I'm pretty sure these materials are like the Rosetta Stone of note taking. Thanks Marie!!!
LEARNING OBJECTIVES FOR CARBS, NUCLEOTIDES, & ENZYMES (Ch. 3/6) 1. Recognize the general structures of monosaccharides, amino acids, and nucleotides, and describe the chemical properties of each. 3.2.1, 3.3.2, 3.4.1 monosaccharides: simplest sugar, C-H bonds with as few as 3 carbon atoms (plays central role in energy storage=6 carbons); linked by covalent bonds— structural isomers determine sweetness
amino acids: central carbon atom, amino group (-NH2), carboxyl group (-COOH), functional side group (R); linked by peptide bonds—chemical character is determined by R group
nucleotides: 5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines-AG or pyrimidines-CT); linked by phosphodiester bonds—OH on sugar ring = RNA, H on sugar ring = DNA
2. Differentiate between glycosidic linkage, peptide bond, and phosphodiester bond.
glycosidic linkage: covalent bond between a sugar molecules and another group (may or may not be carbohydrate)
peptide bond: covalent bond between two amino acids
phosphodiester bond: covalent bond between nucleotides to form nucleic acids 3. Describe the functions of carbohydrates in cells. 3.2
-building blocks for carbon skeletons
-cell identity on outer surface
-energy storage (glucose, glycogen, starch—alpha linkage)
-structure (cellulose, chitin—beta linkage)
4. How do the structures of starch, glycogen and cellulose affect their functions? 3.2
-starch and glycogen: alpha branching, allows for longer food reserve, easier to be broken due to branching rather than linkage
-cellulose: beta linkage, stronger than alpha branching à linkage is better for structures; resists tension, compression, and hydrolysis
5. Describe the functions of nucleotides in cells. 3.4.4
-nucleic acid building blocks (DNA, RNA)
-cellular energy carriers (ATP, GTP)
-electron acceptor/donor (NAD, NADP, FAD)
-carrier of chemical groups (ATP, CoA, UDP)
-regulatory (signaling) molecules (GTP, cAMP)
6. Explain how a catalyst increases the rate of a chemical reaction. 6.4.1 A catalyst lowers activation energy and makes the transition state more stable. 7. Describe the characteristics of enzymes. 6.4.2
Don't forget about the age old question of biol 201 concordia
-mostly proteins, some RNA
-lowers activation energy by stressing specific bonds
-different enzymes catalyze different, specific reactions
-can be reused
8. Explain how enzymes lower activation energies. 6.4.2
Enzymes stress specific chemical bonds in order to allow new bonds to form more easily.
9. Distinguish between substrate, active site, enzyme-substrate complex, and induced fit. 6.4.3 Don't forget about the age old question of algebra notes for 9th grade
If you want to learn more check out mkt 250
substrate: the ligand that binds to an enzyme
active site: the site where the substrate (ligand) binds to an enzyme enzyme-substrate complex: the substrate fits into the enzyme and binds induced fit: the term that describes how the enzyme must alter its shape slightly for the substrate to fit and bind properly
10. Identify the different types of molecules that may act as enzymes. 6.4.4 -RNA: ribozymes may catalyze other molecules (intermolecular catalysis) or themselves (intramolecular catalysis)—rRNA play a key catalytic role in RNA production, with proteins providing the framework to correctly orient RNA subunits with respect to each other
11. Distinguish between enzyme cofactors and coenzymes. 6.4.4 -cofactor: additional chemical component, often metal ions found in active site, that assist enzyme function
-coenzyme: cofactor that is a nonprotein, organic molecule
12. Explain the effects of pH and temperature on enzyme activity. 6.4.5 -pH: when pH is not at optimal pH, the rate is not as fast as it has the potential to be. High pH = ionization, low pH = nonionization (affects ionization of R groups) -temperature: increase in temp increases collisions, thereby speeding up rate, BUT when the temperature gets too high, the protein will change shape (denaturation/unfolding)—an increase in temperature can cause renaturation/refolding in some cases If you want to learn more check out the average victim of anorexia nervosa is ____ percent below normal body weight.
13. Distinguish between competitive and noncompetitive enzyme inhibition. 6.4.5 competitive enzyme: will block substrate at active site
noncompetitive enzyme: will block substrate by entering enzyme at different site than where substrate binds
14. Explain allosteric regulation of enzymes. 6.4.5
Allosteric regulation can activate or inhibit enzymes—can bind to an area other an active site to stabilize an active form or inactive form (noncovalent/reversible) 15. Explain the control of protein function by phosphorylation. 9.1.3 Phosphorylation acts as a switch; if the protein is “off” before adding a phosphate, phosphorylation will turn it “on” and vice versa. The concentration of kinase will affect amount of phosphorylation (lots of kinase = lots of phosphorylation).
LEARNING OBJECTIVES FOR ENERGY AND METABOLISM (Ch. 6) 1. Define energy and distinguish between potential and kinetic energy. 6.1.1 -energy: capacity to do work Don't forget about the age old question of is the ability of persons, groups, or institutions to influence political developments.
-potential energy: energy of motion (active energy)
-kinetic energy: stored energy (energy at rest)
2. State the First Law of Thermodynamics. 6.2.1
Energy cannot be created or destroyed; it can only change from one form to another (e.g. potential to kinetic).
