Defence Against Pathogens

Pathogens need to Enter an Organism for it to Spread Disease
Most Organisms have specific Defences in place to Prevent this from happening:

Skin - Physical Barrier Blocking Pathogens from Entering the Body. It is Also a Chemical Barrier because it Produces Chemicals that are Anti-Microbial and can Lower pH,  Inhibiting the Growth of Pathogens.

Mucous Membranes - Protect Body Openings exposed to the environment (Mouth, Nostrils, Ears e.t.c.) Some Membranes Secrete Mucous that Traps Pathogens and Contains Antimicrobial Enzymes.

Blood Clotting - A blood clot is a Mesh of Protein Fibres. Blood clots Plug Wounds to Prevent Pathogen Entry and Blood Loss. They're Formed by a series of Chemical Reactions that take place when Platelets are Exposed to Damaged Blood Vessels

Inflammation - Swelling, Pain, Heat and Redness. Triggered by Tissue Damage which Releases Molecules which Increase the Permeability of Blood Vessels so they Leak Fluid to the Surrounding Area causing Swelling and helps Isolate any Pathogens. The Molecules cause Vasodilation (Blood Vessels get Wider) which Increases Blood Flow to the affected area. This makes the area Hot and brings White Blood Cells to the affected area to Fight Off any Pathogens.

Wound Repair - The Skin is able to Repair Itself in the event of an Injury. It reforms a Barrier against Pathogen Entry. The Surface is Repaired by the Outer Layer of Skin Cells Dividing and Migrating to the Edges of the Wound. It then Contracts to bring the Edges of the Wound Closer Together. It is Repaired using Collagen Fibres. If there are too many collagen fibres, you'll get a Scar.

Expulsive Reflexes - This is basically Coughing and Sneezing. A Sneeze is when the Mucous Membranes of the Nostrils become Irritated by things such as Dust or Dirt. A Cough is when the Lining of the Respiratory Tract becomes Irritated. Both Coughing and Sneezing are an attempt to Expel Foreign Objects, including Pathogens, from the body. They happen Automatically.

Plants
Plants have both Physical and Chemical Defences too
PHYSICAL

• Most plant Leaves and Stems have a Waxy Cuticle, which is a Physical Barrier against Pathogen Entry. It may also Stop Water Collecting on the Leaf which will Reduce Risk of Infection by Pathogens Transmitted through Water.
• Plant Cells are surrounded by Cell Walls, another Physical Barrier against Pathogens that make it Past the Waxy Cuticle
• Plants produce a Polysaccharide called Callose. It gets Deposited between Plant Cell Walls and Plasma Membranes during times of Stress, i.e. Pathogen Invasion. Callose Deposition might make it Harder for Pathogens to enter Cells. Callose Deposition at the Plasmodesmata (Small Channels in Cell Walls) may Limit Spread of Viruses Between Cells.

CHEMICAL

Plants also produce Antimicrobial Chemicals (Including Antibiotics) which either Kill Pathogens or Inhibit their Growth.

E.g.

• Some plants produce chemicals called Saponins. These Destroy Cell Membranes of Funghi and other Pathogens.
• Plants also Produce Chemicals called Phytoalexins, which Inhibit the Growth of Funghi and other Pathogens.

Other chemicals secreted by plants are Toxic to Insects - This reduces the amount of insects feeding on plants, therefore, Reduces the Risk of Infection by Plant Viruses carried by Insect Vectors.

Pathogens and Communicable Diseases

• DISEASE - A Condition that Impairs the Normal Functioning of an Organism.
• PATHOGEN - An Organism that Causes Disease. Different Types include Bacteria, Viruses, Fungi and Protoctista).
• COMMUNICABLE DISEASE - A Disease that can Spread between 2 Organisms.

See This Free Website for a Table of Stuff we Need To Learn

DIRECT TRANSMISSION

When a Disease is Transmitted Directly from one Organism to Another. This can happen in several ways. (Droplet Infection (Coughing or Sneezing tiny Droplets of Mucous or Saliva onto someone) Sexual Intercourse, or Touching an Infected Organism
e.g.
HIV - Transmitted via Sexual Intercourse
Athlete's Foot - Transmitted via Touch.

INDIRECT TRANSMISSION
When a Disease is Transmitted from one Organism to Another via an Intermediate. An Intermediate can be Air, Water, Food, or Another Organism (Vector)
E.g.
Potato/Tomato Late Blight - Transmitted when Spores are Carried Between Plants. First in the Air, then in Water.
Malaria - Spread between Humans via Mosquitoes (feed on  blood). The Mozzies are Vectors. They Don't Cause Malaria, but they Do Spread the Protoctista that Causes it.

Factors that Affect Disease Transmission
OVERCROWDING
Overcrowded Living Conditions Increase Transmission of many Communicable Diseases.
e.g. TB - Spread via Droplet Infection and is Indirectly Spread because Bacteria can Stay in the Air for a Long Time.

CLIMATE
e.g.
Potato/Tomato Late Blight - Becomes Common during Wet Summers because the Spores need Water to Spread.
Malaria - Common in Tropical Countries because they are Humid and Hot. These are Ideal Conditions for Mosquitoes to breed.

SOCIAL FACTORS
e.g. HIV - The Risk of Infection is High when there is Limited Access to:

• Good Healthcare - Less likely to be Diagnosed and Treated and the Most Effective Drugs would be less likely to be Available, so it is More Likely to be Passed on.
• Good Health Education - Informing people about How it is Transmitted and How it can be Avoided (i.e. Safe Sex)

Co-factors and Enzyme Inhibition

Cofactor - a Substance that is Required by Enzymes for them to work.
Enzyme Inhibitor - a Substance that Stops Enzymes doing their job. (some are harmful, others can be used for medicines).

Cofactors and Coenzymes
Some Enzymes will Only Work if there is Another Substance Attached to it. These are Non-Proteins and are called Cofactors.

