AS BIOLOGY ( C.I.E ) Notes

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Note : After i finish writing the whole syllabus in the long exhausting way i will make a short hand written one . Also i will try to make classified past papers ..i say i will but i mean i hopeHi , i will be writing the AS biology course as i study it . I thought it's a good idea to share my notes + its also good revision for me. If anyone wants to add or criticize any information , please do that ! I will follow the syllabus. Obviously i can't help with the practicals


A Cell structure
Content
• The microscope in cell studies
• Cells as the basic units of living organisms
• Detailed structure of typical animal and plant cells, as seen under the electron microscope

NB : I have attached  the structure ( i.e diagram )  of typical SECTION ofANIMAL and PLANT cells.
       We have to know how to draw and identify these ORGANELLES by heart. I learn them in an easy way but
       only after i learned the functions of each organelle . Here is the way ( i start from the centre of cell ))
      Nucleolus-> Chromatin -> Nuclear Pore-> Nuclear Envelope->   !I know Nucleolus makes ribosomes!
      Ribosomes->                                                                          !Ribosomes go to the ER for protein synthesis!
      Rough and Smooth Endoplasmic reticulum ->                          !Now ER makes Golgi Apparatus!
     Golgi Apparatus ->                                                                  !Golgi Apparatus makes Golgi vesicles!
      Golgi Vesicles->                                                                     !Vesicles make Lysosomes!
      Lysosomes->                  Only thinking of Nucleolus,i got all this.   !Now what is closest to nucleus ?
***These are all both in ANIMAL AND PLANT CELLS , starting from here ANIMAL,PLANTS,BOTH***
      Centriole->                                                                            !Microtubules (str.diff.2.idntfy) are used together during cell division!
      Microtubules->                                                                      !Now, common sense. The most obvious in both are!
      Mitochondrion->Cytoplasm-> Cell membrane*->                      !Now in animals we just add!
     Microvilli->                                                                             !After cell membrane in plants we just obvious differences in plants
      Chloroplasts -> Grana->Tonoplast->Sap Vacuole->Cell wall->Plasmodesma-> Middle Lamellae
Now the only confusion is with Centriole and microtubules.True,there are NO centrioles in plant cells but there are microtubules in both animal and plant. Just learn this by heart. [ The diagrams are attached at the end of the post. ]
Structures revealed by electron microscope and not light microscope =
Rough & Smooth ER/ribosomes/lysosomes/vesicles/microtubules/nuclear envelope made of 2 membranes/mitochondrion made of 2 membranes/chloroplast made of 2 membranes /centriole seen as 2 structures/ nuclear pores/grana and lamellae in chloroplast
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A Cell structure
Content
• Outline functions of organelles in plant and animal cells

ORGANELLE = A Structurally & Functionally distinct part of a cell , mostly bounded by a membrane
COMPARTMENTATION = Organelles bounded by membrane , so their activities are seperated from cytoplasm , leading to division of labour
MEMBRANE SYSTEM = Organelles that are bounded by membranes or envelopes
TISSUE = A group of cells , with any inter cellular secretions ( Capectate ) produced by them that perform similar functions. In tissue cells may be all of same type (e.g cuboidal epithelium ) or may be of mixed type ( e.g xylem and phloem )
ORGAN = A structure made of different tissues that perform specific functions (i.e flower , leaf , stem , heart , eye )


NUCLEUS
The largest organelle = Bounded by a NUCLEAR ENVELOPE (i.e 2 membranes),which has NUCLEAR PORES- Outer membrane has RIBOSOMES on it -Has CHROMATIN ( DNA & HISTONE proteins in EUKARYOTIC cells),this condenses to form CHROMOSOMES during nuclear division - Has NUCLEOLUS.

• Controls CELL DIVISION & INHERITANCE (by genes on chromosomes )
• Controls cell activities [metabolism]  (by genes on chromosomes ) why? genes makes protiens = enzymes = reactions
• Nucleolus makes RIBOSOMES
• Pores allow mRNA and ribosomes OUT and nutrients IN

LYSOSOMES
SPHERICAL SAC- Bounded by a membrane- Contains HYDROLYTIC (digestive) ENZYMES - 0.1-0.5 mm in DIAMETER

• Digests worn out organelles
• Digests WHOLE CELLS to replace old damaged cells
• Digests bacteria by WHITE BLOOD CELLS
• ACROSOME , a special lysosome in sperm head digests a way into ovum

ENDOPLASMIC RETICULUM [ER]
FLAT SACS (cisternae)- Bounded by a membrane  - Rough ER has ribosomes on it's surface - Smooth ER does not have ribosomes.

• Rough ER= 1. ISOLATES and TRANSPORTS proteins made in RIBOSOMES 2.Makes GOLGI APPARATUS
• Smooth ER= Makes LIPIDS & STERIODS ( cholestrol and sex hormones )

RIBOSOMES
Made in NUCLEOLUS - Made of RNA & PROTEINS - Found in surface of NUCLEAR ENVELOPE & ROUGH ER/ FREE IN THE CYTOPLASM/CHLOROPLAST/MITOCHONDRION -  2 TYPES =
70 s Ribosomes (smaller) 18nm in diameter found in prokaryotic cells
80 s Ribosomes (Larger ) 22 nm in diameter found in eukaryotic cells
"A functional ribosome" = Consists of a LARGE & SMALL ribosomal subunit that float independently if ribosome is not making protein.

• Protein synthesis [Translation of Genetic Code to a sequence of amino acids ]

NB : Strange that , even though it says 80 s ribosomes in eukaryotic cells , but inside CHLOROPLAST & MITOCHONDRION there are 70 s. We have to know that by heart . Also Translation of genetic code has to do with mRNA and tRNA which we will learn later.

