Chapter 4 – Nutrition, Enzymes, and Metabolism

1. Define the following terms: malnutrition, energy, nutrients, macronutrients, micronutrients, essential nutrients, essential amino acids, digestion, chemical reaction, catabolic reaction, anabolic reaction, metabolism, enzyme, active site, substrate, activation energy, minerals, vitamins, cofactor, coenzyme.

   • Malnutrition: Poor nutrition due to insufficient or unbalanced food intake.

   • Energy: The ability to do work, required for body processes.

   • Nutrients: Substances in food needed for growth, repair, and maintenance.

   • Macronutrients: Nutrients required in large amounts (e.g., carbohydrates, proteins, fats).

   • Micronutrients: Nutrients required in small amounts (e.g., vitamins, minerals).

   • Essential Nutrients: Nutrients that cannot be synthesized by the body and must be obtained from diet.

   • Essential Amino Acids: Amino acids that the body cannot produce and must be obtained from food.

   • Digestion: The breakdown of food into smaller, absorbable components.

   • Chemical Reaction: A process where substances change to produce different substances.

   • Catabolic Reaction: A reaction that breaks down molecules into smaller units, releasing energy.

   • Anabolic Reaction: A reaction that builds larger molecules from smaller ones, requiring energy.

   • Metabolism: The sum of all chemical reactions in the body.

   • Enzyme: A protein that speeds up chemical reactions in the body.

   • Active Site: The region on an enzyme where the substrate binds.

   • Substrate: The reactant molecule that binds to an enzyme.

   • Activation Energy: The minimum energy required to start a chemical reaction.

   • Minerals: Inorganic nutrients needed in small amounts for body function.

   • Vitamins: Organic compounds essential for body functions, required in small amounts.

   • Cofactor: A non-protein substance that enhances enzyme activity.

   • Coenzyme: An organic cofactor that assists enzyme function.

2. Malnutrition is always associated with starvation. True/False
   False. Malnutrition can also occur with sufficient calorie intake but lacking essential nutrients.

3. ______ is the number one killer of children around the world, and most deaths occur in sub-Saharan Africa because ______________.
   Malnutrition is the number one killer of children around the world, with most deaths occurring in sub-Saharan Africa because of poverty, limited access to nutritious food, and healthcare.

4. What are some examples of macronutrients? What are their functions in our body?
   Examples of macronutrients include carbohydrates, proteins, and fats. They provide energy, build and repair tissues, and support bodily functions.

5. In the United States, food access is more due to __________ (poverty or scarcity).
   In the United States, food access issues are more due to poverty than scarcity.

6. What should a well-balanced diet be composed of?
   A well-balanced diet should include carbohydrates, proteins, fats, vitamins, and minerals in adequate proportions.

7. Animal products contain more protein per gram than carbohydrates, while most plant products contain more carbohydrates than protein. True/False
   True. Animal products generally have more protein per gram than carbohydrates, while plant products have more carbohydrates than protein.

8. Why are macronutrients broken down by digestion?
   Macronutrients are broken down by digestion so they can be absorbed and used by the body for energy and building blocks.

9. Why are nucleic acids not considered macronutrients?
   Nucleic acids are not considered macronutrients because they are not required in large amounts for energy or basic nutrition.

10. Digestion of carbohydrates, proteins, lipids, and nucleic acids releases subunits that are absorbed into the bloodstream. List these subunits.

    • Carbohydrates: simple sugars (glucose).

    • Proteins: amino acids.

    • Lipids: fatty acids and glycerol.

    • Nucleic acids: nucleotides.

11. How many amino acids are considered essential?
    Nine amino acids are considered essential for humans.

12. What are complete foods?
    Complete foods contain all essential nutrients needed for a balanced diet.

13. What is the purpose of the Peanut Butter Project?
    The purpose of the Peanut Butter Project is to provide a ready-to-use therapeutic food (RUTF) for malnourished children.

14. Why is peanut butter a useful treatment for malnutrition?
    Peanut butter is useful for malnutrition treatment due to its high calorie and nutrient density, including healthy fats and protein.

15. According to physician Mark Manary, founder of the Peanut Butter Project, “If you eat RUTF, you don’t need to eat anything else.” True/False
    False. While RUTF provides balanced nutrition, additional variety may still be beneficial.

16. Enzymes are used in catabolic but not anabolic reactions. True/False
    False. Enzymes are involved in both catabolic and anabolic reactions.

17. Discuss the properties of enzymes.
    Enzyme properties include specificity for substrates, ability to lower activation energy, and speed up reactions without being consumed.

18. Without enzymes, reactions will never occur. True/False
    False. Reactions can still occur without enzymes but would be much slower.

19. How is the activation energy affected by enzymes – Do enzymes reduce or increase the activation energy?
    Enzymes reduce the activation energy needed for reactions, making them occur more quickly.

20. Enzymes add energy to a reaction. True/False
    False. Enzymes do not add energy but lower the activation energy threshold.

21. How is an enzyme–substrate complex formed?
    An enzyme-substrate complex forms when the substrate binds to the enzyme's active site.

22. Discuss the ‘induced fit’ model of enzyme activity.
    The 'induced fit' model suggests that the enzyme changes shape slightly to fit the substrate tightly once bound.

23. Enzymes are mostly protein molecules. True/False
    True. Enzymes are primarily protein molecules.

24. Enzymes are changed permanently at the end of the reaction. True/False
    False. Enzymes are not permanently changed by reactions and can be reused.

25. What are the functions of micronutrients? What is “hidden hunger?”
    Micronutrients support bodily functions like immunity, bone health, and cellular processes. "Hidden hunger" refers to micronutrient deficiencies without calorie deficiency.

26. List some examples of minerals, vitamins, cofactors, and coenzymes and their functions.

    • Minerals: Iron (carries oxygen in blood), calcium (bone health).

