Succession

• Primary succession
• Begins in a place without soil
• sand dunes
• sides of volcanoes
• landslides
• flooding/land left after glaciation
• Starts with the arrival of living things such as LICHENS that do  not need soil to survive (called PIONEER SPECIES)
• Lichens - mutualistic relationship between algae and fungus
• algae photosynthesis - fungus absorbs water and minerals and cling onto rocks
• Soil starts to form as lichens and the forces of weather and erosion help break rocks into smaller pieces
• when lichens die, they decompose, adding small amounts of organic matter to the rock to make soil
• simple plants like mosses and ferns can grow in the new soil
• the simple plants die adding ore organic material
• the soil layer thickens and grasses and windflowers and other plants begin to take over
• these plants die thus more nutrients added to the soil
• shrubs and trees can survive
• insects smalls birds and mammals have begun to move in
• what was once a bare rock now supports a variety of life
• Secondary succession
• begins ina place that already has soil and was once a home of living organisms
• occurs faster and has different pioneers species than primary successin
• eg. after forest fires
• Climax community
• a stable group of plants and animals that is the end result of succession pricess
• does not always mean big trees
• grasses in prairies
• cacti in deserts

A2 Biology: Biotechnology

Biotechnology involved the exploitation of living organisms or biological processes to improve agriculture, animal husbandry, food science, medicine and industry

Food production

• Yoghurts and cheese
• produced by bacterial growth in milk
• this chnages the texture and flavour
• the bacteria prevent the growth of those bacteria that caue spoilage
• this helps preserve ood
• 'Qourn'
• produced by the growth of a fungus 'Fusarium'
• The fungal mass (mycelium) is processed and shaped into food
• Soy Sauce
• Roasted soya beans are fermented with yeast of fungus such as Aspergillus.

Drugs and pharmaceuticals

• Penicillin
• this is a product of the growth of a fungus called Penicillium.
• It is a by-product of the organisms metabolism
• this is isolated from the growth medium and is used as an antibiotic
• Insulin
• Bacteria such a E.coli are genetically modified to carry human insulin gene
• they secrete insulin as they grow

Bioremediation of waste products

• a variety of bacteria and fungi use organic waste in the water as nutrients and make wast harmless
• e.g. Fusarium grown on corn steep liquor, a waste product of the corn milling industry.

Why use bacteria and Fungi?

• grows rapidly in favourable conditions
• can produce chemicals or proteins that are released into the surrounding medium and ce be harvested
• can be genetically modified to produce specific products
• grow well at relatively low temperatures
• can be grown anywhere in the world - not climate dependant
• generated products that are in a pure form than those generated via chemical processes
• can often be grown using nutrient materials that would otherwise useless or even toxic to humans

GROWTH CURVE

What is a culture?

• it's a growth of micro-organisms
• it may be pure culture (single species) or mixed culture (mix of species)
• they can be cultured in liquid broth or solid nutrient agar gel.

Lag phase - organisms adjusting to conditions, cells active but not reproducing. Population is fairly constant

Log phase - population size doubles each generation. plenty of space and nutrients to reproduce.

Stationery phase - nutrients level decrease, waste products builds up. Death rate = production rate

Death phase - nutrients exhaustion, increased level of toxic waste products. Death rate > reproduction rate.

FERMENTATION

• Fermentation refers to the culturing of micoorganisms
• they could grow both aerobically and anaerobically in tanks called fermenters

Fermenters

• growth of an microorganism on an enormous scale
• begins with a 'start culture' a small pure culture from whicl all microorganis will grown
• conditions
• temperature
• type and tie of addition of nutrients
• O2 concentration
• pH

• Batch culture
• microorganisms mixed with specific quantity of nutrients then grown for a fixed period, no further nutrients added
• advantages and disadvantages
• growth rate slower
• easy to set up and maintain
• if contaminated, one batch is lost
• lless efficient - not operating all the time
• useful for producing secondary metabolites
• Continuous culture
• microorganisms mixed with nutrients and nutrients are added continuously  with products removed continuously throughout the process
• advantages and disadvantages
• growth rate higher
• difficult to set up and maintain
• if contaminated, huge volumes lost.
• ore efficient, operated continuously
• useful fro primary metabolites.
• Aseptic technique - asepsis
• unwanted micro-organisms can contaminate the fermentation process
• to avoid this, aseptic technique ensures contamination of the culture does not occur
• contamination may result in products being unsafe
• unwanted micro-organisms
• compete with culture micro-organisms for nutrients and space
• reduce the yield of the product
• may cause spoilage, produce toxic chemicals or destroy the culture micro-organisms

