BIOE120 Exam Two Review Chapter 7: Membrane Structure and Function Central Dogma of Membrane Biology Refers to the

he phospholipid bilayer with proteins (hydrophilic ends and hydrophobic centers) that run through the bilayer in the membrane Fluid-Mosaic Model This model based on the above has been developed, revised, and expanded on over the years Phospholipids Amphipathic - Has both a hydrophobic and hydrophilic region Hydrophilic Head (Phosphate and Glycerol and Choline) Hydrophobic Tail (Fatty Acid Tails)

Langmuir Trough Experiment Dissolved red blood cells (no nucleus or organelles) to get a solution of lipids. Stretched the lipids out to a single layer. Calculated that the surface area of the lipids was double what was calculated for a red blood cell. Determined the existence of the bilayer. Phospholipid Movement Phospholipids have lateral movement 10,000,000 times a second Phospholipids flip-flop sides about once a month Phospholipid Fluidity Depends on whether the fatty acid tails are saturated or un-saturated Unsaturated The lipids are extremely fluid due to the prevention of packing from the kinked double bonds Saturated The tails pack together increasing membrane viscosity Cholesterol is located in the bilayer to help regulate fluidity. In warm temperatures, it discourages fluidity, and in cold temperatures, it encourages fluidity

 Fatty Acids Review Saturated No double bonds Unsaturated Double bonds (kinked) Cis/Trans Unsaturated Cis is healthier and natural (vegetable oil) Trans is extremely unhealthy and artificial (hydrogenation)

Differences in Membrane Lipid Composition Variations in species due to evolutionary adaptions Fish that live in extreme cold conditions have high concentrations of unsaturated hydrocarbon tails Some plants can change the concentration of unsaturated to saturated depending on the seasons (winter wheat) Membrane Proteins and their Functions Two major populations of proteins that are part of the lipid bilayer Integral proteins penetrate the hydrophobic interior. The majority span the entirety of the bilayer and are known as transmembrane proteins, while others only go partway Peripheral proteins not imbedded in the bilayer. They are loosely bound to the surface of the membrane Most proteins are bound to the cytoplasmic side of the cell due to being attached to the cytoskeleton. Six major functions by proteins of the plasma membrane Transport may provide a channel for selective substance movement Enzymatic activity may be an enzyme with its active site exposed to substances in the adjacent solution Signal transduction May have a binding site with a specific shape that fits the shape of a chemical messenger Cell-cell recognition Some glycol proteins serve as identification tags that are specifically recognized by membrane proteins of other cells Intercellular joining May hook together with adjacent cells Attachment to the cytoskeleton and extracellular matric help maintain cell shape and stabilize the location of certain membrane proteins Membrane Permeability

 Nonpolar molecules can cross the lipid bilayer easily, but ions and polar molecules have trouble crossing the hydrophobic interior. Transport proteins facilitate the crossing of these Aquaporins allow 3,000,000,000 molecules of water per second through the cell membrane Transport also depends on the concentration gradient of the molecule trying to enter or leave This type of diffusion, from high to low concentrations is known as passive transport. No energy is needed Osmosis The movement of water across the cell membrane Types of solutions: Isotonic No net movement of water Hypotonic High concentration of particles inside the cell causes water to enter increasing the cells size Hypertonic High concentration of particles outside the cell leads to water leaving and the cell shriving up Animal Cells prefer Isotonic solutions while Plant Cells prefer hypotonic solution (Turgid) Active Transport requires energy to move solutes against their gradients Ion Exchangers utilize conformational changes to selectively maintain gradients for specific ions Ion Pumps can be used to generate ion gradients across membranes. The gradients can then be used to perform work such as solute transport or energy generation Contransport The mechanism of how a single ATP powdered pump can transports a specific solute and indirectly drive the active transport of several other solutes Electrogenic pump Generals voltage across a membrane (sodium-potassium pump) Proton Pump Actively transports hydrogens. The pumping of H atoms transfers the positive charge from the cytoplasm to the extracellular solution Endocytosis - The cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane. Reverse of exocytosis. Human cells use receptor-mediated endocytosis to take in cholesterol for membrane synthesis and steroid synthesis. Ligands (a molecule that binds to a receptor site) act with lipoproteins (LDLs) allowing the cholesterol bound to the LDL to enter the cells. Pinocytosis Generates small amounts of ATP. Small particles are brought into the cell within vesicles. (Usually Liquid) Phagocytosis The cell engulfs extracellular material (Usually Solid) Exocytosis The process where a cell secretes certain biological molecules by the fusion of vesicles with the plasma membrane. Deliver these molecules through Golgi vesicles