Some of these are Inorganic Molecules (or Ions). They work by Helping the Enzyme and Substrate to Bind Together. They Don't directly Participate in the Reaction, so are Not Used up or Change in any way. An example would be Chloride Ions (Cl-) which are Cofactors for Amylase (in Saliva)

Other Cofactors are Organic, these ones are called Coenzymes. Unlike the Inorganic Cofactors, these Do Participate in Reactions and Are Changed by it (They're like a second substrate). They often act as Carriers, moving Chemical Groups between Different Enzymes. They're Continually Recycled during this process. Vitamins are often Sources of Coenzymes.

If a Cofactor is Tightly Bound to the Enzyme, it's known as a Prosthetic Group. For Example, Zinc Ions: (Zn2+) are a Prosthetic Group for Carbonic Anhydrase (An Enzyme in Red Blood Cells) which Catalyses the Production of Carbonic Acid from Water and Carbon Dioxide.The Zinc Ions are a Permanent part of the Enzyme's Active Site.

Inhibitors
Enzyme Activity can be Prevented by Enzyme Inhibitors, which are Molecules that Bind to the Enzyme they Inhibit. There are two types of Inhibitors, Competitive and Non-Competitive:

COMPETITIVE INHIBITION

• These molecules have a Similar Shape to the Substrate molecules.
• They Compete with the Substrate molecules to Bind with the Active Site
• Instead, they Block the Active Site, so No Substrate molecules can Fit in it.
• The Level of Inhibition depends on the Relative Concentrations of  the Inhibitors and the Substrates. e.g. if the Concentration of the Inhibitor is High, it will take up nearly all of the Active Sites, meaning that Fewer Substrates will get to the Active Sites of the Enzymes. Vice Versa, High Conc. of Substrate, Higher Rate of Reaction.

NON-COMPETITIVE INHIBITORS

• These Bind to the Enzymes Away from the Active Site, the point where they attach is called the Allosteric Site.
• This causes the Active Site to Change Shape so Substrates can No Longer Bind to it.
• Increasing the Concentration of Substrate WILL NOT make any Difference to the Reaction Rate.

REVERSIBLE AND IRREVERSIBLE INHIBITORS

The Strength of the Bonds between the Enzyme and the Inhibitor decides which one they are:

• If they're Strong Covalent Bonds, the Inhibitor Cannot be Removed Easily and the Inhibition is Irreversible.
• If they're Weaker Hydrogen Bonds or Weak Ionic Bonds, the Inhibitor Can be Removed Easily and the Inhibition is Reversible.

DRUGS AND POISONS

Some Medicines are Enzyme Inhibitors, e.g.

• Some Antiviral Drugs, Inhibit the Enzyme that Catalyses the Replication of Viral DNA.
• Some Antibiotics (e.g. Penicillin) Inhibits the Enzyme that Catalyses the Formation of Proteins in Bacterial Cell Walls. This Weakens the Cell Wall and Prevents the Bacterium from Regulating its Osmotic Pressure. As a Result, The Cell Bursts and the Bacterium are Killed.

Metabolic Poisons Interfere with Metabolic Reactions (Reactions in Cells) which can cause Illness or even Death.

• Cyanide - an Irreversible Inhibitor of an Enzyme that Catalyses Respiration Reactions. Cells that Can't Respire will Die.
• Malonate - Inhibits another Enzyme that Catalyses Respiration Reactions.
• Arsenic - Also inhibits an enzyme with a silly long name we don't need to know, but we do need to know that it Catalyses Respiration Reactions.

METABOLIC PATHWAYS

A Metabolic Pathway is a Series of Connected Metabolic Reactions - The Product of the First Reaction Takes Part in the Second Reaction and so on. Each Reaction is Catalysed by a Different Enzyme.

Many Enzymes are Inhibited by the Product of the Reaction they Catalyse. This is called Product Inhibition.

End Product Inhibition is when the Final Product of a Metabolic Pathway Inhibits an Enzyme that has Catalysed a Previous Reaction.

End Product Inhibition can be used to Regulate the Pathway and Control the amount of End Product that gets made.

For Example, 

• Phosphofructokinase (That's a great scrabble word) Is an Enzyme that is Involved in the Metabolic Pathway that Produces ATP by Breaking Down Glucose.
• ATP Inhibits the Action of Phosphofructokinase - so a High level of ATP Inhibits the Production of ATP.

Both Product and End-Product Inhibition are Reversible, So when the Level of Product starts to Drop, the Level of Inhibition will start to Drop too, so the Enzyme can start to Function again so More Product can be made.

Factors Affecting Enzyme Activity

P.E.S.T. There are 4 main factors that affect Enzyme Activity. PH Level, Enzyme Concentration, Substrate Concentration, and Temperature. We already know enzymes are picky about their working condition, so anything less than perfect will mean that an enzyme could become Denatured, which means it Shrivels Up and can no longer function the way it is supposed to.

Here it is explained:

pH LEVEL

All Enzymes have an Optimum pH Level. Most Human Enzymes work best at pH Level 7, but there are exceptions such as Pepsin, which is found in the Stomach has an Optimum pH Level of 2, which is Acidic.
If the conditions are Above or Below Optimum pH, the H+ and OH- ions found in Acids and Alkalis can mess up the Ionic Bonds and Hydrogen Bonds that hold the Tertiary Structure in place. This makes the Active Site Change Shape, so the enzyme is Denatured.

ENZYME CONCENTRATION
The More Enzyme Molecules there are in a Solution, the More Likely a Substrate Molecule will Collide with it to form an Enzyme-Substrate Complex. So Increasing the Concentration of the Enzyme Increases the Rate of Reaction.
If the amount of Substrate is Limited, there comes a point where Adding Enzymes has No Further Effect on the Rate of Reaction.

