Biology

Pathogens are microorganisms that cause disease, they can be bacteria, viruses or fungi.

To be considered a pathogen it must:

• Gain entry
• Colonise the tissues
• Resist the defences
• Cause damage to the tissues

Pathogens enter the body through the gas exchange system (water droplets in the air). They can also be carried into the stomach through food and water.

To prevent pathogens entering the body we have:

• Mucus layer to form a sticky barrier
• Enzymes to break down pathogens
• Stomach acid to kill pathogens

Pathogens cause disease by damaging the host tissues, this stops them from functioning properly. They also produce toxins which cause damage to the body.

Risk=a measure of the probability that damage to health will occur as a result of a given hazard.

Factors that increase the risk of cancer

• Smoking
• Diet and Obesity
• No physical activity
• Sunlight

Factors that increase the risk of coronary heart disease

• Smoking
• High blood pressure and cholesterol levels
• Being obese
• Diet-high amounts of salt increase blood pressure and high saturated fats increase cholesterol
• No physical activity

Therefore you can reduce the risk of cancer and CHD by: giving up or not smoking, avoiding being overweight, reduce salf and fat intake, regular exercise, reduce alcohol and increase fibre in diet.

Roles of the major parts of the digestive system

• Mouth-adds amylase to salivia to break carbohydrates into maltose. The oesphagus then carries the food to the stomach.
• Stomach-a muscular sac with an inner layer containing enzymes such as; protease to digest proteins into amino acids. Also has mucus layer to stop the stomach digesting itself.
• Small intestine-a long muscular tube, food is digested by the enzymes produced by its walls and glands. The inner walls of the intestine are folded into villi giving them  large surface area, this is further increase by microvilli.
• Large intestine-absorbs water to form faeces.
• Rectum-where faeces is stored.
• Salivary glands-produces amylase to break down starch into maltose.
• Pancreas-large gland situated below the stomach and produces pancreatic juice. This contains protease to digest proteins, lipase to digest lipids and amylase to digest strach

Physical digestion-food being broken down into smaller pieces by the teeth and the churning of the stomach. This allows us to swallow food and also increases surface area for the enzymes.

Chemical digestion-breaking down large insoluble molecules into smaller soluble ones. This is done by hydrolysis (splitting of molecules by adding water).

Monomer                              Polymer

Glucose                                Carbohydrates

Amino acids                         Proteins

Glycerol and fatty acids       Lipids

A monomer is one individual molecule. Carbon atoms of monomers join to form longer chains. These longer chains are called polymers.

A single monomer is called a monosaccharide. A pair of monosaccharides can be combined to form a disaccharide. They can also be combined in much larger numbers to form polysaccharides.

Test for reucing sugars-Benedicts test

All monosaccharides are reducing sugars. This means that they can donate electrons to produce another chemical.

1)Add an equal amount of benedicts reagent to your liquid sample.

2)Heat the mixture gently in a water bath

3)If a reducing sugar is present then the mixture will turn red

Test for non-reducing sugars

First you have to break them down, to do this you add hydrochloric acid to your sample and heat. You then add hydrogencarbonate to neautralise the acid. Then do the same as a reducing sugar.

2 Monosaccharides form a disaccharide

Glucose+Glucose=Maltose

Glucose+Fructose=Sucrose

Glucose+Galactose=Lactose

When the monosaccharides join, a molecule of water is removed. This is called a condensation reaction. This also forms a glycosidic bond.

Test for starch-add iodine solution and sample will go black if starch is present.

Starch digestion

• Starts in the mouth by being chopped up by the teeth and mixed with salivia
• Salivia contains amylade which breaks starch into maltose
• Starch digestion then continues in small intestine where pancreatic juice contains amylase
• This digests starch to maltose which isnt a useful product so maltase breaks this down into glucoe which is then absorbed.

Sucrose and lactose digestion

• Both pass into the small intestine where sucrase breaks down sucrose into glucose and fructose
• Lactase breaks down lactose to glucose and galactose
• These products are then absorbed

Lactose intolerance-some people cant produce lactase meaning lactose cant be broken down or digested.

Peptide bond-water is removed and the two amino acids join togehter.

Protein structure

Primary-amino acid sequence

Secondary-coiling of the protein to make an alpha helix, formation of hydrogen bonds

Tertiary-the alpha helixes fold and twist more to give a unique 3D structure, disulphide, ionic and hydrogen bonds

Quaternary-final 3D structure of the different polypeptide chains and sometimes non-protein groups.

