BIOCHEM - BLOCK 2 REVIEW PACKET

• Exam breakdown is approximately 57 questions.
• Some questions cross categories, but the closest packet is indicated.

Biological Membranes and Transport

• Six questions are about biological membranes and transport.
• Describe basic structures, assembly & functions of a simple biological membrane.
• Assess the consequences of changes in the membrane components.
• Compare & contrast membrane components and function in terms of membrane fluidity.
• Understand its role as a barrier between environments.
• List cholesterol, lipids, & proteins roles.
• Explain the link between membrane lipids, membrane structures and function.
• Define and explain the role of lipid rafts in signaling.
• Understand how lipid rafts/membrane domains are regulated by lipid composition and interactions.
• Compare and contrast passive and active transport, and explain the roles of components to that transport.
• List types of transport with corresponding provided examples.
• Link transporter type with corresponding ion and activity.
• List factors determining diffusion kinetics, summarizing differences in saturability & kinetics for simple and facilitated diffusion.
• Describe how an electrochemical gradient is generated and its importance in biological systems.
• Compare and contrast resting and action potentials.
• Correlate membrane structures with role in disease development for Parkinson's, Cystic Fibrosis, Menkes & Wilson's diseases.
• Identify the causes and physiological representation for these diseases.
• Regulation, coordination, compartmentalization/partition, and cellular trafficking are roles of biological membranes
• Composition correlates with function and fluidity.
• Shape and fluidity are based on saturated vs. unsaturated fats.
• Lipid rafts have functions and roles for DHA, cholesterol, and sphingolipids.

Understanding Oxygen

• There are nine questions for understanding oxygen
• Evaluate the role of oxygen and oxygen-binding proteins in normal metabolism and disease.
• Describe heme synthesis, heme structure, the role of iron in heme, and the importance of heme to myoglobin and hemoglobin.
• Compare and contrast myoglobin and hemoglobin structure, behavior, localization, and uses.
• Determine functional consequences for changes in form or structure.
• Explain pulse oximetry and its importance to evaluating normal and abnormal oxygen transport.
• Explain the allosteric regulation of oxygen binding to hemoglobin.
• Identify changes to pH (Bohr Effect), CO2 levels, and 2,3-BPG levels.
• Evaluate erythrocyte structure, function, and metabolism.
• List key differences between an erythrocyte and other human cells in terms of cellular structure and contents.
• Summarize the difference between glucose metabolism in erythrocytes compared to other cell types.
• Compare and contrast oxygen and carbon dioxide transport within erythrocytes.
• Explain the role of bicarbonate in carbon dioxide regulation.
• Summarize the roles of the lungs, kidney, tissues, and erythrocytes in CO2 regulation and acid-base balance.
• Explain the importance of the pentose phosphate pathway to erythrocyte function and oxidative phosphorylation.
• Explain the oxidation-reduction reactions in the pentose phosphate pathway.
• Compare the reversible and irreversible steps of this pathway.
• Determine the consequence of loss of function or gain of function changes in the pentose phosphate pathway.
• Hemoglobin and myoglobin synthesis and activity
• Oxygen binding and affinity are key themes
• Hemaglobinopathies: cause and effect relationship
• Allosteric regulation of hemoglobin affinity for oxygen
• Identify effectors and direction of effect
• Additive effects of effectors

Reactive Oxygen Species

• Six questions are about reactive oxygen species.
• Evaluate oxygen free radicals and reactive oxygen species in human metabolism and disease.
• Identify the reactive oxygen's that are generated during normal metabolic processes.
• List ROS & RNOS generated by metabolic processes.
• Summarize the steps involved in lipid peroxidation.
• Critique lipid peroxidation concerning localization and cell consequences.
• Summarize the steps involved in the generation of reactive nitrogen-oxygen species.
• Describe the role of ROS and RNOS in inflammation, phagocytosis, diabetes, and ischemia-reperfusion events.
• Describe the role of ROS and RNOS in vitamin deficiencies.
• Summarize mechanisms of cellular defenses against oxidative damage and the role of vitamin C, vitamin E, GSH, superoxide dismutase, catalase, and copper.
• Lipid peroxidation involves initiation, propagation, and termination.
• There is a link and mechanisms between ROS/NOS and disease.

