BIO 112 Study Guide

LAB 1:

1. Understand the difference between a hypothesis and theory 

• Hypothesis: A hypothesis is a testable and specific prediction about the relationship between two or more variables. It is an educated guess based on observations and prior knowledge that can be tested through experimentation.

• Example: "If athletes engage in weight training, then the density of mitochondria in their skeletal muscles will increase."

Theory: A theory is a broad, well-substantiated explanation of some aspect of the natural world that is based on a large body of evidence. Theories are supported by repeated testing and can help explain patterns observed in multiple hypotheses.

• Example: The Cell Theory, which states that all living organisms are composed of cells and that cells are the basic unit of life, is a well-established scientific theory.

2. Understand the importance of a prediction in a well-crafted hypothesis 

• A prediction is a key component of a hypothesis because it allows scientists to test the hypothesis. It is a statement about what you expect to happen under specific conditions and provides a basis for experimentation.

• A well-crafted hypothesis should lead to a specific prediction that can be measured and tested through experimentation. The prediction should be clear and quantifiable to allow for objective evaluation of results.

• Example: If the hypothesis is that "weight training increases mitochondrial density in skeletal muscles," the prediction might be: "After six weeks of weight training, mitochondrial density in the calf muscles of athletes will be higher than before training."

3. Be able to identify the independent, dependent, and controlled variables in an experiment. 

For example, try identifying the independent and the dependent and the controlled variables in the experiment described below. Dr. X is interested in the effect of weight training on the density of mitochondria in the skeletal muscles of athletes. She chooses an 18-year-old, male, swimmer as her test population. She has measured the mitochondrial density in one of the calf muscles of each swimmer before a regimen of weight training and then again after weight training. 40 swimmers participated in the study. Data is collected from each one. 

Independent Variable: The independent variable is the factor that the researcher changes or manipulates in the experiment. In this case, the weight training regimen is the independent variable because Dr. X is interested in how weight training influences mitochondrial density.

Dependent Variable: The dependent variable is the factor that is measured in the experiment and is expected to change due to the manipulation of the independent variable. In this experiment, the mitochondrial density in the calf muscles of the swimmers is the dependent variable because Dr. X is measuring this after weight training.

Controlled Variables: Controlled variables are factors that must be kept constant to ensure that any changes in the dependent variable are due to the independent variable (weight training) and not other factors. In this experiment, controlled variables might include:

• Age of the swimmers (18 years old)

• Sex of the swimmers (male)

• Specific muscle being tested (calf muscle)

• Duration and intensity of weight training regimen

• Diet and nutrition (if not controlled, could influence mitochondrial density)

• Baseline mitochondrial density measurements (before training)

4. Be able to identify the control group and the experimental group, if appropriate.

• Experimental Group: The experimental group is the group that is exposed to the independent variable. In this case, the athletes who undergo weight training would be the experimental group. This group will be measured for mitochondrial density before and after weight training.
  
  

• Control Group: The control group is a group that is not exposed to the independent variable (in this case, weight training) and serves as a baseline for comparison. Ideally, Dr. X would have another group of athletes who are not involved in weight training but have similar characteristics (age, sex, etc.). They would not undergo the weight training regimen, and their mitochondrial density would be measured before and after a comparable period of time. This allows for comparison to see if the weight training specifically affected mitochondrial density.
  
  

1.What are the standard metric units for volume, mass and length? 

• Volume: The standard metric unit for volume is the liter (L).

• Mass: The standard metric unit for mass is the gram (g).

• Length: The standard metric unit for length is the meter (m)

2. What is the standard metric unit for temperature? The standard metric unit for temperature is the Celsius (°C) scale.

3. What does the prefix kilo- tell you about the relationship of a unit to the base unit? (e.g. kilogram to gram). Be able to answer the same question for centi, milli, micro and nano) 

The kilo- prefix tells you that the unit is 1,000 times larger than the base unit.

• kilo- (k) means 1,000 times the base unit.

  • 1 kilogram (kg) = 1,000 grams (g)

• centi- (c) means 1/100 (one hundredth) of the base unit.
  
  

  • 1 centimeter (cm) = 0.01 meters (m)

  • 1 centiliter (cL) = 0.01 liters (L)

• milli- (m) means 1/1,000 (one thousandth) of the base unit.
  
  

  • 1 millimeter (mm) = 0.001 meters (m)

  • 1 milligram (mg) = 0.001 grams (g)

• micro- (µ) means 1/1,000,000 (one millionth) of the base unit.
  
  

  • 1 micrometer (µm) = 0.000001 meters (m)

  • 1 microgram (µg) = 0.000001 grams (g)

• nano- (n) means 1/1,000,000,000 (one billionth) of the base unit.
  
  

  • 1 nanometer (nm) = 0.000000001 meters (m)

  • 1 nanogram (ng) = 0.000000001 grams (g)

4. How would you represent a number such as 3,456 in Scientific Notation? 

• 3,456 = 3.456 × 10³

5. How would you represent a number such as 0.00568 in Scientific Notation? 

• 0.00568 = 5.68 × 10⁻³

6. Write the number 10,000 as a power of 10 with the correct exponent. 

• 10,000 = 1 × 10⁴

7. Which of the following tools would be most appropriate for measuring 1 mL of water? 500 mL beaker, 250 mL Erlenmeyer flask, 500 mL graduated cylinder, 5 mL pipette. 

• The most appropriate tool for measuring 1 mL of water would be a 5 mL pipette, as it is the most precise for measuring small amounts of liquid.

8. What is the purpose of a weight boat or weighing paper? 

• The weigh boat or weighing paper is used to hold solid samples while they are being weighed on a balance. This ensures that the substance does not come into direct contact with the balance pan, preventing contamination and allowing for easy transfer of the sample.

9. What is the purpose of being able to tare or zero a balance?

• The tare or zero function of a balance allows the user to set the balance to zero before weighing a sample. This accounts for the weight of any container or weigh boat used, so only the weight of the substance being measured is recorded. This ensures accurate measurements by eliminating the container's weight from the final reading.

LAB 2:

1. Be able to identify by name and function, all the parts of the microscope. 

Eyepiece (Ocular lens): The lens through which you look at the specimen. It typically magnifies 10x.