    • Vitamins: Vitamin C (immunity), Vitamin D (bone health).

    • Cofactors: Magnesium (stabilizes enzyme structure).

    • Coenzymes: NAD+ (electron carrier in metabolism).

27. Goiter can result from a deficiency in ______.
    Goiter can result from a deficiency in iodine.
    
    
    
    
    
    
    

Chapter 5 – Energy and Photosynthesis

1. Define the following: biofuel, fossil fuel, energy, potential energy, kinetic energy, chemical energy, heat, autotroph, heterotroph, light energy, photons, chlorophyll, Rubisco, photosynthesis, energy, entropy, visible light, pigment, carbon fixation, stomata.

   • Biofuel: Fuel derived from biological sources, such as plants or algae.

   • Fossil Fuel: Nonrenewable energy sources derived from ancient biological matter, like oil, coal, and natural gas.

   • Energy: The capacity to do work or cause change.

   • Potential Energy: Stored energy based on position or state.

   • Kinetic Energy: Energy of motion.

   • Chemical Energy: Energy stored in the bonds of molecules.

   • Heat: Energy associated with the movement of atoms and molecules in matter.

   • Autotroph: Organism that produces its own food from sunlight or chemicals.

   • Heterotroph: Organism that obtains energy by consuming other organisms.

   • Light Energy: Energy from sunlight.

   • Photons: Particles of light that carry energy.

   • Chlorophyll: Green pigment in plants that absorbs light for photosynthesis.

   • Rubisco: An enzyme that catalyzes carbon fixation in photosynthesis.

   • Photosynthesis: The process by which plants and some organisms convert light energy into chemical energy.

   • Entropy: Measure of disorder or randomness in a system.

   • Visible Light: Portion of the electromagnetic spectrum that can be seen by human eyes.

   • Pigment: A molecule that absorbs specific wavelengths of light.

   • Carbon Fixation: The process of converting inorganic CO₂ into organic compounds.

   • Stomata: Small openings on plant leaves that allow gas exchange.

2. Fossil fuels considered nonrenewable. Why?
   Fossil fuels are nonrenewable because they take millions of years to form and are being used faster than they can be replenished.

3. What is the advantage of using algae as a source of fuel?
   Algae can produce biofuel quickly, require less land, and can grow in non-arable areas, making them a sustainable energy source.

4. Why are the single-celled ‘pond scum’ variety of algae the most useful for making biofuel?
   Single-celled algae can grow rapidly, have a high oil content, and are efficient in converting sunlight into biomass suitable for biofuel production.

5. Apart from oil, what are algae also used for?
   Algae are also used in food products, cosmetics, animal feed, and as a source of nutrients and supplements.

6. Make sure you understand the difference between the first and second laws of thermodynamics. Which one is also called the law of energy conservation?

   • The First Law of Thermodynamics (Law of Energy Conservation): Energy cannot be created or destroyed, only transformed.

   • The Second Law of Thermodynamics: Every energy transfer increases the entropy of the universe. The First Law is also called the law of energy conservation.

7. Use the example of a cyclist to explain the concept of energy transformation.
   A cyclist transforms chemical energy from food into kinetic energy for movement. Some energy is lost as heat due to friction and muscle activity.

8. Energy transformation is always 100% efficient. True/False
   False. Some energy is always lost as heat during transformations.

9. Discuss the three main types of work in a cell.

   • Chemical Work: Building molecules.

   • Transport Work: Moving substances across membranes.

   • Mechanical Work: Physical movement, such as muscle contraction.

10. Is photosynthesis anabolic or catabolic?
    Photosynthesis is anabolic, as it builds glucose from CO₂ and water.

11. What is the organelle of photosynthesis?
    The chloroplast is the organelle where photosynthesis occurs.

12. Define the following: stroma, grana, thylakoid, and thylakoid space.

    • Stroma: The fluid-filled space in the chloroplast where the carbon reactions occur.

    • Grana: Stacks of thylakoids in the chloroplast.

    • Thylakoid: A membrane-bound structure where the light reactions occur.

    • Thylakoid Space: The internal space within the thylakoid.

13. How is photosynthesis advantageous for life on Earth? What role does it play in reducing CO₂ in the environment?
    Photosynthesis produces oxygen and removes CO₂ from the atmosphere, which helps reduce greenhouse gases and supports life by creating energy-rich compounds.

14. How can biofuel producers increase the amount of CO₂ available to algae?
    By supplying additional CO₂ directly to the algae to increase growth and biofuel production.

15. Why are plants and algae considered “carbon neutral?”
    They absorb as much CO₂ during photosynthesis as they release when they die or are used as fuel.

16. Sunlight is a type of energy called electromagnetic energy. True/False
    True.

17. Shorter-wavelength photons have less energy than longer-wavelength photons. True/False
    False. Shorter-wavelength photons have more energy.

18. Wavelengths shorter than those of visible light can damage organic molecules such as nucleic acids and proteins. True/False
    True. Ultraviolet and shorter wavelengths can cause damage.

19. Why do plants appear green to us?
    Chlorophyll reflects green light, which is why plants appear green.

20. All pigments reflect all wavelengths of light. True/False
    False. Pigments absorb specific wavelengths and reflect others.

21. What are carotenoids and what is their function?
    Carotenoids are pigments that protect chlorophyll from damage and absorb light for photosynthesis, especially during the fall.

22. What are the two metabolic stages of photosynthesis?

    • Light Reactions: Capture sunlight to produce ATP and NADPH.

    • Carbon Reactions (Calvin Cycle): Use ATP and NADPH to fix carbon and produce glucose.

23. Where do the two metabolic stages of photosynthesis occur? What are their products?

    • Light Reactions: Occur in the thylakoids; produce ATP, NADPH, and O₂.

    • Carbon Reactions: Occur in the stroma; produce glucose.