 Osmolarity Sum total of particles in solution If you have a 150 mM NaCl solution, you have 150mM Na+ and 150mM of Cladding up to a 300 mM total concentration Written as 300 mOsm/L

Chapter 8: An Introduction to Metabolism Pathways Catabolic Break down molecules to simpler compounds and release energy. An example of this is cellular respiration Anabolic Consumes energy to build complicated molecules from simpler ones. An example of this is the synthesis of an amino acid or protein Thermodynamics Two Laws of Thermodynamics First Law: The energy of the universe is constant. Energy cannot be created or destroyed. It can be transferred. Second Law: Every energy transfer or transformation increases the entropy of the universe (increases disorder) Entropy: the measure of disorder or randomness Transduction of Energy Kinetic (Heat or thermal energy) Potential Gibbs Free Energy G = H-TS Gibbs Free Energy is equal to the change of enthalpy minus the temperature times the change in entropy If G > 0 The reaction is endogonic and non-spontaneous If G < 0 The reaction is exergonic and spontaneous If G = 0 The reaction is in equilibrium (no work can be done) Reaction Kinetics ATP + H2O results in ADP + P (phosphate group) This is non-spontaneous. Energy must be spent Hydrolysis of ATPs terminal phosphate yields ADP and Phosphate and releases energy. Through energy coupling, the exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to a reactant forming a phosphorylated intermediate that is more reactant. Actual G = G + RTln(Products/Reactants) G = -RTln(Keq)

 Calculated at a known and given set of conditions R = 8.314 J/mol K Enzymes Enzymes lower the activation energy needed for a reaction An enzyme does not change the G, it cannot make an endogonic reaction exergonic. They enable the reactant molecules to absorb enough energy to reach the transition state at moderate temperatures. Mechanisms for lowering EA by enzymes Active sites orient substrates appropriately to facilitate reactions Active sites can apply strain to bonds within substrate to regions for reactions The active site can provide a favorable microenvironment Factors that affect enzyme kinetics Temperature Too high temperatures cause denaturation pH Binding Types Normal Binding Competitive inhibition Only the substrate or inhibitor can bind to the active site. Same Vmax, different Km Noncompetitive inhibition Two spots, so both can be bound, but it will still be inhibited Different Vmax, same Km

 Allosteric Regulation Any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site. It may result in either inhibition or stimulation of an enzymes activity Most enzymes known to be allosterically regulated are constructed from two or more subunits The binding of a activator or inhibitor will stabilize the respective active or inactive form A single activator or inhibitor can affect all active sites on an enzyme ATP can bind to several catabolic enzymes allosterically, lowering their affinity for substrate and inhibiting their activity ADP can bind to and acts as an activator for the same enzymes This balance can regulate the supply of ATP and ADP (feedback) Cooperativity The binding of a substrate molecule to an active site of one subunit locks all the subunits in active conformation Hemoglobin

Feedback Inhibition A metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway. ATP allosterically inhibits an enzyme in an ATP generating pathway with ADP

 Michaelss Menten Equations See Notes Lineweaver- Burk Equations See Notes

Chapter 9: Cellular Respiration and Fermentation Catabolic Pathways Fermentation partial degradation of sugars or other organic fuel that occurs without the use of oxygen Aerobic respiration oxygen is consumed as a reactant with organic fuel Cellular respiration - includes both aerobic and anaerobic processes, but generally refers to aerobic Cellular respiration does not oxidize glucose in a single step. It is broken down into a series of steps each catalyzed by an enzyme The hydrogen atoms are not transferred directly to oxygen, but instead are passed first to a coenzyme NAD+ which acts as an oxidizing agent Electron Transport Chain Number of molecules (usually proteins) that are built into the inner membrane of the mitochondria. Electrons removed from glucose are shuttled by NADH to the top, higher-energy end of the chain. At the bottom, lower energy end, O2 captures these electrons along with H_ forming water Glucose to NADH to Electron Transport Chain to Oxygen Steps of Cellular Respiration Glycolysis Pyruvate oxidation and the Citric Acid Cycle Oxidative Phosphorylation: electron transport and chemiosmosis

 Glycolysis Begins the degradation process by breaking down glucose (Takes place in the cytoplasm) Glycolysis can occur whether or not O2 is present, but if it is, the chemical energy stores in pyruvate and NADH can be extracted by pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation Two Phases: Energy Investment and Energy Payoff Energy Investment Two ATP molecules are used to break down glucose Energy Payoff - forms four ATP molecules (net of two), two NADH, two Pyruvate molecules and two H2O molecules.

