Biology 241: Lab Final Study Guide

what is hypothesis?

Lab 1: Introduction to scientific investigation

∙ Hypothesis: Possible answer for question being asked

∙ Null hypothesis (Ho): hypothesis to be tested. It is assumed the null  hypothesis will have no effect

∙ Alternate hypothesis (HA): Once null hypothesis is rejected, alternate  hypothesis is created, which states there is a significant difference  between experimental and control

∙ Independent variable: variable being manipulated in the experiment. ∙ Dependent variable: factor which responds to chance in the  independent variable.

∙ Experimental treatment: Examines the effect of the independent  variable on the dependent variable

∙ Control treatment: examines the effect of other facts besides the  dependent variable

∙ Constants: The factors in an experiment that must remain the same.  These include everything but the manipulated variable

what is Spectrophotometer?

∙ Calculating sample mean

o Sample mean is calculated by the sum of the individual  measurements in a treatment, divided by the number of  

measurements in a treatment

o xx̅ = ∑xi / n 

 xx̅ = sample mean 

 ∑ = Sum of 

 xi = Individual measurements in a treatment 

 n = Number of treatments 

∙ Calculating variance in data

o Found by calculating standard error of the mean (SEM) o SEM = √∑( xx̅ - x)2 / n(n-1) 

o The larger the SEM, the less confident we can be that data is an  accurate representation of a population

o If 2 SEM bars overlap, means are not different

o If 2 SEM bars do not overlap, means can be said to be different ∙ 2 kinds of graphs that can be used

o Line graphs: Used when data on x-axis is numerical and  continuous

o Bar graphs: Used when x-axis variable is non-numerical or  discontinuous

what is the process where green plants, algae and certain bacteria covert light energy and CO2 into chemical energy?

We also discuss several other topics like Why did Roman Women have so much power in the Principate formation and early Principate?

∙ Parts of a microscope

o Ocular lens: what you look through. Provides 10x magnification

o Revolving nose piece: part that holds the other magnifications  (4x, 10x, 40x, 100x)

o Objective lens: attached to nose piece, they are the increased  magnifications (4x, 10x, 40x, 100x)

o Stage clips: secure the slide

o Stage: holds the slide

o Iris diaphragm lever: regulates amount of light coming through o Condenser lens: gathers and focuses light on specimen o Light intensity control knob: makes light dimmer or brighter o Stage control knobs: moves stage around

o Coarse adjustment knob: Raises stage significantly

o Fine adjustment knob: Allows you to finish focusing on specimen ∙ Calculating magnification

o Multiple the ocular lens (10x magnification) by the objective lens  you used (either 4x, 10x, 40x, 100x)

∙ Measuring a specimen

o Use ocular micrometer in left ocular as a ruler

o Count number of units specimen occupies and multiply by  calibration factor of objective lens being used (this converts it to  metric units) If you want to learn more check out what is natural monopoly?
If you want to learn more check out What planets in our solar system have liquid water at the surface today?

 For the 10x objective lens, 1 ocular division = 10 µm 

 For the 40x objective lens, 1 ocular division = 2.5 µm 

 For the 100x objective lens, 1 ocular division = 1 µm 

o Example: if you measure a specimen using 40x objective lens,  and it takes up 5 ocular divisions, multiple 5 by 2.5 µm = 12.5  µm 

∙ Drawing diagrams to scale

o Draw with pencil, no shading

o Label parts of the structure observed, drawing lines from  structure to labels (do not write labels on diagram)

o Draw scale bar below structure indicating length in µm units o Below diagram, write detailed title and total magnification  specimen was observed at

o Indicate magnification of drawing by dividing size of drawing by  actual size of object

Lab 2: Enzymes – Part 1

∙ Enzymes: catalyst that increases reaction rate by lowering activation  energy for a reaction to occur  

o Through process of induced fit, the enzyme changes the  substrate, allowing it to turn into product

o Enzyme is unchanged after reaction, and not consumed

∙ Enzyme-catalyzed reaction: rate of reaction depends on concentration  of enzyme & substrate, the Ph, or compounds that alter enzyme  activity

∙ Enzyme kinetics: Studying how fast enzyme converts substrate to  products

∙ Enzyme activity: Rate or velocity of reaction catalyzed by enzyme o To measure this, measure this, combine substrate and enzyme,  then measure either increase in product of decrease in substrate ∙ Spectrophotometer: Measures light absorbed by solution, relative to  light passing through

∙ Standard curve: used to determine concentration of pigment in  solution. We are given absorbance, then use standard curve to turn  that value into a concentration. If you want to learn more check out what type of market in which a small number of interdependent firms compete behind a barrier to entry?

