LIFE 1_ EXAM 2 Review (2) PDF

EXAM 2 I PLUGGED OUR NOTES INTO AI AND CREATED THIS PODCAST IN CASE ANYONE IS INTERESTED https://notebooklm.google.com/notebook/66ee21fd-0dd5-459e-8134-6e77d24847c1/audio Note: Be able to define terminology and know at least 1-2 relevant examples. May be found in multiple choice, T/F, fill-in-the-...

EXAM 2 I PLUGGED OUR NOTES INTO AI AND CREATED THIS PODCAST IN CASE ANYONE IS INTERESTED https://notebooklm.google.com/notebook/66ee21fd-0dd5-459e-8134-6e77d24847c1/audio Note: Be able to define terminology and know at least 1-2 relevant examples. May be found in multiple choice, T/F, fill-in-the-blank. Important Terminology/Definitions: Allosteric enzymes - enzymes regulated by molecules binding to sites other than the active site, causing activation or inhibition through conformational changes. Inhibitor vs activators (enzymes): Inhibitor - decrease enzyme activity by blocking the active or allosteric site. Activators - increase enzyme activity by enhancing enzyme function. Agonist vs antagonist (receptors): Agonist - activates a receptor, mimicking the natural signal. Antagonist - blocks the receptor, preventing activation. Cell structures (examples): Endoplasmic reticulum- largest internal membrane, contains largest compartment (cisternal space) outside of the cytosol(fluid component of cytoplasm) ROUGH ER: synthesizes proteins on membrane surface and may add carbs to proteins to make glycoproteins. SMOOTH ER: synthesizes carbs, lipids, & steroids; glycogen degradation site; stores calcium = keeps intracellular concentration low so calcium can be a signaling molecule. -(Lecture #8 pg. 8-11) Golgi- sorts, packs, and distributes molecules w/in or outside cell; modifies carbs and/or adds them to proteins; stacked membranes “Amazon packaging” -Pegg Vacuole- Makes up about 90% internal volume in plant cells; stores waste products: maintains internal structure of cell Parts of a chemical reaction: Reactant vs. Product A + B → AB A + B are the reactants or what goes into the reaction → Yields AB is the product or what comes out of the reaction Remember Coefficients and Subscripts Energy:  The capacity of something to do work, where work is a force operating on an object over a distance. Biochemistry: energy is “the capacity for change” Altered chemical composition and molecular properties Remember movement/ the potential for movement Terms for energy in a chemical reaction: Potential Energy: Stored energy of a state or position Subtypes/Examples- 1. Nuclear energy: energy in atomic nuclei 2. Gravitational energy: stored in an object's distance from the center of gravity. 3. Chemical energy: bond energy 4. Elastic energy: objects with elasticity 5. Gradient energy: Chemical concentration or concentration of charges (Electrical energy) Kinetic energy: The energy of movement → Work Subtypes/Examples- 1. Thermal energy: heat energy 2. Mechanical energy: movement 3. Radiant energy: light energy 4. Sound energy: acoustic energy -move fastest through solid and water moves 3x faster than air. Proteins in cell membranes The following proteins are embedded in or associated with the lipid bilayer of the membrane: Transport - channel and carrier proteins help move substances across the membrane Receptors - membrane proteins receive signals from the environment or other cells Enzymatic activity - some proteins catalyze chemical reactions at the membrane Structural support - proteins contribute to the cell’s shape and stability Cell recognition - glycoproteins aid in identifying and interacting with other cells Passive transport proteins: Ex. 1. Channel proteins, 2. Carrier proteins, Ethanol enters our bodies and hits the bloodstream (High to low concentration). -passive transport (cell membrane) does not require an input of chemical-bond energy to drive substance movement. Movement occurs due to a concentration gradient. Active transport proteins: ex of primary transport- Sodium/ Potassium pump (Low to high concentration) (direct ATP usage) -active transport (across membranes) 1. Primary- carrier proteins transport molecules into/out of a cell against the concentration gradient using energy from ATP directly/indirectly. 