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BIOL 1000 MIDTERM/EXAM REVIEW 2024 Learning Strategies (these will be covered throughout the course) • Describe the 5 stage study cycle Preview, Attend Class, Review, Study, Assess. Preview before class, and come to class with ideas, questions, and interests. Attend lectures/class, take notes, engage, think, make connections, and write down questions. Review after lecture/class, review your notes, fill in gaps, identify points of confusion, and questions- make a plan to get them answered. Study the material regularly just before the exam; use a variety of learning strategies, and seek understanding not memorizing. Assess your learning, test yourself, and reflect: is your approach working? What needs more work? What else might you do? • Define metacognition and explain its importance to learning Metacognition refers to the awareness and understanding of one's own thought processes. It involves thinking about how we think, learn, and solve problems. In simpler terms, metacognition is "thinking about thinking." It includes skills such as: Self-awareness of how you approach learning tasks. Monitoring your progress while learning. Evaluating the effectiveness of your strategies and adjusting them as needed. Metacognition is like having a big brain outside of your brain looking at what your brain is doing. Importance to Learning: Metacognition is crucial for effective learning because it allows individuals to take control of their cognitive processes and improve their ability to acquire and retain information. • Explain how you can use Topic Learning Outcomes as a study tool • Describe several effective study strategies 1. Active Recall Active recall involves retrieving information from memory without looking at the source. This strengthens memory retention by practicing the active retrieval of knowledge. Example: After reading a chapter, close the book and write down or say out loud everything you can remember about the material. 2. Spaced Repetition Spaced repetition involves reviewing information at increasing intervals over time. This technique combats the forgetting curve and strengthens long-term retention. Example: Use flashcards (physical or digital, like Anki) and review them in spaced intervals: after 1 day, 3 days, 1 week, and so on. 3. Self-Testing Self-testing involves quizzing yourself or taking practice tests. Testing helps to reinforce learning and shows you what areas need more focus. Example: Create your own quiz questions, take practice exams, or use flashcards to test yourself on key concepts. 4. Chunking Chunking involves breaking down large amounts of information into smaller, manageable units. This method helps with memorizing by grouping related items together. Example: When trying to memorize a long list (e.g., dates or vocabulary), group them into categories or sequences. • Reflect upon your own learning (study strategies, topics that are confusing, etc); identify areas for improvement, create and complete an action plan, successfully monitor your own learning. Introduction and Evolution • Describe the major Characteristics of Life Cellular Organization: Made up of one or more cells. Metabolism: Chemical processes for energy conversion. Homeostasis: Maintains a stable internal environment. Growth and Development: Changes in size and function over time. Reproduction: Can reproduce sexually or asexually. Response to Stimuli: Reacts to environmental changes. Adaptation through Evolution: Evolves over generations for survival. Organization: Complex structures from molecules to systems. Needs energy to survive and reproduce Are made up of membrane-bound cell Process genetic and environmental information Replicate Product of evolution • Compare and contrast "hypothesis" and "theory” when used in a scientific context. [Comprehension, Analysis] Hypothesis: A testable prediction about the relationship between variables. Often formulated based on observations and must be falsifiable. Example: “If plants receive more sunlight, then they will grow taller.” Theory: A well-substantiated explanation of an aspect of the natural world. Supported by a vast body of evidence and has stood up to repeated testing. Example: The Theory of Evolution explains the diversity of life based on evidence from various scientific disciplines. • List and describe the two major unifying theories in Biology – Cell Theory and Evolution [Knowledge, Comprehension] Cell theory: All organisms are made up of cells All cells come from preexisting cells Because all cells come from preexisting cells, all individuals in a population of single-celled organisms are related by common ancestry In multicellular organisms, all of the cells present descend from preexisting cells; connected by common ancestry. Theory of evolution: Characteristics of a population change over time Evolution can occur through selection Species are related by common ancestry • Describe the theory of evolution. [Knowledge] What is Evolution: Mutation Migration Genetic Drift Natural selection Evolution describes a change in a population over time Population change can happen in different ways Evolution cannot just be reduced to “survival of the fittest” A scientific explanation for the diversity of life, proposing that species evolve over time through mechanisms like natural selection and genetic variation. • Explain how both the unity and the diversity of life can be explained by the theory of evolution. [Comprehension] Unity: All living organisms share common biochemical processes and genetic materials (DNA). Fundamental similarities in cellular