o measure the absorbance of solutions of known concentrations by preparing a series of dilutions of a stock solution

o plot the absorbance values as a function of concentration to  obtain a standard curve  

o use standard curve to convert absorbance of sample solutions to  concentration

∙ Micropipetors: Used to measure small quantities accurately. One  measures 10 - 100 µm, another measures 100 – 1000 µm (the one we  used) 

o 0.1 Ml = 100 µm 

o 1.0ML = 1000 µm 

∙ Dilutions: made by pipetting volume of undiluted solution into volume  of liquid (diluent)

o Dilution = volume of original sample / (volume of original sample + diluent)

∙ Concentraton of diluted sample (CD) 

o Cd = Cu x D

o Cd = Concentration of Diluted sample If you want to learn more check out what is the difference between dulusion a hallucination?
We also discuss several other topics like Just Price is a Theory of what?

o Cu = Concentration of undiluted (original) sample

o D = dilution

∙ Key points from Lab 2

o We needed to use an artificial substrate which was pigmented,  which allowed us to measure absorbance

o We measured absorbance at different times, of different  dilutions, this allowed us to determine how effective the enzyme  was at catalyzing the reaction

o An alkaline solution needed to be added to stop the reaction o We needed to use a blank solution between each measurement  to account for absorbance other than that of the desired product

(blanks are made with all components other than that being  measured)

Lab 3: Enzymes – Part 2

 ∙     Vmax: maximum rate of reaction for given enzyme and substrate o At Vmax, all enzyme molecules complexed with substrate  molecules, addition of more substrate will not speed up reaction  ∙     Km: substrate concentration when reaction is at half its maximum  value

 ∙     Competitive inhibitor: similar in shape to enzyme substrate, so  compete with substrate to bind to active site

 ∙     Non-competitive inhibitors: don’t compete with substrate for active  site, bind with other part of enzyme

∙ Key points from Lab 3

o Lineweaver-Burk plots are more accurate than Michaelis-menton  plots, since Vmax is an asymptote in the Michaelis-menton plot.  If you use an equation for the Lineweaver Burk plot you get more accurate Vmax and Km

o Vmax for non-inhibited enzymes are higher than those of  inhibited enzymes

Lab 4: Eutrophication

∙ Oligotrophic: healthy ecosystem with low amount of dissolved nutrients ∙ Eutrophic: high dissolved nutrients. Unhealthy ecosystem, this is an  undesirable state for it to be in.

∙ Eutrophication: the process where a body of water is enriched in  nutrients from terrestrial ecosystems (this can also happen through  natural process’s)

∙ Phytoplankton: foundation of most aquatic food webs, and grow rapidly with increased available nutrients

∙ Zooplankton: feed on phytoplankton

∙ Bacopa: Aquatic plants (the ones we used in the lower chamber) ∙ Brassica rapa: The terrestrial plants we planted in the upper chamber ∙ Key points from lab 4

o We created a microcosm to represent the effect of eutrophication on aquatic ecosystems.

o Bacopa, zooplankton, and phytoplankton were added to the  lower chamber, so they could interact as in a regular ecosystem o Brassica rapa were planted in the upper chamber

o Over 3 weeks, fertilizer would be sprayed over the upper  chamber, which would allow us to see the effect of  

eutrophication on all the elements in the microcosm

Lab 5: Fermentation & Biofuels

∙ Biofuel: Fuel derived directly from living matter, which uses  photosynthesis

∙ Fermentation: Occurs in the absence of oxygen

∙ 2 major pathways of fermentation: 

o Lactic acid fermentation

 Occurs in animals and bacteria

 Pyruvate turns into lactic acid and NAD+ 

o Ethanol fermentation

 Occurs in plants and fungi

 Pyruvate releases CO2 to make acetaldehyde

 Electrons from NADH go to acetaldehyde to make ethanol  and NAD+ 

 ∙     Promising biofuel resources 

o First generation biofuels:  

 Corn, wheat, potatoes

 “food for fuel” argument. Using land that can be put  

towards food instead

o Second generation biofuels

 Fast growing woody plants

 Need less fertilizer, can be grown on unusable land

o Third generation biofuels

 Algae cells

 Take up way less land, grow in wastelands, fed with waste  gas

∙    Key points in lab 5

o Sugar beets produced the most CO2, meaning they were the most promising biofuel. Sugar beats main source of carbohydrates are  sucrose

o After our control, straw produced the least amount of CO2 so it  was the least promising biofuel. Straws main source of  

carbohydrates are cellulose

o Simple carbohydrates are better biofuels since they don’t need  to be broken down before fermenting, or at least not as much. o A drawback of ethanol is its high productions of CO2

o Drawbacks of biofuels

 Large amount of land must be dedicated to them, which  could be used for food instead

 Preparing land for biofuels consumes a large amount of CO2  Requires lots of fertilizer, which leads to erosion