Objective lenses: These are the lenses closest to the specimen. They are typically 4x, 10x, 40x, and 100x. These lenses are used to achieve different magnifications.

Nosepiece: The rotating part that holds the objective lenses and allows you to switch between them.

Stage: The flat platform where you place the slide with the specimen. The stage may have clips to hold the slide in place.

Stage clips: Hold the slide in place on the stage.

Condenser: Focuses light onto the specimen. It is located beneath the stage.

Diaphragm (Iris or Aperture): Controls the amount of light that reaches the specimen.

Coarse focus knob: Used to make large adjustments to the focus, typically used with low-power objectives.

Fine focus knob: Used to make small, precise adjustments to the focus, typically used with high-power objectives.

Arm: Supports the body tube and connects to the base.

Base: The bottom of the microscope that supports the entire structure.

Light source (Lamp): Provides the light needed to illuminate the specimen.

Mirror (if applicable): Reflects light onto the specimen if there is no built-in light source.

2. How many objective lenses are on a PCC microscope? 

• A typical PCC (PowerPoint or standard classroom microscope) has 4 objective lenses: 4x (scanning), 10x (low power), 40x (high power), and 100x (oil immersion).

3. What do the longitudinal and transverse adjustment knobs do? 

• Longitudinal adjustment knob: Typically controls the movement of the stage along the y-axis (forward and backward) to help position the specimen.

• Transverse adjustment knob: Controls the movement of the stage along the x-axis (left and right).

4. What is the only objective lens that you are allowed to use the coarse focus control with? 

• You should only use the coarse focus control with the 4x (scanning) objective lens. Using the coarse focus with higher magnifications (such as 10x, 40x, or 100x) can damage the slide or the objective lens.

5. Where would I find the "specimen holder"? 

• The specimen holder is located on the stage of the microscope. It's typically a pair of clips that hold the slide in place.

6. How do you determine total magnification? 

Multiply the magnification of the eyepiece (ocular lens) by the magnification of the objective lens being used.

• Example: If the eyepiece magnifies 10x and you're using the 40x objective lens, the total magnification is:

  • 10x (eyepiece) × 40x (objective lens) = 400x total magnification.

7. Explain the difference between the image you see through the microscope lenses and what you see on the slide with the naked eye. 

• When you view a specimen with the naked eye, the image is seen in natural size.

• When you use a microscope, the image is magnified, so you can see smaller details, structures, or organisms that are otherwise invisible to the naked eye.

• The image through the microscope is also inverted and reversed (upside down and backwards) compared to the view on the slide.

8. Observations of a new slide always start with which objective lens? 

• When starting observations of a new slide, always begin with the 4x (scanning) objective lens. This is because it has the widest field of view and allows you to locate the specimen before switching to higher magnifications.

9. What is the correct procedure for focusing on a specimen on a slide? 

• Start with the lowest objective lens (4x) to locate the specimen.

• Use the coarse focus knob to bring the specimen into rough focus.

• Once the specimen is roughly in focus, switch to a higher objective lens (10x, 40x).

• Use the fine focus knob to make small adjustments and achieve a sharp image.

• If using the oil immersion lens (100x), add a drop of immersion oil and carefully use the fine focus to bring the image into focus.

10.Explain "parfocal" and "depth of focus". 

• Parfocal: This means that once you focus on the specimen at a low magnification, it will remain approximately in focus when you switch to a higher magnification. Minor adjustments with the fine focus are usually required when changing objective lenses.
  
  

• Depth of focus: The depth of focus refers to the thickness of the specimen that remains in focus at a given magnification. At higher magnifications, the depth of focus is smaller, meaning that only a thin layer of the specimen will be in focus at one time.

11.Define working distance and field of view. 

• Working distance: This is the distance between the objective lens and the specimen. As you increase magnification, the working distance decreases (you get closer to the specimen).
  
  

• Field of view: This refers to the area of the specimen that is visible through the microscope lenses. As magnification increases, the field of view becomes smaller.

12. As magnification changes what happens to: depth of field, field of view, working distance, available light?

• Depth of Field: As magnification increases, the depth of field decreases. At high magnifications, only a thin layer of the specimen is in focus at any given time.
  
  

• Field of View: As magnification increases, the field of view decreases. You see less of the specimen, but in greater detail.
  
  

• Working Distance: As magnification increases, the working distance decreases. You need to get closer to the specimen at higher magnifications.
  
  

• Available Light: As magnification increases, the amount of available light decreases. Higher magnifications require more light to keep the image bright and clear.

13.Which objective lens is used for oil immersion? Can you use that lens without oil? 

• The 100x objective lens is used for oil immersion.

• No, you should not use the oil immersion lens without oil. The oil helps to increase the resolution by reducing light refraction as it travels from the specimen to the objective lens. Using the lens without oil would lead to a blurry image and could potentially damage the lens.

14.Why does oil immersion technique allow you to see a slide more clearly? 

• The oil immersion technique improves clarity because the oil has the same refractive index as glass. This reduces the light refraction (bending of light) that typically occurs when light passes from the glass slide to the air and then into the objective lens. As a result, more light enters the objective lens, which enhances image clarity and resolution at high magnification (100x).

15.How do you properly clean the oil immersion lens? 

• Use lens paper or a soft cloth to gently wipe the oil immersion lens after you are done using it.

• Apply lens cleaner (if necessary) to a piece of lens paper to remove any oil residue.

• Never use tissue or paper towels, as they can scratch the lens.

• Make sure to wipe the lens gently to avoid damaging the lens or the objective lens coating.

16.How should the light intensity control knob be set before turning the microscope off/on?

• Lowest setting 

17.What is the procedure for putting a microscope away? 

1. Lower the stage to its lowest point using the coarse focus knob.

2. Turn off the light and set the light intensity control knob to its lowest setting.

3. Remove any slides from the stage and clean up any materials around the microscope.

4. Rotate the objective lenses to the lowest power (4x) position.

5. Cover the microscope with its dust cover to protect the lenses and components.

6. Unplug the microscope (if applicable), and store it in a safe, dry place.

18.How many microns (micrometers or µm) in a millimeter (mm)? 

There are 1,000 microns (µm) in a millimeter (mm).

• 1 mm = 1,000 µm

19.Be able to estimate the size of an object seen in the field of view of your microscope

• Determine the field of view (FOV) for the current objective lens. For example, under a 10x objective, the FOV might be about 1,500 µm, and under a 40x objective, the FOV might be around 400 µm.
  