2. secondary- Cell junction: additional membrane connecting structures forming after initial cell-cell binding (3 types): 1. Communicating junctions: permit diffusion of small molecules or ions between cells to “talk” to one another. (Gap junctions)- found in animals, connexin and pannexin proteins form a circular channel between cells. (Plasmodesmata)- found in plants, they are circular pores lined with plasma membrane and containing a tubule connecting ER between 2 cells. 2. Septate Junctions: Prevent leakage of water and solutes between cells; form barriers that seal sheets of cells, invertebrates. Tight junctions: A type of septate junction unique to vertebrates, forms claudin-containing walls in tissues. (Ex. blood-brain barrier) 3. Adhesive junctions: mechanically attach cytoskeletons of cells to one another. Desmosome- Unique to vertebrates, joins adjacent cells together via intermediate filaments of cytoskeletons. Bulk transport: Endocytosis (with subtypes) & Exocytosis Endocytosis - process by which cells engulf materials into the cell by forming vesicles from the plasma membrane. Phagocytosis - “cell eating” where large particles like bacteria are engulfed Pinocytosis - “cell drinking” where fluids and dissolved solutes are taken in Receptor-mediated endocytosis - specific molecules are ingested after binding to cell surface receptors. Exocytosis - process by which cells expel materials out of the cell by fusing vesicles with the plasma membrane, releasing their contents to the extracellular space. Chemical signaling systems (autocrine, juxtacrine, paracrine) Autocrine - Cells release signaling molecules that act on ITSELF, binding receptors on the same cell and influencing its own function. Juxtacrine - occurs through DIRECT CONTACT between neighboring cells, where the signal molecule remains attached to the signaling cell’s membrane and interacts with receptors on adjacent cells. Paracrine - cell releases signaling molecules that act on NEARBY cells within a CLOSE RANGE, diffusing through extracellular space to reach target cells. Dissociation constant (Kd ) equation  - measure of the affinity between two binding molecules, commonly used in biochem to describe the interaction between a ligand and a protein. Kd ​= ([P][L])/[PL] [P] is the concentration of the free protein [L] is the concentration of the free ligand [PL] is the concentration of the protein-ligand complex Class of signaling receptors (ion channels, protein kinase receptors, G protein-coupled receptors) Ligand - chemical signaling molecule that binds to a protein receptor to trigger a biological response Ion channel receptors - open or close in response to ligand binding, allowing ions to pass through the membrane Protein kinase receptors - ligand binding activates their intrinsic kinase activity, which phosphorylates target proteins to trigger cellular responses G protein-coupled receptors - ligand binding activates an associated G protein, which then triggers downstream signaling pathways inside the cell Catalysts, transition states and equilibrium Catalysts: Speed up chemical reactions ○ Don’t determine whether or not a reaction occurs. Only the rate of reaction EX: Enzymes Transition States: The point where a molecule(s) are reactive ○ Energy input = Activation Energy EX: Ea + sucrose + water → sucrose-water transition state Equilibrium: A stable system where no reaction is taking place Enzyme classes (Oxidoreductases, ligases, isomerases, etc.) – which ones are common in catabolic and anabolic reactions? 6 Main Categories: Oxidoreductases- Transfer electrons between molecules. ○ EX. NADH, NADPH, NAD+, NADP+, dehydrogenases, & oxidases. Remember that these are important in the glucose oxidation because they are electron CARRIERS.  Transferases- Transfer groups of atoms (functional groups) between molecules. ○ AX + B → A + BX EX. Kinases, transaminase Hydrolases- Add water to covalent bonds to break down molecules Hydrolysis ○ A-B + H2O → A-OH + B-H ESSENTIAL to catabolic reactions EX. Lipase, Protease, Sucrase Lyases- Catalyze breaking of non-hydrolytic bonds ○ I.e., splitting chemicals into smaller molecules without using water May take part in catabolic reactions Often form new bonds during catalysis EX. Decarboxylases, Aldolases, Adenylyl cyclase (ATP → cAMP + PPi) Isomerases- Rearrangement of atoms within a molecule ○ May move entire functional groups Essential to isomer formation EX. Decarboxylases, aldolases Ligases- Join