Metabolism and metabolites

• Metabolites include:
• chemicals such as hormones and enzymes
• waste products e.g. CO2, urea and O2
• these can be nutrients required by other organisms
• primary metbolites
• these are produced by organisms as part of its normal growth
• amino acids
• proteins
• enzymes
• ethanol
• lactate
• secondary metabolites
• these are produced by the organism and are not part of its normal growth
• antibiotic chemicals
• produced y a small number of microorganisms

Industrial enzymes

• Commercial use of enzymes
• Pectinase can be used in fruit juice extraction
• Metabolic enzymes in the bacteria A. niger produce citric acid used in detergents
• Downstreaming
• isolated enzymes can be produced in large quantities through biotechnology
• their extraction from the fermentation medium is known as downstream processing
• this is their separation and purification
• Immoilising enzymes
• when using enzymes in industry they need to be removed after they have served their purpose
• this can be a costly process
• it is possible to immobilise enzymes and prevent them from mixing
• immbolisation
• this is a technique were enzyme molecules are held, separated from the reaction mixture
• substrate molecules can bind to the enzymes and the products are formed go back into the reaction leaving the enzymes in place
• methods
• adsorption
• covalent bonding
• entrapment
• membrane separation 

A2 Biology: Roles of genes and environment in evolution

• The Hardy-Weingberg equation is used to show that population changes over time. (they evolve)

Environmental resistance: combined action of biotic and abiotic factors that limits the growth of a popuation.

Selection pressure: 

• environmental actor that confers greater chances of surviving and reproducing on some members of the population than others
  e.g. Rabbits that are well camouflaged are more likely to escape predation, survive, reproduce and pass on favourable (camouflaged) genes to offspring.
• Selection pressure in this case is predation
• it reduces the chances of white or black coat being passed on
• this keeps the population stable = stabilising selection
• If the environment changes - becomes colder, ore snow - rabbits with white fur would have selective advantage. White rabbits are more likely to survive, reproduce and pass white alleles to the next generation.
• frequency of white alleles would increase  = directional selection
• leads to evolutionary change.

Types of selection

• Driving force behind evolution is natural selection and this occurs in three main ways
• stabilising selection
• most common
• a response to a stable environment
• e.g. birth weight
• under weight babies are less likely to survive
• overweight babies are likely to get stuck during birth killing not only themselves but also their mothers.
• The result is that the population graph gets narrower and taller as selection agaisnt mutations takes place
• bottle neck event - occurs when a population is reduced to just a few breeding individuals (e.g. cheetahs)
• though the total population may later recover, they will all be descendants of the few originals and so will have a much smaller gene pool than the original population.
• directional selection
• results ina population of new trait
• takes place whenever a change occurs in the environment
• an evolutionary force of natual selection
• e.g. resistance. Wararin resistance in rats, DDT resistance in mosquitoes or antiiotic rsistance in bacteria. Resistant individuals soon become the dominant type within the population
• disruptive selection
• less common
• results in two distinct populations
• eventually these two forms may become so distinct they become new species

Isolating mechanism

• A large population of organisms may be split into sub groups that are prevented from interbreeding by
• geographical barriers e.g. rivers, mountain range
• seasonal/temporal barriers e.g. climate
• reproductive mechanism

Genetic drift

• change in allele frequency in a population, as some alleles pass to the next generation and some disappear
• large changes in small populations
• as the size of the population decreases the degree of fluctuation increases

SPECIES

Basic classifcation system

• Domain          Eukaryotes
• Kingdom        Animalia
• Phylum          Chordates
• Class              Vertebrata
• Order             Mammalia
• Family            Primates
• Genus            Great Apes
• Species           Home sapiens

Biological species concept

• a group of similar organisms that can interbreed and produce fertile offspring
• problems with this definition
• some species do not reproduce sexually
• some members of the same species look very different  (e.g. gender)

Phylogenetic species concept

• a group of organisms that have similar
• morphology
• physiology
• embryology
• behaviour
• and occupy the same ecological niche
• Closely related organisms will have similar DNA
• DNA analysis is carried out to compare particular base sequences (haplotype)
• Any differences  in bases is expressed a % divergence
• A clade is a group of all the organisms that share a single common ancestor and therefore have the similar DNa and features. 
• aka a monophyletic group e.g. A single ancestor and all its descendants