Disulphide bonds-really strong and not easily broken

Ionic bonds-formed between different polypeptides. easily broken by changes in pH

Hydrogen bonds-numerous but easily broken

Enzymes are catalysts, they lower the activation energy needed to start a reaction. They do this by having an active site that the substrate can bind to for the reaction to happen.

Lock and key model-enzymes are not rigid structures and other molecules can bind to other sites on the enzyme to change its shape.

Induced fit model-enzyme isnt rigid but flexible, the shaple changes shape slightly to accomodate the substrate. This puts a strain on the substrate molecule, this distorts bonds in the substrate which helps lower activation energy.

Factors that affect enzymes:

• pH-this alters the charge on the amino acids in the active site so substrate can no longer bind
• Temperature-increases kinetic energy but if it gets too high hydrogen bonds can break
• Substrate concentration-increasing this will initially will increase the rate of reaction but there will get to a point when all active sites are full.

When an enzyme is said to be denatured then its active site have changed shape permanenlty and can no longer function.

Competitive inhibitors:

• Similar molecular shape to substrate
• Compete with substrate for active sites
• Inhibitor nor permanently bound so just slows down reaction
• The greater the concentration of the inhibitor the greater the effect

Non-competitive inhibitors:

• Fits in a site other than the active site
• Alters the enzymes shape so substrate molecules fit into the active site but not in a way that allows the reaction to proceed
• Enzyme cant funtion
• Concentration will not decrease the effect of the inhibitor as it alters the substrate.

Lungs

• Air flows into the lungs through the trachea which is a flexible airway supported by rings of cartilage
• The air then flows into the bronchi which are similar in structure to the trachea and contain mucus to trap dirt/dust particles and pathogens to stop them from entering into the lungs. They also have cilli which are tiny hairs that get rid of the used mucus.
• Air then travels into the bronchioles which are smaller divisions of the bronchi, they are made of muscle which allows them to constrict and therefore control the flow in and out of the alveoli
• The air then travels into the alveoli which are tiny air sacs. These allow the oxygen to diffuse into the blood and for the carbon dioxide in the blood to diffuse out and into the air. 

Pulmonary ventilation=Tidal Volume X Ventilation rate

-A measure of how much air is taken in and out of the lungs in a give time

Inspiration

• The intercostal and diaphragm muscles contract
• This causes the ribcage to move upwards and outwards and the diaphragm to flatten, increasing the volume of thorax
• As the volume of the thorax increases the lung pressure decreases to below atmospheric pressue
• This causes air to flow into the lungs
• This is an active process so requires energy

Expiration

• The intercostal and diaphragm muscles relax
• The ribcage moves downwards and inwards and the diaphragm becomes curved
• The thorx volume decreases, causing the air pressure to increase above atmospheric pressure
• Air is foced out of the lungs
• This is a passive process so doesnt require energy

The alveoli are exchange surfaces as they allow oxygen and carbon dioxide to be exchanged to and from the blood.

Exchange surfaces must be/have:

• Large surface area ro volume ratio
• Short diffusion pathway
• Partially permeable (selective about what is transported)
• There must be movement to keep a steep concentration gradient

Alveoli have this to efficiently allow oxygen to diffuse into the blood and carbon dioxide out

Alveoli have a thin exchange surface only one cell thick

They have a large surface area because of the large number

A steep concentration is maintained by the constant flow of blood

Pulmonary TB

It is caused by bacteria and is spread via an infected person coughing or sneezing.

People are more likely to catch TB if:

• Close contact with infected individuals
• Work or live in long-term care facilities
• From countries where TB is common.
• Where there is reduced immunity

Course of infection

• Bacteria grow and divide in the upper regions of the lungs where there is most oxygen
• White blood cells accumulate at site of infection to destroy the bacteria
• This leads to inflammation of lymph nodes, this is primary infection with very few symptoms however some bacteria may remain
• These can re-emerge and cause a second infection in the upper part of the lungs
• The bacteria destroy the tissue of the lungs resulting in cavities (when repaired a scar tissue)
• Sufferer coughs up damaged lung tissue and if infection spreads it can be fatal

Pulmonary fibrosis

• Caused by scars forming on the epithelium of the lungs
• Thickens epithelium irreversibly
• Diffusion of oxygen into the blood is less efficient as diffusion pathway is longer
• The volume of air the lungs can contain is also reduced
• Reduced elasticity so difficulty ventilating the lungs

Effects of fibrosis

• Shortness of breath especially when exercising-due to less oxygen diffusing into the blood
• Chronic dry cough-fibrous tissue obstucts the airway
• Pain and discomfort in the chest-pressure and damage from the mass of fibrous tissue
• Weakness and fatigue-due to the reduced intake of oxygen into the blood so less is available for respiration

