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Chapter 7—Intracellular Transport (p.142 – 162) and Cytoskeleton (p. 163 – 168)
Lecture 12 PPT Review “Inside the Cell: The Dynamic Cell—Intracellular Transport”
1.) How do proteins get targeted to their correct destination in the cell?
a. Localization signal/sequence
2.) Where does protein synthesis occur in the cell? How do mRNAs get out of the nucleus? How do
nuclear proteins get into the nucleus?
a. Ribosomes
b. mRNAs exit through NPCs (facilitated by a unique mRNA-export protein complex)
c. Nuclear proteins require NLS in their protein sequence to get into nucleus
3.) Outline as many components of the nucleus as you can—think about nuclear import, export,
anatomy of nucleus, nucleic acid synthesis.
4.) What structures serve as a passageway/gate into and out of the nucleus?
a. Nuclear Pore Complex (NPC)—I don’t think the components will be 100% crucial, nor
how the proteins interact with the NPC. If any structural components, it may be good
to understand the cytoplasmic filaments on the cytoplasmic side and nuclear basket
on the nuclear side
5.) What is the name of the amino acid sequence present in all nuclear proteins? In terms of
protein structure, what comprises the NLS? What is its function?
a. Nuclear Localization signal
b. NLS is a specific portion of the amino acid sequence with the proteins 1* sequence.
Basic residues are densely represented in these sequences
c. Localizes proteins to the nucleus—allows entry into nucleus
6.) What family of transport proteins interacts with NLSs? What transport proteins interact with
NESs?
a. Importins
b. Exportins
7.) Slide 15 showed the research done in our lab. How did the displayed results help to explain
the role of NLSs in nuclear transport (of thyroid hormone receptor)?
a. Initially, we can see on the left that the GFP-tagged TR is localizing primarily to the
nucleus. However, when the Lysine at position 25 (a basic AA) was changed to an
Alanine (Nonpolar hydrophobic), the GFP-TR instead localized only to the cytoplasm,
showing none in the nucleus. She also explained how the same result was shown with
all other AAs in that sequence. This shows that the AAs from 22 – 29 are required in
TR’s AA sequence in order for it to localize to the nucleus—therefore identifying an
NLS of TR.
8.) Outline the path in the endomembrane system using RNA that has just been
synthesized/transcribed.
a. Ribosome
b. RER
c. Transport to cis golgi
d. Cis to trans golgi
e. Golgi packages (association with vesicle + “tag” added if required) to be released to
destination
9.) What is the signal hypothesis? How does it explain the differences between the “signals”
present within the AA sequence of an ER protein versus a nuclear protein? Include the
modification to the ER protein that we discussed in class.
a. Difference is that the ER signal sequence is cleaved after reaching destination,
whereas nuclear localization signal remains intact. Caused by post translational
modification
10.) What is glycosylation? What type of modification is this an example of? Be sure you can identify
what the macromolecules are on this slide and any other example.
a. Addition of a carbohydrate (sugar) to a molecule
b. Post-translational modification
11.) Why would a protein travel from the ER to the golgi? What is the protein transported in?
a. Proteins getting different places in the cell need to be “packaged” into vesicles to get
to other places—Golgi processes proteins by adding the necessary localization
sequence/structure, allowing them to travel to their required destination
12.) A protein designated for the lysosome would have what unique signal/tag/sequence within its
amino acid sequence?
a. Mannose-6-phosphate
Lecture 9 PPT Review “Inside the Cell: The Dynamic Cytoskeleton”
1.) Why would the cytoskeleton be characterized as dynamic?
a. Expands and contracts over time
2.) What are the three major elements of the cytoskeleton? Arrange them in order of smallest to
largest size
a. Microfilaments
b. Intermediate Filaments
c. Microtubules
3.) What is the globular protein that forms microfilaments? Describe subunits of this protein.