Cladistics

• based on evolutionary ancestry (phylogentic relationships)
• it does not use a fixed number of level such as kingdom, phylum and class
• whereas taxonomic classification focuses on similarities between organisms
• it include both monophyletic and paraphyletic groups

• Use molecule analysis e.g. DNA/RNA sequencing
• computer programs to represent evolutionary tree of life
• makes no distinction between extinct and existing species
• the cladisitic approcach has often confirmed the Linneasen classfication of orgnanisms but has sometime sled to organims being reclassified

Paraphyletic groups

• includes most recent ancestors but not all of its descendants e.g. reptiles
• Class: Reptilia. Reptiles are cold blooded vertebrates which unlike amphibians possess thick, impermeable skin covered y scaled. They have lungs, not gills and usually a three chambered heat. Their eggs are watertight shells. - Paraphyletic as it excludes birds which are descendants of reptiles
• The cl

A2 Biology: The endocrine system

Endocrine uses hormones as its signalling molecules.

Hormones: are molecules that are released by endocrine glands directly into the blood. They act as messengers, carrying a signal from the endocrine gland to a specific target organ or tissue.

• Blood circulation is used to transport hormones
• Transported throughout the body
• Endocrine glands are ductless and release hormones straight into the capillaries running through them

ENDOCRINE gland: is a gland that secretes hormones directly into the blood. They have no ducts.

EXOCRINE gland: is a gland that secretes molecule into a duct that carries the molecules to where they are used e.g. salivary glands.

Adrenaline

• Adrenaline is an amino acid derivative, they cannot enter the target cell. Adrenaline receptor on outside of the plasma membrane ha a shape complimentary to the shape of the adrenaline molecule

Adenyl cyclase

• Adenyl cyclase is an enzyme associated with receptor for many hormones, including adrenaline. It is found on the inside of the plasma membrane.
• Adrenaline receptor is associated with this enzyme.

Action of adrenaline

• Adrenaline in blood binds to a specific receptor
• Adrenaline is first messenger
• Activate adenylcyclase enzyme which converts ATP to cyclic AMP
• cAMP is second messenger inside the cell
• cAMP causes effect inside cell by activating enzymes

Adrenal medulla

• Cells make and release adrenaline hormone in response to stress
• Most cells have adrenaline receptors
• Effect is to prepare for activity

Effects of adrenaline

• Relax smooth muscles in  bronchioles
• Increase stroke volume of heart and increase heart rate
• Causes vasoconstriction to raise blood pressure
• Stimulate glycogen to convert to glucose 
• Dilate pupils
• Increase mental awareness
• Inhibit action of gut and cause body hair to react

Target cells must have specific receptors as hormones binds to receptor and activates a process inside the cell receptors must be specific so the hormone only bind to the correct cells, receptors and hormones have shapes complementary to each other.

A2 Biology: KIDENYS

The kidney functions:

• blood filtration
• selective reabsorption via active transport and passive absorption

• human kidneys are about 12 cm long 7 cm wide
• They are covered by a layer of fat and are part of the urinary system

• Blood enters a kidney through the renal artery and leaves through the renal vein.
• Excretory products are removed from the blood and are collected in the form of urine.
• Urine collects in the central part of the kidney called the pelvis.
• Urine passes from each kidney to the bladder along the ureter tube.
• The outer darker region is called the cortex and the inner and lighter region is called the medulla.

The Nephron

• The nephron is the functional unit of the kidney
• It makes up the bulk of its structure
• There are about 1 million in each kidney
• At one end of each nephron is a cup shaped Bowman's capsule (in the cortex)
• This encloses a dense network of capillaries called the glomerulus
• This capsule leads into a tubule, first part coiled aka the proximal convoluted tubule
• Then it leads to a U shape loop of Henle
• This leads to another coiled section called the distal convoluted tubule
• These join to forma  collecting duct and many of these lead though the medulla and coverage of the renal pelvis where they empty into the ureter which takes urine to the bladder

Function of the nephron

• The kidney works by the processes of ultrafiltration and reabsorption
• The fluid parts of the blood are filtered into the capsular space and the resulting fluid flows along the tubules
• As it does so useful substance are reabsorbed back into the bloodstream

Ultrafiltration 

• Blood is brought to each glomerulus by an afferent arteriole and it leaves via the efferent arteriole. The afferent is wider in diameter than the efferent which results in a relatively high hydrostatic pressure of blood in the glomerular capillaries. This pressure tends to force the fluid part of blood into the Bowman's capsule lumen.

