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Bio Review # 2

This is a set of review cards for Test II made from Dr. Burkirk's handouts for Bio 311C, Fall '07! (I'm not the most detailed or smartest person out there, so take these with a grain of salt).
Explain the "fluid mosaic" model of membrane structure. To what does the word "fluid" refer?
In the "fluid mosaic" model, the membrane is a fluid structure with a "mosaic" of various proteins embedded in or attached to a bilayer of phospholipids.
What is the effect of each of the following on membrane fluidity at cooler temperatures? A) Membrane has more phospholipids with very long hydrocarbon chains; B) Membrane has more phospholipids with unsaturated hydrocarbon chains; C) Membrane has more cholesterol.
B & C increase fluidity. A does not increase fluidity because the long carbon chains tangle up with each other and hold everything together--decreasing fluidity.
What is osmosis? What determines the net (overall) direction of water movement across a semi-permeable membrane? What happens if a cell is placed in an isotonic fluid?
Osmosis is the diffusion of water through a selectively permeable membrane from a high concentration to a low concentration. The concentration of solutes determines the net movement of water. If the cell is placed in an isotonic environment, there is no net movement. Water flows in and out at the same rate.
Distinguish the following gradients across a membrane: A) a pH gradient; B) Electrical charge gradient; C) Concentration gradient for a particular substance (e.g., glucose); D) Solute gradient (will affect the movement of water).
A) A difference in H+ ion concentration across the gradient. B) A difference of positive and negative charge across the gradient. C) The steeper the concentration gradient, the greater the net movement. D) Differences in solute amounts across the gradient.
How does the existence of a gradient represent a source of potential energy to do cell work? Give an example of a gradient doing cell transport with.
The existence of a gradient represents a source of potential energy to do cell work because there can be a need for ATP if a substance is being transported against its gradient. An example of a gradient doing cell transport is the H+ concentration around nerve cells and how they bring sucrose in.
Distinguish these terms: simple diffusion, facilitated diffusion, active transport.
Simple diffusion is the tendency for solutes to spread evenly (high to low concentration). Facilitated diffusion is a passive transport through the use of a protein without the use of ATP (carrier proteins and channel protein [high to low concentration]). Active transport is the process of moving molecules against the concentration gradient through the use of ATP (NA-K pump).
How can cells spend ATP energy to transport water into a cell? [No membrane pumps for H20]
Cells indirectly spend ATP energy to transport water into a cell. The water is bound to ions, and when the ions are pumped in (requiring the use of ATP) the water is also pumped in as a side effect.
If the concentration of K+ is .24 M on the outside of a membrane and .25 M inside, but there is excess negative charge on the inside of the membrane, would K+ ions move through a passive ion channel towards the inside or towards the outside? Why?
K+ ions would move inside because the concentration gradient is very similar. The electric charge gradient takes precedence in this case.
Name 3 molecules that can diffuse directly through a phospholipid bilayer, not through a protein.
Hydrophobic molecules, small uncharged polar molecules (H2O and glycerol), molecules such as O2 and CO2
Name 2 different molecules that cannot diffuse through the bilayer: for each tell why not.
Large, uncharged polar molecules like glucose; they are too big to fit through; Ions (they can't pass the nonpolar interior of the phospholipid bilayer).
Tell the difference between transport proteins that are channels (fluid-filled pores) and transport proteins that act as carriers. (Both do facilitated diffusion).
Channel proteins provide hydrophobic corridors for water or small ions to pass through the membrane. Carrier proteins bind to specific molecules and change their shape to get the molecule across.
Explain the differences between these transport proteins in terms of number of items that can cross the membrane at once and their relative direction: uniport, symport, antiport.
Uniport proteins transport one item one direction. Symports transport two items the same direction. Antiports transport two items different directions.
Explain how protein phosphorylation is involved in active transport.
Protein phosphorylation works in active transport because the ATP is broken down, the P used to bind to a protein to change its shape, which then can help diffuse molecules across the transportation gradient.
Explain the sodium-potassium pump (the role of ATP, what ions transported to each side, etc).
A) 3 Cytoplasmic Na+ binds to the pump. B) Na+ binding stimulates phosphorylation by ATP. C) Phosphorylation causes the pump to change shape, expelling the 3 Na+ outside. D) 2 Extracellular K+ is bound to the pump, releasing the phosphate group. E) The pump returns to its original shape, releasing the 2 K+. F) Repeat.
In the protein-sucrose co-transport system (movement through a symport; this is sometimes called secondary active transport), which gradient pulls sucrose into a cell even though sucrose is moving against its concentration gradient? Does ATP affect the co-transport protein (the symport) directly?
