topic 6 and topic 7 weak spots paper 1

endotoxins

* produced by gram negative bacteria
* lipopolysaccharide embedded in the cell surface membrane
* component embedded in the outer phospholipid of the cell membrane is toxic

which bacteria produce endotoxins?

salmonella

* s. entera invades cells lining the intestinal wall. upon lysis, endotoxins are released which cause inflammation and results in diarrhoea
* s. typhi invades the body via the lymphatic system once ingested and invades body cells once spread around the body via the lymph - when endotoxins are released typhoid fever is caused

which bacteria produces exotoxins?

staphylococcus

* haemolysins: polypeptides that become integrated in cell membranes of host cells, creating pores which cause the cells to lose water and ions
* superantigens: polypeptides that stimulate immune cells and cause massive release of cytokines into the blood, which can cause toxic shock syndrome - high fever, low blood pressure, coma, multiple organ failure

what is a granuloma?

the macrophages that have engulfed tuberculosis bacteria become surrounded by other cells in the immune system

how does a chronic infection of tuberculosis occur?

* occurs when the recipient has a weak immune system
* bacteria secretes hydrolytic enzymes into the host’s cells and digests them
* energy source is cholesterol - component of cell membrane
* cavities appear in lung tissue, blood vessels are broken down, and fluid collects as bacteria digest cells

what is found in a granuloma?

* t-cells: immune cells produce signals that stimulate bacterial killing by macrophages
* a TB -infected macrophage
* ‘caseous necrosis’: characteristic crumbly core material containing dead cells

how does tuberculosis affect a healthy recipient?

* growth of bacteria is restricted in the lungs
* bacteria is engulfed by macrophages in the alveoli and bronchioles
* granuloma is formed
* macrophages kill the bacteria but few survive as a latent infection that could result in infection years later

what is *Ug99*?

* variety of stem rust fungus discovered in uganda in 1999
* devastating crops of wheat in east africa, the middle east, and asia
* has the potential to cause worldwide food scarcity
* computer model predicts it will reach india, one of the world’s largest producers of wheat
* 85% of the worlds population depend on wheat as their only sources of energy
* 60% of the worlds population depend on wheat as their main source of dietary protein

hyphae

stem rust fungus spores germinate and produce threadlike structures

mycelium

a mass of fungal hyphae

how does stem rust fungus digest host cells?

1. secretes digestive enzymes from its hyphae onto the material on which it is growing
2. enzymes digest chemicals in the stem and the fungus absorbs the products of this digestion

how does stem rust fungus infection damage the host plant?

* weakens the stem, often causing the plant to fall over
* makes mechanical harvesting impossible
* uses nutrients that would otherwise be stored in the plant’s seeds
* reduces the harvest
* breaks the outer epidermis of the stem
* increases the rate of water loss from the plant
* makes the plant more susceptible to infection by other plant pathogens

how can fungicides be used to control stem rust fungus spread?

* kill stem rust fungus
* usually expensive - reduces their availability to poor farmers in africa and asia
* can damage delicate ecosystems
* associations between plant roots and fungi are vital to the roots’ efficient absorption of inorganic ions from soil

why is it difficult to control the spread of stem rust fungus?

* stem rust fungus depends on the barberry plant to complete its life cycle
* north america has an ongoing barberry eradication programme, but spores are carried to north america by the wind from southern american states and mexico
* spore dispersal occurs over very large distances

how can gene manipulation control stem rust fungus spreading?

using genetic engineering, scientists have produced cereals resistant to some strains of stem rust fungus - identifying a number of genes that confer resistance to stem rust fungus

* have only been used in australia - worldwide effectiveness is unknown

what does the influenza virus look like?

* eight short strands of RNA - segmented genome
* surrounded by protein capsid
* envelope with outer protein layer and inner lipid layer
* glycoproteins project through the envelope and cover the surface of the virus
* H glycoproteins help the virus particle enter a cell of the host
* N glycoproteins allow newly formed virus cells to escape from a cell of the host

what happens during influenza virus infection?