Barrier

• the barrier between the blood in the capillar and the lumen of the Bowman's capsule consists of three layers:

• Endothelium of the capillary there are pored between the calls hat plasma and dissolved  molecules can pass through.

•  Basement membrane; this is a fine mesh of collagen fibres and glycoproteins. These act as a filter preventing any molecule with a mass greater than 69 000 from passing through. This mean most plasma proteins and blood cells are held in the capillaries. 

•  Podocytes - have specialised shape. They have finger like projections called major and minor processes. These ensure gaps between the cell that fluid can pass through into the Bowman's capsule

Blood contains: Digested food, white blood cells, urea, platelets, hormones, plasma proteins, carbon dioxide, oxygen and red blood cells.
Plasma contains; Carbon dioxide, glucose, amino acids, proteins, minerals, etc.

Selective reabsorption

• As the filtrate flow along the tubules, its composition is altered.
• Reabsorption occurs in both the proximal and distal convoluted tubules.
• Water is also reabsorbed form the collecting ducts.
• Most reabsorption occurs in the proximal convoluted tubule. (85%)

Adaptions for efficient reabsorption

• Epithelial cells of the proximal convoluted tubule have a large surface area due tot he presence of the microvilli on both inner and outer surfaces.
• They also have many mitochondria which can supply energy for active absorption.
• The inner membrane contains special co-transporter proteins that transport glucose or amino acids in association with sodium ions, from the tubule into the cell. This is facilitated diffusion.
• The outer membrane contains sodium-potassium pumps that pump sodium ions out of the cell and potassium ions into the cell.

1. This sodium potassium pumps remove sodium ions from the cells lining in the proximal convoluted tubule.
2. This reduces the concentration of sodium ions in the cell cytoplasm.
3. Sodium ions enter the cells long with glucose or amino acids by facilitated diffusion.
4. As the concentration of glucose an amino acids rise inside the cell, they diffuse out of the cell into the tissue fluid
5. from the tissue fluid they diffuse into the blood and are transported away
6. the reabsorption of sodium, glucose and amino acids reduced the water potential of the cells and increase the water potential of the filtrate
7. this means water will enter the cells and be reabsorbed into the blood by osmosis.

The loop of Henle

• Role of loop of Henle is to produce a low water potential in the tissue of the medulla.
• This will ensure that even more water can be reabsorbed from the fluid in the collecting duct

Ascending Limb

• at base of ascending limb, sodium and chloride ions diffuse out into the tissue fluid. 
• Further up, the ascending limb of the loop of Henle pumps out sodium and chloride ions by active transport.
• This movement makes the tissue fluid surround the Loop of Henle more concentrated 
• Water does not move out of these ions because the wall of the ascending limb is quite thick and is impermeable to water.

The descending limb

• The descending limb is permeable to water and solutes. As the filtrate passes down the descending limb water moved out by osmosis.
• Sodium and chloride ions move in by diffusion.
• The fluid within the descending limb therefore becomes more and more concentrated as it flows towards the bottom of the loop,

A2 Biology: Photosynthesis

• Takes place in green plants
• Light energy from te sun is trapped and concerted into a cheicl energy which can be storeed in molecules of carbohydrate.
• 6CO2 + 6H2O --light energy--> C6H12O6 + 6O2
• The leaf is the main photosynthetic organ.
• The chloroplast is the organelle where photosynthesis is carried out.

Chloroplast features

• Chloroplast envelope - double membrane permeable to glucose, CO2, O2, and some ions
• Ribosome
• Circular DNA
• Thylakoid membranes (stack = graum) - contains chlorophyll for photosynthesis
• Starch grain - insoluble carbohydrate storage product of photosynthesis
• Stroma - matrix of chloroplast
• Lipid droplet - energy store made from sugars during this process

Chloroplast structure

• Outermembrane is permeable to small ions, the inner is less permeable.
• Transport proteins allow movement across.
• Inside the chloroplast is a system of membranes running through a colourless, structureless substance - matrix aka stroma.

Stroma

• gel-like substance which contains enzymes for photosynthesis.
• Site of the light independent stage of photosynthesis (Calvin cycle)
• Other structure found in the stroma of chloroplasts are starch grains, DNA, lipid droplets and ribosomes.

