20 - Midterm 2 Review PDF

Lecture 20: Review Session Nov 8, 2024 Kd emember 1  Lipids vs polysaccharides Feature Lipids Polysaccharides Lipids are ideal for long-term...

Lecture 20: Review Session Nov 8, 2024 Kd emember 1  Lipids vs polysaccharides Feature Lipids Polysaccharides Lipids are ideal for long-term energy storage in a compact, water- free form, but they are slower to Energy Density High Lower access and require oxygen to be Triglycerides in adipose, oils in Glycogen in animals, starch in metabolized Storage Form plants plants Polysaccharides are better for short-term, quick energy due to Accessibility Slower to mobilize Rapidly accessible their rapid mobilization, ability to Oxygen function anaerobically, and role in Requirement Requires oxygen (aerobic only) Can function anaerobically immediate energy needs, despite their lower storage efficiency Hydrophobic, does not bind Water Balance water Hydrophilic, binds water using water Primary Use Long-term, sustained energy Short-term, immediate energy hydrolase Polysaccharides are stored as large polymers to avoid increasing osmotic pressure; however, when broken down into glucose units, they can increase osmotic pressure, especially if rapidly mobilized. Lipids do not affect osmotic pressure due to their hydrophobicity and storage in non-aqueous environments, making them ideal for high-capacity energy storage without impacting cellular water balance 2 Biological membranes Lipid Bilayer Structure Phospholipids: The foundation of biological membranes is the phospholipid bilayer, where phospholipids are arranged with their hydrophilic (water-attracting) heads facing outward and their hydrophobic (water- repelling) tails facing inward. This arrangement generates a semi-permeable barrier Amphipathic Nature: Phospholipids are amphipathic, meaning they have both hydrophilic and hydrophobic regions. This dual nature allows the bilayer to self-assemble and maintain a stable, yet flexible structure Membrane Fluidity Cholesterol: Cholesterol is embedded within the membrane and plays a critical role in regulating its fluidity and stability:: Increase membrane rigidity at higher temperatures by filling in spaces between phospholipids, thus stabilizing the membrane. Prevent membrane solidification at lower temperatures by preventing phospholipids from packing too closely, maintaining fluidity. Fluid Mosaic Model: Membranes are dynamic, with phospholipids and proteins moving laterally within the bilayer, resembling a “mosaic” of components. This fluidity allows flexibility and the movement of membrane proteins 3 Biological membranes Membrane asymmetry refers to the unequal distribution of lipids, proteins, and carbohydrates between the inner and outer layers (leaflets) of the phospholipid bilayer. This asymmetry is essential for various cellular functions and is maintained throughout the life of the cell Biological membranes contain specialized structures that allow cells to carry out specific functions and adapt to environmental needs: Lipid rafts are small, dynamic microdomains within the membrane, rich in cholesterol, sphingolipids, and certain proteins. They are more ordered and less fluid than the surrounding membrane areas. Function: Signal Transduction: Lipid rafts organize proteins involved in cell signaling, concentrating receptors and signaling molecules to facilitate rapid and efficient signal transmission. Pathogen Entry: Some viruses and toxins exploit lipid rafts for entry into cells. Membrane Trafficking: Rafts are involved in sorting proteins for transport to specific membrane regions or for endocytosis 4  Membranes not only define the boundaries of cells but also create distinct, membrane-bound organelles within them, such as mitochondria, lysosomes, and the endoplasmic reticulum. These organelles serve as specialized reaction compartments with unique chemical and physical properties tailored to support specific enzymatic activities Within cells, membrane-bound organelles subdivide the cytoplasm into chemically and physically unique reaction compartments. These compartments are further parsed into unique environments at the level of multi-enzyme assemblies and condensates 5  Enzymes Enzymes are biological catalysts that speed up chemical reactions in living organisms by lowering the activation energy required for the reaction to proceed 6  Enzymes This reduction in activation energy allows reactions to occur more efficiently and at a faster rate than they would spontaneously Enzymes are typically proteins (though some RNA molecules, called ribozymes, also catalyze reactions) RNA “enzyme” (ribozyme) Protein enzyme Chem 153B, not this course unfortunately 7 Nomenclature of Enzymes Naming Convention: Enzyme names generally end in "-ase" to signify their catalytic role Common Names: Many enzymes are recognized by common names that reflect their substrate or function. For example: Urease: Catalyzes the breakdown of urea. Arginase: Catalyzes the hydrolysis of arginine. Chymotrypsin: A digestive enzyme that cleaves peptide bonds in proteins. Systematic Names: Systematic names provide more specific information about the reaction an enzyme catalyzes, including the substrate(s) or products and the enzyme class. For example: Lactate Dehydrogenase: Catalyzes the oxidation of lactate to pyruvate. These naming conventions help convey the function of enzymes, providing insight into their roles in biochemical reactions and metabolic pathways. 