BIO233 Exam 2 Study Guide Fall 2024 PDF

EXAM 2: TEST FORMAT 65 minutes, 20 questions No multiple choice. 100 points, 10% of your Some single word answer, final grade some 1 – 3 sentence answers 4 – 8 points per question, 35% What?, 15% 10 – 14 points per topic. Draw/diagram?, 45% What &...

EXAM 2: TEST FORMAT 65 minutes, 20 questions No multiple choice. 100 points, 10% of your Some single word answer, final grade some 1 – 3 sentence answers 4 – 8 points per question, 35% What?, 15% 10 – 14 points per topic. Draw/diagram?, 45% What & why/how?, 5% Calculate? Questions in order based on material from lectures You are allowed a calculator 9 – 17. and one side of a 3” x 5” notecard for notes.  L13: Membranes: Ion Channels POINTS OF EMPHASIS Classification Action potential L9: Cytoskeleton: Components L14: Intracellular: Organelles Structure Function Membrane-enclosed organelles L10: Cytoskeleton: Muscle Protein sorting Contraction L15: Intracellular: Secretion & Organization Endocytosis Myosin-actin interaction Localization & secretion L11: Membranes: Structure Endocytosis Lipid bilayer L16: Signaling: General Principles Membrane Proteins Rules of thumb L12: Membranes: Transporters Intracellular signaling Principles of transport L17: Signaling: Receptors Transporters GPCR Enzyme-coupled receptors INTERMEDIATE FILAMENTS RESIST RUPTURE (STRETCHING) NUCLEAR LAMINA SUPPORT NUCLEAR MEMBRANE AND POSITION CHROMATIN MICROTUBULES ARE THE (TEMPORARY) HIGHWAYS OF THE CELL GTP/GDP CONTROLS DYNAMIC INSTABILITY OF MICROTUBULES  KINESIN AND DYNEIN ARE MOTOR PROTEINS THAT TRANSPORT CARGO ALONG MICROTUBULES https://www.youtube.com/watch?v=yuuk4Pr2i8 MICROTUBULES TRANSPORT ORGANELLES TO POSITION THEM IN THE CELL MICROTUBULES MAKE UP CILIA & FLAGELLA – CELL MOTILITY ACTIN ALLOWS FOR STABILITY OR CHANGES IN CELL SHAPE Microtubules Actin filaments Thicker: more Thinner: easier things can attach to assemble and to it. disassemble. Functions Functions Cargo Cell shape transport (stable or Organelle change) positioning Cell migration Cell motility ACTIN & MICROTUBULE FORMATION USE SIMILAR MECHANISMS Microtubules Same Actin filaments Subtract from -/+ ends Subtract from – + end Add at + end end - end Small molecule ATP/ADP small anchored to allosteric regulation molecule centrosome of protein Actin protein GTP/GDP Covalent small modification of small molecule molecule: Tubulin Hydrolysis and protein condensation of phosphate bond Triphosphate = add Diphosphate = subtract DYNAMIC ACTIN ADDITION/SUBTRACTION PROMOTES CELL MIGRATION QUESTIONS THAT I COULD ASK ON THE EXAM Describe how X cytoskeletal structure is organized. Draw and label the different organizational levels present in X cytoskeletal structure. How are intermediate filaments in the nucleus different from intermediate filaments in the cytoplasm? What is the primary function of X cytoskeletal structure? How does the structural organization of X cytoskeletal structure contribute to its function? Name # ways how are actin and microtubules are similar/different. What motor proteins interact with microtubules and how do they interact? What are the major components of flagella/cilia, and how do they interact with each other? How does actin promote stability or movement? ANATOMY: LAYERS OF SKELETAL MUSCLE OpenStax Anatomy and Physiology Figures 10.3 & 10.4 SARCOMERE: MYOSIN AND ACTIN Group activity [1 pt. each]: Of the following: a) sarcomere length b) myosin filament length c) actin filament length d) myosin/actin overlap During contraction… What shortens? a What stays the same? b, c What increases? d NERVOUS SYSTEM