Module 4 Flashcards
What is a communicable disease?
illnesses resulting from the infection, presence and growth of pathogens in an individual host
What is a pathogen?
a disease causing organism which takes nutrition, energy and protection from and damages its host. (parasite)
What type of cell is bacteria? How are they classified?
prokaryotes classified by shape- rod (bacilli), spherical (cocci), comma shaped (vibrios), spiralled (spirilla) and corkscrew (spirochaetes)
By cell walls- 2 main types have different structures that react differently to gram staining Gram positive- look purple/ blue and Gram negative look red. The cell wall affects how they react to antibiotics
What is the chain of infection?
infective agent (pathogen)- bacteria, virus, protoctists, fungi
source of infection- the reservoir is the location of the microorganism which must meet needs of pathogen to grow and survive
mode of transmission- direct (skin to skin, bodily fluids) or indirect (pathogen transferee to intermediate that’s not infected but transfers pathogen to host (airborne droplets, insects)
susceptibility of host- young, elderly and those with underlying health conditions often have weaker immune systems
Are viruses living?
What structure do they have?
How do they replicate?
How do they evolve?
What are bacteriophages?
non living and very small
Have DNA/RNA surrounded by a protein
they invade living cells and their genetic material takes over the biochemistry of the host to make more viruses
They evolve my adapting to their host
They can even attack bacteria, using them to replicate and killing them at the same time
What type of cell are protocista? How do they infect?
Eukaryote parasitic using people/ animals as host
What type of cell are fungi?
what is their cell wall made of?
How do they absorb nutrients?
what type of fungi are pathogenic?
How do they affects plants?
How do they spread?
Eukaryote
cell wall of chitin
Can photosynthesise so digest food extracellularly before absorbing nutrients- saprophytic feeders. parasitic ones are as they live off organic matter
stop them photosynthesising as they affect the leaves
when they reproduce they produce millions of tiny spores
Bacterial animal disease
- Name of pathogen
- method of transmission
- symptoms/ method
- Tuberculosis
- mycobacterium tuberculosis
- Direct- droplets through air
- Lung tissue destroyed, immune system suppressed, coughing, fever, fatigue
- Bacterial meningitus
- Neisseria meningitidis, haemophilis influenzae
- direct- droplets though air and exchange of fluids In meninges (tissue surrounding brain to prevent entry of bacteria) of brain but can spread causing blood poisoning and death. Blotchy red rash that doesn’t disappear when a glass is pressed against it shows blood poisoning. Nausea, vomiting, fever, headache, muscle pain
Virus animal disease
- Name of pathogen
- method of transmission
- symptoms/ method
HIV/AIDS
- Human immunodeficiency virus (HIV)
- Direct- contact with bodily fluids, mother to child in breast milk
- Targets T cells in immune system and contains enzyme reverse transcriptase which transcribes RNA to a single strand of DNA in the host cell. HIV is a retrovirus as the process is opposite to usual.
- Flue like illness, fatigue, join and muscle pain
Influenza
- Influenza A, B and C
- Direct- droplets in air
- Sudden fever, body ache, fatigue, dry cough, kills cilia allowing airways to be infected
Protoctist animal disease
- Name of pathogen
- method of transmission
- symptoms/ method
- Malaria
- Plasmodium falciparum
- indirect- female anopheles mosquito.
- reproduce in mosquito then invade red blood cell then liver
- High temperature, headache, vomit, muscle pain, diarrhea
Fungus animal disease
- Name of pathogen
- method of transmission
- symptoms/ method
Cattle ringworm
- Trichophyton verrucosum
- Direct- contact with infected cattle
- grey white areas of skin with ashy circular areas. may be itchy
Athletes foot
- Epidermophyton floccosum, trichopyton rubrum, T. Mentagrophytes
- direct- contact with towels used by infetced people.
- Grows on and digests warm moist skin between toes causing cracking and scaling- itchy and sore
Bacterial plant disease
- Name of disease
- host plant
- names of pathogen
- Method of transmission
- Symptoms
- Ring Rot
- Potato, tomato
- clavibacter, michiganensis
- Direct contact with infected tubers, cultivation spreads it as bacteria remain of machinery damages leaves, tubers and fruit. Infects vascular tissue and blocks them so no water can enter leaves. Once a field is infected can’t grow potatoes for 2 years
Viral plant disease
- Name of disease
- host plant
- names of pathogen
- Method of transmission
- Symptoms
- mosaic
- Tobacco Tobaco mosaic virus (TMV)
- direct- contact with leaves of infected plants
- indirect- via aphids as vectors
- damages leaves, flowers and fruit, stunting growth. Yellow mosaic pattern on leaves. spreads though plasmodesmata and phloem
Fungus plant disease
- Name of disease
- host plant
- names of pathogen
- Method of transmission
- Symptoms
Black sigatoka
- bananas
- mycosphaerella fijiensis
- direct- spores are dispersed through air and spores germinate and grow into leaf through stomata. they are also present in soil
- indirect- fungus on infected plant releases spores and an insect eating the plant picks up the spores and transmits to other plants when it feeds
- yellow spots and black streaks. Hyphae penetrate and digest cells so leaves go black as can’t photosynthesise
Protocist plant disease
- Name of disease
- host plant
- names of pathogen
- Method of transmission
- Symptoms
- late blight
- potato, tomatoes
- phytophthora infestans
- direct- swimming zoospores and aerial spores
- hyphae penetrate host cells and destroy leaves, tubers and fruit.
- Blue/ grey spots, shrivel and go brown
disease transmission
why is it not always successful?
the transfer of pathogens from an infected host to an uninfected one
large numbers of pathogen produced to reach chances of reaching a host
infective stages are small to avoid wasting energy
Direct transmission:
CONTACT: between individuals TMV, RINGROT, RINGWORM kissing or bodily fluid contact HIV, microorganisms from faeces transmitted to hands
SPORES: BLACK SIGATOKA, LATE BLIGHT. Insects carry spores so could be indirect
INGESTION: contaminated food and drink, mouth to hands
ANIMAL BITES/ PUNCTURE WOUNDS (inoculation)
Indirect transmission:
VECTORS:
- wind carries spores
- water allow spores to swim in surface film of water on leaves
- animals carry pathogens and spores from one plant to another when they feed
- humans transmit pathogens and spores by hands, clothing, farming, transporting plants around the world
MALARIA, TMV
DROPLETS: of saliva and mucus in the air when you cough, sneeze and talk contain pathogens and can be inhaled by others
TB, MENINGITIS, FLU
FOMITES: inanimate objects transfer pathogens like door handle and towel
ATHLETES FOOT
WATER maybe soil
Factors affecting direct transmission animals and plants:
Animals/ human: close proximity like schools, hospitals and cramped housing- poverty
Plant: High density monocultures of crop plants
Factors affecting indirect transmission animals and plants:
climate and weather- damp and warm is good for vectors, especially mosquitos. Aphids and mosquitos need 20*c and over. Climate change worsens this as increased rain and wind increases spread, animals vectors are spread to new areas, but drier conditions in some areas could reduce spread there
Factors that affect transmission of human diseases
- poor nutrition
- compromised immune system
- poor waste disposal creates breeding sites for vectors
- culture and infrastructure- medical practices socioeconomic- lack of trained HC workers
- warning when outbreak
- poor sanitation and sewage
- housing contaminated water
- travel and migration bring diseases to populations with no natural resistance or immunity behaviour
- sexually transmitted diseases can be lowered depending on number of partners
Preventing spread of plant diseases:
leave space between plants
rotate crops (bacteria/spores die if no host)
strict hygiene- wash hands, boots machinery control insect vectors ?????
plant crops less susceptible to disease
plenty of minerals so healthier plants with more tolerance to infection
retrovirus
a virus like HIV with single stranded RNA as its genetic material, not DNA. when the retrovirus invades a host cell it uses its enzyme reverse transcriptase to make DNA from RNA template. Other RNA viruses like influenza don’t use their RNA as a template for making DNA
what is a vector:
an organism that transfers a pathogen from an infected host to an uninfected host and is not harmed by the pathogen itself
protoctist definiton
a eukaryotic unicellular organism
epidemic
endemic
pandemic
widespread occurrence of infectious disease in community at a particular time
a disease or condition regularly found in particular people/ place
a disease prevalent over a whole country or world
Comparing primary defences in plants and animals:
permanent physical barrier against infection:
prevent entry of pathogens:
Block movement of pathogens:
Use chemicals:
cellulose cell walls, skin
stomata closing, blood clots around open wound in skin
tyloses and calls, musus and cilia to remove
terpenes, HCL and lysosomes to kill pathogens
first line of defence
physical and chemical defences that prevent entry of pathogens into the body
Non specific defences
work the same way whatever the pathogen and are present from birth
How does the skin work as a primary defence?
