Chapter 14:

What is the difference between substrate-level and oxidative phosphorylation?

Oxidative Phosphorylation – involves the consumption of O2 and the addition of a
phosphate group to ADP to form ATP.
Substrate-Level Phosphorylation - It removes a phosphate directly from a
substrate and transfers it to ADP
Where in the cell (which organelle) does each process occur?
Oxidative phosphorylation occurs in the Mitochondria of the cell while substrate-
level occurs in the Cytosol.
What are the four major complexes involved in the electron transport chain, and
what characteristics do these protein complexes have?
NADH dehydrogenase Complex, Succinate Dehydrogenase complex, cytocrome b-c1
complex, cytochrome oxidase complex.
Each complex consists of multiple proteins with “conductors”
of Fe-S, heme or copper prosthetic groups. There is “current” of e-s.
Complexes I, III and IV are also proton pumps, creating chemiosmotic potential.
What are the mobile elements of the electron transport chain, and what are their
characteristics?
Coenzyme Q and cytochrome C. diffusible electron carriers
In what order do electrons flow from NADH to oxygen?
Complex I NADH dehydroenase complex to coenzyme Q to complex III cytochrom b-c1
to cytochrome C to complex IV cytochrome oxidase complex
From FADH to oxygen?
Complex II succinate dehydrogenase complex to coenzyme Q to complex III cytochrome
b-c1 complex to cytochrome C to complex IV cytochrome oxidase complex
Does the order of electron carriers have to do with their physical proximity to one
another, or with their redox potentials? (Explain)
The order of electron carriers have to do with their redox potentials, each consecutive
complex has a greater electron affinity so it has a greater reduction potential.
What is the role of Fe-S prosthetic groups, or metal ions buried in
the proteins of the electron transport chain?
electrons jump between them in a process known as electron tunneling
(involves quantum mechanics).
What are the individual protein subunits that comprise the quaternary structure of
ATP synthase? Membrane-bound F0 stalk forms barrel (c subunit) for H+ to pass
through. Barrel rotates.
• Coupled by γ subunit which sticks asymmetrically down into αβ subunits of F1 head
like a cylindrical bearing in a sleeve.
• The soluble F1 stalk has three αβ subunits that rotate as H+ goes through
Which are part of the membrane embedded stalk?
Which are part of the cytoplasmic head? Which rotate, and which remain
stationary? F1 is held fixed via δ and β2 (stator stalk)
Where is the pathway for proton movement? Through the rotating stalk into the
matrix Which subunits catalyze ATP formation? This rotation of γ drives the
conformational transitions of the catalytic αβ subunits which, in turn, alters the nucleotide
binding site affinities.
• As a consequence, conformational (kinetic) energy flows from the catalytic subunit into
the bound ADP and Pi to promote their dehydration into ATP.
Can this enzyme work in reverse? Yes If so, what organelle can you think
of that might be a good candidate? (Hint: where is low pH (acidic pH) needed?)
What was the role of ferrous (Fe+2) iron in the early evolution of photosynthesis,
and why was it a good thing there was a lot of it around? What process(es) produces
starch granules in the chloroplast stroma? What is the evolutionary significance of
having many
variations on the chlorophyll molecule? What variations change the absorption
maximum of this molecule? Which chlorophylls are
found in land plants? Which accessory pigments are found in land plants? Why
have a light harvesting complex rather than a few
single chlorophyll molecules in each thylakoid membrane? Describe how electrons
are split from water during photosynthesis,
excited, and sent on their way down the electron transport chain in the thylakoid
membrane. Be as detailed as possible. Include a
description of charge separation.
What are the major roles of Photosystem II and Photosystem I in terms of energy
generation for the cell? Which one is “first” in the
electron transport chain? Which excites electrons to the highest level overall?
Which was named (discovered) first?
Compare and contrast electron transport in the mitochondria and the chloroplast.
How is carbon dioxide “fixed” into organic molecules that can be used by
autotrophs and heterotrophs for energy and biosythesis of
their cells’ component parts? Name the most important enzyme and its substrate
(full names please!). Describe the Calvin cycle in
as much detail as your lecture notes and book give, without memorizing structures.
You will need to know how many carbons are
involved, and whether the compound gets split, reduced, etc. at various steps. How
does ATP get to the cytoplasm, where it is needed
for energy? (Note: it is a very indirect pathway!) What are the possible destinies of
the products of the dark reactions in
photosynthesis?

