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

Apoptosis

Events of apoptosis

• enzymes breaks down the cell cytoskeleton
• cytoplasm becomes dense with organelles tightly packed
• the cell surface membrane changes and small bits called blebs form.
• chromatin condenses and nuclear envelope breaks. DNA breaks into fragments
• the cells breaks into vesicles that are taken up by phagocytosis. the cellular debris is disposed of and does not damage any other cells or tissues

How it's controlled

• Apoptosis is controlled by cell signalling
• some from the inside the cell and some from outside
• these include cytokines made by cells of the immune system, hormones, growth factors and nitric oxide
• nitric oxide works by making the inner mitochondrial membrane more permeable to hydrogen ions
• it would prevent the formation of the proton gradient needed for ATP synthesis
• proteins are released into the cytosol
• these proteins bind to apoptosis inhibitor proteins and allow the process to take place

Apoptosis and development

• apoptosis is an important part of the tissue development. Extensive division and proliferation is followed by pruning through apoptosis. 
• Excess cells undergo apoptosis and their components are reused. Different tissues use different signals to induce it.
• Examples:the removal of ineffective or harmful T lymphocytes during the development of the immune system

How often does apoptosis take place?

• In children between 8-14 years old, 20-30 billion cells per day undergo apoptosis.
• in a year this is equivalent to the total body ass
• in adults the figure is around 50-70 million cells per day
• the rate of cell death should = the rate of mitosis
• however, not enough apoptosis leads to the formation of tumours. 
• too much leads to cell loss and degradation
• cell signalling helps maintain the right balance