SUBSTRATE CONCENTRATION
The Higher the Substrate Concentration, the Faster the Reaction due to a Lower Activation Energy. More Substrate Molecules mean that Collisions between Enzymes and Substrates is More Likely to happen, so more Active Sites will be used.
However, this is only true up to a point, this point is called the Saturation Point. After this point, there are so Many Substrate Molecules, all the Active Sites are Full, so Adding more Substrate Molecules will have No Effect on the Rate of Reaction.
Over time, the Reaction takes place, so the Substrate Concentration Decreases (unless more substrate molecules are added), so if there are no other variables, the Rate of Reaction will Decrease Over Time too. This makes the Initial Rate of Reaction the Highest Rate of Reaction.

TEMPERATURE
The Temperature Coefficient symbolised as Q10, Shows How Much the Rate of Reaction Changes when the Temperature is Raised by 10 Degrees Celcius.
At temperatures before the optimum, the Q10 Value of 2 means the Rate Doubles when the Temperature is Raised by 10 Degrees Celcius. A Q10 Value of 3 means that the Rate of Reaction Trebles.
Most Enzyme Controlled Reactions have a Q10 Value of 2.

(In the exam, you might be asked to calculate the rate of reaction. after I have finished all the content, I will write a separate post on all the horrible calculations).

Enzymes

Enzymes are Biological Catalysts. A Catalyst is a Substance that Speeds Up a Chemical Reaction Without Being Used in the reaction.

Enzymes Catalyse Metabolic Reactions, both within a Cell (e.g. respiration) or within the Organism as a Whole (e.g. Digestion). They can Affect Structures in an organism (i.e. The Production of Collagen which is an important protein in the connective tissues of mammals). Enzyme Action can either be Intracellular (within cells) or Extracellular (outside cells).

EXAMPLES

Catalase (Intracellular)

1. Hydrogen Peroxide (H2O2) is  a By-product of several cellular reactions. It is also Toxic, so if it is left to build up, it can Kill Cells.
2. Catalase is an Enzyme that, inside cells, speeds up the Breakdown of H2O2 to Oxygen (O2) and Water (H2O).

Amylase and Trypsin (Extracellular)

1. Both of these work outside the cells in the Human Digestive System.
2. Amylase is found in Saliva. It is Secreted into the Mouth via the Salivary Glands. It Catalyses the Hydrolysis of Starch Into Maltose in the mouth.
3. Trypsin Catalyses the Hydrolysis of Peptide Bonds - It turns Big Polypeptides into Smaller Polypeptides. The enzyme is Produced in the Pancreas and Secreted into the Small Intestine.

Enzymes are Globular Proteins. They all have an Active Site which has a Specific Shape. The active site is the part of the enzyme that the molecules that interact with it (called Substrates) bind to. The Specific Shape of an Active Site is Determined by the Enzyme's Tertiary Structure. For the enzyme to work, the Substrate Shape has to Fit into the Active Site. Otherwise, the Reaction Would Not be Catalysed. This means that Enzymes usually only work with One Substrate.

Activation Energy

In any reaction, a certain amount of Energy is Required by the Reactants Before the Reaction can Start. This quantity is called the Activation Energy. It is often Heat. 

Enzymes Reduce the amount of Activation Energy required, so reactions can happen at a Lower Temperature than they would without an enzyme. This Speeds Up the Rate of the Reaction.

When a Substance Binds to an enzyme's Active Site, an Enzyme-Substrate Complex is formed. This is what Lowers the Activation Energy. There are two reasons why this happens:

• If two Substrate molecules need to be Joined, Attaching to the Enzyme brings them Closer Together, Reducing any Repulsion between molecules so it is Easier for them to Bind.
• If an Enzyme is Catalysing a Breakdown Reaction, Fitting into the Active Site puts Strain on the Bonds in the Substrate. This means it is Easier for the Substrate to Break Up.

LOCK AND KEY MODEL

Enzymes only work with Substrates that Fit their Active Site. Early scientists came up with this theory, that the Substrate fits into the Enzyme similar to the way a Key fits into a Lock. However, this was found to be Incomplete, as Enzymes were found to Change Shape slightly to complete the fit. The original model was modified into the Induced Fit Model.

INDUCED FIT THEORY
It helps to explain why Enzymes are so Specific. Not only does the Substrate have to be the Right Shape to fit the Active Site, It has to make the Active Site Change Shape in the right way too.

Transcription and Translation

Okay, this is the complicated bit, or it is to me anyway :)
Something to note is that I sometimes use my own Abbreviations because I'm lazy and in need of a coffee, anyone taking the exam: Unless its mRNA, tRNA, DNA, rRNA e.t.c. write it in full (i.e. Write Amino Acids, not AAs) otherwise, you might be marked down for not using proper terminology. 
Feel Free to comment any questions you have :)
TRANSCRIPTION

1. RNA Polymerase (an enzyme) Attaches to the DNA Double Helix at the Beginning of a Gene.
2. The Hydrogen Bonds Break, separating the two strands, so the DNA Molecule Uncoils.
3. One of the Strands is then used as a Template to make an mRNA Copy.
4. The RNA Polymerase lines up free RNA Nucleotides next to the Template Strand.
5. The Complimentary Base Pairs are found (A-T) (C-G) - Except for Adenine (A) which is paired with Uracil (U) instead of Thymine (T).
6. The Complimentary Base Pairs are Joined together forming an mRNA Molecule.
7. RNA Polymerase moves along the DNA Separating Strands and Assembling the mRNA Strand.
8. Hydrogen Bonds Form once the RNA Polymerase has Moved on and the Strands Coil back into a Double Helix.
9. When RNA Polymerase reaches a Stop Codon it Stops making mRNA and Detaches from the DNA.
10. mRNA moves out of the nucleus through a Nuclear Pore and Attaches to a Ribosome in the Cytoplasm.

TRANSLATION

It occurs at the Ribosomes in the Cytoplasm. The AAs are Joined together to make a Polypeptide Chain Following the Sequence of Codons carried by the mRNA.

