior, and in organizing social
behavior. Communication occurs through the following mechanisms:

1. Chemical. Chemicals used for communication are called pheromones.

• Reproductively receptive female moths attract male moths by emitting releaser pheromones into the air.
• Ants secrete a releaser pheromone to mark trails that guide other ants to food.
• Queen bees, queen termites, and queen ants secrete primer pheromones that are eaten by workers. The pheromone
prevents development of reproductive ability.
• Many male mammals spray urine throughout their territories (especially along their borders) to warn other animals of
the same species to keep out.

2. Visual. Many visual displays are observed in animals during displays of aggression (agonistic behavior) or during
courtship preceding reproduction.

3. Auditory. Sounds are commonly used to communicate over long distances, through water, and at night.
Whales’ songs produced at infrasound frequencies (below the audible range of humans) can be heard for hundreds of
miles by other whales.
Related female elephants form herds and use infrasound for greetings, for communicating danger, and for singing
songs that announce reproductive readiness to solitary males who may be miles away.
• Calls of male frogs and male crickets ward off male rivals, attract females, and function in species recognition.
• Songs of male birds provide for species recognition, a display to attract mates, and a warning to other males of
territorial boundaries.

4. Tactile. Touching is common in social bonding, infant care, grooming, and mating. Wolves greet the dominant male
in the pack by licking his muzzle.

Foraging Behaviors (Optimality Hypothesis)

Numerous techniques have evolved to optimize feeding. The goal is to maximize the amount of food eaten while minimizing
the energy expended to obtain it and minimizing the risks of being injured or eaten. Some foraging behaviors follow:

1. Herds, flocks, and schools provide several advantages, as follows:

• Concealment. Most individuals in the flock are hidden from view.
• Vigilance. In a group, individuals can trade off foraging and watching for predators. Further, it is easier to detect
predators if many individuals are watching.
• Defense. A group of individuals can shield their young or mob their predator.

2. Packs enable members to corner and successfully attack large prey.

3. Search images help animals find favored or plentiful food. Birds can easily find food they are accustomed to eating
because they seek a specific, perhaps abbreviated, image of the target.

4
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
Animal Movement
Three kinds of movements are commonly found among animals:

1. Kinesis (plural, kineses) is an undirected (without direction) change in speed of an animal’s movement in response to a
stimulus. The animal slows down in a favorable environment or speeds up in an unfavorable environment. As a result, the
animal remains longer in favorable environments.

2. Taxis (plural, taxes) is a directed movement in response to a stimulus. Movement is directed either toward or away
from the stimulus. Movement in response to light is called phototaxis. Movement in response to chemicals is called
chemotaxis.
• Moths move toward lights at night.
• Sharks move toward food when food odors reach them by diffusion or by bulk flow (ocean currents).
• Female mosquitos find mammals (on which they feed) by moving toward CO2 and lactic acid.)
◦ Movement of WBCs to microorganism and Amoeba to food. (chemotaxis)

3. Migration is the long-distance, seasonal movement of animals. It is usually in response to seasonal availability of
food or degradation of environmental conditions (they usually occur together).
• Whales, birds, elk, insects, and bats are examples of animals that migrate to warmer climates

Turning Behavior in Plants: The Tropisms

The word tropism is derived from the Greek word tropos, which means “to turn,” so tropisms are all turning behaviors
in response to particular stimuli. There are three stimuli that can cause turning: light, gravity, and touch.

Auxin Hormone (IAA) is a plant hormone that is responsible for tropism.

Plants need light. If a plant sits in a room in which sunlight comes in through one window, the plant will, on its own,
bend toward the window. When a plant bends toward light, we call it phototropism (photo = light).

Plants need minerals and water from the earth. Plant roots therefore like to grow downward, in the direction of the
gravitational pull. When roots grow downward, toward the earth, it’s called positive gravitropism. Plant stems and
leaves, on the other hand, grow up, away from the earth. This is called negative gravitropism. Gravitropism is
sometimes referred to as geotropism.

Lastly some plants will grow along a wall or trellis. The physical touch of the plant on the object causes it to grow in that
direction. This is known as thigmotropism (thigmo = touch).

Also, these turning behaviors are induced by plant hormones, called auxins. So remember:

Phototropism means … growth of a plant toward light.

Positive gravitropism means … growth of the roots downward, toward the earth.
Negative gravitropism means … growth of the plant stem upward, away from the earth.
Thigmotropism means … growth of the plant along a surface.

5
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
Animals and Plants Can Tell Time: Biological Clocks
Imagine that a plant predictably opens its leaves at 6 A.M., closes them at noon, opens them again at 6 P.M., and closes them
again at midnight. Imagine, furthermore, that the plant does this even if it is kept in the dark all day and all night. This plant
seems somehow to know when to open and close its leaves, even without being exposed to changing conditions of sunlight.
Something in the plant keeps time. Circadian Rhythm Daily cycles of light and dark set an organism’s biological clock to
approximately 24 hours.
 Day and night rhythms: Diurnal: animals active during day time. Nocturnal: animals active at night.
 Human biological clock is maintained by melatonin.
 Hibernation: extend the period of sleep (dormancy) in winter (minimize body temperature and metabolism) (saving
energy)
 Estivation: extend the period of sleep (dormancy) in summer (prevent excessive water loss)
 Courtship and mating often occur in spring.
 Migration: long-distance seasonal movement in response to seasonal changes in food availability.