24. The most abundant protein in the world is _______. What is its function in photosynthesis?
    Rubisco; it catalyzes the carbon fixation step in the Calvin Cycle.

25. What products of the light reactions are used in the carbon reactions?
    ATP and NADPH.

26. During carbon fixation, what is being “fixed?”
    CO₂ is "fixed" into an organic molecule, beginning the process of forming glucose.

27. What are the sources of the ingredients of photosynthesis in plants?

    • CO₂: From the atmosphere.

    • Water: Absorbed by roots.

    • Sunlight: Absorbed by chlorophyll.

28. Discuss the greenhouse effect. List some greenhouse gases.
    The greenhouse effect traps heat in the Earth's atmosphere due to gases like CO₂, methane, and water vapor, warming the planet.

29. What causes global warming?
    Increased greenhouse gases, mainly from burning fossil fuels and deforestation.

30. Burning of fossil fuels has increased the concentration of CO₂ in the atmosphere. True/False
    True.

31. What are some consequences of global climate change?
    Rising sea levels, extreme weather, loss of biodiversity, and changes in ecosystems.

32. How can photosynthesis moderate global warming?
    Photosynthesis removes CO₂ from the atmosphere, reducing greenhouse gases.

33. How can global warming be reduced generally?
    Using renewable energy, reducing emissions, reforestation, and energy conservation.

34. According to calculations by scientists, the CO₂ released by human activities has increased the average temperature of the planet by about 1°C (1.8°F) since 1900. True/False
    True.

35. Discuss the carbon capture systems (covered in class) that are being explored by scientists.
    Carbon capture involves capturing CO₂ from emissions and storing it underground or using it in products to reduce atmospheric CO₂.

36. What are some challenges facing alternative fuels?
    High production costs, technological limitations, infrastructure requirements, and competition with food production for resources.

37. Photosynthesis provides food and O₂ for almost all living organisms. True/False
True. Photosynthesis is the foundation of the food chain, providing energy-rich compounds and oxygen for other organisms.

38. Sugars also serve as the starting material for other organic compounds such as cellulose. True/False
True. Sugars produced in photosynthesis can be converted into various organic compounds like cellulose, which is essential for plant cell walls.

39. Plants store excess sugar as starch in roots, tubers, and fruits. True/False
True. Plants convert excess glucose into starch and store it in roots, tubers, and fruits as a long-term energy reserve.

Chapter 6 – Dietary Energy and Cellular Respiration

1. Define the following: obesity, body mass index, calorie, Calorie, NEAT, Cellular respiration, glycolysis, citric acid cycle, electron transport chain, fermentation.

   • Obesity: A condition characterized by excessive body fat that increases the risk of health problems.

   • Body Mass Index (BMI): A measure of body fat based on height and weight.

   • Calorie (capital C): A unit of energy, equivalent to 1,000 calories; often used in food labeling.

   • calorie (lowercase c): A unit of energy; the amount of heat needed to raise the temperature of 1 gram of water by 1°C.

   • NEAT (Non-Exercise Activity Thermogenesis): The energy expended for activities other than sleeping, eating, or sports-like exercise.

   • Cellular Respiration: A series of metabolic processes that convert glucose and oxygen into ATP, water, and carbon dioxide.

   • Glycolysis: The first stage of cellular respiration where glucose is broken down into pyruvate, producing a small amount of ATP.

   • Citric Acid Cycle: A stage of cellular respiration that generates electron carriers and releases CO₂.

   • Electron Transport Chain: The final stage of cellular respiration where the bulk of ATP is produced.

   • Fermentation: An anaerobic process that generates energy when oxygen is absent.

2. Why is obesity considered America’s #1 health crisis?
   Obesity is linked to numerous health issues, including diabetes, heart disease, and certain cancers, and affects a significant portion of the population.

3. Since 1960, the percentage of obese and extremely obese adults has grown. True/False
   True.

4. Fundamentally, obesity is a problem of energy imbalance: taking in much more energy than we expend in our activities, over time. True/False
   True.

5. Food is a source of chemical energy. True/False
   True.

6. What is the difference between “calorie” and “Calorie?” Which one will you find on most food labels?
   A calorie (lowercase) is a small unit of energy, while a Calorie (uppercase) is 1,000 calories. Food labels use Calories (uppercase).

7. Each gram of fat stores _____ Calories, while each gram of protein or carbohydrate stores _____ Calories.
   Each gram of fat stores 9 Calories, while each gram of protein or carbohydrate stores 4 Calories.

8. There are three main ways our body expends energy. List them.

   • Basal metabolic rate (BMR)

   • Physical activity

   • Thermic effect of food (digestion and absorption)

9. What are the factors that determine the amount of energy required to meet our daily needs?
   Factors include age, gender, body composition, physical activity level, and overall health.

10. What is NEAT? What are the advantages of NEAT?
    NEAT (Non-Exercise Activity Thermogenesis) is the energy expended for daily activities other than formal exercise. It helps burn calories and manage weight.

11. There is one problem associated with the studies conducted by some researchers regarding the effectiveness of NEAT in managing weight. What is that problem?
    Some studies may not account for all variables affecting NEAT, such as genetic differences and activity choices, leading to mixed results.

12. What is the energy currency in cells?
    ATP (adenosine triphosphate).

13. ATP is a nucleotide. What are its components?
    ATP consists of adenine, ribose, and three phosphate groups.

14. The energy in ATP is stored in the bonds between its phosphate groups, and energy is released when these bonds are broken. True/False
    True.

15. List some functions of ATP in a cell.
    ATP powers muscle contractions, active transport across cell membranes, and biochemical reactions.

16. What is the organelle of cellular respiration?
    The mitochondrion.

17. What is the difference between breathing and aerobic cellular respiration?
    Breathing is the physical process of taking in oxygen, while cellular respiration is the metabolic process of using oxygen to produce ATP.