3. State the Second Law of Thermodynamics and describe how it applies to biological systems. 6.2.2
Disorder in the universe (i.e. entropy) is continually increasing. 4. Define entropy, enthalpy and free energy. Explain how chemical reactions can be predicted based on changes in free energy. 6.2.3
-entropy (S): disorder in the universe
-enthalpy (H): total energy contained in a molecule’s chemical bonds -free energy: availability of energy to do work with temperature and pressure constant; a positive change in free energy means the reaction will not be spontaneous/not favorable while a negative change in free energy means the reaction will be spontaneous/favorable. Don't forget about the age old question of What are you going to work on today?
5. Distinguish between endergonic and exergonic reactions. Explain what is meant by a spontaneous reaction. 6.2.3
-endergonic: requires energy, not spontaneous, typically +ΔG/+ΔH/-ΔS -exergonic: doesn’t require energy to occur, spontaneous, typically -ΔG/-ΔH/+ΔS -spontaneous reaction: additional energy is not required for the reaction to occur *6. Recognize the general structures of nucleotides and describe their chemical properties. 3.4.1
-5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines-AG or pyrimidines-CT); linked by phosphodiester bonds—OH on sugar ring = RNA, H on sugar ring = DNA
*7. Describe the functions of nucleotides in cells. 3.4.4
-nucleic acid building blocks (DNA, RNA)
-cellular energy carriers (ATP, GTP)
-electron acceptor/donor (NAD, NADP, FAD)
-carrier of chemical groups (ATP, CoA, UDP)
-regulatory (signaling) molecules (GTP, cAMP)
8. Describe the three main kinds of work carried out by cells. Fig 6.7 -chemical: biosynthesis, bioluminescence
-transport: voltage, concentration
9. Describe the structure of ATP and explain how ATP hydrolysis drives endergonic reactions. 6.3.1
-structure: 5-carbon sugar (ribose), 2 carbon-nitrogen rings (adenine), 3 phosphates
-ATP hydrolysis driving endergonic reactions: if cleavage of ATP ‘s terminal high energy bond releases more energy than the other reaction consumes, the two reactions can be coupled, resulting in a net release of energy (-ΔG)--almost all endergonic reactions require less energy than released by ATP hydrolysis, so ATP is able to provide most energy a cell needs,
10. Describe energy coupling using ATP hydrolysis.
Energy coupling is the transfer of energy from an exergonic process to an endergonic process. Free energy from ATP hydrolysis is used to drive endergonic reactions.
LEARNING OBJECTIVES FOR CELL ENERGY HARVEST (CH. 7) 1. Distinguish between oxidation and reduction reactions. 6.1.2, 7.1.1 -LEO says GER (Lose Electrons Oxidation/Gain Electrons Reduction) -oxidation: process by which an atom or molecule loses an electron--Lose Electrons Oxidation; atom or molecule that accepts an electron is an oxidizing agent
-reduction: process by which an atom or molecule gains an electron--Gains Electrons Reduction; atom or molecule that donates or gives away an electron is a reducing agent
2. Describe the structure of NAD, its role, and the role of B vitamins in energy metabolism. 7.1.2
Structure: 2 nucleotides (nicotinamide monophosphate-NMP +adenosine monophosphate-AMP) joined head to head; NMP is active part--readily reduced (accepts electrons)
NAD role: major electron carrier; when NAD is reduced by accepting 2
B vitamin role: B Vitamins act as coenzymes that are crucial in aiding enzymes in ATP and fatty acid production.
3. Explain the process of glycolysis, including reactants, products, and energy yield. 7.2.1
Process: anaerobic; glucose is converted into 2 pyruvates; each molecule of glucose yields 2 ATP in this process; consists of 10 rxns, first 5 in energy investment phase (priming, endergonic) and second 5 in energy payoff phase (splitting, exergonic)
Reactants: glucose, 2NAD+, 4 electrons, 2 ATP, 4 H+
Products: 2H+, pyruvate, 2H2O, 4 ATP (total yield of 2 ATP), 2NADH Energy yield: 2 ATP
4. Describe two ways in which ATP is generated in cellular respiration. 7.1.3 (p. 134-135)
a. Substrate-level phosphorylation: ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate or substrate; in glycolysis, the chemical bonds of glucose are shifted around in reactions that provide the energy required to form ATP by substrate-level phosphorylation
b. Oxidative phosphorylation: ATP is synthesized by ATP synthase (which is both an enzyme and a channel) using energy from a proton gradient that is formed by high-energy electrons harvested by the oxidation of glucose and passing down an electron transport chain (how ATP is produced most by eukaryotes and aerobic prokaryotes)
5. Name and describe the four stages of cellular respiration, identifying specifically where in the cell (prokaryotic and eukaryotic) each occurs. Figure 7.5; 7.2. 7.3, 7.4
a. GLYCOLYSIS: cytoplasm in euk and prok
b. PYRUVATE OXIDATION: mitochondria in euk, in cytoplasm and at plasma membrane in prok
c. KREBS CYCLE/CITRIC ACID CYCLE/TCA: mitochondrial matrix/inner membrane of mitochondria in euk, cytosol in prok
d. OXIDATIVE PHOSPHORYLATION: mitochondrial cristae in euk, cell membrane in prok
6. Describe two different metabolic pathways that pyruvate can enter. 7.2.2, 7.3.1, 7.7.2
a. Oxidation of pyruvates--cleaves off one of pyruvate’s 3 carbons which becomes CO2, remaining 2-carbon compound (acetyl) attaches to coenzyme A to produce acetyl-CoA. In this rxn, 2 electrons and 1 proton are transferred to NAD+ to reduce it to NADH with a 2nd proton donated.