Describe polarity for this protein?
a. Actin—the microfilament is composed of polymerizing and depolymerizing actin
subunits
b. Has positive and negative end—but usually “grows” at + end
4.) What is treadmilling?
a. Filaments polymerize (grow) and depolymerize (shrink)—can be simultaneous, hence
the “treadmill” action
5.) What is myosin classified as? How does it perform its function? What reaction is involved?
a. Motor Protein
b. Converts chemical energy in ATP into mechanical work—Converts ATP to ADP which
causes a shape change that extends the head region, attaches it to actin, and then
contracts to pull itself along the actin filament---this shape change causes the actin
and myosin to slide past each other.
c. ATP hydrolysis
6.) What are 3 different types of movement that can occur through actin-myosin interactions?
a. Cell crawling
b. Cell division
c. Cytoplasmic streaming in plants
7.) What is the primary protein that forms intermediate filaments (that we discussed)? What are
two functions of this protein?
a. Keratin
b. Functions = maintain cell shape by resisting tension and anchor nucleus and some
other organelles
8.) Describe polarity and “treadmilling” in intermediate filaments.
a. Each end is identicaldoes not treadmill
9.) What are the proteins that make up the composition of microtubules?
a. Tubulin—Has alpha and beta tubulin dimers
10.) List a few functions of microtubules. (There are two that were outlined in the PPT). Describe the
polarity and “treadmilling” of microtubules.
a. Functions = move organelles and provide tracks for intracellular transport—BUT also
keep in mind the fxns involved in cell division for future PPTs
b. Each end has distinct polaritytreadmilling can occur
11.) What would happen if you treated cells with a drug that disrupts microtubules? What would
happen if you depleted the amount of ATP in the cytoplasm?
a. No vesicle transport
b. Without ATP—movement would be either very slow or ablated
12.) How are microtubules linked with the following: (Also list the motor proteins involved in each)
a. Vesicle movement
i. Kinesin w/ ATP moves cells along microtubule tracks (Watch video)
b. Whole cell movement (think cilia + flagella)
i. Dynein w/ ATP—flagella are made of microtubules that whip back and forth
13.) What is an axenome?
a. Microtubule arrangement in cilia and flagella: 9 microtubule doublets linked with
dynein “arms” + 2 central microtubules. “Spokes” connect the central microtubule
with the outer doublets. Plasma membrane surrounds the entire structure.
Watch “The Inner Life of the Cell” and work on understanding each aspect of the video—always good to
have a visual memory to refer back to when you get stuck on questions!
Chapter 15: DNA and the Gene: Synthesis and Repair (p. 316 – 326)
Lecture 14 “DNA Synthesis in vivo and in vitro” Review
1.) What phase of the cell cycle does DNA synthesis occur?
a. S Phase (of Interphase)
2.) Describe the polarity of DNA—what are the exposed ends of the DNA molecule? (think back to
the nucleic acid lecture)
3.)
4.)
5.)
6.)
7.)
8.)
a. One end has an exposed hydroxyl group on the 3’ carbon of deoxyribose. The other
end has an exposed phosphate group on a 5’ carbon--Hence the 3’ and 5’ ends that are
used to describe the directionality of synthesis
What is semiconservative replication?
a. Demonstrates that the parent strands of DNA are separated and serve as the
template. The new DNA that synthesizes from each parent strand by complementary
base pairing creates the daughter strand. Therefore, with a daughter strand created
bound to a parent (template) strand, each new DNA double helix contains one parent
(template) and one daughter strand.
What is the function of DNA Polymerases with DNA? Include directionality that may be relevant.
a. Catalyzes the formation of phosphodiester bonds between nucleotides by adding
deoxyribonucleotides to the 3’ end of a growing chain. Therefore, it always “reads”
the DNA 3’  5’ but synthesizes in the 5’  3’ direction. In other words, as it’s reading
the DNA 3’  5’, the new strand that is polymerized is being created antiparallel, or 5’
 3’
“If you understand this concept ^^^, you should be able to draw two lines representing a DNA
molecule, assign the 3’ to 5’ polarity of each strand and then label the direction in which DNA
synthesis will proceed for each strand. I guarantee this will be addressed in some way on the
exam.