GOLGI APPARATUS
STACK OF FLAT SACS ( cisternae ) - Bounded by a membrane -At one end being continuously made by SHUTTLE VESSICLES from ROUGH ER , and at other end continuously being budded off as GOGLI VESICLES

• PROCESSES & PACKAGES proteins in GOLGI VESICLES
• Makes LYSOSOMES
• Makes GLYCOPROTEINS
• Makes POLYSACCHARIDES

CENTRIOLE
HOLLOW Cylinders - Occur in PAIRS - the two pairs are at RIGHT ANGLES - Each cylinder is made of a RING OF MICROTUBULES

• Helps form SPINDLE FIBRES during nuclear division in ANIMAL CELLS

LARGE SAP VACUOLE
Bounded by a membrane (TONOPLAST )-has CELL SAP : water , minerals , pigments , enzymes , wastes , oxygen and carbon dioxide

• Fills with water by osmosis , makes cell turgid , supports plant
• Stores food , waste , pigments that give colour for flowers and fruits

MICROVILLI
Increase surface area for absorption or secretion

CELL WALL
5mm THICK- Made of CELLULOSE FIBRES,HEMICELLULOSE,PECTIN= STRONG- in a MATRIX that is strongly HYDROPHILIC and has WATER FILLED CHANNELS - has PLASMODESMATA " CYTOPLASMIC threads linking the CYTOPLASM OF ADJACENT PLANT CELLS , through PORES in cell walls- has MIDDLE LAMELLA which hold plat cells together ( CaPectate)

• SUPPORTS,PROTECTS cell & Give it it's SHAPE
• Allows substances in and out freely
• Allows tugidity to develop , supports plant , prevents osmotic bursting
• Plasmodesmata allow transport of substances between cells

MITOCHONDRION AND CHLOROPLASTS are ATTACHED.

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A Cell structure
Content
• Characteristics of prokaryotic and eukaryotic cells

Prokaryotic cell = Bacteria  [NB : DIAGRAM IS ATTACHED ]

• Size = 0.5-5mm in diameter
• No nucleus , circular DNA
• DNA not associated with protein ( histones ), has plasmids
• 70 s ribosomes
• No ER present
• Very few organelles , none have envelopes
• peptidoglycan cell wall

Eukaryotic cell = protoctists , fungi , plants , animals

• Up to 40 mm
• Linear DNA in a nucleus
• DNA associated with proteins ( Histones ) , no plasmids
• 80 s ribosomes
• ER present
• Many organelles , some have envelopes
• cellulose cell wall in plants

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• MAGNIFICATION : The number of times larger an image is , compared to real size of object.
• MAGNIFICATION = SIZE OF IMAGE /ACTUAL SIZE OF OBJECT
• Maximum magnification of LIGHT microscope = X1500 , of ELECTRON microscope = X250,000-X500,000
• RESOLUTION: The ability to distinguish two separate points
• Maximum resolution of LIGHT microscope = 200nm , of ELECTRON = 0.5nm
• Limit of resolution is about 1/2 the wavelength of radiation used (i.e , light microscope- wave length of visible light 400nm ->200nm)
• In electron microscope we use electrons beam because 1. Have very short wavelength , so great resolution 2. are negatively charged so can be focused on object by electromagnet , but unfortunately picture is black and white , only dead matter can be studied ( as beams will burn the live matter ) , heavy metals used as stains (expensive )

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B Biological molecules
Content
• Structure of carbohydrates, lipids and proteins and their roles in living organisms

The 4 most common elements are :  Carbon , Hydrogen , Oxygen , Nitrogen
Macromolecule : A 'GIANT' molecule
Polymer : A MACROMOLECULE made up of MANY,REPEATED subunits called MONOMERS Examples of polymers ->  Proteins (POLYPEPTIDES) , Carbohydrates (POLYSACCHARIDES),NUCLEIC ACIDS,DNA/RNA(POLYNUCLEOTIDES)

Carbohydrates are made of  the following ELEMENTS: Carbon , hydrogen and Oxygen   General  Formula  : Cx(H2O)y

The Subunits of Carbohydrate are -MONOSACCHARIDES (or hexoses which is the maximum no. of Carbon bonds we are supposed to know)        

Properties of MONOSACCHARIDES

• General Formula : (CH20)x
• Readily*(very) soluble in water, sweet , reducing sugar

Types of MONOSACCHARIDES ->

• Trioses -> C3H6O6 ->Is an INTERMEDIATE product in respiration
• Pentoses* [ eg.Ribose , deoxyribose] -> C5H10O5 -> Ribose (builds RNA & ATP) Deoxyribose (Builds DNA)
• Hexoses (eg. Glucose)-> C6H12O6 ->1. Used in respiration to release energy  & make ATP 2. Used to build di-&polysaccharides

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CONDENSATION REACTION : LOSS OF WATER AND FORMATION OF BONDS
HYDROLYSIS REACTION : GAIN OF WATER AND BREAK BONDS .i.e DIGESTION

Properties of DISACCHARIDES ( Monosaccharides + Monosaccharides )

• General Formula : (C12H22011) loss of a WATER molecule- LOOK AT ATTACHED DIAGRAM TO UNDERSTAND.

• soluble in water , sweet , reducing sugar Except SUCROSE[/b]
• Made of 2 MONOSACCHARIDES by a CONDENSATION REACTION
• Sucrose: Translocated in phloem , lactose : milk sugar , maltose : In germinating seeds

NB : IN DRAWING OF DISACCHARIDE IT IS SUPPOSED TO BE CONDENSATION NOT HYDROLYSIS
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Properties of POLYSACCHARIDES-Macromolecules and polymers made of many MONOSACCHARIDES

• General Formula : (C6/H10/O5)
• More or less insoluble in water , not sweet , not reducing sugars
• Starch: Storage material in plant cells (Chloroplasts , tubers ,seeds).Glycogen : Storage material in animals cells. Cellulose: Cell wall
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  NB: STRUCTURE OF , STARCH AND CELLULOSE AND GLYCOGEN IS VERY IMPORTANT , SEE ATTACHED TO UNDERSTAND
  
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  STRUCTURE OF STARCH [AMYLOSE + AMYLOPECTIN]
  
  • Amylose : Unbranched Chain-Made of Alpha Glucose molecules linked by 1,4 Glycosidic Bonds-Chain coiled into a Helix [ Not to react ] See diagram
  • Amylopectin : branched Chain-Made of Alpha Glucose molecules linked by 1,4 Glycosidic Bonds & 1,6 glycosidic bonds form BRANCHES. See diagram
    PROPERTIES OF STARCH [AMYLOSE + AMYLOPECTIN]
    
    • More or less INSOLUBLE in water , doesn't leave cell
    • Compact , occupies little space
    • Intert , doesn't react in cell ( HELIX + COMPACTNESS AND BRANCHING )
    • Has no osmotic effect
    • Easily hydrolysed to sugar when needed

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STRUCTURE OF GLYCOGEN [AMYLOPECTIN ]

• Amylopectin : branched Chain-Made of Alpha Glucose molecules linked by 1,4 Glycosidic Bonds & 1,6 glycosidic bonds form BRANCHES (MORE BRANCHES THAN STARCH ) . See diagram
  
  
  PROPERTIES OF GLYCOGEN [AMYLOPECTIN]
  SAME AS STARCH EXACTLY BUT IT HAS MORE BRANCHES THEREFORE MORE COMPACT ( OCCUPIES LESS SPACE )

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STRUCTURE OF CELLULOSE

• UNbranched Chain-Made of BETA Glucose molecules linked by 1,4 Glycosidic Bonds . - Chain is FLAT , OH groups stick out , hydrogen bonds form cross links with other chains to form Microfibrils & Fibres . See diagram.