The behavior that arises from biological clocks is instinctive; it isn’t learned.

When a biological clock makes an organism do something on a daily basis, it is referred to as a circadian rhythm. The plant
that opens and closes its leaves predictably several times daily exhibits a circadian rhythm. A plant that loses its leaves in the
fall and regrows them in the spring does NOT reflect a circadian rhythm. The pattern is seasonal, not daily.

Organisms Communicate: Pheromones

Many animals communicate with other members of their species by releasing chemicals called pheromones. A pheromone
is any chemical that (1) is released by one member of a species and (2) affects the behavior of other members of the species
in a predictable way.

Some female animals release chemicals that attract males, and these chemicals are also pheromones. On discovering danger,
some animals release chemicals that signal others of their species to stay away, and these chemicals, too, are pheromones. In
some species, an animal’s dead body releases a chemical that causes survivors of the species to bury it. That chemical is a
pheromone as well.

6
BioMax Chapter 14: Animal Behavior Dr.Amr Alaa 0567573420
Summary

Adaptation is centered on an organism’s ability to change its physical and chemical make up to adjust to its habitat. This

takes a long time to achieve and usually affects the whole group to which it belongs. It is part of the evolution process, which

all living things must undergo in order to cope with the ever changing planet. One good example of adaptation is the camel

and its ability to survive for long periods of time in the desert with very little water.

Acclimation is a form of adaptation that an organism undergoes when transferred to a different habitat. It doesn’t take as

long as evolutionary adaptation and it doesn’t affect the body composition of the entire species. Adjustment is made by

modifying physical reactions to environmental changes, like shivering when exposed to cold weather.

7
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Ecology is the study of the distribution and interactions between living organisms ( Biotic factors) and physical
environment (abiotic factors = non-living) within an area
The following terms provide a foundation for the study of ecology:
1. A population is a group of individuals all of the same species living in the same local area.

2. A community is a group of different populations living in the same local area.

3. An ecosystem describes the interrelationships between the organisms in a community (Biotic=Living) and their

physical environment (abiotic=nonliving).

4. The biosphere is composed of all the regions of the earth that contain living things.

5. The habitat of an organism is the type of place where it usually lives. A description of the habitat may include

other organisms that live there (Biotic factors) as well as the physical and chemical characteristics of the

environment (Abiotic factors) (such as temperature, soil quality, or water salinity).

6. The niche of an organism describes all the biotic (living) and abiotic (nonliving) resources in the environment

used by an organism. Or The organism’s total interrelationships within its environment.

Population Ecology
Population ecology is the study of the growth, abundance, and distribution of populations. Population abundance
and distribution are described by the following terms:

1. The size of a population, symbolically represented by N, is the total number of individuals in the population. Size of
the population depends on
a. The ratio between Birth rate and Death rate. B. Direction of Migration. (Emigration or immigration)

N.B: Migration affects also food change

2. The density of a population is the total number of individuals per area or volume occupied. One sampling technique
commonly used to estimate the size of a population is called mark and recapture. In this technique, organisms are
captured, tagged, and then released. Some time later, the same process is repeated and a special mathematical formula
is used to determine the density of the population.
3. Dispersion describes how individuals in a population are distributed. They may be clumped (like humans in
cities/Fish)), uniform (like trees in an orchard), or random (like trees in some forests).

1
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
4. Age structure is a description of the abundance of individuals of each
age. It is often graphically expressed in an age structure diagram.
Horizontal bars or tiers of the diagram represent the frequency of
individuals in a particular age group. A vertical line down the center of
each tier divides each age group into males and females.
A rapidly growing population is indicated when a large proportion of the
population is young. Therefore, age structure diagrams that are
pyramid-shaped, with tiers larger at the base and narrower at the top,
indicate rapidly growing populations. In contrast, age structure
diagrams with tiers of equal width represent populations that are
stable, with little or no population growth (zero population growth, or
ZPG).
5. Survivorship curves describe how mortality of individuals in a species
varies during their lifetimes

• Type I (Convex curve) high age-specific survival probability in early

and middle life, followed by a rapid decline in survival in later life.
(Much parental care-immunity) Human, Primates, elephants, and
other large mammals

• Type II curves describe organisms in which the length of survivorship

is random, that is, the likelihood of death is the same at any age. Song
birds. Rodents and certain invertebrates (such as Hydra) are
examples.

