Download Lecture 12 “Cellular Respiration and Fermentation: Part I” PPT

Lecture 12 “Cellular Respiration and Fermentation: Part I” PPT review:
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 F6P to F1,6-BP
6.) On slide 11 in the Lecture 12 PPT: 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.) 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+
8.) 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.
9.) 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
10.) The product produced from glycolysis can enter 2 pathways. What are these pathways?
a. Aerobic respiration (CACETC)
b. Fermentation (alcohol or lactic acid)
11.) 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+
12.) 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+
13.) Why is fermentation important for glycolysis?
a. Regeneration of NAD+ which is used in glycolysis
Lecture 13 “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
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)
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 (p. 164 in text).
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
Lecture 14 “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 15 “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
Lecture 16 “Cell Communication I” Review:
1.) In regards to slide 5 on Dr. Hinton lecture—Which signal molecule is lipid soluble? What would
be the properties of each molecule causing their current positioning/interaction?
a. The molecule inside the cytosol is lipid-soluble
b. The molecule in the bound to the receptor in the extracellular space is lipid-insoluble-thus, large or hydrophilic. The molecule inside the cytosol is lipid-soluble and
therefore is hydrophobic or small uncharged (think back to the solubility of the
different molecules we reviewed in previous lectures)
2.) If a signal molecule was sent out from brain cells to all other cells in the body with the
“message” of signaling for dehydration and therefore to conserve water in cells, would all cells
in the body respond to this “message”? Make sure you can explain (not just yes or no).
a. No—in order for a cell to respond to this message it would need to have the
appropriate receptors that are specific for binding to the signal molecule (book uses
this example and states that only certain kidney cells will respond because they’re the
only cells that would have the appropriate receptors for this type of signal p. 210)
3.) What are two outcomes of receptors responding to intensive hormonal stimulation for a
prolonged period of time? (p. 210 in text) What property of receptors is demonstrated by the
action of a beta-blocker or caffeine (only the property here is important not ex. Unless you’re
premed!)
a. 1.) The number of receptors may decline and 2.) the ability of a receptor to bind
tightly to a signaling molecule may decline
b. They both work by blocking receptors from binding to normal hormone (betablockers
block adrenaline from binding—no forceful, rapid heart contractions | caffeine blocks
adenosine from binding—which normally induces drowsiness)
4.) What happens to a signal receptor when a signal molecule binds to it?
a. Undergoes a conformational change (shape change)
5.) What is signal transduction? What is a second messenger?
a. Process by which a stimulus outside a cell is converted into an intracellular signal
required for a cellular response. Usually involves a specific sequence of molecular
events, or signal transduction pathway, that may lead to amplification of the signal
(Text definition)
i. aka the conversion of a signal from one form to another
b. A nonprotein signaling molecule produced or activated inside a cell in response to
stimulation at the cell surface. Commonly used to relay the message of a hormone or
other extracellular signaling molecule (text definition)
6.) How does signal processing differ for lipid-soluble signals versus lipid-insoluble signals?
a. Lipid soluble signals are directly processed without any intermediate steps (diffuse
through PMbind to receptorhormone-receptor complex transports to
Nucleuschange in gene expression
b. Insoluble signals has to initiate an intracellular signal when it binds to cell-surface
receptors, therefore indirect (signal reception on surface receptorssignal
transductionsignal amplification (majority of time)signal response)
7.) What occurs with signal amplification?
a. A single signaling molecule results in numerous secondary signals to be transmitted
8.) Compare and contrast the two signaling mechanisms on slide 10 of Hinton lecture. Make sure
you can distinguish between a kinase and a phosphatase at this point (fully understand this—it’s
a building block for cell signaling)
a. Signaling by phosphorylationa protein kinase adds a phosphate from ATP to the
signaling molecule (makes the molecule active/on)a protein phosphatase can
remove the phosphate from the signal molecule to switch it back off
b. Signaling by GTP-bindinga GTP binding protein is induced to exchange the bound
GDP (of the signaling molecule) for a GTP which activates the signal moleculesignal
molecule can become deactivated if the GTP hydrolyzes and returns back to GDP being
bound to it.
c. Both are activated by addition of phosphate group and both are deactivated by
removal of the phosphate group again
9.) What does RTK stand for? What type of signal transduction occurs in the RTK pathway?
a. Receptor Tyrosine Kinase
b. Signal transduction via enzyme linked receptors
10.) Outline the steps of the RTK signaling pathway. Include the point at which the receptor becomes
active.
1. Hormone binds to receptor
2. Receptors dimerize (receptors are now active)
3. Receptors cross-phosphorylate/auto-phosphorylate using ATP inside the cell
4. Proteins inside the cell (this was grb2 + SOS in the specific PPT example—but these
were specific to example) bind to receptor to form bridge to Ras (a G-protein)
5. Ras exchanges GDP out and brings GTP in (activated Ras)
6. Phosphorylation + activation of protein kinase (we talked about mitogen activated
protein kinases (MAPK))
7. Phosphorylation cascade (essentially, the protein kinases phosphorylate each other)
8. Response triggered in the cell (such as gene activation in nucleus)
11.) What type of protein inactivates the phosphorylation cascade occurring in the RTK-MAPK
pathway (signal deactivation)?
a. MAP Kinase Phosphatases
12.) How does the GPCR (G-protein coupled receptor) pathway differ from the RTK pathway? (text p.