PROPERTIES OF CELLULOSE

• Insoluble in Water
• Compact
• High tensile strength

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LIPIDS   - Triglycerides and Phospholipids

See attached diagram.

Lipids Subunits - GLYCEROL ( BOTH ) FATTY ACID chains/tails ( BOTH ) PHOSPHATE GROUP ( ONLY PHOSPHOLIPIDS )

NB:Glycerol is the SAME in all Lipids

The FATTY ACIDS differ  BY :
the number of hydrocarbons in the chain
If it is Saturated  or Unsaturated

Saturated -> The hydrocarbon chain DOES NOT have any C-C double bonds. Or only has single C-C bonds.
Unsaturated->The hydrocarbon chain has 1 OR MORE  C-C double bonds.

Unsaturated ->Causes lipids to 1. MELT EASIER  2. CAUSE KINK IN HYDROCARBON CHAINS.
NB: If ONE double bond : monoUNSATURATED bond. If MORE than ONE : PolyUNSATURATED. If NO double bonds then : SATURATED

Fatty acid tails are -> NON POLAR ( i.e no charge ) , HYDROPHOBIC ( Hates water ) therefore INSOLUBLE

Animal lipids are often SATURATED (solid at room temperature ) . Plant lipids are often UNSATURATED ( Liquid at room temperature )

• Subunits of Triglycerides:3 [tri]Fatty acid tails ATTACHED TO &glycerol head

 -Bonded by ESTER BONDS . See Diagram

• Subunits of Phospholipids:2 Fatty acids tails ATTACHED TO &glycerol&Phosphate group to make a Glycerol Phosphate Head

See Diagram.

NB : GLYCEROL PHOSPHATE is POLAR ( HAS CHARGE BECAUSE OF PHOSPHATE GROUP ) , HYDROPHILIC(loves water) , Soluble in water.

Roles of Lipids : ( Triglycerides )
Economic storage material ( When used in respiration , release more than double the energy released from carbs or proteins )
Heat insulation ( Adipose tissue underskin)
Electric Insulation ( myelin sheath)
Source of Metabolic water ( during respiration )
Buoyancy
                  : ( Phospholipids)
Form cell membranes.

SEE DIAGRAMS TO UNDERSTAND LIPIDS

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PROTEINS

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Elements : Carbon , Hydrogen , Oxygen , Nitron +- SULFUR +- PHOSPHOROUS
Subunits : Amino Acids

Amino Acids is Made of A carbon atom attached to
CARBOXYL GROUP
AMINE GROUP
AND H ATOM
A RESIDUAL GROUP ( R GROUP ) ( SIDE CHAIN ) , The only part that differs between aminoacids

Proteins can be classified on to the following stuctures :

PRIMARY -> the TYPES & SEQUENCE of amino acids in a POLYPEPTIDE CHAIN
                 Linked by PEPTIDE BONDS

SECONDARY-> the COILING of a POLYPEPTIDE chain into an ALPHA HELIX or a B PLEETED SHEET
                 Linked by HYDROGEN BONDS

TERTIARY-> the folding of the ALHPA HELIX into a 3 dimensional shape
                  Linked by HYDROGEN , IONIC , DISULFIDE bonds AND HYDRPHOBIC interactions

QUARTENARY -> Association of MORE THAN ONE DIFFERENT polypeptide chains (e.g haemog)
                  Linked by same bonds as in tertiary.

DIAGRAMS OF TYPES OF BONDS ARE ATTACHED , THEY MAKE NO SENSE AT ALL BUT THEY ARE TO LEARNED BY HEART.

There are TWO types of Proteins . GLOBULAR ( FUNCTIONAL )  & FIBROUS ( STRUCTURAL )

GLOBULAR                                                                                                      FIBROUS
Coiled into Ball or Globe shape                                                               Long chains or forms helix
Has hydrophilic R groups outside making it soluble in water                           Insoluble in water ( Helix shape )
Has hydrophobic R  groups pointing inside forming
hydrophobic interactions protecting the globe shape
Tertiary structure is important as it helix coils to form                               Secondary structure is important ( only helix )
a 3D structure ( GLOBE )

HAEMOGLOBIN                                                                                  Collagen
Made of 4 polypeptide chains. (2 Alpha , 2 Beta )  Made of 3 polypeptidechains.
Each chain has a HAEM goup that has an IRON ion  Each collagen molecule is
attached that combines with one OXYGEN MOLC.                   formed by a triple helix                                                                                 forming a triple helix held by hydrogen atoms.
 Hb Molecule combine with 4 oxygen        1/3 of AA is small AA Glycine ( has short R groups),
molecules (8 oxygen atoms ) to form        helix have to come close to bond to each other
OXYHAEMOGLOBIN.    Each molecule of collagen forms cross-links with other collagen
                              End of molecule is staggered , so no weak points ->great tensile str.

HAEMOGLOBIN ROLE                                                                     COLLAGEN ROLE
Transport of oxygen as OXYHAEMOGLOBIN from lungs to                       Structural material in skin , bld. vessels , bone
body organs

Other roles of Globular proteins                                       Other roles of fibrous proteins
1.Enzymes( catalyse)2.Hormones3.antibodies4.Found in cell membranes  1.Keratin : from structural material in hair , nails , wool , horn

Prosthetic group : A permanent part of a protein molecule that is not made of amino acids.

WATER [polar - has uneven distrib. of charge ]
Weak Hydrogen bonds form between H+ of one water molecule and O- of another

 Properties of Water :
Solvent properties : Good solvent for Polar molecules ( water molecules are attracted to them and collect around them ) Why is it important ? Metabolic reactions occur in solution and water is a transport medium in plants and animals.

