1. Chapter 11
1.1. The Lipid Bilayer
1.1.1. The most abundant type of lipid in the cell membrane is the phospholipid and it contains two hydrophobic tails attached to a hydrophobic head.
1.1.2. The lipid bilayer allows an amphipathic molecule to exist normally in water by having the hydrophilic heads face the water and hydrophobic tails face each other away from the water.
1.1.3. It is easy to repair the bilayer and any small tear in the bilayer will cause the molecules to spontaneously rearrange in order to restore the bilayer to the way it was originally. A large tear will cause the bilayer to break up into smaller vesicles and fold in on itself.
1.1.4. The bilayer is fluid and can bed and allow molecules to pass through it. The fluidity depend on what type of phospholipid makes up the bilayer.
1.1.5. Unsaturated phospholipids contain double bonds allowing for less hydrogen to attach the the carbon while saturated phospholipids allow the full amount of Hydrogen to bond to the carbon since no double bonds exist in it.
1.1.6. The ER makes the phospholipid bilayers using enzymes. Scramblase is a transporter protein also used in the ER which moves random phospholipids from one side of the bilayer to the other. Once completed, the bilayer can be used in cell organelles or the plasma membrane.
1.1.7. Flippases remove a certain phospholipid from its original position in the bilayer to the side facing the cytosol in animal cells. This is another way to maintain asymmetry of the bilayer.
1.2. Membrane Proteins
1.2.1. There are many types of membrane proteins such as transporter proteins, ion channels, anchors, receptors, and enzymes.
1.2.2. The polypeptide chain of a transmembrane protein forms hydrophobic side chains that interact with the hydrophobic tails of phospholipids within the bilayer.
1.2.3. The polypeptide backbone of a protein is polar and hydrophilic. The aa within this chain form hydrogen bonds with each other since no water is available on the inside of the bilayer that the protein spans across. This is why they form alpha helices.
1.2.4. Beta helices can also be formed in which the hydrophilic amino acids are on the inside of the barrel shaped helices and the hydrophobic amino acids are on the outside of the barrel.
1.2.5. Bacteriorhodopsin is found in a type of archaea and helps pump protons out of the cell.
1.2.6. In plant, bacterial, and yeast cells, a cell wall helps support the plasma membrane while in animal cells, a cell cortex attached to the membrane via transmembrane proteins helps support the cell membrane.
1.2.7. Membrane domains are specialized regions with certain functions on the cell membrane that a cell controls. The cell controls the type of proteins located in that specific area.
2. Chapter 12
2.1. Principles of Transmembrane Transport
2.1.1. Molecules can cross the lipid bilayer through simple diffusion very slowly. Therefore, they require the help of certain proteins to cross the bilayer in a process called facilitated transport.
2.1.2. Small nonpolar molecules and uncharged polar molecules diffuse well across the bilayer and larger polar molecules do not cross as well. Also, the bilayer is impermeable when it comes to letting in charged molecules and substances.
2.1.3. The ion concentrations in cells differ from the ion concentrations outside of cells and cells must maintain these concentrations in order to survive.
2.1.4. The voltage difference across the cell membrane is known as the membrane potential.
2.1.5. The resting membrane potential is a cell's membrane potential when anions and cations are balanced in terms of flow in and out of the cell across the cell membrane. In animal cells the resting membrane potential "can be anywhere between -20 and -200 millivolts (mV)." (Alberts et al., 2019, p. 392)
2.1.6. Two types of membrane transport proteins are found in cells-channels and transporters.
2.1.7. Channels allow molecules and substances to flow in based on their charges and sizes while transporters only allow molecules/substances that bind to the site on the protein.
2.1.8. Passive transport is when solutes flow down their concentration gradients when entering/exiting the cell and does not require the use of energy.
2.1.9. Active transport is when solutes flow up their concentration gradient and requires energy.
2.1.10. Electrochemical gradient is the forces of membrane potential and the tendency of a solute to flow down its concentration gradient that determine which direction the solute will flow-in or out of the cell.
2.1.11. Water moves down its concentration gradient through osmosis in order to cross the cell membrane. The water flows from an area of low to high solute concentration.
2.2. Transporters and their Functions
2.2.1. Passive transport of molecules using transporters relies on the electrochemical gradient of the substance being transported.
