Biology AS1


The Role of Biologically Important Ions

Nitrate- component of Amino Acids, Nucleic Acids and Chlorophyll

Calcium- Calcium Pectate in Plants for middle Lamella, improtant component for bones and teeth and blood clotting and muscle contraction

Iron- part of Haem group in Haemoglobin and important consituent of electron carriers in respiration

Magnesium- chlorophyll

Potassium- maintaining electrical gradients across Neurons

Phosphate- phospholipids, phosphate is important for cell membranes- Major component in ATP and Nucleic Acids

Hydrogencarbonate- Natural Buffer

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Types of Carbohydrates

Monosaccharides- basic carbohydrate monomer ie simple sugars- trioses pentoses or hexoses usually eg. Glucose and Fructose

Disaccharides- double sugars formed from two monosaccharide monomers eg. Sucrose and Maltose

Polysaccharides- complex molecules consisting of many monosaccharide monomers.

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a-glucose and beta- glucose

a-glucose-hydroxyl group on bottom

beta-glucose -hydroxyl group on top

Monosaccharides have the same molecular formula but different structural formula therefore known as Structural Isomers

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Two monosaccharides usually Hexoses react together in  a condensation reaction .This reaction is reversable and is known as Hydrolysis(adding water)

The bond formed between the two monosaccharides is known as a Glycosidic Bond

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Example of Important Disaccharides

Maltose= a-glucose + a-glucose (Formed when starch is digested)

Sucrose = a- glucose + fructose

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Disaccharides Characteristics

Disaccharides have the general formula C12H22O11

They dissolve in water producing sweet tasting solutions

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Complex Carbohydrates with often very long chains

Formed through Condensation and broken by Hydrolysis

Large number of monomers joined together to make a complex Polymer

Not sugar! They are not sweet and are insoluble in water

eg. Starch, Glycogen and Cellulose

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Starch Structure

Amylose= a-glucose linked by a-1,4 glycosidic bond. Coils forming a spiral held together by hydrogen bonds. Due to only a-1,4 bonds Amylose forms a long unbranched chain. Due to the presence of bulky sidegroups that cause the a-glucose molecules to lie at different angles , amylose chains form a coiled configuration

Amylopectin = a-glucose linked by a-1,4 glycosidic bonds and a-1,6 glycosidic bonds. The a-1,6 glycosidic bonds form side brances to produce a branched molecule. This branching occure as often as 1 in every 10 a-glucose monomers


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Why is Starch good for Storage?

Amylose and Amylopectin are both very compact(aided by the coiled configuration). Therefore they contain a rich store of glucose in a small space.

They are insoluble thererefore will not affect the water relations of the cell (Osmotically Inert)

Starch is a large molecule so it can be retained within the cell and will not pass through the cell surface membrade readily

The brancing nature of amylopectin means that there is many terminal ends which can be easily hydrolysed. This aids rapid enzymatic breakdown of starch into its consituent glucose molecules ar times of high respiratory demand

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Storage Carbohydrate in Animal and Fungal Cells - Stored as small granules

a-1,4 glycosidic bonds and a-1,6 glucosidic bonds

Glycogen is more branched and shorter than Amylopectin

Stored in Liver and Muscle Cells

Compact and insoluble

No unbranched chains so more terminal ends so faster hydrolysis when conditions demand

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Not a storage polysaccharide- its role is purely structural

Made from beta-glucose monomers joined together by B-1,4 glycosidic  bonds - must rotate 180 due to the different structure (hydroxyl group on top)

This flipping has 2 effects:

  • Straigher chains as bulky CH2OH groups alternate
  • Hydrogen Bonds can form cross linkages between adjacent chains

Cellulose chains grouped together in microfibrils with each microfibril consisting of many cellulose molecules. Plant cell walls are comprised of many cellulose microfibrils orientated into many planes in a lattice structure to further increase the tensile strength.

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Hydrogen to Oxygen 2:1

Large Molecules

Hydrophobic- not soluble in water

They are soluble in organic solvents such as ether and ethanol

Main Types are Tryglicerides( Oils and Fats) , Phospholipids ( major component of membranes),Waxes and Steroids

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Combination of Glycerol and 3 Fatty Acids( Hydrocarbon Chains).