- Impermeable to most pathogens with a keratinised layer of dead epithelial cells. - Hostile conditions as lactic acid and fatty acids are secreted from sweat and sebaceous glands are acidic. When sweat evaporates it leave salty, dry conditions combined with low pH prevent microorganisms growing and multiplying. - Skin floral healthy microorganisms that outcompete pathogens for space on surface. Also inside body like intestines
Primary defences
skin
mucous membranes
expulsive reflexes
other
Mucous membranes
Line parts of the body likely to come into contact with pathogens eg. airways, digestive tract, genital tracts mucous is secreted by goblet cells in the epithelium and traps pathogens its sticky because its full of glycoprotein molecules which have long carbohydrate chains and contains antimicrobial enzymes cilia on ciliated epithelium in airways waft mucus up where it is swallowed
Expulsive reflexes
coughing and sneezing ejects pathogen-laden mucus from gas exchange system areas prone to infection are sensitive to dust, microorganisms or the toxins they release ? happen automatically to expel foreign bodies
Other primary non specific defences:
lysozymes destroy bacterial and fungal cell walls and are found in blood, sweat, tears and phagocytes remove remaining pathogens.
acidic conditions of stomach and vagina kill pathogens
non pathogenic bacteria live in our digestive/ genital tract and compete with invading organisms
ear canal lined with wax
vomiting and diarrhoea expel contents of gut along with any infective pathogens
what types of defence is blood clotting?
Why is it needed?
Why is the process so complex?
How is it activated?
What is involved?
Name the order of enzymes:
- second line non specific
- Blood clotting is required to provide a temporary seal to prevent infection as if skin is breached pathogens can enter the body
- to avoid clotting where its not needed
- When platelets come into contact with collagen in skin or wall of damaged blood vessel they adhere and begin to secreted several substances
- clotting factors which activate an enzyme cascade (product of one reaction activates the next)
- Thromboplastin converts inactive protease to active protease. Ca2+ catalyst helps prothrombin convert to thrombin which converts soluble fibrinogen to insoluble fibrin. This forms a clot with traps platelets and blood cells, then dries to form a scab.
Apart from the thromoplastin cascade, what is the other clotting method?
serotonin makes the smooth muscle in the walls of the blood vessels contract so they narrow and reduce the supply of blood to the area
What is the second stage of wound repair?
- layer of fibrous collagen starts to form under the scab to give new tissue strength
- granulation tissue fills the would allowing further changes to occur underneath
- The outer layers of stem epidermal cells divide by mitosis, into skin cells and migrate to the edge of the wound.
- Platelets secrete growth factors that attract cells to divide and grow
- The tissue then contracts to draw the edges of the wound together
- new blood vessels form to supply nutrients to the tissue
- death of unwanted cells
- scab falls of once new epidermis reaches normal thickness
Secondary defences
phagocytic and antimicrobial cells that act against the type of microorganism that has breeched the primary defences non specific
inflammation definition What are the signs?
the local response to tissue damage and infection, involving the release of chemical signalling molecules and resulting in an increased blood flow and movement of phagocytes into the infected tissue swelling (oedema), pain, heat and redness
Inflammation process
- Damaged/infected tissue releases histamine molecules from mast cells which increase permeability of blood capillaries.
- Fluid leaks into surrounding tissue fluid which is what causes swelling and pain and phagocytes can leave the blood and enter infected tissues.
- The histamine also cause vasodilation which makes the area hot and brings lots of white blood cells. The raised temperature also helps prevent pathogens reproducing.
- When excess tissue drains into lymphatic system the specific immune response is initiated
- Histamine stimulate infected cells to secrete cytokines. Cytokines (including interleukin) stimulate defences in affected area including binding proteins to material to be digested by phagocytes (these proteins can increase 1000x at the start of an infection!). They also promote inflammation and cause the liver to release acute phase proteins, some of which bind to the surfaces of bacteria and damaged host cells to promote phagocytosis. These signalling molecules are also responsible for causing fever and sleepiness by stimulating the brain
Fever- how does it occur Why is it good?
hypothalamus in brain maintains 37*C. when a pathogen invades, cytokine stimulate the hypothalamus to reset the thermostat and temperature goes up. This inhibits pathogen reproduction and the specific immune system works faster at higher temperatures.
What is a passive defence?
What are the passive plant defences- split into physical and chemical?
there all the time
Physical:
- waxy cuticle over leaf epidermis- stops virus and bacteria entering through wounds made by herbivores
- Casparian strip in root endodermis- stops fungi entering through roots
- bark
- cellulose cell walls
- stomatal closure
Chemical:
- secreting toxic compounds- phenols
- secreting enzyme inhibitors that inhibit enzymes needed for plants to enter the plant- tannins
- Sticky resins in bark prevent spread
- secreting compounds which support growth of microorgainsims that are competitors of pathogens
- receptor molecules on cell surface membranes detect pathogens and activate plant defences
Active plant defences
- Hypersensitivity/ necrosis Immediate death of tissue surrounding infection site to prevent spread of infection. Many pathogens require a living host tissue to survive for energy and nutrients used for growth
- Callose deposition Callose is a large polysaccharide that blocks sieve tubes (phloem) or plasmodesmata preventing the spread of the pathogen. Also deposited in sieve pores to block the transport of phloem sap and impede pathogen movement. Cells walls have it too, along with antimicrobial compounds like hydrogen peroxide
- Tyloses growths that block the xylem by swelling preventing pathogen spreading through plant. they are filled with plant chemicals called terpenes
- Cell signalling using signalling molecules like salicylic acid activate defence mechanisms in uninfected areas. They then have system acquired resistance for some time after the original infection if it returns. They produce defence chemicals- phytoalexins which:
disrupt cell surface membranes of bacteria
delay reproduction of pathogen
disrupt metabolism of pathogen
release chitinases to break down hyphae walls
Name a few plant chemicals we extract for use:
Why can’t plants produce cells that roam all over the body?
insect repellents- citronella from lemon grass
insecticides- caffeine is toxin to insects and fungi
fixed cell walls
What are phagocytes?
What are 3 phagocytes?
when and where are they produced?
what causes them to migrate?
what do they contain
specialised cells in the blood and tissue which engulf and digest pathogens and dead cells
neutrophils macrophages (monocytes) dendritic cells
throughout life by the bone marrow
signalling molecules from damaged cells
lysosomes (vesicle containing digestive enzymes)
What is the most common phagocyte?
what is a special feature of this phagocyte and why is it useful?
what happens during infections? What happens after they ingest bacteria? What is pus mostly made of?
neutrophil
lobed nucleus so they can leave capillary walls as more flexible
travel in blood and enter tissue fluid during infections, large numbers quickly released from bone barrow in infections
short lived- die after ingesting bacteria
dead neutrophils
What do macrophages do?
How are they different to neutrophils?