1. influenza enters lungs through inhaled air droplets
2. enters epithelial cells lining the bronchus and bronchioles by endocytosis
3. replication of the virus occurs in the host cells
4. toxins are released as the host cell lysis - brings about many of the symptoms of influenza, can cause secondary infection

why is influenza having great antigenic variability an issue?

humans have little to no resistance to these new antigens - influenza can easily cause an epidemic

* immune systems have not encountered them before, meaning no memory cells

antigenic variability

variation in the chemical nature of the same type of antigen resulting from frequent gene mutations and, in eukaryotes, different splicing of pre-mRNA molecules transcribed from the same gene

what are the three pre-requisites for a flu pandemic?

* a novel virus strain, unfamiliar to human immune systems, must reach human hosts from its point of origin
* the virus must be able to replicate in humans and cause disease
* the virus must be efficiently transmitted between humans

examples of influenza pandemics

* spanish flu 1918-19
* asian flu 1957-58
* hong kong flu 1968-69

how is malaria transmitted?

* transmission of plasmodium from an infected person to another person is by the anopheles mosquito
* female anopheles takes a blood meal from a human, injecting saliva containing coagulants
* if the female is infected with plasmodium, the saliva contains the sporozoites of plasmodium, causing infection of the human

how does plasmodium infect a human?

1. sporozoites infect cells in the liver and rapidly divide to form thousands of daughter cells called merozoites
2. infected liver cells lose and their merozoites are released into the blood
3. merozoites enter red blood cells, where they digest the haemoglobin as a food source
4. each merozoite undergoes several cell cycles to produce 8-32 new red blood cells
5. the red blood cell bursts releasing the new merozoites, which infect other red blood cells
6. each red blood cell that bursts produces toxins produced during the breakdown of its contents by the merozoites, which cause the symptoms of malaria - raised body temperature, intense fever symptoms, and a swollen spleen

endemic

a disease that occurs frequently, or is constantly present at a low level of infection, in particular areas or among people of a particular population

what are the issues with draining wetland areas where mosquitoes breed?

* not possible to drain large lakes, which are also breeding grounds for mosquitoes
* some people earn their living, or derive their main food source, from wetlands
* successful drainage might involve inter-governmental co-operation, which is not always possible

what are the issues with spraying areas where malaria is endemic with insecticide to kill mosquitoes?

* the areas are vast, much larger than areas treated in europe, and would often involve co-operation between different governments or areas occupied by warring groups
* insecticide would damage other wildlife, including beneficial insects

what are the issues with covering beds with fine-mesh nets, coated with insecticide?

* cheap and effective, as most mosquitoes bite during the night
* however mosquitoes that bite during the day are emerging in many areas where malaria is endemic

what are the issues with releasing sterilised male mosquitoes that could mate with females but not result in viable eggs being laid?

* since releasing more insects in order to reduce the number of insects is counter-intuitive, local groups of people are reluctant to accept its use
* large-scale, and effective, education programmes are needed to convince people to accept such programmes

what are the issues with vaccinating against malaria?

* a vaccine would have to be suitable for use with babies and young children, since malaria is most severe during the first years of life
* pharmaceutical companies need to charge for their products
* countries in which malaria is endemic are often poor and could not afford country-wide vaccination programmes
* plasmodium shows great antigenic variability, making the production of an effective vaccine difficult

t killer cells

destroy body cells infected by viruses

t helper cells

release cytokines that stimulate production of b cells

memory cells

remain in the body and bring about the secondary response

how are the three types of t cell produced in the cell mediated response?

* t cells bind to antigen presenting cell
* activated t helper cell is formed that releases cytokines
* release of cytokines stimulates the activated t cell to divide repeatedly to form a clone

active artificial immunity

antibodies are made following administration of a vaccine

b cells, t cells, and memory cells are made

passive artificial immunity

antibodies are administered by injection (immunisation)

active natural immunity

production of antibodies following infection by, and recovery from, a disease

b cells, t cells, and memory cells are made

passive natural immunity

mother’s antibodies cross placenta to fetus or ingested by baby in mother’s breast milk, especially colostrum

what is the longevity of active immunity?

long-lasting since memory cells are maintained throughout life

what is the longevity of passive immunity?

fades with time, since the recipient has not made memory cells and the antibodies received are themselves treated as non-self antigens and destroyed by recipient’s active immunity

what can the active agent in a vaccine be?

