Biology Skills (Paper 3 and etc.)

1.1) Use of a light microscope to investigate the structure of cells and tissues, with drawing of cells
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1.1) Use of a light microscope to investigate the structure of cells and tissues, with drawing of cells
light microscopes use light and a-lot of lenses to magnify image
- living can be viewed in their color
- structures clearly labelled
- title included
- magnification included
1.1) Calculation of the magnification of drawings and the actual size of structures and ultrastructures shown in drawings or micrographs
magnification: image size (with ruler) / actual size (according to scale bar)
1.2) Drawing of the ultrastructure of prokaryotic and eukaryotic cells based on electron micrographs
prokaryote:
- pili (single lines like hair)
- flagella (tail shown as longer line)
- ribosome (70S)
- cell wall
- shape
- size

eukaryote:
- nucleas (double membrane with pores)
- mitochondria (double membrane with folds inside
- golgi (wifi)
- endoplasmic reticulum: something like wifi but rough one has dots around it
- ribosomes: dots
- cytosol: cytoplasm basically so fluid
1.2) Interpretation of electron micrographs to identify organelles and deduce the function of specialised cells
- alot of mitochondria means that cell undergo energy consuming processes (neurons, muscle)
- alot of ER means secretory activities (plasma and exocrine gland)
- alot of lysosomes means digestive processes (phagocytes)
- alot of chloroplast undergo photosynthesis (plant leaf)
1.3) Drawing of fluid mosaic model
Image: 1.3) Drawing of fluid mosaic model
1.3) Analysis of evidence from electron microscopy that lead to proposal of Davson Danielli model
- membrane exhibit trilaminar appearance where there are 2 dark outer and lighter inner region

Davson Danielli:
- two proteins sandwiching central phospholipid bilayer
- lipid layer between two protein layers
- dark segments identifies as two protein layers
1.3)Analysis of falsification of Davson Danielli that lead to Singer Nicholson model
problems with DD:
- assumed that membrane were uniformly thick
- assume all membrane have symmetrical surfaces
- did not account for permeability
- temperatures in which the membrane solidify did not correlate with proposed model

falsified:
- proteins discovered to be water insoluble and varied in size so they cannot form a uniform and continuous layer

how is it falsified?
antibody tagging showed they were mobile
- when two cells fused, markers of red and green become mixed throughout membrane

freeze fracturing used to split open and revealed irregular rough surfaces
- rough surface interpreted as transmembrane protein so its not localised
1.4) Estimation of osmolarity in tissues by bathing samples in hypotonic and hypertonic solution
- tissue will lose water when placed in hypertonic and gain water when placed in hypotonic
- water loss/gain determined by weighing sample before/after
- tissue osmolarity identified through no weight change
1.6) Identification of phases of mitosis in cells viewed with a microscope
interphase:
- DNA present as uncondensed chromatin
- contained within nucleus
- organelles duplicated
- cell enlargened

prophase:
- chromosome condense
- chromosome joined at centromere
- centrosome move to opposite poles and form spindle fibres
- membrane breaks down and nucleus dissolve

metaphase:
- fibres connect to centromere of each chromosome
- depolymerisation cause spindle fibres to shorten and contract, making them align along centre

anaphase:
- contraction cause sister chromatids to seperate
- move to opposite poles of cell

telophase:
- fibres dissolve and chromosome decondense
- membrane reform around each chromosome set
- cell split into 2
Image: 1.6) Identification of phases of mitosis in cells viewed with a microscope
1.6) Determination of a mitotic index from a micrograph
mitotic index: number of cells in mitosis / total cells