What does dNTP stand for? Why is DNA polymerization, specifically during replication,
considered an exergonic reaction?
a. dNTP = deoxyribonucleoside triphosphate
b. dNTPs contain a triphosphate, however, the phosphodiester bonds formed in the DNA
helix require only one of these phosphates. Therefore, two of the phosphates are
cleaved off. Keep in mind that, similar to ATP, these phosphates have repulsion
caused by the (-) charges of the phosphates, which are storing potential energy—so
energy is released when you break this repulsion (deeming it a favorable reaction—a
characteristic of exergonic reactions)
What is the term used to describe the starting position of DNA replication? What enzyme is
responsible for separating the two strands? How does it cause this to occur? What is the
resulting “structure” that forms at the position that this enzyme separates the strands?
a. Origin of replication/replication origins/origins
b. DNA helicase
c. Helicase breaks the hydrogen bonds between the base pairs of the two strands in the
helix.
d. Forms the replication fork
What is the function of single-strand DNA-binding proteins (SSBPs)? What is the function of
topoisomerase?
a. SSBPs attach to the separated strands which prevents the strands from re-connecting
back into the double helix structure (after helicase has separated them)—it’s more
energetically favorable for the bases to H-bond to each other, therefore, will be
spontaneously re-forming H-bonds without the SSBPs
b. Topoisomerase prevents the DNA helix from becoming coiled ahead of the replication
fork (following strand separation by helicase) by making cuts in the DNA, which allows
them to unwind, and then rejoins them ahead of the replication fork.
What is different about origins of replication for bacterial DNA replication versus that of
eukaryotes? What is a plausible reason to explain this?
a. During DNA replication, bacterial DNA is synthesized from a single origin of replication
whereas eukaryotes have numerous origins of replication.
b. This is likely due to the size of the bacterial genome versus that of the eukaryotic
genome
9.) In order for DNA polymerase to be able to initiate synthesis of the new strand, what has to be
synthesized first on the new strand? What enzyme is responsible for this? Why is this external
enzyme required rather than DNA Pol?
a. An RNA primer with a free 3’ end must be synthesized with complementary basepairing to the template strand.
b. Primase (a type of RNA Polymerase) is responsible for this.
c. RNA polymerase does not require a primer to initiate transcription—therefore, since
DNA Pol DOES require a primer DNA replication, it makes sense to use the enzyme
(primase) which does have the ability to freely synthesize the primer, even though it’s
RNA
10.) Due to the fact that DNA Polymerase can only synthesize DNA in the 5’  3’ direction, how are
lagging strands of DNA fully synthesized into a continuous strand? Explain why they have to be
synthesized this way instead of the way that the leading strand is synthesized.
a. Primase synthesizes many short segments of primers on the lagging strand. DNA
Polymerase then elongates the strand from the 3’ end of these primers. The resulting
linear collection of short segments are termed Okazaki fragments.
b. The direction of the replication fork allows the leading strand to continuously run in
the same direction of the replication fork (it would look like the strand is running into
the wedge portion of the fork where the two strands separate). However, the
directionality of the DNA Pol forces the lagging strand to be synthesized in the
opposite direction of the fork (so the strand is traveling away from the fork.
Therefore, primers have to be continuously placed to account for the strand moving
away (I’ve had a handful of you confused with this so far--if you don’t understand it
then email one me, mac, or ashlyn—crucial concept!)
11.) Why do we need Ligase and what is its function?
a. The strand of DNA, particularly those formed in the lagging strand, are discontinuous.
Once the RNA primers have been replaced with DNA, ligase is the enzyme that joins
the adjacent fragments into one continuous unit (Keep in mind that the leading strand
also starts from an RNA primer).
12.) What happens if DNA Polymerase adds an incorrect base to the DNA—what type of enzymatic
capabilities does DNA Pol have to handle this situation?
a. A SUBUNIT of DNA Pol has 3’  5’ exonuclease activity—this allows it to recognize
when it has added the incorrect base, causing it to “reverse” (hence the 3’  5’) and
remove the base and replace it with the correct one.
i. ^^In short, this is because it’s energetically favorable to have the correct bases
paired with each other for H-bonding (stability) and there’s a way in which
DNA Pol recognizes this when it’s polymerizing to the 3’ end of the incorrectly
added base.
13.) Name two common in vitro DNA synthesis reactions performed in molecular biology labs.
a. PCR and DNA sequencing
14.) What components are required to perform DNA synthesis in vitro? Explain why the others are
not required.
a. DNA template, Taq Polymerase, DNA Primer, dNTPs
b. No helicase bc we use heat in the rxn to separate.
