Bio week5

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Feb 20, 2024

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BIOL230W Week 5 — Membrane Trafficking Over the three weeks, we have transcribed protein coding regions of DNA to make mature mRNA, translated the mRNA into functional proteins and briefly discussed how proteins in the ER are transported through the endomembrane system. This week we will focus on the molecular mechanism allowing membrane transport, thereby finalizing the flow of information to the plasma membrane. Day 1 Learning Objectives . Compare and contrast the different classes of membrane proteins. 1 2. Define lipidation and its role in membrane proteins. 3. Review how location of protein translation and/post-translational modifications contributes to final protein location including inner membrane vs. outer membrane leaflet. 4. Analyze how changing the structure of a membrane protein (hydrophobic vs. hydrophilic regions) may alter its function or interaction with a lipid bilayer. Protein Domains: Finish from Last Week Mini-Lecture: Membrane Proteins and Lipidation 1. Where are the three main destinations of translated proteins? oplam (‘;‘;\M"‘V"'C ordanelen (mitschondaa 3 ddeofat ndomemiorane 4 2. What macromolecule can be post-translationally added to a protein, so it localizes to the inner (or outer leaflet) of the cell membrane? Why? o Lipd 3. What does the word exocytosis mean? Vesicle T paxess that alls rtlease Wostanes pram inide chlte fe olhiide cll endrommens: e Lt Knowledge Check: Recap Protein Associations with the Membrane 4. Proteins translated in the ER and destined to the cell membrane (i.e., exocytosis) have three fates: export to the extracellular space, a transmembrane protein, or associated with the outer leaflet of the cell membrane. In the spaces below, draw a vesicle and draw where the protein is in the vesicle before fusion with the cell membrane. The small image above may help and show vesicle fusion for FATE #1: Export to extracellular space (cargo=protein). Fate 1: Fate 2: Fate 3: g Lipd Export to extracellular space | Transmembrane protein Outer leaflet of cell membrane o ’
BIOL230W Week 5 — Membrane Trafficking At home practice: Proteins translated in the cytoplasm can still interact with the cell membrane. Draw an intracellular peripheral protein interaction. Label the protein, lipidation, inner leaflet of lipid bilayer and outer leaflet of lipid bilayer. Day 2 Learning Objectives 1. Analyze the characteristics of fatty acids that impact membrane fluidity using a temperature vs. membrane conversion chart Define anterograde vs. retrograde transport in a cell. Describe the role of coat proteins in vesicle formation. Describe the structure of clathrin (and a triskelion). Define the role of dynamin in endocytosis. Compare and contrast vesicle budding (fission) vs. fusion. ENE R Small Group Activity: Compare and Contrast Membrane Fluidity Membrane fluidity is primarily determined by characteristics of the phospholipid atty acids chains. Below is an image showing two phospholipid bilayers: left = low fluidity, right = high fluidity. Please use Figure 2 (below) and your knowledge from the exploration homework to answer the questions. lower fluidity higher fluidity 1. What forces commonly occur between atoms of the fatty acid chains? \lan Der Waalg 2. What two characteristics of the fatty acid chains are show in this image? sakuraron § lengile o faiv acds 3. How do the characteristics you listed above influence forces present between the fatty acid chains and, ultimately, membrane fluidity. This concept is important to understanding fluidity. more #igltly packed = grativ Von Day Waale foreen. [bmd hjhgpr&mw$8¢wdha Mini-Lecture — Lipid Packin 4. What membrane characteristics result in the most fluid membrane? untahiwatid & Swrter | looely packed 5. What membrane characteristics results in the most crystal-like (i.e. solid) membrane? Sawwahad € lonqen :""3\‘*{3 packed 6. What other molecule can be found in the membrane that alters fluidity? Cudlatodt ) e 10 T4 Grwlme aMplientic like Vkmqholcp.'JA
T LGV e Small Group Activity: Analyzing Membrane Fluidity f il 1 . . ‘ Figure 3. Applying heat to a phospholipid bilayer causes the membrane to “convert” from an ordered, solid state to a disordered, fluid state. ¢ The y-axis is measuring the degree (%) of this B && %&& conversion (0=100% solid, 0% fluid and 1=0% % solid, 100% fluid). The x-axis is measuring 5 05 - P oy temperature. This is analogous to double-stranded 3 red, 3 . 