Abiotic factors in a habitat
- solar energy input
- Topography (altitude, slope etc)
- Oxygen availability
- Edaphic (factors that are connected with soil)
Biotic factors in a habitat
Biotic factors are usually density dependent: the effects are related to the size of the population relative to the area available.
Anthropogenic factors are those arising from human activity.
Primary succession and its pionerr phase
- starts in newly formed habitats where there has not been a community before.
- it can occur on bare rock, sand, and open water.
- Succession usually continues until a stable community is formed.
- first organisms to colonise bare rock are algae.
- they start to break up the rock surface, making the beginnings of soil.
- They change the conditions in the habitat making them suitable for other species to colonise.
- wind-blown moss spores start to grow.
- the moss builds up more organic matter in the soil, which can then hold water.
- the development of soil lets shallow rooted plants grow.
- as the conditions get better seeds from larger and taller plants appear.
- they compete with the plants already present and win and replace the existing community.
- the end habitat is usually dominated by trees.
- a climax community has been reached.
- this often does not change unless the conditions in the habitat change.
Secondary succession and Deflected succession
- Happens on bare soil where an existing community has been cleared.
- plants, animals and wind bring seeds to the soil.
- pioneer species that start the new community usually have the adaptations of:
- seeds can be dispersed by wind.
- rapid growth
- short life cycle
- abundant seed production
Is a community that remains stable because human activity prevents it from changing any further.
Producers and productivity
- The rate in which energy is incorporated into organic molecules in an ecosystem
Produces (or autotrophs):
- organisms that can make their own organic compounds from inorganic compounds.
Non coding blocks in DNA are called introns, and the coding regions are called exons.
In introns DNA sequences are repeated many times, this is called short tandem repeats (STR's).
A DNA profile is produced using gel electrophoresis, In which DNA fragments produced by restriction enzymes can be separated according to their size.
- A single band shows when a persons maternal and paternal chromosomes have the same number of repeat units.
- two bands occur when the two chromosomes have a different number of repeats at a locus. ( a locus is a place where the same STR's occur.)
Polymerase chain reaction
Polymerase chain reaction is used to copy DNA.
- A sample of DNA is added to detergent to release the DNA from cells.
- DNA polymerase, DNA primers with fluorescent markers and nucleotides are added.
- (at 95 degrees) the DNA splits into two strands.
- (at 55 degrees) primers attach at the start of the STR repeated sequence.
- (at 70 degrees ) DNA polymerases attach nucleotides are added the DNA sequence is replicated.
DNA profiling continued
How a DNA profile is made using gel electrophoresis:
- double-stranded DNA is added to a restriction enzyme which cuts the DNA into fragments.
- fragments of double-stranded DNA are loaded into the wells of an agarose gel in a tank using micropipette.
- the negatively charged DNA moves towards the positive electrode. The fragments separate into the invisible bands.
- DNA is transferred to a nylon or nitrocellulose membrane by solution drawn up through the gel. DNA double strands split and stick to the membrane.
- Membrane placed in a bag with DNA probe. Single-stranded DNA probe binds to fragments with a complimentary sequence.
- if DNA is radioactive x-ray film is used to detect fragments, if fluorescent it is seen using UV light.
Determinging the time of death
Body temperature can be used as the body cools soon after death, there are many factors that will affect this process:
- body size
- body position
- air movement
- temperature of surroundings
If the body is in water it will cool more quickly, as water is a better conductor of heat than air.
These factors need to be taken into account.
After death the muscles relax then suddenly stiffen, this is known as rigor mortis. The steps at which this occurs are:
- cells become starved of oxygen, oxygen dependent reactions stop.
- respiration in the cells becomes anaerobic and produces lactic acid.
- the pH of the cells fall, inhibiting enzymes and then inhibiting anaerobic respiration.
- the ATP needed for muscle contraction is not produced, bonds between muscle proteins become fixed.
- the proteins can no longer move over one another to shorten the muscle.
- this fixes the muscles and joints.
This usually happens 6-9 hours after death.
Decomposition (or putrefacation)
- First sign is a greenish discoloration of the skin of the lower abdomen, due to a formation of sulphaemoglobin. (36-72 hours after death)
- it spreads across the rest of the body. It darkens to reddish-green then to purple-black.
- gas or liquid blisters can appear on the skin.
- due to the action of bacteria gases including hydrogen sulphide, methane, carbon dioxide, ammonia and hydrogen form i the intestines causing bloating.(after a week)
- as decomposition continues the gas is released and the body deflates.
- temperature best for decomposition is 21-38 degrees as the enzymes become denatured.