• Type III curves describe species in which most individuals die young,
with only a relative few surviving to reproductive age and beyond.
Concave curves have the greatest mortality (lowest age-specific
survival) early in life, with relatively low rates of death (high probability of survival) for those surviving this bottleneck.
This type of curve is characteristic of species that produce a large number of offspring. This includes most marine
invertebrates, arthropods and amphibian
6. Population Growth: The following terms are used to describe population growth:
a. The biotic potential is the maximum growth rate of a population under ideal conditions, with unlimited
resources and without any growth restrictions (no competition).. The following factors contribute to the biotic potential
of a species:
• Age at reproductive maturity
• Frequency of reproduction cycles
• Reproductive lifetime. ( life span)
• Survivorship of offspring to reproductive maturity

b. The carrying capacity (K) is the maximum number of individuals of a population that can be sustained by a
particular habitat.

2
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
c. Limiting factors are those elements that prevent a population from attaining its biotic potential. Limiting
factors are categorized into density-dependent and density-independent factors, as follows:

• Density-dependent factors are those agents whose limiting effect becomes more intense as the population
density increases. Examples include parasites and disease , competition for resources (food, space, sunlight
for photosynthesis), and the toxic effect of waste products, and predation.

Decomposers has the least effect on population density of a species as the will feed on it just after its death.

• Density-independent factors occur independently of the density of the population. Natural disasters (fires,
earthquakes, volcanic eruptions) and extremes of climate (storms, frosts) are common examples.

The growth of a population can be described by the following equation:

In this equation, r is the reproductive rate (or growth rate), and N is the population size at the beginning of the interval
for which the births and deaths are counted. The numerator of the equation is the net increase in individuals. If, for
example, a population of size N = 1000 had 60 births and 10 deaths over a one-year period, then r would equal (60 –
10)/1000, or 0.05 per year.

Population ecologists describe two general patterns of population

growth, as follows:
1. Exponential growth occurs whenever the reproductive rate is greater
than zero. On a graph where population size is plotted against time, a
plot of exponential growth rises quickly, forming a J-shaped curve.

2. Logistic growth occurs when limiting factors restrict the size

of the population to the carrying capacity of the habitat. In this
case, the equation for reproductive rate given above is
modified as follows:

K represents the carrying capacity. In logistic growth, when the

size of the population increases, its reproductive rate decreases
until, at carrying capacity (that is, when N = K), the reproductive
rate is zero and the population size stabilizes. A plot of logistic
growth forms an S-shaped, or sigmoid, curve

3
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
For Reading:
Population cycles there are fluctuations in population
size in response to limiting factors. For example, since
many limiting factors are density-dependent, they will
have a greater effect when the population size is large
as compared to when the population is small. In
addition, a newly introduced population may grow
exponentially beyond the carrying capacity of the
habitat before limiting factors inhibit growth. When
limiting factors (limiting resources) do bring the
population under control (competition)(density
dependent) , the population size may decline to levels
lower than the carrying capacity (or it may even crash
to extinction). Once reduced below carrying capacity,
however, limiting factors may ease, and population
growth may renew. In some cases, a new carrying
capacity, lower than the original, may be established (perhaps because the habitat was damaged by the excessively
large population or Natural disasters) (density independent factors). The population may continue to fluctuate about
the carrying capacity as limiting factors exert negative feedback on population growth when population size is large.
When population size is small, limiting factors exert little negative feedback, and population growth renews.

Reproductive Strategies:
Exponential and logistic growth patterns are associated with two kinds of life-history strategies, as follows:
1. An r-selected species (r-strategists) exhibits rapid growth (J-shaped curve). This type of reproductive strategy is
characterized by opportunistic species, such as grasses and many insects, which quickly invade a habitat, quickly
reproduce, and then die. They produce many offspring that are small, mature quickly, and require little, if any, parental
care.
2. A K-selected species (K-strategists) is one whose population size remains relatively constant (at the carrying capacity,
K). Species of this type, such as humans, produce a small number of relatively large offspring that require extensive
parental care until they mature. Reproduction occurs repeatedly during their lifetimes

r-strategists K-strategists

Little or no parenting Intensive parenting

Rapid maturation Slow maturation
Reproduce once Reproduce many times
Many, small young Few, large young
Example: insects Example: mammals

4
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Human Population Growth
About a thousand years ago, the human population began exponential growth. By increasing the carrying capacity of
the environment and by immigrating to previously unoccupied habitats, the following factors made exponential growth
possible:
1. Increases in food supply.
2. Reduction in disease.
3. Reduction in human wastes.
4. Expansion of habitat. Better housing, warmer clothing, easy access to energy.

Community structure and Population Interactions

Communities are made of populations that interact with the environment and with each other. These interactions are
very complex but can be divided into 3 categories: competition, predation, and Symbiosis (parasitism, mutualism,
and commensalism)

1. Competition
Competition = limited resources or Common Niche

Forms of Competition: a. Intraspecies (between members of the same population)

b. Interspecies (between members of different population species)

Results of Competition:
1. The competitive exclusion principle (Gause’s principle). When two species compete for exactly the same resources
(or occupy the same niche), one is likely to be more successful. As a result, one species outcompetes the other, and
eventually, the second species is eliminated. The competitive exclusion principle, formulated by G. F. Gause, states that
no two species can sustain coexistence if they occupy the same niche.