Asthma

A localised allergic reaction caused by the release of a histamine. Histamine has the following effects:

• Lining of airways  becomes inflamed 
• Lining cells secrete more mucus than usual
• Fluid leaves the capillaries and enters the airways
• Muscle surrounding the bronchioles contracts and constricts the airways

Effects of asthma:

• Difficulty breathing-due to a greater resistance to air flowing into the lungs
• Wheezing sound when breathing-due to air passing through constricted airways
• Tight feeling in the chest-not being able to ventilate the lungs properly 
• Coughing-reflex response to the obstructed bronchi and bronchioles in an effort to clear them

Emphysema

• Normal lungs contain lots of elastic tissue which helps them inflate and deflate
• Emphysema develops in smokers
• Lung tissue's elastin in permanently stretched so they are no longer able to force air out of the alveoli
• Surface area of the alveoli is reduced and they are known to burst
• Little gas exchange takes place across the stretched and damaged air sacs

Effects of emphysema

• Shortness of breath-concentration gradients are reduced as air is struggled to be forced from the lungs and replaced with fresh oxygen rich air
• Chronic cough-body's effort to remove the damaged lung tissue and mucus that cannot be removed naturally due to the cillia being destroyed
• Bluish skin coloration-due to the low levels of oxygen in the blood as a result of poor gas exchange

• Aorta-carries oxygenated blood to the body
• Vena cava-carries deoxygenated blood to the heart from the body
• Pulmonary artery-carries deoxygenated blood to the lungs
• Pulmonary vein-carries oxygenated blood from the lungs to the heart

Cardiac cycle

1.Blood enters the atria and ventricles from pulmonary veins and vena cava. The semi-lunar valves are closed and the left and right atrioventricular valves are open. Atria are relaxed and fill with blood. Ventricles are also relaxed (diastole)

2.Atria contract (atrial systole), pushing blood into the ventricles which remain relaxed. The left and right atrioventricular valves are open and semi-lunar valve is closed.

3.Blood pumpled into pulmonary arteries and the aorta. Semi-lunar valves are open and atrioventricular vlaves are closed. The atria is relaxed and the ventricles contract (ventricular systole), pushing blood away from the heart through pulmonary arteries and the aorta.

The cardiac cycle is controlled by two nodes that pass electrical activity to each other and the muscle in order to make the heart contract-these are the atrioventricular node and the sinoatrial node.

• A wave of electrical activity spreads from the SAN to both atria causing them to contract
• A layer of non-conductive tissue stops this passing to the ventricles
• This wave of electrical activity then passes to the AVN which delays sending the reponse 
• This allos the atria to fully empty and the atrioventricular valves to close preventing the blood flowing back into the atria
• The AVN after this short delay then sends a wave of electcial activity to the bundle of his. These are exposed muscle fibres in the ventricle walls
• This then makes the ventrcles contract quickly and at the same time forcing the blood out of the heart

Cardiac output=heart rate X stroke volume

Atheroma

• Fatty deposit the forms on the wall of an artery
• Accumulations of white blood cells that have taken on low density lipoproteins
• These enlarge and form an atheromatous plaque on the wall of the artery
• Made up of cholesterol, fibres and dead muscle cells
• These cause the lumen to narrow restricting the flow of blood
• This increases the chances of thrombosis and aneurysms

Thrombosis

• Formed when an atheroma brekas through the lining of the artery forming a rough surface
• As the body tries to repair a blood clot may form (thrombus)
• This may block the blood vessel preventing the supply of blood to the tissues beyond it
• This tissue noramally dies 
• The clot may also detach and move with the blood blocking another artery.

Aneurysm

• Caused by thrombosis weakening artery walls which swell to form blood filled balloons
• These can burst causing haemorrhaging and blood loss, if in the brain this is a stroke

Defence mechanisms-Non-specific-Physical barrier-Phagocytosis

Defence mechanisms-Specific-Cell mediated response-Humoral response

Non-specific response=its immediate and the same for all pathogens

Specific response=Is slower and specific to each pathogen

Barriers to entry

• Skin-physical barrier, pathogens find it hard to penetrate
• Epithelia covered in mucus-pathogens stick to mucus and removed from body by the cillia
• Hydrochloric acid in stomach-such a low pH enzymes in pathogens denature

Phagocytosis

1)The phagocyte is attracted to the pathogen by chemoattractants. It moves towards the pathogen along a concentration gradient.

2)The phagocyte binds to the pathogen

3)Lysosomes within the phagocyte migrate towards the phagosome formed by engulfing the bacterium

4)The lysosomes release their lytic enzymes into the phagosome, where they break down the bacterium

5)The breakdown products of the bacterium are absorbed by the phagocyte.    