Thermal properties :
1. Has high specific heat capacity ( large amount of energy needed to raise its temperature   Why is it important ? Bodies of water are a stable habitat and keeps body temperatue stable
2. Has high latent heat of vaporisation ( large amount of energyy needed to change to gas )
Why is it important ? Water on earth has not evaporated so life goes on and eveaporation is effective in cooling the body
3.To change to solid ( ice )  large amount of energy is need, so less likely to freeze Why? Bodies of water are stable habitat .

Density and freezing properties
Below 4* water starts to decrease in density so ice floats and insulates water beneath it ( Bodies of water will not freeze completely therefore its a stable habitat )

Cohesion : Water molecules stick to each other [ due to large no. of hydrogen bonds] Why is it important ?  For transport in vascular tissues in plants and causes high surface tenstion

High Surface Tension :  The force that causes the surface of the liquid to contract to occupy lease area { due to cohesion due to large no of hydrogen bonds } why is it important ? water surface is a habitat for organisms i.e pond skater

Roles of Water
Solvent for metabolic reactions in cells
Reactant in metabolic reaction in cells like hydrolysis and photosynthesis
Keeps temp of cells constant
Keeps plant Turgid to support plant

Inorganic ions.
Calcium: Component in bones and teeth
Iron : To build haemoglobin that transports oxygen
Sodium ions : For nerve impulse transmission along neurones
Potassium : For nerve impulse transmission along neurones
Magnesium: To build chlorophyll that traps light
Nitrate ions : In plants to make amino acids and nucleotides
Phosphate : To make nucleotides , ATP
Chloride : To balance the +ve charge of cations in and around cells



              

  

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ENZYMES

 " Globular Proteins that act as biological catalysts"
  " Biological catalysts: Chemicals made in living cells that speed up rate of metabolic reaction ( converting substrate into product) and not used up or changed in reaction"
 " Substrate: The molecule that can fit into the active site of an enzyme to be converted to product "

How enzymes work :

Each enzyme is a globular protein , soluble in water
Each enzyme has specific active site ( a depression ) with a specific shape to which only one type of substrate can fit into like a lock and key
Enzyme-Substrate complex is formed holding enzyme and substrate tightly , R groups of enzymes interact with  substrate ( Bonds are either built or broken)
Product leaves active site
Enzyme is a biological catalyst because it lowers the activation energy ( energy needed to start a reaction ) substrate is held tightly in a way that molecules react more easily)


See attached diagrams for the next half  of enzyme chapter explanation.
Effect of enzyme controlled reaction
Time-Course of an enzyme-catalysed reaction
Effect of enzyme concentration on initial rate of reaction of an enzyme-catalysed reaction
Effect of Substrate concentration on initial rate of reaction of an enzyme-catalysed reaction
Effect of Temperature on initial rate of reaction of an enzyme-catalysed reaction
Effect of pH on initial rate of reaction of an enzyme-catalysed reaction
Effect of enzyme inhibitors on initial rate of reaction of an enzyme-catalysed reaction
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Effect of enzyme inhibitors on initial rate of reaction
A -INHIBITORS THAT BIND TO ACTIVE SITE OF AN ENZYME
Temporarily- Competitive , reversible inhibition. Shape of inhibitor is like shape of substrate. Both compete for active site depending on the concentrations . If substrate concentration is increased  , inhibition is reduced or reversed .
Example : Ethanol inhibits an enzyme that changes ethylene glycol to oxalic acid that damages the kidney
Permanently-Non-competitive irreversible inhibition. As above but increasing substrate concentration does not reduce or reverse inhibition.
Example : Penicillin inhibits enzymes that build bacterial cell walls
B - INHIBITORS THAT BIND TO A PLACE OTHER THAN ACTIVE SITE OF ENZYME
Temporarily- Competitive , reversible inhibition .Alters shape of enzyme & active site , cannot bind to substrate . The end product binds to enzyme to stop a metabolic reaction. Or lead arsenic or other heavy metals used  
Permanently -Non-competitive irreversible inhibition . As Above!

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Cell Surface Membrane (7nm) [Fluid mosaic model]

Why fluid mosaic?
Fluid : Phospholipids and proteins move about in monolayer,
Mosaic : The patter of scattered proteins when seen from above.
GENERAL FUNCTION : 1.Allows entry and exit of substance   2.Gives cell its shape
See attached diagram to understand.
Structure and Function of Phospholipid Bilayer

• Phospholipid Polar heads pointing  Outwards and their non-polar tails pointing  inwards, facing each other
• Hydrophobic interaction occur between monolayers [holding each other]
• Phospholipid tails  [ some saturation and some unsaturated ]move by diffusion  in monolayer
• Allows passage of oxygen and carbon dioxide gas by diffusion
• Allows passage of water by osmosis
• Acts as a barrier to polar molecules ( Glucose and Amino acids ) and polar ions
• Helps in regulating the fluidity of the  membrane

Structure and Function of Proteins

• Globular proteins scattered in mosaic pattern. Some EMBEDDED in external surface , some in inner surface and some span the whole membrane
• Allows facilitated diffusion and active transport of polar molecules and ions
• Acts enzymes
• Held by hydrophobic interactions between R groups of amino acids and tails of phospholipids

Structure and Function of Glycoproteins  

• Globular proteins with short , branching carbohydrate chains on the external surface of th emembrane
• Specific receptors for chemicals
• Their carbohydrate chains form hydrogen bonds with water & stabilises the membrane
• Act as antigens for cells to recognise each other

Structure and Function of Glycolipids

• Specific receptor for chemicals
• Their carbohydrate chains form hydrogen bonds with water & stabilises the membrane

Structure and Function of Cholesterol  

• Has polar head and 2 non-polar tails
• Embedded between phospholipid moloecules
• Regulates fluidity of membrane
• Regulates Stability of membrane
• Acts as a barrier to polar molecules and ions.
• Held by hydrophobic interaction between tails of cholesterol and tails of phospholipds.