Where are they found?
where are they made?
consume and destroy any pathogens they encounter
larger and long lived, and initiate a specific immune response as they display antigens from the pathogens to lymphocytes
found in organs/ lymph not the blood. common in lungs as stuff enters there
bone marrow as monocytes (called macrophages once reach organs)
What is a special feature of dendritic cells?
where are they found?
what happens to them after phagocytosis?
have long processes to give a large surface area to interact with pathogens and lymphocytes and are antigen presenting cells (APC’s) like macrophages?
mainly found in areas near to surfaces like skin, digestive tract, mucous membranes
they migrate to the lymph nodes
Describe the process of phagocytosis include process of antigen presentation
- chemotaxis (phagocyte moves in response to chemicals produced by pathogens) and adherence of microbe to phagocyte. can recognise non human proteins on pathogen (not specific)
- ingestion of microbe to phagocyte by endocytosis and invagination
- formation of a phagosome (phagocytic vesicle)
- formation of a phagolysosome ( when lysosome fuses with phagosome)
- digestion of ingested microbe by enzymes from lysosome
- formation of residual body containing indigestible material
- discharge of waste materials my exocytosis and antigens from surface of pathogen absorbed so they can be displayed and used to tell lymphocytes which antibodies to make much quicker, without the real pathogen there to cause damage. The antigens from the pathogen surface membrane combine with special glycoproteins from cytoplasm called major hostocompatability complex (MHC) which moves them to the phagocyte surface membrane becoming APC
How does histamine increase effectiveness of phagocytes?
when cells are under attack they release histamine which makes capillaries more leaky so extra fluid in the blood leaves to become tissue fluid this means more fluid enters the lymphatic system, flushing pathogens towards the macrophages waiting in the lymph nodes so the specific immune response can begin sooner
When are cytokines released and how do they help phagocytes?
what do opsonins do and how do they help?
cytokines are released by a pathogen when it engulfs the phagocyte and they tell other phagocytes the body is under attack and stimulate them to move to the site of the infection
opsonins are chemicals eg. antibodies that bind to and tag the pathogen making it more easily recognised by the phagocyte they also bind to receptors on phagocytes membranes which help the pathogen be engulfed
3 features of antigens:
What do they do?
What are they specific to?
what is specific to antigens?
- proteins or glycoproteins
- large molecules
- have a specific shape on or in the cell surface membrane
they stimulate a immune response eg. production of antibodies
the organism
antibodies
What is another name for antibodies?
what produces them?
what structure do they have?
immunoglobulins
lymphocytes in response to an infection
globular proteins with 4 or more polypeptides
In the antibody structure: what is the function of the variable region?
What is the function of the hinge region?
what is the function of the constant region?
What are the light chains?
What are the heavy chains?
Where is the antigen binding site?
What bonds are involved?
it changes due to different sequence of aa giving it a different 3D shape so is specific for different antibodies
allows flexibility so the antibody can bind to 2 separate antigens
its the same for all antibodies of the same class, and is a receptor binding site on the phagocyte surface so it can detect pathogens labelled by antibodies for phagocytosis
2 smaller polypeptides on the outside
2 larger polypeptides on the inside
at the top of the y and involves all 4 polypeptides- there are 2 identical ones
disulphide bridges form between polypeptides and within polypeptides
What is it called when the antigen and antibody bind?
antigen-antibody complex
How do antibodies work?
Agglutination- antibodies bind to 2 identical antigens on 2 or more pathogens which makes them clump together so they are less likely to spread and and easier for engulfing. bigger antigens are better for this as there are more binding sites
Immobilisation- some attach to the bacterial flagella making them less active and easier for phagocytes to engulf
Opsonins- some act as these by acting as labels coating the pathogen so the phagocyte can identify it. The phagocytes have receptors for the constant region of antibodies
Some block the binding sites on the pathogen so its unable to bind to a host cell (neutralisation)
Antitoxins- they block toxins they are complementary to them so combine with them to make them harmless eg, for those causing diphtheria and tetanus
They also can attach to the membrane and puncture or burst it
Describe trend in graph and explain why for primary and secondary response
low numbers of antibodies in blood as there is a lag phase until antibodies are produced.
small and gradual peak which is short lived.
if the first infection passes the antibody concentration required for immunity then if a second infection occurs with the same pathogen the lymphocytes can quickly make the same antibodies again- the previous ones don’t stay in the blood.
immediate and stronger response shown by a steeper and higher peak.
Due to the presence of memory cells made during the response it is long lived. The graph declines slower too why long lived due to memory cells??
What is the specific immune system?
when lymphocytes and antibodies act against specific pathogens
What is the difference between the specific and no specific immune system?
specific is much slower as only have a small no of each as there are so many lymphocytes so there is a lag time between being infected and producing antibodies due to clonal selection and expansion
also not born with it but can produce when there’s an infection
Immune response
the sequence of events that occur as the specific immune system responds to foreign antigens involving activation of cloning of B cells and T cells specific to antigens
Where do B and T cells originate and mature?
stem cells in bone marrow where they differentiate into mature cells that spread out through the body’s lymphatic system in bone marrow but migrate to thymus gland to mature then spread across lymphatic system
What types of T cells are there?
What types of B cells are there?
T helper cells
T killer cells
T memory cells
T regulator cells
Plasma cells
B memory cells
What do T helper cells do?
have CD4 receptors on cell surface membranes which bind to surface of antigens on APC’s
produce interleukins when they bind- interleukin 1 produced by macrophage which enhances T cell activation, and T cell releases interleukin 2 which causes the proliferation of other helper T cells (positive feedback) and helps activate plasma cells and T killer cells
interferon may also be produced stimulating killer T cell activity
What do killer T cells do?
destroy pathogens and infected cells (they display antigens on surface)
produce chemical perforin which has proteins that channel through membranes so toxins can enter, killing the pathogen
What do T memory cells do?
part of immunological memory
have encountered specific antigens before so can respond quickly and strongly if that antigen is encountered again by dividing to form killer T cells
What do T regulator cells do?
control the immune system by stopping the immune response when no more antigens are present
they also make sure the body recognises self antigens so doesn’t set up an autoimmune response
What do B lymphocytes do?
produce antibodies to a particular antigen which inactivate circulating antigens
only live for a few days but produce 2,000 antibodies/ second
What do B memory cells do?
live for a very long time and provide immunological memory
remember a very specific antigen and if its encountered again they can rapidly differentiate into plasma cells
more antibodies are produced and they last longer
What types of immunity are there?
Active: natural and artificial. involves an immune response, long term but takes a long time for enough B and T cells to be produced for an effective response
Passive: Natural and artificial. no contact with antigen, no immune response, quick
Describe the types of active immunity:
Natural:
- Acquired due to infection When you meet a pathogen your immune system is activated and antibodies are formed to destroy antigens.
- T and B memory cells are produced so if you meet the pathogen again your immune system recognises the antigen it can immediately destroy the pathogen before it causes symptoms
- Active as body has acted itself to produce antibodies/ memory cells
Artificial:
- Some diseases will kill us before the immune system makes the antibodies they need so medical science can give us immunity without any live pathogen contact A vaccine gives the antibody an antigen through an injection into the bloodstream so the body is stimulated to make its own antibodies and memory cells- primary immune response
- The antigen is either dead, inactivated, weakened, genetically engineered, toxin molecules detoxified
- Then if you come into contact with a live pathogen the secondary immune response is triggered and the pathogen is rapidly destroyed before get symptoms so you have long term immunity
- they can also be used in an epidemic to prevent the spread of a communicable disease
Describe the types of passive immunity:
Natural:
- The immune system of a new born baby isn’t mature and can’t make antibodies for the first couple of months. To protect itself, some antibodies cross the placenta from mother to foetus in uterus
- Colostrum is the first milk a mammalian mother makes with lots of IgA antibodies
- The infant gut allows these glycoproteins to pass into the bloodstream without being digested so within a few days of birth a breast fed baby will have the same level of antibody protection against the disease as mother
- Lasts until the immune system can make its own antibodies Only against disease the mother had but usually from environment baby will live in
Artificial:
- For potentially fatal diseases, antibodies are formed in 1 individual, extracted and injected into the bloodstream of another
- Gives temporary immunity but instantly prevents development of disease
What is an autoimmune disease?
Why does it occur?
What is the downside to the treatment?
When the immune system stops recognising self cells and starts to attack healthy body tissue
May be because immune system responds abnormally to mild pathogen or normal body microorganisms, or T regulator cells don’t work effectively
Immunosuppressants prevent the immune system working so has less defence against communicable diseases
What are the areas affected, symptoms and treatments for rheumatoid arthrits?
affects the joints, starting with fingers and hands, ankles and feet then progressing to shoulders etc.
constant pain and muscle spasms, tendons become inflamed and people become lethargic
no cure, but anti-inflammatory drugs, steroids, immunosuppressants and pain relief
What are the areas affected, symptoms and treatments for lupus (systemic lupus erythematosus- SLE)
skin and joints, and specific organs like the heart, lungs, kidney, liver, brain
different each time it flares up, butterfly rash across face, joint pain, fatigue
no cure but treatment involves anti-inflammatory drugs, steroids, immunosuppressants
What are the areas affected, symptoms and treatments for multiple sclerosis?
affects neurons, cells of brain and spinal cord
fatigue, pain, bladder and bowel issues, sexual disfunction, movement and coordination problems visual problems, cognition and emotional changes
symptomatic treatments- pain killers
therapies- CBT, physio
management techniques- pace so manage fatigue
rehab and aid equipment for day to day living
Herd vaccination
Ring vaccination
- where everyone possible gets vaccinated which protects those who don’t have immunity so there is less chance of an outbreak as its hard to spread.
