1. Data will fall into three categories: AP Lab Skills Guide 1. Parametric (normal) data 2. Nonparametric data 3. Frequency or count data - Normal distribution around mean - Mean and SD can predict future observations Ex. Heart rate, plant height, body temp - Does not fit normal distribution - May include large “outliers” - Counting how many of an item fit into a category Ex) Doing a genetic cross (Aa x Aa) and counting how many offspring are AA, Aa and aa. Ex2) Data collected as percentages like the percentage of cells in interphase of a root tip…you are just counting.

2. AP Lab Skills Guide Ex2) Data collected as percentages like the percentage of cells in interphase of a root tip…you are just counting.

3. AP Lab Skills Guide

5. Scatterplots - Comparing two MEASURED VARIABLES - If a linear relationship is predicted, a linear regression can be performed (best fit line; Figure 3) - R 2 (R-squared or coefficient of determination) Typically ranges from 0 to 1 Describes “goodness of fit” or how well the line drawn fits the points. R 2 = 0 implies not relationship R 2 = 1 implies prefect relationship (all points on line)

6. AP Lab Skills Guide Box-and-Whisker Plots (Boxplot) - Used with nonparametric data (data that is not assumed to follow a normal distribution). - Vertical lines indicate highest and lowest points in dataset - Horizontal line represents the median 70 32 Upper Quartile Lower Quartile median - Top of box shows upper quartile and bottom shows lower quartile. Determining Lower (Q1) and Upper (Q3) Quartiles: You are simply dividing the data into quarters by medians…the upper quartile is the median of the upper half of the data and vice versa… (Q2) (Q3 - upper) (Q1 - lower)

7. AP Lab Skills Guide Box-and-Whisker Plots (Boxplot) Determine the upper and lower quartile of the sycamore and beech leaf data: 33 35 40 44 48 52 63 Median (Q2) Equals 42 Lower Quartile(Q1) Equals 37.5 Upper Quartile (Q3) Equals 50 Notice how the upper and lower quartile range give you a sense of the center of the data without the influence of outliers that might exist in nonparametric data!! Sycamore:

8. AP Lab Skills Guide Box-and-Whisker Plots (Boxplot) Determine the upper and lower quartile of the sycamore and beech leaf data: 11 15 19 21 26 32 34 Median (Q2) Equals 42 Lower Quartile(Q1) Equals 37.5 Upper Quartile (Q3) Equals 50 Beech: http://www.brainingcamp.com/resources/math/box-plots/questions.php

9. AP Lab Skills Guide Histograms Used to determine if a given set of measurements, like plant height from art. sel. lab, approximates a normal distribution (parametric) or if data is nonparametric. Histogram showing parametric data Histogram showing NONparametric data

10. AP Lab Skills Guide Warning

11. AP Lab Skills Guide

15. AIM: How do scientists describe population growth? Population growth rates http://bcs.whfreeman.com/thelifewire/content/chp54/5402002.html http://www.brown.edu/Courses/BI0020_Miller/week/2/eco-1-handout.pdf Birth rate (B) = #born per total population size per unit time For example, if the population size is 100 and 5 individuals are born in a year then the birth rate = 5/100 or 0.05 born per individual per year r max = maximum population growth rate, which only occurs when there are no population limiting factors. R max is a constant for a given species. For example, r max for bacteria is much greater than r max for humans as they reproduce at a much greater rate. Death rate (D) = #die per total population size per unit time For example, if the population size is 100 and 10 individuals die in a year then the death rate = 10/100 or 0.1 die per individual per year Overall Rate of population growth (r) = Birth rate – Death rate Calculate the growth rate (r) for the above example: r =.05 -.1 = -0.05 or for every 100 individuals in the population, at this moment, 5 die per year…therefore the population is…. Decreasing!!

16. AIM: How do scientists describe population growth? http://www.youtube.com/watch?v=c6pcRR5Uy6w Exponential Growth

17. AIM: How do scientists describe population growth? Logistic Growth http://www.youtube.com/watch?v=rXlyYFXyfIM

18. AP Lab Skills Guide http://www.youtube.com/watch?v=UQWWSmGM0yQ

19. AP Lab Skills Guide http://www.youtube.com/watch?v=UQWWSmGM0yQ

20. AP Lab Skills Guide

22. Tube 1 (substrate) Tube 2 (enzyme) H 2 O 2 Guaiacol Distilled H 2 O Peroxidase Distilled water + Mix contents Begin Timing Tube 3 (tubes 1 + 2) Begin Timing

23. AP Lab Skills Guide Tube 3 (tubes 1 + 2) Begin Timing Each minute for 5 min compare the color of tube 3 to the standard Time (min)Color 11 22 34… Graph the data…

24. AP Lab Skills Guide Each minute for 5 min compare the color of tube 3 to the standard Time (min)Color 11 22 32 43 55 66 78 810 You are determining how long to let the reaction go to get a value of “5” as your baseline for comparisons in the next step…you will see…we will run all future reactions for 5 minutes and look at color and compare to enzyme in distilled water….