Thylakoids

• membrane system is the site of the light dependant stage of photosynthesis.
• membrane system consists of any flattened fluid filled sacs called thylakoids.
• forms stacks called grana at intervals
• membrane provides a large surface area covered with photosynthetic pigments, enzymes and electron carriers.
• The grana are interconnected with intergranal thylakoids/lamellae

Photosynthetic pigments

• photosynthetic pigments absorb light of certain wavelengths and reflects others.
• They are found in funnel shaped structure called photosystems which harvest lights and are situated in the thylakoid membranes.
• These include chlorophylls and the carotenoids, carotene and xanthophyll. 

Chlorophyll

• Two types: chlorophyll a (P680) and chlorophyll a (P700)
• Both absorb red light but at slightly different wavelengths and appear yellow/green.
• Found at the centre of the photosystems and are known as primary pigment reaction centre.

Chlorophyll and photosystems

• Chlorophyll a (p700) is found in photosystem I and has a peak absorption of 700 nm
• Chlorophyll a (P680) is found in photosystem II and has a peak absorption of 680 nm.

Breakdown of photosynthesis.

Two main reactions

1. Light Dependant Reaction - Produces energy from the photons (solar power) in form of ATP and NADPH - takes place in thylakoid membrane

2. Light Independent Reaction/Calvin Cycle/Carbon Fixation - Uses energy ATP and NADPH from light reaction to make glucose. - takes place in stroma]

LIGHT DEPENDENT STAGE

3 major events:

• Photolysis of water
• Light harvesting
• photophosphorylation

Photolysis of Water

• In photosystem II there is an enzyme in presents of light that can split water into protons, electrons and oxygen. This is called photolysis.
• H2O   2e- + 2H+  + 1/2O2
• Oxygen is lost through the stomata into the air
• Electrons replaces those lost by the chlorophyll during energy tansduction
• Protons are used in chemiosmosis to produce ATP and reduce the coenzyme NADP (both needed for light independent stage)

Light harvesting

• 2 distinct light harvesting systems: PS.I and PS.II
• This is where all the light energy is harvested by the chlorophylls is transferred to the few chlorophyll molecules t the centre of the two reaction centres.
• These are known as primary pigment reaction centre molecule and absorb wavelength of 700 nm in PSI and 68 in PS.II

PHOTOSYSTEM I

Cyclic phosphorylation

• Excited electrons pass to an electron acceptor and back to the chlorophyll molecule from which they were lost.
• No photolysis of water and no generation of reduced NADP.
• Small amounts of ATP made by chemiosmosis.
• This may be used in the light dependant reaction or y the guard cells to open the stomata.

PHOTOSYSTEM I & II

Non cyclic-phosphorylation

• PS.II contains chlorophyll a molecules called p680
• after excitation these molecules  by light, a pair of e- are ejected from primary pigment centre
• these pass to electron carriers and the energy released is used to synthesis ATP by chemiosmosis.

• PS.I contains chlorophyll a p700
• after excitation of these molecules by light, e- are rejected from primary pigment reaction centre
• These e- along with protons (H+) join NADP (coenzyme) and it is reduced
• The e- from PS.II will now replace e- lost by PS.I
• e- from photolysis of water replace the electrons lost by PS.II
• Protons from photolysis of water takes part in chemiosmosis to make ATP and the join with NADP

Photophosphorylation 

• Energy is released a electrons pass along the chain of electron carer in the thylakoid membrane.
• this pumps proton across the thylakoid membranes into the thylakoid space where they accumulate
• a proton gradient is formed across the membrane and protons flow down their gradient through channels associated with ATP synthase enzymes.
• this flow is called chemiosmosis. it produces a force that join ADP and Pi to make ATP. 
• kinetic energy from the proton flow is converted to chemical energy in the ATP
• this formation of ATP and occurs through the processes of cyclic and non-cyclic phosphorylation

LIGHT INDEPENDENT STAGE

• Takes place in the stroma of chloroplast
• aka Calvin Cycle
• products of light dependent stage are used
• CO2 is the source of carbon for the production of organic molecules.

