BIO+202+Lecture+Exam+2+Study+Guide+SP+25

Lecture 5: Binding Sites and Protein Interactions

Binding Sites

• A binding site is a specific location on a protein where molecules can attach. This interaction can involve substrates, ions, or other proteins, leading to various physiological responses.

Chemical Specificity and Affinity

• Chemical specificity refers to the ability of a binding site to preferentially bind a particular ligand over others. This ensures that proteins interact accurately within the cellular environment.

• Affinity indicates the strength of the interaction between a protein and its ligand. Higher affinity means tighter binding.

• While specificity is about which ligands bind, affinity describes how strongly they bind.

Saturation of Proteins

• A protein is said to be fully saturated when all available binding sites are occupied by ligands. Saturation affects protein functionality and efficiency.

• Two factors that affect saturation include:

  • Concentration of the substrate/ligand: More ligands lead to more saturation.

  • Affinity of the protein for the ligand: Higher affinity increases saturation at lower ligand concentrations.

Allosteric Modulation

• Allosteric modulation refers to the alteration of a protein's activity through the binding of a molecule at a site other than the active site. Allosteric regulators can enhance or inhibit protein activity.

• Two binding sites in allosteric proteins:

  • Regulatory site: Binds allosteric modulators, influencing the protein’s overall shape and function.

  • Active site: Where the substrate binds after the conformational changes induced by the allosteric modulator.

Covalent Modulation

• Covalent modulation involves the addition or removal of chemical groups (like phosphate groups) to a protein, altering its activity. This contrasts with allosteric modulation, which is reversible and not through covalent bonds.

Factors Affecting Reaction Rates

• Four key factors that influence reaction rates:

  • Substrate concentration: Increasing substrates increases reaction rate until saturation.

  • Temperature: Higher temperatures generally increase rates until proteins denature.

  • pH levels: Each enzyme has an optimal pH; deviations reduce activity.

  • Enzyme concentration: More enzymes can lead to faster reactions, assuming ample substrate.

Enzymes and Active Sites

• Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy.

• The active site is the part of the enzyme where the substrate binds, facilitating the conversion to products.

Cofactors

• Cofactors are non-protein molecules that assist enzymes in catalyzing reactions. They can be metal ions or organic molecules (coenzymes).

Enzyme Reaction Rates

• Four factors affecting enzyme reaction rates:

  1. Substrate concentration

  2. Temperature

  3. pH

  4. Presence of inhibitors or activators

Lecture 6: Macronutrients and Cellular Respiration

Macronutrients

• The three main macronutrients are carbohydrates, proteins, and fats. They provide energy and building blocks for growth.

• Digestible components absorbed include glucose from carbohydrates, amino acids from proteins, and fatty acids from fats.

Essential vs. Non-Essential Nutrients

• Essential nutrients cannot be synthesized by the body and must be obtained from the diet, whereas non-essential nutrients can be produced internally.

Cellular Respiration

• Cellular respiration is the process by which cells convert biochemical energy from nutrients into ATP, involving three main steps:

  1. Glycolysis: Glucose is broken down into pyruvate, yielding ATP and NADH.

  2. Krebs Cycle (Citric Acid Cycle): Acetyl-CoA combines with oxaloacetate, producing ATP, NADH, and FADH2.

  3. Electron Transport Chain: Uses NADH and FADH2 to generate ATP, and oxygen is the final electron acceptor.

• Overall ATP production varies, with a total of approximately 30-32 ATP per glucose molecule.

Lactic Acid Formation

• Lactic acid formation occurs during anaerobic respiration when oxygen levels are low, allowing glycolysis to continue while preventing energy loss.

Aerobic State

• In an aerobic state, pyruvate enters the mitochondria, where it is converted to acetyl-CoA for further processing in the Krebs cycle.

Electron Transport Chain

• The electron transport chain requires NADH and FADH2, producing about 2.5 ATP per NADH and 1.5 ATP per FADH2.

• ATP synthesis happens via chemiosmosis facilitated by ATP synthase protein.

Metabolic Processes

• Glycogenesis: Formation of glycogen from glucose; occurs when energy supply is high.

• Glycogenolysis: Breakdown of glycogen into glucose; occurs during fasting or energy demand.

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors; occurs during prolonged fasting.

• Lipogenesis: Formation of fat from excess energy intake; occurs when energy is plentiful.

• Lipolysis: Breakdown of fat for energy; occurs during fasting or exercise.

• Protein catabolism: Breakdown of proteins into amino acids; not ideal as it leads to muscle loss during energy deficits.

Lecture 7: Diffusion and Osmosis

Definitions

• Diffusion: The movement of molecules from an area of higher concentration to lower concentration.

• Osmosis: The movement of water across a semipermeable membrane driven by concentration gradients.

Movement of Solutes and Water

• Students should be able to determine the direction of solute or water movement given concentration gradients of two compartments.

Plasma Membrane Permeability

• Small nonpolar molecules passively diffuse through the plasma membrane, while larger or charged molecules require specific channels for transport.

Fick's Law of Diffusion

• Fick's law states that the rate of diffusion is proportional to the concentration gradient, surface area, and permeability of the membrane, and inversely proportional to the thickness of the barrier.

• Factors that affect diffusion rates include:

  • Concentration gradient

  • Surface area

  • Diffusion distance

  • Temperature

Net Flux and Membrane Potential

• Net flux refers to the overall movement of molecules across a membrane. A net flux of "0" indicates equilibrium between compartments.