two molecules together ○ Often through hydrolysis of a functional group on one of the reactants. Ab + C → A-C + b Important in many anabolic reactions EX. DNA ligase, chelatases Saturation point, activation energy, substrates (how do enzymes respond to substrate concentration?) Saturation Point: The point in which all enzymes are bound to a substrate. Activation energy: The energy barrier that must be overcome for a reaction to proceed. Substrates: The reactant, or part that physically attaches to the enzyme protein, which is then catalyzed by the enzyme. Glycolysis, Citric Acid Cycle & Electron Transport Inputs vs. Outputs Glycolysis: Input- Glucose, ATP (x2) Output- Pyruvate (x2), ATP (Use 2, Make 4, Net 2), NADH (x2) Citric Acid Cycle: Input- Acetate, water, GDP, NAD+, FAD Output- Carbon Dioxide, NADH, FADH2, GTP Electron Transport: Input- NADH FADH2 (electrons), O2, H+ (protons), ADP, Phosphate Output- ATP, NAD+, FAD+, H2O Oxidation vs reduction (where do these reactions occur during aerobic cellular respiration). Oxidation: Loss of electrons. Happens during glycolysis when NAD+ becomes NADH and happens during the citrate cycle during steps 3, 4, 6, and 8 Reduction: Gain of electrons Happens during fermentation when NADH becomes NAD+ Chemiosmosis Chemiosmosis refers to the chemical process where ATP is formed by combining a free-roaming phosphate group with a molecule of ADP through the use of the enzyme ATP synthase. ATP synthase is powered by the passive diffusion of protons (H+) into the F0 unit causing a reaction where the F1 unit spins, mashing the ADP and phosphate group together. This process is done on the inner mitochondrial membrane and utilizes the proton gradient from the intermembrane space of the mitochondria. Note: Discussion questions do not need to be very long, a paragraph, a few sentences or even a well labeled drawing are acceptable for many of these topics. Discussion Question Topics (may not be all inclusive): Comparison of receptor antagonists to agonists: Agonists activate receptors by mimicking natural ligands, triggering a biological response. Antagonists bind to receptors but block activation, preventing the natural ligand or agonist from producing a response. Agonists stimulate receptor activity/ Antagonists inhibit it. Types and functions of signaling molecules Primary vs. secondary signaling molecules: what is the difference and provide examples. Signaling molecules - substances that cells use to communicate. Separated into primary and secondary based on their roles in the signaling process. Primary: Extracellular molecules initiating signaling. These bind to receptors on the surface of target cells or inside them. This is the first step in the pathway. Examples: hormones, neurotransmitters, growth factors, cytokines, ligands Secondary: Intracellular molecules that are produced in response to the binding of primary signaling molecules to receptors. These molecules propagate the signal inside the cell, amplifying the effect initiated by primary. Examples: cAMP - a common second messenger that activates enzymes Phospholipids Calcium ions Gasses (like nitric oxide) Comparison of enzyme inhibitor types Competitive Inhibitors: Binds to the active site of an enzyme Prevents normal substrate from binding to the active site Uncompetitive Inhibitors: Binds to the enzyme substrate complex Prevents the release of products Allosteric (Non-Competitive) Inhibitors: Binds to other parts of an enzyme (not the active site) Changes the enzyme structure so that normal substrate binding cannot occur Major classes of enzymes – function and examples “Over The HILL” Kinda did this already a couple questions up, remember the types of enzymes by the mnemonic Over (Oxidoreductases) The (Transferases) H (Hydrolases) I (Isomerases) L (Lyases) L (Ligases) Eukaryotes vs Prokaryote structures Where is genetic material found ? Membrane bound internal structures (one or both cell types)? Type of energy synthesizing pathways present? Eukaryotes: Genetic material found in nuclei has membrane bound mitochondria, golgi, ER, chloroplast Energy synthesizing pathways: ○ Aerobic respiration (with oxygen) - primarily use mitochondria. Glucose is broken down to produce ATP (energy) through glycolysis, the krebs cycle (citric acid cycle), and the electron transport chain (oxidative phosphorylation). ○ Photosynthesis - eukaryotic plants and algae perform this in chloroplasts to convert sunlight into chemical energy ~ which then produces glucose to fuel respiration. ○ Anaerobic respiration (absence of oxygen) - cells produce energy by using alternative electron acceptors (like nitrate or sulfate) instead of oxygen. Fermentation - a type of anaerobic energy production. Pyruvate from glycolysis is converted into lactic acid (in animals) or ethanol (in yeast) producing small amounts of ATP. It also regenerates NAD+ needed for glycolysis to cont. Prokaryotes: Genetic material found in the nucleoid and plasmids [DOES NOT have membrane bound nucleus]. Nucleoid - irregularly-shaped region in the cytoplasm where DNA is located. Prokaryotes LACK membrane-bound organelles. Perform aerobic or anaerobic respiration in the cytoplasm and across the plasma membrane. Cell membrane composition - composed mainly of phospholipids, proteins, cholesterol, and carbohydrates, forming a fluid mosaic structure (bilayer) Role of phospholipids? Form the bilayer [hydrophobic interior/ hydrophilic exterior] which acts as a selective barrier for molecules. Stability of the membrane: environmental and structural aspects? Environmental - temp affects fluidity (heat increases fluidity/ cold decreases) Structural - proteins, phospholipids, and cholesterol contribute to membrane integrity and flexibility.  Role of cholesterol? Maintains membrane fluidity by preventing phospholipid packing in cold and providing structure in heat. (stabilizes membrane) Mechanism: Sodium/Potassium pump 1. Sodium ions (x3) and ATP bind to pump. 2. Phosphorylation causes phosphate to detach from ATP and attach to pump. 3. Pump changes shape due to phosphorylation which releases sodium ions (x3) out. 4. Potassium ions (x2) on other side bind to pump. 5. Potassium ion binding to pump causes dephosphorylation (release of phosphate). 6. Pump changes shape again which releases potassium ions (x2) and is ready to start cycle over again. Mechanism: G-couple protein receptors A ligand binding to the extracellular domain of the receptor, causing conformational change that activates a G protein, leading to the dissociation of its alpha, beta, gamma subunits which then independently trigger downstream signaling pathways Types of cellular signaling pathways Autocrine - cell releases signaling molecule that binds to receptors on its own surface. Allows the cell to regulate its own behavior. Paracrine - occurs when cells release signaling molecules that affect nearby cells. Used for localized communication between neighboring cells. Endocrine - involves signaling molecules (hormones) that are released into the bloodstream and travel to distant targets. Coordinates responses in different parts of the body over long distances. Juxtacrine - cells must be in direct contact for the signaling molecules to be transferred between them (usually involves cell membrane proteins or gap junctions. Enables direct cell-to-cell communication. Factors influencing catalytic reactions Substrate concentration Enzyme concentration Temperature pH Cofactors and coenzymes Inhibitors Allosteric regulation Enzyme-substrate affinity Potential vs. Kinetics energy in cells, food chains, etc. Potential: Stored energy due to position or structure. In cells, it is found in chemical bonds (ATP, glucose) and gradients (proton gradient, chemiosmosis). In food chains, energy stored in biomass is transferred between trophic levels. Kinetic: Energy of motion. In cells, it’s seen in processes like molecular movement, enzyme activity, and active transport. In food chains, kinetic energy is released as organisms metabolize food and perform activities. Relationship between free energy, enthalpy, and entropy (ΔG, ΔH, ΔS respectively) Relationship with regards to reaction activity? Draw the formula: ΔG=ΔH−TΔS ΔG: change in free energy ΔH: change in enthalpy (heat energy) T: temperature (in kelvin) ΔS: change in entropy (disorder) What values of free energy favor product formation? What values favor reactant formation (assuming a reversible reaction). If ΔG < 0 (negative) then rxn favors product formation (spontaneous rxn) If ΔG > 0 (positive) then rxn favors reactant formation Reaction activity: If ΔH < 0 then the reaction is exothermic (releases heat) If