Lab 6: Photosynthesis

∙ Photosynthesis is the process where green plants, algae, and certain  bacteria convert light energy and CO2 into chemical energy ∙ The hill reaction:

o The hill reaction produces oxygen when exposed to light and in  the presence of water and electrons. It reduces an electron  acceptor. Since it requires an input of light, it occurs during the  light-dependent process of photosynthesis, so it occurs in the  thylakoid membrane 

∙ Photolysis: light splitting

∙ The oxygen from photosynthesis comes from the splitting of water ∙ Key points from lab 6

o Our buffer contained chloroplast solution, buffer, and distilled  water. It did not contain DCPIP, as DCPIP was the independent  variable.

o Our light constant was chloroplast solution, DCPIP, and buffer o Our dark constant was chloroplast solution, DCPIP, and buffer,  but it was covered in tinfoil while the reaction took place.  

o The last 3 tests we did were to measure the effect of an inhibitor  ( DCMU) at different concentrations on the hill reaction.  o We can use DCPIP to study the hill reaction since it is a stronger  oxidizing agent than NADP+, and replaces it as the oxidizing  agent in light dependent reactions. It is pigmented, unlike  NADP+, so we can measure absorbance

Lab 7: Harvesting Microbiomes

∙ Measuring chlorophyll content of pond water

o We poured the pond water over filter paper, and used the filter to measure chlorophyll content

o After mixing the filter with ethanol and centrifuging, we used the  solute and calculated the absorbance

o Chlorophyll content was calculated with an equation given o With the chlorophyll content calculated, we could estimate the  population of phytoplankton in the water

∙ Measuring zooplankton population

o We mixed some pond water with iodine to kill the zooplankton,  so we could count them under the microscope

∙ Harvesting aquatic plants

o We plotted the plants dry and weighed them to obtain biomass ∙ Terrestrial plants

o We cut the plants and measured their height

∙ Chlorophyll in terrestrial plants

o After cutting a circle from a leaf, we mixed it with ethanol and  ground it up. Then centrifuged

o We used equation to calculate chlorophyll content after obtaining absorbance

∙ We also obtained ammonium and phosphate concentration from pond  water

Lab 8: Presentations  

∙ Eutrophication on terrestrial plants

o With added fertilizer, shoot height started to increase. After a  certain amount of fertilizer was added it became detrimental to  plant growth and shoot height decreased

o Chlorophyll content followed the same pattern as shoot height.  Initially there was an increase in chlorophyll content, but once it  reached a certain point it started to decrease

o If there is a nitrogen deficiency, the leaves will be less green ∙ Eutrophication on aquatic plants

o The limiting factors of plant growth are sunshine, lack of oxygen,  and lack of nutrients

o Biomass increased, which allowed greater food availability for  other organisms

∙ Eutrophication on phytoplankton

o Phytoplankton increased to a point until it plateaued  

o Eutrophication leads to large population growth in phytoplankton, which can have detrimental effects on the rest of the ecosystem o An algal bloom is extreme growth in algae in an aquatic  ecosystem, which deprives other organisms of sunlight, produces gross amounts of CO2 when they die, and can lead to anoxic  environments with a very small amount of oxygen

∙ Eutrophication of zooplankton

o As fertilizer increased, Tetrahymena decreased

∙ Effect of eutrophication on nitrogen

o Nitrogen can be difficult to obtain in usable forms, and is  important for growth and reproduction

o It cycles between terrestrial and aquatic ecosystems

o Stimulates growth of algae and aquatic plants

o Humans input nitrogen from fertilizer

∙ Eutrophication on P levels

o P is deposited in soil from rocks and fertilizer, and is essential to  all living organisms

o It is an important indicator of health of an ecosystem

o Terrestrial plants consume P through diffusion through roots,  while aquatic organisms absorb it through their surroundings.

Lab 9: SimBio Virtual Lab: Isle Royale

∙ Population ecology: study of changes in the size and composition of  populations and factors that cause those changes

∙ Rmax: population increasing at its maximum per capita rate. Also  known as intrinsic rate of increase

∙ Dn/dt: instantaneous change

∙ K: carrying capacity. Max number of individuals of a certain species  that local environment can support

∙ Exponential growth: when population is small, it increases slowly, but it quickly increases more and more as population expands ∙ Logistic population growth: a more realistic model of population  growth, since it shows the exponential increase and then levels off at  the carrying capacity

∙ Limiting factors of population growth

o Predation

o Food availability

o Competition over resources

∙ Key points from lab 9

o A population is at its healthiest when there is abundant food, and their population is being controlled. Predators attack the weak,  old, young, or ill animals, which leaves the healthiest ones to  maintain the population

o Predatory/prey populations fluctuate based on the amount in  each

o Even if a certain number of animals are added or taken away, the population will eventually return to its carrying capacity, since  that is the amount the environment can support