Biology 1208 Final Study Guide

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1 * If there are any mistakes, fix them! * Laboratory Safety: Always wear closed-toed shoes (Sandals are NOT acceptable footwear) Long hair should be tied back to keep it out of your eyes and away from anything that could result in harm Food and drinks may never be brought into the laboratory Always wash hands prior to and immediately after leaving the laboratory Cell phones on silent and put away Never return materials to the stock containers Broken glassware goes in the broken glassware container All sharps (small sharp glass, metal or plastic objects e.g., coverslips, razor blades) must be placed in the Sharps Containers located in each room All gloves, swabs, and disposable pipettes that may have contacted blood, bacteria, etc in a disposable autoclave bag (biohazard bag) Glassware that has come in contact with biohazardous material (e.g., blood) should be rinsed with a 10% bleach solution and placed in location designated by your lab instructor. Always assume hot plates are hot Eyewash: eyewash is located in preparation room adjacent to the lab. Turn on cold-water faucet, and then pull the knob located in the center of the eyewash unit. Hold your eye or eyes open and place them in the stream(s) of water. The wash should be continued for a minimum of 15 minutes and then you should go immediately to the student health center Fire Extinguisher: the first extinguisher, fire blanket, and first aid kit are located along the rear wall of the laboratory. Pipettes: Mechanical Pipettes, or micropipettes, are used for very small transfers (i.e., less than 1 ml) where a high degree of precision is required They come in several sizes. Depending on the size, different color-coded disposable tips are used. The three most common ranges are 1-20uL(yellow tips), uL(yellow tips), and uL (blue tips) Volumetric Pipettes are designed to deliver a single precise volume. The volume of the pipette is indicated near the top of the pipette. Graduated Pipettes: You should try to use the pipette that is just big enough for the volume you are going to transfer. For example, if the volume you need to transfer were 1.5 ml, the best pipette to accomplish this with the highest accuracy would be a 2mL pipette (not a 1 ml or 5mL or larger). o Mohr: The gradation markings on the Mohr pipette do not go all the way to the tip of the pipette but stop before the pipette begins to narrow.

2 Spectrometer: o Serological Pipette: are graduated to deliver (there is no base mark). The appropriate amount of fluid is drawn into the pipette and the entire amount is transferred. o Pi-Pump: Blue for pipettes up to 2mL and green for 5 or 10mL pipettes As the concentration of a substance in solution increases, the amount of light absorbed by the solution increases. We can use a spectrophotometer to measure the concentration of CoCl2 in a solution as a function of the absorbance Enzymes: A catalyst increases the rate of a chemical reaction without being consumed or changed during the process It reduced the activation energy between the reactants and products The chemical reactions that are part of life are made by organic catalysts, known as enzymes Typically, a single enzyme molecule will catalyze only one type of chemical reaction Most enzymes are proteins (hence, NOT ALL) Enzyme Lab Specific Background: Catechol to benzoquinone Catechol + 1/2O 2 à Benzoquinone o Enzyme is called catechol oxidase Enzymes are typically given the suffix ase and named for the reaction they catalyze Catechol is colorless and benzoquinone is a yellowish-brown substance First lab is to determine the rate of the reaction by observing the increase in the product over time According to the induced-fit model of substrate binding to an enzyme, the enzyme undergoes a change in its three dimensional structure during substrate binding. Note: As concentration increases, absorbance increases and transmittance decreases The relative color intensity of the solution in our experiment s reaction tubes is a consequence of production of Benzoquinone, an indicator of enzyme activity, and may differ depending on the ph, temperature, or the concentration of the substrate Note: BOTH shape of the enzyme and the shape of the substrate are important

3 Scientific Method Part II Kinetics: o Generally speaking, you should only manipulate ONE variable in an experiment o Know about dependent, independent, control variables, and replicates o Also know about null and alternative hypothesis Movement of Material Across the Cell Membrane I: Membranes allow cells and organism to control their internal chemical environment Biological membranes are typically comprised of phospholipid bilayers Hydrophilic head (polar)- these charges heads interact with polar water Hydrophobic nonpolar tails The phospholipid bilayers of biological membranes have protein molecules (both integral and peripheral) associated with their structure. The membrane is selectively permeable (some things can cross, some things can t) Water (polar) is able to cross the phospholipid bilayer because of its small size o These molecules are moving across the membranes at all times The force causing this net movement of water is a change in the free energy of the water molecules. Water can move in these ways: o Lower solute concentration to Higher solute concentration Higher free energy of water to lower free energy of water Higher water potential to lower water potential Higher water concentration to lower water concentration Lower osmotic concentration to higher osmotic concentration Higher osmotic potential to lower osmotic potential Lower osmotic pressure to higher osmotic pressure Note: the increased organization, or decreased disorder has a higher free energy When other material is put in solution this material disrupts the pattern of the water molecules thereby increasing the disorder of the water molecules and consequently, then there will be a decrease in organization or free energy o Osmosis: Osmosis results in a net movement of water from a solution that has a lower osmotic concentration to a solution that has a higher osmotic concentration o Red Blood Cells: RBCs placed in a hypotonic solution (water) will rapidly swell and rupture (hemolysis) RBCs placed in a hypertonic solution (salt water) will rapidly shrink and crenate

