Bio Lab Basics: a QuickStudy Laminated Reference Guide [2 ed.] 1423238613, 9781423238614

Table of contents :
LAB SAFETY & FIRST AID
ESSENTIAL METHODS & TOOLS
SCIENTIFIC METHOD
MEASUREMENTS
Metric System
Common Metric Units
Metric Conversions
Unit Conversions
STATISTICS
COMMON BIOLOGY LAB EQUIPMENT
MICROSCOPY
Compound Light Microscope Usage
ESSENTIAL CONCEPTS
CELL STRUCTURE
CELL TRANSPORT
RESPIRATION
PHOTOSYNTHESIS
ENZYME ACTIVITY
ORGANISMAL DIVERSITY
MITOSIS
MEIOSIS
MOLECULAR GENETICS
MENDELIAN GENETICS
Solving Inheritance Problems
FIELD BIOLOGY
Mark & Recapture
GIS Mapping
Quadrats

Citation preview

WORLD’S #1 ACADEMIC OUTLINE

Essentials of lab concepts, use & safety—including helpful hints & tips

LAB SAFETY & FIRST AID

ESSENTIAL METHODS & TOOLS

Biology labs should be interesting and informative, but most importantly they need to be safe. Because biology labs often manipulate living organisms, there are several chemicals and pieces of equipment that can be dangerous if used improperly. The following are some basic safety guidelines common to most introductory biology labs. ●● Pre-lab preparation ––Read and understand the lab materials. The most important step a student can take is to be well prepared and familiar with what will be covered in lab for each session. Lack of preparation makes labs take longer to complete properly. Uncertainty can easily lead to carelessness and accidents; having to redo work is always time consuming. ●● Specific lab safety guidelines ––No food or drink in the lab at any time. Chemicals someone else used and didn’t clean up properly can get on your food. ––Do not apply cosmetics or contact lenses. You really don’t want to put strange chemicals into your eyes. ––Keep the lab bench clear of unnecessary items (e.g., books, laptops, and cell phones). ––Never touch a hot plate to determine its temperature. ––Test tubes that are being heated should be aimed away from you and others. ––Wear appropriate gloves, goggles, and lab coats when required. ––Dispose of all chemicals, specimens, and sharp objects/tools (e.g., scalpels and broken glass) in designated containers. Discarded sharp objects have injured many janitors. ––Long hair should be tied back. ––Wear appropriate clothing. It shouldn’t be too loose and should cover most of your body. Always wear closed-toe shoes—never sandals. ––Wash hands with soap and water after every lab (and possibly multiple times during a lab, depending on the activity) so you don’t take chemicals home with you. ––Know the location of fire extinguishers, fire blankets, gas shutoff valves, fume hoods, safety showers, eye washes, and first-aid kits and how to use them. »» Fire extinguishers come in several different types and their effectiveness depends on what is burning. Only trained personnel should handle fire extinguishers. »» Fire blankets are used when a person’s clothing is on fire. They are used to smother the fire by wrapping a person inside one. »» Gas shutoff valves are located in particular locations (usually near fire extinguishers). In case of a gas fire, gas to the entire room can be shut down quickly. »» Fume hoods are intended to protect the user from chemicals inside the hood. Room air is pulled into the hood and expelled through special chemical scrubbers to detoxify and protect against airborne chemicals. »» Safety showers are intended to wash away larger chemical spills on a person just like taking a shower at home cleans away dirt. »» Eye washes are located near certain sinks and are used to squirt water into the eyes and wash chemicals from them. Eyes are very fragile and extra care should be taken to avoid getting chemicals in them. One should never put gloved hands to the face; if your hands need protection, your face will too! ●● First aid ––Labs are required to have a first aid kit; however, students will not normally administer first aid to another student. »» All accidents, regardless of severity, should be reported immediately to the lab instructor. »» These guidelines are for the instructor and injured student; in all cases of severe injury and/or intense pain, the instructor should immediately contact medical professionals. ––Specific injury recommendations »» Small cut: In consultation with the instructor, wash the cut with water and then use topical antibiotic ointments and bandages from the first-aid kit. »» Large cut: In consultation with the instructor, apply pressure to the injured area to stop the bleeding; immediately contact medical professionals. »»Small burn: In consultation with the instructor, apply cold water until the pain subsides; if necessary, contact medical professionals. »»Large burn: In consultation with the instructor, immediately contact medical professionals. »» Eye injuries: In consultation with the instructor, the eye wash station should be used for chemical or fluid splashes. All eye injuries are potentially serious; thus, immediate contact with medical professionals is recommended. »» Additional injuries or medical conditions of many kinds and severity can occur in labs (just as they can anywhere else); thus, it is best to be safe. In consultation with the instructor, medical professionals should be contacted.