T lymphocyte

Matures in the thymus gland. Involved in cell-mediated immunity. Responds to foreign material inside body cells. Responds to own cells altered by viruses or cancer and transplanted tissues.

Produces memory cells that circulate in the blood and tissue fluid in readiness to respond to the future infection by the same pathogen. Stimulates B cells to divide and phagocytosis by phagocytes. Kills infected cells by making holes in their cell surface membranes.

B lympocytes

Matures in bone marrow. Involved in humoral immunity. Produces antibodies. Responds to foreign material outside body cells. Responds to bacteria and viruses.

Primary response=attach to antigens on pathogen and destroy it

Secondary response=circulate in blood and tissue fluid in readinisess to respond to future infection by the same pathogen by dividing and developing into plasma cells that produce antibodies

Antibody

• Polypeptide chains (proteins)
• Antigen binding sites are specific to one antigen
• Antigen-antibody complexes are formed

Monoclonal antibodies-target one specific antigen, this is grown outside the body and is used for:

• Separation of a chemical from a mixture
• Calculating the amount of substance in a mixture (pregnancy tests)
•  Cancer treatment
• Transplant surgery to stop rejection

Vaccination is the introduction of a substance into the body, with the intention of the body producing antigens against it and destroying it in order to produce memory cells so that when the pathogen enters the body again, you dont have any of the symptoms of the disease.

Magnification=Size of image/size of object

Resolution is the minimum distance apart two objects can be for them to appear as separate items. Depends on the size of the wavelengh used.

Transmission electron microscope & scanning electron microscope

• Uses electrons with a short wave lengh
• High magnification (SEM less than TEM)
• Resolution TEM=0.1nm SEM=10-20nm
• No coloured images
• TEM produces 2D images SEM produces 3D
• Thin samples needed in a vacuum
• Complex staining process

Optical light microscope- uses light to get an image with a ling wavelength. Has a low magnification with a resolution of 200nm. Produces a 2D coloured image. Light needs to be able to penetrate the sample. No vacuum is needed and no complex staining process.

Cell fractionation 

Preparation

• Ice cold-slows down enzyme activity
• Isotonic-prevents cells bursting or shrinking due to water potential gradient
• Buffer solution-constant pH

Homogenation

• Cells are broken open to release organelles in a homogeniser
• homogenate is filtered to remove any cells and large pieces of cell membrane

Ultracentrifugation

• Tube containing filtered homogenate is spun at any speed, pellet will form at the bottom with the heaviest organelles. 
• Supernatant is spun at a faster speed to separate more organelles
• Low speed-nuclei Medium-mitochondria High-ribosomes

The nucleus

• Nuclear envelope-double membrane that controls entry and exit of cells
• Nuclear pores-allows the passage of large molecules
• Nucleoplasm-granular jelly that makes up bulk of nucleus
• Chromatin-DNA found in the nucleoplasm
• Nucleolus-small spherical structure within the nucleus that manufactures RNA and assembles ribosomes

Functions of the nucleus

• Controls the cell
• Retain the genetic material of the cell as DNA of chromosomes
• Manufacture RNA and ribosomes

Mitochondria

• Double membrane-outer one controlling entry and exit of materials,inner one folder to form cristae
• Cristae-provide large surface are for the attachment of enzymes involved in respiration
• Matrix-fluid that is semi-rigid and contains protein lipids and some DNA that allows it to produce the enzymes involved in respiration

Function-site of certain stages of respiration and responsible for the production of ATP

Endoplasmin reticulum

• Rough ER has ribosomes present on surface and its functions are to provide a large surface are for the synthesis of proteins and to provide a pathway for the transport of materials throughout the cell
• Smooth ER synthesise, stores and transports lipids and carbohydrates

Golgi apparatus

• Transports materials across the cell surface membrane using vesicles
• Add carbohydrates to proteins to make glycoproteins
• Produce secretory enzymes (work outside the cell)
• Secretes carbohydrate 
• Transports,modifies and stores lipids
• Forms lysosomes

Lysosomes are vesicles made by golgi that contain enzymes. They are used to isolate potentially harmful enzymes from the rest of the cell.

• Release enzymes to break down pathogens
• Release enzymes outside of the cell
• Digest worn out organelles
• Break down cells after they have died

Ribosomes are important in protein synthesis. 80S type in eukaryotic and 70S in prokaryotic cells.