8 Enzymatic classes - Oxidoreductases – Transfer of electrons, changes oxidation state of atom - Transferases – Transfer of functional group from one molecule to another - Hydrolases – Breakdown of substrate into two products using water - Lyases – Removal of a group to form a double bond - Isomerases – Intramolecular rearrangement (isomerization) changes within a single molecule - Ligases – Forms one product from two substrates - Translocases – A new EC Class: catalyze the movement of ions or molecules across membranes or their separation within membranes. Several of these involve the hydrolysis of ATP and had been previously classified as ATPases (EC 3.6.3.-), although the hydrolytic reaction is not their primary function 9 1. Oxidoreductases (EC 1): Catalyze oxidation-reduction (redox) reactions, where electrons are transferred between 5. Isomerases (EC 5): Isomerization reactions, rearranging molecules. atoms within a molecule Lactate dehydrogenase: Converts lactate to pyruvate, Phosphoglucose isomerase: Converts glucose-6- essential in glycolysis phosphate to fructose-6-phosphate in glycolysis Cytochrome c oxidase: Part of the electron transport Triose phosphate isomerase: Interconverts DHAP and chain, reducing oxygen to water G3P in glycolysis 2. Transferases (EC 2): Transfer a functional group (like a 6. Ligases (EC 6): Joining of two molecules with the input of methyl, phosphate, or amino group) from one molecule to energy (usually from ATP) another DNA ligase: Joins DNA strands together, crucial in Hexokinase: Phosphorylates glucose to glucose-6- DNA repair and replication phosphate in glycolysis Glutamine synthetase: Synthesizes glutamine from Alanine transaminase: Transfers an amino group, glutamate and ammonia involved in amino acid metabolism 7. Translocases (EC 7): Catalyze the transport or movement 3. Hydrolases (EC 3): Hydrolysis reactions, where a bond is of ions or molecules across membranes or within cellular broken with the addition of water compartments, often powered by ATP hydrolysis or other Trypsin: Cleaves peptide bonds in proteins, part of energy sources digestion ATP synthase: Translocates protons across the Lipase: Breaks down fats into fatty acids and glycerol mitochondrial membrane to drive ATP synthesis. 4. Lyases (EC 4): Add or remove groups without water Essential for energy production in the electron Aldolase: Splits fructose-1,6-bisphosphate into two transport chain. three-carbon sugars in glycolysis Fumarase: Converts fumarate to malate in the citric 10 acid cycle The active site of an enzyme is a specialized region where substrate binding and catalysis occur 11 Active site The active site has a unique three-dimensional shape that fits only specific substrates, determined by the enzyme’s amino acid sequence. This specificity used to be referred to as the "lock and key" model, although in reality, enzymes often undergo slight conformational changes to bind substrates more effectively (induced-fit model) Binding and Orientation: The active site binds substrates with high specificity and orients them in an optimal position for the reaction to occur Catalytic Residues: Within the active site, certain amino acids (known as catalytic residues) directly participate in the reaction. These residues can act as acid-base catalysts, nucleophiles, or stabilize transition states Microenvironment: The active site provides a unique microenvironment that can be hydrophobic or hydrophilic, depending on the enzyme's function. This environment stabilizes the transition state and lowers activation energy, making the reaction more efficient Temporary Interactions: During catalysis, the enzyme may form temporary bonds or interactions (hydrogen bonds, ionic bonds, or covalent bonds) with the substrate. These interactions are transient, allowing the enzyme to release the product and repeat the process Regulation and Inhibition: The active site is often the target of regulatory molecules, such as inhibitors or activators, that modulate enzyme activity by altering substrate binding or catalytic efficiency 12  Active