- This helps people who are unable to be vaccinated like immunocompromised as they have low chance of coming into contact with the disease
- vaccinating only those who are most likely to be infected like those who live or work near an infected person or their contacts to prevent them catching and spreading it/ vulnerable
Why are vaccines necessary
even though many of the diseases are very rare in the UK, they still exist in the world and could be introduced by travellers from areas where there is still endemic
What are the problems with vaccines?
1. hard to get them against eukaryotic organisms as because they have many genes that code for cell surface antigens, which change as it passes through the body becoming different strains eg. Plasmodium. It also remains inside the liver and red blood cells where antibodies have no effect. They do this by: Antigenic drift- small changes in structure and shape of antigens within the same strain of virus Antigenic shift- major changes in antigens within the same strain cross breeding- different strains of viruses invading the same cell, with the formation of new viruses with antigens from different strains When this happens, new vaccines must be made as no one will have immunity to this strain, and if there was. pandemic then stocks would struggle to cope
2. small risk of side effects and complications, swell as false news like MMR and autism mean people dont want vaccines and puts risk to herd immunity and those who aren’t vaccinated
3. People used to be compelled by law but protests over the compulsory smallpox vaccination saw this dropped
4. Historically prisoners and mental institution patients were used to trail vaccines but that is no longer occurring. However, children need to be in the subject population, to test vaccines during and beyond childhood which brings issue of informed consent. in developing countries this can be a problem where cultural and social differences may interfere with effective communication of research aims and key terms may be lost in translation, whilst regulatory boards may not be experienced to protect population from exploitation
5. Vaccines needed for developing countries may be considered low priority in developed countries as won’t make money. developing countries also trial vaccines putting themselves at risk for a vaccine they dot need and which is used in developing nations
Cell mediated immunity
- non specific defence system
- macrophages engulf and digest pathogens in phagocytosis forming APC’s
- The receptors on some of the T helper cells fit the antigens which activates them to produce interleukins etc. (clonal selection)
- interleukins cause more T cells to divide my mitosis producing clones and they may develop into T memory cells, producing interleukins that stimulate phagocytosis and stimulate B cells to divide into plasma cells and stimulate the development of clones of killer T cells specific to the presented antigen so they can destroy infected cells (clonal expansion)
- T cells also recognise antigen fragments presented by infected cells
Humoral immunity
- Responds to antigens found outside cells so produces antibodies that are soluble in the blood and tissue fluid and not attached to cells?? when are they?
- B lymphocytes have antibodies on their cell surface membrane and each b lymphocyte has different antibodies
- A pathogen carry’s specific antigens or produces toxins that act as antigens and the complementary B cell antibodies bind (clonal selection)
- The B cell engulfs and processes the antigens to become an APC???. Then an activated T helper cell binds to the B cell APC selecting the B cell for cloning??
- The B cell then divides by mitosis to give clones of plasma cells and memory cells (clonal expansion)
- Plasma cells then produce antibodies that fit the specific antigen which is the primary immune response- can take a while which is when we get symptoms
- Secondary immune response is by memory cells
What is biodiversity?
What are the three levels it can be studied at?
the variety of living organisms present in an area
Habitat biodiversity
species biodiversity
genetic biodiversity
What is a habitat?
What is habitat biodiversity and how does it affect species?
What places have large habitat biodiversity in UK?
Where has lower?
What does habitat biodiversity provide?
Why can it be hard to measure?
NICHE-
- a place where species live
- The number of different habitats found in an area. each habitat can support a number of different species so more habitat biodiversity means greater species biodiversity
- Meadow, woodland, river, sand dune Farmed
- countryside has lower as only one crop
- resources organisms need to survive like light, CO2, water, mineral ions, food, water, shelter and somewhere to breed
- lots of species feed in 1 ecosystem and roost in another or are seasonal
- role of a species in an ecosystem, like the position in the food web or how it interacts with factors in the environment
What does species diversity involve?
species richness- the number of different species living in a particular area species
evenness- number of individuals of each species living in a community
What is genetic biodiversity?
What is a gene pool?
What are alloenzymes and what do they affect?
When is genetic diversity limited and why?
What problems does this cause?
- the variety of genes that make up a species. For some genes they are the same for all individuals within a species but some have different alleles (different versions)
- Gene pool consists of all the alleles of all the genes within a species
- different forms of an enzyme that have different primary sequences because of different alleles on the genes coding for the enzymes . This can sometimes have an affect on phenotype. Alleles have different nucleotide sequences leading to different amino acids.
- in small populations because inbreeding leads to homozygous genes.
- genes caused by recessive alleles are then more common
What factors affect biodiversity?
Population growth due to improvements in medicine, hygiene, housing and infrastructure allowing people to live longer (habitat loss, overexploitation)
Agriculture
Climate change
What causes habitat loss?
What is the land used for?
What are the negative affects?
Due to deforestation and urbanisation, forest fires and acid rain. marine habitat loss is due to dynamiting coral reefs (extreme way to catch fish), trawl nets pulled across ocean floor and dredging of coastal waters, pollution from rivers full of sediment due to runoff from roads, urban areas and removed trees losing sediment and development along the coast
cleaning land for agriculture, industry, housing, transport, leisure water storage and waste disposal
- causes habitat fragmentation which can cause inbreeding and local extinction
- flooding and soil erosion which looses nutrients
- reduces number of trees present in an area and if 1 type of tree is felled the species diversity is reduced
- reduced number of animal species present as their habitats are destroyed, and food source. This has a ripple effect through the food chain and may also cause them to migrate
- replanting of trees is not as effective as only commercially available trees are used
- coral reefs are also damaged
Examples of overexploitation:
- trees are felled at a faster rate than they can regenerate especially slow growing hardwoods like teak and mahogany
- fish stocks are also overexploited like Atlantic cod which have failed to recover from the 1990’s even after no further fishing. When large predatory fish like cod are removed, less food is available for larger fish, marine animals and seabirds further reducing biodiversity
- in poorer parts of the world, wild animals are overexploited as roads for logging provide easy access for hunting bush meat, especially monkeys
- plants can also be overexploited like hunting as food or to sell
How does agriculture lower biodiversity and what negative affects does this have?
- monoculture is the production of 1 crop only which really lowers biodiversity and few animals will be supported EG. palm oil plantations and livestock farming top feed the growing population
- pests are more common because there is an unlimited supply of food so more chemicals are needed to maximise food production
- deforestation to increase land available for growing crops or rearing animals
- removal of hedgerows due to mechanisation as it allows them to use big machines to plant, fertilise an harvest crops and create more land. Hedgerows are habitats for many species like blackbirds, hedgehogs and mice
- agrochemicals like pesticides to kill pests, however they may also kill non target species and the insect pests are pollinators so important in the habitat and may be a food source for other organisms.
- herbicides kill weeds which compete with crops for light, minerals and water but can also kill non target species. however killing them reduces plant biodiversity and animal biodiversity by removing their food source.
- Fertilisers are needed because of intensive farming but encourage growth of plants which can limit light for lower growing species
- chemicals can pollute rivers as rain washes them in, causing eutrophication. This is when nutrients like nitrate and phosphate ions are too high so more frequent algae blooms which block sunlight so less photosynthesis and plants die. they can also cause large growths of plankton which quickly die and are consumed by bacteria depleting the waters of oxygen, as does age blooms which kills fish.
- Land drainage causes soil invertebrates to live deeper in the soil so less accessible to birds and mammals
What is the trend in global warming?
What aspects of global warming are there?
warming trend in last 50 years is nearly 2x larger than previous 100 years
water vapour levels have increased since 1980’s due to warmer air and more precipitation and more extreme weather
ocean is expanding as it has been absorbing over 80% of the heat added to the climate system
1.8mm/yr from 1961-2003 sea level rise also caused by glacier and ice cap melt due to increasing arctic temperatures CO2 levels increase, trapping thermal energy and acidifying oceans
How does global warming affect biodiversity?