SCIENTIFIC METHOD

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●● Children learn by experimentation: they learn about the world through how they interact with it. When they touch a hot burner on a stove, it hurts. ––The child then most likely speculates that if he/she touches hot stoves again, a burn will ensue. ●● The scientific method works the same way. Scientists observe phenomena and formulate testable, repeatable hypotheses about the world they observe. ––Hypotheses that are untestable are of little use in science. ––Observations that are not repeatable cannot be used to predict future events. ●● The scientific method is formalized into four distinct stages: 1. Observation: Viewing or examining events as well as the circumstances of the event. 2. Hypothesis: A prediction or educated guess about what is being observed. 3. Experiment: A test of the hypothesis, usually involving a manipulation of some variable that might affect the observation. a. Treatment: The part of an experiment where a variable is manipulated. b. Control: The part of an experiment where no manipulation takes place (i.e., a baseline). 4. Theory: A prediction that is checked by at least one (but usually many) experiments. ●● There are specific mathematical tests for comparing treatments and controls. These are known as statistics, with different tests depending upon what data has been collected. ●● Methods used to test hypotheses should be repeatable. Can other people carrying out the same experiment get the same results? ––Introductory biology lab exercises involve doing experiments in which data about the living world can be recorded and analyzed to increase our understanding of how science actually reaches its conclusions.

MEASUREMENTS ●● Scientists make two different types of measurements: ––Qualitative measurements: A relative description characterizing an important aspect of a phenomenon (e.g., a bear displayed its teeth aggressively). ––Quantitative measurements: A numerical description of an aspect of a phenomenon (e.g., a bear displayed its teeth 4 times during a 30-minute observation period while growling at 52 decibels). ●● There are two major systems of measurement: Characteristic Measured

American Standard

Metric System

length

inches/feet/yards/miles

centimeters/meters/kilometers

volume

cups/gallons/barrels

milliliters/liters/hectoliters

temperature

Fahrenheit (°F)

Celsius (°C)/Kelvin (K)

weight

ounces/pounds

grams/kilograms

Science almost exclusively uses the metric system.

Metric System

The metric units all have a base unit of measure (e.g., meter, liter, and gram), and when appropriate, also have a prefix before. Metric Prefixes Prefix

Symbol

Power of 10

Prefix

Symbol

Power of 10

peta

P

10

deci

dc

10-1

tera

T

10

centi

c

10-2

giga

G

109

milli

m

10-3

mega

M

10

micro

µ

10-6

kilo

k

10

nano

n

10-9

hecto

h

102

pico

p

10-12

deca

dk

10

femto

f

10-15

15 12

6 3

1

Essential Methods & Tools (continued) Common Metric Units Measurement

Units

Abbreviation

mass

grams

g

volume

liters

L

distance

meters

m

temperature

Celsius

o

Kelvin

K

calories

cal

joules

J

pascal

Pa

atmospheres

atm

time

seconds

s or sec

force

newtons

N

energy pressure

Unit Conversions

Lab Equipment

C

●● Volume to cubic distances: 1 mL = 1 cm3 ●● Energy to temperature: 1 cal = the energy needed to raise 1 g of water 1°C ●● Mass to volume: 1 g = mass of 1 cm3 of water or 1 mL ●● Pressure to force: 1 Pa = 1 newton per square meter (N/m2) Many other conversion factors are used in chemistry, physics, and engineering. In the lab, it is important to differentiate between precision and accuracy in measurements. ●● Precision: How close a series of measurements are to one another. ●● Accuracy: How close a measurement is to the true characteristic of an object. An analogy can best demonstrate the relationship of these two closely related terms. ●● Mass is frequently measured with balances (scales). If an item’s mass is measured 10 different times on the same balance, and each time the measurement is 52.1 grams, then the scale is precise. ●● If the same item is measured 10 times on another balance, and the mass is 54.1 grams, while both balances are precise, the accuracy of one or both balances is questionable.

Goggles Bunsen burner Graduated cylinder

Pipet bulb

Forceps

Stirring rod Evaporating dish

Watch glass

Beaker Test tube

Volumetric flask

Balance

Buret

STATISTICS Spot plate

Crucible tongs

Funnel

In the natural world, there is a lot of variation; some people are taller than others, some oak leaves are broader than others, and some trout are longer than others. In order to study variation, mathematicians have developed tools and techniques to decide if two populations (groups of related individuals) are the same or different from each other. In most cases, it is not possible to collect every individual; scientists take samples (ideally random samples) and use distributions (idealized descriptions of variation) to compare them. Here are some of the more common techniques used: ●● Mean/Average: The sum of all measurements being compared divided by the number of individuals being counted. ●● Median: The middle point of a population where half the population is larger and half is smaller. It is less influenced by extreme measurements than means. ●● Range: The largest and smallest measurements being compared. ●● n: The number of observations or measurements being compared. The larger the n, the more confident you can be in your results. ●● Probability: The likelihood of a particular event or conclusion being true. ●● Confidence interval: The likelihood that the true value of the population is between two numbers. It is often listed at 95% or 99%, but occasionally as small as 50%. ●● Standard deviation: A measure of how much a population differs from the mean. Larger standard deviations mean that there is a lot of difference within the population. ●● Student’s t-test: A method for comparing two groups of measurements to see if they are from different populations (given as a probability). ●● Expected value: The number of events being predicted by the probability based on the total number of measurements or events in a sample. ●● Actual value: The number of events or measurements that occurred during the experiment. ●● Chi-square test: A mathematical way of comparing whether the actual values are consistent with the expected value of an experiment. It is usually given as a confidence interval.