25. AP Lab Skills Guide

26. Tube 1Tube 2Tube 3Tube 4 Tube 5 Tube 6 Peroxidase H 2 O 2 pH 2 buffer Peroxidase H 2 O 2 pH 4 buffer Peroxidase H 2 O 2 pH 6 buffer Peroxidase H 2 O 2 pH 8 buffer Peroxidase H 2 O 2 pH 10 buffer Peroxidase H 2 O 2 pH 12 buffer Cover with parafilm, gently mix and measure color at 0 minutes and color change at time determined in part 1 (5 minutes)...

27. AP Lab Skills Guide pHColor 21 42 65 83 101 121 Of course, we should combine the class data, take averages, SD, SE and graph with error bars…

28. AP Lab Skills Guide

33. Big Idea 3 – Investigation (Lab) 8

34. Recall how a gene of interest is obtained (PCR), inserted into a plasmid using restriction enzymes / DNA ligase, and transformed into a bacterium for copying or expression to get protein…review chapter 20 powerpoint if you have forgotten. SUBCLONING Big Idea 3 – Investigation (Lab) 8

36. Procedure 1. In this lab you will simply take an E. coli colony, put it in a tube containing the CaCl2 solution, and either add pAMP plasmid (+) or not (-). Tube 1 (-)Tube 2 (+) E. coli (1 colony) 240ul CaCl2 solution 10 ul water E. Coli (1 colony) 240ul CaCl2 solution 10ul of Amp r plasmid (0.005 ug/ul) pAMP plasmid - Amp r gene coding for β-lactamse (enzyme that cuts up ampicillin). - ORI – origin of replication - MCS – multiple cloning sites (restriction sites) Big Idea 3 – Investigation (Lab) 8

37. Procedure 2. You now of course heat shock to transform the cells. The (-) tube is obviously a negative control. The CaCl2 helps with the efficiency of the heat shock. Right after the heat shock, 250ul of liquid LB (nutrient solution) is added to tubes so that cells can begin to recover and grow. Tube 1 (-)Tube 2 (+) E. coli (1 colony) 240ul CaCl2 solution 10 ul water 250 ul liquid LB E. Coli (1 colony) 240ul CaCl2 solution 10ul of Amp r plasmid (0.005 ug/ul) 250 ul liquid LB Big Idea 3 – Investigation (Lab) 8

38. Procedure 3. Plate 100ul of the 500ul cell solution on agar plates both without and amp and with ampicillin to kill untransformed cells. This is what you should see…If you grow either tube on straight LB agar then tons of colonies are observed like plates 1 and 3. If you grow the cells from each tube on LB agar +AMP then you should not see any cells for the (-) tube and only a dozen or two for the transformed (+) cells…. Big Idea 3 – Investigation (Lab) 8

39. 1.Simple…just count the number of colonies you observed…this is how many cells got transformed because each colony comes from a single cell undergoing multiple rounds of binary fission. Let’s say you counted 32 colonies… 2. Now we need to know how much DNA in ug it took to get those colonies you just counted. Remember that you added 100ul of this solution: Tube 2 (+) E. Coli (1 colony) 240ul CaCl2 solution 10ul of Amp r plasmid (0.005 ug/ul) 250 ul liquid LB Figure out how much DNA you added…. Big Idea 3 – Investigation (Lab) 8

40. Remember that you added 100ul of this solution: Tube 2 (+) E. Coli (1 colony) 240ul CaCl2 solution 10ul of Amp r plasmid (0.005 ug/ul) 250 ul liquid LB 1. You added 10ul at 0.005ug/ul. Therefore you have.05ug of plasmid in the tube. 2. The total volume is 500ul. Therefore you have 0.05ug/500ul or 0.0001ug/ul. 3. You took 100ul of this solution: 100ul x 0.0001ug/ul =.01ug of plasmid It took.01 ug of plasmid to get those 32 colonies! = 32/0.01 or 32 colonies per 0.01 ug of plasmid = 3200 colonies per ug plasmid http://www.sciencegateway.org/tools/transform.htm Big Idea 3 – Investigation (Lab) 8

42. Big Idea 3 – Investigation (Lab) 9 We did a variation of this lab at the Cold Spring Harbor DNA Learning Center West… The next few slides highlight the differences between what you did and what this lab specifically asked that you do…which is to pretend that you are working a crime scene, have a DNA sample, and will cut with restriction enzymes to look for restriction fragment length polymorphisms (RFLP’S)