18. What is the function of the coenzyme NAD+ in cellular respiration? What does it become when it accepts electrons?
    NAD+ transports electrons during cellular respiration and becomes NADH after accepting electrons.

19. What is misleading about the following statement? “Plant cells perform photosynthesis, and animal cells perform cellular respiration.”
    It’s misleading because plant cells also perform cellular respiration to generate ATP.

20. What are the three stages of cellular respiration and where do they occur?

    • Glycolysis: Cytoplasm

    • Citric Acid Cycle: Mitochondrial matrix

    • Electron Transport Chain: Inner mitochondrial membrane

21. What are the products of glycolysis, the citric acid cycle, and the electron transport chain?

    • Glycolysis: ATP, NADH, pyruvate.

    • Citric Acid Cycle: ATP, NADH, FADH₂, CO₂.

    • Electron Transport Chain: ATP and water.

22. What stage of cellular respiration produces FADH₂, and what is its function?
    The Citric Acid Cycle produces FADH₂, which carries electrons to the electron transport chain.

23. What is the final electron acceptor in cellular respiration? What is it converted to?
    Oxygen is the final electron acceptor and is converted to water.

24. Make sure you know the number of ATP molecules produced from the stages of cellular respiration as well as the total yield.
    Glycolysis: 2 ATP, Citric Acid Cycle: 2 ATP, Electron Transport Chain: ~32-34 ATP; Total yield: ~36-38 ATP.

25. Which step of cellular respiration produces most of the ATP molecules?
    The Electron Transport Chain.

26. How do cyanide, oligomycin, and carbon monoxide affect cellular respiration?
    They disrupt the electron transport chain, preventing ATP production.

27. Why do mitochondria in brown fat produce heat?
    Brown fat mitochondria produce heat by uncoupling the electron transport chain, generating warmth instead of ATP.

28. Brown fat is found only in babies. True/False
    False. Brown fat is also present in adults, though in smaller amounts.

29. In cold environments, the brown fat of lean people is less active than in overweight people. True/False
    False. Lean people’s brown fat is typically more active in cold environments.

30. Distinguish between cellular respiration and fermentation. Which one is more efficient?
    Cellular respiration is aerobic and produces more ATP than anaerobic fermentation.

31. The ATP produced during fermentation is from glycolysis. True/False
    True.

32. NAD+ is regenerated during fermentation. True/False
    True.

33. Distinguish between alcohol fermentation and lactic acid fermentation. Where do these processes take place (examples of organisms or cells)?

    • Alcohol Fermentation: Produces ethanol and CO₂, occurs in yeast and some bacteria.

    • Lactic Acid Fermentation: Produces lactic acid, occurs in muscle cells and some bacteria.

34. CO₂ is produced in both alcohol fermentation and lactic acid fermentation. True/False.
    False. CO₂ is produced in alcohol fermentation but not in lactic acid fermentation.

35. Both alcohol fermentation and lactic acid fermentation operate anaerobically. True/False.
    True.

36. A child is born with a rare disease in which mitochondria are missing from skeletal muscle cells. However, the muscles still function. Physicians find that:
    a) the muscles contain large amounts of lactate following even mild physical exercise.

37. Why do cells carry out fermentation if there is no more ATP produced?
    To regenerate NAD+ so glycolysis can continue producing small amounts of ATP.

38. Distinguish between short-term energy storage and long-term energy storage. Include the storage molecules involved (glycogen or fat).

    • Short-term: Glycogen stores glucose in muscles and liver.

    • Long-term: Fat stores energy for prolonged use.

39. Photosynthesis and respiration form a continuous cycle. What does this mean?
    Photosynthesis produces oxygen and glucose, which are used in respiration, while respiration produces CO₂ and water, used in photosynthesis.

40. In the presence of oxygen, humans use ____ for ATP production, and plants use ____ for ATP production from stored sugars
    c) Aerobic respiration, aerobic respiration

During aerobic respiration, how does NADH give up electrons to regenerate NAD+?
d) by giving electrons to the electron transport chain





Chapter 7 – DNA Structure and Replication

1. Definitions: DNA, chromosome, nucleotide, DNA profile, DNA replication, helicase, primer, DNA polymerase, PCR, complementary, genome, STRs, gel electrophoresis, genotype, phenotype, CODIS

   • DNA (Deoxyribonucleic Acid): The molecule that carries genetic information in living organisms.

   • Chromosome: A structure of nucleic acids and protein that carries genetic information in the form of genes.

   • Nucleotide: The building block of DNA, consisting of a sugar, phosphate group, and nitrogenous base.

   • DNA Profile: A unique set of DNA markers used to identify individuals.

   • DNA Replication: The process of copying DNA before cell division.

   • Helicase: An enzyme that unwinds the DNA double helix during replication.

   • Primer: A short segment of DNA or RNA that initiates DNA synthesis.

   • DNA Polymerase: An enzyme that synthesizes new DNA strands by adding nucleotides.

   • PCR (Polymerase Chain Reaction): A technique used to amplify small amounts of DNA.

   • Complementary: Refers to the matching base pairs in DNA (A with T, C with G).

   • Genome: The complete set of genetic material in an organism.

   • STRs (Short Tandem Repeats): Repeated DNA sequences used for DNA profiling.

   • Gel Electrophoresis: A technique to separate DNA fragments by size.

   • Genotype: The genetic makeup of an individual.

   • Phenotype: The physical expression of an individual's genotype.

   • CODIS (Combined DNA Index System): A database used to store DNA profiles for forensic purposes.

2. How many chromosomes does a human cell contain?
   A human cell contains 46 chromosomes.

3. If the nucleus is so small, how do the chromosomes all fit?
   DNA is tightly coiled and folded into chromatin, allowing it to fit into the small space of the nucleus.