Why do scientists like the metric system? It is simpler. How many miles is 1 million inches? Well, you can remember there are 12 inches in a foot and 5,280 feet in a mile, so 1,000,000/ (12 × 5,280) is about 15.78 miles. However, a simpler calculation would be: 1 million centimeters or 1,000,000 cm = 1 × 106 cm = 1 × 104 m = 10 km or kilometers. Because the metric prefixes are built on factors of 10, it is easy to convert long numbers into short prefixes. Instead of saying 0.000000001 meters, 1 nanometer says the same thing.

Metric Conversions

To convert metric units, take the numerical value of the starting prefix and divide by the numerical value of the ending prefix. It’s that simple. When converting between any units, always check your final answer using this simple rule: Do I have more of my smaller units? Think it through: it isn’t possible to have more meters than millimeters after the conversion. EX: Convert 3 terabytes into megabytes, take the prefix for tera (1012), and divide by the prefix for mega (106), leaving 10(12-6) = 3 × 106 megabytes. (Dividing by exponents means subtracting them.) Now check: Are there are more megabytes than terabytes? Yes. EX: Convert 16 micrometers into millimeters, take the prefix micro (10-6), and divide by the prefix milli (10-3), leaving 10(-6-(-3)) = 16 × 10-3 millimeters. Now check: Are there more micrometers than millimeters? Yes. More Examples: You can also solve the problems by canceling out units. Here again, there should always be more of the smaller units present. EX: Convert 4,500 milligrams to grams. Start with 10-3 (.001). The ending base is 1. 10-3/1 = .001. 4,500 mg × .001 g/mg. mg cancels out, leaving 4,500 × .001 = 4.5 grams. Double check: Do I have more milligrams than grams? Yes.

COMMON BIOLOGY LAB EQUIPMENT Biologists conduct experiments or make observations with equipment. The finer (and more expensive) the equipment, the more accurate and precise the observations tend to be. There are a number of pieces of equipment commonly used in biology labs. ●● Balance: Also known as a scale, balances are used to weigh objects and chemicals. Most lab balances weigh down to 0.01+/- .01 g, but more accurate analytical balances can measure 0.0001g. Generally, the more accurate the balance is (i.e., how many mg differences can be resolved), the lower the overall capacity of the balance. ●● Bunsen Burner: A device attached to a natural gas supply that creates an open flame used to heat test tubes, sterilize bacterial spreaders, etc. It includes a gas shutoff valve and a way to regulate air intake. When properly adjusted, the burner has a clear blue flame with a lighter core and is quiet (i.e., it does not make a hissing sound). ●● Centrifuge: A device that holds a set of tubes or plates and spins them rapidly. Denser items move toward the bottom of the tube while the lighter material floats to the top. Solids at the bottom of a centrifuged tube are the precipitate; the liquid over it is the supernatant. Note: Centrifuges must be properly balanced or permanent damage can result! ●● Chromatography: A method for separating chemicals based on some chemical property. ––The stationary phase is the part of the system that does not move—things that bind to the stationary phase move more slowly. ––The mobile phase is the liquid part of the system that moves—things that bind more strongly to the mobile phase move faster. ––Depending upon the choice of mobile and stationary phases, the scientist controls the separation of the chemicals of interest. ●● Flasks and beakers: Varieties of containers (usually glass) that hold liquids during experiments and have somewhat inaccurate measurements printed on them. They are useful for various purposes such as growing cultures, collecting samples, temporarily holding liquids, etc. ●● Fume hood: Also known as a chemical fume hood, this device draws in air from the room so that chemical vapors inside the hood do not come into contact with the person in front of the hood. It is used extensively with organic solvents.

EX: Convert 1.5 meters to centimeters. The starting base is 1 and the ending base is 10-2. 1/10-2 = 100. 1.5 m × 100 cm/m. m cancels out, leaving 1.5 × 100 = 150 centimeters. Double check: Do I have more centimeters than meters? Yes. EX: Convert 672 milliliters to kiloliters. 672 mL/L × .001 mL/L × .001 kL/L = 0.672 × 10-3 kiloliters. Double check: Do I have more milliliters than kiloliters? Yes. With any unit conversion, it is easy to use the wrong factor. Always double-check before using the data. The second reason scientists love the metric system is because they convert between units. Have you ever heard the saying “A pint’s a pound the world around?” It’s convenient, as a U.S. pint of water weighs just about a pound (1.04375 pounds, actually). In Britain, however, an imperial pint weighs 1.25 pounds. But why use 16 ounces in a pint or a pound anyway? In metric, all units are able to convert into one another. EX: 1 milliliter or 1 mL = 1 cm3 (as everyone who watches medical dramas knows: “Give me 3 cc’s of adrenaline”). Converting between units and making such calculations is critical as one progresses in science.

2

microscopes can reach much higher magnifications than light microscopes can. Electron microscopes require special chemicals (usually metals) to either block or reflect the electrons. Because electrons are absorbed by water, biological samples must be dehydrated and therefore dead to observe them. »» Scanning electron microscopes: These bounce electrons off of samples that have been coated with metal. They are excellent at showing detailed surface structures, but not so good at seeing what is inside a sample. They have a maximum resolution of roughly 50,000 times. »» Transmission electron microscopes: These shoot electrons through a very thin tissue section that has been stained with special chemicals (often heavy metals) that will block electrons from passing through particular structures in the sections. These microscopes have the highest magnifications available (over 1,000,000 times), but are expensive and hard to use so are generally not used in introductory biology labs.