Oxidation of Pyruvate to Acetyle CoA The pyruvate molecules enter the mitochondrion via active transport and transformed into the acetyl coenzyme A. This step links Glycolysis with the Citric Acid Cycle Pyruvate enters loses its carboxyl group and given off as a molecule of CO2 The remaining fragment is oxidized forming acetate. The extracted electrons are transferred to NAD+ storing energy Coenzyme A attaches to the acetate forming acetyl CoA (has high potential energy) d

 The Citric Acid Cycle Functions as a metabolic furnace that oxidizes organic fuel derived from pyruvate The cycle generates one ATP per turn by substrate-level phosphorylation Substrate-level phosphorylation: An enzyme transfers a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation The cycle has eight steps. For each Acetyl CoA group entering the cycle, three NAD+ are reduced to NADH, electrons are transferred to FAD becoming FADH2, A GTP molecule is formed by substrate-level phosphorylation (can be used to make ATP), and two ATP molecules are formed Oxidative Phosphorylation (forms 26 to 28 ATP) After glycolysis and the Citric Acid Cycle, only four molecules of ATP are produced. At this point NADH accounts to most of the energy Consists of an electron transport chain and chemiosmosis Electron transport chain NADH transfers H+ through proteins. NADH (can create three ATP) and FADH2 (can create two ATP) is oxidized, and energy is derived

Chemiosmosis The process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP H+ flows through the chamber and activates catalytic sides produces ATP form ADP and phosphate The whole ATP yield from one molecule of glucose is about 30 or 32 ATP Fermentation and Aerobic respiration Alcohol fermentation pyruvate is converted to ethanol in two steps

 Lactic Acid fermentation pyruvate is reduced directly by NADH to form lactate With glycolysis, two ATP are produced (substrate-level phosphorylation), without, the net outcome is zero Proteins and Fats Proteins can be converted directly to the Pyruvate, Acetyl CoA, and Citric Acid Cycles Fats Glycerol goes into the Glycolysis Fatty Acids go straight to Acetyl CoA

Chapter 6: Cell Structure The cytoskeleton A network of fibers extending throughout the cytoplasm that plays a major role in organizing the structures and activities of the cell Roles of the cytoskeleton Structure and Support Stabilized by a balance between opposing forces exerted by elements. The cytoskeleton also provides anchorage for organelles Intracellular Transport Motor proteins use the cytoskeleton to travel by cilia or flagella. They attach to receptors on vesicles along microtubules Kinesin (Anterograde Transport) - Transports away from cell body Cytoplasmic Dynein (Retrograde Transport) Transports towards the cell body Contractility and Mobility Spatial Organization Components of the cytoskeleton Microtubules (Tubulin Polymers) Diameter: 25nm Consist of alpha and beta tubulin. Responsible for maintenance of cell shape, chromosome movements, etc. Hollow tubes, wall consist of 13 columns of tubulin molecules. Extremely unstable, they can collapse at any time. GTP and GDP bound. Make up cilia, flagella, centrosomes and centrioles Microfilaments (Acton Filaments) Diameter: 7nm Consists of Actin, two intertwined strands Have a + and a end. The + end adds faster than the end. Bear tension and pulling forces Myosin works as a motor protein that walk along actin filaments, allowing contraction of muscle cells G-actin with bound ATP forms F-Actin

 Cell Traction See Notes Kymograph See Notes

Statistics Variable Categorical Quantitative Discrete Limited number of values Continuous Can take any value within a given bound Distribution describes the values a variable takes and how often they occur Mean Median Standard Deviation Measure of variation in the data from the mean Skew Mean < Median = Skew left Mean > Median = Skew right