Advanced higher biology course notes

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spindle microtubules. This is followed by cytokinesis, in which the cytoplasm is separated into two daughter cells. Mitosis) Consists of prophase, metaphase, anaphase and telophase PRO Dou pola Prophase Metaphase Anaphase Telophase Prophase) DNA condenses into chromosomes; the nuclear membrane breaks down; and spindle microtubules extend from MTOC by polymerization and attach to chromosomes via their kinetochores in the centromere region. Metaphase) Chromosomes are aligned at the metaphase plate (equator of the spindle) Anaphase) Spindle microtubules shorten by depolymerization, sister chromatids are separated and the chromosomes are pulled to opposite poles Telophase) The chromosomes decondense and the nuclear membranes are formed around them c) Control of the cell cycle • Explain what is meant by a checkpoint in the cell cycle? • Explain the processes which occur at the G1 and G2 checkpoints? • Explain what is being checked for at the metaphase checkpoint? • State the problems caused by uncontrolled cell division and describe the mutation of a proto-oncogene? Checkpoints) Progression through the cell cycle is controlled by checkpoints that assess the condition of the cell during the cell cycle and halt progression to the next phase until certain requirements are met. Cyclin) Cyclin proteins that accumulate during cell growth are involved in regulating the cell cycle. Cyclins combine with and activate cyclin-dependent kinases (CDK's). Active cyclin-CDK complexes phosphorylate proteins that regulate progression through the cell cycle; if sufficient phosphorylation is reached, progression can occur. G1 checkpoint) At the G1 checkpoint, retinoblastoma protein (Rb) acts as a tumour suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication. Phosphorylation by G1 cyclin-CDK inhibits the Rb protein. Inhibition of Rb allows transcription of the genes that code for proteins needed for DNA replication, and cells progress from G1 to S phase. active Rb protein inactivated transcription factor inactive p53 active G1-Cdk cell cycle arrest DNA repair G2 checkpoint) At the G2 checkpoint, the success of DNA replication and any damage to DNA is assessed DNA damage triggers the activation of several proteins including p53 that can stimulate DNA repair, arrest the cell cycle or cause cell death DNA damage cell cycle abnormalities inactivated Rb protein active p53 cell cycle restart active transcription factor apoptosis S-phase gene transcription death and elimination of damaged cells cellular and genetic stability Metaphase checkpoint) A metaphase checkpoint controls progression from metaphase to anaphase. At the metaphase checkpoint, progression is haunted until the chromosomes are aligned correctly on the metaphase plate and attached to the spindle microtubules. Prometaphase chromosomes associated to mitotic spindle metaphase checkpoint Metaphase chromosomes Anaphase sister chromatid aligned on the metaphase plate separation An uncontrolled reduction) in the rate of the cell cycle may result in degenerative disease An uncontrolled increase) in the rate of the cell cycle may result in tumour formation cancer-promoting proto-oncogene agent (UV light, chemicals etc.) Proto-oncogene) A proto-oncogene is a normal gene, usually involved in the control of cell growth or division, which can mutate to form a tumour-promoting oncogene AAR AND oncogene CAR cancerous cell d) Control of programmed cell death (apoptosis) Apoptosis) is programmed cell death which is triggered by cell signals that can be external or internal. E nucleus condensing (pyknosis) apoptotic body B nucleus fragmenting (karyorrhexis) ES apoptotic cells nucleus cell shrinkage 88 blebs (bulges in the membrane) phagocyte engulfs apoptotic bodies Death signal molecules) The production of death signal molecules from lymphocytes is an example of an external death signal External death signal molecules) bind to a surface receptor protein and trigger a protein cascade within the cytoplasm An internal death signal) resulting from DNA damage causes activation of p53 tumour suppressor protein internal pathway DNA damage/ lack of growth factor DNA fragmentation initiator initiator caspases caspases executioner caspases breakdown of cytoskeleton membrane bleb (bulge in the membrane) external pathway receptor-ligand interactions S apoptotic body phagocyte S ligands for phagocytic cell receptors caspases) Both types of death signal result in the activation of caspases (types of protease enzyme) that cause the destruction of the cell metamorphosis) Apoptosis is essential during development of an organism to remove cells no longer required as development progresses or during metamorphosis Growth factors) Cells may initiate apoptosis in the absence of growth factors Summary Describe the structure and function of the cytoskeleton in eukaryotic cells? Describe the role of microtubules in cell division? Describe the processes which lead to the formation and breakdown of microtubules? • Name the two phases of the cycle? • List the phases involved in interphase? Describe what happens during both stages of the mitotic phase? List the stages of mitosis and describe what happens in each? • Explain what is meant by a checkpoint in the cell cycle? • Explain the processes which occur at the G1 and G2 checkpoints? Explain what is being checked for at the metaphase checkpoint? • State the problems caused by uncontrolled cell division and describe the mutation of a proto-oncogene? Unit 2 - Organisms and Evolution KA1) Field techniques for Biologists a) Health and safety (a) Health and Safety Explain the specific hazards and control measures used in field studies ● Hazard) Something that could cause harm (eg- adverse weather conditions, difficult terrain, problems associated with isolation, and contact with harmful organisms) Risk) The likelihood of harm arising due to the exposure of a hazard (isolation, contact with harmful organisms) ● Risk assessment) Risk assessment involves identifying possible risks and control measures to minimise them (in the field these may include appropriate equipment, footwear, clothing and a means of communication - as well as appropriate training) b) Sampling of wild organisms (b)Sampling of Wild Organisms Explain how sampling is made ethical Discuss different detection and capture techniques How sampling is made ethical) Sampling should be carried out in a way that minimises the impact on wild