●● Gel box: A device (usually an acrylic box) with electrodes on each side, used to hold a gel plate or gel tray during electrophoresis. ––Vertical gel boxes hold polyacrylamide gels vertically and are used to separate proteins. ––Horizontal gel boxes are used with agarose gels and are used to separate nucleic acids, both DNA and RNA. ●● Graduated cylinder: A plastic or glass cylinder with a base and pouring spout that has accurate markings on it for volumes ranging from roughly 10 mL to 4 L, depending on size. ●● Hot plate: An adjustable ceramic bench top heater that often includes a magnetic stirrer for safely heating and stirring liquids. ●● Incubator: An enclosed device used to maintain a constant environment (usually temperature) to achieve maximal growth of various organisms. Several varieties are common in biology labs, including: ––Bacterial incubators that only specialize in temperature control. ––Shaking incubators that have temperature control and rotate samples to increase aeration and growth rates. ––Cell culture incubators that are optimized for growing mammalian cell cultures at particular temperatures and atmospheric conditions (usually adjustable carbon dioxide concentration). ●● pH meter: A specialized electrical conductivity detector optimized to measure the concentration of hydrogen ions that determine pH. The meter has accurate bench top units with a corded, interchangeable electrode for particular types of measurements or a less accurate but more convenient dippable pen-shaped device. Both types must be standardized against liquids of known pH before use. ●● Pipetteman: A mechanical air-displacement device that can measure out microliter quantities of liquids. It uses color-coded disposable tips for different volumes and specialized applications. Most dispense one volume at a time, but there are multichannel pipettemen that can dispense up to 12 at a time, as well as repeating pipettes that can dispense the same volume over and over. ●● Pipette: A glass or plastic tube with a tapered end at one side and a place to attach a pipette bulb or electronic pipette pump at the other end. Pipettes are quite accurate within their range and typically measure mL quantities. ●● Spectrophotometer: A device that measures the absorbance of light of a liquid sample at an adjustable wavelength. It is typically designed to use square or rectangular cuvettes made of plastic, glass, or quartz (depending on the liquid and wavelength being used) and with a 1 cm path length. The most common type in biology labs use visible or ultraviolet light, although chemists have several other types available. ●● Water bath: A bench-top device used to heat water to a constant temperature. It is often used because the water maintains its temperature more consistently and heats tubes/flasks more quickly than air does. ––A dry bath uses a metal block with precisely drilled holes or filled with sand to heat test tubes and maintain their temperature accurately.

Compound Light Microscope Usage

1. Turn the turret containing the objective lenses so that the lowest usable magnificaOcular lens tion lens is in line with the rest of the microscope. (Some low magnification Coarse focus lenses are too low to see small organisms.) Fine focus 2. Place the sample on the stage of the microscope, often held Objectives in place using clips. Stage a. If necessary, move the sample on the microscope Condenser stage so that it is visible through the ocular lens, Light source or eyepiece. 3. Use the coarse focus knob to bring the microscope slide into focus. 4. Use the fine focus knob to get a sharp focus on your sample. 5. If the sample is too bright, you can adjust the light intensity directly or close the condenser located just below the stage of the microscope. Closing the condenser can also increase the contrast of the sample under certain conditions, so it is something to try. 6. After the observations are made, turn the turret so that the magnification lens one level higher is over your sample. Do not adjust the coarse focus—most microscope lenses regardless of magnification are designed to focus at the same distance from the turret (parfocal). a. Higher magnification lenses let in less light than low magnification lenses, so here is another place to adjust the light intensity using the condenser. 7. The highest magnification objectives on light microscopes use oil immersion to capture more light from the sample. Never use oil on lenses designed for air. It will destroy them. a. If a lens says “oil” on it, it is for oil immersion. To use an oil immersion lens, rotate the turret halfway out of the way and place a small drop of oil directly on the slide over the specimen. Never use the coarse focus knob with an oil lens. Rotate the oil immersion lens into the drop of oil. The lens should touch the oil drop and create a column of oil between the slide and the lens. b. Use the fine focus only with oil immersion lenses. Be careful, as the lens gets very close to the slide and moving the lens too far down can easily crack the slide. c. Never switch back and forth between an oil lens and an air lens without cleaning both the slide and the lens. d. When finished, rotate the turret and remove the slide. Wipe excess oil off the slide with a tissue and use a cleaning solution with detergent to remove the last traces of oil from the slide. e. To clean the lens, use lens paper only! Wipe oil off of the lens with lens paper, wet a corner of the lens paper with cleaning solution, and use that to finishing cleaning the oil off the lens on the microscope. Never leave oil on the lens—it collects dust.

