Biology Lab Practical I PDF

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Dr. Luque notes from lab for the practical...

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Biology Lab Practical I Study Review 

Science: our knowledge of all the natural world o Limits:

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Does not make moral judgement

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Does not make aesthetic judgements

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Does not make decisions about applications of science

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Does not make conclusions about the supernatural

Scientific Method: ongoing process used to describe how science works o Observations of a phenomenon  Personally or indirectly o Ask questions pertaining to the observations  Why is this phenomenon occurring? o A testable hypothesis is created  Can be very specific or very broad o A prediction is developed based on the hypothesis o Hypothesis is tested by conducting an experiment  Purpose of experiment is to determine whether observations agree with or conflict with predictions derived from hypothesis o Based upon data collected, hypothesis is rejected or accepted and a conclusion is drawn o Other components required  Replication ▫ Ability to reproduce experiment multiple times to prevent mistakes from occurring ▫ Measure of experimental error is often included when reporting results ▫ Repetition confirms validity  External review ▫ Involves evaluation of experiments by others in the field ▫ Does not certify the correctness of the result, only that in the opinion of the reviewer, the experiments were sound  Data recording and sharing ▫ Findings are carefully recorded and archived ▫ Can be used to compare other experiments of those who have replicated it

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Developing Hypothesis and Prediction o Hypothesis: proposed explanation for an observation  A reasoned explanation, NOT a guess  Usually based on prior experiences and scientific background or knowledge  May have an alternative hypothesis o Requirements  Testability: can be verified or falsifiable  Parsimony: simpler hypotheses are preferred over more complex ones  Scope: neither too specific nor too general  Fruitfulness: the prospect that a hypothesis may explain further phenomena than in the future  Conservatism: the degree of "fit" with existing recognized knowledge or systems o How to write a hypothesis  Establishment of variables  Are you able to design an experiment from this hypothesis? o Null hypothesis  The hypothesis that chance alone is responsible for the results of  Assumes no relationship between the independent and dependent variables  Hypothesis that says there is no statistical significance between the two variables  Results from experiment will either reject or accept ▫ When rejected, this only provides evidence that supports the alternative hypothesis o Alternative hypothesis  The hypothesis that is hoped or expected to be true instead of the null hypothesis  Proposes that the observations are the result of a real effect o Prediction: forecasts the outcome of an experiment in a lab or the observation of a phenomenon in nature  May invoke statistics and only talk about probabilities  A statement about what will happen in the future (outcome of an experiment, etc.)  Expectation derived from a phenomenon o How to write a prediction  The use of the word "will" Experimental Design o Experiment: procedure carried out to make a discovery, test a hypothesis, or demonstrate a known fact

Will hold its ground under questioning and will focus criticism on conclusions rather that potential experimental errors o Characteristics of a good experimental design  Discrimination ▫ should be able to clearly discriminate between different hypothesis  Replication ▫ Must be repeated enough times for the results to be analyzed statistically  Controls ▫ Provide a reliable baseline to compare the results with ▫ Allow researchers to eliminate and isolate variables ▫ Positive control ♦ Group is expected to have a result that shows that the procedure is working and capable of producing results ♦ If there is no result evident in this group, something is wrong with the experiment ♦ Reduce chance of false negatives ▫ Negative control ♦ Makes sure that no cofounding variable has affected the results ♦ Not expected to produce any results  Measurement ▫ Accuracy ♦ Ability of method to give an unbiased answer on average ♦ Proximity of measurement results to the true value ▫ Precision ♦ An index of the methods reproducibility ♦ A measure of the spread of data collected ♦ Proximity of the measurements to each other ▫ Together accuracy and precision can help judge the reliability of data ▫ Both help in judging how many sig figs you need in the report ▫ When variables are difficult to measure it is necessary to isolate measurable components of the variable o Variables  In an experiment, 1+ variables are manipulated in order to determine the effect of manipulation on another variable  Independent variable ▫ A variable that is changed or manipulated in a scientific experiment 