Calvin Cycle

• CO2 (enters via stomata) combines with ribulose bisphosphate (RuBP) (5C) to make 2 molecules of glycerate 3-phosphate (GP) (2 x 3C)
• The enzyme RUBISCO catalyses this reaction
• CO2 has now been fixed
• GP is phosphorylated and reduced to form triose-phosphate (TP) using AT and reduced NADP from the light dependent stage
• 5/6 f TP molecules are recycled back to 3 molecules of RuBP which fixes more CO2 in a cycle. The rest of the TP is used to make other compounds such as lipids, amino acids or carbohydrates.

A2 Biology: Anaerobic respiration

• Occurs in the absence of oxygen
• Only consists of glycolyis
• therefore takes place in the cytoplasm
• Net ATP made: 2
• Produces lactate (in animals) or ethanol (in plants) as a waste product.

Only glycolysis occurs as oxygen is the final electron acceptor; without it the ETC cannot function. The reduced NAD is not re-oxidised (lose H) and ergo there is an absence NAD for the Krebs cycle to function. Fungi, such as yeast, use ethanol fermentation and animals use lactate fermentation.

LACTATE FERMENTATION

• Pryuvate (3C) -----lactate dehydrogenase----> Lactate (3C)
                      Reduced NAD -- NAD -- glycolysis
• During this process pryuvate is acting a an aternativ H acceptor
• Lactate is carried away from the muscles to the liver. It is converted back to pryuvate when oxygen is present again.
• Muscle fatigue is not caused by the lactate but the drop in the pH that results from its formation, buffers in muscle help prevent this.

ALCOHOLIC FERMENTATION

• Pryuvate (3C) --pryuvate decarboxylase--> Ethanal (2C) --ethanal dehydrogenase--> Ethanol (2C)
•                                                                  gives out CO2         reduced NAD -> NAD

A2 Biology: Celluar Respiration

Cellular respiration is the process ofusing enrgy in complex organic molecules to produce ATP

Glucose + Oxygen > Carbon Dioxide + Water + ATP

Metabolic reactions that build large molecules are called anabolic and those that break large molecules are called catabolic.  We require energy for: active transport, endocytosis and excocytosis, replication of DNA and movement.

ATP = Adenosine Triphosphate

 ATP is formed during a condensation reaction between ADP and Pi (it is phosphorylated)  The enzyme responsible for this is ATP synthase. The energy to produce the bond that is formed comes from the breakdown of organic substrate (such as glucose) during cellular respiration. ATP provides your cells with energy without it we would be dead.

• We get energy from ATP by breaking down the high-energy bonds between the last two phosphates in ATP.
• When ATP reaches the site of energy using processes in the cell it is hydrolysed back to ADP.
• When hydrolysed to ADP + Pi it yield 30.6kJ or energy per mol. This means energy is available to the cell in small manageable amounts.
• Respiration in which glucose is completely oxidised to form carbon dioxide using oxygen is called aerobic respiration.
• The second and third phases of aerobic respiration takes place in the mitochondria and so it is necessary to recall the structure of a mitochondrion.

The mitchondria matrix is the site of link reaction and Krebs cycle. The inner cristae membrane is the site of the electron transport chain (glycolysis takes place in the cytoplasm)

Phosphorylation - addition of an inorganic phosphate gorup.

Hydrolysis - the splitting of large molecules into smaller molecules through the addition of water.

Oxidation - this is when the substrate donates hydrogen to a hydrogen accepted (dehydrogenation)

Reduction - this is when a hydrogen accepter gains a hydrogen.

Coenzymes are needed during glcolysis, the link reacton and the Krebs cycle, H atoms are removed from the substrte molecules in the oxdation reachtion. These eactions are catalysed by dehydrogenase enzymes. 

This occurs in the mitochondria during respiration and the chloroplast during photosynthesis. 

Stages of respiration:

Glycolysis (cytoplasm)

The link reaction (matrix of mitochondria)

Krebs cycle (matrix of the mitchondria)

Oxidative phosphorylation (cristae of mitochondria)

GLYCOLYSIS

• This occurs int he cytoplasm of all cells. t is a series of reactions, each catalysed by a different enzyme. 
• It works under anaerobic conditions (without oxygen)
• Glucose 6(C) -*-> Glucose 6-phosphate (6C) --> Fructose 6-phosphate (6C) -*->Fructose 1,6-bisphosphate (6C) (Hexose 1,6-bisphosphate)

• (-*-> = ATP > ADP) 

