BIO LAB MIDTERM

Where does chemical waste get disposed of?

There are some chemicals you will use this semester that need to be disposed of in a specific waste container. This waste container will be stored in the hood.

What is an autoclave?

An autoclave is a machine that sterilizes whatever is put into it with high pressure, heat, an/or steam.

Where are bacteria plates and waste disposed of?

The bacteria plates and any gloves that were used to touch the bacteria plates should be thrown out in the medical waste bin.

What is an assay?

An assay is a tool used in science that helps to quantitatively measure the amount of a single part of a total sample.

How does a LabQuest 2 and Vernier work?

This system facilitates the collection of data by replacing chemical techniques, providing real time graphical presentations, and saving information directly in an electronic form.

What can affect the activity of proteins?

The activity of proteins is very often dependent on the pH, salt concentrations, and temperature of the reaction mixture.

What is a buffer?

an aqueous solution mixture, function to resist changes in hydrogen ion concentration

What is stock solution?

concentrate solution that last over a long. period of time

What is the dilution factor?

factor by which the concentration of the dilute solution is reduced compared to the concentration of the stock solution

How do you calculate the dilution factor?

DF \= C1/C2 \= V2/V1

What is a serial dilution?

a stepwise dilution where the stock solution for each dilution in the series is the dilute solution from the previous dilution.

What is the total dilution factor?

the product of the dilution factors for each dilution step.

What is a spectrophotometer?

A machine that can measure absorbance or transmittance of a pigmented solution and biologists commonly us them to quantify the concentration of materials in a solution.

How does a spectrophotometer work?

This instrument produces a beam of light with a specific wavelength that passes through the sample before entering a photometer that measure the amount of light. This measurement is transformed electronically to a reading on a meter quantifying the amount of light absorbed.

What is important about the absorbance and concentration of a sample?

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

Why are standard used?

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

What is another way to determine the concentration of an unknown sample?

Making a standard curve.

What is a standard curve?

a tool that scientists use to determine the unknown concentration of a sample.

How is a standard curve generated?

by measuring the absorbance of a series of standards and graphing the absorbance as a function of concentration. The unknown concentration of a sample can be determined by the interpolation on the graph.

What is the blank?

a sample that is used to calibrate zero absorbance on the spectrophotometer.

What is a cuvette?

a small tube used to hold samples for measurements with a spectrophotometer.

How far must the cuvette be filled to obtain an accurate measurement with the SpectroVis?

at least 1 ml.

What is linear regression?

a statistical method for modeling the relationship between two variables, x and y.

What is a linear trendline?

A straight line is best fit to the data points by minimizing the deviation of the data points from the line.

What is the R-squared value?

how well the trendline fits

What is discovery science?

Discovery science used large amounts of data or surveys of natural systems to discover patterns and correlations. Discovery science may be considered as the first step of hypothesis-driven science.

What is hypothesis-driven science?

Hypothesis-driven science utilizes what is generally referred to as the scientific method, a series of steps a scientist uses to develop knowledge.

What is a hypothesis?

When a patten is identified a scientist desires to understand its cause. A statement that purports to explains the cause of a pattern or relationship is a scientific hypothesis.

What are the steps of the scientific method?

1. The problem or observation
2. Collection of background information
3. State the hypothesis using inductive reasoning
4. State predictions using deductive reasoning
5. Test predictions
6. Draw conclusions
7. Report conclusions

What happens if even one prediction is wrong?

Logically there is something wrong with the hypothesis. For the hypothesis to be accepted none of the predictions can be incorrect.

What happens if all of the predictions are right?

The hypothesis is likely to be correct, however, it has not been proven correct.

Can a hypothesis ever really be proven?

The never-ending possibility of additional new predictions that could be incorrect means that hypotheses can never be proven.

What three variables must be considered in experimental design?

the independent variable, the dependent variable, and the controlled variable.

What is the independent variable?

The parameter that is changed by the researcher.

What is the dependent variable?