• Gause mixed two species of Paramecium that competed for the same food. One population grew more rapidly,
apparently using resources more efficiently. Eventually, the second species was eliminated.

2. Resource partitioning. (minimize competition and maximize success) Some species coexist in spite of apparent
competition for the same resources. They occupy slightly different niches.

Ex: Five species of bird coexist in trees by feeding on insects in different regions of the tree and by using different
feeding behaviors to obtain the insects.
3. Character displacement (niche shift). As a result of resource partitioning, certain characteristics may enable
individuals to obtain resources in their partitions more successfully. Selection for these characteristics reduces
competition with individuals in other partitions and leads to a divergence of features, or character displacement.
• Two species of finches that live on two different Galapagos Islands have similar beaks, both suited for using the same
food supply (seeds). On a third island, they coexist, but due to evolution, the beak of each bird species is different. This
minimizes competition by enabling each finch to feed on seeds of a different size.

5
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
2. Symbiosis
Symbiosis is a term applied to two species that live together in close contact during a portion (or all) of their lives. A
description of three forms of symbiosis follows. A shorthand notation for describing the relationship is provided, where
a “+” indicates that one individual benefits, a “–” indicates one is harmed, and a “0 or +/-” indicates no effect.
1. Mutualism is a relationship in which both species benefit (+,+) (coevolution)
• Certain acacia trees provide food and housing for ants. In exchange, the resident ants kill any insects or fungi found
on the tree. In addition, the ants crop any neighboring vegetation that makes contact with the tree, thereby providing
growing space and sunlight for the acacia.
• Lichens, symbiotic associations of fungi and algae, are often cited as examples of mutualism. The algae supply sugars
produced from photosynthesis and the fungi provide minerals, water, a place to attach, and protection from herbivores
and ultraviolet radiation.
2. Commensalism, one species benefits, while the second species is neither helped nor harmed (+,0).
• Many birds build their nests in trees. Generally, the tree is neither helped nor harmed by the presence of the nests.
• Egrets gather around cattle. The birds benefit because they eat the insects aroused by the grazing cattle. The cattle,
however, are neither helped nor harmed.
• Remora and Shark.
3. Parasitism, the parasite benefits from the living arrangement, while the host is harmed but not killed (+,–).
• There are two types of parasites:
a. Ecto-parasite: Live On host (Ticks-Fleas) b. Endo-parasite: Live inside host: Tape worm

● Vectors: Organisms that carry parasites or pathogens.

3. Predation
In a general sense, a predator is any animal that totally or partly consumes a plant or another animal. (Predator: an
animal that naturally preys on others) (Prey: an animal or plant that is hunted and killed by another for food)

Animals and plants (preys) have evolved defenses against predation.

Plant Defense:
 Physical Defense: thorns – spikes – trichomes
 Chemical Defense: poisons such as strychnine, mescaline, morphine, and nicotine to defend off attack by animals.
Animal Defense: ● Active defense: Hidings – Fleeing – defending themselves.
● Passive defense: cryptic coloration (camouflage) or Mimicry

A. Camouflage (or cryptic coloration) is any color, pattern, shape, or behavior that enables an animal to blend in with
its surroundings. Both prey and predator benefit from camouflage.
• The fur of the snowshoe hare is white in winter (a camouflage in snow) and brown in summer (a camouflage against
the exposed soil).
• The larvae of certain moths are colored so that they look like bird droppings.
• The markings on tigers and many other cats provide camouflage in a forested background. In contrast, the yellow-
brown coloring of lions provides camouflage in their savanna habitat.
• Some plants escape predation because they have the shape and color of the surrounding rocks.

6
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
B. Mimicry occurs when two or more species resemble one another in appearance. There are three kinds of mimicry:
A. APOSEMATIC COLORATION. The very bright, often red or orange coloration of poisonous animals is a warning
that possible predators should avoid them.
B. BATESIAN MIMICRY. This is copycat coloration, where one harmless animal mimics the coloration of another
that is poisonous. One example is the viceroy butterfly that is harmless but looks very similar to the monarch
butterfly that stores poisons in its body that it absorbs from the milkweed plant.
C. MULLERIAN MIMICRY. Two or more poisonous species resemble each other and gain an advantage from their
combined numbers. Predators learn more quickly to avoid any prey with that appearance.

Ecological Succession
process of sequential rebuilding of the ecosystem
Ecological succession is the change in the composition of species over time. The traditional view of succession describes
how one community with certain species is gradually and predictably replaced by another community consisting of
different species. Eventually, a final successional stage of constant species composition, called the climax community,
is attained.

The plants and animals that are first to colonize a newly exposed habitat are called pioneer species. They are typically
opportunistic, r-selected species that have good dispersal capabilities, are fast growing, and produce many progeny
rapidly.