Please study the two “big picture” slides at the end of Lecture 14.
Chapter 17:
What is the role of actin?
Actin filaments allow eukaryotic cells to adopt a variety of shapes and perform a
variety of functions. These include muscle contractions, cell motility, cell division and
cytokinesis.
Intermediate filaments?
Intermediate filaments form a strong, durable network in the cytoplasm of the
cell. Their main function is to enable cells to withstand the mechanical stress that occurs
when cells are stretched. They are the toughest and most durable of the three
cytoskeleton filaments. They are also found in the nucleus
Microtubules?
Microtubules are long stiff hollow tubes of protein that can disassemble in one
location and reassemble in another. They grow out from the centrosome and extend to
the outside of the cell, creating a system of tracks within the cell. They support and
strengthen the nuclear envelope. They form the mitotic spindle during mitosis. They can
form permanent structures such as flagella or cilia for motility. Made from tubulin.

Which of these are found in cilia? Microtubules Muscles? actin Lamellipodia? actin
What motor proteins are associated with the cytoskeleton? Myosin, Kinesin, Dynein
Which directions to they go?
Kinesin – Moves away from centrosome, towards the + end of the microtubule
Dynein – Moves toward the centrosome, and towards the – end of the microtubule.
Describe how microtubules and actin filaments have inherent directionality
(polarity).
There is a negative a-tubulin and a positive b-tubulin end. Actin – Each filament is a
twisted chain of identical globular actin molecules all of which point in the same
direction along the axis of the chain (+ end, - end). Which end of MTs is found in the
centrosome? The negative a-tubulin end
What causes microtubules to be stabilized? Microtubules growing out from the
centrosome can be stabilized if it’s plus end is attached to another molecule or cell
structure to prevent tubulin depolymerization. What about actin filaments? Depending
on their association with different actin binding proteins, stable structures can be formed.
Describe the molecular mechanics of skeletal muscle contraction. The myosin
filament has two sets of heads pointing in opposite directions. One set binds to actin
filaments in one orientation and moves them one way, the other binds to other actin
filaments in the opposite orientation and moves in the opposite way. The overall effect is
to slide sets of oppositely oriented actin filaments passed one another, therefore if actin
filaments and myosin filaments are organized together in a bundle – the bundle generates
a contractile forces

Chapter 18:
What are the phases within the cell cycle?
M-Phase: nucleus divides (mitosis) / Cell splits in two (cytokinesis)
Interphase:
G1-Phase: the interval between the completion of M-Phase and beginning
of S-phase
S-Phase: (synthesis) cell replicates it’s DNA
G2-Phase: the interval between end of s-phase and beginning of M-Phase

How does the cell decide to progress from one phase to another?
During gap phases the cell monitors the internal and external environments to
ensure that conditions are suitable and its preparations are complete before it completes
itself to s-phase and mitosis.
What are cyclin-CDKs and what do they have to do with all of this?
Cyclin-dependent protein kinases – protein kinases control the cell cycle; they
must be bound with cyclin in order to become enzymatically active.

What form of post-translational modification is rampant in the control of the cell

cycle?

How are cyclin-dependent kinases regulated (both positively and negatively)?