* the intact pathogen that has been inactivated (stop it causing infection) or attenuated (reducing ability to cause infection)
* purified components of the pathogen that have been found to have antigenic properties but do not cause disease
* toxoids - modified toxins - to develop active immunity against toxin-based diseass
* genetically engineered dna - which can be desgined to stimulate particular target cells of the immune system

what do vaccines do?

cause the recipient’s immune system to make antibodies against the pathogen without suffering an infection, and then to retain the appropriate memory cells

herd immunity

provided a large enough proportion of a population are immune to a particular contagious disease, the likelihood of the causative pathogen being transmitted to a member of the population who is not immune is negligible

what do the complement proteins on phagocytes (macrophages and neutrophils) do?

* attract more phagocytes to the site of infection
* binding to, and forming pores in, the surface membranes of foreign cells, leading to the lysis of these cells
* binding to surface membranes of foreign cells, aiding the attachment of a phagocyte to a foreign cell
* proteins are called opsinins - cause opsonisation

what do b lymphocytes do?

secrete antibodies and produce the humoral immune response

what do t lymphocytes do?

attack infected cells, producing the cell-mediated response, and assist b cells

how are t cells produced?

produced by multipotent stem cells in bone marrow

leave the bone marrow and complete their maturation in the thymus gland

how are b cells produced?

produced by multipotent stem cells in bone marrow

complete their maturation in the bone marrow they were formed in

major histocompatability complex proteins

glycoproteins found on the cell surface membrane of a cell that are unique to that individual

identify cells

what is the first step of the humoral immune response?

a pathogen enters the body; its surface has non-self antigens on it

collides with a b cell randomly which has an antigen receptor on its surface that is complementary to a non-self antigen on the pathogen

other pathogen cells are attacked by non-specific macrophages

what is the second step of the humoral immune response?

the b cell engulfs the antigen and digests it

the b cell then displays fragments of the antigen on its cell surface membrane, bound to its own mhc proteins

what is the third stage of the humoral immune response?

the macrophage digests antigen-carrying pathogen and displays fragments of antigen bound to the mhc proteins on its cell membrane

what is the fourth stage of the humoral immune response?

antigen-presenting macrophage comes into contact with a t cell that has antigen-receptor protein complementary to one of the pathogen’s antigens now displayed on the macrophage

the two cells bind

the t cell is activated, which is now called an activated t helper cell

what is the fifth stage of the humoral immune response?

an activated t helper cell now binds to a b cell displaying the same antigen on its cell membrane, which activates the b cell

what is the sixth stage of the humoral immune response?

stimulated by secretion of cytokines from activated t helper cell, the activated b cell divides by mitosis and forms plasma cells

antibody is mass-produced and exported from plasma cell by exocytosis

what is the seventh stage of the humoral immune response?

a few activated b and cell cells remain in the body as memory cells

form the basis of natural immunity

epigenetic modification

stable, long-term changes in the ability of a cell to transcribe its genes

changes are inherited but they are not caused by changes to the base sequence of the dna

what do promoters do?

short base sequences that lie closed to their target genes

initiate transcription by enabling rna polymerase to bind to the gene they regulate

what do enhancers do?

short base sequences that lie some distance from their target genes

stimulate promoters causing an increase in the rate of transcription of the genes they regulate

what do regulatory sequences do?

stimulate the transcription of genes

transcription factor

a protein, or assembly of several proteins, that regulate the production of mrna

specific transcription factor binds to a promoter region upstream of its target gene and either promotes or inhibits the binding of rna polymerase to the target gene

isoforms

different arrangements of exons in mature messenger rna transcribed from a singe eukaryotic gene

different isoforms result in different polypeptides being produced from one gene

what does alternative splicing do?

alternative splicing of pre-mrna produced from a single gene can result in the production of completely different polypeptides

how is mature mrna formed?