  

• Estimate the size of the object by comparing it to the size of the field of view. For instance, if the object is about half the width of the FOV under the 40x objective, you can estimate its size to be approximately 200 µm.

LAB 3:

1. What is pH? 

• pH is a measure of the hydrogen ion concentration (H⁺) in a solution. It indicates how acidic or basic (alkaline) a solution is. pH is measured on a scale from 0 to 14, with 7 being neutral. A pH lower than 7 indicates an acidic solution, and a pH higher than 7 indicates a basic (alkaline) solution.

2. Explain why pH is such an important factor in the life of an organism. 

• pH affects the shape and function of proteins, including enzymes, which are critical for biochemical reactions in living organisms. Extreme pH values can denature proteins and disrupt cellular functions. Many biochemical processes, such as respiration, digestion, and nerve function, are optimized to occur at specific pH levels. For example, human blood must maintain a pH close to 7.4 for proper functioning of enzymes and other cellular components.

3. Describe what makes a solution acidic? Basic? 

• Acidic solution: A solution is acidic if it has a higher concentration of hydrogen ions (H⁺) compared to hydroxide ions (OH⁻). The pH of an acidic solution is less than 7.
  
  

• Basic (alkaline) solution: A solution is basic if it has a higher concentration of hydroxide ions (OH⁻) compared to hydrogen ions (H⁺). The pH of a basic solution is greater than 7.

4. What is the difference between pH units? (A solution with a pH of 9 is how many times more basic that a solution with a pH of 8?) 

• pH is a logarithmic scale. This means that a one-unit change in pH represents a tenfold change in H⁺ concentration. A solution with a pH of 9 has ten times fewer hydrogen ions (H⁺) than a solution with a pH of 8. Therefore, the solution with a pH of 9 is 10 times more basic than the solution with a pH of 8.

5. Which has a greater concentration of H+, a solution with a pH of 4 or a solution with a pH of 8? 

• A solution with a pH of 4 has a greater concentration of hydrogen ions (H⁺) than a solution with a pH of 8. Since pH is inversely related to the concentration of H⁺ ions, a lower pH corresponds to a higher concentration of hydrogen ions. The pH 4 solution is 10,000 times more acidic than the pH 8 solution (4 units difference = 10,000 times).

6. Describe the activity of bromothymol blue. 

• Bromothymol blue is a pH indicator that changes color based on the pH of a solution. It is yellow in acidic conditions (pH < 6), green in neutral conditions (pH ~7), and blue in basic conditions (pH > 7). This makes it useful for determining whether a solution is acidic, neutral, or basic.

7. Why does water become acidic when you blow into it with a straw? 

• When you blow into water, you are releasing carbon dioxide (CO₂). This CO₂ dissolves in the water and reacts with water molecules to form carbonic acid (H₂CO₃). The carbonic acid dissociates, releasing hydrogen ions (H⁺) and making the solution acidic. This is why water becomes more acidic when you blow into it.

8. What components of red cabbage extract make it useful as a pH indicator? Why? 

• Red cabbage contains a pigment called anthocyanin, which changes color depending on the pH of the solution it is in. In acidic solutions, it appears red; in neutral solutions, it appears purple, and in basic solutions, it appears green or yellow. Anthocyanin is useful as a pH indicator because of its ability to undergo structural changes that alter its color in response to pH variations.

9. Describe the function of a buffer 

• A buffer is a substance that helps maintain the pH of a solution by neutralizing small amounts of added acid (H⁺) or base (OH⁻). Buffers typically consist of a weak acid and its conjugate base, or a weak base and its conjugate acid. They resist changes in pH within a certain range, which is important for maintaining homeostasis in biological systems.

10.Give an example of a biological buffering system (Challenge question: Explain how the carbonic acid-bicarbonate buffering system contributes to the pH stability of human blood.)

Carbonic acid-bicarbonate buffer is an important buffering system in the human body that helps maintain the pH of blood around 7.4.

• Carbonic acid (H₂CO₃) dissociates into hydrogen ions (H⁺) and bicarbonate ions (HCO₃⁻).

• If the blood becomes too acidic (pH drops), bicarbonate ions (HCO₃⁻) act as a base and neutralize excess hydrogen ions.

• If the blood becomes too basic (pH rises), carbonic acid (H₂CO₃) releases hydrogen ions to lower the pH.

This dynamic equilibrium helps maintain a stable pH in the blood. 

11.Explain the difference between a buffer’s pH range and its buffering capacity. 

• pH range: This refers to the range of pH values over which the buffer effectively resists changes in pH. It is the range in which the buffer can maintain its function.
  
  

• Buffering capacity: This refers to the amount of acid or base a buffer can absorb without causing a significant change in pH. A buffer with a higher buffering capacity can absorb more acid or base before the pH changes significantly.

12.From a titration curve, determine the pH range and buffering capacity of a buffer.

• pH range: The pH range of a buffer is typically determined by examining the flat region of the titration curve, where the pH changes very little despite the addition of acid or base. This region indicates the effective working range of the buffer.
  
  

• Buffering capacity: The buffering capacity can be determined by looking at how much acid or base is needed to cause a significant change in pH. The steep parts of the titration curve indicate where the buffer capacity is being exceeded. The larger the flat region, the higher the buffering capacity.

LAB 4:

1. Describe the structure of a monosaccharide, disaccharide, and a polysaccharide. Give examples of each type of carbohydrate. 

​​Monosaccharide: A monosaccharide is the simplest form of sugar and consists of a single sugar unit. It is composed of carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1. The general formula is C6H12O6C_6H_{12}O_6C6​H12​O6​. Monosaccharides can be classified by the number of carbon atoms they contain (e.g., glucose and fructose are hexoses because they have six carbon atoms).

• Example: Glucose, Fructose.

Disaccharide: A disaccharide consists of two monosaccharide molecules linked by a glycosidic bond. It is formed through a condensation reaction (where a water molecule is released). Disaccharides are used for short-term energy storage.

• Example: Sucrose (glucose + fructose), Lactose (glucose + galactose), Maltose (glucose + glucose).

Polysaccharide: A polysaccharide is a long chain of monosaccharides linked by glycosidic bonds. These molecules serve as energy storage or structural components in organisms.