Many pioneer species can tolerate harsh conditions such as intense sunlight, shifting sand, rocky substrate, arid
climates, or nutrient-deficient soil.
There are two kinds of succession, as follows:

1. Primary succession the rebuilding begins in a lifeless area where even soil has been removed.

The vegetation sequence of plants in a new ecosystem ( annual herbs (mosses) → shrubs (bushes)→ immature trees
→ mature trees)

The biotic sequence in a new ecosystem (Lichens → annual herbs (mosses) → shrubs (bushes)→ immature trees →
mature trees)
●The progression of a climax community in an aquatic environment. This community starts with a pond:
 Step 1—pond. This pond contains plants such as algae and pondweed and animals such as protozoa, water insects,
and small fish.
 Step 2—shallow water. The pond begins to fill in with reeds, cattails, and water lilies.
 Step 3—moist land. The former pond area is now filled with grass, herbs, shrubs, willow trees, frogs, and snakes.
 Step 4—woodland. Pine or oak becomes the dominant tree of the climax community.

7
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
2. Secondary succession when an existing community has been cleared by some disturbance that leaves the soil intact.
For example, secondary succession begins in habitats damaged by fire, floods, insect devastations, overgrazing, and
forest clear-cutting and in disturbed areas such as abandoned agricultural fields, vacant lots, roadsides, and
construction sites. Because these habitats previously supported life, secondary succession, unlike primary succession,
begins on substrates that already bear soil.

Primary Succession:

Secondary Succession

8
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Ecosystems
Plants and animals are organized into groups called trophic levels that reflect their main energy source, as follows:

1. Primary producers are autotrophs that convert sun energy into chemical energy. They include plants, photosynthetic
protists ( Phytoplankton, Diatoms and algae= Aquatic ecosystem), cyanobacteria, and chemosynthetic bacteria.

2. Primary consumers, or herbivores, eat the primary producers. grasshoppers and zooplankton (microscopic
arthropods

3. Secondary consumers, or primary carnivores, eat the primary consumers. frogs and small fish

4. Tertiary consumers, or secondary carnivores, eat the secondary consumers. Top of the food chain
 Fewer of these (less biomass) than any organism in the food chain
 Least stable trophic level and most sensitive to fluctuations in populations of the other trophic levels
 Examples: hawk or larger fish

5. Detritivores are consumers that obtain their energy by consuming dead plants and animals (detritus). The smallest
detritivores, called decomposers, include fungi and bacteria. Other detritivores include nematodes, earthworms,
insects, and scavengers such as crabs, vultures, and jackals.

Ecological pyramids are used to show the relationship between trophic levels. Horizontal bars or tiers are used to represent
the relative sizes of trophic levels, each represented in terms of energy (also called productivity), biomass, or numbers of organisms.
The tiers are stacked upon one another in the order in which energy is transferred between levels. The result is usually a pyramid-
shaped figure, although other shapes may also result.

The arrows used in the flow chart indicate the direction of energy flow.
1. A food chain is a linear flow chart of who eats whom. For example, a food chain depicting energy flow in a savanna may look
like this: grass → zebra → lion → vulture

9
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
(The Base of Aquatic food chain(Producer) is Phytoplankton)
2. A food web: Multiple overlapped food chains. Arrows connect all organisms that are eaten to the animals that eat them, that
is, in the direction of energy flow. Detritivores may also be included in the food web.

Energy and Productivity in Food Chains is the rate at which organic matter is created by producers.
 Gross primary productivity (GPP) is the amount of energy converted to chemical energy by photosynthesis per
unit time in an ecosystem.
 Net primary productivity (NPP) is the gross primary productivity minus the energy used by the primary producers
for respiration.
 Respiration Rate (R): is the rate at which energy is consumed in respiration.
NPP= GPP-(R+ assimilations)
The Biomass of each successive trophic level of an ecosystem decreases due to the conversion of food energy to
heat energy by the organisms.
Biological Magnification
Organisms occupying higher trophic levels have greater concentration of accumulated toxins stored in their bodies
than those at lower trophic levels. This is called biological magnification. The bald eagle almost became extinct because
Americans sprayed crops heavily with the pesticide DDT in the 1950s. DDT entered the bottom of the food chain and
accumulated in the bald eagle, at the top of the food chain. Because DDT interferes with the deposition of calcium in
eggshells, the thin-shelled eggs were broken easily and few eaglets hatched. DDT is now outlawed, and the bald eagle
was saved from extinction.