No topoisomerase (and SSBP) bc it’s ssDNA so no kinks/tangling
No primase bc we construct and add the primers instead
No ligase bc there are no fragments being synthesized
Chapter 9: Metabolism (p.189 – 209)
1.) What are the 3 “stages” of cellular respiration?
a. Glycolysis
b. Citric Acid Cycle
c. Electron Transport Chain/Oxidative Phosphorylation
2.) Is glycolysis an aerobic or anaerobic pathway? If you oxidize one molecule of glucose, what is
the approximate net yield of ATP?
a. Anaerobic
b. 29 ATP
3.) The reactions of glycolysis can all be categorized into one type of chemical reaction, what are
these reactions called? How many total reactions occur in glycolysis? What is the starting
substrate?
a. Redox reactions
b. 10 reactions
c. Glucose
4.) Where in the cell does glycolysis take place?
a. Cytosol
5.) What occurs at both steps 1 and 3 in glycolysis? What enzyme catalyzes this reaction in step 1?
What enzyme catalyzes the reaction in step 3? What occurs at step 2?
a. ATPADP + Pi (energy release)
b. Hexokinase (step 1)
c. Phosphofructokinase (step 3)
d. Step 2 causes reorganization of G6P to F6P
6.) What happens to phosphofructokinase when ATP binds to the regulatory site? What type of
regulation is this an example of?
a. Causes feedback inhibition
b. Allosteric Inhibition
7.) Explain how the concentrations of ATP, AMP, Acetyl CoA, and Citrate may all play into the
regulation of PFK.
a. High [ATP], [Citrate], and [Acetyl CoA] would cause inhibition of PFK
High [AMP] would activate PFK
8.) What occurs at step 4? What occurs at step 5? What occurs at step 6?
a. Step 4: 6-C sugar splits into 2 3-C molecules
b. Step 5: Rearrangement
c. Step 6: 1.) Oxidation of glyceraldehyde phosphate 2.) Reduction of NAD+
9.) What specific type of phosphorylation occurs during glycolysis? Which steps does this reaction
occur at? Explain this type of phosphorylation.
a. Substrate-level phosphorylation (2ADP2ATP)
b. Occurs at steps 7 and 10
c. Text definition—Production of ATP or GTP by the transfer of a phosphate group from an
intermediate substrate directly to ADP or GDP. Occurs in glycolysis and in the citric acid
cycle.
10.) What is the end product of glycolysis? What is the NET yield of glycolysis from one molecule of
glucose?
a. Pyruvate
b. 2 pyruvate, 2 ATP, and 2 NADH
11.) The product produced from glycolysis can then enter 2 pathways. What are these pathways?
a. Aerobic respiration (CACETC)
b. (Anaerobic) Fermentation (alcohol or lactic acid)
12.) What redox reactions are occurring in lactic acid fermentation (reactantsproducts)?
a. 1.) Reduction of PyruvateLactate and 2.) NADH being oxidized back to NAD+
13.) What redox reactions are occurring in alcohol fermentation (same as above)?
a. 1.) Pyruvateacetaldehyde (CO2 released)ethanol and 2.) NADH being oxidized back
to NAD+
14.) Why is fermentation important for glycolysis?
a. Regeneration of NAD+ which is used in glycolysis
Lecture 18 “Cellular Respiration: Part 2” PPT review:
1.) Where are most citric acid cycle enzymes located?
a. Mitochondrial Matrix
2.) Outline the components involved in converting Pyruvate to Acetyl-CoA. What redox reactions
are occurring? What enzyme facilitates this reaction?
a. One of the carbons is oxidized to CO2, the remaining 2-Carbon ‘acetyl unit’ of pyruvate
is transferred to CoA to form Acetyl CoA, and NAD+ is reduced to NADH during this.
i. Pyruvate, NAD+, and CoA are reactants|CO2, NADH, and Acetyl CoA are
products
b. Pyruvate Dehydrogenase (complex)
3.) “Key Points” slide: Carbons donated by acetyl group are ________(oxidized or reduced?) to CO2
a. Oxidized
4.) What is the energy yield of the citric acid cycle? What type of phosphorylation produces the
GTP?
a. 3 NADH, 1 FADH2, 1 GTP (ATP) per molecule of pyruvate
b. Substrate-level phosphorylation
5.) Summarize the overall net energy yield for 1 molecule of glucose that undergoes glycolysis and
the CAC—It may be helpful to include the energy reactants and products
a. C6H12O6 + 10 NAD+ + 2 FAD + 4 ADP + 4 Pi ----> 6 CO2 + 10 NADH + 2 FADH2 + 4 ATP
6.) Explain how the concentration of ATP would affect reaction rates—(how is CAC regulated?)
