BCH3033 Biochemistry 1 Chapter 11a PDF

BCH3033: Biochemistry 1 Chapter 11 a 03.20.2024 Donella Beckwith, Ph.D. [email protected] 1 Composition and Architecture of Membranes Transport & Phospholipids Cytoplasm The biological membrane is a lipid bilayer with proteins of various functions (enzymes, transporters) embedded in or associated wi...

BCH3033: Biochemistry 1 Chapter 11 a 03.20.2024 Donella Beckwith, Ph.D. [email protected] 1 Composition and Architecture of Membranes Transport & Phospholipids Cytoplasm The biological membrane is a lipid bilayer with proteins of various functions (enzymes, transporters) embedded in or associated with the bilayer Also known as the plasma membrane: most important structure of the cell 2 Why Is Plasma Membrane So Important? Think of the cell as a really popular nightclub, the membrane is the bouncer It decides what enters and exits the cell Found around both eukaryotic and prokaryotic cells 3 Plasma Membrane Plasma membrane: thin barrier separating the inside of the cell (cytoplasm) from the outside environment – Function: Isolate cell’s contents from the outside environment Regulates exchange of substances between the inside and outside of the cell Affords communication with other cells The hydrophobic effect stabilizes structures (lipid bilayers and vesicles) in which lipids with some polar and some nonpolar regions can protect their nonpolar regions from interaction with the very polar solvent, water Membrane proteins are associated with the lipid bilayer more or less tightly, and proteins and lipids are both allowed limited lateral motion in the plane of the bilayer Note: Membranes also exist within cells forming various compartments where different biochemical processes occur 4 The Endomembrane System Is Dynamic and Functionally Differentiated Within eukaryotic cells, these are the components that carry lipids and proteins t/o the cell single membrane surrounds: – endoplasmic reticulum (ER) – Golgi apparatus – lysosomes – various small vesicles double membrane surrounds: – nucleus – mitochondrion – chloroplasts (in plants) 5 Bilayer bilayer: double layer (twodimensional sheet) of aggregating lipids – Hydrophilic end forms the outer border – Hydrophobic tails form the inner layer – Favored when the crosssectional areas of the head group and acyl side chain(s) are similar Extracellular fluid Hydrophilic heads Hydrophobic tails Cytoplasm 6 The Lipid Bilayer Is Stable in Water glycerophospholipids, sphingolipids, and sterols: – virtually insoluble in water – spontaneously form microscopic lipid aggregates when mixed with water hydrophobic interactions: the clustering of hydrophobic molecule surfaces in an aqueous environment reduces the hydrophobic surface area exposed to water – They are finding the lowest-energy environment by clustering together Micelles: spherical structures containing amphipathic molecules arranged with hydrophobic regions in the interior and hydrophilic head groups on 7 the exterior Micelle Formation 8 Vesicle Formation vesicle (liposome) = forms spontaneously when a bilayer sheet folds back on itself to form a hollow sphere important because this allows bilayers to achieve maximal stability in their aqueous environment Uses in research: promising and versatile drug vehicles – outstanding properties for protecting the encapsulated drug Encapsulated drug 9 Question Micelles were constructed for delivery of a hydrophobic chemotherapeutic drug. What change would INCREASE the diameter of the micelles? A. B. C. D. increasing the concentration of cholesterol increasing the length of the acyl chains used to make them increasing the concentration of polyunsaturated fatty acids using lipids with head groups having greater polarity 10 Question Which amphipathic lipid aggregate is favored to form when glycerophospholipids are mixed with water? A. B. C. D. No aggregate will form. micelle bilayer vesicle (liposome) 11 Bilayer Architecture Underlies the Structure and Function of Biological Membranes fluid mosaic = pattern formed by individual lipid and protein units in a membrane – pattern can change while maintaining the permeability membrane Function of the membrane: – Permits shape changes accompanying cell growth and movement – Molecular gatekeepers – Permit exocytosis, endocytosis, and cell division Recognition protein Transport and receptor proteins 12 Proteins and Enzymes In and On Membranes Transport proteins: regulate the movement of specific organic solutes and inorganic ions across the membrane – Channel proteins: Na+ channels – Carrier proteins: glucose transporter Receptor proteins: sense extracellular signals and trigger molecular changes in the cell Recognition proteins: allow cells to recognize and or attach to one another – Glycoproteins: proteins with attached carbohydrate group Ion channels: mediate electrical signaling between cells and speed the passage of ions across membranes through an aqueous path Adhesion molecules: mediate cells interaction and hold neighboring cells together (example: Integrins) 13 Question Which statement is false? A. All biological membranes have the same composition. B. All biological membranes contain lipids. C. Amphipathic molecules may form micelles rather than bilayers, depending on their structures. D. Biological membranes typically contain proteins. 