CdK inhibitor proteins – block the assembly or activity of one or more cyclin cdk
complexes
Cyclin concentraion regulates cyclin cdk activity
1. association with cyclins
2. activating phosphorylation of threonin around position 160
3. inhibitory phosphorylatio of threonin 14 and tyrosine 15
4. association with cdk inhibitors (cki’s)
the activities of cdk’s is regulated by cyclin degradation
What actions does “active” M-Cdk do to promote mitosis?
Triggers the condensation of the replicated chromosomes into compact rod like
structures, readying them for segregation and it also induces the assembly of the mitotic
spindle that will separate the condensed chromosomes.
M cdk activation begins with the accumulation of M cyclin. The increase in M cyclin
protein leads to a corresponding acculuation of M cdk complexes that are initially
inactive. The activatio of a protein phosphatase revmoes the inhibitory phosphates that
are holding m cdk activity in check. Once activated each m cdk complex indirectly
activates more m cdk by phosphorylating and activating more cdc25. Activated m cdk
also inhibits the inhibitory kinse weel further promoting the activation of m cdk. The
consequence is tha once the activation of m cdk begins there is an explosive increase in
mcdk activity that drives the cell abruptly from G2 into M phase.
What actions does S-Cdk do to promote DNA replication (synthesis)?
Origin recognition complexes (ORCs) remain associated with origins of replication
throughout the cell cycle. In early G1 he regulatory protein Cdc6 associates with the
ORC. Aided by Cdc6, additional proteins bind to the adjacent DNA, resulting in the
formation of a prereplicative complex, which includes th proteins and the DNA to which
they are bound. S Cdk hen triggers origin firing by causing the assembly of the protein
complexes that initiate DNA synthesis. S Cdk also helps block re replication b helping to
phosphorylate Cdc6, which dissociates from the origin and is degraded.
Describe the steps in mitosis.
1. prophase: the replicated chromosomes condense and the mitotic spindle begins to
assemble outside the nucleus
2. prometaphase: the nuclear envelope breaks down allowing the spindle
microtubules to bind to the chromosome
3. metaphase: the mitotic spindle gathers all of the chromosomes to the center of the
spindle
4. anaphase: the two sister chromatids in each replicated chromosome
 synchronously split apart and the spindle draws them to opposite poles of the cell
5. telophase: nuclear envelope reassembles around each of the separated
chromosomes to form two nuclei. Cyokinesis is complete by end of the telophase.
Keep thinking about mitosis. Which steps are regulated by cyclin-dependent
kinases?

What does the anaphase-promoting complex do?

1. Ubiquinates M-cyclin
2. Triggers proteolysis of cohesins that held sister chromatids together
What generates tension at the spindle apparatus?
Kinesin and dynein MT motors attached at:
1. interpolor microtubules (push apart poles)
2. kinetochore (releasing tension to permit destabilization and shortening)
3. cell cortex (beneath cell membrane), pulling centrosomes poleward
When does the centrosome replicate? How is dynamic instability important to
this process?
Which microtubules are stable, like anchors?
Astral MTs are anchored to cell membrane by proteins.

Describe cytokinesis.
Cytokinesis is the process by which the cytoplasm is cleaved in two, completing
m-phase.

How is the midline marked by the cell?

The cleavage furrow forms in the middle and occurs in a plane that runs perpendicular to
the long axis of the mitotic spindle. Astral microtubules and interpolar microtubules
signal the cell cortex to initiate the assembly of the contractile ring at the midway point.

How does it differ between plants and animals?

Animals: Contractile ring made of actin and myosin assembled during anaphase.
Starts with the “puckering and furrowing” of the plasma membrane during anaphase.
The cleavage furrow forms in the middle and occurs in a plane that runs perpendicular to
the long axis of the mitotic spindle
Plants: Two daughter cells are separated by the construction of a new cell wall
that forms inside the dividing cell. The position of the new well precisely determines the
position of the two daughter cells relative to the neighboring cells. The new cell wall
starts to assemble in the cytoplasm, between the two sets of segregated chromosomes at
the store of telophase. The process is guided by phragmoplast, which is formed by the
remains of the interpolar microtubules at the equator of the old mitotic spindle.