b. Fermentation--uses reduction of all or part of pyruvates to oxidize NADH back to NAD+, executed copiously by bacteria
7. Identify the reactants and products of pyruvate oxidation. 7.3.1 (p. 139) -Reactants: pyruvates, NAD+, CoA
-Products: acetyl-CoA, NADH, CO2, H+
8. Identify the reactants and products of the Krebs cycle and describe its role. 7.3.2 (p.139-140)
-Reactants: acetyl-CoA, 3NAD+, FAD, ADP + P, OAA
-Products: 1 ATP, 3 NADH, 1 FADH2, CO2, CoA-SH, OAA
9. Describe how the movement of electrons along the electron transport chain generates a proton gradient. 7.4.1 (p.143)
-The first protein to receive the electrons is the membrane-embedded enzyme NADH dehydrogenase.
-A carrier called ubiquinone then passes the electrons to a protein-cytochrome complex called the bc1 complex.
-The electrons are then carried by cytochrome C to the cytochrome oxidase complex. This complex uses 4 electrons to reduce a molecule of oxygen; each oxygen then combines with 2 protons to form water. -Protons are produced when electrons are transferred to NAD+.
-As the electrons are passed along the ETC, the energy they release transports protons out of the matrix and into the intermembrane space (concentration gradient).
***The flow of highly energetic electrons induces a change in the shape of pump proteins, causing them to transport protons across the membrane. The increasing electronegativity with each pump propels the protons down the ETC.
10. Explain chemiosmosis, including a description of how ATP synthase works. 7.4.2 (p.144)
-Chemiosmosis: ATP is driven by a diffusion force similar to osmosis. Because the mitochondrial matrix is negative compared with the intermembrane space, protons are attracted to the matrix. The higher outer concentration of protons drives protons back in by diffusion, but because membranes are relatively impermeable to ions, this occurs slowly.
-ATP synthase: enzyme channel that uses the energy of the gradient to catalyze the synthesis of ATP; the new ATP is transported by facilitated diffusion to the many places in the cell where enzymes require energy to drive endergonic reactions
11. Explain the maximum yield of ATP from a molecule of glucose and the efficiency of this energy conversion. 7.5
The maximum yield is approx. 30-32 ATP. oxidizing glucose to pyruvates via glycolysis yields 2 ATP directly, and 2 × 2.5 = 5 ATP from NADH, oxidation of pyruvates to acetyl-CoA yields another 2 × 2.5 = 5 ATP from NADH, the Krebs
cycle produces 2 ATP directly, 6 × 2.5 = 15 ATP from NADH, and 2 × 1.5 = 3 ATP from FADH2; NADH produced in the cytoplasm by glycolysis needs to be transported into the mitochondria by active transport, which costs one ATP per NADH transported (causing 30 vs 32 ATP)
12. Explain why the maximum yield of ATP is rarely obtained. 7.8, Figs. 23.7, 31.1 (symport)
The max yield is limited by the fractional number of ATP produced by NAHD and FADH2, which NADH shuttle transported to the mitochondria, the other uses the proton motor force is used for (moving ADP to matrix, proton symport), and intermediates in anabolism.
13. Explain feedback regulation and describe two keys points at which it is used to regulate cellular respiration. 6.5.2, 7.6.1 (The 3rd paragraph in 6.5.2, beginning with ”In the hypothetical pathway…”, refers to something that is not in our text.) -Feedback regulation: control mechanism whereby an increase in the concentration of some molecules inhibits the synthesis of that molecule. a. in glycolysis: control point at phosphofructokinase (which catalyzes the conversion of fructose phosphate to fructose bisphosphate); first reaction of glycolysis that is not readily reversible; ATP itself and citrate (Krebs cycle intermediate) are allosteric inhibitors--high levels of both ATP and citrate inhibit phosphofructokinase. When ATP is in excess or when the Krebs cycle is producing citrate faster than it is being consumed, glycolysis is slowed. b. in pyruvate oxidation: control point at pyruvate dehydrogenase (which converts pyruvate to acetyl-CoA); inhibited by high levels of NADH; another control point in the Krebs cycle is citrate synthetase (which catalyzes the first reaction, the conversion of oxaloacetate and acetyl-CoA into citrate)--high levels of ATP inhibit citrate synthetase (as well as phosphofructokinase, pyruvate
dehydrogenase, and two other Krebs cycle enzymes), slowing down the entire catabolic pathway.
