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biology 115 (Stern) > bio lab manual > Flashcards

bio lab manual Flashcards

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1
Q

what is an assay?

A

a tool used in science that helps to quantitatively measure the amnt of a single part of a total sample

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2
Q

what is a labquest 2 and what do we use it for?

A

this system facilitates the collection of data by replacing chemical techniques, providing real time graphical presentations, and saving info directly in electronic form

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3
Q

what is accuracy?

A

refers to how close a measurement is to its true value

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4
Q

what is percision?

A

refers to the ability to repeatedly measure a value in a fixed situation and get the same results

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5
Q

what are the three rules for sig figs?

A
  1. non zero digits are always significant
  2. zeros btwn two significant digits are also significant
  3. a final zero or trailing zeros in the decimal portion are ONLY significant
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6
Q

what is p20 used for and what are the increments?

A

2-20ul, 0.1ul increments

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7
Q

what is p200 used for?

A

20-200ul, 1ul increments

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8
Q

what is p1000 used for?

A

100-1000ul, 10ul increments

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9
Q

how do you calculate percent error?

A

((theoretical-measured)/theoretical)x100

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10
Q

what is v1?

A

the volume of the stock solution needed to make dilute solution (transfer volume)

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11
Q

what is c1?

A

the concentration of stock solution

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12
Q

what is v2?

A

the final volume of the diluted stock solution (total volume)

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13
Q

what is c2?

A

the concentration of the diluted solution

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14
Q

how do you calculate the dilution factor?

A

df=(v2/v1)

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15
Q

how do you calculate the total dilution factor?

A

you multiply each step by the dilution factor, for example if the dilution factor is 2 the next value would be 4, then 8, 16, 32, etc.

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16
Q

how to determine the amnt needed to make the dilute solution?

A

v2-v1

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17
Q

how do you make a serial dilution?

A
  1. fill out the table using the information provided
  2. obtain 6 cuvettes, label the tops 0-4 and B for blank w/ a sharpie (REMEMBER: section, team, initials, and descp)
  3. add xmL amt of stock solution into cuvette labeled “0” using one of the micropipettes (ex: if asked to add 2ml of bromophenol blue stock solution, use p1000 twice)
  4. fill each cuvettes labeled 1-4 w/ xmL of TAE buffer using a micropipette
  5. switch vortexer to “on” and set to 6
  6. transfer v1 of stock solution from cuvette 0 to cuvette 1. put cap on cuvette and vortex
  7. uncap and transfer v1 from cuvette 1 to cuvette 2, cap and vortex/ repeate this procedure thru cuvette 4 and discard excess v1 from cuvette 4 into rinsate beaker
  8. prepare blank by adding (v1-v2) of buffer into cuvette B
  9. cap all cuvettes and set aside!
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18
Q

what is a spectrovis/spectrophotometer?

A

a machine that can measure absorbance or transmittance of a pigmented solution and biologists commonly use them to quantify the concentration of materials in a solution. the amount of light absorbed at different wavelengths is quantified using a spectrophotometer, the spectrovis itself is producing the beam of light with a specific wavelength.

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19
Q

how would you determine the concentration of an unknown sample?

A

since the absorbance of a sample is directly proportional to the concentration of material in a sample

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20
Q

what is a blank and what is it used for?

A

the blank is used to calibrate zero absorbance on the spectrophotometer, it contains everything except the compound of interest which absorbs light so that any measured absorbance is due to the presence of the compound of interest

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21
Q

how should a cuvette be placed in the spectrovis?

A

there is an arrow on the cuvette, the arrow should be oriented toward the arrow on the spectrovis cuvette holder

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22
Q

what are standards and what are they used for?

A

they have a known amnt of material being assayed and are used to calculate the amnt of material in the unknowns.

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23
Q

what is Cs?

A

concentration of the standard

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24
Q

what is Cu?

A

concentration of the unknown

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25
Q

what is As?

A

absorbance of standard

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26
Q

what is Au?

A

absorbance of unknown

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27
Q

what is the equation that related concentrations and absorbance?

A

Cs/Cu=As/Au, absorbance is directly proportional to concentration

28
Q

what are the steps in measuring absorbance?