Factors that affect fluidity of the membrane

• Type of fatty acids in membrane : The more unsaturated fatty acids the more fluid the membrane because they have kinks so fit together more loosely
• Temperature : The more the temperature the more the movement of phospholipids by diffusion , the more the fluidity of membrane
• Amount of Cholesterol : The more cholesterol the less the fluidity

Methods of transporation

1.Diffusion [ oxygen and carbon dioxide] (passive ):  The movement of molecules from a region of THEIR higher concentration to a region of THEIR  lower concentration down a concentration gradient
Rate depends on : Concentration gradient
                          Temperature
                          Surface area of diffusion
                          Size of molecules
2. Facilitated diffusion  [ Polar molecules and ions ] (passive ) : Molecules pass on specific transport(carrier , channel) proteins down their concentration gradient
Rate depends on : No. of carrier/channel/transport proteins
                          If channels open or not.
3.Active Transport (polar molecules and ions ) : Movement of particles from a region of their lower concentration to a region of their higher concentration , against a concentration gradient.
Molecules pass on specific transport proteins against their concentration gradient , so need ATP to make the transport protein change it's shape and deliver molecule to other side.
 ACTIVE : Consumes metabolic energy ( ATP)
Rate depends on : No. of specific transport proteins
                         No. Of mitochondria
4.Osmosis ( passive ) [water] : Movement of water molecules from a region of their higher concentration to a region of their lower concentration down a concentration gradient through a partially permeable membrane.
5.By bulk transport : Transport of large quantities of materials in or out of a cell,
  A. Endocytosis : Transport of large quantities of materials into a cell.
a) Phagocytosis : Transport of large quantities of solid materials into a cell.
b) Pinocytosis    : Transport of large quantities liquid materials into a cell
  B. Exocytosis   : Transport of large quantities of materials out of cells
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About osmosis :
Importance=  Absorption of water from soil and movement of water across root to xylem in plants
                   Fills sap vacuole with water , makes cell turgid , supports plant
                   Movement of water in and out of organisms
Hypertonic : More concentrated than cell or tissue
Hypotonic : Less concentrated than cell or tissue
isotonic : Same concentration as cell or tissue

Water potential : The tendency of water molecules to move from one place to another
Solute potential : How much a solute helps water molecules to move from one place to another
Pressure potential: The turgor pressure that pushes water out of a plant cell
[See attached diagram for symbols and equation]

Water potential of pure water is zero.
Any solute put in it will lower its water potential
Water potential of any solution is negative.

Effect of osmosis on cells
Animal : If water potential outside animal cell is higher than inside cell , water moves into cell  by osmosis --> cell swells or bursts
           If water potential outside animal cell is lower than inside cell, water moves outside cell by osmosis--> cell shrinks
Plants : If water potential outside plant cell is higher than inside cell, water moves into cell by  osmosis --> cell turgid
           If water potential outside plant cell is less than inside cell, water move outside cell by osmosis --> cell is plasmolysed

Plasmolysis :When protoplast ( living part of cell ) shrinks and is pulled away from cell wall..

 
                

[WARRIOR]

GENETIC CONTROL AND INHERITENCE

Functions of DNA
1. Is the genetic material inherited in nuclear (cell ) division
2. Initiates and guides protein synthesis ( including enzymes  so controls all cell activities ( metabolic reaction )


Structure Of DNA

• A MACROMOLECULE  and POLYMER made of of monomers called : NUCLEOTIDES
• NUCLEOTIDES : A pentose sugar ( Deoxyribose ) + Phosphate group + Nitrogenous base (part that varies ). See Diagram to understand.
• A polynucleotide is made by condensation reaction controlled by DNA POLYMERASE enzyme , P group of nucleotide is joined to C3 of next nucleotide  , this is repeated to form a poly nucleotide strand [ Sugar phosphate backbone + bases stick out at side ]
• DNA is a DOUBLE HELIX made of two , twisted , complementary , anti-parallel  polynucleotide strands which are help by their nitrogenous bases linked by hydrogen bonds

Types of bases
Pyrimidine ( single -ringed ) - Thymine ( T )  & Cytosine (C)
Purine ( double -ringed )     - Adenine  ( A )  & Guanine  ( G)
One  pyrimidine base pairs with one purine !
T with A ( complementary ) & C and G (complementary )
T and A linked by two hydrogen bonds . C and G linked by three hydrogen bonds


The Process of SEMICONSERVATIVE REPLICATION  of DNA

• DNA molecule UNWINDS and UNZIPS (hydrogen bonds broken by DNA HELICASE enzyme)
• In nucleus , there are ACTIVATED NUCLEOTIDES  ( to which to extra phosphate groups have been added to activated them
• Each polynucleotide strand acts as a template ( mould ) to form a complementary strand : Bases of activated nucleotides pair with their complementary bases on the strands by hydrogen bonds / DNA polymerase enzymes links the sugar and the original phosphate groups together
• The 2 extra phosphate groups are realeased
• DNA molecules  rewinds

Why called semiconservative ?
Each polynucleotide strand ( half DNA molecule ) is conserved and acts as a template to make a complementary strand .

Differences between RNA & DNA

RNA                                                                    DNA
Pentose sugar is ribose                                       Deoxyribose
Made of on polynuclotide strand                             2 ( double helix)
Has Cytosine , Guanine , Adenine                      No Uracil
,Uracil but no Thymine

RNA has three types
mRNA ( messenger RNA )
rRNA ( ribosomal RNA )
tRNA ( Transfer RNA )
----------------------------------------------------------------------------------------
Define :
Genetic Code : A sequence of bases or nucleotides in a DNA molecule that codes for a sequence  amino acids in a polypeptide

Gene : A part of DNA , a sequence of nucleotides at a specific locus that code for just one polypeptide

Genome : Total set of genes in a cell , that represents the genetic code of the organism

Codon : A sequence of bases on an mRNA  that code for 1 amino acid

---------------------------------------------------------------------------------------
Protein synthesis  ( SEE DIAGRAM TO UNDERSTAND )
1.  Transcription of mRNA from DNA in nucleus
a)Part of DNA unwinds and unzips  ( hydrogen bonds broken by DNA helicase Enzyme )
b)One polynucleotide strand acts as a template  to form one complementary mRNA strand  thats is built by RNA polymerase enzyme
c) mRNA carries genetic code in the form of codons through the nuclear pore to cytoplasm to ribosome

2.In cytoplasm
a)There are tRNA molecules
b)At one end of a tRNA molecule there is a base triplet ( anticodon ) and at other end a site at which a specific amino acid can bind
c)Each tRNA with a specific anti-codon binds to a specific amino acid

3.mRNA binds to ribosome
a)mRNA binds to ribosome , 6 bases at time (2 codons ).
b)The first three bases are always AUG ( start codon ).
c)A tRNA with a complementary anti-codon UAC and carrying amino acid methionine enter.                  Codon and anti-codon base-pair by hydrogen bonds

4.A second tRNA
a)A second tRNA binds with next 3 bases (codon ) it carries a specific amino acid. The two amino acids held close together form a peptide bond ( between carboxyl group of an AA which loses a hydroxyl group and an amine group of other AA which loses a hydrogen atom) in a condensation reaction controlled by peptidyl transferase enzyme ( made in small ribosomal unit )

5. Ribosome moves along mRNA
a)A third codon
b)A third codon brings another complementary anti-codon ( tRNA ) with a specific amino acids
c)third amino acid forms a peptide bond
d)first tRNA leaves ribosome without its amino acid and goes to cytoplasm to replace it.