species and habitats. Consideration must be given to rare and vulnerable species and habitats that are protected by legislation. Sampling techniques) The chosen sampling technique must be appropriate to the species being sampled Point counts) Involve the observer recording all the individuals seen from a fixed point count location. This can be compared to other point count locations or with data from the same location gathered at other times Quadrats) Of suitable size and shape, or transects are used for plants or other sessile or slow-moving species Mobile species) Capture techniques such as traps and nets are used for mobile species Elusive species) Can be sampled directly using camera traps or an indirect method such as a scat sample (faeces) 5% ----) ½ ● 164 --% 4% 5 5% Species: PUMA 10B/L 1% 2 2% 3 ate:29/11/2004 c) Identification and taxonomy (c) Identification and taxonomy Explain how organisms are identified once sampled Discuss the use of taxonomy in field studies Give the uses of phylogenetics Justify the use of model organisms Identification) Organisms can be classified by both taxonomy and phylogenetics. Identification of an organism in a sample can be made using classification guides, biological keys, analysis of DNA or protein and naming of organisms and their classification into groups based on shared characteristics Taxonomy) Involves the identification and naming of organisms, and their classification into groups based on shared characteristics (eg- morphology, dentition) Phylogenics) The study of the evolutionary relationships and history among individuals or groups of organisms. Phylogenics uses heritable traits such as morphology, DNA sequences and protein structure to make inferences about an organism's evolutionary history and create a phylogeny or phylogenetic tree Phylogenetic tree) A diagrammatic hypothesis of its relationship to other organisms. Genetic evidence) can reveal relatedness obscured by divergent or convergent evolution. Divergent evolution represents the evolutionary pattern in which species sharing a common ancestry become more distinct due to differential selection pressure which gradually leads to speciation over an evolutionary time period. convergent evolution is defined as the process whereby distantly related organisms independently evolve similar traits to adapt to similar necessities. Taxonomic groupings) Familiarity with taxonomic groupings allows predictions and inferences to be made about the biology of an organism from better-known model organisms. Nematodes, arthropods and chordates are examples of taxonomic groupings Model organisms) (eg- E.Coli, Arabidopsis thaliana and C.Elegans, drosophila melanogaster, mice, rat and zebrafish have all been important in the advancement of modern biology) Organisms that are either studied easily or have been well studied. Information obtained from model organisms can be applied to other species that are more difficult to study directly. C.elegans nematode, drosophila = arthropod, rat= chordate d) Monitoring populations (d) Monitoring Populations Describe the use of indicator species to a monitor the environmental conditions in an ecosystem. Describe the process of mark and recapture. Explain how we can mark animals in an ethical manner. ● INDICATOR Stonefly SPECIES nymph Indicator species) The presence, absence or abundance of an indicator species can provide about environmental qualities, such as the presence of a pollutant. Susceptible and favoured species can be used to monitor an ecosystem. The absence of an indicator species or reduced population indicates it is susceptible to some factor in the environment; its abundance or increased population indicates that it is favoured by the conditions. POLLUTION LEVEL Day 1 Day 2 Low (stream) Dragonfly nymph Low (pond) Freshwater shrimp Slight Hoglouse Medium Tubifex worm N= High No life Mark and recapture) A technique used to estimate population size using the formulae N=MC/R. It is assumed that all individuals have an equal chance of capture, there is no immigration or emigration and that individuals that are marked and released can mix fully and randomly with the population MC R Extreme M= Number Marked first time (10) C= Number Captured second time(10) R= Number of marked individuals recaptured (5) N= Total population = 10x10/5 = 20 Methods of marking) Include banding, tagging, surgical implantation, painting and hair clipping. The methods of marking and subsequent observation must minimise the impact on the study species. e) Measuring and recording animal behaviour (e) Measuring and Recording Animal Behaviour Explain how animal behaviour is quantified. Give the features and uses of an ethogram. 1 Discuss the implications of anthropomorphism. Methods used to quantify animal behaviour) Include latency- the time between stimulus occurring and the response behaviour, frequency- the number of times a behaviour occurred within the observation period and dur tion- length of time the behaviour occurs within the observation period. Ethogram) is a list of species-specific behaviours shown by a species in a wild context that allows the construction of time budgets Summary ● 44% (a) Health and Safety Explain the specific hazards and control measures used in field studies (b)Sampling of Wild Organisms Explain how sampling is made ethical Discuss different detection and capture techniques (c) Identification and taxonomy Explain how organisms are identified once sampled Discuss the use of taxonomy in field studies Give the uses of phylogenetics Justify the use of model organisms 15% Time budget) recording the duration of each of the behaviours in an ethogram, together with the total time of observation, allows the proportion of time spent on each behaviour to be calculated as a time budget Anthropomorphism) is the attribution of human characteristics or behaviours and emotions to an animal's behaviours. It is important to avoid anthropomorphism when analysing behaviour as it can lead to invalid conclusions due to our preconceived ideas. 