SIGNALING OF T- TUBULES PROMOTES RELEASE OF CALCIUM IONS FROM SARCOPLASMIC RETICULUM Nervous system signaling of T-tubules promotes release of calcium ions from sarcoplasmic reticulum TROPOMYOSIN BLOCKS THE MYOSIN BINDING SITE ON ACTIN  MYOSIN IS A MOTOR PROTEIN: MOTOR PROTEINS USE ATP HYDROLYSIS TO MOVE ATP binding to motor protein = allosteric regulation ATP itself is covalently modified (hydrolysis) STEPS TO EXPOSE ACTIN TO MYOSIN BINDING 1. Electrical signal from nerve (covered when we talk about Membranes – Ion Channels) 2. Electrical signal to transfer (T)-tubules. 3. T-tubules signal Ca2+ release from sarcoplasmic reticulum (SR) 4. Ca2+ binds to troponin. 5. Troponin changes structure when Ca2+ binds, pulling tropomyosin off myosin binding site on actin. 6. Myosin head can now bind to actin DEPENDING ON WHAT MOLECULE IS BOUND TO IT No ATP: Myosin head bound to actin and contracted (Muscle contracts) ATP: Myosin head releases from actin, but still contracted (Muscle relaxed) ADP + Pi = Myosin head relaxes (Muscle relaxed) ADP = Myosin head bound to actin, relaxed (Muscle relaxed) QUESTIONS THAT I COULD ASK ON THE EXAM What are the levels of structural organization in a muscle? Draw a sarcomere. Label X, Y, and Z in the drawing. What would happen to muscle contraction in X scenario (use class activity for examples), and why? What are the confirmational changes in myosin, and what molecules drive each confirmational change? PHOSPHOLIPIDS ARE AMPHIPATHIC OTHER MEMBRANE LIPIDS ARE ALSO AMPHIPATHIC THE LIPID BILAYER  MOLECULES IN THE LIPID BILAYER ARE DYNAMIC (2D FLUID) Cholesterol slows down dynamic lipid flow IN ER (LIPID SYNTHESIS): In other membranes SCRAMBLASE (different functions): RANDOMIZES Flippase organizes TRANSMEMBRANE PROTEIN FUNCTIONS DIFFERENT TRANSMEMBRANE STRUCTURES TRANSMEMBRANE PROTEINS FOLD DIFFERENTLY THAN CYTOPLASMIC PROTEINS DETERGENTS ARE AMPHIPATHIC THE CELL CORTEX SUPPORTS THE CELL MEMBRANE IN ANIMALS Methods to limit membrane protein diffusion A)Anchor to cell cortex B)Anchor to an external protein C)Anchor by binding to another cell’s protein D)Diffusion barriers QUESTIONS THAT I COULD ASK ON THE EXAM Why do phospholipids form lipid bilayers? Draw a lipid bilayer. Label which part is hydrophobic and which part is hydrophilic. Why can phospholipids diffuse laterally and rotate in the lipid bilayer? What are the two proteins that promote flip-flopping of phospholipids in the lipid bilayer, and how does each protein function? What are the four general functions of transmembrane proteins. How is transmembrane protein structures X and Y different from each other? What is the most common structure in a transmembrane protein, and why? Why are detergents used to isolate membrane proteins for study? What is the function of the cell cortex, and how is it organized? What are two ways how membrane proteins can be limited in their diffusion?  Osmosis always goes with the concentration gradient! OSMOSIS: MOVEMENT OF WATER WHERE THE SALT IS TO BALANCE SALT CONCENTRATIONS http://encyclopedia.lubopitko- GLUCOSE TRANSPORTER: PASSIVE TRANSPORT WITH THE CONCENTRATION GRADIENT PUMPS: ACTIVE TRANSPORT AGAINST THE CONCENTRATION GRADIENT CELLS USE PUMPS TO MAINTAIN ION GRADIENTS ACROSS THE CELL MEMBRANE ION GRADIENTS CAN DRIVE THE ACTIVE TRANSPORT OF SOLUTES QUESTIONS THAT I COULD ASK ON THE EXAM Name the type of membrane transport required for the following scenarios. (class activity) What types of molecules can be transported used X membrane transport term, and why? Using terms discussed in class, describe the pumps depicted in the following diagrams. Why do cells use pumps to maintain ion gradients? What is the source of energy in a gradient-driven pump, and why does that prevent gradient-driven pumps from being uniport?  