• Example: Starch (energy storage in plants), Glycogen (energy storage in animals), Cellulose (structural component in plant cell walls).

2. What are the primary functions of carbohydrates in living organisms? 

• Energy Source: Carbohydrates are a primary energy source for cells. Simple sugars like glucose are broken down during cellular respiration to produce ATP (adenosine triphosphate), which powers cellular processes.
  
  

• Energy Storage: Polysaccharides like starch (plants) and glycogen (animals) store energy for later use.
  
  

• Structural Role: Carbohydrates like cellulose in plants and chitin in arthropods provide structural support.
  
  

• Cell Signaling: Carbohydrates on the surface of cells (in glycoproteins and glycolipids) play a role in cell recognition and signaling.

3. What is the name of a key functional group found in carbohydrates. (Remember functional groups are atoms or groups of atoms bonded to a carbon atom that give an organic compound certain chemical properties) 

• The key functional group found in carbohydrates is the hydroxyl group (-OH). This functional group is responsible for the solubility of sugars in water and their chemical reactivity.

4. Differentiate between an aldose and a ketose. 

• Aldose: A monosaccharide that contains an aldehyde group (-CHO) at the end of the molecule. Aldoses are typically found in sugars like glucose and galactose.
  
  

• Ketose: A monosaccharide that contains a ketone group (C=O) within the molecule, not at the end. Fructose is an example of a ketose.

5. Explain the use and interpretation of the Benedict’s test. What color(s) indicates a positive result? What color(s) indicates a negative result? Would you expect any other changes in the solution besides color if the test was positive? 

Benedict’s test is used to detect reducing sugars (sugars with a free aldehyde or ketone group).

• Positive Result: A color change from blue to green, yellow, orange, or red, depending on the concentration of reducing sugars present.
  
  

• Negative Result: The solution remains blue if no reducing sugars are present.
  
  

• Other Changes: In addition to the color change, you may observe the formation of a precipitate in the positive test, indicating the reduction of copper ions to copper oxide.

6. Explain why sucrose would test negative using the Benedict’s test? 

• Sucrose is a non-reducing sugar because its anomeric carbon atoms are involved in a glycosidic bond, and it does not have a free aldehyde or ketone group. As a result, sucrose does not reduce the copper ions in Benedict's reagent, so it would test negative in the Benedict's test.

7. If a disaccharide such as lactose tested positive using Benedict’s test, what would that tell you about the position of the carbonyl functional group in the ring structure? 

• If lactose (a disaccharide) tested positive for Benedict’s test, it would indicate that at least one of the monosaccharides in the disaccharide has a free aldehyde group (as lactose is a reducing sugar). This suggests that the carbonyl group is not involved in the glycosidic bond and is available to reduce copper ions in the Benedict’s reagent, making the solution test positive.

8. Why did we use controls in the tests you conducted for this lab? Explain why water was an appropriate control. 

• Controls are used to ensure that the test is working correctly and to eliminate confounding variables. Water is an appropriate control because it does not contain any sugars or other substances that would interfere with the test, so it should show a negative result. By comparing the experimental results to the control, we can determine if the substance being tested contains the component we are investigating (e.g., reducing sugars or starch).

9. Explain the use and interpretation of a test using I2 KI (Lugol's iodine). What color indicates a positive result? What color indicates a negative result? 

I2 KI (Lugol’s iodine) is used to test for the presence of starch.

• Positive Result: The iodine will react with starch and turn blue-black in color.
  
  

• Negative Result: The solution will remain yellow-brown if starch is not present.

10.Describe the structure of a protein molecule.

A protein is a polymer made up of amino acids, which are linked by peptide bonds. The structure of a protein can be described in four levels:

• Primary Structure: The sequence of amino acids in a polypeptide chain.
  
  

• Secondary Structure: The folding of the polypeptide chain into alpha-helices or beta-pleated sheets, stabilized by hydrogen bonds.
  
  

• Tertiary Structure: The three-dimensional shape of the protein, formed by the interactions between the side chains (R groups) of amino acids (such as hydrogen bonds, ionic bonds, and disulfide bridges).
  
  

• Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) that work together as a functional protein.

Proteins perform a wide variety of functions, such as catalyzing reactions (enzymes), transporting molecules, and providing structural support in cells.

11.What is the basic building block (monomer) for a protein? What functional groups characterize this monomer? 

The basic building block (monomer) of a protein is an amino acid.

Amino acids have two key functional groups:

• Amino group (-NH2): This group contains nitrogen and can accept a proton, acting as a base.

• Carboxyl group (-COOH): This group contains a carbonyl and hydroxyl group, and it can donate a proton, acting as an acid.

In addition to these groups, each amino acid has a unique side chain (R group) that varies between different amino acids and gives each amino acid its specific properties.

12.List the functions of proteins in living organisms. 

Proteins have a wide variety of functions in living organisms, including:

1. Enzyme Catalysis: Proteins called enzymes speed up biochemical reactions.

2. Structural Support: Proteins like collagen and keratin provide structure to cells and tissues.

3. Transport: Proteins like hemoglobin transport molecules like oxygen across the body.

4. Movement: Proteins like actin and myosin are involved in muscle contraction and cell movement.

5. Defense: Antibodies are proteins that help protect the body from foreign invaders.

6. Signaling: Proteins such as hormones (like insulin) regulate various physiological processes.

7. Storage: Proteins can store nutrients (e.g., ferritin stores iron).

8. Gene Expression: Some proteins are involved in regulating the expression of genes and controlling the cell cycle.

13.Explain the use and interpretation of the biuret test. What color indicates a positive result? What color indicates a negative result? 

The Biuret test is used to detect the presence of proteins.

• Positive Result: A color change to violet indicates that proteins (or polypeptides) are present. This is due to the peptide bonds in proteins reacting with the Biuret reagent.

• Negative Result: The solution remains blue if no proteins are present.

14.Be able to name the reagent used to test for the presence of reducing sugars, starch, and protein. 

• Reducing Sugars: Benedict's solution (Benedict's test) is used to test for reducing sugars. A positive result gives a color change from blue to green, yellow, orange, or red depending on the sugar concentration.
  
  

• Starch: Iodine solution (I2 KI) is used to test for starch. A positive result gives a color change to blue-black.
  