8% 5% Loom for Chrome is sharing y 0% 11% Behaviour □■■□ 目 observing eating drinking sleeping swimming barking defecating (d) Monitoring Populations Describe the use of indicator species to a monitor the environmental conditions in an ecosystem. Describe the process of mark and recapture. Explain how we can mark animals in an ethical manner. ● (e) Measuring and Recording Animal Behaviour Explain how animal behaviour is quantified. Give the features and uses of an ethogram. Discuss the implications of anthropomorphism. KA2) Evolution a) Drift and selection https://www.youtube.com/watch?v=_Ultz 71MIO . Explain what is meant by evolution? • Explain what is meant by natural selection and the types of change that may occur? Explain what is meant by sexual selection and the two methods by which this may take place? • Explain how genetic drift acts on genetic variation in a population Describe the importance of bottleneck and founder effects on genetic drift Evolution) Evolution is the change over time in the proportion of individuals in a population differing in one or more inherited traits During evolution, changes in allele frequency occur through the non-random processes of natural selection and sexual selection, and the random process of genetic drift Allele Frequency WW WW WW IX Population of peas Ww. WW. WW WW GENOTYPE FREQUENCY: Freq; of WW = 6/9 = 0.67 Freq; of Ww=1/9 = 0.11 Frea of ww = 2/9 = 0.22 Z How often PHENOTYPE FREQUENCY: Frea of purple = 7/9 = 0.78 Freq; of white = 2/9 = 0.22 biology ALLELE FREQUENCY: 2 p = Freq; of W = 13/18 = 0.72 q=Freq. of w = 5/18 = 0.28 Iwe see each allele combo WW, Ww, or ww 2 How often Iwe see white vs. purple How often we see each allele Warw Natural selection) acts on genetic variation within a population (which occurs due to mutation). Natural selection is the non-random decrease in deleterious DNA sequences and the non-random increase in DNA sequences which aid with survival. *Mutation) The original source of new sequences of DNA and these sequences can be novel alleles. Most mutations are deleterious or neutral, but in rare cases, they may be advantageous to the individual. Sexual selection) is the non-random process involving the selection of alleles that increase the individual's chances of mating and producing offspring. Sexual selection may lead to sexual dimorphism. Sexual selection can be due to male-male rivalry and female choice Male-male rivalry) the larger size of weaponry increases access to females through success in conflict Female choice) involves females assessing the fitness of males Genetic drift) Genetic drift occurs when chance events cause unpredictable fluctuations in allele frequencies from one generation to the next. Genetic drift is more important in small populations, as alleles are more likely to be lost from the gene pool BBS DD With each subsequent generation, the red allele is less likely to be picked for reproduction Ⓡe The population bottleneck effect) Is an example of genetic drift that can occur when population size is reduced for at least one generation Parent population with significant genetic variation. Bottlenecking event Post-bottleneck population where all but the green and yellow alleles have been lost. Founder effects) are examples of genetic drift that occur through the isolation of a few members of a population from a larger population and a gene pool of the new population is not representative of that in the original gene pool. A gene pool is altered by genetic drift because certain alleles may be under-represented or over-represented and allele frequencies change ANCESTRAL POPULATION Colonisers Selection pressures) are the environmental factors that influence which individuals in a population pass on their alleles (biotic-competition, predation, disease, parasitism/ abiotic= temp, humidity, light, pH, salinity) Where selection pressures are strong, the rate of evolution can be rapid b) Fitness The Hardy-Weinberg (HW) principle) states that, in the absence of evolutionary influences, allele and genotype frequencies in a population will remain constant over the generations. The HW principle can be used to determine whether a change in allele frequency is occurring in a population over time. Changes suggest evolution is occurring No selection, no mutation, no migration, interbreeding, large population size •What is fitness? What is relitive fitness? What is absolute fitness? • Fitness) is an indication of an individual's ability to be successful at surviving and reproducing. It refers to the contribution made to the gene pool of the next generation by individual genotypes Absolute fitness) is the ratio between the frequency of individuals of a particular genotype after selection, to those before selection. If the absolute fitness is 1, then the frequency of that genotype is stable. A value greater than 1 conveys an increase in the genotype and, therefore, a value less than 1 conveys a decrease. absolute fitness relative fitness frequency of a particular genotype after selection frequency of a particular genotype before selection number of surviving offspring per individual of a particular genotype number of surviving offspring per individual of the most successful genotype Relative fitness) is the ratio of the number of surviving offspring per individual of a particular genotype to the number of surviving offspring per individual of the most successful genotype. Calculating relative fitness Relative fitness can be a measure of the reproductive success of a particular organism compared to other members of the population, or the success of a particular genotype within a population. Either way, this is calculated by dividing the absolute fitness by the average fitness within the population. For example, if a dormouse has 6 surviving offspring in a population where the average number of surviving offspring is only 4, this mouse has a relative fitness of 6 + 4 = 1.5. Alternatively, a dormouse in this population with only 2 surviving offspring will have a relative fitness of just 0.5. The concept of relative fitness can be extended further to consider genotype. The genotype with the greatest fitness is given a value of 1. Let's say that dark green (DD) toads are the fittest, averaging 10 surviving offspring each. To calculate the relative fitness of brown (dd) toads with an average of 6 surviving offspring, 6 + 10 = 0.6. c) Co-evolution - Uhat is co-evolution? - what is symbiosis? -Types of symbiosis - What is the 2x² Queen Hypotteris? Co-evolution) is the process by which two or more species evolve in response to selection pressures imposed by each other. A change in the traits of one species acts as a selection pressure on the other species. Co-evolution is frequently seen in pairs of species that have symbiotic interactions Symbiosis) is a co-evolved intimate relationship between members of two different species. The impacts of symbiotic relationships can be positive, negative or neutral for the individual species