4. A human chromosome is composed of DNA only. True/False
   False. Human chromosomes are composed of both DNA and proteins.

5. What are sex chromosomes? How many sex chromosomes are typically found in human males and females, and which ones are they?
   Sex chromosomes determine biological sex: females typically have two X chromosomes (XX), while males have one X and one Y chromosome (XY).

6. All the cells in a multicellular organism have the same genome. True/False
   True. All cells in an organism generally contain the same DNA.

7. Describe the structure of DNA. What forms the “backbone” and what forms the “rungs?”
   DNA is a double helix. The “backbone” is formed by sugar-phosphate groups, and the “rungs” are pairs of nitrogenous bases (A with T, C with G).

8. What is the complementary base pairing rule?
   Adenine (A) pairs with Thymine (T), and Cytosine (C) pairs with Guanine (G).

9. What two functions of DNA comprise the central dogma of molecular biology?
   Replication (copying DNA) and Transcription/Translation (making proteins from DNA).

10. The specific sequence of nucleotides along a strand of DNA is unique to each individual. True/False
    True.

11. Each chromosome contains:
    c) DNA and proteins

12. Which of the following is FALSE?
    b) Each cell in your body has a different genome since they have different functions
    (Each cell in the body has the same genome, even though they perform different functions).

13. Both DNA replication and transcription depend on base-pairing properties of nucleotides. True/False
    True.

14. Describe the semiconservative model of DNA replication.
    In the semiconservative model, each new DNA molecule consists of one original strand and one newly synthesized strand.

15. What are the roles of the enzymes, helicase and DNA polymerase, in DNA replication?

    • Helicase: Unwinds the DNA double helix.

    • DNA Polymerase: Adds nucleotides to synthesize a new DNA strand.

16. The process of DNA replication is fast and 100% accurate. True/False
    False. DNA replication is fast but not 100% accurate, though errors are rare due to proofreading mechanisms.

17. What is the purpose of PCR?
    PCR is used to amplify small amounts of DNA, creating millions of copies for analysis.

18. In PCR, what ingredients do scientists put in the test tube?
    DNA sample, primers, DNA polymerase (usually Taq polymerase), and nucleotides.

19. During PCR, the DNA is first heated and then cooled. Why?
    Heating separates the DNA strands, and cooling allows primers to bind so DNA polymerase can add nucleotides.

20. What is the purpose of the primer in PCR?
    Primers provide a starting point for DNA synthesis by DNA polymerase.

21. What are the similarities and differences between PCR and DNA replication?

    • Similarities: Both rely on base-pairing and DNA polymerase to synthesize new DNA.

    • Differences: PCR occurs outside cells in a test tube, using heat instead of helicase to separate DNA strands.

22. What are short tandem repeats (STRs), and why are they used to distinguish individuals from one another?
    STRs are repeating sequences of DNA that vary in length between individuals, making them useful for DNA profiling.

23. How is DNA profiling done? Include PCR and gel electrophoresis in your discussion.
    DNA is extracted, STR regions are amplified using PCR, and gel electrophoresis is used to separate STRs by size, creating a unique DNA profile.

24. What is a molecular “fingerprint?”
    A unique DNA profile based on STR patterns that can identify individuals.

25. In a paternity test, how many of the child’s STR bands should match bands from the father:
    b) One half

26. Why is it important to use multiple STR regions in forensic science?
    Using multiple STR regions increases accuracy and ensures a unique profile, reducing the chance of false matches.

Why would it be better to use DNA evidence rather than just bite marks or hair?
DNA evidence is more reliable and unique to each individual, whereas bite marks and hair can be similar among different people.




Chapter 8 – Genes to Proteins

1. Define the following: amino acids, spidroin, gene, gene expression, regulatory sequence, coding sequence, transcription, translation, mRNA, RNA polymerase, ribosome, codon, tRNA, anticodon, genetic code, transgenic, recombinant gene, genetic engineering, vector, GMO, gene therapy.

   • Amino Acids: Building blocks of proteins, each with a specific side chain.

   • Spidroin: Protein that makes up spider silk, known for its strength and elasticity.

   • Gene: A sequence of DNA that codes for a protein or functional molecule.

   • Gene Expression: The process by which a gene produces its product and carries out its function.

   • Regulatory Sequence: DNA segment controlling when, where, and how much a gene is expressed.

   • Coding Sequence: DNA segment that determines the amino acid sequence of a protein.

   • Transcription: The process of copying a gene’s DNA sequence into mRNA.

   • Translation: The process of synthesizing a protein based on the mRNA sequence.

   • mRNA: Messenger RNA; carries genetic information from DNA to ribosomes.

   • RNA Polymerase: Enzyme that synthesizes mRNA from a DNA template during transcription.

   • Ribosome: Cell structure where proteins are synthesized.

   • Codon: A three-base sequence on mRNA that specifies an amino acid.

   • tRNA: Transfer RNA; brings amino acids to the ribosome during protein synthesis.

   • Anticodon: Three-base sequence on tRNA complementary to an mRNA codon.

   • Genetic Code: Set of rules by which information in DNA/RNA is translated into proteins.

   • Transgenic: Organism containing genes from another species.

   • Recombinant Gene: Gene that has been artificially formed by combining DNA from different organisms.

   • Genetic Engineering: Manipulation of an organism's DNA to alter its traits.

   • Vector: A vehicle (such as a plasmid) used to insert genetic material into cells.

   • GMO (Genetically Modified Organism): Organism with altered genes.

   • Gene Therapy: Treatment of disease by modifying a person's genes.

2. What are some properties and advantages of spider silk?
   Spider silk is lightweight, strong, flexible, and biodegradable, making it useful for various applications.

3. List some applications of spider silk.
   Spider silk is used in medical sutures, artificial ligaments, and biodegradable materials.

