Bio lab midterm (background Information)

sig figs (ph)

individual measurements are reported with 3 sig figs

sig figs (even number before 5)

stays the same

sig figs (odd number before 5)

round up

mega

one million

mega

10^6

kilo

one thousand

kilo

10³

milli

one thousandth

milli

10^-3

micro

one millionth

micro

10^-6

nano

one billionth

nano

10^-9

pico

one-trillionth

pico

10^-12

P-20 pipette

2-20uL

P-200 pipette

20-200 uL

P-1000

100-1000 uL

sterile technique

aseptic technique

percent error

buffer

an aqueos solution containing a specific mixture of salts, buffering agents, and reducing agents, detergents, or cofactors. optimize reaction

basic function of buffer

resist changes in hydrogen ion concentration

stock solutions are diluted with

water

using stock solutions is beneficial because

save time, reduce storage space, and improve accuracy

X factor (ex. 5X, 10X)

5X concentrated solution will be diluted 5-fold

equation to make a specific volume of a dilute solution from a stock solution

C1V1=C2V2

C1

concentration of stock solution

C2

final concentration of dilute solution

V1

volume of stock solution needed to make a dilute solution

V2

final volume of dilute solution

Dilution factor (DF)

the concentration of the dilute solution is reduced compared to the concentration of the stock solution

DF equation

C1/C2=V2/V1

standard curve

is a graph that shows the relationship between the concentration of a substance and its corresponding absorbance

discovery science

uses large amounts of data or surveys of natural systems to discover patterns or correlations

hypothesis driven science

scientific method

scientific method (step 1)

the problem or observation

scientific method (step 2)

collection of background information

scientific method (step 3)

state the hypothesis

scientific method (step 4)

state predictions

scientific method (step 5)

Test predictions

scientific method *step 6)

draw conclusions

scientific method final step

report conclusions

for a hypothesis to be supported

none of the predictions can be incorrect

if the predictions are correct

then hypothesis is supported and likely to be correct, it has not been proven correct

controlled experiment

three variables independent, dependent, and controlled)

independent variable

parameter that is changed by the researcher

The dependent variable

is a parameter that responded to the changes in the independent variable and is the variable measured by the researcher

controlled variables

other factors that can affect the depended variable and thus should be kept constant or controlled by the researcher

experimental group

the independent variable is added and or changed

control group

independent variable is either not included or kept constant in its natural state

example: fertilizer with increase in growth rate of tomato plants (independent)

fertilizer concentration

example: fertilizer with increase in growth rate of tomato plants (dependent)

growth rate

example: fertilizer with increase in growth rate of tomato plants (control)

amount of water, soil, water, temperature

example: fertilizer with increase in growth rate of tomato plants (control group)

no fertilizer

example: fertilizer with increase in growth rate of tomato plants (experimental group)

fertilizer of different concentrations

p-value greater than 0.05

not significant

p-value less than 0.05

significant

9 parameters to test Water Quality

temperature, pH, DO, BOD, TS, Turbidity, Nitrates, Fecal Coliform, and Total Phosphate

Fecal coliform test

is about whether or not sewerage may be entering the system.

The presence of fecal coliform means

there is bacteria in the water

lotic sources

moving water like a stream

lentic sources

pond or lake still water

non-point source pollution

generates from runoff, acid rain, and atmospheric disposition. caused by rainfall or snowmelt

increased water temperature

increase the photosynthetic rate of aquatic plants ad algae leading to plant growth and algal blooms (harm ecosystem)

changes in Ph can happen due to

algal blooms, industrial processes resulting in a release of bases or acids, or the oxidation go sediments

streams and lakes have a pH of

7 to 8 sometimes 8.5

capstone project is an example of

hypothesis driven sciee

nitrates are important for plant and animals

to synthesize amino acids and proteins

nitrogen is found

in the atmosphere in the form go Nitrogen gas through a process called nitrogen cycle

major source of nitrate pollution is

livestock in feedlots, fertilizer runoff

Eutrophication

a process by which nutrients particularly phosphorus and nitrogen become highly concentrated in a body of water leaded to increased growth of organisms such as algae or cyanobacteria

most common fecal coliform

Escherichia coli

feacal coliform is a type of bacteria that

lives in the intestinal tracts of animals and humans. their presence indicated that other pathogens of fecal orginins like viruses and parasites may be present

High E. coli levels happen from

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

coliform bacteria

facultative aerobes that can tolerate oxygen but can survive without it that ferment lactose to produce gas

phosphorus

limiting factor in plant and algal growth

excess phosphorus can lead to

eutrophication

eutrophication can

lower levels of DO in water

High level of phosphate

increased BOD and decreased DO

DNA barcoding

the use of specific DNA sequences DNA markers and genes to identify organisms to species level

DNA barcoding is a technique

that determines the taxonomic identity of biological specimens using DNA sequences

DNa barcodin

helps to identify to a species level

General DNA barcoding process

collect sample,extraction from samples, barcodes are amplified by PCR using taxa specific primers, visualized via agarose gel electrophoresis, and DNA sequenced, then BLASTn, identify specimen

DNA barcoding process for bacteria

collect water/ bacteria sample, barcodes are direct amplified by PCR (16S rRNA), visualized via agarose gel electrophoresis, and DNA sequenced, then BLASTn, identify specimen

PCR is used

to amplify specific fragment of DNA from a complex mixture of DNA

PCR steps

denaturation at 95 degrees C, then primer annealing drops temp to 50 degrees C, Synthesis temp raised to 72 C allows Taq polymerase to work

PCR uses

DNA polymerase, dNTPS, taq polymerase, primers,

master mix

helps reduce pipetting errors and time to set up reaction

positive control

known sample of DNA and it is used to show that the primers and PCR conditions successfully amplify the DNA barcode fragment

negative control

sample without DNA and it is used to show no contamination of the basic PCR.

Agragrose gel electrophoresis

separate based on size , identify, and purify DNA fragments

the phosphate groups on the DNA backbone confer a

net negative charge on the molecule

if a solution of DNA is placed into an electric field

DNa molecules will migrate towards the positevely charged electrode

setting up agragrose gel

agarose is melted in a buffer and then cooled in a casting tray to form a jello consistency, then place I plastic combs to create wells, hardenend gel then palced into a box with electrodes and covered in buffer.

loading dye consists of g

lycerol and two tracking dyes xylene cyan and bromophenol blue

glycerol is dense

so DNA samples will sink to the bottom of the wells

the two tracking dyes allow for

monitoring how far the DNA has migrated in the gel