The parameter that responds to changes in the independent variable and is the variable that is measured by the researcher.

What is the controlled variable?

Other factors that can affect the dependent variable and, thus, must be kept constant (or controlled) by the researcher so that only the effect of the independent variable is measured.

What two kinds of groups are needed in a controlled experiment?

An experimental group and a control group.

What is an experimental group.

the group in which the independent variable is added and/or changed.

What is a control group?

the group in which the independent variable is either not included or is kept constant in its natural state.

What is qualitative data?

Qualitative data is descriptive rather than a measure. Qualitative data is not numerical; to describes a character state but does not provide a precise measure of that character state. Qualitative data is not conducive to statistical analyses.

What is quantitative data?

Numerical, often a measure like weight, height, distance, or a count of occurrence. Quantitative data are precise and unambiguous. Most importantly, scientists can use statistics to analyze differences between groups

What are the levels of protein structure?

Primary, seconday, tertiary, and quaternary.

Primary

covalent bonds

Secondary

hydrogen bonds

Tertiary

hydrogen bonds not at R groups

Quaternary

Van der Waals

What are enzymes?

organic catalysts that work by lowering the activation energy required for a reaction to take place. The enzyme binds to a substrate.

What is a substrate?

the substance that enzyme acts on. The substrate binds to a region on the enzyme called the active site to form the enzyme-substrate complex.

What is temperature?

the average kinetic energy of the particles, regardless of volume.

Why is pH important to enzymes?

pH affects how a solution will act.

What is Cytochrome C oxidase?

an oxidase capable of converting reduced cytochrome c to oxidized cytochrome c.

What is an oxidase?

an enzyme that catalyzes the removal of electrons from other molecules.

What color is cytochrome c? (Substrate)

pink

What color is OXIDIZED cytochrome c? (Products)

dark red

How do you calculate the rate of reaction?

|Absorbance final - Absorbance initial| / |Time final - Time initial|

What are measures of dispersion?

numerical summaries that describe the variability, or spread, of the values in the data set. Three measure include the range, variance, and standard deviation.

What are the standard deviations and variance?

both describe the variability in the data with respect to the mean and include all value in the data set. they increase as the dispersion in the data gets larger.

What is a normal distribution function?

symmetrical around the mean, and the median and mean are equal.

What is inferential statistics?

used to make estimates and draw conclusions, or inferences, about the population based on the sample. can also be used to compare two groups and draw conclusions about observed differences between them.

What is a t-test?

difference between the means of two samples is significantly different.

What is a p-value?

the probability that the means difference occurred strictly by chance.

What are some effects temp can have on water quality?

More gas can be dissolved in cold water than in warm water, so animals that require high levels of dissolved oxygen can only thrive in cold water.

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Increased temp can also increase the photosynthetic rate leading to increased plant growth and algal blooms, which can harm the local ecosystem.

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When the temp becomes too hot or too cold organisms become stressed, lowering their resistance to pollutants, diseases, and parasites.

What are some reasons the water temp will rise.

Thermal pollution

Runoff is usually warmer than the water,

Shade and the removal of shade by humans, the temp of the air above the water. The influence has a lot to do with the depth of the water.

What can cause changes in the pH of water?

Algal blooms (more basic), industrial processes resulting in the release of bases or acids (raising or lowering pH), or the oxidation of sulfide containing sediments (more acidic). Rainfall can be slightly acidic.

What is the primary contributor to total solids in rivers and streams?

siltation

What are factors of total solids?

soil erosion, naturally occurring rocks or minerals in the soil such as halite, NaCl, or limestone, CaCO3, various types of runoff, industrial wastes, effluent from water treatment plants, and urban runoff. Bottom-dwelling aquatic organisms stir up the sediment that has built up on the bottom of the stream. Organic matter such as plankton or decaying plant and animal matter.

What affect can total solids have on WQI?

if they are too high or too low it can impact the health of the stream and the organisms that live there. Reduces the clarity of the water, which decreases the amount of sunlight able to penetrate the water and decreases the photosynthetic rate. Cloudy water warms faster.

