Bio 1 exam 3
*How many CO2 molecules are produced from the complete oxidation of glucose?* Where is each one produced?
*6 CO2* 4 CO2 are made in the citric acid cycle 2 CO2 are made in pyruvate oxidation per glucose molecule: 6 CO2 molecules (2 pyruvate oxidation, 4 CAC) 4 ATP (2 glycolysis, 2 CAC) 10 NADH molecules (2 glycolysis, 2 pyruvate oxidation, 6 CAC) 2 FADH2 molecules (2 CAC)
ATP hydrolysis can be COUPLED to an endergonic reaction to make that reaction happen. For example, an unfavorable reaction with a G of _____ could be driven (or fueled) by a mole of ATP.
+5.5 kcal/mole The delta G of ATP hydrolysis—an exergonic reaction—is −7.3 kcal/mole. ATP hydrolysis can be used to fuel an endergonic reaction—one with a positive G—that requires LESS THAN 7.3 kcal/mole.
Units of weight: grams vs. Daltons" How much does one molecule/one mole of glucose weigh?
1 molecule= 180 daltons 1 mol= 180 grams
What are the three parts of a photosystem, and how do they function together to harvest light? *Identify the first redox reaction of photosynthesis.*
1. 100s of chlorophylls antennae complex 2. oxidizing agent primary electron acceptor 3. chlorophylls next to the PEA reaction center chlorophylls Their reaction center chlorophylls have slightly different absorbance peaks with allows for the specialization of function. In the first redox reaction, light enters and travels through the pigment molecules until an electron reaches the primary acceptor. reaction center is oxidized, 1 degree electron acceptor is reduced
What are the three phases of the Calvin Cycle, and what does each accomplish? In which decade did Melvin Calvin, Andrew Benson, and colleagues work out the cycle (a.k.a. the Calvin-Benson Cycle)? When did Calvin receive the Nobel Prize in Chemistry? (He is going to appear on the Forever Stamp!)
1. Carbon fixation CO2 + organic molecule (C-H bond) --> carbon made organic 2. Reduction Reduce carbon by adding H+ 3. Regeneration of CO2 acceptor Published in in 1948 Calvin recieved the nobel prize in chemistry in 1961
Describe three ways that cells localize their enzymes for more efficient functioning in metabolic pathways.
1. in organelles 2. as membrane proteins 3. in multi-enzyme COMPLEXES... physically bound together.
Describe the steps of the light reactions, as presented in lecture. I am not so interested in the step numbers, but that you understand WHAT happens and why. Summarize the path energy takes from entering the light reactions as a photon to moving onward as energized electrons.
1. photosytem II absorbs light and electron is transferred to 1 degree electron acceptor reaction center is oxidized, 1 degree electron acceptor is reduced uh-oh! the reaction center lost its electron! 2. obtain an electron from WATER H2O is split by an enzyme Highly endergonic H2O --> 2e- + 2H+ + ½ O2 ... oxygen is produced what allows the electrons to be stripped from water? light energy! 3. the excited electron is transfered to an ETC and ATP is made by chemiosomsis (same as mitochondria) thylakoid membrane/ inner membrane = high H+ concentration stroma/ matrix = low H+ concentration photosystem I is reduced 4. Photosystem I absorbs light and is re-excited by another photon transferred to a 2nd 1 degree electron acceptor 5. excited electron is transferred to a 2nd etc 6. electron passed to NADP+ --> NADPH 4 photons are required to make NADPH
Explain how substrate concentration, enzyme concentration, temperature, and pH affect the rate of an enzyme catalyzed reaction. Which of these are subject to change in cells?