BIOMES
Biomes are very large regions of Earth whose distribution depends on the amount of rainfall and the temperature in
an area. Each biome is characterized by different vegetation and animal life. There are many biomes, including
freshwater, marine, and terrestrial biomes.
Aquatic Biomes
Planktons are microscopic algae, plants, and other organisms that float on the surface of water biomes. They need
sunlight to survive. Phytoplankton are important producers in water biomes. They are the first step in many aquatic
food chains

A. Fresh Water Biomes

Freshwater contains little or no salt, so it has a LOW salinity.
1. Flowing freshwater = rivers and streams 2. Still Freshwater = lakes and ponds

a.Streams: The faster a stream flows the greater the amount of dissolved oxygen in it. ↑Faster water flow =↑oxygen
The fish that live in streams are adapted to fast moving water

b. Rivers: Water moves slower in a river and debris settles on the bottom. Because of this, rivers tend to have more
nutrients and less dissolved oxygen. ↑nutrients and ↓oxygen

c. Ponds: Small, shallow bodies of water. Sunlight penetrates all the way to the bottom. Most completely filled with
plant material. Very high amount of nutrients

d. Lakes: Larger and deeper than ponds. Plant growth is limited to the shoreline. Sunlight does NOT penetrate to the
bottom= no plants after a certain depth.

10
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420

B. Saltwater Biomes: About 95% of the water on Earth has a high concentration of salt. (High salinity)

Marine
The largest biome, covering three-fourths of Earth's surface. The most stable biome, with temperatures that vary little
because water has the ability to absorb lots of heat and there is such an enormous volume of water. Provides most of
Earth's food and oxygen.

A. Estuaries (Wetlands): Area where a river meets an ocean Mix of salt and freshwater .Located near coastlines, border
land. Extremely fertile. Nutrient levels are higher than both salt and freshwater. The highest NPP on earth and greatest
oxygen production due to the present of greatest abundance of photosynthetic phytoplankton.

B. Seashores (INTERTIDAL ZONE) portion of the shoreline that is covered with water at high tide and exposed to the
air at low tide. Various temperature with periods of dryness. Sponge, Small fish, clams, snails, crabs, other mussels are
trapped in the TIDAL POOLS during low tide.

C. Oceans: Can be divided into 2 main life zones

1. Photic zone: (Sunlight penetrates) (above 200m). Plant life and animal life is abundant. Phytoplankton dominates
2. Aphotic zone: NO sunlight. There are no plants. Animal life is highly specialized. Organisms in this zone of Deep
Ocean have a special adaptation known as bioluminescence.

Continental slop →

11
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Land Biomes
Biome Location Climate Soil Plants Animals
↑ Temperature greatest diversity of any biome;
near the ↑ Rain (Heavy) nutrient-poor vines, orchids, ferns, trees insects, reptiles, and amphibians than
Tropical equator ↑ Humidity (water drain Canopy: high trees with great anyplace else; monkeys, other small and
Rainforest (Greatest Most productive Biome nutrients out of branches that shade the floor large mammals, including in some places
Biodiversity 20% Food production the soil) ↑ Epiphyte: Plants the grow on elephants, all sorts of colorful birds
4% of earth land the top of trees to obtain light
generally very dry hot days, cacti, yuccas, bunch grasses,
Rodents, snakes, lizards, tortoises, insects,
cool nights; (Temp. poor in animal and shrubs, and a few trees
and some birds. The Sahara in Africa is
fluctuation) plant decay (Poor vegetation) Waxy leaves-
Desert midlatitudes home to camels, gazelles, antelopes, small
less than 10 inches of rainfall products but often Stomata open at nights)
foxes, snakes, lizards, and gerbils
per year; not even grasses rich in minerals Dry-resisting plants – Shallow
Hide at day time- Active at night
can survive roots
The dry summer makes the chaparral
midlatitudes,
biome sensitive to fires.
Chaparral (Bet desert Moderate rain fall (more Trees -Shrubs Jack rabbit –wild goats- gray fox-
animals are nocturnal
(Shrubs) and grass than desert) (plentiful) spotted skunks - coyotes,
border than desert biome.
land)

midlatitudes, Prairie dogs, foxes, small mammals,

mostly grasses and small shrubs,
(main food uneven seasonal occurrence snakes, insects, various birds elephants,
Grassland rich topsoil some trees near sources of water
source of of rainfall lions, zebras, giraffes. (Grazing animals)
( adapted to face fire)
human)
Hardwoods trees such as oaks,
beeches, hickories, maples, birch Wolves, deer, bears, and a wide variety of
Deciduous Relatively long mild summers rich topsoil over
midlatitudes and cotton -Loose their leaves in small mammals, birds, amphibians,
Forest and cold winters. clay
fall (deciduous) (↑ reptiles, and insects. (dormant in winter)
decomposers→ ↑ soil fertility)
acidic, mineral-
Taiga (conifer Rodents (squirrels), snowshoe hares, lynx,
mid- to high very cold winters, cool poor, decayed pine
forests) conifers, and other evergreens , bears (black bears), wolves, birds in
latitudes summers, Heavy snow and needles on
(Boreal Forest) summer (migrate in winter
leaves
Tundra
(Permafrost:
nutrient-poor, musk oxen, migrating caribuou, arctic
Frozen layer of very cold, harsh, and long
high northern permafrost layer a grasses, wildflowers, mosses, foxes, weasels, snowshoe hares, owls,
soil prevents winters; short and cool
latitudes few inches down small shrubs hawks, various rodents, occasional polar
root growth summers;
(↓decaying) bears
and rain drain)
(frozen desert)

12
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Biogeochemical Cycles

1. Carbon cycle. Carbon is required for the building of all organic compounds.

The Carbon cycle has two sides: Fast: (Photosynthesis and respiration) which has the greatest impact on carbon cycle.
Slow: rock part (Decaying- formation of fossil fuel – Burning of fossil fuel). Fast side affects more on the cycle than
the slow side as that circulates in rock very slowly.