structure (e.g., cell membranes, ribosomes). Diversity: Adaptations to different environments lead to varied traits and forms. Evolution explains how different species arise from common ancestors. • Describe “Natural Selection”, and provide/identify a biological example of this process. [Knowledge] Definition: The process where organisms better adapted to their environment tend to survive and produce more offspring. Example: Peppered Moths: In polluted areas, darker moths were favored as they blended in with soot-covered trees, while lighter moths were more visible to predators, therefore the lighter moths died and there were more darker moths as they were able to survive. Evolution by natural selection: ?Variation in a population ?Variation is heritable ?Differential survival and reproduction ?Frequency of selected traits in next generation ? A change in the traits of a population over time (Evolution) Evolution by natural selection: ?Variation in a population ?Variation is heritable ?Differential survival and reproduction ?Frequency of selected traits in next generation ? A change in the traits of a population over time (Evolution) Evolution by natural selection: ?Variation in a population ?Variation is heritable ?Differential survival and reproduction ?Frequency of selected traits in next generation ? A change in the traits of a population over time (Evolution) Evolution by natural selection: ?Variation in a population ?Variation is heritable (genetic) ?Differential survival and reproduction ?Frequency of selected traits in next generation ? A change in the traits of a population over time (Evolution) • Given a particular example of evolution, describe how the change could arise by Natural Selection. [Application, Analysis] Example: Antibiotic Resistance: Bacteria that survive antibiotic treatment reproduce, passing on resistant traits. Over time, the population becomes predominantly resistant due to selective pressure from the antibiotics. • Compare Natural Selection and Artificial Selection [Comprehension] Natural Selection: Occurs naturally through environmental pressures. Leads to adaptations that enhance survival and reproduction. Artificial Selection: Involves human intervention to select for desired traits in organisms. Example: Breeding dogs for specific characteristics like size or temperament. • Relate the cell theory to the theory of evolution. [Comprehension, Analysis] Both theories emphasize commonalities: all organisms are made of cells, and all cells share a common ancestry. Evolution explains how cellular structures and functions have adapted over time, leading to the diversity of life forms we see today. Cells • Identify and briefly describe the three domains of life. Bacteria: Prokaryotic, unicellular organisms with peptidoglycan cell walls. Example: E. coli. Archaea: Prokaryotic, unicellular organisms with unique lipids in cell membranes. Often extremophiles. Example: Methanogens. Eukarya: Eukaryotic organisms, which can be unicellular or multicellular, with complex cellular structures. Examples: Plants, animals, fungi. • Describe the common components and characteristics of all cells (including protein and protein structure). [Knowledge] – Self-review. Common Components of All Cells Cell Membrane: Structure: A semi permeable phospholipid bilayer embedded with proteins. Function: Acts as a barrier, regulating the movement of substances in and out of the cell and facilitating communication with the external environment. Cytoplasm: Structure: Gel-like substance within the cell, composed of water, salts, and organic molecules. Function: Site for metabolic reactions and contains organelles in eukaryotic cells. Genetic Material (DNA/RNA): Structure: DNA is usually organized into chromosomes in eukaryotes and exists as a single circular molecule in prokaryotes. RNA is single-stranded and involved in protein synthesis. Function: Contains the genetic blueprint for the organism, directing cellular activities and inheritance. Ribosomes: Structure: Composed of ribosomal RNA (rRNA) and proteins; can be free-floating or attached to the endoplasmic reticulum (in eukaryotes). Function: Sites of protein synthesis, translating mRNA into polypeptide chains. Common Characteristics of All Cells Cellular Organization: All cells are organized structures that can be unicellular or multicellular. Metabolism: Cells carry out biochemical processes to extract energy from nutrients, including catabolic (breaking down) and anabolic (building up) pathways. Homeostasis: Cells maintain a stable internal environment, regulating factors like pH, temperature, and ion concentrations. Reproduction: Cells have the ability to reproduce, either through binary fission (in prokaryotes) or mitosis/meiosis (in eukaryotes). Response to Stimuli: Cells can respond to environmental changes or signals, which is essential for survival and adaptation. Proteins and Protein Structure Proteins are essential macromolecules made up of amino acids and perform a wide variety of functions within cells. Here’s a brief overview of protein structure: Amino Acids: The building blocks of proteins, consisting of an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain). Levels of Protein Structure: Primary Structure: The linear sequence of amino acids in a polypeptide chain. Secondary Structure: Local folding into structures like alpha helices and beta sheets, stabilized by hydrogen bonds. Tertiary Structure: The overall three-dimensional shape of a protein, formed by interactions among R groups (side chains) and between R groups and the environment. Quaternary Structure: The assembly