involved. Mutualism) is a symbiosis in which the species in the interaction are interdependent on each other for resources or other services and, since both species gain the interaction is (+/+) Commensalism) is a symbiosis in which only one of the species substantially benefits and for the other, the relationship is neither substantially positive or negative (neutral) and so the interaction is (+/0) Parasitism) is a symbiosis in which the parasite species benefits in terms of energy or nutrients while the host is harmed by the loss of these resources (+/-) Red queen-hypothesis) States that, in co-evolutionary relationships, change in the traits of one species act as a selection pressure on the other species, which must adapt to avoid extinction. Parasites and their hosts Parasitism involves a relationship whereby a parasite lives on a host, gaining resources and a place to live. This is of benefit to the parasite, while the host is harmed, and is written as (+/-). Co-evolution has been documented between the parasite that causes malaria, the mosquito that acts as a vector for this parasite and humans, which are the host. Current fossil evidence suggests that the parasite started to spread extensively about 100,000 years ago. This coincides with evidence to suggest when the first major human migrations took place. More recently, about 10,000 years ago, DNA sequence evidence suggests that both the parasite and mosquitoes underwent rapid evolution. Both of these events provide strong evidence for the complicated co-evolution between the parasite and the two other species; humans and mosquitoes. (hosts better adapted to resist parasites have greater fitness --- puts selection pressure on parasites to adapt) ● Summary Explain what is meant by evolution? Explain what is meant by natural selection and the types of change that may occur? Explain what is meant by sexual selection and the two methods by which this may take place? • Explain how genetic drift acts on genetic variation in a population ● Describe the importance of bottleneck and founder effects on genetic drift what is fitness? -What is relitive fitness? •What is absolute fitness? what is co-evolution? - what is symbiosis? -Types of symbiosis What is the Lut Queen Hypotteris? KA3) Variation and sexual reproduction a) Costs and benefits of sexual and asexual reproduction ● Explain what is meant by sexual reproduction and give the costs and benefits? Explain why co-evolutionary interactions may select for sexual reproduction? Explain what is meant by asexual reproduction and give the costs and benefits? Describe asexual reproduction in eukaryotes (vegetative cloning and parthenogenesis)? Give the conditions which favour asexual reproduction? ● ● ● Asexual reproduction Metabolic costs are lower because it is based on the normal cell cycle and produces many identical offspring. The production of offspring can be rapid because the process is relatively simple and every member of the population can reproduce. Successful parental genomes persist in the population. Sexual reproduction Metabolic costs are higher since gametes are made by a special type of cell division and many fail to achieve fertilisation. Only half the population - the females - can actually produce offspring, so the reproductive rate is much slower. Successful parental genomes are disrupted since only half of each parent's genome is passed onto offspring. Costs and benefits) Sexual and asexual reproduction both have costs and benefits Sexual reproduction costs) Half of the population (males) are unable to produce offspring. And each parent is only able to pass on half of their genetic material rather than the full 100%. Sexual reproduction benefits) Increases the genetic variation within the population Genetic variation) Provides the raw material required for adaptation, giving sexually reproducing species a better chance of survival under changing selection pressures. Red queen hypothesis) Without such genetic variety, the Red Queen's arms race would stop. In other words, this variation can drive selection and evolution should the different genes and alleles provide the individual with an advantage and, therefore, an increased chance of survival. If hosts reproduce sexually, the genetic variability in their offspring decreases the chances that all of the individuals will be susceptible to infection by parasites. This means that the host will be able to resist and tolerate parasitism, therefore showing greater fitness. Asexual reproduction) Can be a successful reproductive strategy as whole genomes are passed on from parent to offspring. In asexual reproduction, just one parent can produce offspring and establish a colony of virtually unlimited size over time. Benefits) Maintaining the genome of the parent is an advantage, particularly in very narrow, stable niches or when recolonising habitats. Offspring can be reproduced more often and in greater numbers by asexual reproduction. Vegititive cloning) in plants, such as reproduction via bulbs, e.g. onions and daffodils, and runners, e.g. spider plants and strawberry plants - all of the resulting offspring will be genetically identical to the original parent plant; Parthenogenesis) animals lack fertilisation - embryos result from unfertilised eggs and, therefore, the resulting offspring will be haploid. Examples When kept in captivity for several years with no male contact, female Komodo dragons have been known to reproduce without fertilisation. It appears that, for the continuation of the species, this is how the female responds to isolation. This would be advantageous should females become isolated in the wild or should males die. The offspring of parthenogenesis in Komodo dragons are always male. Conversely, stick insects can also reproduce asexually in the absence of males; however, all of the offspring are female in this case. Cooler climates) Parthenogenesis is found to be more common in cooler climates with low parasite diversity. Adaptations) Asexually reproducing populations are not able to adapt easily to changes in their environment, but mutations can occur that provide some degree of variation and enable some natural selection and evolution to occur Horizontal gene transfer) Organisms that reproduce principally by asexual reproduction also often have mechanisms for horizontal gene transfer between individuals to increase variation, for example, the plasmids of bacteria and yeasts b) Meiosis Define the process of meiosis? Describe what happens during meiosis l? • Explain