4. Spidroin is longer than the average animal protein. True/False
   True.

5. Polypeptide chain folds into a 3-D protein based on the sequence of amino acids, and this determines the shape and function of the protein. True/False
   True.

6. How do the amino acids, alanine, and glycine, in spidroin contribute to its toughness and strength?
   Alanine and glycine allow for tight packing and hydrogen bonding, making spidroin tough and resilient.

7. What role do hydrophobic and hydrophilic amino acids play in the structure of spidroin?
   Hydrophobic regions help stabilize the protein structure, while hydrophilic regions make it flexible and resilient.

8. Discuss the difference between the coding sequence and the regulatory sequence of a gene.
   The coding sequence specifies the protein’s amino acid sequence, while the regulatory sequence controls when, where, and how much the gene is expressed.

9. What were the advantages and disadvantages of nylon?
   Nylon is strong, durable, and flexible but non-biodegradable, contributing to environmental waste.

10. Where do proteins come from? What is gene expression? What are the steps involved in gene expression, and where do they occur?
    Proteins are synthesized based on genes. Gene expression includes transcription (nucleus) and translation (cytoplasm).

11. What is mRNA, and where is it synthesized in eukaryotic cells?
    mRNA is messenger RNA, synthesized in the nucleus during transcription.

12. What is the role of RNA polymerase in transcription?
    RNA polymerase binds to DNA, unwinds it, and synthesizes mRNA by adding complementary nucleotides.

13. In the cytoplasm, the mRNA attaches to the _________ upon which translation occurs.
    Ribosome.

14. Why is a codon called a “word?”
    Each codon represents a specific amino acid, acting as a “word” in the genetic code.

15. How are amino acids delivered to the ribosome?
    Amino acids are delivered to the ribosome by tRNA molecules.

16. How is the tRNA like an “interpreter?”
    tRNA “interprets” mRNA codons by matching them with the correct amino acids.

17. An anticodon is complementary to the codon. True/False
    True.

18. How many bases does a codon or anticodon contain?
    Three bases.

19. mRNA and tRNAs can be used only once. True/False
    False. mRNA and tRNAs can be used multiple times for protein synthesis.

20. Which statement about DNA or RNA is true?
    a. DNA is completely replicated but only partially transcribed.

21. What is the universal code? Why is it said to be universal, redundant but not ambiguous?
    The genetic code is universal (used by almost all organisms), redundant (multiple codons for some amino acids), but not ambiguous (each codon codes for only one amino acid).

22. What are the functions of the start codon and stop codons?
    The start codon (AUG) signals the beginning of translation, while stop codons (UAA, UAG, UGA) signal the end of translation.

23. An organism’s genetic information is stored within the sequence of ___________. This information is transcribed into a sequence of ____________ which are then translated into a sequence of ___________.
    4 DNA bases, RNA bases, amino acids

24. Only spiders have been genetically engineered to produce spider silk. True/False
    False. Other organisms, like yeast, have been engineered to produce spider silk proteins.

25. Describe the process of genetic engineering of spider silk using yeast. Why is a vector used in this process?
    A spider silk gene is inserted into yeast using a vector. The yeast then produces spider silk protein. The vector is essential for delivering the gene into yeast cells.

26. What are the advantages of using yeast in the production of spider silk?
    Yeast grows quickly, is easy to modify, and produces spider silk proteins without requiring spiders.

27. List some examples in which the field of agriculture has benefited from genetic engineering.

    • Pest-resistant crops (Bt corn)

    • Herbicide-resistant crops (Roundup Ready soybeans)

    • Drought-tolerant crops.

28. List some examples in which the field of medicine has benefited from genetic engineering.

    • Production of insulin

    • Development of gene therapy

    • Creation of vaccines (e.g., HPV vaccine).

29. What are some of the challenges facing genetic engineering?

    • Ethical concerns

    • Environmental risks (e.g., gene transfer to wild species)

    • Public acceptance and regulatory challenges.

Study guide 2

Chapter 4 – Nutrition, Enzymes, and Metabolism

1. Define the following terms: malnutrition, energy, nutrients, macronutrients, micronutrients, essential nutrients, essential amino acids, digestion, chemical reaction, catabolic reaction, anabolic reaction, metabolism, enzyme, active site, substrate, activation energy, minerals, vitamins, cofactor, coenzyme.

2. Malnutrition is always associated with starvation. True/False

3. ______ is the number one killer of children around the world and most deaths occur in sub-Saharan Africa because ______________.

4. What are some examples of macronutrients? What are their functions in our body?

5. In the United States, food access is more due to __________ (poverty or scarcity).

6. What should a well-balanced diet be composed of?

7. Animal products contain more protein per gram than carbohydrates while most plant products contain more carbohydrates than protein. True/False

8. Why are macronutrients broken down by digestion?

9. Why are nucleic acids not considered macronutrients?

10. Digestion of carbohydrates, proteins, lipids, and nucleic acids releases subunits that are absorbed into the bloodstream. List these subunits.

11. How many amino acids are considered essential?

12. What are complete foods?

13. What is the purpose of the peanut butter project?

14. Why is peanut butter a useful treatment for malnutrition?

15. According to physician Mark Manary, founder of the Peanut Butter Project, “If you eat RUTF, you don’t need to eat anything else.” True/False

16. Enzymes are used in catabolic but not anabolic reactions. True/False

17. Discuss the properties of enzymes.

18. Without enzymes, reactions will never occur. True/False

19. How is the activation energy affected by enzymes – Do enzymes reduce or increase the activation energy?

20. Enzymes add energy to a reaction. True/False

21. How is an enzyme–substrate complex formed?

22. Discuss the ‘induced fit’ model of enzyme activity.

23. Enzymes are mostly protein molecules. True/False

24. Enzymes are changed permanently at the end of the reaction. True/False

25. What are the functions of micronutrients? What is “hidden hunger?”

26. List some examples of minerals, vitamins, cofactors, and coenzymes and their functions.

27. Goiter can result from a deficiency in ______.

Chapter 5 – Energy and Photosynthesis

1. Define the following: biofuel, fossil fuel, energy, potential energy, kinetic energy, chemical energy, heat, autotroph, heterotroph, light energy, photons, chlorophyll, Rubisco, photosynthesis, energy, entropy, visible light, pigment, carbon fixation, stomata.