14. Describe two ways that prokaryotes can produce ATP entirely anaerobically. 7.7
-anaerobic respiration: many prokaryotes use sulfur, nitrate, carbon dioxide, or even inorganic metals as the final electron acceptor in place of oxygen--amount of free energy released is lower than with oxygen because of lower electronegativity; ATP production is less
-fermentation: the electrons generated by glycolysis are donated to organic molecules
15. Describe fermentation, explain its role, and distinguish between ethanol and lactic acid fermentation. 7.7.2
-Fermentation: anaerobic process that occurs after pyruvate has been produced through glycolysis; allows cells to regenerate NAD+ for glycolysis -Ethanol fermentation: occurs in yeast, the molecule that accepts electrons from NADH is derived from pyruvates, the end-product of glycolysis, Yeast enzymes remove a terminal CO2 group from pyruvate through decarboxylation, producing a 2-carbon molecule called acetaldehyde. The CO2 released causes bread made with yeast to rise. The acetaldehyde accepts a pair of electrons from NADH, producing NAD+ and ethanol, source of the ethanol in wine and beer -Lactic acid fermentation: regeneration of NAD+ in the absence of oxygen without decarboxylation; for example, muscles use the enzyme lactate dehydrogenase to transfer electrons from NADH back to the pyruvates that is produced by glycolysis. This reaction converts pyruvates into lactic acid and regenerates NAD+ from NADH, allowing glycolysis to continue as long as glucose is available
16. Briefly describe how proteins and fats can be used to make ATP in cellular respiration. 7.8
-Proteins: first broken down into their individual amino acid (deamination), and a series of reactions converts the carbon chain that remains into a molecule that enters glycolysis or the Krebs cycle. The reactions of cellular respiration then extract the high-energy electrons from these molecules and put them to work making ATP
-Fats: broken down into fatty acids plus glycerol, oxidized in the matrix of the mitochondrion. Enzymes progressively remove 2-carbon acetyl groups from the terminus of each fatty acid, nibbling away at the end until the entire fatty acid is converted into acetyl groups (figure 7.22). Each acetyl group is combined with coenzyme A to form acetyl-CoA. This process is known as β oxidation. This process is oxygen-dependent, which explains why aerobic exercise burns fat, but anaerobic exercise does not.
How much ATP does the catabolism of fatty acids produce? Let's compare a hypothetical 6-carbon fatty acid with the 6-carbon glucose molecule, which we've said yields about 30 molecules of ATP in a eukaryotic cell. Two rounds of β oxidation would convert the fatty acid into three molecules of acetyl-CoA. Each round requires one molecule of ATP to prime the process, but it also produces one molecule of NADH and one of FADH2. These molecules together yield four molecules of ATP (assuming 2.5 ATPs per NADH, and 1.5 ATPs per FADH2). The oxidation of each acetyl-CoA in the Krebs cycle ultimately produces an additional 10 molecules of ATP. Overall, then, the ATP yield of a 6-carbon fatty acid is approximately: 8 (from two rounds of β oxidation) – 2 (for priming those two rounds) + 30 (from oxidizing the three acetyl-CoAs) = 36 molecules of ATP. Therefore, the respiration of a 6-carbon fatty acid yields 20% more ATP than the respiration of glucose.
Moreover, a fatty acid of that size would weigh less than two-thirds as much as glucose, so a gram of fatty acid contains more than twice as many kilocalories as a gram of glucose. You can see from this fact why fat is utilized as a storage molecule for excess energy in many types of animals. If excess energy were
stored instead as carbohydrate, as it is in plants, animal bodies would be much heavier.
Chapter 8 Photosynthesis
1. Describe the four ways that organisms obtain carbon and energy. 23.4.1 a. Photoautotroph: energy source = light; carbon source = CO2, HCO3-, or related compound
2. Write the balanced equation for photosynthesis and identify which molecules are oxidized or reduced. 8.1.1
6CO2 + 12H2O + sunlight → C6H12O6 (glucose) + 6H2O + 6O2 In photosynthesis, CO2 is reduced to glucose using electrons gained from the oxidation of water. The oxidation of H2O and the reduction of CO2 requires energy that is provided by light.
3. Compare the structure of a chloroplast with that of a mitochondrion. 8.1.2 A mitochondrion's complex structure of internal and external membranes contribute to its function. The same is true for the structure of the chloroplast. The internal membrane of chloroplasts, called the thylakoid membrane, is a continuous phospholipid bilayer organized into flattened sacs that are found stacked on one another in columns called grana (singular, granum). The thylakoid membrane contains chlorophyll and other photosynthetic pigments for capturing light energy along with the machinery to make ATP. Connections between grana are termed stroma lamella. Surrounding the thylakoid membrane system is a semiliquid substance called stroma. The stroma houses the enzymes needed to assemble organic molecules from CO2 using energy from ATP coupled with reduction via NADPH. In the thylakoid membrane, photosynthetic pigments
are clustered together to form photosystems, which act as large antennas, gathering the light energy harvested by many individual pigment molecules.
4. Describe the endosymbiotic origin of chloroplasts. 24.1.3
All chloroplasts are likely derived from a single line of cyanobacteria, but the organisms that host these chloroplasts are not monophyletic. This apparent paradox is resolved by considering the possibility of secondary, and even tertiary endosymbiosis. Red and green algae both obtained their chloroplasts by engulfing photosynthetic cyanobacteria. The brown algae most likely obtained their chloroplasts by engulfing one or more red algae, a process called secondary endosymbiosis.