MICROSCOPY Because biologists depend on microscopy for so many of their observations, microscopes deserve special attention. Much of life can be observed directly by using our eyes; that is, macroscopically. Cells that make up life, however, are mostly smaller than the unaided eye can see. In order to study them, scientists use microscopes of various sorts. 0.1 nm

1 nm

10 nm

100 nm

100 µm

Electron microscope

1 cm

0.1 m

}

T2 Phage

Protein

1 mm

Fish egg

Chloroplast

Lipids Small molecules

10 µm

}

}

}

}

} Atoms

1 µm

Plant & animal cells Most bacteria

Butterfly

Light microscope

●● There are two basic types of microscopes: ––Light microscopes: Use glass lenses and a bright light source to observe cells and tissues. These are the most common microscopes used in introductory biology classes. There are two basic types of light microscopes: »» Dissecting (stereoscopic) light microscopes: Relatively low magnification (less than 100 times); used for relatively large or thick microscopic items. Has a large working distance between the lens and the object to allow manipulation of the object while it is still under the microscope (i.e., dissection). »»Compound light microscopes: Higher magnification (anywhere from less than 100 times up to roughly 1,000 times); used for detailed examination of thin sections of material. It is the most common type of microscope used for histology (study of cells), medical diagnosis, or biology research. There are many special types of compound light microscopes that take advantage of different properties of light, such as polarized light microscopy, dark field microscopy, and fluorescence microscopy. ––Electron microscopes: Use high-intensity electron beams focused using electromagnetic fields. Since the electrons have more energy (smaller wavelengths), these 3

ESSENTIAL CONCEPTS CELL STRUCTURE

○○ Hypertonic: One solution has more solutes than the other. ○○ Hypotonic: One solution has fewer solutes than the other.

●● Prokaryotic cells are the simplest form of life. They: ––Have smallish circular DNA genomes. ––Lack intracellular membrane structures. ––Typically only a few micrometers in diameter. ●● Eukaryotic cells may be either single- or multi-celled organisms. ––Genomes are organized into chromosomes. ––They contain multiple different membrane-bound organelles. ––They are often larger and more diverse in appearance. ●● Archea are the third major type of organism that has characteristics intermediate between those of the eukaryotes and prokaryotes. They: ––Have a unique cell membrane that uses different lipids than prokaryotes or eukaryotes. ––Are single-celled organisms without membrane-bound organelles similar to prokaryotes. ––Have transcription and translation processes more similar to eukaryotes. ––Often live in extreme environments, including salt-loving halophiles, hot springloving thermophiles, and methane-generating methanogens. ●● Cytology: The study of cell structure and function. ●● Prokaryotes are often described based on their shape under the microscope and their pattern of growth. They are usually visualized with particular chemical stains such as a gram stain. ––Cocci: Spherical ––Bacilli: Rod shaped ––Spirilli: Spiral shaped ––Strepto: Prefix meaning cells grow in chains of cells ––Staphylo: Prefix meaning cells grow in clusters ●● Organelles are membrane-bound structures found in eukaryotic cells. ––Organelles visible under a light microscope with appropriate stains include: »» Nucleus: Contains DNA and synthesizes RNA. It is the largest organelle and is often stained with haematoxylin. »» Chloroplast: Organelle in plant cells and used in photosynthesis. It appears green without staining due to the light-absorbing chlorophyll molecules. »» Mitochondria: Organelle that generates most ATP in eukaryotes. It is often stained with acid fuschine or newer fluorescent dyes. »» Cytoplasm: The liquid inside eukaryotic cells surrounding organelles. It is often stained by eosin. ––Other organelles are visible in the electron microscope, including: »» Endoplasmic reticulum: Membrane folds used to make lipids and membrane proteins. »» Golgi complex: A series of layered folds of membranes used to sort vesicles to different cellular locations. »» Lysosome: A digestive organelle that breaks down cellular waste. »» Peroxisome: An organelle that compartmentalizes reactions involving hydrogen peroxide. »» Vacuoles: Storage organelles most prominent in plants but also found in animals. Introductory biology lab exercises often use light microscopy to examine cell structure and function.

98% water 2% sucrose

100% water (distilled) Bag solution Beaker solution

90% water 10% sucrose

98% water 2% sucrose

Hypotonic

Isotonic

hypertonic

hypotonic Hypertonic

Isotonic

Introductory biology labs frequently use dialysis membranes or blood cells in each of the above conditions to demonstrate the passive transport of water. Contact lens wearers can attest to this water imbalance if they ever have to substitute tap water (which is hypotonic to tears) for saline solution (which is isotonic to tears). The corneal surface will be noticeably uncomfortable until fluids on both sides reach equilibrium once again. ––Active transport relies on the cell providing energy to physically move a substance across the membrane. There are three forms of active transport: »» Membrane pumps: Permease used to move substance, usually from an area of low to high concentration (e.g., kidneys help regulate salt balance in the body by using membrane pumps). »» Endocytosis: Solids (phagocytosis) and liquids (pinocytosis) are brought into cells in bulk by pinching off membrane sacks called vesicles. »» Exocytosis: Materials are expelled from cells by releasing vesicles. Synapses in the nervous system release neurotransmitters by exocytosis and allow signals to pass from one neuron to another. Chloroplasts use energy from sunlight to move hydrogen ions across membranes in the chloroplast, which is how plants “harvest” sunlight for food. Introductory biology labs do not usually attempt to demonstrate active transport mechanisms, as higher-level procedures and technology are typically required.