212)
a. Downstream in the pathway, the production of second messengers elicits a response
rather than the phosphorylation cascade in RTK (there are exceptions to this and it’s
good to be aware, but this is the general difference)
I spoke with Dr. Allison and she’s informed me that it’s unlikely that information about MK-STYX will be
on the exam
Lecture 17 “Cell Communication II” Review:
1.) What general forces does the extracellular matrix of cells protect against?
a. 1.) Cross-linked network of filaments protects against stretching forces
2.) Stiff ground substance protects against compression
2.) What is the primary cell wall composed of? What type of macromolecule is this? How is it
packaged and arranged in the cell wall? What molecule fills the space between this cell wall
material and what type of macromolecule is this?
a. Primary cell wall composed of cellulose
b. Carbohydrate (polysaccharide)
c. Consists of long cellulose strands bundled together into structures called microfibrils
(fibers)
d. Space between these is composed of Pectin—a carbohydrate (polysaccharide)
3.) What material makes up the “cross-linked filaments” of plant cell ECM? Ground substance?
a. Cross-linked filaments = cellulose microfibrils
b. Ground substance = Pectin
4.) What is turgor pressure?
a. The force exerted against the plant cell wall caused by increasing cell volume (could be
due to water uptake)
5.) In regards to composition, what is the difference between plant ECM and animal ECM? What
makes up the fibrous component of animal ECM? What type of macromolecule is this? What
makes up the matrix that surrounds the fibrous component?
a. Animal ECM contains much more protein relative to carbohydrate than does a cell
wall
b. Collagen makes up the fibrous component
c. Collagen is a protein
d. Matrix is composed of gel-forming proteoglycans
6.) Where are most ECM components synthesized in animal cells? Where are they processed? How
are they secreted from the cell?
a. Rough ER
b. Processed in Golgi
c. Secreted via exocytosis
7.) What will dictate variation in both the amount of and composition of ECM in animals?
a. Location—the tissue type of the cells will cause it to adopt different composition or a
varying amount of ECM (p. 203 in text for more)
8.) Why are integrins an important protein for cell-cell interaction?
a. Integrins are extracellular proteins that bind to other proteins that connect to the
cytoskeleton. Therefore, these proteins form a linkage between the ECM and
cytoskeleton which helps adjacent cells adhere to each other
9.) What is the example we discussed that demonstrates one possibility of cells losing their cellECM connection
a. Cancer metastasis—increased cell motility
10.) Describe tight junctions. If a line of cells connected by tight junctions were to come in contact
with a solution, how would the solution cross beyond the barrier of cells?—Why is this
important?
a. Tight junctions allow cells to form a watertight seal with cells adjacent to them.
b. Tight junctions force solution to instead pass through the cells rather than past them.
c. ^^Therefore, the cells can regulate or restrict movement of substances between the
cells and the rest of the body which is why these cell connections are important in
locations such as the intestines or skin layers.
11.) What is selective adhesion? What type of cell adhesion proteins did we discuss in lecture?
Where are these proteins found? What is their significance?
a. Cells of the same tissue type and species (of cell) have specific adhesion molecules
that allow them to adhere to each other
b. Cadherins
c. Found in Plasma membranes
d. Cadherins only bind to cadherins of the same type. Therefore, they allow cells of the
same tissue type to attach specifically to one another.
12.) Adjacent cells have specializes proteins that assemble in their membranes which form structures
that allow a channel to form and thus serve as communication portals. What is the name of
these structures in animal cells? What are they in plant cells? What type of molecules would
pass through these channels?
a. Gap junctions in animal cells
b. Plasmodesmata in plant cells
c. They admit water, ions, and small molecules—AA, CHOs, and nucleotides
Lecture 20 “DNA Replication” Review
1.) Describe the polarity of DNA—what are the exposed ends of the DNA molecule? (think back to
the nucleic acid lecture)
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
2.) What is semiconservative replication?
a. Demonstrates that the parent strands of DNA are separated and serve as the
template. The new DNA that binds with 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.
3.) 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
synthesizes in the 5’  3’ direction.
4.) Helpful hint in the book: “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.
5.) 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)
6.) 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
“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
7.) 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)
b. Topoisomerase prevents the DNA helix from become 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.
8.) 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?
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.
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 come to review session or email me—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 (a mechanism that I can’t imagine you need to
know), 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 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.) If an error in the recently synthesized DNA isn’t recognized by DNA Pol, what is another way that
can assist?
a. Repair enzymes specialized for these DNA errors can come and correct the errors
(Again, I don’t think she expects you to know these enzymes nor their mechanisms—
just be aware that it’s an alternative)
14.) Name two common in vitro DNA synthesis reactions performed in molecular biology labs.
a. PCR and DNA sequencing
15.) What components are required to perform DNA synthesis in vitro?
a. DNA template, Taq Polymerase, DNA Primer, dNTPs