2. Fossil fuels considered nonrenewable. Why?

3. What is the advantage of using algae as a source of fuel?

4. Why are the single-celled ‘pond scum’ variety of algae the most useful for making biofuel?

5. Apart from oil, what are algae also used for?

6. Make sure you understand the difference between the first and second laws of thermodynamics. Which one is also called the law of energy conservation?

7. Use the example of a cyclist to explain the concept of energy transformation.

8. Energy transformation is always 100% efficient. True/False

9. Discuss the three main types of work in a cell.

10. Is photosynthesis anabolic or catabolic?

11. What is the organelle of photosynthesis?

12. Define the following: stroma, grana, thylakoid, and thylakoid space.

13. How is photosynthesis advantageous for life on Earth? What role does it play in reducing CO2 in the environment?

14. How can biofuel producers increase the amount of CO2 available to algae?

15. Why are plants and algae considered “carbon neutral?”

16. Sunlight is a type of energy called electromagnetic energy. True/False

17. Shorter-wavelength photons have less energy than longer-wavelength photons. True/False

18. Wavelengths shorter than those of visible light can damage organic molecules such as nucleic acids and proteins. True/False

19. Why do plants appear green to us?

20. All pigments reflect all wavelengths of light. True/False

21. What are carotenoids and what is their function?

22. What are the two metabolic stages of photosynthesis?

23. Where do the two metabolic stages of photosynthesis occur? What are their products?

24. The most abundant protein in the world is _______. What is its function in photosynthesis?

25. What products of the light reactions are used in the carbon reactions?

26. During carbon fixation, what is being “fixed?”

27. What are the sources of the ingredients of photosynthesis in plants?

28. Discuss the greenhouse effect. List some greenhouse gases.

29. What causes global warming?

30. Burning of fossil fuels has increased the concentration of CO2 in the atmosphere. True/False

31. What are some consequences of global climate change?

32. How can photosynthesis moderate global warming?

33. How can global warming be reduced generally?

34. According to calculations by scientists, the CO2 released by human activities has increased the average temperature of the planet by about 1°C (1.8°F) since 1900. True/False

35. Discuss the carbon capture systems (covered in class) that are being explored by scientists.

36. What are some challenges facing alternative fuels?

37. Photosynthesis provides food and O2 for almost all living organisms. True/False

38. Sugars also serve as the starting material for other organic compounds such as cellulose. True/False

39. Plants store excess sugar as starch in roots, tubers, and fruits. True/False

Chapter 6 – Dietary Energy and Cellular Respiration

1. Define the following: obesity, body mass index, calorie, Calorie, NEAT, Cellular respiration, glycolysis, citric acid cycle, electron transport chain, fermentation.

2. Why is obesity considered America’s #1 health crisis?

3. Since 1960, the percentage of obese and extremely obese adults has grown. True/False

4. Fundamentally, obesity is a problem of energy imbalance: taking in much more energy than we expend in our activities, over time. True/False

5. Food is a source of chemical energy. True/False

6. What is the difference between “calorie” and “Calorie?” Which one will you find on most food labels?

7. Each gram of fat stores _____ Calories, while each gram of protein or carbohydrate stores _____ Calories.

8. There are three main ways our body expends energy. List them.

9. What are the factors that determine the amount of energy required to meet our daily needs?

10. What is NEAT? What are the advantages of NEAT?

11. There is one problem associated with the studies conducted by some researchers regarding the effectiveness of NEAT in managing weight. What is that problem?

12. What is the energy currency in cells?

13. ATP is a nucleotide. What are its components?

14. The energy in ATP is stored in the bonds between its phosphate groups, and energy is released when these bonds are broken. True/False

15. List some functions of ATP in a cell.

16. What is the organelle of cellular respiration?

17. What is the difference between breathing and aerobic cellular respiration?

18. What is the function of the coenzyme NAD+ in cellular respiration? What does it become when it accepts electrons?

19. What is misleading about the following statement? “Plant cells perform photosynthesis, and animal cells perform cellular respiration.”

20. What are the three stages of cellular respiration, and where do they occur?

21. What are the products of glycolysis, the citric acid cycle, and the electron transport chain?

22. What stage of cellular respiration produces FADH2, and what is its function?

23. What is the final electron acceptor in cellular respiration? What is it converted to?

24. Make sure you know the number of ATP molecules produced from the stages of cellular respiration as well as the total yield.

25. Which step of cellular respiration produces most of the ATP molecules?

26. How do cyanide, oligomycin, and carbon monoxide affect cellular respiration?

27. Why do mitochondria in brown fat produce heat?

28. Brown fat is found only in babies. True/False

29. In cold environments, the brown fat of lean people is less active than in overweight people. True/False

30. Distinguish between cellular respiration and fermentation. Which one is more efficient?

31. The ATP produced during fermentation is from glycolysis. True/False

32. NAD+ is regenerated during fermentation. True/False

33. Distinguish between alcohol fermentation and lactic acid fermentation. Where do these processes take place (examples of organisms or cells)?

34. CO2 is produced in both alcohol fermentation and lactic acid fermentation. True/False.

35. Both alcohol fermentation and lactic acid fermentation operate anaerobically. True/False.

36. A child is born with a rare disease in which mitochondria are missing from skeletal muscle cells. However, the muscles still function. Physicians find that: a) the muscles contain large amounts of lactate following even mild physical exercise
    b) the muscles contain large amounts of carbon dioxide following even mild physical exercise
    c) the muscles require extremely high levels of oxygen to function
    d) the muscles cannot split glucose to pyruvate.
    e) the muscles require extremely large amounts of carbon dioxide to function

37. Why do cells carry out fermentation if there is no more ATP produced?

38. Distinguish between short-term energy storage and long-term energy storage. Include the storage molecules involved (glycogen or fat).

