Review Questions Exam 1 BIOL 3300

1. What are the properties of living organisms?

• Organization: Living organisms have a complex and organized structure.

• Metabolism: They undergo chemical reactions to maintain life.

• Homeostasis: They regulate their internal environment to maintain a stable state.

• Growth and Development: They grow and develop according to specific instructions coded in their DNA.

• Reproduction: They can reproduce to create new organisms.

• Response to Stimuli: They can respond to environmental changes.

• Adaptation: They evolve over time through adaptations to their environment.

2. What is the cell theory?

• All living organisms are composed of one or more cells.

• The cell is the basic unit of life.

• All cells arise from pre-existing cells.

3. Who was the first scientist to identify cells and what type of cells did he observe?

• Robert Hooke was the first scientist to identify cells in 1665. He observed the cell walls in a slice of cork, which are the remains of dead plant cells.

4. All types of cells are divided into what two types?

• Prokaryotic Cells: These cells do not have a nucleus or other membrane-bound organelles.

• Eukaryotic Cells: These cells have a nucleus and other membrane-bound organelles.

5. Describe the main differences between these two main types of cells.

• Nucleus: Prokaryotic cells lack a nucleus, while eukaryotic cells have a nucleus.

• Size: Prokaryotic cells are generally smaller than eukaryotic cells.

• Complexity: Eukaryotic cells are more complex, with multiple organelles, while prokaryotic cells are simpler.

• DNA Structure: Prokaryotic cells have circular DNA, while eukaryotic cells have linear DNA.

• Reproduction: Prokaryotic cells reproduce by binary fission, while eukaryotic cells reproduce by mitosis and meiosis.

6. What are model organisms? Explain some of the different types and what aspects of scientific inquiry are they used mostly for?

• Definition: Model organisms are non-human species that are extensively studied to understand particular biological phenomena. They are chosen because they are easy to maintain and breed in a laboratory setting and have particular experimental advantages.

• Types and Uses:

  • Bacteria (e.g., Escherichia coli): Used for studying basic cellular processes and genetics.

  • Yeast (e.g., Saccharomyces cerevisiae): Used for studying cell cycle and genetics.

  • Fruit Fly (Drosophila melanogaster): Used for studying genetics, development, and behavior.

  • Nematode (Caenorhabditis elegans): Used for studying development and neurobiology.

  • Mouse (Mus musculus): Used for studying mammalian genetics, development, and disease models.

  • Zebrafish (Danio rerio): Used for studying development and genetics.
    

7. What is the basic structure of an atom?

• Nucleus: Contains protons (positively charged) and neutrons (neutral).

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

8. What does the atomic number and atomic mass represent?

• Atomic Number: Represents the number of protons in the nucleus of an atom. It defines the element.

• Atomic Mass: Represents the total number of protons and neutrons in the nucleus.

9. Why does an atom interact with another atom?

• Atoms interact to achieve a more stable electron configuration. This often involves filling their outer electron shells, which can be achieved by sharing, donating, or receiving electrons.

10. What different types of interaction occur between atoms?

• Covalent Bonds: Atoms share electrons to fill their outer shells.

• Ionic Bonds: Atoms transfer electrons from one to another, resulting in positively and negatively charged ions that attract each other.

• Hydrogen Bonds: Weak bonds between a hydrogen atom in one molecule and an electronegative atom in another molecule.

• Van der Waals Forces: Weak attractions between molecules due to temporary dipoles.

11. What are organic compounds?

• Organic compounds are molecules that contain carbon atoms bonded to hydrogen atoms, and often include other elements such as oxygen, nitrogen, sulfur, and phosphorus. They are the basis of all known life.

12. What are the common types of organic compounds in living organisms?

• Carbohydrates: Sugars and starches that provide energy.

• Lipids: Fats and oils that store energy and make up cell membranes.

• Proteins: Made of amino acids, they perform a wide range of functions including catalyzing reactions (enzymes), providing structure, and regulating processes.

• Nucleic Acids: DNA and RNA, which store and transmit genetic information.

13. Describe the structure and functions of each macromolecules. What types of molecules are found in each group and how are the structures similar and different?

• Carbohydrates:

  • Structure: Composed of carbon, hydrogen, and oxygen atoms, typically in a ratio of 1:2:1.

  • Functions: Provide energy, serve as structural components (e.g., cellulose in plants), and are involved in cell recognition processes.