prophase: condensed but confined in nuclear region
metaphase: align along equator of cell
anaphase: chromosome apparent at different poles of cell
telophase: 2 nuclear region present within single cell
Image: 1.6) Determination of a mitotic index from a micrograph
2.1) Drawing molecular diagrams of glucose, ribose, saturated fatty acid and generalised amino acidcarbohydrates (monosaccharides) - exist in pentose and hexose form (alpha d glucose has right OH on the bottom while beta d glucose has right OH on top) lipids - fatty acids are long chains of hydrocarbons that may or may not have double bonds protein: - consist of central carbon connected to amine group (NH2) and carboxyl group (COOH) - variable group gives different properties nucleic acid: - nucleotide consist of pentose sugar, phosphate group and nitrogenous base2.1) Identification of biochemicals such as sugars, lipids or amino acids from molecular diagramsglucose: - form of glycogen, cellulose and starch lipids: - triglycerides (glycerol with 3 fatty acids) , phospholipids (2 fatty acids, phosphate and glycerol) and steroids (4 fused hydrocarbon rings) protein: - amino acids into dipeptide + water2.3) Use of molecular visualisation software to compare cellulose, starch and glycogencellulose: - beta glucose units with 1-4 bonds - linear chains for cell wall structure starch: amylose - alpha glucose units in helical chains for energy storage amylopectin - alpha glucose units in branched chains (1-4 bonds and 1-6 bonds) for energy storage in plants glycogen: - alpha glucose units with branched chains for energy storage in animals2.3) Determination of body mass index by calculation or use of nomogrambody mass index: mass in kg / (height in m) squared2.4) Drawing molecular diagram to show formation of peptide bondpeptide bonds formed between amine and carboxylic acid groups - amine loses hydrogen atoms - carboxylic group loses hydroxyl (OH) - Forms H20 as byproduct2.5) Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymesthree key decisions: - which factor to investigate - which enzyme / substrate reaction to use - how to measure the enzyme activity measuring activity: gas production - count bubble formation - time for enzyme disc to rise in substrate solution - displacement of syringe with increasing volume of gas - pressure change in sealed environment (data logger) digestion of solid - calculate change in weiht - change in diameter - production of volume digestion of liquid - dialysis tube color change -starch with iodine (purple) - peptide bonds stained via Biuret Blue test - Benedict's reagent2.6) Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentose and bases5 carbon pentose sugar drawn in pentagon attached to phosphate base (circle) in the 5' carbon atom (left point and nitrogenous base (rectangle) attached to 1' carbon atom (right point)2.7) Use genetic code to deduce which codons correspond to which amino acid2.7) Analysis of Meselson and Stahl's results to obtain support for semi-conservative theoryconservative: entirely new molecule synthesised from template semi-conservative: new molecule consist of one new strand and one template strand dispersive: molecules made up of segments of old and new DNA test validity using radioactive isotopes of nitrogen - DNA molecules prepared using N15 while replicated DNA was tagged with N14 - DNA seperated through centrifugation to determine composition of DNA results: - after one division, DNA molecules contain mix of N14 and N15 (which disproves conservative0) - after two division, some molecules only consist of N14 so (disproves dispersive)2.7) Use table of mRNA codons and corresponding amino acids to deduce sequence of amino acidsmRNA transcript organised into codons (triplets) - reading frame starts with AUG and reads proteins in triplets until termination codon - blocked reading frame interrupted by termination codons start (AUG) , end (UGA)2.7) Deducing the DNA base sequence for the mRNA strandconverting mRNA into DNA: - cytosine replaced with guanine (C with G) - uracil replaced with adenine (U with A) - adenine replaced with thymine (A with T)2.8) Analysis of results from experiments involving measurement of respiration rates in germinating seeds/invertebrates using respirometerrespirometer is a device that determines organism's respiration rate (measuring rate of exchange between O2 and CO2) - specimen enclosed in sealed container - CO2 production measured with data logger of pH changes in water - when alkali included to absorb CO2, oxygen consumption can be measured as change in pressure within system (through data logger or U-tube manometer) factors affecting rates include: temperature, hydration, light, age and activity levels - increase in CO2 is increase in respiration - decrease in 02 is increase in respiration2.9) Drawing absorption spectrum for chlorophyll and action spectrum for photosynthesisabsorption spectrum: wavelength of lights absorbed by each pigment action spectrum: rate of photosynthesis at each wavelength of light correlation between absorption and action spectrum - both display peaks in blue region and smaller peak in red region - both display trough in green/yellow portion2.9) Design of experiments to investigate effect of limiting factors on photosynthesisphotosynthesis measured through uptake of CO2 or production of O2 or change in biomass (levels could be influenced by cell respiration in tissue) CO2 Uptake: - place leaf tissue in closed space with water - water free of dissolved CO2 produced by boiling and cooling water - C02 interacts with water molecules to produce bicarbonate and hydrogen ions (changing pH_ - increase uptake of C02 lowers concentration and increase alkalinity - also can be measured with data logger 02 Production: - submerge plant in closed space with water attached to gas syringe - oxygen produced will bubble out of solution and measured in change of syringe level - measured by time taken for submerged leaf discs to surface - data logger Biomass: - glucose production measured by change in biomass - tissue dehydrated beforehand to ensure that weight is organic content not water content - measure in change of starch levels - starch identified through iodine staining and quantified through colorimeter2.9) Separation of photosynthetic pigments by chromatographphotosynthetic organisms rely on combined action of many pigments to absorb light (including chlorophyll, xanthophyll and carotenes) chromatograph is experimental technique that helps pigments to be seperated - mixture dissolved in fluid and passed through static material (mobile phase to stationary phase) - components of mixture travel at different speed - Rf value = distance component traveled + distance solvent travels methods: - paper chromatography (using celulose) - thin layer chromatography (using adsorbent) which runs faster and have better seperation3.3) Drawing diagrams to show stages of meiosis resulting in formation of four haploid cellsMeiosis: P1: chromosomes condense, membrane dissolved, chromosomes form bivalents and crossing over occurs M1: spindle fibres from opposing centromered connect to bivalents and align them along middle of cell A1: fibres contract and split bivalent, chromosomes move to opposite poles of cell TI: chromosomes decondense, membrane reforms, cell divides and form 2 haploid daughter cells P2: chromosomes condense, membrane dissolve and centrosomes move to opposite poles M2: fibres attach to chromosome and align along equator A2: fibres contract and seperate sister chromatids, moving to opposite poles T2: chromosome decondense, membrane reforms and cell divides to form 4 haploid daughter cell3.4) Construction of Punnett grids for predicting outcome of monohybrid genetic crossesProcess of calculating Monohybrid crosses: - designate letters to represent alleles - write down genotype and phenotype of parents - write down genotype of parental gametes - draw grid with maternal gametes along top and paternal gametes along left - complete punnet grid to determine potential genotypes and phenotypes of offspring3.4) Comparison of predicted and actual outcome of genetic crosses using real datapredictions from Punnettt grids are only probabilities and dont reflect actual trends - larger data sets more likely to yield positive correlation - Gregor Mendel performed 5,000 crosses - he crossed different varieties of pea plants and recorded characteristics - he crossbred purebred dominant and purebred recessive to produce heterozygotes - he self pollinated heterozygotes to produce third generation and counted dominant and recessive phenotypes - expected ratio (dominant 3: recessive 1)3.4) Analysis of pedigree charts to deduce patterns of inheritance of genetic diseasespedigree chart: chart of genetic history Autosomal Dominant: - if both parents affects and offspring is unaffected, the trait must be dominant - if both parents unaffected, all offspring must be unaffected Autosomal Recessive - if both parents are affected and offspring is affected, trait recessive - if both parents showed trait, offspring must exhibit that trait X linked Dominant: - if male shows trait, all daughters and his mother should show trait - unaffected mother cannot have affected sons X linked Recessive: - if female shows trait, sons as well as her father should too - unaffected mother can have affected sons if she's a carrier3.5) Design of experiment to assess one factor affecting rooting