The H+ gradient pulls sucrose into the cell even though sucrose is moving against its concentration gradient. ATP is involved in this system only indirectly—it is used to move H+ outside the membrane.
A nerve cell membrane at rest has many gradients across it, as indicated by Figure 48.10 (over) and the inside is negative with respect to the outside. A) Name a pump that could help create/maintain some of the ion gradients shown. B) If membrane protein gates for Na+ ions were suddenly open, would Na+ flow into or out of the cell? C) If membrane protein gates for K+ ions were suddenly open, would K+ flow into or out of the cell?
A) NaK pump B) The Na would flow into the cell (Na is more concentrated on the outside of the cell) C) K would flow outside the cell (K is more concentrated on the inside of the cell)
Compare and contrast exocytosis and endocytosis. What is receptor-mediated endocytosis?
Endocytosis and exocytosis are both methods of transporting bulk molecules across the membrane. Exocytosis is the excretion of molecules. Endocytosis is the engulfing of large molecules (phagocytosis [cell eating] and pinocytosis [cell drinking]). Receptor-mediated endocytosis enables bulk amounts of specific things to be acquired, inward budding of vesicles with proteins with receptors specific to the molecules taken in.
Describe the structure of plasmodesmata. What can pass from cell to cell through plasmodesmata?
Plasmodesmata are channels that perforate plant cell walls that link each cell together. Cytosol, water, and small solutes can pass freely from cell to cell, but also specific proteins and RNA molecules.
The extra-cellular matrix of animal cells consists of what types of molecules?
The extra-cellular matrix consists of glycoprotein, proteins with covalently bonded carbohydrates, usually with a short chain of sugars.
Define and tell the function of the following animal cell-cell junctions: A) tight junctions, B) gap junctions, C) desmosomes.
A) Tight junctions occur when the membranes of neighboring cells are pressed tightly together, bound by specific proteins. These form seals that prevent leakage of extracellular fluid across a layer of epithelial cells; B) Gap junctions provide channels for the cytoplasm from one cell to another adjacent one. It is a special membrane protein that surrounds a pore through which ions, sugars, amino acids, and other small molecules may pass. These are necessary for communication.; C) Desmosomes function as rivets, fastening cells together into strong sheets. Intermediate filaments made of keratin proteins anchor desmosomes in the cytoplasm..
Define potential energy and kinetic energy, and give examples of each form.
Potential energy is the energy something possesses because of location or position. Example: water behind a dam. Kinetic energy is the energy of motion. Example: Water gushing over a dam.
Define these terms: oxidation, reduction. Explain electron transfer in redox reactions. What becomes oxidized? Reduced?
Oxidation is a loss of electrons. Reduction is a gain of electrons. In redox reactions, the reducing agent loses electrons and becomes oxidized. The oxidizing agent gains electrons and becomes reduced.
State the first and second laws of thermodynamics. What is entropy?
The first law of thermodynamics states that energy in the universe is constant, but energy constantly changes forms. The second law of thermodynamics states that every energy transformation increases the entropy of the system. Entropy is disorder, or randomness.
What does the second law of thermodynamics predict about changes in disorder (randomness)?
The second law of thermodynamics predicts that although order can increase locally, there is an unstoppable trend toward randomization.
Examine figure 8.5 and explain why each of the examples at the top of the figure has more free energy (potential energy) than the corresponding example at the bottom of the figure.
The person on the diving board has more potential energy because he has gravitational motion. Objects move spontaneously from a higher altitude to a lower one. The undiffused molecules have higher free energy because it has the capacity to diffuse until they are randomly dispersed. The top figure in the chemical reaction has more free energy because it has the capacity to react and break into smaller parts.
Use an example from figure 8.5 and explain why a system with higher entropy can do less work.
A system with higher entropy can do less work because it is more stable with less free energy; it just wants to sit there because it is already stable.
Use an example from figure 8.5 and explain why a system with more free energy is less stable.
A system with more free energy is less stable because it has more free energy and a greater work capacity; it has the potential to do more things instead of being stable.
Write the Gibbs free energy equation and state what each term means.
ΔG (the change in free energy) = ΔH (change in enthalpy [bond energy, heat energy] - T (temperature in Kelvin)ΔS (change in entropy [randomness, disorder]);
Compare ATP and ADP. Which contains more free energy? Which is more stable (less reactive?)
ATP has more free energy. ADP has less free energy and thus is more stable.
ATP hydrolysis is exergonic. Explain how ATP --> ADP + P provides energy for cell work.