• Lipids:

  • Structure: Composed mainly of carbon and hydrogen atoms, with a small amount of oxygen. They include fats, phospholipids, and steroids.

  • Functions: Store energy, make up cell membranes (phospholipids), and act as signaling molecules (steroids).

• Proteins:

  • Structure: Made up of amino acids linked by peptide bonds, forming polypeptide chains that fold into specific three-dimensional shapes.

  • Functions: Catalyze biochemical reactions (enzymes), provide structural support, transport molecules, and regulate cellular processes.

• Nucleic Acids:

  • Structure: Made up of nucleotides, which consist of a sugar, a phosphate group, and a nitrogenous base.

  • Functions: Store and transmit genetic information (DNA) and play a role in protein synthesis (RNA).

14. How are the polymers formed? Which macromolecules are described as polymers.

• Polymers are formed through dehydration synthesis (condensation reactions), where monomers are joined together by covalent bonds with the removal of a water molecule.

• Macromolecules Described as Polymers: Carbohydrates (polysaccharides), proteins (polypeptides), and nucleic acids (DNA and RNA).

15. What is energy?

• Definition: Energy is the capacity to do work or bring about change. It exists in various forms, including kinetic, potential, thermal, chemical, and electrical energy.

16. What is metabolism?

• Metabolism refers to all the chemical reactions that occur within a living organism to maintain life. These reactions are divided into two categories: catabolic and anabolic pathways.

17. Describe catabolic pathways vs. anabolic pathways.

• Catabolic Pathways: These pathways break down complex molecules into simpler ones, releasing energy in the process. For example, the breakdown of glucose during cellular respiration.

• Anabolic Pathways: These pathways build complex molecules from simpler ones, consuming energy in the process. For example, the synthesis of proteins from amino acids.

18. What are the two laws of thermodynamics?

• First Law (Law of Energy Conservation): Energy cannot be created or destroyed, only transformed from one form to another.

• Second Law: In any energy transfer or transformation, the total entropy (disorder) of a system and its surroundings always increases.

19. How is energy transferred in cells?

• Energy is transferred in cells primarily through the molecule ATP (adenosine triphosphate). ATP stores energy in its high-energy phosphate bonds and releases it when these bonds are broken, providing energy for cellular processes.

20. Why are enzymes essential to cells?

• Enzymes are essential to cells because they act as catalysts, speeding up chemical reactions that would otherwise occur too slowly to sustain life. They lower the activation energy required for reactions to proceed.

21. How do they decrease the activation energy? (Hint: the enzyme lysozyme can be used as an example)

• Enzymes decrease activation energy by stabilizing the transition state and providing an alternative reaction pathway. For example, the enzyme lysozyme binds to its substrate and distorts its structure, making it easier for the reaction to occur.

22. What are the structural features and properties of enzymes?

• Enzymes are proteins with a specific three-dimensional shape that includes an active site where the substrate binds. They are highly specific, meaning each enzyme typically catalyzes only one type of reaction. Enzymes can be regulated by factors such as temperature, pH, and the presence of inhibitors or activators.

23. How do cells accomplish unfavorable reactions?

• Cells accomplish unfavorable reactions by coupling them with favorable ones. This often involves the use of ATP, where the energy released from ATP hydrolysis drives the unfavorable reaction.

24. What is ∆G?

• ∆G represents the change in free energy during a chemical reaction. It indicates whether a reaction is spontaneous (negative ∆G) or requires energy input (positive ∆G).

25. Describe the ∆G of unfavorable and favorable reactions?

• Favorable Reactions: Have a negative ∆G, meaning they release free energy and occur spontaneously.

• Unfavorable Reactions: Have a positive ∆G, meaning they require an input of free energy to proceed.

26. How does the ratio of reactants to products influence the ∆G?

• The ratio of reactants to products influences the ∆G of a reaction. According to the equation ΔG = ΔG∘ + RT ln⁡ ([products]/[reactants]), where ΔG∘ΔG∘ is the standard free energy change, R is the gas constant, and T is the temperature in Kelvin. If the ratio of products to reactants is high, the reaction is less likely to proceed forward, making ∆G more positive. Conversely, if the ratio of reactants to products is high, the reaction is more likely to proceed forward, making ∆G more negative.

27. What are proteins comprised of and what part of the cell specifies the order of amino acids in each type of protein?

• Proteins are comprised of amino acids linked together by peptide bonds. The order of amino acids in each type of protein is specified by the sequence of nucleotides in the DNA of the cell.

