BIOLOGY UNIT 4 THE NATURAL ENVIRONMENT AND SPECIES SURVIVAL

Topic 5 On the wild side

Adenosine triphosphate (ATP)

ATP is a nucleotide with three phosphate groups attached. The chemical energy stored in the phosphate bonds are made available to cells to use in synthesising or breaking bonds. The third phosphate bond is usually broken by a hydrolysis reaction, catalysed by the enzyme ATPase and resulting in ADP and a free inorganic phosphate group (Pi) and energy. ATP + H20 + ATPase = ADP + Pi + energy (used in cell). This is a reversible reaction. Energy to synthesise ATP comes from redox reactions, providing an immediate supply of energy when needed.

Making ATP
Formed from ADP and inorganic phosphate Two hydrogen atoms are removed from a compound and are picked up by a hydrogen carrier/acceptor, making it reduced. Electrons from the hydrogen atoms are then passed along an electron transport chain through redox reactions, which each release a small amount of energy used to drive the synthesis of ATP.

Chloroplasts
The membranes within a chloroplast are arranged in stacks called grana. The individual membrane disks within this are known as thylakoids. The pigment molecules are arranged on the membrane. The light-dependent reaction occurs in the thylakoids. The light-independent reaction occurs in the stroma. The stroma contains all the enzymes needed for photosynthesis.

The light-dependent reaction

Two main functions to produce ATP, and to split water molecules in photochemical reactions (photolysis). Photons of light hit a chlorophyll molecule which excites the electrons, causing them to leave the chlorophyll. The election is then picked up by an electron acceptor , which passes down an electron transport chain to produce energy to synthesise ATP. Electrons return to the chlorophyll molecule and can be excited again. This involves only PSI. (cyclic photophosphorylation) Water always dissociates spontaneously, so there are plenty H+ and OH- ions in the cell. In non-cyclic photophosphorylation, an electron from PSI is picked up by NADP. The NADP also picks up a free hydrogen ion to form reduced NADP.

The light-dependent reaction

At the same time, an electron from PSII is picked up by another electron acceptor and passes down an electron transport chain, creating energy to make ATP. When it reaches PSI, it replaced the previously lost electron. Now PSII is short of one electron, which must be replaced through photolysis (splitting of water through light). There are many hydroxide ions left in the cell (hydrogen ions have been removed by NADP), which react together to form this water that can then be split with light to create free electrons. This process can then be repeated, but it requires the presence of light in order for it to take place.

The light-independent reaction

Uses the reduced NADP and ATP previously formed within the light-dependent reaction. Consists of a series of reactions known as the Calvin cycle, and takes place in the stroma.

1 Ribulose bisphosphate (RuBP) combines with CO2 in the air, with help from the enzyme RUBISCO, to form a 6-carbon compound which is unstable, and immediately splits into two molecules of glycerate 3-phosphate (2 GP). 2 - GP is then reduced as hydrogen is added to it from reduced NADP and ATP, to form glyceraldehyde 3-phosphate (2 GALP). 3 - Much of this passes through to replace the RuBP, but some is synthesized into the 6-carbon simple sugar glucose, used for respiration in the plant. 4 Glucose can also be converted to sucrose for transport, starch for storage, and cellulose for structural support.

The light-independent reaction

The Calvin cycle takes place in both the light and the dark. The reactions only stop when the products of the light reaction run out, leaving no reduced NADP or ATP available. Glucose and nitrates are used as a building block for amino acids Glucose and phosphates help create nucleic acids The products of photosynthesis also produce lipids

Ecology key terms

Ecosystem a life-supporting environment including all living organisms, the nutrient that cycle through the system, and the physical and chemical environment in which they live. Habitat the place where an organism lives e.g. tropical rainforest Population A group of organisms of the same species living and breeding together in a habitat. Community all the populations of a different species of organisms living in a habitat at any one time. Niche the role of an organism in the community, e.g. what it eats, how it behaves, place in food chain. Abiotic factor non-living elements of the habitat of an organism. Biotic factor living elements of a habitat.

Succession
Succession is the process by which communities of animals and plants colonise an area and change over time until a climax community is reached. Primary succession starts with an empty inorganic surface such as bare rock or a sand dune, e.g. after a volcano. The first plants are pioneer species, which help break down the surface and allow other organisms to colonise. Secondary succession the evolution of an ecosystem from existing soil cleared of vegetation, e.g. after fires or floods. The soil is already formed, so the number of plants and animals present at the start is much higher. In both cases, eventually a climax community is reached. This is selfsustaining and usually the most productive group of organisms the environment can support.

