Lecture 12.105 Membranes, Glysolysis

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Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 1 Office hours today in 3072 SLB Last time we were talking about two-tailed lipids. They form bilayers, membranes and liposomes Lipid membranes undergo phase transitions The lipids are mobile. The tail regions wag about when the membrane is in its fluid state. Can go below a temperature at which the tails are free to wag, and instead are packed in more ordered arrays. This temperature is called the phase transition temperature, below which lipid motion is relatively restricted, and above which lipid motion is much freer. Gel to liquid crystalline phase change. Plot mobility (or membrane fluidity) vs. temperature. There is a change in the packing order of the lipids during this transition. In going from gel to liquid crystalline, the membrane increases in surface area and the width decreases. Basic Picture of Biological Membranes • Picture to hold in your mind during this lecture: "proteins floating in a sea of lipids" some icebergs are floating on top of the water, some are submerged 1/2 way through, some a sunk all the way through the membrane, some make holes in the membrane, some are mostly out of the membrane, some are mostly in the membrane. We'll consider these specifics.

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 2 Look at slide from text. Membranes are composed of numerous types of proteins and lipids. Often the proteins are the main focus of attention when considering the function of a particular membrane, but the different types of lipids confer specific characteristics on the membrane and should not be forgotten. The great variety of different lipids in different membranes infers as much. • Basic Components: LIPIDS & PROTEINS by WEIGHT → myelin sheath around nerve bundles <25% protein inner mitochondrial membrane up to 75% PROTEIN typical numbers are 50% protein by NUMBERS → typically 1 mole protein per 50-100 moles lipid, or 1 protein molecule per 50-100 lipid molecules Other Components: Carbohydrates → just as you have glycolipids, you also have glycoproteins IV. FLUID MOSAIC MODEL • We have seen the players involved (lipids, types of membrane proteins) in our "proteins floating in a sea of lipids), now let’s consider in finer detail this image, more officially known as the Fluid Mosaic Model

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 3 Fluid mosaic model : states that there is a lateral diffusion of proteins and lipids in the liquid crystalline lipid bilayer. Proteins are free to rotate, but not flip-flop, while lipids though less common than lateral diffusion can still flip-flip between the leaflets of the bilayer. • Evidence for this model: I’ll show you one experiment 1. FRAP (Fluorescence Recovery After Photobleaching) Use fluorescently labeled lipids -- recovery in seconds Use fluorescently labeled proteins -- recovery in minutes Picture of FRAP Experiment:

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Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 4 Types of Membrane proteins • Membrane proteins are proteins that are associated specifically with membranes: we will consider two types 1) intrinsic and 2) extrinsic ; but if a protein isn't a membrane protein what is it? SOLUBLE protein • INTRINSIC MEMBRANE PROTEINS: integral to the membrane (characterized by surviving a high pH (11.5) bicarbonate membrane wash) 1. Protein possesses some portion that is hydrophobic and resides in the hydrophobic interior of the lipid bilayer. Can and often does pass through the entire membrane. 2. hydrophobic aa are the main type of aa found within these membrane residing domains, often find charged and polar aa flanking membrane associated regions and interacting with polar head groups of lipids 3. Schematic diagram of intrinsic membrane protein:

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 5 4.  -helix is the most common membrane spanning structure: Average membrane thickness: 30 Å How many aa in an  -helix required to cross membrane?  -helix: 30 Å /1.5 Å/amino acid = 20 amino acids ; 3.6 aa/turn = 25-30 aa to span the membrane Picture of  -helix spanning membrane: 5. Can span the membrane 1 time or multiple times: e.g. Bacteriorhodopsin spans the membrane 7 times 6. Integral membrane proteins can be solubilized with detergents, which dissolve membranes, but are resistant to salt washes. 7. Intrinsic proteins are often transporters or components of transporters • TECHNIQUES to determine the Structure of Intrinsic Membrane proteins: how can we "see" what these proteins look like 1. Hydropathy Plots : can be done on both soluble and membrane proteins, but particularly useful on intrinsic membrane proteins → can indicate the number and location of membrane spanning domains • Accomplished by examining the average hydrophobicity of a "window" of aa in the primary sequence of the protein. A plot of the window's value over the entire aa sequence can indicate stretches of hydrophobicity.