1. substrate (changing concentrations): more substrate, increase in reaction rate 2. enzyme (changing concentrations): more enzyme, increase in reaction rate 3. temperature (altering 3D shape): every enzyme has an optimal temperature so it depends. increase in temp in optimal range leads to increase in rate. ex. human enzyme, 0-50 celsius; bacteria, 40-90 celsius 4. pH (altering 3D shape): every enzyme has an optimal pH so it depends. ex. stomach enzyme, pH = acidic; intesintal enzyme, pH = basic 5. binding of regulartory molecules (altering 3D shape): competitve and noncompetitve inhibition 6. localization: having enzymes all in one place makes it go faster. temperature and pH: all cells are adapted to function in enviroment based on PROTEIN STRUCTURE
How many CO2 molecules are produced in ONE cycle of the citric acid cycle? How many cycles are required to complete the catabolism of a molecule of glucose?
2 CO2 molecules are produced in ONE cycle TWO cycles are required to complete the catabolism of glucose
Covalent bonding: orbitals and hybridization" How many atoms in glucose have undergone sp3 hybridization?
5
Write the summary equation for the process of photosynthesis. Indicate which reactant becomes oxidized and which reactant becomes reduced. Explain how each reactant is imported into a leaf, and how each product is exported from the leaf.
6CO2 +6H2O + light = C6H12O6 +6O2 H2O is oxidized to O2--> reducing agent CO2 is reduced C6H12O6--> oxidizing agent Through the leaf pores CO2 enters and O2 leaves H2O enters through the roots, goes up the stem, and goes out the leaves converts light into chemical energy stored in sugars. *for euks, in the chloroplasts for plants, in the leaves.* why are we seperating them like they arent the same thing?
The citric acid cycle is run by _____ different enzymes.
8 This pathway has eight 'steps' or reactions, which requires eight different enzymes.
During coupling, HOW is ATP actually USED to make a reaction happen (see Figure 8.10)?
A phosphate is transferred from ATP to a reactant. Phosphorylation is the basic mechanism by which ATP is used to do work. Either a REACTANT (as seen in Figure 8.10) or a PROTEIN (as seen in Figure 7.15) may be phosphorylated. And in steps 1 and 3 of glycolysis (Chapter 9), phosphorylation is used to boost the energy of chemical intermediates of the pathway!
How exactly does ATP drive the sodium-potassium pump (see Figure 7.15)?
A phosphate is transferred from ATP to the pump.
In which stage(s) of cellular respiration is ATP made? *In which stage(s) is it consumed?* In which stage(s) are coenzymes reduced? In which stage(s) are coenzymes oxidized? Make a table tabulating the number of 'earned' and 'spent' ATPs and reduced coenzymes in the various parts of cellular respiration.
ATP Made: Glycolysis (2 ATP) Citric Acid Cycle (2 ATP) Oxidative Phosphorylation [Electron Transport & Chemiosmosis] (26-28 ATP) TOTAL: 30-32 ATP ATP Used: initial investment in glycolysis (2 ATP) NAD and FAD are oxidized in pyruvate oxidation , and NAD is reduced to NADH during citric acid. printed slide
What two products are made by the light reactions for use in the Calvin Cycle? (See Fig. 10.5)
ATP and NADPH
What type of monomer is ATP? List its parts. *How is its chemical energy liberated?* How do cell's use ATP to drive endergonic reactions? What other function does ATP have in cells?
ATP= adenosine TRIphosphate -a nucleotide used to make RNA -base is adenine -three phosphates -energy rich chemical energy transforms by adding phosphates to adenosine... AMP, ADP, ATP catabolism releases energy "-7.3 kcal/mol" anabolism requiress energy "3.4 kcal/mol" then there is some left over! "-3.9kcal/mol" ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant. --recipient molecule is now phosphorylated. ATP is used in the Na+/K+ pump. The pump gets ATP because it is phophorylated!!!! CELLULAR RESPIRATION energy from catabolism -> ATP +H2O -> energy for ceullar work -> ADP + P (atp) -> cycle around again
Covalent bonding: atoms, covalent bonds, and molecules" How many atoms/bonds are found in glucose?
Atoms: 24 Bonds: 24
Write out an equation which summarizes the process of cellular respiration as the complete oxidation of glucose. Explain when in the process of cellular respiration each reactant or product is consumed or produced, respectively.