of multiple polypeptide chains into a functional protein complex (not all proteins have this level). Functions of Proteins: Enzymatic: Catalyze biochemical reactions. Structural: Provide support and shape to cells and tissues (e.g., collagen). Transport: Carry substances across membranes or within organisms (e.g., hemoglobin). Regulatory: Control cellular processes, including gene expression (e.g., transcription factors). Defense: Protect against pathogens (e.g., antibodies). • Explain what is meant by metabolic diversity in bacteria and archaea. Provide examples. [Knowledge, Comprehension] Definition: The variety of metabolic pathways found in these domains, enabling survival in diverse environments. Examples: Bacteria: Some perform photosynthesis (cyanobacteria), while others are chemolithotrophic (use inorganic molecules for energy). Archaea: Methanogens produce methane, while halophiles thrive in high-salt environments • Describe the general structure of bacterial and archaeal cells, relating structure to function and using appropriate terminology. [Comprehension] Structure: Cell Wall: Provides shape and protection; composed of peptidoglycan in bacteria, pseudopeptidoglycan in archaea. Cell Membrane: Phospholipid bilayer; may contain unique lipids in archaea. Nucleoid: Region where DNA is located, not membrane-bound. Ribosomes: Smaller than eukaryotic ribosomes, involved in protein synthesis. Function: The cell wall supports structure, while the cell membrane regulates transport. • Describe the similarities and differences of chromosomal and plasmid bacterial DNA [Knowledge, Comprehension] Chromosomal DNA: Typically a single, circular chromosome. Contains essential genes for survival and reproduction. Plasmid DNA: Small, circular DNA molecules independent of chromosomal DNA. Carry non-essential genes, such as those for antibiotic resistance. • Describe the structure and function of the eukaryotic cell and its organelles (including nucleus and other elements of the endomembrane system, ribosomes, lysosomes, mitochondria, chloroplasts). [Knowledge, Comprehension] - Self-review Structure of Eukaryotic Cells Cell Membrane: A phospholipid bilayer that regulates the movement of substances in and out of the cell, providing protection and support. Nucleus: Contains genetic material; site of transcription. Cytoplasm: A gel-like substance where organelles are suspended and metabolic processes occur. Key Organelles and Their Functions: Nucleus: Structure: Surrounded by a double membrane (nuclear envelope) with nuclear pores. Function: Stores genetic information; site of transcription and RNA processing. Ribosomes: Synthesize proteins; can be free-floating or attached to the RER. Structure: Small, made of RNA and proteins; can be free in the cytoplasm or attached to the endoplasmic reticulum. Function: Sites of protein synthesis. Endomembrane System: Structure: Network of membranes; rough ER has ribosomes, while smooth ER does not. Function: Rough Endoplasmic Reticulum (RER): Studded with ribosomes; synthesizes and modifies proteins. Smooth Endoplasmic Reticulum (SER): Synthesizes lipids; detoxifies substances. Golgi Apparatus: Structure: Stacked membranes. Function: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles. Lysosomes: Contain digestive enzymes for waste processing. Structure: Membrane-bound vesicles containing digestive enzymes. Function: Breaks down waste materials and cellular debris; involved in autophagy. Mitochondria: Structure: Double membrane with inner folds (cristae) that increase surface area. Function: Produces ATP through cellular respiration, often called the "powerhouse of the cell." Chloroplasts (in plant cells): Site of photosynthesis in plant cells Structure: Double membrane with thylakoids containing chlorophyll. Function: Site of photosynthesis, converting solar energy into chemical energy (glucose). Cytoskeleton: Structure: Network of protein filaments and tubules. Function: Provides structural support, enables cell movement, and plays a role in intracellular transport. Centrioles (in animal cells): Structure: Paired structures made of microtubules. Function: Involved in cell division and the organization of the mitotic spindle. • Explain how transport into and out of the nucleus is regulated. Nuclear Transport in Eukaryotic Cells Nuclear Envelope: Double membrane surrounding the nucleus. Contains Nuclear Pore Complexes (NPCs) for transport regulation. Nuclear Pore Complexes (NPCs): Large protein structures that form channels through the nuclear envelope. Allow selective transport of proteins, RNA, and small molecules. Transport Types: Passive Diffusion: Small molecules (e.g., ions) diffuse freely through NPCs. Active Transport: Larger molecules require specific signals: Nuclear Localization Signals (NLS): On proteins entering the nucleus; bind to importin proteins. Nuclear Export Signals (NES): On proteins exiting the nucleus; bind to exportin proteins. Ran Protein Gradient: Ran-GTP: Predominantly in the nucleus, promotes import. Ran-GDP: Predominantly in the cytoplasm, facilitates export. This gradient is crucial for the disassembly of transport complexes. Gram-Positive Bacteria Cell Structure: Thick Peptidoglycan Layer: Provides structural support. No Outer Membrane: Cell membrane is more directly accessible. Transport Mechanisms: Nutrient uptake occurs mainly through the cell membrane. Thick cell wall limits passive diffusion but allows specific transport proteins. Gram-Negative Bacteria Cell Structure: Thin Peptidoglycan Layer: Located between inner and outer membranes. Outer Membrane: Contains lipopolysaccharides (LPS) and porins. Transport Mechanisms: Outer membrane acts as an additional barrier. Porins: Allow small molecules to passively diffuse. Active Transport Systems: Needed for larger molecules and nutrients. Efflux Pumps: Actively transport antibiotics and toxins out of the cell, contributing to antibiotic resistance. Summary Nuclear transport in eukaryotic cells is regulated by NPCs, specific signaling sequences, and the Ran protein gradient. Gram-positive bacteria have a simpler transport mechanism due to their thick peptidoglycan layer, while gram-negative bacteria require more complex mechanisms due to their dual membrane structure. Nuclear Pores: Complex structures that allow selective transport of molecules. Import/Export Signals: Proteins contain specific signals that direct their transport through nuclear pores. • Compare and contrast the features of plant and animal cells. [Comprehension, Analysis] – Self-review Similarities: Both have a nucleus, ribosomes, mitochondria, and endomembrane system. Differences: Cell Wall: Present in plant cells, absent in animal cells. Chloroplasts: Present in plant cells, absent in animal cells. Shape: Plant cells typically have a fixed, rectangular shape; animal cells are more varied • Explain the structural and functional relationships between different members of the endomembrane system. [Comprehension, Application] Proteins and lipids are synthesized in the ER (rough ER for proteins, smooth ER for lipids) and transported via vesicles to the Golgi apparatus for modification. After processing in the Golgi, vesicles deliver proteins and lipids to their target destinations: the plasma membrane, lysosomes, or secretion outside the cell. Lysosomes receive digestive enzymes from the Golgi, and vesicles formed at the plasma membrane can fuse with lysosomes for degradation. Endosomes interact with both lysosomes and the plasma membrane for the recycling and degradation of internalized materials. • Describe the process by which proteins are targeted to the RER and other parts of the endomembrane system. [Knowledge, Comprehension] Signal Sequence: Newly synthesized proteins have a signal sequence that directs them to the RER. Translocation: Ribosomes dock on the RER, allowing proteins to enter the lumen for folding and modification. 1. Synthesis of Proteins Ribosomes: Protein synthesis begins on ribosomes in the cytosol. Ribosomes can be either free in the cytosol or bound to the RER. Signal Sequence: Proteins destined for the RER typically have a short signal peptide (or signal sequence) at their N-terminus. This sequence is usually composed of hydrophobic amino acids and serves as a recognition signal for the RER. 2. Recognition and Targeting Signal Recognition Particle (SRP): As the ribosome synthesizes the signal peptide, it is recognized and bound by the signal recognition particle (SRP). This binding pauses translation. SRP-Ribosome Complex: The SRP-ribosome complex is then directed to the RER membrane, where it interacts with an SRP receptor. 3. Translocation into the RER Docking: Upon binding to the SRP receptor, the ribosome docks onto a protein translocation channel in the RER membrane known as the translocon. Resumption of Translation: The SRP is released, and translation resumes, with the growing polypeptide being threaded through the translocon into the lumen of the RER. Signal Peptidase: Once inside the RER, the signal peptide is typically cleaved off by an enzyme called signal peptidase. 4. Folding and Modifications Inside the RER lumen, proteins undergo proper folding, assisted by chaperone proteins. They may also undergo post-translational modifications such as glycosylation (addition of sugar groups). 5. Quality Control The RER has a quality control system that ensures only properly folded and assembled proteins are transported to the next stage. Misfolded proteins may be retained and eventually targeted for degradation. 6. Transport to the Golgi Apparatus Once the proteins are correctly folded, they are packaged into transport vesicles that bud off from the RER. These vesicles carry the proteins to the Golgi apparatus for further processing and sorting. 7. Sorting in the Golgi Apparatus In the Golgi, proteins are further modified, sorted, and packaged into vesicles that will either be sent to lysosomes, incorporated into the plasma membrane, or secreted outside the cell. Each protein has specific sorting signals that direct it to its correct destination. 8. Final Targeting The vesicles containing the proteins bud off from the Golgi and travel to their specific destinations, where they will perform their functions. • List and describe the major eukaryotic cytoskeletal elements and associated motor proteins, their basic structure and their roles in the cell/organism. [Knowledge, Comprehension] Microfilaments: Provide structural support and are involved in cell motility. Microtubules: Maintain cell shape, form cilia/flagella, and facilitate intracellular transport. Intermediate Filaments: Provide mechanical strength. Motor Proteins: Kinesin: Moves materials along microtubules toward the plus end. Dynein: Moves materials toward the minus end. Myosin: Interacts with actin for muscle contraction and movement. • Compare and contrast kinesin, dynein and myosin [Analysis]. Given a description of a cellular process predict which motor protein is involved. [Application, Evaluation] Kinesin: Moves toward the cell periphery (plus end of microtubules). Dynein: Moves toward the cell center (minus end of microtubules). Myosin: Primarily interacts with actin filaments for muscle movement. • Compare and