exons and introns are coped into the base sequence of an rna molecule - pre-mrna

molecule is spliced; the introns are removed and the exons are rejoined, to form mature mrna

mrna migrates into the cytoplasm where is base sequence is translated by ribosomes

how does miRNA destroy mrna?

miRNA moleule binds to a protein to form a RISC

the miRNA within the RISC will bind to mRNA in the cytoplasm

the two RNA molecules bind by the formation of hydrogen bonds between base pairs, but the pairs are not fully complementary, forming ‘bulges’ which prevent mRNA being transcribed

how does siRNA destroy mrna?

bind with a protein complex to form a RISC

proteins within the RISC unwind the rna and remain bound to one of the strands

this single-stranded, antisense rna, bound within the RISC, that binds to the target mRNA

bound mRNA is hydrolysed by yet another RNA hydrolase

what does dna methylation do?

methylated dna prevents the activation of rna polymerase

target genes of these promoters are silenced

what happens when histones are acetylated?

the binding of the histones changes and they become more loosely packed

loosening of the histone frees the gene, so that the transcription factors and RNA polymerase can now gain access to it

how are induced pluripotent stem cells produced?

scientists identified genes which were vital to embryonic stem cell function

these genes were transferred into mouse fibroblasts using retroviruses as vectors

devised a technique which enabled them to find which cells had become pluripotent

found four genes which induced change from adult fibroblast to pluripotent stem cell

how can ips cells be used in medical research?

* produce new types of cell that directly replace those affected by disease
* generate new types of cell that can be used in the laboratory to test the effectiveness and safety of new drugs, reducing need for animal and human experimentation

why must ips cells be used with caution?

* scientists do not know how to control the differentiation of pluripotent stem cells
* two genes that produce ips cells are oncogenes
* conversion of adult cells to ips cells is currently slow and the success rate is very low
* growing cells for therapies will require specialist systems and research centres, so access to therapies may be limited to areas with suitable facilities
* the safety aspects of introducing pluripotent stem cells into recipients must be trialled
* clinical trials take a long time and are expensive

what are the reagents of PCR?

* primers: short lengths of single-stranded DNA that are complementary to the base sequence of part of the 3’ ends of the strands of target DNA to be copied
* free DNA nucleotides, each with an adenine, cytosine, guanine, or thymine base
* thermostable DNA polymerase

what are the steps of PCR?

1. separate chains of double stranded DNA with known end sequences by heating to 95oC
2. make primer that matches the end sequences of the DNA fragment to be copied. cool to 45oC to allow the primer to stick each strand
3. add heat tolerant taq polymerase and nucleotides, and heat to 75oC

what can recombinant dna do in genetically modified soya beans to increase the crop yield?

* resistance to glyphosate, a commonly used weed killer that would also affect the soya plant
* resistance to pests, including fungi, nemotade worms, and insects
* tolerance to drought and to soil salinity

how can recombinant dna change biochemical components of soya beans?

* the balance of fatty acids, increasing the percentage of oleic acid and reducing the percentage of linoleic acid
* during cooking, linoleic acid is more easily oxidised to produce trans fats that oleic acids - trans fats are harmful to human health
* production of active pharmacological ingredients - molecular pharming

how have bacteria been used to insert recombinant dna into soya plants?

when the transgenic bacteria infects the plant it transfers its own dna into the cells of the infected plant, creating tumours

transgenic bacteria infect soya tissue cultures, resulting in soya plants in which all the cells contain the desired genes

what is a ‘knockout’ mouse?

a laboratory mouse in which scientists have inactivated one of its genes

how are ‘knockout’ mice created?

add a piece of foreign dna that disrupts transcription of a gene into the genome of a mice

scientists begin with embryonic stem cells from an early mouse embryo

using a virus the scientists insert the artificial gene into the stem cells

these cells are cultured in a laboratory before injecting them into new mouse embryos, which are transplanted into the uterus of a female mouse

some tissues of the pups will have the inactivated gene - crossbred to produce mice which are homozygous for the target gene (all tissues have the targeted gene inactivated)

how can ‘knockout’ mice be used in research?

research scientists can investigate the function of the gene they knockout

mice and humans have many genes in common - understand the function of human genes

heart disease, cancer, and parkinson’s disease research