what is meant by crossing over and random assortment and how these increase genetic variability? Describe what happens during meiosis II? sister chromatids homologous chromosomes FIL THIID genetic material swapped during crossing over Meiosis) is the division of the nucleus that results in the formation of haploid gametes from a diploid gametocyte In diploid cells) chromosomes typically appear as homologous pairs, these are chromosomes of the same size, same centromere position and the same genes at the same loci. They do however have different alleles as they have been inherited by a different parent. Meiosis I Replication) The chromosomes, which have replicated prior to meiosis I, each consist of two genetically identical chromatids attached at the centromere zygote Charismata) The chromosomes condense and the homologous chromosomes pair up. Chiasmata form at points of contact between the non-sister chromatids of a homologous pair and sections of DNA are exchanged Linked genes) are those on the same chromosome and crossing over can result in new combinations of the alleles on these genes Crossing over) Of DNA is random and produces genetically different chromosomes through recombination. Independent assortment) Spindle fibres attach to the homologous pairs and line them up at the equator of the spindle. The orientation of the pairs of homologous chromosomes at the equator is random and each pair of homologous chromosomes is positioned independently from the other pairs, irrespective of their maternal or parental origin - this is independent assortment. Meiosis II zygote Cytokinesis) The chromosomes of each homologous pair are separated and move towards opposite poles Cytokinesis occurs and two daughter cells form gametes / plant and fungi meiospores .00 zygote (c+c=2c, n+ n = 2n) zygote mother cells of gametes or meiospores telophase II (c, n+c, n) (c, n+c, n) cytokinesis (c, n) (c, n) (c, n) (c, n) (8²8) interphase S interphase G¹ (2cx 2 = 4c, 2n) prophase I (2c, 2n) (4c, 2n) interphase G² (4c, 2n) anaphase II (c, n+c, n) (c, n+c, n) meiosis II crossing-over metaphase II (2c, n) (2c, n) metaphase I (4c, 2n) anaphase I (2c, n + 2c, n) prophase II (2c, n) (2c, n) BA meiosis I telophase I (2c, n + 2c, n) Meiosis II) Each of the two cells produced in meiosis I undergo a further division called meiosis II during which the sister chromatids of each chromosome are separated. A total of 4 haploid cells are produced as a result of meiosis. c) Sex determination Explain how the presence of specific chromosomes determines the sex of birds, mammals and some insects Name the gene on the Y chromosome which determines the development of male characteristics ● ● • • Explain how the shape of the sex chromosomes can result in sex-linked patterns of inheritance Explain what is meant by chromosome inactivation and how this prevents harm to individual females Define what is meant by a hermaphrodite and how this can benefit individual members of the species Give examples of environmental factors which can determine sex and sex ratio Sex chromosomes) The sex of birds, mammals and some insects is determined by the presence of sex chromosomes SRY gene) In most mammals the SRY gene on the Y chromosome determines development of male characteristics Heterogametic (XY) males) lack most of the corresponding homologous alleles on the shorter (Y) chromosome. This can result in sex-linked patterns of inheritance as seen with carrier females (XBXb) and affected males (Xb Y) Double dose) In homogametic females (XX) one of the two X chromosomes present in each cell is randomly inactivated at an early stage of development. X chromosome inactivation prevents a double dose of gene products, which could be harmful to cells. Carriers are less likely to be affected by any deleterious mutations on these X chromosomes. As the X chromosome inactivated in each cell is random, half of the cells in any tissue will have a working copy of the gene in question. Hermaphrodites) are species that have functioning male and female reproductive organs in each individual They produce both male and female gametes and usually have a partner with which to exchange gametes The benefit) to the individual organism is that if the chance of encountering a partner is an uncommon event, there is no requirement for that partner to be of the opposite sex Enviormental factors) can also determine the sex and sex ratio of a species. Sex can change within individuals of some species as a result of size, competition, or parasitic infection. In some species the sex ratio of offspring can be adjusted in response to resource availability Summary Explain what is meant by sexual reproduction and give the costs and benefits? Explain why co-evolutionary interactions may select for sexual reproduction? ● Explain what is meant by asexual reproduction and give the costs and ● benefits? Describe asexual reproduction in eukaryotes (vegetative cloning and parthenogenesis)? ● Give the conditions which favour asexual reproduction? ● Define the process of meiosis? Describe what happens during meiosis l? • Explain what is meant by crossing over and random assortment and how these increase genetic variability? Describe what happens during meiosis II? ● Explain how the presence of specific chromosomes determines the sex of birds, mammals and some insects Name the gene on the Y chromosome which determines the development of male characteristics • Explain how the shape of the sex chromosomes can result in sex-linked patterns of inheritance • Explain what is meant by chromosome inactivation and how this prevents harm to individual females Define what is meant by a hermaphrodite and how this can benefit individual members of the species Give examples of environmental factors which can determine sex and sex ratio KA4) Sex and behaviour a) Parental Investment ● Describe what is meant by parental investment? ● Compare the production of sperm and eggs in relation to number and energy store? Compare female investment in mammals and non-mammals? • Explain the classification of organisms as r-strategists or K-strategists and give the characteristics of each? Compare the costs and benefits of external and internal fertilisation? b) Reproductive behaviours and mating systems in animals Summary Unit 3 - Investigative Biology KA1) Scientific principles and processes a) Scientific method (a) The Scientific Method • Give the stages of the scientific cycle Explain why scientists discuss theories rather than facts. • Describe a 'null