contrast cells of bacteria, archaea and eukaryotes, identifying structural and functional similarities and differences . [Comprehension, Analysis] Bacteria: Prokaryotic, peptidoglycan cell walls, circular DNA. Archaea: Prokaryotic, unique membrane lipids, circular DNA. Eukaryotes: Eukaryotic, complex organelles, linear DNA in multiple chromosomes. • Explain why eukaryotic cells are typically much larger than bacterial & archaeal cells. [Comprehension] Eukaryotic cells are typically much larger than bacterial and archaeal cells primarily due to differences in cellular structure, organization, and complexity. Several factors explain why eukaryotic cells can maintain a larger size: 1. Internal Compartmentalization Membrane-bound organelles: Eukaryotic cells contain numerous membrane-bound organelles (e.g., nucleus, mitochondria, endoplasmic reticulum, and Golgi apparatus) that compartmentalize various cellular functions. This internal organization allows eukaryotic cells to maintain a high level of efficiency and manage complex biochemical processes. Specialized functions: Organelles allow for localized environments within the cell, where specific reactions can occur more efficiently, contributing to the cell's ability to grow larger without losing functionality. 2. Surface Area-to-Volume Ratio Volume increase: As a cell grows larger, its volume increases faster than its surface area. This limits the rate at which materials (e.g., nutrients, gases, waste) can diffuse across the cell membrane. Eukaryotic cells solve this problem by developing organelles that facilitate intracellular transport and metabolism. Endomembrane system: The eukaryotic endomembrane system, including the ER and Golgi apparatus, assists in the distribution of proteins and lipids, which reduces the dependency on the cell’s surface area and supports larger cell sizes. 3. Cytoskeleton Structural support and intracellular transport: Eukaryotic cells possess a complex cytoskeleton made of microtubules, microfilaments, and intermediate filaments. This system provides structural support, maintaining cell shape, and also facilitates the transport of materials within the cell. This allows eukaryotic cells to grow larger without losing mechanical stability or efficiency in internal transport. 4. Energy Requirements Mitochondria and energy production: Eukaryotic cells have mitochondria, which enable efficient energy production through aerobic respiration. Mitochondria produce significantly more ATP per glucose molecule than anaerobic processes used by many bacteria and archaea, allowing eukaryotic cells to meet the higher energy demands of larger cells. Efficiency of ATP production: The high efficiency of ATP production in eukaryotic cells supports the metabolic needs of larger cells and allows them to maintain energy-intensive processes. 5. Genome Size and Regulation Larger and more complex genome: Eukaryotic cells have larger genomes than prokaryotic cells (bacteria and archaea), encoding more genes involved in regulating cellular processes and differentiation. The presence of a nuclear membrane also allows for more complex gene regulation and RNA processing, which supports more elaborate cellular functions. Gene expression regulation: Eukaryotic cells can regulate gene expression more efficiently, allowing them to coordinate activities across a larger cell volume. 6. Multicellularity and Specialization Cell differentiation: In multicellular organisms, eukaryotic cells can differentiate into specialized cell types with distinct functions, enabling larger organisms to evolve. The ability to specialize reduces the pressure for individual eukaryotic cells to perform all functions, contributing to larger cell sizes and more efficient functioning in larger organisms. 7. Endosymbiosis Theory According to the endosymbiotic theory, eukaryotic cells originated through the engulfment of prokaryotic cells (like mitochondria and chloroplasts) by an ancestral eukaryote. This symbiotic relationship allowed eukaryotic cells to gain energy through more efficient means (aerobic respiration), enabling them to grow larger and support more complex cellular structures. In Contrast: Bacteria and Archaea Lack of internal compartmentalization: Bacteria and archaea do not have membrane-bound organelles. Their smaller size allows for efficient diffusion of materials throughout the cell, which would not be effective in larger cells without organelles to assist. Simple structure: Their smaller genomes, lack of complex cytoskeletal systems, and simpler biochemical pathways make them highly efficient at smaller sizes but limit their ability to scale up in size while maintaining function. • Describe the likely origin of eukaryotic cells: hypothesis for origins of endomembrane system, endosymbiotic theory of the origin and evolution of mitochondria and chloroplasts and the evidence supporting this theory. [Knowledge, Comprehension] The origin of eukaryotic cells is explained through two main hypotheses: Origin of the Endomembrane System: Eukaryotic cells likely evolved through the inward folding of the plasma membrane in an ancestral prokaryote. This formed internal membranes, including the nuclear envelope and organelles like the endoplasmic reticulum and Golgi apparatus, enabling compartmentalization and specialization of cellular functions. Endosymbiotic Theory: Mitochondria and chloroplasts originated from free-living bacteria (aerobic bacteria and cyanobacteria, respectively) that were engulfed by an early eukaryotic cell. Over time, these bacteria formed symbiotic relationships with the host cell and evolved into