What affect does DO have on the diversity of organisms?

The diversity of organisms is greatest at higher DO concentrations.

How is oxygen gas dissolved?

diffusion between the atmosphere and water at its surface, aeration as water flows over rocks and other debris, churning of water by waves and wind, and photosynthesis of aquatic plants.

What factors affect DO?

temp, stream flow, air pressure, aquatic plants, decaying organic matter, and human activities.

What could be the cause of large fluctuations in DO over the a short time period?

Algal blooms. Following an algal bloom oxygen levels can be so low that fish and other aquatic organisms suffocate and die.

What happens in a healthy stream with oxygen?

oxygen is replenished faster than it is used by aquatic organisms.

What causes this cloudiness (turbidity)?

light reflecting off of particles in the water; therefore, the more particles in the water, the higher the turbidity.

What can contribute to turbidity?

an increase in stream flow due to heavy rains or a decrease in stream-bank vegetation can speed up the process of soil erosion, runoff, bottom dwellers.

What affect can turbidity have?

high turbidity will decrease the amount of sunlight able to penetrate the water, decreasing the photosynthetic rate; the water will warm faster.

Why are nitrates important in water?

Nitrates are an important source of nitrogen necessary for plants and animals to synthesize amino acids and proteins.

What manmade sources can raise the concentration of nitrates in the water?

animal feedlots, runoff from fertilized fields, or treated municipal wastewater being returned to streams.

What are total phosphates?

condensed + orthphosphates + organically bound

How are phosphates added to the water?

through industrial and agricultural wastes, fertilizers enter through runoff and soil erosion, and from excrement of animals living in or near the water.

What do fecal coliform bacteria tests test for?

It tests for intestinal E. Coli and other coliform bacteria.

What are coliform bacteria?

they are facultative anaerobes that ferment lactose to produce gas.

How does E. coli get into the water?

leaking septic or sewer systems, polluted runoff that has picked up animal waste en route to the stream, waterfowl in the stream, or wading cows.

What is DNA barcoding?

Sequencing a short stretch of DNA. The DNA provides a unique way to identify the species, much like UPC barcodes on products in stores that are used to uniquely identify the product.

What is agar?

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

What is direct amplification?

when the specific DNA fragments are amplified.

What is the second step in barcoding?

purifying the DNA from the tissue, removing the proteins, RNA, and other cellular components before PCR. So, in other words, isolating the DNA.

PCR VS Gel Electrophoresis

PCR copies, Gel separates DNA so its easier to visualize

What is a conserved region of DNA?

a nucleotide sequence that has little to no variation across species.

What marker is used for animal samples?

COI gene

What marker is used for plant samples?

rbCL gene

What marker is used for bacteria samples?

Since bacteria do not have mitochondria and chloroplasts another gene is used as a DNA barcode marker. The 16S rRNA gene that codes for the 16S ribosomal RNA that is part of the bacteria ribosome complex is used. It should generate around a 1500 bp fragment.

What is a master mix?

Instead of adding each reagent individually to each sample, you can make a PCR master mix.

What does the master mix consist of?

It consists of DNA polymerase, dNTPs, forward and reverse primers, and water in the quantity needed to perform multiple PCR reactions for a given primer set.

What are the benefits of using a master mix?

Help reduce pipetting errors and time spent running the reaction.

What is added to the sample after the master mix is added?

An aliquot

What is an aliquot?

a small portion of genomic DNA or bacterial to the PCR tube with the appropriate primer set.

What does spot plating do?

spot plating of serial dilutions allows for the direct count of CFUs through the number of colonies found growing in the spots.

What is gel electrophoresis?

the standard method used to separate, identify, and purify DNA fragments.

Describe the net negative charge.

the phosphate groups on the DNA backbone confer a net negative charge on the molecule.

Describe gel electrophoresis.

DNA moves through the gel it must "snake" through the agarose, fitting through the pores.