- A persons time of death can also be estimated by using entomology.
- The rate of maggot development can be used as they accumulate on the body shortly after death.
- its stage of development can tell us its age.
- usually blowflies will lay eggs within one day of finding the body.
- some factors can increase the maggots development such as cocaine.
Succession on corpses:
- as each organism feeds on a body it changes it
- this change makes it more attractive to other species of organism which changes the body for the next group
- until the body is reduced to a skeleton
bacteria are prokaryotic which means they do not have a nucleus among other things. They produce asexually by binary fission.
A bacterium is made from:
- cell wall
- cell surface membrane
- ribosomes = site of protein synthesis
- capsule = a mucus layer for protection
- flagellum = used for cell movement
- mesosome = in-folding of the cell surface membrane, site of respiration
- main circular DNA
- plasmids = small circles of DNA
- pilus = protein tubes that allow bacteria to attach to surfaces
- a strand of DNA or RNA (Viral DNA can be single or double stranded.)
- protein coat
How viruses reproduce:
- virus attaches to a hosts cell
- virus inserts nucleic acid
- the viral DNA replicates
- viral protien coats are made
- new virus particles are formed
- virus particles are released
Transmission of HIV and TB
TB can be transmitted by:
- is carried through the air in droplets of mucus
- this is caused by people coughing or sneezing
HIV can be transmitted by:
- sharing needles
- unprotected sex
- direct blood to blood transfer
- maternal transmission from mother to child
Non-specific responses to infection
- an enzyme that breaks down the cell walls of bacteria, found in tears and saliva.
- when a cut lets microbes enter the body the inflammatory response destroys them.
- White blood cells release chemicals such as histamine which cause the arterioles to dilate increasing blood flow to the site.
- are white blood cells that engulf bacteria
- lymphocytes (B cells and T cells)
- monocytes (become macrophages)
- and other white cells which produce histamine
Non-specific responses to infection continued
Engulfing of bacteria:
- bacterium with antigens on surface
- engulfed by neutropil or macrophage
- enclosed in vacuole
- lysosomes fuse with vacuole releasing enzymes that destroy the foreign material.
- tissue fluid drains into lymphatic vessels
- the lymph fluid flows along lymph vessels
- as lymph passes through the lymph nodes any pathogens present activate lymphocytes and macrophages which then destroy the microbes
-prevents viruses from multiplying
- secrete antibodies in response to antigens
- special protein molecules of a class known as immunoglobulins
- B cell produces antibodies which which bind to bacteria with antigens on surface this labels them as 'non self'
- antibody binds to antibody receptor on a macrophage
- macrophage engulfs antibodies and bacterium
- lysosomes fuse with vacuole releasing enzymes which destroy the bacteria.
specific immunity continued
are produced in the bone marrow. they have specific antigen receptors which bind to antigens with the complimentary shape.
- T helper cells = stimulate B cells to divide and become cells capable of producing antibodies. also enhance the activity of phagocytes.
- T killer cells = destroy any cells with antigens on the surface that have been labeled as 'non self'.
Activation of T helper cells
- bacterium with antigens on surface
- bacterium engulfed by macrophage
- macrophage presents antigens on its surface and becomes an antigen presenting cell (APC)
- APC binds to T helper cell with complimentary CD4 receptors
- the T helper cell is activated and divides
- clone of T memory cells and clone of active T helper cells are produced
- bacterium with antigens on surface
- antigen binds to B cell with complimentary receptor
- B cell becomes an antigen-presenting cell (APC)
- activated T helper cell with complimentary receptor binds to APC and produces cytokines (proteins) that stimulate B cell.
- the B cell divides to give B memory cells and B effector cells
- B effector cells differentiate into plasma cells
- plasma cells secrete antibodies which bind to antigens identifying them for destruction.
The role of T killer cells
- Bacterium infects cell of host
- the cell presents the antigens and becomes an APC
- T killer cell with complimentary receptor binds to the APC
- the T killer cell divides to form two clones active T killer cells and memory T killer cells. Cytokines from T helper cells stimulate the differentiation.
- The active T killer cells bind to infected cells presenting antigens.
- T killer cell releases chemicals that cause pores to form in the infected cell causing it to explode.
- The infected cell dies.