3. Nitrogen cycle. Nitrogen is required for the manufacture of all amino acids and nucleic acids. (has gaseous form) (as
legumes roots and Nitrogen fixing bacteria)
• Reservoirs: atmosphere (N2); soil (NH4+ or ammonium, NH3 or ammonia, NO2 – or nitrite, NO3 – or nitrate).
• Assimilation: plants absorb nitrogen either as NO3 – or as NH4 +; animals obtain nitrogen by eating plants or other
animals. The stages in the assimilation of nitrogen are as follows:

Nitrogen fixation: N2 to NH4+ by nitrogen-fixing prokaryotes (in soil and root nodules). (↑ Soil Fertility)

Nitrification: NH4+ to NO2– and NO2– to NO3 – by various nitrifying bacteria.NH4 + or NO3 – to organic compounds by plant
metabolism. (↑ Soil Fertility)

• Release: denitrifying bacteria (decomposers) convert NO3 – back to N2 to the atmosphere (↓ Soil Fertility)

4. Phosphorus cycle. Phosphorus is required for the manufacture of ATP and all nucleic acids. Biogeochemical cycles
of other minerals, such as calcium and magnesium, are similar to the phosphorus cycle. (No Gaseous form)

13
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420

14
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
HUMANS AND THE BIOSPHERE
As the human population has grown in size, we have intruded upon and altered or destroyed many ecosystems.
We are responsible for the deforestation (Deforestation, clearance or clearing is the removal of a forest or
stand of trees where the land is thereafter converted to a non-forest use of millions of acres of land and the
destruction of vast wetlands. We have caused groundwater contamination and depletion, the elimination of
habitats, and the loss of biodiversity..

Eutrophication of the Lakes ( Change lake to land)

Run off from sewage and manure to lake → nutrients increase in the lake → excessive growth of plants and algae →
oxygen depletion → death of aquatic organism and accumulate in the bottom of lake → decomposition → decrease
the depth of lake

Acid Rain (pH= 4.5-4.5)

Pollutants in the air cause acid rain from the combustion of fossil fuels. Nitrogen and sulfur oxides pollutants in the
air turn into nitric, nitrous, sulfurous, and sulfuric acids, which cause the pH of the rain to be less than 5.6. This causes
the death of the organisms in lakes and damages ancient stone architecture.

Toxins
Most cattle and chicken feeds contain antibiotics and hormones to accelerate animal growth but may have serious ill
effects on humans who eat the chicken and beef. Any carcinogens or teratogens (causing birth defects) that get into
the food chain accumulate and remain in our body's fatty tissues.

Global Warming
Excessive burning of fossil fuels has caused the concentrations of carbon dioxide in the air to increase to such high
levels that it causes the greenhouse effect. This means that carbon dioxide and water vapor (Green house gases)in
the air absorb much of the infrared radiation reflecting off of Earth, causing the average temperature on Earth to
rise. This increase in temperature is called global warming and could have disastrous effects for Earth. An increase
of 1.0°C on average temperature worldwide would cause the polar ice caps to melt, raising the level of the seas and
causing tremendous changes in weather patterns, including an increase in occurrences of violent storms.
Eventually, major U.S. coastal cities, including New York and Miami could be under w ater.

Depleting the Ozone Layer

The accumulations in the air of chlorofluorocarbons, chemicals used for refrigerants and aerosol cans, have caused
the formation of a hole in the protective ozone layer. This allows more ultraviolet (UV) light to reach Earth, which in
turn is responsible for an increase in the incidence of skin cancer worldwide.

Introduction of New Species (destruction of native communities due to the competition

with the non-native or exotic species)
Humans have moved species from one area to another with serious consequences. Two examples are the "killer"
honeybees and the zebra mussel.

15
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Pesticides vs. Biological Control
Pesticides, chemicals that kill organisms that we consider to be undesirable. These include insecticides, herbicides,
fungicides, and mice and rat killers. On the one hand, these 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). On the other hand, exposure to pesticides can cause cancer in humans. Moreover, spraying with
pesticides ensures the development of resistant strains of pests through natural selection. The pests come back
stronger than before. This problem requires that we spray more and more, which means more people will be
exposed to these toxic chemicals.