A
  1. complete table
  2. connect spectrovis to labquest w/ USB plug
  3. power on labquest
  4. Go to meter screen, sensors, calibrate and wait 90s for warm up to finish. Next add blank and click “finish calibration”, once calibration is finished click “OK.”
  5. Go to sensors, data collection, change mode to timebased and click ok
  6. tap on large red box, change wavelength, enter the given value or 550 and click ok. this is the wavelength you will be reading the absorbance of your solution.
  7. remove cuvette b and place cuvette 0 into spectrovis
  8. click play button and collect data for at least 10s, click stop when sample run is complete
  9. go to analyze, statistics, select your run, record avg.
  10. remove cuvette 0 and place cuvette 1, press play, discard previous data and start data collection for cuvette 1
  11. repeat steps for all 5 samples
  12. if finding concentrations of unknowns, record absorbacnes of unknowns and use the equation Cu=Au(Cs)/As
29
Q

what is discovery science?

A

uses large amnts of data or surveys of natural systems to discover patterns and correlations. (ex: while using biochemical techniques to identify molecules in cells, you may observe that a certain protein is found in muscle cells but not neurons.)

30
Q

what is hypothesis driven science?

A

the development and verification of a hypothesis is the core of the scientific method and hence this system is often referred to as hypothesis driven science.

31
Q

what is the process of science?

A
  1. Problem/observation
  2. collection of background info
  3. state hypothesis
  4. state prediction
  5. test predictions
  6. draw conclusions
  7. report conclusions
32
Q

what are the four levels for protein structure and what are the bonds at each level?

A
  1. Primary: covalent, peptide
  2. secondary: hydrogen, peptide
  3. teriarty: hydrogen, ionic
  4. quaternary: several polypeptides
33
Q

what are enzymes?

A

organic catalysts that work by lowering the activation energy req. for a reaction to take place

34
Q

what is the enzyme we used in lab?

A

cytochrome c oxidase

35
Q

how do you measure a reaction rate?

A

x

36
Q

how to use pH probe?

A
  1. plug pH sensor into channel 1
  2. mix solution that is being measured by inverting 5-6 times
  3. remove pH sensor from storage bottle, rinse tip with distilled water, gently blot extra moisture w/ kimwipe (you dont want to add distilled water to the sample water, will not give accurate results)
  4. place tip of probe into unknown pH buffer, submerge sensor top to a depth of 3-4 cm. before collecting, allow pH to stabilize in new env,
  5. begin data collection by pressing play, collect for 10s. press stop
  6. analyze, statistics, select run, record avg.
  7. repeat
37
Q

what are descriptive statistics and what are they used for?

A

used to describe and summarize data. it includes measures of central tendency, dispersion, and distributions. (mean, median, mode)

38
Q

what are inferential statistics and what are they used for?

A

they are used to make estimates, draw conclusions, or inferences, about the population based on the sample. provides methods for generalizing the sample data to the larger population from which the sample was selected. (t-test

39
Q

what is a t-test and what are they possible conclusions that can be drawn with a t-test?

A

used to determine if the difference between the means of two samples is significantly different. t-test gives the p-value. if p-value is 0.05 there is a 5% probability the difference btwn the two means is due to chance, smaller the p-value, the more confident the difference btwn the two means is real and is statistically significant.

40
Q

what is the water quality index (WQI)?

A

created in 1970 by the National Sanitation Foundation, the water quality index is used for quantifying and tracking the quality of water sources. There are nine separate test parameters that are combined to determine if a water body is healthy!

41
Q

what are the nine parameters of the WQI?

A
  1. Temp
  2. pH
  3. Dissolved Oxygen
  4. Biochemical Oxygen Demand
  5. Total Solids
  6. Turbidity
  7. Nitrates
  8. Fecal Coliform
  9. Total Phosphate
42
Q

what is the fecal coliform test?

A

indicates whether sewage may be entering the system, the presence of coliform bacteria is a public health issue

43
Q

how does the WQI work?

A

each test parameter has a graph that represents the relationship btwn the measured parameter and its associated quality value. the graphs are used to convert the measurements to q-values that are expressed on a scale from 0-100. once the q-value is determined, it is multiplied by a weighing factor. each test parameter is weighted based on its relative importance to overall water quality. all nine weighted q-values are then added together to arrive at an overall water quality index score.

44
Q

what is a lotic source?

A

moving waters like a stream or river

45
Q

what is a lentic source?

A

a pond/lake

46
Q

what is point source pollution?

A

any contaminant that enters the environment from an easily identified and confined space

47
Q

what is nonpoint-source pollution?

A

generally results from many diffuse (general) sources such as runoff, precipitation, and atmospheric deposition. (as the runoff moves it picks up and carries away natural and man-made pollutants.