- melting of polar ice caps could lead to extinction of plants and animals species eg. algae is on the underside of ice is a producer for birds and marine animals.
- Some species are moving further north from the arctic to find the conditions they want where they may have to compete for survival
- rising sea levels can cause floods which reduces terrestrial habitats, and salt water can flow further up fresh rivers which reduces habitats of fresh water species
- High temperatures and less rain mean plants can die so rough resistant ones become dominant.
- Animal species dependent on plant species would suffer and new animal species invade
- Insect life cycles and populations change as they adapt to climate change will affect plants as they are key pollinators. Plants may go extinct. Insects carry plant and animal pathogens so could spread tropical diseases to poles
- decrease in pH due to CO2 dissolving makes it harder for organisms to make shells of calcium carbonate which acts as a sink for carbon so less long term stores of carbon
- stratification is when surface waters don’t mix with nutrient rich water deep in the ocean due to warming so phytoplankton won’t grow and divide to produce for the oceans
Positive about climate change
- if climate change is slow species can adapt by migration or finding a new food source.
- You may loose nature species but would gain new ones so no biodiversity lost even though species mix changes
however climate change is occurring much faster than before
Ecological reasons for maintaining biodiversity
interdependence of organisms- removal of one species may affect others through a food source or habitat
keystone species- play and important role in maintaining the structure of a community compared to their size or number so need to be protected to avoid drastic change in a habitat and keep it stable whilst maintaining biodiversity. They can be top/ apex predators or not
Gene pool- higher biodiversity means higher stability in the ecosystems so can withstand environmental change like storms better and recover better. They become unstable due to loss of populations at different trophic levels eg. loss of top predators like lions causes increase in herbivores so overgrazing and erosion and loss of biodiversity
Economic reasons for maintaining biodiversity: agricultural
soil erosion and loss of nutrients and desertification caused by deforestation reduces the countries ability to grow crops and feed its people so they rely on other countries.
monoculture also causes soil depletion as crops are harvested so nutrients aren’t replenished and crops become weaker and more vulnerable to pests so chemicals are used to maintain productivity. rotting material also helps bind soil
high biodiversity provides protection against abiotic stresses like extreme weather so a change in conditions don’t destroy whole crops EG Irish potato famine only relied on 2 varieties of potato.
plant varieties needed for cross breeding so get better disease resistance or increased yield characteristics so less land needed
Economic reasons for maintaining biodiversity: materials
food - hardwood timber is an important resource but removed unsustainably which will result in the collapse of an industry in an area as it will no longer be economically viable
undiscovered species in tropical rainforests may have chemical or medical uses so biodiversity loss causes them to go extinct and they would have had economic importance
when habitats are destroyed so are populations of commonly grown plants and without genetic diversity, plant breeders struggle to breed to new varieties reducing horticultural industry income
Economic reasons for maintaining biodiversity: services
- plants transpire water passing to the water cycle which gives us drinking water. they also filter it through the soil and rock and organic waste material in water is broken down in water is broken down
- nutrient cycling maintains soil fertility
- reefs and mangroves protect from erosion
- habitats moderate floods, droughts and extremes of wind and temperature
- insects pollinate crops
- forests and peat bogs absorb CO2
Aesthetic reasons for maintaining biodiversity
health and well being- patients recover quicker from stress and injury when in natural environment and helps everyday people relax and enrich their lives
attractive environment- inspires musicians and writers who provide pleasure for readers so landscapes must be protected economic for tourism like ecotourism
What are the methods of maintaining biodiversity in situ?
- internationally designated areas
- nationally protected areas
- nature reserves
- marine conservation zones
What is in situ conservation?
Why is it preferred?
Why may it not be good?
conservation of species in its natural habitat
- preferred option as have all the resources they need
- are adapted to their environment
- continue to evolve in their natural environment
- help interdependent species
- larger species have more space
- animals more likely to breed if in natural environment
- if populations are small they risk poaching
Wildlife reserves
internationally designated areas: designated by organisations like UNESCO. 28 world heritage sites in UK (important physical or cultural sites) and 5 biosphere reserves promoting sustainable development and preventing hunting etc.
Nationally protected areas like national parks- 15 in England, Scotland and Wales with separate authority for each. Also areas of outstanding natural beauty- 46 in England, Wales and N Ireland
nature reserves can be national and protect sensitive ecosystems and provide outdoor labs for research administered by natural England to maintain conditions for rarest species
local nature reserves under control of local authorities through ownership or lease with landowner and are for natural species
sites of special scientific interest give legal protection to the best sites for wildlife and geology so landowners can’t change the management of the are without permission
Marine conservation zones
- marine and coastal access act 2009 set up these 28 zones
- they include refuge areas where fish populations can build up
- also protect the habitats
- ban commercial fishing zones
- can turn an area devoid of life to support a diverse community
What are some other general ways of maintaining biodiversity?
controlled grazing- particular area or amount of time so can recover
restricting human access- no beach access in seal reproductive season, paths
controlled poaching- defences to prevent access, fines, remove rhino horns
feeding animals- help them survive to reproductive age
reintroduction of species- if locally extinct or in low numbers
remove invasive species- they compete for resources
halting succession- so doesn’t become woodland by controlled grazing which eat seedlings
create new habitats- digging ponds, sinking ships for coral to colonise
Ex situ conservation examples
what is it?
why is it needed?
botanical gardens, seed banks and zoos
removal of species from wild to a protected place
necessary due to mining, road construction, development, grazing, logging and poaching. May not be able to conserve in natural habitat as its shrinking and fragmented
Botanical gardens
- grow plants that are extinct in the wild hoping they can be reintroduced
- they are given all the resources they need
- protect populations of plants collected from wild so there’s enough for people to buy so they don’t have to take endangered from wild
- researching methods of growth and reproduction so can be grown in appropriate conditions
- researching conservation methods so can be reintroduced
- used to educate public of role of plants in ecosystems and economic value
What are seed banks?
How are the seeds collected and stored?
What are they used for?
What happens if the seeds can’t be stored?
A gene bank where seeds are stored so new plants can be grown in the future and are stores of genetic diversity
Collected from the wild or crops, sorted, dried to slow metabolism and reduce ice crystal damage and stored at very cold temperatures. They are checked at 5 yr intervals to see if their still viable by attempting to germinate them. They remain viable for centuries as it slows down the rate they loose their ability to germinate
- Used for future breeding programmes
- To genetically modify plants for economic gain
- A store of material for medicines
- To prevent extinction
some can’t be stored so can be kept as tissue cultures or grown as mature plants in fieldworker gene banks
What do zoos do?
How do they maintain diversity?
- protect endangered and vulnerable species
- research biology of species to gain a better understanding of breeding habitats and habitat requirements
- contribute to reintroduction schemes
- educate public about wildlife and conservation
frozen
- can hold a lot of genetic diversity for a long time and include frozen eggs
- can be damaged due to ice crystals which damage internal membranes
captive breeding programmes
- provides animals shelter, food, no predators and veterinary treatment before release
- may not be able to survive as have no resistance to local disease
- have behaviour issue, don’t know how to hunt for food (try to hide it in cages).
- The genetic population of captive may be so different to original they can’t interbreed
- natural habitat may be destroyed or not big enough to support more individuals
- to avoid small gene pools they exchange specimens or use artificial insemination from frozen sperm banks and take part in breeding programmes to prevent inbreeding
International union for the conservation of nature
- Assess the status of world animal and plant species as animals don’t respect countries boundaries so international cooperation is needed
- once a year they publish a red list detailing current status of threatened animals
- They also established CITES
Conservation agreements
ICUN
CBD
CITES
CSS
What does CBD stand for?
What does it do?
1992 rio conventions biological diversity meeting of 172 nations
- earths summit ensured national strategies for sustainable development to maintain biodiversity
- convention of climate change to stabilise greenhouse gas concentrations
- conservation to combat desertification by reducing effect of drought
What does CITES stand for
What does it do?
What are the disadvantages?
convention of international trade in endangered species- 1973 145 countries signed the agreement. 35,000 species protected
- regulates international trade of endangered species to prevent over exploitation eg. pet trade and materials like ivory which is illegal
- has 3 appendix depending on how at risk of extinction species are
- if trade is illegal, price increases so its more worthwhile to break the law
- trade spikes when new species are announced to go on the list eg. poaching of elephants as increased as illegal trade of ivory increases in response to demand from china
What are local countryside stewardship schemes?