Fatty Acids are organic acids that form long hydrocarbon tailes linked to a Carboxyl Group (COOH)

Ester Bond forms between Glycerol and Hydrocarbon Tail

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Saturation and Unsaturation

Saturated Fatty Acids contain the maximum number of hydrogen atoms . Linked by a C-C single bond. eg.Stearic Acid

Unsaturaturated Fatty Acids contain atleast one C=C double bonds in the Oleic Acid

If there is one C=C double bond it is monounsaturated.

If there is more than one C=C double bond it is Polyunsaturated

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Tryglcerides as Energy Stores

Tryglycerides are an excellent energy store as they release more energy per unit per mass than carbohydrates.

 Fats are also important for insulation and are stored in a layer below the body surface in many animals. Many body organs are protected by a layer of fat. Fat is important for boyancey in marine life etc

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One Glycerol, 2 Fatty Acids and a Phosphate.

The fatty acid molecules repel water and are insoluble in water forming hydrophobic tails whereas phosphate gives the glycerol parts of the molecule are hydrophillic properties and is soluble in Water. Phospholipids are polar molecules and this property is important in determining their orientation and function in the cell surface membrane


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Contains Carbon, Oxygen, Hydrogen,Nitrogen and Usually Sulfur

They are large Polymers formed form amino acid sub-units.

Proteins are determined by the sequence of the amino acids in the protein.

The Amino Acids differ due to them having different R-groups

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Amino Acids are linked together by peptide bonds . These condensation reactions with hte loss of water. The Condensation reaction takes place between the amino group of one of the amino acids and the carboxyl group of another.This link is between the Nitrogen and Carbon Atoms involved.Thebond formed is a Dipeptide.


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Primary Protein Structure

The sequence of amino acids in the polypeptide chains. Its when the amino acids are linked by the peptide bonds


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Secondary Protein Structure

The Orientation of how the Hydrogen bonds are orientated.

a-helix- Hydrogen bonds formed at regular intervals between amino acids. The bonds twist the chain of amino acids into a spiral or helical shape

B-pleated sheets- more rigid and less flexible configurations that the a-helix,

They are sections formed by the polypeptide chain, orientated in oppiside (anti-parrallel) directions, laying adjacent to eachother. Hydrogen bonds form between the C=O and NH groups


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Tertiary Protein Structure

Further folding of the secondary structure. Unique 3-D Shape and is a consequence of the range of bonds formed between the R-Groups of the Amino acids in the chain,

 Hydrogen Bonds-numerous and relatively weak and easily broken

Ionic Bonds- between amino and carboxyl groups. Stronger than hydrogen bonds but damaged by changes in pH

Disulfide Bonds- covalent bonds formed between R-groups of sulfur containing Amino Acids. Very Strong bonds and important in giving structual strength to fibrous proteins eg Collagen

Hydrophobic Interactions- Amino Acids with hydrophobic R-groups whoch tend to take up positions within the molecule surrounded by other parts of the polypeptide further influencing the tertiary structure.

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Quaternary Protein Structure

Two or more polypeptides bonded together.

Some Quaternary Structures contain prostethic groups that are integral to their function.

These conjugated proteins include glycoproteins important for membrane structure

Haemoglobin is a conjugated protein that consists of 4 polypeptide chains and 4 Iron Rich Haem groups which is essential for the transport of 02 in the blood.

Fibrous Proteins- polypeptides arranged in chains that form fibres or sheets. The parallel chains are linked by cross bridges which form very stong and stable molecules. Fibrous Protiens are invariably structural in function. eg Collagen- Found in tendons which link muscle to bone

Globular Proteins- have metabolic role and include Enzymes and Antibodies. The ability of the protein to form a very specific 3D shape is crucial to their role are enzymes and antibodies eg. Haemoglobin

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Particular type of Protein found in Mammals and in some other animal groups. Found in the Nervous System and is thought to be involved in synaptic transmissionThe Normal Prion Protein can convert to the disease casuing Prion (PrPc to PrPSc)Normal PrPc consists of more a-helices  however PrPSc constins more B-pleated Sheets.Leads to a chain reaction - leads to Neurodegenerative disorders in the brain and other nervous tissues and eventually death

Prions can arise

  • Through Consumption of contaminated Protein
  • Sproadically/Spontaneously
  • Mutations in DNA that codes for the normal PrPc Protein