C6H12O6 + 6O2 ---> 6 CO2 + 6 H2O + Energy (ATP + heat) C6H12O6= oxidized 6O2= reduced The water and oxygen gain electrons while the glucose and carbon dioxide lose electrons. 1. glycolsis (cytosol) 2. pyruvate oxidation (mitochondria matrix) 3. citric acid cycle (mitochondria matrix) 4. electron transport chain (mitochondria matrix) 1-3 catabolize glucose through oxidation --many NAD+ are reduced into NADH --makes little ATP 4 electrons are transferred --NADHs are oxidized -- makes the most ATP
Explain what carbon fixation is. Why is it important for both animal and plant life?
CO2 + organic molecule (C-H bond) making carbon organic Carbon fixation is important because it allows plants and animals to respire
What are coenzymes? (See Chapter 8 for a description.) Explain how the coenzyme NAD+ is chemically altered when it is reduced, and when it is re-oxidized (i.e. what exactly is added and removed?). Where does this happen on the molecule?
Coenzymes: Small molecules required by some enzymes Can be easily reduced then oxidizied, so it takes electrons from one molecule, and gives them to another. They are molecular "handles" NAD+ is reduced by gaining a hydrogen and 2 electrons to become NADH. little energy is lost. *Reduction happens in cytosol and matrix Oxidation happens in ETC in matrix*
Beyond providing energy as ATP, what do catabolic pathways provide to anabolic pathways that enables them to build biomolecules?
Divert intermediates into anabolic pathways and use CARBON as building material-- build cell, build yourself catabolating in uterus when growing DNA synthesis RNA synthesis protein synthesis
Which of the following statements best describes enzyme function?
Enzymes increase the rate of chemical reactions by lowering activation energy barriers.
How many steps do the catabolic pathways glycolysis, pyruvate oxidation, and the citric acid cycle have? What distinguishes a cyclic pathway from a linear one?
Glycolysis has 10 steps Pyruvate oxiation has 3 steps Citric Acid cycle has 8 steps a cyclic pathway uses its products as reactants
Why is the cycle discovered by Hans Krebs called the citric acid cycle? List 3 molecules produced by the cycle that store valuable chemical energy. In which decade did Krebs work out the cycle? When did he receive the Nobel Prize in Physiology or Medicine?
Hans showed that a 2-carbon atom molecule derived from food combines with a 4-carbon enzyme in the cell to create a 6-carbon compound - citric acid. Citric Acid is a product of the cycle. 2 ATP, 6 NADH, 2 FADH2 1930s then won the nobel prize in 1953 Nobel prize in medicine
How does aerobic glucose catabolism (cellular respiration) compare with processes like the combustion of methane or wood (made of cellulose, a glucose polymer)? How is it different?
LIKE combustion of methane: EXERGONIC Just as in the combustion of methane, in respiration; the fuel (glucose) is oxidized and oxygen is reduced. The electrons lose potential energy along the way and energy is released. Oxidation of glucose transfers electrons to lower energy state, liberating the energy that becomes available for ATP Synthesis. UNLIKE combustion of methane: MANY STEPS, catabolism requires many steps
The oxidizing agent for the first three stages of cellular respiration is _____.
NAD+ The coenzyme FAD is an oxidizing agent for the citric acid cycle; NADP+ is an oxidizing agent for photosynthesis. What does coenzyme A carry, and when?
If the activity of threonine deaminase is completely inhibited, would you expect greater concentrations of threonine to increase activity?
NO, greater concentrations of threonine would not be able to out-compete the inhibitor, so inhibition would continue. Competition between the substrate and the regulatory molecule occurs when both molecules are capable of binding to the active site; this is known as competitive inhibition.
How many CO2 molecules are consumed in one cycle of the Calvin Cycle? How many CO2 must enter the cycle to produce one molecule of the sugar product of the cycle? How many cycles would be required for a leaf cell to make one molecule of glucose from this sugar product? Name the sugar product of photosynthesis.