1. The mRNA Attaches itself to a Ribosome and Transfer RNA molecules (tRNA) carry AAs to the Ribosome.
2. A tRNA molecule with the Anticodon (A-U-G's Anticodon is U-A-C) and Attaches itself to the mRNA  by Complimentary Base Pairing.
3. A Second tRNA molecule Attaches itself to the Next Codon on the mRNA in the Same Way.
4. rRNA in the Ribosome Catalyses the Formation of a Peptide Bond between the Two AAs attached to the tRNA molecules. This joins the AAs together. The First tRNA molecule Moves Away leaving the AA behind.
5. A Third tRNA Binds to the Next Codon on the mRNA. Its AA Binds to the First Two and the Second tRNA Moves Away.
6. This Process Repeats producing a Chain of Linked AAs (Polypeptide Chain) Until there is a Stop Codon on the mRNA molecule
7. The Polypeptide Chain Moves Away from the Ribosome and the process is complete.

Genes and Protein Synthesis

INSTRUCTIONS
DNA contains Genes which are Instructions for Making Proteins.

• A Gene is a Sequence of DNA Nucleotides that Codes for a Polypeptide.
• The Sequence of Amino Acids (AAs) in a Polypeptide chain forms the Primary Structure of a Protein.
• Different Proteins have a Different Number and Order of AAs
• The Order of the Nucleotide Bases in a Gene that determines the Order of AAs in a particular Protein.
• Each AA is Coded for by a Sequence of 3 Bases (called a Triplet) in a Gene.
• Different Sequences of Bases code for Different AAs, So the Sequence of Bases in DNA is a Template used to make Proteins during Protein Synthesis

DNA IS COPIED INTO RNA

• DNA is found in the Nucleus of the cell. However, the Organelles that make Proteins are found in the Cytoplasm.
• DNA is Too Big to move Out Of The Nucleus.
• A Section of DNA is Copied into mRNA. This bit is called Transcription.
• The mRNA Leaves the Nucleus and Joins with a Ribosome in the Cytoplasm, where it can Synthesise a Protein

RNA

RNA is a Single Polynucleotide Strand and is similar to a single DNA strand, but instead of Thymine (T) it contains Uracil (U). There are 3 types of RNA we need to know about:

MESSENGER RNA (mRNA)

• It is Made in the Nucleus.
• Three Adjacent Bases are called a Codon.
• It Carries the Genetic Code from the DNA in the Nucleus to the Cytoplasm where it is used for Protein Synthesis (Translation)

TRANSFER RNA (tRNA)

• Found in the Cytoplasm
• It has an AA Binding Site at one end and a Sequence of 3 Bases at the other end, which is called an Anticodon.
• It Carries the AAs that are used to make Proteins with the Ribosomes during Translation.

RIBOSOMAL RNA (rRNA)

• Forms the Two Subunits in a Ribosome.
• The Ribosome Moves along the mRNA strand during Protein Synthesis. The rRNA in the Ribosome helps to Catalyse  the Formation of Peptide Bonds between the AAs.

THE GENETIC CODE

The Genetic Code is the Sequence of Base Triplets (Codons) in DNA or mRNA. It Codes for Specific AAs.

Within the genetic code, each Codon is Read in Sequence, separate from the codon before and after it.

Base Triplets don't share their Bases, so they are 'Non-Overlapping'.

There are More Possible Combinations of Triplets Than there are AAs (20AAs = 64 Possible Triplets). We call this Degenerate. Because of this, some AAs are coded for by More Than One Base Triplet, i.e. Tyrosine can be coded for by either UAU or UAC

Some triplets tell the cell when to Start/Stop Production of the Protein, unsurprisingly, these are called Start and Stop Signals. (or Start/Stop Codons). They're found at the Beginning and End of the Gene. An example is UAG (Stop)

The genetic code is also Universal. The Same Specific Triplets Code for the Same AAs in All living organisms.

Polynucleotides & DNA

Nucleotides --> Polynucleotides

• The Nucleotides Join Together between the Phosphate group of one nucleotide, and between a Sugar of another. This forms a Phosphodiester Bond (made up of the phosphate group and two ester bonds - Phospho-Di-Ester)
• The chain of Sugars and Phosphates is known as the Sugar-Phosphate Backbone
• Polynucleotides can be Broken Down into Nucleotides again by Breaking the Phosphodiester Bonds.

Double Helix

• Two Polynucleotides join together by Hydrogen Bonding Between the Bases.
• Each base can only bond with a particular partner: this is called Complimentary Base Pairing.
• Adenine (A) always pairs with Thymine (T) and Cytosine (C) always pairs with Guanine (G) (I remember it as the straight letters go together, and the curly letters go together)
• A Pyrimidine always pairs with a Purine.
• 2 Hydrogen bonds form between A-T and 3 Hydrogen Bonds form between G-C
• Two Antiparallel (going in opposite directions) polynucleotide Strands Twist to form the DNA Double Helix

Purifying DNA - Precipitation Reaction

1. Break Up Cells using a blender
2. Make a mixture of washing up liquid, salt, and distilled water, this mixture is called the Detergent
3. Add broken cells to a beaker containing the detergent
4. Put the beaker in a Water Bath (60°C) for 15 Minutes.
5. Now, put the beaker in an Ice Bath, then Filter the mixture.
6. Transfer a small amount of the filtered mixture to a clean boiling tube.
7. Add Protease Enzymes
8. Slowly Dribble some cold ethanol down the side of the boiling tube so it forms a Layer on top of the mixture.
9. Leave it for a few minutes and a White Precipitate should form, which can be removed with a Glass Rod.