Forms of Prions Disease

  • Scrapie- Sheep
  • BSE-Cows
  • vCJD- Humans
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Nucleic Acid

Consists of

  • Pentose Sugar
  • Phosphate Group
  • Nitrogenous Base

The three components are joined by condensation reactions./ broken down by Hydrolysis

Phosphodiester bond links pentose sugar to the phosphate (Sugar-Phosphate Backbone)

Adjacent Nucleotides can be joined together to create the Nucleic Acid. The Nucleic Acid is a chain of Nucleotides.(Polynucleotide)

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Nucleic Acid

Consists of

  • Pentose Sugar
  • Phosphate Group
  • Nitrogenous Base

The three components are joined by condensation reactions./ broken down by Hydrolysis

Phosphodiester bond links pentose sugar to the phosphate (Sugar-Phosphate Backbone)

Adjacent Nucleotides can be joined together to create the Nucleic Acid. The Nucleic Acid is a chain of Nucleotides.(Polynucleotide)

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Three Types

  • messanger RNA(mRNA)

Carries code from the DNA in the nuceus to a ribosome in the cytoplasm where protein systhesis occurs

  • transfer RNA(tRNA)

Carries the Amino Acids to the mRNA/Ribosome where the protein synthesis is taking place. It is a single chain folded into a clover leaf shape.

  • ribosomal (rRNA)

Made in the Nucleolus and forms over half the mass of each individual ribosome

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DNA Replication

Semi Conservative Mechanism- genetic replication in which a double-stranded molecule of nucleic acid separates into two single strands each of which serves as a template for the formation of a complementary strand that together with the template forms a complete molecule.

1. The enzyme DNA Helicase breakes the Hydrogen Bonds between the base pairs and 'unzips' part of the DNA double helix revealing two strands

2. The DNA Polymerase moves along each strand which acts as a template fot the synthesis of a new strand

3. DNA Polymerase catalyses the joining of free deoxyribonucleotides to each of the exposed original strands according to base pairing rules that the new complimentary strands form.

4. The process of unzipping and joining for new nucleotides continues alond the whole length of the DNA molecule

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Meselson and Stahl Experiment

Meselson and Stahl tested the hypothesis of DNA replication. They cultured bacteria in a 15N medium. 15N is a heavy isotope of nitrogen so the DNA synthesized is of heavy density. They then shifted the bacteria to a 14N medium,   After one generation, the DNA was all of intermediate density.

After two generations , two bands of DNA were seen, one of intermediate density and one of light density. This result is exactly what the semiconservative model predicts: half should be 15N-14N intermediate density DNA and half should be 14N-14N light density DNA. This result rules out the dispersive replication model, which predicts that after replication cycle 1, the DNA density of all DNA molecules will gradually become lower, so no intermediate density DNA should remain at 2nd Generation. The semiconservative model is correct.

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Enzymes- Structure and Function

Enzymes are Biological Catalysts which speed up the rate of Metabolic Reactions.

Enzymes are globular proteins which is advantageous

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Activation Energy changes

Enzymes lower the activation energy to overcome the energy barrier.

This reduction in activation energy enables reactions to take place at a more rapid rate needed to sustain life.


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Enzyme Action

Anabolism= building up of material

Metabolism= breaking down of material

Enzymes have specific active sites ( Enzyme Specificity)

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Lock and Key Hypothesis

Substrate and Enzyme Active Site complimentary.- Proves enzyme specificity


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Induced Fit Model

The active site moulds itself around the substrate forming a precise fit. The active site is therefore flexible and as it changes shape to fit the substrate the enzyme is able to put pressure on the substrate breaking particular bonds and therefore lowering the activation energy required for the reaction to take place- When products released the activesite returns to pre-reaction shape.


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Non-protein substances that enzymes require in order to function.

Examples include Metal Ions (such as Mg2+, Ca2+ and Fe3+ ). They form attachments to the enzyme and change the shape of the active site, enabling the reaction to take place.


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Particuar Type of co-factor. They are non-protein ,organic molecules necessary ot the enzymes active. Unlike some other cofactors theyre are not permanently attached . Co-enzymes are very important in the biochemistry of respiration and photosynthesis. The coenzymes NAD and FAD act as the hydrogen acceptors in Respiration


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Substrate Concentration

The Rate of reaction increases as substrate concentration increases. Substrate molecules all occupy activesites and substrate availability limits the rate of the reaction with some of the active sites unused.