1. Mitosis
a. Plants, fungi, and diatoms have gamma tubulin clusters in the nuclear
membrane rather than in exterior centrosomes.
b. Plants also lack centrioles.
2. Cell division
Animal cytokinesis occurs via plasma membrane furrowing due
 to contraction of cytoplasmic actin filaments.
Plant cytokinesis is accomplished by vesicle fusion and synthesis of
new cell wall material by phragmoplast.

What maintains homeostasis in terms of organ and body size?

1. Cell growth
Size increase
Interphase (G1, S, G2)
Stimulated by growth factors
2. Cell proliferation
Cell division
M phase = mitosis, cytokinesis
Stimulated by mitogens
(example of a mitogen: PDGF, signal for platelet proliferation
during wound healing)
3. Cell death
Apoptosis = a-puh-toasis)
Stimulated by caspase cascade
Inhibited by survival factors

Why is the “death” part of this process (apoptosis) also referred to as

“pruning” – what other important function(s) does apoptosis fill?
1. Tissues no longer needed
2. Organ size maintenance: cell division = cell death
3. Disease (self sacrifice)

Two types of cell death:

1. Necrosis
a. caused by acute injury
b. swelling, bursting, spilling of contents
c. triggers immune response
2. Apoptosis
a. Programmed by cell itself – caspase proteins (see book)
b. Orderly
1. Shrinking/condensation
2. Cytoskeleton collapses
3. Nuclear envelope disassembles, DNA fragments
4. Phagocytes are recruited to “clean up”

Explain why meiosis is a reductive division.

• Daughter cells have half the chromosome complement of parent cells
• Daughter cells become gametes (germ line, as opposed to somatic cells)
Compare and contrast mitosis and meiosis.

Differences between meiosis and mitosis

1) Mitosis forms two identical daughters; meiosis forms four gametes that
are not identical.
2) Meiotic Prophase I: Crossing over occurs, forming recombinant
chromosomes.
3) Meiotic Interphase II: No DNA replication.
4) Prophase is considerably lengthened, relative to mitosis. In mammalian
females, prophase begins in gestation and continues until the oocyte

Name the two reasons that offspring of a diploid organism like you can be so
different from either the male or female parent. Be specific – name to processes, and
discuss the stage in meiosis at which each process occurs.
1. Crossing over at Prophase I (homologs pair)
2. Independent assortment of chromosomes at anaphase I (random
alignment/separation at metaphase I)
Describe all the opposing forces on the spindle apparatus during metaphase.
Kinesin and dynein MT motors attached at:
1. interpolor microtubules (push apart poles)
 2. kinetochore (releasing tension to permit destabilization and shortening)
3. cell cortex (beneath cell membrane), pulling centrosomes poleward
How do these forces change during anaphase?
What filaments form the contractile ring in animal cell cytokinesis?
Actin and myosin. It assembles at anaphase and is attached to membrane associated
proteins on the cytoplasmic face of the plasma membrane.
What organelle is the source of vesicles that coalesce to form the phragmoplast
during late anaphase in plant cells?
Phragmoplast formed by remains of interpolar microtubules at equator of old mitotic
spindle. Small membrane enclosed vesicles largely derive from golgi apparatus and filled
with polysaccharides and glyco proteins required for the cell wall matrix are transported
along microubules to the phragmoplast.
What goodies are inside the vesicles?
Polysaccharides and glycoproteins
What is the fate of these molecules (e.g. what will they eventually become, in the
daughter cells)?
They form the cell wall.
What is the fate of the membrane of the phragmoplast?

What is the difference between a haploid organism and a diploid organism?

Haploid organisms have one set of chromosomes and diploid organisms have two sets of
chromosomes
Can an organism contain more than 2 sets of each chromosome?
Yes.
What is the ploidy level of your own cells during Anaphase I?
haploid
Anaphase II?

Just after telophase 2? What process has

to happen between Telophase II and embryonic development to get your somatic
cells to the correct ploidy level?