14 How Are Substances Transported Across Membranes? Concentration Gradients Concentration: number of molecules in a given unit of volume (e.g., grams/liter; moles/liter) Gradient: difference between two regions of space such that molecules move from one region to the other 15 Diffusion Diffusion: (process) movement of molecules from an area of high concentration to an area of low concentration The greater the concentration gradient, the faster diffusion occurs Diffusion will continue until the gradient is eliminated (equilibrium) Diffusion cannot move molecules rapidly over long distances 16 Types of Movement Across Membranes 1. Passive Transport: Requires NO energy Substances move down concentration gradients ([higher] to [lower]) 3 types to discuss 2. Active Transport: Requires energy Substances move against concentration gradients 3. Endocytosis: movement of large particles into cells (vesicle formation) 4. Exocytosis: movement of large particles out of cells (e.g., hormones) 17 Passive Transport A 1. Passive Transport: Requires NO energy Substances move down concentration gradients ([higher] to [lower]) 3 types to discuss ❖ Simple Diffusion: small molecules pass directly through the phospholipid bilayer (e.g., CO2, H2O, O2) Rate depends on: Molecule size Concentration gradient Lipid solubility 18 Passive Transport B 1. Passive Transport: Requires NO energy Substances move down concentration gradients ([higher] to [lower]) 3 types to discuss ❖ Facilitated Diffusion: molecules need assistance of channel proteins or carrier proteins (e.g., ions, amino acids, sugars) Rate depends on: Temperature Concentration gradient Selectivity 19 Passive Transport C 1. Passive Transport: Requires NO energy Substances move down concentration gradients ([higher] to [lower]) 3 types to discuss ❖ Osmosis: movement of water from an area of high water concentration to an area of low water concentration across a semi-permeable membrane Rate depends on: Concentration of the solute Concentration gradient Pressure gradient 20 Osmosis and Living Cells Isotonic solution: outside of the cells have same [solute] as the inside of cells Hypertonic solution: outside of the cells has a higher [solute] than the inside of the cell Hypotonic solution: the inside of the cell has a higher [solute] than the outside of the cell 21 Active Transport 2. Active Transport: Requires energy Substances move against concentration gradients Examples: sodium-potassium pump, calcium pump 22 3. Endocytosis: movement of large particles into cells (vesicle formation) a) Pinocytosis: cell drinking – Uptake of fluid droplets b) Receptor-mediated endocytosis – Uptake of specific molecules via coated pits c) Phagocytosis: cell eating – Uptake of large particles (e.g., bacteria) 23 Endocytosis Plasma membrane pathogen 24 4. Exocytosis: movement of large particles out of the cells (e.g., hormones) 25 Question Which type of transport requires energy? A. B. C. D. active diffusion osmosis passive 26 Question The picture represents which type of cellular transport? A. B. C. D. exocytosis endocytosis osmosis Passive transport 27 Question If particles are too large to enter the membrane (shown in image) and they need help from channel proteins but require no energy what type of transport is represented? A. B. C. D. Facilitated diffusion osmosis Active transport Passive transport 28 Lipid Composition of the Plasma and Organelle Membranes the functional specialization of each membrane type is reflected in its unique lipid composition 29 Changes in Lipid Composition During Membrane Trafficking sphingolipids and cholesterol largely replace phosphatidylcholine Reminder: phosphatidylcholine is a glycerophospholipid Do you remember what the polar head group is? 30 Lipid Transfer Proteins (LTPs) lipid transfer proteins (LTPs) = soluble proteins that contain a hydrophobic lipid-binding pocket to carry a lipid from one membrane to another through the cytosol – can be bispecific 31 Question Which statement is false regarding lipid transfer proteins (LTPs)? A. B. C. D. They are soluble in water. They have a hydrophilic pocket for binding lipids. In some cases, ATP is needed to drive the process. The rate of lipid movement from one membrane to another in vivo is significantly greater than the rate of vesicle budding and fusion. 