hypothesis' • Explain why a lack of findings does not invalidate a theory. Explain how conflicting data is resolved. Explain the importance of independent confirmation of results ● Formulation of new hypotheses. Evaluation of results, conclusions drawn Construction of a testable hypothesis Recording and analysis of < Experimental design Gathering data 0:58/5:16 The scientific cycle) The scientific cycle involves observation, the construction of a testable hypothesis, experimental design, gathering, recording and analysis of data, evaluation of results and conclusions and the formation of a revised hypothesis when necessary. Refinement) In science, the refinement of ideas is the norm, and scientific knowledge can be thought of as the current best explanation, which may then be updated after evaluation of further experimental evidence Null hypothesis) The null hypothesis proposes that there will be no statistically significant effect as a result of the experimental treatment. If there is evidence for an effect, unlikely due to chance, the null hypothesis will be rejected (eg- Shell colour did not affect predation by birds) Negative result) Failure to find an effect ( a negative result) is valid finding, as long as an experiment is well designed. Conflicting data or conclusions can be resolved through careful evaluation or can lead to further experimentation. Independently) Scientific ideas only become accepted once they have been checked independently. Effects must be reproducible, one-off results are treated with caution b) Scientific literature and communication . (b) Scientific literature and communication Suggest why a clear and complete write up is required for publication in a journal Give the role of a peer reviewer • Give ways which scientific advances are shared Repete) Publication of methods, data, analysis and conclusions in scientific reports is important so that others can repeat an experiment. Methods of sharing) Common methods of sharing original scientific findings include seminars, talks and posters at conferences and publishing in academic journals. Peer review) Most scientific publications use peer review. Specialists with expertise in the relevant field access the scientific quality of an investigation and critically review the findings, then they make recommendations regarding its suitability for publication. Review articles) Review articles which summarise current knowledge and recent findings in a particular field are essential to scientists undertaking new research in that field c) Scientific ethics (c) Scientific ethics • Describe the features of professional integrity Explain how animal studies can be made ethical Explain why 'replication' is important in ensuring professional integrity. • List the rights that humans participating in an experimental trial have • List the individuals whose safety must be taken into account during a study • Explain why risky trials can still often be carried out and suggest who may regulate these trials • List factors which may prevent an ideal experiment being carried out Plagiarism) The unbiased presentation of results, citing, providing references and avoiding plagiarism is important Replication) While judgements and interpretations of scientific evidence may be disputed, integrity and honesty are of key importance in science. Replication of experiments by others reduces the opportunity for dishonesty or the deliberate misuse of science Animal studies) In animal studies, the Beforeconcepts of replacement, reduction and refinement are used to reduce harm to animals Replacement Methods which avoid or replace the use of animals The 3Rs Reduction Methods which minimise the number of animals used per experiment Refinement Methods which minimise suffering and improve animal welfare Human studies) Informed consent, the right to withdraw and confidentiality in human studies Value) The value or quality of science investigations must be justifiable in terms of the benefits of its outcome, including the pursuit of scientific knowledge. As a result of the risks involved, many areas of scientific knowledge are highly regulated and licensed by governments Risk) The risk to and safety of subject species, individuals, investigators and the environment must be taken into account, so studies must be carried out only if they have realistic outcomes for science Legislation) Legislation, regulation, policy and funding can all influence scientific research. Legislation limits the potential for misuse of studies or data, funding also has its influence. KA2) Experimentation General Terminology • Validity • Control confounding variable • Reliability Consistent values in repeats • Independent Replicates Accuracy • Data/ Means close to actual value • Precision Measurements concurrent Accurate, precise Inaccurate, precise Accurate, imprecise Inaccurate, imprecise Accuracy and precision 1) General terminology Validity) Refers to whether conclusions drawn from a set of results are credible. Valid results rely on sound experimental design and execution (control of confounding variables) Accuracy) A measure of how close the data is to the actual true value Reliability) Refers to whether a procedure yields consistent results each time it is repeated Precision) The closeness of related measurements to one another a) Pilot studies (a) Pilot Study Explain why pilot studies are carried out. Describe how pilot studies can improve an experimental method What) A pilot study is used to help plan procedures, assess validity and check techniques (volumes, temperature) Benefits) This allows the evaluation and modification of the experimental design, an appropriate range of values for the independent variable and the number of repeat experiments required to give a representative value for each independent datum point. b) Experimental design (b) Experimental Design Explain which variable is 'Independent' and which is 'Dependent'. Explain why a placebo may be used. Suggest how an experimental design can be altered to deal with confounding variables. Describe the placebo effect. Describe the difference between simple and multifactorial experiments. Explain the differences between observational and experimental approaches. Explain how in vitro and in vivo studies differ Independent Changed by experimenter X axis variable ● Dependent Measured -13 dh Continuous) Quantitative data can be measured and has an infinite number of values within a given range Discrete) Data could be categorised and easily counted Simple Y axis variable 