Self-Replication

DNA can Copy Itself before cell division

1. DNA  Helicase (Enzyme) Breaks the Hydrogen Bonds Between Two polynucleotide DNA Strands - The helix Unzips.
2. Each Original Strand becomes a Template for a new strand. Free-Floating DNA Nucleotides Join to the exposed bases of each original strand by Complementary Base Pairing.
3. The Nucleotides of the New Strand are joined together by DNA Polymerase (Another Enzyme). This forms the Sugar-Phosphate Backbone. Hydrogen Bonds Form between the bases on the Original and New Strand. It then Twists to form a Double Helix.
4. Each new DNA molecule contains One strand from the Original DNA Molecule and One New Strand

Nucleotides

• A Nucleotide is yet another type of Biological Molecule, it's made from a Pentose Sugar, a Nitrogenous Base and a Phosphate Group.
• All Nucleotides contain the elements, Phosphorus, Oxygen, Nitrogen, Carbon and Hydrogen 

• Nucleotides are the Monomers that make up DNA and RNA
• ADP and ATP are Special types of Nucleotides used to Store and Transport Energy in cells

Deoxyribose (Shown Above)

• The pentose sugar in a DNA nucleotide is 'Deoxyribose'
• Each DNA Nucleotide has the Same Sugar and Phosphate Group, it is the Base on each DNA nucleotide that Varies.
• There are 4 possible bases, Adenine (A), Thymine (T), Guanine (G) and Cytosine (C)
• Adenine and Guanine are a type of base called Purine.
• Thymine and Cytosine are a type of base called Pyrimidine.

• Purine: contains 2 Carbon-Nitrogen Rings joined together
• Pyrimidine: Only 1 Carbon-Nitrogen Ring - so it is Smaller than purine.
• A Molecule of DNA contains Two Polynucleotide Chains - each chain having lots of nucleotides joined together.

Ribose 

• RNA contains Nucleotides with a Ribose sugar instead of deoxyribose.
• An RNA molecule also has a Phosphate group, and one of four different bases.
• However, in RNA, Uracil (U), which is a Pyrimidine, Replaces Thymine as a base.
• An RNA molecule is made up of a Single Polynucleotide Chain

ADP and ATP

• To Phosphorylate a nucleotide, you Add One or More Phosphate Groups to it.
• ADP (Adenosine Diphosphate) contains the base Adenine, the sugar Ribose and Two Phosphate Groups.
• ATP (Adenosine Triphosphate) contains the base Adenine, the sugar Ribose, and Three Phosphate Groups.

ADP, ATP and Energy

• ATP provides Energy for Chemical Reactions in the Cell.
• ATP is Synthesised from ADP and Inorganic Phosphate (Pi) using the Energy From an Energy-Releasing Reaction, (e.g. the breakdown of glucose in respiration.
• The ADP is Phosphorylated to form ATP and a Phosphate Bond is formed.
• Energy is Stored in the Phosphate Bond. When this Energy is Needed by a cell, ATP is Broken Back Down into ADP and Inorganic Phosphate (Pi). The Energy is Released from the Phosphate Bond and Used by the Cell.

Biochemical Tests and Separating Molecules

Biosensors
A Biosensor is a device that uses a Biological Molecule, such as an Enzyme to detect a Chemical.
The biological molecule produces a Signal (i.e. a chemical  signal) which is Converted into an Electrical Signal by a Transducer.
The electrical signal is then processed and can be used to work out other information.

Example:
A Glucose Biosensor is used to determine the Concentration of Glucose in a Solution.
It does this using the enzyme 'Glucose Oxidase' and Electrodes.
The enzyme Catalyses the Oxidation of glucose at the Electrodes. this creates a Charge, which is Converted into an Electrical Signal by the Electrodes (Transducer)
The Electrical Signal is then Processed to work out the Initial Glucose Concentration

Chromatography
The main use is Separating.
Once a solution is separated, we can Identify the Components.
It can be used to Identify Biological Molecules such as Amino Acids, Carbohydrates, Vitamins and Nucleic Acids.
There are loads of different types of chromatography, but we only need to know two, Paper Chromatography and Thin-Layer Chromatography.

Both methods of chromatography have two basic phases:
A MOBILE PHASE

• Where the Molecules Can Move
• in both paper and thin-layer chromatography, the Mobile Phase is a Liquid Solvent, such as Ethanol or Water.

A STATIONARY PHASE

• Where the Molecules Can't Move
• In Paper chromatography, the stationary phase is a piece of Paper.
• In Thin-Layer Chromatography, the stationary phase is a Thin (<0.5mm) Layer of a Solid, i.e. Silica Gel, Glass or Plastic.

They both use the same basic method:

1. The Mobile Phase moves Through or Over the Stationary Phase, 
2. The Components in the mixture spend Different amounts of Time in the Mobile phase And the Stationary phase.
3. The Components that spend Longer in the Mobile phase travel Faster or Further.
4. The time spent in the different phases is what separates out the components of the mixture.

PAPER CHROMATOGRAPHY

1. Draw a pencil line near the bottom of the chromatography paper and put a concentrated spot of the mixture of amino acids on it.
2. Add a small amount of prepared Solvent in a beaker and Dip the bottom of the paper into it. Cover it with a lid to stop the solvent evaporating.
3. As the solvent spreads up the paper, the different amino acids move with it, but at different rates, so they separate out.
4. When the solvent's nearly reached the top, Take the paper Out and Mark the Solvent Front (the highest point the solvent has reached), now leave the paper to Dry before analysing it.
5. Since amino acids are colourless, Spray them with Ninhydrin solution to turn the amino acids purple, then use the Rf values to Identify the separated molecules.

Colorimetry

Colorimetry is used to determine the Concentration of a Glucose Solution.

• To do this, we need to use Benedict's Reagent and a Colorimeter to get an Estimate of how much Reducing Sugar there is in a solution.
• A Colorimeter measures the strength of a coloured solution by detecting how much Light Passes Through it, the More Concentrated the colour, the Higher the Abundance of Reducing Sugars

PAST PAPER QUESTION!

Describe how the concentration of a reducing sugar can be measured using a colorimeter?