28. How do amino acids interact together to form a polypeptide chain?

• Amino acids interact together to form a polypeptide chain through peptide bonds, which are formed by dehydration synthesis. The carboxyl group of one amino acid reacts with the amino group of another, releasing a molecule of water and forming a covalent bond.

29. What types of interactions occur between amino acids result in the 3-dimensional shape of a protein?

• The interactions between amino acids that result in the 3-dimensional shape of a protein include hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges. These interactions help stabilize the protein's structure.

30. Describe the different structural levels of protein folding. Be sure to include details about each level and interactions that stabilize these levels.

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

• Secondary Structure: Local folding patterns such as alpha-helices and beta-sheets, stabilized by hydrogen bonds.

• Tertiary Structure: The overall 3D shape of a single polypeptide chain, stabilized by various interactions between side chains.

• Quaternary Structure: The arrangement of multiple polypeptide chains (subunits) into a functional protein complex.

31. What are protein domains?

• Protein domains are distinct functional and/or structural units within a protein. Each domain can fold independently and often has a specific function. Proteins can have one or multiple domains.

32. Describe the different locations of hydrophobic and hydrophilic amino acids in a folded protein.

• In a folded protein, hydrophobic amino acids are typically located in the interior, away from the aqueous environment, while hydrophilic amino acids are usually found on the surface, interacting with the surrounding water.

33. Describe the methods used to determine the structure of proteins (advantages and disadvantages of each).

• X-ray Crystallography: Provides high-resolution structures but requires crystallization of the protein, which can be challenging.

• Nuclear Magnetic Resonance (NMR) Spectroscopy: Useful for studying proteins in solution but is limited to smaller proteins.

• Cryo-Electron Microscopy (Cryo-EM): Allows visualization of large protein complexes and does not require crystallization, but the resolution can be lower compared to X-ray crystallography.

34. How do proteins work?

• Proteins work by binding to other molecules, which can be other proteins, small molecules, or ions. This binding often induces a conformational change in the protein, allowing it to perform its specific function, such as catalyzing a reaction, transporting molecules, or signaling.

35. What is a molecule called that a protein binds and what types of interactions occur to create this binding?

• A molecule that a protein binds is called a ligand. The interactions that create this binding include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals forces. These interactions are typically non-covalent and reversible.

36. Describe the structure of antibodies. How does this structure relate to function? What cells make antibodies and what is the overall function of these protein?

• Structure: Antibodies are Y-shaped molecules composed of two heavy chains and two light chains, connected by disulfide bonds. Each chain has a variable region that binds to a specific antigen and a constant region that determines the antibody's class.

• Function: The variable regions allow antibodies to recognize and bind to specific antigens, marking them for destruction by the immune system.

• Production: Antibodies are produced by B cells (a type of white blood cell) in response to antigens.

• Overall Function: Antibodies help neutralize pathogens, mark them for destruction by other immune cells, and activate other components of the immune system.

37. Describe the general properties of enzymes. What does vmax and km values mean when studying enzyme kinetics?

• Vmax: The maximum rate of an enzyme-catalyzed reaction when the enzyme is saturated with substrate.

• Km: The substrate concentration at which the reaction rate is half of Vmax. It reflects the affinity of the enzyme for its substrate; a lower Km indicates higher affinity.

38. What reaction is mediated by lysozyme? What role does this enzyme play in the human immune system? How does it mechanistically bind to its substrate and mediate production of product?

• Reaction: Lysozyme catalyzes the hydrolysis of the glycosidic bonds in the peptidoglycan layer of bacterial cell walls, leading to cell lysis.

• Role in Immune System: Lysozyme is part of the innate immune system and helps protect against bacterial infections by breaking down bacterial cell walls.

• Mechanism: Lysozyme binds to its substrate (peptidoglycan) and distorts the bonds, making them easier to break. This lowers the activation energy required for the reaction.

39. Describe the different mechanisms used by cells to regulate the activity of proteins ( “off” and “on” states).

• Allosteric Regulation: Proteins can be regulated by molecules that bind to sites other than the active site, causing a conformational change that affects activity.

• Phosphorylation: The addition or removal of phosphate groups can activate or deactivate proteins.

• Proteolytic Cleavage: Some proteins are activated by the cleavage of specific peptide bonds.

• Feedback Inhibition: The end product of a metabolic pathway can inhibit an enzyme involved in the pathway, preventing overproduction.

• Protein-Protein Interactions: Interactions with other proteins can modulate activity.