•  Hexose 1,6 bisphosphate splits into 2 Triose phosphate (3C)
• Triose phosphate ----NAD>2xreduced nAD------ADP>2xATP----> Intermediate compound (3C)
• Intermediate compound (3C) ----ADP>ATP----> Pryuate (3C)

Glycolysis: One molecule of glucose produces:

Net gain: 2 ATP (4 ATP in total)

2 reduced NAD

2 molecules of pryuvate

THE LINK REACTION

• Pryuvate diffuses into the matrix of the mitochondria
• 3 stages:
• Decarboxylation of pryuvate by pryuvate decarboxylase
• Dehydrogenation (oxidation) of pryuvate by pryuvate dehydrogenase to form acetate
• Coenzyme A combines with the acetate to give two molecules of Acetyl CoA - enters Krebs cycle

KREBS CYCLE

• The carbon doxide is produced by decarboxylation
• The NAD and FAD are reduced to dehydrogenation during the conversion of citrate into oxaloacetate
• ATP is produced by substrate level phosphorylation where the energy taken directly from a substrate is used to add a phosphate group to ADP.

=6x reduced NAD

=2x reduced FAD

=4x CO2

=2x ATP 

Electron transport chain (ETC)

A number of reduced NAD and FAD have been produced during the first three phases of aerobic respiration  In the ETC these molecules are re-oxidised (lose H) by dehydrogenase enzymes. It takes place in the cristae of mitochondria.

• Each electron carrier is an enzyme, each associated with a coenzyme.
• The coenzyme can accept e- (become reduced) or donate e- (become oxidised)
• They are oxidoreductase enzymes
• Electron pass along the chain of carriers losing energy
• Some coenzymes use this energy to pump protons H+ from matrix to intermembranous space.
• The electrons from each reduced NAD can pump H+ into the space.
• Protons (H+) accumulate in the intermembranous space and build up a proton gradient (high conc)
• Stalked particles allows H+ to pass through them which generates ATP
• Each reduced NAD generates 2.6 molecules of ATP

Chemiosmosis: the process when protons flow down the proton gradient through the ATP synthase enzymes from intermembrane space into the matrix.

• The force of this flow rotates the enzyme and allows ADP + Pi join to form ATP
• aka oxidative phosphorylation - formation of ATP by adding a phosphate group to ADP in the presence of oxygen which is the final electron acceptor
• Oxygen is the final hydrogen acceptor
• when electrons are released from the chain they combine with the H+ ions to form hydrogen.
• The hydrogen then combines with oxygen to form water, so it is the final H or e- acceptor.
• There this stage will only take place in aerobic conditions.

AS Biology: Plants' transport system: Xylem and Phloem

Plants need a transport system as every cell of a multicellular plant needs a regular supply of water and nutrients. Cells inside the plant would not be able to receive enough nutrients and water to survive simply by diffusion.

Plants require:

• Carbon dioxide for photosynthesis
• Oxygen for aerobic respiration
• Organic nutrients for growth

PHLOEM transports sugars from the leaves  - it's also for amino acids. - they can move upwards or downwards.

XYLEM transports water, minerals up from roots. 

Vascular tissue is distributed throughout the plant and it helps with the plant transport. Xylem and phloem are found together in vascular bundles which also contains other tissues. It helps transport water from toots to leaves via the stem. The xylem and phloem run the entire length of the plant from the roots to the midrib and veins of the leaf.

Xylem vessels are empty tube shaped cells/ Their cytoplasm has been removed by the plant and their walls are strengthened and thickened with lignin. The lignin strengthens the tubes and help support the plant by giving rigidity to the xylem. Minerals from the soil are also carried in the xylem, they are needed by the plants in many of its chemical reactions.

Features:

• Wall thickened by lignin prevents collapse under tension and adhesion to lignin
• Hollow tubes means that there is less resistance to flow
• No end walls so there's a continuous columns so there is less resistance to flow
• Pits inside the walls allows lateral movement
• Narrower the lumen the higher water will rise by capillarity
• Stacked end to end develops as a continuous water filled column; allows tension to pull water up

Phloem (sieve) tubes carry sugar around the plant. Phloem cells are alive and have a cytoplasm unlike hollow xylem vessels. It's is made up of two types of cells: sieve tubs and companion cells.

Sieve tubes: the ends walls of the tube cells have pores which dissolved sucrose is transported from cell to cell. They have sieve plates at the end with pores so sugar can get through. they have no nucleus, the cytoplasm is controlled by companion cell nucleus. The vacuoles of the tube are joined and sugary sap flow along them.