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 6 • Number of parameters that can be changed in such an analysis: size of the window (range from 5 to 20 aa), function of the window (rectangular, trapezoidal, Gaussian -- assigns varying weights based on the position of the aa within the window), hydrophobicity scale used • Can INDICATE possible topology of a protein but should be followed by direct experimental evidence. Picture of a typical hydropathy plot: • A stretch of 20 aa indicator of membrane spanning domain (bilayer's hydrophobic interior is about 3 nm thick) • EXTRINSIC MEMBRANE PROTEINS: specifically associated with the membrane 1. proteins associated with, but not inserted into the membrane 2. most often associated with integral proteins through ionic interactions 3. can often be solubilized by washing with salts, which diminish the ionic interactions by shielding charges 4. extrinsic proteins often have structural roles i.e. spectrin which lines the inner surface of plasma membranes, providing points of anchor for cytoskeletal components Picture of Extrinsic membrane protein -- associated with intrinsic membrane protein:

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Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 7 If a protein is not a membrane protein, then it is a soluble protein. We will move on to Metabolism Organisms show remarkable similarities in their metabolism. Despite relatively endless possibilities from organic chemistry, there are relatively few and common pathways. This provides strong evidence that all life descended from one ancestral form. Having said that, there are some differences between metabolic pathways in various organisms. Can be categorized by metabolic possibilities. Type C source Energy source Electron donors Examples Photoautotrophs CO 2 light H 2 O, H 2 S, S, inorganic compounds Green plants Photoheterotrophs Organic compounds light organic compounds Non-sulfur purple bacteria Chemoautotrophs CO 2 redox reactions Inorganic compounds, H 2 , H 2 S, NH 4 + Nitrifying bacteria; H, S, Fe bacteria Chemoheterotrophs organic compounds redox reactions organic compounds, glucose animals, etc.

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 8 Role of O 2 : Energy gained or released in oxidation /reduction reactions. The ultimate electron acceptor is oxygen. More about redox reactions later, but for now, in general, the more electrons and hydrogens on a carbon, the more reduced it is. OR, the more bonds to oxygen, the more oxidized it is. Carbon can exist in one of five (5) oxidation states, depending on what it is bound to. From the most reduced to most oxidized (more reduced, more energy): Some organisms must use O 2 as the terminal e - acceptor – obligate aerobes (humans). Some can use O 2 when it is available – facultative aerobes (E. coli, baker’s yeast). Some are poisoned by O 2 – obligate anaerobes (Clostriduim botulinum). Catabolism – breakdown, energy-producing pathways Anabolism – synthesis, energy-requiring pathways In general, the energy produced or consumed is often in the form of ATP. Recall ATP + H 2 O  ADP + P i ΔG°’ = -30.5 kJ/mol The other compound with some energy currency value is nicotinamide adenine dinucleotide, NAD.

Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 9 With R = two nucleotides, not to memorize. This is the business part of the molecule. Look at the reduction/oxidation reaction. NAD + + 2 e - + 2 H +  NADH + H + There is a variant of this molecule that is phosphorylated on the R group, NADP NADP + + 2 e - + 2 H +  NADPH + H+ NAD + /NADH + H + is generally used for carrying e - s during catabolism, whereas NADP + /NADPH + H + is generally used for reductive synthesis (anabolic) reactions. Note that these are both 2 electron reductions. They link catabolic and anabolic reactions. Catabolism and anabolism linked through energy-rich compounds ATP and NADPH

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Biological Sciences 105 Lecture 12, November 9, 2017 Copyright Steven M. Theg, 2017 All federal and state copyrights reserved for all original material presented in this course through any medium, including lecture or print. 10 Catabolism overview: Catabolism of glucose: C 6 H 2 O 6 + 6 O 2  6 CO 2 + 6 H 2 O ΔG°’ = -2,840 kJ/mol There is a lot of energy in glucose. If you just burned it, a lot of energy would be lost to the environment as heat. Metabolism is a slow controlled burn, so the energy liberated from glucose can be captured and put to use in the cell.