6. Termination
Polypeptide chain continues to grow until a stop codon ( UAA,UGA,UAG ) is exposed on ribosome.
---------------------------------------------------------------------------------------

[Romeesa-Chan]

haha thanks for the rep =]!

Welcome ...

Keep the notes coming!

[silvercameron]

hey your notes are reallyy good.=).but could you upload them in a way that i can download them in pdf format?pls?
Besides even i have started my A/AS level in september.so i need all help i can get.iwanna know which books you study from.i have got the cie biology revision guide and its really helpful.i will definitely post the link from where u'll be able to download it but i cant find at the moment.i'll post it soon.
Revision guides are a must for studying  A level subjects.but i'm not able to find them for chem and phy.do you know where i can download them from?
P.S. Could you give me some references?
Thanks.=)

[WARRIOR]

 

GENETIC CONTROL AND INHERITENCE Contd.

Chromosomes

• A Double structure made of two identical CHROMATIDS ( due to semi-conservative replication of DNA in interphase )
• Each Chromatid has one DNA & HISTONES (proteins)
• Chromatids are held by a CENTROMERE at a POSITION CHARACTERISTIC to a PARTICULAR CHROMOSME
• It is linear and only visible during nuclear devision

---------------------------------------------------------------------------------------
Mitosis
Daughter cells have same number of chromosomes as parent cells
Daughter cells are genetically identical
Uses of mitosis:
Growth of somatic cells and zygote
Repair of tissues and replacement of cells
Basis of asexual reproduction
NOTE : Interphase  is not a stage of mitosis !
Interphase

• DNA replicates
• Centriole replicate
• Cell builds up energy for all stages
• Cell grows to normal size

Starting from here mitosis begins.SEE DIAGRAMS ALSO.
1. PROPHASE

• Chromosomes coil up , become shorter , thicker , denser , take more stain and become visible
• Nucleolus and nuclear envelope disappear
• Centrioles start moving to poles

2.Metaphase

• Centrioles reach poles and forms spindle
• Chromosomes line up at equator of spindle fibres that attaches to their centromeres

3.Anaphase

• Centromeres divide into two
• Chromatids move to opposite poles , centromeres first by shortening of spindle microtubules

4.Telophase

• Chromatids at poles will now uncoil to form chromatin. DNA will replicate in interphase
• Cytokinesis : Constriction of cell membrane to divide cytoplams and cell into two
• Nuclear envelope and nucleolus reappear

Meiosis
Reduction division to make gametes as it
halves the number of chromosomes , so gametes are haploid to fuse in fertilisation to give zygote
Causes genetic variation

----------------------------------------------------------------------------------------
Oncogenes : The mutated form of genes that control cell divison
Carcinogens : Factors that increase chance cancer
Mutagens : Factor that increase chance of mutations
Genetic mutation
Carcinogens combine with DNA
Genetic mutation occurs in a gene that control cell division
Oncogenes made
Cancerous cell appears
Divided repeatedly and rapidly  by mitosis and it is different in shape and size from cells
Malignant tumor forms and enlarges and is supplied by blood and lymphatic vessels
It's malignant cells spread 1.directly to surrounding tissues 2. by lymphatics 3 by blood vessels to give metastasis in distant organs

Carcinogens
1.Chemicals : Carcinogens in tar of tobacco smoke
2.Radiations : X-rays
4.Virus infection : Cancer of cervix
5.Hereditary predispositions: The susceptibility to carcinogens  is inherited but cancer itself is not.


 

[silvercameron]

thanks for your info.=)here is the download link for cie biology revision guide

http://ebookee.org/go/?u=http://depositfiles.com/files/u2nlaaw9u
just go to this link and click 'free downloading'.

you are lucky that you 've got a teacher who gives you excellent notes.my teachers dont give us priper notes at all!!!!infact they just make us write whatever is in the book!!!whats the point?thats why i have to rely on revision guides and other references.
From whereever i have searched i cant find the cie revision guides maybe cuz they were published this year in jan.anyways,if you find the guides or anyone else you know does pls let me know and thanks for your help.
Keep posting more notes.

[WARRIOR]

Energy and Ecosystem

Habitat :  A place where an organism lives

Niche    : Role of an organism in an ecosystem

Population : A group of organisms of same species at the same place at the same time and can interbreed

Community : All organisms of all species  living in a habitat

Ecosystem : An interacting community of living organisms and the non-living parts of the
environment with which they interact

Producer : Organism that obtains light energy .That gets is carbon from an inorganic source (C02) . Has chlorophyll . Does photosynthesis .  Makes it's own food

Consumer : Organism that obtains chemical energy. That gets it's carbon from an organic source.Does not have chlorophyll , does not photosynthesise . Takes it's food from other organisms

Decomposer : Organism that obtains chemical energy . Gets it's carbon from an organic source by secreting enzymes of dead organsims and digesting them to liquid form  and absorbing it.

Food Chain : Diagram showing the flow of food and energy between organisms in linear form

Food web : Diagram showing flow of food and energy between organisms in network form (shows all food chains )

Trophic level : The feeding position of an organism in a food chain or a food web

Gross Primary Productivity : Total amount of light energy converted to chemical energy
Net Primary Productivity : Total amount of Chemical energy left after a plant does respiration.