(p.162 in text)
a. If [ATP] is low, then reaction rates will be high. If [ATP] is high, reaction rates will be low.
7.) How is the energy yield from the CAC used to produce more ATP?
a. The NADH and FADH2 produced during CAC then carry into the electron transport chain
(ETC)
8.) Where in the cell does the electron transport chain occur? Are the NADH and FADH2 being
oxidized or reduced during the ETC?
a. Inner membrane and cristae of mitochondria
b. Oxidized
9.) What is the relationship between electron movement, energy release, and proton movement in
the ETC?
a. “As electrons are passed from one molecule to another in the chain, the energy released
by the redox reaction is used to move protons across the inner membrane of the
mitochondria” (p. 166)
10.) What type of phosphorylation produces ATP in the ETC?
a. Oxidative phosphorylation
11.) Outline the steps required to get electrons from both of the following molecules to Coenzyme
Q (Ubiquinone). ALSO include which complex of the ETC each is occurring in: 1.) NADH 2.)
FADH2
a. In ETC complex 1--NADH donates e- to FMN (Flavin-containing protein) which then
donates to Fe•S (iron and sulfur-containing protein) and then passes electron to Q.
b. In ETC complex 2--FADH2 donates electrons directly to Fe•S which then passes to Q.
12.) What is happening to the amount of potential energy as electrons move from the NADH or
FADH2 to the final electron acceptor?
a. Relative potential energy (or relative free-energy) is decreasing as electrons step down
13.) What component of Cytochrome C is important for acting as an electron carrier?
a. Heme group (it may be helpful to look at the structure so that you could recognize it
without the name being provided)
14.) From PPT example involving the consumption of hydrocyanic acid (HCN)--Which component of
the electron transport chain is inhibited (after consumption)?
a. Cyanide binds to Fe which blocks cytochrome c from being activated (due to Fe in heme
group being bound already to cyanide)—which, as we discussed, can cause death.
15.) Outline the steps that allow ATP Synthase to catalyze the phosphorylation event of ADP + Pi 
ATP.
a. Higher concentration of H+ in Intermembrane space of mitochondria (as opposed to
lower concentration in mitochondrial matrix) causes H+ to move into the ATP synthase
Chapter 10: Photosynthesis (Lectures 19/21)
Lecture 19 “Photosynthesis Part I” Review:
1.) In the overall process of photosynthesis
a. What two types of reactions occur?
i. Energy-capturing reactions
ii. Carbon-fixing reactions
b. What is occurring in this biochemical process?
i. CO2 + light being converted to sugars
2.) In which organelle do the photosynthetic reactions take place in?
a. Chloroplast
3.) What are pigments? What causes a pigment to display a color? What component of chloroplasts
contains pigments?
a. Molecules that absorb only certain wavelengths of light while other wavelengths are
either reflected or transmitted
b. The color displayed by pigments are the wavelengths of light that they do not absorb
c. Thylakoid membrane possesses pigments
4.) Carrying out a thin layer chromatography of a leaf followed by analyzing the results with a
spectrophotometer will reveal what two properties of a particular leaf extract (to understand
this it may be helpful to review the experimental process in text from p.179-180—the exp
design doesn’t seem crucial, but it will help you understand why they’re doing each step)
a. It will reveal the pigments that are present and what wavelengths each absorbs
5.) What are the two major pigment classes in plant leaves?
a. 1.) Chlorophylls 2.) Carotenoids
6.) What does an action spectrum for photosynthesis reveal?
a. It tells us what wavelengths cause the highest rates of photosynthesis
7.) On slide about structure of pigments: what compound does this structure resemble?
a. Heme group—briefly discussed during explanation of electron transport chain and
elsewhere
8.) How do the different parts of chlorophyll differ in function?