ΔS > 0 then disorder increases Active vs passive transport Active - moves molecules across the cell membrane against their concentration gradient (low concentration to high) using ATP Passive - moves molecules along their concentration gradient (high areas of concentration to low) without using energy (ATP) Exocytosis vs endocytosis Exocytosis - discharge of waste materials Endocytosis - ingestion of microbe by phagocyte Pg.127 Eukaryotic cells: chloroplasts, mitochondria, and their origin via the Endosymbiotic Theory Chloroplasts - organelles in plant and algal cells responsible for photosynthesis. Mitochondria - organelles found in nearly all eukaryotic cells that generate ATP through aerobic respiration [Powerhouse of the cell] Endosymbiotic theory - explains the origin of mitochondria and chloroplasts as once free-living prokaryotes that were engulfed by an ancestral eukaryotic cell and over time formed a symbiotic relationship with the host cell. Cell communication & separation of somatic and reproductive functions Molecules that “partner” and activate enzymes Ex. What are cofactors and how do they activate an enzyme? How do enzymes lower activation energy (at least 3 methods)? 1. Substrate Orientation: The diagram that Pegg gave in the powerpoint doesn’t give a great representation of what this means in words. I found a good quote that explains  it, “One of the ways the activation energy is lowered is having the enzyme bind two of the substrate molecules and orient them in a precise manner to encourage a reaction. This can be thought of as lining the binding pockets up for the substrates so that it is not left to random chance that they will collide and be oriented in this way.” 2. Inducing Strain: The enzyme can put strain on a substrate, causing its shape to change, which then puts stress on the bonds of the substrate, and something with less bonds is easier to react with. Kinda like how double bonds for trans fats are bad. 3. Adding Chemical Groups: Adding chemical groups to a substrate can make the environment of the active site more favorable for the substrate. If a negative charge is added to a substrate that has a positive active site, it will make the bonding of the two easier. Mechanism: glycolysis Location: cytoplasm Input: 1 glucose, 2 NAD+, 2 ATP Output: 2 pyruvate, 2 NADH, 4 ATP (net gain of 2 ATP) The 2 pyruvate produced enter the mitochondria and they are converted into acetyl-CoA so they can enter the citric acid cycle. Remember only one molecule can enter the citric acid cycle at a time. So since 2 pyruvates come from ONE glucose, the citric acid cycle must cycle twice. Mechanism: Citric acid cycle step 1: two-carbon acetyl group is oxidized, Acetyl CoA is used to initiate the cycle step 2: citrate step 3:NADH is formed from NAD+, 2 molecules of CO2 are released. step 4:NADH is formed from NAD+, 2 molecules of CO2 are released. step 5: formation of GTP from GDP and phosphate molecule, which can be converted into ATP. step 6: FADH2 is formed from FAD+ step 7: H20 is added step 8: NADH is formed from NAD+, the four-carbon acceptor molecule, oxaloacetate, is regenerated and ready to accept another acetate group from acetyl CoA. Inputs - acetate, water, GDP, NAD+, FAD Outputs - carbon dioxide, NADH, FADH2, GTP Mechanism: chemiosmosis What specific membrane bound structure is making ATP? ATP synthase in the inner mitochondrial membrane (or thylakoid membrane in chloroplasts) How does it function?  Uses the flow of protons (H+) down their electrochemical gradient to synthesize ATP from ADP and inorganic phosphate Components? Source of potential energy? Components: F0 subunit - proton channel embedded in the membrane F1 subunit - ATPase catalytic site that produces ATP in the matrix (mitochondria) or stroma (chloroplast) Source of potential energy: Proton gradient created by the electron transport chain (ETC) across the membrane, establishing a high concentration of H+ in the intermembrane space. The gradient drives protons through ATP synthase. Cellular aerobic respiration vs. fermentation. Where do they occur in a cell? Inputs? Outputs? Aerobic respiration: Location - mitochondria (euk) or cytoplasm (prok) Input - Glucose, oxygen Output - CO2, H2O, ~38 ATP Fermentation: Location - cytoplasm Input - glucose Output - lactate or ethanol, CO2, ~ 2 ATP