RESPIRATION ●● Every day of our lives, our respiratory and circulatory systems ensure that we bring in oxygen and expel carbon dioxide; these two gases are key components of cellular metabolism (cell respiration). ●● The specific form of energy “currency” used by all cells is adenosine triphosphate (ATP). ●● Aerobic respiration, the production of ATP using oxygen, is very efficient and produces roughly 36 molecules of ATP from a single glucose molecule, giving off carbon dioxide. ●● Anaerobic metabolism (also known as fermentation) does not produce nearly as much energy per glucose molecule but does not require oxygen. ––In fermentation, one glucose molecule becomes two carbon dioxide and two ethanol molecules. ●● Glycolysis is the initial breakdown of glucose and takes place with or without oxygen. ●● In aerobic metabolism, the Krebs cycle takes what was left over from glycolysis and breaks it down further so that mitochondria can use chemiosmotic phosphorylation to extract more energy, breaking that former glucose all the way down into carbon dioxide and water.

CELL TRANSPORT ●● Biological membranes serve to separate two different compartments in living cells, such as separating the inside of the cells from the outside. ●● Cell membranes are semipermeable, meaning that certain materials can pass through membranes and other materials cannot. ●● The interiors of cell membranes are hydrophobic, as they repel water (it literally means “fear of water”), just like grease and oil. ––Nonpolar molecules (e.g., oxygen gas, carbon dioxide gas, steroid hormones) pass through cell membranes easily, as they are hydrophobic. ––Molecules that are hydrophillic (it literally means “water loving”) such as ions or water cannot pass through easily. ●● There are two different mechanisms cells use to move things across their membranes: ––Passive transport relies on the thermal energy of matter. The cell does not have to put energy into these. »» Diffusion: Movement from an area of high to low concentration. For an example of passive transport, add a tea bag to a clear glass of hot water and watch diffusion occur as brownish tea particles spread into areas of clear water. »» Facilitated diffusion: A permease, or enzyme that exists in the membrane, carries substances from high to low concentrations. »» Osmosis: A form of diffusion across a barrier (such as a cell membrane) where a solvent (such as water) moves to reduce the concentration of a salt (i.e., water moves from a lower to a higher salt concentration). »» Tonicity: Relative solute concentration of two (or more) solutions. There are three possible situations: ○○ Isotonic: Both solutions have the same amount of solutes (no diffusion).

Enzymes

4

C6 H 12 O 6 + 6O 2

6CO + 6H O + 36ATP

C H O + 6O

6CO + 6H O + 36ATP

2 2 Enzymes Glucose Oxygen Carbon Water Chemical dioxide energy 6 12 6 2 2 2 Glucose single-celled Oxygen organisms) Carboncan survive Waterwithout Chemical Enzymes ●● Some cells (including oxygen; thus, they dioxide energy use only glycolysis in fermentation reactions to produce ATP at a very slow rate. 6 12 Enzymes 6 3 2 2 Glucose Ethanol Carbon Chemical dioxide energy 6 12 6 3 2 2 Glucose Ethanol Carbon Chemical dioxide energy 2 2 6 12 6 2 Carbon Watercell Chlorophyll Sugar ●● Muscle cells (and several other types) can engage in Oxygen a kind of fermentation dioxide Sunlight reaction that produces2lactic acid 2 (which lowers 6 12the6pH in our2tissues, triggering muscle fatigue and soreness). Carbon Water Chlorophyll Sugar Oxygen dioxide Sunlight

CH O

2CH CH OH + 2CO + 2ATP

CH O

2CH CH OH + 2CO + 2ATP

6CO + 6H O

C H O + 6O

6CO + 6H O

C H O + 6O

Essential Concepts (continued) Introductory biology labs can easily demonstrate respiration by taking a growing organism (e.g., germinating plant seed) and recording how much carbon dioxide is released via respiration under different experimental conditions. ♦♦ Carbon dioxide (which forms a weak acid in solutions) levels can be estimated by measuring the pH change in solutions housing the growing organisms; specifically, color indicators illustrate differing pH levels. Enzymes ♦♦ Additional simple methods can quantify oxygen consumption and carbon dioxide production. 6 12 6 2 2 2 PHOTOSYNTHESIS Glucose Oxygen Water Chemical Carbon dioxide energy ●● Almost all natural food comes directly from plants, an animal that ate a plant, an animal that ate an animal that ate a plant, etc. Enzymes ●● Most life on earth relies on photosynthetic organisms that use sunlight to convert carbon dioxide for storage. 6 and 12 water 6 into sugars 3 (glucose) 2 2 ●● The followingGlucose chemical reactionEthanol summarizes theCarbon photosynthetic Chemicalprocess; notice that it is essentially the opposite direction of cell dioxide respiration:energy

C H O + 6O

CH O

MITOSIS ●● From the moment of conception, the single fertilized egg cell (i.e., zygote) divides and divides repeatedly, ultimately resulting in an adult with up to 100 trillion total cells.

6CO + 6H O + 36ATP

2CH CH OH + 2CO + 2ATP

6CO 2 + 6H 2 O Carbon dioxide

Introductory labs use this approach, which typically involves a wide range of protocols—from microscopy to dissections.