5. Identify specifically the location of the light reactions and carbon fixation in the chloroplast.
-light reactions: photosystems (photosynthetic pigments clustered together in thylakoid membrane)
-carbon fixation: stroma
6. Identify the reactants and products of the Calvin cycle 8.6.2 -reactants: 6CO2, 18ATP, 12NADPH, H20
-products: 2 G3P, 16 Pi, 18 ADP, 12 NADP+
7. Describe the three major phases of the Calvin cycle and the role of Rubisco. 8.6.1, 8.6.2
a. Carbon fixation: generates 2 molecules of PGA
-3 RuBP + 3 CO2 → 6 PGA
b. Reduction: PGA is reduced to G3P by reverse-glycolysis rxns -6 PGA + 6 ATP + 6 NADPH → 6 G3P
c. Regeneration: PGA is used to regenerate RuBP
-5 G3P + 3 ATP → 3 RuBP
**G3P is product; 3 turns of cycle are needed to produce one molecule of G3P; 6 turns needed to synthesize one glucose molecule
-Rubsico: enzyme that carries out carbon fixation; catalyzes primary chemical reaction by which inorganic enters the biosphere; 16-subunit enzyme found in stroma; most abundant protein on earth, though slow
8. Describe the nature of electromagnetic radiation and visible light. 8.3.1 Light is a form of electromagnetic energy. The wave nature of light produces an electromagnetic spectrum based on wavelength and frequency. The shorter the wavelength, the greater the energy. Visible light occupies a very small part of the spectrum, approx. 400 nm to 740 nm (VIBGYOR--violet, indigo, blue, green, yellow, orange, red--with violet at 400 nm and red at 740 nm).
9. Identify which wavelengths/colors of visible light are most effective in photosynthesis. 8.3.2
Chlorophyll a and chlorophyll b absorb violet-blue and red light best. Neither absorb photons with wavelengths between approx. 500-600 nm; rather, light of these wavelengths get reflected. Chlorophyll b’s absorption spectrum is shifted toward the green wavelengths. Because chlorophyll b can absorb green wavelength photons that chlorophyll a cannot, this greatly increases the proportion of photons in sunlight that plants can harvest. The action spectrum (relative effectiveness of different wavelengths of light in promoting photosynthesis corresponds to the absorption spectrum of chlorophylls.
10. Identify the major pigments involved in plant photosynthesis and the roles of each. 8.3.2, 8.3.3
-chlorophylls (principal photosynthetic pigments): absorb photons within narrow energy ranges (violet-blue and red) at high efficiency
-carotenoids (accessory pigments): absorb photons with a wide range of energies but with less efficiency, capture energy from light composed of
wavelengths not efficiently absorbed by chlorophylls; also can act as general purpose antioxidants to lessen damage of free radicals (aka certain redox rxns that occur in the chloroplast)
11. Differentiate between photosystem, antenna complex, reaction center. 8.4.2 -photosystem: an organized complex of chlorophyll, other pigments, and proteins that traps light energy as excited electrons
-antenna complex: complex of hundreds of pigment molecules in a photosystem that collects photons and feeds the light energy to a reaction center, light harvesting complex captures photons from sunlight and channels them to the reaction center chlorophylls. In chloroplasts, light-harvesting complexes consist of a web of chlorophyll molecules linked together and held tightly in the thylakoid membrane by a matrix of proteins. Varying amounts of carotenoid accessory pigments may also be present. The protein matrix holds individual pigment molecules in orientations that are optimal for energy transfer.
- The excitation energy resulting from the absorption of a photon passes from one pigment molecule to an adjacent molecule on its way to the reaction center . After the transfer, the excited electron in each molecule returns to the low-energy level it had before the photon was absorbed. Consequently, it is energy, not the excited electrons themselves, that passes from one pigment molecule to the next. The antenna complex funnels the energy of many excited electrons to the reaction center.
-reaction center: transmembrane protein complex in a photosystem that receives energy from the antenna complex, exciting an electron that is passed to an acceptor molecule.
• reaction center of purple photosynthetic bacteria is simpler than the one in chloroplasts--a pair of bacteriochlorophyll a molecules acts as a trap for photon energy, passing an excited electron to an acceptor precisely positioned as its neighbor. In this reaction center, what is transferred is the excited electron itself, and not just the energy, as was
the case in the pigment–pigment transfers of the antenna complex. This difference allows the energy absorbed from photons to move away from the chlorophylls, and is the key conversion of light into chemical energy.
12. Explain the functions of photosystem I and of photosystem II. Explain why two photosystems are required to reduce NADP. 8.5.2, 8.5.3 (p. 166-169) -Photosystem I: absorption peak = 700 nm; reaction center pigment = P700; transfers electrons ultimately to NADP+, producing NADPH; absorbs photons, exciting electrons used to reduce NADP+ to NADPH; electrons replaced by electron transport from photosystem II
-Photosystem II: absorption peak = 680 nm; reaction center pigment = P680; generates oxidation potential high enough to oxidize water to replace its electrons transferred to photosystem I; absorbs photons, exciting electrons that are passed to plastoquinone (PQ)
-Cyclic photophosphorylation limits electron sources. This noncyclic transfer of electrons allows the oxidation of water to serve as an alternative source of electrons. An overall flow of electrons from water to NADPH is created.
13. Explain how photosynthesis generates O2. 8.2.3 (p. 160)
van Niel’s generalized equation for photosynthesis: CO2 + 2H2A + light energy → (CH2O) + H20 + 2 A
In this equation, H2A = an electron donor (which is water in photosynthesis). The product “2 a” comes from splitting the H2A. In real life, O2 is the product of the splitting of H2O.
14. Describe how a proton gradient drives ATP synthesis in the chloroplast. 8.5.4 (p. 168)
The chloroplast has ATP synthase enzymes in the thylakoid membrane that form a channel, allowing protons to go back to the stroma. As protons pass out of the
thylakoid through the ATP synthase channel, ADP is phosphorylated to ATP and released into the stroma.