site, activation energy, and transition state The enzyme’s active site has a unique shape and charge distribution that is highly complementary to the transition state rather than to the substrate itself. This specificity allows the enzyme to stabilize the high-energy transition state (represented by the lower peak in the red curve of the image). By stabilizing the transition state, the enzyme lowers the activation energy (ΔG‡_cat), enabling the reaction to occur more quickly Within the active site, specific catalytic residues participate directly in the reaction. These residues might donate or accept protons, form temporary covalent bonds, or stabilize charged intermediates, helping push the substrate toward the transition state. This aligns with the energy-lowering effect shown in the image, where the enzyme’s environment (shaped by these catalytic residues) 13 reduces the activation barrier  Active site, activation energy, and transition state The enzyme’s active site has a unique shape and charge distribution that is highly complementary to the transition state rather than to the substrate itself Enzymes can bind to substrates in a way that slightly distorts or strains their molecular structure. This strain brings the substrate closer to the shape of the transition state, which reduces the energy needed to reach it Within the active site, specific catalytic residues participate directly in the reaction. These residues might donate or accept protons, form temporary covalent bonds, or stabilize charged intermediates, helping push the substrate toward the transition state. This aligns with the energy-lowering effect shown in the image, where the enzyme’s environment (shaped by these catalytic residues) 14 reduces the activation barrier  Transition state analogs are competitive inhibitors Enzymes evolved to bind very tightly to the transition Proline racemase (PR) state of a reaction, which is the high-energy, temporary shape the substrate takes as it’s being converted into a product. Because of this, if we design molecules that look like the transition state—called transition state analogs—these molecules will fit very well into the enzyme’s active site but won’t actually react. They just sit there, blocking the active site and preventing the enzyme from working on its real substrate. This makes transition state analogs powerful enzyme inhibitors. PR inhibitor binds 160x better than proline Transition state analogs bind the active site, and therefore compete with the substrate 15  Transition state analogs won’t react because, while they resemble the shape and charge distribution of the transition state, they are chemically stable and lack the reactive groups required for the reaction to proceed: Lack of Necessary Chemical Groups: These analogs often don’t have the exact atoms or bonds that would make them reactive, meaning they can’t undergo the same transformations that the actual substrate does Stability: Transition states are inherently unstable, but analogs are designed to mimic their shape without sharing their instability. They have modified structures that make them chemically "inert" in the enzyme’s active site Non-ideal Bonding Arrangement: Although the analog’s shape is similar to the transition state, it isn’t a perfect match for the bonds or electron configuration needed for the enzyme to perform the catalysis. So, while the enzyme binds it tightly, the analog simply "sits" in the active site without triggering the reaction 16 active site of an enzyme, showing three key catalytic residues involved in the reaction: this active site is structured to facilitate a multi-step reaction with distinct roles for each residue—one acting as an acid, one as a base, and another as a nucleophile—allowing 17 precise control over the reaction mechanism. Propensity of amino acids to be catalytic in active sites Histidine is one of the most common catalytic residues in enzyme active sites, largely due to the unique properties of its imidazole side chain With a pKa in the range of 6 to 7, histidine's imidazole group is close to neutral pH, allowing it to accept or donate a proton readily EC 1, oxidoreductases EC 3, hydrolases EC 5, isomerases EC 2, transferases EC 4, lyases EC 6, ligases 18  Induced fit model The induced fit model describes how an enzyme’s active site changes shape slightly to better fit the substrate upon binding. Unlike the earlier lock-and-key model, which suggested that the enzyme and substrate fit together perfectly from the start, the induced fit model proposes that the enzyme is more flexible The induced-fit model states a substrate binds to an active site and both change shape slightly, creating an ideal fit for catalysis 19  Induced-fit model 20 https://www.youtube.com/watch?v=yk14dOOvwMk