Infection of TB
- TB bacteria can survive inside the macrophages
- they have think waxy walls making them hard to break down
- they can lie dormant until the immune system weakens and they are activated
- TB bacteria can suppress T cells this reduces antibody production and attack by killer T cells
Symptoms of TB:
- coughing (can even cough up blood)
- shortness of breath
- loss of appetite and weight loss
- fever and extreme fatigue
The role of fever
A person infected with TB can get a fever. This is caused by:
- as part of the inflammatory response fever causing substances are released from neutrophils and macrophages
- these chemicals affect the hypothalamus and alter the set point for the core body temperature to a higher temperature
-effectors act to warm up the body to the new set point
- a raised temperature enhances immune function and phagocytosis
- bacteria and viruses may reproduce slower at higher temperatures
- although a high temperature can be harmful to the patient as it denatures enzymes
How is TB diagnosed?
Skin and blood tests:
- small amount of tuberculin is injected under skin
- positive result shows inflamed area
- antibodies in the blood cause this inflammation showing TB antigens already present
Identification of bacteria:
-a sample of sputum coughed up by a patient is taken
- it is then cultured to see what bacteria are present
- stains are then used to identify the bacteria
Chest x-rays: x-rays can be used to see the extent of damage in the lungs in a person with TB, damaged areas show up as red.
HIV and AIDS
AIDS is caused by infection with the human immunodeficiency virus HIV.
HIV invades T helper cells
HIV invades I helper cells within the immune system:
- gp120 bind to the CD4 receptors on the surface of T helper cells
- they then combine with a second receptor allowing the envelope to fuse with the T helper cell membrane
- the viral RNA then enters the cell
- macrophages also have CD4 receptors so the virus can infect them too
How the virus replicates:
-uses an enzyme called reverse transcriptase
- it makes a DNA copy of the RNA
- the DNA is copied to make a double strand that can be inserted into the human genome
- it is then integrated into the hot cell's genome using intergrase
Transcription and Translation
- RNA polymerase attaches to the DNA
- hydrogen between the paired bases break and the DNA unwinds
- RNA nucleotides with complimentary bases to the ones on the template strand bond together forming mRNA
- mRNA then leaves the nucleus through a pore in the nuclear envelope
- mRNA attaches to a ribosome
-the anticodons on tRNA are complimentary to the mRNA codons for the amino acid
- free amino acids attach to the correct tRNA molecule which carry it to the ribosome
- the anticodons bind to the codons and form a chain of amino acids which are held together with a peptide bond
- RNA is often edited
- the non-coding introns are removed
- the remaining sequences which are coding regions are called exons
- that means several proteins can be formed from one length of mRNA if it is spliced in different ways
How HIV destroys T helper cells
- HIV binds to cell receptors virus envelope fuses with cell surface membrane
- virus reverse transcription copies viral RNA into viral DNA
- intergrase inserts viral DNA into host DNA
- transcription occurs
- translation of virus envelope proteins
- virus envelope proteins are incorporated into the cell membrane
- the virus mRNA is translated
- virus particle budding becomes wrapped in cell membrane, forming the virus protein
The course of the disease - AIDS
the acute phase:
- HIV antibodies appear in the blood after 3-12 weeks
- the infected person starts to either get symptoms or have no symptoms
- there is a rapid replication of the virus and loss of T helper cells
- after a few weeks infected T helper cells are recognised by T killer cells which start to destroy them
- this greatly reduces the rate of virus replication
The chronic phase:
- immune system weakens and more symptoms can occur
- dormant diseases can reactivate
The disease phase:
- the increased number of viruses in circulation and low number of T helper cells indicates the onset of AIDS and can leave the immune system vulnerable to other diseases
Preventing entry of pathogens
- the skins keratin (hard protein) outer layer stops entry of microorganisms
- entry can occur through wounds but blood clotting stops further enrty
- large numbers of microbes called skin flora live on the skin surface they prevent colonisation of other bacteria
- the mucus membranes line the airways and gut and provide easier routes into the body
- entry of microbes into the lungs is limited by the action of mucus and cilia
- the mucus traps microbes and the cilia carry the mucus to the throat where it is swallowed
- tears and saliva contain lysozyme which breaks down bacterial cell walls
Preventing entry of pathogens continued
In the digestive system:
gastric juices secreted by gastric glands in the stomach walls will contain hydrochloric acid giving a pH of less than 2.0 this kills most bacteria that enter with food
- bacteria are found in the small and large intestines
- natural flora benefit from living within the gut where conditions are ideal
- the bacteria can aid in the digestive process as they secrete chemicals like lactic acid which are useful in the defense against pathogens
You can become immune to a disease in these ways:
-active artificial immunity = being vaccinated against specific diseases, this vaccine stimulates specific immune responses which give her immunity to the disease
- passive artificial immunity = when a patient who is in danger of getting a disease is given specific antibodies to stop them from getting a particular disease
- active natural immunity = when a person has had a disease in the past and has made specific B memory and T memory cells to help combat the disease if the person gets it again
- passive natural immunity = when a baby has just been born its immune system is undeveloped, but its mother has given it antibodies via the placenta
Vaccines may contain the following:
- Attenuated viruses = these viruses have been weakened so they are harmless
- Killed bacteria = vaccines may contain bacteria that has been killed
- a toxin that has been altered into a harmless form
- an antigen-bearing fragment of the pathogen
when enough people are immunised the disease is less likely to be transferred to others.