organelles. Evidence Supporting the Endosymbiotic Theory: Double membranes in mitochondria and chloroplasts. Own circular DNA similar to bacterial DNA. Bacterial-like ribosomes and binary fission replication. Genetic similarity between mitochondria and alpha-proteobacteria, and between chloroplasts and cyanobacteria. Sensitivity to antibiotics that affect bacteria but not eukaryotic cells. Together, these processes led to the energy efficiency and complexity of modern eukaryotic cells. Energy and Enzymes • Define key terms: enthalpy, entropy, endergonic, exergonic, free energy (G), activated carrier molecule, activation energy, active site, substrate, reactants, catalysis, cofactor, coenzyme, enzyme inhibitor (competitive, non-competitive), allosteric site, feedback inhibition. [Knowledge] Enthalpy: Total heat content of a system; reflects internal energy and pressure. Entropy: Measure of disorder or randomness in a system; higher entropy means greater disorder. Endergonic: Reactions that absorb energy; ?G is positive. Exergonic: Reactions that release energy; ?G is negative. Free Energy (?G): Energy available to do work in a system. Activated Carrier Molecule: Molecules like ATP or NADH that store and transfer energy within cells. Activation Energy: Minimum energy required to initiate a chemical reaction. Active Site: Region on an enzyme where substrate molecules bind. Substrate: Reactant molecules that enzymes act upon. Reactants: Starting materials in a chemical reaction. Catalysis: The acceleration of a chemical reaction by a catalyst (like an enzyme). Cofactor: Non-protein substances that assist enzymes in catalyzing reactions. Coenzyme: Organic molecules that function as cofactors (e.g., vitamins). Enzyme Inhibitor: Substances that decrease enzyme activity. Competitive Inhibition: Inhibitor competes with substrate for the active site. Non-competitive Inhibition: Inhibitor binds to a site other than the active site, changing the enzyme's shape. Allosteric Site: Site on an enzyme where molecules can bind and change enzyme activity. Feedback Inhibition: Process where the end product of a metabolic pathway inhibits an earlier step. • Describe the difference between potential energy and kinetic energy and illustrate with examples. Potential Energy: Energy stored in an object due to its position or arrangement. Example: A boulder perched on a hill. Kinetic Energy: Energy of motion. Example: A rolling boulder. • Briefly describe the first two laws of thermodynamics, and apply them to living organisms. First Law: Energy cannot be created or destroyed, only transformed. Application: In living organisms, energy from food is converted into ATP. Second Law: In any energy transfer, the entropy of the universe increases. Application: Living organisms maintain order by using energy, which increases overall entropy. • Relate the use of energy and enzymes to metabolism. [Comprehension] Metabolism refers to the sum of all chemical reactions in a cell or organism, involving both the breakdown of molecules (catabolism) and the building of molecules (anabolism). Energy and enzymes play crucial roles in regulating and driving metabolic processes. 1. Energy in Metabolism: ATP as an energy currency: Cells use adenosine triphosphate (ATP) to store and transfer energy. During catabolic reactions, energy is released from the breakdown of molecules like glucose, and this energy is used to synthesize ATP. ATP then provides the necessary energy for anabolic reactions, which build complex molecules (e.g., proteins, nucleic acids) from simpler ones. Energy coupling: Metabolism relies on energy coupling, where energy released from exergonic (energy-releasing) reactions, such as the breakdown of ATP, is used to drive endergonic (energy-requiring) reactions, enabling cells to perform work (e.g., building molecules, transporting substances). 2. Enzymes in Metabolism: Lowering activation energy: Enzymes are biological catalysts that speed up metabolic reactions by lowering the activation energy required for reactions to occur. Without enzymes, many reactions in metabolism would be too slow to sustain life. Specificity: Each enzyme is highly specific to a substrate, ensuring that the right reactions occur at the right time in metabolic pathways. Regulation: Enzymes regulate metabolic pathways through mechanisms like feedback inhibition, where the end product of a pathway inhibits the enzyme that initiates the pathway. This prevents overproduction and maintains balance in metabolic processes. • Briefly describe redox (reduction – oxidation) reactions (Self Review) and why they are significant in living systems. [Knowledge, Comprehension] Definition: Reactions involving the transfer of electrons between substances. Reduction: Gain of electrons. Oxidation: Loss of electrons. Significance: Critical for energy transfer (e.g., cellular respiration). LEO says GER L oss of G ain of E lectrons is E lectrons is O xidation R eduction • Relate anabolic and catabolic pathways to an organism’s metabolism. [Analysis] Anabolic Pathways: Build complex molecules from simpler ones; require energy (endergonic). Example: Synthesis of proteins from amino acids. Catabolic Pathways: Break down complex molecules into simpler ones; release energy (exergonic). Example: Breakdown of glucose during cellular respiration. • Explain how cells use activated carrier molecules to couple reactions in metabolism. [Comprehension] Cells use activated carriers (like ATP and NADH) to shuttle energy and electrons between metabolic reactions, coupling exergonic and endergonic processes. cells use activated carrier