One cycle takes in one CO2 THREE CO2 are needed to produce a molecule of sugar THREE cycles would be required for a leaf cell to make one molecule of sugar SIX cycles required for glucose G3P --> glyceraldehyde-3 phosphate (G3P)
Explain what redox reactions are, and give examples as discussed in lecture and your textbook. Explain the meaning of the terms oxidation, reduction, oxidizing agent and reducing agent.
Oxidation reduction reactions involve a TRANSFER of electrons. sometimes redox changes the degree of electron sharing between atoms oxidation is the loss of electrons and H+ reducing agent is what loses H+, electron donor if product is positive reduction is the gain of electrons and H+ oxidizing agent is what gains H+, electron acceptor if product is negative
List all the products of pyruvate oxidation. How many of each product is produced per glucose? In what way are the enzymes catalyzing pyruvate oxidation 'localized' (this concept was explained at the end of Chapter 8)? Draw the structure of an acetyl group.
Products: 2 acetyl CoA, 2 NADH, 2 H, 2 CO2 Per glucose, 10 NADH & 6 CO2 Catalyzed by a COMPLEX of enzymes = localization. they are all together promoting efficientcy O double bonded to C bonded to C bonded to 3H
In glycolysis, what is meant by 'energy investing' and 'energy harvesting'? What all is invested and what all is harvested, and at which steps?
Stages 1-5 are "energy investing" meaning the first 5 steps spend ATP to make glucose even more energy rich Stages 5-10 are making ATP and NADH: "energy payoff" or "energy harvesting" 1-5 invest ATP to make glucose more energy rich 5-10 harvest ATP and NADH
What is the activation energy(EA) of a reaction? What type of kinetic energy allows reactants to overcome the EA? How do enzymes help reactants to overcome EA?
The activation energy is the energy needed to break the bonds and allow the reaction to occur. thermal energy--> CATALYSTS cells accomplish catalysis with enzymes. 1. they do not damage cells 2. the are specific they work by REDUCING ACTIVATION ENERGY without altering delta G
Describe how the energy stored in reduced coenzymes is used to create a proton gradient (a.k.a. a proton motive force), and ultimately stored in ATP by chemiosmosis.
The chain proteins use the energy of electrons (REDOX) to transfer protons across the inner membrane... As electrons are transferred (by electron carriers such as NADH and FADH2) and cause H+ ions to be taken up and released into the surrounding solution, in Euks, the electron carriers are spatially arranged in the inner mitochondrial membrane in a such a way that H+ is accepted from the mitochondrial matrix and deposited in the intermembrane space, the H+ gradient that results is Proton Motor Force. chemiosmosis: using a proton gradient to make ATP ATP synthase is carrier for protons-- another example of coupling
Which coenzyme carries electrons in photosynthesis? How is it similar and different from NAD+? Where in photosynthesis—the light reactions or the Calvin Cycle—is the coenzyme reduced? Where is it oxidized?
The lower energy form, NADP+, picks up a high energy electron and a proton and is converted to NADPH. When NADPH gives up its electron, it is converted back to NADP+. NADPH has a phosphate group the conenzyme NADP+ is reduced in light reactions the conenzyme NADPH is oxidized in the calvin cycle when NADPH is oxidized to NADP+ and CO2 is reduced to glucose.
What is the original source of electrons for the manufacture of sugar? What by product is created when electrons are stripped away? With what energy are the electrons excited?
WATER... H2O --> 2e- + 2H+ + ½ O2 oxygen LIGHT ENERGY
What is the name of the barrier that must be overcome before products are formed in a spontaneous reaction?
activation energy
If an enzyme in solution is saturated with substrate, the most effective way to obtain a faster yield of products is to
add more of the enzyme.