15. Compare chemiosmosis in chloroplasts and mitochondria. 7.4.2, 8.5.4 (p. 168)
Both use a proton gradient by electron transport that generates ATP by chemiosmosis. In mitochondria, the protons reenter the matrix through ATP synthase, and in chloroplasts, protons reenter the stroma.
16. Compare the roles of CO2 and H2O in respiration and photosynthesis. In cellular respiration, a glucose molecule combines with oxygen to form ATP with CO2 and H2O as waste products. Oxygen is absorbed and carbon dioxide is released. In photosynthesis, carbon dioxide and water are combined as reactants, yielding glucose and oxygen as products. Carbon dioxide is absorbed and oxygen is released.
PRACTICE TEST QUESTIONS:
Ch 6 and Redox
1. When you have a severe fever, what grave consequence may occur if the fever is not controlled?
a. destruction of your enzymes' primary structure
b. removal of amine groups from proteins
c. change in the tertiary structure of your enzymes
d. removal of the amino acids in the active sites of your enzymes e. binding of your enzymes to inappropriate substrates
2. The reaction phosphoenolpyruvate + ADP → pyruvate + ATP (Δ G = -7.5 kcal/mole)
a. is an endergonic reaction.
b. is not spontaneous.
c. Is an exergonic reaction
d. involves the transfer of a phosphate to phosphoenolpyruvate. e. involves the transfer of energy from ATP to phosphoenolpyruvate.
3. To form NADH from NAD+, two electrons and a proton are removed from an organic molecule. What term best describes the reaction in which electrons and a proton are removed from an organic molecule? a. Isomerization
4. Enzymes function as catalysts by
a. bringing the substrates together at the active site, in effect concentrating them.
b. bringing the substrates together at the active site correctly oriented for the reaction.
c. bringing the substrates together at the active site, in effect concentrating them and bringing the substrates together at the active site correctly oriented for the reaction.
d. none of the choices
5. Which of these statements is NOT a consequence of the second law of thermodynamics?
a. While the total amount of energy is unchanged, the energy lost as heat is no longer useful to the cell in doing work.
b. Reactions that occur spontaneously are those that increase the amount of useful energy in a system.
c. The amount of disorder in the universe is always increasing.
d. To maintain organization of a cell, a continual input of energy is required.
6. Once ATP donates its phosphate to a coupled reaction it becomes ADP. The ADP
a. becomes the needed potential energy source for another coupled reaction. b. is a waste product that must be broken down.
c. can be recharged in an endergonic reaction to form ATP. d. can be recharged in an exergonic reaction to form ATP. e. can be recharged in an oxidation reaction to form ATP.
7. Competitive inhibition of enzymes occurs
a. when the product, or other substances, instead of the reactant, bind to the active site of the enzyme.
b. when a substance other than the substrate binds to the active site of the enzyme.
c. when the product, instead of the reactant of a reaction binds to the active site.
d. when a substance binds to an enzyme at a site away from the active site. e. by blocking the production of an enzyme.
8. In this pathway, B C is coupled with ADP ATP. Categorize the reactions as endergonic or exergonic.
a. B C is endergonic and ADP ATP is exergonic.
b. B C is exergonic and ADP ATP is endergonic.
c. Both B C and ADP ATP are endergonic.
d. Both B C and ADP ATP are exergonic.
9. Which process involves an increase in the entropy of the system? a. formation of raindrops
b. any spontaneous process
c. freezing of ice
d. synthesis of cellulose
e. combustion of paper
10. The primary function of an enzyme or any biological catalyst is to a. reduce the energy of activation of a reaction and increase the rate of a reaction.
b. reduce the energy of activation of a reaction.
c. increase the rate of a reaction.
d. increase the rate of a reaction and change the direction of a reaction. e. change the direction of a reaction.
11. Which statement describes the currently accepted theory of how an enzyme and its substrate fit together?
a. As the product is released, the enzyme breaks down.
b. The active site is permanently changed by its interaction with the substrate.
c. The substrate is like a key that fits into the enzyme, which is like a lock. d. As the substrate binds to the enzyme, the shape of the protein changes to accommodate the reaction.
12. A particular reaction has a positive delta G. However, this reaction takes many years to proceed in the absence of enzyme. Why is this the case?
a. This reaction does not obey the second law of thermodynamics. b. The initial free energy of the reactants is much less than the final free energy of the products.
c. This reaction does not proceed spontaneously.
d. A certain amount of activation energy is required for the reaction to proceed.
13. What is the function of a protein kinase?
a. To phosphorylate GDP to generate GTP
b. To remove phosphate groups from proteins
c. To add phosphate groups from proteins
d. To cleave membrane phospholipids
14. A new antibiotic has been developed. It acts as a noncompetitive inhibitor. How will this antibiotic affect delta G for the enzyme-catalyzed reaction?
a. Delta G will increase
b. Delta G will decrease
c. Delta G will remain unaffected
15. Which statement is NOT true about how various conditions will effect the activity of an enzyme?
a. Higher temperatures generally increase the activity of an enzyme up to a point.
b. Above a certain range of temperatures, the protein of an enzyme is denatured.
c. A change in pH can cause an enzyme to be inactivated.
d. An enzyme's activity is generally reduced by an increase in substrate concentration.
e. When sufficient substrate is available, the active site will nearly always be occupied.