The addition of extra substrate molecules has no effect as all the activesites are in use. The Number of enzyme active sites limits the rate of the reaction


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Enzyme Concentration

As more enzymes and active sites become available more enzyme-substrate compleces can form and reactions can take place.

 Enzyme Activity levels off as the number of substrate molecules becomming limiting.

Normally in living systems activity continues to increase as substrate is sledom limiting


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Increasing Temperature, increases the KE, molecules vibrate more vigourously and this leads to more bonds to break which effects the tertiary structure of the globular protein to be affected. This causes the Active site to change shape to cause little/no enzyme substrate complexes to form.


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Each enzyme has an optimum pH range in which the enzyme works best at . At either side of this optimum changes in pH will reduce the activity. This is caused by the changes in pH disrupting the bonds that are improtant in determining the protein shapr. The Ionic Bonds in particular are subject to disruption when in non opetimal pH. The further the pH is from the optimum the greater the degree of disruption to the bonding until eventuallt denaturing results.


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Competitive Inhibition

Inhibitor Substances competes with the usual substrate for the active site. Competitive inhibitors are very similar in shape to the usual substrate

If the quantity of the inhibitor substance is low compared to the substrate it will have little or no effect. If it is relatively high it can significantly affect the enzyme activity


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Non-Competitive Inhibititon

The inhibitor attaches itself to an allosteric site-other than the active site

The presence of the non competitive inhibitor leads to the active site changing shape so that it is no longer complementary to the substrate molecule.

Increasing the substrate concentration does not reduce the effect of the inhibitor as the two molecules are not in direct comeptition

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Elastase as Biomarker

Elastase is an enzyme released by white blood cells as a consequence of lung infection. - breaks down the bacterial pathogens and is apart of the immune response

Elastase breakes down the protein Elastin which is an important component of lung tissue that contributes to the elasticity of the alveoli.The elastin allows the alveoli to stretch and recoil. Normally when its not broken downs the elastase inhibitor alpha-1-antitrypsin prevents the Elastase activity after the infection has been cleared

However cigarette smoke causes too much Elastase to be released in the lungs with little A1AT present to control the elastase effectively . Therefore the elastin in the Alveoli is broken down resulting in Elastase-Induced Emphysema

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Enzyme Inhibitors as Therapuetic Drugs

A1AT- used medically to reduce the harmful effects arising from Lung Infection

ACE(Angiotensin Convering Enzyme)- used to treat HBP and other Cardiovasular disases by inhibiting an enzyme that leads to the constriction of the blood vessels . The ACE inhibitors reduce the constriction of blood vessels - lowering BP

Penicillin- inhibiting enzymes involved in cell wall formation in bacteria. Some antiviral drugs inhibit DNA/RNA Polymerase preventing viral replication

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Enzyme Immobilisation

Adsorption- Attached by weak forces onto an inert substance such as glass or a matrix.

Entrapment- trapped within polymers such as alginate beads or microspheres

Encapsulation- trapped inside a selectively permeable membrane such as Nylon

Cross-Linkage- covalenly bonded to a matrix such as Cellulose as consequnce of chemical reactions

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Enzyme Immobilisation Advantages

Increased Themal Stability /pH Stability

More resistant to changes in pH

Can be Retained and Reused

Commercial processes continuous- faster and less waste

No contamination of end product- simplifying downstreaming process reducing purification costs and avoiding any allergic reactions to consumers.

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Enzyme Immobilisation Disadvantages

Reduced speed of diffusion


Enzyme may be wasted

Active site might be in wrong orientation

Active site may change shape

Research costs high

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Light Microscope vs TEM

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Eukaryotic Cell

Cell with Nucleus

Consist of cell surface membrane and cytoplasm and Nucleus with organelles


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Animal Cells


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Lysosomal Activity

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Plant Cells


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Plant Cell Layers

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Chloroplast structure


Lipid droplets also present

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Fungal Cells


Chitin Cell Wall


Nuclei can be multinulceate


Glycogen Granules

Hyphae- long thread like structures-englongated cells

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Cell Surface Membrane

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Function of the Phospholipid Bilayer

The backbone of the cell surface membrane

Gives the membrance its selectivity or differentially permaeble properties

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Increases Membrane Stability by restricting the sideways movement of the phospholipid molecules at high temerature.