When the bonds between the phosphate groups in ATP are broken to form ADP, energy (approximately 7.3) is released. This energy can be coupled with other reactions to power them.
What is the activation energy of a reaction? How does it relate to ΔG??
The activation energy of a reaction amount of energy it takes to get it started. It has nothing to do with ΔG.
What is the effect of adding a catalyst on the ΔG of a reaction? What is the effect of adding a catalyst on activation energy?
There is no effect on the ΔG when a catalyst is added. The activation energy is lowered when a catalyst is introduced (the reaction speeds up).
What does the term "induced fit" mean when used to describe enzymes?
Enzyme changes shape so active site fits substrates.
What, physically, can an enzyme do that makes it easier for a reaction to occur? Explain how an enzyme protein could thus help to "energy-couple" two reactions together.
The enzyme stresses bonds of the substrate to make it "fit"; the enzyme lines up substrates in their correct positions to "bind snugly" to promote the reaction. The enzymes would have to be in very close proximity and occur at the exact same time for an "energy coupled" reaction to occur.
From what you know about proteins, explain how enzymes can be highly substrate-specific.
The specificity of an enzyme results from its 3D shape—a consequence of its amino acid sequence.
From what you know about proteins, explain why enzymes have optimal pH and temperatures.
At high (optimal) temperatures the substrates are moving around faster and binding faster with the active site. At too high of a temperature the enzyme can denature and become inactive (loses its shape-specificity of a certain substrate). Optimal pH allows the enzyme to have perfect conditions for reactions; too high or too low of a pH can hinder enzyme activity by stressing the bonds and eventually denaturing the enzyme.
Explain the difference between competitive and non-competitive enzyme inhibitors.
Competitive inhibitors bind at the enzyme's active site to "block" the binding of a particular substrate. A non-competitive inhibitor binds at a different spot on the enzyme to change its shape and therefore make the enzyme lose its shape-specificity with the substrate.
Allosteric inhibitors slow reaction rates. Explain specifically how they affect enzymes. How do allosteric activators have a different effect than allosteric inhibitors?
Allosteric inhibitors deactivate an enzyme by binding to a regulatory site and changing the enzyme to its inactive form. Allosteric activators activate an enzyme by binding to a regulatory site and change the enzyme to its active form.
Explain the concept of feedback inhibition of enzymes, using the example of end-product inhibition of an enzyme-controlled pathway. What's the advantage of having the end-product inhibit an enzyme early in the pathway (first committed step) rather than later?
When the end product of a reaction pathway achieves its desired concentration, the end product of the reaction binds allosterically to the first enzyme to stop production. The first enzyme is inhibited so as not to waste resources in production (so there are no intermediate products).
What are coenzymes (such as NAD, FAD), and what is their function?
Coenzymes are enzyme helpers that are dinucleotides from B vitamins in a diet. They carry electrons and shuttle H atoms in redox reactions.
What is the main function of the processes that altogether we call cellular respiration?
To make ATP!
What are coenzymes (such as NAD, FAD, coenzyme A) and what is their function?
Coenzymes are enzyme helpers that are dinucleotides from B vitamins in a diet. They carry electrons and shuttle H atoms in redox reactions.
What type of organic molecule is NAD? What kind of enzyme (name) oxidizes NAD? Of NAD+ and NADHH+ which has more free energy? Which of the two is more oxidized? More reduced?
NAD is a nucleic acid. Dehydrogenase oxidizes NAD. NADHH+ has more free energy (reduced forms of things have more free energy). NAD is oxidized, NADHH+ is reduced.
The two general ways of making ATP from ADP + phosphate are substrate-level phosphorylation and oxidative phosphorylation. Explain how each occurs (from where does the phosphate come? What is the exergonic process that drives this endergonic phosphorylation?).
Substrate-level phosphorylation begins with a phosphate attached to a "substrate" and ends with phosphate in ATP. Oxidative phosphorylation begins with phosphate ions loose in the solution. This always involves a proton gradient across the membrane and a proton complex called ATP synthase. This process is known as chemiosmosis.
List the molecules that enter glycolysis and those produced in glycolysis.
Glucose, 2 ATP, and NAD go into glycolysis. 4 ATP, 2 NADH, and Pyruvate are produced by glycolysis.
What is the oxidized product of glycolysis? What is the reduced product of glycolysis?
The oxidized product of glycolysis is pyruvate. The reduced product of glycolysis is NADH.
When cells have plenty of glucose but no O2, why don't they just stop at pyruvic acid?