1 One Independent Variable More Controlled than in field Not generalisable Multifactorial) Uses several different independent variables and is more generalisable, less valid and reliable Observational studies) Independent variable not controlled by the investigator for either ethical or logistical reasons (eg- a group of zebras). Good at detecting correlation but not causation as a hypothesis is not directly investigated. Confounding variables) Must be kept constant or monitored. (ii) Confounding Variables • Variables other than the independent variable which could affect the dependent variable. • Age • Sex • Medical History • Fitness • Other Medications Randomised block design) Used when confounding variables cannot be controlled. Groups are split in such a way that the influence of any confounding variable is likely to be reduced. (iii) Controls Compare with treatment group Negative Absence of treatment Positive • Checks system can detect positive results Placebo • Placebos • Treatment without independent variable Placebo effect •measurable change in dependent variable. • Expectation rather than treatment ● c) Sampling (c) Sampling Explain why only a sample of a population may be used in an experiment Suggest which factors may affect sample size. ● Describe how sampling is made random. Describe how sampling is made systematic. • Describe how sampling is made stratified. ● In vitro vs. in Vivo ● • In Vitro • Controlled environment outside organism • Culture medium/ proteins in solution, purified organelles. • In Vivo ● • Whole living organism • More realistic • Less easy to control/ replicate . Sample size (d) Reliability Explain how variation in experimental results can be caused. Describe how the reliability of a measuring instrument can be found. Describe how variation in a biological material can be measured. Explain what the range of measured values suggests. • Describe how the overall reliability of an experiment can be found. • Pilot Study • Variation in population Large variation - Larger sample size. •Sample size and population - same variation and means Random sampling) members of a population have an equal chance of being selected (common within ecological studies) Systematic sampling) Members of a population are selected at equal intervals Stratified) The population is divided into categories which are then divided proportionally d) Reliability • Variation ● Reliability of measurement methods Variation in specimens (causes) The reliability of a procedure can be determined by repeatedly measuring a single data point, the variation observed indicates the precision of the measurement instrument or the procedure but not necessarily its accuracy Prior to a large study, it is common to calibrate any equipment against a sample of know quantity to see the degree of accuracy and precision of the equipment Precision • Concurrent results Accuracy • Close to known value (Measurements) Natural variation in a biological sample) Can be determined by measuring a sample of individuals from a population (mean indicatesHarvard true value/ range gives the extent of variation of the results eg- narrow range= narrow variation in the population) Natural Variation •Good sample • Population •Variation •Mean •Range e) Presentation of data (e) Presentation of Data • Describe the features of Qualitative data. • Describe the features of Quantitative data. • Describe the features of Ranked data. . • • . Describe how the mean' is calculated. Describe how the median' is calculated. Describe how the 'mode' is calculated. Create a box plots to show variation within and between data sets using their median, lower quartile, upper quartile and inter-quartile range. Explain what a correlation between two variables demonstrates. • • Explain the difference between correlation and causation • Describe the meaning of a positive correlation. • Describe the meaning of a negative correlation • Describe what the strength of correlation denotes Qualitative) Subjective and descriptive Quantitative) Measured with a numerical value Ranked) data sorted from lowest to highest and numbered based on this order R squared •Correlation •R values •Strength Dominant frequency (Hz) 800 600 400 Harvarddependant variable (its correlation) (lower the better) Dominant frequency (Hz) vs Body length (mm) - Trend line for series 1 R² = 0.885 200 0 40 Variable A 50 Variable A Variable B Strong positive Variable B Weak positive 60 00 Body length (mm) 70 Variable A Correlation Variable B Strong negative Variable B Weak negative 80 90 values indicate how likely it is that the independent variable is affecting the Data Analysis 1,2,2,3,3,3,4,6, Mean • 1+2+2+3+3+3+4+6 = 24/8 = 3 Median 3 • 1,2,2,3,3,3,4,6 Mode • 1,2,2,3,3,3,4,6 Range • 6-1 or 5 Box Plots Median- Lower ORT Upper QRT IOR 93-91 3 overlap 25% of data higehr than this value smallest value 50% of data higher than this value lower quartile, Q, 12 3 4 5 median, Q, 6 upper quartile, Q, range Error bars) indicate the variability of the data around the mean less overlap 25% of data lower than thi value 7 8 9 10 11 12 13 14 shoe sizes Box plot largest value no overlap a) b) c) Figure 3.11 a) When standard deviation error bars overlap a lot, it's a clue that the difference is not statistically significant; (b) when standard deviation error bars overlap a little, it's a clue that the difference is probably not statistically significant; c) when standard deviation error bars do not overlap, it's a clue that the difference may be statistically significant, but in each case a statistical test would be needed to draw a reliable conclusion KA3) Reporting and critical evaluation of biological research a) Background research (a) Background information Give the features of an effective background information section. Give the features of an effective title. Give the features of an effective abstract. Give the features of an effective aim. Give the features of an effective introductory section. Effective background information section. . . . • Clear • Relevant • Unambiguous Title, Abstract, Introduction, Aim Title) Clear explanation of the study without too much information Abstract) Outlines the aims and findings of the study Effective Abstract section. • Aims and findings of the study. Brief • Justification • Method • Findings Conclusions Aim) Links the independent and dependant variables is Confirmationrepresentative Before effect of X on Y) Introduction) Should provide any information needed to support the method, result, discussion and