of stem cuttingsstem cutting is seperated portion of plant stem that can regrow into a new clone through vegetative propagation - all stems possess nodes from which a root can grow out of, region between nodes is called internodes - cuttings typically placed in soil with lower nodes covered and upper nodes exposed - it is a common method employed to rapidly propagate plant species (sugar, grapes) factors influencing successful rooting of cutting: - cutting position (above or below a node, and proximity of cut to node) - length of cutting (how many nodes remain in cutting) - growth medium (left in soil, water, potting mix etc.) - use of growth hormones - temperature (optimal growth during spring and summer) - water (ground water or humidity) - pH, light3.5) Analysis of data on risks to monarch butterflies of Bt cropsBt corn is genetically modified maize that incorporates insecticide in producing gene from bacteria - insecticide lethal to certain types of larvae concerns: - Bt corn can also impact survival rate of monarch butterflied - monarch butterfly larvae feed exclusively on milkweed, windborne pollen from Bt pollen can dust nearby milkweeds - from study, caterpillars exposed to Bt corn found to have eaten less, grew slower and have higher mortality rates but, resuts may lack validity since no reflection on natural conditions: - higher amount of Bt pollen on leaves than natural - larva restricted in diet since they can avoid eating pollenated leaves second study conducted: - no significant increase in mortality when larva placed near Bt corn field - no significant risk to population = answer4.1) Classifying species as autotrophs, consumers, detritivores or saprotrophs from a knowledge of their mode of nutritionautotrophs produce their own organic molecules using light energy or energy from oxidation consumers ingest molecules from living or recently killed things detritivores: ingest organic molecules from non-living remnant of organisms (scavenger) saprotrophs: release digestive enzyme and then absorb external products of digestion (decomposers)4.1) Testing for association between two species using the chi-squared test with data obtained by quadrat samplingpresence of 2 species dependant on their potential interaction - if species typically found on same habitat: positive correlation (predator-pray or symbiotic) - if specific tend to not occur in same habitat: negative correlation (competition for resources) - negative correlation could lead to competitive exclusion or resource partitioning - if 2 species do not interact, no association quadrat sampling: - quadrats placed in define area of random arrangement or of design (transect) - number of individuals counted or estimates through percentage coverage - repeated alot to gain representative data set - in each quadrat, presence or absence is identified chi squared uses data from quadrat sampling: - identify hypotheses (null vs. alternative) - construct table of frequencies (observed vs. expected) - apply chi-squared formulas - determine degree of freedom - identify p value (<)0.054.1) Recognising and interpreting statistical significance of chi squaredstep 1: identify hypotheses - null (no significant difference so random) - alternative (there is significant difference between distribution so associated) step 2: construct table of frequencies - table constructed to find expected distribution for each species - expected frequency = (row total x column total) / grand total step 3; apply chi squared formula - x squared = sum of (observed - expected) squared.... divided by expected step 4: degree of freedom - df = (number of rows - 1) times (number of columns - 1) - when distribution patterns compared, degree of freedom should always be 1 step 5: p value - if p is <0.05 then results are statistically significant and null hypothesis is rejected and alternate hypothesis accepted - identify positive or negative4.2) Quantitative representations of energy flow using pyramids of energypyramid never inverted since energy always lost upon transfer - each level to be one tenth of preceding level - bottom level present producers and so on presents consumers4.3) Construct a diagram of the carbon cyclecarbon cycle: where carbon is exchanged between different earth-spheres (atmosphere, lithosphere, hydrosphere and biosphere) exchanged through: - gases (CO2 and methane) - oceanic carbonates (bicarbonates dissolved in water and calcium carbonate in corals/shells) - organic materials (carbs, lipids found in living things - non living remain (fossil fuels)5.3) Construction of dichotomous keys for use in identifying specimensd-key: method of identification - with each division, more information is revealed about specific