They don't stop at pyruvic acid because going into fermentation (although yielding no ATP) will produce tons of reduced electron carriers (NADH and FADH).
Explain "glycolysis has an energy-investment phase followed by an energy-payoff phase."
In order to produce ATP, ATP must be invested into the reaction. There is a moment where nothing happens and no ATP is produced, but in the end, ultimately 4 ATP (net 2 ATP) is produced.
The enzyme PFK catalyzes reaction #3 of glycolysis and is the main regulator of the process. Explain how AMP and ATP regulate PFK.
AMP is the allosteric activator of PFK. ATP is the allosteric inhibitor of PFK. When there is too much ATP, it will act in feedback regulation and allosterically bind to PFK, halting production. When there is not enough ATP, AMP will activate PFK and production will continue.
Why is fermentation necessary under conditions of no O2? What is the difference between lactic acid fermentation and alcohol fermentation? Which of these produces ATP from pyruvic acid breakdown?
Fermentation provides a mechanism in which some cells can oxidize organic fuel and generate ATP without oxygen. In alcohol fermentation pyruvate is converted to ethanol in two steps: 1) Releases carbon dioxide from the pyruvate to form acetaldehyde. 2) Acetaldehyde is reduced by NADH to ethanol. This regenerates NAD for glycolysis. During lactic acid fermentation, pyruvate is reduced by NADH to form lactate as an end product with no release of CO2. Lactic acid fermentation produces ATP from pyruvic avid breakdown.
List the molecules that enter Krebs Cycle and those released from Krebs Cycle (you don't have to know the intermediates). Why is it called the citric acid cycle? Is O2 used directly in Krebs Cycle?
Acetyl, NAD and FAD enter the Krebs Cycle. CO2, FADH and NADH exit the Krebs Cycle. It is sometimes called the citric acid cycle because Acetyl CoA turns into citric acid during step 2. 02 is not directly used in the Krebs Cycle but the lack of oxygen will put the Pyruvate into fermentation instead of the Kreb's Cycle.
In cellular respiration, exactly where (in what steps) is O2 used and where is CO2 produced?
0¬2 is used in oxidative phosphorylation and CO2 is produced in the Krebs Cycle.
What carriers bring electrons into the electron transport chain? What is the final acceptor of electrons in the electron transport chain?
Reduced electron carriers (NADH and FADH) bring electrons into the ETC. O2 is the final acceptor of electrons in the ETC.
What specific reactions will stop if the cell has no oxidized NAD or oxidized FAD?
Glycolysis and the Krebs Cycle
In the oxidation of methane (CH4), what becomes oxidized and what becomes reduced?
CH4 becomes oxidized and 02 becomes reduced.
Cyanide can bind to, and permanently reduce, cytochrome a3, the last cytochrome in the electron transport chain, so a3 can no longer accept electrons. How, therefore, is cyanide a "respiratory" poison?
Cyanide is a respiratory poison because it also permanently reduces cytochrome a3. The electrons get backed up and the ETC chain stops. When the electrons cease flowing, the H+ ions cannot go through the intermembrane space and the energy is lost as heat.
A respiratory "uncoupling agent" allows H+ ions to diffuse across the inner mitochondrial membrane at sites other than through ATP synthase. Explain the effects of such an agent.
These agents greatly reduce the mitochondria's ability to make ATP through oxidative phosphorylation because if all the H+ ions are diffusing back through the membrane in sites other than ATP synthase, there are less H+ ions that CAN go through ATP synthase.
How does the structure of the mitochondrion help its function in cellular respiration?
Mitochondria have a double-layered membrane. These two layers allow there to be intermembrane space, a place for the H+ ions to go and wait to go through ATP synthase. The inner membrane also bends and curves upon itself, which allows a greater surface area for oxidative phosphorylation to occur.
The complete aerobic respiration of one glucose molecule provides energy for 36-38 ATP. Tell which steps produce ATP and whether it is by substrate-level or oxidative phosphorylation.
Glycolysis produces 2 ATP through substrate-level phosphorylation; the Krebs cycle produces 2 ATP through substrate level-phosphorylation; the ETC and chemiosmosis produces about 32-34 ATP through oxidative phosphorylation.
What is the general reaction of photosynthesis? Overall, what becomes reduced?
The general reaction of photosynthesis is CO2 + H2O --(light energy)--> sugars + 02. Overall, carbon becomes reduced.
With what molecules do plant cells absorb light? Where, specifically, are these located?
Plant cells absorb light through chlorophyll, which are specifically located in the chloroplasts.