Energy loss in producer by : Heat loss & Respiration
Energy loss by primary consumer : Not all plant are eaten
                                              Respiration and heat loss
                                              Defaecation
                                              Excretion
Energy loss by secondary consumer : Respiration & heat loss
                                                   Defaecation
                                                   Exctretion

Nitrogen Cycle
Nitrogen fixation : By Rhizobium in nodules and in soil , Lightning  , Haber Process
Decomposition and Ammonification : By Decomposer Bacteria and fungi
Nitrification of Ammonium into Nitrites : Nitrosomonas
Nitrification of Nitrites into Nitrates : Nitrobacter
Denitrification : By denitrifying bacteria

Nitrogen from airs turns into :

1.ORGANIC NITROGEN  in leguminous plants (By bacteria in root nodules of leguminous plants , RHIZOBIUM  by nitrogen fixation ) . The plants then die and turn into HUMUS ( ORGANIC N in soil ) . OR the plant gets eaten by animals who EITHER die and turn into HUMUS or excrete UREA into soil. The UREA and HUMUS turns into  AMMONIUM in soil   by decomposition and ammonification  ( By decomposer bacteria and fungi ) . The   AMMONIUM in soil turns into NITRITES by Nitrification ( By nitrifying bacteria called NITROSOMONAS) . NITRITES are turned into   NITRATES by Nitrification ( By Nitrifying bacteria called [/u]NITROBACTER) [/u].NITRATES are either absorbed by plants or leached into waterways or are turned into NITROGEN GAS by Denitrification (By Denitrifying Bacteria )

2.ORGANIC NITROGEN by nitrogen fixation ( By nitrogen-fixing bacteria living in soil , Rhizobium )  . The ORGANIC NITROGEN is then turned to  AMMONIUM in soil   by decomposition and ammonification  ( By decomposer bacteria and fungi ) . The   AMMONIUM in soil turns into NITRITES by Nitrification ( By nitrifying bacteria called NITROSOMONAS) . NITRITES are turned into   NITRATES by Nitrification ( By Nitrifying bacteria called [/u]NITROBACTER) [/u].NITRATES are either absorbed by plants or leached into waterways or are turned into NITROGEN GAS by Denitrification (By Denitrifying Bacteria ).

[u3.]AMMONIUM SALTS AND NITRATES  [/u] by nitrogen fixation ( By Haber process ).The Nitrates enter the soil as Nitrates . And the AMMONIUM SALTS is then turned to  AMMONIUM in soil   by decomposition and ammonification  ( By decomposer bacteria and fungi ) . The   AMMONIUM in soil turns into NITRITES by Nitrification ( By nitrifying bacteria called NITROSOMONAS) . NITRITES are turned into   NITRATES by Nitrification ( By Nitrifying bacteria called [/u]NITROBACTER) [/u].[/u].NITRATES are either absorbed by plants or leached into waterways or are turned into NITROGEN GAS by Denitrification (By Denitrifying Bacteria ).

4.NITRATES by LIGHTNING [ Also Nitrogen fixation ][/u].NITRATES are either absorbed by plants or leached into waterways or are turned into NITROGEN GAS by Denitrification (By Denitrifying Bacteria ).

[emzie]

Thnaxx alot!! these notes are amazing! i started preparing for bio this September, and this isreally helpful 

[WARRIOR]

IMMUNITY

ANTIGEN : A large molecule ( GLYCOPROTEIN ) that the body recognises as FOREIGN and stimulates an IMMUNE RESPONSE

ANTIBODY : A GLYCOPROTEIN , made by the immune system as a response to the presence of ANTIGEN and is SPECIFICALLY targeted at it .

IMMUNE RESPONSE : LYMPHOCYTES response to the presence of antigen by producing ANTIBODIES


White blood cells are divided into the following
1. Neutrophils                   2. Macrophages                3. T Cells                     4. B cells
  Phagocyte                          Phagocyte                      Lymphocyte               Lymphocyte
  LARGE                                 LARGEST                      SMALL                          SMALL
 Lobed Nucleus with           Kidney shaped                   Large rounded               Large Rounded
3-5 lobes                             Nucleus                            Nucleus                        Nucleus
Granular cytoplasm          Non-granular cytoplasm      Non-Granular cytoplsm   Non-Granular cytplsm
Matures in                   Monocyte in Bone marrow            Matures in                   Matures in
Bone marrow             but matures in cells & organs    Thymus Gland                   Bone Marrow

Phagocytes
Neutrophils : 60% of white blood cells , Short lived ,Squeeze out of capillary gaps ,  Increase rapidly during infection , They phagcytose
 
How they work?
Attraction : Neutrophils attracted to site of infection by CHEMOTAXIS due to a) Histamine released by body cells under attack b)Chemicals from bacteria
Attachment : Bacteria attached to cell surface membrane of neutrophils either directly of after being labelled by antibody
Endocytosis : Infolding of neutrophil's cell surface to engulf bacteria
Bacteria in Phagosome
Lysosome fuse with phagosome to form phagolysosome
Bacteria killed by enzymes or hydrogen peroxide

Macrophages :Long lived , Cut pathogen in antibodies and displays them on their surface to be recognised by lymphocytes

Clonal Selection : Only T and B cells with specific  receptors specific to antigen will respond
Clonal Expansion : Clonal selection increase in number by mitosis

Lyphocytes: T cells and B cells
 T cells develop specific Tcell  receptor . 2 types of cells are developed
 Take care cells ( cytotoxic cell ) Th cells  ( Helper cells )

Take care cells : Punches holes in cell surface membrane of infected body cell and secretes toxic chemicals that kill cell.
 Divided by mitosis to form memory T cells
Th cells : Secretes cytokines that : Stimulate B cells to differentiate into plasma cells that secrete specific antibodies and form memory B cells by mitosis  .
 Divided by mitosis to form memory T cells

B cells : Stimulated by Cytokines to divide by mitosis to and differentiate into plasma cells that secrete specific antibodies and memory B cells.