This means that anyone who did not get the virus is also protected. When this happens it is called herd immunity.
Treating AIDS and TB
There are two types of drugs that reduce the the production of more viruses.
- reverse transcriptase inhibitors = prevent the viral RNA from making DNA for integration into the hosts genome
- protease inhibitors = inhibit the proteases that catalyse the cutting of larger proteins into small polypeptides for use in the construction of more viruses
- active TB bacteria can be killed by antibiotics
- this goes on for 6 months until all dormant bacteria are destroyed
How antibiotics work
There are two types of antibiotics:
- bactericidal = antibiotics that destroy bacteria
- bacteriostatic = antibiotics that prevent the multiplication of bacteria, the hosts own immune system can then destroy the pathogens
How antibiotics disrupt bacterial cell growth and division:
- inhibition of bacterial cell wall synthesis (this can lead to bursting of the cell)
- disruption of the cell membrane causing changes in permeability
- inhibition of nucleic acid synthesis, replication and transcription which prevents cell division
- inhibition of protein synthesis meaning that essential proteins are not produced
- inhibition of specific enzymes found in the bacterial cell
Why do we still have diseases like TB?
Bacterial populations evolve very quickly because:
- bacteria reproduce very fast
- bacterial population sizes are usually in billions, so the number os cells containing mutations is vast
- some of these random mutations can be beneficial to the bacteria. Such mutations can make the bacteria:
-use different food sources
- reproduce more quickly
- infect other cells more successfully
Selection pressures and Conjugation
- When a constraint of any kind is put on an ecosystem it will put pressure on all species within the system to adapt to the constraint in order to survive.
- So if an antibiotic is injected into the host with bacteria present the bacteria will fight to mutate and adapt to the antibiotic before they are destroyed.
Conjugation (or horizontal evolution):
- a resistant bacterial plasmid cell carrying a gene for antibiotic resistance finds a non-resistant bacterial cell
- one strand of the plasmid DNA is transferred to the non-resistant cell
- each bacteria replicates the strand to make a complete plasmid
- both bacteria are now resistant
Antibiotic resistance and hospital aquired infecti
- hand wash stations
- hand wash signs
- no wearing ties, watches or long sleeves
Preventing the development and spread of resistant bacteria:
- antibiotics should only be used when needed
- patients should complete their treatment even when they feel better so that all bacteria is destroyed
- infection control should be used in hospitals to prevent bacteria spreading
Releasing hydrogen from water:
- the splitting of water into hydrogen and oxygen requires energy
- photosynthesis uses energy from light to split water
- this is known as photolysis of water
Storing hydrogen from water:
- the hydrogen reacts with carbon dioxide in order to store hydrogen
- carbon dioxide is then reduced to form the carbohydrate fuel glucose
Using the glucose:
- The fuel has the potential to release large amounts of energy when the hydrogen stored in the carbohydrate reacts with oxygen during respiration
- in aerobic respiration glucose is pulled apart and the hydrogen combines with oxygen to make water, energy and carbon dioxide are released
How photosynthesis works
There are two main stages:
Light-dependent reactions =
- use energy from light and hydrogen from photolysis of water to produce reduced NADP, ATP and the waste product oxygen
- the oxygen is then either used directly in respiration or released into the atmosphere
Light-independent reactions =
- use the reduced NADP and ATP from the light-dependent reaction to reduce carbon dioxide to carbohydrates
The co-enzyme NADP is reduced when electrons are added during photosynthesis.
Structure of a chloroplast
Thylakoid membrane - a system of interconnected flattened fluid-filled sacs. Proteins and embedded in the membranes and are involved in the light-dependent reactions.
DNA loop - chloroplasts contain genes for some of their proteins
Stroma - the fluid surrounding the thylakoid membranes. contains all the enzymes needed to carry out the light-independent reactions
Thylakoid space - fluid within the thylakoid membrane sacs contains enzymes for photolysis.