––Stem cells are cells that can form different types of cells in an organism. »» One type of stem cell is found in bone marrow and can form any of the types of cells found in your blood. »» Embryonic stem cells can form any type of cell in the adult organism (a characteristic known as pluripotency) and are found only in the very early embryo stage or are specifically induced in the lab.

C H O + 6O 2

6 12 6 Water Chlorophyll Sugar Sunlight

Oxygen

●● Photopigments (e.g., chlorophylls) are molecules that absorb light energy and channel it into chemical energy. Introductory biology labs usually demonstrate several aspects of the photosynthetic process, including: ♦♦ A spectral analysis of light to show which wavelengths are most important, using a spectrophotometer. Note that green is not one of them: it is reflected, making plants appear green. ♦♦ Chromatography, which may be used to separate the various photopigments. ♦♦ Volumetric measurements, which may be used to directly measure oxygen production.

ENZYME ACTIVITY ●● Enzymes are proteins made by cells that speed up chemical reactions. Reactants, also known as substrates, bind to enzymes in a specialized pocket known as the active site. ––When they are bound, enzymes change their shape just like a baseball player changes the shape of his glove by squeezing it when the ball comes into it. ––Changing the shape of the enzyme causes the reactant to change shape as well (known as the induced fit model of enzyme activity). ––Once the reactant has changed its shape, it becomes easier for the reactant to become the product rather than go back to being the reactant. ––The energy it takes to squeeze the reactant to its intermediate form is known as the activation energy. ––Any chemical that lowers the activation energy of a reaction is known as a catalyst, so enzymes are often called biological catalysts. ––DNA controls which enzymes get made, so it can indirectly control which chemical reactions take place in the cell.

●● Critical to mitosis is a mechanism ensuring that a complete set of genetic information resides in each cell. ●● Mitosis involves making exact copies of the DNA and creating two new, identical nuclei. ––Introductory biology labs often include dividing cells showing different stages of mitosis. ––Cytokinesis, the separation of one cell into two cells, only occurs after mitosis.

MEIOSIS ●● Unless you have an identical twin, your siblings are different from you. ––While all siblings will show many similar traits from both parents, the processes that produce sperm and eggs ensure there are also differences. Note: Mutations (changes in the DNA sequence) are also important sources of genetic variation. ●● Sexual reproduction involves gametes Chiasmata (sperm and egg) from two different individuals combining to create similar but unique offspring. ●● Meiosis is a special type of cell division to make gametes (or spores in some organisms) with two distinguishing characteristics: ––A haploid amount of DNA so that gametes will have one half the number of copies that the parent organism had (i.e., humans have two copies of their DNA (diploid), so gametes only have one copy). ––The original pairs of chromosomes from each parent switch sections of their DNA through crossovers known as chiasmata. This makes sure that the chromosome of the gamete is unique to only that one gamete and allows variation to form. Introductory biology labs frequently use models to illustrate the meiotic process, as it is much more complex than mitosis, and subsequently harder to follow using prepared microscopic slides alone.

ORGANISMAL DIVERSITY

MOLECULAR GENETICS

Evidence of the diversity of life is apparent all around us; biologists, however, take more than just a casual interest in these organisms. ●● Introductory biology labs present a sampling of species diversity, which could involve literally millions of species. ●● Certain animals, plants, fungi, protists, and bacteria have become standard representatives of the multitude of life. ●● The organism’s morphology, or shape, becomes the focus of comparison, not only to show differences, but also similarities among species.

●● Once DNA was discovered as the major informational molecule of inheritance, a revolution in biology ensued—molecular biology. ●● Much of modern discovery in many disciplines of biology has been due to incorporating molecular biological techniques. ●● Introductory biology labs can incorporate some of the simpler techniques to isolate and identify DNA or its components (e.g., nucleic acids). ●● Plasmids are pieces of circular DNA that can replicate on their own and are often used in molecular biology experiments. 5

Essential Concepts (continued) EX: One common plasmid carries a piece of DNA from jellyfish (the gene for the protein GFP) that causes bacteria to glow green under ultraviolet light. ●● Pieces of DNA can be separated by agarose gel electrophoresis using horizontal gel boxes and seen under UV light. ●● Genetic engineering is the manipulation of DNA and the mixing of DNA from various sources. ●● Enzymes that cut DNA at particular bases are known as restriction endonucleases and enable genetic engineering. ––By cutting plasmid DNA, genes from other organisms such as humans can be joined to the plasmid DNA by an enzyme called DNA ligase. ––The human gene can then be made in bacteria to produce a protein such as insulin or human growth hormone because all organisms use the same DNA codes. ●● Polymerase chain reaction (PCR) allows the amplification of a small sequence of DNA to obtain large amounts of specific DNA from even a small sample. ––PCR is a common way of obtaining a human gene to insert it into a plasmid. ●● DNA cloning is the process of making identical copies of DNA. Plasmids are used to clone most genes before they are used experimentally or for therapies. ––DNA cloning is different from reproductive cloning, which is making genetically identical copies of organisms.