Primary Response :  During primary infection it takes time for clonal selection and clonal expansion for the specific antibodies to specific antigens to made. After infection no. of antibodies in blood decreases but memory cells remain

Secondary Response :  When infection enters the body , memory cells divide rapidly making more plasma cells . Therefore response is faster and higher conc of antibodies in blood , and more memory cells are made for future infections

STRUCTURE OF ANTI-BODIES
Glycoprotein
Made of 4 polypeptide chains : 2 heavy/long chains and 2 light/short chains
Held together by Disulfide bonds
The heavy chains have a sugar branch
Hinge region to provide flexibility to bind to antigen
Variable region specific to each type of antigen

Roles of Antibodies
Immobilise bacteria by sticking to flagellae
agglutinate (clump ) bacteria
Label bacteria to be phagocytosed
Neutralise toxins
Lysis of bacteria by making holes in their cell walls and water enters by osmosis and bacteria burst


Types of Immunity
Natural passive immunity : Where antibodies is passed from one individual to another of same species . No memory cells made , so protects for short time ( e.g Antibodies from colostrum )
Artificial passive  Immunity : Giving a serum ( antibodies from one individual injected to another individual of same or different species ) , no memory cells made , so protects for short time ( e.g Antitetanus serum from horse given to MAN )
Natural Active immunity : Body exposed to infection , so body makes it's antibodies . Memory cells made so protects for a long time
Artficial active immunty : giving a vaccine , antigens , body makes its antibodies , memory cells made to protects for a long time


 

[Most UniQue™]

Kimo Please refrain from double posting the same thing as you did in the earlier posts. All of them have been removed. I hope this wont happen again....

[WARRIOR]

Infectious Diseases

Diseases Caused by pathogens that can spread from infected people to uninfected people.

Carrier of a disease : People that carry pathogen , spreads it , but has no symptoms or disease

Incubation Period : Period between entry of pathogen into person and the appearance of disease

Acute disease : Sudden , short term
Chronic : Long term

Opportunistic infection : Pathogens that infect a body with low immunity  

Prophylaxis :  A measure taken to prevent a disease before it happens.

endemic : Always found in population
epidemic : spreads rapidly infecting many people
pandemic : spreads worldwide !

Cholera
Pathogen : Vibrio Cholerae ( Bacterium )
Method of transmission : Food borne , water borne
Incubation period : 1-5 days
Site of action of pathogen : Walls of small intestine
Symptoms : Diarrhoea , loss of water and salts , dehydration , weakness
Diagnosis : Microscopical examination of faeces
Distribution : ASIA , AFRICA , LATIN AMERICA due to
1) No clean water supply
2) No sewage system or treatment
3)Eating raw  vegetable irrigated by sewage
Control : Buy clean water supply
            Cook vegetable
             Buy sewage system
            Isolate patient
            Give oral rehydration solution

Tuberculosis
Pathogen : Mycobacterium Tuberculosis , Mycobacterium Bovis
Transmitted by : Air-borne droplets ( Tuberculosis ) , Food-Borne ( Bovis) [infected meat or unpasteurised milk ]
Incubation period : Few week or months
Clinical features : racking cough , coughing blood , fever , sweating , chest pain , weight loss , breathlessness
Site of action : Lungs , lymph nodes , bones , gut
Method of diagnosis :  Microscopical examination of sputum for bacteria
                               Chest X-RAY
Global Distribution : Worldwide , but mainly Asia  , Africa and Latin America
Reasons : Malnutrition -> Less protein -> Less antibody -> less immunity -> TB is an opportunistic infection
            HIV-> Low immunity -> TB is n opportunistic infection
           Overcrowded areas spread air-borne infections
            More immigrants and refugees
Control : Isolation of patient
             Treat by anti-tuberculous drugs : Rifampicin , Isoniazid
            Several drugs  at a time to reduce appearance of drug resistant strains
            Tracing contancts and screening for TB
            BCG vaccine as prohylaxis
           Milk pasteurisation and TB testing of cattle

MDRTB- multiple drug resistant strains of tuberculosis  , due to stopping taking of drugs early , and because patient feels good
DOTS : Direct observation treatment  short course . Health workers and family members ensure patient takes drugs for 6-8 months.

AIDS
Pathogen : HIV - HUMAN IMMUNODEFICIENCY VIRUS
Method of transmission :  In semen and vaginal fluid during heterosexual and homosexual intercourse  
                                   In blood transfusion
                                  Contaminated syringes
                                 From mother to foetus through placenta
                                 From mother to foetus in colostrum
Incubation period :  a few weeks , but up to 10 years or more for symptoms of AIDS to develop
Clinical features  HIV - flu-like symptoms , then symptomless
                       AIDS - opportunistic infections ( pneumonia , tb , cancers , weight loss , fever )
Site of Action : T helper lymphocyts , brain
Diagnosis : Blood test for HIV antibodies
Global distribution : WORLDWIDE , SUBSAHHARAN AFRICA , SOUTHEAST ASIA  , NORTH AMERICA (DUE TO INCREASE IN HOMOSEXUALS )
Control :  Advise people to use condoms or femidom
             Advise people to have 1 sexual partner
              Advise people to use sterile syringes
            Advise people not to donate blood if they have HIV
          Screening and heat-treating donated blood
            Contact tracing
 Drugs like Zidovudine (similar to DNA nucleotide that has thmine ) slows down onset of AIDS by stopping  viral infection
AIDS is difficult to control because :
It has a long incubation period ( so carrier can spread AIDS without symptoms appearing on him)
Virus mutates  , not detected by immune system , cannot make vaccine
Not all cases are diagnosed or reported
Widespread HIV testing would be an infringement of personal freedom , so governments dont do it

Malaria
Pathogen : Plasmodium Malariae , P.Ovale , P.Vivax , P.Falciparum
Method of transmission : Insect vector is the female Anopheles mosquito that bites an infected person , takes gametes of plasmodium that develops in its body to infective stage. It then bites an uninfected person  and injects an anti-coagulant to prevent blood clot .
Incubation period : A week to a year
Clinical Features : Anaemia , fever , sweating , enlarged liver adn spleen
Site of action : Liver , Red blood cells , brain
diagnosis : Microscopical examination of red blood cells for protoctists
Global distribution : Tropics and Sub-tropics , Asia , Latin Ameerica , africa
Control : Oil spread on ponds , ditches to kill pupae and larvae
             Using fish in ponds that eat larvae
              Sprayng bacteria in ponds that kill larvae , not other organisms
            Screening houses
            Mosquito nets
            Avoid exposure of skin at dusk
            Use anti-malarial drugs , before , during , after visit to area where malaria is endemic ( Chloroquine )
If someone is infected with malaria in an area where malaria is endemic it gives him immunity !But if he leaves the area he becomes sick
Plasmodium mutates become resistant to anti-malarial drugs
Mosquito mutates become resistant to DDT

[WARRIOR]

No problem ! As long as you can fix it there is no problem at all . Like you said i have space for one more chapter after that you can delete romeesa's post or do whatever you mods do ill inbox you when i want to add another chapter. Thanks !