  

• Proteins: Biuret reagent is used to test for proteins. A positive result gives a color change to violet.

15.What are the limits of these tests? (What information is not provided by these tests?)

• Benedict's Test: This test only detects reducing sugars. It does not distinguish between different types of sugars (e.g., glucose vs. fructose) and cannot detect non-reducing sugars like sucrose unless they are hydrolyzed.
  
  

• Iodine Test: This test only detects starch. It cannot differentiate between different types of polysaccharides (e.g., starch vs. glycogen or cellulose) or other carbohydrates.
  
  

• Biuret Test: This test detects peptide bonds and is used to test for proteins, but it does not provide specific information about the type of protein, its structure, or function. It also cannot detect small peptides (short chains of amino acids) that may not have fully formed proteins yet.

LAB 5:

1. What is the driving force (energy) that powers passive processes? powers active processes? 

• Passive Processes: The driving force for passive transport is the concentration gradient, meaning substances move from an area of higher concentration to an area of lower concentration. No energy (ATP) is required. Examples of passive processes include diffusion and osmosis.
  
  

• Active Processes: The driving force for active transport is the direct use of energy, typically in the form of ATP. Active transport moves substances against their concentration gradient (from low to high concentration). Examples include active transport through pumps like the sodium-potassium pump.

2. What does it mean for a membrane to be semi-permeable? 

A semi-permeable membrane means that the membrane allows some molecules or ions to pass through while blocking others. Typically, small, non-polar molecules can pass through easily, while larger, charged, or polar molecules are restricted. The degree of permeability depends on factors like size, charge, and whether the molecule can interact with the hydrophobic interior of the membrane.

3. What is diffusion? What is osmosis? Is osmosis an example of an active or passive process? 

• Diffusion: Diffusion is the movement of molecules or ions from an area of higher concentration to an area of lower concentration, driven by the kinetic energy of the molecules. It continues until equilibrium is reached.
  
  

• Osmosis: Osmosis is a type of diffusion that specifically refers to the movement of water molecules across a semi-permeable membrane. Water moves from an area of low solute concentration to an area of high solute concentration.
  
  

• Osmosis is a passive process because it doesn't require energy (ATP); it relies on the concentration gradient of water.

4. How are simple diffusion and facilitated diffusion different? 

• Simple Diffusion: In simple diffusion, molecules move directly through the lipid bilayer without the help of transport proteins. This typically happens with small, non-polar molecules like oxygen or carbon dioxide.
  
  

• Facilitated Diffusion: In facilitated diffusion, larger or polar molecules (like glucose) require the help of transport proteins (such as channels or carriers) to cross the membrane. The molecules still move down their concentration gradient, and energy is not required.

5. Describe a solution that is hypotonic, hypertonic, or isotonic to the contents of the cell? 

• Hypotonic Solution: A solution that has a lower concentration of solutes compared to the inside of the cell. Water will enter the cell, causing it to swell or even burst (lysis).
  
  

• Hypertonic Solution: A solution that has a higher concentration of solutes compared to the inside of the cell. Water will leave the cell, causing it to shrink (crenation in animal cells or plasmolysis in plant cells).
  
  

• Isotonic Solution: A solution where the concentration of solutes is equal to that inside the cell. There is no net movement of water, and the cell maintains its shape.

6. How do cells with cell walls differ from cells without cell walls when put in a hypotonic environment? a hypertonic environment? an isotonic environment? 

In a Hypotonic Environment:

• Cells with cell walls (e.g., plant cells) will swell due to the influx of water, but the cell wall prevents bursting. The cell becomes turgid (firm).

• Cells without cell walls (e.g., animal cells) will swell and may lyse (burst) if the excess water is not removed.

In a Hypertonic Environment:

• Cells with cell walls (e.g., plant cells) will undergo plasmolysis, where the cell membrane pulls away from the cell wall due to the loss of water.

• Cells without cell walls (e.g., animal cells) will shrink and may become crenated due to water loss.

In an Isotonic Environment:

• Cells with cell walls (e.g., plant cells) will maintain a flaccid state (not fully turgid but not plasmolyzed either).

• Cells without cell walls (e.g., animal cells) will maintain their normal shape, with no net movement of water.

7. Understand the terms turgid, flaccid, plasmolysis, lyse, and crenate with respect to osmosis. 

• Turgid: A state where plant cells are firm and swollen due to water intake in a hypotonic solution. The cell wall prevents further expansion.
  
  

• Flaccid: A state where plant cells have lost some water and are not firm. This happens in an isotonic solution where there is no net movement of water.
  
  

• Plasmolysis: The process where plant cell membranes pull away from the cell wall due to water loss in a hypertonic solution.
  
  

• Lyse: The bursting of an animal cell due to excessive water intake in a hypotonic solution.
  
  

• Crenate: The shrinking of an animal cell due to water loss in a hypertonic solution.

8. If all other parameters are equal which would diffuse faster: a small or a large molecule?

• Small molecules would diffuse faster than large molecules because they have less mass and can move more easily through the membrane and the surrounding medium. 

9. Was glucose able to pass through the dialysis tubing in Supplemental Act. 4? Was the starch able to pass through the dialysis tubing in Act. 4? Why is it important to know that glucose is a monosaccharide and starch is a polysaccharide for your conclusions?

• Glucose (monosaccharide) is small enough to pass through the dialysis tubing (which typically has pores that allow small molecules to pass), so it would likely be able to diffuse through the tubing.
  
  

• Starch (polysaccharide) is much larger and would not pass through the dialysis tubing because the pores in the tubing are too small to allow large molecules to pass through.
  
  

Knowing that glucose is a monosaccharide and starch is a polysaccharide helps explain this because monosaccharides are smaller and can diffuse through the pores of the dialysis tubing, while polysaccharides are too large to pass through.

LAB 6:

1. What molecule is formed (for energy usage in the cell) as a result of all processes that catabolize glucose? 

• The molecule formed is ATP (adenosine triphosphate). ATP is the primary energy currency of the cell, used to power cellular processes.

2. What is meant by a metabolic pathway? What does the term catabolism mean? 

• Metabolic Pathway: A metabolic pathway refers to a series of interconnected biochemical reactions that occur within a cell, where the product of one reaction becomes the substrate for the next. These pathways often involve enzymes that catalyze the reactions.
  