48
Q

what is temp and how does it affect WQI?

A

water temps outside of the normal range can harm aquatic organisms. generally the change in temp of the water over a section of a stream is measured. water temp can effect the solubility of gasses, more gas can be dissolved in cold water than warm. animals like salmon require high levels of DO and will only thrive in cold water. increased water temp can also increase the photosynthetic rate of plants which can lead to increased plant growth and algal blooms.

49
Q

what is pH and how does it affect WQI?

A

pH is a measure of relative concentrations of OH- and H+ ions in a solution. a change from pH 7 to pH 8 in a lake/stream reps a ten-fold increase in the OH- ion concentration. small changes in pH can endanger many kinds of plants and animals.

50
Q

what is DO and how does it affect WQI?

A

some organisms require high concentrations of DO, other can survive at lower. the diversity of organisms is greatest at higher DO concentrations. DO levels fluctuate throughout the day, so they should be performed at the same time each day. DO is measured in mg/L.

51
Q

what is percent saturation?

A

often used for water quality comparisons. It is the dissolved oxygen reading in mg/L divided by the 100_ DO value for water.

52
Q

what is biochemical oxygen demand and how does it affect WQI?

A

in healthy streams, oxygen is replenished faster than used by aquatic organisms. however, in water bodies, aerobic bacteria decompose such a large volume of organic material that oxygen is depleted from the stream faster than it can be replaced. The resulting decrease in DO is known as biochemical oxygen demand. if the amnt of decomposing organic material is too high, DO levels can be severely reduced and BOD levels will be high

53
Q

what is total solids and how does it affect WQI?

A

a measure of all suspended, colloidal, and dissolved solids in a sample of water including dissolved salts such as sodium chloride, and particles such as silt and plankton. high levels of total solids will reduce the clarity of the water.

54
Q

what is turbidity and how does it affect WQI?

A

a measure of a body of waters lack of clarity. water with high turbidity is cloudy, while water with low turbidity is clear.

55
Q

how to find dissolved oxygen levels?

A
  1. plug DO prove into channel 1 of the labquest
  2. unscrew the protective clear plastic case
  3. rinse the tip of the prove with water, gently dry w/ kimpwipe
  4. set the switch on the DO probe to collect data in % saturation
  5. submerge the probe tip in Nalgene bottle of sample water to a depth of 4-6cm, ensure that metal contacts on side of the probe are submerged, DO NOT DROP PROBE INTO NALGENE BOTTLE
  6. hold the probe in water for 40s to allow time for the automatic temp compensation. allow for the probe to stabilize reading before proceeding to the next step
  7. begin data collection and collect for 10s
  8. record avg data from 10s reading in appendix A
  9. once data collection is complete, rinse DO prove top with distilled water, dry with kimwipe, screw protective clear case when done.
56
Q

how to find BOD? (day 0 steps)

A
  1. use tape and label each BOD bottle with section, team, sample #
  2. fill each BOD bottle up to the neck of the bottle with sample water
  3. plug the DO probe into channel 1 of the labquest
  4. unscrew the protective clear plastic case, rinse tip of probe with water and gently dry with a kimpwipe
  5. set the switch on the DO probe to collect data in mg/L
  6. submerge the probe tip in the first BOD bottle to a depth of 4-6cm, ensuring that the metal contacts on the side of the probe are submerged
  7. hold the probe in the water for 40s to allow time for the automatic temp compensation
  8. begin data collection and collect data for at least 10s
  9. when the sampling run is complete, stop data collection
  10. determine the initial DO concentration by going to analyze, statistics, record avg mg/L in the BOD table in your data sheets packet under “initial DO”
  11. repeat steps 5-12 to measure the mg/L for the remaining 2 bottles
  12. at the end, rinse probe tip, blot dry with kimwipe, replace cap with damp sponge
  13. use water from nalgene bottle to bring water level to top of bottle, no air in bottle, replace the stopper
  14. place BOD bottles in a dark cabinet as directed by TA at abt 20C. the bottles should remain in the cabinet for one week until you are ready to perform the final DO measurement in the day 7 procedure below in the next lab meeting
57
Q

how to find BOD? (Day 7 steps)

A
  1. collect BOD bottles from storage
  2. measure the DO in mg/L for all 3 bottles, record the avg mg/L in the BOD table in your data sheets packed under “final DO”
  3. when all readings have been taken, rinse probe tip, blot dry with kimpwipe, replace cap with damp sponge, do not overtighten the cap
  4. wash and rinse BOD bottles. place each bottle upside down on the padded counter to dry properly
58
Q

why are BOD bottles black to block out all light?