Abiotic factors
Light the amount of light in a habitat has a direct effect on the number of organisms found there, as plants are dependent on light for photosynthesis. Some plants reproduce early to avoid the shade caused by larger plants. Other plants are able to photosynthesise in low light. Seasonal light changes can also affect reproductive patterns within animals. Temperature temperature can affect the rate of enzyme-controlled reactions in plants and ectothermic animals. Many animals have evolved behaviours to allow them to cope with extremes of temperatures. Wind and water currents wind increases water and heat loss from the body and adds to the environmental stress an organism has to cope with, so fewer species survive in areas of strong wind. For fast water currents, animals must be strong swimmers of be able to cling to substrate to resist the force of the water. Water availability Water is vital for living organism, so limited supplies can cause major problems. Increases in water can cause large increases in organism numbers.

Abiotic factors
Oxygen availability in water, if temperature rises or water becomes still, the oxygen content will drop, making it more difficult for organisms to survive. The spaces between soil often contain plenty of oxygen, but waterlogged soil refills these spaces and leads to deprivation of oxygen. Soil structure and mineral content sand has loose, shifting structure that allows very little to grow on it. Certain colonising plants will bind the sand together to allow other plants to thrive, e.g. marram grass. Water also passes easily through sand, leaching the minerals and reducing population density of plants. Different types of plants have evolved to grow well in different soil types, but will not thrive in other soils.

Biotic factors
Predation following mathematical models, populations will oscillate in a repeating cycle. As a prey population increases there is more food for the predator, so the predator population grows too. The predator will increase to the point where they eat more prey than are replaced, so prey decrease, reducing the food supply. In turn, predators will then produce less offspring, so the numbers will fall. However, in natural habitats, this is often more complex, as more factors are present. Finding a mate the likelihood of finding a mate/achieving pollination will affect the organisms found in any habitat. Availability of mates has a big effect on the abundance of animals. Territory the type and size of territory will help to determine which species live in a particular community. Parasitism and disease diseased animals will be weak and often cannot produce successfully. Sick predators cannot hunt well, and diseased prey are more likely to be caught. Parasites and diseases spread more rapidly when population density is high.

Competition
Intraspecific competition competition for a limited resource between members of the same population or species. As a result of this, some individuals may not survive/reproduce, and so population growth slows. If resources are plentiful, numbers will increase quickly.

Interspecific competition occurs when different species within a community compete for the same resources. Competition will reduce the abundance of the competing species. If there is a greater density of one species or it has a faster reproduction rate, then competing species may become extinct in that area.

Energy transfer
Net primary productivity = Gross primary productivity respiration NPP = GPP R Food chains are made of different tropic levels Energy used to make new animal biomass is known as secondary production Much energy is used to drive respiration, or is lost in heat energy or through excretion

The carbon cycle

There are massive abiotic and biotic carbon sinks in nature. These are reservoirs where carbon is removed from the atmosphere and locked up in organic or inorganic compounds. Biotic carbon removed by photosynthesis, stored in living organisms Abiotic Rocks, e.g. limestone and chalk, and fossil fuels hold carbon stores

Greenhouse gases
Greenhouse gases include carbon dioxide, methane and water vapour These gases reduce heat loss from the surface of the Earth through the greenhouse effect Radiation from the sun reaches the Earth, and some is reflected back. Infrared radiation in particular warms the Earths surface, and some of it is reradiated back to the Earth by greenhouse gas molecules in the atmosphere. The more greenhouse gases, the more radiation is reflected back and so the hotter the Earths surface becomes.

Methane is produced by the decay of organic material by bacteria, and the digestion of some herbivores such as cows.

Measuring climate change

Frozen isotopes Ice cores provide a record of climate change going back thousands of years. Records of the oxygen isotopes in melted ice reflect the air temperature at the time the ice layer was laid down, and so gives scientists data on the air temperature. Atmospheric carbon dioxide levels can also be measured. Dendrochronology the dating of past events using tree ring growth. When there is plenty of moisture and trees are growing quickly, new cells are large. As conditions get more difficult, new cells become smaller. This contrast produces a ring. Counting the rings allows us to determine an approximate age for the tree, whilst the thickness of rings can give information about the conditions within certain years.

Gene and allele frequency

A genome is all the DNA of an individual. The proteome is all of the proteins produced from that DNA. Mutations can increase the gene pool of a population by increasing the number of different alleles available. The relative frequency of a particular allele is known as the allele frequency. If a mutation produces an advantageous feature, the frequency of that allele will increase. Changes in allele frequency can lead to the evolution of new species. Groups of closely related genes are known as gene families.

Reproductive barriers
Reproductive isolation is crucial to speciation and occurs when fertilization is prevented (prezygotic) or when zygote fails or is unable to breed (postzygotic). Prezygotic barriers: Habitat isolation, temporal isolation (mating periods out of synch), mechanical isolation, behavioural isolation, gametic isolation (male gamete cannot penetrate female gamete etc.). Postzygotic barriers: Low hybrid zygote vigour (zygote fails to develop properly), low hybrid adult viability: (offspring fail to thrive and grow), hybrid infertility.