NERNST EQUATION AT 37 DEGREES C: V = 62 LOG10 (CO/CI) Group questions (4 pts per correct answer to the 0.0001, 3 to 0.001, etc.) If membrane potential (V) = -60 mV (-0.06 V), what is the ratio of concentrations of positively charged ions outside/inside the cell (Co/Ci)? 0.9978 What if V = +40 mV (0.04V)? 1.0015 What if V = 0 mV? 1 EXAMPLE OF ION CHANNEL: K+ LEAK CHANNEL GATED ION CHANNELS ANATOMY OF A NEURON NA+/K+ PUMP MAINTAINS A NON-ZERO MEMBRANE POTENTIAL (NEGATIVE INSIDE CELL) VOLTAGE GATED NA+ AND K+ CHANNELS Na+ channel opens ~ -40mV, closes ~ +40 mV K+ channel opens ~+40 mV, closes ~-40mV ELECTRICAL SIGNAL GETS CONVERTED TO CHEMICAL SIGNAL AT SYNAPTIC CLEFT NEUROTRANSMITTERS ARE EXTRACELLULAR LIGANDS FOR LIGAND-GATED ION CHANNELS DEPENDING ON WHAT TYPE OF CHANNEL THEY OPEN, NEUROTRANSMITTERS CAN BE EXCITATORY (+) OR INHIBITORY (-) MANY AXONS CAN CONNECT TO ONE CELL ACETYLCHOLINE IS THE NEUROTRANSMITTER CONNECTING NERVES TO MUSCLES AT NEUROMUSCULAR JUNCTIONS (NMJ) NEURONS CONNECT TO TRANSVERSE (T) TUBULES AT THE NMJ Change in voltage of T-tubules promotes release of calcium ions from sarcoplasmic reticulum QUESTIONS THAT I COULD ASK ON THE EXAM Using the listed Nernst equation, if membrane potential is X, what is the ratio of concentration of cations outside vs. inside of the cell? What are two properties that all ion channels have? What are the three general types of gated ion channels? Why is the membrane potential of a neuron negative? What are the specific ion channels used in an action potential, and how does each one function? Draw an action potential. Label when X channel opens/closes. What type of ion channels are at the synaptic cleft, and how do they propagate a signal between two neurons? ORGANELLES IN DIAGRAMS ARE NOT TO SCALE SIGNAL SEQUENCES ENABLE PROTEIN LOCALIZATION THREE GENERAL MECHANISMS OF PROTEIN TRANSPORT NUCLEAR PORE COMPLEX GTP/GDP MODIFICATION OF RAN (ALLOSTERIC REGULATION) DRIVES NUCLEAR IMPORT RECEPTOR RECYCLING PROTEIN TRANSLOCATORS UNFOLD PROTEINS FOR TRANSPORT ACROSS MEMBRANES PROTEIN TRANSLOCATOR IN THE ER IS TIED TO PROTEIN SYNTHESIS (ROUGH ER) ER signal sequence in protein being synthesized is bound by the signal recognition particle (SRP) for localization to the rough ER.  THREE DIFFERENT WAYS PROTEINS CAN BE SYNTHESIZED IN THE ER In ER In ER membrane ER signal sequence – cleaved Start transfer sequence – not cleaved Stop transfer sequence – not cleaved CLATHRIN PROMOTES VESICLE FORMATION VESICLE FUSION WITH TARGET MEMBRANES VESICLE TRANSPORT ALLOWS FOR ENDOCYTOSIS AND EXOCYTOSIS (SECRETION) QUESTIONS THAT I COULD ASK ON THE EXAM What is the main function of X organelle? What organelles are unrealistically depicted in the textbook, and why are they unrealistically depicted? What enables protein localization, and how was that shown? What type of transport is used to transport a protein to each of the following organelles? Name the protein responsible for each of the following protein sorting functions. What organelle utilizes more than one protein sorting mechanism, and why? LOCALIZATION & SECRETION INSIDE THE ER MODIFIES PROTEINS FOR LOCALIZATION & SECRETION Chaperone proteins Covalent modifications GOLGI ORGANIZES MOLECULES BY TYPE OF SECRETION AND LOCALIZATION TO PLASMA MEMBRANE THREE TYPES OF ENDOCYTOSIS Phagocytosis: White blood cells & protists Pinocytosis: Unregulated vesicle formation from plasma membrane, counters