a. Ring structurering structure that absorbs light
b. Tail structureHelps anchor chlorophyll to the thylakoid membrane
9.) What are the roles of carotenoids?
a. Absorb wavelengths of light that are not absorbed by chlorophyll and relay the energy
on to chlorophyll
b. Stabilize free radicals by accepting or stabilizing unpaired electrons
10.) What happens to electrons when pigments absorb light? What are the possible consequences?
a. Electrons are moved to a higher energy state (Excited state)
b. 1.) Energy is re-emitted as light energy of a longer wavelength plus heat (fluorescence)
2.) Electrons at higher energy level is transferred to an electron acceptor
3.) Transferring the energy—but not the electron—directly to a neighboring
chlorophyll molecule (resonance energy transfer)
4.) Emitted as heat alone
******I highly recommend reading p. 182 in text under the heading “When Light is Absorbed, e- Enter
an Excited State” to understand the relationship between photons, electron excitability, and colorwavelength being emitted. Read it more than once!
11.) Where does photosystem II take place in chloroplast?
a. Thylakoid membrane
12.) Outline the steps of Photosystem II (Include where the electrons that drive the system originate
from)
1. Photons excite electrons in the chlorophyll molecules of photosystem II’s antennae
complex
2. Energy in excited electrons is transferred to reaction center
3. Electrons with P680 enter excited state (P680*)
4. P680* passes excited electrons to pheophytin
5. Pheophytin is reduced which transfers the high-energy e- to an ETC
6. Electron is gradually stepped down in PE through redox rxns among a series of
quinones and cytochromes
7. Using energy released by the redox reactions, PQ carries protons across the thylakoid
membrane, from the stroma to the lumen
8. ATP synthase uses the resulting proton-motive force to phosphorylate ADP creating
ATP (Photophosphorylation)
9. Once e- reaches the end of the cytochrome complex, they are passed to a PC
10. PC diffuses through the lumen of the thylakoid and donates electrons to an oxidized
reaction center pigment in Photosystem I
13.) Why is Plastocyanin (PC) crucial to the Photosystems?
a. Creates link between PSII and PSI by not only transferring electrons between the two
PS but also replaces e- that are carried away from the pair of pigments in the PSI
reaction center
14.) Where do the electrons that fuel the photosystems come from? (The reaction would be helpful
to know)
a. Originates from incoming water molecules: 2 H2O  4H+ + O2 yielding 4e15.) Outline the steps in Photosystems I starting with Plastocyanin.
1. Electrons from plastocyanin replace electrons at PSI with the specialized pair of
chlorophyll called P700
2. Photons emitted and cause e- in P700 to reach excited state (P700*)
3. E- from P700* are then transferred to ferredoxin
4. Ferredoxin passes e- to an enzyme that catalyzes reduction of NADP+ to NADPH
16.) How do the light reactions set up a proton gradient? Where does the proton gradient form?
Ultimately, what molecule is generated by the proton gradient?
a. 1.) The protons released from e- being pulled off of H2O (that provide the
photosystems with e-) and 2.) For every 2 e- passing through the complexes (PQ to
plastocyanin via a cytochrome complex—don’t need to know but know where in
photosystem this is occurring) 4 protons are pumped
b. Protons are pumped in the thylakoid lumen
c. Used to generate ATP
17.) What is photophosphorylation?
a. The capture of light energy by photosystem II to produce ATP
Lecture 21 “Photosynthesis Part II” Review:
1.) How do terrestrial plants differ from aquatic plants in the way that they obtain CO2 from the
environment?
a. Aquatic plants obtain dissolved CO2 directly from surrounding H2O.