3 solid like fluid like DNA converting to single-stranded DNA. Tm = g temperature in which the phospholipid bilayer is 50% solid and 50% fluid. | Tm 0 b / 20 40 Temperature, T (°C) 7. What interactions in the phospholipid bilayer are disrupted by applying heat? \lm dov Waale fron 8. How do the interactions differ compared to those found in DNA denaturation? Bonds Aot WAL wy myeRaes e diffeve nt ( Ohe Vem dov Waala fwian) and plyo e rdasonship b ol agda is disvupied - 9. If an experimental phospholipid bilayer was compared to the control shown above (Figure 3), which way would the line shift if the experimental sample had shorter fatty acid chains compared to the control. Why? To fw o, thevay s veak W 10. Which way would the line shift if the ex chains compared to the control? Why? TAu \ub) Fales \en enevay o break 11. Which way would the line shift if the experimental sample had more saturated fatty acid chains compared to the control? Why? To A volk, 4aha voe LNQAY B brean w0 Mini-Lecture: Coat Proteins and Dynamin 12. Describe the quaternary structure of clathrin? e v 3 neavy € 3 ght duain oy proteis all aftaded @y ond, (dvisketow) D ey weatr, @ clafwoin ok - perimental sample had more unsaturated fatty acid
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BIOL230W Week 5 — Membrane Trafficking 0 40f7 What is one outcome if clathrin failed to function? MNomioants wowuld net be progerly coted 14. What is the role of dynamin in vesicle budding? Cifas ceass phosphati off 3 GOP Chdoiys)- finat veoicle buddieg ( prewewcba cpqonne o Wduophdei seim § vescide dunving buctdivas) 15. What is one outcome if dynamin failed to function? T vesude womt Yor ressed Day 3 Learning Objectives 1. Describe the general pattern of cytoskeleton location as related to vesicle transport. 2. Identify where a G-protein is active in a cellular process, like vesicle transport. 3. Outline the role of small G-proteins and SNARE proteins in vesicle fusion and analyze what may occur if proteins fail to function. 4. Review major topics from Sci Lit Week 4 (Ricin). Mini-Lecture: Cytoskeleton and SNARE proteins 1. What is the general pattern of cytoskeletal elements in a cell? Grovlas cell avronged wf a wtls Sy \act $ micrstitbes with mund nockews ‘nade Hro call 2A. How do T-SNARESs and V-SNAREs differ in location? U-SNARES 4asqec veacdeo vembrone- T-SNAREs toger o BIOL230W Week 5 — Membrane Trafficking 2B. Figure 4 shows the role of SNARE proteins and Rab G-protein |Rabs in Vesicle TPy s m—m—"
BIOL230W Week 5 — Membrane Trafficking |Rabs in Vesicle Formation & Fusion ] C Donor Qrgane!!e’__‘pJ 2B. Figure 4 shows the role of SNARE proteins and Rab G-protein in vesicle transport. In which of the following steps of vesicle transport is the G-protein Rab active; budding, vesicle transport, fusion or G-protein recycling? @\GEF ‘2 Rab-GDP % “&d'fi Rab-GTP (1] binds to Vesicle v-SNARE ‘ GEF formation Rab-GDP ’ Rab de- phosphorylates GTP Vesicle fuses ! with target organelle -y B S . z Target Organelle O'Day Mini-Lecture: Protein Trafficking and Ricin Key Terms to know: RIP, lectins, A- and B-chains, endocytosis, retrograde transport, sec61 (translocon) 3. What is the function of a RIP? 4. What is the function of a lectin? 5. Describe the function of A-chain vs. B-chain of lectin.
(O 7o0f7 BIOL230W Week 5 — Membrane Trafficking Protein Structure Practice For Home Use Figure 6 to answer the next four questions about CFTR structure. Cor> Gieop) Figure 6. Cystic fibrosis transmembrane conductance regulator (CFTR) is a 1,480-amino acids protein @rsE0 (@00 inserted into the cell membrane. CFTR has five f 1T 1 domains: two transmembrane domains (TMD1/2 - e containing six alpha-helices and are joined by two intracellular loops and three extracellular loops each), ! l 09990000009 and with glycosylated residues linked in the W &, B B s o o Bl B o, @, 9.0 extracellular loop 4 (N894, N900); two nucleotide- ’ = & B WA ‘.“::‘“:m:? binding domains (NBD1/2) with highly conserved sequenced for ATP-binding and hydrolysis; and one regulatory domain (RD) with multiple phosphorylation sites. TMDs form the gate where chlorine ions can diffuse through the membrane. The positions denoted 5 g e into the boxes correspond to the first and last amino o Pxaposprayimon e aC1d O €ach fragment. © PKC phosphorylabon stes wan2 Lopes-Pacheco, M. (2016). CFTR modulators: shedding light on precision medicine for cystic fibrosis. Frontiers in pharmacology, 7, 275. 7. How many domains are found in the CFTR protein? 9 lowains 8. In which cellular space is CFTR translation completed: cytoplasm or pndoplasmic reticulum) Circle the correct answer and explain why? fo post - rong|akinak acki; ¢ agiond 9. The transmembrane domains (TMDI1 and 2) consist of (charged 0 amino acids. Circle the correct answer and explain why? . vk v onng 08 O Sighle inbtfgatin O poaen W W kd BN easvina e QR unctini] A BNOM o biane, g«*cfm 10. The intracellular and extracellular loops consist off @ or non-polar) amino acids. Circle the correct answer and explain why? Plavs K pv potev fwncion € atablly o e gwttin witain igid Bloyer 11. What is the major molecular function of the CFTR regarding symptoms of cystic fibrosis? Maidtain the balance o ik § waker on mamy gurfaces n -th.v-’dj
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