Extracellular Matrix

• Nine questions are about the extracellular matrix.
• Understand the ECM's general structure and identify the macromolecules within the 2 important layers.
• Define the structure & function of the following ECM components: laminin, non-fibrillar collagen, integrin, nidogen, perlecan, fibrillar collagen, fibronectin, elastin, glycosaminoglycans.
• Explain the structure and function of hyaluronan and aggrecan and identify their role in cartilage structure.
• Compare and contrast different types of cellular junctions in location, function & important adhesion molecules.
• Recognize the clinical presentation of diseases associated with the ECM and cellular junctions and identify the defective component.
• Laminin is cross-shaped and held together by disulfide bonds and requires calcium.
• Integrin's function is linkage of epithelium to basement membranes.
• Elastin molecules are cross-linked and covalently bound.
• Hyaluronan is withstanding compressive force.
• Aggrecan is a major cartilage component

Protein Degradation and Proteolysis

• Six questions are about protein degradation and proteolysis.
• Explain protein/enzyme regulation basics and define domain, motif, half-life, and proteolysis.
• Explain the relationship between protein structure and protein degradation with factors that increase/reduce protein half-life.
• Assess the role of protein targeting and degradation in regulation of cellular processes.
• List five general initiating mechanisms of protein degradation and match them to their corresponding targets.
• Summarize the process of protein degradation with emphasis on the enzymes and steps involved in protein targeting and recognition.
• Identify the role of ubiquitin and explain ubiquitylation process.
• Explain relationship between proteolysis and autophagy.
• Summarize autophagy stages, emphasizing autophagy utilization to eliminate proteasomes.
• Summarize and explain Edman Degradation steps and its role in defining protein sequence.
• Assess causes and consequences of reduced or altered proteolysis.

Cell Signaling Introduction

• Five questions are about cell signaling introduction.
• Summarize basics of cellular signaling and the difference between direct enzymatic activity and mediated enzymatic activity for receptors.
• Compare and contract autocrine, juxtacrine, paracrine, and endocrine signaling.
• Compare and contrast protein-binding ligand models.
• Compare/contrast types of ligands with lipid/water for soluble hormones actions.
• The three major components to all signaling pathways are Ligands, Receptors, Mediators, and alterations can lead to adverse consequences.
• The key features of signaling are Initiation, Propagation, and Termination/Reset.

Cell Signaling Transduction

• Six questions are about cell signaling transduction.
• Identify signaling mediators for a given receptor or pathway, with emphasis on G-coupled protein receptors, inositol triphosphate, integrin signaling, Pl3K & insulin signaling.
• Explain how signal transduction can be collaborative or concomitant.
• Recognize the steps that lead to signal amplification and explain how low levels of ligand can lead to significant biological responses
• Summarize the conceptual framework of coincident, gated, and feedback mechanisms of signal transduction and apply using discussed pathways.
• Assess consequences for changes in the initiation, propagation, or termination/reset of a given pathway from ligands, receptors, mediators or transcription factors.

Cytoskeleton, Pumps, and Channels

• Five questions are about the cytoskeleton, pumps and channels.
• Explain the structures/functions of actin filaments, microtubules, and intermediate filaments in the cell.
• Explain Taxane family (paclitaxel specifically) and Omeprazole mechanisms of action and assess the consequences of treating a cell/organism with these.
• Summarize steps in activation of sodium/potassium pumps, proton pumps, and calcium channels with emphasis on ion movement and consequences of movement.
• Explain the symport activities that enable absorption of glucose in the intestine and the role of sodium/potassium pumps in the process.
• Summarize and explain the consequences of pathogenic variation in SCL5A1.
• Both sodium/potassium and calcium ATPases are P-ATPases

Cellular Homeostasis and Clinical Correlates

• Five questions are about cellular homeostasis and clinical correlates.
• Identify the following molecules and match their activity to specific steps in cell cycle regulation: p53, pRb, p21, E2F and E2F promoter, CHK1 and CHK2, cyclins, CDKs, cyclin/CDK complexes, and INK4 family.
• Assess the consequences of changes in binding at E2F promoter, Rb phosphorylation, cyclin availability, p53 activity, p21 activity, and INK4 family activity.
• Recognize the clinical consequences for changes in cellular components.
• Link changes in signaling with additional disorders & summarize unique features/corresponding disorders including cancer & proteus syndrome.
• Connect condition with pathways or processes altered and identify condition clinical features.
• How transitions work with requirements to progress through from one phase requires necessary components
• Disorders can be simplified by only using class components
• Pay attention to bolded works in past class packets and connections with the disorders from class

Explore biological membranes: structure, function, and assembly. Learn about membrane fluidity, components like cholesterol, lipids, and proteins, and their roles. Compare passive and active transport mechanisms and lipid rafts in signaling.