What do they do?
in England it operated 1991-2014 involved payments from governments to farmers to make conservation a part of normal practice. now replaced by similar environmental stewardship scheme
- ensure land is well managed
- retains traditional character
- protect historic features and natural resources
- improve and create new habitats
- resort neglected land
- conserve traditional livestock and crops
- have opportunities for people to visit and learn about the countryside
classification
taxonomy
phylogeny
the process of sorting living things into groups
the study of the principles of classification
the study of the evolutionary relationships between organisms often presented as a phylogenetic tree which shows how different species have evolved from a common ancestor, with earliest at base and newests at tips. Based on physical characteristics as used to only be able to see external and internal (microscope) and genetic makeup. 2 groups that branch from the same node (branch) are sister groups. linen classification uses phylogeny
Why do we classify?
- convenience, makes studying living organisms more manageable
- makes it easier to identify organisms both new and old
- helps us see interspecies relationships
- creates a world wide record of all living organisms
- helps communication worldwide to share research
- see evolutionary links as species in the same group probably share characteristics as they have evolved from common ancestors
How do we classify?
- historically it has been based on observable features
- more recently it has been on DNA and biochemistry- molecular biology because if characteristics change so must the proteins and so much the DNA which codes for them
What did carl Linnaeus found?
the binomial system of nomenclature and the hierarchal system of classification which is largely based on observable features which represent evolutionary relationships
What are the taxonomic groups in the hierarchal system?
Kingdom: largest group of organisms sharing common features
Phylum: major subdivision of a Kingdom
Class: group of related orders, subdivision of phylum
Order: group of related families, subdivision of a class
Family: group of closely related genera, subdivision of order
Genus: group of related species, subdivision of family
Species: breed freely with one another. smallest group and most specific/ least diversity
What do you need to remember about binomial nomenclature?
- Genus and species
- Only G capital letter
- italics or underline if handwritten
species
what is not a species?
- the smallest basic taxonomic unit used to define living organisms
- a group of individuals with similar key features but show variation and can interbreed and produce fertile offspring (doesn’t take into account simple organisms that reproduce asexually)
- mule from a male donkey and a female horse
- hinny from male horse and female donkey can’t produce fertile offspring
Are you more related if your species or genus are the same?
How do you find the most closely related species on a phylogenetic tree?
genus
doesn’t matter which direction, but closest branch
What are the advantages of phylogeny?
produces a continuous tree whereas classification requires discrete taxonomic groups so scientists don’t have to put organisms into a specific group if they dont quite fit in heirachal structure
Linnean classification can be misleading as it implies different groups in the same rank are equivalent, whereas in reality they may have longer history, different levels of diversity so aren’t comparable
Homology
shared features that are inherited from a common ancestor but may not be used for same function
eg bats wings and human arms have same bone pattern so are homologous but are used in different ways
The more recently 2 species shared a common ancestor the more homologies they will have and the more similar those homologies will be
divergent
Using antibodies for molecular evidence in classification
- Antibodies to a specific antigen can be produced by injecting an animal with that antigen.
- Their blood is taken a week later and prepared as an antiserum by removing all cells and adding anticlotting agent. The antiserum contains antibodies from the plasma cells.
- The serum can then be used to test the blood of other species to see if they same antigen is present
Can be done by spinning human blood in a centrifuge to remove red and white blood cells then treating for clotting. Sample of plasma is injected into mouse and then later a sample of blood is taken from the mouse. The antiserum conaytins antibodies against all proteins in human blood plasma. So when combined with blood, they would attatch to human antigens and precipitate. The degree of precipitation is compared to mouse antibodies and human blood plasma.
Using DNA sequencing for molecular evidence in classification
- Sequence of amino acids is determined by sequence of bases in genes that code for them.
- Its easier to sequence DNA than proteins, and its more detailed and specific due to the degenerative nature of the code. May get silent mutations- changes in base pairs still result in same amino acid.
- Neutral mutations change the amino acid but not the R group, so they don’t affect function.
- Protein sequences are determined from DNA sequnces now.
- Genes that code for rRNA change slowly so are useful in sorting out relationships between higher taxa like domains, kingdoms and phyla.
- Rapidly changing genes show relationships between species and even between isolated populations of species.
- DNA is also more stable than a protein so can sequence DNA from extinct organisms.
- Most useful genes to analyse are the genes that code for proteins required for fundamental features all organisms have.
Using protein sequencing for molecular evidence in classification
Comparing sequences of amino acids.
The sequences are created from a 1 letter code.
Tree diagrams can be drawn, with the lengths of branches proporinal to number of differences in primary sequence.
Using DNA hybridisation for molecular evidence in classification
- Each DNA molecule is made of 2 strands of nucleotides and heating to around 90*C the DNA molecules causes the hydrogen bonds to break between them.
- The strands separate and can be isolated. Two species can then have their single stranded DNA mixed.
- When cooled, the attraction of the nucelotides will make the hydrogen bonds reform.
- As there are genetic differences, the match between the 2 strands is not perfect and the hydrogen bonding will be weaker, so can be broken with little heat.
- The closer the match the more heat required to break the strands.
How has molecular evidence changed classification?
Used to use anatomy, morphology, behaviour, physiology and cell structure
now can study sequences of amino acids in proteins and the sequence of nucleotides in DNA- molecular phylogeny
Features of the 5 kingdoms
Sources of medicines
example of plant and microorganism based medicines
- complex computer programmes can design new drugs
- many commonly used drugs come from plants and microorgaisms
- Penicillin (mould) is an antibiotic
- Aspirin (willowbark) is a painkiller, anticoagulent, antiinflammatory
- digoxin (foxgloves) for heart failure
- vancomycin (soil fungus) most powerful antibiotic
Personalised medicine
Why does it work?
how can it be used?
example
What is pharmacogenomics?
the combination of drugs that work with your individual combination of genetics and disease
people have different genes so produce different enzymes and proteins so certain medicines are more effective on some poeple than others
by testing someones genome its possible to identify the effectiveness of drugs so they are mre precise and have less side effects
EG. HER2 gene mutation for trastuzumab
interweaving knowlege of drug actions with personalised genetic material
Why is synthetic biology needed?
What 2 ways can it be useed
examples
some drugs are difficult or expensive to produce
genetic engirneering can be used to develop bacteria which produces these drugs by inserting a genome into a bacterial cell with removed DNA and letting it divideto relpicate the DNA. can be exisiting DNA sequences or create new ones
Nonotechnology uses tiny synthetic particles to deliver drugs to a very sepcific site within a cell
EG E.Coli and yeasts are genetically modified to produce a precursor (drug that will be activated to become the drug) of an antimalarial drug
EG mamals can also be genetivally modified to produce drugs in their milk EG goats produce human antithrombin which prevents blood clotting
how do antibiotics work?
examples
history of antibiotics
whats happening now?
antibiotics interfere with the metabolism of bacteria without affecting the matabolism of human cdells- selective toxicity
they were the 1st time medicines were effective against bacteria so were widely used and commuicable disease deaths dropped
EG. steptomycis, vancomycin, penicillin
are now used for minor infections which the immune system could handle
resistance started with penicillin but some microorgansms are resistant to all
how does antibiotic resistance occur?
where is it common?
- antibiotics work as theres a binding site for the drug and a metabolic pathway affected by it
- random mutations can produce bacteria not affected by the antibiotic and this is best fitted to survive and reproduce
- it passes it mutation to daughter cells and reproduces rapidly
- bacteria have 1 copy of a gene- a single loop of double stranded DNA so mutations have an immediate effect
- antibiotics can then kill the weaker ones so that the restant bacteria become more common so you get a resistant strain
- common in care homes and hospitals where antibiotics are often used and people have weak immune system
MRSA and clostridium difficile
MRSA
- bacterium carried in 30% of population on sin and nose
- enters through cut or medical procedure
- causes boils, abcesses and potentially fatal scepticaemia and neumonia
- was treated effectively with methicillin, a penicillin like antibiotic but mutated to be resistant strains
C.Difficile
- bacteria in guts of 5%
- produces toxins that damage the lining of intestines cauing dirrhoea, bleeding and death
- no problem for healthy people but when antibiotics kill of helpul bacteria in gut it can survive and reproduce rapidly
how to prevent resistant bacteria
- need to minimise use and ensure complete course so resistan individuals are less likely to survive and become a resistant strain
- good hygiene
Graph for priamry and secondary response
why is there no vaccine for malaria?
it spends time in erythrocytes so it is protected by self antigens and its own antigens reshuffle
What are the diffferent methods if classification?
biological/ species/ physiological- by observing homologous structures which show common ancestry
phylogeny- based on ancestry and molecular similarities such as DNA and RNA
what is convergent evolution?