Companion cells - proves the energy for the sieve tube cells. The nuclei tends to be large to compensate for the lack of nucleus in the sieve tube.

Features:

• Both cells are living which allows active processes
• Plasmodesmata (connections between sieve tube and companion cell) allows exchange between cells.
• Companion cell have many mitochondria to make energy and a nucleus to control functions both cells.
•  Sieve tubes have little cytoplasm and elongated cells so there's less resistance of fluid flow
• Sieve plates allow material through, it also joins end to end to provide continuous tubes.
• Sieve tubes are bi-directional which allows sugar to go to sink or it can travel either direction.

A2 Biology: Respiration - Glycolysis

Glycolysis

• Happens in the cytoplasm of all cells
• It can take place in anaerobic or aerobic conditions.
• Glucose (6C sugar) is broken down to 2 molecules of pryuvate (3C compound)

Stage 1. Phosphorylation

• Glucose (6C sugar) - very stable - needs to be activated to be split
• An ATP molecule is hydrolysed - phosphate group attached to glucose at carbon 6
• Glucose > Fructose 6 phosphate
• Another ATP is hydrolysed - phosphate group attached to fructose 6 phosphate at carbon 1
• Activated - fructose 1,6 bisphosphate aka hexose, 1,6-bisphosphate
• Energy from hydrolysed ATP activates the sugar and prevents it from going out of the cell

2. Splitting hexose 1,6 bisphosphate

• each molecules of hexose 1,6 bisphosphate is splt into 2 x triose phosphate 

3. Oxidation of triose phosphate

• 2H atoms are removed from triose phosphate (involves dehydrogenase enzymes)
• These are helped by NAD which is a H acceptor - combines with H and becomes 'reduced NAD'
• 2 ATP formed - substrate level phosphorylation

4. Conversion triose phosphate > pryuvate

• 4 enzyme-catalysed reactions convert each phosphate to a pryuvate
• during this, 2 molecule of ADP are phosphorylysed to 2 ATP

So overall, 2 molecules of ATP (=net amount - 4 have been made but 2 are used again)

There are also 2 molecules of reduced NAD and 2 pryuvate which ill be used in next stage of respiration

My revision notes: A2 Biology: Urea + Ornithine cycle + detoxification of alcohol

Deamination is the process where ammonia (NH3) is produced. Ammonia is very soluble and highly toxic. It also produces an organic keto acid which is then used in respiration. Ammonia is converted into Urea which is less soluble and less toxic. Urea travels in the blood and is transported to the kidneys where it is filtered out of the blood and stored into the bladder until released from the body.

The ornithine cycle

2NH + CO2 > CO(NH2)2 + H2O

ammonia + carbon dioxide > urea + water

Detoxification of alcohol

Alcohol can be bad for us but it also contains chemical potential energy which could be used in respiration.

• Alcohol is broken down b hepatocytes by the action of enzyme ehtanol dehydrogenase
• In result of this ETHANAL is made
• it is then dehydrogenated again by ethanal dehydrogenase
• Which produces ethanoate (acetate)
• combined with coenzyme A to form acetyl coenzyme A which enters respiration.
• Ethanol > Ethanal > Ethanoic acid > Acetyl coenzyme A

My revision notes: A2 Biology: Control of Heart Rate

All cells, e. muscle cells have different requirements, depending on the activity e.g. exercising - muscle cells require an increase in oxygen, glucose and removal of carbon dioxide.

The average heart rate is 70 beats / min
SAN controls this with no need of neurone impulses

If you exercise you need to increase:

• Heart rate
• strength of contraction
• stroke of volume  volume of blood pumped / beat

When you exercise you produce more CO2 - which dissolves to form carbonic acid - lowers pH

> This is detected by chemoreceptors in carotid arteries (going to head and aorta)

> They send an impulse to the cardiovascular centre which in turn sends an impulse down an accelerator nerve to SAN 

> So heart beats faster and stronger

Why are the chemoreceptors in the head and aorta?

Carotid artery is going to the brain ensures that the blood is not acidic

Going for aorta as its the biggest artery as it has the most amount of blood passing through

If you eercise you got receptors in muscles > gets stretched > impulse sends to cardiovascular neurone > SAN  > Increase in heart rate

Stop eercising > decrease in CO2/muscle receptors not stretched > impulse vagus nerves > SAN > slows heart rate back to normal