When can an exergonic reaction drive/fuel an endergonic one? What is the specific exergonic reaction that is commonly 'coupled' to endergonic ones in cells?
an exergonic fuels an endergonic one through metabolic pathways. catabolism -> atp -> anabolism (not direct) catabolism produces ATP to give to anabolism. transforming energy in the form of ATP energy from ATP hydrolysis can make ATP. 1 phosphate= AMP 2 phosphates= ADP 3 phosphates= ATP more phosphate= more energy
Define the terms autotroph and heterotroph. Identify to which group each of the following organisms (from the lab course) belong: onion, Elodea, potatoes, yeast, cyanobacteria, lactobacillus, Paramecia, Amoebae, Euglena, rotifers, and humans.
autotrophs make organic compounds from CO2 (or other inorganic materials) heterotrophs must obtain their required organic compounds from others onion- autotrophs elodea- autotrophs potatoes- autotrophs yeast- heterotroph cyanobacteria- autotrophs lactobacillus- heterotrophs paramecia- heterotrophs amoebae- heterotrophic euglena- both rotifers- heterotrophs humans- heterotrophs
According to the absorption spectrum of chlorophyll, which wavelengths/colors of visible light does it absorb? Which wavelengths are reflected and transmitted?
blue and red are absorbed green is refelcted
Aside from glucose, what other metabolic fuels can be used to make ATP? *Summarize how each fuel is hydrolyzed, then enters into one of the first three stages of cellular respiration.*
carbs -fructose (mono) -sucrose, maltose, lactose (di) -strach (poly) lipids (fats) -fatty acids -glycerol (much like monosaccharide) proteins -amino acids image on slide 98
Compare and contrast competitive inhibition with noncompetitive inhibition. Which can be overcome by additional substrate?
competitive inhibition is when a competitive inhibitor blocks the ssubstrate from binding to the active site. noncompetitive inhibition is when a noncompetitive inhibitor binds to the allosteric site and changes the shape of the active site. both can turn enzymes on or off Competitive inhibition can be overcome by additional substrate because more substrate wins the competition
Does ALLOSTERIC regulation STIMULATE or INHIBIT an enzyme's activity?
either stimulates or inhibits
exergonic vs endergonic
exergonic, ΔG< 0 endergonic, ΔG> 0
Relate the terms exergonic and endergonic to free energy change. Then explain how the total energy and the entropy change in an exergonic or an endergonic reaction or process. Apply the terms favorable/spontaneous and unfavorable/nonspontaneous. Finally, state whether stability increases/decreases for each case.
exothermic = releases energy neg delta G H down and/ or S up product is MORE stable favorable reaction 'spontaneous' course of reaction free energy, start from top: reactants, amaount of energy released, products In an exergonic chemical reaction where energy is released, entropy increases because the final products have less energy inside them holding their chemical bonds together. endothermic= absorbs energy pos delta G H up and/or S down product is LESS stable unfavorable reaction 'nonspontaeous' course of reaction free energy, start from bottom: reactants, amaount of energy required, products The change in entropy (S) decreases.
Explain how feedback inhibition regulates the abundance of a given biomolecule.
feedback inhibition: the PRODUCT of a pathway controls its own production by regulating an enzyme that catalyzes an EARLY STEP of the pathway. typically by noncompetitive inhibition. ex. isoleucine biosynthesis isoleucine is made from threonine in 5 steps (=5 enzymes) Enzyme #1 has an allosteric site to which isoleucine binds Binding by isoleucine SHUTS OFF the enzyme--> stops making isoleucine
What is the transformation of the energy of a proton gradient into the energy of ATP a demonstration of?
first law of thermodynamics Energy cannot be created; it can only be transformed into a variety that you can make use of.
Explain the first two laws of thermodynamics and how they apply to cells. Why must cells be open systems?
first law: energy can only be transformed second law: entropy, disorder (S), or universe increased. you always lose energy= heat cells must conform to both!!! Energy is exchanged between cells and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. organization of inside of cell creates disorder in the outside of the cell in the form of heat.
What is free energy? *how what does it have to do with cellular work?* *How does free energy change in chemical reactions or processes?* How is delta G calculated? What does the SIGN of delta G (negative/positive) tell you about a reaction or process?
free energy is an energy of system that can do work (at uniform system temp). The portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system chemical reactions... free energy-> metabolism -> aquiring free energy for cellular work. ATP, coupling delta g = delta H (change in enthalpy) - T (temp in K) delta S (change in entropy) delta g = Gprod - Greact Negative delta G is exothermic Positive delta G is endothermic
NADH is produced by this pathway.
glycolysis pyruvate oxidation citric acid cycle A lot of folks got the last question right, then missed this one. If NAD+ is the oxidizing agent for each of these stages (question #4), then NADH must be made by each!