An alternative to wide scale spraying with pesticides is called biological control. The following are some biological
solutions to get rid of pests without using dangerous chemicals.
1. Use crop rotation—change the crop planted in a field.
2. Introduce natural enemies of the pests—you must be careful, however, that you do not disrupt a delicate
ecological balance by introducing an invasive species.
3. Use natural plant toxins instead of synthetic ones.
Use insect birth control—male insect pests can be sterilized by exposing them to radiation and then releasing them
into the environment to mate unsuccessfully with females

16
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
Summary

17
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
 Omnivores: Organisms that feed on both plant and animals. (human – sparrows)
 Omnivores can secure the survival by depending more on producers that any other level as produces contain
the highest NNP and present in great numbers.
 Omnivores and decomposers can depend on more than one trophic level.
 Prairies are ecosystems considered part of the temperate grasslands, savannas, and shrublands biome by
ecologists, based on similar temperate climates, moderate rainfall, and a composition of grasses, herbs, and
shrubs, rather than trees, as the dominant vegetation type.
 A population of insects is identified as society when it assigns specific work to specific members. (bees)
 By limited resources, competition happens.
 Carbon fixation = Photosynthesis
 Organisms that live in Lacks (ponds) polluted by sewage can suffer from oxygen depletion. (Eutrophication)
 Identifying an organism as omnivore is clearly known from Feed web not food chain as in food chain the
organism behaves with single attitude. (either eating plants or eating animals)
 Weasels is a carnivore mammals .
 All the following can be useful in describing the population’s growth rate:
a. Fertility
b. Mortality (death)
c. Survivorship
d. Age structure
 Each habitat has special characters as the annual pattern of rainfall, the average ratio between O 2 and CO2,
The annual pattern of daily Temperature range, The rate of rock weathering into soil.
 Rock weathering is the process of breaking rocks down either by physical of chemical means. (slow)
 Rock Erosion: is the process of transporting the weathered rocks from site of weathering to other sites.
 Replacement an organism by another in the ecosystem is an action of succession. (as plant replaces other
plant)
 Stream and river ecosystems differ from other aquatic ecosystems that stream and river ecosystems move
continuously in one direction and have nutrients content that is depend on location.
 Each Trophic level within an ecosystem is best characterized by the nutrient source of organism in each level.
 Biological control refers to the using of an organism to limit the growth of another organism.
 Any biome has tree as vegetation form must have plentiful rain fall.
 In area: the side that is exposed to prevailing wind will experience less vegetation. (sparse=less
dense=Scattered)

18
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
 The advantages of two distinct life stages in an organism is that allow organism to occupy different niche
(different requirement = Limit the competition) at different life stage.
 Phenotype is a description of the individual rather than population.
 The effect of the removal of a trophic level will firstly appear on the level below (↑ N) and the level after (if it
present will ↓ N.
 Most of the energy is lost at each step of the food chain as respiration energy consumed by organism.
 Natural insect predators will die as a consequence of the accumulation of toxins from insecticide control of
insect population.
 The vegetation sequence of plants in a new ecosystem ( annual herbs (mosses) → shrubs (bushes)→ immature
trees → mature trees)
 The biotic sequence in a new ecosystem (Lichens → annual herbs (mosses) → shrubs (bushes)→ immature
trees → mature trees)
 Grass Land is the biome that supplies largest amount of food for human.
 Bog plants are carnivores that feed on insect in adaptation tom the soil that poor especially in N2.
 Fungi have dual role in ecosystem as they act as decomposers (saprophyte) and parasites.
 The first step to preserve any ecological diversity is studying the population dynamics and its ecology.
 Biological Control is a control mechanism is applied by using a living organism.
 Bioremediation a waste management technique that involves the use of organisms to neutralize pollutants
from a contaminated site.
 Mid Successional Forests Sun-loving, fast-growing pioneer plants are short-lived. As they grow, they change
the forest environment, shading the forest floor.
 Late Successional Forests Shade-tolerant trees are fir, spruce, hemlock, beech, sugar maple.
 Ecological Succession is the process of rebuilding an ecosystem. It involves the replacement of organism by
another (especially plants)
 Extinction the end of an organism or of a group of organisms (taxon), normally a species. The moment
of extinction is generally considered to be the death of the last individual of the species.
 There are two types of extinction: background extinction, which is a natural part of evolution, and
mass extinction, which typically means some form of catastrophic event (such as a volcano eruption or an
asteroid hitting the Earth) has decimated plant and animal life. Every mass extinction is followed by adaptive
radiation.
 Oxygen is highly reactive, but nonetheless (inspite of that) required for human survival.
 Sulfur oxides (SO2) contributes mostly to production of acid rain.

19
BioMax SAT 2 Chapter 15: Ecology Dr. Amr Alaa 0567573420
 Layers of Atmosphere: (from earth surface to up)
a. Troposphere: most of gases and most weather changes.
b. Stratosphere: Ozone layer (prevention from the harmful U.V radiation
c. Mesosphere: the middle coldest layer. (Meteors and meteoroids are burned)
d. Ionosphere: Wireless communication.
e. Thermosphere: Hottest Top layer.
 Net primary productivity can be expressed as increase in biomass.

20