CO2 cannot directly diffuse into land plants (due to cuticle coating), therefore they
have stomata (pair of guard cells + the pore that forms between them) that allows
CO2 to diffuse into the cell (p. 193 in text)
2.) What are the three general phases of the calvin cycle? What is the overall reaction for each
phase (this isn’t essential but could be beneficial to recall for certain questions on test)
1. Fixation: 3 RuBP + 3 CO2  6 3-phosphoglycerate
2. Reduction: 6 3-phosphoglycerate + 6 ATP + 6 NADPH  6 G3P
3. Regeneration: 5 G3P + 3 ATP  3 RuBP
3.) In the first phase of the calvin cycle, what two molecules interact and what is the product of this
interaction (Include how many molecules are used for each and how many carbons are in each
molecule)
a. 3 molecules of RuBP (5C molecule) interact with 3 molecules of CO2 (1C molecule)
yielding 6 molecules of 3-phosphoglycerate (3C molecule)
4.) Two high energy molecules enter the calvin cycle from the light reactions. What are these
molecules and what type of reaction is each undergoing during the calvin cycle?
a. ATP is undergoing ATP hydrolysis to yield 6 ADP + 6 Pi
b. NADPH is undergoing oxidation to yield 6 NADP+ + 6 H+
5.) In lecture, we discussed ways in which this cycle (and others for the same reason) could be
regulated. Aside from controlling input of substrates into the cycle, what is the primary source
of regulation for the calvin cycle?
a. Each step is catalyzed by a specific enzyme. Therefore, the concentration of enzyme is
a powerful point of regulation for the cycle.
6.) What molecule from the calvin cycle is used to synthesize glucose? What is the set of reactions
called that allows the conversion of this molecule to glucose? What are the 2 fates of glucose
(that we discussed) following this conversion?
a. Glyceraldehyde-3-phosphate (G3P)
b. Gluconeogenesis
c. Glucose can be converted to sucrose or starch
7.) State the reactions that Rubisco is involved in (It will be useful to think about the carbons in
each of the products) Why is Rubisco considered an inefficient enzyme?
a. 1.) RuBP + CO2  2 3PG and
2.) RuBP + O2 3PG + 2PG
b. It will catalyze the addition of either O2 or CO2 to RuBP—Oxygen and carbon dioxide
compete for Rubisco’s active sites, which slows the rate of CO2 reduction
8.) How is Rubisco involved in photorespiration? When photorespiration occurs, what happens to
the rate of photosynthesis (think back to previous question)? Under what conditions would
photorespiration serve as a survival/protective measure for the plant?
a. When rubisco catalyzes the reaction between RuBP + O2, one of the products
produced (2PG) is processed in reactions that results in photorespiration
b. Rate of photosynthesis will decreased when photorespiration occurs
c. When the plant is under conditions of high light and low CO2 this mechanism could be
beneficial
9.) In C3 plants, what happens to growth under hot and dry conditions? As a result, what will the
orientation of stomata be? Will the resulting concentrations of CO2 and O2 be high or low?
a. Slow growth when hot and dry
b. Stomata will close to conserve water as a result
c. [CO2] will be low and [O2] will be high
10.) What reaction is occurring in the C4 plant Hatch-Slack pathway? Include enzyme catalyzing rxn.
a. 3C compound + CO2  4C molecule (reaction catalyzed by PEP carboxylase
11.) Is it possible to find the C3 and C4 pathway on the same leaf of a plant? Explain.
a. Yes—PEP carboxylase (C4 pathway) is found in mesophyll cells near surface of leaves
while rubisco is found in bundle-sheath cells that surround vascular tissue in the leaf
interior.
12.) Why would the C4 pathway be considered as a way to improve the efficiency of the calvin cycle?
What is the drawback?
a. The C4 pathway increases the concentration of CO2 in cells where rubisco is active.
Therefore, it increases the ratio of CO2 to O2 in photosynthesizing cells which will
cause less O2 to bind to rubisco. Since more CO2 is binding as a result which is then
used in the calvin cycle, it improves the efficiency.
b. Drawback is that it uses more ATP than C3 (30 used in C4 as opposed to 18 if C3
pathway)
13.) Aside from improving efficiency, why might a plant close to dehydration still utilize C4 even
given the drawbacks? (p. 194—touched on in lecture as well)
a. Affinity for CO2 by PEP carboxylase is much higher than that of rubisco—therefore
stomata can be open for shorter periods than if utilizing the C3
14.) In plants where the C4 pathway still doesn’t prevent dehydration, what other method is
utilized? Explain how this method is similar to C4 but differs in its relationship to C3.
a. Crassulacean acid metabolism—it is also a CO2 concentrator and generates a 4C
compound, however, it occurs at a different time (at night) than C3 as opposed to a
different place like C4’s relationship with C3