In what aqueous compartment of a eukaryotic cell do glycolysis, pyruvate oxidation, and the citric acid cycle occur? Name the initial reactants and the end products for all three pathways. What is OXIDIZED and what is REDUCED during all 3 processes?
glycolysis= cytosol pyruvate oxidation= matrix citric acid cycle= matrix Glycolysis: -Reactant: 1 glucose molecule, 2 ATP -Products: 2 pyruvate, 2 NET ATP, 2 NADH. Pyruvate oxidation: -Reactants: 2 pyruvate, 2 NAD, 2 CoA -Products are 2 acetyl CoA, 2 NADH, 2 H, 2 Co2. Citric acid cycle: -Reactants: 2 ATP, 2 NADH. -Products: 2 ATP, 6 NADH, 2 FADH's *Glycolysis: the NAD is being reduced and the G3P is oxidized Pyruvate oxidation: pyruvate is oxidized while NAD is reduced to NADH Citric acid cycle: acetyl CoA gets oxidized and NADH/FADH gets reduced.*
Enzymes are described as catalysts, which means that they __________.
increase the rate of a reaction without being consumed by the reaction This permits enzyme molecules to be used repeatedly.
Review where electrons come FROM and *where they END UP in cellular respiration and in photosynthesis. * *In which process do electrons LOSE potential energy and in which do they GAIN it?*
initially from glucose then NADH/FADH2 in cellular respiration and water then PS2/etc/PS1/etc then NADPH in photosynthesis
Isoleucine biosynthesis is regulated by FEEDBACK INHIBITION; an early step of its metabolic pathway is blocked at high concentrations of _____.
isoleucine As the concentration of the final product increases it binds more often to the enzyme of this step, effectively shutting off the pathway from that point onward. The pathway will remain off until the product's concentration drops again. Note that it is not always the first step of the pathway that is regulated, but an early step. For example, cellular respiration (Chapter 9) is regulated through the enzyme PFK which catalyzes the THIRD step of GLYCOLISIS.
The electron transport chain removes protons from which part of mitochondria?
matrix A mitochondrion has TWO membranes and TWO aqueous compartments; be familiar with all of them.
The enzyme ATP synthase can also be described as a _____.
membrane transport protein You should be familiar with all of these terms, and understand why ATP synthase—an enzyme and a protein—cannot logically be any of the others.
Explain the terms metabolism, catabolism, and anabolism and how they are related.
metabolism is all of the cells chemical reactions = biochem. The sum of the physical and chemical processes in an organism by which its material substance is produced, maintained, and destroyed, and by which energy is made available. catabolism, destructive metabolism, is the breaking down compounds, hydrolysis, releases energy anabolism, constructive metabolism, is building complex compounds, biosynthesis, dehydration, endothermic, requires energy catabolic reactions produce energy for anabolic reactions through metabolic pathways.
During feedback inhibition of isoleucine synthesis, which of the following molecule(s) stops being made?
more than one of these answers are correct isoleucine, intermediate A First, the product of the reaction that is catalyzed by the deactivated enzyme (in this case, intermediate A) stops being made. The remaining 'A' will be converted to 'B', 'B' will be converted to 'C', and so on until all of these intermediates run out and isoleucine stops being made. As mentioned above, the pathway remains off until isoleucine becomes scarce again.