  

• Catabolism: Catabolism refers to the breakdown of larger, complex molecules into smaller ones, often releasing energy. In the case of glucose, catabolic processes break it down into carbon dioxide and water, releasing energy that is used to form ATP.

3. Explain how the processes of aerobic respiration and fermentation differ? In what ways are they similar? 

Aerobic Respiration:

• Occurs in the presence of oxygen.

• Involves three main stages: Glycolysis, Krebs Cycle (Citric Acid Cycle), and Electron Transport Chain.

• Produces a large amount of ATP (about 36-38 molecules per glucose).

• The final electron acceptor is oxygen, forming water.

Fermentation:

• Occurs in the absence of oxygen (anaerobic conditions).

• Involves only glycolysis; no citric acid cycle or electron transport chain.

• Produces much less ATP (2 ATP per glucose).

• The final electron acceptor is an organic molecule (like pyruvate or acetaldehyde, depending on the type of fermentation).

Similarities: Both processes begin with glycolysis, where glucose is broken down into pyruvate, and both processes ultimately generate ATP.

4. Identify the final electron acceptor used for aerobic respiration and fermentation. 

• Aerobic Respiration: The final electron acceptor is oxygen. Oxygen accepts electrons and combines with protons (H+) to form water.
  
  

• Fermentation: The final electron acceptor is typically an organic molecule. For example, in alcoholic fermentation, acetaldehyde acts as the final electron acceptor and is reduced to ethanol.

5. Is glucose the only source of energy? Explain your answer. 

• No, glucose is not the only source of energy. While glucose is a major energy source, cells can also utilize other molecules such as fatty acids, amino acids, and lactic acid for energy production. These molecules can enter cellular respiration at various stages (e.g., fatty acids enter the Krebs cycle, amino acids can be converted into intermediates for glycolysis or the Krebs cycle).

6. Know the summary equations for both cellular respiration and anaerobic fermentation. 

Cellular Respiration (aerobic):
C6H12O6+6O2→6CO2+6H2O+ATP

This equation shows that glucose and oxygen are converted into carbon dioxide, water, and energy (ATP).

Anaerobic Fermentation:

• Alcoholic Fermentation (by yeast):
  C6H12O6→2C2H5OH+2CO2+2ATP
  Glucose is converted into ethanol, carbon dioxide, and ATP.
  
  

• Lactic Acid Fermentation (in muscle cells):
  C6H12O6→2C3H6O3+2ATP
  Glucose is converted into lactic acid and ATP.

7. Know the purpose of all equipment and all experimental treatments in the experiments to detect respiration in germinating peas. What was the specific purpose of KOH? 

• Equipment: The experiment typically uses a respirometer to measure oxygen consumption and carbon dioxide production. The setup may include germinating peas, a sealed container, a syringe to adjust air volume, and a KOH solution.
  
  

• Purpose of KOH: Potassium hydroxide (KOH) is used to absorb carbon dioxide produced during cellular respiration. As CO₂ is absorbed by KOH, it prevents a build-up of CO₂ in the respirometer, ensuring that any volume changes observed are due to oxygen consumption.

8. What are the waste products formed during fermentation by yeast cells? 

• The waste products of alcoholic fermentation in yeast cells are ethanol and carbon dioxide. In lactic acid fermentation, the waste product is lactic acid.

9. Explain how the rate of alcoholic fermentation can be measured using fermentation tubes.

• In the experiment with fermentation tubes, the rate of fermentation is often measured by the production of gas (CO₂). As yeast ferments sugar, CO₂ is produced and can be captured in an inverted tube or by measuring the displacement of liquid in a manometer. The more gas produced, the faster the rate of fermentation. The amount of CO₂ produced can be used as an indirect measure of the fermentation rate.

LAB 7:

1. What is a nucleotide?

• A nucleotide is the basic building block of nucleic acids like DNA and RNA. It is composed of three components: a phosphate group, a sugar molecule (deoxyribose in DNA and ribose in RNA), and a nitrogenous base.

2. What are the three parts of a nucleotide?

• The three parts of a nucleotide are:

  • Phosphate group: Contains a phosphorus atom bonded to four oxygen atoms.

  • Sugar molecule: In DNA, the sugar is deoxyribose, and in RNA, the sugar is ribose.

  • Nitrogenous base: There are four nitrogenous bases in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G). In RNA, thymine is replaced by uracil (U).

3. What 4 bases are found in the DNA molecule?

The four nitrogenous bases in DNA are:

1. Adenine (A)

2. Thymine (T)

3. Cytosine (C)

4. Guanine (G)

4. Can you use Chargaff’s rules? e.g. An organism’s DNA is analyzed and found to be 30% cytosine. Can you predict the percentage of guanine, adenine, and thymine?

Chargaff's rules state that in any DNA molecule:

• The amount of adenine (A) equals the amount of thymine (T).

• The amount of cytosine (C) equals the amount of guanine (G).

If the DNA of an organism is found to be 30% cytosine (C), then it will also be 30% guanine (G), because C pairs with G.

Since A = T, the remaining percentage (100% - 30% C - 30% G = 40%) must be split equally between adenine (A) and thymine (T). Thus:

• A = 20%

• T = 20%

5. Know the Watson & Crick model of the DNA double-helix.

The Watson & Crick model of DNA describes the structure of DNA as a double helix (two intertwined strands). The key features of this model include:

• DNA consists of two strands that run in opposite directions, which are antiparallel.

• Each strand is made of a backbone of sugar and phosphate groups.

• The nitrogenous bases of the two strands are paired via hydrogen bonds: adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).

• The bases form complementary base pairs, which help stabilize the structure and allow for accurate DNA replication.

6. What was the purpose of the sports drink during DNA extraction? Contrast this with the purpose of the cell lysate solution.

Sports drink: The sports drink often contains sodium and salts that help stabilize the DNA and make the extraction process easier. It helps to prevent the DNA from degrading and helps to "coat" the DNA, aiding in its extraction.

Cell lysate solution: The purpose of the cell lysate solution is to break open the cells (by disrupting the cell membrane and nuclear envelope) and release the DNA. This solution typically contains a detergent, such as SDS (sodium dodecyl sulfate), which breaks down the lipid membranes and releases the DNA into the solution. The lysate also often contains salts to neutralize the charge on the DNA and stabilize it.