What is evidence foe this?
what are analogous structures?
what are homologous strctures?
why does alll of this mean classifying species can be less accurate and how can you be more accurate?
some animals are unrelated but have evolves similar adaptations to their environment
anatomical adaptations
EG birds, bats and insects all have evolved with wings but are very different
serve the same purpose but are structually veyr different
EG bird and insect wings
structures that have developed from the same limb
EG bat and bird wings
- more accurate to DNA type them
What methods enabled another assessment of the classification system by Woese in 1990 to 3 domains?
What protein can be used to determine evolutionary links?
now study genetics and biological molecules. when you eveolve, your internal and external features change so therefore DNA does too as it determines the proteins therefore the characteristics. it uses differences in sequence of nucleotides in cells rRNA and lipid membranes structure as each domain is different
haemoglobin has 4 polypeptide chains with a fixed number of amino acids
chimpanzees only have 1 different aa, gorillas have 3, indicating common ancestory
What are the 3 domains?
which are prokartotes?
bacteria forming eubacteria
archaea forming archaeabacteria
eukaryotes forming protoctista , plantae, fungi and animalia
eubacteria and arcjaea are both prokaryotes
Features of domains
What does it mean if 1 branch is smaller at an equivalent time on a tree?
extinct
Why can recalssification necessary?
archaea ad eukaryotes had lots in common
- similar cell membrane structure
- simialr flagella structure
- same form of RNA polymerase
- proteins bound to genetic material
- similar mechanisms for DNA replication and building RNA
what is the purpose for cytochrome C?
is a protein used in respiration in all living organisms (not chemosynthetic organisms)
made from a sequence of aa which varies slightyl from species to species
if thr sequence is very similar between 2 species we can infer they are closely related
we could also comapre DNA or RNA sequqnces
What is an adaptation?
What makes a well adapted organism?
a characteristic that increases an organisms chance of survival and reproduction in its environment
- find enough food or photosynthesise well
- find enough water
- defend itself against predators and disease
- survive physical conditions of environment
- respond to changes in its environment
- have enough energy to allow successful reproduction
What is the main difference and similarity betwen the marsupial and placental mole?
different taxa as reproduce different and seperated from common ancestor 100 mill years ago
Placental- placenta connects embryo to mothers circulatory system in the uterus so the embryo reaches a high level of maturity before birth. dark grey
Marsupial- start life in the uterus but leave and enter the marsupium pouches when they are still embryos and suvk milk to mature here. light brown/orange
adapted same due to similar conditons
both burrow throughsoft soil to find worms and grubs and have modified fore limbs for digging. velvety fur for smooth movement and simialr shape (long)
What types of adaptations are there?
anatomical (physical features internal and external)
physiological (internal processes and functions of the body systems)
behavioural (inherited or learnt)
What tyoes of anatomical adaptations are there and examples?
body covering- feathers, hair and shells for flying, warmth and protection
mimicry appearance- think harmful/ poisonous eg hoverfly mimics wasp
camoflauge- white snows have white hair in winter and brown in summer
teeth- tigers and sharp and big to kill prey
behavioural
survival behaviour - possoms play dead
courship- elaborate to attract mate and more chance of reproducing eg scorpois dance
seasonal behaviour- migration for climate and food andhibernation where they are inactive and have reduced HR + temp to conserve enegy eg brown bear in winter
innate- genes eg spiders make their webs
learned- from experience or watchign others eg sea otter uses stones to hammer shells off rocks
physiological adaptations and examples
poison production- reptiles produce venom to kill prey
antibiotic production- bacteria try to kill other bacteria species
water holding- cacti
Blue gum example for adaptations
Structural: vertical leaves to reduce light exposure and transpiration, thick bark to protect from fire
Behavioural: releases seeds after a fire so less competition from other plants
Physiological: Leaves produce toxic compounds to deter grazing
Fennec fox example for adaptations
Structural: large ears for hearing and heat loss, eyes for predation, thick fur for the cold nights hunting
Behavioural: Nocturnal to avoid heat and predation from eagles and are in underground burrows in day
Physiological: kidneys reabsorb most water to concentrate urine to avoid dehydration
thermophilic archae example for adaptations
Structural: membranes have strong ether linkages . DNA has a high proportion C-G and so compact to withstand heat. Proteins have many polar amino acids to stabilise the tertiary structure
Behavioural: form a matrix that sticks bacteria to a biofilm to help withstand the high temperatures
Physiological: produce heat shock proteins to protect the cell. A heat resistant polymerase so replication still occurs at high temperatures.
whay cant differences in DNA data tell us what weather to put species in the same genus?
- There is no clear definition of what a genus is and what criteria should be used for placing different species in the same genus.
- If we use DNA sequences in this way, there is no agreement about whether it is more valid to look at every part of the DNA in a species or whether we should concentrate on particular areas, such as the coding
- We can also question whether sheer numbers of differences in DNA bases can justifiably be used to determine classification, or whether we should take into account their effects as well.
are the five-kingdom and the three-domain classifications completely different from one another, or could they possibly be used together
The three domains are the highest taxa.
It is possible to have the domain Eukarya, with the kingdoms Protoctista, Fungi, Plantae and Animalia as subdivisions of it.
However, we cannot keep the kingdom Prokaryota, as that is now split at a higher level.
What is variation?
- The presence of variety/ difference between individuals leading to adaptations and evolution (natural selection)
- Can occur within a species (intra specific variation), or between species (inter specific variation)
What are the types of variation?
Continuous
- 2 extremes and a full range of intermediates.
- Most individuals are close to the mean value, with the number of individuals at the extremes being low.
- EG. Height or length of leaves.
- Can be due to genetic or environment and usually a combination of many different alleles and genes (polygenic) and then affected by environment too.
- Often assigned numerical values but not always lie eye and skin colour.
Discontinuous
- 2 or more distinct categories with no intermediate values, often categories have a label not a number.
- Members of a species may be evenly or unevenly distributed between categories.
- EG. Human blood groups, colour of flowers, drug resistant and drug susceptible TB.
- Mainly due to genetic variation and little influence of environment, and often determined by a single gene with one 2 or 3 possible alleles. (largely monogenic)
What are the 2 main causes of variation?
Genetic
- alleles are different forms of the same gene, all organisms have different combinations of different alleles.
- In sexually reproducing organisms it comes from events in meiosis- crossing over in prophase 1, independent assortment in metaphase, random fusion of gametes, and you inherit alleles from each parent so is different from parents.
- It may also arise from random mutations in DNA. Mutations must occur at the gamete so new cells can be passed onto future generations not just the individual itself. If thy occur in somatic cells (body) then only the individual is affected. Both cause variation.
- Allozymes are enzyme variants that are coded by different alleles of the same gene. Isozymes all catalyse the same reaction but are coded by different genes. They may be able to work at different temps.
Environment
- not all genes are active at once. The environment can affect which genes are active at a time.
- Food- obesity, sun- skin colour.
- It is not inherited.
- Plants are more affected by environmental variation as they can move less.
- Scars are completely environmental.
Can be a combination
- if you have tall parents you will probably inherit genes to grow tall but if you eat a poor diet and suffer from disease you may not be tall
What were darwins 4 observations?
- All organisms reproduce to give far more offspring than are going to survive
- Populations of organisms fluctuate but don’t tend to increase and decrease significantly over time- their number remain fairly constant
- There is variation among individuals in many of their characteristics- intraspecific variation caused by sexual reproduction
- Offspring resemble their parents- features are transmitted from one feature to the next.
What were Darwins 4 inferences?