4 IMPORTANT NOTE: The amount of time that it takes for hemolysis or crenation to occur is directly related to the rate of osmosis across the cell membrane Movement Across the Cell Membrane: If the potato cells decreased in mass what was lost from the cells? o Water Red blood cells (RBCs) placed in a hypotonic solution (water) will hemolyze Why does it take glycerol longer to cause hemolysis than propanol? o Glycerol is larger than propanol and glycerol is more polar than propanol The excess water can introduce error in the measurements Certain molecules have difficulty crossing from one side to the other of cellular membranes. If you were designing a drug that you wanted to easily pass through the cellular membrane, would you try to make the compound more or less hydrophobic? o More (make it more polar) Hemolysis is the name of the process by which red blood cells burst, or explode. In lab, we induced hemolysis to occur and timed how long it took. What was the first process that occurred after we mixed the RBC solution with the propanol/glycol solutions? o DIFFUSION o THEN OSMOSIS directly causes the red blood cells to burst Photosynthesis: Figure: The relationship between photosynthesis and respiration Photosynthesis consists of two stages known as the light reactions (or energy capturing reactions) and the Calvin cycle (dark reactions) In the light reactions, light energy is absorbed by the pigments in the chloroplasts and converted to chemical energy in the form of ATP and the reduced form of NADPH. Water is split in the process and oxygen is released as a by-product to the atmosphere The Calvin cycle uses the ATP and NADPH from the light reactions and CO2 from the atmosphere to produce carbohydrates (sugars)

5 TO SUMMARIZE: the chloroplasts use light energy to make sure by linking the two stages of photosynthesis. Water, sunlight, and CO2 are inputs Oxygen and sugar are the outputs Chromatography: A process used to separate mixtures of compounds Solvent is going to run up the paper Paper is polar Solvent is nonpolar Pigments that are very polar are going to stick to paper and not travel very far and stay at origin Less polar are going to go intermediate Very non-polar will move right along with the solvent Background information on Pigments and Chloroplasts: Chloroplasts of most plants contain several photosynthetic pigments: chlorophyll a, a blue-green pigment; chlorophyll b, a yellow-green pigment; xanthophyll s, yellow pigments; and carotenes, yellow-orange pigments These pigments are located in the thylakoid membrane Chlorophyll a and chlorophyll b are large molecules They have identical chemical structures, except chlorophyll b has a CHO group in place of the CH3 group The carotene and xanthophyll molecules have a very non-polar molecular nature that makes their integration into the thylakoid membrane NOTE: There are TWO phases: mobile phase and stationary phase o Mobile: the solvent that moves along the paper (non-polar) o Stationary: the solvent that stays near the bottom and doesn t move (polar) Important Background Information on Absorption and Transmission of Light: White light is a continuum of wavelengths o It is composed of all the wavelengths (colors) in the spectrum of visible light These wavelengths are measured in nanometers (nm) and range from approximately 380 to 750 nm. o This is the part of the electromagnetic spectrum that drives the photosynthetic process When light strikes an object, it may be reflected, transmitted, or absorbed Substances that absorb light are called pigments (located in thylakoid membranes) Pigments selectively absorb certain wavelengths of visible light and reflect or transmit others

6 Therefore, an object s color is composed on of those wavelengths of light reflected or transmitted o For example, a leaf appears green because it reflects and transmits green wavelengths but absorbs all other wavelengths (colors) of light When a chlorophyll solution is exposed to white light, the pigment molecules absorb light and become chemically excited. However, since there are now no molecules to accept the absorbed energy, it is re-emitted as light energy of a longer wavelength (red), a phenomenon known as fluorescence Under light saturating conditions, this phenomenon of fluorescence can occur in the intact leaves, although Why do photosynthetic organisms have different types of pigments? o To absorb different wavelengths of light In order for photosynthesis to occur in green plants, PIGMENT must be present for the absorption of light Which of the following is a device useful for viewing the spectrum of light is a: spectroscope Based on your results from the laboratory, a pigment that absorbs red and blue light and reflects green light is chlorophyll a Based on your findings, if you had to use colored lights to grow plants, which color would you choose? o Red! Say you are looking at light, which has been passed through a prism so that you can see all of its colors. You then hold up a filter and notice that you can see very color except green. What conclusions can you make about the filter? o Green is the only color being absorbed. The rest are being reflected Whenever you shine white light on a flask of chlorophyll, you notice that the solution turns green but then upon removing the light, the solution glows red. What does this tell you about the nature of chlorophyll? o It reflects green light when illuminated, and emits red light when not illuminated IMPORTANT NOTE:

7 Photosynthesis Overview II: We are using whole plant cells/whole leaves So we not only have to think about photosynthesis, but also have to think about what is going on with cellular respiration We measure the decrease in the amount of CO2 So as the rate of photosynthesis increases, the amount of CO2 should decrease since it is an input Background information: Photosynthesis rates and the rate of CO2 used by photosynthesis is directly proportionate to the light available at low light intensities The linear relationship is the result of the rate of photosynthesis being limited by the rate of the light reactions Under low light conditions the pigments in the leaf receive insufficient photons to produce enough ATP and NADPH The qubit measures CO2 levels using an infrared gas analyzer (IRGA) Net photosynthesis rate = photosynthesis rate respiration rate The net amount of CO 2 used by a leaf is equal to the amount of CO 2 consumed by photosynthesis minus the amount of CO 2 generated by respiration. Qubit Setup For Photosynthesis and Fermentation: ^Photosynthesis ^ <Fermentation