molecules, such as ATP, NADH, and NADPH, to couple reactions in metabolism by temporarily storing and transferring energy from exergonic (energy-releasing) reactions to endergonic (energy-requiring) reactions. These carriers temporarily store energy released from favorable reactions and then transfer it to drive reactions that require an energy input, allowing the cell to perform essential metabolic functions efficiently. • Describe and be able to identify the structure of ATP. [Knowledge, Comprehension] Adenosine Triphosphate (ATP): Composed of: Adenine base Ribose sugar -63523876000Three phosphate groups (negatively charged) • Explain, at a general level, the role of ATP in metabolism. [Comprehension] 1. Energy Transfer High-Energy Bonds: ATP contains high-energy phosphate bonds, particularly between the second and third phosphate groups. When ATP is hydrolyzed to adenosine diphosphate (ADP) and inorganic phosphate (Pi), energy is released. This energy is harnessed to drive various cellular processes. Immediate Energy Source: ATP serves as an immediate energy source for many biological reactions, allowing cells to respond quickly to energy demands. 2. Coupling Reactions Energy Coupling: ATP hydrolysis is often coupled with endergonic reactions (energy-consuming processes) within the cell. This means that the energy released from ATP can be directly used to power reactions such as: Biosynthesis: The synthesis of macromolecules (proteins, nucleic acids, lipids) requires energy, which is supplied by ATP. Active Transport: ATP powers transport proteins that move substances across cell membranes against their concentration gradients. Muscle Contraction: ATP is essential for the contraction of muscle fibers, as it provides the energy needed for the sliding of myosin and actin filaments. 3. Regulatory Role Metabolic Regulation: ATP levels within the cell are closely monitored. When ATP levels are high, it indicates sufficient energy availability, while low ATP levels signal a need for increased energy production. This regulatory mechanism ensures that metabolic pathways are activated or inhibited according to the cell’s energy status. 4. Intermediary Metabolism Linking Pathways: ATP plays a key role in connecting different metabolic pathways. For example, during cellular respiration, glucose is broken down to produce ATP, which is then used in anabolic pathways for building complex molecules. This interplay between catabolism (breaking down molecules to release energy) and anabolism (using energy to build molecules) is central to cellular metabolism. 5. Versatile Functions Phosphorylation: ATP can donate its phosphate group to other molecules in a process known as phosphorylation, which often activates or deactivates enzymes and alters the activity of proteins, further regulating metabolic pathways. • Describe what occurs when ATP is hydrolyzed (in terms of reactants, energy). [Comprehension] Process: ATP + H2O ? ADP + Pi + energy Reactants: ATP and water. Energy: Released for cellular work. when ATP is hydrolyzed, it reacts with water to form ADP and inorganic phosphate, releasing energy in the process. This energy is crucial for powering various cellular activities and metabolic reactions, emphasizing ATP's role as the energy currency of the cell. • Describe the role of enzymes in biological reactions. [Comprehension] Enzymes speed up reactions by lowering activation energy, enabling the transformation of substrates into products efficiently. Catalysis Lowering Activation Energy: Enzymes accelerate reactions by lowering the activation energy required for a reaction to occur. This means that reactions can proceed faster and at lower temperatures than they would without the enzyme. Transition State Stabilization: Enzymes stabilize the transition state of a reaction, which is the intermediate state during the conversion of reactants to products. This stabilization makes it easier for the reaction to proceed. Specificity Substrate Binding: Enzymes have specific active sites that bind to particular substrates (the reactants in the reaction). The structure and chemical properties of the active site determine the enzyme's specificity, allowing it to catalyze only specific reactions. Induced Fit Model: The binding of the substrate often induces a conformational change in the enzyme, enhancing the fit between the enzyme and substrate, which further facilitates the reaction. Regulation Allosteric Regulation: Enzymes can be regulated by molecules that bind to sites other than the active site (allosteric sites). This can activate or inhibit enzyme activity, allowing cells to regulate metabolic pathways according to their needs. Feedback Inhibition: In many metabolic pathways, the end product can inhibit the activity of an enzyme involved earlier in the pathway. This prevents the overproduction of the product and helps maintain metabolic balance. Cofactors and Coenzymes Assistance in Catalysis: Some enzymes require additional non-protein molecules called cofactors (inorganic ions like metal ions) or coenzymes (organic molecules, often derived from vitamins) to function effectively. These molecules can help in the catalytic process or assist in substrate binding. Biological Significance Metabolism: Enzymes play a vital role in metabolic pathways, facilitating both catabolic (breaking down molecules to release energy) and anabolic (building molecules using energy) reactions. Homeostasis: By regulating metabolic reactions, enzymes help maintain homeostasis in organisms, ensuring that cellular processes occur efficiently and responsively to changes in the