A

to make sure no growth happens

59
Q

what are nitrates and why are they important?

A

nitrate ions found in freshwater result from a variety of natural and manmade sources. nitrates are an important source of nitrogen necessary for plants and animals to synthesize amino acids and proteins

60
Q

what is a fecal coliform bacteria test?

A

determines whether escherichia coli bacteria is in the water, E coli are types of bacteria that live in the intestinal tracts of animals and humans. e coli is a good sewage indication bc it is not normally present in water or soil, it is relatively easy to identify, and survives a little longer in water than other enteric bacteria. to see if high amnts of e coli are present, you observe the amount of gas (usually CO2) produced in a tube.

61
Q

how to prepare nitrate ISE…

A

nitrate ion selective electrode must be soaked in nitrate standard solution for 30 mins
1. attach probe clamp to support stand
2. carefully insert the nitrate ISE to the probe clamp, make sure it is setup vertically
3. raise clamp to allow room for rinsate beaker to be placed under the nitrate ISE probe
4. rinse nitrate ISE probe with distilled water squeeze bottle, blot dry with kimpwipe
5. uncap nitrate high standard. swap rinsate beaker for the nitrate high standard, placing the standard directly under the nitrate ISE
6. carefully lower the probe clamp so the white dot on nitrate ISE is submerged int he Nitrate high Standard, but not touching the bottom of the bottle
7. soak nitrate ISE in Nitrate High Standard for 30 mins

62
Q

how to take measurements using nitrate ISE…

A
  1. plug ISE sensor into channel 1 of labquest
  2. go to sensors, calibrate, nitrate ISE, calibrate now, while the ISE is in HIGH standard wait for “live voltage” reading and then enter 100 for value 1 and press keep
  3. remove nitrate ISE from the nitrate standard by raising probe clamp, swap nitrate high standard for rinsate beaker, rinse the ISE thoroughly with distilled water and gently blot it with kimpwipe
  4. swap out rinsate beaker for nitrate LOW standard, lower probe clamp until nitrate ISE is sumberged in low standard, wait for “live voltage” reading to stabalize, enter 1 for known value 2 and press Keep
  5. rinse ISE with distilled water and gently blot with kimwipe
  6. place tip of ISE into sample water in nalgene bottle, make sure ISE is not resting at bottom and the small white reference contacts are immersed
  7. leave probe sumberged for 60s before collecting data
  8. begin data collection for at least 10s
  9. go to analyze, statistics, record avg nitrate concentration
  10. CLEANUP: rinse probe with DI water and gently dry with kimwipe, make sure sponge at bottom of long term solution bottle is moist (use DI water if not), loosen lid of long term storage bottle and insert porbe, the tip should not be touching the sponge and the white junctions should be submerged, once positioned, tighten lid and return to proper drawer
63
Q

how to perform the fecal coliform bacteria test…

A
  1. set up 3 DSLB bottles and 6 SSLB bottles, use sharpie to label directly on each tube with section, team, and amnt of water dispensed
  2. invert SAMPLE water 4-5 times
  3. transfer 10mL of sample water to each DSLB tubes
  4. transfer 1mL of sample water to each of the middle set of three SSLB tubes
  5. transfer 100uL of sample water to the last three SSLB tubes
  6. return tubes to section rack, they will be incubated for 24hrs in 44.5C and then refrigerated.
64
Q

how to initiate a CFU assay…

A
  1. complete a serial dilutions table
  2. shake out 6 microfuge tubes and label 0-5 (DO NOT CONTAMINATE MICROFUGE CONTAINER)
  3. dispense STERILE water into each microfuge tube according to your calculations in table 4
  4. gently invert the 50mL conical tube with water sample A/B 5 times to resuspend all organisms in the water. Add 900 uL of pond/stream water to tube 0 per serial dilutions table and vortex tube 0.
  5. complete serial dilutions.
65
Q

what is DNA barcoding?

A

the use of specific DNA sequences to identify organisms to species level. In this technique DNA sequence provides a unique way to identify the species, much like UPC Barcodes on products in stores that are used to uniquely identify the product.

66
Q

what is agar?

A

a solid matrix of agarose and agaropectin that, with added nutrients, provides a growth medium for bacteria

67
Q

how do you convert phosphate into phosphorus?

A

biology 115 (Stern) (4 decks)

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