32 Posttranslational Modification of Membrane Proteins Proteins that undergo posttranslational modification pass through the ER and the Golgi apparatus Glycosylation: attachment of oligosaccharides to proteins – typically on the outer face of the plasma membrane attachment of 1+ lipids: serve as hydrophobic anchors to hold proteins to the membrane or as tags to target proteins PTM discussed further in Ch. 27 33 Membrane Proteins Differ in the Nature of Their Association with the Membrane Bilayer integral membrane proteins = firmly embedded within the lipid bilayer (transporters, channels, enzymes) peripheral membrane proteins = associate with the membrane through electrostatic interactions and hydrogen bonding (electron transport chains) amphitropic proteins = associate reversibly with membranes – found in both membranes and the cytosol 34 Integral, Peripheral, and Amphitropic Proteins associate reversibly with membranes (found in both membranes and the cytosol) glycosylphosphatidylinositol associate with the membrane through electrostatic interactions and hydrogen bonding (electron transport chains) firmly embedded within the lipid bilayer (transporters, channels, enzymes) 35 Question An amphitropic protein: A. has both basic and acidic surfaces. B. switches from one face of a membrane to the other. C. is sometimes associated with a membrane and sometimes not. D. is never a peripheral membrane protein. 36 Monotopic Proteins (Integral) monotopic = have small hydrophobic domains that interact with only a single leaflet of the membrane 37 Bitopic Proteins (Integral) bitopic = span the bilayer once, extending on either surface (glycophorin) – have a single hydrophobic sequence somewhere in the molecule 38 Polytopic Proteins (Integral) polytopic = cross the membrane several times – have multiple hydrophobic sequences of ~20 residues that each cross the membrane when in the α-helical conformation bacteriorhodopsin 39 Question Which statement is true? A. Monotopic integral proteins have small hydrophilic domains that hold the proteins to the membrane. B. Bitopic proteins span the bilayer twice. C. A hydrophobic sequence of 20 amino acid residues will span the lipid bilayer when in the α-helical conformation. D. Membrane proteins do not co-crystallize with phospholipids. 40 The Topology of an Integral Membrane Protein Can Often Be Predicted from Its Sequence an α-helical sequence of 20-25 residues (each 1.5 Å) is just long enough to span the thickness (30 Å) of the lipid bilayer – stabilized by intrachain hydrogen bonding and the hydrophobic effect in many organisms, 20-30% of proteins are integral proteins What if we want to determine the hydrophobicity of a sequence? 41 Hydropathy Index hydropathy index: expresses the free-energy change associated with the movement of an amino acid side chain from a hydrophobic environment to water – ranges from highly exergonic to highly endergonic overall hydropathy index: estimated by summing the free energies of transfer for the residues in the sequence the larger the number, the more hydrophobic the amino acid 42 Hydropathy Index for the 20 Common Amino Acids the larger the number, the more hydrophobic the amino acid 43 Hydropathy Plots hydropathy plot: average hydropathy index plotted against residue number – Window: segment of given length – hydropathy index (y-axis): average hydropathy for a window – residue number (x-axis): the residue in the middle of the window 44 Question Which statement is true regarding hydropathy plots? A. A negative hydropathy index indicates the residue number is hydrophobic. B. A region with more than 20 residues of high hydropathy index is presumed to be a transmembrane segment. C. An integral protein must have at least one sequence of 20 hydrophilic residues. D. Hydropathy plots plot residue number (y-axis) against average hydropathy index (x-axis). 45 β Barrel β barrel = structural motif in which 20+ transmembrane segments form β sheets that line a cylinder – stabilized by intrachain hydrogen bonds porins = proteins that allow certain polar solutes to cross the outer membrane of gram-negative bacteria – have β barrels lining the transmembrane passage 46 β Strands of Membrane Proteins in β conformation: – seven to nine residues are needed to span a membrane – alternating side chains project above and below the sheet in β strands of membrane proteins: – every second residue in the membrane-spanning segment is hydrophobic and interacts with the lipid bilayer aromatic side chains are commonly found at the lipidprotein interface 47 Amino Acid Locations Relative to the Bilayer Tyr and Trp side chains serve as membrane interface anchors positive-inside rule = positively charged Lys and Arg residues in the extramembrane loop of membrane proteins occur more commonly on the cytoplasmic face 48 Amino Acid Locations Relative to the Bilayer Tyr and Trp side chains serve as membrane interface anchors positive-inside rule = positively charged Lys and Arg residues in the extramembrane loop of membrane proteins occur more commonly on the cytoplasmic face Crystals 2021, 11(9), 1032; https://doi.org/10.3390/cryst11091032 49