Using Known Concentrations of reducing sugar (1)

Heat with Benedict's Solution at least 80°C (1)

The Colour Changes to  green, yellow, orange, brown or (brick) red (1)

Then press zero on the colorimeter by using  a Blank Cuvette With Benedict's solution. (1)

Then take a Reading of Transmission (how much light passes through the cuvette) of the Solution. (1)

Plot a Calibration Curve for Transmission against Reducing Sugar Concentration then use the reading of the Unknown Sugar Solution and read off graph to find the Concentration of the Unknown sugar solution (1)

Biochemical Tests for Molecules

This is just loads of practicals involving biological molecules we need to know how to do.

Benedict's Test for Sugars
Sugar is a general term for Monosaccharides and Disaccharides. All sugars can be classed as Reducing or Non-Reducing. The Benedict's Test Differs depending on the Type of Sugar you are testing for.

BENEDICT'S TEST FOR REDUCING SUGARS

• Reducing sugars include All Monosaccharides (i.e. glucose) and some Disaccharides (i.e. maltose and lactose)
• To the sample, we need to add Benedict's Reagent (It's blue).
• now we need to heat it up and Bring it to the Boil. This is usually done in a Water Bath.
• The colour should go: BLUE>GREEN>YELLOW>ORANGE>BRICK-RED
• If the test is Positive, the Precipitate will Change Colour. The Higher the Concentration of reducing sugars, the Further the Colour Change will go.
• We can use this to compare the amount of reducing sugar in different solutions, however, weighing would be a more reliable alternative.

BENEDICT'S TEST FOR NON-REDUCING SUGARS

• If the result of the above test is negative, it could still have non-reducing sugars in the solution, such as sucrose. But first, we have to Break Them Down into Monosaccharides.
• For this, you will need a New Sample of the Test Solution.
• Add Dilute Hydrochloric Acid and Heat It in a water bath that has been Brought to the Boil.
• Then Add Sodium Hydrogencarbonate to neutralise the solution. Then carry out Benedict's test for Reducing Sugars as explained above. 
• If the solution forms a precipitate which is not blue, the solution contains non-reducing sugars.
• If the solution remains blue, there are no sugars present.

Test Strips for Glucose

Glucose can be tested for using Test Strips coated in a Reagent. The strips are Dipped in a Test Solution and Change Colour if Glucose is Present. The test strip can be Compared to a Chart to Estimate the Concentration of Glucose present. This is used in Urine Tests, which may indicate Diabetes.

Iodine Test for Starch

• Add iodine dissolved in Potassium Iodide solution to the test sample.
• If Starch is Present, the sample will change from brown/orange to Blue/Black.
• If there's no starch, the sample will stay brown/orange

Biuret Test for Proteins.

There are 2 stages:

1. The test solution must be alkaline, so we need to add a few drops of Sodium Hydroxide solution.
2. Then add Copper (II) Sulphate solution.

If Proteins are Present, the solution turns purple.

If no proteins are present, the solution will stay blue.

Emulsion Test for Lipids

• Add Ethanol to the Test Sample, and Shake Well for 60s.
• Then pour the solution into a test tube of Water.

If Lipids are Present, the solution will turn Milky.

If no lipids are present, the solution will remain clear.

Inorganic Ions

• An Ion is an Atom (or group of atoms) with an Electric Charge
• An Ion with a Positive charge is a Cation
• An Ion with a Negative charge is an Anion
• An Inorganic Ion is one that Doesn't Contain Carbon (mostly!)

We need to know about 5 cations and 5 anions:

Name of Ion	Chemical Symbol	Examples of roles in biological processes.
Calcium	Ca2+	The Transmission of Nerve Impulses and the Release of Insulin from the pancreas. It acts as a Cofactor for many enzymes. Also important in Bone formation
Sodium	Na+	For Generating Nerve Impulses for Muscle Contraction and for Regulating Fluid Balance in the body.
Potassium	K+	Generating Nerve Impulses, for Muscle Contraction and Regulating Fluid Balance. It activates Enzymes needed for Photosynthesis in plants
Hydrogen	H+	Affects the pH of Substances  if the amount of H+ is greater than the amount of OH- then it is an acid, vice versa is an alkali. Also Important for Photosynthesis Reactions in the thylakoid membranes inside chloroplasts
Ammonium	NH4+	Absorbed from the Soil by the plants and is an important Source of Nitrogen (used to make amino acids and nucleic acids)
Nitrate	NO3-	Exactly the same as NH4+
Hydrogencarbonate	HCO3-	Acts as a Buffer to help maintain the pH of the Blood
Chloride	Cl-	Involved in the 'Chloride Shift' which helps to Maintain pH of the Blood during Gas Exchange. Acts as a Cofactor for Amylase (an enzyme). Also involved in some Nerve Impulses
Phosphate	PO43-	Involved in Photosynthesis and Respiration Reactions. It is needed for the Synthesis of many Biological Molecules such as Nucleotides including ATP, Phospholipids and Calcium Phosphate (strengthens bones)
Hydroxide	OH-	Affects the pH of Substances (see H+)

Biological Molecules

Water

Water makes up 70-80% of a cell.
FUNCTIONS

• It's a reactant in important chemical reactions, including Hydrolysis.
• It's a Solvent - which means substances can dissolve in it. Most biological reactions take place in a solution.
• It Transports substances. it is good at this because it is a Liquid and is a Solvent.
• It helps with Temperature Control because it has a High Specific Heat Capacity and a High Latent Heat of Evaporation.
• Water is a Habitat. many organisms can survive and reproduce in it.

STRUCTURE

• H₂O is the chemical formula for water. This means that in every molecule of water, there are 2 Hydrogen atoms, and 1 Oxygen atom. The hydrogen atoms are joined to the oxygen atom by a Covalent Bond, which simply means it Shares Electrons.

• Because the Shared Negative Hydrogen Electrons are pulled Towards the Oxygen atom, each hydrogen atoms are left with a Slight Positive Charge.
• The Unshared Electrons on the Oxygen atom give it Slight Negative Charge.
• This makes water a Polar Molecule. its slightly negatively charged on one side, and slightly positively charged on the other.

