Exam 2 Flashcards
L8. Sketch the organization of a mitochondrion of a plant cell. Label the inner and outer membranes, the matrix, and the intermembrane space.
Diagram
B-oxidation and TCA occur in matrix
Electron carriers for OxPhos are in the inner membrane (cyt C is in the IMS)
ATP synthase is in the inner membrane, with catalytic heads facing the matrix.
L8. Where do the reactions of B-oxidation and the TCA cycle take place? Where are the electron carriers of oxidative phosphorylation? The ATP synthase?
B-oxidation and TCA occur in matrix
Electron carriers for OxPhos are in the inner membrane (cyt C is in the IMS)
ATP synthase is in the inner membrane, with catalytic heads facing the matrix.
L8. Diagram the electron transport reactions of oxidative phosphorylation on a redox/energy diagram. Indicate at which stages and in what form the energy released during electron transport is “harvested” and “stored”?
Diagram (!!!!!!!)
Energy is harvested by using the flow of electrons to pump protons across the inner membrane. Energy is then stored in a proton gradient.
L8. Diagram the electron transport chain of oxidative phosphorylation in the mitochondrial membrane. Indicate at which stages and in what form the energy released during electron transport is “harvested” and “stored”?
Diagram(!!!!)
The major electron
transport complexes (NADH
deHyd , the b-c1 complex,
cytochrome oxidase) act as a
proton pumps. In addition,
protons are pumped as CoQ transfers a pair of electrons from NADH dehydrogenase to Cyt b-c1.
Protons are pumped across the inner membrane into the IMS/cytoplasm (the outer
membrane is permeable to protons), creating a H +
gradient across the IM, high in the cytoplasm,
low in the matrix.
L8. The inner mitochondrial membrane in brown fat cells, which are abundant in infants, contain a protein that allows protons to flow across the membrane without generating ATP. Considering the first law of thermodynamics, what do you think happens to the potential energy of the proton gradient in brown fat cells? Why might that be beneficial to young babies?
1st law: Energy is neither created or destroyed, merely conserved.
Protons flow through the membrane carriers in the inner membrane of the mitochondria in brown fat cells, the PE of the proton gradient is dissipated as heat, which helps keep the baby warm.
L8. If radiolabeled Oxygen was used to trace the fate of the oxygen during the complete oxidative metabolism of stearate to Carbon Dioxide and Water, what would be the first chemical compound into which radiolabeled oxygen atoms were incorporated? explain
H2O
The only place molecular O is used in fatty acid metabolsim is as an electron acceptor during oxPhos, and it ends up in water.
L8. Sketch a chloroplast, identifying all of its important features and compartments.
Sketch
L8. Given a sample of chloroplasts isolated from leaf mesophyl cells, how might you physically separate ribulose bisphosphate carboxylase (rubisco) from cF0 cF1 ATP synthase?
Gently break open the chloroplasts and spin in a centrifuge to separate the membrane fragments from soluble components. The ATP synthase will be in the membrane fraction, Rubisco will be found in the soluble fraction.
L8. Diagram the electron transport chain of non-cyclic photosynthesis. Indicate at which stages and in what form the energy released during electron transport is “harvested” and “stored”?
Diagram
Energy is harvested by pumping/using/releasing protons, generating a proton gradient across the thylakoid membrane.
Energy stored in this gradient will be used by ATP synthase to synth. ATP
L8. Compare the roles of chlorophyll in the antenna complexes with those in the reactoin centers of PSII and PSI during photosynthesis
Chlorphyls in the antenna complex absorb photons, and pass energy to other chlorophyll molecules by a quantum effect known as resonance energy transfer. in RET, energy is passed form electron to electron, but the electrons are not themselves passed from one molecule to the next.
The reaction center chlorophyll molecules accept energy from the antenna complex, boosting electrons to a higher energy state P680* in PSII and p700* in PSI. These electrons are then stripped from the reaction center chlorophylls and passed along the ETC
L8. Diagram the “Calvin-Benson” cycle by which plants fix Carbon Dioxide into carbohydrates, indicating important reactants and intermediates and where/what form energy is required.
Diagram
What is the energy cost (In ATP equivalents) required to synthesize a molecule of glyceraldehyde-3-phosphate in the “Calvin-Benson” cycle? Assume NADPH=NADH=2.5ATP
Each G3P made in CAlvin cycle requires:
6 NADPH+9 ATP
Total: 24 ATP equivalents.