2.2.1.1. Glucose transporter transports glucose in or out f cells depending on its concentration gradient.
2.2.2. Transmembrane pumps use active transport to pump solutes across a membrane when they need to go against their electrochemical gradient in order to maintain the correct concentrations of the solutes in the cells.
2.2.2.1. They carry out transport in three ways-"(i) transport of one solute across a membrane to the downhill transport of another; (ii) ATP-driven pumps use the energy released by the hydrolysis of ATP to drive uphill transport; and (iii) light-driven pumps." (Alberts et al., 2019, p. 397)
2.2.3. Na+ pump uses ATP hydrolysis to pump out three Na+ ions and in two K+ ions. The pump maintains a large concentration of sodium on the outside of the cell generating enough energy to allow the cell to continue functioning normally for several minutes if ouabain where used to stop the Na+ pump. The pump also maintains the correct concentration of Na+ and K+ ions in the cell.
2.2.4. Ca2+ pump keeps the concentration of Calcium ions low in the cytosol so the cell can be more sensitive to changes of calcium concentration.
2.2.5. The gradient-driven pumps can use the movement of one solute to drive the movement of another solute.
2.2.6. Antiports use the movement of a solute in one direction to move another solute in the opposite direction.
2.2.6.1. Na+-H+ exchanger p.401
2.2.7. Symports are the opposite of antiports and move both solutes in the same direction.
2.2.7.1. 12-16 glucose-Na+ symporter p. 401
2.2.8. Uniports are transporters that move a single type of molecule down their concentration gradient.
2.2.8.1. 12-9 glucose transporter p. 396
2.2.9. Plants, yeast, and bacteria rely on H+ pumps instead of an Na+ pump (animal cells) to maintain an electrochemical gradient. This pumps only H+ out of the cell an creates a sort of acidic pH in the membrane around the cell.
2.3. Ion Channels and the Membrane Potential
2.3.1. Ion channels are selective to certain ions only which means only those ions can pass through those channels. Ion channels are also not open all the time. They open briefly and the close and repeat. The channels can be gated which means they require a certain stimuli to open or close.
2.3.2. Altering the permeability of the cell membrane to a certain ion can cause a change in membrane potential.
2.3.3. K+ leak channels allow K+ to flow inn and out of the cell. These channels are open when a cell is resting and lower the membrane potential making it more negative.
2.3.4. The Nernst equation can be used to calculate a cell's resting membrane potential. V=62log10(C outside/C inside) V is the voltage and c is the concentration.
2.3.5. Patch-clamp recording can measure the current flowing through an ion channel and can tell us about the behavior of an ion channel. It uses a microelectrode(fine glass tube) to trap a small yet sufficient amount of a cell membrane. This piece of membrane could contain an ion channel and modern tech can measure the current of ion channels so we can observe them and figure out how they work.
2.3.6. Voltage-gated channels are opened and closed based on membrane potential. They can directly alter a membrane potential as well.
2.3.7. Ligand-gated channels open and close based on the binding of a a ligand to the channel itself.
2.3.8. Mechanically gated channels are opened and closed based on some mechanical force on the channel.
2.4. Ion Channels and Nerve Signaling
2.4.1. Neurons consist of a cell body(nucleus with long extensions coming out of it), axon(passes electrical signals from cell body to other target cells), dendrites(Come out of cell body and receive signals from other axons), and a nerve terminal(found at the end of a neuron and aids in passing the signal to other neurons).
2.4.2. Passive spread is when a localized change in the membrane potential send a weak signal down an axon/dendrite.
2.4.3. An action potential is a nerve impulse. It uses a burst of energy to send a continuous positive feedback loop along the axon membrane allowing to travel long distances without losing any strength.
2.4.4. A stimuli large enough to cause the depolarization of a neuron's cell membrane can cause voltage-gated sodium channels to open. Sodium will then enter the cell and causes further depolarization leading to more voltage-gated channels being opened and the process repeats in a continuous positive feedback loop.
2.4.5. The voltage-gated channels inactivate very quickly in order to stop too much sodium form entering the cell. The channels become inactivated and once the membrane potential returns to resting, they become closed.
2.4.6. Neurotransmitters turn electric signals coming form presynaptic cells to chemical signals in order to cross the synaptic cleft. Once the signal crosses the synaptic cleft, it is changed back to an electric signal by transmitter-gated ion channels.