• The δ sign is called 'Delta' and just means 'Slight', so δ- is delta negative, so it has a slightly negative charge. δ+ is delta positive, so it has a slightly positive charge.
• The slightly negatively charged Oxygen atoms Attract the slightly positively charged Hydrogen atoms of Other Water Molecules. this is called Hydrogen Bonding and gives Water some of its useful properties.

PROPERTIES

• High Specific Heat Capacity
• specific heat capacity is the energy needed to increase the temperature of 1 gram of a substance by 1°C.
• Hydrogen Bonds between water molecules can Absorb a lot of Energy
• Basic terms - it takes a Lot of Energy to Heat It Up.
• Water doesn't have rapid temperature changes, meaning it is a Good Habitat - the temperature underwater is likely to be more stable than it is on land.
• High Latent Heat of Evaporation
• It takes a Lot of Energy to Break the Hydrogen Bonds between water molecules.
• Therefore, lots of energy is used up when it evaporates.
• this is great for organisms because water is Good at Cooling things down. This is why some mammals sweat when they're too hot. when sweat evaporates, it cools the surface of the skin.
• Very Cohesive
• Cohesion is the Attraction Between Molecules of the Same Type. Water molecules are very cohesive because they are polar.
• This helps water to Flow, making it good for Transporting Substances.
• It also helps water to be Transported Up Plant Stems in the transpiration stream.
• Good Solvent
• Lots of important substances are Ionic (e.g. salt) which means they consist of one positively charged atom or molecule, or one negatively charged atom or molecule
• Because water is polar, the delta positive end of a water molecule will be attracted to the negative ions and vice-versa. (Opposites Attract!)
• This means the Ions will get Completely Surrounded by Water Molecules, i.e. they dissolve.
• Less Dense When Solid
• At low temperature, water freezes - it turns from liquid to solid.
• In ice, Water Molecules are Held Further Apart than they are in a liquid state, because each molecule forms four hydrogen bonds to other water molecules, making a Lattice Shape. because of this, ice is less dense than water and this explains why ice floats.
• This is useful for organisms because, in cold temperatures, Ice Forms an Insulating Layer on top of the water, which is why the Water Below Doesn't Freeze. So organisms that live in water don't freeze and can still move around when it's cold.

Carbohydrates

Carbohydrates are Polymers. This simply means it is a molecule made up of many similar, smaller molecules (Monomers) bonded together.
The monomers that make up carbohydrates are called Monosaccharides.
Glucose is a monosaccharide with Six Carbon Atoms. This means it is a HEXose monosaccharide.
There are two forms of glucose, Alpha (α) and Beta (β). They both have a Ring Structure.

In this diagram, each line represents a bond between atoms or molecules. As you can see, the H and OH, highlighted in blue and pink, are opposite in the Alpha and Beta Glucose Molecules.
The structure of Glucose is related to its function as the Main Energy Source in animals and plants. the ring structure makes it Soluble so it can be Easily Transported. the bonds contain a lot of energy.
Ribose is a structure with 5 Carbon Atoms - so it is a Pentose Monosaccharide. Unfortunately, this is another silly diagram we need to know how to draw. (NOTE: WE DO NOT NEED O LEARN ABOUT DEOXYRIBOSE! ... I couldn't crop the picture...Also, we can ignore the numbers, that's chemistry stuff!)

Monosaccharides are joined together by Glycosidic Bonds.
During synthesis, (The combination of components to make a connected whole), Hydrogen atom on one monosaccharide bonds to a hydroxyl Group (OH) on the other Releasing a Molecule of Water. this is called a Condensation Reaction. The opposite of this is called Hydrolysis. This is where a Molecule of Water Reacts with the Glycosidic Bond, breaking it apart.
A Disaccharide is when Two Monosaccharides join together.
There are a few more disaccharides we need to know about:
Maltose - When Two Alpha Glucose molecules are joined together by a glycosidic bond.
Sucrose - Alpha Glucose and Fructose
Lactose - Beta Glucose and Galactose
Amylose - Lots of Alpha Glucose joined by glycosidic bonds, this is a Polysaccharide (when More Than Two Monosaccharides are joined together).

The three main Polysaccharides we need to know about are:

STARCH

1. Cells get energy from glucose. Plants Store Excess Glucose as Starch. So when a plant needs more energy, it Breaks Down Starch to Release the Glucose
2. Starch is a mixture of two polysaccharides, Amylose and Amylopectin:

Amylose	Amylopectin
A Long, Unbranched chain of Alpha Glucose.	A long, Branched chain of Alpha Glucose.
Angles of the glycosidic bonds make a Coiled Structure, almost cylindrical	The Side Branches allow the Enzymes that break down the molecule to get to the Glycosidic Bonds Easily.
This makes it Compact, so it's really Good for Storage because you can fit more in a small space.	This means the Glucose can be Released Quickly

  3.  Starch is Insoluble In Water, so it doesn't enter cells by osmosis, which would make them swell. This makes it good for storage.

GLYCOGEN

1. Animal cells get energy from glucose too. But Animals Store Excess Glucose as Glycogen, which is another polysaccharide of alpha glucose.
2. The structure of glycogen is very similar to amylopectin, except it has Lots more Side Branches, which allows stored glucose to be Released Quickly when it is needed.
3. It's also very Compact, making it Good for Storage.

CELLULOSE

1. Cellulose is made of long Unbranched Chains of Beta-Glucose.
2. When Beta-Glucose molecules bond, they Form Straight Cellulose Chains.
3. The chains are linked together by Hydrogen Bonds to form strong fibres called Microfibrils. The strong fibres mean cellulose provides Structural Support for cells, i.e. in Cell Walls.

Lipids

Simple terms: Fatty Oily Things. Some of them are just straight-forward fats, but others have additional parts. We need to know about 3 types of lipids:

• Triglycerides
• Phospholipids
• Cholesterol

All Lipids contain Carbon, Hydrogen and Oxygen atoms.