What is the yield (in ATP equivalents) of the complete aerobic metabolsim of one molecule of glyceraldehyde-3-phosphate?
Complete aerobic metabolism of one G3P yields:
3 ATP (2 in glycolysis and 1 in CAC)
4 NADH
2 FADH2
Total: 16 ATP equivalents.
Why do plants expend so much enery synthesizing G3P from Carbon Dioxide?
The G3P made in the dark RXN’s of photosynthesis provide the precursors for EVERY biomolecule in plant cells. Thus for most biomolecules on Earth
L8. Considering photosynthesis, Which reactant is the source of the oxygen atoms liberated as O2 during photosynthesis? B) IN which product would you find the oxygen atoms derived from CO2 during photosynthesis
A) H20
B) CH2O
L8. Make simple sketches the show the location of the electron transport carriers, direction of proton pumping, ATP synthase, and direction of proton flow through ATP synthase in
A) a respiring prokayote
B) mitochondrion
C) Chloroplast
D) can you think of an evolutionary pathway that connects the topology of proton flow and the ATP synthase in these examples
DIAGRAM(!!!!!!!) A B C D: Inner membrane of mitos is topologically identical to the plasma membrane of respiring proks with infoldings to increase surface area. The thylakoid membrane is also similar in orientation, if we consider it to be "budded off" from the inner membrane. Both mito IM and chloroplast TM may be evolutionarily derived from the plasma membrane of endosymbiotic bacteria.
L8. Although chloroplasts and mitochondria both generate and use proton gradients to power ATP synthesis, the mitochondrial proton gradient has a larger electrical component, while the chloroplast’ gradient has a large chemical component. Why might this be so?
Mitochondria are pumping protons to the IMS, which is the same as the cytoplasm. Although
they can raise the matrix pH to ~8, they cannot greatly acidify the cytoplasm without affecting
other chemical reactions. Thus, the cytoplasm stays at pH ~7… and the concentration gradient is
only ~10-fold. However, there is a significant electrical component to the proton motive force
Chloroplasts, on the other hand, pump protons into a small, distinct compartment… the
thylakoid lumen (or space). There are less strict constraints on the pH of the thylakoid… which is
acidified to a pH of ~5. The Stromal pH is ~8, so the chemical gradient is ~1000-fold. However,
other ions balance much of the electrical component of the thylakoid proton gradient, so that the
proton motive force is mostly chemical.
L8. According to the first law of thermodynamics, energy is neither created nor destroyed, but can be converted from one form to another. What are three “forms” of stored energy used by cells. How are these forms interconverted?
- Chemical energy of high energy phosphate bonds (ATP
- Chemical energy and reducing power of electrons in NADH and FADH2
- The potential energy of electrochemical ion gradients
L10. Draw the structure of the tri-deoxyribonucleotide ATG (remember 5’-3’) with 5’ triphosphate and free 3’ hydroxyl. circle a phosphoester bond
Diagram
L10. What causes melting temp. of DNA to be higher?
More GC bonds, because they have 3 H-bonds between them
Larger double helices make more H bonds, therefore they have higher melting points.
L10. Briefly outline or diagram the packaging of DNA into chromatin in a euk. What are the major structural proteins found in chromatin?
Diagram
Double Helix
-Core Histone H2A, H2B, H3, H4
Beads on a string(nucleosomes)
30 nm fiber (solenoid)
-non-histone chromosomal proteins
Chromatin loops
“condensins
Mitotic Chromatin.
Two copies each of histones H2A, H2B, H3, and H4 (the “core” histones) constitute the histone core, around which are wrapped ~146 bp of DNA. The “linker” histone H1 binds the nucleosome linker DNA and coils the nucleosomes into the 30 nm fiber or “solenoid.” Additional proteins (“non-histone chromosomal proteins,” incl “condensins”) organize the chromatin into loops and higher order structures.
L10. What provides energy for adding nucleotides to a growing DNA or RNA strand? How much energy (ATP) equivalents is required to add each nucleotide?
Beta and Gamma phosphates are cleaved off and released as PPi, which is then cleaved to 2Pi. These reactions, which are equivalent to using 2 ATP, provide the energy for adding the nucleotide to the growing strand.
