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.