Lipids       Roles:

• Plasma membrane-provide flexibility and enable lipid soluble materials to pass through it
• Energy source-oxidised lipids provide more than twice the energy of the same mass of carbohydrate
• Waterproofing-lipids arent soluble in water so are effective for waterproofing
• Insulation-slow conductors of heat so help the body stay warm
• Protection-often stored around delicate organs

Saturated-no carbon to carbon double bonds

Mono-unstaturated-1 carbon to carbon double bonds

Poly-unsaturated-more than 1 carbon to carbon double bond

Phospholipids-two fatty acids and a phosphate attached

• Hydrophillic head-attracted to water
• Hydrophobic tail-stays away from water

Test for lipids-emulsion test

1)Add 2cm of the sample and 5cm of ethanol

2)Shake test tube to dissolve lipid

3)Add 5cm of water

4)A cloudy white indicates the presence of a lipid

Proteins

• Extrinsic-occur on either side of the phospholipid bilayer but dont go all the way through
• Instrinsic-go through the bilayer from one side to the other

Function of the proteins is to provide structural support and act as a carrier to transport things through the membrane.

Fluid mosaic model

• Fluid-individual phospholipids can move relative to each other
• Mosaic-the proteins thate are embedded in the phospholipid bilayer vary in shape, size and patteren. Like a mosaic.

Diffusion

Diffusion is the net movement of molecules or ions from an area of high concentration to an area of low concentration.

Rate of diffusion depends on

• Concentration gradient
• Surface area-the larger the area of an exchange surface the faster the rate of diffusion
• Thickness of an exchange surface-the thinner the diffusion pathway the faster the rate of diffusion

Facilitated diffusion

• Passive process so requires no energy from respiration
• Channels are selective-only open for one particular molecule
• Water filled channels-on transport things that are water-soluble
• Same factors effect rate as diffusion but the number of pores avalable to a particular substance also increases rate

Osmosis

Osmosis is the passage of water from a region of high water potential to a region of low water potential through a partially permeable membrane.

Pure water has a water potential of 0, anything added to the water decreases water potential.

Solution has higher water potential than the cell (less negative)

• Water enters the cell which swells and bursts
• Hypotonic solution

Solution has equal water potential to cell

• No netmovement of water particles and no change in cell
• Solution is isotonic

Solution has a lower water potential than cell (more negative)

• Water leaves cell which will shrink
• Solution is hypertonic

Active transport

The movement of molecules or ions into of out of a cell from a region of low concentration to a region of high concentration using ATP and carrier molecules.

Features-Requires energy, molecules/ions move against a concentration gradient, carrier proteins needed which are specif so only certain molecules can be transported.

Active transport of a single molecule

• Carrier proteins accept the molecule to be transported
• Molecule enters one side of the transport protein
• Molecule binds to carrier protein
• ATP is used to swivel the protein in the membrane
• Molecule is released on the other side of the membrane
• This causes the carrier protein to go back to normal

Villi are the folds inside the lining of the small intestine. Microvilli are finger-like projections from the surface of the cells lining the intestine. These increase surface area for absorption.

Glucose absorption-when carbohydrates are first broken down, theres a higher concentration of glucose in the small intestine than the blood. Glucose moves across the epithelial cells of the small intestine into the blood by diffusion. Then the concentration in the lumen becomes lower than in the blood diffusion stops. The remaining glucose is absorbed by active transport:

• Sodium ions are pumped out of the cell due to the action of the sodium potassium pump. This is actively transported requiring ATP, this creates a concentration gradient
• This causes sodium ions to diffuse from the small intestine lumen into the cell. They do this via the sodium-glucose co-transporter proteins.
• The co-transporter carriers glucose into the cell with the sodium. As a result the concentration of glucose inside the cell increases
• Glucose diffuses out of the cell, into the blood, down its concentration gradient through a protein channed by facilitated diffusion.

Prokaryotic cells (bacteria)

• 70S type ribosomes
• Flagella
• Cell wall
• Capsule
• Cell membrane

Eukaryotic cells (animals and cells)

• Nucleus
• Nucleolus
• Membrane bound organelles
• 80S type ribosomes
• Cell membrane
• Cellulose cell wall in plants

How Chlolera causes disease

• They use their flagella to propel themselves through the mucus lining
• Then produce a toxic protein which causes the ion channels in the cell to open and chloride ions that are usually stored within the cell flood into the lumen of the small intestine
• This causes the water potential in the small intestine to drop which draws water in from the surrounding cells and this causes diarrhoea

Oral rehydration solutions

• Water for rehydration
• Sodium ions to replace the ones lost from the epithelium
• Glucose to provide energy and stimulate the uptake of sodium ions
• Potassium ions to replace those lost and to stimulate appetite
• Other electrolytes to prevent an imbalance