TRIGLYCERIDES

• Triglycerides are Macromolecules - they're complex, with a relatively large molecular mass.
• Triglycerides have one molecule of Glycerol, with 3 Fatty Acids attached to it.
• The Fatty Acids have a Long Tail made of Hydrocarbons (hydrogen and carbon only) which are Hydrophobic, so they repel water molecules. this makes them Insoluble in Water.

• All fatty acids have the same basic structure, but the hydrocarbon tail varies. 
• The picture below shows the chemical structure of a fatty acid: C is carbon, O is oxygen, H is hydrogen. As you can see, there is a double bond between the C and the O. The rest are single bonds. The R represents the Variable Hydrocarbon Tail.

• Triglycerides are Synthesised by the formation of an Ester Bond between each Fatty Acid and the Glycerol molecule.
• The Ester Bond is Formed by a Condensation Reaction (water molecule released) This process is called Esterification.
• Triglycerides Break Down when the Ester Bonds are Broken. Each Ester Bond is Broken by a Hydrolysis Reaction (when a water molecule is used up).

There are two types of fatty acids: Saturated, and Unsaturated.

SATURATED

• Saturated means it has No Double Bond between Two Carbon Atoms. 
• The General formula is something we just have to learn and know how to use it. 
• For Saturated fatty acids, the formula is C_nH_(2n+1)COOH

UNSATURATED

• Unsaturated means it has, At Least One Double Bond between Two Carbon Atoms.
• The General Formula is the same as saturated fatty acids, so the only real difference is the double bond.

PHOSPHOLIPIDS

Phospholipids are also Macromolecules, so they look pretty similar to triglycerides, but instead of having one glycerol to 3 fatty acids, they have One Glycerol to Two Fatty Acids and One Phosphate Group

The Phosphate Group is Hydrophilic, so it attracts water molecules.

Structures & Functions of Triglyceride, Phospholipids and Cholesterol.

TRIGLYCERIDES	PHOSPHOLIPIDS	CHOLESTEROL
Energy Storing molecules	Found in the Cell Membranes of all Eukaryotes and Prokaryotes.	Hydrocarbon Ring  attached to  a Hydrocarbon Tail.
In Bacteria, it is used to Store Carbon too	They make up the Phospholipid Bilayer	Has a Polar Hydroxyl (OH) Group. (polar means it has a slightly negatively charged bit and a slightly positively charged bit).
They  are good for storage because: Long Hydrocarbon Tails  contain lots of Chemical Energy which is released when broken down Hydrophobic Tails  forces Triglycerides to bundle together as Insoluble Droplets with tails facing inwards, shielding themselves from water with their glycerol heads.	Phospholipid Heads are Hydrophilic, and their Tails are Hydrophobic, so they make a Double Bilayer with their heads facing outwards.	Small in size and Flattened shape - allowing Cholesterol to fit In Between the Phospholipid molecules in the Membrane
	The Centre of the Bilayer is Hydrophobic, so water soluble substances can't pass through easily.	They Bind to the Hydrophobic Tails of the Phospholipids, causing them to Pack more closely together - this makes the Membrane Less Fluid and More Rigid.

^^^Triglyceride - Insoluble droplets^^^

^^^Phospholipid Bilayer ^^^

^^^Cholesterol in the Bilayer^^^

Proteins
There are Millions of different proteins and they are essential to life.

• Proteins are Polymers.
• Amino Acid is the Monomer.
• A Dipeptide is when Two Amino Acids join together.
• A Polypeptide is when More Than Two Amino Acids join together.
• Proteins are made of one or more Polypeptides.

Amino Acids
All amino acids have the Same General Structure.

• 1 Carboxyl Group (-COOH)
• 1 Amino Group (-NH2)
• All attached to a Carbon Atom
• The only difference is the part labelled 'R' which is a Variable Atom

Peptide Bonds join Amino Acids together to form Dipeptides or Polypeptides. A Molecule of Water is Released during the reaction and the reverse of this reaction breaks the peptide bond (hydrolysis)

Primary Structure - The Sequence of amino acids:

Secondary Structure - The chain does not stay straight and flat. Hydrogen Bonds form Between the Amino Acids making it either coil into an α Helix or it folds into a β Pleated Sheet.

Tertiary Structure - The coiled and folded chain of amino acids is Coiled and Folded Further. For proteins made out of a single polypeptide chain, this phase forms their final 3D structure.

Quaternary Structure - Some proteins are made of more than one polypeptide chain. This phase is where the Different Polypeptide Chains are Assembled. i.e. haemoglobin is made of 4 polypeptides.

Different bonds hold together different structures of proteins:

1. Primary Structure - Peptide Bonds
2. Secondary Structure - Hydrogen Bonds between amino acids
3. Tertiary Structure - there's a few:
1. Ionic Interactions - Weak Attractions between the Positive and Negative parts of the molecule.
2. Disulphide Bonds - only when Two Molecules of an amino acid called Cysteine come Close Together, a Sulphur atom from Each Cysteine Join together.
3. Hydrophobic and Hydrophilic Interactions - when Hydrophobic Groups are Close together, they tend to Clump together, Pushing the Hydrophilic groups to the Outside
4. Hydrogen Bonds
4. Quaternary Structure - All of the above.

The shape of proteins relates to its function. There are two examples we need to know:

COLLAGEN

• A Fibrous protein
• Forms Supportive Tissues in animals, so it needs to be Strong.
• Made of 3 Polypeptide Chains Tightly Coiled into a Triple Helix.
• Chains are Interlinked by Strong Covalent Bonds
• Minerals can Bind to the Triple Helix to Increase its Rigidity.

HAEMOGLOBIN

• A Globular protein
• Contains a Haem Group with Iron in it that Binds to Oxygen, carrying it around the body.
• It has a Curled Up Structure.
• Hydrophilic Side Chains are on the Outside of the molecule, and Hydrophobic Side Chains face Inwards.
• This makes it Soluble in Water which makes it Good for Transport in the Blood.