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▫ Found on the x-axis  Dependent Variable ▫ The variable being tested and measured in a scientific experiment ▫ Found on the y-axis  Best to manipulate one variable at a time to truly determine the effect this independent variable has on the dependent variable o Quantitative experiments  Provide a mathematical outcome that can be analyzed using statistics  Minimum replicates for each experiment must be three ▫ Every added replicate mathematically increases confidence in the conclusions o Qualitative experiment  Understanding Beer's Law o Solution: homogeneous mixture composed of two or more substances  Solvent: makes up a majority of the solution ▫ Usually water ♦ Aka: aqueous solution  Solute: minor components of the solution ▫ Amount of solute in a solution ♦ Total quantity of solute in a solution ♦ Generally measured in weight or volume ▫ Concentration ♦ Amount of solute per unit of solution ♦ Ex: 10 g of sucrose in 2 L of solution (concentration = 10g/2L or 5g/L (5 grams per liter) o Beer's Law  "absorbance is directly proportional to the solute concentration" Calculate Rate of Reaction o The speed at which reactants are converted into products o Steps  Draw a tangent to the curve (a straight line that represents the gradient at that point)  Draw a vertical line and horizontal line to form a right-angled triangle with the line from step 1  Read off the change in amount of product (vertical line of the triangle)  Read off the change in time (horizontal line in the triangle)  Calculate the gradient (step 3 / step 4) (amount of product/change in time) o Reaction rate = mg starch degraded per minute  Don’t use absorbance to calculate reaction rates

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o Calculate initial amounts of starch  o Determine the time it takes to degrade half of the initial amount of starch  

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Spectrophotometer o Instrument that makes a measurement of light absorbance o Important method for assessing the concentrations or amounts of solutes o Blanking  Iodine absorbs light at 620 nm  Solve for an unknown concentration using absorbance and a known concentration and absorbance ▫  Interpret how concentration changes in a quantitative or qualitative setting ▫ ▫ Environmental effects on enzymes o Temperature  Increasing the temperature increases the rate of reaction  If a temperature gets too high, it can denature the protein ▫ Weakens hydrogen bonds losing the active conformation  As temperature increases, the molecules in the substrate moves faster and the enzymes collide with the substrates which makes the reaction rate increase o Substrate concentration  Increasing ▫ Will increase the enzyme activity ▫ Saturation of enzymes will cause the reaction rate to level off ▫ More substrate is in the solution to bind with the enzymes, so the reaction rate increases until the enzyme active sites are all filled then the reaction rate will level off  Decreasing ▫ Reaction rate will be the same ▫ If there is not as much substrate to break down, the reaction rate will not change o Enzyme concentration  Decreasing the enzyme concentration will increase the reaction rate up until the enzyme is saturated and then the reaction rate will level off  Less enzymes will cause the substrate to bind to all the enzymes and when all the enzyme active sites are busy, the reaction rate will level off o pH

Decreasing the pH of the environment to 4.5 will increase the reaction rate, however decreasing it too low can cause denaturing of the protein  Increasing the pH can slow the reaction rate  Changes is pH can alter the charge of an amino acid side chain group and weaken or destroy ionic bonds, leading o protein denaturing Standard Deviation and Standard Error o Standard deviation: measures the variability within a single sample 

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 o Standard error: quantitative measurement of uncertainty   Standard deviation of the sampling distribution of a statistic (most commonly the mean)  Standard error of the mean estimates the variability between samples Raw data: data that is collected from the source and has not been processed for use o Data must be reduced and analyzed so others can understand and read it better T-test o A statistical test that can determine whether there are differences between two independent sample groups P-value o The probability of finding the observed, or more extreme, results when the null hypothesis of a study question is true o If the p value is less than 0.05, then the null hypothesis is rejected o If the p value is greater than or equal to 0.05, then the null hypothesis is not rejected Graphing o Know what components are necessary for proper figures  Axes labels, title, legend, etc....