conclusions. It should explain why the study has been carried out and place the study in the context of any previous understanding Effective Introduction sectior • Supports • choices of method/organism • Results • Discussion. • Justification for study Key points identified and weighed • Context • Sources ( Citations) Several sources should be selected to support information, linked with appropriate citations and references in a standard form (harvard or Vancouver method) b) Reporting and evaluating experimental design (b) Reporting and evaluating experimental design • Give the features of an effective methods section. Suggest how the validity of an experiment be compromised. • Explain the effect of selection bias on representative sampling. Explain the effect of sample size on representative sampling. Method section) Should contain enough information for another investigator to repeat your work, methods are often adapted from previous studies which either cover similar aims or use the same organisms Design of method) should contain the intended experimental aim and test the hypothesis, an experimental design that fails to address the intended aim/hypothesis is not valid as it does not allow for a satisfactory conclusion Validity is compromised) when confounding variables are not controlled and affect the dependent or independent variable. (to combat that a randomised block design may be used) Selection bias) The selection of a sample in a non-random way so that the sample is not representative of the whole population Good Sampling •Random Represents whole population Sample size c) Data analysis (c) Data Analysis Give the features of an effective results section. • Suggest how outlier or anomalous results can be dealt with in analysis. • Suggest how statistical testing may be used in data analysis. Explain the role of error bars in graphical presentations. . . Results section) must be presented clearly and logically suitable for analysis, consideration must be given to outlying and anomalies results •Statistical tests •Difference in means of data due to chance? (eg- mean;mode; median; range; standard deviation;graphs;confidence intervals;error bars;t-test.) Error bars) indicate variation around mean (if they don't overlap= a statistically significant difference) d) Evaluating results and conclusions (d) Evaluating results and conclusions • Give the features of an effective conclusion section. Conclusions Refer to Aim, Results, and Hypothesis When appraising a paper • Validity •Reliability Correlation/ Causation • Reference to existing knowledge Application In order to reach a valid conclusion, procedures must be evaluated Summary (a) The Scientific Method • Give the stages of the scientific cycle Explain why scientists discuss theories rather than facts. • Describe a 'null hypothesis' . Explain why a lack of findings does not invalidate a theory. Explain how conflicting data is resolved. Explain the importance of independent confirmation of results (b) Scientific literature and communication • Suggest why a clear and complete write up is required for publication in a journal Give the role of a peer reviewer • Give ways which scientific advances are shared (c) Scientific ethics • Describe the features of professional integrity • Explain how animal studies can be made ethical • Explain why 'replication' is important in ensuring professional integrity. • List the rights that humans participating in an experimental trial have • List the individuals whose safety must be taken into account during a study Explain why risky trials can still often be carried out and suggest who may regulate these trials • List factors which may prevent an ideal experiment being carried out (a) Pilot Study Explain why pilot studies are carried out. Describe how pilot studies can improve an experimental method Validity Accuracy Reliability Precision (b) Experimental Design Explain which variable is 'Independent' and which is 'Dependent'. Explain why a placebo may be used. Suggest how an experimental design can be altered to deal with confounding variables. Describe the placebo effect. Describe the difference between simple and multifactorial experiments. Explain the differences between observational and experimental approaches. Explain how in vitro and in vivo studies differ (c) Sampling Explain why only a sample of a population may be used in an experiment Suggest which factors may affect sample size. Describe how sampling is made random. Describe how sampling is made systematic. Describe how sampling is made stratified. . ● (d) Reliability Explain how variation in experimental results can be caused. • Describe how the reliability of a measuring instrument can be found. Describe how variation in a biological material can be measured. Explain what the range of measured values suggests. • Describe how the overall reliability of an experiment can be found. ● ● . (e) Presentation of Data • Describe the features of Qualitative data. Describe the features of Quantitative data. • Describe the features of Ranked data. • Describe how the mean' is calculated. Describe how the median' is calculated. • Describe how the 'mode' is calculated. Create a box plots to show variation within and between data sets using their median, lower quartile, upper quartile and inter-quartile range. • Explain what a correlation between two variables demonstrates. • Explain the difference between correlation and causation. • Describe the meaning of a positive correlation. • Describe the meaning of a negative correlation. • Describe what the strength of correlation denotes . (a) Background information • Give the features of an effective background information section. • Give the features of an effective title. • Give the features of an effective abstract. • Give the features of an effective aim. • Give the features of an effective introductory section. (b) Reporting and evaluating experimental design • Give the features of an effective methods section. . . Suggest how the validity of an experiment be compromised. Explain the effect of selection bias on representative sampling. Explain the effect of sample size on representative sampling. (c) Data Analysis • Give the features of an effective results section. Suggest how outlier or anomalous results can be dealt with in analysis. Suggest how statistical testing may be used in data analysis. Explain the role of error bars in graphical presentations. • . . (d) Evaluating results and conclusions • Give the features of an effective conclusion section.