In the absence of oxygen, some organisms or cell types can subsist on the ATP made by fermentation. *Which REACTANT of glycolysis must be recycled in order to keep glycolysis running? * Describe two ways this may be done (i.e. two types of fermentation).
no oxygen = NADH cannot be oxidized = NAD levels drop = chain fills with electrons and stops functioning derive ATP from glycolysis ONLY and oxidize NADH using pyruvate. *NAD+ is recycled* Lactic acid fermentation: pyruvate reduced directly by NADH to form lactate as an end product. toxin --> shifted to liver alchol fermentation: pyruvate converted to ethanol (alcohol) SINGLE CELLED LIFE ALSO RUN ON AEROBIC CEULLULAR RESPIRATION INCLUDING BACTERIA AND YEAST
Regulation occurs through the enzyme threonine deaminase, whose activity is curtailed through _____.
noncompetitive inhibition Notice in the diagram that the enzyme has an allosteric site in addition to its active site!
Explain how ATP is made by photophosphorylation, (FROM what reactants, and WITH what energy source) and *where in chloroplasts it occurs. * Where is this ATP USED?
photophosphorylation is making ATP fromn ADP and an inorganic phosphate powered by LIGHT ENERGY
Covalent bonds: polar vs. nonpolar" How many polar covalent bonds/nonpolar covalent bonds does glucose contain? (Note: Count double bonds as TWO covalent bonds.)
polar covalent bonds: 12 nonpolar covalent bonds: 12
A _____ gradient is created in mitochondria during the last stage of cellular respiration.
proton gradient Across which membrane is it created?
ATP is produced in all stages of cellular respiration EXCEPT _____.
pyruvate oxidation Be clear on what is made when, and how many. In particular you should tally the number of NADH, FADH2, ATP, and CO2 produced by each of the first three pathways, per glucose consumed. Write it out again and again until it becomes imprinted in your brain!
Why are several different pigments used in photosystems? What is the main pigment used?
so they can absorb energy from a wide range of wavelengths. chlorophyll, the primary pigment used in photosynthesis, reflects green light and absorbs red and blue lightmost strongly
Which step of what pathway does the enzyme phosphofructokinase catalyze? Explain how cellular respiration is regulated through PFK, including the three metabolites involved, whether they stimulate or inhibit PFK, and how two of these regulate their own production by feedback inhibition. In these cases, is competitive inhibition or noncompetitive inhibition involved?
step 3 in glycolysis production of ATP is controlled by feedback inhibition. PFK has allosteric sites where ADP, citrate, and ATP bind to PFK to turn off. abundance of ADP and AMP indicates low on energy. AMP stimulates in step 3. citrate inhibits. citrate (first product of CAC) turns off PFK too noncompetitve inhibition because they bind to allosteric sites.
Why does a substrate bind to an enzyme's active site? How does it bind? Give examples of what active sites physically do to substrates to speed up chemical reactions.
substrate binds to an enzymes active site because this complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process. weak interactions *1. orients two substrates: increases rate tremendously* *2. puts stress on bonds: breaking covalent bonds* *3. creates a micro-environments: electron flow*
Contrast ATP production by substrate-level phosphorylation and by oxidative phosphorylation. For each mechanism, give the specific REACTANTS from which ATP is made and the SOURCE OF ENERGY used to make it (in each case they are different!). Finally, indicate in which stages of cellular respiration ATP is produced by each mechanism.
substrate level phosphorylation: making ATP by transferring a phosphate from an organic subsstrate to ADP endergonic no energy, comes from substrate SUGAR PHOSPHATE IS ORGANIC ADP + Sugar-P (substrate) --> ATP GLYCOLYSIS oxidative phosphorylation: making ATP from ADP and phosphate, powered by redox reactions of e.t.c. endergonic energy provided by proton gradient INORGANIC PHOSPHATE ADP + energy (proton gradient) + Pi --> ATP ELECTRON TRANSPORT CHAIN
Acidic and basic "In a catabolically active cell, which side of the mitochondrial inner membrane is slightly basic?"
the MATRIX side of the mitochondrial inner membrane
Which of the following is NOT a way in which an enzyme can speed up the reaction that it catalyzes?
the active site can provide heat from the environment that raises the energy content of the substrate enzyme can speed up reaction by: the enzyme *binds a cofactor that interacts with the substrate to facilitate the reaction* the active site of the enzyme can provide a *microenvironment with a different pH that facilitates the reaction* the binding of *two substrates in the active site provides the correct orientation for them to react to form a product binding of the substrate to the active site can stretch bonds in the substrate that need to be broken* An enzyme cannot extract heat from the environment to speed a reaction.; it can only lower the activation energy barrier so that more substrates have the energy to react.