environment. Enzyme Kinetics Reaction Rates: Enzymes influence the rate of biochemical reactions. Factors such as substrate concentration, temperature, and pH can affect enzyme activity and, consequently, the rate of the reaction. Michaelis-Menten Kinetics: Many enzymes follow a specific kinetic pattern (Michaelis-Menten kinetics) that describes how reaction rates change with varying substrate concentrations, which helps in understanding enzyme efficiency and regulation. • Explain how enzymes serve as catalysts for biological reactions. [Comprehension] Enzymes act as catalysts by lowering the activation energy required for biological reactions, increasing the reaction rates without being consumed. Their specificity, ability to stabilize transition states, and various catalytic mechanisms make them essential for facilitating the myriad of biochemical processes necessary for life. Through regulation and optimal conditions, enzymes ensure that metabolic pathways operate efficiently and responsively to the needs of the cell. • List and describe the factors that affect enzyme activity. [Knowledge, Comprehension] Temperature: Each enzyme has an optimal temperature; high temperatures can denature enzymes. pH: Each enzyme has an optimal pH; deviations can affect activity. Substrate Concentration: Higher concentrations can increase reaction rates until saturation occurs. Enzyme Concentration: More enzymes generally increase reaction rates, assuming sufficient substrate. • Correctly predict the effect of various factors on enzyme activity, (such as enzyme concentration, reaction conditions, etc). [Application] Increased Enzyme Concentration: Increases rate of reaction. Higher Temperature (within optimal range): Increases activity; too high can denature the enzyme. Higher pH (within optimal range): Increases activity; extreme pH can denature. • Predict and explain how non-optimal conditions (e.g., temperatures, pH) affect enzyme activity. [Comprehension, Analysis, Synthesis] Temperature Increased Temperature: Initially speeds up reaction rates due to increased molecular motion, but excessive heat can lead to denaturation, causing loss of enzyme structure and function. Decreased Temperature: Slows down molecular motion and reaction rates; enzyme activity generally decreases, but it does not typically cause denaturation. pH Levels Each enzyme has an optimal pH range. Deviations can disrupt the enzyme's structure and active site: Low or High pH: Can lead to denaturation and altered substrate binding due to changes in ionization. Substrate Concentration At low substrate levels, increasing concentration raises reaction rates until a saturation point is reached: Beyond saturation, additional substrate does not further increase the rate, and low substrate levels result in decreased activity. Enzyme Concentration Increasing enzyme concentration can boost reaction rates if substrate is available. However: If substrate is limited, excess enzyme becomes ineffective, not enhancing the reaction rate. Inhibitors and Activators Inhibitors: Competitive inhibitors block substrate binding, reducing activity; non-competitive inhibitors change enzyme shape and reduce activity regardless of substrate concentration. Activators: Enhance enzyme activity but may be ineffective under non-optimal conditions. Cofactors and Coenzymes Enzymes often depend on cofactors or coenzymes. Non-optimal conditions affecting these molecules can reduce enzyme activity. • Interpret an enzyme curve. [Application] Michaelis-Menten Curve: Shows how reaction velocity increases with substrate concentration until it plateaus (Vmax) when the enzyme is saturated. • Explain how reaction rates and enzyme activity can be regulated. [Comprehension] Allosteric Regulation Allosteric Sites: Regulatory molecules bind to sites other than the active site, inducing conformational changes that can activate or inhibit enzyme activity. Feedback Inhibition End Product Inhibition: The final product of a metabolic pathway inhibits an enzyme involved earlier in the pathway, preventing overproduction and conserving resources. Competitive and Non-Competitive Inhibition Competitive Inhibition: Inhibitors compete with substrates for the active site; increasing substrate concentration can overcome this. Non-Competitive Inhibition: Inhibitors bind to an allosteric site, reducing activity regardless of substrate concentration. Post-Translational Modifications Covalent Modifications: Changes such as phosphorylation can activate or deactivate enzymes. Proteolytic Cleavage: Inactive precursors (zymogens) are activated through cleavage. Enzyme Concentration Regulation Gene Expression: Regulation of enzyme synthesis at the genetic level alters enzyme levels. Degradation: Targeting enzymes for degradation decreases their activity. Environmental Factors Temperature and pH: Deviations from optimal conditions can lead to decreased activity or denaturation. Substrate Concentration: Rates increase with substrate concentration until saturation, beyond which further increases do not enhance activity. Coenzymes and Cofactors Availability: The presence of necessary cofactors or coenzymes influences enzyme activity. • Compare and contrast competitive inhibition of enzymatic activity to non-competitive inhibition. [Comprehension, Analysis] Competitive Inhibition: Inhibitor competes with substrate for the active site. Can be overcome by increasing substrate concentration. Non-Competitive Inhibition: Inhibitor binds to an allosteric site, changing enzyme shape regardless of substrate concentration. Cannot be overcome by increasing substrate concentration.