What two products of non-cyclic photophosphorylation are NOT produced in cyclic?
NADPH and 02.
Consider the light reactions and the Calvin Cycle as two phases of photosynthesis, and name the substances that are used and produced in each phase. How are the two phases linked together?
In the light reactions of photosynthesis, light energy is trapped and transformed into chemical bond energy. In the Calvin cycle, sugar is produced. The two phases are linked together because the sugar can only form if NADPH and ATP (from the light cycle) are present.
Chloroplasts generally have both cyclic and non-cyclic photophosphorylation—what's the difference?
In cyclic photophosphorylation, electrons go through the ETC and return to a chlorophyll in the same photosystem. A proton gradient is built across the thylakoid membrane and ATP synthase is used to produce ATP. In non-cyclic photophosphorylation, electrons go through a different ETC ending up in chlorophyll in a different photosystem (H+ ion gradient still formed, ATP made by chemiosmosis). Light is absorbed, and the electrons enter another ETC, ending up by reducing NADP into NADPH2, which then inters the Calvin cycle.
Be able to distinguish within each of the following pairs of terms: A) endergonic reaction and exergonic reaction; B) Positive ΔG and negative ΔG; C) change in bond energy and change in entropy.
A) Endergonic reactions require energy. The products have more energy than the reactants. Exergonic reactions give off energy. The products have less energy than the reactants. B) Positive ΔG is an endergonic reaction. Negative ΔG is an exergonic reaction and is spontaneous. C) Change in bond energy is a change in heat energy, change in entropy is a change in disorder or randomness.
What are energy-coupled reactions? Give examples of energy-coupling in cells using the ATP/ADP cycle and through phosphorylation.
Energy-coupling is the use of an exergonic process to drive an endergonic one. An example of this is the coupling of the H+ gradient flowing through ATP synthase (exergonic) with the formation of ATP (endergonic.
The energy from the hydrocarbon chain of fats enters respiration at which point? In the form of what molecule?
It enters respiration at the Krebs Cycle in the form of Acetyl.
Why does the Krebs Cycle (citric acid cycle) stop under anaerobic conditions (no O2)?
The Krebs Cycle stops under anaerobic conditions because although it is the ETC that needs oxygen directly, when it stops production of oxidized NAD and FAD stops also. These are needed in the Krebs cycle.
Yeast cells can conduct either aerobic or anaerobic respiration, depending on conditions. (In the case of anaerobic, they do alcohol fermentation.) Why do yeasts use much more glucose per ATP produced in anaerobic respiration than in aerobic?
Aerobic is much more efficient than anaerobic respiration. To gain the same amount of ATP, yeast cells need to use more glucose and run through more chains of glycolysis/fermentation.
In "carbon fixation", CO2 is joined to what molecule to begin the Calvin cycle?
CO2 is joined to a five carbon sugar named ribulose biphosphate (RuBP).
What is the Calvin Cycle reaction catalyzed by the enzyme "rubisco"?
Carbon fixation
Compare and contrast mitochondria and chloroplasts, in structure and reactions within them.
Both generate ATP by chemiosmosis; both have ETCs, both have potential energy in the form of a H+ ion gradient, both have ATP synthase, both have similar cytochromes. Mitochondria use food as their energy source and chloroplasts use light. In the mitochondria, the H+ gradient is in the intermembrane space while in the chloroplasts' H+ gradient is in the thylakoid space.
Is light used directly in Calvin cycle reactions? Why will they stop in the absence of light?
Light isn't use directly in the Calvin cycle reactions, but they will stop in the absence of light because the products produced in the light cycle (NADPH and ATP, which requires light) will be absent.
O2 and CO2 compete with each other for rubisco's active site. If O2 is very abundant, rubisco binds it and starts what process? Why is this process a drain on plant cell resources?
Photorespiration; this process is such a drain on plant cell resources because no ATP or sugars are produced but all the materials are used up.
What are two types of adaptations to reduce photorespiration? How do they differ?
CAM plants and C4 plants; CAM plants separate CO2 by timing (storing CO2 by night and releasing it by day) and C4 plants separate CO2 by location (CO2 is kept in different cells).
Why isn't all of the reduced Calvin cycle product (G3P) used to make sugar as soon as it is made?
G3P not only is used to make sugars but it is also used by the cell as "raw material" for a lot of other processes (to build amino acids,etc...). It is also used to replenish the cycle and complete the chain so that the Calvin cycle can actually be a cycle.
In photosynthesis, does ATP synthesis occur by substrate-level or by oxidative phosphorylation?
Oxidative phosphorylation.