16 . Cells use ATP for which of the following processes? Check all that apply.
c. Concentration gradients
d. Intracellular transport
e. Protein phosphorylation
17. Zinc, an essential nutrient for most organisms, is present in the active site of the enzyme carboxypeptidase. The zinc most likely functions as a(n) a. competitive inhibitor of the enzyme.
b. allosteric activator of the enzyme.
c. cofactor necessary for enzyme activity.
d. noncompetitive inhibitor of the enzyme.
18. A serving of 30 grams of almonds may have 190 Calories listed on a nutrition label. This represents
a. enough energy to raise the temperature of 30 kilograms of water 190 °C. b. enough energy to raise the temperature of 190 grams of water 1 °C. c. enough energy to raise the temperature of 30 grams of water 190 °C. d. enough energy to raise the temperature of 190 kilograms of water 1 °C.
Ch 7 plus 8.1, 8.6, 23.4
1. Inside the chloroplast, where are organic molecules made? a. Inside the thylakoid
b. On the thylakoid membrane
d. on the cristae
e. Between the outer and inner membranes
2. Only a small amount of ATP is produced during glycolysis because most of the energy stored in a glucose molecule remains in the bonds of a. NADH.
b. None of the answer choices are correct.
c. carbon dioxide.
3. Cellular respiration produces the most ATP from which of the following? a. the citric acid cycle
b. substrate-level phosphorylation
c. oxidative phosphorylation
d. production of lactate
4. The process of carbon dioxide fixation refers to
a. release of carbon dioxide during catabolic reactions.
b. reduction of carbon dioxide and incorporation into organic molecules. c. oxidation of carbon dioxide and incorporation into organic molecules. d. release of carbon dioxide during anabolic reactions.
e. reaction of carbon dioxide with water to form carbonic acid.
5. Arsenic poisoning can lead to organ failure and death and is thought to be due mainly to inhibition of enzymes involved in both pyruvate oxidation
and the Krebs cycle. As a result, this compound must be able to enter what cellular compartment(s)?
a. The cristae
b. The mitochondrial matrix
c. The cytosol
d. The cytosol and mitochondrial matrix.
e. The intermembrane space of the mitochondria
6. The TCA cycle enzymes are located in the _________ in bacterial and archaeal cells.
a. plasma membrane
7. Which of the following is false regarding ATP synthases? a. They require proton motive force to make ATP.
b. They span the inner membrane of mitochondria.
c. Protons flow out into the intermembrane space during ATP synthase. d. The catalytic subunits of ATP synthase undergo conformational changes during ATP production.
8. In addition to ATP, what are the end products of glycolysis? a. CO2 and NAD
b. H2O, NADH, and citrate
c. CO2 and pyruvate
d. CO2 and H2O
e. NADH and pyruvate
9. In the reaction: pyruvate + CoA + NAD+ → acetyl CoA + CO2 + NADH. a. Pyruvate is oxidized and NAD+ is reduced.
b. Pyruvate is reduced and NAD+ is oxidized.
c. Pyruvate is reduced and CoA is oxidized.
d. Pyruvate is oxidized and CoA is reduced.
10. Why would yeast need to perform ethanol fermentation in the absence of oxygen?
a. NADH is necessary to reduce pyruvate to lactate.
b. To produce NAD+ allowing glycolysis to continue.
c. To produce CO2 for respiration.
d. To produce NAD+ allowing the electron transport chain to run. e. To consume excess pyruvate that cannot enter the Krebs cycle.
11. In prokaryotes, the respiratory electron transport chain is located in the a. mitochondrial inner membrane.
b. mitochondrial outer membrane.
d. Plasma membrane
e. bacterial outer membrane.
12. Which is usually true of catabolic pathways?
a. They produce energy in the process of polymerizing monomers into larger polymers.
b. They consume energy while breaking large molecules into smaller parts. c. They use energy to polymerize monomers into larger polymers. d. They break large molecules into smaller parts and produce energy.
13. In the absence of oxygen, can cells utilize the respiratory electron transport chain?
a. Yes, some prokaryotes can use a terminal electron acceptor other than oxygen and make use of the ETC.
b. No, oxygen is the primary electron acceptor in electron transport chains in all cell types.
c. No, oxygen is a required cofactor for the complexes in the electron transport chain.
d. Yes, all cells can make use of the electron transport chain in the absence of oxygen via fermentation.
14. _______ is the product of the Calvin Cycle that is used to form glucose phosphate, amino acids or fatty acids.
b. ribulose bisphosphate (RuBP)
c. glyceraldehyde-3-phosphate (G3P)
e. carbon dioxide
15. Cyanide and carbon monoxide block the final step in the electron transport chain. What effect would this have on ATP production in the mitochondria?
a. ATP production would not change, because protons cross the outer mitochondrial membrane to produce ATP.
b. ATP production would decrease, because protons would not be able to move across the inner mitochondrial membrane.
c. ATP production would decrease, because electrons would not move through the ETC and the proton gradient would decrease.
d. ATP production would increase, because this would spontaneously establish a stronger proton gradient.
e. ATP production would increase, because this would make more oxygen available in the mitochondrial matrix.
f. ATP production would decrease, because protons would not be able to move across the inner mitochondrial membrane.