39. Photosynthesis and respiration form a continuous cycle. What does this mean?

40. In the presence of oxygen, humans use ____ for ATP production, and plants use ____ for ATP production from stored sugars:
    a) Aerobic respiration, photosynthesis
    b) Fermentation, aerobic respiration
    c) Aerobic respiration, aerobic respiration
    d) Fermentation, glycolysis

41. During aerobic respiration, how does NADH give up electrons to regenerate NAD+? a) by giving electrons directly to O₂
    b) by giving electrons to pyruvate
    c) by giving electrons to another NAD+
    d) by giving electrons to the electron transport chain

Chapter 7 - DNA Structure and Replication

1. Definitions: DNA, chromosome, nucleotide, DNA profile, DNA replication, helicase, primer, DNA polymerase, PCR, complementary, genome, STRs, gel electrophoresis, genotype, phenotype, CODIS.

2. How many chromosomes does a human cell contain?

3. If the nucleus is so small, how do the chromosomes all fit?

4. A human chromosome is composed of DNA only. True/False

5. What are sex chromosomes? How many sex chromosomes are typically found in human males and females, and which ones are they?

6. All the cells in a multicellular organism have the same genome. True/False

7. Describe the structure of DNA. What forms the “backbone” and what forms the “rungs?”

8. What is the complementary base pairing rule?

9. What two functions of DNA comprise the central dogma of molecular biology?

10. The specific sequence of nucleotides along a strand of DNA is unique to each individual. True/False

11. Each chromosome contains: a) DNA only
    b) Proteins only
    c) DNA and proteins
    d) The same number of genes

12. Which of the following is FALSE? a) The 46 chromosomes in a typical human cell are found in the nucleus
    b) Each cell in your body has a different genome since they have different functions
    c) A human female has a pair of X chromosomes
    d) A nucleotide is composed of a base, a sugar, and a phosphate group

13. Both DNA replication and transcription depend on base-pairing properties of nucleotides. True/False

14. Describe the semiconservative model of DNA replication.

15. What are the roles of the enzymes, helicase and DNA polymerase, in DNA replication?

16. The process of DNA replication is fast and 100% accurate. True/False

17. What is the purpose of PCR?

18. In PCR, what ingredients do scientists put in the test tube?

19. During PCR, the DNA is first heated and then cooled. Why?

20. What is the purpose of the primer in PCR?

21. What are the similarities and differences between PCR and DNA replication?

22. What are short tandem repeats (STRs), and why are they used to distinguish individuals from one another?

23. How is DNA profiling done? Include PCR and gel electrophoresis in your discussion.

24. What is a molecular “fingerprint?”

25. In a paternity test, how many of the child’s STR bands should match bands from the father?
    a) All
    b) One half

26. Why is it important to use multiple STR regions in forensic science?

27. Why would it be better to use DNA evidence rather than just bite marks or hair?

Chapter 8 – Genes to Proteins

1. Define the following: amino acids, spidroin, gene, gene expression, regulatory sequence, coding sequence, transcription, translation, mRNA, RNA polymerase, ribosome, codon, tRNA, anticodon, genetic code, transgenic, recombinant gene, genetic engineering, vector, GMO, gene therapy.

2. What are some properties and advantages of spider silk?

3. List some applications of spider silk.

4. Spidroin is longer than the average animal protein. True/False

5. Polypeptide chain folds into a 3-D protein based on the sequence of amino acids, and this determines the shape and function of the protein. True/False

6. How do the amino acids, alanine, and glycine, in spidroin contribute to its toughness and strength?

7. What role do hydrophobic and hydrophilic amino acids play in the structure of spidroin?

8. Discuss the difference between the coding sequence and the regulatory sequence of a gene.

9. What were the advantages and disadvantages of nylon?

10. Where do proteins come from? What is gene expression? What are the steps involved in gene expression, and where do they occur?

11. What is mRNA, and where is it synthesized in eukaryotic cells?

12. What is the role of RNA polymerase in transcription?

13. In the cytoplasm, the mRNA attaches to the _________ upon which translation occurs.

14. Why is a codon called a “word?”

15. How are amino acids delivered to the ribosome?

16. How is the tRNA like an “interpreter?”

17. An anticodon is complementary to the codon. True/False

18. How many bases does a codon or anticodon contain?

19. mRNA and tRNAs can be used only once. True/False

20. Which statement about DNA or RNA is true?
    a. DNA is completely replicated but only partially transcribed.
    b. DNA is partially replicated but completely transcribed.
    c. RNA is completely replicated but only partially translated.
    d. DNA is completely replicated and completely translated.
    e. DNA is partially replicated but completely translated.

21. What is the universal code? Why is it said to be universal, redundant but not ambiguous?

22. What are the functions of the start codon and stop codons?

23. An organism’s genetic information is stored within the sequence of ___________. This information is transcribed into a sequence of ____________, which are then translated into a sequence of ___________.

1. DNA bases, amino acids, RNA bases

2. RNA bases, DNA bases, amino acids

3. Amino acids, DNA bases, RNA bases

4. DNA bases, RNA bases, amino acids

24. Only spiders have been genetically engineered to produce spider silk. True/False

25. Describe the process of genetic engineering of spider silk using yeast. Why is a vector used in this process?

26. What are the advantages of using yeast in the production of spider silk?

27. List some examples in which the field of agriculture has benefited from genetic engineering.

28. List some examples in which the field of medicine has benefited from genetic engineering.

29. What are some of the challenges facing genetic engineering?