2.4.7. Channel rhodopsin allows sodium to flow into a cell through the use of blue light.
3. Chapter 13
3.1. The Breakdown and Utilization of Sugars and Fats
3.1.1. Cells make ATP in two ways-either through coupling energetically favorable reactions to the reaction of adding a phosphate group to ADP to make ATP or through oxidative phosphorylation.
3.1.2. Food molecules are broken down in three stages-1) enzymes breakdown polymers into monomers, 2) glycolysis breaks down the glucose obtained from the polymers and creates pyruvate. 3) citric acid cycle
3.1.3. Glycolysis uses 2 ATP to break down glucose into 2 pyruvate and also creates 4 ATP and 2 NADH. Pyruvate(contains three C atoms) is used in the matrix where it is converted to acetyl-coA and CO2 and NADH is produced as well.
3.1.4. The citric acid cycle occurs in the mitochondria. The acetyl group is oxidized to CO2 and a lot of NADH is made. The electrons in NADH are then transferred to the electron transport chain (turning NADH into NAD+) which is key for oxidative phosphorylation.
3.1.5. ATP synthesis using coupled favorable reactions is called substrate level phosphorylation since a phosphate group is directly transferred to ADP.
3.1.6. Fermentation uses the pyruvate and NADH made during glycolysis to make products such as lactate that are excreted by the cell. The NADH ultimately loses it electrons and is converted to NAD+ to be used in glycolysis again.
3.1.7. Pyruvate dehydrogenase complex decarboxylates pyruvate in the matrix. CO2, NADH, and acetyl-coA are made.
3.1.8. The citric acid cycle oxidizes the carbons of the acetyl group by transferring them to oxaloacetate making citric acid.
3.1.9. The cycle produces 3 NADH, 1 FADH2 and one GTP.
3.2. Regulation of Metabolism
3.2.1. Control mechanisms help regulate the metabolic reactions that occur in a cell.
3.2.2. Gluconeogenesis makes glucose from pyruvate.
3.2.3. Glucose is stored in cells in the form of glycogen which can be used when ATP is needed and not enough of it is generated from food molecules.
3.2.4. Adipocytes are cells made for storing fats in animal cells.
4. Chapter 14
4.1. Mitochondria and Oxidative Phosphorylation
4.1.1. A mitochondria is made up of an outer membrane, intermembrane space, inner membrane, ad a matrix. Refer to 14-8 p.461 for more info.
4.1.2. The citric acid cycle produces high energy electrons which can be stored in the electron carriers NADH and FADH2. these carriers would then transfer their electrons to the electron-transport chain.
4.1.3. The ETC uses the passing of the electrons to oxygen to form water to drive proton pumps which form a proton gradient across the inner membrane. This gradient is then used to help power ATP synthesis(oxidative phosphorylation).
4.1.4. The high energy electrons donated by carriers are passed along the inner membrane through three respiratory enzyme complexes- (1) NADH dehydrogenase complex, (2) cytochrome c reductase complex, and (3) cytochrome c oxidase complex. (Alberts, et al., 2019, p. 464)
4.1.5. ATP synthase is a protein found on the inner membrane. It catalyzes the phosphorylation of ADP using the electrochemical proton gradient across the inner membrane.
4.1.6. ADP is constantly being pulled back into the mitochondria in order to be transformed into ATP once again.
4.1.7. Overall, 30 ATP molecules are produced per glucose molecule.
4.2. Molecular Mechanisms of Electron Transport and Proton Pumping
4.2.1. Water can be used as a reservoir to donate and receive protons.
4.2.2. Redox reactions depend on the change in free energy to be spontaneous.
4.2.3. Redox potential is a measure of the tendency of electron carriers to donate/ accept electrons and the lower it is the more likely they are to donate electrons.
4.2.4. The three complexes in the inner membrane of the mitochondria contain metals. The electrons donated to the complexes can move within them by jumping from one metal to another.
4.2.5. Iron-sulfur centers are present in the early stages of the etc in electron carriers. They have a low affinity for electrons which means they donate electrons easily.
4.2.6. Cytochrome C oxidase has a very high redox potential. This means it accepts electrons very well and it also oxidases cytochrome c. Most of the oxygen we breathe is consumed in cytochrome c oxidase complex.