7. How was the ethanol used during DNA extraction?

• Ethanol (or isopropanol) is used to precipitate the DNA. After the cells are lysed and the DNA is released into the solution, the addition of ethanol causes the DNA to become insoluble and precipitate out of the solution. Since DNA is not soluble in alcohol, it will form visible clumps or a stringy mass that can be collected. Ethanol is also used to wash the DNA, helping to remove any remaining contaminants.

LAB 8:

1. Define what is meant by an allele, point mutation, and polymorphism. 

Allele: An allele is a variant form of a gene found at a specific position (locus) on a chromosome. Each individual has two alleles for each gene, one inherited from each parent. Alleles can be dominant or recessive, influencing traits in different ways.

Point mutation: A point mutation is a change in a single nucleotide base in the DNA sequence. This can lead to a change in the codon, and possibly the amino acid sequence of a protein. Point mutations include substitutions, insertions, and deletions at a specific position in the DNA.

Polymorphism: A polymorphism is a variation in DNA sequence that exists within a population at a frequency greater than 1%. Polymorphisms can result in different traits among individuals, such as eye color or susceptibility to diseases.

2. Identify and understand the purpose of the 3 stages of a single thermocycle (at 95°C, 64C, and 72°C) in the PCR reaction. 

• 95°C (Denaturation): The first stage of PCR is denaturation, where the double-stranded DNA template is heated to 95°C to break the hydrogen bonds between complementary base pairs, resulting in two single-stranded DNA molecules.
  
  

• 64°C (Annealing): In the second stage, the temperature is lowered to about 64°C to allow the primers to bind (anneal) to the complementary sequences on the single-stranded DNA template. The primers are short DNA sequences that initiate DNA synthesis.
  
  

• 72°C (Extension): The final stage occurs at 72°C, which is the optimal temperature for the DNA polymerase (commonly Taq polymerase) to extend the primers and synthesize new strands of DNA by adding nucleotides to the primers. This step builds the new complementary strands.

3. Understand the purpose of the primers in the PCR reaction. 

Primers are short, single-stranded sequences of nucleotides that are complementary to the sequences on the single-stranded DNA templates. Their purpose is to provide a starting point for DNA polymerase to begin synthesizing a new DNA strand. There are two primers in PCR, one for each strand of the DNA template (forward and reverse primers).

4. Understand why the PCR reaction is done in a series of cycles. For example, after 3 cycles, how many copies of your gene of interest would you have? 

• PCR is performed in cycles to amplify the DNA. Each cycle includes denaturation, annealing, and extension, which results in the doubling of the amount of DNA. After 1 cycle, you would have 2 copies of the target DNA. After 2 cycles, you would have 4 copies, and after 3 cycles, you would have 8 copies (2^n, where n is the number of cycles).

5. Explain why the polymerase enzyme in the PCR reaction is able to withstand the repeated heating to 95°C and is active at 72°C. 

• The polymerase enzyme used in PCR is typically Taq polymerase, which is derived from the bacterium Thermus aquaticus. This enzyme is thermostable, meaning it can withstand high temperatures without denaturing. Taq polymerase is active at 72°C, which is the optimal temperature for its activity during the extension step.

6. What does a restriction enzyme do? 

• A restriction enzyme (also known as a restriction endonuclease) is an enzyme that cuts DNA at specific sequences. These sequences are usually 4-8 base pairs long and are called recognition sites. Restriction enzymes are used to cut DNA molecules into smaller fragments, which can be useful in cloning, mapping, and sequencing DNA.

7. How can a restriction enzyme help identify gene differences? 

• Restriction enzymes can be used to identify genetic differences by recognizing specific sequences in DNA. Restriction fragment length polymorphisms (RFLPs) are variations in the lengths of DNA fragments produced when DNA is cut by restriction enzymes. Differences in DNA sequences, such as mutations or polymorphisms, may create or abolish a recognition site for a restriction enzyme, resulting in different fragment patterns that can be detected on a gel.

8. Describe the process of agarose gel electrophoresis. 

• Agarose gel electrophoresis is a technique used to separate DNA fragments based on their size. DNA samples are loaded into wells in an agarose gel, and an electric current is applied. Since DNA is negatively charged due to its phosphate backbone, it moves towards the positive electrode. Smaller DNA fragments move faster through the gel, while larger fragments move more slowly. After electrophoresis, the DNA fragments can be visualized using a dye like ethidium bromide.

9. What is the purpose of a DNA molecular weight standard (DNA ladder)? 

• A DNA molecular weight standard (or DNA ladder) is a mixture of DNA fragments of known sizes. It is run alongside the samples in gel electrophoresis to serve as a reference for estimating the size of unknown DNA fragments based on their migration distance in the gel.

10.In a gel picture, be able to estimate the size of a DNA fragment by comparing to the DNA ladder. 

• To estimate the size of DNA fragments in a gel, you compare the migration distance of your sample bands to the bands of the DNA ladder. The DNA ladder has markers of known sizes (in base pairs), and by matching the position of your bands to the ladder, you can estimate their size.

11.Interpret a gel picture to identify bands that indicate “wild-type” and mutant sickle cell alleles for beta-globin proteins. 

• In sickle cell disease, a point mutation in the beta-globin gene causes a difference in the DNA sequence. This can alter the restriction enzyme recognition site and result in different fragment lengths when the DNA is digested with a restriction enzyme.

  • A wild-type allele would show a pattern of fragments based on the normal sequence.

  • A mutant sickle cell allele would show a different fragment pattern due to the mutation that affects the recognition site.

12.Know the proper set up of the gel, power source, and electrodes for an electrophoresis gel. What is the purpose of the “comb” when preparing the gel? 

The gel electrophoresis setup includes:

1. Agarose gel placed in an electrophoresis chamber.

2. Wells where DNA samples are loaded, created by a comb before the gel solidifies. The comb allows for the formation of the wells, which hold the DNA samples.

3. Electrodes: The positive electrode is placed at the far end of the gel, and the negative electrode is at the end where the samples are loaded. DNA moves towards the positive electrode.

4. Power source: A constant voltage is applied to drive the DNA through the gel.

13.Your dye samples moved through your agarose gel by electrophoresis. Which pieces moved the farthest by molecular weight?