Granum - a stack of thylakoids joined to one another
Smooth inner membrane - which contains transposter molecules
Smooth outer membrane - which is permeable to CO2 and H2O
Starch grain - stores the product of photosynthesis
Light-dependent reactions (chlorophyll)
- energy from the light raises two electrons to a higher energy level
- the electrons leave the chlorophyll and pass along electron carriers
- the electrons pass from one carrier to the next in a series of oxidation and reduction reactions losing its energy in the process
- the energy is used in the synthesis in a process called photophosphorylation
- the electrons lost from the chlorophyll must be replaced
- within the thylakoid space an enzyme catalyses splitting of water to give oxygen gas, hydrogen ions and electrons
- these electrons replace the ones lost in the chlorophyll molecule and the hydrogen ion concentration is raised as a result of photolysis
- the electrons that have passed along the electron transport chain combine with NADP and hydrogen ions from the water to form reduced NADP
Light-independent reactions (stroma)
The reactions form a cyclical pathway called the Calvin cycle:
- CO2 combines with a 5-carbon compound called RuBP. This reaction is catalysed by the enzyme RuBISCO.
- The 6-carbon compound formed is unstable and immediatly breaks down into two 3-carbon molecules, GP.
- this 3-carbon compound is reduced to form a 3-carbon sugar phosphate called GALP.
- The hydrogen for the reduction comes from the reduced NADP from the light-dependent reactions. ATP from the light-dependent reactions provides the energy for the reaction.
- Two out of every 12 GALP's formed are involved in the creation of a 6-carbon sugar called hexose.
- hexose can then be converted into other organic compounds such as amino acids.
Energy transfer and feeding relationships
Hetrotrophs cannot make their own food instead they must consume it. Types of consumers are:
- primary consumers (herbivores) are hetrotrophs that eat plat material
- secondary consumers (carnivores) feed on primary consumers
- tertiary consumers (carnivores) eat other consumers. the carnivores at the top of the food chain are sometimes called top carnivores.
- animals that eat plants and other animals are known as omnivores
- detrivores are primary consumers that feed on dead organic matter (detritus)
- decomposers are species of bacteria that feed on the dead remains of animals
is the way energy is transferred in a ecosystem. The position a species occupies in a food chain is called its trophic level.
How efficient is the transfer of energy through th
What happens to the light when it hits a plant leaf:
- 5% reflected
- 5% transmitted straight through the leaf
- 40% absorbed by chlorophyll in the chloroplast
- 50% of energy not absorbed by chlorophyll but used in evaporating water from leaves
- some is lost during the process to make energy and is transferred to the environment
Limiting factors will also influence the rate of photosynthesis.
Energy in a ecosystem
Gross primary productivity (GPP):
The rate at which energy is incorporated into organic molecules by an ecosystem.
Net primary productivity (NPP):
The rate at which energy is transferred into the organic molecules that make up the new plant biomass.
NPP = GPP - R
Pollen grains and dendrochronology
pollen from peat is useful for reconstructing past climates because:
- plants produce pollen in vast amounts
- pollen grains have a tough outer layer that is very resistant to decay
- each species of plant has a unique type of pollen
- peat forms in layers: the deeper the layer the older the peat
- each species of plant has particular conditions in which it flourishes best
- every year a tree produces a new layer of xylem vessels
- wide vessels are produced in spring and narrow vessels in summer
The greenhouse effect
Solar radiation (visible and ultraviolet):
- most ultraviolet is absorbed by ozone in the stratosphere
- some visible radiation is reflected by the earth
- some is reflected by clouds
- most solar radiation is absorbed by the earths surface which warms it up
Infrared radiation from the earth:
- some infrared is absorbed by greenhouse gasses warming the troposphere
- some infrared emitted by the earth's surface escapes and cools down the earth
The greenhouse effect:
- sun's radiation (mainly visible) passes through the glass
- infrared radiation is emitted by the plants and soil, some infrared radiation is absorbed by the glass
Isolation - preventing species interbreeding
ecological isolation - the species occupy different parts of the habitat
temporal isolation - the species exist in the same area but reproduce at different times
behavioral isolation - the species exist in the same area, but do not respond to each others courtship behavior
hybrid inviability - in some species hybrids are produces but they do not survive long enough to breed
hybrid sterility - hybrids survive to reproductive age but cannot reproduce
Why is CO2 concentration increasing?
if a forest were cut down photosynthesis would drop, in the short term more carbon dioxide would be released then absorbed.
Combustion of fossil fuels:
Fossil fuels lock carbon dioxide inside them instead of releasing it into the atmosphere, this is called a carbon sink. It removes carbon dioxide from the air, but burning them releases its accumulated carbon dioxide.
Volcanoes and acid rain may release CO2:
so an increase in volcanic activity and acid rain could increase the CO2 levels. Acid rain erodes limestone which releases CO2.