exocytosis Receptor-mediated endocytosis: Ligand specific EXAMPLE OF RECEPTOR- MEDIATED ENDOCYTOSIS ENDOSOMES SORT RECEPTORS (& SOMETIMES CARGO) AFTER ENDOCYTOSIS LYSOSOMES BREAK DOWN MACROMOLECULES INTO METABOLIC BUILDING BLOCKS USING HYDROLASES THAT ONLY FUNCTION IN ACIDIC CONDITIONS  Fatty acids, glycerol Lysosomes Endoplasmic reticulum Endosomes Golgi apparatus Plasma membrane Endocytosis Secretion QUESTIONS THAT I COULD ASK ON THE EXAM Draw each of the following pathways of vesicle transport. How does the ER modify proteins for localization and secretion? What are the two types of secretion the Golgi is responsible for, and how do they differ? What are the three types of endocytosis? What are the three fates of vesicles sorted by endosomes? What is the function of lysosomes, and how do they perform that function? TYPES OF SIGNALING CHEMICAL NATURE OF SIGNAL MOLECULE DICTATES TYPE OF RECEPTOR NEEDED PROTEINS = EXTRACELLUAR STEROIDS = INTRACELLULAR ONE SIGNAL MOLECULE CAN INDUCE MANY DIFFERENT RESPONSES DEPENDING ON TARGET CELL THE COMBINATION OF SIGNALS EACH CELL RECEIVES DICTATES CELL FUNCTION CELL RESPONSE CAN BE FAST OR SLOW INTRACELLULAR SIGNALING & PROTEIN MOLECULAR SWITCHES Every arrow is promoting: (A)Protein phosphorylation or dephosphorylation (covalent modification) (B)GTP or GDP binding (allosteric regulation) LOTS OF CROSSTALK BETWEEN SIGNAL TRANSDUCTION PATHWAYS QUESTIONS THAT I COULD ASK ON THE EXAM What are two types of signaling, and how are they different from each other? How do protein and steroid signals differ in mechanism of action/location of receptor, and why? How does intracellular signaling differ during a fast vs. slow cell response? In the following pathway, circle and label one amplification, one positive feedback, and one integration. Draw a pathway using enzymes W, X, Y, and Z with one integration and one negative feedback. What are the two most common mechanisms of activating and inactivating protein molecular switches? G-PROTEIN-COUPLED RECEPTORS SHARE SIMILAR STRUCTURE GENERAL GPCR MECHANISM WHAT ACTIVATED SUBUNITS CAN DO: 1) DIRECT ALLOSTERIC REGULATION WHAT ACTIVATED SUBUNITS CAN DO: 2)COVALENTLY MODIFY SECOND MESSENGERS FOR INDIRECT ALLOSTERIC REGULATION SECOND MESSENGERS CAN ALTER PROTEIN FUNCTION AND/OR GENE EXPRESSION INOSITOL PHOSPHOLIPID PATHWAY: ANOTHER 2ND MESSENGER PATHWAY RECEPTOR TYROSINE KINASES (RTKS) AS AN EXAMPLE OF AN ENZYME- COUPLED RECEPTOR Covalent modifications → Allosteric regulation The Hallmarks of Cancer: Cell RECEPTOR TYROSINE KINASES (RTKS) AS AN EXAMPLE OF AN ENZYME- COUPLED RECEPTOR The Hallmarks of Cancer: Cell Allosteric regulation Covalent modification ONE RTK CAN ACTIVATE MANY DIFFERENT PATHWAYS The Hallmarks of Cancer: Cell  LOTS OF CROSSTALK BETWEEN SIGNAL TRANSDUCTION PATHWAYS The Hallmarks of Cancer: Cell Hanahan and Weinberg, Hallmarks of Cancer. 2000. Cell, 100(1): 57-70. MULTISTEP CASCADES ALLOW FOR AMPLIFICATION AND ADAPTATION QUESTIONS THAT I COULD ASK ON THE EXAM What is the general structure of GPCR? Describe how G proteins are activated/inactivated. Describe one mechanism of action for G protein subunits once activated. How are enzyme-coupled receptors fundamentally different from GPCR’s? What is one way how amplification can be achieved in GPCR’s/enzyme-coupled receptors? What is one example of second messenger, and how are second messengers generally used in signal transduction? In the following signal transduction pathway, what would happen in A scenario (class activity), and why? Why is lots of crosstalk and multistep cascades useful in signal transduction?