What is an allosteric site and how does it affect an enzyme's functioning? Do all enzymes have allosteric sites? What about active sites?
the allosteric site is the site where another substance combines with the enzyme at a site other than the active site, altering the enzyme activity. through noncompetitive inhibition, a substrate binds to the allosteric site changing the shape of the active site. this can turn enzymes on or off. 'allosteric regulation' may be positive. all enzymes have active sites but not allosteric sites.
Which of the following is an example of the LOCALIZATION of enzymes during cellular respiration to help the pathway to function more efficiently? (See the end of Chapter 8 for information about the ways that enzymes are localized.)
the enzymes of pyruvate oxidation are bound together into a multi-enzyme complex citric acid cycle enzymes are located in the mitochondrial matrix electron transport chain proteins and ATP synthase are embedded in the inner membrane of the mitochondria Localizing enzymes of a pathway concentrates the enzymes with their substrates and with each other to make a pathway more efficient.
How are lysosomal hydrolases localized in a cell?
they are confined together within an organelle Confining the hydrolytic enzymes to the lysosome protects the rest of the cell from the enzymes, which are capable of breaking down most types of biological molecules. But how does this work, considering that these enzymes are made in the ER, then transported through the Golgi before every reaching a lysosome? The answer is that the enzymes are only active within the lysosome but not elsewhere. This is accomplished through control of the enzymes by pH; the enzymes are less active at a neutral pH and most active at a pH of 5, and only the interiors of lysosomes have a pH this low! (pH control of lysosomal hydrolases is described in the textbook.)
Name the three membranes and the three aqueous compartments found in a chloroplast. In which membrane are the enzymes of the light reactions embedded? In which compartment are the enzymes of the Calvin Cycle found? Indicate where in photosynthesis—the light reactions or the Calvin Cycle—each reactant is consumed and each product is produced.
three membranes: inner membrane, outer membrane, thylakoid membrane three aqueous compartments: stroma, intermembrane space, thykaloid lumen Enzymes of light reactions are embedded in the thykaloids Enzymes of the calvin cycle are found in the storma Light reactions: reactants...H2O, light, NADP, ADP+Pi products... ATP, NADPH, O2 Calivin cycle: reactants...ATP, NADPH, CO2, products...NADP, ADP, G3P
As mentioned back in Chapter 5 (lipids), coenzymes may be made from _______. One example is NAD+, which is made from 'niacin' (a.k.a. nicotinic acid).
vitamins A 'coenzyme' is a term for a molecule that can carry a cargo of energy or raw material in cells. Coenzymes are not enzymes at all, but are reactants that become loaded with their cargo in enzyme-catalyzed reactions. There are three coenzymes in cellular respiration: the electron carriers NAD+ and FAD, and the acetyl group carrier coenzyme A. (What is an acetyl group?)
Threonine deaminase binds threonine through _____ interactions.
weak (i.e. noncovalent) Binding of threonine occurs at the active site of the enzyme, by weak (noncovalent) interactions.
What is the electron transport chain, and in which specific membrane is it found? How does the potential energy of an electron change as it move down the chain? How do the electronegativities of the chain molecules differ along the chain? How are the chain molecules 'localized' to facilitate their functioning (see the end of in Chapter 8)?
· NADH is OXIDIZED by the E.T.C. · A "chain of protiens" within the inner membrane · Includes FOUR complexes · Several 'cytochrome proteins' · 'transport' = a SERIES of redox reactions · The chain is OXIDIZED by OXYGEN · ELECTRONS MOVE THROUGH TRAIN, PROTONS MOVE FROM MATRIX TO INTERMEMBRANE SPACE As it moves down the chain, potential energy decreases As it moves down the chain, electronegaties increase as they keep getting tighter and closer to the nucleus Localized within inner membrane