• The smaller DNA fragments move the farthest in the gel because they encounter less resistance as they travel through the agarose matrix. Larger fragments move more slowly and travel a shorter distance.

LAB 9:

1. Distinguish between the designations Covid-19 and SARS-Cov-2. 

• COVID-19: This is the name of the disease caused by the virus SARS-CoV-2. "COVID-19" stands for "Coronavirus Disease 2019," referring to the year the disease was first identified.
  
  

• SARS-CoV-2: This refers to the Severe Acute Respiratory Syndrome Coronavirus 2, the virus responsible for causing the disease COVID-19. It is a novel coronavirus related to the SARS-CoV virus that caused the SARS outbreak in 2003.

2. Be able to explain the basic differences between the work done in a clinical diagnostic laboratory and a research laboratory. 

• Clinical Diagnostic Laboratory: These labs focus on testing and diagnosing diseases in individuals. Their primary goal is to provide accurate results for patient care, such as identifying infections or abnormalities in bodily fluids (blood, urine, etc.). These labs typically use well-established, standardized techniques to produce results that can be used for medical decisions.
  
  

• Research Laboratory: Research labs focus on the scientific study of various phenomena, which may include the development of new treatments, the study of disease mechanisms, or exploring new biological processes. The techniques used may be experimental or novel, and the goal is to generate knowledge rather than provide diagnostic results for patient care.

3. Be able to list the major stages in the CDC SARS-Cov-2 diagnostic test protocol. 

The CDC SARS-CoV-2 diagnostic test protocol typically involves the following major stages:

1. Sample Collection: A sample is collected from the patient, usually through a nasopharyngeal or oropharyngeal swab.
   
   

2. RNA Extraction: The viral RNA is extracted from the collected sample.
   
   

3. Reverse Transcription: The RNA is reverse-transcribed into complementary DNA (cDNA) using reverse transcriptase.
   
   

4. Polymerase Chain Reaction (PCR): PCR is used to amplify specific regions of the viral genome, confirming the presence of SARS-CoV-2.
   
   

5. Detection: The amplification products are detected, typically through fluorescent dyes or probes that bind to the target sequences. This step confirms whether the virus is present.

4. Why is it necessary to use reverse transcriptase when testing for this virus? 

• Reverse transcriptase is necessary because SARS-CoV-2 is an RNA virus. In order to perform PCR (which amplifies DNA), the viral RNA must first be converted into complementary DNA (cDNA). This is done using the enzyme reverse transcriptase. Without this step, it would be impossible to amplify the viral genome using standard PCR methods.

5. Know how quantitative PCR (qPCR) differs from standard PCR in terms of components of the reaction, the process of the reaction, and interpretation of results. 

Components:

• qPCR: Includes fluorescent dyes or probes that bind to the DNA, allowing for real-time monitoring of amplification. These components enable quantification of the DNA in each cycle.

• Standard PCR: Does not include any fluorescent probes or dyes for real-time monitoring.

Process:

• qPCR: Quantifies the amount of DNA at each cycle, allowing for the measurement of the starting quantity of DNA. It provides real-time results throughout the amplification process.

• Standard PCR: Only measures the presence or absence of the target DNA at the end of the amplification process. It does not allow for quantification during the reaction.

Interpretation of Results:

• qPCR: The amplification is tracked in real-time, and the amount of fluorescence corresponds to the amount of DNA. The data are used to quantify the initial amount of template in the sample.

• Standard PCR: Results are interpreted qualitatively (positive or negative) based on the presence or absence of bands on a gel after the amplification.

• 6. Be able to interpret a graph from a qPCR report: what type of curves would lead to a conclusion of “positive”, “negative”, or “ambiguous” for the presence of the virus? 

• Positive: A positive qPCR result shows an amplification curve that rises steeply (exponential amplification) at an early cycle number (low Ct value). This indicates the presence of the virus in the sample.
  
  

• Negative: A negative qPCR result shows no amplification, meaning the fluorescence does not rise above the threshold, and there is no detectable virus in the sample.
  
  

• Ambiguous: An ambiguous result shows weak or late amplification with an unclear curve, which may indicate low viral load or other issues with the sample or test.

7. Based on a DNA sequence, predict the sequence of the mRNA that would be produced. 

• To predict the mRNA sequence from a DNA sequence, replace all thymine (T) with uracil (U), and use the complementary bases for the rest:

  • DNA: A-T, C-G

  • mRNA: A-U, C-G, T-A, G-C

For example, if the DNA sequence is 5’-ATG GCG TAA-3’, the corresponding mRNA sequence would be 5’-AUG GCG UAA-3’.

8. From a messenger-RNA sequence, predict the amino acid sequence of the polypeptide that would be synthesized. 

• To predict the amino acid sequence from an mRNA sequence, use the genetic code (codons) to translate the mRNA into amino acids. Each codon (a sequence of three RNA nucleotides) specifies an amino acid.

For example, for the mRNA sequence 5'-AUG GCG UAA-3':

• AUG: Methionine (Start codon)

• GCG: Alanine

• UAA: Stop codon

So, the polypeptide would consist of Methionine - Alanine and then terminate.

9. What is the importance of determining the open reading frame? 

• The open reading frame (ORF) is the part of the gene that has the potential to be translated into a protein. Determining the ORF is crucial because it defines the region that will be read by ribosomes to synthesize the polypeptide. It is essential for identifying where translation starts (at the start codon) and stops (at the stop codon), ensuring that the correct sequence of amino acids is incorporated into the protein.

10. What is the difference between a point mutation, a base insertion, and a base deletion? Which one of these causes a frameshift mutation?

• Point Mutation: A point mutation is a change in a single nucleotide base. This can be a substitution of one base for another (e.g., A → T), which may or may not change the resulting protein.
  
  

• Base Insertion: A base insertion occurs when an extra nucleotide is added into the DNA sequence, which can alter the reading frame of the gene.
  
  

• Base Deletion: A base deletion involves the removal of a nucleotide from the DNA sequence, which can also alter the reading frame.
  
  

Frameshift Mutation: Both base insertion and base deletion can cause a frameshift mutation because they shift the reading frame of the codons, leading to incorrect amino acid sequences and potentially nonfunctional proteins. Point mutations typically do not cause frameshift mutations unless they involve specific types of changes like premature stop codons.