16. What happens to the oxygen that is used in cellular respiration? a. It is used to make glucose
b. It is used to make Krebs cycle intermediates
c. It is reduced to form water.
d. It is converted to carbon dioxide
e. It is converted to acetyl-CoA
17. Regardless of the electron or hydrogen acceptor used, one of the products of fermentation is always:
18. How do high levels of ATP inhibit glycolysis?
a. High levels of ATP hydrolyze the enzyme phosphofructokinase. b. High levels of ATP act as a competitive inhibitor of phosphofructokinase. c. High levels of ATP break down glucose.
d. High levels of ATP bind to the active site of phosphofructokinase. e. High levels of ATP bind to the regulatory site of phosphofructokinase.
19. Glucose is not our only food source, nor the only one we can utilize in our bodies to generate energy. Other primary sources of energy include other sugars, proteins, and fats. What metabolic intermediate are fats primarily converted into?
b. Krebs cycle intermediates
c. Glyceraldehyde 3-phosphate
d. Oxaloacetic acid
20. Which of the following statements is TRUE of both aerobic and anaerobic respiration?
a. Both produce either lactic acid or ethanol as a biproduct. b. Both use glycolysis to oxidize glucose to pyruvate.
c. Both produce NADH as high-energy intermediates. d. Both produce NADH as high-energy intermediates and both produce either lactic acid or ethanol as a bioproduct.
e. Both use glycolysis to oxidize glucose to pyruvate and both produce NADH as high-energy intermediates.
21. Compared to the air a person inhales, the air that they exhale has a. a higher concentration of O2 and a lower concentration of CO2 . b. a lower concentration of O2 and a higher concentration of CO2 c. lower concentrations of both O2 and CO2 .
d. higher concentrations of both O2 and CO2 .
22) High levels of citric acid inhibit phosphofructokinase. This is an example of
a. competitive inhibition.
b. allosteric regulation
c. enzyme-substrate specificity.
d. an enzyme requiring a cofactor.
e. positive feedback regulation.
23) In the reaction, 6CO2 + 6H2O →C6H12O6 + 6O2, which side should energy be placed on?
a. The left side, this is an endergonic reaction.
b. Neither side, the reaction is in equilibrium.
c. The right side, this is an exergonic reaction.
d. The right side, this is an endergonic reaction.
e. The left side, this is an exergonic reaction.
24) During which phases of cellular respiration is ATP produced via substrate level phosphorylation?
1. Glycolysis and pyruvate processing
2. Pyruvate processing and the citric acid cycle
3. Glycolysis and pyruvate processing
4. The citric acid cycle and the electron transport chain
25) A microbiologist is conducting a research project on chemolithoautotrophs. This means that the investigator is examining certain aspects of a bacterium that
a. can oxidize inorganic molecules such as ammonia and sulfur for energy b. is a purple non-sulfur bacteria which depends on light.
c. obtains carbon from organic molecules.
d. can use the energy from sunlight to build organic molecules from carbon dioxide.
5. uses light as its energy source and carbon for organic compounds.
26. When Calvin added 14CO2 as a radioactive tracer into cultures of green algae, which of the following was detected first?
a. Radioactivity first appeared in ribulose bisphosphate.
b. Radioactivity was detected first in glyceraldehyde 3-phosphate. c. Radioactivity was detected first in 3-phosphoglycerate.
d. Radioactivity first appeared in glucose.
e. Radioactivity was detected first in 1,3-bisphosphoglycerate.
27. The six carbons that form glucose in your food, are effectively lost from the cell as a byproduct
a. each time ATP synthase phosphorylates ADP.
b. during the Krebs cycle as intermediate molecules are rearranged c. as pyruvate is oxidized to form acetyl CoA.
d. when the glucose is initially broken apart in glycolysis.
e. both at the oxidation of pyruvate to acetyl CoA, and in the Krebs cycle.
28. When oxygen is unavailable during heavy exercise what process do muscle cells use for energy generation?
a. Glycolysis coupled with lactate fermentation
b. Aerobic respiration.
c. Anaerobic respiration.
d. Glycolysis coupled with alcohol fermentation.
Ch. 6 and Redox Ch. 7, plus 8.1, 8.6, 23.4
1. C 1. C 26. C
2. C 2. E 27. B
3. E 3. C 28. A
4. C 4. B
5. B 5. B
6. C 6. C
7. B 7. C
8. B 8. E
9. E 9. A
10. A 10. B
11. D 11. D
12. D 12. D
13. C 13. A
14. C 14. C
15. E 15. B
16. all 16. C
17. C 17. E
18. D 18. E
KEY THINGS TO KNOW:
- Products & reactants
- Key enzymes & intermediates (acceptor, first product, branch point) - What is going on (endergonic, exergonic, oxidation, reduction, carboxylation, decarboxylation, etc)
- Specific location process is taking place
- Who performs processes (plants vs animals, prokaryotes vs eukaryotes, etc)
HELPFUL THINGS TO REMEMBER:
– “ase” = enzyme; “ose” = sugar
– NAD+ to NADH is reduction; accepts 2 electrons
– Photosynthesis is reverse cellular respiration
– Krebs Cycle = Citric Acid Cycle = TCA
– Most ATP is produced in oxidative phosphorylation
– In the ETC, the proton gradient works because the proteins increase in electronegativity, ending at oxygen
– Glycolysis is 10 rxns broken into 2 stages: energy investment and energy payoff stage
???? When the products of glycolysis start to developing coefficients of 2, tha signals the transition from energy investment to payoff
???? 4 ATP produced - 2 ATP used in investment stage = net yield of 2 ATP
– Reactions in Photosystem II occur before Photosystem I (named by discovery order, not reaction order)