- In ‘on the origin of species’, there is a struggle for life- there is competition between organisms in the same population for limited resources
- The organism that are successful in competing for resources have features that mean they are adapted to their environment. They have a higher chance of surviving than individuals that are not so well adapted. Those that are successful in competition live long enough to reproduce
- The organisms that reproduce pass on inherited characteristics to the next generation which then contains a higher proportion of offspring from the better adapted parents than from those that are less well adapted
- The unequal ability to survive and reproduce leads to a gradual change in a population with certain adaptations increasing in frequency over the generations
What did darwin and Alfred Wallace do?
Darwin noticed that the shape of finches beaks were adapted to food available on different Galapagos islands. When he returned to England he spent many years developing ideas and carried out experimental breeding of pigeons to gain evidence that his ideas may work.
Wallace spent many years travelling and collecting specimens in south America (Borneo) and in south east Asia. He came up with natural selection. They both had similar ideas of evolution so they proposed the theory of evolution though a joint presentation of 2 scientific papers in the Linnean society of London in 1858.
A year later Darwin wrote his book naming the theory as the theory of evolution by natural selection
Evidence of evolution from fossils
- Palaeontology is the study of fossils
- Mineralised animals that have lived and died found in sedimentry rocks
- Only the hard parts mineralise and generally the soft tissues decompose
- Only a small proportion of organisms will be fossilised
- Need specific conditions for fossils to form and are not often present
- We only find a small proportion of fossils so we have a limited view and some are destroyed in volcanoes etc.
- Older fossils show organisms to be smaller and simpler
- We can track fossils over a period of time and observe a sequence of developmental changes and adaptations (evolution)
- Fossils of the simplest organisms like bacteria and simple algae are found in the rocks whilst more complex organisms like vertebrates are in more recent rocks
- The sequence organisms are found matches their ecological link- plants appear before animal fossils as animals need plants to survive
- Can see similarities in anatomy to see how closely related organisms evolved from the same ancestor
- Allow relationships between extinct and living organisms to be investigated
Comparative anatomy and morphology for evidence of evolution
Bones in the front limbs of tetrapod’s- amphibians, reptiles, birds and mammals have basically the same pattern even though there are differences between them, indicating they had a common origin
Homologous structures- appear superficially different but has same underlying structure – vertebrates weather swimming, walking, flying has similar limbs so may have evolved from a common ancestor and common structure. This is evidence for divergent evolution when closely related species diversify to adapt to new habitats as a result of migration or loss of habitat.
Biochemistry/ DNA as evidence for evolution
- Atoms in aa can be arranged to give 2 molecules that are mirror images of each other- left handed and right handed molecules. Only left handed aa exist in nature.
- There are many possible different types of aa but only 20 are used to make proteins and they are the same 20 in all organisms
- The molecules of inheritance in all cellular organisms, prokaryotes and eukaryotes is DNA so slight changes in this can help identify evolutionary links
- The genetic code that specifies an organisms aa is basically the same in all organisms
- ATP is the universal currency for energy in the cells of all organisms
- Analysis of the aa sequences of proteins reveals proteins from closely related organisms are very similar
- Sequencing DNA nucleotides shoes the relationship between different species- nucleotide sequences in the genes of closely related species are found to be very similar. Similarities and differences can group species and deciding the extent of the differences gives us an idea when speciation occurred.
- Also similar key protein structures like DNA polymerase which repairs and copies DNA has only a few differences between its aa sequence for different phyla and even kingdoms. Any significant changes in this enzyme reflect significant events in evolutionary history.
- Ribosomal RNA and cytochrome c, a protein involved in respiration are commonly studied as they are mainly conserved among species. rRNA has a slow rate of substitution so is used with fossil evidence to determine relationships with ancient species
- Neutral evolution- most variability in the structure of a molecule doesn’t affect its function as most variability occurs outside the molecules functional regions which aren’t affected by natural selection
Natural selection
- Genetic variation, selection pressure and reproductive success or failure results in an increased proportion of the population possessing the advantageous characteristic
- Organisms that are best adapted to the environment are more likely to survive and reproduce. As a result of natural selection these adaptations will become more common in the population. Organisms poorly adapted are less likely to survive ad reproduce so characteristics are not passed onto next generation so less of the population displays these characteristics.
- Organisms within a species show variation in their characteristics that are caused by differences in their genes (genetic variation) different alleles for example from mutations
- Organisms whose characteristics are best suited to a selection pressure such as predation, competition or disease have an increased chance of surviving and successfully reproducing. Less well adapted organisms die or fail to reproduce – survival of the fittest
- Successful organisms pass the allele encoding the advantageous characteristic onto their offspring and those without it are less likely to pass it on
- This process is repeated for every generation and over time the proportion of individuals with the advantageous adaptation increases. Therefore the frequency often allele that codes for this particular characteristic increases in the populations gene pool
- Over very long periods of time many generations and often involving multiple gens, this process can lead to the evolution of a new species
Example of natural selection
EG. Peppered moths- dramatic changes to their environment I the 19th century caused changes in the allele frequency. Before the industrial revolution they were pale coloured to camouflage them against light coloured tree bark and increase their chance of survival. Tress got darker in the industrial revolution as covered in soot so loss of lichen cover caused by increased atmospheric pollutants. Darker ones survived and reproduced so increased frequency f ark moths and the dark allele in the population. Now lighter moths again due to clean air act.
Selection pressure
factors that affect the organisms chances of survival or reproductive success (ability to produce fertile offspring)
Pre-adaptation
when an organisms existing trait is advantageous for a new situation.
How has evoltion impacted humans?
- Drug resistance
- Pesticide resistance
- Flavobacterium
Evolutions impact on humans: drug resistance
- Antibiotics soon became less effective as bacteria developed resistance, due to a few bacteria which naturally possessed genes that helped them prevent the effect of the antibiotic
- EG penicillin is effective as it prevents the growth of cell walls in some bacteria. Resistant bacteria have enzymes that can break down penicillin, and when antibiotics are used, they have an advantage as they are adapted to new conditions. There is then less competition for the resistant bacteria as they have been killed so the resistant ones survive and reproduce to pass on their genes to offspring. EG MRSA (methicillin resiatant S. aereus)
Bacteria gain resistance by:
- A gene on the chromosome spontaneously mutating to give a form that codes for a polypeptide that is not affected y the antibiotic
- A bacterium may gain a plasmid with a gene for resistance from another bacterium, even from an individual of a different species
As bacteria only have 1 copy of each gene since they only have a single loop of double stranded DNA. They are essentially haploid so a mutant gene for antibiotic resistance will have an immediate effect on any bacterium with it. They also reproduce very quickly asexually by binary fission.
Usually, the few bacteria that aren’t eliminated will be eliminated by the immune system so eventually the entire population will be killed but if the dose is not correctly followed then the less susceptible bacteria can survive. TMT next time there’s an infection with thin bacteria strain the antibiotic won’t be as effective. Some strains are untreatable.
Ways to reduce resistance:
- Only prescribe antibiotics when absolutely necessary and don’t prescribe them for no bacterial diseases just in case
- Ensure people finish their course of antibiotics
- Rotate antibiotics so that one type is not used continuously in the treatment of a specific disease
- Keep some antibiotics as a last resort
- Invest in research to find new antibiotics
Evolutions impact on humans: pesticide resiatance
- Used to kill pests of crops and vectors of diseases – EG Colorado potato beetles and anopheles tranmit malaria
- Monoculture provides lots of food for insects so if other conditions are good then they will increase in number rapidly
- Resistant insects will survive and reproduce as there is less competition
- The insecticide is the selective agent
- This reduces food security for the future as evolution of resistant strains means we need to find new chemical controls, use them sparingly or rotate them so they’re not used all the time which helps extend the useful life of pesticides. 2 or more pesticides can be mixed which delays the time for resistance to emerge and spread. Also only use them when they know their crops are at risk, not to prevent an invasion of pests
- Biological control is an option where natural parasites and predators of the pest species are released
- Selective breeding can develop new crop varieties that are resistant to pests
- Genetically modifying crops to make toxins that kill pests
Flavobacterium
Most evolution occurs as a negative result of selection pressure, but some occurs due to opportunities that have arisen in their environment. A new strain of flavobacterium is living in waste water from factories that produce nylon 6, that makes toothbrushes and violin strings. Humans use it to digest and clear u factory waste as they contain enzymes called nylonases which provides them with a source of nutrients. These enzymes were probably caused by a mutation.