At low temperatures the cholesterol helps to maintain the membrane fluidity by acting as a wedge between adjacent phospholipid molecules and stopping adjacent molecules sticking together.

 In effect Cholesterol helps make the membrane less fluid at high temperatures and more fluid at low temperatures

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Proteins in Membrane

  • Help provide stability and support as they anchor the phospholipid moleules.
  • They may also act as Enzymes.
  • Some proteins act as adhesion sites - areas where adjacent cells are held together
  • Also some proteins are involved in cell recognition and as receptors or antigens

Important in transporting substances across through

  • Channel proteins - span the membrane and work by creating a hydrophillic channel that allows the polar molecules to bypass the hydrphobic centre of the bilayer -gated/non-gated
  • Carrier Proteins - carry specific ions and molecules across the membrane. May be because the moleucles/ ions have been moved against their concentration gradient. The Carrier Protiens can change shape to carry the substance from one side to another
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Polysaccarides bind to the glycoprotein or glycolipid are found on the outise of the cell surface membrane and are peripheral to the protein or phospholipid.

Glycoproteins and Glycolipids involved in

  • Cell-to-Cell recognition
  • Antigens (glycoproteins)
  • Receptor sites- important for hormone action and in the passage of Neurotransmitters between Neurons
  • Glycoproteins and Glycolipids can form Hydrogen Bonds with water molecules outside the membrane so can increase stability of the membrane
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Virus- commonly called phages

Normally have DNA core and are Parasitic on Bacteria

Inside their host cell the viral DNA codes for the production of new protein for new protein coats. The DNA itself replicates to make copeis that are packages within the protein coats forming new viruses .

Eventually due to the build up of viruses in the coat it ruptures releasing the viruses to continue the cell cycle

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Human Immunodeficiency Virus

RNA Core.

Protein coat with a lipid bilayer containing glycoproteins.

 Reverse Transcriptase enzyme catalyses the synthesis of DNA from RNA . DNA them makes new viruses by synthesising new protein coats and viral RNA

These viruses are known as Retroviruses as the viral RNA is used as a template to make DNA . This is the revers of the normal transcription process where DNA is used to make mRNA as part of the protien synthesis.

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In Humans HIV invades the lymphocyte - helper-T-cells.

These T cells are very important for the Immune System when protecting against disease.

 As progressively more T-Cells are destroyed the immune system becomes critically comprimised and medical condition AIDS can develop


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The net movement of a substance from where it is in highter concentration ot where it is in a lower concentration . Its not restricted to occuring across membranes

 Factors Affecting Diffusion-

  • Concentration Gradient - greater the conc. gradient faster diffusion
  • Size of molecule- smaller molecule faster diffusion
  • Temperature- high temp. inc diffusion
  • Thickness of Exchange Surface- thin surface faster diffusion
  • Surface Area of Membrane - greater SA faster diffusion


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Facilitated Diffusion

Channel Proteins- Static- gated/non-gated. Allow charged particals to pass through.

Carrier Proteins- Take in the diffusing moleule such as glucose change shape and release the molecule on the other side of the membrane. These protein carriers have binding sites that match specific moleucles and they assist the movement of these molecules across the membrane


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Active Transport

Moving molecules against their concentration gradient . Energy required- ATP

 Active Transport involves protein carrier molecules(pumps). The substance binds to the carrier protein.

Cells that carryout Active Transport have high number of Mitocondria- important for synthesis of ATP energy

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Endocytosis- movement of substances into the cell- cell wall invaginates and pinches off as vesicle

Exocytosis- movement of substances out of the cell-vesicle fuses with cell membrane

Phagocytosis- transporting solid material into cell

Pinocytosis- transport of fluid into cell


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High water potential to lower water potential

Water potential is the tendancy to take in water by osmosis from pure water across a selectively permaeble membrane. Pure water was solute potential of 0kPa, Solutes decrease solute potential

Solute Potential is the potential of a solution to take in water Pressure Potential is the effect of pressure on the solution ( ONLY IN PLANT CELLS)