features of organism - when organism no longer shares totality of selected characteristics, it has been identified (popsugar quiz) - use no-change features as keys (physical characteristics and biological processes such as reproduction methods work) presented as branching flowchart or as paired statements in numbered sequence5.4) Analysis of cladograms to deduce evolutionary relationshipsfeatures: - root (initial ancestor) - nodes (hypothetical common ancestor) - outgroup (most distantly related species for reference) - clades (common ancestor and descendants6.1) Production of an annotated diagram of the digestive systemfeatures: - stomach should look like j-shaped bag and connected to esophagus and small intestine - liver looks like right angled triangle and positioned to left of stomach - bile duct connected to gall bladder and pancreatic duct should both feed into U shaped bend of small intestine - small intestine thinner in width than large intestine6.1) Identification of tissue layers in transverse sections of the small intestine viewed with a microscope or in a micrographserosa: protective layer of cells reinforced by fibrous tissue muscle layer: outer layer of longitudinal and inner layer of circular muscles (peristalsis v. segmentation) submucosa: connective tissue seperating muscle layer from mucosa mucosa: highly folded inner layer that absorbs material through surface epithelium6.2) Identification of blood vessels as arteries, capillaries or veins from the structure of their wallsstructural differences: arteries: thick walls and narrow lumens to transport blood at high pressure (composed of 3 distinct layers) capillaries: single cell thick to exchange materials (bigger magnification due to small feature) veins: thin walls and wide lumens to transport blood at low pressure (like a big hole with thin outline)6.2) Recognition of the chambers and valves of the heart and the blood vessels connected to it in dissected hearts or in diagrams of heart structurestructure: - 2 atria: chambers on top of heart that collect blood from lungs/body - 2 ventricles: chambers on bottom that pump blood to body/lungs - atrioventricular valves (tricuspid on right carries deoxygenated blue, bicuspid on left carries oxygenated red) - vena cava feed into right atrium, returning deoxygenated blue blood from body - pulmonary artery connect to right ventricle to send deoxygenate blue blood to lungs - pulmonary vein feed into left atrium to return oxygenated red blood from lungs - aorta extends from left ventricle and sends oxygenated red blood around body6.4) Monitoring of ventilation in humans at rest and after mild and vigorous exerciseventilation in humans change in response to physical activity since energy demands change - changes in blood C02 levels detected by chemosensors in arterial walls, sending signals to brainstem - as exercise intensity increase, demand for gas exchange lead ot increase in ventilation exercise influence ventilation: - increase ventilation rate (greater frequency of breaths) - increase tidal volume (increase volume of air taken monitored through: - chest belt and pressure meter - spirometer (brathing in balloon and measuring volume of air in single breath)6.5) Analysis of oscilloscope traces showing resting potentials and action potentialsoscilloscopes: scientific instruments used to measure membrane potential across neuronal membrane resting potential: before - action potential, neuron should be in state of rest - depolarisation: rising spike via sodium influx - repolarisation: falling spike via potassium efflux - refractory period: trace returns to level of resting potential action potential occur if initial depolarisation exceed threshold potential6.6) Annotate diagrams of the male and female reproductive system to show names of structures and their functionsmale structure: - testis: responsible for sperm/testosterone production - epididymis: site where sperm matures and becomes motile until ejaculation - vas deferens: long tube that conducts sperm from testes to prostate during ejaculation - seminal vesicle: secrete fluid containing fructose (nourish), mucus (protect), prostaglandin (contractions) - prostate gland: secretes alkaline fluid to neutralise vaginal acids - urethra: conducts sperm from prostate to outside via penis female structure: ovary: location where oocytes mature prior to release // responsible for estrogen fimbria: muscle tissue that sweep oocyte into oviduct oviduct: transports oocyte to uterus (fertilisation) uterus: where fertilised egg will implant and develop endometrium: membrane lining that thickens in preparation for implantation (or lost via menstruation) vagina: passage leading to uterus where penis can enter