43. Restriction fragment length polymorphisms (RFLP’s = “rif lips”) Amplified section of the DNA from the crime scene Amplified section of the same DNA segment from the suspect. The differences in restriction sites found on homologous chromosomes giving rise to different numbers and lengths of restriction fragments...review chapter 20 powerpoint for more detail. Crime scene DNA Suspect DNA Big Idea 3 – Investigation (Lab) 9

44. A gel showing lambda phage DNA (same DNA you cut at the DNA learning center) cut with three different restrictions enzymes and an uncut negative control. IDEAL GEL Look at chapter 20 for a review of how gel electrophoresis works…

45. Big Idea 3 – Investigation (Lab) 9 Calculating the Standard Curve

46. Big Idea 3 – Investigation (Lab) 9 Calculating the Standard Curve 2.3 3.0 3.5 4.2 5.8 6.3

47. Big Idea 3 – Investigation (Lab) 9 Calculating the Standard Curve 2.3 3.0 3.5 4.2 5.8 6.3 Migration distance (cm) Size of fragment (bp) Relationship between DNA fragment size in bp and migration distance in a 0.8% agarose gel. There appears to be an exponential relationship… Or…small fragments move exponentially quicker than larger fragments… If so, then using a log scale on the y-axis should result in a linear relationship…(next slide)

48. Big Idea 3 – Investigation (Lab) 9 Calculating the Standard Curve 2.3 3.0 3.5 4.2 5.8 6.3 R 2 =0.93057

49. Big Idea 3 – Investigation (Lab) 9 Calculating the Standard Curve 2.3 3.0 3.5 4.2 5.8 6.3 R 2 =0.93057 This is now our standard curve…we can use it to do what? To calculate the sizes of the BamHI and EcoRI bands… Simply measure the distance traveled by the band and then use the curve to determine the size.

50. Big Idea 3 – Investigation (Lab) 9 Calculating Size of Unknown Bands 2.3 3.0 3.5 4.2 5.8 6.3 R 2 =0.93057 Calculate the size of the largest fragment for the BamHI digest. The migration distance is 2.5 cm. Therefore, the size is approximately 14,000 bp (I actually used the formula for the line, which excel can give you, instead of the graph itself, but the AP will require you to use the graph). 14,000 2.5 14,000

51. Big Idea 3 – Investigation (Lab) 9

52. Big Idea 4 – Investigation (Lab) 10

53. Complete metamorphosis

54. AIM: What types of biomes exist on Earth? Primary Productivity: Production of organic material in a given amount of time through the fixation of carbon (CO2) either by photosynthesis or chemosynthesis. Open ocean wins due to its huge area even though its productivity per unit area is generally low as you will see on the next slide..

55. AIM: What types of biomes exist on Earth? Gross Primary Productivity (GPP): Total organic material generated by photo- and chemosynthesis per unit area in a given time. Net Primary Productivity (NPP): When organic material is generated by photo- or chemosynthesis, some will go to cellular respiration and be converted back to CO2 and H2O. What is left in the organisms per unit area per unit time is the net primary productivity. Tropical forests usual win this one in the terrestrial biomes as they have a huge biomass per unit area, while swamps and marshes take it in the aquatics. NPP = GPP – respiration

56. Big Idea 4 – Investigation (Lab) 10 Then how does one monitor NPP (net primary productivity) in plants? Define Primary Productivity, NPP (Net Primary Productivity) and GPP (Gross Primary Productivity). Primary Productivity is the formation of organic molecules from CO2 by photo- or chemosynthesis. Measure the biomass of the plants over time…however, biomass does not include water…therefore you need to either dry the plants out, which would kill them, or estimate the percentage of water in the plant, which is about 75% just like us… GPP – the total amount of organic material formed per unit area time. NPP – the total amount of organic material formed per unit area time after subtracting what is burned in cell resp…(basically, NPP is the biomass that accumulate per unit area time) This means that if the mass of the plant is 120g then the biomass is…90g.

57. Big Idea 4 – Investigation (Lab) 10

59. Step 2. Design an experiment that estimates the NPP of Fast Plants. A. Grow 40 or more plants from seed in identical conditions… B. After 7 days, take 10 plants carefully out of soil, wash off all soil, blot dry and mass them. C. Dry them in an oven to get rid of water and mass them again. D. Calculate amount of energy stored in biomass by assuming 4.35kcal/g and then the NPP per day per plant.

60. Big Idea 4 – Investigation (Lab) 10 Step 2. Design an experiment that estimates the NPP of Fast Plants. E. Wait another 7 days and repeat the procedure with another 10 plants… One should combine all the class data from the groups and calculate a mean, SD, SE for percent biomass, NPP, etc…

61. Big Idea 4 – Investigation (Lab) 10 0.29 kcal/day

62. Big Idea 4 – Investigation (Lab) 10

63. Kcal consumed Biomass (growth) Cell Respiration (heat and IR) Feces (egestion)