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Water Potential Graphs

As cell begins to become more turgid the membrane begins to exert a force on the cell wall( Incipient Plasmolysis)At full Turgor the maximum force betweeen the cell and the cell walWater Potential of the cell is zero so no more water can enter Solute potential is still negative at full turgor as solutes are present in the cell  As the pressure potential becomes positive it begins to hinder the water entering the cell therefore the cell potential and solute potential diverge As the cell takes in water by osmosis its contents become less concentrated therefore the solute potential increcreases. There is no pressure potential to restrict the water intakes therefore the solute potential=cell potential


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Osmosis in Plant Cells

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Osmosis in Animal Cells


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Cell Cycle


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G0 Phase

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Cell Cycle Regulation-Cancer

Cancer is casued by uncontrolled cell division in effect it is Mitosis out of control

Cancer cells cannot enter the G0 phase and cancer involves a breakdown in the ability of the checkpoints in the cycle to regulate the process of cell division.

 Modern Anti-canver drugs- Chemotherapy

Inhibition of Microtubule formation= Vincristine binds to the tubulin in the microtubules ( spindle fibres) and prevents them from functioning properly . This stops the spindle fibres contracting  and pulling the chromatids apart ( prevents Anaphase) VERCRISTINE IS A MITOTIC POISION

Antimetabolies act as S-Phase Inhibitors preventing DNA Synthesis.= Fluoroacil - inhibits an enzyme involved in making nucleotides that contain the base Thyamine. This prevents DNA synthesis. Chemotherapy Drugs can affect the normal cells as well ascancer cells . Anti Cancer drugs can also stop ordinary cells dividing. Leads to unpleasant side effects to the patients recieving Chemotherapy

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Graph for Amount of DNA in Cell Cycle

DNA doubles during DNA replication and chromatid formation.

DNA is then Halved during Cytokinesase as DNA is divided between two daughter cells

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Chromasomes consist of an ectended DNA molecule sipported by special proteins called Histones. Chromatin condenses to form Visible Chromosomes during Nuclear Division

DNA coils tightly around the stack to form a structure called a Nucleosome.

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Difference in Mitosis and Meiosis


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Functions of Cross Sections

  • Serosa = outer layer of connective tissue providing very thin protective and supportive lining for the alimentary canal
  • Muscularis Externa = consists of an outer layer of longitudinal muscle and an inner layer of circular muscle. The Muscle causes pendular movement and contration of the circular muscle cause localised constrictions which churn and mix the food bolus and is transported by the peristalic movements - Antagonistic Contractions
  • Submucosa= largely comprised of connective tissueand contains many blood vessels and lymphatic vessel - crucial for transporting absorbed food products
  • Muscularis Mucosa = thin layer of muscle that lies between the submucosa and the mucosa. It is important in moving the villi that are present in the mucosa. Increases the contact with the digested food in the gut lumen.- characteristic wafting movement of villi
  • Mucosa= layer in contact with the food in the gut lumen. Highly Specialised with increase SA due to presence of Villi and Microvilli
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Cell Functions

Columnar Epilthelium Cells = column-shaped cells .On their free surfaces the cells have microvilli forming brush borders. Since digestive enzymes are bound to the membrane of the microvilli. This provides a hugh surface area for digestion and for the adsorption of the products of digestion. Some substances are taken up partly by diffusion and partly by active transport. Others are taken up by Pinocytosis. Numerous Mitocondria aids ATP energy production. Short lived cells.

Goblet Cells= secrete mucus . Protects the epilthelium from action of digestive enzymes and lubricates the lining as solid material is pushed along.

 Villi= finger like projections which increase the SA for absorption of the digested products. The villi contain blood capillaries into which aminoacids and monosaccharides are absorbed and lacteals into which fats are absorbed.

Crypts of Lieberkuhn =  intestinal glands are found at the base of the villi. Cells along the sides secrete mucus. Stem Cells lining the bottom of the crypts are in a state of continous division. New cells are continously being pushed up by the division of the cells deeper down.

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Structure of Plant Cell


  • Waxy Cuticle - Prevents water loss amd provides waterproofing
  • Palisade Mesophyll Layer- photosynthesis . Rich in Chloroplasts
  • Spongy Mesophyll Layer-gas exchange- intercellular spaces
  • Xylem and Phloem - transport of ions and water moleucles
  • Stomata - Allow gas exchange . Allows water vapour to diffuse out of the leaf
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Niamh Meredith



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