MENDELIAN GENETICS ●● Parents usually give rise to offspring that have similar traits, or phenotypes, to one or both parents. ●● Gregor Mendel worked out the H H basic rules for inheritance almost H G H C 100 years before DNA was H H A T H known to store the information. CH2 O O ●● His “determinants,” which we -O P O O P OO know today as genes, are passed O CH2 H down from parents to offspring A T H CH2 O as part of chromosomes. The O -O P O O P Oparents had two copies, while O O H CH2 G gametes only had one copy. H C H CH2 ●● He noted that the gene that an O O -O P O individual gamete carried was O P OO O random and was not tied to other H CH2 G C H H genes. This is known as the Rule CH2 O O -O P O of Independent Assortment. O P OO ●● Dominant traits would show up O H CH2 G C H in an organism if they received H CH2 O a single copy from either parent. O -O P O O P O●● Recessive traits would only apO O CH2 H pear if the offspring received the A H T same copy from each parent. 5' 3' ●● Although he knew nothing about the molecular basis of inheritance, he realized there had to be “factors” that were passed on by parental organisms to their offspring via gametes. Introductory biology labs usually examine organisms (including humans) to observe and record the distribution of traits, which demonstrate the basic “Laws of Genetics,” as formulated by Mendel. In cases where parental genotypes are known, the distribution of phenotypes can be used to introduce statistics to students.

Solving Inheritance Problems

Organisms usually have two copies of each gene, known as alleles. 1. To figure out what types of offspring are possible, write out the genotype of a cross, a mating of two organisms each with two alleles. 2. Make what is known as a Punnet square with all of the possible male gametes written across the top row and all possible female gametes written down the side. Note: Gametes have only one allele of any given gene, never both. 3. Combine the male and female gametes in the different entries in the table. Each entry represents one type of zygote, with each zygote getting two alleles.

EX: Pea plants can have either purple (P) or white (p) flowers with P (purple) dominant over p (white). If two plants are heterozygous, what percentage of the offspring will be white? 1. Write out the genotype of the cross. Because both are heterozygous, the cross is Pp x Pp. 2. Make the Punnett square with the male gametes across the top and female gametes down the side. P

p

p

Pp

pp

P

PP

Pp

3. Using the genotype of the zygote, count what fraction are white. Since only pp will be white, that fraction is 25% (1/4). When there are more than two genes, the Punnett squares are made exactly the same way. EX: P (purple) is dominant over p (white) and A (axial) is dominant over a (terminal). If a male plant that is heterozygous purple and terminal is crossed to a female white heterozygous axial plant, what percentage of the offspring will be purple axial? 1. Write out the genotype of the cross. Male (heterozygous purple, terminal) = Ppaa x ppAa female (heterozygous white, axial). 2. Make the Punnet square with the male gametes across the top and female gametes down the side. Pa

pa

pA

PpAa

ppAa

pa

Ppaa

ppaa

3. Using the genotypes of the zygotes, count what fraction are purple (either PP or Pp) and axial (AA or Aa). Only 1/4 are both, so 25% of the offspring are purple axial. To calculate the percentage another way, you can do two separate Punnett squares (one for each gene) and multiply their probabilities together. Using the example above, P

p

a

a

p

Pp

pp

A

Aa

Aa

p

Pp

pp

a

aa

aa

50% × 50% = 25%, so 25% are both purple and axial.

FIELD BIOLOGY Many experiments in biology take place in the natural world. There are a few techniques commonly used or discussed in introductory biology labs that are designed to count or study numbers of organisms as well as where they tend to move.

Mark & Recapture

●● This technique uses random sampling to estimate the size of a particular population. ●● In the first sampling session, all individuals captured (not harmed) are counted and marked so they can be identified. ●● In a second sampling session, the number of individuals captured is again counted, as are the number of marked individuals. ●● The estimated size of the population is calculated as follows: number captured first time × number captured second time ÷ number captured both times (i.e., marked). N = K × n/k, where N = population size, K = second capture size, n = first capture size, and k = number of marked individuals recaptured.

GIS Mapping

●● GIS (Graphical information systems): A type

U.S. $6.95 Authors: Randy Brooks, PhD Frank Miskevich, PhD NOTE TO STUDENT: This guide is intended for informational purposes only. Due to its condensed format, this guide cannot cover every aspect of the subject; rather, it is intended for use in conjunction with course work and assigned texts. BarCharts Publishing, Inc., its writers, editors, and design staff are not responsible or liable for the use or misuse of the information contained in this guide. All rights reserved. No part of this publication may be reproduced or transmitted in any form, or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without written permission from the publisher. Made in the USA ©2018 BarCharts Publishing, Inc. 0718

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of computerized map that allows collected data to be overlaid onto the geography so that information can be obtained. ●● GIS mapping usually uses things such as radio collars to track animal movements, but it can include temperature measurements, sunlight measurements, rainfall, etc. ●● GIS mapping allows data to be compared over location and time.

Quadrats

●● Quadrats (a shortened form of quadrants): A technique used to estimate the population density of a large area by closely analyzing a small area. ●● Quadrats uses a standard area (typically 1 m2) where all of the organisms of the desired types (plants, insects, etc.) are individually counted and tabulated. ––Random quadrats are taken from the entire area being studied and the results are averaged together. ––The average from the quadrat of a given size is assumed to be constant over the whole area and is used to estimate the size of the whole population based on the measured sample. ●● This is a common field experiment in an introductory biology course.