• Membrane potential is the voltage difference across a membrane; intracellular matrices are generally negatively charged compared to extracellular environments.

Channel Gating

• Channel gating is the opening and closing of ion channels in response to stimuli. There are three gated channel types:

  • Voltage-gated channels: Open in response to membrane potential changes.

  • Ligand-gated channels: Open when specific molecules bind.

  • Mechanically gated channels: Open in response to physical deformation of the channel.

Mediated Transport

• Mediated transport involves protein carriers to help transport substances across membranes, differing from channel gating.

  • Two types of mediated transport are:

    1. Facilitated diffusion: Passive transport using carrier proteins, no energy required.

    2. Active transport: Requires energy to move substances against their concentration gradient.

Active Transport

• Primary active transport requires ATP to move substances directly, while secondary active transport utilizes energy from the primary transport of another substance. Both types use carrier proteins, but their energy sources are different.

Na+/K+ ATPase Pump

• The Na+/K+ ATPase pump exports three sodium ions (Na+) out of the cell and imports two potassium ions (K+) into the cell per ATP consumed.

Cotransport and Countertransport

• Cotransport involves the simultaneous transport of two substances in the same direction, while countertransport involves their transport in opposite directions.

Osmosis and Osmolarity

• Channels responsible for osmosis are aquaporins. Given osmolarity, students should deduce water movement directions based on solute concentrations.

Tonicity Definitions

• Isotonic solutions have equal solute concentrations inside and outside the cell, hypotonic solutions have lower concentrations outside leading to cell swelling, and hypertonic solutions have higher concentrations outside leading to cell shrinkage.

Endocytosis and Exocytosis

• Three types of endocytosis:

  1. Phagocytosis: Large particles are engulfed.

  2. Pinocytosis: Ingestion of liquid and small particles.

  3. Receptor-mediated endocytosis: Specific receptors mediate uptake of substances.

• Exocytosis is the process of expelling materials from the cell, primarily for secretion and membrane recycling.

Epithelial Cell Membranes

• The apical membrane faces the lumen, while the basolateral membrane faces the interstitial fluid; they have different protein compositions and functions.

• Paracellular pathways allow substances to pass between cells, whereas transcellular pathways involve substances passing through the cell itself.

Lectures 8+9: Receptors and Signal Transduction

Receptor Locations and Binding

• Receptors can be found on the cell surface or within the cell. After a ligand binds, conformational changes lead to internal cellular responses.

Ligand Binding

• Plasma membrane receptors bind ligands externally, while intracellular receptors bind ligands that diffuse across the membrane.

Saturation of Receptors

• Saturation occurs when all receptors are occupied; increasing the ligand concentration can increase saturation to some extent, while excessive ligands may lead to down-regulation of receptor availability.

Competitor Types

• Two types of competitors include:

  • Non-competitive inhibitors: Bind to a site other than the active site, reducing efficacy.

  • Competitive inhibitors: Compete with the substrate for the active site and can be overcome by increasing substrate concentration.

Regulation of Receptors

• Down-regulation reduces receptor numbers or affinity, typically occurring in response to an abundance of hormone or signaling molecules.

• Up-regulation increases receptor numbers or affinity, often due to a lack of stimulation.

Signal Transduction Pathways

• A signal transduction pathway is a series of molecular events triggered by receptor activation, leading to a specific cellular response.

Messengers in Signal Transduction

• Lipid-soluble messengers can cross membranes and bind to intracellular receptors, affecting gene expression. Water-soluble messengers bind to extracellular domains of membrane receptors, triggering cascades internally.

Water Soluble Messengers

• Types of water-soluble messengers include peptide hormones and neurotransmitters. They trigger specific cellular outcomes based on receptor activation.

Cellular Mechanisms of Action

• First messengers bind to cell surface receptors, while second messengers carry signals inside the cell, amplifying responses.

Protein Kinases

• Protein kinases facilitate phosphorylation, altering protein function and activity as part of signal transduction cascades.

Gated Ion Channels

• Ligand-gated ion channels open in response to the binding of specific ligands, allowing ions to flow based on concentration gradients.

Docking Protein Activation

• Receptors that activate or phosphorylate docking proteins initiate downstream signaling pathways linked to cellular responses.

Janus Kinase Function

• Janus Kinase mediates signal transduction for various cytokines and hormones, leading to cellular effects through post-translational modifications.

G-Protein Coupled Receptors (GPCRs)

• GPCRs activate intracellular G-proteins upon ligand binding. Each G-protein subunit has distinct roles in signal propagation, which can be deactivated when GTP is hydrolyzed.

cAMP Production and Action

• cAMP is synthesized from ATP by adenylate cyclase and serves as a second messenger, triggering target protein phosphorylation and subsequent cellular effects.

Signal Amplification

• Signal amplification is crucial as it allows a single ligand to induce a large-scale cellular response through cascading effects.

Cellular Responses Induced by cAMP

• cAMP activates PKA, leading to diverse effects like gene expression changes and enzyme activation.

Phospholipase C Activation

• Phospholipase C is activated by GPCRs, leading to the production of IP3 and DAG, which further mediate intracellular calcium release and other signaling pathways, influencing muscle contraction and secretion.

Calmodulin Function

• Calmodulin binds calcium ions and mediates various cellular processes, such as muscle contraction, by altering the activity of several proteins.

Termination of Signal Transduction

• Signal transduction pathways can be ceased via:

  1. Degradation of signaling molecules.

  2. Receptor internalization or down-regulation.

  3. Inactivation of second messengers.